US20090286962A1 - Chimeric antibodies with part new world primate binding regions - Google Patents

Chimeric antibodies with part new world primate binding regions Download PDF

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US20090286962A1
US20090286962A1 US12/158,034 US15803406A US2009286962A1 US 20090286962 A1 US20090286962 A1 US 20090286962A1 US 15803406 A US15803406 A US 15803406A US 2009286962 A1 US2009286962 A1 US 2009286962A1
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Benjamin P. Woolven
Ian M. Tomlinson
Anthony G. Doyle
Philip A. Jennings
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Teva Pharmaceuticals Australia Pty Ltd
Domantis Ltd
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Definitions

  • the present invention relates to engineered antibody polypeptides. More particularly, the present invention provides antibody polypeptides comprising an antigen binding site, wherein the antigen binding site comprises a human variable domain having at least one New World Primate CDR. In particular the present invention relates to antibody polypeptides directed against TNF- ⁇ .
  • TNF- ⁇ Tumor Necrosis Factor- ⁇
  • RA rheumatoid arthritis
  • Crohn's disease Crohn's disease
  • ulcerative colitis and other bowel disorders
  • psoriasis toxic shock
  • graft versus host disease and multiple sclerosis.
  • the pro-inflammatory actions of TNF- ⁇ result in tissue injury, such as inducing procoagulant activity on vascular endothelial cells (Pober, et al., 1986, J.
  • TNF- ⁇ is synthesized as a 26 kD transmembrane precursor protein with an intracellular tail that is cleaved by a TNF- ⁇ -converting metalloproteinase enzyme and then secreted as a 17 kD soluble protein.
  • the active form consists of a homotrimer of the 17 kD monomers which interacts with two different cell surface receptors, p55 TNFR1 and p75 TNFR2.
  • p55 TNFR1 and p75 TNFR2 cell surface receptors
  • p75 receptor is implicated in triggering lymphocyte proliferation
  • the p55 receptor is implicated in TNF-mediated cytotoxicity, apoptosis, antiviral activity, fibroblast proliferation and NT- ⁇ B activation (see Locksley et al., 2001, Cell 104: 487-501).
  • the TNF receptors are members of a family of membrane proteins including the NGF receptor, Fas antigen, CD27, CD30, CD40, Ox40 and the receptor for the lymphotoxin ⁇ / ⁇ heterodimer. Binding of receptor by the homotrimer induces aggregation of receptors into small clusters of two or three molecules of either p55 or p75.
  • TNF- ⁇ is produced primarily by activated macrophages and T lymphocytes, but also by neutrophils, endothelial cells, keratinocytes and fibroblasts during acute inflammatory reactions. TNF- ⁇ is at the apex of the cascade of pro-inflammatory cytokines (Reviewed in Feldmann & Maini, 2001, Ann. Rev. Immunol.
  • This cytokine induces the expression or release of additional proinflammatory cytokines, particularly IL-1 und IL-6 (see, for example, Rutgeerts et al., 2004, Gastroenterology 126: 1593-1610). Inhibition of TNF- ⁇ inhibits the production of inflammatory cytokines including IL-1, IL-6, IL-8 and GM-CSF (Brennan et al., 1989, Lancet 2: 244-247). Because of its role in inflammation, TNF- ⁇ has emerged as an important inhibition target in efforts to reduce the symptoms of inflammatory disorders.
  • soluble TNF- ⁇ receptors and antibodies specific for TNF- ⁇ .
  • Commercial products approved for clinical use include, for example, the antibody products RemicadeTM (infliximab; Centocor, Malvern, Pa.; a chimeric monoclonal IgG antibody bearing human IgG1 constant and mouse variable regions), HumiraTM (adalimumab or D2E7; Abbott Laboratories, described in U.S. Pat. No. 6,090,382) and the soluble receptor product EnbrelTM (etancrcept, a soluble p75 TNFR2 Fc fusion protein; Immunex).
  • RemicadeTM infliximab
  • Centocor Centocor, Malvern, Pa.
  • HumiraTM adalimumab or D2E7
  • soluble receptor product EnbrelTM etancrcept, a soluble p75 TNFR2 Fc fusion protein
  • TNF- ⁇ is highly expressed in inflamed synovium, particularly at the cartilage-pannus junction (DiGiovine et al., 1988, Ann. Rheum. Dis. 47: 768-772; Firestein et al., 1990, J. Immunol. 144: 3347-3353; and Saxne et al., 1988, Arthritis Rheum. 31: 1041-1045).
  • TNF- ⁇ increases the levels of inflammatory cytokines IL-1, IL-6, IL-8 and GM-CSF
  • TNF- ⁇ can alone trigger joint inflammation and proliferation of fibroblast-like synoviocytes (Gitter et al., 1989, Immunology 66: 196-200), induce collagenase, thereby triggering cartilage destruction (Dayer et al., 1985, J. Exp. Med. 162: 2163-2168; Dayer et al., 1986, J. Clin. Invest.
  • TNF- ⁇ induces increased release of CD14+ monocytes by the bone marrow.
  • Such monocytes can infiltrate joints and amplify the inflammatory response via the RANK (Receptor Activator of NF- ⁇ B)-RANKL signaling pathway, giving rise to osteoclast formation during arthritic inflammation (reviewed in Anandarajah & Richlin, 2004, Curr. Opin. Rheumatol. 16: 338-343).
  • TNF- ⁇ is an acute phase protein which increases vascular permeability through its induction of IL-8, thereby recruiting macrophage and neutrophils to a site of infection. Once present, activated macrophages continue to produce TNF- ⁇ , thereby maintaining and amplifying the inflammatory response.
  • TNF- ⁇ Titration of TNF- ⁇ by the soluble receptor construct etanercept has proved effective for the treatment of RA, but not for treatment of Crohn's disease.
  • the antibody TNF- ⁇ antagonist infliximab is effective to treat both RA and Crohn's disease.
  • the mere neutralization of soluble TNF- ⁇ is not the only mechanism involved in anti-TNF-based therapeutic efficacy. Rather, the blockade of other pro-inflammatory signals or molecules that are induced by TNF- ⁇ also plays a role (Rutgeerts et al., supra).
  • the administration of infliximab apparently decreases the expression of adhesion molecules, resulting in a decreased infiltration of neutrophils to sites of inflammation.
  • infliximab therapy results in the disappearance of inflammatory cells from previously inflamed bowel mucosa in Crohn's disease.
  • This disappearance of activated T cells in the lamina propria is mediated by apoptosis of cells carrying membrane-bound TNF- ⁇ following activation of caspases 8,9 and then 3 in a Fas dependent manner (see Lugering et al., 2001, Gastroenterology 121: 1145-1157).
  • membrane- or receptor-bound TNF- ⁇ is an important target for anti-TNF- ⁇ therapeutic approaches.
  • infliximab binds to activated peripheral blood cells and lamina intestinal cells and induces apoptosis through activation of caspase 3 (sec Van den Brando et al., 2003, Gastroenterology 124: 1774-1785).
  • TNF- ⁇ Intracellularly, the binding of trimeric TNF- ⁇ to its receptor triggers a cascade of signaling events, including displacement of inhibitory molecules such as SODD (silencer of death domains) and binding of the adaptor factors FADD, TRADD, TRAF2, c-IAP, RAIDD and TRIP plus the kinase RIP1 and certain caspases (reviewed by Chen & Goeddel, 2002, Science 296: 1634-1635, and by Muzio & Saccani in :Methods in Molecular Medicine: Tumor Necrosis Factor, Methods and Protocols,” Corti and Ghezzi, eds. (Humana Press, New Jersey; 2004), pp. 81 -99).
  • SODD semiconductor of death domains
  • the assembled signalling complex can activate either a cell survival pathway, through NF- ⁇ B activation and subsequent downstream gene activation, or an apoptotic pathway through caspase activation. Similar extracellular downstream cytokine cascades and intracellular signal transduction pathways can be induced by TNF- ⁇ in other diseases. Thus, for other diseases or disorders in which the TNF- ⁇ molecule contributes to the pathology, inhibition of TNF- ⁇ presents an approach to treatment.
  • Angiogenesis plays an important role in the active proliferation of inflammatory synovial tissue. RA synovial tissue, which is highly vascularized, invades the periarticular cartilage and bone tissue and leads to joint destruction.
  • VEGF Vascular endothelial growth factor
  • VEGF is a secreted, heparin-binding, homodimeric glycoprotein existing in several alternate forms due to alternative splicing of its primly transcript (Leung et al., 1989, Science 246: 1306-1309).
  • VEGF is also known as vascular permeability factor (VPF) due to its ability to induce vascular leakage, a process important in inflammation.
  • VPF vascular permeability factor
  • VEGF expression in the joints increased upon induction of the disease, and the administration of anti-VEGF antisera blocked the development of arthritic disease and ameliorated established disease (Sone et al., 2001, Biochem. Biophys. Res. Comm. 281: 562-568; Lu et al., 2000, J. Immunol. 164: 5922-5927).
  • Antibodies are highly specific for their binding targets and although they are derived from nature's own defence mechanisms, antibodies face several challenges when applied to the treatment of disease inhuman patients.
  • Conventional antibodies are large multi-subunit protein molecules comprising at least four polypeptide chains.
  • human IgG has two heavy chains and two light chains that are disulfide bonded to form the functional antibody.
  • the size of a conventional IgG is about 150 kD. Because of their relatively large size, complete antibodies (e.g., IgG, IgA, IgM, etc.) are limited in their therapeutic usefulness due to problems in, for example, tissue penetration. Considerable efforts have focused on identifying and producing smaller antibody fragments that retain antigen binding function and solubility.
  • the heavy and light polypeptide chains of antibodies comprise variable (V) regions that directly participate in antigen interactions, and constant (C) regions that provide structural support and function in non-antigen-specific interactions with immune effectors.
  • the antigen binding domain of a conventional antibody is comprised of two separate domains: a heavy chain variable domain (VH) and a light chain variable domain (VL: which can be either V ⁇ or V ⁇ ).
  • VH heavy chain variable domain
  • VL light chain variable domain
  • the antigen binding site itself is formed by six polypeptide loops: three from the VH domain (H1, H2 and H3) and three from the VL domain (L1, L2 and L3). In vivo, a diverse primary repertoire of V genes that encode the VH and VL domains is produced by the combinatorial rearrangement of gene segments.
  • C regions include the light chain C regions (referred to as CL regions) and the heavy chain C regions (referred to as CH1, CH2 and CH3 regions).
  • CL regions the light chain C regions
  • CH1, CH2 and CH3 regions the heavy chain C regions
  • a number of smaller antigen binding fragments of naturally occurring antibodies have been identified following protease digestion. These include, for example, the “Fab fragment” (VL-CL-CH1-VH), “Fab′ fragment” (a Fab with the heavy chain hinge region) and “F(ab′)2 fragment” (a dimer of Fab′ fragments joined by the heavy chain hinge region).
  • Recombinant methods have been used to generate even smaller antigen-binding fragments, referred to as “single chain Fv” (variable fragment) or “scFv,” consisting of VL and VH joined by a synthetic peptide linker.
  • VHH domains VHH domains and retain the ability, when isolated as fragments of the VH chain, to bind antigen with high specificity
  • Antigen binding single VH domains have also been identified from, for example, a library of murine VH genes amplified from genomic DNA from the spleens of immunized mice and expressed in E. coli (Ward et al, 1989, Nature 341: 544-546). Ward et al. named the isolated single VH domains “dAbs,” for “domain antibodies”.
  • the term “dAb” will refer herein to a single immunoglobulin variable domain (VH, VHH or VL) polypeptide that specifically binds antigen.
  • a “dAb” binds antigen independently of other V domains; however, as the term is used herein, a “dAb” can be present in a homo- or heteromultimer with other VH or VL domains where the other domains are not required for antigen binding by the dAb, i.e., where the dAb binds antigen independently of the additional VH, VHH or VL domains.
  • Single immunoglobulin variable domains for example, VHH, are the smallest antigen-binding antibody unit known.
  • human antibodies are preferred, primarily because they are not as likely to provoke an immune response when administered to a patient. Isolated non-camelid VH domains tend to be relatively insoluble and are often poorly expressed.
  • WO 03/035694 (Muyldermans) reports that a Trp 103 Arg mutation improves the solubility of non-camelid VH domains, Davies & Riechmann, (1995, Biotechnology N.Y. 13: 475-479) also report production of a phage-displayed repertoire of camelized human VH domains and selection of clones that bind hapten with affinities in the range of 100-400 nM, but clones selected for binding to protein antigen had weaker affinities.
  • the antigen binding domain of an antibody comprises two separate regions: a heavy chain variable domain (VH) and a light chain variable domain (VL: which can be either V ⁇ or V ⁇ ).
  • the antigen binding site itself is formed by six polypeptide loops: three from VH domain (H1, H2 and H3) and three from VL domain (L1, L2 and L3).
  • VH domain H1, H2 and H3
  • VL domain L1, L2 and L3
  • a diverse primary repertoire of V genes that encode the VH and VL domains is produced by the combinatorial rearrangement of gene segments.
  • the VH gene is produced by the recombination of three gene segments, VH, D and JH. In humans, there are approximately 51 functional VH segments (Cook and Tomlinson, 1995, Immunol. Today, 16: 237), 25 functional D segments (Corbett et al., 1997 J. Mol.
  • VH segment encodes the region of the polypeptide chain which forms the first and second antigen binding loops of the VH domain (H1 and H2), whilst the VH, D and JH segments combine to form the third antigen binding loop of the VH domain (H3).
  • the VL gene is produced by the recombination of only two gene segments, VL and JL. In humans, there are approximately 40 functional V ⁇ segments (Schable and Zachau (1993) Biol. Chem.
  • the VL segment encodes the region of the polypeptide chain which forms the first and second antigen binding loops of the VL domain (L1 and L2), whilst the VL and JL segments combine to form the third antigen binding loop of the VL domain (L3).
  • Antibodies selected from this primary repertoire are believed to be sufficiently diverse to bind almost all antigens with at least moderate affinity.
  • High affinity antibodies are produced by “affinity maturation” of the rearranged genes, in which point mutations are generated and selected by the immune system on the basis of improved binding. Analysis of the structures and sequences of antibodies has shown that five of the six antigen binding loops (H1, H2, L1, L2, L3) possess a limited number of main-chain conformations or canonical structures (Chothia and Lesk, 1987, Mol. Biol., 196; 901-917; Chothia al., 1989, Nature, 342: 877-883).
  • the main-chain conformations are determined by (i) the length of the antigen binding loop, and (ii) particular residues, or types of residue, at certain key position in the antigen binding loop and the antibody framework. Analysis of the loop lengths and key residues has enabled us to predict the main-chain conformations of H1, H2, L1, L2 and L3 encoded by the majority of human antibody sequences (Chothia et al., 1992, J. Mol. Biol., 227: 799-817; Tomlinson et al., 1995, EMBO J., 14; 4628-4638; Williams et al., 1996, J. Mol. Biol., 264: 220-232).
  • H3 region is much more diverse in terms of sequence, length and structure (due to the use of D segments), it also forms a limited number of main-chain conformations for short loop lengths which depend on the length and the presence of particular residues, or types of residue, at key positions in the loop and the antibody framework (Martin et al., 1996, J. Mol. Biol, 263: 800-815; Shirai et al., 1996, FEBS Letters, 399: 1-8).
  • Bispecific antibodies comprising complementary pairs of VH and VL regions are known in the art. These bispecific antibodies must comprise two pairs of VH and VLs, each VH/VL pair binding to a single antigen or epitope. Methods described involve hybrid hybridomas (Milstein & Cuello, Nature, 1983, 305:537-40), minibodies (Hu et al., 1996, Cancer Res 30 56:3055-3061), diabodies (Holliger et al., 1993, Proc. Natl. Acad. Sci. USA 90, 6444-6448; WO 94/13804), chelating recombinant antibodies (CRAbs; Neri et al., 1995, J. Mol. Biol.
  • each antibody species comprises two antigen-binding sites, each fashioned by a complementary pair of VH and VL domains. Each antibody is thereby able to bind to two different antigens or epitopes at the same time, with the binding to EACH antigen or epitope mediated by a VH and its complementary VL domain.
  • cross-reactive antibodies have been so described, usually where the two antigens are related in sequence and structure, such as hen egg white lysozyme and turkey lysozyme (McCafferty et al., WO 92/01047) or to free hapten and to hapten conjugated to carrier (Griffiths et al., 1994, EMBO J 13:14 3245-60).
  • WO 02/02773 (Abbott Laboratories) describes antibody molecules with “dual specificity”.
  • the antibody molecules referred to are antibodies raised or selected against multiple antigens, such that their specificity spans more than a single antigen.
  • Each complementary VH/VL pair in the antibodies of WO 02/02773 specifies a single binding specificity for two or more structurally related antigens; the VH and VL domains in such complementary pairs do not each possess a separate specificity.
  • the antibodies thus have a broad single specificity which encompasses two antigens, which are structurally related.
  • natural autoantibodies have been described that are polyreactive (Casali & Nolkins, 1989, Ann. Rev. Immunol. 7, 515-531), reacting with at least two (usually more) different antigens or epitopes mat are not structurally related.
  • Protein engineering methods have been suggested that may have a bearing on this.
  • a catalytic antibody could be created with a binding activity to a metal ion through one variable domain, and to a hapten (substrate) through contacts with the metal ion and a complementary variable domain (Barbae et al, 1993, Proc. Natl. Acad. Sci USA 90,6385-6389).
  • the binding and catalysis of the substrate is proposed to require the binding of the metal ion (second antigen).
  • the binding to the VH/VL pairing relates to a single but multi component antigen.
  • camel heavy chain single domains are unusual in that they are derived from natural camel antibodies which have no light chains, and indeed the heavy chain single domains are unable to associate with camel light chains to form complementary VH and VL pairs.
  • Single heavy chain variable domains have also been described, derived from natural antibodies which are normally associated with light chains (from monoclonal antibodies or from repertoires of domains; see EP-A-0368684). These heavy chain variable domains have been shown to interact specifically with one or more related antigens but have not been combined with other heavy or light chain variable domains to create a ligand with specificity for two or more different antigens. Furthermore, these single domains have been shown to have a very short in viva half-life. Therefore, such domains are of limited therapeutic value.
  • Human/mouse chimeric antibodies have been created in which antibody variable region sequences from the mouse genome are combined with antibody constant region sequences from the human genome.
  • the chimeric antibodies exhibit the binding characteristics of the parental mouse antibody, and the effector functions associated with the human constant region.
  • the antibodies are produced by expression in a host cell, including for example Chinese Hamster Ovary (CHO). NS0 myeloma cells, COS cells and SP2 cells.
  • Such chimeric antibodies have been used inhuman therapy, however antibodies to these chimeric antibodies have been produced by the human recipient. Such anti-chimeric antibodies are detrimental to continued therapy with chimeric antibodies.
  • human monoclonal antibodies are expected to be an improvement over mouse monoclonal antibodies for in vivo human therapy. From work done with antibodies from Old World primates (rhesus monkeys and chimpanzees) it has been postulated mat these non-human primate antibodies will be tolerated in humans because they are structurally similar to human antibodies (Ehrlich PH et al., 1988, Human and primate monoclonal antibodies for in vivo therapy. Clin Chem. 34:9 pg 1681-1688).
  • EP 0 605 442 discloses chimeric antibodies which bind human antigens. These antibodies comprise the whole variable region from an Old World monkey and the constant region of a human or chimpanzee antibody.
  • One of the advantages suggested in this reference for these constructs is the ability to raise antibodies in Old World monkeys to human antigens which are less immunogenic in humans compared with antibodies raised in a mouse host.
  • New World primates comprise at least 53 species commonly divided into two families, the Callithricidae and Cebidae.
  • the Callithricidae consist of marmosets and tamarins.
  • the Cebidae includes the squirrel monkey, titi monkey, spider monkey, woolly monkey, capuchin, uakaris, sakis, night or owl monkey and the howler monkey.
  • Evolutionarily distant primates such as New World primates, are not only sufficiently different from humans to allow antibodies against human antigens to be generated, but are sufficiently similar lo humans to have antibodies similar to human antibodies so that the host does not generate an anti-antibody immune response when such primate-derived antibodies are introduced into a human.
  • the present invention provides a chimeric antibody polypeptide comprising an antigen binding site, wherein the antigen binding site comprises a human variable domain having at least one New World Primate CDR.
  • the present invention provides a method of producing an antibody polypeptide according to the first aspect of the invention, the method comprising the steps of:
  • the present invention provides a chimeric domain antibody (dAb) which binds human TNF- ⁇ , the dAb comprising an immunoglobulin heavy or light chain variable domain, wherein said variable domain comprises at least one New World Primate CDR.
  • dAb chimeric domain antibody
  • the present invention provides a pharmaceutical composition
  • a pharmaceutical composition comprising an effective amount of an antibody polypeptide according to the first or third aspects of the invention, together with a pharmaceutically acceptable carrier or diluent.
  • FIG. 1 shows the amino acid (SEQ ID No:6) and nucleotide sequence (SEQ ID No:5) of the acceptor dAb.
  • FIG. 2 shows the nucleotide and amino acid sequences of eleven (11) marmoset and six. (6) Owl monkey V ⁇ gene segments.
  • FIG. 3 shows the acceptor dAb amino acid and nucleotide sequence (both strands).
  • the restriction digest sites for Kpn I and San DI which excises a region including the CDR2 is indicated in the figure.
  • CDR2 residues removed are indicated in underline.
  • FIG. 4 shows sequence alignments showing oligonucleotides used during cloning and final sequence confirmation of the nucleotide (A) and amino acid (B) sequences shown in FIG. 2 .
  • FIG. 5 demonstrates the ability of CDR2-grafted dAbs to inhibit the binding of TNF to recombinant TNF receptor.
  • FIG. 6 demonstrates the improved ability of Compounds 100 and 123 to neutralise the cytotoxic activity of TNF on mouse L929 fibroblasts relative to Compound 145.
  • the present invention provides a chimeric antibody polypeptide comprising an antigen binding site, wherein the antigen binding site comprises a human variable domain having at least one New World Primate CDR.
  • the present invention provides a chimeric domain antibody (dAb) which binds human TNF- ⁇ , the dAb comprising an immunoglobulin heavy or light chain variable domain, wherein said variable domain comprises at least one New World Primate CDR.
  • dAb chimeric domain antibody
  • the present invention provides a pharmaceutical composition
  • a pharmaceutical composition comprising an effective amount of an antibody polypeptide according to the first or third aspects of the invention, together with a pharmaceutically acceptable carrier or diluent.
  • the human variable domain comprises at least one human framework region having an amino acid sequence encoded by a human germline antibody gene segment, or an amino acid sequence comprising up to 5 amino acid differences relative to the amino acid sequence encoded by the human germline antibody gene segment.
  • the human variable domain preferably comprises four human framework regions, FR1, FR2, FR3 and FR4 having amino acid sequences encoded by a human germline antibody gene segment, or the amino acid sequences which collectively contain up to 10 ammo acid differences relative to the amino acid sequences encoded by said human germline antibody gene segment.
  • the human germline antibody gene segment selected from the group consisting of DP47, DP45, DP48 and DPK9.
  • the New World Primate CDR may be any CDR, however, it is preferred that the New World Primate CDR is CDR2.
  • the New World Primate CDR is CDR1 or CDR3.
  • New World Primate CDR sequence is a germline New World Primate CDR sequence.
  • the antibody polypeptide of the present invention is preferably selected from a dAb, scFv, Fab, (Fab′) 2 , Fv, disulphide bonded Fv, IgG, and a diabody.
  • the antibody polypeptide of the present invention is preferably directed against TNF- ⁇ .
  • the human variable domain amino acid sequence comprises a Kpn1 restriction site spaced from a SanD1 restriction site, said CDR of the human variable domain being between the restriction sites.
  • New World Primate CDR sequence is obtainable from New World Primate DNA by PCR using primer pair VK1BL (SEQ ID No:11)/VK1BL35a (SEQ ID No:12) or primer pair VK1BL (SEQ ID No:11/VK1BL35b (SEQ ID No:13).
  • the present invention also provides a chimeric domain antibody (dAb) which binds to human TNF- ⁇ , wherein the dAb is a human dAb that binds human TNF- ⁇ in which at least one of the CDRs is replaced with the corresponding CDR from a New World Primate.
  • dAb chimeric domain antibody
  • the present invention also provides a method of producing an antibody polypeptide according to the first aspect of the invention, the method comprising the steps of:
  • step (ii) said CDR of said human variable domain is replaced by said donor New World Primate CDR using restriction digestion and annealing of an oligonucleotide encoding the donor CDR into the acceptor sequence.
  • the method further comprises affinity maturing the variable domain produced in step (ii).
  • New World Primate CDR refers to a CDR sequence obtained from a New World Primate.
  • the term encompasses modification of 1, 2 or 3 ammo acids within the sequence which may be used to achieve improved antigen binding characteristics or lower immunogenicity. The term does not, however, extend to cover modifications which result in the New World Primate CDR sequence being identical to a human CDR sequence.
  • human framework region refers to a framework region obtained from a human or a human framework region having an amino acid sequence encoded by a human germline antibody gene segment, or an amino acid sequence comprising up to 5 amino acid differences relative to the amino acid sequence encoded by the human germline gene segment.
  • the term also encompasses modification of the amino acid sequence of the framework region in order to obtain improved antigen binding characteristics or lower immunogenicity such as disclosed in U.S. Pat. No. 4,816,567, U.S. Pat. No. 5,585,089 and US 20030039649 the disclosures of which are incorporated herein by reference in their entirety. Typically where modifications are made the total number of residues changed will be 10 or less collectively over the framework regions.
  • variable domain comprises four framework regions, wherein at least one framework region comprises an amino acid sequence derived from a corresponding framework region encoded by a human germline immunoglobulin gene.
  • the four framework regions comprise amino acid sequences derived from corresponding framework regions encoded by human germline immunoglobulin genes.
  • the human germline immunoglobulin gene is selected from the group consisting of DP47, DP45, DP48 and DPK9.
  • domain as used herein is meant a folded protein structure which retains its tertiary structure independently of the rest of the protein. Generally, domains are responsible for discrete functional properties of proteins, and in many cases may be added, removed or transferred to other proteins without loss of function of the remainder of the protein and/or of the domain.
  • immunoglobulin or antibody “variable domain” as used herein is a term of art, and includes a folded polypeptide domain comprising sequences characteristic of immunoglobulin or antibody heavy or light chain variable domains and which specifically binds an antigen.
  • immunoglobulin refers to a family of polypeptides which retain the immunoglobulin fold characteristic of antibody molecules, which contains two ⁇ sheets and, usually, a conserved disulphide bond.
  • Members of the immunoglobulin superfamily are involved in many aspects of cellular and non-cellular interactions in vivo, including widespread roles in the immune system (for example, antibodies, T-cell receptor molecules and the like), involvement in cell adhesion (for example the ICAM molecules) and intracellular signalling (for example, receptor molecules, such as the PDGF receptor).
  • the present invention is applicable to all immunoglobulin superfamily molecules which possess binding domains.
  • the present invention relates to antibody polypeptides.
  • New World primates comprise at least 53 species commonly divided into two families, the Callithricidae and Cebidae.
  • the Callithricidae consist of marmosets and tamarins.
  • the Cebidae includes the squirrel monkey, titi monkey, spider monkey, woolly monkey, capuchin, uakaris, sakis, night or owl monkey and the howler monkey.
  • Evolutionarily distant primates such as New World primates, are not only sufficiently different from humans to allow antibodies against human antigens to be generated, but are sufficiently similar to humans to have antibodies similar to human antibodies so that the host does not generate an anti-antibody immune response when such primate-derived antibodies are introduced into a human.
  • the New World primate CDR is from the family Callithricidae.
  • the New World primate CDR is selected from the group consisting of marmosets, tamarins, squirrel monkey, titi monkey, spider monkey, woolly monkey, capuchin, uakaris, sakis, night or owl monkey and the howler monkey. More preferably, the New World primate is a marmoset.
  • the at least one New World primate CDR is substantially identical to a CDR encoded by a New World primate germline immunoglobulin gene.
  • antibody as used herein, is intended to refer to immunoglobulin molecules comprised of two heavy chains or immunoglobulin molecules comprised of four polypeptide chains, two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds.
  • Each heavy chain is comprised of a heavy chain variable region (HCVR or V H ) and a heavy chain constant region.
  • the heavy chain constant region comprises three domains, C H 1, C H 2 and C H 3.
  • Each light chain is comprised of a light chain variable region (LCVR or V L ) and a light chain constant region.
  • the light chain constant region is comprised of one domain, C L .
  • V H and V L regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (PR).
  • CDR complementarity determining regions
  • PR framework regions
  • Each V H and V L is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
  • antibody polypeptide refers to a polypeptide comprising one or more components or derivatives of an immunoglobulin that exhibit the ability to bind to an antigen. It has been shown that the antigen-binding function of an antibody can be performed by fragments of a full length antibody.
  • binding fragments encompassed within the term “antibody polypeptide” include (i) a Fab fragment, a monovalent fragment consisting of the V L , V H , C L and C H 1 domains; (ii) a F(ab′) 2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the V H and C H 1 domains; (iv) a Fv fragment consisting of the V L and V H domains of a single arm of an antibody, (v) a dAb fragment (Ward et al, 1989, Nature 341:544-546) which consists of a single V H domain, or a V L domain (van den Beucken et al, 2001, J.
  • V L and V H are coded by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the V L and V H regions pair to form monovalent molecules (known as single chain Fv (scFv); (see eg Bird et al., 1988, Science 242:423-426 and Huston et al., 1988 Proc. Natl. Acad. Sci. USA 85:5879-5883).
  • scFv single chain Fv
  • single chain Fvs are also intended to be encompassed within the term “antigen-binding portion” of an antibody.
  • Other forms of single chain Fvs and related molecules such as diabodies or triabodies are also encompassed.
  • Diabodies are bivalent antibodies in which V H and V L domains are expressed on a single polypeptide chain, but using a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain and creating two antigen binding sites (see e.g., Holliger, et al., 1993, Proc. Natl. Acad. Sci. USA, 90:6444-6448; Poljak, et al., 1994, Structure, 2:1121-1123).
  • the antibody polypeptide is selected from the group consisting of a dAb, scFv, Fab, F(ab′) 2 , Fv, disulphide bonded Fv, a diabody and IgG.
  • the antibody polypeptide further comprises a human or non-human primate constant region sequence.
  • non-human primates include, but are not limited to, chimpanzees, oranguatangs and baboons.
  • the constant region sequence is preferably obtained from a human or non-human primate immunoglobulin sequence.
  • the primate sequence may be a New World primate or an Old World primate sequence. Suitable Old World primates include chimpanzee, or other hominid ape eg. gorilla or orangutan, which because of their close phylogenetic proximity to humans, share a high degree of homology with the human constant region sequence. Sequences which encode for human or primate constant regions are available from databases including e.g. The National Centre for Biotechnology Information protein and nucleotide databases, The Kabat Database of Sequences of Proteins of Immunological Interest.
  • the antibody polypeptide is a domain antibody (dAb).
  • Domain antibodies are small functioning binding units of antibodies and correspond to the variable regions of either the heavy (V H ) or light (V L ) chains of antibodies. Domain antibodies have a molecular weight of approximately 13 kDa, or less than one tenth the size of a full antibody.
  • Antibody light chains are referred to as either kappa or lambda light chains and the heavy chains as gamma, mu, delta, alpha or epsilon.
  • the variable region gives the antibody its specificity.
  • regions of hypervariability otherwise known as complementarity determining regions (CDRs) which are flanked by more conserved regions referred to as framework regions.
  • CDRs complementarity determining regions
  • framework regions Within each variable region are three CDRs and four framework regions.
  • domain antibodies are well expressed in bacterial, yeast and mammalian systems. Their small size allows for higher molar quantities per gram or product, thus providing a significant increase in potency per dose.
  • domain antibodies can be used as a building block to create therapeutic products such as multiple targeting dAbs in which a construct containing two or more variable domains bind to two or more therapeutic targets, or dAbs targeted for pulmonary or oral administration.
  • an increase in binding is demonstrated by a decrease in K D (k off /k on ) for the antibody or antigen binding portion thereof.
  • An increase in potency is demonstrated in biological assays.
  • assays that can be used to measure the potency of the antibody or antigen-binding portion thereof include the TNF ⁇ -induced L929 cytotoxicity neutralisation assay, IL-12-induced human PHA-activated peripheral blood mononuclear cell (PBMC) proliferation assay, and RANKL mediated osteoclast differentiation of mouse splenocytes (Stem, 1990, Proc. Natl. Acad. Sci.
  • the CDR sequences may be obtained from several sources, for example, databases e.g. The National Centre for Biotechnology Information protein and nucleotide databases www.ncbi.nlm.nih.gov, The Kabat Database of Sequences of Proteins of Immunological Interest www.kabatdatabase.com, or the IMGT database www.imgt.cines.fr.
  • the CDR regions can be predicted from the V H and V L domain repertoire (see for example Kabat and Wu, 1971, Ann. NY Acad. Sci. 190:382-393).
  • the CDR sequence may be a genomic DNA or a cDNA.
  • the preferred method of the present invention involves replacement of the CDR2 in the variable region domain via primer directed mutagenesis. This method consists of annealing a synthetic oligonucleotide encoding a desired mutations to a target region where it serves as a primer for initiation of DNA synthesis in vitro, extending the oligonucleotide by a DNA polymerase to generate a double-stranded DNA that carries the desired mutations, and ligating and cloning the sequence into an appropriate expression vector.
  • variable domain sequence into which the CDR is grafted is the “dAb acceptor sequence” (designated Compound 128; SEQ ID No:6) provided in FIG. 1 .
  • chimeric is meant that the antibody polypeptide or domain antibody includes sequences from more than one species.
  • the anti-human TNF- ⁇ dAb according to the invention can be used to detect human TNF- ⁇ for example in a biological sample, such as serum or plasma using a conventional immunoassay, such as an enzyme linked immunosorbent assay (ELISA), a radioimmunoassay (RIA) or tissue immunohistochemistry.
  • a biological sample such as serum or plasma
  • a conventional immunoassay such as an enzyme linked immunosorbent assay (ELISA), a radioimmunoassay (RIA) or tissue immunohistochemistry.
  • ELISA enzyme linked immunosorbent assay
  • RIA radioimmunoassay
  • tissue immunohistochemistry tissue immunohistochemistry.
  • the anti-human TNF- ⁇ dAb according to the invention can be assayed in biological fluids by a competition immunoassay using recombinant human TNF- ⁇ standards label led with a detectable substance and an unlabelled anti-human TNF- ⁇ antibody.
  • the anti-human TNF- ⁇ dAb according to the invention may also be used to detect TNF- ⁇ from species other than humans eg. chimpanzee, marmoset, rhesus, mouse, pig.
  • the anti-human TNF- ⁇ dAb according to the invention may also be used in cell culture applications where it is desired to inhibit TNF- ⁇ activity.
  • the invention also provides a method for treating a disorder characterised by human TNF- ⁇ activity in a human subject, comprising administering to the subject a pharmaceutical composition according to the second aspect of the invention.
  • a disorder characterised by human TNF- ⁇ activity is intended to include diseases and other disorders in which the presence of TNF- ⁇ in a subject suffering from the disorder has been shown to be or is suspected of being either responsible for the pathophysiology of the disorder or a factor which contributes to a worsening of the disorder.
  • the disorder characterised by human TNF- ⁇ activity is selected from the group consisting of inflammation, inflammatory diseases, sepsis, including septic shock, endotoxic shock, gram negative sepsis and toxic shock syndrome; autoimmune disease, including rheumatoid arthritis, rheumatoid spondylitis, osteoarthritis and gouty arthritis, allergy, multiple sclerosis, autoimmune diabetes, autoimmune uveitis and nephrotic syndrome; infectious disease, including fever and myalgias due to infection and cachexia secondary to infection; graft versus host disease; tumour growth or metastasis; pulmonary disorders including adult respiratory distress syndrome, shock lung, chronic pulmonary inflammatory disease, pulmonary sarcoidosis, pulmonary fibrosis and silicosis; inflammatory bowel disorders including Crohn's disease and ulcerative colitis; cardiac disorders; inflammatory bone disorders, hepatitis, coagulation disturbances, burns, reperfusion injury, keloid formation and scar tissue formation
  • the invention provides a pharmaceutical composition
  • a pharmaceutical composition comprising an effective amount of the antibody polypeptide according to the first aspect of the invention or a chimeric domain antibody according to the third aspect of the invention, together with a pharmaceutically acceptable carrier or diluent.
  • a “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal-agents, isotonic and absorption delaying agents, and the like which are physiologically compatible.
  • pharmaceutically acceptable carriers include one or more of water, saline, phosphate buffered saline, dextrose, glycerol, ethanol, and the like as well as combinations thereof.
  • isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride in the composition.
  • Pharmaceutically acceptable substances such as welling or minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives or buffers.
  • the composition may be in a variety of forms, including liquid, semi-solid and solid dosage forms, such as liquid solutions (eg injectable and infusible solutions), dispersions or suspensions, tablets, pills, powders, liposomes and suppositories.
  • the composition is in the form of an injectable solution for immunization.
  • the administration may be intravenous, subcutaneous, intraperitoneal, intramuscular, transdermal, intrathecal, and intra-arterial.
  • compositions typically must be sterile and stable under the conditions of manufacture and storage.
  • the compositions can be formulated as a solution, microemulsion, dispersion, liposome, or other ordered structure suitable to high drug concentration.
  • Sterile injectable solutions can be prepared by incorporating the active compound (i.e. antibody polypeptide) into the required amount in an appropriate solvent with one or a combination of ingredients listed above, followed by filtered sterilisation.
  • composition may also be formulated as a sterile powder for the preparation of sterile injectable solutions.
  • the proper fluidity of a solution can be maintained by for example, use of a coating such as lecithin and/or surfactants.
  • the active compound may be prepared with a carrier that will protect the compound against rapid release, such as a controlled release formulation, including implants, transdermal patches, and microencapsulated delivery systems.
  • a carrier that will protect the compound against rapid release, such as a controlled release formulation, including implants, transdermal patches, and microencapsulated delivery systems.
  • Compatible polymers may be used such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters and polylactic acid.
  • composition may also be formulated for oral administration.
  • the antibody polypeptide may be enclosed in a hard or soft shell gelatin capsule, compressed into tablets, or incorporated directly into the subject's diet.
  • composition may also be formulated for rectal administration.
  • Supplementary active compounds can also be incorporated into the composition.
  • the antibody polypeptide may be co-formulated with and/or co-administered with one or more additional therapeutic agents eg. anti-inflammatory compounds, soluble TNF- ⁇ receptor or a chemical agent that inhibits human TNF- ⁇ production, or antibodies that bind other targets such as cytokines or cell surface molecules.
  • additional therapeutic agents eg. anti-inflammatory compounds, soluble TNF- ⁇ receptor or a chemical agent that inhibits human TNF- ⁇ production, or antibodies that bind other targets such as cytokines or cell surface molecules.
  • a soluble immunochemical reagent such as protein A, C, G or L.
  • An effective amount may include a therapeutically effective amount or prophylactically effective amount of the antibody polypeptide of the invention.
  • a therapeutically effective amount refers to an amount effective at dosages and for periods of time necessary, to achieve the desired therapeutic result.
  • a prophylactically effective amount refers to an amount effective, at dosages and for periods of lime necessary, to achieve the desired prophylactic result.
  • composition is administered to mammals, preferably humans or primates.
  • Marmoset (genus Callidirix , species unknown) and Owl monkey ( Aotus trivirgatus ) genomic DNA were obtained from the European Collection of Cell Cultures (ECACC), catalogue numbers 85011419 and 90110510 respectively. Marmoset DNA was derived from cell line B95-8 while Owl monkey DNA came from cell line OMK 637-69.
  • V ⁇ leader sequences and recombination signal sequences were derived from Walter and Tomlinson, Antibody Engineering: A Practical Approach (1996).
  • the primers used for amplification of germline V ⁇ DNA were as follows:
  • Primer VK1BL AATCKCAGGTKCCAGATG (SEQ ID No: 11) Primer VK1BL35a GTTYRGGTKKGTAACACT (SEQ ID No: 12) Primer VK1BL35b ATGMCTTGTWACACTGTG (SEQ ID No: 13)
  • Genomic PCR (30 cycles) was performed using Taq polymerase with either primer pair VK1BLxVK1BL35a or VK1LxVK1BL35b. There was overlap between the sequences cloned and the two primer sets used.
  • PCR products were cloned into Invitrogen's TOPO TA cloning kit (Cat No K4500-01) and sequenced with M13 forward and pUC reverse primers. Sequence was confirmed in forward and reverse directions. In order to further confirm key sequences were not subject, to PCR errors, the PCR and cloning process was repeated twice for marmoset sequences. Nucleotide (SEQ ID Nos:14-24 and SEQ ID Nos:36-41) and amino acid (SEQ ID Nos:25-35 and SEQ ID Nos:42-47) sequences are given in FIG. 2 . Marmoset sequences 1, 2 and 3 were confirmed. Sequences 4, 5, 6, 7 and 8 were seen only in the initial PCR. Sequences 9, 10 and 11 were seen only in the repeat (i.e. second) PCR and cloning.
  • YAATKLQS (SEQ ID No:1) from Owl monkey sequence 1 (SEQ ID No:42), YEASSLQS (SEQ ID No:2) from Owl monkey sequence 2 (SEQ ID No:43), YEASKLQS (SEQ ID No:3) from Marmoset sequence 1 (SEQ ID No:25), and YSASNLET (SEQ ID No:4) from Marmoset sequence 2 (SEQ ID No:26), were chosen from the amino acid sequences shown in FIG. 2 as indicated.
  • YYASSLQS (SEQ ID No:48) was found to be identical to GI6176295 an Aotus nancymaae (Ma's night monkey) cDNA sequence, all other sequences were unique.
  • acceptor variable region (anti-TNF domain antibody) sequence in the expression vector was digested (25 ⁇ g) sequentially with KpnI and SanDI which excises the majority of FR2 as well as CDR2 as indicated on the restriction digest map. The vector was then gel purified to remove the excised wild-type FR2 and CDR2 sequence.
  • Oligo annealing was performed by incubating oligo pairs (500 pmol of each as shown in FIGS. 4A and 4B ) at 95° C. for 5 minutes followed by 65° C. for 5 minutes and then allowed to reach room temperature slowly on a hot block. Overlaps were then filled in during a Klenow reaction in the presence of dNTPs.
  • the marmoset CDR-grafted dAb Compound 145 (SEQ ID No:7) was affinity matured by constructing 14 separate libraries, each a diversification of the sequence of SEQ ID No:7 at a single amino acid residue. The selected residues are shown shaded below.
  • dAbs diversified in the 14 selected positions were tested for the ability to inhibit the binding of TNF to recombinant TNF receptor 1 (p55). Briefly, Maxisorp plates were incubated overnight with 30 mg/ml anti-human Fc mouse monoclonal antibody (Zymed, San Francisco, USA). The wells were washed with phosphate buffered saline (PBS) containing 0.05% Tween-20 and then blocked with 1% BSA in PBS before being incubated with 100 ng/ml TNF receptor 1 Fc fusion protein (R&D Systems, Minneapolis, USA). Each dAb was mixed with TNF which was added to the washed wells at a final concentration of 10 ng/ml.
  • PBS phosphate buffered saline
  • TNF binding was detected with 0.2 mg/ml biotinylated anti-TNF antibody (HyCult biotechnology, Uben, Netherlands) followed by 1 in 500 dilution of horse radish peroxidase labelled streptavidin (Amersham Biosciences, UK) and then incubation with TMB substrate (KPL, Gaithersburg, USA). The reaction was stopped by the addition of HCl and the absorbance was read at 450 nm. Anti-TNF dAb activity lead to a decrease in TNF binding and therefore a decrease in absorbance compared with the TNF only control ( FIG. 5 ).
  • Anti-TNF dAbs identified by the minilibrary diversification approach including Compounds 100 (SEQ ID No:9) and 123 (SEQ ID No:8), were also tested for the ability to neutralise the cytotoxic activity of TNF on mouse L929 fibroblasts (Evans, T., 2000, Molecular Biotechnology 15, 243-248). Briefly, L929 cells plated in microtitre plates were incubated overnight, with anti-TNF dAb, 100 pg/ml TNF and 1 mg/ml actinomycin D (Sigma, Poole, UK).

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US13/585,192 Abandoned US20130040383A1 (en) 2005-12-20 2012-08-14 Nucleic acid molecules encoding anti-inflammatory domain antibodies

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US20110237780A1 (en) 2011-09-29
US20090226428A1 (en) 2009-09-10
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US8263076B2 (en) 2012-09-11
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WO2007070979A1 (en) 2007-06-28
EP1969009A4 (en) 2009-07-22
CA2634083A1 (en) 2007-06-28
US7981414B2 (en) 2011-07-19
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US20130040383A1 (en) 2013-02-14
JP2009519720A (ja) 2009-05-21

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