isolated heteromultimeric fc construct, composition, use of an isolated heteromultimeric fc construc

专利摘要:
ISOLATED HETEROMULTIMERIC FC CONSTRUCT, COMPOSITION, USE OF AN ISOLATED HETEROMULTIMERIC FC CONSTRUCT, NUCLEIC ACID COMPOSITION AND METHOD TO EXPRESS THE ISOLATED HETEROMULTIMÉRICO FC CONSTRUCT. The structures provided have heavy chains that are asymmetric in several domains (for example, CH2 and CH3) to perform selectivity among the various Fc receptors involved in the modulation of the effector function, in addition to those that can be made with a natural (symmetrical) homodimeric Fc molecule, and stability and increased purity of the resulting Fc variant heterodimers. These new molecules comprise complexes of heterogeneous components designed to alter the natural way in which antibodies act to find use in therapy.
公开号:BR112014010580B1
申请号:R112014010580-4
申请日:2012-11-02
公开日:2021-01-12
发明作者:Thomas SPRETER VON KREUDENSTEIN；Surjit Bhimarao Dixit；Eric Escobar Cabrera；Paula I. Lario；David Kai Yuen Poon
申请人:Zymeworks, Inc.；
IPC主号:

专利说明:

[0001] [0001] The present disclosure generally provides polypeptide heterodimers, compositions thereof and methods for preparing and using these polypeptide heterodimers. More specifically, the present invention relates to multispecific thermostable antibodies, including bispecific ones, comprising a heterodimeric Fc domain. Fundamentals of the Invention
[0002] [0002] Bispecific drugs are antibody-based molecules that can simultaneously bind two separate and separate separate targets or different epitopes of the same antigen. Bispecific antibodies are composed of entities based on the immunoglobulin domain and attempt to structurally and functionally mimic the components of the antibody molecule. One use of bispecific antibodies is to redirect cytotoxic immune effector cells for enhanced killing of tumor cells, as by antibody dependent cell cytotoxicity (ADCC). In this context, one arm of the bispecific antibody binds to a tumor cell antigen, and the other binds to a determinant expressed in effector cells. By cross-linking tumor and effector cells, the bispecific antibody not only brings effector cells within the vicinity of tumor cells, but also simultaneously triggers their activation, leading to effective cell killing. Bispecific antibodies are also used to enrich chemo or radiotherapeutic agents in tumor tissues to minimize the detrimental effects on normal tissue. In this scenario, one arm of the bispecific antibody binds to an antigen expressed on the target cell for destruction, and the other arm releases a chemotherapeutic drug, radioisotope or toxin. Going beyond bispecifics, there is a need for protein medicines to achieve their effectiveness by targeting several modalities simultaneously. These complex and novel biological effects can be achieved with protein medicines by projecting aspects of multi-target and multifunctional binding on the protein.
[0003] [0003] A robust structure that provides a framework for fusing other functional warheads or target protein binding domains to design these multifunctional and multi-target binding drugs is required. Ideally, the framework should not only provide the framework, but also provide a number of other valuable and therapeutically relevant characteristics for the designed drug. A major obstacle in the general development of multifunctional and bispecific antibodies based on antibodies is the difficulty of producing materials of sufficient quantity and quality for preclinical and clinical studies. There is still a need in the art for polypeptide constructs that comprise single variation domains as protein binding domains that are linked to a variant Fc region, said Fc variant comprising CH3 domains, which have been modified to select heterodimers with increased stability and purity . Summary of the invention
[0004] [0004] According to one aspect of the invention, an isolated heteromultimeric Fc construct comprising a modified heterodimeric CH3 domain, said modified CH3 domain comprising: a first modified CH3 domain polypeptide comprising at least three amino acid modifications compared to one wild type CH3 domain polypeptide, and a second modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a wild type CH3 domain polypeptide; wherein at least one of said first and second polypeptides of the CH3 domain comprises an amino acid modification of K392J wherein J is selected from L, I or an amino acid with a side chain volume not substantially greater than the volume of the K side chain ; wherein said first and second modified CH3 domain polypeptides preferably form a heterodimeric CH3 domain with a melting temperature (Tm) of at least about 74 ° C and a purity of at least 95%; and wherein at least one amino acid modification is not an amino acid that is at the interface between said first and said second polypeptide of CH3 domain. In certain embodiments there is a heteromultimeric Fc construct described here, comprising at least one T350X modification, where X is a natural or unnatural amino acid selected from valine, isoleucine, leucine, methionine and derivatives or variants thereof. In some embodiments there is an isolated heteromultimeric Fc construct described here, comprising at least one T350V modification. In one embodiment is an isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C or higher. In one embodiment is the isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a Tm of about 77 ° C or higher. In certain embodiments, the modified CH3 domain has a Tm of about 80 ° C or higher. Provided in certain embodiments is an isolated heteromultimeric Fc construct described herein, wherein at least one CH3 domain polypeptide is a modified CH3 domain polypeptide comprising an amino acid modification of at least one of L351, F405, and Y407. In some embodiments there is an isolated heteromultimeric Fc construct, wherein at least one CH3 domain polypeptide is a modified CH3 domain polypeptide further comprising an amino acid modification of T366. In certain embodiments, there is an isolated heteromultimeric Fc construct described here, wherein the first CH3 domain polypeptide is a modified CH3 domain polypeptide comprising amino acid modifications at positions L351, F405, and Y407, and the second CH3 domain polypeptide is a modified CH3 domain polypeptide comprising amino acid modifications at positions T366, K392, and T394. In one embodiment is the isolated heteromultimeric Fc construct described here, said first CH3 domain polypeptide comprising amino acid modifications L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprising amino acid modifications T366L, K392M, and T394W. In some embodiments is the isolated heteromultimeric Fc construct described here, said first CH3 domain polypeptide comprising amino acid modifications L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprising amino acid modifications T366L, K392L, and T394W. In another embodiment is the isolated heteromultimeric Fc construct described here, said first CH3 domain polypeptide comprising amino acid modifications L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprising amino acid modifications T366I, K392M, and T394W. In some embodiments is the isolated heteromultimeric Fc construct described here, said first CH3 domain polypeptide comprising amino acid modifications L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprising amino acid modifications T366I, K392L, and T394W. In certain embodiments is the isolated heteromultimeric Fc construct described here, wherein at least one of said first and second polypeptides of the CH3 domain is a modified CH3 polypeptide comprising an amino acid modification at the S400 position. In another embodiment is the isolated heteromultimeric Fc construct described here, comprising the S400Z modification, in which Z is selected from a positively charged amino acid and a negatively charged amino acid. In some embodiments, the positively charged amino acid is lysine or arginine and the negatively charged amino acid is aspartic acid or glutamic acid. In certain embodiments is the isolated heteromultimeric Fc construct described here, said first CH3 domain polypeptide comprising a selected amino acid modification from S400E and S400R. In some embodiments, the isolated heteromultimeric Fc construct described herein is provided, wherein at least one of said first and second polypeptides of the CH3 domain is a modified CH3 polypeptide comprising an amino acid modification at the N390 position. In some embodiments, the modification of N3 90 is N3 90Z, where Z is selected from a positively charged amino acid and a negatively charged amino acid. In one embodiment, N390Z is N390R. In certain embodiments of the isolated heteromultimeric Fc construct described herein, said first CH3 domain polypeptide is a modified CH3 domain polypeptide comprising the amino acid modification S400E and said second CH3 domain polypeptide is a modified CH3 domain polypeptide comprising amino acid modification N390R. In some embodiments of the isolated heteromultimeric Fc construct described here, each of the first and second CH3 domain polypeptides is a modified CH3 domain polypeptide, said modified CH3 domain polypeptide comprising the amino acid modification Q347R and the other CH3 domain polypeptide modified comprising the K360E amino acid modification.
[0005] [0005] Provided in one aspect is an isolated heteromultimeric Fc construct comprising a modified heterodimeric CH3 domain, said modified CH3 domain comprising: a first modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a CH3 domain polypeptide of wild type, and a second modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a wild type CH3 domain polypeptide; wherein at least one of said first and second polypeptides of the CH3 domain comprises an amino acid modification of K392J wherein J is selected from L, I or an amino acid with a side chain volume not substantially greater than the volume of the K side chain ; wherein said first and second modified CH3 domain polypeptides preferably form a heterodimeric CH3 domain with a melting temperature (Tm) of at least about 74 ° C and a purity of at least 95%; and wherein at least one amino acid modification is not an amino acid that is at the interface between said first and said second polypeptide of CH3 domain. In certain embodiments there is a heteromultimeric Fc construct described here, comprising at least one T350X modification, where X is a natural or unnatural amino acid selected from valine, isoleucine, leucine, methionine, and derivatives or variants thereof. In some embodiments there is an isolated heteromultimeric Fc construct described here, comprising at least one T350V modification. In one embodiment is an isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C or higher. In one embodiment is the isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a Tm of about 77 ° C or higher. In certain embodiments, the modified CH3 domain has a Tm of about 80 ° C or higher. In one embodiment is the isolated heteromultimeric Fc construct described here, wherein at least one CH3 domain polypeptide is a modified CH3 domain polypeptide comprising an amino acid modification of at least one of K409 and T411. In certain embodiments is the isolated heteromultimeric Fc construct described here, comprising at least one of K409F, T411E and T411D. In some embodiments is the isolated heteromultimeric Fc construct described here wherein at least one CH3 domain polypeptide is a modified CH3 domain polypeptide comprising an amino acid modification of D399. In some embodiments, the D399 amino acid modification is at least one for D399R and D399K.
[0006] [0006] Provided in one aspect is an isolated heteromultimeric Fc construct comprising a modified heterodimeric CH3 domain, said modified CH3 domain comprising: a first modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a CH3 domain polypeptide of wild type, and a second modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a wild type CH3 domain polypeptide; wherein at least one of said first and second polypeptides of the CH3 domain comprises an amino acid modification of K392J wherein J is selected from L, I or an amino acid with a side chain volume not substantially greater than the volume of the K side chain ; wherein said first and second modified CH3 domain polypeptides preferably form a heterodimeric CH3 domain with a melting temperature (Tm) of at least about 74 ° C and a purity of at least 95%; and wherein at least one amino acid modification is not an amino acid that is at the interface between said first and said second polypeptide of CH3 domain. In certain embodiments there is a heteromultimeric Fc construct described here, comprising at least one T350X modification, where X is a natural or unnatural amino acid selected from valine, Isoleucine, leucine, methionine, and derivatives or variants thereof. In some embodiments there is an isolated heteromultimeric Fc construct described here, comprising at least one T350V modification. In one embodiment is an isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C or higher. In one embodiment is the isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a Tm of about 77 ° C or higher. In certain embodiments, the modified CH3 domain has a Tm of about 80 ° C or higher. In certain embodiments of the isolated heteromultimeric Fc construct described here, wherein the first CH3 domain polypeptide is a modified CH3 domain polypeptide comprising at least one selected amino acid modification from K409F, T411E and T411D, and the second CH3 domain polypeptide is a modified CH3 domain polypeptide comprising at least one amino acid modification selected from Y407A, Y407I, Y407V, D399R and D399K. In some embodiments is any of the isolated heteromultimeric Fc constructs described herein, further comprising a first modified CH3 domain comprising one of the amino acid modifications T366V, T366I, T366A, T366M, and T366L; and a second modified CH3 domain comprising the amino acid modification L351Y. In some embodiments is any of the isolated heteromultimeric Fc constructs described herein, comprising a first modified CH3 domain comprising one of the K392L or K392E amino acid modifications; and a second modified CH3 domain comprising one of the amino acid modifications S400R or S400V.
[0007] [0007] An isolated heteromultimeric Fc construct comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide and a second modified CH3 domain polypeptide, each modified CH3 domain polypeptide comprising at least four amino acid mutations, is provided herein. at least one of said first and said second modified CH3 domain polypeptide comprises a selected mutation of N390Z and S400Z, wherein Z is selected from a positively charged amino acid and a negatively charged amino acid, and wherein said first and second CH3 domain polypeptides Preferably modified, they formed a heterodimeric CH3 domain with a melting temperature (Tm) of at least about 70 ° C and a purity of at least 90%. In one embodiment, the isolated heteromultimeric Fc construct is provided, wherein said first modified CH3 domain polypeptide comprising amino acid modifications at positions F405 and Y407 and said second modified CH3 domain polypeptide comprises amino acid modification at position T394. In one embodiment, the isolated heteromultimeric Fc construct, the first modified CH3 domain polypeptide comprising an amino acid modification at position L351, is provided. In certain embodiments, there is the isolated heteromultimer described herein, said second modified CH3 domain polypeptide comprising a modification of at least one of the T366 and K392 positions. In some embodiments, there is the isolated heteromultimer described here, in which the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C and is formed with a purity of at least about 95%. In certain embodiments, there is the isolated heteromultimer described herein, at least one modified CH3 domain polypeptide comprising amino acid modifications of at least one of N390R, S400E and S400R. In some embodiments there is an isolated heteromultimer described here, one of said first and second modified CH3 domain polypeptides comprising amino acid modifications at position 347 and the other modified CH3 polypeptide comprising amino acid modification at position 360. In certain embodiments is the heteromultimer isolate described herein, at least one of said first and second modified CH3 domain polypeptides comprising T350V amino acid modification. In specific embodiments is an isolated heteromultimer described herein, said first modified CH3 domain polypeptide comprising at least one selected amino acid modification from L351Y, F405A and Y407V; and said second modified CH3 domain polypeptide comprising at least one selected amino acid modification from T366L, T366I, K392L, K392M and T394W. In certain embodiments described here is an isolated heteromultimer, the first modified CH3 domain polypeptide comprising amino acid modifications at positions D399 and Y407, and a second modified CH3 domain polypeptide comprising amino acid modification at positions K409 and T411. In some embodiments there is an isolated heteromultimer described here, the first CH3 domain polypeptide comprising amino acid modification at the L351 position, and the second modified CH3 domain polypeptide comprising amino acid modifications at the T366 and K392 position. In specific embodiments, isolated heteromultimers are described herein, at least one of said first and second polypeptides of the CH3 domain comprising amino acid modification of T350V. In certain embodiments, isolated heteromultimers described herein, wherein the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C or higher and is formed with a purity of at least about 95%. Provided in certain embodiments are isolated heteromultimeric Fc constructs described herein, said first modified CH3 domain polypeptide comprising amino acid modifications selected from L351Y, D399R, D399K, S400D, S400E, S400R, S400K, Y407A, and Y407V; and said second modified CH3 domain polypeptide comprising amino acid modifications selected from T366V, T366I, T366L, T366M, N390D, N390E, K392L, K392I, K392D, K392E, K409F, K409W, T411D and T411E.
[0008] [0008] An isolated heteromultimeric Fc construct comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide and a second modified CH3 domain polypeptide, each modified CH3 domain polypeptide comprising at least three amino acid mutations, is provided herein. one of said first and said second modified CH3 domain polypeptide comprises a selected mutation of T411E and T411D, and wherein said first and second modified CH3 domain polypeptides preferably form a heterodimeric CH3 domain with a melting temperature (Tm) of at least about 70 ° C and a purity of at least 90%. In one embodiment, the isolated heteromultimeric Fc construct is provided in which said first modified CH3 domain polypeptide comprising amino acid modifications at positions F405 and Y407 and said second modified CH3 domain polypeptide comprises amino acid modification at position T394. In one embodiment, the isolated heteromultimeric Fc construct, the first modified CH3 domain polypeptide comprising an amino acid modification at position L351, is provided. In certain embodiments, there is the isolated heteromultimer described herein, said second modified CH3 domain polypeptide comprising a modification of at least one of the T366 and K392 positions. In some embodiments, there is the isolated heteromultimer described here, in which the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C and is formed with a purity of at least about 95%. In certain embodiments, there is the isolated heteromultimer described herein, at least one modified CH3 domain polypeptide comprising amino acid modifications of at least one of N390R, S400E and S400R. In some embodiments there is an isolated heteromultimer described here, one of said first and second modified CH3 domain polypeptides comprising amino acid modifications at position 347 and the other modified CH3 polypeptide comprising amino acid modification at position 360. In certain embodiments is the heteromultimer isolate described herein, at least one of said first and second modified CH3 domain polypeptides comprising T350V amino acid modification. In specific embodiments is an isolated heteromultimer described herein, said first modified CH3 domain polypeptide comprising at least one selected amino acid modification from L351Y, F405A and Y407V; and said second modified CH3 domain polypeptide comprising at least one selected amino acid modification from T366L, T366I, K392L, K392M and T394W. In certain embodiments described here is an isolated heteromultimer, the first modified CH3 domain polypeptide comprising amino acid modifications at positions D399 and Y407, and a second modified CH3 domain polypeptide comprising amino acid modification at positions K409 and T411. In some embodiments there is an isolated heteromultimer described here, the first CH3 domain polypeptide comprising amino acid modification at the L351 position, and the second modified CH3 domain polypeptide comprising amino acid modifications at the T366 and K392 position. In specific embodiments, isolated heteromultimers are described herein, at least one of said first and second polypeptides of the CH3 domain comprising amino acid modification of T350V. In certain embodiments, isolated heteromultimers described herein, wherein the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C or higher and is formed with a purity of at least about 95%. Provided in certain embodiments are isolated heteromultimeric Fc constructs described herein, said first modified CH3 domain polypeptide comprising amino acid modifications selected from L351Y, D399R, D399K, S400D, S400E, S400R, S400K, Y407A, and Y407V; and said second modified CH3 domain polypeptide comprising amino acid modifications selected from T366V, T366I, T366L, T366M, N390D, N390E, K392L, K392I, K392D, K392E, K409F, K409W, T411D and T411E.
[0009] [0009] An isolated heteromultimeric Fc construct is provided herein, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications L351Y, F405A and Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T366I, K392M and T394W.
[0010] [00010] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications L351Y, F405A and Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T366I, K392L and T394W.
[0011] [00011] Provided in a certain aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications L351Y, F405A and Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T366L, K392M and T394W.
[0012] [00012] Provided in some respects is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications L351Y, F405A and Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T366L, K392L and T394W.
[0013] [00013] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T350V, L351Y, F405A and Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T350V, T366L, K392L and T394W.
[0014] [00014] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T350V, L351Y, S400R, F405A, Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T350V, T366L, K392M and T394W.
[0015] [00015] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T350V, L351Y, S400E, F405A, Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T350V, T366L, N390R, K392M and T394W.
[0016] [00016] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T350V, L351Y, F405A, Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T350V, T366L, K392L and T394W.
[0017] [00017] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T366V, K392L, K409F and T411E; and a second modified CH3 domain polypeptide comprising amino acid modifications L351Y, D399R, and Y407A.
[0018] [00018] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T366V, K392LE K409F and T411E; and a second modified CH3 domain polypeptide comprising amino acid modifications L351Y, D399R, S400R and Y407A.
[0019] [00019] An isolated heteromultimer comprising an heterodimeric Fc region is provided according to one aspect of the invention, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote heterodimer formation, where the heterodimeric Fc region is still comprises a variant CH2 domain comprising at least one asymmetric amino acid modification to promote selective binding of an Fcgama receptor. In one embodiment, the variant CH2 domain selectively binds to the Fcgama IIIa receptor compared to the wild type CH2 domain. In one embodiment, the modified CH3 domain has a melting temperature (Tm) of about 70 ° C or higher. In certain embodiments, the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C. In some embodiments, the modified CH3 domain has a melting temperature (Tm) of at least about 80 ° C.
[0020] [00020] In another aspect an isolated heteromultimer comprising a heterodimeric Fc region is provided, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations, where the modified CH3 domain has a melting temperature (Tm) of about 70 ° C or higher, and wherein said modified CH3 domain results in the formation of the heterodimeric Fc region with increased stability compared to a CH3 domain that does not comprise amino acid mutations. In one embodiment, the heterodimeric Fc region does not comprise an additional disulfide bond in the CH3 domain relative to a wild type Fc region. In an alternative embodiment, the heterodimeric Fc region comprises at least one additional disulfide bond in the modified CH3 domain relative to a wild-type Fc region, provided that the melting temperature (Tm) of about 70 ° C or higher is in the absence additional disulfide bond. In another embodiment, the heterodimeric Fc region comprises at least one additional disulfide bond in the modified CH3 domain relative to a wild type Fc region, and in which the modified CH3 domain has a melting temperature (Tm) of about 77.5 ° C or higher.
[0021] [00021] An isolated heteromultimer comprising a heterodimeric Fc region is provided in one embodiment, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations, wherein the modified CH3 domain has a melting temperature (Tm) of about 70 ° C or higher and the heterodimeric Fc region is formed with a purity greater than about 90%, or the heterodimeric Fc region is formed with a purity of about 95% or greater or the heterodimeric Fc region is formed with a purity of about 98% or higher.
[0022] [00022] An isolated heteromultimer comprising a heterodimeric Fc region is also provided in certain embodiments, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising one or more amino acid mutations that result in the formation of the heterodimeric Fc region with increased stability compared to a CH3 domain that does not comprise said one or more amino acid mutations, wherein the modified CH3 domain has a melting temperature (Tm) of about 70 ° C or higher or Tm is about 71 ° C or higher or Tm is about 74 ° C or higher. In another embodiment, the heterodimeric Fc region is formed in solution with a purity of about 98% or greater, and Tm of about 73 ° C or where the heterodimeric Fc region is formed with a purity of approximately 90% or greater , and Tm of about 75 ° C.
[0023] [00023] An isolated heteromultimer comprising a heterodimeric Fc region is provided in certain embodiments, wherein the heterodimeric Fc region comprises a first and a second CH3 domain polypeptide, wherein at least one of said first and second CH3 domain polypeptides comprises modification of amino acid T350V. In isolated embodiments, an isolated heteromultimer comprising a heterodimeric Fc region, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising amino acid modification T350V and a second CH3 domain polypeptide also comprising amino acid modification T350V. An isolated heteromultimer comprising a heterodimeric Fc region is provided in certain embodiments, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising amino acid modification at positions F405 and Y407 and a second CH3 domain polypeptide comprising amino acid modification at position T394 . A first CH3 domain polypeptide comprises amino acid modifications at the D399 and Y407 positions and a second CH3 domain polypeptide comprises amino acid modification at the K409 and T411 positions. In isolated embodiments, an isolated heteromultimer comprising a heterodimeric Fc region, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising amino acid modifications L351Y and Y407A and a second CH3 domain polypeptide comprising amino acid modifications T366A and K409F. In one aspect, the first CH3 domain polypeptide or the second CH3 domain polypeptide comprises another amino acid modification at position T411, D399, S400, F405, N390, or K392. The amino acid modification at position T411 is selected from T411N, T411R, T411Q, T411K, T411D, T411E or T411W. The amino acid modification at position D399 is selected from D399R, D399W, D399Y or D399K. The amino acid modification at position S400 is selected from S400E, S400D, S400R, or S400K. The amino acid modification at position F405 is selected from F405I, F405M, F405T, F405S, F405V or F405W. The amino acid modification at position N390 is selected from N390R, N390K or N390D. The amino acid modification at the K392 position is selected from K392V, K392M, K392R, K392L, K392F or K392E.
[0024] [00024] In certain embodiments an isolated heteromultimer comprising a heterodimeric Fc region is provided, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising amino acid modifications T350V and L351Y and a second CH3 domain polypeptide also comprising amino acid modifications T350V and L351Y.
[0025] [00025] In another embodiment an isolated heteromultimer comprising a heterodimeric Fc region is provided, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising amino acid modification Y407A and a second CH3 domain polypeptide comprising amino acid modifications T366A and K409F. In one aspect the first CH3 domain polypeptide or the second CH3 domain polypeptide comprises other amino acid modifications K392E, T411E, D399R and S400R. In another aspect, the first CH3 domain polypeptide comprises amino acid modification D399R, S400R and Y407A and the second CH3 domain polypeptide comprises amino acid modification T366A, K409F, K392E and T411E. In another embodiment, the modified CH3 domain has a melting temperature (Tm) of about 74 ° C or higher and the heterodimer has a purity of about 95% or higher.
[0026] [00026] An isolated heteromultimer comprising a heterodimeric Fc region is provided in another embodiment, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising an amino acid modification at the L351 positions and a Y407A amino acid modification and a second CH3 domain polypeptide comprises an amino acid modification at position T366 and amino acid modification K409F. In one aspect the amino acid change at position L351 is selected from L351Y, L351I, L351D, L351R or L351F. In another aspect, the amino acid modification at position Y407 is selected from Y407A, Y407V or Y407S. In yet another aspect the amino acid modification at position T366 is selected from T366A, T366I, T366L, T366M, T366Y, T366S, T366C, T366V or T366W. In one embodiment, the modified CH3 domain has a melting temperature (Tm) of about 75 ° C or higher and the heterodimer has a purity of about 90% or higher.
[0027] [00027] An isolated heteromultimer comprising a heterodimeric Fc region is provided in another embodiment, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising an amino acid modification at the F405 position and amino acid modifications L351Y and Y407V and a second polypeptide from CH3 domain comprises modification of amino acid T394W. In one aspect the first CH3 domain polypeptide or the second CH3 domain polypeptide comprises an amino acid modification at positions K392, T411, T366, L368 or S400. The amino acid change at position F405 is F405A, F405I, F405M, F405T, F405S, F405V or F405W. The amino acid modification at the K392 position is K392V, K392M, K392R, K392L, K392F or K392E. The amino acid modification at the T411 position is T411N, T411R, T411Q, T411K, T411D, T411E or T411W. The amino acid modification at the S400 position is S400E, S400D, S400R or S400K. The amino acid modification at the T366 position is T366A, T366I, T366L, T366M, T366Y, T366S, T366C, T366V or T366W. The amino acid modification at the L368 position is L368D, L368R, L368T, L368M, L368V, L368F, L368S and L368A.
[0028] [00028] In another embodiment an isolated heteromultimer comprising a heterodimeric Fc region is provided, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising amino acid modifications L351Y, F405A and Y407V and a second CH3 domain polypeptide comprises amino acid modification T394W. In one aspect, the second CH3 domain polypeptide comprises amino acid modification T366L or T366I.
[0029] [00029] In yet another embodiment, an isolated heteromultimer comprising a heterodimeric Fc region is provided, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising at least one of the amino acid modifications Y349C, F405A and Y407V and a second domain polypeptide CH3 comprises modifications of amino acids T366I, K392M and T394W.
[0030] [00030] An isolated heteromultimer comprising a heterodimeric Fc region is provided in certain embodiments, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising amino acid modifications L351Y, F405A and Y407V and a second CH3 domain polypeptide comprising amino acid modifications K392M and T394W, and one from T366L and T366I.
[0031] [00031] In another embodiment, an isolated heteromultimer comprising a heterodimeric Fc region is provided, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising amino acid modifications F405A and Y407V and a second CH3 domain polypeptide comprising amino acid modifications T366L and T394W.
[0032] [00032] In another embodiment, an isolated heteromultimer comprising a heterodimeric Fc region is provided, wherein the heterodimeric Fc region comprises a first CH3 domain polypeptide comprising amino acid modifications F405A and Y407V and a second CH3 domain polypeptide comprising amino acid modifications T366I and T394W.
[0033] [00033] In certain embodiments of the heteromultimer, bispecific antibody or a multispecific antibody is provided.
[0034] [00034] In another embodiment, a composition is provided comprising a heteromultimer of the invention and a pharmaceutically acceptable carrier.
[0035] [00035] In another embodiment, a host cell comprising nucleic acid encoding the heteromultimeric of the invention is provided.
[0036] [00036] In certain embodiments, heteromultimeric is provided, wherein the heteromultimeric comprises at least one therapeutic antibody. In one aspect, the therapeutic antibody is selected from the group consisting of abagovomab, adalimumab, alemtuzumab, aurograb, bapineuzumab, basiliximab, belimumab, bevacizumab, briakinumab, canakinumab, catumaxomab, certolizumab pegol, cetuximab, dalbizbuzb, dumma, bumbizbam, dumma, , golimumab, ibritumomab tiuxetan, infliximab, ipilimumab, lumiliximab, mepolizumab, motavizumab, muromonab, mycograb, natalizumab, nimotuzumab, ocrelizumab, ofatumumab, omalizumab, palivizuma, pertumizumab, rumbumab, atlantizumab trastuzumab, ProxiniumTM, RencarexTM, ustekinumab, and zalutumumab.
[0037] [00037] In another embodiment of the heteromultimer of the invention there is provided a method for treating cancer in a patient with a cancer characterized by a cancer antigen, said method comprising administering to said patient a therapeutically effective amount of a heteromultimer.
[0038] [00038] In another embodiment of the heteromultimer of the invention, a method is provided for treating immune disorders in a patient with an immune disorder characterized by an immune antigen, said method comprising administering to said patient a therapeutically effective amount of a heteromultimer.
[0039] [00039] In certain embodiments, the modified Fc region used in the heteromultimeric construct described here comprises immunoglobulins of type G, for example, immunoglobulins that are defined as immunoglobulins of class 2 (IgG2) or immunoglobulins of class 3 (IgG3). In some embodiments, the modified Fc region used in the heteromultimeric construction described here comprises Immunoglobulin M or IgM. In some embodiments, the modified Fc region used in the heteromultimeric construction described here comprises Immunoglobulin A or IgA. In some embodiments, the modified Fc region used in the heteromultimeric construction described here comprises Immunoglobulin D or IgD. In some embodiments, the modified Fc region used in the heteromultimeric construction described here comprises Immunoglobulin E or IgE. In certain embodiments, the modified Fc region used in the heteromultimeric construct described here comprises all cases of the immunoglobulin G isotypes, for example, immunoglobulins that are defined as class 1 (IgG1), class 2 (IgG2), class 3 (IgG3) ) or class 4 (IgG4). Brief description of the figures
[0040] [00040] Figure 1 is a 3D graphic structure of a wild type antibody showing CH3 (top), CH2 (middle) and receptor regions. The dashed rectangle on the left side is expanded to the right side showing two regions, Region 1 and Region 2, of the target area of CH3;
[0041] [00041] Figure 2 is a 3D graphic representation showing the wild type residue at position 368;
[0042] [00042] Figure 3 is a 3D graphical representation of Region 1 showing the mutated position 368;
[0043] [00043] Figure 4 is a 3D graphical representation of additional mutations in Region 2;
[0044] [00044] Figure 5 is a table of calculations in silico for shock score, difference in interface area, difference in packaging, difference in electrostatic energy and general "affinity score" for the first three variants AZ1, AZ2 and AZ3;
[0045] [00045] Figure 6 shows a 3D graphic image showing variants AZ2 and AZ3, which are "built in" variant AZ1;
[0046] [00046] Figure 7 shows 3D graphic representations of AZ2 and AZ3 variants;
[0047] [00047] Figure 8 shows a table as in Figure 5, but for heterodimers AZ1, AZ2 and AZ3 and potential homodimers. The affinity score is not shown for homodimers, this is not relevant;
[0048] [00048] Figure 9 is a graphical representation of a 3D representation of AZ4 of wild type (left) and mutated (right);
[0049] [00049] Figure 10 is a table as in Figure 5 showing the in silico calculations for the AZ4 heterodimer and potential homodimers;
[0050] [00050] Figure 11 is a graphical representation of the CH3 AZ5 (left) and AZ6 (right) variants;
[0051] [00051] Figure 12 is a table as described for Figure 5 showing in silico data for AZ4, AZ5 and AZ6;
[0052] [00052] Figure 13 is a 3D graphic representation of an antibody on the left, with a drawing of the possibilities of binding characteristics in the receptor region using a heterodimeric approach;
[0053] [00053] Figure 14 is a schematic representation of the IgG molecule;
[0054] [00054] Figure 15 shows the alignment of multiple sequences of Fcγ receptors. Genebank / Uniprot Sequence ID's: FcγRIIA (sp P12318), FcγRIIB (sp P31994), FcγRIIc (gi 126116592), FcγRIIIA (sp P08637), FcγRIIIB (sp O75015);
[0055] [00055] Figure 16 is a schematic of the crystalline structure of the Fc-FcγRIIIb Complex [PDB ID: 1T83, Radaev & Sun]. A 1: 1 complex of the Fc and Fcγ receptor is observed with an asymmetric contact between the two Fc chains and the FcγR;
[0056] [00056] Figure 17 shows a scheme of multifunctional molecules based on the asymmetric Fc structure formed by heterodimeric variants described here: Asymmetric Fc Structure and Asymmetric Fc-Monomeric IgG Arm;
[0057] [00057] Figure 18 shows a scheme of multifunctional molecules based on the asymmetric Fc structure formed by heterodimeric variants described here: Asymmetric IgG Fc-Monospecific Arms and Asymmetric IgG Fc-Bispecific Arms (Common Light Chain);
[0058] [00058] Figure 19 shows an illustration of multifunctional molecules based on the asymmetric Fc structure formed by heterodimeric variants described here: Asymmetric IgG Fc-Bispecific arms and a functional molecule as a toxin;
[0059] [00059] Figure 20 illustrates multifunctional molecules based on the asymmetric Fc structure formed by heterodimeric variants described here: Asymmetric scFv Fc-Unique Arm and Asymmetric scFv Fc-Bispecific Arms;
[0060] [00060] Figure 21 illustrates alternative multifunctional molecules based on the asymmetric Fc structure formed by heterodimeric variants described here: Asymmetric scFv Fc-Triespecific arms and Asymmetric scFv Fc-Tetra-specific arms;
[0061] [00061] Figure 22 shows an asymmetric design of mutations on one side of the Fc for better selectivity. FcγR introduces a productive side for FcγR interactions and a non-productive side with wild type interactions. Mutations on the non-productive side of Fc can be introduced to block interactions with FcR and skew the polarity of Fc in order to interact only on the productive side;
[0062] [00062] Figure 23 shows the amino acid sequence for human wild-type IgG1;
[0063] [00063] Figure 24 shows the iterative process of the Fc heterodimer project, combining positive and negative projection strategies as described in detail below;
[0064] [00064] Figures 25A-25C show the in vitro assay used to determine the purity of the heterodimer. The assay is based on an entire monospecific antibody structure with two heavy Fc chains of different molecular weight; Heavy chain A has a C-terminal HisTag (His) and heavy chain B has a cleavable C-terminal mRFP Tag (RFP). The two heavy chains A (His) and B (RFP) are expressed in different relative ratios, together with a fixed amount of light chain, giving rise to three possible dimer species with different molecular weight: a) Homodimer Chain A (His) / A (His) chain (~ 150kDa); b) Heterodimer Chain A (His) / Chain B (RFP) (~ 175kDa); c) Chain B (RFP) / Chain B (RFP) homodimer (~ 200kDa). After expression, as described in Example 2, the ratio of heterodimer vs the two homodimers was determined by non-reducing SDS-PAGE, which allows the separation of the 3 species of dimer by molecular weight. SDS-PAGE gels were stained with Coomassie Brilliant Blue. Figure 25A: Variants tested were WT Chain A (His) only; WT chain B (RFP) only; WT chain A (His) plus chain B (RFP); Control 1 chain A (His) plus chain B (RFP), which has a reported heterodimer purity of> 95%. The composition of the dimer bands was verified by Western Blot with antibodies directed against IgG-Fc (anti-Fc), mRFP Tag (anti-mRFP) and HisTag (anti-His), as shown above. The SDS-PAGE shows a single band for the His / His homodimer, a double band for the His / RFP heterodimer and several bands for the RFP homodimer. The various bands are an artifact of the mRFP Tag and have been confirmed to have no influence on the physical properties of the Fc heterodimer. Figure 25B: The SDS-PAGE assay has been validated with the published Fc heterodimer variants Controls 1-4 as controls, See Table A. The variants were expressed with different relative ratios of chain A (His) vs chain B (RFP): Specifically, the 1: 3 ratio is equivalent to an LC, HC_His, HC_mRFP ratio of 25%, 10%, 65%; 1: 1 ratio of 25%, 20%, 55% and 3: 1 ratio of 25%, 40%, 35% respectively (the apparent 1: 1 expression of chain A (His) to chain B (RFP) was determined as being close to 20% / 55% (His / RFP) for WT Fc). Figure 25C shows a non-reducing SDS-PAGE assay to determine the heterodimer purity of Structure 1 variants. The Fc variants were expressed with different relative ratios of A (His) vs B-chain (RFP) and analyzed by SDS - Non-reducing page as described in Figure 2. Specifically, the 1: 3 ratio is equivalent to a ratio of LC, HC_His, HC_mRFP of 25%, 10%, 65%; 1: 1 ratio of 25%, 20%, 55% and 3: 1 ratio of 25%, 40%, 35% respectively (the apparent 1: 1 expression of chain A (His) to chain B (RFP) was determined as being close to 20% / 55% (His / RFP) for WT Fc);
[0065] [00065] Figures 26A-26B show Fc heterodimer variants expressed with a specific ratio of chain A (His) vs chain B (RFP) (See Table 2), purified by Protein A affinity chromatography and analyzed by SDS-PAGE non-reducer as described in Figures 25A-25C). Figure 26A illustrates the classification of heterodimers based on purity as seen by visual inspection of the SDS-PAGE results. For comparison, the equivalent amount of the purified Protein A product was loaded onto the gel. This definition of purity based on unreduced SDS-PAGE was confirmed by LC / MS in selected variants (see Figure 28). Figure 26B provides exemplary SDS-PAGE results of selected protein A purified heterodimer variants (AZ94, AZ86, AZ70, AZ33 and AZ34);
[0066] [00066] Figures 27A-27B illustrate DSC analyzes to determine the melting temperature of the heterodimeric CH3-CH3 domain formed by the heterodimeral variants described here. Two independent methods were used to determine the melting temperatures. Figure 27A provides thermograms equipped for 4 independent non-2-state transitions and optimized to generate values for CH2 and Fab transitions close to the values reported in the literature for ~ 72 ° C (CH2) and ~ 82 ° C (Fab ). Figure 27B shows the normalized and baseline-corrected thermograms for the heterodimer variants were subtracted from WT to generate a peak of positive and negative difference for only the CH3 transition;
[0067] [00067] Figure 28 illustrates the LC / MS analysis of the variant of example AZ70, as described in example 2. The expected masses (calculated average) for the glycosylated heterodimer and homodimer are indicated. The region consistent with the heterodimer mass contains major peaks corresponding to the loss of a glycine (-57 Da) and the addition of 1 or 2 hexoses (+ 162 Da and +324 Da, respectively). The purity of the heterodimer is classified as> 90% if there are no significant peaks corresponding to one of the homodimers;
[0068] [00068] Figures 29A-29D show the CH3 interface of Fig2 9AWT Fc; Fig29B AZ6; Fig29C AZ33; Fig29D AZ19. The comprehensive in silico analysis, as described in the detailed description section and the comparison of the variants for the WT indicated that one of the reasons for the inferior WT stability of the initial AZ33 heterodimer is the loss of the Y407 and T366 core interaction / packaging. Initial AZ33 shows the non-ideal packaging in this hydrophobic core as illustrated in Fig29B, suggesting that optimization of this region, particularly at position T366, would improve the stability of AZ33. This is illustrated in Fig 29C and Fig29D with T366I and T366L. The experimental data correlate with this structural analysis and show that T366L generates the greatest increase in Tm. See, Example 5;
[0069] [00069] Figure 30 illustrates the usefulness and importance of dynamic conformational analysis, exemplified in Structure 1 initial variant AZ8. The structure after in silico mutagenesis (structure conformation close to WT) is superimposed with a structure representative of a 50ns Molecular Dynamics simulation analysis. The figure highlights the great conformational difference in the region of the D399-S400 loop of the AZ8 vs WT variant, which in turn exposes the hydrophobic core to the solvent and causes decreased stability of the AZ8 heterodimer;
[0070] [00070] Figures 31A-31C illustrate how comprehensive in silico analysis information was used and MD simulation was used in the described positive design strategy. As illustrated in Figure 30, one of the reasons for the less than WT stability of AZ8 is the weakened interaction of loop 399-400 to 409, which is mainly due to the loss of packaging interactions F405 (see comparison of Fig31A (WT) vs Fig31B (AZ8)). One of the positive design strategies was the optimization of the hydrophobic packaging of the area, to stabilize the conformation of loop 399-400. This was achieved by the K392M mutation that is illustrated in Fig. 31 C. Fig. 31C represents the heterodimer AZ33, which has a Tm of 74 ° vs. 68 ° of the initial negative design of variant AZ8;
[0071] [00071] Figures 32A-32B illustrate the dynamics of the Fc molecule observed using principal component analysis of a molecular dynamics path. Fig. 32A shows a structure trace of the Fc structure as a reference. Fig 32B and C represent an overlap of the dynamics observed along the 2 main modes of movement in the Fc structure. The CH2 domains of the A and B chains show significant opening / closing movements in relation to each other while the CH3 domains are relatively rigid. Mutations in the CH3 interface impact the relative flexibility and dynamics of this open / close movement in the CH2 domains;
[0072] [00072] Figures 33A-33C illustrate the hydrophobic core packaging of two variants of Structure-2 vs. WT. Fig 33A WT Fc; Fig 33B AZ63; and Fig 33C AZ70. Comprehensive in silico analysis of the initial Structure 2 variant suggested that the loss of WT interactions from the Y407-T366 core is one of the reasons for less than WT stability for the initial Structure-2 variants. The loss of Y407-T366 is partially compensated by the K409F mutations, but as illustrated in Fig. 33B, particularly the T366A mutation leaves a cavity in the hydrophobic nucleus, which destabilizes the variant vs. WT. Targeting this hydrophobic nucleus by additional T366V_L351Y mutations, as shown by the Fc AZ70 variant in Fig33C, proved to be successful; AZ70 has an experimentally determined Tm and 75.5 ° C. See Table 4 and Example 6;
[0073] [00073] Figures 34A-34C illustrate the interactions of loop 399-400 of two variants of Structure-2 vs. o WT: Fig 34A WT Fc; Fig 34B AZ63; and Fig 34C AZ94. Comprehensive in silico analysis of the initial Structure-2 variant suggested that the loss of the WT K409-D399 salt bridge (Fig. 34A) due to the K4 0 9F mutation and the then unmet D399 (Fig34B) causes a more 'open' conformation 'handle 399-400. This further leads to greater exposure to the hydrophobic core solvent and further destabilization of the variant vs. WT. One of the strategies used to stabilize loop 399-400 and compensate for the loss of the K409-D399 interaction was the projection of additional salt bridges D399R-T411E and S400R-K392E, as illustrated in Fig34C for the AZ94 variant. The experimental data showed a purity of> 95% and Tm of 74 ° C. See Table 4 and Example 6. In addition, although AZ94 has considerably higher purity and stability compared to the initial Structure-2 variant (purity <90%, Tm 71 ° C), AZ94 hydrophobic core mutations they are less preferred than the 'best' mutations in the hydrophobic nucleus identified in the AZ70 variant (Figure 33). Since the mutations in the hydrophobic nucleus at AZ7 0 (T366V_L351Y) are distal from the AZ94 salt bridge mutations in loop 399-400, the combination of the AZ70 amino acid mutations and the additional AZ94 mutations should have a higher melting temperature higher than AZ70 or AZ94. This combination can be tested as described in Examples 1-4;
[0074] [00074] Figure 35 illustrates the association constant (Ka (M-1)) of homodimeric IgG1 Fc, the heterodimeric variants het1 (Control 1): A: Y349C_T366S_L368A_Y407V / B: S354C_T366W and het2 (Control 4): A: K409D_K392D / B: D399K_D356K connecting to the six Fcgama receivers. Heterodimeric Fc variants tend to show slightly altered binding to Fcgama receptors compared to wild-type IgG1 Fc. See Example 7.
[0075] [00075] Figure 36A shows the relative binding strength of a wild-type IgG1 Fc and its various forms of homodimeric and asymmetric mutants for IIbF, IIBY and IIaR receptors, based on the wild-type binding strength as a reference. (Homo Fc + S267D) refers to the binding strength of a homodimeric Fc with the S2 6 7D mutation in both strands. (Het Fc + asym S267D) refers to the binding strength of a heterodimeric Fc with the S267D mutation introduced in one of the two chains in Fc. The average binding strength obtained by introducing the mutation into either of the two Fc chains is reported. The introduction of this mutation in a chain reduced the binding force to approximately half the force observed for the same mutation in a homodimeric manner. (Het Fc + asym S267D + asym E269K) refers to the binding force of a heterodimeric Fc with the S267D and E269K mutations introduced asymmetrically in one of the chains of the two Fc chains. The E269K mutation blocks the interaction of the FcgR to one side of the Fc and is capable of decreasing the binding force by approximately half that seen for the asymmetric S267D variant (Het Fc + S267D) alone. Fc Het here is made up of CH3 mutations as indicated for the het2 variant (Control 4) in Figure 35;
[0076] [00076] Figure 36B shows the association constant (Ka (M-1)) of several Fcs and their variants with a series of FcgRIIa, FcgRIIb, and FcgRIIIa allotypes. The Ka of the wild-type IgG1 Fc for various Fcg receptors is represented as columns with horizontal shadow. The bars with vertical shadows (base2 homodimer) represent the homodimeric Fc Ka with the S239D / D265S / I332E / S298A mutations. The columns with the slanted shadow represent the Ka of the heterodimeric Fc with asymmetric mutations A: S239D / D265S / I332E / E269K and B: S239D / D265S / S298A in the CH2 domain. The introduction of asymmetric mutations is able to achieve greater selectivity between receptors IIIa and IIa / IIb. The heterodimeric Fc here is made up of CH3 mutations as indicated for the het2 variant (Control 4) in Figure 35;
[0077] [00077] Figure 36C shows the association constant (Ka (M-1)) for wild-type IgG1 and three other variants involving homodimeric or asymmetric mutations in the CH2 domain of the Fc region. The Ka of the wild type Fc is represented in the shaded column with grids. The Ka of the Fc variant with the base mutation S239D / K326E / A330L / I332E / S298A introduced homodimerically (base homodimer 1) in both Fc chains is shown with the slant pattern column. The introduction of asymmetrically related mutations in the A and B chains of a heterodimeric Fc (heterobase 1) is shown with horizontal lines. The column with shaded vertical lines represents the asymmetric variant including the E269K mutation (hetero base 1 + PD). The heterodimeric Fc here is made up of CH3 mutations as indicated for the het2 variant (Control 4) in Figure 35;
[0078] [00078] Figure 37 - Table 6 is a list of CH3 domain variants based on the third phase of the project as described in Example 5 for Structure 1;
[0079] [00079] Figure 38 - Table 7 is a list of CH3 domain variants based on the third phase of the project as described in Example 6 for Structure 2;
[0080] [00080] Figures 39A-39B illustrate the determination of the purity of variants without any C-terminal Tags using LC / MS. Fig. 3A shows the LC / MS spectra of a representative variant (AZ162: L351Y_F405A_Y407V / T366L_K392L_T394W). The variant was expressed by transient coexpression, as described in the Examples using 3 different A-Heavy to B-Heavy Chain ratios of 1: 1.5 (AZ133-1), 1: 1 (AZ133-2) and 1.5 : 1 (AZ133-3). The samples were purified and deglycosylated with Endo S for 1 hour at 37 ° C. Before MS analysis, the samples were injected into a Poros R2 column and eluted in a gradient with 20-90% ACN, 0.2% FA in 3 minutes. The peak of the LC column was analyzed with an LTQ-Orbitrap XL mass spectrometer (Cone Voltage: 50 V Lens tube: 215 V; FT Resolution: 7,500) and integrated with the Promass software to generate molecular weight profiles. Fig. 39B shows the LC / MS spectra of the Control 2 sample, which represents the Knobs-into-Holes variant. The variant was expressed by transient coexpression, as described in the Examples using 3 different A-Heavy to B-Heavy Chain ratios of 1: 1.5 (Control 2-1), 1: 1 (Control 2-2) and 1 , 5: 1 (Control 2-3). The samples were purified and deglycosylated with Endo S for 1 hour at 37 ° C. Before MS analysis, the samples were injected into a Poros R2 column and eluted in a gradient with 20-90% ACN, 0.2% FA in 3 minutes. The peak of the LC column was analyzed with an LTQ-Orbitrap XL mass spectrometer (Cone Voltage: 50 V Lens tube: 215 V; FT Resolution: 7,500) and integrated with the Promass software to generate molecular weight profiles;
[0081] [00081] Figures 40A-40B Bispecific binding has been demonstrated using an anti-HER2 heterodimer and anti-HER3 scFvs fused to the N-terminus of the A-Chain and B-Chain of the Fc heterodimer. The variants resulting from bispecific HER2 / HER3 variants and the two monovalent-monospecific HER2, HER3 variants are illustrated in Figure 40-A (A-chain in dark gray; B-chain in lighter gray). Figure 40-B demonstrates a bispecific binding test;
[0082] [00082] Figure 41 illustrates a computational model comparing the Fc of wild type IgG1 and AZ3003. The computational model for AZ3002 is the same for AZ3003 in the T350 position. The table summarizes the selected heterodimer variants and the stabilizing effect of the T350V mutation on the CH3 fusion temperature. The figure shows heterodimer variants that were expressed and purified as described in Example 11. DSC was performed as detailed in Example 3 and LC / MS quantification was performed as detailed in Example 11;
[0083] [00083] Figure 42 illustrates a comparison of the crystal structure and the predicted model of the main heterodimer. The residues of the mutant interface (indicated in the table) are highlighted in the representation of the drawings;
[0084] [00084] Figure 43 shows the analysis of the glycosylation pattern of the purified main heterodimer;
[0085] [00085] Figure 44 illustrates the results of the forced degradation assessment of the purified main heterodimer;
[0086] [00086] Figure 45 shows an industry standard antibody purification process scheme; and
[0087] [00087] Figure 46 shows an evaluation of the Downstream Purification Summary of the AZ3003 heterodimer variant showing the yields and step recovery (see Example 15 for details). The heterodimer was produced in 10L of transient CHO as described in detail in Example 11. Detailed Description
[0088] [00088] Modified CH3 domains comprising specific amino acid modifications to promote heteromultimer formation are provided here. In one embodiment, the modified CH3 domains comprise modifications of specific amino acids to promote the formation of heterodimer (See, for example, Tables 1.1-1.3). In another embodiment, the modified CH3 domains comprise modifications of specific amino acids to promote the formation of heterodimer with increased stability (See, for example, Table 4, Table 6 and Table 7). Stability is measured as the melting temperature (Tm) of the CH3 domain and increased stability refers to a Tm of about 70 ° C or higher. The CH3 domains form part of the Fc region of a multispecific heteromultimeric antibody. They are provided here in a heteromultimer modality comprising a heterodimeric Fc region, where the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote heterodimer formation in which the modified CH3 domains are selected from the variants listed in Table 1. In a second embodiment, heteromultimers are provided comprising a heterodimeric Fc region, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, wherein the modified CH3 domain has a melting temperature ( Tm) of about 70 ° C or higher.
[0089] [00089] Amino acid modifications used to generate a modified CH3 domain include, among others, insertions, deletions, substitutions, and rearrangements of amino acids. Modifications to the CH3 domain and modified CH3 domains are referred to herein collectively as "CH3 modifications", "modified CH3 domains", "modified CH3 domains" or "CH3 variants". In certain embodiments, the modified CH3 domains are incorporated into a molecule of choice. Accordingly, in one embodiment, molecules, for example, polypeptides, are provided, such as immunoglobulins (for example, antibodies) and other binding proteins, comprising an Fc region (as used here, "Fc region" and similar terms include any region domain. heavy chain constant comprising at least part of the CH3 domain) incorporating a modified CH3 domain. Molecules comprising Fc regions comprising a modified CH3 domain (for example, a CH3 domain comprising one or more insertions, deletions, substitutions, and rearrangements of amino acids) are referred to herein as "Fc variants", "heterodimers" or "heteromultimers". The Fc variants present comprise a CH3 domain that has been modified asymmetrically to generate heterodimer Fc regions or variants. The Fc region is composed of two heavy-chain constant domain polypeptides - Chain A and Chain B, which can be used interchangeably, as long as each Fc region comprises a chain A and chain B polypeptide. Amino acid modifications are introduced into CH3 asymmetrically, resulting in a heterodimer when two modified CH3 domains form an Fc variant (See, for example, Table 1). As used here, asymmetric amino acid modifications are any modifications in which an amino acid at a specific position in a polypeptide (for example, "Chain A") is different from the amino acid in the second polypeptide (for example, "Chain B") at the same position of the heterodimer or Fc variant. This can be a result of modifying just one of the two amino acids or modifying both amino acids to two different amino acids of the Fc variant, Chain A and Chain B. The modified CH3 domains are understood to comprise one or more asymmetric amino acid modifications.
[0090] [00090] An amino acid that is at the interface between the first and the second said polypeptide of the CH3 domain is any amino acid in the first or second polypeptide of the CH3 domain that interacts with an amino acid in the other polypeptide of the CH3 domain resulting in the formation of the dimeric CH3 domain. An amino acid that is not at the interface between the first and the second said CH3 domain polypeptide is any amino acid in the first or second CH3 domain polypeptide that does not interact with an amino acid in the other CH3 domain polypeptide. In embodiments described here, a modified amino acid that is not at the interface between the first and the second said CH3 domain polypeptide is any amino acid in the first or second CH3 domain polypeptide which, after being modified as described here, does not interact with an amino acid in the another CH3 domain polypeptide. For example, in certain embodiments described here, modifications of the amino acid position T350 are provided. As demonstrated by the crystal structure provided in Example 12 and shown in Figure 42, T350 is not involved in interactions between the two CH3 domain polypeptides. Any T350 modifications were shown to have negligible impact on the formation of CH3 dimers, as described by Carter et al. Biochemistry 1998, 37, 9266. In the heteromultimeric Fc constructs described here, changes in the T350 positions have shown to have an unexpected stabilizing effect on the CH3 variant domains despite not being directly involved in the formation of the CH3 dimer itself. For example, variants comprising at least one T350X modification, where X is a natural or non-natural amino acid selected from valine, isoleucine, leucine, methionine, and derivatives or variants thereof, form very stable variant CH3 domains. In some embodiments, isolated heteromultimeral Fc constructs described herein are described here, comprising at least one T350V modification. In certain embodiments, the first and second polypeptide variant of the CH3 domain comprises the T350V modification which provides unexpected stability for the CH3 variant domain compared to the corresponding CH3 domain not comprising the modification.
[0091] [00091] In the present description, any concentration range, percentage range, ratio range or entire range should be understood to include the value of any integer within the recited range and, where appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise stated. As used herein, "about" means ± 10% of the indicated range, value, sequence or structure, unless otherwise stated. It should be understood that the terms "one" and "one" as used herein refer to "one or more" of the listed components unless otherwise indicated or dictated by their context. The use of the alternative (for example, "or") must be understood to mean one, two, or any combination of the alternatives. As used here, the terms "includes" and "comprises" are used interchangeably. In addition, it is to be understood that the individual single chain polypeptides or heterodimers derived from various combinations of the structures and substituents (e.g., modified CH3 domains) described herein are disclosed by the present application to the same extent as if each single chain or heterodimer polypeptide were established individually. Thus, the selection of particular components to form individual single chain polypeptides or heterodimers is within the scope of the present disclosure.
[0092] [00092] The "first polypeptide" is any polypeptide that must be associated with a second polypeptide, also referred to herein as "Chain A". The first and second polypeptides meet at an "interface". The "second polypeptide" is any polypeptide that is to be associated with a first polypeptide via an "interface", also referred to herein as "Chain B". The "interface" comprises those amino acid residues in "contact" on the first polypeptide that interact with one or more amino acid residues in "contact" on the interface of the second polypeptide. As used herein, the interface comprises the CH3 domain of an Fc region that is preferably derived from an IgG antibody and most preferably a human IgG1 antibody.
[0093] [00093] As used herein, "isolated" heteromultimer means a heteromultimer that has been identified and separated and / or recovered from a component of its natural cell culture environment. Contaminating components of its natural environment are materials that can interfere with diagnostic or therapeutic uses for the heterodimer and can include enzymes, hormones and other protein or non-protein solutes.
[0094] [00094] An amino acid with a side chain volume "not substantially greater" than a first amino acid is any amino acid that has a side chain volume no more than 20Å3 greater than the first amino acid based on the chain volume values lateral view of AA Zamyatnin, Prog. Biophys. Mol. Biol. 24: 107-123, 1972. In certain embodiments, the volume is no more than 10Å3 greater than the first amino acid. In some embodiments, the volume is no more than 5Å3 greater than the first amino acid. For example, in certain embodiments described here are lysine (K) mutations such as K392J in which J is selected from L, I or an amino acid with a volume of the side chain not substantially greater than the volume of the side chain of K.
[0095] [00095] Fc variant heterodimers are generally purified for substantial homogeneity. The phrases "substantially homogeneous", "substantially homogeneous form" and "substantial homogeneity" are used to indicate that the product is substantially devoid of by-products originating from undesirable polypeptide combinations (for example, homodimers). Expressed in terms of purity, substantial homogeneity means that the amount of by-products does not exceed 10%, and is preferably less than 5%, more preferably less than 1%, more preferably less than 0.5%, where the percentages are in Weight.
[0096] [00096] The terms understood by those skilled in the art of antibody technology are each given the meaning acquired in the art, unless expressly defined otherwise here. Antibodies are known to have variable regions, a hinge region and constant domains. The function and structure of immunoglobulin are reviewed, for example, in Harlow et al, Eds., Antibodies: A Laboratory Manual, Chapter 14 (Cold Spring Harbor Laboratory, Cold Spring Harbor, 1988).
[0097] [00097] The design of the Fc variant heterodimers of wild-type homodimers is illustrated by the positive and negative design concept in the context of protein engineering, balancing stability vs. specificity, in which mutations are introduced in order to direct the formation of heterodimer in relation to the formation of homodimer when polypeptides are expressed in cell culture conditions. Negative design strategies maximize unfavorable interactions for homodimer formation, introducing bulky side chains in one chain and small side chains in the opposite, for example, the knobs-into-holes strategy developed by Genentech ((Ridgway JB, Presta LG, Carter P. 'Knobs-into-holes' engineering of antibody CH3 domains for heavy chain heterodimerization.Protein Eng. 1996 Jul; 9 (7): 617-21; Atwell S, Ridgway JB, Wells JA, Carter P.Stable heterodimers from remodeling the domain interface of a homodimer using a phage display library. J Mol Biol. 270 (1): 26-35 (1997))), or by the electrostatic projection that leads to the repulsion of homodimer formation, for example the electrostatic steering strategy developed by Amgen (Gunaskekaran K, et al. Enhancing antibody Fc heterodimer formation through electrostatic steering effects: applications to bispecific molecules and monovalent IgG. JBC 285 (25): 19637-19646 (2010)). In these two examples, asymmetric point mutations of negative design were introduced in the wild type CH3 domain to direct the formation of heterodimer. To date, only negative design strategies are used to develop Fc heterodimers. Published results show that heterodimers designed using only a negative design approach leads to high specificity with> 95% heterodimers, but destabilizes the complex considerably (Supra). These negative design heterodimers have a melting temperature, of the modified CH3 domain, of 69 ° C or less, additional disulfide bond missing compared to the wild type. See table A below.
[0098] [00098] The melting temperature for wild-type IgG1 is shown as a range of 81-83 since the values in the literature vary according to the assay system used, we report a value of 81.5 ° C in our test system.
[0099] [00099] In contrast to the negative design, a general concept used to design proteins is the positive design. In this case, amino acid modifications are introduced into polypeptides to maximize favorable interactions within or between proteins. This strategy assumes that when several mutations are introduced that specifically stabilize the desired heterodimer while neglecting the effect on homodimers, the net effect will be better specificity for the desired heterodimer interactions on homodimers and, consequently, greater specificity of the heterodimer. It is understood in the context of engineering design that positive design strategies optimize the stability of desired protein interactions, but rarely reach> 90% specificity (Havranek JJ & Harbury PB. Automated design of specificity in molecular recognition. Nat Struct Biol. 10 (1): 45-52 (2003); Bolon DN, Grant RA, Baker TA, Sauer RT. Specificity versus stability in computational protein design. Proc Natl Acad Sci US A. 6; 102 (36): 12724-9 (2005 ); Huang PS, Love JJ, Mayo SL. A new designed protein protein interface Protein Sci. 16 (12): 2770-4 (2007)). Prior to this disclosure, positive design strategies were not used to design Fc heterodimers as more attention was paid to specificity compared to stability for the development and manufacture of therapeutic antibodies. In addition, beneficial positive design mutations can be difficult to predict. Other methodologies for improving stability, such as additional disulfide bonds, have attempted to improve stability in Fc heterodimers with success or limited improvement for the molecule. (See Table A). This may be because all the disulfide bonds of the projected CH3 Fc domain are exposed to the solvent, which results in a short disulfide bond life and therefore a significant impact on the long-term stability of the heterodimer - especially when the projected CH3 domain has a Tm below 70 ° C, without the additional disulfide bond (as in Control 4, which has a Tm of 6 9 ° C without the disulfide (see Control 2). Other methodologies for improving stability, such as bonds disulfide, can also be used with the Fc variants present, provided that the intrinsic stability (measured as melting temperature) of the CH3 domain is 70 ° C or higher without the disulfide bond, in particular when the intrinsic stability (measured as melting temperature) ) of the CH3 domain is 72 ° C or higher without the disulfide bond.
[0100] [000100] Therefore, here we reveal a new method for designing Fc heterodimers that results in the formation of stable and highly specific heterodimer. This design method combines positive and negative design strategies together with protein projection techniques guided by computational and structural modeling. This powerful method allowed us to design new combinations of mutations in the CH3 domain of IgG1 in which, using only standard cell culture conditions, heterodimers were formed with more than 90%, purity in relation to homodimers and the resulting heterodimers had a melting temperature of 70 ° C or higher. In exemplary embodiments, the variant Fc heterodimers have a melting temperature of 73 ° C or higher and a purity greater than 98%. In other exemplary embodiments, the Fc variant heterodimers have a melting temperature of 75 ° C or higher and a purity greater than 90%. In certain embodiments of the variant Fc heterodimers described herein, the variant Fc heterodimers have a melting temperature of 77 ° C or higher and a purity greater than 98%. In some embodiments of the variant Fc heterodimers described herein, the variant Fc heterodimers have a melting temperature of 78 ° C or higher and a purity greater than 98%. In certain embodiments of the variant Fc heterodimers described herein, the variant Fc heterodimers have a melting temperature of 79 ° C or higher and a purity greater than 98%. In certain embodiments of the variant Fc heterodimers described herein, the variant Fc heterodimers have a melting temperature of 80 ° C or higher and a purity greater than 98%. In certain embodiments of the variant Fc heterodimers described herein, the variant Fc heterodimers have a melting temperature of 81 ° C or higher and a purity greater than 98%.
[0101] [000101] In certain embodiments, an isolated heteromultimer comprising a heterodimeric Fc region is provided wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, wherein the modified CH3 domain has a melting temperature (Tm) of 70 ° C or higher. As used herein "increased stability" or "stable heterodimer", refers to a modified CH3 domain, in the formation of heterodimer, with a melting temperature of about 70 ° C or higher. In certain embodiments, "increased stability" or "stable heterodimer" refers to a modified CH3 domain, in the formation of heterodimer, with a melting temperature of about 72 ° C or higher. In certain embodiments, "increased stability" or "stable heterodimer" refers to a modified CH3 domain, in the formation of heterodimer, with a melting temperature of about 74 ° C or higher. In certain embodiments, "increased stability" or "stable heterodimer", refers to a modified CH3 domain, in the formation of heterodimer, with a melting temperature of about 75 ° C or higher. In certain embodiments, "increased stability" or "stable heterodimer" refers to a modified CH3 domain, in the formation of heterodimer, with a melting temperature of about 76 ° C or higher. In certain embodiments, "increased stability" or "stable heterodimer", refers to a modified CH3 domain, in the formation of heterodimer, with a melting temperature of about 78 ° C or higher. In certain embodiments, "increased stability" or "stable heterodimer", refers to a modified CH3 domain, in the formation of heterodimer, with a melting temperature of about 79 ° C or higher. In certain embodiments, "increased stability" or "stable heterodimer", refers to a modified CH3 domain, in the formation of heterodimer, with a melting temperature of about 80 ° C or higher. In certain embodiments, "increased stability" or "stable heterodimer", refers to a modified CH3 domain, in the formation of heterodimer, with a melting temperature of about 81 ° C or higher. In addition, the term "to promote heterodimer formation" is understood to refer here to amino acid mutations in the CH3 domain that result in more than 90% heterodimer formation in relation to homodimer formation.
[0102] [000102] In another embodiment, this increased stability is in the absence of an additional disulfide bond. Specifically, the increased stability is in the absence of an additional disulfide bond in the CH3 domain. In one embodiment, the modified CH3 domain does not comprise an additional disulfide bond as compared to the wild type CH3 domain. In an alternative embodiment, the modified CH3 comprises at least one disulfide bond compared to the wild type CH3 domain, provided that the modified CH3 has a melting temperature of 70 ° C or higher in the absence of the disulfide bond. In one embodiment, the modified CH3 domain comprises at least one disulfide bond as compared to the wild type CH3 domain, and the modified CH3 domain has a melting temperature (Tm) of about 77.5 ° C or higher. In one embodiment, the modified CH3 domain comprises at least one disulfide bond as compared to the wild type CH3 domain, and the modified CH3 domain has a melting temperature (Tm) of about 78 ° C or higher. In another embodiment, the modified CH3 domain comprises at least one disulfide bond as compared to the wild type CH3 domain and the modified CH3 domain has a melting temperature (Tm) of more than about 78 ° C, or greater than about 78.5 ° C, or above about 79 ° C, or above about 79.5 ° C, or above about 80 ° C, or above about 80.5 ° C, or above 81 ° C, or greater than about 81.5 ° C, or greater than about 82 ° C, or greater than about 82.5 ° C, or greater than about 83 ° C.
[0103] [000103] In one embodiment, the modified CH3 domain has a melting temperature of more than about 70 ° C, or greater than about 70.5 ° C, or greater than about 71 ° C, or greater than about 71.5 ° C, or above about 72 ° C, or above about 72.5 ° C, or above about 73 ° C, or above about 73.5 ° C, or above 74 ° C, or above about 74.5 ° C, or above about 75 ° C, or above about 75.5 ° C, or above about 76 ° C, or above about 76.5 ° C, or above about 77 ° C, or above about 77.5 ° C, or above about 78 ° C, or above about 78.5 ° C, or above 79 ° C, or above about 79.5 ° C, or above about 80 ° C, or above about 80.5 ° C, or above about 81 ° C, or above about 81.5 ° C, or above about 82 ° C, or above about 82.5 ° C, or above about 83 ° C. In another embodiment, the modified CH3 domain has a melting temperature of about 70 ° C, or about 70.5 ° C, or about 71 ° C, or about 71.5 ° C, or about 72 ° C, or about 72.5 ° C, or about 73 ° C, or about 73.5 ° C, or about 74 ° C, or about 74.5 ° C, or about 75 ° C, or about 75.50C, or about 76 ° C, or about 76.5 ° C, or about 77 ° C, or about 77.5 ° C, or about 78 ° C, or about 78 , 5 ° C, or about 79 ° C, or about 79.5 ° C, or about 80 ° C, or about 80.5 ° C, or about 81 ° C. In yet another embodiment, the modified CH3 domain has a melting temperature of about 70 ° C to about 81 ° C, or about 70.5 ° C to about 81 ° C, or about 71 ° C to about 81 ° C, or about 71.5 ° C to about 81 ° C, or about 72 ° C to about 81 ° C, or about 72.5 ° C to about 81 ° C, or about 73 ° C to about 81 ° C, or about 73.5 ° C to about 81 ° C, or about 74 ° C to about 81 ° C, or about 74.5 ° C to about 81 ° C, or about 75 ° C to about 81 ° C, or about 75.5 ° C to about 81 ° C, or 76 ° C to about 81 ° C, or about 76.5 ° About 81 ° C, or about 77 ° C to about 81 ° C, or about 77.5 ° C to about 81 ° C, or about 78 ° C to about 81 ° C, or about 78.5 ° C to about 82 ° C, or about 79 ° C to about 81 ° C. In yet another embodiment, the modified CH3 domain has a melting temperature of about 71 ° C to about 76 ° C, or about 72 ° C to about 76 ° C, or about 73 ° C to about 76 ° C, or about 74 ° C to about 76 ° C.
[0104] [000104] In addition to the improved stability, the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote heterodimer formation. These amino acid mutations to promote heterodimer formation are understood to be as compared to homodimer formation. This heterodimer formation as compared to the homodimer formation is known together here as "purity" or "specificity" or "heterodimer purity" or "heterodimer specificity". It is understood that the heterodimer purity refers to the percentage of the desired heterodimer formed compared to homodimer species formed in solution under standard cell culture conditions prior to selective purification of the heterodimer species. For example, a 90% heterodimer purity indicates that 90% of the dimer species in solution is the desired heterodimer. In one embodiment, the variant Fc heterodimers have a purity of more than about 90%, or greater than about 91%, or greater than about 92%, or greater than about 93%, or greater than about 94% , or greater than about 95%, or greater than about 96%, or greater than about 97%, or greater than about 98%, or greater than about 99%. In another embodiment, the variant Fc heterodimers have a purity of about 90%, or about 91%, or about 92%, or about 93%, or about 94%, or about 95%, or about 96%, or about 97%, or about 98%, or about 99%, or about 100%.
[0105] [000105] In a specific embodiment, the isolated heteromultimer comprising a heterodimeric Fc region in which the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, wherein the modified CH3 domain has a temperature melting point (Tm) of 70 ° C or higher and the resulting heterodimer has a purity greater than 90%. In one aspect, the resulting Fc variant heterodimer has a purity of over 98% and the modified CH3 domain has a melting temperature of more than about 70 ° C, or greater than about 71 ° C, or greater than about 72 ° C, or above about 73 ° C, or above about 74 ° C, or above about 75 ° C, or above about 76 ° C, or above about 77 ° C, or above at about 78 ° C, or above about 79 ° C, or above about 80 ° C or above about 81 ° C. In another aspect, the modified CH3 domain has a melting temperature of 70 ° C or higher and the resulting Fc variant heterodimer has a purity greater than about 90%, or greater than about 91%, or greater than about 92% , or greater than about 93%, or greater than about 94%, or greater than about 95%, or greater than about 96%, or greater than about 97%, or greater than about 98%, or more than about 99%.
[0106] [000106] In order to design these Fc variants with improved purity and stability, we use an iterative process of computational projection and experimental screening to select the most successful combinations of positive and negative design strategies (See Figure 24).
[0107] [000107] Specifically, in the initial design phase, different negative design Fc variant heterodimers were prepared and tested for expression and stability as described in Examples 1-3. The initial design phase included Fc AZ1-AZ16 variant heterodimers (See, Table 1). From that initial set of negative design Fc variant heterodimers, which were expected to have low stability (for example, a Tm below 71 ° C), the variant Fc heterodimers with more than 90% purity and a melting temperature of about 68 ° C or higher were selected for further development. This included variant heterodimers Fc AZ6, AZ8 and AZ15. In the second phase of the project, those selected Fc variant heterodimers were further modified to target stability and purity using positive design strategies after a detailed computational and structural analysis. The selected Fc variant heterodimers (AZ6, AZ8 and AZ15) were each analyzed with computational methods and comprehensive structural function analysis to identify the structural reasons for these Fc variants to have less stability than the wild type Fc homodimer, which is 81 ° C for IgG1. See, Table 4 for the list of Fc variant heterodimers and the Tm values.
[0108] [000108] In certain embodiments, the modified CH3 domain is selected from AZ1, or AZ2, or AZ3, or AZ4, or AZ5, or AZ6, or AZ7, or AZ8, or AZ9, or AZ10, or AZ11, or AZ12, or AZ13, or AZ14, or AZ15 or AZ16. In selected modalities, the modified CH3 domain is AZ6, or AZ8 or AZ15.
[0109] [000109] The computational and structure-function analysis tools included, among others, molecular dynamic analysis (MD), side chain / structure repackaging, potential Knowledge Base (KBP), packaging analysis (hydrophobic) and cavity (LJ , CCSD, SASA, dSASA (carbon / all atoms)), electrostatic GB calculations, and coupling analysis. (See Figure 24 for an overview of computational strategy).
[0110] [000110] One aspect of the protein projection approach was based on the combination of structural information from the IgG Fc protein derived from X-ray crystallography with computational modeling and the simulation of wild type and variant forms of the CH3 domain. This allowed us to gain new structural and physicochemical perspectives in relation to the function of individual amino acids and their cooperative actions. These structural and physico-chemical perspectives obtained from several modified CH3 domains, together with the resulting empirical data regarding their stability and purity, helped us to develop an understanding for the relationship between purity and stability of the Fc heterodimer compared to the Fc and homodimers the simulated structural models. In order to carry out our simulations, we started by building complete and realistic models and refining the quality of the wild type Fc structure of an IgG1 antibody. Protein structures derived from X-ray crystallography lack details about certain characteristics of proteins in an aqueous medium under physiological conditions and our refinement procedures have addressed these limitations. These include construction regions absent from the protein structure, often flexible parts of the protein such as loops and some residual side chains, assessment and definition of the protonation states of the neutral and charged residues and placement of potentially functionally relevant water molecules associated with the protein .
[0111] [000111] Molecular dynamics (MD) algorithms are a tool that we use, simulating the protein structure to assess the intrinsic dynamic nature of the Fc homodimer and the modified CH3 domain in an aqueous environment. Molecular dynamics simulations track the dynamic trajectory of a molecule resulting from movements resulting from interactions and forces that act between all atomic entities in the protein and its local environment, in this case, the atoms that make up the Fc and its surrounding water molecules. After molecular dynamics simulations, several aspects of the trajectories were analyzed to gain knowledge about the structural and dynamic characteristics of the Fc homodimer and Fc variant heterodimer, which we use to identify specific amino acid mutations to improve the purity and stability of the molecule.
[0112] [000112] Therefore, the generated MD trajectories were studied using methods such as principal component analysis to reveal the intrinsic low-frequency modes of movement in the Fc structure. This provides insight into the potential conformational substates of the protein (See Figure 32). While the critical protein-protein interactions between the A and B chains in the Fc region occur at the interface of the CH3 domains, our simulations indicated that this interface functions as a hinge in a movement involving the "opening" and "closing" of the N ends -terminal of the CH2 domains in relation to each other. The CH2 domain interacts with FcgR's at that end, as seen in Figure 16. Thus, while one does not want to be bound by a theory, it appears that the introduction of amino acid mutations at the CH3 interface affects the magnitude and nature of the open / close movement at the N-terminal end of the Fc and, therefore, how the Fc interacts with the FcgR's. See example 4 and Table 5.
[0113] [000113] The MD paths generated were also studied to determine the mutability of the specific amino acid residue positions in the Fc structure based on profiling its flexibility and analyzing its environment. This algorithm allowed us to identify residues that can affect the structure and function of the protein, providing a unique knowledge of the characteristics and mutability of the residue for the subsequent design phases of the modified CH3 domains. This analysis also made it possible to compare various simulations and assess the mutability based on outliers following the creation of the profile.
[0114] [000114] The MD paths generated were also studied to determine the correlated residue movements in the protein and the formation of waste networks as a result of coupling between them. Finding dynamic correlations and residue networks within the Fc structure is a critical step in understanding the protein as a dynamic entity and for developing knowledge about the effects of mutations at distal sites. See, for example, Example 6.
[0115] [000115] Thus, we study in detail the impact of mutations on the local environment of the site of the mutation. The formation of a tightly packed nucleus at the CH3 interface between the A and B strands is critical for the spontaneous pairing of the two strands in a stable Fc structure. Good packaging is the result of strong structural complementarity between molecular partners interacting, together with favorable interactions between contact groups. Favorable interactions result from buried hydrophobic contacts well removed from solvent exposure and / or the formation of complementary electrostatic contacts between hydrophilic polar groups. These hydrophobic and hydrophilic contacts have enthalpic and entropic contributions to the free energy of dimer formation at the CH3 interface. We employ a variety of algorithms to accurately model packaging at the CH3 interface between chain A and chain B and subsequently evaluate the thermodynamic properties of the interface by scoring the number of relevant physicochemical properties.
[0116] [000116] We employ a series of protein packaging methods including flexible structures to optimize and prepare model structures for the large number of variants that we screen computationally. After packaging, we evaluated a series of terms including contact density, shock score, hydrogen bonds, hydrophobicity and electrostatics. The use of solvent models has allowed us to more accurately address the effect of the solvent environment and to contrast differences in free energy after the mutation of specific positions in the protein to alternative waste types. Contact density and shock score provide a measure of complementarity, a critical aspect of effective protein packaging. These sorting procedures are based on the application of knowledge-based potentials or coupling analysis schemes dependent on the calculation of energy and entropy of residue interaction by pairs.
[0117] [000117] This comprehensive in silico analysis provided a detailed understanding of the differences of each Fc variant compared to the wild type with respect to the main interface points, asymmetry sites, poorly packed cavities and regions, structural dynamics of individual sites and unveiling sites place. These combined results from the computational analysis described identified specific residues, sequence / structural motifs and cavities that were not optimized and in combination responsible for the lowest stability (for example, Tm of 68 ° C) and / or lower specificity of <90% of purity. In the second design phase, we use positive target design to specifically address these assumptions by additional point mutations and test these by in silico projection using the methodology and analysis described above (see, Figure 24). The variant Fc heterodimers designed to improve the stability and purity for each design targeted in phase two (variant Fc AZ17-AZ101 heterodimers) have been experimentally validated for expression and stability, as described in Examples 1-4.
[0118] [000118] In certain embodiments, isolated heteromultimers comprising a heterodimeric Fc region are provided herein, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, in which the modified CH3 domain is AZ17 , or AZ18, or AZ19, or AZ20, or AZ21, or AZ22, or AZ23, or AZ24, or AZ25, or AZ26, or AZ27, or AZ28, or AZ29, or AZ30, or AZ21, or AZ32, or AZ33, or AZ34, or AZ35, or AZ36, or AZ37, or AZ38, or AZ39, or AZ40, or AZ41, or AZ42, or AZ43, or AZ44, or AZ45, or AZ46, or AZ47, or AZ48, or AZ49, or AZ50, or AZ51, or AZ52, or AZ53, or AZ54, or AZ55, or AZ56 or AZ57, or AZ58, or AZ59, or AZ60, or AZ61, or AZ62, or AZ63, or AZ64, or AZ65, or AZ66, orAZ67, or AZ68, or AZ69, or AZ70, or AZ71, or AZ72, orAZ73, or AZ74, or AZ75, or AZ76, or AZ77, or AZ78, or AZ79, or AZ80, or AZ81, or AZ82, or AZ83, or AZ84, or AZ85, or AZ86, or AZ87, or AZ88, or AZ89, or AZ90, or AZ91, the u AZ92, or AZ93, or AZ94, or AZ95, or AZ96, or AZ97, or AZ98, or AZ99, or AZ100 or AZ101. In an exemplary embodiment, the modified CH3 domain is AZ17, or AZ18, or AZ19, or AZ20, or AZ21, or AZ22, or AZ23, or AZ24, or AZ25, or AZ26, or AZ27, or AZ28, or AZ29, or AZ30 , or AZ21, or AZ32, or AZ33, or AZ34, or AZ38, or AZ42, or AZ43, or AZ 44, or AZ45, or AZ46, or AZ47, or AZ48, or AZ49, or AZ50, or AZ52, or AZ53, or AZ54, or AZ58, or AZ59, or AZ60, or AZ61, or AZ62, or AZ63, or AZ64, or AZ65, or AZ66, orAZ67, or AZ68, or AZ69, or AZ70, or AZ71, or AZ72, orAZ73, or AZ74, or AZ75, or AZ76, or AZ77, or AZ78, or AZ79, or AZ81, or AZ82, or AZ83, or AZ84, or AZ85, or AZ86, or AZ87, or AZ88, or AZ89, or AZ91, or AZ92, or AZ93, or AZ94, or AZ95, or AZ98, or AZ99, or AZ100 or AZ101. In a specific embodiment, the modified CH3 domain is AZ33 or AZ34. In another embodiment, the modified CH3 domain is AZ70 or AZ90.
[0119] [000119] In an exemplary embodiment, the CH3 domain comprises a first and second polypeptides (also referred to herein as Chain A and Chain B) in which the first polypeptide comprises amino acid modifications L351Y, F405A, and Y407V and in which the second polypeptide comprises amino acid modifications T366I, K392M and T394W. In another embodiment, a first polypeptide comprises amino acid modifications L351Y, S400E, F405A and Y407V and the second polypeptide comprises amino acid modifications T366I, N390R, K392M and T394W.
[0120] [000120] This iterative process of computational structure-function analysis, targeted design and experimental validation was used to design the remaining Fc variants listed in Table 1, in the subsequent phases of the project and resulting in Fc heterodimers with a purity greater than 90% and increased stability with a melting temperature of the CH3 domain greater than 70 ° C. In certain embodiments, the Fc variants comprise amino acid mutations selected from AZ1 to AZ136. In other embodiments, the Fc variants comprise mutations of selected amino acids from the Fc variants listed in Table 4.
[0121] [000121] From the first and second phase of the project, two nucleus structures were identified, Structure 1 and Structure 2, in which additional amino acid modifications were introduced in these structures to fine tune the purity and stability of Fc variant heterodimers. See Example 5 for a detailed description of the development of Structure 1 including AZ8, AZ17-62 and the variants listed in Table 6. See Example 6 for a detailed description of the development of Structure 2 including AZ15, AZ63-101 and the variants listed in Table 7.
[0122] [000122] The mutations in the nucleus of Structure 1 comprise L351Y_F405A_Y407V / T394W. Structure 1a comprises amino acid mutations T366I_K392M_T394W / F405A_Y407V and Structure 1b comprises amino acid mutations T366L_K392M_T394W / F405A_Y407V. See Example 5.
[0123] [000123] In certain embodiments, the modified CH3 domain comprises a first and second polypeptides (also referred to herein as Chain A and Chain B) in which the first polypeptide comprises amino acid modifications L351Y, F405A and Y407V and the second polypeptide comprises amino acid modification T394W. In one aspect, the modified CH3 domain still comprises point mutations at positions F405 and / or K392. Such mutations at the K392 position include, but are not limited to, K392V, K392M, K392R, K392L, K392F or K392E. These mutations at the F405 position include, but are not limited to, F405I, F405M, F405S, F405S, F405V or F405W. In another aspect, the modified CH3 domain still comprises point mutations at positions T411 and / or S400. Such mutations at the T411 position include, but are not limited to, T411N, T411R, T411Q, T411K, T411D, T411E or T411W. Such mutations at the S400 position include, but are not limited to, S400E, S400D, S400R or S400K. In yet another embodiment, the modified CH3 domain comprises a first and second polypeptides in which the first polypeptide comprises amino acid modifications L351Y, F405A and Y407V and the second polypeptide comprises amino acid modification T394W, wherein the first and / or second polypeptide comprises others amino acid modifications at positions T366 and / or L368. Such mutations at the T366 position include, but are not limited to, T366A, T366I, T366L, T366M, T366Y, T366S, T366C, T366V or T366W. In an exemplary embodiment, the amino acid mutation at position T366 is T366I. In another exemplary embodiment, the amino acid mutation at the T366 position is T366L. Mutations at the L368 position include, but are not limited to, L368D, L368R, L368T, L368M, L368V, L368F, L368S and L368A.
[0124] [000124] In certain embodiments, the modified CH3 domain comprises a first and second polypeptide (also referred to herein as Chain A and Chain B) in which the first polypeptide comprises amino acid modifications L351Y, F405A and Y407V and the second polypeptide comprises amino acid modifications T366L and T394W. In another embodiment, the modified CH3 domain comprises a first and second polypeptides in which the first polypeptide comprises amino acid modifications L351Y, F405A and Y407V and the second polypeptide comprises amino acid modifications T366I and T394W.
[0125] [000125] In certain other embodiments, the modified CH3 domain comprises a first and second polypeptides (also referred to herein as Chain A and Chain B) in which the first polypeptide comprises modifications of amino acids L351Y, F405A and Y407V and the second polypeptide comprises modifications of amino acids T366L, K392M and T394W. In another embodiment, the modified CH3 domain comprises a first and second polypeptide where the first polypeptide comprises amino acid modifications L351Y, F405A and Y407V and the second polypeptide comprises amino acid modifications T366I, K392M and T394W.
[0126] [000126] In yet another embodiment, the modified CH3 domain comprises a first and second polypeptides (also referred to herein as Chain A and Chain B) in which the first polypeptide comprises amino acid modifications F405A and Y407V and the second polypeptide comprises modifications of T366L amino acids , K392M and T394W. In another embodiment, the modified CH3 domain comprises a first and second polypeptides in which the first polypeptide comprises amino acid modifications F405A and Y407V and the second polypeptide comprises amino acid modifications T366I, K392M and T394W.
[0127] [000127] In certain embodiments, the modified CH3 domain comprises a first and second polypeptides (also referred to herein as Chain A and Chain B) in which the first polypeptide comprises amino acid modifications F405A and Y407V and the second polypeptide comprises amino acid modifications T366L and T394W. In another embodiment, the modified CH3 domain comprises a first and second polypeptide in which the first polypeptide comprises amino acid modifications F405A and Y407V and the second polypeptide comprises amino acid modifications T366I and T394W.
[0128] [000128] In an exemplary embodiment, isolated heteromultimers comprising a heterodimeric Fc region are provided herein, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, wherein the modified CH3 domain has a melting temperature (Tm) of about 74 ° C or higher. In another embodiment, isolated heteromultimers are provided here comprising a heterodimeric Fc region, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, wherein the modified CH3 domain has a temperature of melt (Tm) of about 74 ° C or more and the heterodimer has a purity of about 98% or more.
[0129] [000129] In certain embodiments, the isolated heteromultimer comprising a heterodimeric Fc region, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, wherein the modified CH3 domain has a temperature melting point (Tm) greater than 70 ° C and the modified CH3 domains are selected from Table 6.
[0130] [000130] The mutations in the nucleus of Structure 2 comprise L351Y_Y407A / T366A_K409F. Structure 2a comprises amino acid mutations L351Y_Y407A / T366V_K409F and Structure 2b comprises amino acid mutations Y407A / T366A_K409F. See Example 6.
[0131] [000131] In certain embodiments, the modified CH3 domain comprises a first and a second polypeptide (also referred to herein as Chain A and Chain B) wherein the first polypeptide comprises amino acid modifications L351Y and Y407A and the second polypeptide comprises amino acid modifications T366A and K409F. In one aspect, the modified CH3 domain still comprises point mutations at positions T366, L351, and Y407. Such mutations at the T366 position include, but are not limited to, T366I, T366L, T366M, T366Y, T366S, T366C, T366V or T366W. In a specific embodiment, the mutation at position T366 is T366V. Mutations at position L351Include, among others, L351I, L351D, L351R or L351 F. Mutations at position Y407 include, but are not limited to, Y407V or Y407S. See, CH3 AZ63-AZ70 variants in Table 1 and Table 4 and Example 6.
[0132] [000132] In an exemplary embodiment, the modified CH3 domain comprises a first and a second polypeptide (also referred to herein as Chain A and Chain B) wherein the first polypeptide comprises amino acid modifications L351Y and Y407A and the second polypeptide comprises amino acid modification T366V and K409F.
[0133] [000133] In an exemplary embodiment, isolated heteromultimers comprising a heterodimeric Fc region are provided herein, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, wherein the modified CH3 domain has a melting temperature (Tm) of about 75.5 ° C or higher. In another embodiment, isolated heteromultimers are provided here comprising a heterodimeric Fc region, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, wherein the modified CH3 domain has a temperature of melt (Tm) of about 75 ° C or greater and the heterodimer has a purity of about 90% or greater. In certain other embodiments, the modified CH3 domain comprises a first and a second polypeptide (also referred to herein as Chain A and Chain B) where the first polypeptide comprises amino acid modifications L351Y and Y407A and the second polypeptide comprises amino acid modification T366A and K409F, wherein the modified CH3 domain comprises one or more amino acid modifications at positions T411, D399, S400, F405, N390, and / or K392. These mutations at the D399 position include, but are not limited to, D399R, D399W, D399Y or D399K. Mutations at the T411 position include, but are not limited to, T411N, T411R, T411Q, T411K, T411D, T411E or T411W. Mutations at the S400 position include, but are not limited to, S400E, S400D, S400R, or S400K. Mutations at the F405 position include, but are not limited to, F405I, F405M, F405S, F405S, F405V or F405W. Mutations at the N390 position include, but are not limited to, N390R, N390K or N390D. Mutations at the K392 position include, but are not limited to, K392V, K392M, K392R, K392L, K392F or K392E. See, CH3 AZ71-101 variants in Table 1 and Table 4 and Example 6.
[0134] [000134] In an exemplary embodiment, the modified CH3 domain comprises a first and second polypeptides (also referred to herein as Chain A and Chain B) wherein the first polypeptide comprises amino acid modification Y407A and the second polypeptide comprises amino acid modification T366A and K409F . In one aspect, that modified CH3 domain still comprises amino acid modifications K392E, T411E, D399R and S400R. In another embodiment, the modified CH3 domain comprises a first and second polypeptides in which the first polypeptide comprises amino acid modification D399R, S400R and Y407A and the second polypeptide comprises amino acid modification T366A, K409F, K392E and T411E. In an exemplary embodiment, isolated heteromultimers comprising a heterodimeric Fc region are provided herein, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, where the modified CH3 domain has a temperature melting point (Tm) of about 74 ° C or higher. In another embodiment, isolated heteromultimers are provided here comprising a heterodimeric Fc region, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, wherein the modified CH3 domain has a temperature of melt (Tm) of about 74 ° C or higher and the heterodimer has a purity of about 95% or greater.
[0135] [000135] In certain embodiments, isolated heteromultimers comprising a heterodimeric Fc region are provided herein, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, where the modified CH3 domain has a melting temperature (Tm) greater than 70 ° C and the modified CH3 domains are selected from Table 7.
[0136] [000136] Furthermore, this new method of designing Fc variant heterodimers with increased purity and stability can be applied to other classes and isotypes of Fc regions. In certain embodiments, the Fc region is a human IgG Fc region. In other embodiments, the human IgG Fc region is a human IgG1, IgG2, IgG3 or IgG4 Fc region. In some embodiments, the Fc regions are from an immunoglobulin selected from the group consisting of IgG, IgA, IgD, IgE and IgM. In some modalities, IgG is a subtype selected from the group consisting of IgG1, IgG2a, IgG2b, IgG3 and IgG4. Table 1.1: CH3 domain amino acid modifications for the generation of Fc variant heterodimers.
[0137] [000137] The Fc region as defined herein comprises a CH3 domain or fragment thereof and may additionally comprise one or more domains of constant addition region or fragments thereof, including hinge, CH1 or CH2. It will be understood that the numbering of the Fc amino acid residues is that of the EU index as in Kabat et al., 1991, NIH Publication 91-3242, National Technical Information Service, Springfield, Va. The "EU index as established in Kabat" refers to refer to the EU index numbering of the human Kabat IgG1 antibody. For convenience, Table B provides the amino acids numbered according to the EU index as established in Kabat of the human IgG1 CH2 and CH3 domain.
[0138] [000138] According to one aspect of the invention, an isolated heteromultimeric Fc construct comprising a modified heterodimeric CH3 domain, said modified CH3 domain comprising: a first modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a polypeptide wild-type CH3 domain, and a second modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a wild-type CH3 domain polypeptide; wherein at least one of said first and second polypeptides of the CH3 domain comprises an amino acid modification of K392J wherein J is selected from L, I or an amino acid with a side chain volume not substantially greater than the volume of the K side chain ; wherein said first and second modified CH3 domain polypeptides preferably form a heterodimeric CH3 domain with a melting temperature (Tm) of at least about 74 ° C and a purity of at least 95%; and wherein at least one amino acid modification is not an amino acid that is at the interface between said first and said second polypeptide of CH3 domain. In certain embodiments there is a heteromultimeric Fc construct described here, comprising at least one T350X modification, where X is a natural or unnatural amino acid selected from valine, isoleucine, leucine, methionine, and derivatives or variants thereof. In some embodiments there is an isolated heteromultimeric Fc construct described here, comprising at least one T350V modification. In one embodiment is an isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C or higher. In one embodiment is the isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a Tm of about 77 ° C or higher. In certain embodiments, the modified CH3 domain has a Tm of about 80 ° C or higher. Provided in certain embodiments is an isolated heteromultimeric Fc construct described herein, wherein at least one CH3 domain polypeptide is a modified CH3 domain polypeptide comprising an amino acid modification of at least one of L351, F405, and Y407. In some embodiments there is an isolated heteromultimeric Fc construct, wherein at least one CH3 domain polypeptide is a modified CH3 domain polypeptide further comprising an amino acid modification of T366. In certain embodiments, there is an isolated heteromultimeric Fc construct described here, wherein the first CH3 domain polypeptide is a modified CH3 domain polypeptide comprising amino acid modifications at positions L351, F405, and Y407, and the second CH3 domain polypeptide is a modified CH3 domain polypeptide comprising amino acid modifications at positions T366, K392, and T394. In one embodiment is the isolated heteromultimeric Fc construct described here, said first CH3 domain polypeptide comprising amino acid modifications L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprising amino acid modifications T366L, K392M, and T394W. In some embodiments is the isolated heteromultimeric Fc construct described here, said first CH3 domain polypeptide comprising amino acid modifications L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprising amino acid modifications T366L, K392L, and T394W. In another embodiment is the isolated heteromultimeric Fc construct described here, said first CH3 domain polypeptide comprising amino acid modifications L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprising amino acid modifications T366I, K392M, and T394W. In some embodiments is the isolated heteromultimeric Fc construct described here, said first CH3 domain polypeptide comprising amino acid modifications L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprising amino acid modifications T366I, K392L, and T394W. In certain embodiments is the isolated heteromultimeric Fc construct described here, wherein at least one of said first and second polypeptides of the CH3 domain is a modified CH3 polypeptide comprising an amino acid modification at the S400 position. In another embodiment is the isolated heteromultimeric Fc construct described here, comprising the S400Z modification, in which Z is selected from a positively charged amino acid and a negatively charged amino acid. In some embodiments, the positively charged amino acid is lysine or arginine and the negatively charged amino acid is aspartic acid or glutamic acid. In certain embodiments is the isolated heteromultimeric Fc construct described here, said first CH3 domain polypeptide comprising a selected amino acid modification from S400E and S400R. In some embodiments, the isolated heteromultimeric Fc construct described herein is provided, wherein at least one of said first and second polypeptides of the CH3 domain is a modified CH3 polypeptide comprising an amino acid modification at the N390 position. In some embodiments, the modification of N 3 90 is N 3 90 Z, where Z is selected from a positively charged amino acid and a negatively charged amino acid. In one embodiment, N390Z is N390R. In certain embodiments of the isolated heteromultimeric Fc construct described herein, said first CH3 domain polypeptide is a modified CH3 domain polypeptide comprising the amino acid modification S400E and said second CH3 domain polypeptide is a modified CH3 domain polypeptide comprising amino acid modification N390R. In some embodiments of the isolated heteromultimeric Fc construct described here, each of the first and second CH3 domain polypeptides is a modified CH3 domain polypeptide, said modified CH3 domain polypeptide comprising the amino acid modification Q347R and the other CH3 domain polypeptide modified comprising the K360E amino acid modification.
[0139] [000139] Provided in one aspect is an isolated heteromultimeric Fc construct comprising a modified heterodimeric CH3 domain, said modified CH3 domain comprising: a first modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a CH3 domain polypeptide of wild type, and a second modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a wild type CH3 domain polypeptide; wherein at least one of said first and second polypeptides of the CH3 domain comprises an amino acid modification of K392J wherein J is selected from L, I or an amino acid with a side chain volume not substantially greater than the volume of the K side chain ; wherein said first and second modified CH3 domain polypeptides preferably form a heterodimeric CH3 domain with a melting temperature (Tm) of at least about 74 ° C and a purity of at least 95%; and wherein at least one amino acid modification is not an amino acid that is at the interface between said first and said second polypeptide of CH3 domain. In certain embodiments there is a heteromultimeric Fc construct described here, comprising at least one T350X modification, where X is a natural or unnatural amino acid selected from valine, isoleucine, leucine, methionine, and derivatives or variants thereof. In some embodiments there is an isolated heteromultimeric Fc construct described here, comprising at least one T350V modification. In one embodiment is an isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C or higher. In one embodiment is the isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a Tm of about 77 ° C or higher. In certain embodiments, the modified CH3 domain has a Tm of about 80 ° C or higher. In one embodiment is the isolated heteromultimeric Fc construct described here, wherein at least one CH3 domain polypeptide is a modified CH3 domain polypeptide comprising an amino acid modification of at least one of K409 and T411. In certain embodiments is the isolated heteromultimeric Fc construct described here, comprising at least one of K409F, T411E and T411D. In some embodiments is the isolated heteromultimeric Fc construct described here wherein at least one CH3 domain polypeptide is a modified CH3 domain polypeptide comprising an amino acid modification of D399. In some embodiments, the D399 amino acid modification is at least one for D399R and D399K.
[0140] [000140] Provided in one aspect is an isolated heteromultimeric Fc construct comprising a modified heterodimeric CH3 domain, said modified CH3 domain comprising: a first modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a CH3 domain polypeptide of wild type, and a second modified CH3 domain polypeptide comprising at least three amino acid modifications compared to a wild type CH3 domain polypeptide; wherein at least one of said first and second polypeptides of the CH3 domain comprises an amino acid modification of K392J wherein J is selected from L, I or an amino acid with a side chain volume not substantially greater than the volume of the K side chain ; wherein said first and second modified CH3 domain polypeptides preferably form a heterodimeric CH3 domain with a melting temperature (Tm) of at least about 74 ° C and a purity of at least 95%; and wherein at least one amino acid modification is not an amino acid that is at the interface between said first and said second polypeptide of CH3 domain. In certain embodiments there is a heteromultimeric Fc construct described here, comprising at least one T350X modification, where X is a natural or unnatural amino acid selected from valine, isoleucine, leucine, methionine, and derivatives or variants thereof. In some embodiments there is an isolated heteromultimeric Fc construct described here, comprising at least one T350V modification. In one embodiment is an isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C or higher. In one embodiment is the isolated heteromultimeric Fc construct described here, in which the modified CH3 domain has a Tm of about 77 ° C or higher. In certain embodiments, the modified CH3 domain has a Tm of about 80 ° C or higher. In certain embodiments of the isolated heteromultimeric Fc construct described here, wherein the first CH3 domain polypeptide is a modified CH3 domain polypeptide comprising at least one selected amino acid modification from K409F, T411E and T411D, and the second CH3 domain polypeptide is a modified CH3 domain polypeptide comprising at least one amino acid modification selected from Y407A, Y407I, Y407V, D399R and D399K. In some embodiments is any of the isolated heteromultimeric Fc constructs described herein, further comprising a first modified CH3 domain comprising one of the amino acid modifications T366V, T366I, T366A, T366M, and T366L; and a second modified CH3 domain comprising the amino acid modification L351Y. In some embodiments is any of the isolated heteromultimeric Fc constructs described herein, comprising a first modified CH3 domain comprising one of the K392L or K392E amino acid modifications; and a second modified CH3 domain comprising one of the amino acid modifications S400R or S400V.
[0141] [000141] An isolated heteromultimeric Fc construct comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide and a second modified CH3 domain polypeptide, each modified CH3 domain polypeptide comprising at least four amino acid mutations, is provided herein. at least one of said first and said second modified CH3 domain polypeptide comprises a selected mutation of N390Z and S400Z, wherein Z is selected from a positively charged amino acid and a negatively charged amino acid, and wherein said first and second CH3 domain polypeptides Preferably modified forms formed a heterodimeric CH3 domain with a melting temperature (Tm) of at least about 70 ° C and a purity of at least 90%. In one embodiment, the isolated heteromultimeric Fc construct is provided, wherein said first modified CH3 domain polypeptide comprising amino acid modifications at positions F405 and Y407 and said second modified CH3 domain polypeptide comprises amino acid modification at position T394. In one embodiment, the isolated heteromultimeric Fc construct, the first modified CH3 domain polypeptide comprising an amino acid modification at position L351, is provided. In certain embodiments, there is the isolated heteromultimer described herein, said second modified CH3 domain polypeptide comprising a modification of at least one of the T366 and K392 positions. In some embodiments, there is the isolated heteromultimer described here, in which the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C and is formed with a purity of at least about 95%. In certain embodiments, there is the isolated heteromultimer described herein, at least one modified CH3 domain polypeptide comprising amino acid modifications of at least one of N390R, S400E and S400R. In some embodiments there is an isolated heteromultimer described here, one of said first and second modified CH3 domain polypeptides comprising amino acid modifications at position 347 and the other modified CH3 polypeptide comprising amino acid modification at position 360. In certain embodiments is the heteromultimer isolate described herein, at least one of said first and second modified CH3 domain polypeptides comprising T350V amino acid modification. In specific embodiments is an isolated heteromultimer described herein, said first modified CH3 domain polypeptide comprising at least one selected amino acid modification from L351Y, F405A and Y407V; and said second modified CH3 domain polypeptide comprising at least one selected amino acid modification from T366L, T366I, K392L, K392M and T394W. In certain embodiments described here is an isolated heteromultimer, the first modified CH3 domain polypeptide comprising amino acid modifications at positions D399 and Y407, and a second modified CH3 domain polypeptide comprising amino acid modification at positions K409 and T411. In some embodiments there is an isolated heteromultimer described here, the first CH3 domain polypeptide comprising amino acid modification at the L351 position, and the second modified CH3 domain polypeptide comprising amino acid modifications at the T366 and K392 position. In specific embodiments, isolated heteromultimers are described herein, at least one of said first and second polypeptides of the CH3 domain comprising amino acid modification of T350V. In certain embodiments, isolated heteromultimers described herein, wherein the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C or higher and is formed with a purity of at least about 95%. Provided in certain embodiments are isolated heteromultimeric Fc constructs described herein, said first modified CH3 domain polypeptide comprising amino acid modifications selected from L351Y, D399R, D399K, S400D, S400E, S400R, S400K, Y407A, and Y407V; and said second modified CH3 domain polypeptide comprising amino acid modifications selected from T366V, T366I, T366L, T366M, N390D, N390E, K392L, K392I, K392D, K392E, K409F, K409W, T411D and T411E.
[0142] [000142] An isolated heteromultimeric Fc construct comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide and a second modified CH3 domain polypeptide, each modified CH3 domain polypeptide comprising at least three amino acid mutations, is provided herein. one of said first and said second modified CH3 domain polypeptide comprises a selected mutation of T411E and T411D, and wherein said first and second modified CH3 domain polypeptides preferably form a heterodimeric CH3 domain with a melting temperature (Tm) of at least about 70 ° C and a purity of at least 90%. In one embodiment, the isolated heteromultimeric Fc construct is provided in which said first modified CH3 domain polypeptide comprising amino acid modifications at positions F405 and Y407 and said second modified CH3 domain polypeptide comprises amino acid modification at position T394. In one embodiment, the isolated heteromultimeric Fc construct, the first modified CH3 domain polypeptide comprising an amino acid modification at position L351, is provided. In certain embodiments, there is the isolated heteromultimer described herein, said second modified CH3 domain polypeptide comprising a modification of at least one of the T366 and K392 positions. In some embodiments, there is the isolated heteromultimer described here, in which the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C and is formed with a purity of at least about 95%. In certain embodiments, there is the isolated heteromultimer described herein, at least one modified CH3 domain polypeptide comprising amino acid modifications of at least one of N390R, S400E and S400R. In some embodiments there is an isolated heteromultimer described here, one of said first and second modified CH3 domain polypeptides comprising amino acid modifications at position 347 and the other modified CH3 polypeptide comprising amino acid modification at position 360. In certain embodiments is the heteromultimer isolate described herein, at least one of said first and second modified CH3 domain polypeptides comprising T350V amino acid modification. In specific embodiments is an isolated heteromultimer described herein, said first modified CH3 domain polypeptide comprising at least one selected amino acid modification from L351Y, F405A and Y407V; and said second modified CH3 domain polypeptide comprising at least one selected amino acid modification from T366L, T366I, K392L, K392M and T394W. In certain embodiments described here is an isolated heteromultimer, the first modified CH3 domain polypeptide comprising amino acid modifications at positions D399 and Y407, and a second modified CH3 domain polypeptide comprising amino acid modification at positions K409 and T411. In some embodiments there is an isolated heteromultimer described here, the first CH3 domain polypeptide comprising amino acid modification at the L351 position, and the second modified CH3 domain polypeptide comprising amino acid modifications at the T366 and K392 position. In specific embodiments, isolated heteromultimers are described herein, at least one of said first and second polypeptides of the CH3 domain comprising amino acid modification of T350V. In certain embodiments, isolated heteromultimers described herein, wherein the modified CH3 domain has a melting temperature (Tm) of at least about 75 ° C or higher and is formed with a purity of at least about 95%. Provided in certain embodiments are isolated heteromultimeric Fc constructs described herein, said first modified CH3 domain polypeptide comprising amino acid modifications selected from L351Y, D399R, D399K, S400D, S400E, S400R, S400K, Y407A, and Y407V; and said second modified CH3 domain polypeptide comprising amino acid modifications selected from T366V, T366I, T366L, T366M, N390D, N390E, K392L, K392I, K392D, K392E, K409F, K409W, T411D and T411E.
[0143] [000143] An isolated heteromultimeric Fc construct is provided here, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications L351Y, F405A and Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T366I, K392M and T394W.
[0144] [000144] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications L351Y, F405A and Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T366I, K392L and T394W.
[0145] [000145] Provided in some aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications L351Y, F405A and Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T366L, K392M and T394W.
[0146] [000146] Provided in some respects is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications L351Y, F405A and Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T366L, K392L and T394W.
[0147] [000147] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T350V, L351Y, F405A and Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T350V, T366L, K392L and T394W.
[0148] [000148] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T350V, L351Y, S400R, F405A, Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T350V, T366L, K392M and T394W.
[0149] [000149] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T350V, L351Y, S400E, F405A, Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T350V, T366L, N390R, K392M and T394W.
[0150] [000150] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T350V, L351Y, F405A, Y407V; and a second modified CH3 domain polypeptide comprising amino acid modifications T350V, T366L, K392L and T394W.
[0151] [000151] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T366V, K392L, K409F and T411E; and a second modified CH3 domain polypeptide comprising amino acid modifications L351Y, D399R, and Y407A.
[0152] [000152] Provided in one aspect is an isolated heteromultimeric Fc construct, comprising a modified CH3 domain comprising a first modified CH3 domain polypeptide comprising amino acid modifications T366V, K392LE K409F and T411E; and a second modified CH3 domain polypeptide comprising amino acid modifications L351Y, D399R, S400R and Y407A.
[0153] [000153] In certain embodiments, the Fc variant comprises a CH2 domain. In some embodiments, the CH2 domain is a variant CH2 domain. In some embodiments, the variant CH2 domains comprise asymmetric amino acid substitutions in the first and / or second polypeptide chain. In some embodiments, the heteromultimer comprises asymmetric amino acid substitutions in the CH2 domain so that a chain of said heteromultimer binds selectively to an Fc receptor.
[0154] [000154] In certain embodiments, the heteromultimer selectively binds to an Fc receptor. In some embodiments, the Fc receptor is a member of the Fcγ receptor family. In some embodiments, the receptor is selected from FcγRI, FcγRIIa, FcγRIIb, FcγRIIc, FcγRIIIa and FcγRIIIb. In one embodiment, the CH2 domain comprises asymmetric amino acid modifications that promote selective binding to Fcgama receptors.
[0155] [000155] In some embodiments, the heteromultimer selectively binds to FcγRIIIa. In some embodiments, the heteromultimer comprises asymmetric substitutions of amino acids selected from S267D, K392D and K409D. In some embodiments, the heteromultimer selectively binds to FcγRIIa. In some embodiments, the heteromultimer comprises asymmetric substitutions of amino acids selected from S239D, K326E, A330L and I332E. In some embodiments, the heteromultimer binds selectively to FcγRIIb. In some embodiments, the heteromultimer comprises asymmetric substitutions of amino acids selected from S239D, D265S, E269K and I332E. In some modalities, the heteromultimer binds selectively to FcγRIIIa and FcγRIIa. In some embodiments, the heteromultimer comprises asymmetric substitutions of amino acids selected from S239D, D265S, and S298A. In some embodiments, the heteromultimer binds selectively to FcγRIIIa and FcγRIIb. In some embodiments, the heteromultimer comprises asymmetric substitutions of amino acids selected from S239D, S298A, K326E, A330L and I332E. In some modalities, the heteromultimer selectively binds to FcγRIIa and FcγRIIb. In some embodiments, the heteromultimer comprises asymmetric substitutions of amino acids selected from S239D, D265S, S298A and I332E.
[0156] [000156] In certain embodiments, a method is provided for designing multifunctional drugs comprising heteromultimer described here. In some embodiments, a method is provided for designing bifunctional drugs comprising an Fc variant heterodimer. In some embodiments, a method is provided to design asymmetric mutations in the CH2 domain of a variant Fc heterodimer derived with mutations in the CH3 domain. In some modalities, a method is provided to project selectivity for the different Fcgama receptors based on mutations in the asymmetric Fc. In certain embodiments, a method is provided to design mutations that skew the binding of Fcgama receptors to one side of the Fc molecule. In certain embodiments, a method is provided to design polarity conductors that skew Fcγ receptors to interact with only one side of the asymmetric Fc structure of the heteromultimer described here.
[0157] [000157] In some embodiments, a polypeptide is provided comprising mutations in the asymmetric Fc CH2 domain that lead to the preferred Fcgama receptor selectivity profiles. In some embodiments, mutations in the CH3 domain lead to preferential formation of heterodimeric Fc. In certain embodiments there is a method for designing bispecific therapeutic entities based on the asymmetric Fc described here. In certain embodiments there is a method for designing multispecific therapeutic entities based on the asymmetric Fc described here.
[0158] [000158] Monoclonal antibodies such as IgG are symmetrical molecules composed of two heavy and two equivalent light polypeptide chains (Figure 14), each comprising several immunoglobulin (Ig) structural domains. The IgG class of mAb exists in one of four isoforms IgG1, IgG2, IgG3 or IgG4. The heavy chain is composed of four (VH, CH1, CH2 and CH3) and light chains of two (VL and CL) Ig domains, respectively. The VH and CH1 domains of each of the heavy chains combine with the VL and CL domains of the light chain to form the two Fab arms ("antigen binding fragment") of the mAb. The CH3 and CH2 domains of the two heavy chains interact through protein-protein contact in all CH3 domains and glycosylation in the CH2 domains to form the homodimeric Fc region ("crystallizable fragment"). The binding region between the CH1 and CH2 domains of the antibody constitutes the hinge region of the antibody molecule. In addition to connecting the Fab and Fc regions of the mAb, the hinge also maintains disulfide bonds between the two heavy chains and holds them together. The number of amino acids and disulfide bonds in the hinge region is strikingly different among the four IgG isotypes. The pattern of glycosylation in IgG molecules can be significantly different, about 30 different carbohydrate fractions have been observed in IgG molecules [Arnold J.N .; Wormald M.R .; Yes R.B .; Rudd P.M. and Dwek R.A. (2,007) Annual Reviews of Immunology 25, 21-50].
[0159] [000159] The symmetrical nature of the monoclonal antibody structure results in both Fab arms having their affinity for the ability to bind to the matured antigen to recognize the same epitope. At the other extreme, the Fc fraction of the antibody molecule is involved in interactions with various receptor molecules in immune or "effector" cells, and some of these interactions are responsible for mediating effector functions such as antibody-dependent cell cytotoxicity (ADCC), cell phagocytosis antibody-dependent (ADCP) and complement activation. Generally, the effector function involves immune responses leading to neutralization and elimination of the pathogen or toxin, activation of the complement and phagocytic response of the humoral immune system. The Fcγ receptor (FcγR) molecules in the effector cells contact the activated IgG antibody Fc involved in the integral antibody-antigen immune complex to mediate and regulate the effector response. The optimization of the interaction of therapeutic agents based on monoclonal antibodies with these Fcγ receptors can lead to improvements in the effectiveness of these drug candidates.
[0160] [000160] In humans, there are three known classes of FcγR with other polymorphic types within each class. The Fc in the IgG1 molecule is known as the FcγRI ligand (CD64), with dissociation constants in the nanomolar interval while binding to FcγRII (CD32) and FcγRIII (CD16) occurs in the micromolar interval [Bruhns P .; Iannascoli B .; England P .; Mancardi D.A .; Fernandez N .; Jorieux S. and Daeron M. (2009) Blood 113: 3716-25]. High-affinity FcγRI receptors can bind IgG in monomeric forms, while low-affinity FcγRII and FcγRIII receptors can only bind to antigen-antibody immunocomplexes or IgG aggregates as a result of the effects of avidity. The different forms of IgG have different affinities for different FcγR's; in particular, IgG1 and IgG3 show stronger activity. Fcγ receptors are the extracellular domains of transmembrane proteins and have cytoplasmic domains that are involved in the regulation of signaling pathways within the cell. When grouped on the surface of immune cells in association with antibody-mediated immunocomplexes, depending on the nature of the signaling units attached to the FcγR at the cytoplasmic end of these cell surface receptors, these molecules regulate the effector response [Nimmerjahn F. and Ravetch J.V. (2008) Nature Immu Rev 8 (1): 34-47].
[0161] [000161] At the human chromosomal level, three genes encode FcγRI (FcγRIA, FcγRIB, FcγRIC) and FcγRII (FcγRIIA, FcγRI IB, FcγRIIc) and two genes encode FcγRIII (FcγRIIIA, FcγRIIIB). Among human IgG-binding Fcγ receptors, FcγRIA, FcγRIC and FcγRIIIA have been shown to be associated with the membrane with a common γ-chain signal adapter protein, which contains a tyrosine-based activation motif of the cytoplasmic immunoreceptor (ITAM) that leads to activation of the effector function. FcγRIIA and FcγRIIc also comprise a cytoplasmic ITAM, but without the common γ-chain signal adapter protein. At the same time, FcγRIIB is linked to an immunoreceptor tyrosine-based inhibitory motif (ITIM). The activation of FcγRIIB, resulting in phosphorylation of ITIM results in the inhibition of the activation signaling cascade. FcγRIIIB, while devoid of tyrosine-based immunomodulatory cytoplasmic tails, has a GPI anchor (glycosyl-phosphatidyl-inositol) that has been shown to contribute to the activation of some granulocytes in the presence of FcγRIIA.
[0162] [000162] While the functional role of ITAM and ITIM motifs and the associated receptor molecules are known, the nature and mechanisms of signaling modulation in combination are not fully understood, especially when combined with the activity of a host of other receptors of immune cell surface and adapter molecules (eg, BCRs, CD22, CD45, etc.) involved in signal transduction. In this context, the design of Fc type molecules that can interact with these Fcγ receptors with exquisite selectivity profiles is a valuable structure in any attempt to deconvolve and modulate the effect of these receptor molecules with sudden regulatory activities.
[0163] [000163] In the context of the projection of antibody molecules that can differentiate FcγR's, the effort is complicated by the fact that the extracellular binding sections of the types of FcγRII and FcγRIII receptors show high sequence similarity (Figure 15), which can be attributed, at least in part, to ancestral segment duplication. The two main types of FcγRII receptors, A and B, have 69% sequence identity, while FcγRIIA and FcγRIIIA have about 44% sequence identity. FcγRIIB and FcγRIIc differ by only 2 residues in the extracellular region, despite being significantly different in the intracellular region, notable being the presence of ITIM and ITAM motifs respectively. As a result, it can be anticipated that therapeutic antibody molecules needed to bind to a receptor can also potentially bind to other classes of receptors, possibly resulting in unintended therapeutic effects.
[0164] [000164] To complicate things further, each of the receptor classes has several single nucleotide polymorphisms (SNPs) and copy number variations (CNVs). The diversity of the resulting receptor differentially impacts its affinity for IgG's and their mechanism of action. These genetic variations could affect the affinity of particular IgG subclasses for Fcγ receptors, alter effector events downstream or impact mechanisms that alter levels of receptor expression resulting in functionally relevant phenotypes, functionally unknown or non-functional receptor variants ( Bournazos S .; Woof JM; Hart SP and Dransfield I. (2009) Clinical and Experimental Immunology 157 (2): 244-54). These potentially lead to complex effects, altering the balance between activation and inhibitory receptor signaling, resulting in the creation of phenotypes susceptible to the disease.
[0165] [000165] Some of the allelic variations are listed in Table C. Notably, the R131 variant in FcγRIIa is a high respondent with IgG1, while the alternative H131 variants show more efficient interactions with IgG2 and IgG3. In the case of FcγRIIIa, homozygous donors for V at position 158 show increased NK cell activity compared to F / F158 homozygous individuals due to the greater affinity of the old allotype for humans IgG1, IgG3 and IgG4. The allelic variants NA1 and NA2 of FcγRIIIb are the result of a substitution of four amino acids, which in turn leads to differences in receptor glycosylation. The NA1 allele has potentiated binding and phagocytosis of the immune complex by neutrophils. FcγRIIB has two known allelic variants, 232I and 232T. The 232T variant is known to be strongly committed to its negative regulatory activity. The frequencies of polymorphisms in the FcγR and their associations for differential responsiveness to infections or predisposition to disease conditions, such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), vasculitis, immunity-mediated thrombotic purpura, myasthenia gravis, sclerosis Multiple (MS) and immune neuropathies (Guillain-Barre syndrome (GBS)) have been reported.
[0166] [000166] Variation in the number of copies at the locus of the FcγR genes, in particular for FcγRIIIB, FcγRIIc and FcγRIIIA, has been demonstrated, and another correlation of these differences for cell surface expression of these receptors has been observed. In contrast, FcγRIIa and FcγRIIb show no variation in the number of copies of the gene. The low number of copies of FcγRIIIb has actually been associated with glomerulonephritis in autoimmune disease systemic lupus erythematosus (SLE) [Aitman TJ et al. (2006) Nature 16; 439 (7078): 851-5]. This is particularly interesting, given the fact that a non-signaling GPI module anchors the FcγRIIIb receptor. This could be the hypothesis that the presence of these FcγRIIIb receptors could potentially act as a competitive inhibitor of Fc interactions with other signaling FcγR's. The effect of varying the copy number on FcγRIIc is also especially interesting. A C / T SNP at position 202 in FcγRIIc converts a glutamine residue into a stop codon preventing the generation of a functional protein. The FcγRIIc functional open reading frame is expressed in 9% of healthy individuals (white population), and there is a significant over-representation (19%) of the allele in the ITP population, implying a predisposition of these phenotypes to ITP [Breunis WB et al. (2008) Blood111 (3): 1029-38]. It has been shown that in individuals who express functional FcγRIIc in NK cells, the achieved ADCC is mediated by these receptors to a greater extent than FcγRIIIa. These complexities associated with these polymorphisms and genetic variations highlights the need for personalized treatment strategies that require highly designed drugs.
[0167] [000167] The various effector cells differ in the presentation of these Fcγ receptors, as well as in their humoral and tissue distribution, thus contributing to variations in their activation and action mechanisms [Table D]. Adjusting the selectivity of therapeutic antibodies for the recognition of specific types of FcγR and modulating the impact of certain classes of effector cells, leads to the optimization of the effector mechanism for particular disease conditions. This is done to selectively activate or inhibit specific effector modalities, depending on the condition of the disease being treated.
[0168] [000168] In addition, FcγR's are also expressed by follicular dendritic cells, endothelial cells, microglial cells, osteoclasts and mesangial cells. Currently, the functional significance of FcγR expression in these other cells is not known.
[0169] [000169] FcγRI of high affinity is composed of three domains of superfamily of type C immunoglobulin (IgSF) while FcγRII and FcγRIII of low affinity are constituted of two IgSF type C domains. The structure of FcγRIIa, FcγRIIb, FcγRIIIa and FcγRIIIb was resolved by crystallography. The two IgSF domains in these structures are positioned 50-55 degrees in relation to each other and are connected by a hinge.
[0170] [000170] The public structure of an Fc-FcγR cocomplex is that of the Fc-FcγRIIIb system and the FcγR geometry in the complex is kept very close to that observed in the apo state of the protein [Sondermann P .; Huber R .; Oosthuizen V. and Jacob U. (2000) Nature 406, 267-273 .; Radaev S .; Motyaka S .; Fridman W .; Sautes-Fridman C. and Sun P.D. (2001) J Biol Chem 276, 1646916477; Sondermann P. et al. Biochem Soc Trans. 2002 Aug; 30 (4): 481-6; Sondermann P, Oosthuizen V. Immunol Lett. 2 002 Jun 3; 82 (1-2): 51-6; Radaev S, Sun P. Mol Immunol. 2002 May; 38 (14): 1073-83.] [Figure 16]. The strong structural and sequence similarity between the receptors forms the basis of the comparative models of the Fc linked to the other receptors. On the other hand, the structural and sequence similarity between these molecules of the receptor also makes the Fc design with exquisite selectivity between the receptors and their various isotypes challenging.
[0171] [000171] Before the structural evaluation of the Fc-FcγR complex based on crystallography, there were doubts whether the duplicated axis of symmetry in the Fc molecule means two potential binding sites and an effective 2: 1 stoichiometry for the association of Fc-FcγR. Studies based on nuclear magnetic resonance (NMR) of Fc-FcγR interactions indicate that the binding of an Fc to an FcγR on one side of the molecule induces a conformational change that prevents the binding of a second FcγR molecule to the Fc of the same antibody molecule [Kato K. et al (2000) J Mol Biol. 295 (2): 213-24]. The geometry of the available cocrystal complex of Fc-FcγRIIIb confirms the association of FcγR to Fc in an asymmetric orientation with a 1: 1 stoichiometry. As shown in Figure 16, the FcγR binds to a fissure at one end of the horseshoe-shaped Fc molecule and is in contact with the CH2 domains of both chains.
[0172] [000172] Alanine scan mutagenesis [Shields RL et al. (2001) JBC 276 (9): 6591-604] provides information about the residues of the Fc interface with the different types of receptors and, therefore, involved in the Fc-FcγR interaction and recognition. Traditionally, optimization of therapeutic antibodies has focused on mutations that have increased binding to FcγRIII activation receptors [US Patent 6,737,056] or decreased affinity for FcγRIIb [US2009 / 0010920A1]. In all of these alternative variants, mutations are introduced simultaneously in both strands.
[0173] [000173] Monoclonal antibodies often show their therapeutic activities by inducing spatial localization of effector and target immune cells. A natural antibody mediates this by interacting with the target using its Fab domains and the effector cell using the Fc domain. They are capable of juxtaposing the immune complex vis-à-vis the effector cell so that the cell-mediated response can be included. The effects of avidity required for FcγR signaling, originating from the formation of immunocomplexes involving the targeting of a single target by several antibody molecules, is another example of the importance of spatio-temporal organization in immune action.
[0174] [000174] There is also a space-time aspect for cell signaling that is induced as part of the effector activity of mAb molecules. Cell signaling like those based on the activation of the FcγR molecule involves the location of the relevant receptor molecules within a region of the membrane domain referred to as lipid rafts. Lipid rafts are enriched with glycosphingolipids and cholesterol and several classes of signal transducers upstream, including the kinases of the Src family. After cellular stimulation, several signaling molecules, adapter proteins and signaling kinases as well as phosphatases are recruited. Molecular assembly in lipid rafts is important for signal transduction.
[0175] [000175] An unnatural design strategy, combining different antigen specificities and greater avidity to provide better binding properties is the basis of the bispecific therapeutic design. Bispecific antibodies or other forms of bispecific or multifunctional protein drugs are designed to mediate interactions between the target and a variety of effector cells [Muller & Kontermann (2010) BioDrugs 24 (2): 89-98]. Multispecific therapeutic molecules are designed to redirect Helper T cells or other immune effector cells against specific target cells.
[0176] [000176] In another embodiment, the invention relates to a method for identifying variant Fc polypeptides in silico based on the calculated binding affinities for FcγRIIa, FcγRIIb and / or FcγRIIIa. In another embodiment, the method also comprises calculating electrostatic, solvation, packaging effects, packing density, hydrogen bonding and in-silico entropic effects of said Fc variant polypeptides. In yet another embodiment, the method of the present invention further includes the construction of an Fc variant polypeptide and expression of said polypeptides in the context of a therapeutic antibody and also expressing said antibody in mammalian cells. In yet another embodiment, the method of the present invention comprises building a variant Fc polypeptide identified in silico by site-directed mutagenesis, PCR-based mutagenesis, cassette mutagenesis or de novo synthesis.
[0177] [000177] The factors taken into account when designing the synthetic Fc structure include in silico calculations of steric repulsion, change in the buried interface area, relative contact density, relative solvation and electrostatic effect. All of these matrices were used to reach an affinity score.
[0178] [000178] In one aspect, this application describes a molecular design to achieve exquisite FcγR selectivity profiles through the design of an asymmetric structure built on a heterodimeric Fc. This structure allows for asymmetric mutations in the CH2 domain to achieve a variety of new selectivity profiles. In addition, the structure has inherent characteristics for the projection of multifunctional therapeutic molecules (bi, tri, tetra or pentafunctional).
[0179] [000179] In certain embodiments, the asymmetric structure is optimized for pH-dependent binding properties to the neonatal Fc receptor (FcRn) to allow better recycling of the molecule and enhance its half-life and related pharmacokinetic properties.
[0180] [000180] The asymmetric structure can be optimized for connection with functionally relevant FcγRI receptor allotypes. FcγRI is a prominent marker in macrophages that are involved in chronic inflammatory disorders, such as Rheumatoid Arthritis, Atopic Dermatitis, Psoriasis and a number of lung diseases.
[0181] [000181] The asymmetric structure can be optimized for binding to protein A. Binding to protein A is often employed for separation and purification of antibody molecules. Mutations can be introduced into the asymmetric structure to prevent aggregation of the drug during storage.
[0182] [000182] Therefore, it is specifically envisaged that the Fc variants of the invention may contain, among others, one or more substitutions, modifications and / or mutations of additional amino acid residues, which result in an antibody with preferential characteristics including, among others: increased serum half-life, increased binding affinity, reduced immunogenicity, increased production, enhanced or reduced ADCC or CDC activity, altered glycosylation and / or disulfide bonds and modified binding specificity.
[0183] [000183] It is envisaged that the Fc variants of the invention may have other altered characteristics, including increased in vivo half lives (e.g., serum half lives) in a mammal; in particular, a human, increased in vivo stability (e.g., serum half-lives) and / or in vitro (e.g., shelf-life) and / or increased melting temperature (Tm) with respect to a comparable molecule. In one embodiment, a variant Fc of the invention has an in vivo half-life greater than 15 days, greater than 20 days, greater than 25 days, greater than 30 days, greater than 35 days, greater than 40 days, greater than 45 days, over 2 months, over 3 months, over 4 months, or over 5 months. In another embodiment, a variant Fc of the invention has an in vivo half-life (for example, liquid or powder formulation) greater than 15 days, greater than 30 days, greater than 2 months, greater than 3 months, greater than 6 months, or more than 12 months, or more than 24 months, or more than 36 months, or more than 60 months.
[0184] [000184] It will also be appreciated by one skilled in the art that the Fc variants of the invention may have altered immunogenicity when administered to a subject. In this sense, it is anticipated that the modified CH3 domain, which minimizes the immunogenicity of an Fc variant, is generally more desirable for therapeutic applications.
[0185] [000185] The Fc variants of the present invention can be combined with other Fc modifications, including, among others, modifications that alter the effector function. The invention includes combining an Fc variant of the invention with other Fc modifications to provide additive, synergistic or novel properties in antibodies or proteins of the Fc fusion. Such modifications may be in the hinge, CH1 or CH2 domains (or CH3 provided that this does not negatively alter the stability and purity properties of the present modified CH3 domain) or a combination thereof. It is envisaged that the Fc variants of the invention enhance the property of a modification with which they are combined. For example, if an Fc variant of the invention is combined with a mutant known as an FcγRIIIA ligand with a greater affinity than a comparable molecule comprising a wild-type Fc region; the combination with a mutant of the invention results in a greater potentiation in the affinity of FcγRIIIA.
[0186] [000186] In one embodiment, the Fc variants of the present invention can be combined with other Fc variants known as those disclosed in Duncan et al, 1988, Nature 332: 563-564; Lund et al., 1991, J Immunol 147: 2657-2662; Lund et al., 1992, Mol Immunol 29: 53-59; Alegre et al, 1994, Transplantation 57: 1537-1543; Hutchins et al., 1995, Proc Natl. Acad Sci USA 92: 11980-11984; Jefferis et al, 1995, Immunol Lett. 44:11 1-117; Lund et al., 1995, Faseb J 9: 115119; Jefferis et al, 1996, Immunol Lett 54: 101-104; Lund et al, 1996, Immunol 157: 4963-4969; Armor et al., 1999, Eur J Immunol 29: 2613-2624; Idusogie et al, 2000, J Immunol 164: 4178-4184; Reddy et al, 2000, J Immunol 164: 1925-1933; Xu et al., 2000, Cell Immunol 200: 16-26; Idusogie et al, 2001, J Immunol 166: 2571-2575; Shields et al., 2001, J Biol Chem 276: 6591-6604; Jefferis et al, 2002, Immunol Lett 82: 57-65; Presta et al., 2002, Biochem Soc Trans 30: 487-490); US Patent 5,624,821; 5,885,573; 6,194,551; US Patent Applications 60 / 601,634 and 60 / 608,852; PCT publications WO 00/42072 and WO 99/58572.
[0187] [000187] One skilled in the art will understand that the Fc variants of the invention may have altered Fc ligand binding properties (for example, FcγR, C1q) (examples of binding properties include, among others, binding specificity, the constant of equilibrium dissociation (KD), dissociation and association rates (Koff and Kon, respectively), avidity and / or binding affinity) and that certain changes are more or less desirable. It is well known in the art that the equilibrium dissociation constant (KD) is defined as koff / kon. In general, it is understood that a binding molecule (for example, an antibody) with a low KD is preferred to a binding molecule (for example, an antibody) with a high KD. However, in some cases, the kon or koff value may be more relevant than the KD value. A person skilled in the art can determine which kinetic parameter is most important for the application of a particular antibody. For example, a modification in CH3 and / or CH2 that potentiates the binding of Fc to one or more positive regulators (for example, FcγRIIIA), leaving unchanged or even reducing the binding of Fc to the negative regulator FcγRIIB would be more advantageous to improve activity ADCC. Alternatively, a CH3 and / or CH2 modification that reduced binding to one or more positive regulators and / or potentiated binding to FcγRIIB would be advantageous for reducing ADCC activity. In this sense, the binding affinity ratio (for example, equilibrium dissociation constant (KD)) can indicate whether the ADCC activity of a variant Fc is increased or decreased. For example, a decrease in the equilibrium dissociation constant (KD) FcγRIIIA / FcγRIIB ratio will correlate with improved ADCC activity, while an increase in the ratio will correlate with decreased ADCC activity.
[0188] [000188] As part of the characterization of the Fc variants they were tested for their binding affinities for FcγRIIIA (CD16a) and FcγRIIB (CD32b) reported as a ratio compared to wild-type IgG1. (See, Example 4 and Table 5). In this case, it was possible to evaluate the impact of CH3 domain mutations in the binding to these activation and inhibition Fc receptors. In one embodiment, isolated heteromultimers are provided here comprising a heterodimeric Fc region, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, wherein the modified CH3 domain has a temperature of melt (Tm) greater than 70 ° C, where the heteromultimer that binds to CD16a is approximately the same as compared to wild type homodimer. In certain embodiments, the heteromultimer that binds to CD16a is increased compared to wild-type homodimer. In an alternative embodiment, the heteromultimer that binds to CD16a is reduced in comparison to wild type homodimer.
[0189] [000189] In certain embodiments, isolated heteromultimers comprising a heterodimeric Fc region are provided herein, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, where the modified CH3 domain has a melting temperature (Tm) greater than 70 ° C, where the heteromultimer that binds to CD32b is approximately the same as compared to wild type homodimer. In certain embodiments, the heteromultimer that binds to CD32b is increased in comparison to wild type homodimer. In an alternative embodiment, the heteromultimer that binds to CD32b is reduced in comparison to wild type homodimer.
[0190] [000190] One skilled in the art will understand that, instead of reporting the CD16a and CD32b binding KD as a ratio of Fc variant to wild type homodimer, KD can be reported as a ratio of Fc variant binding to CD16a for Fc variant linking to CD32b (data not shown). This ratio would provide an indication of the mutation of the ADCC-modified CH3 domain, both unchanged and increased to decreased compared to the wild type, described in more detail below.
[0191] [000191] The affinity and binding properties of the Fc variants of the invention to an FcγR are initially determined using in vitro assays (biochemical or immunological based assays) known in the art to determine Fc-FcγR interactions, that is, region specific binding Fc for an FcγR, including, but not limited to, ELISA assay, surface plasmon resonance assay, immunoprecipitation assays (See section entitled "Characterization and Functional Assays" below) and other methods such as indirect binding assays, competitive inhibition assays , fluorescence resonance energy transfer (FRET), gel electrophoresis and chromatography (for example, gel filtration). These and other methods may use a marker on one or more of the components to be examined and / or use a variety of detection methods, including, but not limited to, chromogenic, fluorescent, luminescent or isotopic markers. A detailed description of binding affinity and kinetics can be found in Paul, W. E., ed., Fundamental Immunology, 4th Ed., Lippincott-Raven, Philadelphia (1999), which focuses on antibody-immunogen interactions.
[0192] [000192] It is anticipated that the binding properties of the molecules of the invention are also characterized by functional in vitro assays for the determination of one or more functions of FcγR mediating effector cells (See section entitled "Characterization and Functional Assays" below). In certain embodiments, the molecules of the invention have similar binding properties in in vivo models (as described and disclosed here) as those in in vitro based assays. However, the present invention does not exclude molecules of the invention that do not exhibit the desired phenotype in in vitro based assays, but do exhibit the desired phenotype in vivo.
[0193] [000193] The invention includes Fc variants that bind to FcγRIIIA (CD16a) with increased affinity, with respect to a comparable molecule. In a specific embodiment, the Fc variants of the invention bind to FcγRIIIA with greater affinity and bind to FcγRIIB (CD32b) with a binding affinity that is unchanged or reduced, in relation to a comparable molecule. In yet another embodiment, the Fc variants of the invention have an equilibrium dissociation constant (KD) ratio FcγRIIIA / FcγRIIB that is decreased relative to a comparable molecule.
[0194] [000194] Also included in the present invention are Fc variants that bind to FcγRIIIA (CD16a) with decreased affinity with respect to a comparable molecule. In a specific embodiment, the Fc variants of the invention bind to FcγRIIIA with decreased affinity for a comparable molecule and bind to FcγRIIB with a binding affinity that is unchanged or increased with respect to a comparable molecule.
[0195] [000195] In one embodiment, the Fc variants bind with increased affinity for FcγRIIIA. In a specific embodiment, said Fc variants have an affinity for FcγRIIIA that is at least 2 times, or at least 3 times, or at least 5 times, or at least 10 times, or at least 10 times, or at least 20 times, or at least 30 times, or at least 40 times, or at least 50 times, or at least 60 times, or at least 70 times, or at least 80 times, or at least 90 times, or at least 100 times, or at least at least 200 times that of a comparable molecule. In other embodiments, the Fc variants have an affinity for FcγRIIIA that is increased by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60% , or at least 70%, or at least S0%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, with respect to a comparable molecule.
[0196] [000196] In another embodiment, the Fc variant has an equilibrium dissociation constant (KD) for an Fc ligand (for example, FcγR, C1q) which is decreased between about 2 times and 10 times, or between about 5 times and 50 times, or between about 25 times and 250 times, or between about 100 times and 500 times, or between about 250 times and 1000 times in relation to a comparable molecule.
[0197] [000197] In another embodiment, said Fc variants have an equilibrium dissociation constant (KD) for FcγRIIIA that is reduced by at least 2 times, or at least 3 times, or at least 5 times, or at least 7 times, or at least 10 times, or at least 20 times, or at least 30 times, or at least 40 times, or at least 50 times, or at least 60 times, or at least 70 times, or at least 80 times, or at least 90 times, or at least 100 times, or at least 200 times, or at least 400 times, or at least 600 times, in relation to a comparable molecule. In another embodiment, the Fc variants have an equilibrium dissociation constant (KD) for FcγRIIIA that is reduced by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50 %, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, with respect to a comparable molecule .
[0198] [000198] In one embodiment, the Fc variant binds to the FcγRIIB with an affinity that is unchanged or reduced. In a specific embodiment, said Fc variants have an affinity for FcyRIIB that is unchanged or reduced at least 1 time, or at least 3 times, or at least 5 times, or at least 10 times, or at least 20 times, or at least 50 times, or at least 100 times, in relation to a comparable molecule. In other embodiments, the Fc variants have an affinity for FcyRIIB that is unchanged or reduced by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, with respect to a comparable molecule.
[0199] [000199] In another embodiment, the Fc variants have an equilibrium dissociation constant (KD) for FcyRIIB that is unchanged or increased by at least 2 times, or at least 3 times, or at least 5 times, or at least 7 times , or at least 10 times, or at least 20 times, or at least 30 times, or at least 40 times, or at least 50 times, or at least 60 times, or at least 70 times, or at least SO times, or at least 90 times, or at least 100 times, or at least 200 times in relation to a comparable molecule. In another specific embodiment, the Fc variants have an equilibrium dissociation constant (KD) for FcγRIIB that is unchanged or increased by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, in relation to a comparable molecule.
[0200] [000200] In yet another modality, the Fc variants bind to FcγRIIIA with increased affinity, in relation to a comparable molecule and bind to FcγRIIB with an affinity that is unchanged or reduced, in relation to a comparable molecule. In a specific embodiment, the Fc variants have an affinity for FcγRIIIA that is increased at least 1 time, or at least 3 times, or at least 5 times, or at least 10 times, or at least 20 times, or at least 50 times, or at least 100 times, in relation to a comparable molecule. In another specific embodiment, the Fc variants have an affinity for FcγRIIB that is unchanged or reduced by at least 2 times, or at least 3 times, or at least 5 times, or at least 7 times, or at least 10 times, or at least 20 times, or at least 50 times, or at least 100 times, in relation to a comparable molecule. In other embodiments, the Fc variants have an affinity for FcγRIIIA that is increased by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60% , or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, with respect to a comparable molecule and the Fc variants have an affinity by FcγRIIB which is unchanged or increased by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, with respect to a comparable molecule.
[0201] [000201] In yet another modality, the Fc variants have an equilibrium dissociation constant (KD) ratio FcγRIIIA / FcγRIIB that is decreased in relation to a comparable molecule. In a specific embodiment, the Fc variants have an equilibrium dissociation constant (KD) ratio FcγRIIIA / FcγRIIB that is decreased by at least 1 time, or at least 3 times, or at least 5 times, or at least 10 times, or at least 20 times, or at least 50 times, or at least 100 times, in relation to a comparable molecule. In another specific modality, the Fc variants have an equilibrium dissociation constant (KD) ratio FcγRIIIA / FcγRIIB that is decreased by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, in relation to to a comparable molecule.
[0202] [000202] In another embodiment, the Fc variants bind to FcγRIIIA with a decreased affinity for a comparable molecule. In a specific embodiment, said Fc variants have an affinity for FcγRIIIA that is reduced by at least 1 time, or at least 3 times, or at least 5 times, or at least 10 times, or at least 20 times, or at least 50 times, or at least 100 times, in relation to a comparable molecule. In other embodiments, the Fc variants have an affinity for FcγRIIIA that is decreased by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60% , or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, with respect to a comparable molecule.
[0203] [000203] In yet another modality, the Fc variants bind to FcγRIIIA with decreased affinity and bind to FcγRIIB with an affinity that is unchanged or increased, in relation to a comparable molecule. In a specific embodiment, the Fc variants have an affinity for FcγRIIIA that is reduced by at least 1 time, or at least 3 times, or at least 5 times, or at least 10 times, or at least 20 times, or at least 50 times, or at least 100 times in relation to a comparable molecule. In another specific embodiment, the Fc variants have an affinity for FcγRIIB that is at least 2 times, or at least 3 times, or at least 5 times, or at least 10 times, or at least 10 times, or at least 20 times, or at least 50 times, or at least 100 times, greater than that of a comparable molecule. In other embodiments, the Fc variants have an affinity for FcγRIIIA that is decreased by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60% , or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, with respect to a comparable molecule and the Fc variants have an affinity by FcyRIIB which is increased by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, with respect to a comparable molecule.
[0204] [000204] In yet another modality, the Fc variants have an equilibrium dissociation constant (KD) for FcγRIIIA that is increased by at least 1 time, or at least 3 times, or at least 5 times or at least 10 or at least 20 times, or at least 50 times when compared to that of a comparable molecule. In a specific embodiment, said Fc variants have equilibrium dissociation constant (KD) for FcγRIIB which are decreased at least 2 times, or at least 3 times, or at least 5 times, or at least 7 times, or at least 10 times , or at least 20 times, or at least 50 times or at least 100 times, in relation to a comparable molecule. CH2 variations for FcγR selectivity
[0205] [000205] The protein-protein interaction of Fc-FcγR in this complex indicates that the two chains in the Fc molecule interact with two distinct sites on the FcγR molecule. Although there is symmetry in the two heavy chains in the natural Fc molecules, the local FcγR environment around residues in a chain is different from the FcγR residues that surround the same position as the residue in the opposite Fc chain. The two positions with related symmetry interact with different selection of FcγR residues.
[0206] [000206] Given the asymmetry in the association of Fc to FcγR, simultaneous mutations in the A and B chain of the Fc molecule do not impact interactions with FcγR in a symmetrical way. When introducing mutations to optimize interactions in a Fc chain with its local FcγR environment, in a homodimeric Fc structure, the corresponding mutation in the second chain may be favorable, unfavorable or not contribute to the necessary FcγR binding and selectivity profile.
[0207] [000207] Using an approach guided by structure and computation, asymmetric mutations are designed in the two Fc chains to overcome these limitations of traditional Fc projection strategies, which introduce the same mutations in both Fc chains. It is possible to achieve better binding selectivity between the receptors if the two Fc chains are independently optimized for potentiated binding with their corresponding side of the receptor molecule.
[0208] [000208] For example, mutations at a particular position in an Fc chain can be designed to enhance the selectivity of a particular waste, a positive design effort, while the same position of the residue can be mutated to interact unfavorably with its local environment in an alternative type of Fcγ receptor, a negative design effort, in order to achieve better selectivity between the two receptors. In certain embodiments, a method is provided for designing asymmetric amino acid modifications in the CH2 domain that selectively binds to an Fcgamma receptor compared to a different Fggamma receptor (for example, selectively binds to FcgRIIIa instead of FcgRIIb). In certain other embodiments, a method is provided for designing asymmetric amino acid modifications in the CH2 domain of a variant Fc heterodimer comprising amino acid modifications in the CH3 domain to promote heterodimer formation. In another embodiment, a method is provided to design selectivity for different Fcgamma receptors based on a variant Fc heterodimer comprising asymmetric amino acid modifications in the CH2 domain. In yet another embodiment, a method is provided to design asymmetric amino acid modifications that skew the binding of Fcgama receptors to one side of the Fc molecule. In certain other embodiments, a method is provided for designing polarity conductors that skew Fcgama receptors to interact with only one side of the Fc variant heterodimer comprising asymmetric amino acid modifications in the CH2 domain.
[0209] [000209] The asymmetric design of mutations in the CH2 domain can be designed to recognize the FcγR on one side of the Fc molecule. This constitutes the productive side of the asymmetric Fc structure, while the opposite side is prone to interaction similar to the wild type without the projected selectivity profile and can be considered an unproductive side. A negative design strategy can be employed to introduce mutations on the non-productive side to block FcγR interactions for this side of the asymmetric Fc structure, thereby forcing the desired interaction trends for Fcγ receptors. Table E: Potentially Interesting Fc Selectivity Profiles for Different Fcγ
[0210] [000210] The present invention also relates to fusion polypeptides comprising a binding domain fused to an Fc region, wherein the Fc region comprising a modified CH3 domain, comprising amino acid mutations to promote the formation of heterodimer with increased stability, in the modified CH3 domain has a melting temperature (Tm) greater than 70 ° C. It is specifically envisaged that molecules comprising a heterodimer comprising a modified CH3 domain can be generated by methods known to a person skilled in the art. Briefly, these methods include, among others, combining a variable region or binding domain with the desired specificity (for example, a variable region isolated from a phage or expression display library or derived from a human or non-human antibody or a domain from receptor binding) with Fc variant heterodimers. Alternatively, one skilled in the art can generate an Fc variant heterodimer by modifying the CH3 domain in the Fc region of a molecule comprising an Fc region (for example, an antibody).
[0211] [000211] In one embodiment, the Fc variants are antibodies or Fc fusion proteins. In a specific embodiment the invention provides antibodies comprising an Fc region, comprising a modified CH3 domain, comprising mutations of amino acids to promote the formation of heterodimer with increased stability, in which the modified CH3 domain has a melting temperature (Tm) greater than 70 ° Ç. Such antibodies include IgG molecules that naturally comprise an Fc region containing a CH3 domain that can be modified to generate an Fc variant, or derivatives of antibodies that have been designed to contain an Fc region comprising a modified CH3 domain. Fc variants of the invention include any antibody molecule that preferably binds specifically (i.e., competes for nonspecific binding as determined by immunoassays known in the art to assess specific antigen-antibody binding) an antigen comprising an Fc region incorporating a domain CH3 modified. Such antibodies include, but are not limited to, polyclonal, monoclonal, monospecific, bispecific, multispecific, human, humanized, chimeric antibodies, single chain antibodies, Fab fragments, F (ab ') 2 fragments, disulfide-linked Fvs and fragments containing a VL domain or VH or even a complementarity determining region (CDR) that specifically binds to an antigen, in certain cases, designed to contain or fused to an Fc variant heterodimer.
[0212] [000212] "Antibody-dependent cell-mediated cytotoxicity" or "ADCC" refers to a form of cytotoxicity in which the secreted antibody binds to Fc receptors (FcRs) present in certain cytotoxic cells (for example, Natural Killer cells ( NK), neutrophils and macrophages) allow these effector cytotoxic cells to specifically bind to a target antigen-curing cell and subsequently kill the target cell with cytotoxins. High affinity specific IgG antibodies directed to the surface of target cells "strengthen" cytotoxic cells and are absolutely necessary for such an induction of death. The lysis of the target cell is extracellular, requires direct cell-to-cell contact and does not involve complement.
[0213] [000213] The ability of any particular antibody to mediate lysis of the target cell by ADCC can be assessed. To assess ADCC activity, an antibody of interest is added to the target cells in combination with effector immune cells, which can be activated by the antigen-antibody complexes resulting in cytolysis of the target cell. Cytolysis is usually detected by releasing the marker (for example, radioactive substrates, fluorescent dyes or natural intracellular proteins) from the lysed cells. Effector cells useful for these assays include peripheral blood mononuclear cells (PBMC) and Natural Killer cells (NK). Specific examples of in vitro ADCC assays are described in Wisecarver et al., 1985, 79: 277; Bruggemann et al., 1987, J Exp Med 166: 1351; Wilkinson et al., 2001, J Immunol Methods 258: 183; Patel et al., 1995 J Immunol Methods 184: 29 and here (See section entitled "Characterization and Functional Assays" below). Alternatively, or in addition, the ADCC activity of the antibody of interest can be assessed in vivo, for example, in an animal model such as that disclosed in Clynes et al., 1998, PNAS USA 95: 652.
[0214] [000214] It is envisaged that the Fc variants of the invention are characterized by functional in vitro assays for the determination of one or more functions of FcγR-mediating effector cells. In specific embodiments, the molecules of the invention have similar binding and effector cell functions in in vivo models (such as those described and disclosed here) as those in in vitro based assays. However, the present invention does not exclude molecules of the invention that do not exhibit the desired phenotype in in vitro based assays, but do exhibit the desired phenotype in vivo.
[0215] [000215] The present invention further provides Fc variants with enhanced CDC function. In one embodiment, the Fc variants have increased CDC activity. In one embodiment, the Fc variants have CDC activity that is at least 2 times, or at least 3 times, or at least 5 times, or at least 10 times, or at least 50 times, or at least 100 times greater than that of a comparable molecule. In another embodiment, the Fc variants bind to C1q with an affinity that is at least 2 times, or at least 3 times, or at least 5 times, or at least 7 times, or at least 10 times, or at least 20 times , or at least 50 times, or at least 100 times, greater than that of a comparable molecule. In yet another modality, the Fc variants have CDC activity that is increased by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, with respect to a comparable molecule. In a specific embodiment, the Fc variants of the invention bind to C1q with increased affinity; have enhanced CDC activity and specifically bind to at least one antigen.
[0216] [000216] The present invention also provides Fc variants with reduced CDC function. In one embodiment, the Fc variants have reduced CDC activity. In one embodiment, the Fc variants have CDC activity that is at least 2 times, or at least 3 times, or at least 5 times or at least 10 times or at least 50 times or at least 100 times less than that of a molecule comparable. In another embodiment, an Fc variant binds to C1q with an affinity that is reduced at least 1 time, or at least 3 times, or at least 5 times, or at least 10 times, or at least 20 times , or at least 50 times, or at least 100 times, in relation to a comparable molecule. In another embodiment, the Fc variants have CDC activity that is decreased by at least 10%, or at least 20%, or at least 30%, or at least 40%, or at least 50%, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 100%, or at least 150%, or at least 200%, with respect to a comparable molecule. In a specific embodiment, the Fc variants bind to C1q with decreased affinity, have reduced CDC affinity and specifically bind to at least one antigen.
[0217] [000217] In some embodiments, the Fc variants comprise one or more designed glycoforms, that is, a carbohydrate composition that is covalently linked to a molecule comprising an Fc region. Projected glycoforms can be useful for a variety of purposes, including, but not limited to, increasing or reducing effector function. Projected glycoforms can be generated by any method known to a person skilled in the art, for example, using projected or variable expression strains, by coexpression with one or more enzymes, for example, β (1,4) -N-acetylglycosaminyltransferase III (GnTIl 1), by the expression of a molecule comprising an Fc region in several organisms or cell lines of several organisms, or by the modification of carbohydrates after the molecule comprising the Fc region has been expressed. Methods for generating projected glycoforms are known in the art and include, among others, those described in Umana et al, 1999, Nat. Biotechnol 17: 176-180; Davies et al., 20017 Biotechnol Bioeng 74: 288-294; Shields et al, 2002, J Biol Chem 277: 26733-26740; Shinkawa et al., 2003, J Biol Chem 278: 34663473) US patent 6,602,684; US 10 / 277,370; US 10 / 113,929; PCT WO 00 / 61739A1; PCT WO 01 / 292246A1; PCT WO 02 / 311140A1; PCT WO 02/3 0 954A1; Potillegent ™ technology (Biowa, Inc. Princeton, N.J.); GlycoMAb ™ glycosylation projection technology (GLYCART biotechnology AG, Zurich, Switzerland). See, for example, WO 00061739; EA01229125; US 20030115614; Okazaki et al., 2004, JMB, 336: 1239-49.
[0218] [000218] Fc variants are expected to include antibodies comprising a variable region and a heterodimeric Fc region, wherein the heterodimeric Fc region comprises a modified CH3 domain comprising amino acid mutations to promote the formation of heterodimer with increased stability, in the modified CH3 domain has a melting temperature (Tm) greater than 70 ° C. Fc variants, which are antibodies, can be produced "de novo" by combining a variable domain, or fragment thereof, that specifically binds at least one antigen with a heterodimeric Fc region comprising a modified CH3 domain. Alternatively, the Fc variant heterodimer can be produced by modifying the CH3 domain of an Fc region containing antibody that binds to an antigen.
[0219] [000219] Antibodies of the invention may include, but are not limited to, synthetic antibodies, monoclonal antibodies, recombinantly produced antibodies, intrabodies, monospecific antibodies, multispecific antibodies, bispecific antibodies, human antibodies, humanized antibodies, chimeric antibodies, synthetic antibodies, chain FvFcs (scFvFc), single-chain Fvs (scFv) and anti-idiotypic antibodies (anti-Id). In particular, antibodies used in the methods of the present invention include immunoglobulin molecules and immunologically active parts of immunoglobulin molecules. The immunoglobulin molecules of the invention can be of any type (for example, IgG, IgE, IgM, IgD, IgA and IgY), class (for example, Igd, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass of molecule of immunoglobulin.
[0220] [000220] The antibodies of the invention can be of any animal origin including birds and mammals (for example, human, murine, donkey, sheep, rabbit, goat, guinea pig, camel, horse or chicken). In a specific embodiment, the antibodies are human or humanized monoclonal antibodies, in particular bispecific monoclonal antibodies. As used herein, "human" antibodies include antibodies having the amino acid sequence of a human immunoglobulin and include antibodies isolated from human immunoglobulin libraries or from mice expressing antibodies to human genes.
[0221] [000221] Antibodies, like all polypeptides, have an Isoelectric Point (pI), which is generally defined as the pH at which a polypeptide carries no net charge. It is known in the art that protein solubility is usually lower when the pH of the solution is equal to the isoelectric point (pI) of the protein. It is possible to optimize solubility by changing the number and location of ionizable residues in the antibody to adjust the pI. For example, the pI of a polypeptide can be manipulated by making the appropriate amino acid substitutions (for example, by replacing a charged amino acid like lysine with an uncharged residue like alanine). Without wishing to be bound by any particular theory, amino acid substitutions of an antibody that result in changes in the pI of said antibody can improve the solubility and / or stability of the antibody. One skilled in the art will understand which amino acid substitutions would be most appropriate for a particular antibody to achieve the desired pI. The pI of a protein can be determined by a variety of methods, including, but not limited to, isoelectric focus and several computer algorithms (see, for example, Bjellqvist et al., 1993, Electrophoresis 14: 1023). In one embodiment, the pI of the Fc variants of the invention is between pH 6.2 and pH 8.0. In another embodiment, the pI of the antibodies of the invention is between pH 6.8 and pH 7.4. In one embodiment, substitutions resulting in changes in the pI of an Fc variant of the invention will not significantly decrease its binding affinity for an antigen. It is anticipated that the modified CH3 domain with increased stability can also result in a change in pI. In one embodiment, variant Fc heterodimers are chosen specifically to effect increased stability and purity and any desired change in pI.
[0222] [000222] The antibodies of the invention can be monospecific, bispecific, triespecific or have greater multispecificity. Multispecific antibodies can specifically bind to different epitopes of the desired target molecule or can bind specifically to the target molecule, as well as a heterologous epitope, such as a heterologous polypeptide or solid support material. See, for example, International Publication WO 94/04690; WO 93/17715; WO 92/08802; WO 91/00360; and WO 92/05793; Tutt, et al., 1991, J. Immunol. 147: 60-69; US patent 4,474,893; 4,714,681; 4,925,648; 5,573,920 and 5,601,819 and Kostelny et al., 1992, J. Immunol.148: 1547).
[0223] [000223] Various modalities of multifunctional target molecules can be designed based on this asymmetric structure, as shown in Figure 20.
[0224] [000224] Multispecific antibodies have binding specificity for at least two different antigens. While these molecules will normally only bind to two antigens (i.e., bispecific antibodies, BsAbs), antibodies with additional specificities such as triespecific antibodies are included in the present invention. Examples of BsAbs include, but are not limited to, those with one arm directed against a tumor cell antigen and the other arm directed against a cytotoxic molecule, or both arms are directed against two different tumor cell antigens, or both arms are directed against two different soluble ligands, or one arm is directed against a soluble ligand and the other arm is directed against a cell surface receptor, or both arms are directed against two different cell surface receptors. Methods for preparing bispecific antibodies are known in the art.
[0225] [000225] According to a different approach, antibody variable domains with the desired binding specificities (antibody-antigen combination sites) are fused to immunoglobulin constant domain sequences. The fusion can be with an immunoglobulin heavy chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. The first heavy chain constant region (CH1) containing the site necessary for light chain binding is predicted to be present in at least one of the fusions. The DNAs encoding the immunoglobulin heavy chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors and are cotransfected into an appropriate host organism. This provides great flexibility in adjusting the mutual proportions of the three polypeptide fragments in modalities when unequal ratios of the three polypeptide chains used in the construction provide the ideal yield. See, Example 1 and Table 2. However, it is possible to insert the coding sequences for two or all three polypeptide chains in an expression vector when, the expression of at least two polypeptide chains in equal ratios results in high yields or when reasons are not of particular significance.
[0226] [000226] Bispecific antibodies include cross-linked or "heteroconjugate" antibodies. For example, one of the antibodies in the heteroconjugate can be coupled to avidin, the other to biotin. These antibodies, for example, have been proposed to target immune cells to unwanted cells (US Patent 4,676,980) and for the treatment of HIV infection (WO 91/00360, WO 92/200373, and EP 03089). Heteroconjugate antibodies can be prepared using any convenient cross-linking methods. Suitable crosslinking agents are well known in the art, and are disclosed in US Patent 4,676,980, along with a number of crosslinking techniques.
[0227] [000227] Antibodies with more than two valences incorporating modified CH3 domains and Fc heterodimers resulting from the invention are predicted. For example, specific antibodies can be prepared. See, for example, Tutt et al. J. Immunol. 147: 60 (1991).
[0228] [000228] Antibodies of the present invention also include those that have half-lives (for example, serum half-lives) in a mammal, (for example, a human), greater than 15 days, greater than 20 days, greater than 25 days, greater over 30 days, over 35 days, over 40 days, over 45 days, over 2 months, over 3 months, over 4 months, or over 5 months. The increased half-lives of the antibodies of the present invention in a mammal, (for example, a human), result in a higher serum titer of said antibodies or antibody fragments in the mammal and thus, reduce the frequency of administration of said antibodies or fragments of antibodies and / or reduces the concentration of said antibodies or antibody fragments to be administered. Antibodies having increased in vitro half lives can be generated by techniques known to those skilled in the art. For example, antibodies with increased in vivo half-lives can be generated by modifying (for example, replacing, deleting or adding) amino acid residues identified as involved in the interaction between the Fc domain and the FcRn receptor (see, for example, International Publication WO 97 / 34631; WO 04/029207; US Patent 6,737,056 and US Patent Publication 2003/0190311).
[0229] [000229] In a specific embodiment, the variant heterodimer Fc comprising the modified CH3 domain is a multispecific antibody (referred to herein as an antibody of the invention), the antibody of the invention specifically binds to an antigen of interest. In particular, the antibody of the invention is a bispecific antibody. In one embodiment, an antibody of the invention specifically binds to a polypeptide antigen. In another embodiment, an antibody of the invention specifically binds to a non-polypeptide antigen. In yet another embodiment, administration of an antibody of the invention to a mammal suffering from a disease or disorder can result in a therapeutic benefit for that mammal.
[0230] [000230] Virtually any molecule can be targeted by and / or incorporated into a variant Fc heterodimer construct provided here (e.g., antibodies, Fc fusion proteins) including, but not limited to, the following list of proteins, as well as subunits, domains , reasons and abstracts belonging to the following list of proteins: renin, a growth hormone, including human growth hormone and bovine growth hormone, growth hormone releasing factor; parathyroid hormone, thyroid stimulating hormone; lipoproteins; alpha-1-antitrypsin; chain A insulin; B-chain insulin; proinsulin; follicle stimulating hormone; calcitonin; luteinizing hormone; glucagon, coagulation factors such as factor VII, factor VIIIC, factor IX, tissue factor (TF), and von Willebrands factor, anticoagulation factors such as Protein C; atrial natriuretic factor; pulmonary surfactant; a plasminogen activator, such as urokinase or human urine or tissue-type plasminogen activator (t-PA); bombesin; thrombin; hematopoietic growth factor; tumor necrosis factor-alpha and beta; encephalinase; RANTES (regulated in the activation of normally expressed and secreted T cells); inflammatory human macrophage protein (MIP-1-alpha); a serum albumin like human serum albumin; Muellerian inhibitory substance, relaxin A chain; relaxin B chain; pro-relaxin; peptide associated with mouse gonadotropin, a microbial protein, such as beta-lactamase; DNase; IgE, an associated cytotoxic T lymphocyte antigen (CTLA), such as CTLA-4; inhibin; activin; vascular endothelial growth factor (VEGF); receptors for hormones or growth factors, such as EGFR, VEGFR; interferons such as alpha interferon (α-IFN), beta interferon (β-IFN) and gamma interferon (γ-IFN); protein A or D, rheumatoid factors, a neurotrophic factor such as bone-derived neurotrophic factor (BDNF), neurotrophin-3, -4, -5, or -6 (NT-3, NT-4, NT-5, or NT - 6), or a nerve growth factor; platelet-derived growth factor (PDGF), fibroblast growth factor, such as AFGF and PFGF; epidermal growth factor (EGF); transforming growth factor (TGF) such as TGF-alpha and TGF-beta, including TGF-1, TGF-2, TGF-3, TGF-4, or TGF-5; insulin-like growth factor I and II (IGF-I and IGF-II); des (1-3) -IGF-I (cerebral IGF-I), insulin-like growth factor-binding proteins; CD proteins, such as CD2, CD3, CD4, CD8, CD11a, CD14, CD18, CD19, CD20, CD22, CD23, CD25, CD33, CD34, CD40, CD40L, CD52, CD63, CD64, CD80 and CD147, erythropoietin; osteoinductive factors; immunotoxins; a bone morphogenetic protein (BMP); an interferon like interferon-alpha, -beta and -gamma; colony stimulating factors (CSFs), such as M-CSF, GM-CSF and G-CSF; interleukins (IL), for example, IL-1 to IL-13; TNFα, superoxide dismutase, T cell receptors; surface membrane proteins; decay acceleration factor; viral antigens such as a portion of the AIDS envelope, for example, gp120; transport proteins; forwarding receivers; adressins; regulatory proteins; cell adhesion molecules such as LFA-1, Mac 1, p150.95, VLA-4, ICAM-1, ICAM-3 and VCAM, a4 / p7 integrin, and (Xv / p3 integrin including the same or subunits of the same, integrin alpha subunits such as CD49a, CD49b, CD49c, CD49d, CD49e, CD49f, alfa7, alfa8, alfa9, alfaD, CD11a, CD11b, CD51, CD11c, CD41, alphaIIb, alfaIELb; beta integrin subunits such as, CD29, CD18, CD61, CD104 , beta5, beta6, beta7 and beta8; integrin subunit combinations, including, but not limited to, αVβ3, αVβ5 and α4β7, a member of an apoptosis pathway, IgE; blood group antigens; flk2 / flt3 receptor; obesity receptor (OB ); mp1 receptor; CTLA-4; protein C; an Eph receptor like EphA2, EphA4, EphB2, etc.; a human leukocyte antigen (HLA), like HLA-DR; complement proteins, such as the complement receptor CR1, C1Rq and other complement factors, such as C3 and C5, a glycoprotein receptor such as Gplbα, GPIIb / IIIa and CD200, and fragments of any of the polypeptides listed above.
[0231] [000231] Also provided are antibodies of the invention that specifically bind to cancer antigens, including, but not limited to, ALK receptor (pleiotrophin receptor), pleiotrophin, KS 1/4 pan carcinoma antigen; ovarian carcinoma antigen (CA125); prostatic acid phosphate; prostate specific antigen (PSA); antigen associated with p97 melanoma; gp75 melanoma antigen; high molecular weight melanoma antigen (HMW-MAA); prostate-specific membrane antigen; carcinoembryonic antigen (CEA); polymorphic epithelial mucin antigen; human milk fat globule antigen; antigens associated with colorectal tumor such as: CEA, TAG-72, CO17-1A, GICA 19-9, CTA-1 and LEA; Burkitt-38.13 lymphoma antigen; CD19; human B-CD20 lymphoma antigen; CD33; specific melanoma antigens such as GD2 ganglioside, GD3 ganglioside, GM2 ganglioside and GM3 ganglioside; tumor-specific transplantation cell surface antigen (TSTA); virally induced tumor antigens, including T-antigen, DNA tumor viruses and RNA tumor virus envelope antigens; oncofetal antigen-alpha-fetoprotein, such as colon CEA, oncofetal trophoblast glycoprotein 5T4 and oncofetal bladder tumor antigen; differentiation antigen such as L6 and L20 human lung carcinoma antigens; fibrosarcoma antigens; human T cell leukemia antigen Gp37; neoglycoprotein; sphingolipids; breast cancer antigens such as EGFR (epidermal growth factor receptor); NY-BR-16 antigen; NY-BR-16 and HER2 (p185HER2); polymorphic epithelial mucin (PEM); malignant human lymphocyte antigen-APO-1; differentiation antigen as antigen I found on fetal erythrocytes; primary endoderm I antigen found in adult red blood cells; pre-implantation embryos; I (Ma) found in gastric adenocarcinomas; M18, M39 found in the breast epithelium; SSEA-1 found in myeloid cells; VEP8; VEP9; MyI; Va4-D5; D156-22 found in colorectal cancer; TRA-1-85 (blood group H); SCP-1 found in the testis and ovarian cancer; C14 found in colon adenocarcinoma; F3 found in lung adenocarcinoma; AH6 found in gastric cancer; Y hapten; Ley found in embryonic carcinoma cells; TL5 (group A blood); EGF receptor found on A431 cells; series E1 (blood group B) found in pancreatic cancer; FC10.2 found in embryonic carcinoma cells; gastric adenocarcinoma antigen; CO-514 (Lea blood group) found in adenocarcinoma; NS-10 found in adenocarcinomas; CO-43 (Leb blood group); G49 found at the A431 EGF cell receptor; MH2 (blood group ALeb / Ley) found in colon adenocarcinoma; 19.9 found in colon cancer; gastric cancer mucins; T5A7 found in myeloid cells; R24 found in melanoma; 4.2, GD3, D1.1, OFA-1, GM2, OFA-2, GD2 and M1: 22: 25: 8 found in embryonic carcinoma cells and SSEA-3 and SSEA-4 found in embryos from cell stage 4 to 8; cutaneous lymphoma T cell antigen; MART-1 antigen; Sialy Tn antigen (STn); colon cancer antigen NY-CO-45; lung cancer antigen NY-LU-12 A brave; ART1 adenocarcinoma antigen; Brain-testicular cancer antigen associated with paraneoplasia (MA2 onconeuronal antigen; paraneoplastic neuronal antigen); ventral neuro-oncological antigen 2 (NOVA2); Hepatocellular carcinoma antigen gene 520; tumor-associated CO-029 antigen; tumor-associated MAGE-C1 antigens (cancer antigen / CT7 testis), MAGE-B1 (MAGE-XP antigen), MAGE-B2 (DAM6), MAGE-2, MAGE-4-a, MAGE-4-be MAGE- X2; testicular cancer antigen (NY-EOS-1) and fragments of any of the polypeptides listed above.
[0232] [000232] In certain embodiments, the heteromultimer described here, comprises at least one therapeutic antibody. In some embodiments, the therapeutic antibody binds to a cancer-targeting antigen. In one embodiment, the therapeutic antibody can be selected from the group consisting of abagovomab, adalimumab, alemtuzumab, aurograb, bapineuzumab, basiliximab, belimumab, bevacizumab, briakinumab, canakinumab, catumaxomab, certolizumab pegol, cetuximab, dacizimabal, cetuximab, dacizimabal, cetuximab, dalizumab, cibizima, , gemtuzumab ozogamicin, golimumab, ibritumomab tiuxetan, infliximab, ipilimumab, lumiliximab, mepolizumab, motavizumab, muromonab, mycograb, natalizumab, nimotuzumab, ocrelizumab, ranatizumabuma, ranbizbuma, rumaizumabuma, , tositumomab, trastuzumab, ProxiniumTM, RencarexTM, ustekinumab, zalutumumab, and any other antibodies.
[0233] [000233] The antibodies of the invention include derivatives that are modified (i.e., by the covalent bonds of any type of molecule to the antibody of that covalent bond). For example, but not by way of limitation, antibody derivatives include antibodies that have been modified, for example, by glycosylation, acetylation, pegylation, phosphorylation, amidation, derivatization by known protecting / blocking groups, proteolytic cleavage, binding of a cell ligand or other proteins, etc. Any of the numerous chemical modifications can be carried out by known techniques, including, among others, specific chemical cleavage, acetylation, formylation, metabolic synthesis of tunicamycin, etc. In addition, derivatives may contain one or more non-classic amino acids.
[0234] [000234] Antibodies or fragments thereof with increased in vivo half lives can be generated by linking polymer molecules such as high molecular weight polyethylene glycol (PEG) to antibodies or antibody fragments. PEG can be linked to antibodies or antibody fragments with or without a multifunctional linker through site-specific conjugation of PEG to the N- or C-terminal of said antibodies or antibody fragments or through amino-epsilon groups present in lysine residues . Derivatization of linear or branched polymers that results in minimal loss of biological activity will be used. The degree of conjugation will be monitored closely by SDS-PAGE and mass spectrometry to ensure the correct conjugation of PEG molecules to antibodies. Unreacted PEG can be separated from antibody-PEG conjugates by, for example, size exclusion chromatography or ion exchange.
[0235] [000235] In addition, antibodies can be conjugated to albumin to make the antibody or antibody fragment more stable in vivo or to have a longer in vivo half-life. The techniques are well known, see, for example, International Publications WO 93/15199, WO 93/15200, and WO 01/77137; and European Patent EP 413,622. The present invention includes the use of antibodies or fragments of the same conjugates or fused to one or more fractions, including, but not limited to, peptides, polypeptides, proteins, fusion proteins, nucleic acid molecules, small molecules, mimetic agents, synthetic drugs, inorganic molecules and organic molecules.
[0236] [000236] The present invention includes the use of antibodies or fragments of them fused recombinantly or chemically conjugated (including covalent and non-covalent conjugations) to a heterologous protein or polypeptide (or fragment thereof, for example, for a hair polypeptide at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90 or at least 100 amino acids) to generate fusion proteins. The fusion does not necessarily have to be direct, but it can occur through sequences of ligands. For example, antibodies can be used to target heterologous polypeptides to particular cell types, in vitro or in vivo, by fusing or conjugating antibodies to specific antibodies to particular cell surface receptors. Antibodies fused or conjugated to heterologous polypeptides can also be used in immunoassays and in vitro purification methods using methods known in the art. See, for example, International Publication WO 93/21232; European patent EP 439,095; Naramura et al., 1994, Immunol. Lett. 39: 91-99; US patent 5,474,981; Gillies et al., 1992, PNAS 89: 1428-1432; and Fell et al., 1991, J. Immunol. 146: 2446-2452.
[0237] [000237] The present invention further includes compositions comprising heterologous proteins, peptides or polypeptides fused or conjugated to antibody fragments. For example, heterologous polypeptides can be fused or conjugated to a Fab fragment, Fd fragment, Fv fragment, F (ab) 2 fragment, a VH domain, a VL domain, a VR CDR, a CDR VL or fragments thereof. Methods for fusing or conjugating polypeptides to parts of antibodies are known in the art. See, for example, US Patent 5,336,603; 5,622,929; 5,359,046; 5,349,053; 5,447,851 and 5,112,946; European patents EP 307,434 and EP 367,166; International Publications WO 96/04388 and WO 91/06570; Ashkenazi et al., 1991, Proc. Natl. Acad. Sci. USA 88: 10535-10539; Zheng et al., 1995, J. Immunol. 154: 55905600; and Vil et al., 1992, Proc. Natl. Acad. Sci. USA 89: 11337-11341.
[0238] [000238] Additional fusion proteins, for example, antibodies that specifically bind to an antigen (for example, above) can be generated using gene scrambling, motif scrambling, exon scrambling and / or codon scrambling (collectively referred to as "DNA shuffling"). DNA shuffling can be used to alter the activities of the antibodies of the invention or fragments thereof (for example, antibodies or fragments thereof with higher affinities and lower dissociation rates). See, in general, US Patent 5,605,793; 5,811,238; 5,830,721; 5,834,252 and 5,837,458 and Chris Patten et al., 1997, Curr. Opinion Biotechnol. 8: 724-33; Harayama, 1998, Trends Biotechnol. 16 (2): 76-82; Hansson, et al., 1999, J. Mol. Biol. 287: 26576; and Lorenzo and Blasco, 1998, Biotechniques 24 (2): 308-313. Antibodies or fragments thereof, or the encoded antibodies or fragments thereof, may be altered by being subjected to random mutagenesis by error-prone PCR, random nucleotide insertion or other methods before recombination. One or more parts of a polynucleotide encoding an antibody or antibody fragment whose parts specifically bind to an antigen can be recombined with one or more components, motifs, sections, parts, domains, fragments, etc. of one or more heterologous agents.
[0239] [000239] The present invention further includes uses of the variant Fc heterodimers or fragments thereof conjugated to a therapeutic agent.
[0240] [000240] An antibody or fragment thereof can be conjugated to a therapeutic fraction, such as a cytotoxin, for example, a cytostatic or cytocidal agent, a therapeutic agent, or a radioactive metal ion, for example, alpha emitters. A cytotoxin or cytotoxic agent includes any agent that is harmful to cells. Examples include ribonuclease, monometillauristatin E and F, paclitaxel, cytochalasin B, gramicidin D, ethidium bromide, emetin, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, doxorubicin, daunomycin, dihydroxy anthracine, mitomycin, actin, mitoxin, actin, mitosis 1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, puromycin, epirubicin and cyclophosphamide and analogues or homologues thereof. Therapeutic agents include, but are not limited to, antimetabolics (eg, methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil decarbazine), alkylating agents (eg, meclorethamine, chlorambucil thiotepa, melphalan, carmustine (BCNU) and lomustine (BCNU) and lomustine CCNU), cyclophosphamide, busulfan, dibromomanitol, streptozotocin, mitomycin C and cisdichlorodiamine platinum (II) (DDP) cisplatin), anthracyclines (eg daunomycin (formerly daunomycin) and doxorubicin), antibiotics (eg, dactinomycin) bleomycin, mitramycin and anthramycin (AMC)) and antimitotic agents (eg vincristine and vinblastine). A more extensive list of therapeutic fractions can be found in PCT publication WO 03/075957.
[0241] [000241] In addition, an antibody or fragment thereof can be conjugated to a therapeutic agent or drug fractions that modify a given biological response. Therapeutic agents or drug fractions should not be understood as limited to classical chemical therapeutic agents. For example, the drug fraction can be a protein or polypeptide having a desired biological activity. Such proteins may include, for example, a toxin such as abrin, ricin A, Onconase (or another cytotoxic RNase), pseudomonas exotoxin, cholera toxin, or diphtheria toxin; a protein such as tumor necrosis factor, α-interferon, β-interferon, nerve growth factor, platelet-derived growth factor, tissue plasminogen activator, an apoptotic agent, for example, TNF-α, TNF-β, AIM I (see International Publication WO 97/33899), AIM II (see International Publication WO 97/34911), Ligante Fas (Takahashi et al., 1994, J. Immunol., 6: 1567), and VEGI (see International Publication WO 99/23105), a thrombotic agent or an antiangiogenic agent, for example, angiostatin or endostatin; or, a biological response modifier such as a lymphokine (for example, interleukin-1 ("IL-1"), interleukin-2 ("IL-2"), interleukin-6 ("IL-6") , granulocyte macrophage colony stimulating factor ("GM-CSF"), and granulocyte colony stimulating factor ("G-CSF")), or a growth hormone (for example, growth hormone ("GH" )).
[0242] [000242] In addition, an antibody can be conjugated to therapeutic fractions such as radioactive materials or macrocyclic chelators useful for conjugating radiometal ions (see radioactive material examples above). In certain embodiments, the macrocyclic chelator is 1,4,7,10-tetrazacyclododecane-N, N ', N' ', N' '- tetraacetic acid (DOTA) which can be linked to the antibody via a linker molecule. These binding molecules are commonly known in the art and described in Denardo et al., 1998, Clin Cancer Res. 4: 2483; Peterson et al., 1999, Bioconjug. Chem. 10: 553; and Zimmerman et al., 1999, Nucl. Med. Biol. 26: 943.
[0243] [000243] Methods for fusing or conjugating antibodies to polypeptide fractions are known in the art. See, for example, US Patent 5,336,603; 5,622,929; 5,359,046; 5,349,053; 5,447,851 and 5,112,946; EP 307,434; EP 367,166; PCT publications WO 96/04388 and WO 91/06570; Ashkenazi et al., 1991, PNAS USA 88: 10535; Zheng et al., 1995, J Immunol 154: 5590; and Vil et al., 1992, PNAS USA 89: 11337. The fusion of an antibody to a fraction does not necessarily have to be direct, but it can occur through sequences of ligands. These binding molecules are commonly known in the art and described in Denardo et al., 1998, Clin Cancer Res 4: 2483; Peterson et al., 1999, Bioconjug Chem 10: 553; Zimmerman et al., 1999, Nucl Med Biol 26: 943; Garnett, 2002, Adv Drug Deliv Rev 53: 171.
[0244] [000244] Recombinant expression of a variant, derivative, Fc analogue, or fragment thereof (for example, an antibody or fusion protein of the invention), requires the construction of an expression vector containing a polynucleotide encoding an Fc variant (for example antibody, or fusion protein). Once a polynucleotide that encodes an Fc variant (for example, antibody, or fusion protein) has been obtained, the vector for producing an Fc variant (for example, antibody, or fusion protein) can be produced by Recombinant DNA using well-known techniques. Thus, methods for preparing a protein by expressing a polynucleotide containing a nucleotide sequence that encodes an Fc variant (for example, antibody or fusion protein) are described here. Methods that are well known to those skilled in the art can be used to construct expression vectors containing Fc variant coding sequences (e.g., antibody or fusion protein) and appropriate transcriptional and translational control signals. Such methods include, for example, in vitro recombinant DNA techniques, synthetic techniques and in vivo genetic recombination. The invention thus provides replicable vectors comprising a nucleotide sequence that encodes an Fc variant of the invention, operably linked to a promoter. Such vectors may include the nucleotide sequence that encodes the constant region of the antibody molecule (see, for example, Patent Publication WO 86/05807; Patent Publication WO 89/01036; US Patent 5,122,464 and the antibody variable domain or a polypeptide to generate an Fc variant can be cloned into an entire antibody chain expression vector (e.g., light or heavy chain), or full Fc variant comprising a fusion of a non-antibody derived polypeptide and an Fc region incorporating at least the modified CH3 domain.
[0245] [000245] The expression vector is transferred to a host cell by conventional techniques and the transfected cells are then cultured by conventional techniques to produce an Fc variant of the invention. Thus, the invention includes host cells containing a polynucleotide that encodes an Fc variant of the invention, operably linked to a heterologous promoter. In specific modalities for the expression of Fc variants comprising antibodies with double chains, vectors encoding both heavy and light chains can be coexpressed in the host cell for expression of the entire immunoglobulin molecule, as detailed below.
[0246] [000246] A variety of vector expression host systems can be used to express the Fc variants of the invention (for example, antibody or fusion protein molecules) (see, for example, US Patent 5,807,715). Such host expression systems represent vehicles by which the coding sequences of interest can be produced and subsequently purified, but they also represent cells that can, when transformed or transfected with the appropriate nucleotide coding sequences, express an Fc variant of the invention in situ. These include, but are not limited to, microorganisms such as bacteria (e.g., E. coli and B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA expression vectors or cosmid DNA containing Fc variant coding sequences; yeast (for example, Saccharomyces Pichia) transformed with recombinant yeast expression vectors containing Fc variant coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing Fc variant coding sequences; plant cell systems infected with recombinant virus expression vectors (for example, cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (for example, plasmid Ti) containing Fc variant coding sequences; or mammalian cell systems (eg COS, CHO, BHK, 293, NS0 and 3T3 cells) harboring recombinant expression constructs containing promoters derived from the mammalian cell genome (eg, metallothionein promoter) or mammalian viruses (for example, the adenovirus late promoter; the vaccinia virus 7.5 K promoter). In certain embodiments, bacterial cells, such as Escherichia coli or eukaryotic cells, are used for the expression of an Fc variant, which is a recombinant antibody or fusion protein molecules. For example, mammalian cells, such as Chinese hamster ovary (CHO) cells, in conjunction with a vector, as the strong promoter element of the human cytomegalovirus intermediate early gene is an effective antibody expression system (Foecking et al., 1986, Gene 45: 101; and Cockett et al., 1990, Bio / Technology 8: 2). In a specific embodiment, the expression of nucleotide sequences encoding an Fc variant of the invention (for example, antibody or fusion protein) is regulated by a constitutive promoter, inducible promoter or tissue specific promoter.
[0247] [000247] In bacterial systems, a series of expression vectors can be advantageously selected depending on the intended use of the Fc variant (for example, antibody or fusion protein molecules) expressed. For example, when a large amount of this protein must be produced, for the generation of pharmaceutical compositions of an Fc variant, vectors that direct the expression of high levels of fusion protein products that are readily purified may be desirable. These vectors include, among others, the E. coli expression vector pUR278 (Ruther et al., 1983, EMBO 12: 1791), in which the Fc variant coding sequence can be individually linked to the vector in the frame with the region lac Z encoding so that a lac Z fusion protein is produced; pIN vectors (Inouye & Inouye, 1985, Nucleic Acids Res. 13: 3101-3109; Van Heeke & Schuster, 1989, J. Biol. Chem. 24: 5503-5509); and the like. PGEX vectors can also be used to express foreign polypeptides such as glutathione 5-transferase (GST) fusion proteins. In general, these fusion proteins are soluble and can be easily purified from cells lysed by adsorption and binding in the matrix of glutathione-agarose beads followed by elution in the presence of free glutathione. The pGEX vectors are designed to include thrombin protease or factor Xa cleavage sites so that the cloned product of the target gene can be released from the GST fraction.
[0248] [000248] In an insect system, Autographs californica nucleopoliedrovirus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The coding sequence for the Fc variant (for example, antibody or fusion protein molecules) can be cloned individually into non-essential regions (for example, the polyhedrin gene) of the virus and placed under the control of an AcNPV promoter (for example, the promoter polyhedrin).
[0249] [000249] In mammalian host cells, a number of virus-based expression systems can be used. In cases where an adenovirus is used as an expression vector, the Fc variant coding sequence (for example, antibody or fusion protein molecules) of interest can be linked to an adenovirus transcription / translation control complex, for example , the late promoter and tripartite leader sequence. This chimeric gene can then be inserted into the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome (for example, E1 or E3 region) will result in a recombinant virus that is viable and capable of expressing the Fc variant (for example, antibody or fusion protein molecules) in infected hosts ( for example, see Logan & Shenk, 1984, Proc. Natl. Acad. Sci. USA 81: 355-359). Specific initiation signals may also be required for efficient translation of the inserted antibody coding sequences. These signals include the ATG initiation codon and adjacent sequences. In addition, the start codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert. These exogenous translational control signals and initiation codons can come from a variety of sources, both natural and synthetic. The effectiveness of expression can be enhanced through the inclusion of appropriate transcription enhancing elements, transcription terminators, etc. (see, for example, Bittner et al., 1987, Methods in Enzymol. 153: 516-544).
[0250] [000250] The expression of an Fc variant (for example, antibody or fusion protein molecules) can be controlled by any promoter or enhancer element known in the art. Promoters that can be used to control the expression of the gene encoding an Fc variant (for example, antibody or fusion protein molecules) include, but are not limited to, the SV40 early promoter region (Bernoist and Chambon, 1981, Nature 290: 304 -310), the promoter contained in the 3 'long end repeat of Rous sarcoma virus (Yamamoto, et al., 1980, Cell 22: 787-797), the herpes thymidine kinase promoter (Wagner et al., 1981, Proc. Natl. Acad. Sci. USA 78: 1441-1445), the regulatory sequences of the metallothionein gene (Brinster et al., 1982, Nature 296: 3942), the tetracycline (Tet) promoter (Gossen et al., 1995, Proc. Nat. Acad. Sci. USA 89: 5547-5551); prokaryotic expression vectors such as the β-lactamases promoter (Villa-Kamaroff et al, 1978, Proc. Natl. Acad. Sci. USA 75: 3727-3731), or the tac promoter (DeBoer et al., 1983, Proc. Natl. Acad. Sci. USA 80:21 -25; see also "Useful proteins from recombinant bacteria" in Scientific American, 1980, 242: 7494); plant expression vectors comprising the nopaline synthase promoter region (Herrera-Estrella et al., Nature 303: 209-213) or the cauliflower mosaic virus 35S RNA promoter (Gardner et al., 1981, Nucl Acids Res. 9: 2871), and the photosynthetic enzyme ribulose carboxylase biphosphate promoter (Herrera-Estrella et al., 1984, Nature 310: 115-120); promoter elements of yeast or other fungi such as the Gal 4 promoter, ADC promoter (alcohol dehydrogenase), PGK promoter (phosphoglycerol kinase), alkaline phosphatase promoter and the following transcriptional animal control regions, which have tissue specificity and are used in transgenic animals: control region of the elastase I gene that is active in pancreatic acinar cells (Swift et al., 1984, Cell 38: 639-646; Ornitz et al., 1986, Cold Spring Harbor Symp. Quant. Biol. 50: 399-409; MacDonald, 1987, Hepatology 7: 425-515); control region of the insulin gene that is active in pancreatic beta cells (Hanahan, 1985, Nature 315: 115-122), control region of the immunoglobulin gene that is active in lymphoid cells (Grosschedl et al., 1984, Cell 38 : 647-658; Adames et al., 1985, Nature 318: 533-538; Alexander et al., 1987, Mol. Cell. Biol. 7: 1436-1444), mouse mammary tumor virus control region that is active in the testis, breast, lymphoid cells and mast cells (Leder et al., 1986, Cell 45: 485-495), region of control of the albumin gene that is active in the liver (Pinkert et al., 1987, Genes and Devel. 1: 268-276), control region of the alpha-fetoprotein gene, which is active in the liver (Krumlauf et al., 1985, Mol. Cell. Biol. 5: 1639-1648; Hammer et al., 1987, Science 235 : 53-58; alpha 1 antitrypsin gene control region that is active in the liver (Kelsey et al., 1987, Genes and Devel. 1: 161-171), beta-globin gene control region that is active in myeloid cells (Mogram et al., 1985, Nature 31 5: 338-340; Kollias et al., 1986, Cell 46: 89-94); control region of the basic myelin protein gene that is active in oligodendrocyte cells in the brain (Readhead et al., 1987, Cell 48: 703-712); control region of the myosin light chain 2 gene that is active in skeletal muscle (Sani, 1985, Nature 314: 283-286); specific neuronal enolase (NSE), which is active in neuronal cells (Morelli et al., 1999, Gen. Virol. 80: 571-83); control region of the brain-derived neurotrophic factor (BDNF) gene that is active in neuronal cells (Tabuchi et al., 1998, Biochem. Biophysic. Res. Com. 253: 818823); glial fibrillary acid protein (GFAP) promoter that is active in astrocytes (Gomes et al., 1999, Braz J Med Biol Res 32 (5): 619-631; Morelli et al., 1999, Gen. Virol. 80: 571 -83) and gonadrotopic release hormone gene control region that is active in the hypothalamus (Mason et al., 1986, Science 234: 1372-1378).
[0251] [000251] Expression vectors containing inserts of a gene encoding an Fc variant of the invention (for example, antibody or fusion protein molecules) can be identified by three general approaches: (a) nucleic acid hybridization, (b) a presence or absence of "marker" gene functions and (c) expression of inserted sequences. In the first approach, the presence of a gene encoding a peptide, polypeptide, protein or a fusion protein in an expression vector can be detected by nucleic acid hybridization using probes comprising sequences that are homologous to an inserted gene encoding the peptide , polypeptide, protein or the fusion protein, respectively. In the second approach, the recombinant host / vector system can be identified and selected based on the presence or absence of certain functions of the "marker" gene (for example, thymidine kinase activity, antibiotic resistance, transformation phenotype, body formation baculovirus occlusion, etc.) caused by the insertion of a nucleotide sequence that encodes an antibody or fusion protein in the vector. For example, if the nucleotide sequence encoding the Fc variant (for example, antibody or fusion protein molecules) is inserted into the sequence of the vector marker gene, recombinants containing the gene encoding the antibody or protein insert fusion can be identified by the absence of the marker gene function. In the third approach, recombinant expression vectors can be identified by evaluating the gene product (for example, antibody or fusion protein molecules) expressed by the recombinant. These assays can be based, for example, on the physical or functional properties of the fusion protein in in vitro assay systems, for example, binding with antibioactive molecule antibody.
[0252] [000252] In addition, a host cell strain can be chosen in a way that modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific way desired. The expression of certain promoters can be high in the presence of certain inducers; thus, the expression of the genetically modified fusion protein can be controlled. In addition, different host cells have specific and characteristic mechanisms for post-translational and translational processing and modification (eg, glycosylation, protein phosphorylation). Appropriate cell lines or host systems can be chosen to ensure correct modification and processing of the expressed foreign protein. For example, expression in a bacterial system will produce a non-glycosylated product and expression in yeast will produce a glycosylated product. Eukaryotic host cells that have cellular machinery for the proper treatment of primary transcription (for example, glycosylation and phosphorylation) of the gene product can be used. Such mammalian host cells include, but are not limited to, CHO, VERY, BHK, Hela, COS, MDCK, 293, 3T3, WI38, NS0, and in particular, neuronal cell lineage such as human neuroblastomas SK-N-AS , SK-N-FI, SK-N-DZ (Sugimoto et al., 1984, J. Natl. Cancer Inst. 73: 51-57), human neuroblastoma SK-N-SH (Biochim. Biophys. Acta, 1982, 704: 450-460), human cerebellar medulloblastoma Daoy (He et al., 1992, Cancer Res. 52: 1144-1148) glioblastoma cells DBTRG-05 MG (Kruse et al., 1992, In Vitro Cell. Dev. Biol 28A: 609-614), human neuroblastoma IMR-32 (Cancer res., 1970, 30: 2110-2118), human astrocytoma 1321 N1 (Proc. Natl. Acad. Sci. USA, 1977, 74: 4816), astrocytoma human MOG-G-CCM (Br. J. Cancer, 1984, 49: 269), human glioblastoma-astrocytoma U87MG (Acta Pathol. Microbiol. Scand., 1968, 74: 465-486), human glioblastoma A172 (Olopade et al ., 1992, Cancer Res. 52: 2523-2529), C6 rat glioma cells (Benda et al., 1968, Science 161: 370-371), ca neuroblastoma Neuro-2a mundongo (Proc. Natl. Acad. Sci. USA, 1970, 65: 129-136), mouse neuroblastoma NB41A3 (Proc. Natl. Acad. Sci. USA, 1962, 48: 1184-1190), SCP sheep choroid plexus (Bolin et al., 1994, J. Virol. Methods 48: 211-221), G355-5, normal astrocyte PG-4 (Haapala et al., 1985, J. Virol. 53: 827-833), ferret brain Mpf (Trowbridge et al., 1982, In Vitro 18: 952-960) and normal cell lines, such as the brain cortex of normal CTX TNA2 mice (Radany et al., 19 92, Proc. Natl. Acad. Sci. USA 89: 6467- 6471) such as, for example, CRL7030 and Hs578Bst. In addition, different vector / host expression systems can affect processing reactions to different extents.
[0253] [000253] In the long term, the production of recombinant proteins with high yield, stable expression is preferable. For example, cell lines that stably express an Fc variant of the invention (for example, antibody or fusion protein molecules) can be designed. Instead of using expression vectors that contain viral origins of replication, host cells can be transformed with DNA controlled by the appropriate expression of control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc. .) and a checkmark. After the introduction of the foreign DNA, the projected cells can grow for 1-2 days in an enriched medium and then are placed in a selective medium. The selection marker on the recombinant plasmid confers resistance to selection and allows cells to integrate the plasmid into their chromosomes in a stable manner and grow to form foci that, in turn, can be cloned and expanded into cell lines. This method can be used advantageously to design cell lines that express an Fc variant that specifically binds to an antigen. These designed cell lines can be particularly useful in screening and evaluating compounds that affect the activity of an Fc variant (for example, a polypeptide or a fusion protein) that specifically binds to an antigen.
[0254] [000254] A number of selection systems can be used, including, but not limited to, herpes simplex virus thymidine kinase (Wigler et al., 1977, Cell 11: 223), hypoxanthine-guanine phosphoribosyltransferase (Szybalska & Szybalski, 1962, Proc. Natl. Acad. Sci. USA 48: 2026), and adenine phosphoribosyltransferase genes (Lowy et al., 1980, Cell 22: 817) can be used in tk, hgprt or aprt cells, respectively. Also, antimetabolic resistance can be used as the basis of selection for dhfr, which confers resistance to methotrexate (Wigler et al., 1980, Natl. Acad. Sci. USA 77: 3567; O'Hare et al., 1981, Proc Natl. Acad. Sci. USA 78: 1527); gpt, which confers resistance to mycophenolic acid (Mulligan & Berg, 1981, Proc. Natl. Acad. Sci. USA 78: 2072); neo, which confers resistance to the aminoglycoside G-418 (Colberre-Garapin et al., 1981, J. Mol. Biol. 150: 1); and hygro, which confers resistance to hygromycin genes (Santerre et al., 1984, Gene 30: 147).
[0255] [000255] Since the Fc variant (for example, antibody or fusion protein) of the invention was produced by recombinant expression, it can be purified by any method known in the art for purification of a protein, for example, by chromatography ( for example, ion exchange, affinity, particularly affinity for the specific antigen after protein A, and size column chromatography), centrifugation, difference in solubility, or any other standard protein purification technique.
[0256] [000256] The Fc variant is generally recovered from the culture medium as a secreted polypeptide, although it can also be recovered from the host cell lysate when produced directly without a secretory signal. If the Fc variant is attached to the membrane, it can be released from the membrane using an appropriate detergent solution (for example, Triton-X 100).
[0257] [000257] When an Fc variant is produced in a recombinant cell that is not of human origin, it is completely free of proteins or polypeptides of human origin. However, it is necessary to purify the Fc variant of recombinant cell proteins or polypeptides to obtain preparations that are substantially homogeneous as to the Fc variant. As a first step, the culture medium or lysate is usually centrifuged to remove debris from cell particles.
[0258] [000258] Fc heterodimers having antibody constant domains can be conveniently purified by hydroxylapatite chromatography, gel electrophoresis, dialysis or affinity chromatography, with affinity chromatography being the preferred purification technique. Other protein purification techniques such as fractionation on an ion exchange column, ethanol precipitation, reverse phase HPLC, silica chromatography, Sepharose heparin chromatography, chromatography on an anion or cation exchange resin (such as a polyaspartic acid column ), chromatofocusing, SDS-PAGE and ammonium sulfate precipitation are also available depending on the polypeptide to be recovered. The suitability of protein A as an affinity linker depends on the species and isotype of the immunoglobulin Fc domain that is used. Protein A can be used to purify immunoglobulin Fc regions that are based on human heavy chains γ1, γ2 or γ4 (Lindmark et al., J. Immunol. Meth. 62: 1-13 (1983)). Protein G is recommended for all isotypes of mice and for human γ3 (Guss et al., EMBO J. 5: 15671575 (1986)). The matrix to which the affinity linker is attached is often agarose, but other matrices are available. Mechanically stable matrices such as controlled porosity glass or poly (styrenodivinyl) benzene allow for faster flow rates and shorter processing times than can be achieved with agarose. The conditions for binding an immunoadhesin to the protein A or G column are dictated entirely by the characteristics of the Fc domain; that is, their species and isotypes. Generally, when the appropriate binder is chosen, efficient binding occurs directly from the unconditioned culture fluid. Linked Fc heterodimers can be efficiently eluted at acidic pH (at or above 3.0), or in a neutral pH buffer containing a weak chaotropic salt. This affinity chromatography step can result in a Fc variant heterodimer preparation that is> 95% pure.
[0259] [000259] The expression levels of an Fc variant (for example, antibody or fusion protein molecules) can be increased by amplifying the vector (for a review, see Bebbington and Hentschel, The use of vectors based on gene amplification for the expression of cloned genes in mammalian cells in DNA cloning, Vol. 3. (Academic Press, New York, 1987). For example, when a marker in the vector system that expresses an antibody or fusion protein is amplifiable, increasing the level of inhibitor present in the host cell culture will increase the number of copies of the marker gene. Since the amplified region is associated with the antibody gene, production of the antibody or fusion protein will also increase (Crouse et al., 1983, Mol. Cell. Biol. 3: 257).
[0260] [000260] The host cell can be cotransfected with two expression vectors of the invention. For example, the first vector that encodes a polypeptide derived from heavy chain and the second vector that encodes a polypeptide derived from light chain. The two vectors can contain identical selection markers that allow for equal expression of light and heavy chain polypeptides. Alternatively, a single vector can be used that encodes and is capable of expressing, the fusion protein or both heavy and light chain polypeptides. The coding sequences for the fusion protein or heavy and light chains can comprise cDNA or genomic DNA. Characterization and Functional Tests
[0261] [000261] Fc variants (e.g., antibodies or fusion proteins) of the present invention can be characterized in a variety of ways. In one embodiment, the purity of the Fc variant heterodimers is assessed using well-known techniques, including, but not limited to, SDS-PAGE gels, Western blots, densitometry or mass spectrometry. Protein stability can be characterized using a set of techniques, including size exclusion chromatography, UV-visible and CD spectroscopy, mass spectroscopy, differential light scattering, bench stability testing, thawing along with other techniques characterization, differential scanning calorimetry, differential fluorometric scanning, hydrophobic interaction chromatography, isoelectric focus, receptor binding assays or relative protein expression levels. In an exemplary embodiment, the stability of the variant Fc heterodimers is assessed by the melting temperature of the modified CH3 domain, compared to the wild type CH3 domain, using well-known techniques such as differential scanning flourimetry and differential scanning calorimetry.
[0262] [000262] Fc variants of the present invention can also be evaluated for the ability to specifically bind to a ligand, (for example, FcγRIIIA, FcγRIIB, C1q). This test can be performed in solution (eg, Houghten, Bio / Techniques, 13: 412-421, 1992), in granules (Lam, Nature, 354: 82-84, 1991), in chips (Fodor, Nature, 364: 555-556, 1993), bacteria (US Patent 5,223,409) on plasmids (Cull et al., Proc. Natl. Acad. Sci. USA, 89: 1865-1869, 1992) or on phage (Scott and Smith, Science, 249: 386-390, 1990; Devlin, Science, 249: 404-406, 1990; Cwirla et al., Proc. Natl. Acad. Sci. USA, 87: 6378-6382, 1990; and Felici, J. Mol. Biol., 222: 301-310, 1991). Molecules that have been identified to specifically bind to a ligand, (for example, FcγRIIIA, FcγRIIB, C1q or an antigen) can then be evaluated for their affinities for the ligand.
[0263] [000263] Fc variants of the invention can be evaluated for specific binding to a molecule as an antigen (e.g., cancer antigen and cross-reactivity with other antigens) or a linker (e.g., FcγR) by any method known in the art. Immunoassays that can be used to analyze specific binding and cross-reactivity include, but are not limited to, competitive and non-competitive assay systems using techniques such as western blots, radioimmunoassays, ELISA (enzyme-linked immunosorbent assay), "sandwich" immunoassays, immunoprecipitation assays , precipitation reactions, gel diffusion precipitation reactions, immunodiffusion assays, agglutination assays, complement fixation assays, immunoradiometric assays, fluorescent immunoassays, protein A immunoassays, to name just a few. Such assays are routine and well known in the art (see, for example, Ausubel et al., Eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York).
[0264] [000264] The binding affinity of the Fc variants of the present invention for a molecule such as an antigen or a ligand, (for example, FcγR) and the rate of dissociation of the interaction can be determined by competitive binding assays. An example of a competitive binding assay is a radioimmunoassay comprising incubation of labeled ligand, such as FcγR (for example, 3H or 125I with a molecule of interest (for example, Fc variants of the present invention) in the presence of an increasing amount of non-ligand labeled, such as FcγR, and the detection of the molecule bound to the labeled linker The affinity of the molecule of the present invention for the linker and rates of dissociation of the link can be determined from the saturation data by scatchard analysis.
[0265] [000265] The kinetic parameters of an Fc variant can also be determined using any surface plasmon resonance (SPR) analysis known in the art (for example, BIAcore kinetic analysis). For a SPR-based technology review, see Mullet et al., 2000, Methods 22: 77-91; Dong et al., 2002, Review in Mol. Biotech., 82: 303-23; Fivash et al., 1998, Current Opinion in Biotechnology 9: 97-101; Rich et al., 2000, Current Opinion in Biotechnology 11: 54-61. In addition, any of the SPR instruments and SPR-based methods for measuring protein-protein interactions described in US Patent 6,373,577; 6,289,286; 5,322,798; 5,341,215; 6,268,125 are provided for in the methods of the invention.
[0266] [000266] Fluorescence activated cell separation (FACS), using any of the techniques known to those skilled in the art, can be used to characterize the binding of the Fc variants to a molecule expressed on the cell surface (for example, FcγRIIIA, FcγRIIB). Flow separations are able to quickly examine a large number of individual cells that contain library inserts (for example, 10-100 million cells per hour) (Shapiro et al., Practical Flow, Cytometry, 1995). Flow cytometers for separation and examination of biological cells are well known in the art. Known flow cytometers are described, for example, in US Patent 4,347,935; 5,464,581; 5,483,469; 5,602,039; 5,643,796; and 6,211,477. Other known flow cytometers are the FACS Vantage ™ system manufactured by Becton Dickinson and Company, and the COPAS ™ system manufactured by União Biometrica.
[0267] [000267] The Fc variants of the invention can be characterized by their ability to mediate FcγR-mediated effector cell function. Examples of effector cell functions that can be assessed include, but are not limited to, antibody dependent cell mediated cytotoxicity (ADCC), phagocytosis, opsonization, opsonophagocytosis, C1q binding and complement dependent cell mediated cytotoxicity (CDC). Any cell-based or cell-free assay known to those skilled in the art to determine the activity of effector cell function can be used (for effector cell assays, see Perussia et al., 2000, Methods Mol. Biol. 121: 179- 92; Baggiolini et al., 1998 Experientia, 44 (10): 841 -8; Lehmann et al., 2000 J. Immunol. Methods, 243 (1-2): 229-42; Brown E J. 1994, Methods Cell Biol., 45: 147-64; Munn et al., 1990 J. Exp. Med., 172: 231 -237, Abdul-Majid et al., 2002 Scand. J. Immunol. 55: 70-81; Ding et al., 1998, Immunity 8: 403-411).
[0268] [000268] In particular, the Fc variants of the invention can be evaluated for FcγR-mediated ADCC activity in effector cells, (for example, natural killer cells) using any of the standard methods known to those skilled in the art (see, for example, Perussia et al., 2000, Methods Mol. Biol. 121: 179-92). An exemplary assay to determine the ADCC activity of the molecules of the invention is based on a 51Cr release assay comprising: target cells labeled with [51Cr] Na2CrO4 (this molecule permeable to the cell membrane is commonly used to label once it binds to proteins cytoplasmic and although spontaneously released from cells with slow kinetics, it is released massively after necrosis of the target cell); opsonize target cells with the Fc variants of the invention; combining opsonized radiolabeled target cells with effector cells on a microtiter plate in an appropriate ratio of target cells to effector cells; incubate the cell mixture for 16-18 hours at 37 ° C; collect supernatants; and analyze radioactivity. The cytotoxicity of the molecules of the invention, then, can be determined, for example, using the following formula:% of lysis = (experimental cpm-cpm originating from the target) / (cpm of detergent lysis-cpm originating from the target) x 100% . Alternatively,% lysis = (ADCC-AICC) / (maximum release-spontaneous release). Specific lysis can be calculated using the formula: specific lysis =% lysis with the molecules of the invention-% lysis in the absence of the molecules of the invention. A graph can be generated by varying any target: effector cell ratio or antibody concentration.
[0269] [000269] Method for characterizing the ability of the Fc variants to bind to C1q and to mediate complement-dependent cytotoxicity (CDC) are well known in the art. For example, to determine C1q binding, a C1q binding ELISA can be performed. An exemplary assay can comprise the following: assay plates can be coated overnight at 4 ° C with variant polypeptide or start (control) polypeptide in the coating buffer. The plates can then be washed and blocked. After washing, an aliquot of human Clq can be added to each well and incubated for 2 hours at room temperature. After an additional wash, 100 μl of an antibody conjugated to sheep complement C1q peroxidase can be added to each well and incubated for 1 hour at room temperature. The plate can again be washed with wash buffer and 100 µl of substrate buffer containing OPD (O-phenylenediamine dihydrochloride (Sigma)) can be added to each well. The oxidation reaction, observed by the appearance of a yellow color, can continue for 30 minutes and be stopped by adding 100 ul of 4.5 NH2 SO4. The absorbance can then be read at (492-405) nm.
[0270] [000270] To assess complement activation, a CDC complement-dependent cytotoxicity assay can be performed (as described in Gazzano-Santoro et al., 1996, J. Immunol. Methods 202: 163). Soon, various concentrations of Fc variant and human complement can be diluted with buffer. The cells expressing the antigen to which the Fc variant binds can be diluted to a density of about 1 x 106 cells / ml. Mixtures of the Fc variant, diluted human complement and cells expressing the antigen can be added to a 96-well plate of flat-bottomed tissue culture and incubated for 2 hours at 37C and 5% CO2 to facilitate the complement mediate the lysis of the cell. 50 µL of alamar azul (Accumed International) can be added to each well and incubated overnight at 37 ° C. Absorbance is measured using a 96-well fluorometer with excitation at 530 nm n and emission at 590 nm. The results can be expressed in relative fluorescence units (RFU). Sample concentrations can be computed from a standard curve and the percentage of activity, relative to a comparable molecule (ie, a molecule comprising an Fc region with an unchanged or wild-type CH3 domain) is reported for the Fc variant of interest.
[0271] [000271] Complementary tests can be performed with human serum, guinea pig or rabbit. Complementary lysis of target cells can be detected by monitoring the release of intracellular enzymes such as lactate dehydrogenase (LDH), as described in Korzeniewski et al., 1983, Immunol. Methods 64 (3): 313-20; and Decker et al., 1988, J. Immunol Methods 115 (1): 61-9; or the release of a marker such as europium, chromium 51 or indium 111 in which target cells are marked. Methods
[0272] [000272] The present invention includes administering one or more Fc variant of the invention (e.g., antibodies) to an animal, in particular a mammal, specifically a human, to prevent, treat, or ameliorate one or more symptoms associated with a disease , disorder or infection. The Fc variants of the invention are particularly useful for treating or preventing a disease or disorder in which altered efficacy of the effector cell function (for example, ADCC, CDC) is desired. The Fc variants and compositions thereof are particularly useful for treating or preventing primary or metastatic neoplastic disease (i.e., cancer) and infectious diseases. The molecules of the invention can be provided in pharmaceutically acceptable compositions, as known in the art or as described herein. As detailed below, the molecules of the invention can be used in methods to treat or prevent cancer (particularly in passive immunotherapy), autoimmune disease, inflammatory disorders or infectious diseases.
[0273] [000273] The Fc variants of the invention can also be advantageously used in combination with other therapeutic agents known in the art to treat or prevent cancer, autoimmune disease, inflammatory disorders or infectious diseases. In a specific embodiment, Fc variants of the invention can be used in combination with monoclonal or chimeric antibodies, lymphokines or hematopoietic growth factors (such as, for example, IL-2, IL-3 and IL-7), which, for example , serve to increase the number or activity of effector cells that interact with the molecules and, increase the immune response. The Fc variants of the invention can also be advantageously used in combination with one or more drugs used to treat a disease, disorder or infection, such as, for example, anti-cancer agents, anti-inflammatory agents or antiviral agents.
[0274] [000274] Accordingly, the present invention provides methods for preventing, treating or ameliorating one or more symptoms associated with cancer and related conditions by administering one or more Fc variants of the invention. Although not intended to be linked to any mechanism of action, an Fc variant of the invention that binds to FcγRIIIA and / or FcγRI IA with a higher affinity than a comparable molecule and still binds to FcγRIIB with a lower affinity than a comparable molecule , and / or said Fc variant has an enhanced effector function, for example, ADCC, CDC, phagocytosis, opsonization, etc. will result in selective targeting and efficient destruction of cancer cells.
[0275] [000275] The invention further includes administering one or more Fc variants of the invention in combination with other therapies known to those skilled in the art for the treatment or prevention of cancer, including, but not limited to, current standard or experimental chemotherapies, hormonal therapies, biological therapies, immunotherapies, radiation therapies or surgery. In some embodiments, the molecules of the invention can be administered in combination with a therapeutically or prophylactically effective amount of one or more anti-cancer agents, therapeutic antibodies or other agents known to those skilled in the art for the treatment and / or prevention of cancer. Examples of dosage schedules and therapies that can be used in combination with the Fc variants of the invention are well known in the art and have been described in detail elsewhere (see, for example, PCT publications WO 02/070007 and WO 03/075957) .
[0276] [000276] Cancers and related disorders that can be treated or prevented by the methods and compositions of the present invention include, but are not limited to, the following: leukemias, lymphomas, multiple myelomas, bone and connective tissue sarcomas, brain tumors, breast cancer, cancer adrenal, thyroid cancer, pancreatic cancer, pituitary cancers, eye cancers, vaginal cancers, vulvar cancers, cervical cancers, uterine cancers, ovarian cancers, esophageal cancers, stomach cancers, colon cancers, rectal cancers, liver cancers, gallbladder cancers, cholangiocarcinomas, lung cancers, testicular cancers, prostate cancers, penal cancers; oral cancers, pharyngeal cancers and salivary gland cancers, skin cancers, kidney cancers, bladder cancers (for a review of these disorders, see Fishman et al., 1985, Medicine, 2d Ed., JB Lippincott Co., Philadelphia and Murphy et al., 1997, Informed Decisions: The Complete Book of Cancer Diagnosis, Treatment, and Recovery, Viking Penguin, Penguin Books USA, Inc., United States of America).
[0277] [000277] The invention further contemplates projecting any of the antibodies known in the art to treat and / or prevent cancer and related disorders, so that the antibodies comprise an Fc region incorporating a modified CH3 domain of the invention.
[0278] [000278] In a specific embodiment, a molecule of the invention (for example, an antibody comprising an Fc variant heterodimer inhibits or reduces the growth of the primary tumor or cancer cell metastasis by at least 99%, at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 60%, at least 50%, at least 45%, at least 40%, at least 45%, at least at least 35%, at least 30%, at least 25%, at least 20%, or at least 10% in relation to primary tumor growth or metastasis in the absence of said molecule of the invention.
[0279] [000279] The present invention includes the use of one or more Fc variants of the invention to prevent, treat or manage one or more symptoms associated with an inflammatory disorder in a subject. Although not intended to be linked to any mechanism of action, Fc variants with enhanced affinity for FcγRIIB will lead to an attenuation of activation receptors and, therefore, an attenuation of the immune response and have therapeutic efficacy to treat and / or prevent an autoimmune disorder. In addition, antibodies that bind to more than one target, such as bispecific antibodies comprising an Fc variant heterodimer, associated with an inflammatory disorder can provide synergistic effects over monovalent therapy.
[0280] [000280] The invention further includes administering the Fc variants of the invention in combination with a therapeutically or prophylactically effective amount of one or more anti-inflammatory agents. The invention also provides methods for preventing, treating, or managing one or more symptoms associated with an autoimmune disease, further comprising administering to said subject an Fc variant of the invention in combination with a therapeutically or prophylactically effective amount of one or more immunomodulatory agents. Examples of autoimmune diseases that can be treated by administering the Fc variants of the invention include, but are not limited to, alopecia areata, ankylosing spondylitis, antiphospholipid syndrome, autoimmune Addison's disease, autoimmune diseases of the adrenal gland, autoimmune hemolytic anemia, autoimmune hepatitis, oophoritis and orchitis autoimmune, autoimmune thrombocytopenia, Behcet's disease, bullous pemphigoid, cardiomyopathy, celiac dermatitis-disease, chronic fatigue immune dysfunction syndrome (CFIDS), chronic inflammatory demyelinating polyneuropathy, Churg-Strauss syndrome, scar pemphigoid, CREST syndrome, aglutin disease cold, Crohn's disease, discoid lupus, essential mixed cryoglobulinemia, fibromyalgia-fibromiositis, glomerulonephritis, Graves' disease, Guillain-Barré syndrome, Hashimoto's thyroiditis, idiopathic pulmonary fibrosis, idiopathic thrombocytopenic purpura (ITP), juvenile neuropathy, IgA lichen planus, lupus erythematosus, Meniere's disease, mixed connective tissue, multiple sclerosis, type 1 or immune-mediated diabetes mellitus, myasthenia gravis, pemphigus vulgaris, pernicious anemia, polyarteritis nodosa, polychondritis, polyglandular syndromes, polymyalgia rheumatica, polymyositis and dermatomyositis, primary agamaglobulinemia, primary arthritis, arthritis primary, cirrhosis psoriatic, Raynauld's phenomenon, Reiter's syndrome, rheumatoid arthritis, sarcoidosis, scleroderma, Sjogren's syndrome, rigid person syndrome, systemic lupus erythematosus, lupus erythematosus, takayasu arteritis, temporal arteritis / giant cell arteritis, ulcerative colitis, uveitis vasculitis such as vasculitis of herpetiform dermatitis, vitiligo and Wegener's granulomatosis. Examples of inflammatory disorders include, but are not limited to, asthma, encephalitis, inflammatory bowel disease, chronic obstructive pulmonary disease (COPD), allergic disorders, septic shock, pulmonary fibrosis, undifferentiated spongylarthropathy, undifferentiated arthropathy, arthritis, inflammatory osteolysis and resulting chronic inflammation of chronic viral or bacterial infections. Some autoimmune disorders are associated with an inflammatory condition, so there is an overlap between what is considered to be an autoimmune disorder and an inflammatory disorder. Therefore, some autoimmune disorders can also be characterized as inflammatory disorders. Examples of inflammatory disorders include those that can be prevented, treated or managed according to the methods of the invention include, but are not limited to, asthma, encephalitis, inflammatory bowel disease, chronic obstructive pulmonary disease (COPD), allergic disorders, septic shock, pulmonary fibrosis , undifferentiated spongyloarthropathy, undifferentiated arthropathy, arthritis, inflammatory osteolysis and chronic inflammation resulting from chronic viral or bacterial infections.
[0281] [000281] Fc variants of the invention can also be used to reduce the inflammation experienced by animals, particularly mammals, with inflammatory disorders. In a specific embodiment, an Fc of the invention reduces inflammation in an animal by at least 99%, at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70 %, at least 60%, at least 50%, at least 45%, at least 40%, at least 45%, at least 35%, at least 30%, at least 25%, at least 20%, or at least at least 10% in relation to inflammation in an animal, which is not administered with said molecule.
[0282] [000282] The invention further contemplates designing any of the antibodies known in the art to treat and / or prevent autoimmune disease or inflammatory disease, so that the antibodies comprise the Fc variant heterodimer of the invention.
[0283] [000283] The invention also includes methods for treating or preventing an infectious disease in a subject comprising administering a therapeutically or prophylactically effective amount of one or more Fc variants of the invention. Infectious diseases that can be treated or prevented by the Fc variants of the invention are caused by infectious agents, including, but not limited to, viruses, bacteria, fungi, viruses and protozoa.
[0284] [000284] Viral diseases that can be treated or prevented using the Fc variants of the invention, in conjunction with the methods of the present invention include, among others, those caused by hepatitis type A, hepatitis type B, hepatitis type C, influenza, chickenpox, adenovirus, herpes simplex type I (HSV-I), herpes simplex type II (HSV-II), rinderpest, rhinovirus, ecovirus, rotavirus, respiratory syncytial virus, papillomavirus, papova virus, cytomegalovirus, echinovirus, arbovirus, huntavirus, virus coxsackie, mumps virus, measles virus, rubella virus, polio virus, smallpox, Epstein-Barr virus, human immunodeficiency virus type I (HIV-I), human immunodeficiency virus type II (HIV-II) and agents viral diseases such as viral meningitis, encephalitis, dengue or smallpox.
[0285] [000285] Bacterial diseases that can be treated or prevented using the Fc variants of the invention, in conjunction with the methods of the present invention, which are caused by bacteria include, among others, mycobacteria rickettsia, mycoplasma, neisseria, S. pneumonia, Borrelia burgdorferi (Lyme disease), Bacillus antracis (anthrax), tetanus, streptococcus, staphylococcus, mycobacterium, tetanus, pertissus, cholera, plague, diphtheria, chlamydia, S. aureus and legionella. Protozoal diseases that can be treated or prevented using the molecules of the invention in conjunction with the methods of the present invention, which are caused by protozoa include, but are not limited to, leishmania, kokzidioa, trypanosoma or malaria. Parasitic diseases that can be treated or prevented using the molecules of the invention in conjunction with the methods of the present invention, which are caused by parasites include, but are not limited to, chlamydia and rickettsia.
[0286] [000286] In some embodiments, the Fc variants of the invention can be administered in combination with a therapeutically or prophylactically effective amount of one or more additional agents known to those skilled in the art for the treatment and / or prevention of an infectious disease. The invention contemplates the use of the molecules of the invention in combination with other molecules known to those skilled in the art for the treatment and prevention of an infectious disease, including, but not limited to, antifungal agents, antibiotics and antiviral agents.
[0287] [000287] The invention provides pharmaceutical methods and compositions comprising Fc variants of the invention (for example, antibodies, polypeptides). The invention also provides methods for treating, prophylaxis, and ameliorating one or more symptoms associated with a disease, disorder or infection by administering to a subject an effective amount of at least one Fc variant of the invention, or a pharmaceutical composition comprising at least least one Fc variant of the invention. In one aspect, the Fc variant is substantially purified (i.e., substantially free of substances that limit its effect or produce undesirable side effects including homodimers and other cellular material). In a specific embodiment, the subject is an animal, like a mammal including non-primates (for example, cows, pigs, horses, cats, dogs, mice, etc.) and primates (for example, monkey like a cynomolgous monkey and a human ). In a specific modality, the subject is a human. In yet another specific embodiment, the antibody of the invention is of the same species as the subject.
[0288] [000288] The route of administration of the composition depends on the condition to be treated. For example, intravenous injection may be preferable for treating a systemic disorder such as lymphatic cancer or a tumor with metastasis. The dosage of the compositions to be administered can be determined by the person skilled in the art without undue experimentation in conjunction with standard dose-response studies. Relevant circumstances to be considered in making these determinations include the condition or conditions to be treated, the choice of composition to be administered, the age, weight and response of the individual patient and the severity of the patient's symptoms. Depending on the condition, the composition can be administered orally, parenteral, intranasal, vaginal, rectal, lingual, sublingual, buccal, intrabucal and / or transdermal to the patient.
[0289] [000289] In this sense, compositions designed for oral, lingual, sublingual, buccal and intraoral administration can be prepared without undue experimentation by means known in the art, for example, with an inert diluent or with an edible carrier. The composition can be filled into gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the pharmaceutical compositions of the present invention can be incorporated with excipients and used in the form of tablets, capsule lozenges, elixirs, suspensions, syrups, chewing gums and the like.
[0290] [000290] Tablets, pills, capsules, lozenges and the like may also contain binders, containers, disintegrating agents, lubricants, sweetening agents, and / or flavoring agents. Some examples of binders include microcrystalline cellulose, tragacanth gum and gelatin. Examples of excipients include starch and lactose. Some examples of disintegrating agents include alginic acid, corn starch and the like. Examples of lubricants include magnesium stearate and potassium stearate. An example of a lubricant is colloidal silicon dioxide. Some examples of sweetening agents include sucrose, saccharin and the like. Examples of flavoring agents include peppermint, methyl salicylate, orange flavor and the like. Materials used to prepare these various compositions must be pharmaceutically pure and non-toxic in the amounts used.
[0291] [000291] The pharmaceutical compositions of the present invention can be administered parenterally, such as, for example, by intravenous, intramuscular, intrathecal and / or subcutaneous injection. Parenteral administration can be carried out by incorporating the compositions of the present invention into a solution or suspension. Such solutions or suspensions may also include sterile diluents, such as water for injection, saline, fixed oils, polyethylene glycols, glycerin, propylene glycol and / or other synthetic solvents. Parenteral formulations can also include antibacterial agents, such as, for example, benzyl alcohol and / or methyl parabens, antioxidants, such as, for example, ascorbic acid and / or sodium bisulfite and chelating agents, such as EDTA. Buffers, such as acetates, citrates and phosphates and agents for the regulation of tonicity, such as sodium chloride and dextrose, can also be added. The parenteral preparation can be placed in ampoules, disposable syringes and / or multi-dose vials made of glass or plastic. Rectal administration includes administering the composition to the rectum and / or large intestine. This can be done using suppositories and / or enemas. Suppository formulations can be prepared by methods known in the art. Transdermal administration includes percutaneous absorption of the composition through the skin. Transdermal formulations include adhesives, ointments, creams, gels, plaster and the like. The compositions of the present invention can be administered nasally to a patient. As used herein, administering via nasal or nasal administration includes administering the compositions to the mucous membranes of the nasal cavity and / or nasal passage of the patient.
[0292] [000292] The pharmaceutical compositions of the invention can be used in accordance with the methods of the invention to prevent, treat or ameliorate one or more symptoms associated with a disease, disorder or infection. It is envisaged that the pharmaceutical compositions of the invention are sterile and in a form suitable for administration to a subject.
[0293] [000293] In one embodiment, the compositions of the invention are pyrogenic formulations that are substantially free of endotoxins and / or related pyrogenic substances. Endotoxins include toxins that are confined within a microorganism and are released when the microorganisms are destroyed or die. Pyrogenic substances also include fever inducers, thermostable substances (glycoproteins) in the outer membrane of bacteria and other microorganisms. Both substances can cause fever, hypotension and shock if administered to humans. Due to the potential harmful effects, it is advantageous to remove even low amounts of endotoxins from the pharmaceutical solution administered intravenously. The Food & Drug Administration ("FDA") has set a maximum limit of 5 units of endotoxin (EU) per dose per kilogram of body weight over a period of one hour for intravenous drug applications (The The United States Pharmacopeial Convention, Pharmacopeial Forum 26 (1): 223 (2000) When therapeutic proteins are administered in amounts of several hundred or thousands of milligrams per kilogram of body weight, as is the case with monoclonal antibodies, it is advantageous to remove any trace of endotoxin. , levels of endotoxins and pyrogen in the composition are less than 10 EU / mg, or less than 5 EU / mg, or less than 1 EU / mg, or less than 0.1 EU / mg, or less than 0.01 EU / mg, or less than 0.001 EU / mg.
[0294] [000294] The invention provides methods for preparing, treating, or ameliorating one or more symptoms associated with a disease, disorder or infection, said method comprising: (a) administering to a subject in need thereof a dose of a quantity prophylactically or therapeutically efficacy of a composition comprising one or more Fc variants and (b) administering one or more subsequent doses of said Fc variants, to maintain a plasma concentration of the Fc variant at a desirable level (for example, about 0.1 to about 100 μg / mL), which continuously binds to an antigen. In a specific embodiment, the plasma concentration of the Fc variant is maintained at 10 μg / ml, 15 μg / ml, 20 μg / ml, 25 μg / ml, 30 μg / ml, 35 μg / ml, 40 μg / ml, 45 μg / ml or 50 μg / ml. In a specific modality, said effective amount of Fc variant to be administered is between at least 1 mg / kg and 8 mg / kg per dose. In a specific embodiment, said effective amount of Fc variant to be administered is between at least 4 mg / kg and 5 mg / kg per dose. In yet another specific modality, said effective amount of Fc variant to be administered is between 50 mg and 250 mg per dose. In yet another specific modality, said effective amount of Fc variant to be administered is between 100 mg and 200 mg per dose.
[0295] [000295] The present invention also includes protocols to prevent, treat or ameliorate one or more symptoms associated with a disease, disorder or infection in which an Fc variant is used in combination with a therapy (e.g., prophylactic or therapeutic agent) other than an Fc variant and / or variant fusion protein. The invention is based, in part, on the recognition that the Fc variants of the invention have enhanced and synergistic effects with, and increase the effectiveness of, improve the tolerance of, and / or reduce the side effects caused by other cancer therapies, including current standard and experimental chemotherapies. Combination therapies have additive potency, an additive therapeutic effect or a synergistic effect. The combination therapies of the invention allow for lower dosages of therapy (for example, therapeutic or prophylactic agents) used in conjunction with Fc variants to prevent, treat or ameliorate one or more symptoms associated with a disease, disorder or infection and / or less frequently administering such therapeutic or prophylactic agents to a subject with a disease or infection disorder to improve the quality of life of said subject and / or to achieve a prophylactic or therapeutic effect. In addition, the combination therapies of the invention reduce or avoid undesirable or adverse side effects associated with the administration of current single agent therapies and / or existing combination therapies, which in turn improve patient compliance with the treatment protocol. Numerous molecules that can be used in combination with the Fc variants of the invention are well known in the art. See, for example, PCT publications WO 02/070007; WO 03/075957 and US Patent Publication 2005/064514.
[0296] [000296] The present invention provides kits comprising one or more Fc variants with altered binding affinity for FcγRs and / or C1q and altered CDC and / or ADCC activity that specifically bind to an antigen conjugated or fused to a detectable agent, therapeutic agent or drugs, in one or more containers, for use in monitoring, diagnosing, preventing, treating or ameliorating one or more symptoms associated with a disease, disorder, or infection. EXAMPLES
[0297] [000297] The following examples are given in order to illustrate the practice of this invention. They are not intended to limit or define the scope of this invention. Example 1: Generation of Bivalent Monospecific Antibodies with Fc Heterodimer Domains.
[0298] [000298] The genes encoding the antibody's light and heavy chains were constructed through gene synthesis using codons optimized for expression in humans / mammals. Fab sequences were generated from a known Her2 / neu binding Ab (Carter P. et al. (1992) Humanization of an anti P185 Her2 antibody for human cancer therapy. Proc Natl Acad Sci 89, 4285.) and Fc it was an IgG1 isotype (SEQ NO ID: 1). The final gene products were subcloned into the mammalian expression vector pTT5 (NRC-BRI, Canada) (Durocher, Y., Perret, S. & Kamen, A. High-level and high-throughput recombinant protein production by transient transfection of suspension-growing human HEK293- EBNA1 cells. Nucleic acids research 30, E9 (2002)). Mutations in the CH3 domain were introduced through site-directed mutagenesis of the pTT5 model vectors. See Table 1 and Table 6 and Table 7 for a list of mutations prepared from the modified CH3 domain.
[0299] [000299] In order to estimate the formation of heterodimers and to determine the ratio of homodimers vs heterodimers, the two heavy chains of the heterodimer were designed with C-terminal extensions of different size (specifically, A-chain with HisTag C-terminal and B-chain with C-terminal mRFP plus Strep TagII). This difference in molecular weight allows the differentiation of homodimers vs heterodimers in non-reducing SDS - PAGE as illustrated in FIGURE 25A.
[0300] [000300] HEK293 cells were transfected in an exponential growth phase (1.5 to 2 million cells / mL) with 1 mg / mL 25kDa aqueous polyethylenimine (PEI, Polysciences) in the ratio of 2.5: 1 PEI: DNA . (Raymond C. et al. A simplified polyethylenimine-mediated transfection process for large-scale and high-throughput applications. Methods. 55 (1): 44-51 (2011)). To determine the ideal concentration range for the formation of heterodimers, DNA was transfected at three different ratios than the two heavy chains. For example, this was done in a volume of 2ml of culture and transfection DNA, composed of 5% GFP, 45% salmon sperm DNA, 25% light chain and 25% total heavy chains, in which the plasmid heavy chain A (with His-Tag C-terminal) and heavy chain B plasmid (with StrepTagII C-terminal plus RFP) at 65% / 55% / 35% or 10% / 20% / 40%) were sampled in 3 different relative ratios (string_A (His) / string_B (mRFP)) of 10% / 65%; 20% / 55%; 40% / 35% (the apparent 1: 1 expression ratio of a WT_His / WT_mRFP heterodimer was determined to be close to the 20% / 55% DNA ratio). Between 4 to 48 hours after transfection in free medium if serum F17 (Gibco), peptone TN1 is added to a final concentration of 0.5%. Expressed antibody was analyzed by SDS-PAGE to determine the best light to heavy chain ratio for ideal heterodimer formation (see Figure 25B and C).
[0301] [000301] A selected DNA ratio, for example, plasmid with 50% light chain, plasmid with 25% heavy chain A, 25% heavy chain B of AZ33 and AZ34, with 5% GFP and 45% DNA of salmon sperm was used to transfect 150mL of cell culture, as described above. Transfected cells were collected after 5-6 days with culture medium collected after centrifugation at 4000 rpm and clarified using a 0.45μm filter. See Table 2 below for a list of the percentage of light and heavy chain plasmids A and B used in the step transfection assays for each of the antibodies with CH3 mutations generated for further analysis, including determination of purity and fusion temperature.
[0302] [000302] The clarified culture medium was loaded onto a MabSelect SuRe protein-A column (GE Healthcare) and washed with 10 column volumes of pH 7.2 PBS buffer. The antibody was eluted with 10 column volumes of citrate buffer at pH 3.6 with the combined fractions containing the antibody neutralized with TRIS at pH 11. The protein was finally desalted using an Econo-Pac 10DG column (Bio-Rad). The C-terminal mRFP tag on heavy chain B was removed by incubating the antibody with enterokinase (NEB) in a 1: 10,000 ratio overnight in PBS at 25oC. The antibody was purified from the mixture by gel filtration. For gel filtration, 3.5 mg of the antibody mixture was concentrated to 1.5 mL and loaded onto a Sephadex 200 HiLoad 16/600 200 pg column (GE Healthcare) via AKTA Express FPLC at a flow rate of 1 mL / min. PBS buffer at pH 7.4 was used at a flow rate of 1 mL / min. The fractions corresponding to the purified antibody were collected, concentrated to ~ 1 mg / mL and stored at -80 ° C.
[0303] [000303] The formation of heterodimers, in comparison with homodimers, was analyzed using non-reducing SDS-PAGE and mass spectrometry. The protein A purified antibody was run on an SDS-PAGE with a 4-12% gradient, non-reducing gel to determine the percentage of heterodimers formed prior to enterokinase treatment (see Figure 26). For mass spectrometry, all Trap LC / MS (ESI-TOF) experiments were performed on an Agilent 1100 HPLC system interfaced with a Waters Q-TOF2 mass spectrometer. Five μg of purified antibody with gel filtration was injected into a Protein MicroTrap protein (1.0 by 8.0 mm), washed with 1% acetonitrile for 8 minutes, a gradient of 1 to 20% acetonitrile / 0.1% formic acid for 2 minutes, then eluted with a gradient of 20 to 60% acetonitrile / 0.1% formic acid for 20 minutes. The eluate (30-50μL / min) was directed to the spectrometer with spectrum acquired every second (m / z 800 to 4,000). (See Figure 28) Variants with more than 90% heterodimers were selected for further analysis, with the exception of AZ12 and AZ14 which each had more than 85% heterodimer formation. Example 3: Determination of the Stability of Monospecific Bivalent Antibodies with heterodimeric Fc Domains using Differential Scanning Calorimetry (DSC).
[0304] [000304] All DSC experiments were performed using a GE VP-Capillary instrument. The proteins were exchanged in the buffer in PBS (pH 7.4) and diluted to 0.4 to 0.5 mg / mL with 0.137 ml loaded into the sample cell and measured at a scan rate of 1 ° C / min. 20 to 100 ° C. The data were analyzed using Origin software (GE Healthcare) with the subtracted PBS buffer. (See, Figure 27). See Table 3 for a list of tested variants and a determined melting temperature. See Table 4 for a list of variants with a melting temperature of 70 ° C and above and the specific Tm for each variant. Table 3: Fusion temperature measurements of modified CH3 domains in an IgG1 antibody having 90% or more heterodimer formation compared to homodimer formation
[0305] [000305] All binding experiments were performed using a BioRad ProteOn XPR36 instrument at 25 ° C with 10mM HEPES, 150mM NaCl, 3.4 mM EDTA and 0.05% Tween 20 at pH 7.4. Recombinant HER-2 / neu (p185, ErbB-2 (eBiosciences, Inc.)) was captured on the activated GLM sensor chip by injecting 4.0μg / mL in 10 mM NaOAc (pH 4.5) at 25μL / min up to approximately 3000 resonance units (RUs) are immobilized with the remaining active groups interrupted. 40μg / mL of purified anti-HER-2 / neu antibodies comprising the modified CH3 domains were captured indirectly on the sensor chip by binding with the Her-2 / neu protein when injected at 25μL / min for 240s (resulting in approximately 500RUs) after a buffer injection to establish a stable base. Concentrations of Fcgama (CD16a (allotype f) and CD32b) (6000, 2000, 667, 222 and 74.0nM) were injected at 60μL / min for 120s with a dissociation phase of 180s to obtain a set of binding sensograms. Resulting KD values were determined from binding isotherms using the Balance Adjustment model with values reported as the average of three independent runs. Comparisons were made with the wild-type IgG1 Fc domain and binding is expressed as a ratio of the WT kD to the kD variant (See Table 5). Table 5: Ratio of binding of wild-type IgG1 kD to the CH3 domain antibody modified independently of CD16a and CD32b
[0306] [000306] To obtain AZ variants with high purity and stability, the structural and computational strategies described above were used. (See Figure 24) For example, the AZ8 depth structure-function analysis provided a detailed understanding for each of the introduced AZ8 mutations, L351Y_V397S_F405A_Y407V / K392V_T394W compared to human wild-type IgG1 and indicated that the nucleus mutations of important heterodimers were L351Y_F405A_Y407V / T394W, while V397S, K392V were not relevant for the formation of heterodimer. The nucleus mutations (L351Y_F405A_Y407V / T394W) are referred to here as "Structure 1" mutations. The analysis further revealed that the major interface points that are missing with respect to the formation of wild type homodimer (WT) are the interactions of WT-F405-K409, Y407-T366 and the packaging of Y407- Y407 and - F405 (see Figure 29). This was reflected in the packaging, cavity and analysis of MD, which showed a great conformational difference in the loop region D399-S400-D401 (see Figure 30) and the associated β sheets in K370. This resulted in the loss of K409-D399 inter-chain interactions (see Figure 30) and weakening of the strong hydrogen bond K370 to E357 (K370 is no longer in direct contact with S364 and E357, but is fully exposed to the solvent). In the WT IgG1 domain CH3, these regions chain the interface at the edge that protects core interactions from volume solvent competition and increases the dynamic occurrence of favorable hydrophobic van der Waals interactions. The consequence was a smaller buried surface area of AZ8 compared to WT and greater accessibility of the hydrophobic core solvent. This indicates that the most important factors for the lower stability of AZ8 compared to the stability of WT were a) the loss of the WT-F405-K409 interaction and F405 packaging and b) the loss of the strong packaging interaction of Y407-Y407 and Y407-T366. See Figure 29.
[0307] [000307] Consequently, we have identified the main residue / sequence motifs responsible for the low stability of AZ8 compared to WT. To improve the stability and specificity of the AZ8 heterodimer, subsequent positive projecting efforts were therefore specifically focused on stabilizing the loop conformation of positions 399-401 in a more 'closed' WT conformation (see Figure 30) and compensating for the overall slightly decreased (freer) packing of the hydrophobic core at positions T366 and L368 (see Figure 29).
[0308] [000308] To achieve this stabilization of the conformation of the handle of positions 399-401, the computational approach described was used to evaluate our different targeted design ideas. Specifically, three different independent options for the Fc AZ8 variant were analyzed to optimize the main regions identified to improve stability. First, the connection pocket near position K409 and F405A was evaluated for better hydrophobic packaging to protect the hydrophobic core and stabilize the 399-400 conformation loop (see Figure 30). Those included, but were not limited to, additional point mutations at positions F405 and K392. Second, options for improving electrostatic interactions at positions 399-409 were evaluated, to stabilize the 399-400 loop conformation and protect the hydrophobic core. This included, but was not limited to, additional point mutations at positions T411 and S400. Third, the connection pocket in the T366, T394W and L368 core packaging positions was evaluated to improve the hydrophobic core packaging (see Figure 29). Those included, but were not limited to, additional point mutations at positions T366 and L368. The different independent positive design ideas were tested in silico and certain good variants using the computational tools (AZ17-AZ62) were experimentally validated for expression and stability as described in Examples 1-4. See Table 4 for a list of certain Fc-based heterodimer constructs comprising this design strategy, with a melting temperature of 70 ° C or higher.
[0309] [000309] Variant Fc AZ33 is an example of the development of an Fc variant in which Structure 1 has been modified resulting in mutations in Structure 1a to improve stability and purity. This Fc variant was designed based on AZ8 with the goal being to improve hydrophobic packaging in positions 392-394-409 and 366 to protect the hydrophobic core and stabilize the 399-400 loop confirmation. This Fc AZ33 variant heterodimer has two additional point mutations different from the core mutations of AZ8, K392M and T366I. T366I _K392M_T394W / F405A_Y407V mutations are referred to here as "Structure 1a" mutations. The K392M mutation was designed to improve packaging in the cavity close to position K409 and F405A to protect the hydrophobic core and stabilize the 399-400 loop conformation (see Figure 31). T366I was designed to improve the packaging of the hydrophobic core and eliminate the formation of T394W chain homodimers (see Figure 29). Experimental data for AZ33 show significant improvement in stability over other negative design Fc variants such as AZ8 (Tm 68 ° C) where AZ33 has a Tm of 74 ° C and a heterodimer content of> 98%. (see Figure 25C) Development of Fc variants using Structure 1 mutations in phase three design of Fc variant heterodimers
[0310] [000310] Although AZ33 provides a significant improvement in stability and specificity (or purity) over the initial AZ8 variant at the beginning, our analysis indicates that further improvements to the stability of an Fc variant heterodimer can be made with other amino acid modifications using the data AZ33 experiments and the design methods described above. Different design ideas have been tested independently for expression and stability, but independent design ideas are transferable and the most successful heterodimer will contain a combination of different designs. Specifically, for the optimization of AZ8 packaging mutations in the cavity close to K409-F405A-K392, they were independently evaluated based on mutations that optimize the nucleus packaging in L366T-L368 residues. These two regions, 366-368 and 409-405-392 are distal from each other and are considered independent. Variant Fc AZ33, for example, was optimized for packaging in 409-405-392, but not in 366-368, because these optimization mutations were evaluated separately. The comparison of mutations 366-368 suggests that T366L has an improved stability over T366 and also T366I, the point of mutation used in the development of the Fc AZ33 variant. Consequently, the experimental data presented immediately suggest further optimization of AZ33 by introducing T366L instead of T366I, for example. Therefore, amino acid mutations in the CH3 domain T366L_K392M_T394W / F405A_Y407V are referred to herein as "Structure 1b" mutations.
[0311] [000311] Similarly, complete experimental data were analyzed to identify point mutations that can be used to further improve the Fc AZ33 heterodimer variant. These identified mutations were analyzed using the computational approach described above and classified to generate the list of additional Fc variant heterodimers based on AZ33, as shown in Table 6. Example 6: Rational design of Fc variants using design Fc_CH3 - Structure 2 (a and b) and, the development of AZ63-101 and AZ2199-AZ2524
[0312] [000312] To improve the initial negative design phase Fc variant AZ15 for stability and purity, the structural and computational strategies described above were employed (see Figure 24). For example, the analysis of the structure-function depth of the Fc AZ15 variant provided a detailed understanding for each of the introduced AZ15 mutations, L351Y_Y407A / E357L_T366A_K409F_T411N compared to human wild-type (WT) IgG1 and indicated that the heterodimer mutations of the important nuclei were L351Y_Y407A / T366A_K409F, while E357L, T411N were not directly relevant to the formation and stability of heterodimer. Nucleus mutations (L351Y_Y407A / T366A_K409F) are referred to herein as "Structure 2" mutations. The analysis further revealed that the major interface points that are missing with respect to the formation of wild type homodimer (WT) are the saline bridge D399-K409, the hydrogen bond Y407-T366 and the packaging of Y407- Y407 . The detailed analysis, provided below, describes how we improved the stability of our original Fc AZ15 variant and the positions and amino acid modifications made to achieve these Fc variants with improved stability. Development of Fc variants using Structure 2 mutations and the further development of Structure 2a mutations.
[0313] [000313] In silico analysis indicated a non-ideal packaging of previous Fc variant designs such as AZ15 K409F_T366A_Y407A mutations and a general decreased packaging of the hydrophobic core due to the loss of interactions of WT-Y407 Y407. The heteromultimers described here are designed with the most ideal packaging. Some of the positive design efforts described here have focused on point mutations to compensate for packaging deficits in the initial Fc AZ15 variant. Target residues included positions T366, L351, and Y407. Different combinations of these were tested in silico and the Fc variants best classified using the computational tools (AZ63-AZ70) were experimentally validated for expression and stability as described in Examples 1-4.
[0314] [000314] The Fc AZ70 variant is an example of the development of an Fc variant in which Structure 2 has been modified resulting in mutations in Structure 2a to improve stability and purity. This Fc variant was designed based on AZ15 in order to achieve better packaging in the hydrophobic core as described above. The Fc AZ70 variant has the same mutations as the Structure 2 core (L351Y_Y407A / T366A_K409F), as described above except that T366 was mutated to T366V instead of T366A (FIGURE 33). The L351Y mutation improves the melting temperature of the 366A_409F / 407A variant from 71.5 ° C to 74 ° C, and the further change from 366A to 366V improves the Tm to 75.5 ° C. (See, AZ63, AZ64 and AZ7 0 in Table 4, with a Tm of 71.5 ° C, 74 ° C and 75.5 ° C, respectively). Nucleus mutations (L351Y_Y407A / T366V_K409F) are referred to herein as "Structure 2a" mutations. Experimental data for the Fc AZ70 variant showed a significant improvement in stability over the initial negative design Fc variant AZ15 (Tm 71 ° C) where AZ70 has a Tm of 75.5 ° C and a heterodimer content> 90% (FIGURE 33 and 27). Development of Fc variants using Structure 2 mutations and further development of Structure 2b mutations.
[0315] [000315] Molecular Dynamics (MD) simulation and packaging analysis showed a more 'open' preferential conformation of loop 399-400, which was probably due to the loss of the WT K409-D399 salt bridge. This also results in the unsatisfied D399, which in turn, preferred a compensatory interaction with K392 and induced a more 'open' conformation of the handle. This more 'open' conformation of the loop results in decreased overall packaging and greater solvent accessibility of the interface residues of the core of the CH3 domain, which in turn significantly destabilized the heterodimer complex. Therefore, one of the efforts of the positive targeted project was the chaining of this loop in a more 'closed' conformation, type WT with additional point mutations that compensate for the loss of the D399-K409 salt bridge and the K409 packaging interactions. The target residues included positions T411, D399, S400, F405, N390, K392 and combinations thereof. Different strategies for positive electrostatic and hydrophobic packaging design were tested in silico in relation to the above positions and the best classified Fc variants determined using the computational tools (AZ71-AZ101) were experimentally validated for expression and stability as described in Examples 1-4 .
[0316] [000316] The Fc AZ94 variant is an example of the development of an Fc variant in which Structure 2 has been modified resulting in mutations in Structure 2b together with additional point mutations to improve stability and purity. This Fc variant was designed with the objective of linking the 399-400 loop into a more 'closed' conformation, type WT and compensating for the loss of the D399-K409 salt bridge as described above. The Fc AZ94 variant has four additional point mutations to Structure 2 (L351Y_Y407A / T366A_K409F) and returns L351Y to wild type L351Leave (Y407A / T366A_K409F) as the core mutations for this Fc variant. Mutations of the Y407A / T366A_K409F nucleus are referred to herein as "Structure 2b" mutations. The four additional point mutations of AZ94 are K392E_T411E / D399R_S400R. The T411E / D399R mutations were designed to form an additional salt bridge and compensate for the loss of the K409 / D399 interaction (FIGURE 34). In addition, this salt bridge has been designed to prevent homodimer formation by disadvantaging the charge-charge interactions in both potential homodimers. The additional K392E / S400R mutations were intended to form another salt bridge and thus further tie the 399_400 loop into a more 'closed' conformation, type WT (FIGURE 34). Experimental data for AZ94 show better stability and purity over the negative design Fc variant AZ15 (Tm 71 ° C,> 90% purity) where the Fc AZ94 variant has a Tm of 74 ° C and a heterodimer or purity content > 95%. Development of Fc variants using Structure 2 mutations in phase three design of Fc variant heterodimers
[0317] [000317] FC, AZ70 and AZ94 variants provide a significant improvement in stability and purity over the initial negative design Fc variants like AZ15, but our analysis and comparison of AZ70 and AZ94 directly indicates that unexpected improvements to the stability of a variant heterodimer Fc can be made with more amino acid modifications. For example, variants Fc AZ70 and AZ94 were designed to target two distinct regions not optimized in the initial AZ15 variant, which was accomplished by improving the hydrophobic core packaging and mutating outside the core interface residues resulting in salt bridges and additional hydrogen bonds to stabilize the loop conformation of positions 399-401. The additional point mutations of the Fc, AZ70 and AZ94 variants are distal from each other and are therefore independent and transferable to other Fc variants designed around the same mutations in the Structure 2 nucleus, including mutations 2a and 2b. Specifically, AZ70 only carries the optimized L351Y_Y407A / T366A_K409F core mutations, but no additional salt bridge, while AZ94 comprises four additional electrostatic mutations (K392E_T411E / D399R_S400R), but has one less mutation in the hydrophobic core interface (Y407A / T409A40) . These Structure 2b mutations are less stable than AZ70 (See, for example, AZ63, which has equivalent core mutations such as AZ94 and 72 ° C Tm), but are compensated for by the addition of K392E_T411E / D399R_S400R mutations. The experimental data presented for stability and purity indicate that the combination of AZ70 mutations, which optimize the hydrophobic nucleus, and AZ94 electrostatic mutations should further improve the stability and purity of an Fc variant heterodimer. Similarly, complete experimental data for Structure 2 Fc variants (AZ63-101) were analyzed to identify point mutations that can be used to further improve the Fc AZ70 and AZ 94 variant heterodimers. These identified mutations were further analyzed by the approach computational described above and classified to generate the list of additional Fc variant heterodimers based on AZ70 and AZ94, as shown in Table 7. Example 7: Effect of heterodimeric CH3 on FcgR binding
[0318] [000318] As a prototypical example of heterodimeric Fc activity with FcgR, two variant antibodies with heterodimeric Fc region were tested A: K409D_K392D / B: D399K_D356K (Control 1 (het 1 in Figure 35) and A: Y349C_T366S_L368A_Y407V / B3C 4 (het 2 in Figure 35) with Her2-binding Fab arms in a SPR assay described in Example 4 for FcgR binding. As shown in Figure 35, we observed that the Fc heterodimeric regions bind to different Fcgama receptors with the same relative strength of the wild-type IgG1 Fc region, but in general, the binding of the heterodimeric Fc region to each of the FcgRs is slightly better than that of the wild-type antibody, indicating that mutations at the Fc CH3 interface may impact the binding strength of the Fc region for Fcgama receptors in all CH2 domains, as observed in our analyzes and molecular dynamics simulations. Example 8: Effect of Asymmetric CH2 Mutations of a heterodimeric Fc on FcgR binding
[0319] [000319] Serine mutation at position 267 in the CH2 domain of the Fc region for an aspartic acid (S267D) is known to potentiate binding to Fcgama IIbF, IIbY & IIaR receptors when introduced homodimerically into the two chains of the CH2 domain. This mutation can be introduced in only one of the CH2 domains in a heterodimeric Fc molecule to obtain about half the improvement in binding strength compared to when this mutation is introduced into a homodimeric Fc CH2 as indicated by the data shown in Figure 36A. On the other hand, the E269K mutation in a homodimeric CH2 domain of Fc prevents binding of the Fc region to FcgR. We present a scheme for potentiated manipulation of the binding force of the Fc region for Fcg receptors by the asymmetric introduction of these favorable and unfavorable mutations in one of the two chains in the CH2 domain of Fc. The introduction of an E269K mutation asymmetrically in a CH2 chain in a heterodimeric Fc acts as a polarity conductor blocking the FcgR bond on the side where it is present, while letting the other side of the Fc interact with the FcgR in a normal way. The results of this experiment are shown in Figure 36A. The opportunity to selectively alter the binding strength across both Fc chains independently provides greater opportunity to manipulate the binding strength and selectivity between Fc and Fcg receptors. Thus, this asymmetric design of mutations in the CH2 domain allows us to introduce positive and negative design strategies to favor or disadvantage certain connection models, providing a greater opportunity to introduce selectivity.
[0320] [000320] In a subsequent experiment, we changed the selectivity profile of the base Fc mutant S239D_D265S_I332E_S298A which shows increased binding strength to Fcgama IIIaF and IIIaV receptors, while continuing to present weaker binding to Fcgama IIaR, IIbF and IIbY receptors. This is shown in the connection profile shown in Figure 36B. By introducing asymmetric E269K mutations in chain A and avoiding the I332E mutation in chain B, we are able to generate a new FcgR binding profile that further weakens binding to receptor IIa and IIb and makes Fc more specific for binding to receptor IIIa.
[0321] [000321] In another example shown in Figure 36C, asymmetric mutations are highlighted in relation to the homodimeric Fc involving a S239D / K326E / A330L / I332E / S298A mutation in the CH2 domain. In relation to the wild type IgG1 Fc, this variant shows increased binding to the IIIa receptor but also binds to the Ia and IIb receptors slightly more strongly than the wild type Fc. The introduction of these mutations in an asymmetric form A: S239D / K326E / A330L / I332E and B: S298A while reducing the binding of IIIa, also increases the binding to the IIa / IIb receptor, losing selectivity in the process. By introducing an asymmetric E269K mutation in this heterodimeric variant, ie A: S239D / K326E / A330L / I332E / E269K and B: S298A, the binding of IIa / IIb is reduced back to wild-type levels. This highlights the fact that the use of asymmetric mutations in the CH2 domain of Fc is able to provide a significant opportunity to project increased FcgamaR selectivity.
[0322] [000322] The reagents used in the examples are either commercially available or can be prepared using commercially available instrumentation, methods or reagents known in the art. The above examples illustrate various aspects of the invention and practice of the methods of the invention. The examples are not intended to provide an exhaustive description of the many different embodiments of the invention. Thus, although the above invention is described in detail by way of illustration and example for the sake of clarity of understanding, those skilled in the art will easily realize that many changes and modifications can be made to them without departing from the spirit or scope of the attached claims. . Example 9: FcRn binding determined by SPR.
[0323] 1. Fluindo o heterodímero variante sobre FcRn imobilizado: Neste experimento, superfícies de alta densidade, aproximadamente 5000 RUs foram preparadas usando o acoplamento padrão NHS/EDC. 100nM de WT e cada variante foram injetados em triplicata a 50 uL min para 120s com dissociação de 600s em tampão de execução MES pH6. 2 . Fluindo FcRn sobre heterodímeros variantes indiretamente capturados: Neste experimento SPR, uma superfície de IgG anti-humano de cabra foi usada para capturar indiretamente os anticorpos (aproximadamente 400RUs cada), seguidos por uma injeção de uma série de diluição de 3 vezes FcRn (cone alto 6000nM) . O tampão de execução foi 10mM de MES/150mM de NaCl/3,4 mM de EDTA /0,05 de Tween20 em pH6. Não houve ligação significativa de FcRn à superfície policlonal da cabra. Todas as variantes mostram sensogramas semelhantes ao WT. A Tabela 8 abaixo mostra o Kd determinado pela imobilização indireta com fluxo de FcRn (2.). Tabela 8: Kd determinado pela imobilização indireta com fluxo de FcRn.
[0324] [000324] Bispecific binding has been demonstrated using an Fc heterodimer with A-chain mutations: L351Y_F405A_Y407V, B-chain: T366L_K392M_T394W and anti-HER2 and anti-HER3 scFvs fused to the N-terminal of the H-chain and F-chain H-chain of the F-chain and B-chain. The variants resulting from bispecific HER2 / HER3 variants and the two monovalent-monospecific HER2, HER3 variants are illustrated in Fig. 40A. To test bispecific binding, a dose range of the two monovalent variants (monovalent anti-HER2 and monovalent anti-HER2, shown in Fig. 40A) and the bispecific anti-HER2 / HER3 heterodimer was incubated with MALME-M3 melanoma cells in a row FACS analysis to determine the apparent binding affinity of each molecule. (Shown in Fig. 40B) The assay system was configured according to the protocols described in: "Antitumor activity of a novel bispecific antibody that targets the ErbB2 / ErbB3 oncogenic unit and inhibits heregulin-induced activation of ErbB3", McDonagh CF et al., Mol Cancer Ther. 11 (3): 582-93 (2012). Example 11: Expression and Purification of Bivalent Monospecific Antibodies with Fc Heterodimer Domains and quantification of purity by LC / MS.
[0325] [000325] AZ133 heterodimeric variants (A: L351Y / F405A / Y407V, B: T366L / K392M / T394W), AZ138 (A: F405A / Y407V, B: T366L / K392M / T394W), AZ3002 (A: T350V / L351 / Y407V, B: T350V / T366L / K392M / T394W), AZ3003 (A: T350V / L351Y / F405A / Y407V, B: T350V / T366L / K392L / T394W), and other AZ3000-AZ3021 constructs were generated and purified as per described in Examples 1 and 2. In order to estimate the strength of the heterodimer formation and the effect of the excess of one of the heterodimer chains on the purity of the heterodimer, the selected heterodimers were transiently expressed using 3 different DNA ratios of the two heavy chains A and B (for example, ratios A: B = 1: 1.5; 1: 1; 1.5: 1).
[0326] [000326] The genes encoding the heterodimer light and heavy chains were constructed by gene synthesis using codons optimized for expression in humans / mammals, as described in detail in Example 1. The Fab sequences were generated from an Ab of known Her2 / neu linkage (Carter P. et al. (1992) Humanization of an anti P185 Her2 antibody for human cancer therapy. Proc Natl Acad Sci 89, 4285) and the Fc was an IgG1 isotype (SEQ NO ID: 1). The variant was expressed by transient coexpression, as described in Examples 1-2 using 3 different heavy chain-A to heavy chain-B ratios of 1: 1.5, 1: 1 and 1.5: 1. The samples were purified by protein-A affinity chromatography and preparative gel filtration (see Example 2 for details). The purified samples were deglycosylated with PNGaseF overnight at 37 ° C. Before MS analysis, the samples were injected into a Poros R2 column and eluted in a gradient with 20-90% ACN, 0.2% FA in 3 minutes. The peak of the LC column was analyzed with an LTQ-Orbitrap XL mass spectrometer (Cone Voltage: 50 V Lens tube: 215 V; FT Resolution: 7,500) and integrated with the Promass software to generate molecular weight profiles.
[0327] [000327] The relative peak heights for heterodimers and homodimers were used to estimate the heterodimer purity (see Figure 39). Example 12: Crystalline structure of AZ3002 and AZ3003 heteromultimers:
[0328] 1. Kabsch, W. XDS. Acta Crystallogr D Biol Crystallogr, 125132 (2010). 2. McCoy, A.J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr.D.Biol.Crystallogr. 63, 32-41 (2007). 3. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr.D.Biol.Crystallogr. 60, 2126-2132 (2004) . 4. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr.D.Biol. Crystallogr. 53, 240-255 (1997). [000328] AZ3002 and AZ3003 heterodimeric Fc constructs were transiently expressed in CHO and purified for homogeneity by pA and SEC. The purified Fc heterodimers were crystallized at 18 ° C, after ~ 24 hours of incubation by means of a vapor drop diffusion method in a 2: 1 ratio above a 5% (v / v) mother liquor solution composed of ethylene glycol, 18% (w / v) polyethylene glycol 3350 and 0.15 M ammonium iodide with the aid of micropropagation. The crystals were cryoprotected, increasing the concentration of ethylene glycol to 30% (v / v) and, subsequently, cooled in a flash in liquid nitrogen. Diffraction data from both crystals were collected at 100 K, using oscillations from 0.5 degrees to 200 degrees total, and processed with XDS.1 The AZ3002 structure was resolved by molecular substitution with Phaser using PDBID: 2J6E as a protein consultation.2 The AZ3002 framework was then used to resolve AZ3003 in a similar way. In order to accommodate the mayor duo, the reciprocity relationship of the Azimetric heterodimer present in the asymmetric crystallographic unit (for example, the occupation of molecule A can also be described by molecule B and vice versa), two possible heterodimer pairs, each with 0.5 atomic occupations, they were modeled with Coot, refined with Refmac.3.4 Diffraction data processing and structure refinement statistics are shown in Table 9.
[0329] [000329] An overlap of the crystal structures is shown in Figure 42. The crystal structure of the AZ3002 and AZ3003 heterodimers shows very good agreement with in silico models (RMSD every atom = 0.706Å, RMSD structure = 0.659Å for the CH3 domain) and confirms the expected conformations of the critical core packaging waste. Example 13: AZ3003 Glycosylation Analysis
[0330] [000330] The AZ3003 heterodimer was expressed and purified as described in Example 11. Glycans were analyzed with GlykoPrep ™ Rapid N-Glycan Preparation with InstantAB ™ (Prozyme) using the manufacturer's standard protocol.
[0331] [000331] The results are shown in Figure 43 and illustrate that AZ3003 has a typical glycosylation pattern. Example 14: Assessment of AZ3003 stability under forced degradation conditions
[0332] [000332] The stability of the AZ3003 heterodimer was assessed by incubation under forced degradation conditions. The stability of an mAb under conditions of forced degradation can be a good estimate for long-term stability and formulation.
[0333] [000333] The purified heterodimer sample (expression and purification as described in Example 11) was concentrated to 100mg / ml with no signs of aggregation. The sample was diluted in an appropriate buffer and evaluated under conditions of forced degradation, as described in Table 10 below. The treated samples were analyzed by SDS-PAGE and HPLC-SEC.
[0334] [000334] SDS-PAGE was performed in reducing (R) and non-reducing (NR) conditions and precast gradient gels purchased from LONZA. The protein bands were visualized by staining with Coomassie Brilliant Blue G-250.
[0335] [000335] Analytical SEC-HPLC was performed using a Phenomenex HPLC column, BIOSEP-SEC-S4000 or BioRad Bio-Sil TSK 4000 at a flow rate of 0.8 ml / min with 10 mM sodium phosphate, 0.14 M NaCl, 10% isopropanol as an execution buffer. This allowed for the quantification of higher and lower molecular potential with species.
[0336] [000336] The results are shown in Figure 44 and demonstrate that the AZ3003 heterodimer is stable and has a stability profile that is consistent with those of industry standard mAbs. Example 15: Assessment of Purification Downstream of AZ3003
[0337] [000337] AZ3003 manufacturing capability assessment was performed to assess the behavior of AZ3003 using the industry standard antibody purification process scheme as shown in Figure 45. This process involves a three column step platform comprising chromatography of protein A affinity for product capture, followed by cation exchange chromatography (CEX) for removal of leached aggregates, protein A and HCP and finally, anion exchange chromatography (AEX) in the flow mode to capture viruses, Negatively charged DNA and contaminants. This assessment is used to identify potential manufacturing problems (eg, process stability, product stability and quality) with early drug candidates in the research and development phase.
[0338] [000338] During the evaluation of the manufacturing capacity, the chromatographic behavior, protein stability and product quality were evaluated using the standard purification process shown in Figure 46. Table 11 (below) lists the main criteria used for the evaluation, that is, stage yields, high molecular weight aggregate (HMW) content and elution volume. High step yields and low elution volumes during purification indicate a stable, well-performing protein. Monitoring HMW content and removing it during purification is vital, since the presence of protein aggregates (HMW species) in the final product can lead to decreased activity, immunogenic reactions in the patient, and / or particle formation during shelf life of the pharmaceutical product. The expression of Mabs with minimum initial HMW content (<4%) is desirable, since high levels of aggregates will require additional purification steps for removal, increasing the time and cost of manufacture.
[0339] [000339] Standard industrial purification processes were used to check the stability, chromatographic behavior and product quality of AZ3003. 1.1 Protein A Capture
[0340] [000340] CM expressing AZ3003 was filtered 0.22μm using a Millipore bottle neck (PES) filter and applied to the Mab Select SuRe column (1.6 x 25 cm) balanced with 5 CV of 20 mM Tris- HCl, 0.14 M NaCl, pH 7.5. After loading, the column was washed extensively with equilibration buffer until absorbance A280 reached a stable base. AZ3003 was eluted with 0.1 M acetate buffer, pH 3.6 and immediately titrated to pH 5.2 by adding 1/10 volume of 1 M tris base.
[0341] [000341] After the elution step, the column is washed with 0.1 M acetate, pH 3.0. Analysis with SDS-PAGE shows that all Mabs were linked to the column since no Mab was detected in the FT column. Highly purified mab was detected in the pH 3.6 elution buffer. The initial capture and purification step using Protein A affinity chromatography produces a product with> 90% purity. 1.2 Low pH Maintenance Study
[0342] [000342] The next step in the downstream process is maintenance at low pH, which is performed to inactivate viruses. After eluting the protein A column, the Mab (~ 10 mg / ml, pH 4.0) was titrated to pH 3.6 with 10% acetic acid and incubated in RT with shaking for 90 min. The stability of AZ3003 against low pH treatment was assessed by SDS-PAGE, SEC-HPLC and by turbidity measurements at A410 nm. AZ3003 tolerated the low pH maintenance step well, with no changes in SDS-PAGE or SEC-HPLC. In addition, no increase in turbidity was detected after incubation for 90 min, indicating the absence of the formation of insoluble aggregates that can be problematic during purification (ie, clogging of filters and columns in the process, loss of product). These data show that AZ30003 is stable at the low pH maintenance stage. 1.3 Cation Exchange Chromatography (CEX)
[0343] [000343] CEX was investigated as the second step in the purification process. Two resins were evaluated: Fractogel EMD SO3 (M) by Merk Millipore and SP HP by GE Lifesciences.
[0344] [000344] Fractogel EMD SO3 (M), pH 5.2: The combined Mab Select SuRe (35mg) was titrated to pH 5.2 by adding 10% (v / v) of 1M tris base and then 2 times diluted with equilibration buffer, 20 mM acetate, pH 5.2. This combination was applied to a Fractogel EMD S03 (M) column equilibrated with 5 CV of 20 mM acetate, pH 5.2. The column was washed with equilibration buffer until absorbance A280 reached a stable base. The Mab was eluted from the column with a linear salt gradient from 0 to 600 mM NaCl, pH 5.2 over 10 CV. The remaining contaminants were removed from the column with 20 mM acetate, 1 M NaCl, pH 5.2 followed by treatment with 1 N NaOH. The analysis by SDS-PAGE and SEC-HPLC was performed to monitor HMW levels and their removal of the main Mab fraction in that column. The step yield (based on A280 nm readings) was 73%.
[0345] [000345] SP HP, pH 5.2: The combined Mab Select SuRe (50mg) was titrated to pH 5.2 by adding 10% (v / v) of 1 M tris base and then equally diluted with buffer equilibrium, 20 mM acetate, pH 5.2. This combination was applied to an SP HP column (1.6 x 2.5 cm / 5 ml) equilibrated with 5 CV of 20 mM acetate, pH 5.2 (Fig. 21). The column was washed with equilibration buffer until absorbance A280 reached a stable base. The Mab was eluted from the column with a linear salt gradient from 0 to 600 mM NaCl, pH 5.2 over 10 CV. The remaining contaminants were removed from the column with 20 mM acetate, 1 M NaCl, pH 5.2 followed by treatment with 1 N NaOH. Analysis by SDS-PAGE and SEC-HPLC was performed to monitor the levels of aggregation and their separation in this column. The step yield (based on A280 nm readings) was 87%. 1.4 Anion Exchange Chromatography (AEX)
[0346] [000346] Anion exchangers (eg, quaternary amine, Q) have been widely used in the purification of the monoclonal antibody. The AEX medium is operated in flow mode, with the Mab appearing in FT while allowing the retention of HCP, DNA, viruses and endotoxins.
[0347] [000347] The combined Fractogel SO 3 M pH 5.2 (25 mg) was titrated to pH 7.0 with 1 M tris base and applied to 1 ml of HiTrap Q FF balanced with 5 CV of 10 mM phosphate, pH 7.0. The column was washed with equilibration buffer. However, in this case, a stable baseline has not been reached. Consequently, the column was washed with PBS to elute any residual coupled Mab. Then, the column was washed with 10 mM phosphate, 1 M NaCl, pH 7.0 to remove any bound contaminants. This step needs further optimization so that the entire fraction of Mab is present in the flow. The step yield (based on A280 nm readings) was 82% with an estimated purity> 98% by HPLC-SEC. 1.5 Analysis by SDS-PAGE of Downstream Purification
[0348] [000348] SDS-PAGE (Fig. 35) was performed on eluates from each stage of purification to monitor the removal of contaminants throughout the process to assess the purity and quality of the final product. The gel analysis showed the expected pattern of migration to a Mab under reducing and non-reducing conditions. The comparison of the gel of the combined CEX resins shows that there are no major differences in the product profile. The final combinations of CEX, CHT and HIC pH 5.0 and pH 7.0 all look similar with respect to the purity and contamination bands. 1.7 Estimation of Purity by HPLC-SEC
[0349] [000349] AZ3003 purified after Protein A three column chromatography steps; CEX; AEX flow mode; was assessed by SEC (size exclusion) -HPLC under native conditions (Figure 46).
[0350] [000350] AZ3003 shows a single elution peak within the expected region of 150 kDa for native IgG1. Purity has been estimated to be> 98%. 1.8 Process Yield for Purification of AZ3003
[0351] [000351] The process yields were calculated for the downstream purification process and listed in Figure 46. The step yields for AZ3003 were typical for purified IgG using the industry standard three column purification process.
[0352] [000352] AZ3003 has been successfully purified from CM using the industry standard purification process (Protein A affinity resin, CEX, followed by AEX).
[0353] [000353] These results indicated that AZ3003 is comparable to standard mAb's in total recovery yield (see Kelley B. Biotechnol. Prog. 2007, 23, 995-1008) and minimally observed aggregation. AZ3003 was also evaluated for maintenance at low pH & CHT (ceramic hydroxyapatite) and HIC (hydrophobic interaction chromatography) (Phenyl HP pH 5 and pH 7) with good aggregate-free recovery. Figure 46 illustrates that the heterodimer has been successfully purified from CM using the industry standard purification process (Protein A affinity resin, CEX, followed by AEX).
[0354] [000354] All publications, patents and patent applications mentioned in this specification are incorporated herein by reference in the specification, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated here by reference.

权利要求:
Claims (26)
[0001]
Isolated heteromultimeric Fc construct, characterized by the fact that it comprises a modified heteromultimeric CH3 domain comprising: - a first CH3 domain polypeptide and a second CH3 domain polypeptide, each of the first and second CH3 domain polypeptides independently comprise amino acid substitutions when compared to the CH3 domain of the heavy chain IgG1 sequence as represented in SEQ ID NO: 1, with the substitution of amino acids promoting the formation of a heterodimeric CH3 domain when compared to a homodimeric CH3 domain; the first CH3 domain polypeptide comprising amino acid substitutions at the F405 and Y407 positions, and the second CH3 domain polypeptide comprising amino acid substitutions at the T366 and T394 positions; the amino acid substitution at position F405 being F405A, F405S, F405T or F405V; amino acid substitution at position Y407 is Y407A, Y407I or Y407V; the amino acid substitution at the T366 position is T366I, T366L, T366M or T366V, and the amino acid substitution at the T394 position is T394W; both the first CH3 domain polypeptide and the second CH3 domain polypeptide or both the first and the second CH3 domain polypeptides further comprising amino acid substitution T350V, T350I, T350L or T350M; where the modification of the heterodimeric CH3 domain has a melting temperature (Tm) of 74 ° C or greater and a purity of 95% or greater; the heteromultimeric Fc construct being an antibody or Fc fusion protein; and where the numbering of the amino acid residues is in accordance with the EU index represented in Kabat.
[0002]
Isolated heteromultimeric Fc construct, according to claim 1, characterized by the fact that it comprises at least one T350V substitution.
[0003]
Isolated heteromultimeric Fc construct, according to claim 1, characterized in that each of the first and second polypeptides of the CH3 domain comprises the amino acid substitution T350V.
[0004]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 3, characterized in that the modified heterodimeric CH3 domain has a melting temperature (Tm) of 75 ° C or higher, 77 ° C or higher, or 80 ° C or higher.
[0005]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 3, characterized in that the modified heterodimeric CH3 domain has a melting temperature (Tm) of 77 ° C or higher.
[0006]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 3, characterized in that the modified heterodimeric CH3 domain has a melting temperature (Tm) of 80 ° C or higher.
[0007]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 6, characterized in that the first CH3 domain polypeptide comprises the L351Y amino acid substitution.
[0008]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 7, characterized in that the second polypeptide of the CH3 domain comprises the substitution of amino acids K392, K392 l or K392M.
[0009]
Isolated heteromultimeric Fc construct, according to claim 8, characterized by the fact that: (a) said first CH3 domain polypeptide comprises amino acid substitutions L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprises amino acid substitutions T366L, K392M, and T394W; (b) said first CH3 domain polypeptide comprises amino acid substitutions L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprises amino acid substitutions T366L, K392L, and T394W; (c) said first CH3 domain polypeptide comprises amino acid substitutions L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprises amino acid substitutions T366I, K392M, and T394W; or (d) said first CH3 domain polypeptide comprises amino acid substitutions L351Y, F405A, and Y407V, and said second CH3 domain polypeptide comprises amino acid substitutions T366I, K392L, and T394W.
[0010]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 9, characterized in that the first CH3 domain polypeptide or second CH3 domain polypeptides or both the first and second CH3 domain polypeptides comprise the S400Z modification, where Z is selected from a positively charged amino acid and a negatively charged amino acid.
[0011]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 10, characterized in that the first CH3 domain polypeptide or second CH3 domain polypeptide or both the first and second CH3 domain polypeptides comprise the N390Z modification, where Z is selected from a positively charged amino acid and a negatively charged amino acid.
[0012]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 11, characterized in that said first CH3 domain polypeptide comprises substitution of amino acid S400E or S400R, and said second polypeptide of domain CH3 comprises substitution of amino acid N390R .
[0013]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 12, characterized in that one of said first and second polypeptide of the CH3 domain comprises the amino acid substitution Q347R and the other polypeptide of the CH3 domain comprises the amino acid substitution K360E.
[0014]
Isolated heteromultimeric Fc construct, according to claim 8, characterized by the fact that: (a) the first CH3 domain polypeptide comprises amino acid substitutions T350V, F405A, and Y407V, and the second polypeptide of CH3 domain comprises amino acid substitutions T350V, T366L, K392M, and T394W; (b) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, F405A, and Y407V, and the second polypeptide of CH3 domain comprises amino acid substitutions T350L, T366L, K392M, and T394W; (c) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, F405A, and Y407V, and the second polypeptide of CH3 domain comprises amino acid substitutions T350V, T366L, K392L, and T394W; (d) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, S400R, F405A, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, T366L, K392M, and T394W; (e) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, S400E, F405A, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, T366L, N390R, K392M, and T394W; (f) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, S400E, F405A, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, T366L, N390R, K392M, and T394W; (g) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, S400E, F405T, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, T366L, N390R, K392M, and T394W; (h) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, S400E, F405S, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, T366L, N390R, K392M, and T394W; (i) the first CH3 domain polypeptide comprises amino acid substitutions T350V, S400E, F405A, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, T366L, N390R, K392M, and T394W; (j) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, S400E, F405A, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, T366L, N390R, K392M, and T394W; (k) the first CH3 domain polypeptide comprises amino acid substitutions Q347R, T350V, L351Y, S400E, F405A, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, K360E, T366L, N390R, K392M, and T394; (l) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, S400R, F405A, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, T366L, N390D, K392M, and T394W; (m) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, S400R, F405A, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, T366L, N390E, K392M and T394W; (n) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, S400E, F405A, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, T366L, N390R, K392L and T394W; (o) the first CH3 domain polypeptide comprises amino acid substitutions T350V, L351Y, S400E, F405A, and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, T366L, N390R, K392L, and T394W; (p) the first CH3 domain polypeptide comprises amino acid substitutions Y349C, T350V, L351Y, S400E, F405A and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, S354C, T366L, N390R, K392M and T394W; (q) the first CH3 domain polypeptide comprises amino acid substitutions Y349C, T350V, S400E, F405A and Y407V, and the second CH3 domain polypeptide comprises amino acid substitutions T350V, S354C, T366L, N390R, K392M and T394W; or (r) the first CH3 domain polypeptide comprises amino acid substitutions Y349C, T350V, F405A and Y407V, and the second polypeptide of CH3 domain comprises amino acid substitutions T350V, S354C, T366L, K392M and T394W.
[0015]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 14, characterized in that said heteromultimeric Fc construct is a bispecific antibody or a multispecific antibody.
[0016]
Isolated heteromultimeric Fc construct according to any of claims 1 to 15, characterized by the fact that it comprises one or more domains of binding to the antigen that binds to a cancer antigen.
[0017]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 15, characterized in that it comprises one or more therapeutic antibody binding domains.
[0018]
Isolated heteromultimeric Fc construct according to claim 17, characterized in that the therapeutic antibody is selected from the group consisting of abagovomab, adalimumab, alemtuzumab, aurograb, bapineuzumab, basiliximab, belimumab, bevacizumab, briakinumab, canakinumabol, cokmamaumabol, cokmakumabumab, cokmakumabumab, cokmakumabumab, cokmakumabumab, cokmakumabumab. , cetuximab, daclizumab, denosumab, efalizumab, galiximab, gemtuzumab ozogamicin, golimumab, ibritumomab tiuxetan, infliximab, ipilimumab, lumiliximab, mepolizumab, motizizuma, ranbuma, oma, bizbum, mybogrbum, mybogrbum, mycogrb, natal , reslizumab, rituximab, teplizumab, tocilizumab / atlizumab, tositumomab, trastuzumab, Proxinium ™, Rencarex ™, ustekinumab, and zalutumumab.
[0019]
Isolated heteromultimeric Fc construct according to either claim 17 or claim 18, characterized in that it comprises a first antigen-binding domain and a second antigen-binding domain, where: (a) the first and second antigen-binding domains are obtained from the same therapeutic antibody, or (b) the first and second antigen-binding domains are obtained from different therapeutic antibodies.
[0020]
Isolated heteromultimeric Fc construct according to any one of claims 1 to 19, characterized in that the heteromultimeric Fc construct is conjugated to a therapeutic agent.
[0021]
Composition, characterized by the fact that it comprises the isolated heteromultimeric Fc construct, as defined in any one of claims 1 to 20 and a pharmaceutically acceptable carrier.
[0022]
Use of an isolated heteromultimeric Fc construct, as defined in any one of claims 1 to 20, characterized by the fact that it is directed towards the manufacture of a medicine for the treatment of a disease, disorder or infection.
[0023]
Nucleic acid composition, characterized by the fact that it comprises one or more polynucleotides encoding the isolated heteromultimeric Fc construct, as defined in any of claims 1 to 19.
[0024]
Composition according to claim 23, characterized by the fact that one or more polynucleotides are comprised in one or more expression vectors.
[0025]
Composition according to claim 23, characterized by the fact that one or more polynucleotides are comprised of a multi-cistronic expression vector.
[0026]
Method for expressing the isolated heteromultimeric Fc construct, as defined in any one of claims 1 to 19, said method being characterized by the fact that it comprises: (a) transfecting mammalian cells with the nucleic acid composition defined in any one of claims 23 to 25, to produce transient or stably transfected mammalian cells; and (b) culturing transient or stably transfected mammalian cells under conditions suitable for expression of the isolated heteromultimeric Fc construct.

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同族专利:

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公开号 | 公开日

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US20150284470A1|2015-10-08|

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US9988460B2|2018-06-05|

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EP2773671B1|2021-09-15|

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RU2675319C2|2018-12-18|

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US20180030150A1|2018-02-01|

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AU2017245451B2|2019-08-22|

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US9732155B2|2017-08-15|

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HK1200465A1|2015-08-07|

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MX2014005348A|2014-11-12|

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AU2012332021A1|2014-06-19|

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WO2013063702A1|2013-05-10|

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EP2773671A4|2015-06-03|

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CA2854233C|2020-05-12|

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KR20140092370A|2014-07-23|

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PL2773671T3|2022-01-24|

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CN104080811A|2014-10-01|

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CN109897103A|2019-06-18|

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BR112014010580A2|2017-05-02|

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DK2773671T3|2021-11-15|

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AU2012332021B8|2017-10-12|

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US9574010B2|2017-02-21|

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US20130195849A1|2013-08-01|

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CA2854233A1|2013-05-10|

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AU2017245451A1|2017-11-02|

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PT2773671T|2021-12-14|

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AU2012332021A8|2017-10-12|

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US10457742B2|2019-10-29|

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RU2014121832A|2015-12-10|

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RU2018142832A|2019-03-21|

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AU2017245451B9|2019-08-29|

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JP2014533243A|2014-12-11|

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US20180016347A1|2018-01-18|

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EP2773671A1|2014-09-10|

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KR102052774B1|2019-12-04|

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MX358862B|2018-09-06|

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US20200087414A1|2020-03-19|

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法律状态:
2018-01-23| B07D| Technical examination (opinion) related to article 229 of industrial property law [chapter 7.4 patent gazette]|

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2018-03-27| B06F| Objections, documents and/or translations needed after an examination request according [chapter 6.6 patent gazette]|

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2020-05-05| B07E| Notification of approval relating to section 229 industrial property law [chapter 7.5 patent gazette]|

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2020-06-09| B07A| Application suspended after technical examination (opinion) [chapter 7.1 patent gazette]|

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2020-11-03| B09A| Decision: intention to grant [chapter 9.1 patent gazette]|

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2021-01-12| B16A| Patent or certificate of addition of invention granted [chapter 16.1 patent gazette]|Free format text: PRAZO DE VALIDADE: 20 (VINTE) ANOS CONTADOS A PARTIR DE 02/11/2012, OBSERVADAS AS CONDICOES LEGAIS. |

优先权:

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申请号 | 申请日 | 专利标题

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US201161556090P| true| 2011-11-04|2011-11-04|

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US61/556,090|2011-11-04|

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US201161557262P| true| 2011-11-08|2011-11-08|

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US61/557,262|2011-11-08|

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US201261645547P| true| 2012-05-10|2012-05-10|

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US61/645,547|2012-05-10|

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PCT/CA2012/050780|WO2013063702A1|2011-11-04|2012-11-02|Stable heterodimeric antibody design with mutations in the fc domain|

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