# Patent

## Title
PD-1 antibodies

## Abstract

A humanised agonistic antibody which binds human PD-1 comprising a heavy chain and a light chain wherein the variable domain of the heavy chain comprises the sequence given in SEQ ID NO:1 for CDR-H1, the sequence given in SEQ ID NO:2 for CDR-H2 and the sequence given in SEQ ID NO:3 for CDR-H3 and the variable domain of the light chain comprises the sequence given in SEQ ID NO:4 for CDR-L1, the sequence given in SEQ ID NO:5 for CDR-L2 and the sequence given in SEQ ID NO:7 for CDR-L3. The invention also extends to therapeutic uses of the antibody molecules, compositions and methods for producing said antibody molecules.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims priority to U.S. Application Ser. No. 61/312,702, filed on Mar. 11, 2010, under 35 U.S.C. §119(e), which is incorporated by reference in its entirety.


FIELD OF THE INVENTION
The present invention relates to antibody molecules having specificity for antigenic determinants of human PD-1 and compositions comprising the same. The present invention also relates to the therapeutic uses of the antibody molecules, compositions and methods for producing said antibody molecules.
BACKGROUND OF THE INVENTION
Programmed Death 1 (PD-1), also known as CD279; gene name PDCD1; accession number NP—005009 is a cell surface receptor with a critical role in regulating the balance between stimulatory and inhibitory signals in the immune system and maintaining peripheral tolerance (Ishida, Y et al. 1992 EMBO J 11 3887; Kier, Mary E et al. 2008 Annu Rev Immunol 26 677-704; Okazaki, Taku et al. 2007 International Immunology 19 813-824). It is an inhibitory member of the immunoglobulin super-family with homology to CD28. The structure of PD-1 is a monomeric type 1 transmembrane protein, consisting of one immunoglobulin variable-like extracellular domain and a cytoplasmic domain containing an immunoreceptor tyrosine-based inhibitory motif (ITIM) and an immunoreceptor tyrosine-based switch motif (ITSM). Expression of PD-1 is inducible on T cells, B cells, natural killer (NK) cells and monocytes, for example upon lymphocyte activation via T cell receptor (TCR) or B cell receptor (BCR) signaling (Kier, Mary E et al. 2008 Annu Rev Immunol 26 677-704; Agata, Y et al 1996 Int Immunol 8 765-72). PD-1 has two known ligands, PD-L1 (B7-H1, CD274) and PD-L2 (B7-DC, CD273), which are cell surface expressed members of the B7 family (Freeman, Gordon et al. 2000 J Exp Med 192 1027; Latchman, Y et al. 2001 Nat Immunol 2 261). Upon ligand engagement, PD-1 recruits phosphatases such as SHP-1 and SHP-2 to its intracellular tyrosine motifs which subsequently dephosphorylate effector molecules activated by TCR or BCR signaling (Chemnitz, J et al. 2004 J Immunol 173 945-954; Riley, James L 2009 Immunological Reviews 229 114-125) In this way, PD-1 transduces inhibitory signals into T and B cells only when it is engaged simultaneously with the TCR or BCR.
PD-1 has been demonstrated to down-regulate effector T cell responses via both cell-intrinsic and cell-extrinsic functional mechanisms. Inhibitory signaling through PD-1 induces a state of anergy or unresponsiveness in T cells, resulting in the cells being unable to clonally expand or produce optimal levels of effector cytokines. PD-1 may also induce apoptosis in T cells via its ability to inhibit survival signals from co-stimulation, which leads to reduced expression of key anti-apoptotic molecules such as Bcl-XL (Kier, Mary E et al. 2008 Annu Rev Immunol 26 677-704). In addition to these direct effects, recent publications have implicated PD-1 as being involved in the suppression of effector cells by promoting the induction and maintenance of regulatory T cells (TREG). For example, PD-L1 expressed on dendritic cells was shown to act in synergy with TGF-β to promote the induction of CD4+ FoxP3+ TREG with enhanced suppressor function (Francisco, Loise M et al. 2009 J Exp Med 206 3015-3029).
The first indication of the importance of PD-1 in peripheral tolerance and inflammatory disease came from the observation that PD-1 knockout (Pdcd1−/−) mice develop spontaneous autoimmunity. Fifty percent of Pdcd1−/− mice on a C57BL/6 background develop lupus-like glomerulonephritis and arthritis by 14 months of age and BALB/c-Pdcd1−/− mice develop a fatal dilated cardiomyopathy and production of autoantibodies against cardiac troponin I from 5 weeks onwards (Nishimura, H et al. 1999 Immunity 11 141-151; Nishimura, H et al. 2001 Science 291 319-322). Furthermore, introduction of PD-1 deficiency to the non-obese diabetic (NOD) mouse strain dramatically accelerates the onset and incidence of diabetes resulting in all NOD-Pdcd1−/− mice developing diabetes by 10 weeks of age (Wang, J et al. 2005 Proc Natl Acad Sci USA 102 11823). Additionally, using induced murine models of autoimmunity such as experimental autoimmune encephalomyelitis (EAE), or transplantation/graft-versus-host (GVHD) models, several groups have shown that blocking the PD-1-PD-L interaction exacerbates disease, further confirming the key role of PD-1 in inflammatory diseases. Importantly, evidence suggests that PD-1 has a comparable immune modulatory function in humans as mice, as polymorphisms in human PDCD1 have been associated with a range of autoimmune diseases including systemic lupus erythematosus (SLE), multiple sclerosis (MS), type I diabetes (TID), rheumatoid arthritis (RA) and Grave's disease (Okazaki, Taku et al. 2007 International Immunology 19 813-824; Prokunina, L et al. 2002 Nat Genet 32 666-669; Kroner, A et al. 2005 Ann Neurol 58 50-57; Prokunina, L et al 2004 Arthritis Rheum 50 1770).
Several therapeutic approaches to enhance PD-1 signaling and modulate inflammatory disease have been reported, using murine models of autoimmunity. One such approach tried was to generate artificial dendritic cells which over-express PD-L1. Injection of mice with antigen-loaded PD-L1-dendritic cells before or after induction of EAE by MOG peptide immunisation reduced the inflammation of the spinal cord as well as the clinical severity of the disease (Hirata, S et al. 2005 J Immunol 174 1888-1897). Another approach was to try to cure lupus-like syndrome in BXSB mice by delivering a PD-1 signal using a recombinant adenovirus expressing mouse PD-L1. Injection of this virus partially prevented the development of nephritis as shown by lower frequency of proteinuria, reduced serum anti-dsDNA Ig and better renal pathology (Ding, H et al. 2006 Clin Immunol 118 258). These results suggest that enhancing the PD-1 signal could have therapeutic benefit in human autoimmune disease. An alternative therapeutic approach more appropriate as a human drug treatment would be to use an agonistic monoclonal antibody against human PD-1. Binding of this agonistic antibody would ideally independently transduce inhibitory signals through PD-1 whilst also synergising with ongoing endogenous signals emanating from the natural PD-1-PD1-L interaction. An agonistic anti-PD-1 mAb would be predicted to modulate a range of immune cell types involved in inflammatory disease including T cells, B cells, NK cells and monocytes and would therefore have utility in the treatment of a wide range of human autoimmune or inflammatory disorders.
Whilst a number of antagonistic anti-PD-1 antibodies have been described, to date the only PD-1 agonistic antibodies described in the literature, to the best of the inventors knowledge, still also block the PD-1-PD1L and PD1-PD2L interaction. See for Example, WO2004/056875.
Accordingly there is still a need in the art for improved agonistic anti-PD-1 antibodies suitable for treating patients, in particular those which do not block the PD1-PDL1 or the PD1-PDL2 interaction.
We have now identified high affinity agonistic anti-PD-1 antibodies suitable for use in the treatment or prophylaxis of immune disorders, for example by reducing the T cell response. Non limiting examples of immune disorders that can be treated via the administration of PD-1 specific antibodies to a subject include, but are not limited to, rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, Crohn's disease, systemic lupus erythematosus, type I diabetes, transplant rejection, graft-versus-host disease, hyperproliferative immune disorders, cancer and infectious diseases.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows amino acid sequences relating to antibody 949 according to the disclosure
FIGS. 2-12 shows certain amino acid or DNA sequences relating to an antibody according to the disclosure
FIG. 13 shows Inhibition of human CD4+ T cell proliferation by antibody 949.
FIG. 14 Ligand blocking assay with antibody 949 and humanised versions.
FIG. 15 Stimulation of SEAP from the human PD-1/CD28/Zeta reporter cell line by antibody 949.
FIG. 16 Species Cross-reactivity of 949 chimeric and humanised grafts with PD-1
FIG. 17 shows an alignment of the light chains for the murine, acceptor frameworks and humanised light chains.
FIG. 18 shows an alignment of the heavy chains for the murine, acceptor frameworks and humanised heavy chains.
FIG. 19 shows an amino acid sequence of a heavy chain of antibody 949 in a huIgG4 format
FIG. 20 shows a nucleic acid sequence of a heavy chain of antibody 949 in a huIgG4 format
FIG. 21 shows an amino acid sequence of a heavy chain, including the signal sequence, of antibody 949 in a huIgG4 format
FIG. 22 shows a nucleic acid sequence of a heavy chain, including the signal sequence, of antibody 949 in a huIgG4 format
FIG. 23 shows an amino acid sequence of a heavy chain of antibody 949 in a huIgG1 format
FIG. 24 shows a nucleic acid sequence of a heavy chain of antibody 949 in a huIgG1 format
FIG. 25 shows an amino acid sequence of a heavy chain, including the signal sequence, of antibody 949 in a huIgG1 format
FIG. 26 shows a nucleic acid sequence of a heavy chain, including the signal sequence, of antibody 949 in a huIgG1 format
FIGS. 27 to 30 show various amino acid or nucleotide sequences for a variable region wherein CDR3 has been amended to remove a deamidation site.
FIGS. 31 to 38 show various amino acid or nucleotide sequences for a variable region, and variable region plus constant region.
FIG. 39 shows the results of PD-1 ligand blocking binding assay.
FIGS. 40 and 41 shows activated T-cell binding assay with various constructs
FIGS. 42a) and b) show the cross-reactivity of various antibody constructs with human PD-1 and cyno PD-1
FIG. 43 shows an alignment of the light chains for the murine, acceptor frameworks and humanised light chains



DETAILED DESCRIPTION OF THE INVENTION
The parental murine antibody hybridoma from which the humanised antibodies are derived is referred to herein as Clone 19. The cloned recombinant antibody derived from Clone 19 is referred to herein as antibody CA051—00949 also referred to herein as 949.
The residues in antibody variable domains are conventionally numbered according to a system devised by Kabat et al. This system is set forth in Kabat et al., 1987, in Sequences of Proteins of Immunological Interest, US Department of Health and Human Services, NIH, USA (hereafter “Kabat et al. (supra)”). This numbering system is used in the present specification except where otherwise indicated.
The Kabat residue designations do not always correspond directly with the linear numbering of the amino acid residues. The actual linear amino acid sequence may contain fewer or additional amino acids than in the strict Kabat numbering corresponding to a shortening of, or insertion into, a structural component, whether framework or complementarity determining region (CDR), of the basic variable domain structure. The correct Kabat numbering of residues may be determined for a given antibody by alignment of residues of homology in the sequence of the antibody with a “standard” Kabat numbered sequence.
The CDRs of the heavy chain variable domain are located at residues 31-35 (CDR-H1), residues 50-65 (CDR-H2) and residues 95-102 (CDR-H3) according to the Kabat numbering system. However, according to Chothia (Chothia, C. and Lesk, A. M. J. Mol. Biol., 196, 901-917 (1987)), the loop equivalent to CDR-H1 extends from residue 26 to residue 32. Thus unless indicated otherwise ‘CDR-H1’ as employed herein is intended to refer to residues 26 to 35, as described by a combination of the Kabat numbering system and Chothia's topological loop definition.
The CDRs of the light chain variable domain are located at residues 24-34 (CDR-L1), residues 50-56 (CDR-L2) and residues 89-97 (CDR-L3) according to the Kabat numbering system.
As used herein, the term ‘agonistic antibody’ describes an antibody that is capable of stimulating the biological signaling activity of PD-1, leading to phosphatase recruitment to its intracellular domain and hence inactivation of T or B cell receptor signaling and phenotypic characteristics associated with activation.
Antibodies for use in the present invention may be obtained using any suitable method known in the art. The PD-1 polypeptide/protein including fusion proteins, for example PD-1-Fc fusions proteins or cells (recombinantly or naturally) expressing the polypeptide (such as activated T cells) can be used to produce antibodies which specifically recognise PD-1. The PD-1 polypeptide may be the ‘mature’ polypeptide or a biologically active fragment or derivative thereof. Suitably the PD-1 polypeptide is the mature human polypeptide or the extracellular domain or fragment thereof. The extracellular domain typically comprises amino acids 21-170 of the PD-1 protein (SWISS PROT entry Q15116). PD-1 polypeptides may be prepared by processes well known in the art from genetically engineered host cells comprising expression systems or they may be recovered from natural biological sources. In the present application, the term “polypeptides” includes peptides, polypeptides and proteins. These are used interchangeably unless otherwise specified. The PD-1 polypeptide may in some instances be part of a larger protein such as a fusion protein for example fused to an affinity tag. Antibodies generated against the PD-1 polypeptide may be obtained, where immunisation of an animal is necessary, by administering the polypeptides to an animal, preferably a non-human animal, using well-known and routine protocols, see for example Handbook of Experimental Immunology, D. M. Weir (ed.), Vol 4, Blackwell Scientific Publishers, Oxford, England, 1986). Many warm-blooded animals, such as rabbits, mice, rats, sheep, cows, camels or pigs may be immunized. However, mice, rabbits, pigs and rats are generally most suitable.
Monoclonal antibodies may be prepared by any method known in the art such as the hybridoma technique (Kohler & Milstein, 1975, Nature, 256:495-497), the trioma technique, the human B-cell hybridoma technique (Kozbor et al., 1983, Immunology Today, 4:72) and the EBV-hybridoma technique (Cole et al., Monoclonal Antibodies and Cancer Therapy, pp 77-96, Alan R Liss, Inc., 1985).
Antibodies for use in the invention may also be generated using single lymphocyte antibody methods by cloning and expressing immunoglobulin variable region cDNAs generated from single lymphocytes selected for the production of specific antibodies by, for example, the methods described by Babcook, J. et al., 1996, Proc. Natl. Acad. Sci. USA 93(15):7843-78481; WO92/02551; WO2004/051268 and International Patent Application number WO2004/106377.
Screening for antibodies can be performed using assays to measure binding to human PD-1 and/or assays to measure the ability to agonise PD1 activity. An example of a binding assay is an ELISA, in particular, using a fusion protein of human PD-1 and human Fc, which is immobilized on plates, and employing a conjungated secondary antibody to detect anti-PD-1 antibody bound to the fusion protein. Examples of suitable agonism and ligand blocking assays are described in the Examples herein.
Humanised antibodies (which include CDR-grafted antibodies) are antibody molecules having one or more complementarity determining regions (CDRs) from a non-human species and a framework region from a human immunoglobulin molecule (see, e.g. U.S. Pat. No. 5,585,089; WO91/09967). It will be appreciated that it may only be necessary to transfer the specificity determining residues of the CDRs rather than the entire CDR (see for example, Kashmiri et al., 2005, Methods, 36, 25-34). Humanised antibodies may optionally further comprise one or more framework residues derived from the non-human species from which the CDRs were derived.
The present invention provides agonistic humanised antibodies having specificity for human PD-1.
An agonistic murine anti-PD-1 antibody (Clone 19) was described in PCT/IB2009/06940 (unpublished) and the sequences of the variable regions and CDRs of this antibody are provided in FIG. 1. In particular the CDRs of this antibody are provided in FIG. 1(c), SEQ ID NOs 1-6.
An improved version of the CDRL3 (SEQ ID NO:6) derived from Clone 19 is provided in FIG. 2(a) (SEQ ID NO:7) in which a potential deamidation site has been modified. Accordingly, in one embodiment the present invention provides a humanised agonistic antibody which binds human PD-1 comprising a heavy chain and a light chain wherein the variable domain of the heavy chain comprises the sequence given in SEQ ID NO:1 for CDR-H1, the sequence given in SEQ ID NO:2 for CDR-H2 and the sequence given in SEQ ID NO:3 for CDR-H3 and the variable domain of the light chain comprises the sequence given in SEQ ID NO:4 for CDR-L1, the sequence given in SEQ ID NO:5 for CDR-L2 and the sequence given in SEQ ID NO:7 for CDR-L3.
As used herein, the term ‘humanised antibody molecule’ refers to an antibody molecule wherein the heavy and/or light chain contains one or more CDRs (including, if desired, one or more modified CDRs) from a donor antibody (e.g. a murine monoclonal antibody) grafted into a heavy and/or light chain variable region framework of an acceptor antibody (e.g. a human antibody). For a review, see Vaughan et al, Nature Biotechnology, 16, 535-539, 1998. In one embodiment rather than the entire CDR being transferred, only one or more of the specificity determining residues from any one of the CDRs described herein above are transferred to the human antibody framework (see for example, Kashmiri et al., 2005, Methods, 36, 25-34). In one embodiment only the specificity determining residues from one or more of the CDRs described herein above are transferred to the human antibody framework. In another embodiment only the specificity determining residues from each of the CDRs described herein above are transferred to the human antibody framework.
When the CDRs or specificity determining residues are grafted, any appropriate acceptor variable region framework sequence may be used having regard to the class/type of the donor antibody from which the CDRs are derived, including mouse, primate and human framework regions. Suitably, the Humanised antibody according to the present invention has a variable domain comprising human acceptor framework regions as well as one or more of the CDRs provided in FIG. 1(c) or FIG. 2(a). Thus, provided in one embodiment is an agonistic humanised antibody which binds human PD-1 wherein the variable domain comprises human acceptor framework regions and non-human donor CDRs.
Examples of human frameworks which can be used in the present invention are KOL, NEWM, REI, EU, TUR, TEI, LAY and POM (Kabat et al., supra). For example, KOL and NEWM can be used for the heavy chain, REI can be used for the light chain and EU, LAY and POM can be used for both the heavy chain and the light chain. Alternatively, human germline sequences may be used; these are available at: http://vbase.mrc-cpe.cam.ac.uk/
In a humanised antibody of the present invention, the acceptor heavy and light chains do not necessarily need to be derived from the same antibody and may, if desired, comprise composite chains having framework regions derived from different chains.
Once such suitable framework region for the heavy chain of the humanised antibody of the present invention is derived from the human sub-group VH1 sequence 1-3 1-46 together with JH4 (SEQ ID NO:52). Accordingly, in one example there is provided an agonistic humanised antibody comprising the sequence given in SEQ ID NO:1 for CDR-H1, the sequence given in SEQ ID NO:2 for CDR-H2 and the sequence given in SEQ ID NO:3 for CDRH3 wherein the heavy chain framework region is derived from the human subgroup VH1 sequence 1-3 1-46 together with JH4. The sequence of human JH4 is as follows: (YFDY)WGQGTLVTVS (Seq ID No: 56). The YFDY motif is part of CDR-H3 and is not part of framework 4 (Ravetch, J V. et al., 1981, Cell, 27, 583-591).
Another suitable framework region for the heavy chain of the humanised antibody of the present invention is derived from the human sub-group VH1 sequence 1-2 1-e together with JH4 (SEQ ID NO:54). Accordingly, in one example there is provided an agonistic humanised antibody comprising the sequence given in SEQ ID NO:1 for CDR-H1, the sequence given in SEQ ID NO:2 for CDR-H2 and the sequence given in SEQ ID NO:3 for CDRH3 wherein the heavy chain framework region is derived from the human subgroup VH1 sequence 1-2 1-e together with JH4, see for example SEQ ID NO:46). The sequence of human JH4 is as follows: (YFDY)WGQGTLVTVS (Seq ID No: 56). The YFDY motif is part of CDR-H3 and is not part of framework 4 (Ravetch, J V. et al., 1981, Cell, 27, 583-591). In one example the heavy chain variable domain of the antibody comprises the sequence given in SEQ ID NO:46.
A suitable framework region for the light chain of the humanised antibody of the present invention is derived from the human germline sub-group VK1 sequence 2-1-(1) L23 together with JK4 (SEQ ID NO:48). Accordingly, in one example there is provided an agonistic humanised antibody comprising the sequence given in SEQ ID NO:4 for CDR-L1, the sequence given in SEQ ID NO:5 for CDR-L2 and the sequence given in SEQ ID NO:6 or SEQ ID NO:7 for CDRL3 wherein the light chain framework region is derived from the human subgroup sequence 2-1-(1) L23 together with JK4. The JK4 sequence is as follows: (LT)FGGGTKVEIK (Seq ID No: 57). The LT motif is part of CDR-L3 and is not part of framework 4 (Hieter, P A., et al., 1982, J. Biol. Chem., 257, 1516-1522).
Another suitable framework region for the light chain of the humanised antibody of the present invention is derived from the human germline sub-group VK3 sequence 6-1-(1) A27 together with JK4 (SEQ ID NO:50). Accordingly, in one example there is provided an agonistic humanised antibody comprising the sequence given in SEQ ID NO:4 for CDR-L1, the sequence given in SEQ ID NO:5 for CDR-L2 and the sequence given in SEQ ID NO:6 or SEQ ID NO:7 for CDRL3 wherein the light chain framework region is derived from the human subgroup sequence VK3 6-1-(1) A27 together with JK4. The JK4 sequence is as follows: (LT)FGGGTKVEIK (Seq ID No: 57). The LT motif is part of CDR-L3 and is not part of framework 4 (Hieter, P A., et al., 1982, J. Biol. Chem., 257, 1516-1522).
Also, in a humanised antibody of the present invention, the framework regions need not have exactly the same sequence as those of the acceptor antibody. For instance, unusual residues may be changed to more frequently-occurring residues for that acceptor chain class or type. Alternatively, selected residues in the acceptor framework regions may be changed so that they correspond to the residue found at the same position in the donor antibody (see Reichmann et al., 1998, Nature, 332, 323-324). Such changes should be kept to the minimum necessary to recover the affinity of the donor antibody. A protocol for selecting residues in the acceptor framework regions which may need to be changed is set forth in WO 91/09967.
Suitably, in a humanised antibody molecule of the present invention, if the acceptor heavy chain has the human VH1 sequence 1-3 1-46 together with JH4, then the acceptor framework regions of the heavy chain comprise, in addition to the three donor CDRs (SEQ ID NOs:1, 2 and 3), a donor residue at at least one of positions 25, 37, 41, 48, 71, 73 and 76 (according to Kabat et al., (supra)). Accordingly, in one example there is provided a humanised antibody, wherein at least the residues at each of positions 25, 37, 41, 48, 71, 73 and 76 of the variable domain of the heavy chain are donor residues, see for example the sequence given in SEQ ID NO:30. In one example there is provided a humanised antibody, wherein at least the residues at each of positions 25, 37, 41 and 48 of the variable domain of the heavy chain are donor residues, see for example the sequence given in SEQ ID NO:38. In one example there is provided a humanised antibody, wherein at least the residue at position 25 of the variable domain of the heavy chain is a donor residue, see for example the sequence given in SEQ ID NO: 40.
Suitably, in a humanised antibody molecule of the present invention, if the acceptor heavy chain has the human VH1 sequence 1-2 1-e together with JH4, then the acceptor framework regions of the heavy chain comprise, in addition to the three donor CDRs (SEQ ID NOs:1, 2 and 3), a donor residue at at least one of positions 25, 37, 41, 48, 71, 76 and 78 (according to Kabat et al., (supra)). Accordingly, in one example there is provided a humanised antibody, wherein at least the residues at each of positions 25, 37, 41, 48, 71, 76 and 78 of the variable domain of the heavy chain are donor residues, see for example the sequence given in SEQ ID NO:42. In one example there is provided a humanised antibody, wherein at least the residues at each of positions 25, 37, 41 and 48 of the variable domain of the heavy chain are donor residues, see for example the sequence given in SEQ ID NO:44.
Suitably, in a humanised antibody molecule according to the present invention, if the acceptor light chain has the human sub-group VK1 sequence 2-1-(1) L23 together with JK4, then the acceptor framework regions of the light chain comprise, in addition to three donor CDRs (SEQ ID NOs:4, 5 and 6 or 7), a donor residue at at least one of positions 1, 2, 3, 4, 47, 60 and 70. Accordingly, in one example there is provided a humanised antibody, wherein at least the residues at each of positions 1, 2, 3, 4, 47, 60 and 70 of the variable domain of the light chain are donor residues, see for example SEQ ID NO:10. In one example there is provided a humanised antibody, wherein at least the residues at each of positions 1, 2, 3, and 4 of the variable domain of the light chain are donor residues, see for example SEQ ID NO:18 or SEQ ID NO:20. In one embodiment the antibody comprises a sequence as shown in SEQ ID NO. 66. In one example there is provided a humanised antibody, wherein at least the residues at each of positions 1, 2 and 3 of the variable domain of the light chain are donor residues, see for example SEQ ID NO:22 or SEQ ID NO:24.
Suitably, in a humanised antibody molecule according to the present invention, if the acceptor light chain has the human sub-group VK3 sequence 6-1-(1) A27 together with JK4, then the acceptor framework regions of the light chain comprise, in addition to the three donor CDRs (SEQ ID NOs:4, 5 and 6 or 7), a donor residue at at least one of positions 2, 47, 58, 70, 71 and 85. Accordingly, in one example there is provided a humanised antibody, wherein at least the residues at each of positions 2, 47, 58, 70, 71 and 85 of the variable domain of the light chain are donor residues, see for example, SEQ ID NO:26 or SEQ ID NO:28.
Donor residues are residues from the donor antibody, i.e. the antibody from which the CDRs were originally derived. Donor residues may replace human acceptor framework residues (acceptor residues) at one or more of the positions listed below.










VK1 Light chain 2-1(1) L23








Kabat position
Human acceptor residue











1
Alanine


2
Isoleucine


3
Arginine


4
Methionine


47
Phenylalanine


60
Serine


70
Aspartic acid



















VK3 Light chain 6-1-(1) A27








Kabat position
Human acceptor residue











2
Isoleucine


47
Leucine


58
Isoleucine


70
Aspartic acid


71
Phenylalanine


85
Valine



















VH1 Heavy chain 1-3 1-46








Kabat position
Human acceptor residue





25
Serine


37
Valine


41
Proline


48
Methionine


71
Arginine


73
Threonine


76
Serine



















VH1 Heavy chain 1-2 1-e








Kabat position
Human acceptor residue





25
Serine


37
Valine


41
Proline


48
Methionine


71
Alanine


76
Serine


78
Alanine









The antibody molecules of the present invention suitably comprise a complementary light chain or a complementary heavy chain, respectively. Accordingly, in one embodiment the present invention provides a humanised agonistic antibody which binds human PD-1 having a heavy chain comprising a sequence selected from the group consisting of: SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44 and SEQ ID NO:46 and a light chain comprising a sequence selected from the group consisting of SEQ ID NO: 10, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26 and SEQ ID NO:28.
The antibody molecules of the present invention suitably comprise a complementary light chain or a complementary heavy chain, respectively. Accordingly, in one embodiment the present invention provides a humanised agonistic antibody which binds human PD-1 having a heavy chain comprising a sequence selected from the group consisting of: SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44 and SEQ ID NO:46 and a light chain comprising a sequence selected from the group consisting of SEQ ID NO: 10, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28 and SEQ ID NO:66.
In one embodiment the heavy chain comprises a sequence selected from SEQ ID NO: 30 and SEQ ID NO: 46 and the light chain comprises a sequence according to SEQ ID NO: 66.
It will be appreciated that one or more amino acid substitutions, additions and/or deletions may be made to the CDRs or other sequences (e.g variable domains) provided by the present invention without significantly altering the ability of the antibody to bind to PD-1 and to agonise PD-1 activity. The effect of any amino acid substitutions, additions and/or deletions can be readily tested by one skilled in the art, for example by using the methods described herein, in particular in the Examples, to determine PD-1 binding and PD-1 agonism.
In another embodiment, an antibody of the present invention comprises a heavy chain, wherein the variable domain of the heavy chain comprises a sequence having at least 60% identity or similarity to the sequence given in any one of SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44 or SEQ ID NO:46. In one embodiment, an antibody of the present invention comprises a heavy chain, wherein the variable domain of the heavy chain comprises a sequence having at least 70%, 80%, 90%, 95% or 98% identity or similarity to the sequence given in any one of SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44 or SEQ ID NO:46.
“Identity”, as used herein, indicates that at any particular position in the aligned sequences, the amino acid residue is identical between the sequences. “Similarity”, as used herein, indicates that, at any particular position in the aligned sequences, the amino acid residue is of a similar type between the sequences. For example, leucine may be substituted for isoleucine or valine. Other amino acids which can often be substituted for one another include but are not limited to:

    phenylalanine, tyrosine and tryptophan (amino acids having aromatic side chains);
    lysine, arginine and histidine (amino acids having basic side chains);
    aspartate and glutamate (amino acids having acidic side chains);
    asparagine and glutamine (amino acids having amide side chains); and
    
        cysteine and methionine (amino acids having sulphur-containing side chains). Degrees of identity and similarity can be readily calculated (Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing. Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part 1, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987, Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991, the BLASTTM software available from NCBI (Altschul, S. F. et al., 1990, J. Mol. Biol. 215:403-410; Gish, W. & States, D. J. 1993, Nature Genet. 3:266-272. Madden, T. L. et al., 1996, Meth. Enzymol. 266:131-141; Altschul, S. F. et al., 1997, Nucleic Acids Res. 25:3389-3402; Zhang, J. & Madden, T. L. 1997, Genome Res. 7:649-656,).
    
    


In another embodiment, an antibody of the present invention comprises a light chain, wherein the variable domain of the light chain comprises a sequence having at least 60% identity or similarity to the sequence given in any one of SEQ ID NO: 10, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26 or SEQ ID NO:28
In one embodiment the antibody of the present invention comprises a light chain, wherein the variable domain of the light chain comprises a sequence having at least 70%, 80%, 90%, 95% or 98% identity or similarity to the sequence given in any one of SEQ ID NO: 10, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26 or SEQ ID NO:28.
In one embodiment the antibody of the present invention comprises a sequence having at least 70%, 80%, 90%, 95% or 98% identity or similarity to the sequence given herein, for example SEQ ID NO:66 or SEQ ID NO:70.
In one embodiment the antibody of the present invention comprises a sequence having at least 70%, 80%, 90%, 95% or 98% identity or similarity to the sequence given herein, for example SEQ ID NO: 34, SEQ ID NO:58, SEQ ID NO:62, SEQ ID NO:76 or SEQ ID NO:80.
In another embodiment of the invention, the antibody comprises a heavy chain and a light chain, wherein the variable domain of the heavy chain comprises a sequence having at least 60% identity or similarity to the sequence given in any one of SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44 or SEQ ID NO:46 and the variable domain of the light chain comprises a sequence having at least 60% identity or similarity to the sequence given in any one of SEQ ID NO: 10, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26 or SEQ ID NO:28.
Suitably, the antibody comprises a heavy chain, wherein the variable domain of the heavy chain comprises a sequence having at least 70%, 80%, 90%, 95% or 98% identity or similarity to the sequence given in any one of SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44 or SEQ ID NO:46 and a light chain, wherein the variable domain of the light chain comprises a sequence having at least 70%, 80%, 90%, 95% or 98% identity or similarity to the sequence given in any one of SEQ ID NO: 10, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26 or SEQ ID NO:28.
In another embodiment of the invention, the antibody comprises a heavy chain and a light chain, wherein the variable domain of the heavy chain comprises a sequence having at least 60% identity or similarity to the sequence given in any one of SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO: 58, SEQ ID NO: 62, SEQ ID NO:76 or SEQ ID NO:80 and the variable domain of the light chain comprises a sequence having at least 60% identity or similarity to the sequence given in any one of SEQ ID NO: 10, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:66 or SEQ ID NO:70.
Suitably, the antibody comprises a heavy chain, wherein the variable domain of the heavy chain comprises a sequence having at least 70%, 80%, 90%, 95% or 98% identity or similarity to the sequence given in any one of SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO: 58, SEQ ID NO: 62, SEQ ID NO:76 or SEQ ID NO:80 and a light chain, wherein the variable domain of the light chain comprises a sequence having at least 70%, 80%, 90%, 95% or 98% identity or similarity to the sequence given in any one of SEQ ID NO: 10, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO: 66 or SEQ ID NO: 70.
The antibody molecules of the present invention may comprise a complete antibody molecule having full length heavy and light chains or a fragment thereof and may be, but are not limited to Fab, modified Fab, Fab′, modified Fab′, F(ab)2, Fv, single domain antibodies (e.g. VH or VL or VHH), scFv, bi, tri or tetra-valent antibodies, Bis-scFv, diabodies, triabodies, tetrabodies and epitope-binding fragments of any of the above (see for example Holliger and Hudson, 2005, Nature Biotech. 23(9):1126-1136; Adair and Lawson, 2005, Drug Design Reviews—Online 2(3), 209-217). The methods for creating and manufacturing these antibody fragments are well known in the art (see for example Verma et al., 1998, Journal of Immunological Methods, 216, 165-181). Other antibody fragments for use in the present invention include the Fab and Fab′ fragments described in International patent applications WO2005/003169, WO2005/003170 and WO2005/003171. Multi-valent antibodies may comprise multiple specificities e.g bispecific or may be monospecific (see for example WO 92/22853, WO05/113605, WO2009/040562 and WO2010/035012).
In one embodiment there is a provided a heavy chain selected from SEQ ID NO: 58, SEQ ID NO: 62, SEQ ID NO: 76 or SEQ ID NO:80 in combination with a light chain comprising SEQ ID NO: 66.
In one embodiment there is provided a heavy chain selected from SEQ ID NO: 58 in combination with a light chain comprising SEQ ID NO: 66.
In one embodiment there is provided a heavy chain selected from SEQ ID NO: 62 in combination with a light chain comprising SEQ ID NO: 66.
In one embodiment there is provided a heavy chain selected from SEQ ID NO: 76 in combination with a light chain comprising SEQ ID NO: 66.
In one embodiment there is provided a heavy chain selected from SEQ ID NO: 80 in combination with a light chain comprising SEQ ID NO: 66.
In one embodiment there is provided a heavy chain selected from SEQ ID NO: 58, SEQ ID NO: 62 or SEQ ID NO: 76 in combination with a light chain according to SEQ ID NO: 70.
In one embodiment there is provided a heavy chain selected from SEQ ID NO: 58 in combination with a light chain according to SEQ ID NO: 70.
In one embodiment there is provided a heavy chain selected from SEQ ID NO: 62 or in combination with a light chain according to SEQ ID NO: 70.
In one embodiment there is provided a heavy chain selected from SEQ ID NO: 76 in combination with a light chain according to SEQ ID NO: 70.
In one embodiment there is provided a heavy chain selected from SEQ ID NO: 80 in combination with a light chain according to SEQ ID NO: 70.
In one embodiment the antibody according to the present disclosure is provided as PD-1 binding antibody fusion protein which comprises an immunoglobulin moiety, for example a Fab or Fab′ fragment, and one or two single domain antibodies (dAb) linked directly or indirectly thereto, for example as described in WO2009/040562.
In one embodiment the fusion protein comprises two domain antibodies, for example as a variable heavy (VH) and variable light (VL) pairing, optionally linked by a disulphide bond.
In one embodiment the Fab or Fab′ element of the fusion protein has the same or similar specificity to the single domain antibody or antibodies. In one embodiment the Fab or Fab′ has a different specificity to the single domain antibody or antibodies, that is to say the fusion protein is multivalent. In one embodiment a multivalent fusion protein according to the present invention has an albumin binding site, for example a VH/VL pair therein provides an albumin binding site.
The constant region domains of the antibody molecule of the present invention, if present, may be selected having regard to the proposed function of the antibody molecule, and in particular the effector functions which may be required. For example, the constant region domains may be human IgA, IgD, IgE, IgG or IgM domains. In particular, human IgG constant region domains may be used, especially of the IgG1 and IgG3 isotypes when the antibody molecule is intended for therapeutic uses and antibody effector functions are required. Alternatively, IgG2 and IgG4 isotypes may be used when the antibody molecule is intended for therapeutic purposes and antibody effector functions are not required, e.g. for simply agonising PD-1 activity. It will be appreciated that sequence variants of these constant region domains may also be used. For example IgG4 molecules in which the serine at position 241 has been changed to proline as described in Angal et al., Molecular Immunology, 1993, 30 (1), 105-108 may be used. It will also be understood by one skilled in the art that antibodies may undergo a variety of posttranslational modifications. The type and extent of these modifications often depends on the host cell line used to express the antibody as well as the culture conditions. Such modifications may include variations in glycosylation, methionine oxidation, diketopiperazine formation, aspartate isomerization and asparagine deamidation. A frequent modification is the loss of a carboxy-terminal basic residue (such as lysine or arginine) due to the action of carboxypeptidases (as described in Harris, R J. Journal of Chromatography 705:129-134, 1995). Accordingly, the C-terminal lysine of the antibody heavy chain, for example as given in FIG. 8(a), SEQ ID NO: 36, may be absent.
In one embodiment there is provided an antibody heavy chain comprising or consisting of a sequence as per SEQ ID NO:58.
In one embodiment there is provided an antibody heavy chain comprising or consisting of a sequence as per SEQ ID NO:62.
In one embodiment there is provided an antibody heavy chain comprising or consisting of a sequence as per SEQ ID NO:76.
In one embodiment there is provided an antibody heavy chain comprising or consisting of a sequence as per SEQ ID NO:80.
In one embodiment there is provided a light chain comprising or consisting of a sequence as per SEQ ID NO: 70.
In one embodiment the antibody heavy chain comprises a CH1 domain and the antibody light chain comprises a CL domain, either kappa or lambda.
Biological molecules, such as antibodies or fragments, contain acidic and/or basic functional groups, thereby giving the molecule a net positive or negative charge. The amount of overall “observed” charge will depend on the absolute amino acid sequence of the entity, the local environment of the charged groups in the 3D structure and the environmental conditions of the molecule. The isoelectric point (pI) is the pH at which a particular molecule or solvent accessible surface thereof carries no net electrical charge. In one example, the PD-1 antibody and fragments of the invention may be engineered to have an appropriate isoelectric point. This may lead to antibodies and/or fragments with more robust properties, in particular suitable solubility and/or stability profiles and/or improved purification characteristics.
Thus in one aspect the invention provides a humanised PD-1 antibody engineered to have an isoelectric point, different to that of the originally identified antibody 949. The antibody may, for example be engineered by replacing an amino acid residue such as replacing an acidic amino acid residue with one or more basic amino acid residues. Alternatively, basic amino acid residues may be introduced or acidic amino acid residues can be removed. Alternatively, if the molecule has an unacceptably high pI value acidic residues may be introduced to lower the pI, as required. It is important that when manipulating the pI care must be taken to retain the desirable activity of the antibody or fragment. Thus in one embodiment the engineered antibody or fragment has the same or substantially the same activity as the “unmodified” antibody or fragment.
Programs such as ** ExPASY http://www.expasy.ch/tools/pi_tool.html, and http://www.iut-arles.up.univ-mrs.fr/w3bb/d_abim/compo-p.html, may be used to predict the isoelectric point of the antibody or fragment.
The antibody molecules of the present invention suitably have a high binding affinity, in particular nanomolar. Affinity may be measured using any suitable method known in the art, including BIAcore, as described in the Examples herein, using isolated natural or recombinant PD-1 or a suitable fusion protein/polypeptide. In one example affinity is measured using recombinant human PD-1 extracellular domain as described in the Examples herein. In one example the recombinant human PD-1 extracellular domain used is a monomer. Suitably the antibody molecules of the present invention have a binding affinity for isolated human PD-1 of about 6 nM or better. In one embodiment the antibody molecule of the present invention has a binding affinity of about 5 nM or better. In one embodiment the antibody molecule of the present invention has a binding affinity of about 4 nM or better. In one embodiment the antibody molecule of the present invention has a binding affinity of about 3 nM or better. In one embodiment the present invention provides a humanised antibody with a binding affinity of about 5 nM or better.
It will be appreciated that the affinity of antibodies provided by the present invention may be altered using any suitable method known in the art. The present invention therefore also relates to variants of the antibody molecules of the present invention, which have an improved affinity for PD-1. Such variants can be obtained by a number of affinity maturation protocols including mutating the CDRs (Yang et al., J. Mol. Biol., 254, 392-403, 1995), chain shuffling (Marks et al., Bio/Technology, 10, 779-783, 1992), use of mutator strains of E. coli (Low et al., J. Mol. Biol., 250, 359-368, 1996), DNA shuffling (Patten et al., Curr. Opin. Biotechnol., 8, 724-733, 1997), phage display (Thompson et al., J. Mol. Biol., 256, 77-88, 1996) and sexual PCR (Crameri et al., Nature, 391, 288-291, 1998). Vaughan et al. (supra) discusses these methods of affinity maturation.
In one embodiment the antibody molecules of the present invention agonise human PD-1 activity. Assays suitable for determining the ability of an antibody to agonise PD-1 are described in the Examples herein. In a preferred embodiment, the antibodies of the present invention do not block the interaction between PD-1 and its ligand PD-1 L. Suitable assays for determining whether antibodies block PD-1 interaction with its ligand PD-1L are described in the examples herein (Freeman, Gordon et al. 2000 J Exp Med 192 1027; Butte, Mannish et al, 2007 Immunity 27(1) 2007).
If desired an antibody for use in the present invention may be conjugated to one or more effector molecule(s). It will be appreciated that the effector molecule may comprise a single effector molecule or two or more such molecules so linked as to form a single moiety that can be attached to the antibodies of the present invention. Where it is desired to obtain an antibody fragment linked to an effector molecule, this may be prepared by standard chemical or recombinant DNA procedures in which the antibody fragment is linked either directly or via a coupling agent to the effector molecule. Techniques for conjugating such effector molecules to antibodies are well known in the art (see, Hellstrom et al., Controlled Drug Delivery, 2nd Ed., Robinson et al., eds., 1987, pp. 623-53; Thorpe et al., 1982, Immunol. Rev., 62:119-58 and Dubowchik et al., 1999, Pharmacology and Therapeutics, 83, 67-123). Particular chemical procedures include, for example, those described in WO 93/06231, WO 92/22583, WO 89/00195, WO 89/01476 and WO 03/031581. Alternatively, where the effector molecule is a protein or polypeptide the linkage may be achieved using recombinant DNA procedures, for example as described in WO 86/01533 and EP0392745.
The term effector molecule as used herein includes, for example, antineoplastic agents, drugs, toxins, biologically active proteins, for example enzymes, other antibody or antibody fragments, synthetic or naturally occurring polymers, nucleic acids and fragments thereof e.g. DNA, RNA and fragments thereof, radionuclides, particularly radioiodide, radioisotopes, chelated metals, nanoparticles and reporter groups such as fluorescent compounds or compounds which may be detected by NMR or ESR spectroscopy.
Examples of effector molecules may include cytotoxins or cytotoxic agents including any agent that is detrimental to (e.g. kills) cells. Examples include combrestatins, dolastatins, epothilones, staurosporin, maytansinoids, spongistatins, rhizoxin, halichondrins, roridins, hemiasterlins, taxol, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and puromycin and analogs or homologs thereof.
Effector molecules also include, but are not limited to, antimetabolites (e.g. methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil decarbazine), alkylating agents (e.g. mechlorethamine, thioepa chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (II) (DDP) cisplatin), anthracyclines (e.g. daunorubicin (formerly daunomycin) and doxorubicin), antibiotics (e.g. dactinomycin (formerly actinomycin), bleomycin, mithramycin, anthramycin (AMC), calicheamicins or duocarmycins), and anti-mitotic agents (e.g. vincristine and vinblastine).
Other effector molecules may include chelated radionuclides such as 111In and 90Y, Lu177, Bismuth213, Californium252, Iridium192 and Tungsten188/Rhenium188; or drugs such as but not limited to, alkylphosphocholines, topoisomerase I inhibitors, taxoids and suramin. Other effector molecules include proteins, peptides and enzymes. Enzymes of interest include, but are not limited to, proteolytic enzymes, hydrolases, lyases, isomerases, transferases. Proteins, polypeptides and peptides of interest include, but are not limited to, immunoglobulins, toxins such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin, a protein such as insulin, tumour necrosis factor, α-interferon, β-interferon, nerve growth factor, platelet derived growth factor or tissue plasminogen activator, a thrombotic agent or an anti-angiogenic agent, e.g. angiostatin or endostatin, or, a biological response modifier such as a lymphokine, interleukin-1 (IL-1), interleukin-2 (IL-2), granulocyte macrophage colony stimulating factor (GM-CSF), granulocyte colony stimulating factor (G-CSF), nerve growth factor (NGF) or other growth factor and immunoglobulins.
Other effector molecules may include detectable substances useful for example in diagnosis. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, radioactive nuclides, positron emitting metals (for use in positron emission tomography), and nonradioactive paramagnetic metal ions. See generally U.S. Pat. No. 4,741,900 for metal ions which can be conjugated to antibodies for use as diagnostics. Suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; suitable prosthetic groups include streptavidin, avidin and biotin; suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride and phycoerythrin; suitable luminescent materials include luminol; suitable bioluminescent materials include luciferase, luciferin, and aequorin; and suitable radioactive nuclides include 125I, 131I, 111In and 99Tc.
In another example the effector molecule may increase the half-life of the antibody in vivo, and/or reduce immunogenicity of the antibody and/or enhance the delivery of an antibody across an epithelial barrier to the immune system. Examples of suitable effector molecules of this type include polymers, albumin, albumin binding proteins or albumin binding compounds such as those described in WO05/117984.
Where the effector molecule is a polymer it may, in general, be a synthetic or a naturally occurring polymer, for example an optionally substituted straight or branched chain polyalkylene, polyalkenylene or polyoxyalkylene polymer or a branched or unbranched polysaccharide, e.g. a homo- or hetero-polysaccharide.
Specific optional substituents which may be present on the above-mentioned synthetic polymers include one or more hydroxy, methyl or methoxy groups.
Specific examples of synthetic polymers include optionally substituted straight or branched chain poly(ethyleneglycol), poly(propyleneglycol) poly(vinylalcohol) or derivatives thereof, especially optionally substituted poly(ethyleneglycol) such as methoxypoly(ethyleneglycol) or derivatives thereof.
Specific naturally occurring polymers include lactose, amylose, dextran, glycogen or derivatives thereof.
“Derivatives” as used herein is intended to include reactive derivatives, for example thiol-selective reactive groups such as maleimides and the like. The reactive group may be linked directly or through a linker segment to the polymer. It will be appreciated that the residue of such a group will in some instances form part of the product as the linking group between the antibody fragment and the polymer.
The size of the polymer may be varied as desired, but will generally be in an average molecular weight range from 500 Da to 50000 Da, for example from 5000 to 40000 Da such as from 20000 to 40000 Da. The polymer size may in particular be selected on the basis of the intended use of the product for example ability to localize to certain tissues such as tumors or extend circulating half-life (for review see Chapman, 2002, Advanced Drug Delivery Reviews, 54, 531-545). Thus, for example, where the product is intended to leave the circulation and penetrate tissue, for example for use in the treatment of a tumour, it may be advantageous to use a small molecular weight polymer, for example with a molecular weight of around 5000 Da. For applications where the product remains in the circulation, it may be advantageous to use a higher molecular weight polymer, for example having a molecular weight in the range from 20000 Da to 40000 Da.
Suitable polymers include a polyalkylene polymer, such as a poly(ethyleneglycol) or, especially, a methoxypoly(ethyleneglycol) or a derivative thereof, and especially with a molecular weight in the range from about 15000 Da to about 40000 Da.
In one example antibodies for use in the present invention are attached to poly(ethyleneglycol) (PEG) moieties. In one particular example the antibody is an antibody fragment and the PEG molecules may be attached through any available amino acid side-chain or terminal amino acid functional group located in the antibody fragment, for example any free amino, imino, thiol, hydroxyl or carboxyl group. Such amino acids may occur naturally in the antibody fragment or may be engineered into the fragment using recombinant DNA methods (see for example U.S. Pat. No. 5,219,996; U.S. Pat. No. 5,667,425; WO98/25971, WO2008/038024). In one example the antibody molecule of the present invention is a modified Fab fragment wherein the modification is the addition to the C-terminal end of its heavy chain one or more amino acids to allow the attachment of an effector molecule. Suitably, the additional amino acids form a modified hinge region containing one or more cysteine residues to which the effector molecule may be attached. Multiple sites can be used to attach two or more PEG molecules.
Suitably PEG molecules are covalently linked through a thiol group of at least one cysteine residue located in the antibody fragment. Each polymer molecule attached to the modified antibody fragment may be covalently linked to the sulphur atom of a cysteine residue located in the fragment. The covalent linkage will generally be a disulphide bond or, in particular, a sulphur-carbon bond. Where a thiol group is used as the point of attachment appropriately activated effector molecules, for example thiol selective derivatives such as maleimides and cysteine derivatives may be used. An activated polymer may be used as the starting material in the preparation of polymer-modified antibody fragments as described above. The activated polymer may be any polymer containing a thiol reactive group such as an α-halocarboxylic acid or ester, e.g. iodoacetamide, an imide, e.g. maleimide, a vinyl sulphone or a disulphide. Such starting materials may be obtained commercially (for example from Nektar, formerly Shearwater Polymers Inc., Huntsville, Ala., USA) or may be prepared from commercially available starting materials using conventional chemical procedures. Particular PEG molecules include 20K methoxy-PEG-amine (obtainable from Nektar, formerly Shearwater; Rapp Polymere; and SunBio) and M-PEG-SPA (obtainable from Nektar, formerly Shearwater).
In one embodiment, the antibody is a modified Fab fragment or diFab which is PEGylated, i.e. has PEG (poly(ethyleneglycol)) covalently attached thereto, e.g. according to the method disclosed in EP 0948544 or EP1090037 [see also “Poly(ethyleneglycol) Chemistry, Biotechnical and Biomedical Applications”, 1992, J. Milton Harris (ed), Plenum Press, New York, “Poly(ethyleneglycol) Chemistry and Biological Applications”, 1997, J. Milton Harris and S. Zalipsky (eds), American Chemical Society, Washington, D.C. and “Bioconjugation Protein Coupling Techniques for the Biomedical Sciences”, 1998, M. Aslam and A. Dent, Grove Publishers, New York; Chapman, A. 2002, Advanced Drug Delivery Reviews 2002, 54:531-545]. In one example PEG is attached to a cysteine in the hinge region. In one example, a PEG modified Fab fragment has a maleimide group covalently linked to a single thiol group in a modified hinge region. A lysine residue may be covalently linked to the maleimide group and to each of the amine groups on the lysine residue may be attached a methoxypoly(ethyleneglycol) polymer having a molecular weight of approximately 20,000 Da. The total molecular weight of the PEG attached to the Fab fragment may therefore be approximately 40,000 Da.
Particular PEG molecules include 2-[3-(N-maleimido)propionamido]ethyl amide of N,N′-bis(methoxypoly(ethylene glycol) MW 20,000) modified lysine, also known as PEG2MAL40K (obtainable from Nektar, formerly Shearwater).
Alternative sources of PEG linkers include NOF who supply GL2-400MA2 (wherein m in the structure below is 5) and GL2-400MA (where m is 2) and n is approximately 450:




That is to say each PEG is about 20,000 Da.
Further alternative PEG effector molecules of the following type:




are available from Dr Reddy, NOF and Jenkem.

In one embodiment there is provided an antibody which is PEGylated (for example with a PEG described herein), attached through a cysteine amino acid residue at or about amino acid 226 in the chain, for example amino acid 226 of the heavy chain (by sequential numbering).
The present invention also provides an isolated DNA sequence encoding the heavy and/or light chain(s) of an antibody molecule of the present invention. Suitably, the DNA sequence encodes the heavy or the light chain of an antibody molecule of the present invention. The DNA sequence of the present invention may comprise synthetic DNA, for instance produced by chemical processing, cDNA, genomic DNA or any combination thereof. DNA sequences which encode an antibody molecule of the present invention can be obtained by methods well known to those skilled in the art. For example, DNA sequences coding for part or all of the antibody heavy and light chains may be synthesised as desired from the determined DNA sequences or on the basis of the corresponding amino acid sequences.
DNA coding for acceptor framework sequences is widely available to those skilled in the art and can be readily synthesised on the basis of their known amino acid sequences.
Standard techniques of molecular biology may be used to prepare DNA sequences coding for the antibody molecule of the present invention. Desired DNA sequences may be synthesised completely or in part using oligonucleotide synthesis techniques. Site-directed mutagenesis and polymerase chain reaction (PCR) techniques may be used as appropriate.
Examples of suitable DNA sequences are provided in FIGS. 2-12, in particular SEQ ID NOs 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45 and 47.
Other examples of suitable DNA sequences are provided in FIGS. 20, 22, 24 and 26-38, in particular SEQ ID NO: 65, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81 and SEQ ID NO: 83.
The present invention also relates to a cloning or expression vector comprising one or more DNA sequences of the present invention. Accordingly, provided is a cloning or expression vector comprising one or more DNA sequences encoding an antibody of the present invention. Suitably, the cloning or expression vector comprises two DNA sequences, encoding the light chain and the heavy chain of the antibody molecule of the present invention, respectively and suitable signal sequences. In one example the vector comprises an intergenic sequence between the heavy and the light chains (see WO03/048208).
General methods by which the vectors may be constructed, transfection methods and culture methods are well known to those skilled in the art. In this respect, reference is made to “Current Protocols in Molecular Biology”, 1999, F. M. Ausubel (ed), Wiley Interscience, New York and the Maniatis Manual produced by Cold Spring Harbor Publishing.
Also provided is a host cell comprising one or more cloning or expression vectors comprising one or more DNA sequences encoding an antibody of the present invention. Any suitable host cell/vector system may be used for expression of the DNA sequences encoding the antibody molecule of the present invention. Bacterial, for example E. coli, and other microbial systems may be used or eukaryotic, for example mammalian, host cell expression systems may also be used. Suitable mammalian host cells include CHO, myeloma or hybridoma cells.
The present invention also provides a process for the production of an antibody molecule according to the present invention comprising culturing a host cell containing a vector of the present invention under conditions suitable for leading to expression of protein from DNA encoding the antibody molecule of the present invention, and isolating the antibody molecule.
The antibody molecule may comprise only a heavy or light chain polypeptide, in which case only a heavy chain or light chain polypeptide coding sequence needs to be used to transfect the host cells. For production of products comprising both heavy and light chains, the cell line may be transfected with two vectors, a first vector encoding a light chain polypeptide and a second vector encoding a heavy chain polypeptide. Alternatively, a single vector may be used, the vector including sequences encoding light chain and heavy chain polypeptides.
The antibodies and fragments according to the present disclosure are expressed at good levels from host cells. Thus the properties of the antibodies and/or fragments are optimised and conducive to commercial processing.
As the antibodies of the present invention are useful in the treatment and/or prophylaxis of a pathological condition, the present invention also provides a pharmaceutical or diagnostic composition comprising an antibody molecule of the present invention in combination with one or more of a pharmaceutically acceptable excipient, diluent or carrier. Accordingly, provided is the use of an antibody of the invention for the manufacture of a medicament. The composition will usually be supplied as part of a sterile, pharmaceutical composition that will normally include a pharmaceutically acceptable carrier. A pharmaceutical composition of the present invention may additionally comprise a pharmaceutically-acceptable adjuvant.
The present invention also provides a process for preparation of a pharmaceutical or diagnostic composition comprising adding and mixing the antibody molecule of the present invention together with one or more of a pharmaceutically acceptable excipient, diluent or carrier.
The antibody molecule may be the sole active ingredient in the pharmaceutical or diagnostic composition or may be accompanied by other active ingredients including other antibody ingredients, for example anti-TNF, anti-IL-1β, anti-T cell, anti-IFNγ or anti-LPS antibodies, or non-antibody ingredients such as xanthines.
In a further embodiment the antibody, fragment or composition according to the disclosure is employed in combination with a further pharmaceutically active agent, for example a corticosteroid (such as fluticasonoe propionate) and/or a beta-2-agonist (such as salbutamol, salmeterol or formoterol) or inhibitors of cell growth and proliferation (such as rapamycin, cyclophosphmide, methotrexate) or alternative a CD28 and for CD40 inhibitor. In one embodiment the inhibitor is a small molecule. In another embodiment the inhibitor is an antibody specific to the target.
The pharmaceutical compositions suitably comprise a therapeutically effective amount of the antibody of the invention. The term “therapeutically effective amount” as used herein refers to an amount of a therapeutic agent needed to treat, ameliorate or prevent a targeted disease or condition, or to exhibit a detectable therapeutic or preventative effect. For any antibody, the therapeutically effective amount can be estimated initially either in cell culture assays or in animal models, usually in rodents, rabbits, dogs, pigs or primates. The animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
The precise therapeutically effective amount for a human subject will depend upon the severity of the disease state, the general health of the subject, the age, weight and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities and tolerance/response to therapy. This amount can be determined by routine experimentation and is within the judgment of the clinician. Generally, a therapeutically effective amount will be from 0.01 mg/kg to 50 mg/kg, for example 0.1 mg/kg to 20 mg/kg. Pharmaceutical compositions may be conveniently presented in unit dose forms containing a predetermined amount of an active agent of the invention per dose.
Compositions may be administered individually to a patient or may be administered in combination (e.g. simultaneously, sequentially or separately) with other agents, drugs or hormones.
The dose at which the antibody molecule of the present invention is administered depends on the nature of the condition to be treated, the extent of the inflammation present and on whether the antibody molecule is being used prophylactically or to treat an existing condition.
The frequency of dose will depend on the half-life of the antibody molecule and the duration of its effect. If the antibody molecule has a short half-life (e.g. 2 to 10 hours) it may be necessary to give one or more doses per day. Alternatively, if the antibody molecule has a long half life (e.g. 2 to 15 days) it may only be necessary to give a dosage once per day, once per week or even once every 1 or 2 months.
The pharmaceutically acceptable carrier should not itself induce the production of antibodies harmful to the individual receiving the composition and should not be toxic. Suitable carriers may be large, slowly metabolised macromolecules such as proteins, polypeptides, liposomes, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers and inactive virus particles.
Pharmaceutically acceptable salts can be used, for example mineral acid salts, such as hydrochlorides, hydrobromides, phosphates and sulphates, or salts of organic acids, such as acetates, propionates, malonates and benzoates.
Pharmaceutically acceptable carriers in therapeutic compositions may additionally contain liquids such as water, saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents or pH buffering substances, may be present in such compositions. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries and suspensions, for ingestion by the patient.
Suitable forms for administration include forms suitable for parenteral administration, e.g. by injection or infusion, for example by bolus injection or continuous infusion. Where the product is for injection or infusion, it may take the form of a suspension, solution or emulsion in an oily or aqueous vehicle and it may contain formulatory agents, such as suspending, preservative, stabilising and/or dispersing agents. Alternatively, the antibody molecule may be in dry form, for reconstitution before use with an appropriate sterile liquid.
Once formulated, the compositions of the invention can be administered directly to the subject. The subjects to be treated can be animals. However, in one or more embodiments the compositions are adapted for administration to human subjects.
Suitably in formulations according to the present disclosure, the pH of the final formulation is not similar to the value of the isoelectric point of the antibody or fragment, for example if the pH of the formulation is 7 then a pI of from 8-9 or above may be appropriate. Whilst not wishing to be bound by theory it is thought that this may ultimately provide a final formulation with improved stability, for example the antibody or fragment remains in solution.
In one embodiment the pharmaceutical formulation at a pH in the range of 4.0 to 7.0 comprises: 1 to 200 mg/mL of an antibody according to the present disclosure, 1 to 100 mM of a buffer, 0.001 to 1% of a surfactant, a) 10 to 500 mM of a stabiliser, b) 10 to 500 mM of a stabiliser and 5 to 500 mM of a tonicity agent, or c) 5 to 500 mM of a tonicity agent.
For example the formulation at approximately pH6 may comprise 1 to 50 mg/mL of antibody, 20 mM L-histadine HCl, 240 mM trehalose and 0.02% polysorbate 20. Alternatively a formulation at approximately pH 5.5 may comprise 1 to 50 mg/mL of antibody, 20 mM citrate buffer, 240 mM sucrose, 20 mM arginine, and 0.02% polysorbate 20.
The pharmaceutical compositions of this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, transdermal, transcutaneous (for example, see WO98/20734), subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, intravaginal or rectal routes. Hyposprays may also be used to administer the pharmaceutical compositions of the invention. Typically, the therapeutic compositions may be prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared.
Direct delivery of the compositions will generally be accomplished by injection, subcutaneously, intraperitoneally, intravenously or intramuscularly, or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Dosage treatment may be a single dose schedule or a multiple dose schedule.
It will be appreciated that the active ingredient in the composition will be an antibody molecule. As such, it will be susceptible to degradation in the gastrointestinal tract. Thus, if the composition is to be administered by a route using the gastrointestinal tract, the composition will need to contain agents which protect the antibody from degradation but which release the antibody once it has been absorbed from the gastrointestinal tract.
A thorough discussion of pharmaceutically acceptable carriers is available in Remington's Pharmaceutical Sciences (Mack Publishing Company, N.J. 1991).
In one embodiment the formulation is provided as a formulation for topical administrations including inhalation.
Suitable inhalable preparations include inhalable powders, metering aerosols containing propellant gases or inhalable solutions free from propellant gases. Inhalable powders according to the disclosure containing the active substance may consist solely of the abovementioned active substances or of a mixture of the abovementioned active substances with physiologically acceptable excipient.
These inhalable powders may include monosaccharides (e.g. glucose or arabinose), disaccharides (e.g. lactose, saccharose, maltose), oligo- and polysaccharides (e.g. dextrans), polyalcohols (e.g. sorbitol, mannitol, xylitol), salts (e.g. sodium chloride, calcium carbonate) or mixtures of these with one another. Mono- or disaccharides are suitably used, the use of lactose or glucose, particularly but not exclusively in the form of their hydrates.
Particles for deposition in the lung require a particle size less than 10 microns, such as 1-9 microns for example from 0.1 to 5 μm, in particular from 1 to 5 μm. The particle size of the active ingredient (such as the antibody or fragment) is of primary importance.
The propellant gases which can be used to prepare the inhalable aerosols are known in the art. Suitable propellant gases are selected from among hydrocarbons such as n-propane, n-butane or isobutane and halohydrocarbons such as chlorinated and/or fluorinated derivatives of methane, ethane, propane, butane, cyclopropane or cyclobutane. The abovementioned propellant gases may be used on their own or in mixtures thereof.
Particularly suitable propellant gases are halogenated alkane derivatives selected from among TG 11, TG 12, TG 134a and TG227. Of the abovementioned halogenated hydrocarbons, TG134a (1,1,1,2-tetrafluoroethane) and TG227 (1,1,1,2,3,3,3-heptafluoropropane) and mixtures thereof are particularly suitable.
The propellant-gas-containing inhalable aerosols may also contain other ingredients such as cosolvents, stabilisers, surface-active agents (surfactants), antioxidants, lubricants and means for adjusting the pH. All these ingredients are known in the art.
The propellant-gas-containing inhalable aerosols according to the invention may contain up to 5% by weight of active substance. Aerosols according to the invention contain, for example, 0.002 to 5% by weight, 0.01 to 3% by weight, 0.015 to 2% by weight, 0.1 to 2% by weight, 0.5 to 2% by weight or 0.5 to 1% by weight of active ingredient.
Alternatively topical administrations to the lung may also be by administration of a liquid solution or suspension formulation, for example employing a device such as a nebulizer, for example, a nebulizer connected to a compressor (e.g., the Pari LC-Jet Plus® nebulizer connected to a Pari Master® compressor manufactured by Pari Respiratory Equipment, Inc., Richmond, Va.).
The antibody of the invention can be delivered dispersed in a solvent, e.g., in the form of a solution or a suspension. It can be suspended in an appropriate physiological solution, e.g., saline or other pharmacologically acceptable solvent or a buffered solution. Buffered solutions known in the art may contain 0.05 mg to 0.15 mg disodium edetate, 8.0 mg to 9.0 mg NaCl, 0.15 mg to 0.25 mg polysorbate, 0.25 mg to 0.30 mg anhydrous citric acid, and 0.45 mg to 0.55 mg sodium citrate per 1 ml of water so as to achieve a pH of about 4.0 to 5.0. A suspension can employ, for example, lyophilised antibody.
The therapeutic suspensions or solution formulations can also contain one or more excipients. Excipients are well known in the art and include buffers (e.g., citrate buffer, phosphate buffer, acetate buffer and bicarbonate buffer), amino acids, urea, alcohols, ascorbic acid, phospholipids, proteins (e.g., serum albumin), EDTA, sodium chloride, liposomes, mannitol, sorbitol, and glycerol. Solutions or suspensions can be encapsulated in liposomes or biodegradable microspheres. The formulation will generally be provided in a substantially sterile form employing sterile manufacture processes.
This may include production and sterilization by filtration of the buffered solvent/solution used for the formulation, aseptic suspension of the antibody in the sterile buffered solvent solution, and dispensing of the formulation into sterile receptacles by methods familiar to those of ordinary skill in the art.
Nebulizable formulation according to the present disclosure may be provided, for example, as single dose units (e.g., sealed plastic containers or vials) packed in foil envelopes. Each vial contains a unit dose in a volume, e.g., 2 mL, of solvent/solution buffer.
The antibodies disclosed herein may be suitable for delivery via nebulisation.
It is also envisaged that the antibody of the present invention may be administered by use of gene therapy. In order to achieve this, DNA sequences encoding the heavy and light chains of the antibody molecule under the control of appropriate DNA components are introduced into a patient such that the antibody chains are expressed from the DNA sequences and assembled in situ.
The present invention also provides an antibody molecule (or compositions comprising same) for use in the control of inflammatory diseases, for example acute or chronic inflammatory disease. Suitably, the antibody molecule (or compositions comprising same) can be used to reduce the inflammatory process or to prevent the inflammatory process. In one embodiment there is provided an in vivo reduction of activated T cells, in particular those involved in inappropriate inflammatory immune responses, for example recruited to the vicinity/location of such a response.
Reduction of activated T cells, as employed herein, may be a reduction, 10, 20, 30, 40, 50, 60, 70, 80, 90 or more percent in comparison to before treatment or without treatment. Advantageously, treatment with an antibody, fragment or composition according to the present invention, may allow the reduction in the level of activated T cells, without reducing the patients general level of T cells (unactivated T cells). This may result in fewer side effects, and possibly prevent T cell depletion in the patient.
The present invention also provides the antibody molecule of the present invention for use in the treatment or prophylaxis of an immune disorder. The immune disorder, may, for example be selected from the group consisting of infections (viral, bacterial, fungal and parasitic), endotoxic shock associated with infection, arthritis, rheumatoid arthritis, asthma, COPD, pelvic inflammatory disease, Alzheimer's Disease, inflammatory bowel disease, Crohn's disease, ulcerative colitis, Peyronie's Disease, coeliac disease, gallbladder disease, Pilonidal disease, peritonitis, psoriasis, vasculitis, surgical adhesions, stroke, Type I Diabetes, lyme disease, arthritis, meningoencephalitis, autoimmune uveitis, immune mediated inflammatory disorders of the central and peripheral nervous system such as multiple sclerosis, lupus (such as systemic lupus erythematosus) and Guillain-Barr syndrome, Atopic dermatitis, autoimmune hepatitis, fibrosing alveolitis, Grave's disease, IgA nephropathy, idiopathic thrombocytopenic purpura, Meniere's disease, pemphigus, primary biliary cirrhosis, sarcoidosis, scleroderma, Wegener's granulomatosis, other autoimmune disorders, pancreatitis, trauma (surgery), graft-versus-host disease, transplant rejection, heart disease including ischaemic diseases such as myocardial infarction as well as atherosclerosis, intravascular coagulation, bone resorption, osteoporosis, osteoarthritis, periodontitis and hypochlorhydia, or infertility related to lack of fetal-maternal tolerance.
In one embodiment the antibody according to the invention is employed in the treatment of allergy, COPD, autoimmune disease or rheumatoid arthritis.
The present invention also provides an antibody molecule according to the present invention for use in the treatment or prophylaxis of pain, particularly pain associated with inflammation.
The present invention further provides the use of an antibody molecule, fragment or composition according to the present invention in the manufacture of a medicament for the treatment or prophylaxis of an immune disorder, in particular the immune disorder is rheumatoid arthritis, asthma or COPD.
The present invention further provides the use of an antibody molecule, fragment or composition according to the present invention in the manufacture of a medicament for the treatment or prophylaxis of one or more medical indications described herein.
An antibody molecule, fragment or composition of the present invention may be utilised in any therapy where it is desired to increase the effects of PD-1 in the human or animal body.
In one embodiment the antibody molecule of the present invention or a composition comprising the same is used for the control of inflammatory disease, e.g. as described herein.
The present invention also provides a method of treating human or animal subjects suffering from or at risk of an immune disorder, the method comprising administering to the subject an effective amount of the antibody molecule of the present invention, or a composition comprising the same.
In one embodiment there is provided a process for purifying an antibody (in particular an antibody or fragment according to the invention) comprising the steps:

    performing anion exchange chromatography in non-binding mode such that the impurities are retained on the column and the antibody is eluted.


Suitable ion exchange resins for use in the process include Q.FF resin (supplied by GE-Healthcare). The step may, for example be performed at a pH about 8.
The process may further comprise an initial capture step employing cation exchange chromatography, performed for example at a pH of about 4 to 5, such as 4.5. The cation exchange chromatography may, for example employ a resin such as CaptoS resin or SP sepharose FF (supplied by GE-Healthcare). The antibody or fragment can then be eluted from the resin employing an ionic salt solution such as sodium chloride, for example at a concentration of 200 mM.
Thus the chromatograph step or steps may include one or more washing steps, as appropriate.
The purification process may also comprise one or more filtration steps, such as a dia filtration step.
Thus in one embodiment there is provided a purified anti-PD-1 antibody or fragment, for example a humanised antibody or fragment, in particular an antibody or fragment according to the invention, in substantially purified from, in particular free or substantially free of endotoxin and/or host cell protein or DNA.
Purified form as used supra is intended to refer to at least 90% purity, such as 91, 92, 93, 94, 95, 96, 97, 98, 99% w/w or more pure.
Substantially free of endotoxin is generally intended to refer to an endotoxin content of 1 EU per mg antibody product or less such as 0.5 or 0.1 EU per mg product.
Substantially free of host cell protein or DNA is generally intended to refer to host cell protein and/or DNA content 400 μg per mg of antibody product or less such as 100 μg per mg or less, in particular 20 μg per mg, as appropriate.
The antibody molecule of the present invention may also be used in diagnosis, for example in the in vivo diagnosis and imaging of disease states involving PD-1.
Comprising in the context of the present specification is intended to meaning including.
Where technically appropriate embodiments of the invention may be combined.
Embodiments are described herein as comprising certain features/elements. The disclosure also extends to separate embodiments consisting or consisting essentially of said features/elements.
The present invention is further described by way of illustration only in the following examples, which refer to the accompanying Figures, in which:
EXAMPLES


    FIG. 1 in detail:
    a) Light chain V region of antibody 949 (SEQ ID NO:8)
    b) Heavy chain V region of antibody 949 (SEQ ID NO:9)
    c) CDRH1 (SEQ ID NO:1), CDRH2 (SEQ ID NO:2), CDRH3 (SEQ ID NO:3), CDRL1 (SEQ ID NO:4), CDRL2 (SEQ ID NO:5), CDRL3 (SEQ ID NO:6) of antibody 949)
    FIG. 2
    
        a) Modified CDRL3 (deamidation site modified)
        b) 949 VK1 gL1 V region (SEQ ID NO:10)
        c) 949 VK1 gL1 V region DNA (SEQ ID NO:11)
        d) 949 VK1 gL1 V region with signal sequence (SEQ ID NO:12)
        e) 949 VK1 gL1 V region DNA with signal sequence (SEQ ID NO:13)
        f) 949 VK1 gL1 light chain V+constant (SEQ ID NO:14)
    
    
    FIG. 3
    
        a) 949 VK1 gL1 light chain V+constant DNA (SEQ ID NO:15)
        b) 949 VK1 gL1 light chain V+constant with signal sequence (SEQ ID NO:16)
        c) 949 VK1 gL1 light chain V+constant DNA with signal sequence (SEQ ID NO:17)
        d) 949 VK1 gL9 V region (SEQ ID NO:18)
    
    
    FIG. 4
    
        a) 949 VK1 gL9 V region DNA (SEQ ID NO:19)
        b) 949 VK1 gL11 V region (SEQ ID NO:20)
        c) 949 VK1 gL11 V region DNA (SEQ ID NO:21)
        d) 949 VK1 gL12 V region (SEQ ID NO:22)
        e) 949 VK1 gL12 V region DNA (SEQ ID NO:23)
        f) 949 VK1 gL14 V region (SEQ ID NO:24)
    
    
    FIG. 5
    
        a) 949 VK1 gL14 V region DNA (SEQ ID NO:25)
        b) 949 VK3 gL1 V region (SEQ ID NO:26)
        c) 949 VK3 gL1 V region DNA (SEQ ID NO:27)
        d) 949 VK3 gL11 V region (SEQ ID NO:28)
        e) 949 VK3 gL11 V region DNA (SEQ ID NO:29)
        f) 949 gH1a V region (SEQ ID NO:30)
    
    
    FIG. 6
    
        a) 949 gH1a V region DNA (SEQ ID NO:31)
        b) 949 gH1a V region with signal sequence (SEQ ID NO:32)
        c) 949 gH1a V region with signal sequence DNA (SEQ ID NO:33)
        d) 949 gH1a V region and constant region (SEQ ID NO:34)
    
    
    FIG. 7
    
        a) 949 gH1a V region and constant region DNA (SEQ ID NO:35)
    
    
    FIG. 8
    
        a) 949 gH1a V region and constant region with signal sequence (SEQ ID NO:36)
    
    
    FIG. 9
    
        a) 949 gH1a V region and constant region with signal sequence DNA (SEQ ID NO:37)
    
    
    FIG. 10
    
        a) 949 gH8a V region (SEQ ID NO:38)
        b) 949 gH8a V region DNA (SEQ ID NO:39)
        c) 949 gH20a V region (SEQ ID NO:40)
        d) 949 gH20a V region DNA (SEQ ID NO:41)
        e) 949 gH1b V region (SEQ ID NO:42)
        f) 949 gH1b V region (SEQ ID NO:43)
    
    
    FIG. 11
    
        a) 949 gH8b V region (SEQ ID NO:44)
        b) 949 gH8b V region DNA (SEQ ID NO:45)
        c) 949 gH20b V region (SEQ ID NO:46)
        d) 949 gH20b V region DNA (SEQ ID NO:47)
        e) Human VK1 2-1-(1) L23 JK4 acceptor framework (SEQ ID NO:48)
        f) Human VK1 2-1-(1) L23 JK4 acceptor framework DNA (SEQ ID NO:49)
    
    
    FIG. 12
    
        a) Human VK3 6-1-(1) A27 JK4 acceptor framework (SEQ ID NO:50)
        b) Human VK3 6-141) A27 JK4 acceptor framework DNA (SEQ ID NO:51)
        c) Human VH1 1-3 1-46 JH4 acceptor framework (SEQ ID NO:52)
        d) Human VH1 1-3 1-46 JH4 acceptor framework DNA (SEQ ID NO:53)
        e) Human VH1 1-2 1-e JH4 acceptor framework (SEQ ID NO:54)
        f) Human VH1 1-2 1-e JH4 acceptor framework DNA (SEQ ID NO:55)
    
    
    FIG. 13 shows Inhibition of human CD4+ T cell proliferation by antibody 949. CD4+ T cells were purified from human PBMCs by negative selection and cultured with Dynalbeads coated with anti-CD3 plus control (BSA) or anti-PD-1 antibodies/recombinant PD-L2. Proliferation (y-axis) was measured by 3H-thymidine incorporation at day 6. Bars represent the % of maximal response (anti-CD3/BSA) and are the mean+/−S.E.M. of 4 different donor cultures.
    FIG. 14 Ligand blocking assay with antibody 949. PD-1 expressing HEK293 cells were pre-incubated with purified chimeric 949 or humanised 949, or isotype matched positive and negative controls, followed by incubation with recombinant PD-L2. Blocking of PD-L2 to PD-1 by antibody 949 was assessed by revealing PD-L2 binding with an anti-mouse IgG H+L PE conjugated antibody. Figures in parentheses denote calculated concentration in μg/mL of humanised 949 added during the pre-incubation stage.
    FIG. 15 Stimulation of SEAP from the human PD-1/CD28/TCRζ SEAP reporter cell line by antibody 949. Dilutions of antibody were incubated with reporter cells and the released SEAP determined. Data was plotted as fold induction (signal/background signal).
    FIG. 16 Cross-reactivity of 949 chimeric and humanised grafts with PD-1 from Cynomolgus and Rhesus monkeys. Binding of 949 grafts to HEK293 cells transfected with empty vector (d), or PD-1 from human (a), cynomolgus (b) or rhesus (c) was measured by flow cytometry. Data is presented as geomean of PD-1 antibody associated fluorescence.
    FIG. 17 shows an alignment of the light chains for the murine, acceptor frameworks and humanised light chains. CDRs are in bold and underlined. Donor residues are in bold, italic and are highlighted.
    FIG. 18 shows an alignment of the heavy chains for the murine, acceptor frameworks and humanised heavy chains. CDRs are in bold and underlined. Donor residues are in bold, italic and are highlighted.
    FIG. 19 shows 949gH1a heavy chain (V+constant−hu IgG4P delta Lys) (SEQ ID NO:58)
    FIG. 20 949gH1a heavy chain (V+constant−hu IgG4P delta Lys, exons underlined) (SEQ ID NO:59)
    FIG. 21 949gH1a heavy chain (V+constant−hu IgG4P delta Lys) with signal sequence underlined and italicised (SEQ ID NO: 60)
    FIG. 22 949gH1a heavy chain (V+constant−hu IgG4P delta Lys, exons underlined) with signal sequence underlined and italicised (SEQ ID NO: 61)
    FIG. 23 949gH1a heavy chain (V+constant−hu IgG1 delta Lys) (SEQ ID NO: 62)
    FIG. 24 949gH1a heavy chain (V+constant−hu IgG1 delta Lys, exons underlined) (SEQ ID NO: 63)
    FIG. 25 949gH1a heavy chain (V+constant−hu IgG1 delta Lys) with signal sequence underlined and italicised (SEQ ID NO:64)
    FIG. 26 949gH1a heavy chain (V+constant−hu IgG1 delta Lys exons underlined) with signal sequence underlined and italicised (SEQ ID NO: 65)
    FIG. 27
    (a) 49 VK1 gL15 V-region amino acid and nucleic acid sequence and a corresponding amino acid sequence where a signal sequence is included. (SEQ ID NO: 66)
    (b) 949 VK1 gL15 V-region (SEQ ID NO: 67)
    (c) 949 VK1 gL15 V-region with signal sequence underlined and italicised (SEQ ID NO: 68)
    FIG. 28
    (a) 949 VK1 gL15 V-region nucleic acid sequence including a signal sequence. Also shown is an amino acid sequence of a light chain variable region and constant region. (SEQ ID NO: 69)
    (b) 949 VK1 gL15 light chain (V+constant) (SEQ ID NO: 70)
    FIG. 29
    (a) 949VK1 gL15 light chain variable and constant region nucleic acid sequence. Also shown is a light chain amino acid sequence including a signal sequence. (SEQ ID NO: 71)
    (b) 949 VK1 gL15 light chain with signal sequence underlined and italicised (SEQ ID NO: 72)
    FIG. 30
    (a) 949 VK1 gL15 light chain with signal sequence underlined and italicised (SEQ ID NO:73)
    FIG. 31
    (a) 949gH20b V-region with signal sequence underlined and italicized (SEQ ID NO:74)
    (b) 949gH20b V-region with signal sequence underlined and italicized (SEQ ID NO: 75)
    (c) 949gH20b heavy chain (V+constant−hu IgG4P delta Lys) (SEQ ID NO:76)
    FIG. 32
    (a) 949gH20b heavy chain (V+constant−hu IgG4P delta Lys) (SEQ ID NO:77)
    FIG. 33
    (a) 949gH20b heavy chain (V+constant−hu IgG4P delta Lys) with signal sequence underlined and italicized (SEQ ID NO: 78)
    FIG. 34
    (a) 949gH20b heavy chain (V+constant−hu IgG4P delta Lys, exons underlined) with signal sequence underlined and italicised (SEQ ID NO: 79)
    FIG. 35
    (a) 949gH20b heavy chain (V+constant−hu IgG1 delta Lys) (SEQ ID NO:80)
    FIG. 36
    (a) 949gH20b heavy chain (V+constant−hu IgG1 delta Lys, exons underlined) (SEQ ID NO:81)
    FIG. 37
    (a) 949gH20b heavy chain (V+constant−hu IgG1 delta Lys) with signal sequence underlined and italicized (SEQ ID NO:82)
    FIG. 38
    (a) 949gH20b heavy chain (V+constant−hu IgG1 delta Lys, exons underlined) with signal sequence underlined and italicised (SEQ ID NO: 83)
    FIG. 39 Ligand blocking binding assay for 949 VK1 gL9 gH20b, 949 VK1 gL15 g8a, 949 VK1 gL15 g8b, 949 VK1 gL15 gH20a, VK1 gL15 gH20b.
    FIGS. 40 and 41 Activated T-cell binding assay with various constructs
    FIGS. 42a) and b)—The various antibody constructs cross react with human and cyno PD-1
    FIG. 43 shows an alignment of the light chains for the murine, acceptor frameworks and humanised light chains. CDRs are in bold and underlined. Donor residues are in bold, italic and are highlighted.


Example 1
Methods for Generation of Anti-PD-1 Antibody Clone 19
The generation of antibody clone 19 has already been described in international application WO2010/029434.
1.1 Myeloma Cell Line
For fusion the myeloma cell line SP2/0-Ag14 from the German Collection of Microorganisms and Cell Cultures (DSMZ GmbH, Braunschweig) was used. This cell line is a hybrid between BALB/c spleen cells and the myeloma cell line P3x63Ag8. The cells have been described as not synthesizing or secreting immunoglobulin chains, being resistant to 8-azaguanine at 20 μg/ml, and not growing in HAT (Hypoxanthine, Aminopterin, Thymidine) medium. The SP2/0 cells are routinely maintained in tissue culture flasks in standard growth medium (with 10% FCS). A new aliquot of frozen SP2/0 cells was used after a period of 2 weeks in order to avoid the implementation of HGPRT-positive revertants. The myeloma cells were shown to be negative in all mycoplasma tests.
1.2 Antigens for Immunization and Screening
The recombinant protein PD-1Fc was prepared using the methods described for the production of CD28Fc (Evans et al. Nat Immunol. 6, 271-9 (2005)) and concentrated to 5.1 mg/ml in 0.01 M HEPES, 150 mM NaCl, pH 7.4. SDS-PAGE analysis of the antigen run under reducing and non-reducing conditions established the purity of the protein to be >95%.
1.3 Immunization
Five mice (about 8 weeks old) were immunized via the intraperitoneal cavity using an immunization protocol over 60 days. For immunization an alum precipitate of the immunogen was prepared. The alum precipitate was freshly prepared for each boost. The mice were immunized with 50 μg protein and boosted with 25 μg protein. Three mice were used for fusion.
1.4 General Handling of Cells
Cells were handled under sterile conditions using a laminar air-flow system, sterile materials and sterile solutions. Cells were incubated at 37° C. in a humid atmosphere containing 5% carbon dioxide. For cultivation of the hybridoma cells a complete growth medium (CGM) containing DMEM with supplements 2-mercaptoethanol, L-Glutamine, GlutaMax, HT, non essential amino acids, sodium pyruvate, antibiotics/antimycotic solution (in concentrations recommended by the supplier) and FCS at different concentrations (10%, 15% or 20%) was used.
1.5 Preparation of Spleen Cells and Cell Fusions
After asphyxiation of the three immunized mice in CO2 spleens were aseptically removed. A single cell suspension of pooled spleens was prepared. The spleen cells and the myeloma cells were washed several times with DMEM and fused twice in the presence of 1 ml 50% (w/v) PEG 3550 (ratio spleen cells to SP2/0 2.5:1 and 2.4:1). The hybridomas produced were resuspended in CGM containing 20% FCS and aminopterin (HAT medium). The cell suspension (140 Cl/well) of each fusion was plated out into eight 96-well tissue culture flat-bottom plates (Corning-Costar) containing 140 Cl/well peritoneal exudate cells as feeder cells in CGM with 20% FCS. The plates were incubated for 10 days. During this period cells were fed two times with HAT medium. An aliquot of the spleen cell preparation (about 8×106 spleen cells) was cultivated 10 days in a well of a 24-well plate and the cell culture supernatant served as positive control in ELISA.
1.6 Screening Assay
An ELISA was used for screening of IgG in cell culture supernatants. 96 well flat-bottom polystyrene microtiter plates (Greiner, Cat. No 655061) were coated with 50 μl/well PD-1Fc antigen (5 μg/ml) in 0.5 M carbonate/bicarbonate buffer, pH 9.6. After incubation overnight in a moist chamber at 4° C. the plates were washed with tris-buffered saline (TBS, 50 mM Tris, pH 7.8, 500 mM sodium chloride) containing 0.01% Triton X-100 (washing buffer) and blocked with 200 μl/well 2% FCS in TBS (blocking buffer) for 1 hour at room temperature (RT) on a shaker. The wells were washed with washing buffer and 100 μl cell culture supernatant was added in the appropriate well. Cell culture supernatant from SP 2/0 myeloma cells was used as a negative control. As positive control cell culture supernatant from spleen cell culture was used. The plates were incubated on a shaker for 1 h at RT, followed by several washes. For detection of bound antibodies plates were incubated with 50 μl/well goat anti-mouse IgG (Fab specific) conjugated to alkaline phosphatase (1:5000) in blocking buffer for 1 h at RT on a shaker, followed by several washes and addition of 150 μl/well substrate buffer (2 mM 4-nitrophenyl phosphate in 5% diethanolamine+0.5 mM MgCl2, pH 9.8). The optical density (OD) was estimated in a 12-channel Dynex Opsys MR microplate reader at 405 nm. Wells with OD405 nm 2-fold higher than the OD405 nm of the average plate value were selected as positive.
1.7 Selection of Stable Antibody Producers
Cells from positive IgG producing cultures were transferred into wells of a 48-well plate and cultivated for several days (depending on the growth characteristics of the cells). An ELISA on PD-1Fc and without precoated antigen in order to select the specific binders was carried out. The cells from ELISA-positive wells were frozen in freezing medium (90% FCS, 10% DMSO). An aliquot of the cells was further cultivated for production of cell culture supernatants for further characterization.
1.8 Limiting Dilution Cloning
As soon as positive wells were identified, hybridoma cells were cloned to reduce the risk of overgrowth by non-producing cells (first cloning). To ensure that the antibodies are truly monoclonal the hybridomas were cloned again (second cloning). The method of limiting dilution was used for both cloning procedures. IgG producing cells were distributed into one 96 well plate containing feeder cells at a density of 1-3 cells per well. After 8-10 days (depending on growth characteristics) all plates were visually inspected under the microscope for detection of monoclonal growth. Culture supernatants from such wells were screened for specific immunoglobulin content using the above-described screening assay. The appropriate clones concerning growth characteristic and ELISA signal were selected, transferred into wells of a 24-well plate and cultivated for some days. A screening assay was performed. This procedure was repeated two to three times. The appropriate subclone was selected respectively for the second cloning procedure or cultivation for cryopreservation. This procedure resulted in the production of an anti-PD-1 antibody known as Clone 19.
1.9 Preparation and Isotyping of Antibodies
Hybridoma supernatant was prepared and diluted into sterile, azide-free PBS. Purified stocks of monoclonal antibodies were isotyped at 1 μg/ml in PBS using the IsoStrip Mouse Monoclonal Antibody Isotyping Kit (Santa Cruz; sc-24958). Clone 19 was found to be isotype IgG1K.
1.10 Sequencing of Clone 19
The genes encoding clone 19 were cloned and sequenced and are provided in FIG. 1. This antibody was named antibody CA051—00949 (often abbreviated to 949).
Example 2
Characterisation and Selection of Antibody 949
2.1 Rationale for Antibody Selection
In order to generate a therapeutic reagent which is able to transduce an inhibitory signal to T cells through PD-1, an agonistic anti-PD-1 monoclonal antibody was selected. Targeting the membrane proximal epitope with this antibody will ensure that it does not block the binding of the endogenous ligands for PD-1 (PD-L1 or PD-L2). Therefore, the agonistic antibody will act in addition to, and may potentiate, any natural inhibitory signals from the ligands being transduced through PD-1. Humanised versions of this antibody will have potential therapeutic utility in a wide range of human diseases which involve inappropriate levels of T or B lymphocyte activation.
2.2 Analysis of PD-1 Agonism Induced by Antibody 949 on Human CD4+ T Cells
To demonstrate that antibody 949 (parental variable regions, murine IgG1) can induce signaling through PD-1, it was tested for its ability to inhibit T cell receptor (TCR)-derived activating signals. This was achieved by covalently coupling 949, along with a TCR-activating anti-CD3 antibody, to Dynalbeads. The beads were then added to cultures of primary human CD4+ T cells and the resultant proliferation measured by 3H-thymidine incorporation after 6 days.
Tosyl-activated 4.5 μm Dynalbeads (M450; Invitrogen) were washed in 0.1M sterile phosphate buffer (pH 7.5) and loaded with 2 μg of anti-human CD3 (clone OKT3) per 1×107 beads at 37° C. for 8 h with continuous inversion mixing. The beads were then washed to remove unconjugated anti-CD3 and aliquots were secondarily coated with 3 μg of BSA, a non-agonistic control anti-PD-1 antibody, 949 or recombinant human PD-L2.mFc per 1×107 beads at 37° C. for 19 h with continuous inversion mixing. Beads were subsequently washed and incubated in 0.2M Tris/0.1% BSA (pH 8.5) for 3 hours to inactivate free tosyl groups, followed by washing and re-suspension of beads in PBS/0.1% BSA/2 mM EDTA (pH 7.4). Equal anti-CD3 and antibody/ligand coating of the bead sets was confirmed by staining the beads with fluorochrome-labelled isotype-specific antibodies and analysing by flow cytometry.
For human T cell proliferation studies, fresh heparinised blood was diluted 1:1 with RPMI and the lymphocytes isolated by density gradient separation (Ficoll Hypaque). CD4+ T cells were purified from the whole PBMCs by negative selection using MACS (CD4+ T cell isolation Kit II; Miltenyi Biotec). 1×105 human CD4+ T cells/well were cultured at a 1:1 ratio with the coated beads in 96-well round-bottomed plates and incubated at 37° C./5% CO2/100% humidity for 6 days. Proliferation was measured after 6 days by addition of 0.5 μCi/well 3H-thymidine for the last 6 hours of culture. Cells were harvested onto glass-fibre filters and incorporated 3H-thymidine was measured by β-scintillation counting.
2.3 Results
The results in FIG. 13 show the day 6 proliferative response by human CD4+ T cells measured in the presence of anti-CD3 plus anti-PD-1 antibody or BSA control coated beads. The data are expressed as percentage of the maximal response (anti-CD3 plus BSA control) and are the mean of 4 different donor responses. CD4+ T cell proliferation was inhibited by antibody 949, so that the average proliferation observed was only 51.6% of the maximum. Similar inhibition of CD4+ T cell proliferation was seen with recombinant human PD-L2, utilised as a positive control for PD-1 signaling. In comparison, a non-agonistic anti-PD-1 mAb was used, which showed no effect on CD4+ T cell proliferation in this assay as expected. This demonstrates that antibody 949 is capable of inducing agonistic signaling through PD-1, which leads to inhibition of human CD4+ T cell responses.
Example 3
Humanisation of Antibody CA051—00949
Antibody CA051—00949 was humanised by grafting the complementarity determining regions (CDRs, FIG. 1c) from the mouse antibody V-regions onto human germline antibody V-region frameworks. In order to recover the activity of the antibody, a number of framework residues from the mouse V-regions were also retained in the humanised sequence. These residues were selected using the protocol outlined by Adair et al. (1991) (Humanised antibodies. WO91/09967). Alignments of the mouse antibody (donor) V-region sequences with the human germline antibody (acceptor) V-region sequences are shown in FIGS. 17 and 18 together with the designed humanised sequences.
The CDRs grafted from the donor to the acceptor sequence are as defined by Kabat (Kabat et al. Sequence of proteins of immunological interest (1987). Bethesda, Md., National Institutes of Health, US), with the exception of CDR-H1 where the combined Chothia/Kabat definition is used (see Adair et al. (1991) Humanised antibodies. WO91/09967).
The heavy chain CDRs of antibody 949 were grafted onto the human V-region VH1 1-3 1-46 plus JH4 J-region (V BASE, http://vbase.mrc-cpe.cam.ac.uk/). The heavy chain framework residues are all from the human germline gene, with the exception of residues 25, 37, 41, 48, 71, 73 and 76 (Kabat numbering), where the donor residues Phenylalanine (F25), Methionine (M37), Histidine (H41), Isoleucine (148), Valine (V71), Lysine (K73) and Threonine (T76) were retained, respectively. The Glutamine residue at position 1 of the human framework was replaced with Glutamic acid (E1) to afford the expression and purification of a homogeneous product: the conversion of Glutamine to pyroGlutamate at the N-terminus of antibodies and antibody fragments is widely reported. The resulting humanised sequence was named 949 gH1a. An alternative humanised heavy chain sequence, 949 gH1b, was created by grafting the CDRs onto human V-region VH1 1-2 1-e plus JH4 J-region (V BASE, http://vbase.mrc-cpe.cam.ac.uk/). The heavy chain framework residues are all from the human germline gene, with the exception of residues 25, 37, 41, 48, 71, 76 and 78 (Kabat numbering), where the donor residues Phenylalanine (F25), Methionine (M37), Histidine (H41), Isoleucine (148), Valine (V71), Threonine (T76) and Valine (V78) were retained, respectively. The Glutamine residue at position 1 of the human framework was replaced with Glutamic acid (E1) to afford the expression and purification of a homogeneous product.
Human V-region VK1 2-1-(1) L23 plus JK4 J-region (V BASE, http://vbase.mrc-cpe.cam.ac.uk/) was chosen as the acceptor for the light chain CDRs. The light chain framework residues are all from the human germline gene, with the exception of residues 1, 2, 3, 4, 47, 60 and 70 (Kabat numbering), where the donor residues Glutamaic acid (E1), Asparagine (N2), Valine (V3), Leucine (L4), Tryptophan (W47), Aspartic acid (D60) and Serine (S70) were retained, respectively. The resulting humanised sequence was named 949 VK1 gL1. An alternative humanised light chain sequence, 949 VK3 gL1, was created by grafting the CDRs onto human V-region VK3 6-1-(1) A27 plus JK4 J-region (V BASE, http://vbase.mrc-cpe.cam.ac.uk/). The light chain framework residues are all from the human germline gene, with the exception of residues 2, 47, 58, 70, 71 and 85 (Kabat numbering), where the donor residues Asparagine (N2), Tryptophan (W47), Valine (V58), Serine (S70), Tyrosine (Y71) and Threonine (T85) were retained, respectively.
Genes encoding the humanised 949 VK1 gL1, 949 VK3 gL1, 949 gH1a and 949 gH1b light and heavy chain V-region sequences were designed and constructed by an automated synthesis approach by Entelechon GmbH. Oligonucleotide-directed mutagenesis was used to modify the genes to create variants of the humanized heavy chains (gH2a through to gH20a, and gH2b through to gH20b) and light chains (VK1 gL2 through to gL17, and VK3 gL2 through to gL17), and in some cases a deamidation site in CDRL3 was modified (FIG. 2a). FIG. 27a shows a light chain gL15 comprising a modified CDRL3. The humanised 949 light chain V-region gene sequences were cloned into the UCB-Celltech human light chain expression vector pKH10.1, which contains DNA encoding the human Kappa chain constant region (Km3 allotype). The humanised 949 heavy chain V-region gene sequences were cloned into the UCB-Celltech human gamma-4 heavy chain expression vector pVhγ4P FL, which contains DNA encoding the human gamma-4 heavy chain constant region with the hinge stabilising mutation S241P (Angal et al., Mol Immunol. 1993, 30(1):105-8), and also into a version of the human gamma-4P heavy chain vector in which the codon for the C-terminal Lysine residue has been removed, pVhγ4P delta Lys. The humanised 949 heavy chain V-region gene sequences were also cloned into the UCB-Celltech human gamma-1 heavy chain expression vector pVhγ1 delta Lys, which contains DNA encoding the human gamma-1 heavy chain constant region with the C-terminal Lysine residue removed. Transient co-transfection of light and heavy chain vectors into HEK293 suspension cells was achieved using 293 Fectin (12347-019 Invitrogen), and gave expression of the humanised, recombinant 949 antibodies.
A number of different variants of the humanised heavy and light chains were generated by including the CDRs in FIG. 1(c) derived from antibody 949 and 2(a) CDRL3 from clone 19 with a modified deamidation site, and one or more of the donor residues listed below, depending on the framework used. The sequences are provided in FIGS. 2-11 and FIGS. 17 to 38.










3.1 Ab949 residues for humanization


VK1 Light chain 2-1-(1) L23








Kabat position 
Human acceptor residue











1
Alanine


2
Isoleucine


3
Arginine


4
Methionine


47
Phenylalanine


60
Serine


70
Aspartic acid



















VK3 Light chain 6-1-(1) A27








Kabat position
Human acceptor residue











2
Isoleucine


47
Leucine


58
Isoleucine


70
Aspartic acid


71
Phenylalanine


85
Valine



















VH Heavy chain 1-3 1-46








Kabat position
Human acceptor residue





25
Serine


37
Valine


41
Proline


48
Methionine


71
Arginine


73
Threonine


76
Serine



















VH Heavy chain 1-2 1-e








Kabat position
Human acceptor residue





25
Serine


37
Valine


41
Proline


48
Methionine


71
Alanine


76 
Serine


78 
Alanine









Example 4
Characterisation of the Humanised Antibodies Generated in Example 3
4.1 Affinity
Binding Affinity Measurements
The assay format involved capture of 949 or humanised version thereof by immobilised anti-human Fc and subsequent titration of the human PD-1 over the captured surface.
BIA (Biamolecular Interaction Analysis) was performed using a BIAcore 3000 (BIAcore AB). Affinipure F(ab′)2 Fragment, goat anti-human IgG, Fc fragment specific (Jackson ImmunoResearch) was immobilised on a CM5 Sensor Chip via amine coupling chemistry to a capture level of ≈6000 response units (RUs). A blank surface was prepared in a similar way, omitting the Fc fragment from the procedure. HBS-EP buffer (10 mM HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005% Surfactant P20, BIAcore AB) was used as the running buffer with a flow rate of 10 μl/min. A 10 μl injection of 949 IgG at  ̃1 μg/mL was used to give  ̃200RU capture by the immobilised anti-human IgG-Fc. Human PD-1 was titrated over the captured 949 or humanised variants at various concentrations (50 nM or below) at a flow rate of 30 μL/min. The surface was regenerated by a 10 μL injection of 40 mM HCl, followed by a 5 μL injection of 5 mM NaOH at a flowrate of 10 μL/min.
Background subtraction binding curves were analysed using the BIAevaluation software (version 3.2) following standard procedures. Kinetic parameters were determined from the fitting algorithm.
Data for 949 and the various humanised versions are shown in Table 1. For all grafts tested except for 1, (VK1 gL11gH1a) affinity for PD-1 was improved compared to the 949 parental antibody. The chimeric contained the 949 variable regions with human IgG4 constant domains.







TABLE 1







4.2 Analysis of ligand blocking activity of antibody


949 and humanised versions of 949












Antibody
ka (1/Ms)
kd (1/s)
KD (nM)







949 parental
2.66E+05
1.35E−03
5.07



949 chimeric
1.95E+05
1.17E−03
5.98



949 VK1gL1 gH1a
2.11E+05
7.82E−04
3.71



949 VK1 gL1 gH1b
1.91E+05
5.56E−04
2.92



949 VK1 gL11 gH1a
2.07E+05
1.15E−03
5.54



949 VK1 gL9 gH8a
2.45E+05
5.74E−04
2.35



949 VK1 gL9 gH20a
2.30E+05
7.27E−04
3.17



949 VK1 gL9 gH8b
2.27E+05
5.32E−04
2.34



949 VK1 gL9 gH20b
2.47E+05
6.58E−04
2.66



949 VK1 gL12 gH8a
2.34E+05
5.74E−04
2.46



949 VK1 gL12 gH20a
2.26E+05
7.66E−04
3.38



949 VK1 gL12 gH8b
2.22E+05
6.14E−04
2.77



949 VK1 gL12 gH20b
2.20E+05
8.35E−04
3.80



949 VK1 gL14 gH8a
2.09E+05
9.92E−04
4.75



949 VK1 gL14 gH8b
2.03E+05
8.88E−04
4.38



949 VK3 gL1 gH1a
2.10E+05
8.44E−04
4.02



949 VK3 gL1 gH1b
2.07E+05
6.50E−04
3.14



949 VK3 gL11 gH1a
2.23E+05
1.09E−03
4.89



949 VK1 gL15 Gh2
2.37E+05
8.56E−04
3.61










PD-1 ligand binding assays were performed to determine if antibody 949 (chimeric human IgG4 (parental V region), and humanised transient clones of 949) had the capacity to block ligand binding. In these assays PD-1 expressing HEK cells were incubated with purified or transiently expressed antibody supernatants for 30 minutes, followed by incubation with recombinant human PD-L2.mFc fusion protein. Binding of the PD-L2.mFc to cell expressed PD-1 was then revealed with a PE-conjugated anti-mouse IgG H+L antibody.
Method
HEK293 cells were transiently transfected by culturing at 5×106/well with 5 μg human PD-1 DNA and 293 fectin (Invitrogen) overnight in 6 well plates. The following day PD-1 expressing HEK293 cells were added to 96 well U-plate at 1×105/well in 50 μL and pre-incubated for 30 mins on ice with 50 μL of either human IgG4 control (10 μg/mL), or purified chimeric 949 (10, 3.3 or 1.1 μg/mL), or control anti-PD-1 antibody (10, 3.3 or 1.1 μg/mL), or 150 μL neat humanised 949 transient supernatants. Recombinant human PD-L2.mFc fusion protein was added to the cells at 0.3 μg/mL final concentration for a further 30 minutes on ice. HEK cells were washed twice in FACS buffer. Phycoerythrin conjugated anti-mouse H+L IgG was diluted 1/200 and added to the cell pellets at 50 μL per well. Cells were incubated on ice for 30 minutes. Cells were washed twice in FACS buffer and immediately acquired on the flow cytometer.
Results
The data in FIG. 14 shows PD-L2.mFc binding to PD-1 transfected HEK cells when pre-blocked with either control IgG4 or anti-PD-1 antibodies. Control IgG4 did not inhibit binding of PD-L2 to the cells as indicated by an increase in geometric mean fluorescent intensity. Purified, chimeric 949 antibody did not inhibit PD-L2 binding to PD-1 expressing cells at concentrations between 1 and 10 μg/mL. A control anti-PD-1 antibody with known ligand blocking properties did block PD-L2 binding to PD-1 expressing cells at the concentrations tested, confirming that ligand blocking could be detected in this assay format. All humanised versions of antibody 949 also did not inhibit PD-L2 binding to PD-1 expressed on cells.
4.3 Analysis of Functional Activity of Antibody 949 and Humanised Versions thereof
A reporter gene assay was developed using a Jurkat cell line which stably expresses a chimeric receptor comprising the extracellular ligand binding and transmembrane domains of human PD-1 and human CD28 signaling and human TCRζ intracellular domains. These cells have a reporter gene under the control of an NFκB-dependent promoter and the cells produce secreted alkaline phosphatase (SEAP) when stimulated with recombinant human PD-Ligand 1 or 2, demonstrating that this reporter assay is capable of detecting PD-1 agonism. The assay was used to compare the functional agonistic activity of the parental murine antibody 949 with a range of humanised constructs.
The human PD-1/CD28/TCRζ chimera construct was generated according to the methods described in International Application WO 2007/060406. Jurkat cells were stably transfected with the human PD-1/CD28/TCRζ chimera in the SEAP reporter vector. Cells were prepared in bulk and stored in liquid nitrogen until used. Cells were thawed and dispensed in 15 μL aliquots of medium containing 30,000 cells per 384 well. The antibody/construct was prepared at 4× final concentration in NM6 medium, and a 5 μL volume added to duplicate wells. After 18 hours incubation, 4 μL of supernatant was assayed for SEAP activity as described in the pack leaflet (Clontech, Great EscapeTM SEAP). Activity was calculated as fold induction (signal divided by background signal).
The data in FIG. 15 shows antibody 949 stimulated release of SEAP from the Jurkat human PD-1/CD28/TCRζ SEAP reporter cell line. The control human antibody, CAN-1, did not stimulate release of SEAP. The original CA949 construct, cLcH, and the construct VK1 gL12 gH8b produced similar titrations in the assay. Table 2 indicates that all the humanised constructs tested generated a SEAP response in this assay, demonstrating that they have maintained their agonistic function after humanisation.







TABLE 2







Comparison of humanised versions of 949 in the human


PD-1/CD28/TCRζ SEAP reporter assay. EC50 values


were calculated as the concentration of antibody required to


generate 50% of the maximal signal generated by that antibody









EC50 (ug/mL)














VK1 gL9 gH8a
0.22



VK1 gL9 gH8b
0.23



VK1 gL9 gH20a
0.25



VK1 gL9 gH20b
0.27



VK1 gL12 gH8a
0.29



VK1 gL12 gH8b
0.20



VK1 gL12 gH20a
0.18



VK1 gL12 gH20b
0.18



VK1 gL14 gH8a
0.15



VK1 gL14 gH8b
0.11



949 cLcH
0.08










4.4 Flow Cytometry Analysis of 949 Chimeric and 949 Humanised Grafts Binding to HEK293 Human, Cynomolgus and Rhesus PD-1

To confirm that the humanised grafts of antibody 949 maintained cross-reactivity with non-human primate PD-1, flow cytometry assays were carried out with HEK293 suspension cells which had been transiently transfected with DNA encoding full length human, cynomolgus or rhesus PD-1. HEK293 cells were transiently transfected by culturing at 5×106/well with 5 μg DNA and 293 fectin (Invitrogen) overnight in 6 well plates. The following day human, cynomolgus or rhesus PD-1 expressing HEK293 cells were resuspended in 0.2% BSA (w/v) PBS+0.09% sodium azide and incubated for 1 hr at 4° C. with stated concentrations of 949 chimeric, 949 humanised grafts, 949 chimeric (purified) or control antibodies. Cells were washed with PBS and incubated with secondary antibody—1:1000 FITC (Fab)2 Goat anti Human Fc specific (109-006-098 Jackson) for 1 hr at 4° C. Analyses were performed on a FACSCalibur (Becton Dickinson).
The results are shown in FIG. 16. They indicate that i) all the grafts bind specifically to PD-1 expressing cells (FIG. 16a, d), ii) they all retain human PD-1 binding equivalent to the original sequence (FIG. 16a) and iii) they all cross-react with PD-1 from cynomolgus (FIG. 16b) and rhesus (FIG. 16c) monkeys.
4.5 Ligand Blocking Assay
PD-1 transfect HEK293 cells with test antibody for 30 minutes on ice. Then a control CAN1.Fc or PD-L2mFc were added at 0.3 μg/mL for a further 30 minutes on ice after which cells were washed and the ligand binding revealed with anti mouse IgG H+L PE. The results are shown in FIG. 39. In summary the results show that the various 949 constructs do not prevent ligand binding.
4.6 Activated T-Cell Binding Assay
Human T cells isolated from whole blood via MACS (pan T cell kit) and activated with PHA-L (1 μg/ml) & IL-2 (1 ng/ml) for 3 days
Cells washed in FACS buffer and added to a 96-well plate at  ̃1×105 cell/well
Cells were incubated with samples for 1⁄2 hour on ice, and then washed twice in FACS buffer.
Antibody samples (in duplicate) diluted 1⁄3 from 10 μg/ml or neat (6-point titration curve)
Samples include Clone 19 hIgG4, CDP850 (hIgG4 control) and transient samples:

    
    
        Transient #1=949 VK1 gL9 gH 20b (10.3 μg/ml)
        Transient #2=949 VK1 gL15 gH 8a (8.5 μg/ml)
        Transient #3=949 VK1 gL15 gH 8b (8.4 μg/ml)
        Transient #4=949 VK1 gL15 gH 20a (8.53 μg/ml)
        Transient #5=949 VK1 gL15 gH 20b (6.8 μg/ml)
        Transient #6=mock (tested neat)
    
    


Cells were then incubated with reveal antibody (anti-human IgG H+L, PE conjugated, diluted to 1/200 in FACS buffer) for 1⁄2 hour on ice.
Cells were washed twice in FACS buffer and read on FACSCalibur 2 (acquired  ̃10 000 lymphocytes per sample). The results are shown in FIG. 40.
The EC50's were all between 1-6 μg/ml
EC50's (ng/ml):
Clone 19 hIgG4: −1197 (unconstrained curve) or 3611 (top part curve constrained to  ̃45 geo mean)
Transient #1: 1142
Transient #2: 3147
Transient #3: 6092
Transient #4: 2889
Transient #5: 4096
It will of course be understood that the present invention has been described by way of example only, is in no way meant to be limiting, and that modifications of detail can be made within the scope of the claims hereinafter. Preferred features of each embodiment of the invention are as for each of the other embodiments mutatis mutandis. All publications, including but not limited to patents and patent applications, cited in this specification are herein incorporated by reference as if each individual publication were specifically and individually indicated to be incorporated by reference herein as though fully set forth.

## Claims

1. A humanised agonistic antibody which binds human PD-1 comprising a heavy chain and a light chain wherein the variable domain of the heavy chain comprises the sequence given in SEQ ID NO:1 for CDR-H1, the sequence given in SEQ ID NO:2 for CDR-H2 and the sequence given in SEQ ID NO:3 for CDR-H3 and the variable domain of the light chain comprises the sequence given in SEQ ID NO:4 for CDR-L1, the sequence given in SEQ ID NO:5 for CDR-L2 and the sequence given in SEQ ID NO:7 for CDR-L3.

2. A humanised agonistic antibody according to claim 1, which binds human PD-1 comprising a heavy chain wherein the variable domain of the heavy chain comprises the sequence given in SEQ ID NO:1 for CDR-H1, the sequence given in SEQ ID NO:2 for CDR-H2 and the sequence given in SEQ ID NO:3 for CDR-H3 and the heavy chain framework region is derived from human sub-group sequence VH 1-3 1-46+JH4 (SEQ ID NO: 52).

3. A humanised antibody according to claim 2 wherein the residue at at least one of positions 25, 37, 41, 48, 71, 73 and 76 of the variable domain of the heavy chain is a donor residue.

4. A humanised antibody according to claim 3 having the heavy chain variable domain sequence given in SEQ ID NO:30, SEQ ID NO:38 or SEQ ID NO:40.

5. A humanised agonistic antibody according to claim 1, which binds human PD-1 comprising a heavy chain wherein the variable domain of the heavy chain comprises the sequence given in SEQ ID NO:1 for CDR-H1, the sequence given in SEQ ID NO:2 for CDR-H2 and the sequence given in SEQ ID NO:3 for CDR-H3 and the heavy chain framework region is derived from human sub-group sequence VH 1-2 1-e+JH4 (SEQ ID NO: 54).

6. A humanised antibody according to claim 5 having the heavy chain variable domain sequence given in SEQ ID NO:46.

7. A humanised antibody according to claim 5 wherein the residue at, at least one of, positions 25, 37, 41, 48, 71, 76 and 78 of the variable domain of the heavy chain is a donor residue.

8. A humanised antibody according to claim 7 having the heavy chain variable domain sequence given in SEQ ID NO:42 or SEQ ID NO:44.

9. A humanised agonistic antibody according to claim 1, which binds human PD-1 comprising a light chain wherein the variable domain of the light chain comprises the sequence given in SEQ ID NO:4 for CDR-L1, the sequence given in SEQ ID NO:5 for CDR-L2 and the sequence given in SEQ ID NO:7 for CDR-L3 and the light chain framework region is derived from human sub-group sequence VK1 2-1(1) L23+JK4 (SEQ ID NO:48).

10. A humanised antibody according to claim 9 wherein the residue at, at least one of positions 1, 2, 3, 4, 47, 60 and 70 of the variable domain of the light chain is a donor residue.

11. A humanised antibody according to claim 10 having the light chain variable domain sequence given in SEQ ID NO:20, SEQ ID NO:24 or SEQ ID NO:66.

12. A humanised agonistic antibody according to claim 1, which binds human PD-1 comprising a light chain wherein the variable domain of the light chain comprises the sequence given in SEQ ID NO:4 for CDR-L1, the sequence given in SEQ ID NO:5 for CDR-L2 and the sequence given in SEQ ID NO:7 for CDR-L3 and the light chain framework region is derived from human sub-group sequence VK3 6-1-(1) A27+JK4 (SEQ ID NO:50).

13. A humanised antibody according to claim 12 wherein the residue at least one of positions 2, 47, 58, 70, 71 and 85 of the variable domain of the light chain is a donor residue.

14. A humanised antibody according to claim 13 having the light chain variable domain sequence given in SEQ ID NO:28.

15. A humanised agonistic antibody according to claim 1 having a heavy chain comprising a sequence selected from the group consisting of: SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44 and SEQ ID NO:46 and a light chain comprising a sequence selected from the group consisting of SEQ ID NO:20, SEQ ID NO:24, SEQ ID NO:28 and SEQ ID NO:66.

16. A humanised agonistic antibody according to claim 1 having a heavy chain comprising a sequence selected from the group consisting of: SEQ ID NO:46, SEQ ID NO:58, SEQ ID NO:62, SEQ ID NO:76 and SEQ ID NO:80 and a light chain comprising a sequence selected from the group consisting of SEQ ID NO:20, SEQ ID NO:24, SEQ ID NO:28, SEQ ID NO:66 and SEQ ID NO:70.

17. An agonistic antibody molecule according to claim 1, wherein the antibody molecule is selected from the group consisting of: a complete antibody molecule having full length heavy and light chains or a fragment thereof, such as a Fab, modified Fab′, Fab′, F(ab′)2, Fv, VH, VL or scFv fragment.

18. A humanised agonistic antibody according to claim 1, wherein the variable domain of the light chain comprises a sequence having at least 80% identity or similarity to the light chain variable domain of a light chain comprising a sequence selected from the group consisting of SEQ ID NO:20, SEQ ID NO:24, SEQ ID NO:28 and SEQ ID NO:66; and wherein the variable domain of the heavy chain comprises a sequence having at least 80% identity or similarity to the heavy chain variable domain of a heavy chain comprising a sequence selected from the group consisting of: SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44 and SEQ ID NO:46.

19. A humanised agonistic antibody according to claim 1, wherein the variable domain of the light chain comprises a sequence having at least 80% identity or similarity to the light chain variable domain of a light chain comprising a sequence selected from the group consisting of SEQ ID NO: 20, SEQ ID NO:24, SEQ ID NO:28, SEQ ID NO:66 and SEQ ID NO:70; and wherein the variable domain of the heavy chain comprises a sequence having at least 80% identity or similarity to the heavy chain variable domain of a heavy chain comprising a sequence selected from the group consisting of: SEQ ID NO:46, SEQ ID NO:58, SEQ ID NO:62, SEQ ID NO:76 and SEQ ID NO:80.

20. A humanised agonistic antibody according to claim 1 having a binding affinity for isolated human PD-1 (for example human extracellular domain) of less than 5 nM.

21. A pharmaceutical composition comprising an antibody according to claim 1, in combination with one or more of a pharmaceutically acceptable excipient, diluent or carrier.

22. A pharmaceutical composition according to claim 21, additionally comprising other active ingredients.

23. A humanised agonistic antibody according to claim 1, wherein the heavy chain framework region is derived from human sub-group sequence VH 1-2 1-e+JH4 (SEQ ID NO: 54), and the residue at, at least one of, positions 25, 37, 41, 48, 71, 76 and 78 of the variable domain of the heavy chain is a donor residue; or derived from human sub-group sequence VH 1-3 1-46+JH4 (SEQ ID NO: 52), wherein a residue at at least one of positions 25, 37, 41, 48, 71, 73 and 76 of the variable domain of the heavy chain is a donor residue; and the light chain framework region is derived from human sub-group sequence VK1 2-1(1) L23+JK4 (SEQ ID NO:48), and the residue at, at least one of, positions 2, 47, 58, 70, 71 and 85 of the variable domain of the light chain is a donor residue; or derived from human sub-group sequence VK1 2-1(1) L23+JK4 (SEQ ID NO: 50), and the residue at, at least one of, positions 2, 47, 58, 70, 71 and 85 of the variable domain of the light chain is a donor residue.