isolated ctla-4 polypeptide, host cell, composition and use of a ctla-4 polypeptide

专利摘要:
ISOLATED CTLA-4 POLYPEPTIDE, HOST CELL, COMPOSITION, METHOD OF PRODUCTION OF ANOTHER CTLA-4 POLYPEPTIDE AND USE OF A CTLA-4 POLYPEPTIDE. Cytotoxic T lymphocyte antigen 4 (CTLA-4) variants with high affinity, activity and stability. High concentration formulations of CTLA-4 variants for subcutaneous or intravenous administration, for example, at monthly or less frequent dosing intervals. Use of CTLA-4 variants in the treatment of rheumatoid arthritis and other inflammatory diseases. Fusion of CTLA-4 with IgG Fc having improved stability and a longer in vivo half-life.
公开号:BR112014026718B1
申请号:R112014026718-9
申请日:2013-03-11
公开日:2021-05-18
发明作者:Ralph Minter；Julie Douthwaite；Jacques Moisan；Michael Bowen；Steve Rust；Cyril Privezentzev
申请人:Medimmune Limited.；
IPC主号:

专利说明:

Reference to electronically submitted sequence listing
[001] The contents of the sequence listing submitted electronically in an ASCII text file (Name CTLA4101P1Sequencelisting.txt; Size: 107,814 bytes; and Creation Date: May 11, 2012) submitted with the application is incorporated herein by reference in its entirety . Invention Area
[002] This invention relates to compositions comprising variants of cytotoxic T lymphocyte antigen 4 (CTLA-4), optionally fused to IgG Fc, and their therapeutic use to inhibit T cell activation, especially in the context of inflammatory conditions such as rheumatoid arthritis (RA). Background
[003] It is thought that the activation of native T cells is performed by a two-signal mechanism. Upon encountering an antigen presenting cell (APC), the T cell receptor (TCR) interacts with the major histocompatibility complex (MHC) peptide and thus provides the first activation signal for the T cells. This initial signal is insufficient to trigger T cell activation and a second signal from costimulatory receptors is an absolute requirement. One of the most important and best described costimulatory receptors is CD28, which interacts with CD80 (B7.1) and CD86 (B7.2) on the surface of macrophages, dendritic cells, as well as activated B and T lymphocytes.
The CD86 gene encodes a type I membrane protein (Swiss-Prot Acc-No P33681). Alternative amendments result in two transcriptional variants of the CD86 gene that encode different isoforms. Other transcript variants have been described, but their full-length sequences have not been determined.
The CD80-related protein (Swiss-Prot Acc-No P42081) has a secondary structure similar to CD86. CD80 shares 26% and 46% identical or similar amino acid residues with CD86, respectively. CD80 is only expressed at low levels on resting APCs, but may be up-regulated after activation. CD80 recognizes the same receptors on T cells as CD28 and CD152 (CTLA-4), but binds to the latter with an affinity about 2 to 4 times higher than the affinity for CD86.
No shared linear peptide epitope had been identified as being responsible for binding to CD28 and/or CTLA-4 (Ellis et al., J Immunol., 156, 2700-2709), but residues conserved in secondary structures (leaves CD80 and CD86 IgV) have been found to interact with CTLA-4 (Swartz et al. Nature, 410, 604-608).
[007] Signal transduction from CD28 leads to T cell activation and CTLA-4 co-inhibitor receptor upregulation. CTLA-4 is a member of the immunoglobulin superfamily. It binds to CD80 and CD86 with greater affinity and avidity compared to CD28 and effectively decreases the expression of activation signals.
[008] Several theories have been postulated about the relative roles of CD80 and CD86 in binding to CTLA-4. Slavik et al. (Immunol. Res. 19(1): 1-24, 1999) analyzed the signaling and function of the CD28/CTLA-4 and CD80/CD86 families. Sansom (Immunology 101: 169-177 2000) summarizes some studies where differences between CD80 and CD86 were investigated.
[009] Odobasic et al. (Immunology 124: 503-513 2008) investigated the role of CD80 and CD86 in effector T cell responses. This study investigated the effect of anti-CD80 and anti-CD86 monoclonal antibodies in a mouse model induced by arthritis antigens. It was reported that blocking both CD80 and CD86 caused a trend towards reduced disease severity compared to antibody-treated control mice. Based on the results of treatment with the individual antibodies, the authors concluded that CD80 exacerbates arthritis by down-regulating systemic IL-4 and increasing T-cell accumulation in joints, whereas CD86 increases disease severity by up-regulating IL- 17 and increase the accumulation of effector T cells in joints without affecting Th1 or Th2 development. However, the study reports that no further reduction in arthritis severity was seen when both CD80 and CD86 were blocked, suggesting that inhibition of the costimulatory molecule was adequate to obtain maximum disease amelioration. This model was based on a recall response to antigen (BSA, in this study), injected directly into the joint space.
[0010] Another study used a murine model of collagen-induced arthritis, which involves breaking tolerance to an endogenous antigen (collagen). In this study, blocking of both CD80 and CD86 was reported to be necessary for maximum benefit (Webb et al. Eur J. Immunol 26 (10): 2320-2328, 1996).
A recombinant fusion protein comprising the extracellular domain of CTLA-4 linked to a modified IgG1 Fc domain ("CTLA-4 - Ig") has been shown to bind CD80 and CD86 in vivo and effectively suppress the CD28-mediated T cell activation (Kliwinski et al., J Autoimmun. 2005;25(3):165-71).
[0012] CTLA-4 fusion proteins have been developed as therapeutic agents for rheumatoid arthritis (RA). RA is a progressive degenerative disease leading to cartilage and bone destruction. There is evidence that many branches of the immune system are involved in the inflammatory process, leading to fibroblast-like synoviocytes and osteoclast-mediated joint damage and cartilage and bone destruction. Several studies have shown an increased activation of T cells in the synovial membrane and up to 50% of the cells that infiltrate the inflamed pannus are T lymphocytes. In addition, T cells in the synovia of RA patients exhibit an activated effector phenotype exhibiting an increase in expression of markers associated with activation, such as CD44, CD69, CD45RO, VLA-1 and CD27.
Activated T cells have been shown to play an essential role in the establishment and maintenance of the pathological inflammatory response found in the RA synovial membrane*. Activated T cells are an important source of pro-inflammatory cytokines, such as IFNY, IL-17 and TNFα. These factors are potent activators of fibroblast-like synoviocytes (FLS) and macrophage-like synoviocytes (MLS) that lead to the secretion of matrix metalloproteinases (MMP), which are mediators of cartilage destruction, as well as the secretion of inflammatory mediators such as IL-6, IL-1 and TNFα. Activated CD4 + cells can also provide assistance to B lymphocytes, leading to the production of antibodies, such as rheumatoid factor (RF), which contributes most to disease progression.
Abatacept (Orencia®) is a CTLA-4 Ig fusion protein, containing the extracellular domain of CTLA-4 fused to IgG1 Fc. The resulting soluble protein is a dimer with a molecular weight of approximately 92 kDa. It has been shown to have beneficial effects in the treatment of patients with RA in the clinic, which demonstrates that inhibition of the costimulation pathway involving CD80 and CD86 is a viable therapeutic approach for rheumatoid arthritis. RA therapy with Abatacept is given either as a monthly intravenous or weekly subcutaneous injection.
Abatacept contains in its CDR3-like loop the hexapeptide amino acid domain MYPPPY, which is shared between CD28 and CTLA-4 and is said to be required to bind B7 ligands. Mutation of the first tyrosine (Y) in this domain to alanine (A) suppressed binding to CD80, but also resulted in reduced binding to CD86, whereas a phenylalanine (F) substitution allows retention of full affinity for CD80 with a total loss of CD86 binding (Harris et al., J. Exp Med. (1997) 185:177-182). Other residues in regions similar to CDR3 and CDR1 are also important for the interaction of Abatacept with its ligands. Thus, a mutant molecule with glutamic acid (E) instead of leucine (L) at position 104 and tyrosine (Y) instead of alanine (A) at position 29 has approximately twice the binding avidity for CD80 (B7 -1) and approximately 4 times greater binding avidity for CD86 (B7-2) than Abatacept. This LEA-29Y compound (Belatacept, Nulojix®) is reported to have similar affinity for binding to CD80 as to CD86 (3.66 nM and 3.21 nM, respectively). Belatacept has been developed as an immunosuppressant for transplantation (Larsen et al., Am J. Transplantation (2005) 5:443-453; Gupta & Womer Drugs Des Develop Ther 4: 375-382 2010) and has recently been approved for prophylaxis of organ rejection in adult patients undergoing a kidney transplant. Abatacept itself shows limited efficacy against transplant rejection, a finding that has been attributed to its low CD86-dependent inhibition as opposed to CD80-dependent costimulation (Gupta & Womer, supra).
[0016] Abatacept and Belatacept formulations for subcutaneous administration are described in WO2007/07654.
[0017] Selections for increased affinity and stability have previously been performed using ribosome visualization to isolate improved CTLA-4 variants. Both error-prone PCR mutagenesis to mutate the complete gene sequence and site-directed mutagenesis to target mutations in key regions have been successful for protein evolution. For example, WO2008/047150 reports CTLA-4 protein variants, showing increased activity and greater stability compared to wild type.
Maxygen, Inc. reported a therapeutic CTLA-4-Ig molecule, designated ASP2408, being developed by Perseid Therapeutics LLC in collaboration with Astellas Pharma Inc. for the treatment of RA. CTLA-4-Ig has been reported to show increased potency compared to Orencia® (Abatacept) (WO2009/058564).
US 6,750,334 (Repligen Corporation) describes CTLA-4-Cy4 as being a soluble fusion protein comprising CTLA-4 fused to a portion of an immunoglobulin. The immunoglobulin constant region, which comprises a hinge region and CH2 and CH3 domains, is modified by substitution, addition or deletion of at least one amino acid residue to reduce complement activation or Fc receptor interaction.
[0020] Xencor, Inc. recently described a CTLA4-Ig molecule, comprising a variant of the CTLA-4 portion and an immunoglobulin Fc region (WO2011/103584). A number of amino acid substitutions in the sequence of the CTLA-4 portion have been described for the generation of CTLA4-Ig variants with increased T cell inhibitory activity. WO2011/103584 also describes Fc modifications, e.g. binding to FcyRs, enhancing Fc-mediated effector functions and/or extending the in vivo half-life of CTLA4-Ig. Invention Summary
[0021] In a first aspect, the invention provides CTLA-4 polypeptides that are variants of wild-type CTLA-4. The CTLA-4 polypeptides of the invention may have one or more improved properties, such as higher potency, greater affinity for CD80 and/or CD86, increased selectivity for CD80 over CD86, good cross-reactivity and/or for a higher stability compared to wild type.
Improvements in CTLA-4 can be obtained by mutating the amino acid sequence of the wild-type extracellular domain of human CTLA-4, also known as soluble CTLA-4. One or more amino acid mutations, which can be an amino acid substitution, insertion, or deletion, can be introduced into a CTLA-4 amino acid sequence to produce an enhancement to the CTLA-4 polypeptide, as described herein. The polypeptide may, for example, exhibit increased potency, affinity and/or stability relative to wild-type CTLA-4.
The extracellular domain of CTLA-4 comprises the wild-type amino acid sequence SEQ ID NO: 35. SEQ ID NO: 35 is not the entire extracellular domain, but is the region employed in Abatacept (Orencia®).
The CTLA-4 polypeptides of the present invention may or may not include other CTLA-4 residues or sequences in addition to the region corresponding to SEQ ID NO: 35. Preferably, a CTLA-4 polypeptide of the invention is soluble. It generally does not comprise the transmembrane region of CTLA-4.
A number of mutations within the CTLA-4 amino acid sequence have been identified herein which are associated with increased potency, affinity and/or stability or which can be introduced for other purposes, such as to influence dimerization.
Examples of wild-type CTLA-4 amino acid substitutions are as follows: R, S, V or T in I16; T in A24; N or P in S25; S in G27; I in V 32; G in D41; G in S42; And in V44; K or V in M54; S or G in N56; A, G, S or P in L58; S or A in T59; T in F 60; Q or P in L61; G in D 62; Y in D63; P in S 64; N, D, V or T in I65; A, T, M or H in S70; R in Q80; Q, S, V, R, K or L in M85; S at T87; Q, H, T, E or M in K93; R, Q or E in L104; V in I106; D or S in N108; V or F in I115 and S in C120. An example of an amino acid deletion is the T51 deletion. Residue numbering is with reference to the CTLA-4 sequences shown in Figure 1A and Figure 2, numbered with the first residue position 1 "sequence numbering". Figure 1 also shows the Swiss Prot numbering for comparison.
A CTLA-4 variant can have, for example, up to twelve or up to twenty amino acid mutations in wild-type human soluble CTLA-4. Mutations can include any or all of the amino acid mutations listed above, and optionally one or more different mutations, e.g., different substitutions, at these or other residue positions. The variant amino acid sequence may comprise wild-type human CTLA-4 of the sequence SEQ ID NO: 35 with one or more, for example, at least five, six or seven of the listed amino acid mutations.
The CTLA-4 polypeptide may comprise or consist of an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%, 96%, 97%, 98% or 99% sequence identity with SEQ ID NO: 35.
[0029] Examples of CTLA-4 variant amino acid sequences according to the invention include those of SEQ ID NOS: 36-55 shown in Figure 1A. A CTLA-4 variant may comprise the CTLA-4 amino acid sequence "1299" encoded by the deposited nucleic acid with NCIMB accession number 41948. Nucleic acid with NCIMB accession number 41948 encodes the 1299 CTLA-4 polypeptide fused to an immunoglobulin Fc region. The encoded CTLA-4 1299 polypeptide, the encoded Fc region, and the encoded polypeptide comprising the CTLA-4 1299 polypeptide fused to the Fc region, are all encoded by the deposited nucleic acid with accession number NCIMB 41948, being individual modalities of present invention.
[0030] Preferred mutations are amino acid substitutions selected from the following: R, S or V in I16; T in A24; N in S25; S in G27; K in M54; S at N56; A or G in L58; S in T59; T in F 60; Q at L61; Y in D63; P in S 64; N or D in I65; A at S70; R in Q80; Q or S in M85; Q or H in K93; and S at C120. Thus, the variant amino acid sequence may comprise wild-type human CTLA-4 of sequence SEQ ID NO: 35 with one or more, for example, at least five or six, or all, of these amino acid residue positions replaced with one. different residue as specified.
[0031] A CTLA-4 polypeptide sequence preferably comprises: R, I, S or V at position 16; T or A at position 24; N at position 25; S or G at position 27; M or K at position 54; N or S at position 56; A, L or G at position 58; T or S at position 59; F or T at position 60; L or Q at position 61; D or Y at position 63; S or P at position 64; I, N or D at position 65; A or S at position 70; Q or R at position 80; Q, M or S at position 85; Q or H at position 93; and/or C or S at position 120. Other residue positions may be wild-type human, or may be subject to one or more additional mutations.
[0032] A CTLA-4 polypeptide may comprise N at position 25, which represents a wild-type S substitution at this position. The polypeptide may comprise Q or H at position 93, which represents a wild-type K substitution at this position. As illustrated in the examples described below, it is believed that these substitutions at residues 25 and 93 may be strongly associated with improvements in CTLA-4 affinity, activity and/or stability.
A preferred amino acid domain, which has been observed in several high potency variants, is STQDYPN (SEQ ID NO:69). This domain, located at residues 59-65, is a loop region, which appears to be in close proximity to CD80 and CD86 in the linked structure. Thus, in certain embodiments, a CTLA-4 polypeptide comprises SEQ ID NO: 69 at residues 59-65. Residue numbering is as shown in Figure 1A (top row of numbering, starting at 1) and Figure 2. When insertions or deletions are present, the actual numbering of polypeptide residues may differ from the reference sequence. Figure 1A also shows the Swiss Prot numbering for comparison.
[0034] It may also be desirable to mutate C at position 120, for example, by substitution of S, in order to remove a disulfide bridge formed between CTLA-4 molecules at this site, and to inhibit CTLA-4 dimerization. In other situations, it is desirable to retain or promote CTLA-4 dimerization or higher multimerization (eg, tetramer formation). This can be achieved, for example, by retaining C120 and/or by adding dimerization domains, such as by conjugating CTLA-4 to an IgG Fc region. The addition of such domains and the formation of CTLA-4 comprising macromolecules will be discussed further below.
The CTLA-4 polypeptide may comprise the amino acid sequence SEQ ID NO:68, or may comprise SEQ ID NO:68 with one or more mutations. For example, a CTLA-4 polypeptide can comprise SEQ ID NO: 68 with up to twelve mutations, up to ten amino acid mutations or up to five mutations, for example one, two or three amino acid mutations. SEQ ID NO: 68 illustrated in Figure 2, is a consensus sequence of residues found in the group of six CTLA-4 polypeptides with exceptionally good functional activity, which were produced as described in the Examples. The six polypeptides have the amino acid sequences shown in Figure 1A, with the SEQ ID NOS as follows: SEQ ID NO: 43 (variant 1299), SEQ ID NO: 37 (variant 1322), SEQ ID NO: 38 (variant 1321 ), SEQ ID NO: 36 (variant 1315), SEQ ID NO: 42 (variant 1115), SEQ ID NO: 47 (variant 1227). These six sequences and variants with one or more amino acid mutations, for example up to twelve, for example, up to ten amino acid mutations, for example, up to five mutations, for example one, two or three amino acid mutations in any one of these six sequences, represent examples of the invention. The CTLA-4 polypeptide may comprise the CTLA-4 polypeptide sequence "1299" deposited under accession number NCIMB 41948, with one or more amino acid mutations, e.g., up to twelve, e.g., up to ten amino acid mutations, per for example, up to five mutations, for example one, two or three amino acid mutations.
The CTLA-4 polypeptides according to the invention may comprise or consist of an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90% or at least minus 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 68, to any of SEQ ID NOS: 36-55, or to the CTLA-4 "1299 polypeptide sequence" " filed under accession number NCIMB 41948.
[0037] The mutation or mutations may comprise or consist of amino acid substitutions and may optionally be selected from the following:
T at residue 16; P at residue 25; I at residue 32; G at residue 41; G at residue 42; And at residue 44; V at residue 54; G at residue 56; S or P at residue 58; A at residue 59; P at residue 61; G at residue 62; V or T at residue 65; T, M or H at residue 70; V, R, K or L at residue 85; S at residue 87; T, E or M at residue 93; R, Q or E at residue 104; V at residue 106; D or S at residue 108; V or F at residue 115; S at residue 120; deletion at residue 51.
Preferably, a polypeptide comprises N at position 25, and/or comprises Q or H at position 93. A polypeptide may optionally comprise S at position 120.
[0040] As noted above, preferably a polypeptide comprises R, I, S or V at position 16; T or A at position 24; N at position 25; S or G at position 27; M or K at position 54; N or S at position 56; A, L or G at position 58; T or S at position 59; F or T at position 60; L or Q at position 61; D or Y at position 63; S or P at position 64; I, N or D at position 65; A or S at position 70; Q or R at position 80; Q, M or S at position 85; Q or H at position 93; and/or C or S at position 120. Thus, the polypeptide comprises one or more, for example, at least five or six, or more, of the following amino acid substitutions relative to wild-type CTLA-4 of SEQ ID NO : 35: R, S or V in I16; T in A24; N in S25; S in G27; K in M54; S at N56; A or G in L58; S in T59; T in F 60; Q at L61; Y in D63; P in S 64; N or D in I65; A at S70; R in Q80; Q or S in M85; Q or H in K93.
Mutations in SEQ ID NOS: 36-55 compared to wild type are illustrated in Figure 1A. A polypeptide according to the invention may comprise wild-type CTLA-4 of SEQ ID NO: 35, with one or more mutations exemplified in such variants, for example with the combination of mutations present in any one of SEQ ID NOS: 36- 55. A polypeptide may optionally comprise other mutations as discussed above, for example, optionally, one or two additional mutations.
[0042] For example, a polypeptide can comprise a combination of mutations selected from:
[0043] - the 1315 mutations, that is, S in I16; N in S25; G in L58; A at S70; R in Q80; S in M85; and Q in K93;
[0044] - the 1322 mutations, that is, N in S25; S in G27; K in M54; S at N56; S in T59; T in F60; Q at L61; Y in D63; P in S64; N in I65; and Q in K93;
[0045] - the 1321 mutations, that is, S in I16; N in S25; K in M54; G in L58; A at S70; R in Q80; S in M85; and Q in K93;
[0046] - the 1115 mutations, that is, V in I16; N in S25; G in L58; A at S70; Q in M85; and Q in K93;
[0047] - the 1299 mutations, i.e., R in I16; T in A24; N in S25; S in G27; A at L58; A at S70; Q in M85; and Q in K93; and
[0048] - the 1227 mutations, that is, S in I16; N in S25; S in G27; A at L58; A at S70; Q in M85; and H in K93.
Therefore, a CTLA-4 polypeptide may be one that comprises the combination of residues substituted in any one of SEQ ID NOS: 36-55 relative to wild type, for example, may comprise:
[0050] - S at residue 16; N at residue 25; G at residue 58; A at residue 70; R at residue 80; S at residue 85; and Q at residue 93;
[0051] - N at residue 25; S at residue 27; K at residue 54; S at residue 56; S at residue 59; T at residue 60; Q at residue 61; Y at residue 63; P at residue 64; N at residue 65; and Q at residue 93;
[0052] - S at residue 16; N at residue 25; K at residue 54; G at residue 58; A at residue 70; R at residue 80; S at residue 85; and Q at residue 93;
[0053] - V at residue 16; N at residue 25; G at residue 58; A at residue 70; Q at residue 85; and Q at residue 93;
[0054] - R at residue 16; T at residue 24; N at residue 25; S at residue 27; A at residue 58; A at residue 70; Q at residue 85; and Q at residue 93; or
[0055] - S at residue 16; N at residue 25; S at residue 27; A at residue 58; A at residue 70; Q at residue 85; and H at residue 93.
[0056] The mutation is preferably a substitution and may be a conserved substitution. By "conserved substitution" is meant a replacement of a first amino acid residue with a different second amino acid residue, wherein the first and second amino acid residues have side chains, which have similar biophysical characteristics. Similar biophysical characteristics include hydrophobicity, charge, polarity, or the ability to provide or accept hydrogen bonds. Examples of conservative substitutions include the change from serine to threonine or tryptophan, glutamine to asparagine, lysine to arginine, alanine to valine, aspartate to glutamate, valine to isoleucine, asparagine to serine.
[0057] Polypeptides according to the invention may include one or more mutations in the amino acid sequences (substitution, deletion and/or insertion of an amino acid residue) and less than about 15 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3 or 2.
Mutations normally do not result in loss of function, so that a polypeptide comprising an amino acid sequence thus altered may retain an ability to bind to human CD80 and/or CD86. It may retain the same binding affinity or function as a polypeptide, wherein the alteration is not effected, for example, as measured in an assay described herein.
[0059] The mutation may comprise replacing one or more amino acid residues with a non-standard or non-naturally occurring amino acid, modifying one or more amino acid residues into a non-standard and non-naturally occurring form, or inserting one or more non-standard amino acids or non-naturally occurring in the sequence. Examples of numbers and locations of sequence alterations of the invention are described elsewhere herein. Naturally occurring amino acids include the 20 "standard" amino acids identified as G, A, V, L, I, M, P, F, W, S, T, N, Q, Y, C, K, R, H, D, E by their standard single letter codes. Non-standard amino acids include any other residue that can be incorporated into a polypeptide backbone or result from modification of an existing amino acid residue. Non-standard amino acids can be naturally occurring or non-naturally occurring. Several naturally occurring non-standard amino acids are known in the art, such as 4-hydroxyproline, 5-hydroxylysine, 3-methylhistidine, N-acetylserine, etc. [Voet & Voet, Biochemistry, 2nd Edition, (Wiley) 1995]. Those amino acid residues that are derived at their N-alpha position will only be located at the N-terminus of an amino acid sequence. Typically, in the present invention an amino acid is a l-amino acid, but it can be a d-amino acid. The change may then comprise modifying an l-amino acid to, or replacing it with, a d-amino acid. Methylated, acetylated and/or phosphorylated forms of amino acids are also known and the amino acids in the present invention can undergo such modification.
The amino acid sequences in the polypeptides of the invention may comprise unnatural or non-standard amino acids described above. Non-standard amino acids (eg, d-amino acids) can be incorporated into an amino acid sequence during synthesis, or by modification or substitution of the "original" standard amino acids after the synthesis of the amino acid sequence.
[0061] The use of non-standard and/or non-naturally occurring amino acids increases structural and functional diversity and may thus increase the potential to achieve desired neutralizing and binding properties. Additionally, d-amino acids and analogues have been shown to have different pharmacokinetic profiles compared to standard l-amino acids, due to the in vivo degradation of polypeptides having l-amino acids after administration to an animal, eg a human, which means that d-amino acids are advantageous for some in vivo applications.
[0062] Variants can be generated through the use of random mutagenesis of one or more selected VH and/or VL genes to generate mutations within the entire variable domain. Such technique is described by Gram et al. [Gram et al., 1992, Proc. Natl. Academic Sci., USA, 89:3576-3580], who used an error-prone PCR. Another method that can be used is to target mutagenesis to particular regions or locations on the polypeptide. Such techniques are revealed by Barbas et al. [Barbas et al., 1994, Proc. Natl. Academic Sci., USA, 91:3809-3813] and Schier et al. [Schier et al., 1996, J. Mol. Biol. 263:551-567].
[0063] All of the techniques described above are known as such in the art and the person skilled in the art will be able to use such techniques to provide polypeptides of the invention using methodology routine in the art.
Algorithms that can be used to calculate the % identity of two amino acid sequences include, for example, BLAST [Altschul et al. (1990) J. Mol. Biol. 215: 405 to 410], FASTA [Pearson and Lipman (1988) PNAS USA 85: 2,444 to 2,448], or the Smith-Waterman algorithm [Smith and Waterman (1981) J. Mol Biol. 147: 195 to 197], for example, which employ standard parameters.
[0065] According to the invention, compositions containing CTLA-4 polypeptides can be provided having a better biological activity, such as increased selectivity for CD80 over CD86, a higher affinity and/or higher potency and/or can exhibit good cross-reactivity, improved stability and/or prolonged half-life compared to wild-type CTLA-4. As discussed in detail here, such properties may contribute to greater therapeutic efficacy and may allow therapeutic benefits to be achieved at reduced or less frequent dosages. Improved stability can facilitate manufacture and formulation into pharmaceutical compositions.
[0066] The CTLA-4 polypeptide according to the invention is optionally conjugated to an IgG Fc region, for example, as a fusion protein. The Fc region can be manipulated to increase the in vivo half-life of the molecule and to contribute to the overall stability of the composition by avoiding unwanted Fc effector functions. Improved stability facilitates formulation of the product at high concentrations, for example, for subcutaneous administration. Brief description of the drawings
Figure 1. (A) Alignment of CTLA-4 variant sequences (SEQ ID NOS: 36-55) with wild type human CTLA-4 (SEQ ID NO: 35). Wild-type mutations are shown in gray boxes. The top line of numbering, starting from 1, is the numbering referred to in this description, unless otherwise specified. Swiss Prot numbering is shown below for comparison. (B) IgG1 Fc Sequence Alignment SEQ ID NOS: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59 and SEQ ID NO: 60. The top row of numbering, starting from 1 , is the numbering referred to in this description, unless otherwise specified. Swiss Prot numbering is shown below for comparison.
Figure 2. CTLA-4 polypeptide sequence SEQ ID NO: 68. With sequential numbering from Met as position 1, SEQ ID NO: 68 has 124 residues, with variability at residues 16, 24 27, 54, 56 , 58, 59, 60, 61, 63, 64, 65, 70, 80, 85 and 93. The amino acid residue at each of these variable positions is selected from the group of residues indicated in each case.
Figure 3. IC50 profiles of wild-type CTLA-4 variants of CTLA-4 in Fc fusion format in: (A) the dual Raji-Jurkat cell assay; (B) the primary human CD4+ T cell assay; (C) Cynomolgus monkey mixed lymphocyte reaction assay.
[0070] Figure 4. The specificity of CTLA-4 variants for CD80 and CD86 compared to other related protein ligands. (A) variant 1299. (B) variant 1322.
[0071] Figure 5. Demonstration of the null effector function (ADCC and CDC) for CTLA-4 variants with TM and YTE modifications. (A) ADCC. (B) CDC.
[0072] Figure 6. Improvements in monovalent affinity relative to CD80 and CD86 of CTLA-4 variants compared to wild-type CTLA-4 in Fc fusion format.
[0073] Figure 7. (A) Construction of the design for the CTLA-4 tetrameric protein. (B) Comparison of potency in the Raji Jurkat assay for wild-type CTLA-4 in Fc versus tetrameric CTLA-4 fusion format. Detailed Description
[0074] CTLA-4 residue numbering, which is used throughout this specification, is as shown in Figure 1A (top row, sequence numbering) and Figure 2, unless otherwise indicated. CTLA-4 has a leader sequence that is cleaved and at least two different mature protein numbering systems are possible. The CTLA-4 sequence can start with, inter alia, Ala at position 1 (US 5,434,131) or with Met at position 1 (Larsen et al, Am J. Transplantation (2005) 5:443-453). Unless the context clearly indicates otherwise, the numbering system used here is one where position 1 is Met. This also corresponds to the numbering that is generally used to refer to the residues of the Abatacept product.
[0075] The FC residue numbering, which is used throughout this specification, is as shown in Figure 1B (top line, starting from 1), unless otherwise indicated.
[0076] The following numbered clauses represent aspects of the invention.
1. An isolated CTLA-4 polypeptide having a greater binding affinity for human CD80, greater potency and/or greater stability compared to wild type CTLA-4 SEQ ID NO:35, the polypeptide comprises an amino acid sequence that is a variant of SEQ ID NO:35, wherein the variant comprises five or more of the following amino acid mutations in SEQ ID NO:35:
[0078] R, S, V or T in I16;
[0079] T in A24;
[0080] N or P in S25;
[0081] S in G27;
[0082] I in V 32;
[0083] G in D41;
[0084] G in S42;
[0085] And in V44;
[0086] K in M54;
[0087] S or G in N56;
[0088] A, G, S or P in L58;
[0089] S or A in T59;
[0090] T in F 60;
[0091] Q or P in L61;
[0092] G in D 62;
[0093] Y in D63;
[0094] P in S 64;
[0095] N, D, V or T in I65;
[0096] A, T, M or H in S70;
[0097] R in Q80;
[0098] Q, S, V, R, K or L in M85;
[0099] S in T87;
[00100] Q, H, T, E or M in K93;
[00101] R, Q or E in L104;
[00102] V in I106;
[00103] D or S in N108;
[00104] V or F in I115;
[00105] S at C120;
[00106] deletion in T51.
[00107] 2. A CTLA-4 polypeptide according to clause 1, wherein the polypeptide comprises an amino acid sequence at least 70% identical to SEQ ID NO: 35.
[00108] 3. A CTLA-4 polypeptide according to clause 1 or 2, comprising five or more of the following amino acid mutations:
[00109] R, S or V in I16;
[00110] T in A24;
[00111] N in S25;
[00112] S in G27;
[00113] K in M54;
[00114] S at N56;
[00115] A or G in L58;
[00116] S in T59;
[00117] T in F60;
[00118] Q in L61;
[00119] Y in D63;
[00120] P in S64;
[00121] N or D in I65;
[00122] A at S70;
[00123] R in Q80;
[00124] Q or S in M85;
[00125] Q or H in K93;
[00126] S in C120.
[00127] 4. The CTLA-4 polypeptide according to clause 1 or 2 comprises the substitution S25N or S25P.
[00128] 5. The CTLA-4 polypeptide according to any one of clauses 1 to 3, comprising the substitution S25N, K93Q or K93H.
[00129] 6. The CTLA-4 polypeptide according to any one of clauses 1 to 5, comprising an amino acid sequence at least 70%, 80%, 90%, 95% or 98% identical to any one of the SEQ NOS ID: 36-55, or an amino acid sequence at least 70%, 80%, 90%, 95%, 98 or 99% identical to the CTLA-4 amino acid sequence encoded by the deposited nucleic acid with the number of NCIMB access 41948.
[00130] 7. The CTLA-4 polypeptide according to any one of clauses 1 to 6, comprising the amino acid domain with SEQ ID NO: 69 at residues 59-65, wherein the residue numbering begins with reference to SEQ ID NO: 35.
[00131] 8. The CTLA-4 polypeptide according to any one of clauses 1 to 6, comprising a combination of mutations selected from:
[00132] - the 1315 mutations, that is, S in I16; N in S25; G in L58; A at S70; R in Q80; S in M85; and Q in K93;
[00133] - the 1322 mutations, that is, N in S25; S in G27; K in M54; S at N56; S in T59; T in F60; Q at L61; Y in D63; P in S64; N in I65; and Q in K93;
[00134] - the 1321 mutations, that is, S in I16; N in S25; K in M54; G in L58; A at S70; R in Q80; S in M85; and Q in K93;
[00135] - the 1115 mutations, that is, V in I16; N in S25; G in L58; A at S70; Q in M85; and Q in K93;
[00136] - the 1299 mutations, i.e., R in I16; T in A24; N in S25; S in G27; A at L58; A at S70; Q in M85; and Q in K93; and
[00137] - the 1227 mutations, that is, S in I16; N in S25; S in G27; A at L58; A at S70; Q in M85; and H in K93.
[00138] 9. The CTLA-4 polypeptide according to any of the preceding clauses, comprising an amino acid sequence selected from SEQ ID NOS: 36-55, or comprising the CTLA-4 amino acid sequence encoded by the nucleic acid deposited under accession number NCIMB 41948 or comprising a variant of one of these sequences with up to ten amino acid mutations.
10. The CTLA-4 polypeptide according to any of the preceding clauses, comprising an amino acid sequence selected from SEQ ID NOS: 36-55, or comprising the CTLA-4 amino acid sequence encoded by the nucleic acid deposited under accession number NCIMB 41948 or comprising a variant of one of these sequences with up to five amino acid mutations.
[00140] 11. The CTLA-4 polypeptide according to clause 10, comprising an amino acid sequence selected from SEQ ID NOS: 36-55, or comprising the CTLA-4 amino acid sequence encoded by the nucleic acid deposited with NCIMB accession number 41948 or comprising a variant of one of these sequences with up to three amino acid mutations.
12. The CTLA-4 polypeptide according to clause 1 or clause 2, comprising an amino acid sequence selected from SEQ ID NOS: 36-55 or comprising the CTLA-4 amino acid sequence encoded by the nucleic acid deposited with accession number NCIMB 41948.
[00142] 13. The CTLA-4 polypeptide according to clause 12, comprising an amino acid sequence selected from SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 47 or the CTLA-4 amino acid sequence encoded by nucleic acid deposited under accession number NCIMB 41948.
14. An isolated CTLA-4 polypeptide having a greater binding affinity for human CD80, greater potency and/or greater stability compared to wild-type CTLA-4 SEQ ID NO: 35, wherein the polypeptide comprises:
[00144] (i) amino acid sequence SEQ ID NO: 68, SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 42 or SEQ ID NO: 47 ;
[00145] (ii) an amino acid sequence that is a variant of (i) containing up to ten amino acid mutations, wherein residue 25 is unmutated and is N;
(iii) an amino acid sequence which is a variant of (i) which comprises one or more amino acid mutations, wherein residue 25 is not mutated and is N, the variant has at least 70% sequence identity I ate); or
(iv) a CTLA-4 amino acid sequence encoded by the nucleic acid deposited under accession number NCIMB 41948.
[00148] 15. The CTLA-4 polypeptide according to clause 14, comprising the sequence SEQ ID NO: 68, SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 42 or SEQ ID NO: 47, or a variant of one of these sequences with up to five amino acid mutations.
[00149] 16. The CTLA-4 polypeptide according to clause 15, comprising the sequence SEQ ID NO: 68, SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 42 or SEQ ID NO: 47, or a variant of one of these sequences with up to three amino acid mutations.
17. A CTLA-4 polypeptide according to clause 14, wherein the polypeptide comprises an amino acid sequence having at least 80% sequence identity with SEQ ID NO: 68, SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 42 or SEQ ID NO: 47.
18. A CTLA-4 polypeptide according to clause 17, wherein the polypeptide comprises an amino acid sequence having at least 90%, 95%, 98% or 99% sequence identity with SEQ ID NO :68, SEQ ID NO:43, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:36, SEQ ID NO:42 or SEQ ID NO:47.
[00152] 19. A CTLA-4 polypeptide according to any of the preceding clauses, having an affinity of 50 nM or less for the binding of human CD80, wherein the affinity is Kd, as determined by surface plasma resonance .
[00153] 20. A CTLA-4 polypeptide according to clause 19, having an affinity of 20 nM or less for the binding of human CD80, wherein the affinity is Kd, as determined by surface plasma resonance.
21. A CTLA-4 polypeptide according to any of the preceding clauses, wherein the polypeptide has a greater affinity than wild-type CTLA-4 (SEQ ID NO: 35) for binding to human CD86.
[00155] 22. The CTLA-4 polypeptide according to any one of clauses 14 to 21, comprising:
[00156] - S at residue 16; N at residue 25; G at residue 58; A at residue 70; R at residue 80; S at residue 85; and Q at residue 93;
[00157] - N at residue 25; S at residue 27; K at residue 54; S at residue 56; S at residue 59; T at residue 60; Q at residue 61; Y at residue 63; P at residue 64; N at residue 65; and Q at residue 93;
[00158] - S at residue 16; N at residue 25; K at residue 54; G at residue 58; A at residue 70; R at residue 80; S at residue 85; and Q at residue 93;
[00159] - V at residue 16; N at residue 25; G at residue 58; A at residue 70; Q at residue 85; and Q at residue 93;
[00160] - R at residue 16; T at residue 24; N at residue 25; S at residue 27; A at residue 58; A at residue 70; Q at residue 85; and Q at residue 93; or
[00161] - S at residue 16; N at residue 25; S at residue 27; A at residue 58; A at residue 70; Q at residue 85; and H at residue 93.
23. The CTLA-4 polypeptide according to any one of clauses 14 to 22, comprising the amino acid sequence SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 42 or SEQ ID NO: 47, with up to three amino acid mutations.
24. The CTLA-4 polypeptide according to any one of clauses 14 to 18, comprising: R, I, S or V at position 16; T or A at position 24; S or G at position 27; M or K at position 54; N or S at position 56; A, L or G at position 58; T or S at position 59; F or T at position 60; L or Q at position 61; D or Y at position 63; S or P at position 64; I, N or D at position 65; A or S at position 70; Q or R at position 80; Q, M or S at position 85; Q or H at position 93; and C or S at position 120.
[00164] 25. The CTLA-4 polypeptide according to any one of clauses 1 to 6, wherein the amino acid mutations are selected from: T substitution at residue 16; substitution of I at residue 32; substitution of G at residue 41; substitution of G at residue 42; substitution of E at residue 44; substitution of G at residue 56; substitution of S or P at residue 58; substitution of A at residue 59; substitution of P at residue 61; substitution of G at residue 62; substitution of V or T at residue 65; substitution of T, M or H at residue 70; substitution of V, R, K or L at residue 85; substitution of S at residue 87; substitution of T, E or M at residue 93; substitution of R, Q or E at residue 104; substitution of V at residue 106; substitution of D or S at residue 108; substitution of V or F at residue 115; substitution of S at residue 120; deletion of residue 51.
26. The CTLA-4 polypeptide according to clause 14, comprising the amino acid sequence SEQ ID NO: 68, SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 42 or SEQ ID NO: 47 or comprising the CTLA-4 amino acid sequence encoded by the deposited nucleic acid under accession number NCIMB 41948.
[00166] 27. An isolated CTLA-4 polypeptide that has at least 10 times greater binding affinity for CD80 than for CD86.
28. A CTLA-4 polypeptide according to clause 27, which has at least 50 times greater binding affinity for CD80 than for CD86.
29. A CTLA-4 polypeptide according to clause 27 or clause 28, wherein the polypeptide is as defined in any one of clauses 1 to 26.
30. A CTLA-4 polypeptide according to any of the preceding clauses, conjugated to an IgG Fc amino acid sequence.
[00170] 31. A CTLA-4 polypeptide according to clause 30, wherein the IgG Fc is human IgG1 Fc modified to reduce Fc effector function and comprises a native human IgG1 Fc hinge region.
32. A CTLA-4 polypeptide according to clause 30 or clause 31, wherein the IgG Fc amino acid sequence comprises a human IgG1 Fc region, wherein one or both of the following groups of residues are substituted as follows:
[00172] F at residue 20; And at residue 21; S at residue 117; and
Y at residue 38, T at residue 40, E at residue 42,
[00174] the numbering of the residues begins with reference to SEQ ID NO: 56.
33. The CTLA-4 polypeptide according to any one of clauses 30 to 32, wherein the IgG Fc amino acid sequence is SEQ ID NO:59.
34. An isolated CTLA-4 polypeptide comprising the amino acid sequence of CTLA-4-Ig 1299 encoded by the deposited nucleic acid with accession number NCIMB 41948.
35. A CTLA-4 polypeptide according to any one of the preceding clauses, wherein the polypeptide is a multimer.
[00178] 36. A CTLA-4 polypeptide according to clause 35, wherein the CTLA-4 polypeptide is a dimer.
[00179] 37. A CTLA-4 polypeptide according to clause 35, wherein the CTLA-4 polypeptide is a tetramer.
38. A CTLA-4 polypeptide according to clause 37, wherein the tetramer comprises two pairs of CTLA-4 polypeptides each pair comprising a CTLA-4 polypeptide fused to an antibody light chain constant region and one CTLA-4 polypeptide fused to the constant region of an antibody heavy chain.
39. A host cell containing the nucleic acid, wherein the nucleic acid comprises the nucleic acid sequence of CTLA-4-Ig 1299 deposited under accession number NCIMB 41948.
[00182] 40. A composition comprising:
[00183] a CTLA-4 polypeptide according to any one of the preceding clauses; and
[00184] one or more pharmaceutical excipients.
[00185] 41. A composition comprising:
[00186] a CTLA-4 polypeptide comprising the amino acid sequence SEQ ID NO: 68, SEQ ID NO: 43, SEQ ID NO: 47, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 47 or the CTLA-4 amino acid sequence encoded by the nucleic acid deposited under accession number NCIMB 41948, conjugated to an IgG Fc amino acid sequence; and
[00187] one or more pharmaceutical excipients.
42. A composition according to clause 40 or clause 41, wherein CTLA-4 polypeptide is conjugated to an IgG Fc amino acid sequence comprising SEQ ID NO:59.
[00189] 43. A composition according to clause 42, wherein CTLA-4 polypeptide conjugated to IgG Fc comprises the amino acid sequence SEQ ID NO: 13, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO :14, SEQ ID NO:15 or SEQ ID NO:16.
44. A composition comprising the CTLA-4-Ig 1299 polypeptide encoded by the deposited nucleic acid with accession number NCIMB 41948 and one or more pharmaceutical excipients.
45. A composition according to any one of clauses 40 to 44, comprising the CTLA-4 polypeptide at a concentration of at least 70 mg/ml.
[00192] 46. A composition according to clause 45, which comprises the CTLA-4 polypeptide at a concentration of at least 100 mg/ml.
47. A CTLA-4 polypeptide according to any one of clauses 1 to 38, or a composition according to any one of clauses 40 to 46, for use in a method of treating a patient, either subcutaneously or intravenously. .
48. A CTLA-4 polypeptide according to any one of clauses 1 to 38, or a composition according to any one of clauses 40 to 46, for use in a method of treating rheumatoid arthritis, multiple sclerosis, asthma, Crohn's disease, ulcerative colitis, systemic lupus erythematosus, or transplant rejection.
49. A CTLA-4 polypeptide according to any one of clauses 1 to 38, or a composition according to any one of clauses 40 to 46, for use in a method of treatment comprising administering said CTLA- polypeptide 4 or said composition to a patient at intervals of 28 days.
50. A method of producing another CTLA-4 polypeptide by mutating an amino acid sequence of the CTLA-4 polypeptide selected from SEQ ID NOS 36-55 or the CTLA-4 amino acid sequence encoded by nucleic acid deposited with accession number NCIMB 41948, the method comprising:
[00197] providing a CTLA-4 polypeptide, comprising or consisting of the amino acid sequence SEQ ID NOS 36-55 or the CTLA-4 amino acid sequence encoded by the deposited nucleic acid with accession number NCIMB 41948;
[00198] introduction of one or more mutations in the amino acid sequence to provide another CTLA-4 polypeptide;
[00199] test the stability, affinity and/or potency of the other CTLA-4 polypeptide; and
[00200] formulating more CTLA-4 polypeptides into a composition comprising one or more pharmaceutical excipients.
51. A method according to clause 50, wherein the other CTLA-4 polypeptide is conjugated to an Fc region. Biological potency
[00202] Soluble CTLA-4 competes with CD28 expressed on the surface of T lymphocytes, inhibiting the binding of CD80 (B7.1) and CD86 (B7.2) ligands to CD28, which would otherwise result in co-stimulation and activation Thus, soluble CTLA-4 inhibits T lymphocyte activation. The potency of this inhibition by soluble exogenous CTLA-4 can be determined in in vitro assays. CTLA-4 can optionally be conjugated to another molecule, for example, as a fusion protein. For example, an IgG Fc can be present as described herein. The assay can be used to qualitatively determine whether a CTLA-4 polypeptide is more or less potent than wild-type, using wild-type CTLA-4 (optionally Fc-conjugated, as appropriate) as a control and can also provide quantitative information regarding the magnitude of the power difference. Methods for performing these tests and for analyzing the statistical significance of the data reliably to produce qualitative or quantitative information are known in the art.
Binding of a CTLA-4 polypeptide can be measured through IL-2 production, since CTLA-4 binding to CD80 and CD86 attenuates IL-2 production. Suitable assays may comprise detecting the amount of IL-2 produced, for example by ELISA.
[00204] A reduction in the amount of IL-2 production can be partial or total. A CTLA-4 polypeptide can reduce IL-2 production by at least 50%, 75% or 80%, preferably at least 85%, 90% or 95%, at the concentrations tested.
A dual cell assay can be used to identify CTLA-4 polypeptides with a higher potency than wild-type. CTLA-4 polypeptides are assayed to measure inhibition of signaling. Co-culture of T cells expressing CD28 (eg Jurkat cells) and B cells expressing CD80 and CD86 (eg Raji cells) results in the production of IL-2 due to the interaction between CD28 and the ligands CD80 and CD86 in the presence of phytohemagglutinin (PHA). IL-2 is then detected by ELISA. See Example 3 for a detailed example of this assay.
[00206] Human primary T cell activation assays can be used to assess the potency of selected polypeptides. CTLA-4 polypeptides can be classified by their ability to inhibit CD80/86-mediated IL-2 secretion from primary human CD4+ T lymphocytes. CTLA-4 polypeptides can also be classified by their ability to inhibit anti-CD3 stimulated proliferation of human CD4+ T lymphocytes in the presence of Raji cells expressing CD80 and CD86. Proliferation can be assayed using a homogeneous luminescence assay (ATP lite). An advantage of this test is that it measures the potency of CTLA-4 polypeptides to block the activation of primary human CD4+ lymphocytes. See Example 4 for a detailed example of this assay.
Certain CTLA-4 polypeptides according to the invention have been shown to bind CD80 and CD86 with high potency in the assay for measuring T cell activation. CTLA-4 polypeptides block CD80 and CD86 ligands , thus preventing additional activation signals from these molecules and leading to reduced IL-2 production.
The potency of CTLA-4 polypeptides can be determined or measured using one or more assays known to one of skill in the art and/or as described or referred to herein. Potency is a measure of activity expressed in terms of the amount needed to produce an effect. Typically, a titer of a polypeptide is compared in a cell assay and IC50 values are reported. In functional assays, the IC50 is the concentration of a product that reduces a biological response by 50% of its maximum. IC50 can be calculated by plotting % maximal biological responses as a function of the log of the product concentration and using a software program such as Prism (GraphPad) to fit a sigmoid function to the data to generate the IC50 values. The lower the IC50 value the more potent the product.
CTLA-4 polypeptides can be described as having increased potency as less is needed compared to a reference (e.g. wild type) of CTLA-4 polypeptide to produce inhibition of IL-2 production . This is also reflected in the reported IC50 values. Preferred CTLA-4 polypeptides have increased potency compared to wild-type human CTLA-4 (SEQ ID NO: 35).
A CTLA-4 polypeptide according to the invention may have a higher potency relative to the wild type of SEQ ID NO: 35, wherein the potency is a reduction in IC50, in an IL-2 production assay using T cells activated by B cells. The potency can be at least 10-fold, at least 15-fold, at least 20-fold, at least 30-fold, at least 40-fold, or at least 50-fold greater than wild-type. As described in the Examples, a polypeptide of SEQ ID NO: 36 (variant 1315) was found to have about 120 times greater potency than wild type CTLA-4. The potency can, for example, be up to 150 times, up to 130 times, up to 120 times, up to 100 times, up to 80 times, up to 70 times or even 60 times greater than in wild type. The improvement in potency can, for example, be in the range of 10-fold to 100-fold greater than in wild type.
The potency of a CTLA-4 polypeptide can be determined with reference to CTLA-4 polypeptide sequences exemplified herein, rather than (or as well) with reference to wild type, e.g., potency can be compared to any one of SEQ ID NO: 37 (variant 1322), SEQ ID NO: 38 (variant 1321), SEQ ID NO: 43 (variant 1299), SEQ ID NO: 36 (variant 1315), SEQ ID NO: 42 (variant 1115), SEQ ID NO: 47 (variant 1227) or variant 1299 as encoded by nucleic acid deposited with accession number NCIMB 41948. Thus, one of these CTLA-4 variants can be used as a control in the assay. A CTLA-4 polypeptide can be at least as potent as one or more of these variants, for example, at least as potent as SEQ ID NO: 43 (variant 1299) or SEQ ID NO: 47 (variant 1227). A CTLA-4 polypeptide can have a potency that is approximately the same or less than the potency of SEQ ID NO: 36 (variant 1315). Affinity
[00212] The affinity of a CTLA-4 polypeptide for binding CD80 or CD86 can be determined as the monovalent affinity, using surface plasma resonance to determine Kd. See Example 8 for a practical example of using surface plasma resonance to measure binding affinity and determine Kd. The resulting Kd can be compared to wild-type CTLA-4 of SEQ ID NO:35 or compared to one of the CTLA-4 polypeptides of SEQ ID NO:37 (variant 1322), SEQ ID NO:38 (variant 1321) , SEQ ID NO: 43 (variant 1299), SEQ ID NO: 36 (variant 1315), SEQ ID NO: 42 (variant 1115), SEQ ID NO: 47 (variant 1227) or variant 1299 as encoded by the nucleic acid deposited with the NCIMB accession number 41948 to determine relative affinity. A CTLA-4 polypeptide can have a greater binding affinity for human CD86 and/or human CD80 as compared to the affinity of wild-type CTLA-4.
A CTLA-4 polypeptide may have a binding affinity for human CD80 that is greater than that of wild-type CTLA-4, e.g., at least 10-fold, at least 15-fold, at least 20-fold, at least at least 30 times, at least 40 times, at least 50 times, at least 100 times, or at least 140 times greater than in wild type. The CTLA-4 polypeptide can have at least the binding affinity for human CD80 of one or more of SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO :42 and SEQ ID NO:47, or at least the affinity of the 1299 CTLA-4 variant as encoded by the deposited nucleic acid with accession number NCIMB 41948. A CTLA-4 polypeptide can have an affinity for binding to human CD80 that is approximately the same as or less than the affinity of SEQ ID NO: 37. Kd for human CD80 binding may be 50 nM or less, e.g. 25 nM or less, 20 nM or less, or 10 nM or less . For example, Kd can be in the range of 5 to 50 nM.
A CTLA-4 polypeptide may have a binding affinity for human CD86 that is greater than that of wild-type CTLA-4, e.g., at least 2-fold, at least 3-fold, at least 4-fold, at least at least 5 times or at least 10 times greater than in wild type. The CTLA-4 polypeptide can have at least the binding affinity for human CD86 of one or more of SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO :42 and SEQ ID NO:47 or at least the affinity of the 1299 CTLA-4 variant as encoded by the deposited nucleic acid with accession number NCIMB 41948. A CTLA-4 polypeptide can have an affinity for binding to human CD86 that is approximately the same as or less than the affinity of SEQ ID NO: 37. Kd for human CD86 binding may be 2 nM or less, e.g. 1.5 nM or less or 1 nM or less. For example, Kd can be in the range of 0.5 to 2 nM. Selectivity for CD80 over CD86
The CTLA-4 polypeptides described herein can bind to both CD80 and CD86, but can selectively bind to CD80 in preference to CD86. It is known that wild-type CTLA-4 has a higher binding affinity for CD80 compared to CD86, and a CTLA-4 polypeptide according to the invention may also have a higher binding affinity for CD80 than for CD86. However, a CTLA-4 polypeptide may have greater selectivity for binding to CD80, preferably to CD86, compared to wild-type CTLA-4. For example, in surface plasma resonance assays as described herein, wild-type CTLA-4 exhibited about 4-fold greater binding affinity for CD80 than for CD86. In contrast, CTLA-4 polypeptides can exhibit greater than 10-fold, greater than 20-fold, greater than 30-fold, greater than 40-fold, or greater than 50-fold greater binding affinity for CD80 than for CD86. For example, a CTLA-4 polypeptide may have 120-fold or 130-fold greater binding affinity for CD80 than for CD86. Thus, when compared to wild-type CTLA-4 affinity, a CTLA-4 polypeptide may show a greater increase in affinity for CD80 than for CD86. The selective preference for CD80 over CD86 can be seen with human CD80 and human CD86.
[00216] Furthermore, the same selective preference can be retained with cynomolgus monkey CD80 and CD86. The difference in affinity for binding CD80 relative to CD86 may be approximately the same for human and cynomolgus CD80 and CD86.
[00217] Improvements in binding affinity to CD80 should provide a better biological profile for medical use. Through binding to CD80, which is upregulated on antigen-presenting cells in the context of an active immune response, CTLA-4 inhibits the binding of CD80 to CD28 on T cells, thereby blocking the T cell activation signal. a CTLA-4 polypeptide can be used to attenuate the T cell response in vivo and to treat conditions where this is beneficial, as described herein.
[00218] By engineering a CTLA-4 polypeptide that selectively targets CD80 over CD86, large gains in binding affinity for CD80 can be obtained. Although the literature is inconclusive as to the relative functions of CD80 and CD86, the polypeptides of the present invention selectively bind to CD80 over CD86 and exhibit excellent biological profiles suitable for therapeutic use, as shown in various assays. Without being limited by theory, the attributes of the present CTLA-4 polypeptides may be attributable, at least in part, to the high affinity for binding to CD80 and/or to the preferential binding of CD80 over CD86.
[00219] Several data point to a role of CD80 in delivering a greater activation signal to T lymphocytes. For example:
CD80 transduced CHO cells induce an increase in IL-2 production from primary human T cells compared to CD86 transduced CHO cells (Slavik et al. JBC 274(5):3116-3124 1999);
[00221] CD80 induces increased activity of NFkB and AP-1 transcription factor compared to CD86 on Jurkat T cells (important factors for the production of cytokines such as IL-2) (Olsson et al. Int. Immunol 10(4):499-506 1998);
[00222] CD80 induces increased expression of CD25 on CD8+ T cells that interact with virus-infected dendritic cells, compared to CD86 (important for T cell survival and proliferation) (Pejawar-Gaddy & Alexander-Miller, J Immunol.177:4495-4502 2006); and
[00223] in a murine model of allergic asthma, using a mutated CTLA-4 Ig molecule, it was found that CD80, but not CD86, is an important factor in pulmonary eosinophilia (Harris et al. J. Exp. Med. 185(1 ) ) 1997).
[00224] Preferably, the increased affinity of CTLA-4 to CD80 can thus lead to a better inhibition of T cell activation by directing the most efficient pathway of activation of CD80 T cells.
[00225] Furthermore, there is some evidence that CD86 signaling may have a beneficial anti-inflammatory effect in some disease models. For example, in a rat model for sepsis, mortality and severity have been observed to be associated with CD80 upregulation and concomitant CD86 downregulation (Nolan et al. PLoS ONE 4(8):6600 2009). Thus, a selective binding of CD80 over CD86 may provide an advantage, as it can inhibit the binding of CD80 to CD28, while at the same time reducing the interaction of CD28 to a lesser degree.
Both CD80 and CD86 positive cells can be found in the joints of patients with rheumatoid arthritis, and the binding of both B7 molecules can contribute to the therapeutic effect, while the selectivity for CD80 over CD86 can contribute to the desirable qualitative and quantitative effects in inhibiting T cell activation. Thus, the CTLA-4 polypeptides of the invention can bind to both CD80 and CD86 and can have a greater affinity for CD80 than wild-type CTLA-4. and may also have a higher affinity for CD86 than wild-type CTLA-4. cross reactivity
Preferably, the CTLA-4 polypeptides according to the invention maintain the wild-type cross-reactivity profile of CTLA-4.
The CTLA-4 polypeptide can show cross-reactivity for binding cynomolgus and/or rat CD80 and CD86, as well as human CD80 and CD86. The difference in affinity for cynomolgus CD80 compared to human CD80 can be within 10-fold, within 5-fold, within 2-fold, about 1.5-fold or 1.2-fold. The difference in affinity for cynomolgus CD86 compared to human CD86 can be within 10-fold, within 5-fold, within 2-fold, about 1.5-fold or 1.2-fold. The difference in affinity for mouse CD80 compared to human CD80 can be within 10-fold, within 5-fold, within 2-fold, about 1.5-fold or 1.2-fold. The difference in affinity for mouse CD86 compared to human CD86 can be within 10-fold, within 5-fold, within 2-fold, about 1.5-fold or 1.2-fold.
[00229] The CTLA-4 polypeptide can inhibit the activation of cynomolgus T lymphocytes, for example, measured as the inhibition of IL-2 production in a mixed lymphocyte reaction using peripheral blood mononuclear cells from cynomolgus monkeys. The polypeptide may have greater potency than wild-type CTLA-4 in an assay for inhibition of cynomolgus T lymphocyte activation.
[00230] Data for cross-reactive species, e.g., CTLA-4 polypeptides of the invention are shown in Example 8.
[00231] The CTLA-4 polypeptide can show specific binding to CD80 and CD86 in preference to other related proteins in the B7 family. Thus, there may be a lack of cross-reactivity with PD-L2, B7-H1, B7-H2, B7-H3 and B7-H3B.
[00232] Assays to determine specificity are known in the art. For example, an enzyme immunoassay can be used. See Example 6 for an example of this suitable assay. Stability
A CTLA-4 polypeptide preferably retains at least the stability of wild-type CTLA-4 and is preferably more stable than wild-type, e.g., as measured for CTLA-4 alone. or CTLA-4 conjugated to (e.g., fused) an Fc region, as described below.
It is believed that more stable CTLA-4 Fc conjugates ("CTLA-4 Ig") will be better able to tolerate the formulation at the high (eg, >100 mg/mL) concentrations required for subcutaneous delivery.
[00235] Stability can be tested in a degradation test. Typically this comprises incubating the product at a fixed temperature (eg 5 °C or 25 °C) for a period of time, for example for a month, and determining the extent of the loss of purity (degree of degradation) throughout that month. Aggregation and/or fragmentation can contribute to the loss of purity and each can be measured separately to determine the percentage for two values, adding to the % loss of purity. Examples of degradation tests are set forth in Example 9 and Example 10.
[00236] A CTLA-4 polypeptide with improved stability may be more amenable to routes of administration, such as subcutaneous administration, due to reduced aggregation, which not only increases efficacy, but also reduces the risk of neutralization or binding to antibodies to be induced. Conjugation of Fc
In one embodiment, the invention provides an optimized affinity of the CTLA-4 Ig molecule, optionally with an extended half-life (e.g. including a YTE mutation, further described herein), for subcutaneous or intravenous formulation and for monthly dosing interval , 28 days or less frequently, for the treatment of moderate to severe RA, or other conditions as described.
The invention provides a polypeptide that consists of a CTLA-4 polypeptide sequence or that comprises or is conjugated to a peptide or polypeptide sequence, for example, to an antibody molecule or a part of an antibody molecule. For example, a CTLA-4 polypeptide can be conjugated to an antibody Fc amino acid sequence, e.g., IgG Fc. An Fc region comprises a hinge, a CH2 and CH3 region. Preferably IgG is human IgG, for example IgG1, IgG2 or IgG4.
[00239] Allotype variants of IgG1 are known. Preferably, an IgG1 Fc region comprises E at residue 142 and M at residue 144 (numbering corresponding to SEQ ID NO: 56, starting from 1, as shown in Figure 1). This allotype is well represented in the general population. An alternative IgG1 Fc region representing a different allotype comprises D at residue 142 and L at residue 144. This allotype is employed in Abatacept.
The IgG Fc amino acid sequence may comprise the human IgG Fc amino acid sequence (for example IgG1 or IgG4) with certain mutations. For example, where IgG1 human IgG is, the amino acid sequence can be mutated to reduce or suppress Fc effector functions, e.g., complement dependent cytotoxicity (CDC) and antibody dependent cellular cytotoxicity (ADCC). Removal of Fc effector functions can be confirmed through known routine tests. See Example 7 for exemplary assays for determining ADCC and CDC.
[00241] It is known that the effector function of IgG1 can be reduced by mutating the hinge region of IgG1 Fc. An example of this is in the Abatacept CTLA-4 - IgG1 Fc construct, which incorporates a mutated hinge sequence in the IgG1 Fc region, where wild type C is mutated to S. The IgG1 region of Abatacept includes an amino acid sequence SEQ ID NO: 71, which corresponds to the amino acid sequence of wild type human IgG1 Fc SEQ ID NO: 70 with wild type C replaced by S. Substitutions are at residues 6, 12 and 15 of the Fc region.
[00242] SEQ ID NO: 70 VEPKSCDKTHTCPPCPAPE
[00243] SEQ ID NO: 71 QEPKSSDKTHTSPPSPAPE
In the context of the present invention it was surprisingly found that this mutation reduces the stability of the FC domain, so that CTLA4 Abatacept - IgG1 Fc fusion has a lower stability than CTLA-4 - IgG1 Fc fusion, in which the sequence of wild-type IgG1 Fc is used. This loss of stability is undesirable, but it is important to reduce or prevent the effector function of IgG1 Fc.
An Fc region conjugated to a CTLA-4 polypeptide of the invention preferably does not comprise SEQ ID NO: 71. Preferably, the cysteine at residues 6, 12 and/or 15 of the Fc are retained. Preferably, a CTLA-4-Fc conjugate according to the invention comprises a human wild-type human IgG1 Fc hinge region. Preferably, the Fc region comprises SEQ ID NO: 70. The Fc region may be the Fc region of the 1299 CTLA4-Ig polypeptide as encoded by the nucleic acid deposited under accession number NCIMB 41948.
[00246] While the reversion of Fc Abatacept to wild type suppresses the instability caused by the Fc mutation, it also restores the effector functions of IgG1 Fc, which is undesirable in many therapeutic applications. Therefore, this mutation improves the stability of the Abatacept Fc domain but only at the expense of reintroducing undesirable effector function.
[00247] Other regions of IgG fc with low or no effector function can be used, for example, IgG2.
[00248] The present invention provides a way to use IgG1 Fc in which effector functions are lacking, while overcoming the problem of reduced stability inherent in the Abatacept mutation. An Fc region according to the invention may be an IgG1 Fc which comprises a triple mutation (TM) L20F, L21E, P117S (Oganesyan et al 2008 Acta Crystallogr D Biol Crystallogr. 64:700-4). This mutation reduces Fc effector function without reducing stability. Therefore, such an Fc domain facilitates the formulation of CTLA-4-Fc constructs at high concentrations, which are suitable for the production of compositions for subcutaneous administration.
[00249] Still other benefits can be achieved by incorporating a "YTE" mutation into the Fc region (Dall'Acqua et al 2006 J Biol Chem. 281:23514-24). The YTE mutation provides a prolonged in vivo half-life, which may improve therapeutic efficacy and/or may allow therapeutic benefits to be achieved with reduced or less frequent dosing, such as monthly dosing. An Fc domain used in the products of the invention may comprise Y at residue 38, T at residue 40 and E at residue 42. This represents M38Y, S40T, T42E mutations in human IgG1 Fc.
Other than the above-mentioned YTE and/or triple mutation, it is preferable that the other Fc domain residues are wild-type residues of human IgG. Some human IgG1 Fc variation is known and the Fc region can comprise any human IgG1 with YTE and/or triple mutation.
Preferably, the CTLA-4 polypeptide is conjugated to an IgG1 Fc amino acid sequence SEQ ID NO: 59. This includes a human IgG1 Fc hinge region, lacking the Abataceptde C to S mutation, incorporates the triple mutation to reduce the effector function and includes the YTE half-life extension.
The improved Fc regions described herein can be used in conjunction with wild-type CTLA-4, providing even more benefit when conjugated to a CTLA-4 polypeptide according to the invention. A CTLA-4 polypeptide can be conjugated from its C-terminus to the N-terminus of an Fc region, optionally via one or more linker amino acids or a linker peptide. Preferably, the conjugate is a CTLA-4 - Fc fusion protein.
[00253] For example, a CTLA-4 polypeptide comprising the amino acid sequence SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 42 or SEQ ID NO: 47 can be conjugated to an IgG1 Fc amino acid sequence SEQ ID NO: 59 or to an IgG1 Fc amino acid sequence SEQ ID NO: 60.
According to the invention the CTLA-4 - IgG Fc fusion protein may comprise SEQ ID NO: 13, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO: 16.
The CTLA-4 - IgG Fc 1299 polypeptide encoded by the deposited nucleic acid with accession number NCIMB 41948 is an embodiment of the invention. The CTLA-4 1299 polypeptide encoded by the deposited nucleic acid with accession number NCIMB41948 may alternatively be conjugated to a different Fc region, if desired. CTLA-4 Polypeptide Products
[00256] CTLA-4 polypeptides, including CTLA-4 - Fc, can be monomeric or multimeric, for example, dimeric, trimeric, tetrameric or pentameric. As discussed here, CTLA-4 can form dimers. This natural dimerization can be promoted through the conjugation of CTLA-4 to an Fc domain or other dimerization domain.
[00257] Polypeptide multimers comprising a plurality of CTLA-4 polypeptides are an aspect of the invention. The plurality of CTLA-4 polypeptides within the multimer can be identical or different from one another. A multimer may comprise some identical polypeptides and/or some different polypeptides. A multimer may comprise one or more CTLA-4 polypeptides according to the invention and one or more other polypeptides. The one or more other polypeptides can include, for example, a wild-type CTLA-4 and/or a polypeptide that is not a CTLA-4 polypeptide.
The multimer may be a dimer comprising two CTLA-4 polypeptides according to the invention, which may be identical (a homodimer) or different (a heterodimer).
The multimer can be a tetramer composed of four CTLA-4 polypeptides according to the invention, which can all be identical (a homotetramer) or can include one or more different CTLA-4 polypeptides according to the invention (a heterotetramer ). The multimer may be a tetramer consisting of two CTLA-4 polypeptides according to the invention (identical or different from each other) and two other CTLA-4 polypeptides, such as wild-type CTLA-4 polypeptides.
Where CTLA-4 is in multimeric form, the CTLA-4 polypeptide is optionally conjugated to an immunoglobulin Fc region and/or an antibody molecule. The conjugate may or may not include an antigen binding site from an antibody, VH or VL domain.
One aspect of the invention is a conjugate comprising one or more, for example two, three, four or five CTLA-4 polypeptides and an antibody molecule or an antibody domain, preferably human. Dimerized CTLA-4 domains can be conjugated to antibody heavy-light chain pairs. An antibody molecule can comprise two heavy-light chain pairs, each heavy chain comprising a VH domain and one or more heavy chain constant domains (for example, CH1, CH2 and CH3), and each light chain comprising a VL domain and a light chain constant region, in which the two heavy-light chain pairs are linked through dimerization of the heavy chain constant domains and in which four CTLA-4 polypeptides are conjugated to the antibody molecule, a CTLA-4 linked to each of the four variable domains. The constant region of the light chain can be the lambda or kappa light chain. A pair of CTLA-4 molecules can be linked to each pair of VH-VL domain, wherein the CTLA-4 polypeptide linked to the VH domain forms a dimer with the CTLA-4 polypeptide linked to the VL domain. Preferably, the C-terminus of CTLA-4 is fused to the N-terminus of the VH or VL domain. Preferably, the VH and VL pairing does not confer any binding to known human antigens.
Optionally, some or all of the VH and/or VL domain antibodies are deleted such that a CTLA-4 polypeptide is included in place of, or in place of part of, the VH and/or VL. A dimer may suitably comprise a pair of CTLA-4 polypeptides, one fused to an antibody light chain constant region and one fused to an antibody heavy chain constant region. The tetramer can comprise two pairs of CTLA-4 polypeptides each pair comprising a CTLA-4 polypeptide fused to an antibody light chain constant region and a CTLA-4 polypeptide fused to an antibody heavy chain constant region. As noted above, a heavy chain constant region comprises one or more heavy chain constant domains, for example CH1, CH2 and CH3, and a light chain constant region which may be lambda or kappa.
The invention also includes CTLA4 pentamers. Five CTLA4 polypeptides can be assembled to form a pentamer, optionally through pentamerization of Fc regions of bound antibodies. Pentamer formation is facilitated using the Fc region of IgM, which is naturally pentameric. Thus, five CTLA4-Fc polypeptides including the Fc region of IgM, preferably human IgM, can be provided as a pentamer. Pentameric CTLA4 has been described (Yamada et al. Microbiol. Immunol. 40(7):513-518 1996).
Polypeptides in a multimer can be covalently linked, for example, by disulfide bonds. Covalent bonds can be present between the CTLA4 polypeptide and/or between any Fc region linked to the CTLA-4 polypeptide. When using Fc regions and/or other antibody domains, the polypeptides can be linked in the same manner as naturally occurs in such Fc domains and/or other antibody domains. The formation of disulfide bonds between cysteine residues of CTLA-4 polypeptides is described elsewhere in this document.
Such multimers and conjugates can be used in any method or for any use, as described herein for CTLA-4 polypeptides. The multimeric structure can promote the biological activity of CTLA-4, e.g., inhibition of T cell activation. Inhibition of wild-type CTLA-4 is shown to be enhanced in the tetrameric form (Example 11, Figure 7).
[00266] The CTLA-4 polypeptide can be labeled or unlabelled. A tag can be added to the CTLA-4 sequence or to an Fc region conjugated thereto.
[00267] CTLA-4 and/or the Fc region can be glycosylated or non-glycosylated. Preferably, CTLA-4 and/or Fc support its normal human glycosylation.
[00268] CTLA-4 polypeptides as described herein can be further modified and developed to provide other improved or altered variants. For example, the amino acid sequence of a CTLA-4 polypeptide in accordance with the invention described herein can be modified by introducing one or more mutations, e.g., substitutions, to provide another CTLA-4 polypeptide, which can then be tested for potency, affinity (to CD80 and/or CD86) and/or its stability, for example, as already described herein.
[00269] CTLA-4 polypeptides preferably retain one or more desired functional properties as described herein. Such properties include the ability to bind CD80 and/or CD86, the ability to bind CD80 and/or CD86 with an affinity greater than wild-type CTLA-4, and/or a potency, affinity and/or stability, such as as described herein for CTLA-4 polypeptides of the invention, e.g., Kd for human CD80 binding of 50 nM or less, as determined by surface plasma resonance. As described herein, a polypeptide according to the invention typically has a greater binding affinity for human CD80, greater potency and/or greater stability compared to wild-type CTLA-4 SEQ ID NO: 35.
The CTLA-4 polypeptide may comprise or consist of an amino acid sequence having at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% with as SEQ ID NOS: 36-55, for example with SEQ ID NO: 43, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 42 or SEQ ID NO: 47. The CTLA-4 polypeptide can comprise or consist of an amino acid sequence having at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% with the SEQ ID NO: 68. The CTLA-4 polypeptide may comprise or consist of an amino acid sequence having at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% with the CTLA-4 amino acid sequence encoded by the nucleic acid deposited under accession number NCIMB 41948.
The CTLA-4 polypeptide may comprise or consist of any SEQ ID NOS: 36-55, SEQ ID NO: 68 or the CTLA-4 amino acid sequence encoded by the nucleic acid deposited under accession number NCIMB 41948, with one or more mutations in the amino acids. For example it may comprise up to twelve mutations, up to ten amino acid mutations, for example up to five mutations, for example one, two or three amino acid mutations. Examples of mutations are described here.
[00272] Following the introduction of one or more mutations, the CTLA-4 polypeptide can be tested for desired functional properties, such as the ability to bind to CD80 and/or CD86, ability to bind to CD80 and/or CD86 with a greater affinity than wild-type CTLA-4 and/or a potency, affinity and/or stability as described herein for CTLA-4 polypeptides of the invention, e.g., Kd for human CD80 binding of 50 nM or less , as determined by surface plasma resonance.
[00273] One aspect of the invention is a method comprising
[00274] provide a CTLA-4 polypeptide, which comprises or consists of an amino acid sequence of CTLA-4 polypeptide as described herein;
[00275] introducing one or more mutations in the amino acid sequence to provide another CTLA-4 polypeptide; and
[00276] test the stability, affinity and/or potency of the other CTLA-4 polypeptide.
The CTLA-4 polypeptide amino acid sequence can comprise or consist of, for example, any one of SEQ ID NOS 36-55 or SEQ ID NO: 68 or the CTLA-4 amino acid sequence encoded by the deposited nucleic acid with NCIMB accession number 41948. For example, the amino acid sequence can be SEQ ID NO: 43, 37, 36, 38, 42 or 47.
[00278] (i) Between one and twenty included mutations, optionally, may be introduced and may include substitutions, deletions, insertions or a mixture of any of these. For example, one or more substitutions, for example between one and twenty substitutions can be introduced.
[00279] (ii) Examples of assays to test the stability, affinity and/or potency of the other CTLA-4 polypeptide are described herein. The other polypeptide may have a stability, affinity, and/or potency that is not significantly lower, or greater, than the CTLA-4 polypeptide from which it was derived.
[00280] (iii) The method may comprise determining which other CTLA-4 polypeptides have a potency, affinity and/or stability as described herein for CTLA-4 polypeptides of the invention, e.g., which has Kd for binding of human CD80 of 50 nM or less, as determined by surface plasma resonance.
[00281] (iv) Another CTLA-4 polypeptide identified as having potency, affinity and/or stability, as described herein for CTLA-4 polypeptides of the invention, may then be formulated into a pharmaceutical composition or used in therapeutic methods , including the methods as described herein.
[00282] (v) The method comprises formulating more CTLA-4 polypeptides into a composition comprising one or more pharmaceutical acceptable excipients. Such compositions, their use and formulation are described in more detail here. The CTLA-4 polypeptide can be provided in any format described herein, for example, it can be conjugated to an Fc region as described.
A nucleic acid molecule encoding a CTLA-4 polypeptide, for example a CTLA-4 - Fc construct, can be produced. For example, a nucleic acid molecule can encode any amino acid sequence of the CTLA-4 polypeptide or the CTLA-4 amino acid sequence - Fc, according to the invention. The nucleic acid may comprise the nucleic acid sequence deposited under accession number NCIMB 41948 which encodes the 1299 CTLA-4-Ig polypeptide or encodes at least the CTLA-4 polypeptide region thereof. The nucleic acid molecule can be isolated and can be included in a vector, for example, a recombinant vector for expressing the nucleic acid in a cell. An in vitro cell can comprise the vector and can be used for expression of the CTLA-4 polypeptide or CTLA-4 Fc product. The polypeptide can be expressed by the deposited E. coli cell line NCIMB with accession number 41948.
[00284] A CTLA-4 polypeptide as described herein can be produced by a method that includes expression of the polypeptide from encoding nucleic acid. This may conveniently be accomplished by growing a host cell in culture, containing such a vector, under suitable conditions that cause or allow expression of the CTLA-4 polypeptide. CTLA-4 polypeptides can also be expressed in in vitro systems such as reticulocyte lysate. After production of a CTLA-4 polypeptide by expression, its activity, for example, its ability to bind to CD86 or CD80, can be routinely tested.
Systems for cloning and expressing a polypeptide in a variety of different host cells are well known, and can be employed for the expression of the CTLA-4 polypeptides described herein, including CTLA-4 -Fc polypeptides. Suitable host cells include bacteria, eukaryotic cells such as mammalian and yeast, and baculovirus systems. Mammalian cell lines available in the area for expression of a heterologous polypeptide include Chinese hamster ovary cells, HeLa cells, baby hamster kidney cells, COS cells and many others. A preferred common bacterial host is E. coli. Suitable vectors can be shrunk or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator sequences, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate. Vectors can be plasmids, viral, e.g. bacteriophage, or phagemid, as appropriate. Many techniques and protocols for nucleic acid manipulation, for example, in the preparation of nucleic acid constructs, mutagenesis, sequencing, introduction of DNA into cells and gene expression and protein analysis are known.
Generally, the nucleic acid encoding a CTLA-4 polypeptide according to the present invention is provided as an isolate, in isolated and/or purified form, or free or substantially free of contaminants. Nucleic acid can be fully or partially synthetic and can include genomic DNA, cDNA or RNA.
The nucleic acid may be provided as part of a replicable vector, and also provided by the present invention is a vector including nucleic acids encoding a CTLA-4 polypeptide of the invention, particularly any expression vector from which the polypeptide encoded can be expressed under appropriate conditions, and a host cell containing any such vector or nucleic acid. An expression vector, in this context, is a nucleic acid molecule, including nucleic acid encoding a polypeptide of interest and regulatory sequences suitable for expression of the polypeptide, in an in vitro expression system, eg, reticulocyte lysate , or in vivo, for example, in eukaryotic cells such as COS or CHO cells, or in prokaryotic cells such as E. coli.
A host cell may contain nucleic acid as disclosed herein. The nucleic acid of the invention can be integrated into the genome (e.g., chromosome) of the host cell. Integration can be promoted by including sequences that promote recombination with the genome, in accordance with standard techniques. Nucleic acid can be on an extrachromosomal vector within the cell.
Nucleic acid can be introduced into a host cell. Introduction, which may be (particularly for in vitro introduction) generally referred to without limitation as "transformation" or "transfection", may employ any available technique. For eukaryotic cells, suitable techniques may include calcium phosphate transfection, DEAE-Dextran, electroporation, liposome-mediated transfection and transduction using retroviruses or another virus, e.g. smallpox or, for insect cells, baculovirus. For bacterial cells, suitable techniques may include calcium chloride transformation, electroporation and transfection using bacteriophage.
Marker genes such as antibiotic resistance or sensitivity genes can be used in identifying clones that contain the nucleic acid of interest, as is well known in the art.
Introduction can be followed by causing or allowing expression from the nucleic acid, for example, by culturing host cells (which may include actually transformed cells although more likely the cells are descendants of the transformed cells) under conditions for expression of the gene so that the encoded polypeptide is produced. If the polypeptide is expressed coupled to an appropriate signal leader peptide, it can be secreted from the cell into the culture medium. Following production by expression, a polypeptide may be isolated and/or purified from the host cell and/or culture medium, as the case may be, and subsequently used as desired, for example, in formulating a composition which may include a or more additional components, such as a pharmaceutical composition that includes excipients, one or more pharmaceutically acceptable vehicles or carriers (for examples, see below).
The CTLA-4 polypeptide according to the present invention can be isolated and/or purified (for example, using an antibody) for example, after production, by expression from the encoding nucleic acid. Thus, a CTLA-4 polypeptide can be provided free or substantially free of contaminants. A CTLA-4 polypeptide can be provided free or substantially free of other polypeptides. Isolated and/or purified CTLA-4 polypeptide can be used in formulating a composition, which can include at least one additional component, for example, a pharmaceutical composition including a pharmaceutically acceptable excipient, vehicle or carrier. A composition including a CTLA-4 polypeptide according to the invention may be used in prophylactic and/or therapeutic treatment as discussed elsewhere herein.
Accordingly, one aspect of the invention is a composition comprising or consisting of a CTLA-4 polypeptide of the invention, optionally a CTLA-4 polypeptide conjugated to IgG Fc and one or more pharmaceutical excipients. Numerous examples of CTLA-4 polypeptides according to the invention are described herein and any can be conjugated to an Fc region.
[00294] For example, the composition may comprise or consist of:
[00295] a CTLA-4 polypeptide comprising the amino acid sequence SEQ ID NO: 43 (variant 1299), SEQ ID NO: 37 (variant 1322), SEQ ID NO: 38 (variant 1321), SEQ ID NO: 36 (variant 1315), SEQ ID NO: 42 (variant 1115) or SEQ ID NO: 47 (variant 1227), conjugated to an IgG Fc amino acid sequence SEQ ID NO: 59; and
[00296] one or more pharmaceutical excipients.
The composition comprising or consisting of the CTLA-4 Ig 1299 polypeptide encoded by the deposited nucleic acid with accession number NCIMB 41948 and one or more pharmaceutical excipients.
[00298] For example, the CTLA-4 polypeptide can comprise the amino acid sequence SEQ ID NO: 13, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO : 16.
[00299] A composition according to the invention may comprise a CTLA-4 polypeptide at a concentration of at least 70 mg/ml, for example at least 80 mg/ml, at least mg/ml or at least 100 mg /mL. Concentration is calculated as the mass of the polypeptide, including glycosylation, and includes the Fc region when present. The concentration of the polypeptide can be determined by standard methods of spectrophotometric measurement using an extinction coefficient based on the calculated mass of the polypeptide, including glycosylation (if present). Whenever glycosylation is present, it can be considered to be complete. Suitable methods are illustrated in the Examples. For example, an extinction coefficient of 1.09 can be used for concentration determination, as exemplified for CTLA-4-Fc 1299. Formulation and Medical Use
[00300] CTLA-4 polypeptides of the present invention may be administered monthly or less frequently. Low frequency of administration is generally desirable to reduce the burden on patients and clinicians, but may be associated with the risk of less therapeutic efficacy and/or the need to increase the dose of product. Improvements in potency, affinity and/or half-life in accordance with the present invention reduce risks and offer the possibility of lower or less frequent dosing compared to previous administration regimens.
[00301] For many patients, treatment will be required over prolonged periods of time, for example, for many years, and possibly for the entire lifetime of the patient. Therefore, it is anticipated that several doses will be administered. Intervals between dosages can be on the order of days, a week or a month. Preferably, administration is at intervals of at least at or about 14, 21 or 28 days. Preferably, administration to a patient is via subcutaneous delivery with a dosage interval of 28 days or longer, for example, monthly administration.
Administration may be intravenous or by any other appropriate route of administration. For example, CTLA-4 polypeptide can be administered by subcutaneous injection, facilitating self-administration by patients at home and offering the potential advantage of reducing patient visits to the clinic compared to intravenous administration regimens.
Formulating CTLA-4 in small volumes suitable for subcutaneous administration typically requires a higher concentration of CTLA-4 product compared to formulation for intravenous administration. Concentrations of at least 70 mg/ml are typically preferred for subcutaneous administration, more preferably at least 100 mg/ml. Improved stability of CTLA-4 compositions in accordance with the present invention facilitates formulation at a high concentration, for example, for subcutaneous administration.
[00304] Pharmaceutical compositions according to the present invention, and for use according to the present invention, may include, in addition to the active ingredient, an excipient, carrier, buffer, stabilizer or other pharmaceutically acceptable materials well known to those skilled in the art. in technique. Such materials must be non-toxic and must not interfere with the effectiveness of the active ingredient. The precise nature of the carrier or other material will depend on the route of administration, which can be any suitable but most likely route of injection (with or without a needle), especially subcutaneous injection. Other preferred routes of administration include administration by inhalation or intranasal administration.
[00305] For intravenous, subcutaneous or intramuscular injection, the active ingredient will be in the form of a parenterally acceptable aqueous solution that is free of pyrogen and has adequate pH, isotonicity and stability. Those of relevant skill in the art will be well able to prepare suitable solutions using, for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection or Lactated Ringer's Injection. Preservatives, stabilizers, buffers, antioxidants and/or other additives may be included as required.
[00306] The CTLA-4 polypeptide according to the present invention can be used in a method of diagnosis or treatment of the human or animal body, preferably human.
Methods of treatment may comprise administering a CTLA-4 polypeptide according to the invention, for example administering a pharmaceutical composition comprising the CTLA-4 polypeptide. The CTLA-4 polypeptide or composition comprising a CTLA-4 polypeptide as described herein may be for use in a method of treating a patient, either subcutaneously or intravenously.
[00308] A CTLA-4 polypeptide may be administered to an individual, preferably by administering a "prophylactically effective amount" or a "therapeutically effective amount" (as the case may be, although prophylaxis may be considered therapy), this being sufficient to present benefit to the individual. The actual amount administered and the rate and time of administration will depend on the nature and severity of which you are being treated. Prescription of treatment, eg decisions on dosage etc., is the responsibility of general practitioners and other physicians.
[00309] A composition can be administered alone or in combination with other treatments, or simultaneously or sequentially depending on the condition being treated.
CTLA-4 polypeptides are useful for attenuation of the T cell response and thus can be used for the treatment of conditions where attenuation of the T cell response is beneficial. Clinical indications in which a CTLA-4 polypeptide can be used to provide therapeutic benefit include autoimmune diseases and/or inflammatory diseases. Examples of therapeutic indications are rheumatoid arthritis (RA), juvenile rheumatoid arthritis, psoriatic arthritis, psoriasis, multiple sclerosis, asthma, Crohn's disease, lupus nephritis, systemic lupus erythematosus, ankylosing spondylitis, transplant rejection, type I diabetes syndrome Sjogren's and ulcerative colitis, as well as other autoimmune diseases such as alopecia. CTLA-4 polypeptides according to the invention are considered to be particularly suitable for patients with moderate to severe RA.
[00311] Patients treated with CTLA-4 polypeptides or pharmaceutical compositions according to the invention may be those who have moderately to severely active RA despite previous or ongoing treatment with synthetic disease modifying anti-rheumatic drugs (DMARDs) or with biological products other than CTLA-4, for example, other than Abatacept. The CTLA-4 polypeptide according to the invention can be used to treat patients in monotherapy, in combination with conventional DMARDs patients with inadequate responses to conventional DMARDs, or in patients with biological insufficiency.
[00312] The effectiveness of treatment can be monitored and data can be obtained on the progression of joint damage and/or patient function. Examples
[00313] The following CTLA4-Ig sequence has been deposited with NCIMB:
[00314] Escherichia coli DH5a Variant 1299 = NCIMB 41948
[00315] (i) Date of filing = March 13, 2012
[00316] The strategy used to optimize the biological potency of the CTLA-4 Fc fusion molecule consisted of two main activities. One activity was the use of ribosome display to perform directed evolution of the CTLA-4 domain to select a better affinity for CD80 and CD86 ligands, as well as a better stability of this domain. The outputs of the ribosome display selections, which consist of multiple populations of CTLA-4 variants, were sequenced and these unique coding sequences were expressed with an Fc fusion partner for testing directly in in vitro T cell stimulation assays The advantage of this approach is that it classifies several CTLA-4 variants (> 1000 were tested) into a drug format, such as within an Fc domain, which promotes dimerization, in a biologically relevant assay. An additional feature of this strategy was to carry out recombinations of these CTLA-4 mutations that were associated with the improvement of biological function, in order to obtain a greater gain in potency, through synergy.
[00317] This approach was able to simultaneously select for a higher affinity of CTLA-4 variants and for protein stability. Affinity selections employ decreasing concentrations of the target ligand, in this case CD80/86, to selectively enrich the highest affinity CTLA-4 variants. Selections for a better stable use of either a destabilizing agent such as DTT or hydrophobic interaction chromatography (HIC) beads to remove, from the selection set, variants that are less stable or more prone to unfolding. Thus, stability and affinity pressure could be applied to a single selection rather than following parallel approaches.
The second activity was the rational engineering of the Fc domain to introduce mutations known to eliminate Fc-mediated effector functions and to increase the circulating half-life of the molecule in vivo. Different regions of Fc variants were prepared as fusions with CTLA-4 and tested in accelerated in vitro stability studies to select the Fc region with the optimal stability profile.
Following these two parallel activities and subsequent screening, the most potent CTLA-4 domains, as measured by inhibition in various in vitro T cell stimulation assays, were combined with the more stable altered Fc domain, as measured through accelerated in vitro stability studies. Furthermore, in vitro tests for biological potency and protein stability allowed the relative classification of molecules into the final drug format. Example 1 Construction of a library of CTLA-4 variants and selection of ribosomes displayed for increased potency and stability.
Ribosome display was performed on a human domain of monomeric CTLA-4, corresponding to P16410 Swiss-Prot, residues 38-161 of the extracellular domain, without the Fc region attached. This sequence (SEQ ID NO: 35) is also referred to as wild-type CTLA-4. The CTLA-4 ribosome display construct was obtained by cloning the necessary part of human CTLA-4 cDNA into a vector containing regulatory elements at the 5' and 3' ends that are required for ribosome display (Hanes et al, Meth Enzymol (2000) 328:404). This construct comprises a T7 RNA polymerase promoter sequence followed by a prokaryotic ribosome binding site (Shine-Dalgarno sequence) upstream of the CTLA-4 coding sequence. Cysteine at amino acid 120 (or position 157 according to Swiss-Prot P16410 numbering) at the human CTLA-4 dimerization interface was mutated to a serine, in order to avoid dimerization of CTLA-4 molecules in display format of ribosome, which may otherwise interfere with selection for improved CTLA-4 sequences. Downstream of the CTLA-4 sequence, a portion of the filamentous phage gene III protein was included to act as a spacer to allow the CTLA4 variants to be displayed outside the ribosome tunnel. The CTLA-4 ribosome display construct also contained 5' and 3' hairpin loop sequences at the mRNA level to help stabilize mRNA libraries against nuclease degradation. error-prone library
The human CTLA-4 ribosome display construct described above was used as a model, in which there is generation of a library of random variants using error-prone PCR. Error-prone PCR was applied to the CTLA-4 gene using the Diversified Random Mutagenesis PCR Kit (Clontech) according to the manufacturer's instructions. The reactions were adapted to obtain an average of four amino acid mutations per molecule and a library of approximately 2.5x1010 variant molecules. This random mutagenesis procedure was further incorporated into the selection process, where it was applied at the exit of the third round of selection, in order to introduce more diversity into the enriched population of ligands, before proceeding with the selection. Library targeting 'Loop4'
[00322] The CTLA-4 ribosome display construct was also used as a model in which there is generation of a library of variants with targeted mutagenesis to a region of the CTLA-4 molecule, with the potential to contribute to the interaction with CD80 and CD86. The co-crystal structure of human CTLA-4:human CD80 complex (Protein Data Bank (PDB): 1I8L) and human CTLA-4:human CD86 complex (PDB: 1I85) were examined to visualize the binding interaction between the molecules , in particular, the CTLA-4 amino acid side chains, in close proximity to the ligands. A region of the human CTLA-4 protein (SEQ ID 35) comprising amino acid positions 59 to 65 (or positions 96 to 102 according to the SwissProt numbering of CTLA-4 P16410) was seen to form a loop that spans the direction of CD80 and CD86. Each of the residues in this region was completely randomized using saturation mutagenesis (NNS) to create a library of approximately 3.4x1010 variant molecules. This 'Loop 4' library was constructed by standard techniques using the overlapping oligonucleotides (SEQ ID NO: 33 and SEQ ID NO: 34). Selection for improved affinity and stability
Selection to improve binding of CTLA-4 variants to human CD80 and CD86 was performed using ribosome affinity-based selections as described in Hanes et al (Meth. Enzymol. (2000) 328:404). Briefly, CTLA-4 variant DNA libraries were transcribed and then translated into a prokaryotic cell-free translation system, and the translation reactions were disrupted to generate ternary ribosome display selection complexes (mRNA-ribosome -protein), which were then incubated with human CD80 or human CD86 Fc fusion proteins (R&D Systems). CD80 or CD86 binding complexes were captured by incubation with protein G coated on magnetic beads (Dynal) and bound ternary complexes were recovered by magnetic separation, while unbound complexes were washed away. mRNA encoding the linked CTLA-4 variants was recovered by reverse transcription and PCR. To target selection for CTLA-4 variants with binding improvements, the selection process was repeated using decreasing concentrations of CD80 or CD86 over several rounds.
[00324] In conjunction with selection of better affinity for CD80 and CD86, sets of CTLA-4 variants were simultaneously selected by ribosome display for improved stability. In the first rounds of selection (Rounds 1 and 3), DTT was used to apply selection pressure that favored the recovery of the more stable CTLA-4 variants (Jermutus et al., Proc Natl Acad Sci US A. 2001 Jan 2;98( 1): 75-80). A final concentration of 0.5 mM DTT was included in the translation reaction, after the reaction was incubated with a suspension of Sepharose beads (GE Healthcare) from hydrophobic interaction chromatography (HIC), also in the presence of 0.5 mM of DTT. The HIC step was used to capture the misfolded variants and remove them from the reaction by centrifugation, prior to incubation with CD80 and affinity selection as described above. Hotspot Mutagenesis Library and Rational Recombination of Key Mutations
[00325] After initial screening of CTLA-4 variants from error-prone PCR and Loop4-directed libraries, mutations associated with improved activity were identified and used to design new CTLA-4 variants. In one strategy, a Hotspot mutagenesis library was constructed, in which positions 16, 25, 58, 70, 85 and 93 of SEQ ID NO: 35 (or positions 53, 62, 95, 107, 122 and 130, according to the SwissProt numbering of CTLA-4 P16410) were completely randomized in a single library using saturation mutagenesis (NNS). The library was created using the overlapping and mutagenic oligonucleotides (SEQ ID NO: 61 to SEQ ID NO: 67 inclusive). This library was then selected to improve affinity as described above.
[00326] In an alternative approach, a smaller number of mutations, identified from error-prone Hotspot and Loop4 mutagenesis libraries, which were associated with improved activity, were combined by oligonucleotide-directed mutagenesis to create rational recombinants that were then directly tested for biological activity. The mutations chosen for this strategy were: I16S, S25N, S25P, G27S, M54K, N56S, L58G, T59S, F60T, L61Q, L61P, D62G, D63Y, S64P, I65N, I65V, S70A, Q80R, M85S and K93Q (or, numbered according to CTLA-4 SwissProt P16410: I53S, S62N, S62P, G64S, M91K, N93S, L95G, T96S, F97T, L98Q, L98P, D99G, D100Y, S101P, I102N, I102V, S107A, Q117R, MQ12)2S and . Example 2 Expression of wild-type and variant CTLA-4 as Fc fusion proteins
The CTLA-4 variant genes from the display ribosome selections were cloned into the pEU7.1 vector. This vector allows expression of the CTLA-4 gene as an in-frame fusion with the IgG1 Fc region (SEQ ID NO:56). The resultant from the display ribosomes was amplified by PCR and cloned into pEU7.1, before transformation into DH5-alpha E. coli cells. The oligonucleotides used for the PCR cloning were also designed to reverse the serine at position 120 (residue 157 according to Swiss-Prot P16410 numbering) to the wild-type amino acid cysteine. After sequencing individual transformants, a total of over 1000 variants with unique CTLA-4 amino acid sequences were selected for protein expression. In lots of 88 variants, plasmid encoding DNA was purified following supplier protocols (Qiagen) and quantified by spectrophotometry at 260 nm so that the DNA concentration can be used to calculate the proper amount of DNA for transfection. Expression, purification and quantification of CTLA-4 proteins from 24-well plates
[00328] 3 ml Chinese hamster ovary (CHO) cells (ECACC) were grown at 1 million cells per ml in separate wells of a 24-well plate (Whatman 734-2558) in CD-CHO medium (Invitrogen 10743-029) containing 25 µM L-methionine sulfoximine (Sigma M5379). 24-well plates containing cells were sealed with a breathable lid (Applikon biotechnology, Z365001224) and placed in a deep-well plate clamp (Applikon biotechnology, Z365001700). Cells were shaken at 250 rpm, 80% humidity, 5% CO2 and 37 °C. For transfection, 50 µL of 150 mM NaCl containing 3 mg plasmid DNA was mixed with 50 µL containing 21 µg linear PEI of 25 kDa (Polysciences, 23966). The DNA-PEI complex formed was added to the cells, allowing no more than 15 minutes between the start of complex formation and addition to the cells. 16 to 24 hours after transfection, cells were fed by adding 300 µl/well of CD-CHO Efficient Feed B (Invitrogen A10240). Plates were shaken at 250 rpm, 80% humidity, 5% CO2 and 37 °C for an additional 5 to 6 days to allow protein expression into the growth medium. After expression, spent culture medium containing protein was clarified by centrifugation at 3000 rpm for 10 minutes. Clarified supernatants (1.2 mL) were redistributed to 96-well Filter Pads (3M Empore, 12146036) using the Freedom Evo® liquid handling robot (Tecan). Residual cell ethritus was removed by filtration using a vacuum pump and a QIAvac 6S Manifold vacuum (Qiagen). 1.8 ml of clarified and filtered supernatant was processed for purification performed on a liquid handling robot (Perkin Elmer) Minitrack (RTM) using PhyTip Protein A (RTM) affinity columns (Phynexus, PTP-92-20-01) , 20μL resin bed volume). PhyTip (RTM) columns were conditioned by 500 µL 20 mM NaP pH 7.0. PhyTip (RTM) columns were then loaded by passage of crude supernatants in batches of 6x300 μL, washed with 200 μL of D-PBS, 200 μL of 20 mM NaP, pH 7.0, eluted with 120 µL of 100 mM HEPES 140 mM NaCl pH 3 and neutralized with 20 µL of 1M HEPES pH 8.0.
The purified proteins were transferred to a 96-well black polypropylene plate (Greiner, 655209), followed by the addition of 145 µL PBS, 0.02% Tween20, 1 mg/mL BSA, sodium azide buffer at 0.05% (octet buffer). A standard curve was generated using previously purified wild-type CTLA-4 Fc fusion protein in identical buffer. A set of standard concentrations were prepared on the black polypropylene plate in a volume of 150 µL with an initial concentration of 500 µg/mL and 3 dilutions. Using Octet RED Protein A coated biosensors (ForteBio Inc., 18-0004) quantitation was performed using 120 sec read time at a flow rate of 200 rpm. A column of 8 biosensors was used for each 96-well plate of samples. Biosensors were regenerated by adding 200 µL of 10 mM glycine pH1.7 (Sigma, L-7403) to the 96-well plate. Biosensors were neutralized before processing the next samples, adding 200 µL of Octet buffer. 3 cycles of regeneration/neutralization were performed with a time of 30s and a flow rate of 200rpm. The concentrations of the unknown samples were determined by comparing the binding rates between the standard and the unknown curve using the Octet RED data analysis software package. Larger scale expression, purification and quantification of CTLA-4 proteins
[00330] For larger scale preparation of CTLA-4 proteins as Fc fusions, the same general steps as used for the 24-well plate method were applied. Plasmids containing the CTLA-4 variant gene, such as an in-frame fusion to IgG1 Fc, were prepared from E. coli cells. For protein preparation at >100 mg scale, the entire construct containing the CTLA-4 gene directly in frame with the IgG1 Fc gene was prepared by gene synthesis. In all cases, plasmid DNA encoding the protein of interest was prepared and transfected into CHO cells for expression. In place of the 24-well plates, a greater volume of cells were grown in tissue culture flasks or in wave bags, prior to purification from the culture supernatants. Crops were pooled and filtered prior to purification by protein A chromatography. Culture supernatants were loaded onto an appropriately sized Protein A ceramic column (BioSepra) and washed with 50 mM Tris-HCl pH 8.0, 250 mM NaCl. Bound IgG was eluted from the column using 0.1 M sodium citrate (pH 3.0) and was neutralized by the addition of Tris-HCl (pH 9.0). The eluted material was exchanged in buffer to PBS using Nap10 columns (GE, 17-0854-02) and the IgG concentration was determined spectrophotometrically using an extinction coefficient based on the amino acid sequence of the protein. Purified proteins were analyzed for aggregation or degradation using SEC-HPLC and SDS-PAGE. Example 3 Biological activity of CTLA-4 variants in a dual Raji cell (B cell) and Jurkat (T cell) assay
The screening strategy described here includes measuring the biological activity of over 1000 CTLA-4 variants, expressed with an Fc fusion partner, in an in vitro T cell stimulation assay. CTLA-4 variants of all different mutagenesis strategies (including error-prone PCR, targeted mutagenesis, hotspot recombination, and rational recombination) were tested for biological activity and classified according to their biological activity relative to wild-type CTLA- 4 (SEQ ID NO: 35) also expressed in Fc fusion format.
[00332] To determine the biological activity of CTLA-4 variants, samples were added to a dual cell assay consisting of Raji cells (B cells) and Jurkat cells (T cells). The interaction of CD28, expressed by Jurkat cells, with ligands CD80 (B7-1) and CD86 (B7-2), expressed on Raji cells, combined with a co-activation signal for the T cell receptor (such as the PHA (phytohemagglutinin)) results in the release of interleukin-2 (IL-2) from Jurkat cells. Soluble CTLA-4 can bind to CD80 and CD86 ligands, blocking its interaction with CD28 and attenuating this response. Thus, potency of CTLA-4 Ig Ig clones is determined by inhibition of IL-2 release from T cells, as measured by an IL-2 HTRF assay (CisBio 64IL2PEC).
[00333] 384-well low protein binding plates (Greiner # 781280) were used to run eleven 1 in 3 serial dilutions of assay samples, which were made in complete growth medium (RPMI 1640 Glutamax, Invitrogen # 61870, 10% FBS, 1% Penicillin/Streptomycin, Invitrogen # 15140). All sample dilutions were made in duplicate from the 5-30 µg/ml top sample concentration in the cells.
The Raji and Jurkat suspension cells were transferred from culture flasks to centrifuge flasks and centrifuged at 240g for 5 minutes. Both cell lines were resuspended at a concentration of 750,000 cells/ml in growth medium and plated in each at 0.02 ml/well (l= 15,000 cells/cell line/well) into a Maxisorp 384-well plate (Nunc 464718 ). 0.02 mL was transferred from sample dilution plates to cell plates and 0.02 mL and 40 μg/mL of PHA (Sigma # L-1668) (or 0.02 mL of medium to control wells negative) was added to all other wells to give a final concentration of 10 µg/ml and incubated at 37°C with 5% CO2.
After 20 to 24 hours, cell supernatants were collected and IL-2 secretion was measured using a commercial HTRF IL-2 kit (CisBio 64IL2PEC). Briefly; a 'master mix' of anti-hIL-2 cryptate (fluorophore donor) and anti-Hil-2 d2 (recipient fluorophore) was performed by 1/200 dilution in freshly constituted conjugate buffer (0.2% BSA/0, 8M KF/PBS). An eight-point standard curve was generated using IL-2 (NIBSC # 96/504) diluted 1 in 2 in medium with a higher concentration of 2 ng/ml. Equal volumes of the reagent master mix and samples were mixed in a 384-well low volume assay plate (Costar 3676) and incubated 3-168 hours at room temperature. Plates were read on an Envision (Perkin Elmer) using an excitation wavelength of 320 nm and emission wavelengths of 620 nm and 665 nm.
[00336] Specific binding and % delta F values were calculated for each well as follows: % Delta F = (Sample Ratio A665/A620 - Ratio NSB A665/A620) X 100 (Ratio NSB A665/A620) % binding specifies = (% Sample Delta F - % NSB Delta F) X 100 (% Total Delta F - % NSB Delta F)
[00337] Wells with only medium (Min/non-specific binding (NSB)) were used as reference and wells with only PHA (Max/Total) were used to determine the maximum signal for the assays. Results were analyzed using GraphPad Prism software (v5.01) and IC50 concentrations were determined using a non-linear regression curve-fitting model (Log [inhibitor] vs response with variable slope) using the least squares method. of adjustment.
The following table summarizes the number of CTLA-4 variant molecules classified as having a significant improvement in biological potency over wild-type CTLA-4 (SEQ ID NO:35) also expressed in the Fc fusion format:

Following retesting of these 107 CTLA-4 variants, precise IC50 measurements were determined and the improvement in folding over wild-type CTLA-4 (SEQ ID NO:35) in the Fc fusion format was calculated . The table below summarizes these data for some of the most potent CTLA-4 variants of each of the mutagenesis strategies.



[00340] The sequences of these CTLA-4 variants are shown in Figure 1A.
The IC50 profiles of 6 of the most potent CTLA-4 and wild-type CTLA-4 variants (SEQ ID NO: 35) in Fc fusion format in the Raji-Jurkat dual cell assay are shown in Figure 3A. Example 4 Biological Activity of CTLA-4 Variants in a Dual Assay of Raji Cells (B Cells) and Human CD4+ T Cells
Human blood was collected in a CPT Vacutainer tube (BD Biosciences) and 400 µL of CD4+ RosetteSep purification reagent (Stem Cell Technologies) was added. After a 20 minute incubation, the tubes were centrifuged at 1700g for 25 minutes. Cells were collected and transferred to a 50 ml tube and centrifuged at 350g for 10 minutes. Red blood cells were lysed by resuspension in 20 ml Vitalizar reagent and incubated for 30 minutes to 1 hour. Cells were then centrifuged at 350 g for 10 minutes and washed once with T cell media (Xvivo-15 media (Lonza), supplemented with 1% Anti/anti (Invitrogen)). One million cells per ml suspension of Raji cells and primary human CD4+ T cells was prepared in complete T cell medium and kept separate until ready to add to the 96-well assay plate. In a separate (low protein binding) 96-well plate, dilutions of CTLA-4 variant molecules were made in complete T cell medium, starting with an initial concentration of 100 µg/ml and making twelve 1:5 dilutions in series. 100 µL of each of the four concentrations of CTLA variants was dispensed into tissue culture in a 96-well assay plate. The suspension of Raji cells and human CD4+ T cells were mixed in a ratio of 1:1 and the anti-CD3 antibody (clone UCHT1 (BD Bioscience)) was added to a final concentration of 10 µg/ml. 100 µL of the cell suspension was dispensed into each well containing the CTLA-4 variants and incubated for 18 to 24 hours. Plates were then harvested by centrifugation at 350g for 5 minutes and the supernatant transferred to a new 96-well plate. IL-2 secretion was measured using a human IL-2 DuoSet kit according to the manufacturer's protocol (R&D Systems).
A potency comparison with wild-type CTLA-4 (SEQ ID NO: 35) in Fc fusion format in the human primary CD4+ T cell assay for 6 of the most potent CTLA-4 variants is shown in Figure 3B . Example 5 Biological activity of CTLA-4 variants of a mixed lymphocyte reaction using cynomolgus monkey peripheral blood mononuclear cells
Cynomolgus monkey blood from two separate animals was collected in Vacutainer CPT tubes (BD Biosciences) and centrifuged at 1700g for 25 minutes. Cells were collected and transferred to a 50 ml tube and centrifuged at 350 g for 10 minutes. Red blood cells were lysed by resuspension in 20 ml Vitalizar reagent and incubated for 30 minutes to 1 hour. Cells were then centrifuged at 350 g for 10 minutes and washed once with T cell media (Xvivo-15 media (Lonza), supplemented with 1% Anti/anti (Invitrogen)). In a separate (low protein binding) 96-well plate, dilutions of CTLA-4 variant molecules were made in complete T cell medium, starting with an initial concentration of 100 µg/ml and making twelve 1:5 dilutions in series. 100 µL of CTLA-4 Ig dilutions were dispensed into tissue culture 96-well assay plate. The PBMC cell suspension from each animal was mixed at a ratio of 1:1 and 100 µl of the cell suspension was distributed to all wells containing the CTLA-4 Ig dilutions and incubated for 24 hours. Plates were then harvested by centrifugation at 350g for 5 minutes and the supernatant transferred to a new 96-well plate. IL-2 secretion was measured using a cynomolgus IL-2 ELISA kit, according to the manufacturer's protocol (MABTech).
A comparison of potency with wild-type CTLA-4 (SEQ ID NO: 35) in Fc fusion format in the Cynomolgus Monkey Mixed Lymphocyte Reaction Assay for two of the most potent CTLA-4 variants is shown in Figure 3C. Example 6 Specificity of variant binding to CD80 and CD86
CTLA-4 variants were labeled with horseradish peroxidase using the activated HRP labeling kit (Pierce). Fc fusion protein from extracellular domains of B7 family members (R&D Systems) was coated overnight at a concentration of 5 µg/ml in PBS on the Maxisorp plate (Nunc). Plates were blocked with 1% BSA and HRP-labeled CTLA-4 variants were added at various concentrations and the amount of bound protein was determined using a colorimetric substrate (BD OptEIA substrate, BD Biosciences).
The specificity of two of the most potent CTLA-4 variants for CD80 and CD86, compared to other related protein ligands, is shown in Figure 4. Example 7 Analysis of Fc-mediated effector functions
[00348] Antibody-dependent cell-mediated cytotoxicity assay (ADCC)
Human blood was collected in Vacutainer CPT tubes (BD Biosciences) and centrifuged at 1700g for 25 minutes. Cells were collected and transferred to a 50 ml tube and centrifuged at 350g for 10 minutes. Red blood cells were lysed by resuspension in 20 ml Vitalizar reagent and incubated for 30 minutes to 1 hour. Cells were then centrifuged at 350 g for 10 minutes and washed once with T cell media (Xvivo-15 media (Lonza), supplemented with 1% Anti/anti (Invitrogen)). 500,000 PBMC were plated on 200 µL Xvivo-15 media in the presence of various antibodies and Fc fusion proteins. After 24 hours of incubation, B lymphocyte viability was determined by flow cytometry by staining with anti-CD19 antibodies (BD Biosciences) and 7-AAD (Molecular Probes). The number of viable B cells was calculated for each sample by multiplying 500,000 by the percentage of viable cells by the front/side scattering properties which were also CD19+ and 7-AAD-. Complement Dependent Cytotoxicity Assay (CDC)
Human serum was collected in serum separator tubes and added to Xvivo-15 medium at a final concentration of 10% w/v. 100,000 Raji B cells were incubated for 18 hours in medium containing different antibodies and Fc fusion proteins. Raji cell viability was determined using flow cytometry by staining with 7-AAD (Molecular Probes). The number of viable cells was calculated for each sample by multiplying 100,000 by the percentage of viable cells by the front/side diffusion properties which were also 7-AAD-. Medium containing human serum, which were previously heat inactivated for 30 minutes at 56 °C was used as a control to confirm complement-mediated cell cytotoxicity. A demonstration of the null effector function (ADCC and CDC) for two of the most potent CTLA-4 variants with TM modification is shown in Figure 5. Example 8 Kinetic analysis of binding of CTLA-4 variants to human, cynomolgus monkey and mouse CD80 and CD86 Cloning and expression of CD80 and CD86
cDNA molecules encoding the extracellular domains (ECDs) of human and mouse CD80 and CD86 were synthesized by cloning PCR primer extension and cloned into pDONR221 (Invitrogen Cat. No.12536-017). Database sequences were used for human and mouse CD80 and CD86 (see Table 1). Cynomolgus monkey sequences were not available, so based on the high homology between cynomolgus monkey and Rhesus monkey, Rhesus monkey CD80 (accession number ENSMMUG00000016367) and CD86 (accession number ENSMMUG00000000912) were used to design primers capable of amplifying the coding gene sequence in cynomolgus monkeys.
The cDNA fragments coding for the extracellular domains were then transferred to the mammalian expression vector pDEST12.2 (Invitrogen), using the clonase II enzyme from LR Gateway, according to the manufacturer's instructions (Invitrogen Cat. No. 12538-120). The pDEST12.2 vector was modified to include a 10xhis FLAG tag (DYKDDDDKAAHHHHHHHHHH) in frame with the gene of interest inserted, and also by inserting the oriP origin of replication from the pCEP4 vector (Invitrogen cat. No. V044-50), which allows the episomal plasmid replication after transfection of cell lines expressing the EBNA-1 gene product (such as HEK293-EBNA cells). Protein expressed in HEK293-EBNA supernatant was purified using Ni-NTA affinity chromatography (HisTrap HP column (GE Healthcare cat. No. 17-5248-02)) followed by size exclusion chromatography (Superdex 200 column (GE Healthcare) cat. No.17-1069-01)). CD80 extracellular domains
CD86 extracellular domains
Surface plasma resonance (SPR) analysis of binding affinity
The SPR analysis of CTLA-4:CD80 and CD86 interactions was performed on a Biacore 2000 SPR machine. About 200 RU of CTLA4 variants were covalently coupled through primary amine groups to a CM5 Biacore chip (GE Healthcare cat. No. BR-1000-1014) using an amine coupling kit (GE Healthcare cat. No. BR- 1000-1050). CD80 and CD86 titrations in HBS-EP buffer (GE Healthcare cat. No. BR-1001-1088) were performed on immobilized CTLA-4 variants. All traces were double subtracted from the reference. The analysis was performed using Biacore's evaluation software, using a 1:1 mixture of Langmuir model to fit the association and dissociation constants. Where the variants had a very fast equilibrium kinetic analysis.
The monovalent affinity (Kd in nM) of selected CTLA-4 and wild-type CTLA-4 variants (SEQ ID NO:35) in Fc fusion format for human, cynomolgus monkey and rat ligands is shown below.


Improvements in affinity (improvement in folding over wild-type CTLA-4 in Fc fusion format) of selected CTLA-4 variants for human, cynomolgus monkey and rat ligands are shown below.

It was noted that these variants, which were the most potent variants tested in the biological activity assays, demonstrated greater affinity gains for human CD80 ligand than human CD86 ligand (as summarized in Figure 6). A similar pattern of greater affinity gain for CD80 over CD86 was observed using the cynomolgus ligands. Example 9 Accelerated Stability Studies of Wild Type CTLA-4 with Fc Mutations Expression, Purification and Quantitation of CTLA-4 Proteins
The cDNA encoding the extracellular domain of native CTLA4 fused to Fc 1 to 4 variants was cloned into pEE 12.4 (Lonza) and expressed in CHO cells. Briefly, 1 x 106 CHOK1SV cells (Lonza) were transfected with nucleofection (Lonza) using the U-024 program and Solution V with 5 mcg of linearized plasmid DNA. After transfection, cells were cultured in CD-CHO (Invitrogen), 1 x GS supplement and 50 μM MSX. Cells began to grow approximately 2 weeks after transfection, at which time they were expanded into shake flasks for protein production. For purification, a series of steps were used starting with a MabSelect capture step, followed by a SuperQ anion exchange polishing step, followed by SEC for the removed aggregates. Proteins were stored in phosphate buffered saline (PBS) pH 7.2. Stability Studies
[00358] Stability studies were performed on CTLA-4 molecules fused with different Fc variants to compare their stability and to determine the most stable Fc configuration. Molecules that were tested include: CTLA-4 Fc variant-1 (SEQ ID NO: 7); CTLA-4 Fc variant-2 (SEQ ID NO: 8); CTLA-4 Fc variant-3 (SEQ ID NO: 9); and CTLA4 Fc variant-4 (SEQ ID NO: 10). Amino acid differences in the Fc region are highlighted in Figure 1B for variant Fc-1 (SEQ ID NO: 57), Fc variant-2 (SEQ ID NO: 58), Fc variant-3 (SEQ ID NO: 59) and Variant Fc-4 (SEQ ID NO: 60).
[00359] CTLA-4 Fc variant-1 (SEQ ID NO: 7) is the Abatacept molecule, comprising the wild type CTLA-4 (SEQ ID NO: 35) fused to an IgG1 Fc region with a modified hinge (SEQ ID NO: 57).
CTLA-4 Fc variant-2 (SEQ ID NO: 8) is Abatacept modified to incorporate a YTE mutation in the Fc region and comprises the wild type CTLA-4 (SEQ ID NO: 35) fused to IgG1 Fc with a modified hinge and a YTE mutation (SEQ ID NO: 58).
CTLA-4 Fc variant-3 (SEQ ID NO: 9) comprises wild type CTLA-4 (SEQ ID NO: 35) fused to IgG1 Fc in which the observed C>S mutations in Abatacept are reversed, comprising a wild-type hinge, and which further includes a triple mutation (TM) and YTE mutation (SEQ ID NO:59).
CTLA-4 Fc variant-4 (SEQ ID NO: 10) comprises wild type CTLA-4 (SEQ ID NO: 35) fused to IgG4 Fc comprising a YTE mutation and a hinge region comprising the proline mutation at position 111 (SEQ ID NO: 60).
Position 111 in the Swiss Prot numbering corresponds to residue 14 of the corresponding IgG1 sequence SEQ ID NO: 56 as shown in Figure 1, or residue 228, in the full length of the IgG4 constant region. The introduction of a serine to proline mutation at this position is known to stabilize the inter-chain disulfide interaction and therefore minimize the formation of IgG4 molecules (Aalberse and Schuurman, Immunology 105(1):9-19 2002; Van der Neut Kolfschoten et al, Science 307(5844):1554-7 2007; Angal et al, Mol Immunol 30(1):105-8 1993; Schuurman et al Mol Immunol 38(1):1-8 2001), thus , minimizes the challenges associated with drug candidate development. Furthermore, as this proline residue is in the corresponding position of IgG1, no immunogenicity problems are anticipated.
The molecules were received in liquid form at ~10 mg/ml in PBS buffer. The four molecules were concentrated using Amicon μltra centrifugal filters, 30,000 MW cut-off. Molecules were centrifuged at 4200 g until target volume was reached (30 - 60 minutes). Concentrations were measured spectrophotometrically using a standard antibody extinction coefficient of 1.4. Final concentrations were calculated to be between 71-85 mg/ml. Although in the present example an antibody extinction coefficient of 1.4 was used, the actual polypeptide extinction coefficient was subsequently determined to be closer to 1.1. These calculated concentrations actually represent a concentration range of 91-108 mg/mL. A higher concentration can be achieved if desired by continuous ultrafiltration, subject to volume restrictions.
Samples of each Fc variant were incubated at 5°C and 25°C for 1 month. High performance size exclusion liquid chromatography (SE-HPLC) was the stability assay used to determine and compare degradation rates for the four molecules. SE-HPLC was performed according to SOP DV-9525 with a flow rate of 1 ml/min. Any peak that elutes before the monomer peak (with an elution time less than that of the monomer) in the HPLC chromatogram is designated as an aggregate peak. Any peak that elutes after the monomer peak (with an elution time longer than the monomer) is designated as a fragment peak. The total percentage of fragment and aggregate is determined by the area of the aggregate peak(s) and the fragment peak(s) as a fraction of the total area of all protein peaks in the chromatogram. Prior to incubation, SE-HPLC was run on all samples for time 0. Thereafter, SE-HPLC data were collected every week during the 25°C stability study and every 2 weeks for the stability study at 5°C. The total duration for both studies was 1 month. Shown below are the aggregation, fragmentation, and degradation rates, calculated using a linear fit to one-month data. Fees after 1 month at 5 °C
Rates after 1 month at 25 °C

Based on these data, Fc variant-3 (SEQ ID NO:59) was chosen as the ideal fusion partner based on the lowest purity loss rates at both 5°C and 25°C. Example 10 - Accelerated Stability Studies of CTLA-4 Variants Fused with Fc Variant-3
Stability studies were performed on 6 of the most potent variant CTLA-4 molecules fused to Fc variant-3 (SEQ ID NO:59) to determine the most stable CTLA-4 variant. The molecules that were tested in this format were: variant 1115 (SEQ ID NO: 15), variant 1227 (SEQ ID NO: 16), variant 1299 (SEQ ID NO: 13), variant 1315 (SEQ ID NO: 14), variant 1321 (SEQ ID NO: 12), variant 1322 (SEQ ID NO: 11).
The molecules were received in liquid form at ~10mg/ml in PBS buffer. The 6 molecules were concentrated using Amicon μltra centrifugal filters, 30,000 MW cutoff. The molecules were centrifuged at 4200g until the target volume was reached (30 - 60 minutes). Extinction coefficients were calculated using amino acid sequences. The calculated extinction coefficients were 1.10 for 1315 and 1321; and 1.09 for 1115, 1227, 1299 and 1322. Concentrations were measured using the appropriate extinction coefficient. Final concentrations were between 94.6 - 101.6 mg/ml.
[00369] The stability studies were performed at 5 °C and 25 °C following the same guidelines described in the previous section, with the exception of collecting only 0 and 1 month for the stability study at 5 °C. The total duration for both studies was 1 month. Shown below are the aggregation, fragmentation, and degradation rates, calculated using a linear fit to one-month data. Rates after 1 month at 25 °C
Fees after 1 month at 5 °C

Variants 1299 and 1322 were found to have lower levels of loss of purity, in studies at both 5°C and 25°C in more than 1 month. Thus, the stability studies were extended to 6 months at 5 °C for the 1299 and 1322 variants. Shown below are the results obtained from the monthly time points. 1299 stability data at 5°C
% Loss of Purity/year, calculated from linear data = 3.6% Stability data 1322 at 5 °C
% Loss of Purity/year, calculated from linear data = 2.6% Example 11 - Construction of a tetravalent CTLA-4 molecule Design and construction of tetravalent CTLA-4 expression vectors
Using the nitrophenol IgG linker NIP 74 (heavy chain SEQ ID NO: 17; light chain SEQ ID NO: 18) as a support, tetravalent CTLA-4 was produced by fusing CTLA-4 with the amino terminus of both VH and VL chain antibodies (Figure 7A). Expression constructs were produced by fusing CTLA-4 with the VH and VL using a 2-step PCR strategy and then subcloning the PCR products into IgG expression vectors containing the constant domains of antibodies. The primary PCR amplified CTLA-4 and IgG VH and VL with the gene specific primers (SEQ ID NOS 21-28), which was added a flexible linker at the 3' end of CTLA-4 and at the 5' end of VH and VL . Secondary PCR pull-through linked CTLA-4 to the 5' end of VH and VL by hybridization of complementary binding sequences. The final CTLA-4-VH construct was amplified using primers that introduced a BssHII site at the 5' end and a BstEII site at the 3' end (SEQ ID NOS 29-30). The final CTLA-4-VL construct was amplified using primers that introduced an ApaLI site at the 5' end and a PacI site at the 3' end (SEQ ID NOS 31-32). The PCR products were then digested with the respective restriction enzymes before being ligated directly into the pre-digested IgG expression vectors, pEU1.4 for the CTLA-4-VH cassette and pEU3.4 for the CTLA cassette -4-VL, and used to transform chemically competent E. coli DH5-alpha cells. Correct clones, corresponding to SEQ ID NOS 19 and 20, were identified by sequence analysis for expression studies. Expression and purification of tetrameric CTLA-4
For both plasmids required for transfection, one encoding CTLA-4 heavy chain fusion protein and one encoding CTLA-4 light chain fusion protein, a single colony was used to inoculate 100 mL of 2xTY broth containing 100 μg/mL ampicillin. Cultures were incubated overnight (16 hours) at 37°C and 300 rpm. Plasmid DNA was isolated from the bacterial pellet using the EndoFree Plasmid Maxi Kit (QIAGEN; 12362) following the manufacturer's instructions. On the morning of the day of transfection, CHO cells were grown at one million cells per ml in CD-CHO medium (Invitrogen; 10743-029) containing 25 µM L-methionine sulfoximine (Sigma; M5379). Cells were grown in a volume of 500 ml and incubated at 37°C, 140rpm, 80% humidity and 5% CO2. In order to form DNA-PEI complexes for transfection, 250 µg of each vector was mixed and diluted in 150 mM NaCl to yield 500 µg of DNA in a final volume of 1 ml. The DNA was then mixed with 1 ml of 5 mg/ml PEI (Polysciences, 23966) diluted in 150 mM NaCl and incubated at room temperature for 1 minute. The DNA-PEI mixture was then carefully added to the CEP6 culture which was then incubated for 24 hours before adding 150 μl of efficient CD-CHO B feed (Invitrogen; A10240). The culture was then incubated for another six days.
The culture was centrifuged at 2000g for 30 minutes; the clarified culture supernatant was then filtered through 500 ml Stericup (Millipore; SCGVU05RE). Purification of tetravalent CTLA-4 from the clarified culture supernatant was performed using an ÃKTApurifier 10 system (GE Healthcare; 28-4062-64) and affinity chromatography followed by gel filtration chromatography. 5 ml of MabSelect Claro column (GE Healthcare; 11-0034-94) was equilibrated with ten volumes of D-PBS column (Invitrogen; 14040-174). The clarified culture supernatant was passed over the column before the column was washed with more than ten volumes of D-PBS column. Bound protein was eluted with 0.1 M glycine, pH 2.7 and 1 ml fractions were collected. Each fraction was neutralized with 100 µl of 1M Tris, pH 10 and the fractions containing the eluted protein were pooled and concentrated to 2 ml using the Vivaspin, 10,000 MWCO filtration unit (Sartorius Stedim; VS2002) following the manufacturer's instructions. 2 ml of the concentrated sample was loaded onto a HiLoad 16/60 Superdex 200 gel filtration column (GE Healthcare; 17-1069-01), which had been equilibrated in D-PBS. During the entire process 1.2 ml fractions were collected. Fractions containing the correct molecular weight target protein (56 ml retention volume) were pooled, concentrated to 1 ml using Vivaspin, 10,000 MWCO filter units and stored at -80°C.
Purified tetrameric CTLA-4 was profiled alongside wild-type CTLA-4 (SEQ ID NO: 35) in Fc fusion format in the Raji-Jurkat dual cell assay and the data is shown in Figure 8. IC50 values in the tetrameric CTLA-4 assay and wild-type CTLA-4 (SEQ ID NO: 35) in Fc fusion format were 1.93 nM and 11.39 nM, respectively. This indicates a 5.9-fold gain in potency over converting a dimeric Fc fusion format to a tetrameric, IgG-like format.

权利要求:
Claims (13)
[0001]
1. Isolated CTLA-4 polypeptide having greater binding affinity for human CD80, greater potency and/or greater stability compared to wild-type CTLA-4 SEQ ID NO: 35, characterized in that the polypeptide comprises the amino acid sequence of SEQ ID NO: 43.
[0002]
2. CTLA-4 polypeptide according to claim 1, characterized in that it has an affinity of 50 nM or less for binding to human CD80, wherein the affinity is KD as determined by surface plasma resonance, optionally wherein the polypeptide has an affinity of 20 nM or less for binding to human CD80.
[0003]
3. CTLA-4 polypeptide according to claim 1 or 2, characterized in that the polypeptide has a higher affinity than wild-type CTLA-4 (SEQ ID NO: 35) for binding to human CD86.
[0004]
4. CTLA-4 polypeptide according to any one of claims 1 to 3, characterized in that it has at least 10 times more affinity to bind CD80 than to bind CD86, optionally wherein the peptide has at least 50 times more affinity to bind CD80 than to bind CD86.
[0005]
5. CTLA-4 polypeptide according to any one of claims 1 to 4, characterized in that it is conjugated to an IgG Fc amino acid sequence, optionally wherein the IgG Fc is human IgG1 Fc modified to reduce Fc effector function and comprises a native human IgG1 Fc hinge region, optionally wherein the IgG Fc amino acid sequence comprises a human IgG1 Fc region wherein one or more of the following residue groups are substituted as follows: F at residue 20; And at residue 21; S at residue 117; and Y at residue 38, T at residue 40, E at residue 42, The residue numbering being defined with reference to SEQ ID NO: 56.
[0006]
6. CTLA-4 polypeptide according to claim 5, characterized in that the IgG Fc amino acid sequence is SEQ ID NO: 59.
[0007]
7. CTLA-4 polypeptide according to any one of claims 1 to 6, characterized in that the polypeptide comprises the sequence of SEQ ID NO: 13.
[0008]
8. CTLA-4 polypeptide according to any one of claims 1 to 7, characterized in that the polypeptide is in a multimer, optionally wherein the CTLA-4 polypeptide is in a dimer or tetramer, the tetramer comprising two pairs of CTLA-4 polypeptides, each pair comprising a CTLA-4 polypeptide fused to an antibody light chain constant region and a CTLA-4 polypeptide fused to an antibody heavy chain constant region.
[0009]
9. Host cell containing the nucleic acid, characterized in that the nucleic acid encodes a CTLA-4 polypeptide or CTLA-4 IgG Fc fusion protein as defined in any one of claims 1 to 8, wherein the host cell is selected from the group of: bacteria, yeast and baculovirus systems.
[0010]
10. A composition characterized in that it comprises: a CTLA-4 polypeptide or CTLA-4 IgG Fc fusion protein as defined in any one of claims 1 to 8; and one or more pharmaceutical excipients.
[0011]
11. Composition according to claim 10, characterized in that it comprises the CTLA-4 polypeptide or CTLA-4 IgG Fc fusion protein at a concentration of at least 70 mg/ml, optionally a a concentration of at least 100 mg/ml.
[0012]
12. Use of a CTLA-4 polypeptide or CTLA-4 IgG Fc fusion protein as defined in any one of claims 1 to 9 or a composition as defined in claims 10 or 11, characterized in that it is in the preparation of a drug for therapy of a patient by subcutaneous or intravenous administration.
[0013]
13. Use of a CTLA-4 polypeptide or CTLA-4 IgG Fc fusion protein as defined in any one of claims 1 to 9 or a composition as defined in claims 10 or 11, characterized in that it is in the preparation of a drug to treat rheumatoid arthritis, multiple sclerosis, asthma, Crohn's disease, ulcerative colitis, systemic lupus erythematosus, or transplant rejection.

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法律状态:
2018-01-16| 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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2018-06-05| B25A| Requested transfer of rights approved|Owner name: MEDIMMUNE LIMITED. (GB) |

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2019-12-17| B07E| Notice of approval relating to section 229 industrial property law [chapter 7.5 patent gazette]|

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2020-06-09| B07A| Technical examination (opinion): publication of technical examination (opinion) [chapter 7.1 patent gazette]|

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2020-10-13| B06A| Notification to applicant to reply to the report for non-patentability or inadequacy of the application [chapter 6.1 patent gazette]|

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2021-03-02| B09A| Decision: intention to grant [chapter 9.1 patent gazette]|

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2021-05-18| B16A| Patent or certificate of addition of invention granted|Free format text: PRAZO DE VALIDADE: 20 (VINTE) ANOS CONTADOS A PARTIR DE 11/03/2013, OBSERVADAS AS CONDICOES LEGAIS. |

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PCT/US2013/030179|WO2013169338A1|2012-05-11|2013-03-11|Ctla-4 variants|

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