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  • C07K16/24—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
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  • C07K2317/00—Immunoglobulins specific features
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  • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
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  • C07K2317/00—Immunoglobulins specific features
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  • C07K2317/55—Fab or Fab'
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  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
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  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
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  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
  • C07K2317/732—Antibody-dependent cellular cytotoxicity [ADCC]
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  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
• • C—CHEMISTRY; METALLURGY
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  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
  • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

• the invention relates to anti-IL-13 antibodies, crystals of anti-IL-13 antibodies, JJL-13 polypeptide/anti-IL-13 antibody complexes, crystals of IL-13 polypeptide/anti-IL-13 antibody complexes, IL-13R ⁇ l polypeptide/JJL-13 polypeptide/anti-IL-13 antibody complexes, crystals of JJ -13R ⁇ l polypeptide/IL-13 polypeptide/anti-IL-13 antibody complexes, and related methods and software systems.
• BACKGROUND Interleukm-13 is a pleiotropic cytokine involved in immune response conditions, such as atopy, asthma, allergy, and inflammatory response.
• the role of IL- 13 in immune response is facilitated by its effect on cell-signaling pathways.
• IL-13 can promote B cell proliferation, induce B cells to produce IgE, and down regulate the production of proinflammatory cytokines.
• IL-13 can also increase expression of VCAM-1 on endothelial cells, and enhance expression of class II MHC antigens and various adhesion molecules on monocytes.
• IL-13 function is mediated through an interaction with its receptor on hematopoietic and other cell types.
• the human LL-13 receptor (LL-13R) is a heterodimer that includes the interleukin-4 receptor ⁇ chain, H-4R ⁇ , and the LL-13 binding chain, IL-13R ⁇ l.
• the association of IL-13 with its receptor induces the activation of STAT6 (signal transducer and activation of transcription 6) and JAK1 (Janus-family kinase) through a binding interaction with the JX-4R ⁇ chain.
• EL- 13Roc2 which may be found on the cell surface or in soluble form in the circulation, binds to IL-13 with high affinity but does not mediate cellular responses to IL-13. It is thought to function as a decoy receptor.
• the invention features a crystalline antibody.
• the crystalline antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody.
• the invention features a crystalline composition that includes an antibody.
• the antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody.
• the invention features a crystalline complex that includes an IL-13 polypeptide and an antibody.
• the antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody.
• the invention features a crystalline complex that includes an IL-13R ⁇ l polypeptide and an IL-13 polypeptide.
• the invention features a method that includes using a three-dimensional model of an antibody to design an agent that interacts with an IL- 13 polypeptide.
• the antibody is an anti-IL-13 antibody or a Fab fragment of an anti- LL-13 antibody.
• the invention features a method that includes using a three- dimensional model of an IL-13 polypeptide to design an agent that interacts with the JJ -13 polypeptide.
• the invention features a method that includes using a three- dimensional model of an LL-13 polypeptide bound to an IL-13R ⁇ l polypeptide to design an agent that interacts with the JX-13 polypeptide.
• the invention features a method that includes selecting an agent by performing rational drug design with a three-dimensional structure of a crystalline complex that includes an IL-13 polypeptide; contacting the agent with an IL-13 polypeptide; and detecting the ability of the agent to bind the IL-13 polypeptide.
• the invention features a method that includes contacting an B -13 polypeptide with an antibody to form a composition; and crystallizing the composition to form a crystalline complex in which the antibody is bound to the IL-13 polypeptide.
• the antibody is an anti-LL-13 antibody or a Fab fragment of an anti-JJ - 13 antibody, and the crystalline complex can diffract X-rays to a resolution of at least about 3.5 A.
• the invention features a method that includes contacting an agent by performing rational drug design with a three-dimensional structure of a crystalline complex that includes an IL-13 polypeptide; contacting the agent with an IL-13 polypeptide; and detecting the ability of the agent to bind the IL-13 polypeptide
• LL-13 polypeptide with an antibody and an IL-13R ⁇ l polypeptide to form a composition and crystallizing the composition to form a crystalline complex in which the antibody and the IL-13R ⁇ l polypeptide are each bound to the JJ -13 polypeptide.
• the antibody is an anti-IL-13 antibody or a Fab fragment of an anti-LL-13 antibody, and the crystalline complex can diffract X-rays to a resolution of at least about 3.5 A.
• the invention features a software system that includes instructions for causing a computer system to accept information relating to a structure of an JJL-13 polypeptide bound to an antibody, the antibody including an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody.
• the instructions also cause the computer system to accept information relating to a candidate agent and to determine binding characteristics of the candidate agent to the TL- 13 polypeptide. The determination of binding characteristics is based on the information relating to the structure of the IL-13 polypeptide and the information relating to the candidate agent.
• the invention features a computer program residing on a computer readable medium.
• a plurality of instructions is stored on the computer readable medium.
• the one or more processors will accept information relating to a structure of an IL-13 polypeptide bound to an antibody, the antibody being an anti-IL-13 polypeptide or a
• the invention features a method that includes accepting information relating to the structure of an LL-13 polypeptide bound to an antibody and modeling the binding characteristics of the EL-13 polypeptide with a candidate agent.
• the antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody.
• the invention features a computer program residing on a computer readable medium containing a plurality of instructions. When the instructions are executed by one or more processors, the one or more processors will accept information relating to the structure of an IL-13 polypeptide bound to an antibody, the antibody being an anti-IL-13 antibody or a Fab fragment of an anti-IL- 13 antibody; and model the binding characteristics of the JJL-13 polypeptide with a candidate agent.
• the invention features a software system, that includes instructions for causing a computer system to accept information relating to the structure of an IL-13 polypeptide bound to an antibody, and model the binding characteristics of the IL-13 polypeptide with a candidate agent.
• the antibody is an anti-IL-13 antibody or a Fab fragment of an anti-IL-13 antibody.
• the invention features a crystalline antibody.
• the antibody is capable of binding to a site of an IL-13 polypeptide to which an D -4R polypeptide binds in vivo.
• the invention features a crystalline composition that includes an antibody capable of binding a site of an IL-13 polypeptide to which an EL- 4R polypeptide binds in vivo.
• the invention features a crystalline complex that includes an JL-13 polypeptide and an antibody.
• the antibody is capable of binding a site of an IL- 13 polypeptide to which an JL-4R polypeptide binds in vivo.
• the invention features a crystalline complex that includes an IL-13 polypeptide, an JL-13Ral polypeptide, and an antibody.
• the antibody is capable of binding a site of an IL-13 polypeptide to which an IL-4R polypeptide binds in vivo.
• the invention features a method that includes using a three- dimensional model of an antibody to design an agent that interacts with an IL-13 polypeptide.
• the antibody is capable of binding a site of an EL-13 polypeptide to which an EL-4R polypeptide binds in vivo.
• the invention features a method that includes contacting an IL-13 polypeptide, an JL-13Ral polypeptide, and an antibody.
• the antibody is capable of binding a site of an IL-13 polypeptide to which an IL-4R polypeptide binds in vivo.
• the invention features a method that includes contacting an IL-13 polypeptide, an JL-13Ral polypeptide, and an antibody.
• the antibody is capable
• the invention features a method that includes contacting an IL-13 polypeptide with an antibody and an IL-13R ⁇ l polypeptide to form a composition, and crystallizing the composition to form a crystalline complex in which the antibody and the TL-13R ⁇ l polypeptide are each bound to the EL-13 polypeptide.
• the antibody is capable of binding a site of an EL-13 polypeptide to which an EL-4R polypeptide binds in vivo, and the crystalline complex can diffract X-rays to a resolution of at least about 3.5 A.
• the invention features a software system that includes instructions for causing a computer system to accept information relating to a structure of an EL-13 polypeptide bound to an antibody, accept information relating to a candidate agent, and determine binding characteristics of the candidate agent to the EL-13 polypeptide.
• the antibody is capable of binding a site of an EL-13 polypeptide to which an EL-4R polypeptide binds in vivo.
• the determination of binding characteristics of the candidate agent is based on the information relating to the structure of the EL-13 polypeptide and the information relating to the candidate agent.
• the invention features a computer program residing on a computer readable medium containing a plurality of instructions. When the instructions are executed by one or more processors, the one or more processors will accept information relating to a structure of an EL-13 polypeptide bound to an antibody, accept information relating to a candidate agent; and determine the binding characteristics of the candidate agent to the EL-13 polypeptide.
• the antibody is capable of binding a site of an EL-13 polypeptide to which an EL-4R polypeptide binds in vivo.
• the invention features a method that includes accepting information relating to the structure of an EL-13 polypeptide bound to an antibody and modeling the binding characteristics of the EL-13 polypeptide with a candidate agent.
• the antibody is capable of binding a site of an EL-13 polypeptide to which an EL-4R polypeptide binds in vivo.
• the method of accepting information and modeling the binding characteristics is implemented by a software system.
• the invention features a computer program residing on a computer readable medium containing a plurality of instructions.
• the one or more processors When the instructions are executed by one or more processors, the one or more processors will accept information relating to the structure of an EL-13 polypeptide bound to an antibody and model the binding characteristics of the EL-13 polypeptide with a candidate agent.
• the antibody is capable of binding a site of an EL-13 polypeptide to which an EL-4R polypeptide binds in vivo.
• the invention features a software system that includes instructions for causing a computer system to accept information relating to the structure of an EL-13 polypeptide bound to an antibody and model the binding characteristics of the EL-13 polypeptide with a candidate agent.
• the antibody is capable of binding a site of an EL-13 polypeptide to which an EL-4R polypeptide binds in vivo.
• the invention features a method of modulating EL-13 activity in a subject.
• the method includes using rational drug design to select an agent that is capable of modulating EL-13 activity, and administering a therapeutically effective amount of the agent to the subject.
• the invention features a method of treating a subject having a condition associated with EL-13 activity.
• the method includes using rational drug design to select an agent that is capable of effecting EL-13 activity, and administering a therapeutically effective amount of the agent to the subject.
• the invention features a method of prophylactically treating a subject susceptible to a condition associated with EL-13 activity.
• the method includes determining that the subject is susceptible to the condition associated with EL-13 activity, using rational drug design to select an agent that is capable of effecting EL-13 activity, and administering a therapeutically effective amount of the agent to the subject.
• Structural information of a polypeptide or a corresponding ligand can lead to a greater understanding of how the polypeptide functions in vivo. For example, knowledge of the structure of a protein or a corresponding ligand can reveal properties that facilitate ' the interaction of the protein with its ligands, including other proteins, antibodies, effector molecules (e.g., hormones), and nucleic acids.
• Structure based modeling can be used to identify ligands capable of interacting with an EL-13 polypeptide, thus eliminating the need for screening assays, which can be expensive and time-consuming.
• Structural information can also be used to direct the modification of a ligand known to interact with EL-13 to generate an alternative ligand with more desirable properties, such as tighter binding or greater specificity.
• the study of the interaction between an anti-EL-13 antibody and an EL-13 polypeptide and between an EL-13 polypeptide and its receptor can facilitate the design or selection of ligands (e.g., drugs) for modulating the activity of EL-13 in vivo. Such studies can therefore be useful for designing therapeutic agents.
• Activity assays indicated that mAbl3.2 blocked EL-13 function in vitro and in vivo (see Examples 1 and 2 below), including the use of an antibody to identify EL-13-binding agents capable of disturbing the normal function of the protein. Accordingly, it is believed that the crystal structures of the mAbl3.2Fab fragment, the human EL-13/mAbl3.2 Fab fragment complex, and the human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2 Fab fragment complex (see Tables 10-12 below) can be useful for designing or identifying agents that can interact with EL-13 and the EL-13 receptor polypeptide, EL- 13R ⁇ l.
• Such agents may be useful in modulating the activity of EL-13 in immune response conditions, such as, for example, asthma (e.g., nonallergic asthma, or allergic asthma, which is sometimes referred to as chronic allergic airway disease), chronic obstructive pulmonary disorder (COPD), airway inflammation, eosinophilia, fibrosis and excess mucus production (e.g., cystic fibrosis, pulmonary fibrosis, and allergic rhinitis), inflammatory and/or autoimmune conditions of the skin (e.g., atopic dermatitis), inflammatory and/or autoimmune conditions of the gastrointestinal organs (e.g., inflammatory bowel disease (EBD) and/or Crohn's disease), liver (e.g., cirrhosis), inflammatory and/or autoimmune conditions of the blood vessels or connective tissue (e.g., scleroderma), and tumors or cancers (e.g., soft tissue or solid tumors), such as Hodgkin's lymphoma
• FIG. 1 A is the amino acid sequence of the light chain of the mAbl3.2 Fab (fragment antigen binding) fragment (SEQ JD NO:l).
• FIG. IB is the amino acid sequence of the heavy chain of mAbl3.2 Fab fragment (SEQ ED NO:2).
• FIG. 2 A is the amino acid sequence of full-length human EL-13 (Swiss-Prot Accession No. P35225) (SEQ ED NO:3).
• the signal peptide cleavage site is indicated by a slash.
• Alpha helices A, B, C, and D are underlined.
• Helix A is defined by ' amino acids 25-42;
• helix B is defined by amino acids 62-71;
• helix C is defined by amino acids 78-89; and
• helix D is defined by amino acids 112-127.
• FIG 2B is the amino acid sequence of human EL-13 (SEQ ED NO:4) following cleavage of the signal peptide.
• Alpha helices A, B, C, and D are underlined.
• FIG. 3 is a ribbon diagram illustrating the crystal structure of mAbl3.2 Fab fragment (left) with the processed form of human EL-13 (right) (see FIG. 2B). The light chain of mAbl3.2 Fab fragment is shown in dark shading, and the heavy chain in light shading. Helices A, B, C, and D of the EL-13 structure are indicated.
• FIG. 3 is a ribbon diagram illustrating the crystal structure of mAbl3.2 Fab fragment (left) with the processed form of human EL-13 (right) (see FIG. 2B). The light chain of mAbl3.2 Fab fragment is shown in dark shading, and the heavy chain in light shading. Helices A, B, C, and D of the EL-13 structure are indicated.
• FIG. 3 is a ribbon diagram illustrating the crystal structure of mAbl3.2 Fab fragment (left) with the processed form of human EL-13 (right) (see FIG. 2B). The light chain of mAbl3.2 Fab fragment is shown in dark shading, and the heavy chain in light shading. Helices
• FIG. 4 is a graph illustrating the kinetic parameters of three different anti-EL- 13 antibodies (mAbl3.2, mAbl3.4, and mAbl3.9) binding to human EL-13 as determined by Biacore analyses. Kinetic constants for mAbl3.2 are also shown.
• FIG. 5 is a graph illustrating the binding of biotinylated mAbl3.2 to recombinant and native human EL-13. ELISA plates were coated with anti-FLAG M2 antibody. The binding of FLAG-human EL-13 was detected with biotinylated mAbl3.2 and streptavidin-peroxidase.
• FIG. 6 is a graph illustrating the effect of mAbl3.2 and the known inhibitor rhuEL-13R ⁇ 2 on the bioactivity of human EL-13. "cpm" is the measure of H- thymidine taken up into TF1 cells grown in the presence of EL-13 and varying concentrations of mAbl3.2 or rhuEL-13R ⁇ 2 (x-axis).
• cpm is the measure of H- thymidine taken up into TF1 cells grown in the presence of EL-13 and varying concentrations of mAbl3.2 or rhuEL-13R ⁇ 2 (x-axis).
• FIG. 7A is a graph illustrating the effect of recombinant human EL-13 and EL-4 on CD23 expression on CDllb+ monocytes.
• the monocytes were normal peripheral blood mononuclear cells (PBMCs) harvested from a healthy donor. The cells were treated overnight with 1 ng/mL recombinant human EL-13 or EL-4, then assayed for CD23 expression by flow cytometry.
• FIG.7B is a graph illustrating the effect of mAbl3.2 on EL-13-induced CD23 expression on CDllb+ monocytes.
• FIG.7C is a graph illustrating the effect of mAbl3.2 on EL-4 - induced CD23 expression on CD1 lb+ monocytes.
• FIG. 8 is a graph illustrating the effect of mAbl3.2 on EL-13-dependent IgE production by human B cells.
• PBMC from a healthy donor were stimulated with PHA and EL-13. After 3 weeks, each well was assayed for IgE concentrations by ELISA.
• PHA + EL-13 increased the frequency of IgE-producing B cell clones. This effect was inhibited by mAbl3.2, but not by an EL-13 specific nonneutralizing antibody (mAbl3.8) or by control mouse IgG (msIgG).
• FIG. 9A is a Western blot detecting phosphorylated STAT6 protein from HT- 29 human epithelial cells treated with the indicated concentration of JJL-13 for 30 min at 37°C.
• FIG. 9A is a Western blot detecting phosphorylated STAT6 protein from HT- 29 human epithelial cells treated with the indicated concentration of JJL-13 for 30 min at 37°C.
• FIG. 9B is a histogram from flow cytometry experiments that measured the level of cellular phosphorylated STAT6 protein following treatment with JL-13. The shift in phospho-STAT6 staining intensity upon treatment with JJL-13 is indicated by the lightly shaded trace.
• FIG. 9C is a panel of histograms from flow cytometry experiments that measured the level of cellular phosphorylated STAT6 protein following treatment with a sub-optimal concentration of human EL-13 and the indicated antibody. Cells treated with EL-13 and antibody are indicated by the bold trace. Shaded histograms indicate untreated cells. In addition to mAbl3.2, an EL-13 specific nonneutralizing antibody (mAbl3.8) and a control mouse IgGl were also tested.
• FIG. 10 is a graph demonstrating the percentage of eosinophils detected in B AL from Cynomolgus monkeys sensitized to Ascaris suum following lung segmental challenge with Ascaris antigen. Twenty-four hours before challenge, animals had been administered mAbl3.2 i.v. (diamonds) or left untreated (circles). Triangles represent mAbl3-2-treated and re-challenged with Ascaris at three months post-Ab administration. Eosinophils were detected by flow cytometry using depolarized side scatter analysis. FIG.
• FIG. 11A is a graph showing that unlabeled mAbl3.2 (diamonds) or mAbl3.2 Fab fragments (circles) could compete for binding with biotinylated mAbl3.2 in an ELISA assay.
• An "irrelevant antibody” (monoclonal antibody mAbl3.8, which binds EL-13 but does not neutralize its activity) (asterisks) could not compete for binding. Competitor concentration is expressed as picomole (pM) antibody or Fab.
• FIG. 1 IB is a graph showing that unlabeled mAbl3.2 (diamonds) or mAbl3.2 Fab fragment (circles) could compete for binding with biotinylated mAbl3.2 in an ELISA assay.
• FIG. 12A is a graph showing that mAbl3.2 (diamonds) and mAbl3.2 Fab fragment (circles) inhibited EL-13-dependent TF1 cell division.
• Competitor concentration is mAbl3.2 and mAbl3.2 Fab fragment concentration, and concentration is represented as pM competitor binding sites, assuming two binding sites per intact IgG and one binding site per Fab fragment.
• FIG. 12B is a graph showing that mAbl3.2 (diamonds) and mAbl3.2 Fab fragment (circles) inhibited JJL-13 CD23 expression on human PBMCs. Competitor concentration is mAbl3.2 and mAbl3.2 Fab fragment concentration, and the concentration is represented as pM competitor binding sites, assuming two binding sites per intact IgG and one binding site per Fab fragment.
• FIG. 13 is the DNA sequence of the expression vector pAL-981 (SEQ JD NO:5), including a human EL-13 cDNA insert (hEL13coli). The cDNA sequence encoding EL-13 is underlined.
• FIG. 14 is the amino acid sequence of human EL-13R ⁇ l (Swiss-Prot Accession No. P78552) (SEQ JD NO: 12).
• FIG. 15 is a ribbon diagram illustrating the structure of the mAbl3.2
• FIG. 16 is a ribbon diagram illustrating the interaction between EL-13 and Ig domain 1 of EL-13R ⁇ l.
• FIG. 17 is a ribbon diagram illustrating the interaction between EL-13 and Ig domain 3 of EL-13R ⁇ l.
• FIG. 1 A and IB provide amino acid sequence information for the light and heavy chain polypeptides of the mAbl3.2 Fab fragment.
• FIGs. 2A and 2B provide amino acid sequence information for human EL-13.
• FIG. 3 provides structural information for a crystal of a human EL-13/mAbl3.2 Fab fragment complex.
• the mAbl3.2 Fab fragment binds to the EL-4R (JL-4R ⁇ ) binding domain of human EL-13, which includes the amino acids Ser7, Thr8, Ala9, Glul2, Leu48, Glu49, Ile52, Asn53, Arg65, Met66, Ser68, Gly69, Phe70, Cys71, Pro72, His73, Lys74, and Arg86 as defined by SEQ ID NO:4.
• FIG. 14 provides amino acid sequence information for the human JJL-13 receptor polypeptide, human EL-13R ⁇ l.
• FIGs. 15, 16, and 17 provide structural information for a crystal of a human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2
• human EL-13 forms two contacts with the human EL-13R ⁇ l polypeptide, one with Ig domain 1 of the human EL-13R ⁇ l polypeptide, and a second with the Ig domain 3 of the human EL-13R ⁇ l polypeptide.
• the interaction with Ig domain 1 involves residues Thr88, Lys89, Ile90, and Glu91 of human EL-13 as defined by SEQ ED NO:4, and residues Lys76, Lys77, Ile78, and Ala79 of the human EL-13R ⁇ l polypeptide, as defined by SEQ ED NO:12 (see FIG. 16).
• the interaction with Ig domain 3 involves residues Argil, Glul2, Leul3, Ilel4, Glul5, Lysl04, Lysl05, LeulO ⁇ , Phel07, and Argl08 of human EL-13 as defined by SEQ ED NO:4, and residues fle254, Ser255, Arg256, Lys318, Cys320, and Tyr321 of the human IL-13R ⁇ l polypeptide as defined by SEQ ID NO: 12 (see HG 17).
• a crystal of the mAbl3.2 Fab fragment can be prepared as desired.
• the process includes first isolating the mAbl3.2 Fab fragment, and then forming a crystal that contains that mAbl3.2 Fab fragment.
• a crystal containing the mAbl3.2 Fab fragment can be prepared as follows. The intact antibody is cleaved with an appropriate proteolytic enzyme (e.g., papain), and the mAbl3.2 Fab fragment is isolated from the Fc (Fragment crystallizable) fragment. The isolated mAbl3.2 Fab fragment is disposed in an appropriate solution, and the solution is crystallized.
• an appropriate proteolytic enzyme e.g., papain
• the solution can contain, for example, one or more polymers (e.g., polyethylene glycol (PEG)), one or more salts (e.g., potassium sulfate) and optionally one or more organic solvents.
• the crystals can be grown by various methods, such as, for example, sitting or hanging drop vapor diffusion. In general, crystallization can be performed at a temperature of from about 4°C to 60°C (e.g., from about 4°C to about 45°C, such as at about 4°C, about 15°C, about 18°C, about 20°C, about 25°C, about 30°C, about 32°C, about 35°C, about 37°C).
• Structural data describing a crystal of the mAbl3.2 Fab fragment can be obtained, for example, by X- ray diffraction.
• X-ray diffraction data can be collected using a variety of means in order to obtain structural coordinates. Suitable X-ray sources include rotating anodes and synchrotron sources (e.g., Advanced Light Source (ALS), Berkeley, California; or Advanced Photon Source (APS), Argonne, Illinois).
• X-rays for generating diffraction data can have a wavelength of from about 0.5 A to about 1.6 A (e.g., about 0.7 A, about 0.9 A, about 1.0 A, about 1.1 A, about 1.3 A, about 1.4 A, about 1.5 A, about 1.6 A).
• Suitable X-ray detectors include area detectors and/or charge-couple devices (CCDs) can be used as the detector(s).
• a crystal of the mAbl3.2 Fab fragment can diffract X-rays to a resolution of about 3.5 A or less (e.g., about 3.2 A or less, about 3.0 A or less, about 2.8 A or less, about 2.5 A or less, about 2.4 A or less, about 2.3 A or less, about 2.2 A or less, about 2.1 A or less, about 2.0 A or less, about 1.9 A or less, about 1.8 A or less, about 1.7 A or less, about 1.6 A or less, about 1.5 A or less, about 1.4 A or less).
• a crystal of the mAbl3.2 Fab fragment can diffract X-rays to a resolution of from about 1.6 A to about 2.5 A (e.g., from about 1.8 A to about 2.2 A).
• a complex including human EL-13 and the mAbl3.2 Fab fragment can be prepared and crystallized as desired.
• the process is as follows. Human EL-13 is expressed from a DNA plasmid.
• Human EL-13 can be expressed as a fusion protein with a suitable tag (e.g., to facilitate isolation of human EL-13 from cells), such as a glutathione-S-transferase (GST), myc, HA, hexahistidine, or FLAG tag.
• GST glutathione-S-transferase
• a fusion protein can be cleaved at a protease site engineered into the fusion protein, such as at or near the site of fusion between the polypeptide and the tag.
• Human EL-13 can be mixed with the mAbl3.2 Fab fragment prior to purification (e.g., prior to cleavage of a polypeptide tag), or human EL-13 can be mixed with the mAbl3.2 Fab fragment after purification. In some embodiments, the mAbl3.2 Fab fragment can be mixed with human EL-13 prior to purification and again following purification. In some embodiments, human EL-13 polypeptide and the mAbl3.2 Fab fragment are combined in a solution for collecting spectral data for the complex, NMR data for the complex, or for growing a crystal of the complex.
• the solution can contain, for example, one or more salts (e.g., a potassium salt), one or more polymers (e.g., polyethylene glycol (PEG)), and/or one or more organic solvents.
• Crystals can be grown by various methods, such as, for example, sitting or hanging drop vapor diffusion. In general, crystallization can be performed at about 16°C to 24°C (e.g., about 17°C to 23°C, or 18°C to 21°C).
• Structural information for a crystal of a human EL-13/mAbl3.2 Fab fragment complex can be obtained by X-ray diffraction. In general, a crystal of a human
• EL-13/mAbl3.2 Fab fragment complex can diffract X-rays to a resolution of about 3.5 A or less (e.g., about 3.2 A or less, about 3.0 A or less, about 2.8 A or less, about 2.5 A or less, about 2.4 A or less, about 2.3 A or less, about 2.2 A or less, about 2.1 A or less, about 2.0 A or less, about 1.9 A or less, about 1.8 A or less, about 1.7 A or less, about 1.6 A or less, about 1.5 A or less, about 1.4 A or less).
• about 3.5 A or less e.g., about 3.2 A or less, about 3.0 A or less, about 2.8 A or less, about 2.5 A or less, about 2.4 A or less, about 2.3 A or less, about 2.2 A or less, about 2.1 A or less, about 2.0 A or less, about 1.9 A or less, about 1.8 A or less, about 1.7 A or less, about 1.6 A or less, about 1.5 A or less, about 1.4 A or
• a crystal of a human EL-13/mAbl3.2 Fab fragment complex can diffract X-rays to a resolution of from about 1.6 A to about 2.5 A (e.g., from about 1.8 A to about 2.2 A).
• the structure of the complex can be solved to a resolution of 1.8 A.
• a complex including human EL-13, the mAbl3.2 Fab fragment, and a human EL-13R ⁇ l polypeptide can be prepared and crystallized as desired.
• the process is as follows.
• a human EL-13R ⁇ l polypeptide is expressed from a DNA plasmid in the yeast strain Pichia pastoris, such that the expressed polypeptide is glycosylated. Expression from the DNA plasmid can be driven by a promoter, such as an inducible promoter.
• the human EL-13R ⁇ l polypeptide can be expressed as a fusion protein with a suitable tag (e.g., to facilitate isolation of the human EL-13R ⁇ l polypeptide from cells), such as a glutathione-S-transferase (GST), myc, HA, hexahistidine, or FLAG tag.
• GST glutathione-S-transferase
• a fusion protein can be cleaved at a protease site engineered into the fusion protein, such as at or near the site of fusion between the polypeptide and the tag.
• the human EL-13R ⁇ l polypeptide can be mixed with human EL-13 to form a complex, and then the polypeptides of the complex can be deglycosylated by treatment with an enzyme such as endoglycosidase H.
• the mAbl3.2 Fab fragment can be added to the deglycosylated complex to form a human EL-13R ⁇ l polypeptide/human JL-13/mAbl3.2 Fab complex.
• the human EL-13R ⁇ l, human EL-13, and mAbl3.2 Fab fragment are combined in a solution for collecting spectral data for the complex,
• the solution can contain, for example, one or more salts (e.g., a potassium salt), one or more polymers (e.g., polyethylene glycol (PEG)), and/or one or more organic solvents.
• Crystals can be grown by various methods, such as, for example, sitting or hanging drop vapor diffusion. In general, crystallization can be performed at about 16°C to 24°C (e.g., about 17°C to 23°C, or 18°C to 21°C).
• Structural information for a crystal of a human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2 Fab fragment complex can be obtained by X-ray diffraction.
• a crystal of a human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2 Fab fragment complex can diffract X-rays to a resolution of about 3.5 A or less (e.g., about 3.2 A or less, about 3.0 A or less, about 2.8 A or less, about 2.5 A or less, about 2.4 A or less, about 2.3 A or less, about 2.2 A or less, about 2.1 A or less, about 2.0 A or less, about 1.9 A or less, about 1.8 A or less, about 1.7 A or less, about 1.6 A or less, about 1.5 A or less, about 1.4 A or less).
• a resolution of about 3.5 A or less e.g., about 3.2 A or less, about 3.0 A or less, about 2.8 A or less, about 2.5 A or less, about 2.4 A or less, about 2.3 A or less, about 2.2 A or less, about 2.1 A or less, about 2.0 A or less, about 1.9 A or less, about 1.8 A or less, about 1.7
• a crystal of a human TL-13/mAbl3.2 Fab fragment complex can diffract X-rays to a resolution of from about 1.6 A to about 2.5 A (e.g., from about 1.8 A to about 2.2 A).
• the structure of the complex can be solved to a resolution of 2.2 A.
• X-ray diffraction data of a crystal of the mAbl3.2 Fab fragment, human EL-13/mAbl3.2 Fab fragment complex, or human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2 Fab fragment complex can be used to obtain the structural coordinates of the atoms in the antibody or the complex.
• the structural coordinates are Cartesian coordinates that describe the location of atoms in three-dimensional space in relation to other atoms in the complex.
• the structural coordinates listed in Table 10 are the structural coordinates of a crystalline mAbl3.2 Fab fragment. These structural coordinates describe the location of atoms of the mAbl3.2 Fab fragment in relation to each other.
• the structural coordinates listed in Table 11 are the structural coordinates of a crystalline human EL- 13/mAbl3.2 Fab fragment complex. These structural coordinates describe the location of atoms of the human IL-13 in relation to each other, the location of atoms in the human EL-13 in relation to the atoms in the mAbl3.2 Fab fragment, and the location of atoms in the mAbl3.2 Fab fragment in relation to each other.
• the structural coordinates listed in Table 12 are the structural coordinates of a crystalline human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2 Fab fragment complex.
• structural coordinates describe the location of atoms of the EL-13R ⁇ l polypeptide in relation to each other, the location of atoms in the human EL- 13R ⁇ l polypeptide in relation to the atoms in human EL-13, the location of atoms in human EL-13 in relation to each other, the location of atoms in human EL-13 in relation to the atoms in the mAbl3.2 Fab fragment and the location of atoms in the mAbl3.2 Fab fragment in relation to each other.
• the structural coordinates of a crystal can be modified by mathematical manipulation, such as by inversion or integer additions or subtractions. As such, structural coordinates are relative coordinates.
• structural coordinates describing the location of atoms in the mAbl3.2 Fab fragment are not specifically limited by the actual x, y, and z coordinates of Table 10.
• structural coordinates describing the location of atoms in the human EL-13 bound to the mAbl3.2 Fab fragment are not specifically limited by the actual x, y, and z coordinates of Table 11.
• structural coordinates describing the location of atoms in the human EL-13 bound to both the mAbl3.2 Fab fragment and the human EL-13R ⁇ l polypeptide are not specifically limited by the actual x, y, and z coordinates of Table 12.
• the structural coordinates of the mAbl3.2 Fab fragment or human JJL-13/mAbl3.2 Fab fragment complex or human EL-R ⁇ l polypeptide/human JL- 13/mAb 13.2 Fab fragment complex can be used to derive a representation (e.g., a two dimensional representation or three dimensional representation) of the mAbl3.2 Fab fragment, a fragment of the mAbl3.2 Fab fragment, human IL-13, a fragment of human IL-13, the human EL-13R ⁇ l polypeptide, a fragment of the JL-13R ⁇ l polypeptide, the human JL- 13/mAb 13.2 Fab fragment complex or human IL-R ⁇ l polypeptide/human IL-13/mAb 13.2 Fab fragment complex, or a fragment of either complex.
• a representation e.g., a two dimensional representation or three dimensional representation
• a three-dimensional representation can include the structural coordinates of the mAbl3.2 fragment according to Table 10 ⁇ a root mean square deviation from the alpha carbon atoms of amino acids of about 1.5 A or less (e.g., about 1.0 A or less, or about 0.5 A or less).
• a three-dimensional representation can include the structural coordinates of a human EL- 13/mAbl3.2 Fab fragment complex according to Table 11 ⁇ a root mean square deviation from the alpha carbon atoms of amino acids of not more than about 1.5 A (e.g., not more than about 1.0 A, not more than about 0.5 A or less).
• a three-dimensional representation can include the structural coordinates of a human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2 Fab fragment complex according to Table 12 ⁇ a root mean square deviation from the alpha carbon atoms of amino acids of not more than about 1.5 A (e.g., not more than about 1.0 A, not more than about 0.5 A or less).
• Root mean square deviation is the square root of the arithmetic mean of the squares of the deviations from the mean, and is a way of expressing deviation or variation from structural coordinates.
• Conservative substitutions of amino acids can result in a molecular representation having structural coordinates within the stated root mean square deviation.
• two molecular models of polypeptides that differ from one another by conservative amino acid substitutions can have coordinates of backbone atoms within a stated rms deviation, such as less than about 1.5 A (e.g., less than about about 1.0 A, less than about 0.5 A).
• Backbone atoms of a polypeptide include the alpha carbon (C ⁇ or CA) atoms, carbonyl carbon (C) atoms, and amide nitrogen (N) atoms.
• Various software programs allow for the graphical representation of a set of structural coordinates to obtain a representation of a molecule or molecular complex, such as the mAbl3.2 Fab fragment or the human JL-13/mAbl3.2 Fab fragment complex or the human JL-13R ⁇ l polypeptide/human IL- 13/mAb 13.2 Fab fragment complex.
• a representation should accurately reflect (relatively and/or absolutely) structural coordinates, or information derived from structural coordinates, such as distances or angles between features.
• the representation can be a two- dimensional figure, such as a stereoscopic two-dimensional figure, or an interactive two-dimensional display (e.g., a computer display that can display different faces of the molecule or molecular complex), or an interactive stereoscopic two-dimensional display.
• An interactive two-dimensional display can be, for example, a computer display that can be rotated to show different faces of a polypeptide, a fragment of a polypeptide, a complex and/or a fragment of a complex.
• the representation is a three-dimensional representation.
• a three- dimensional model can be a physical model of a molecular structure (e.g., a ball-and- stick model).
• a three dimensional representation can be a graphical representation of a molecular structure (e.g., a drawing or a figure presented on a computer display).
• a two-dimensional graphical representation e.g., a drawing
• a representation can be modeled at more than one level.
• the polypeptide when the three-dimensional representation includes a polypeptide, such as human IL-13 bound to the mAbl3.2 Fab fragment, the polypeptide can be represented at one or more different levels of structure, such as primary structure (amino acid sequence), secondary structure (e.g., ⁇ -helices and ⁇ - sheets), tertiary structure (overall fold), and quaternary structure (oligomerization state).
• the heavy and light chain polypeptides of the mAbl3.2 Fab fragment can also be represented at the one or more different structural levels.
• a representation can include different levels of detail.
• the representation can include the relative locations of secondary structural features of a protein without specifying the positions of atoms.
• a more detailed representation could, for example, include the positions of atoms.
• a representation can include information in addition to the structural coordinates of the atoms in the mAbl3.2 Fab fragment, the human JL-13/mAbl3.2 Fab fragment complex, or the human IL-13R ⁇ l polypeptide/human J -13/mAbl3.2 Fab fragment complex.
• a representation can provide information regarding the shape of a solvent accessible surface, the van der Waals radii of the atoms of the model, and the van der Waals radius of a solvent (e.g., water).
• Other features that can be derived from a representation include, for example, electrostatic potential, the location of voids or pockets within a macromolecular structure, and the location of hydrogen bonds and salt bridges.
• An agent that interacts with the mAbl3.2 Fab fragment, human IL-13, or the human EL-13R ⁇ l polypeptide can be identified or designed by a method that includes using a representation of the mAbl3.2 Fab fragment, a human EL-13, a human IL- 13R ⁇ l polypeptide, a human EL-13/mAbl3.2 Fab fragment complex, or a human EL- 13-R ⁇ l polypeptide/human EL-13/mAbl3.2 Fab fragment complex.
• Exemplary types of representations include the representations discussed above.
• the representation can be of an analog polypeptide, polypeptide fragment, complex or fragment of a complex.
• a candidate agent that interacts with the representation can be designed or identified by performing computer fitting analysis of the candidate agent with the representation.
• an agent is a molecule.
• agents include polypeptides, nucleic acids (including DNA or RNA), or small molecules (e.g., small organic molecules).
• An agent can be a ligand, and can act, for example, as an agonist or antagonist.
• An agent that interacts with a polypeptide e.g., human IL-13, human IL-13R ⁇ l polypeptide
• the interaction can be mediated by any of the forces noted herein, including, for example, hydrogen bonding, electrostatic forces, hydrophobic interactions, and van der Waals interactions.
• X-ray crystallography can be used to obtain structural coordinates of an mAbl3.2 Fab fragment, a human JJL-13/mAbl3.2 Fab fragment complex, or a human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2 Fab fragment complex.
• structural coordinates can be obtained using other techniques including NMR techniques. Additional structural information can be obtained from spectral techniques (e.g., optical rotary dispersion (ORD), circular dichroism (CD)), homology modeling, and computational methods such as those that include data from molecular mechanics or from dynamics assays).
• the X-ray diffraction data can be used to construct an electron density map of the mAbl3.2 Fab fragment, the human EL-13/mAbl3.2 Fab fragment complex, or the human EL-13R ⁇ l polypeptide/human EL- 13/mAb 13.2 Fab fragment complex.
• the electron density map can be used to derive a representation (e.g., a two dimensional representation or a three dimensional representation) of the mAbl3.2 Fab fragment, a fragment of the mAbl3.2 Fab fragment, human EL-13 or a fragment of human EL-13, the human EL-13R ⁇ l polypeptide or a fragment of the human EL-13R ⁇ l polypeptide, the human EL- 13/mAb 13.2 Fab fragment complex, the human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2 Fab fragment complex, or a fragment of either complex. Creation of an electron density map typically involves using information regarding the phase of the X-ray scatter.
• Phase information can be extracted, for example, either from the diffraction data or from supplementing diffraction experiments to complete the construction of the electron density map.
• Methods for calculating phase from X-ray diffraction data include, without limitation, multiwavelength anomalous dispersion (MAD), multiple isomorphous replacement (MER), multiple isomorphous replacement with anomalous scattering (MERAS), single isomorphous replacement with anomalous scattering (SERAS), reciprocal space solvent flattening, molecular replacement, or a combination thereof.
• MAD multiwavelength anomalous dispersion
• MER multiple isomorphous replacement
• MERAS multiple isomorphous replacement with anomalous scattering
• SERAS single isomorphous replacement with anomalous scattering
• reciprocal space solvent flattening molecular replacement, or a combination thereof.
• phase of each diffracted X-ray can be determined by solving a set of simultaneous phase equations.
• the location of heavy atom sites can be identified using a computer program, such as SHELXS (Sheldrick, Institut Anorg. Chemie, G ⁇ ttingen, Germany), and diffraction data can be processed using computer programs such as MOSFLM, SCALA,
• an electron density map of the complex can be constructed.
• the electron density map can be used to derive a representation of a polypeptide, a complex, or a fragment of a polypeptide or complex by aligning a three-dimensional model of a polypeptide or complex (e.g., a complex containing a polypeptide bound to an antibody) with the electron density map.
• the alignment process results in a comparative model that shows the degree to which the calculated electron density map varies from the model of the previously known polypeptide or the previously known complex.
• the comparative model is then refined over one or more cycles (e.g., two cycles, three cycles, four cycles, five cycles, six cycles, seven cycles, eight cycles, nine cycles, ten cycles) to generate a better fit with the electron density map.
• a software program such as CNS (Brunger et al, Acta Crystallogr. D54:905-921, 1998) can be used to refine the model.
• the quality of fit in the comparative model can be measured by, for example, an R work ⁇ r R f r ee value. A smaller value of R work or R f r ee generally indicates a better fit.
• Misalignments in the comparative model can be adjusted to provide a modified comparative model and a lower R W o rk or R ⁇ e value.
• the adjustments can be based on information relating to human EL-13, human EL-13R ⁇ l, the mAbl3.2 Fab fragment, the previously known polypeptide and/or the previously known complex.
• information includes, for example, estimated helical or beta sheet content, hydrophobic and hydrophilic domains, and protein folding patterns, which can be derived, for example, from amino acid sequence, homology modeling, and spectral data.
• an adjustment can include replacing the ligand in the previously known complex with the mAbl3.2 fragment.
• an adjustment can include replacing an amino acid in the previously known polypeptide with the amino acid in the corresponding site of human EL-13.
• a representation of the mAbl3.2 Fab fragment can be derived by aligning a previously determined structural model of a different (but similar) antibody Fab fragment (e.g., a 2E8 Fab antibody fragment, Protein Databank Identification No.
• a representation of a human JL-13/mAbl3.2 Fab fragment complex can subsequently be derived by aligning the previously determined structural model of the mAbl3.2 Fab fragment with the electron density map of the complex.
• a representation of a human J -13R ⁇ l polypeptide/human IL-13/mAbl3.2 Fab fragment complex can subsequently be derived by aligning the previously determined structural model of the human IL- 13/mAb 13.2 Fab fragment complex with the electron density map of the human IL-13R ⁇ l polypeptide/human EL- 13/mAbl3.2 Fab fragment complex.
• a machine such as a computer, can be programmed in memory with the structural coordinates of the mAbl3.2 Fab fragment, a human JL-13/mAbl3.2 Fab fragment complex, or a human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2 Fab fragment complex together with a program capable of generating a three-dimensional graphical representation of the structural coordinates on a display connected to the machine.
• a software system can be designed and/or utilized to accept and store the structural coordinates. The software system can be capable of generating a graphical representation of the structural coordinates.
• the software system can also be capable of accessing external databases to identify compounds (e.g., polypeptides) with similar structural features as human EL-13 or human EL-13R ⁇ l, and/or to identify one or more candidate agents with characteristics that may render the candidate agent(s) likely to interact with human JJL-13 or human EL-13R ⁇ l.
• the software system can also be capable of accessing external databases to identify compounds that interact with human EL-13 or human EL-13R ⁇ l by virtue of the knowledge of the structure of the mAbl3.2 Fab fragment, or human EL-13R ⁇ l polypeptide, and its interaction with human EL-13.
• a machine having a memory containing structure data or a software system containing such data can aid in the rational design or selection of EL-13 ligands, such as agonists or antagonists.
• a machine or software system can aid in the evaluation of the ability of an agent to associate with human EL-13, can aid in the modeling of compounds or proteins related by structural or sequence homology to human EL-13, or can aid in the evaluation of the ability of an agent to interfere with the bioactivity of human EL-13.
• a bioactivity of human EL-13 can be any effect that the polypeptide elicits on or in a cell or tissue in vivo or in vitro. Exemplary bioactivities of human JJL-13 are described herein, such as in Examples 1 and 2.
• a machine having a memory containing structure data or a software system containing such data can aid in the rational design or selection of JL-13R ⁇ l ligands, such as agonists or antagonists.
• a machine or software system can aid in the evaluation of the ability of an agent to associate with a human EL-13R ⁇ l polypeptide, can aid in the modeling of compounds or proteins related by structural or sequence homology to a human JJL-13R ⁇ l polypeptide, or can aid in the evaluation of the ability of an agent to interfere with the bioactivity of a human EL-13R ⁇ l polypeptide.
• a bioactivity of a human EL-13R ⁇ l polypeptide can be any affect that the polypeptide elicits on or in a cell or tissue in vivo or in vitro. Exemplary bioactivities of human EL-13R ⁇ l are described herein, such as in Example 3.
• the machine can produce a representation (e.g., a two dimensional representation or a three dimensional representation) of the mAbl3.2 Fab fragment or a fragment of the mAbl3.2 Fab fragment, human EL-13 or a fragment of human EL- 13, a human EL-13R ⁇ l polypeptide or a fragment of a human JJL-13R ⁇ l polypeptide, a human IL-13/mAbl3.2 Fab fragment complex, a human EL-13R ⁇ l polypeptide/human EL- 13/mAb 13.2 fab fragment complex, or a fragment of either complex.
• a software system for example, can cause the machine to produce such information.
• the machine can include a machine-readable data storage medium including a data storage material encoded with machine-readable data.
• the machine- readable data can include structural coordinates of atoms of the mAbl3.2 Fab fragment or atoms of a fragment of the mAbl3.2 Fab fragment, atoms of human EL-13 or atoms of a fragment of human EL-13, atoms of a human EL- 13/mAb 13.2 Fab fragment complex, atoms of a human EL-13R ⁇ l polypeptide/human EL-13/mAbl3.2 fab fragment complex, or atoms of either complex.
• Machine-readable storage media including data storage material can include conventional computer hard drives, floppy disks, DAT tape, CD-ROM, DVD, and other magnetic, magneto-optical, optical, and other media which may be adapted for use with a computer.
• the machine can also have a working memory for storing instructions for processing the machine-readable data, as well as a central processing unit (CPU) coupled to the working memory and to the machine-readable data storage medium for the purpose of processing the machine-readable data into the desired three-dimensional representation.
• a display can be connected to the CPU so that the three-dimensional representation may be visualized by the user.
• the machine when used with a machine programmed with instructions for using the data (e.g., a computer loaded with one or more programs of the sort described herein) the machine is capable of displaying a graphical representation (e.g., a two dimensional graphical representation, a three-dimensional graphical representation) of any of the polypeptides, polypeptide fragments, complexes, or complex fragments described herein.
• a graphical representation e.g., a two dimensional graphical representation, a three-dimensional graphical representation
• a display (e.g., a computer display) can show a representation of the mAbl3.2 Fab fragment or a fragment of the mAbl3.2 Fab fragment, human EL-13 or a fragment of human EL-13, a human EL-13R ⁇ l polypeptide or a fragment of a human JL-13R ⁇ l polypeptide, a human IL- 13/mAb 13.2 Fab fragment complex, a human J -13R ⁇ l polypeptide/human EL- 13/mAb 13.2 fab fragment complex, or a fragment of either complex.
• the representation can also include an agent bound to human IL-13 or the human IL-13R ⁇ l polypeptide, or the user can superimpose a three-dimensional model of an agent on the representation of human EL-13 or the human JJL-13R ⁇ l polypeptide.
• the agent can be an agonist (e.g., a candidate agonist) of human EL-13 or human EL-13R ⁇ l, or an antagonist (e.g., a candidate antagonist) of human EL-13 or human EL-13R ⁇ l.
• the agent can be a known compound or fragment of a compound.
• the agent can be a previously unknown compound, or a fragment of a previously unknown compound. The user can inspect the resulting representation.
• a representation of the mAbl3.2 Fab fragment or fragment of the mAbl3.2 Fab fragment, human EL-13 or fragment of the human EL-13, the human EL-13Ral polypeptide or fragment of the human EL-13Ral polypeptide, the human EL- 13/mAb 13.2 Fab fragment complex, the human EL-13R ⁇ l polypeptide/human JL-13/mAbl3.2 fab fragment complex, or the fragment of either complex can be generated, for example, by altering a previously existing representation of such polypeptides and polypeptide complexes. For example, there can be a preferred distance, or range of distances, between atoms of the antibody and atoms of the human IL-13 when considering a new representation of a complex or fragment of a complex.
• Distances longer than a preferred distance may be associated with a weak interaction between the agent and active site (e.g., the site of IL-13 receptor binding (such as to an EL-13R ⁇ l receptor polypeptide or an EL-4 receptor polypeptide) on the JJL-13 polypeptide).
• Distances shorter than a preferred distance may be associated with repulsive forces that can weaken the interaction between the agent and the polypeptide. A steric clash can occur when distances between atoms are too short.
• a steric clash occurs when the locations of two atoms are unreasonably close together, for example, when two atoms are separated by a distance less than the sum of their van der Waals radii. If a steric clash exists, the user can adjust the position of the agent relative to the human EL-13 (e.g., a rigid body translation or rotation of the agent), until the steric clash is relieved. The user can adjust the conformation of the agent or of the human EL-13 in the vicinity of the agent in order to relieve a steric clash.
• Steric clashes can also be removed by altering the structure of the agent, for example, by changing a "bulky group,” such as an aromatic ring, to a smaller group, such as to a methyl or hydroxyl group, or by changing a rigid group to a flexible group that can accommodate a conformation that does not produce a steric clash.
• Electrostatic forces can also influence an interaction between an agent and a polypeptide (such as the part of the polypeptide that interacts with a receptor polypeptide, e.g., a human EL-13R ⁇ l polypeptide or a human EL-4R polypeptide).
• electrostatic properties can be associated with repulsive forces that can weaken the interaction between the agent and the EL-13 polypeptide.
• Altering the charge of the agent e.g., by replacing a positively charged group with a neutral group can relieve electrostatic repulsion.
• Similar processes can be performed to design an agent that interacts with a human EL-13R ⁇ l polypeptide, such as in the vicinity of interaction between the human EL-13R ⁇ l polypeptide and human EL-13. Forces that influence binding strength between the mAbl3.2 Fab fragment and human EL-13 can be evaluated in the polypeptide/agent model. Likewise, forces that influence binding strength between human EL-13 and the human EL-13R ⁇ l polypeptide can be evaluated in the polypeptide/agent model.
• These can include, for example, hydrogen bonding, electrostatic forces, hydrophobic interactions, van der Waals interactions, dipole-dipole interactions, ⁇ -stacking forces, and anion- ⁇ interactions.
• the user can evaluate these forces visually, for example by noting a hydrogen bond donor/acceptor pair arranged with a distance and angle suitable for a hydrogen bond. Based on the evaluation, the user can alter the model to find a more favorable interaction between the human IL-13, or human JJL-13R ⁇ l polypeptide, and the agent.
• Altering the model can include changing the three-dimensional structure of the polypeptide without altering its chemical structure, for example by altering the conformation of amino acid side chains or backbone dihedral angles.
• Altering the model can include altering the position or conformation of the agent, as described above. Altering the model can also include altering the chemical structure of the agent, for example by substituting, adding, or removing groups. For example, if a hydrogen bond donor on the human IL-13 is located near a hydrogen bond donor on the agent, the user can replace the hydrogen bond donor on the agent with a hydrogen bond acceptor.
• the relative locations of the agent and the human EL-13, or their conformations, can be adjusted to find an optimized binding geometry for a particular agent to the EL-13 polypeptide. Likewise, the relative locations of the agent and the human EL-13R ⁇ l polypeptide can be adjusted to find an optimized binding geometry for a particular agent to the human EL-13R ⁇ l polypeptide.
• An optimized binding geometry is characterized by, for example, favorable hydrogen bond distances and angles, maximal electrostatic attractions, minimal electrostatic repulsions, the sequestration of hydrophobic moieties away from an aqueous environment, and the absence of steric clashes.
• the optimized geometry can have the lowest calculated energy of a family of possible geometries for a human EL-13 /antibody complex, or a human EL-13/receptor complex.
• An optimized geometry can be determined, for example, through molecular mechanics or molecular dynamics calculations.
• a series of representations of human EL-13 bound to different agents can be generated.
• a series of representations of a human EL-13R ⁇ l polypeptide bound to different agents can be generated.
• a score can be calculated for each representation.
• the score can describe, for example, an expected strength of interaction between human EL-13 and the agent.
• the score can reflect one of the factors described above that influence binding strength.
• the score can be an aggregate score that reflects more than one of the factors.
• the different agents can be ranked according to their scores. Steps in the design of the agent can be carried out in an automated fashion by a machine (e.g., a computer).
• a machine e.g., a computer
• a representation of human IL-13, or a human EL-13R ⁇ l polypeptide can be programmed in the machine, along with representations of candidate agents.
• the machine can find an optimized binding geometry for each of the candidate agents to the site of receptor binding, and calculate a score to determine which of the agents in the series is likely to interact most strongly with human EL-13, or the human EL-13R ⁇ l polypeptide.
• a software system can be designed and/or implemented to facilitate these steps.
• Software systems e.g., computer programs used to generate representations or perform the necessary fitting analyses include, but are not limited to: MCSS, Ludi, QUANTA, Insight ⁇ , Cerius2, CHARMm, and Modeler from Accelrys, Inc. (San Diego, CA); SYBYL, Unity, FleXX, and LEAPFROG from TRIPOS, Inc. (St. Louis, MO); AUTODOCK (Scripps Research Institute, La Jolla, CA), GRJD (Oxford
• the structural coordinates can also be used to visualize the three-dimensional structure of human EL-13 using MOLSCREPT, RASTER3D, or PYMOL (Kraulis, J. Appl. Crystallogr. 24: 946-950, 1991 ; Bacon and Anderson, /. Mol. Graph. 6: 219-220, 1998 ; DeLano, The PYMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA).
• the agent can, for example, be selected by screening an appropriate database, can be designed de novo by analyzing the steric configurations and charge potentials of an unbound human EL-13, or unbound human EL-13R ⁇ l polypeptide, in conjunction with the appropriate software systems, and/or can be designed using characteristics of known cytokine ligands.
• the agent can be tested for an ability to block binding of EL-13 to an EL-4R polypeptide, such as EL-4R ⁇ , or an EL-R ⁇ l polypeptide.
• An agent can be designed for binding to human EL-13 or to the human EL-13R ⁇ l polypeptide.
• the method can be used to design or select agonists or antagonists of human EL-13 or a human EL-R ⁇ l polypeptide.
• a software system can be designed and/or implemented to facilitate database searching, and/or agent selection and design.
• an agent Once an agent has been designed or identified, it can be obtained or synthesized and further evaluated for its affect on human EL-13 activity or on human EL-13R ⁇ l activity.
• the agent can be evaluated by contacting it with human JJL-13 and assaying JJL-13 bioactivity, or by contacting it with a human JL-13R ⁇ l polypeptide and assaying JL-13R ⁇ l bioactivity.
• a method for evaluating the agent can include an activity assay performed in vitro or in vivo.
• An activity assay can be a cell-based assay, for example.
• the agent can act either as an agonist or antagonist of human JJL-13 or EL-13R ⁇ l activity.
• An agonist will cause human EL-13 or human EL- 13R ⁇ l polypeptide to have the same or similar activity, and an antagonist will inhibit a normal function of human EL-13 or the human EL-13R ⁇ l polypeptide.
• An agent can be contacted with the human EL-13 in the presence of an anti-EL-13 antibody (e.g., mAbl3.2 or mAbl3.2 Fab) or a human EL-13 receptor (e.g., an EL-4R polypeptide, such as a human EL-4R ⁇ polypeptide, or an EL-13R polypeptide, such as a human EL- 13R ⁇ l polypeptide) to determine whether or not the agent inhibits binding of the antibody or the receptor to the human EL-13 polypeptide.
• the agent will inhibit binding of one kind of receptor to human IL-13, but will not inhibit binding of another kind of receptor.
• an agent can inhibit binding of a human EL-13 polypeptide to a human EL-4R polypeptide (e.g., the EL-4R ⁇ chain), but not a human EL-13R ⁇ l polypeptide.
• a different agent can inhibit binding of human EL-13 to an EL-13R ⁇ l polypeptide but not to a human EL-4R polypeptide.
• the agent will inhibit binding of the EL-13 polypeptide to a human EL 4R polypeptide (e.g., the EL-4R ⁇ chain) and a human EL-13R ⁇ l polypeptide.
• a crystal containing human EL-13 bound to the identified agent can be grown and the structure determined by X-ray crystallography.
• a second agent can be designed or identified based on the interaction of the first agent with human EL-13.
• Various molecular analysis and rational drug design techniques are further disclosed in, for example, U.S. Patent Nos. 5,834,228, 5,939,528 and 5,856,116, as well as in PCT Application No. PCT/US98/16879, published as WO 99/09148. While certain embodiments have been described, other embodiments are also contemplated. As an example, while embodiments involving human EL-13, the mAbl3.2 Fab fragment, and a human EL-13R ⁇ l polypeptide have been described, more generally, any JJL-13 polypeptide, any JL-13R ⁇ l polypeptide, and/or any anti-IL-13 antibody can be used.
• an JJL-13 polypeptide or an J - 13R ⁇ l polypeptide can originate from a nonmammalian or mammalian species.
• nonhuman mammals include, a nonhuman primate (such as a monkey or ape), a mouse, rat, goat, cow, bull, pig, horse, sheep, wild boar, sea otter, cat, or dog.
• exemplary nonmammalian species include chicken, turkey, shrimp, alligator, or fish.
• an IL-13 polypeptide or an EL-13R ⁇ l polypeptide can generally be a full-length, mature polypeptide, including the full-length amino acid sequence of any isoform or processed form of an EL-13 polypeptide or EL-13R ⁇ l polypeptide.
• An isoform is any of several multiple forms of a protein that differ in their primary structure.
• Full-length EL-13 can be referred to as the precursor form of the protein.
• Full-length EL-13 has a signal peptide cleavage site.
• the EL-13 polypeptide can be the processed polypeptide, such as following cleavage of the signal peptide.
• a human EL-13 polypeptide typically has at least one active site for interacting with a receptor polypeptide (e.g., an EL-4R polypeptide, an EL-13 ⁇ l polypeptide).
• An EL-13 polypeptide can include three active sites for interacting with two different receptor polypeptides.
• An anti-EL-13 antibody can be capable of binding to at least one of the active sites.
• an active site can include a site of receptor polypeptide binding, or a site of phosphorylation, glycosylation, alkylation, acylation, or other covalent modification.
• An active site can include accessory binding sites adjacent or proximal to the actual site of binding that may affect activity upon interaction with the ligand.
• An active site of a human EL-13 polypeptide can include amino acids of SEQ ED NO:4.
• an active site of a human EL-13 polypeptide can include one or more of amino acids Ser7, Thr8, Ala9, Glul2, Leu48, Glu49, ⁇ e52, Asn53, Arg65, Ser68, Gly69, Phe70, Cys71, Pro72, His73, Lys74, and Arg86 as defined by the amino acid sequence of SEQ ID NO:4 (FIG. 2B).
• an agent can interact to within about 2. ⁇ A or less (e.g., about 1.5 A or less, about LOA or less) of one or more amino acids Glu49, Asn53, Gly69, Pro72, His73, Lys74, and Arg86 of EL-13, as defined by the amino acid sequence of SEQ JJD NO:4.
• an active site of a human EL-13 polypeptide can include one or more of amino acids Argl 1, Glul2, Leul3, Ilel4, Glul5, Lysl04, Lysl05, Leul06, Phel07, and Argl08 as defined by the amino acid sequence of SEQ ID NO:4.
• an active site of a human EL-13 polypeptide can include one or more of amino acids Thr88, Lys89, Ile90, and Glu91 as defined by the amino acid sequence of SEQ ED NO:4.
• a human EL-13 polypeptide can include one, two, or all three of the active sites described above.
• a human EL-13R ⁇ l polypeptide typically has at least one active site for interacting with a polypeptide ligand (e.g., a human EL-13 polypeptide).
• An anti- JL-13R l antibody can be capable of binding to at least one of the active sites.
• an active site can include a site of polypeptide ligand binding, or a site of phosphorylation, glycosylation, alkylation, acylation, or other covalent modification.
• An active site can include accessory binding sites adjacent or proximal to the actual site of binding that may affect activity upon interaction with the ligand.
• An active site of a human JL-13R ⁇ l polypeptide can include amino acids of SEQ ID NO: 12.
• an active site of a human EL-13R ⁇ l polypeptide can include one or more of amino acid residues Ele254, Ser255, Arg256, Lys318, Cys320, and Tyr321 as defined by the amino acid sequence of SEQ ED NO: 12.
• an active site of a human EL-13R ⁇ l polypeptide can include one or more of amino acid residues Lys76, Lys77, Ile78, and Ala79 as defined by the amino acid sequence of SEQ ED NO: 12.
• a human EL-13R ⁇ l polypeptide can include one or both of these active sites. The numbering of the amino acids of a human EL-13 polypeptide, a human
• EL-13R ⁇ l polypeptide, and the heavy and light chains of an anti-EL-13 antibody, such as mAbl3.2 Fab may be different than that set forth here, and may contain certain conservative amino acid substitutions, additions or deletions that yield the same three- dimensional structure as those defined by Table 10, ⁇ an rmsd for backbone atoms of less than 1.5 A, or by Table 11, ⁇ an rmsd for backbone atoms of less than 1.5 A, or by Table 12, ⁇ an rmsd for backbone atoms of less than 1.5 A.
• the numbering of a human EL-13 processed polypeptide may be different than that set forth in FIG.
• the sequence of the EL-13 may contain conservative amino acid substitutions but yield the same structure as that defined by the coordinates of Table 11 and illustrated in FIG. 3 or the same structure as that defined by the coordinates of Table 12 and illustrated in FIGs. 15,16 and 17.
• Corresponding amino acids and conservative substitutions in other isoforms or analogs are easily identified by visual inspection of the relevant amino acid sequences or by using commercially available homology software programs (e.g., MODELLAR, MSI, San Diego, CA).
• An analog is a polypeptide having conservative amino acid substitutions.
• Conservative substitutions are amino acid substitutions that are functionally or structurally equivalent to the substituted amino acid.
• a conservative substitution can include switching one amino acid for another with similar polarity, or steric arrangement, or belonging to the same class (e.g., hydrophobic, acidic or basic) as the substituted amino acid.
• Conservative substitutions include substitutions having an inconsequential effect on the three-dimensional structure of an anti-EL-13 antibody or a human EL-13 polypeptide/anti-EL-13 antibody complex or a human EL-13R ⁇ l polypeptide/human IL-13 polypeptide/anti-EL-13 antibody complex with respect to identification and design of agents that interact with the polypeptide (e.g., an EL-13 polypeptide, an EL-13R ⁇ l polypeptide), as well as for molecular replacement analyses and/or for homology modeling.
• an anti-IL-13 antibody is derived from a mouse
• any anti-EL-13 antibody can be used.
• an anti-EL-13 antibody can originate from a human, mouse, rat, hamster, rabbit, goat, horse, or chicken.
• an anti-EL-13 antibody is generated by a certain method, other methods may also be used.
• an anti-EL-13 antibody can be generated by first preparing polyclonal antisera by immunization of female B ALB/c mice with recombinant or native human EL-13. Sera can be screened for binding to human EL-13 by an assay such as ELISA.
• Splenocytes from a mouse demonstrating high serum antibody titers can be fused with a myeloma cell line, such as the P3X63_AG8.653 myeloma cell line (ATCC, Manassas, VA), and plated in selective media. Fusions can be isolated following multiple rounds of subcloning by limiting dilution and the fusions can be screened for the production of antibodies that have a binding affinity to human EL-13.
• An anti-EL-13 antibody can be polyclonal or monoclonal.
• An antibody that binds EL- 13 can be a fragment of an antibody, such as a Fab fragment.
• intact antibodies also known as immunoglobulins
• immunoglobulins are tetrameric glycosylated proteins composed of two light (L) chains of approximately 25 kDa each and two heavy (H) chains of approximately 50 kDa each.
• Each light chain is composed of an N-terminal variable (V) domain (VL) and a constant (C) domain (CL).
• Each heavy chain is composed of an N-terminal V domain (VH), three or four C domains (CHs), and a hinge region.
• the CH domain most proximal to VH is designated as CHI.
• the VH and VL domain consist of four regions of relatively conserved sequence called framework regions, which form a scaffold for three regions of hypervariable sequence (complementarity determining regions, CDRs).
• CDRs contain most of the residues responsible for specific interactions with the antigen.
• CDRs are referred to as CDRl, CDR2, and CDR3.
• CDR constituents on the heavy chain are referred to as HI, H2, and H3, while CDR constituents on the light chain are referred to as LI, L2, and L3 (see Table 4, for example).
• the subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known in the art. For a review of antibody structure, see Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, eds. Harlow et al. (1988).
• the smallest antigen-binding fragment is the Fv (Fragment variable), which consists of the VH and VL domains.
• the Fab (fragment antigen binding) fragment consists of the VH-CH1 and VL-CL domains covalently linked by a disulfide bond between the constant regions. Accordingly, in one aspect, this application features an antibody or an antigen- binding fragment thereof, that binds to and/or neutralizes, EL- 13.
• the antibody or fragment thereof can also be a human, humanized, chimeric, or in vjtro-generated antibody.
• the anti-EL- 13 antibody or fragment thereof is a humanized antibody.
• the antibody includes one or more CDRs that has a backbone conformation of a CDR described in Table 10 ⁇ a root mean square deviation (RMSD) of not more than 1.5, 1.2, 1.1, or 1.0 Angstroms, Table 11 ⁇ an RMSD of not more than 1.5, 1.2, 1.1, or 1.0 Angstroms, or Table 12 ⁇ an RMSD of not more than 1.5, 1.2, 1.1, or 1.0 Angstroms.
• RMSD root mean square deviation
• one, two, or three of the CDRs of the light chain variable domain (e.g., particularly in CDRl, or in at least two CDRs, e.g., CDRl and CDR3, CDRl and CDR2, or in all three CDRs) have an RMSD of not more than 1.5, 1.2, 1.1, or 1.0 Angstroms, relative to those structures.
• the antibody or antigen binding fragment thereof includes a variable domain that, as a whole, has a backbone conformation of a CDR described in Table 10 ⁇ a root mean square deviation (RMSD) of not more than 1.5, 1.2, 1.1, or 1.0 Angstroms, Table 11 ⁇ an RMSD of not more than 1.5, 1.2, 1.1, or 1.0 Angstroms, or Table 12 ⁇ an RMSD of not more than 1.5, 1.2, 1.1, or 1.0 Angstroms.
• RMSD root mean square deviation
• variable domain can also be at least at least 70%, 80%, 85%, 87%, 90%, 92%, 93%, 95%, 96%, 97%, 98%, or 99% identical to an antibody described herein, e.g., in the CDR region and/or framework regions.
• the antibody can be used, e.g., in a method of treatment described herein.
• Anti-EL-13 antibodies are disclosed, for example, in U.S. Provisional Patent Application No. 60/578,473, filed June 9, 2004, U.S. Provisional Patent Application
• Biacore analysis confirmed that mAbl3.2 had a rapid on-rate, slow off -rate, and high affinity for binding to human EL-13 (FIG. 4).
• ELISA assays showed that mAbl3.2 bound to all forms of human EL-13 tested, including native JJL-13 derived from cord blood T cells (FIG. 5).
• ELISA plates were coated with anti-FLAG M2 antibody. The binding of recombinant FLAG-tagged human IL-13 was detected with biotinylated mAbl3.2 and streptavidin-peroxidase.
• This binding could be competed with native human EL-13 isolated from itogen activated, TH2-skewed, cord blood mononuclear cells and with recombinant human EL-13 (FIG. 5).
• Recombinant murine IL-13 could not compete for binding with mAbl3.2.
• Unlabeled mAbl3.2 and unlabeled mAbl3.2 Fab were also able to compete for binding to the flag-tagged JJL-13 with biotinylated mAbl3.2 (FIG. 11 A).
• the JJL-13 specific nonneutralizing monoclonal antibody mAbl3.8 could not compete with biotinylated mAbl3.2 binding.
• mAbl3.2 to neutralize IL-13 bioactivity in vitro was confirmed using a TF1 bioassay, human peripheral blood monocytes, and human peripheral blood B cells.
• a TF1 bioassay human peripheral blood monocytes, and human peripheral blood B cells.
• JJL-13 the proliferation of cells of the human erythroleukemic TF1 cell line can be made IL-13-dependent.
• the TF1 cell line was starved for cytokine, then exposed to a suboptimal concentration (3 ng/mL) of recombinant human EL-13 in the presence of varying concentrations of purified mouse mAbl3.2 or the soluble inhibitor rhuJL-13R ⁇ 2.
• mAbl3.2 caused a dose-dependant inhibition of TF1 proliferation (FIG. 6 and FIG. 12A).
• the IC 50 for this effect, 250 pM, is comparable to the IC 50 of rhuEL-13R ⁇ 2.
• the mAbl3.2 Fab also inhibited CD23 expression human PBMCs. Human PBMCs respond to EL-13 or EL-4 by increasing cell-surface expression of low affinity IgE receptor (CD23) in a dose-dependent manner (see FIG.7A).
• CDllb + monocytes were therefore used to confirm the ability of mAbl3.2 to neutralize IL-13 bioactivity.
• CDllb + monocytes were treated for 12 hours with 1 ng/mL recombinant human EL-13 (FIG. 7B) or EL-4 (FIG. 7C) in the presence of the indicated concentration of purified mouse mAbl3.2.
• Cells were then harvested and stained with CyChrome-labeled anti-CD lib antibodies and PE-labeled anti-CD23 antibodies. Labeling was detected by flow cytometry.
• the mAbl3.2 inhibited EL- 13- induced CD23 expression (FIG. 7B; see also FIG. 12B), but did not inhibit EL-4- induced CD23 expression (FIG. 7C).
• mAbl3.2 were also tested in a model of EL-13-induced IgE production by human peripheral blood B cells.
• PHA phytohemaglutinin
• human B cells undergo an Ig isotype switch recombination to IgE, resulting in higher IgE levels in culture. This effect can be seen as an increased frequency of IgE-producing B cells.
• PBMCs from a healthy donor were cultured in microtiter wells in the presence of autologous irradiated PBMC as feeders, and stimulated with PHA and EL-13.
• STAT6 dimerizes, becomes phosphorylated, and translocates from the cytoplasm to the nucleus, where it activates transcription of cytokine-responsive genes (Murata et al, J. Biol. Chem. 270:30829-36, 1995). Specific antibodies against phosphorylated STAT6 can detect this activation by Western blot or flow cytometry within 30 min of EL-13 exposure.
• mAbl3.2 on EL-13 dependent STAT6 phosphorylation
• cells of the HT-29 human epithelial cell line were treated with the indicated concentration of EL-13 for 30 minutes at 37°C.
• Phospho-STAT6 was detected in cell lysates by Western blot (FIG. 9A) or by flow cytometry (FIGs. 9B and 9C).
• FIG. 9B cells were treated with a saturating concentration of JJL-13 for 30 minutes at 37°C and then fixed, permeabilized, and stained with an Alexa-Fluor 488-labeled mAb against phospho-STAT6.
• FIG. 9C cells were treated with a suboptimal concentration of EL-13 in the presence or absence of an antibody, fixed and stained as described above.
• Example 2 Murine monoclonal antibody mAb 13.2 neutralizes EL-13 bioactivity in vivo.
• the ability of mouse mAbl3.2 to neutralize EL-13 activity in vivo was tested using a model of antigen-induced airway inflammation in Cynomolgus monkeys naturally allergic to Ascaris suum. In this model, challenge of an allergic monkey with Ascaris suum antigen results in an influx of inflammatory cells, especially eosinophils, into the airways.
• mAbl3.2 To test the ability of mAbl3.2 to prevent this influx of cells, the antibody was administered 24 hours prior to challenge with Ascaris suum antigen. On the day of challenge, a baseline lavage sample was taken from the left lung. The antigen was then instilled intratracheally into the right lung. Twenty- four hours later, the right lung was lavaged, and the bronchial alveolar lavage (BAL) fluid from animals treated intravenously with 8 mg/kg ascites purified mAbl3.2 were compared to BAL fluid from untreated animals. Eosinophil counts increased in 4 of 5 untreated animals following challenge, as compared to 1 of 6 animals treated with mAbl3.2 (FIG. 10).
• BAL bronchial alveolar lavage
• the percent BAL eosinophils was significantly increased for the untreated group (p ⁇ 0.02), but not for the antibody-treated group. These results confirmed that mAbl3.2 effectively prevents airway eosinophilia in allergic animals challenged with an allergen.
• The, average serum half -life of mouse mAbl3.2 was less than one week in the monkeys. At the 3-month time point, when all traces of mAbl3.2 would have been gone from the serum, mAbl3.2-treated animals were rechallenged with Ascaris suum to confirm the Ascaris responsiveness of those individuals. Two of six monkeys in the treated group were found to be nonresponders.
• Example 3 Murine monoclonal antibody mAbl3.2 binds to a region of JJL-13 that normally binds to EL-4R ⁇ . JJL-13 bioactivity is mediated through a receptor complex consisting of the EL-13R ⁇ l and EL-4R ⁇ chains. The cytokine first undergoes a relatively low affinity interaction with EL-13R ⁇ l on the surface of cells. This complex then recruits EL-4R ⁇ to form the high affinity receptor (Zurawski et al., EMBO J. 12:2663, 1993; Zurawski et al, J. Biol. Chem. 270:23869. 1995).
• mAbl3.2 was analyzed with a Biacore chip. This analysis was done in several formats. First, EL-4R was bound to the Biacore chip, and a complex of EL-13 prebound to EL-13R ⁇ l was flowed over the chip. In the absence of mAb 13.2, formation of a tri-molecular complex could be demonstrated. However, addition of mAbl3.2 to the mixture of EL- 13 prebound to EL-13R ⁇ l prevented binding to EL-4R on the chip. Second, mAbl3.2 was immobilized on the chip and bound EL-13 was added in solution phase.
• Example 4 Crystal structure of anti-EL-13 antibody mAb!3.2 Fab fragment.
• Monoclonal antibody mAbl3.2 from mouse ascites was purified using a Protein A affinity column.
• the mouse ascites was diluted 2X with Protein A binding buffer (50mM Tris-HCl, 500mM NaCl, pH 8.0) and filtered through a 0.2 mm filter unit.
• the filtered solution was applied to a Poros Protein A column (Applied Biosystems, Framingham, MA) equilibrated with the binding buffer at 4°C. The column was washed with the binding buffer, and the IgG was eluted using 100 mM Glycine (pH 3.0).
• the eluted IgG was neutralized immediately with IM Tris-HCl at pH 8.0.
• the Fab fragment was prepared by digesting the JJL-13 monoclonal IgG with activated papain (Sigma, St. Louis, MO). Papain was activated by diluting the stock
• the dialyzed o solution was loaded onto a tandem Poros HS/Protein A column equilibrated with 50 mM Tris-HCl (pH 7.5) at 4°C to remove the papain and the Fc fragment.
• the flow- through of the tandem columns containing the Fab fragment was then loaded onto a hydroxylapatite column (Bio-Rad, Hercules, CA) equilibrated with 1 mM Sodium Phosphate and 20 mM Tris-HCl, pH 7.5, and eluted with a 1 mM to 125 mM Sodium5 Phosphate gradient at 25°C.
• the eluted Fab fragment solution was dialyzed overnight in 50 mM Tris-HCl (pH 8.0) at 4°C. After dialysis, the solution was loaded onto a Poros HQ column equilibrated with 50 mM Tris-HCl (pH 8.0). The flow-through was collected and ammonium sulfate was adjusted to a final concentration of 1.5 M before loading onto a Polypropyl Aspartamide column (Nest Group, Southborough, MA).0 The Fab fragment was eluted from the column with a 1.5 to 0 M ammonium sulfate gradient at 25°C. The protein was dialyzed in 50 mM Tris-HCl (pH 8.0) at 4°C.
• the isolated mAbl3.2 antibody and mAbl3.2 Fab fragment were tested for their ability to inhibit IL-13 bioactivity.
• purified mAbl3.2 and mAbl3.2 Fab fragment were tested for their ability to compete for binding with biotinylated5 mAbl3.2 in an ELISA assay.
• ELISA plates were coated with anti-FLAG M2 antibody.
• the binding of FLAG-human JJL-13 was detected with biotinylated mAbl3.2 and streptavidin-peroxidase. Both the intact antibody and the Fab fragment were able to compete for binding, while the JJL-13-specific nonneutralizing antibody mAbl3.8 could not compete for binding (FIGs.
• mAbl3.2 and mAbl3.2 Fab fragment were tested for their ability to inhibit EL-13-dependent TF1 cell proliferation and EL- 13 -dependent CD23 expression on PBMCs.
• TF1 cells were incubated with 3 ng/mL recombinant human EL-13 as described in Example 1. The cells were treated with increasing concentrations of purified mAbl3.2 or mAbl3.2 Fab, and cell proliferation was monitored as described. Both the intact antibody and the Fab fragment inhibited EL- 13-de ⁇ endent TF1 cell proliferation (FIG. 12A).
• PBMCs were incubated with 1 ng/mL recombinant human EL-13 as described in Example 1.
• the monocytes were treated with increasing concentrations of mAbl3.2 or mAbl3.2 Fab, and CD23 expression was monitored by flow cytometry as described above.
• the purified intact antibody and the purified Fab fragment were each capable of inhibiting EL-13-dependent CD23 expression (FIG. 12B).
• purified mAbl3.2 Fab was prepared at a concentration of
• R work 2 ⁇ .
• the structure of mAbl3.2 Fab was solved by molecular replacement using the program AMORE (Navaza, Acta Crystallogr. A50: 157-163, 1994).
• the structure of the monoclonal 2E8 Fab antibody fragment (PDB code 12E8) was used as the probe. Prior to refinement, 5% of the data were randomly selected and designated as an R f i. ee test set to monitor the progress of the refinement.
• the structure of the mAb 13.2 Fab was then rebuilt within QUANTA (Accelrys, San Diego, CA) utilizing a series of omit maps. Following six cycles of refinement with CNS (Brunger et al, Acta Crystallogr.
• Example 5 Crystal structure of mAbl3.2 Fab/TJL-13 Complex.
• Recombinant EL-13 (Swiss-Prot Accession Number P35225) and mAbl3.2 Fab were purified for crystallization.
• Recombinant EL-13 was purified as follows.
• E. coli K12 strain GI934 was used for expression of Human EL-13.
• GI934 is an i/vG derivative of GI724 (LaVallie et al, Bio/Technology ⁇ : 187-193, 1993) that contains specific deletions in the two E. coli proteases omp ⁇ and ompP.
• this strain contains the bacteriophage 1 repressor (cl) gene stably integrated into the chromosomal ampC locus.
• the cl gene is transcriptionally regulated by a synthetic Salmonella typhimurium trp promoter.
• E.coli expression vector pAL-981, a derivative of pAL- 781 (Collins-Racie, et al, Bio/Technology 13 ⁇ 982-987, 1995), was used as the basis for construction of a Human EL-13 expression vector.
• a cDNA of the human EL-13 gene was generated from synthetic oligonucleotide duplexes designed to possess silent changes from human EL-13 cDNA (Accession number NM_002188) that was optimized for E.coli codon usage and increased AT content at the 5' end of the gene.
• Three sets of complementary duplexes of synthetic oligonucleotides corresponding to amino acids Gly21 to Asnl32 of the human EL-13 amino acid (SEQ ED NO:3) (FIG. 2A) were used to construct the mature region of human EL-13, which is the amino acid sequence of processed EL-13 (SEQ ED NO:4).
• coli optimized complementary oligonucleotides of duplex 1 were 5 ' -TATGGGTCCAGTTCCACCATCTACTGCTCTGCGTGAACTGATTGAAGAACTGGT TAACATCACCCAGAACCAGAAAGCTCCGCTGTGTAACGGTTCCATGGTTTGGTCCAT CAACCTG-3 ' (SEQ ID NO: 6) with complement
• AACTGGACCCA-3 (SEQ ID NO : 7 ) ; duplex 2 were
• CAGTACATAC-3 ' (SEQ ID NO : 9 ) ; and duplex 3 were 5 ' -TTCTCCTCTCTGCACGTTCGTGACACCAAAATCGAAGTTGCTCAGTTCGTAAAA GACCTGCTGCTGCACCTGAAAAAACTGTTCCGTGAAGGTCGTTTCAACTAATAAT- 3' (SEQ ID NO: 10) with complement
• the first and last duplexes respectively encoded the restriction endonucleases Ndel and Xbal to allow for cloning into an Ndel, Xbal digested and gel purified expression vector pAL-981. All restriction digests, enzymatic phosphorylation of oligonucleotides, DNA fragment isolations and ligations were carried out as described in Sambrook et al., 1989. "Molecular Cloning, a Laboratory Manual, second edition," Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. Ligation mixtures were transformed into electrocompetent GI934 as described (LaVallie et al, Methods Mol Biol. 205:119-140, 2003).
• the resulting plasmid pALHIL13-981 was transformed into GI934. Optimal growth temperature of the culture for production of human EL-13 from plasmid pALHEL13-981 was determined empirically.
• Fermentor medium consisted of 1% casamino-acids, 1.75% w/v glucose, 50mM KH 2 PO 4 , 15mM (NH 4 2 SO 4 , 30mM Na 3 .citrate.2H 0, 20mM MgSO 4 , lOO ⁇ g/ml ampicillin, DM trace metals (300 ⁇ M FeCl 3 , 29 ⁇ M ZnCl 3 , 36 ⁇ M CoCl 2 , 25 ⁇ M Na 2 MoO , 20 ⁇ M CaCl 2 , 22 ⁇ M CuCl 2 , 24 ⁇ M H 3 BO 3 ), and was adjusted to pH 7 with NH 4 OH.
• a 10L fermentor was inoculated to A 550 0.00005 with a fresh culture of GI934 containing ⁇ ALHEL13-981 grown in Fermentor medium at 30°C.
• the fermentor culture was grown at 30°C to A 550 of 1.2, then the temperature was adjusted to 37°C, and the culture was allowed to grow to A5 50 of 7.5.
• Induction of protein synthesis from the pL promoter was initiated and the culture with the addition of tryptophan to 500 ⁇ g/ml.
• the culture was grown at 37°C for 4.25 hours before harvesting the cells by centrifugation.
• the sequence of the expression vector is shown in FIG. 13 (SEQ JD NO:5).
• the protein was essentially completely insoluble. Cells were broken with a microfluidizer and insoluble IL-13 was collected and dissolved at about 2 mg/mL in
• the mAbl3.2 Fab was purified as described in Example 4.
• the Fab:EL-13 complex was prepared by combining the two in a molar ratio of about 1:1.
• EL-13 50 ⁇ M in 40 mM MES and 40 mM NaCl, pH 6.0
• mAbl3.25 Fab 50 ⁇ M in 50 mM Tris.HCl, pH 8.0
• the complex was further purified by a Superdex 75 size exclusion column (Amersham Biosciences, Piscataway, NJ) equilibrated with 50 mM Tris-HCl and 300 mM NaCl, pH 8.0, at 25°C.
• the purified complex was dialyzed in 50 mM Tris-HCl and 50 mM NaCl, pH 8.0, before setting up the crystallization.0
• purified mAb 13.2 Fab/U-13 complex was prepared at a concentration of 11.3 mg/mL in a solution of 50 mM Tris (pH 8.0) and 50 mM NaCl.
• One microliter of protein solution was mixed with 1 ⁇ l of crystallization solution (20% PEG 3350, 50 mM ZnOAc) (Hampton Research, Aliso Viejo, CA).
• the structure of the complex was solved by molecular replacement using the program AMORE, and using the crystal structure of the ui ⁇ i D.z. a ⁇ cbcnut; m 4) as the probe. Prior to refinement, 5% of the data were randomly selected and designated as an R f r ee test to monitor the progress of the refinement. This structure of the mAbl3.2 Fab was then rebuilt within QUANTA using a series of omit maps. During this process, extra density was observed near the hypervariable regions, and these regions sharpened after each cycle of rebuilding. After the Fab fragment had been rebuilt, the NMR structure of EL-13 (Moy et al, J. Mol. Biol.
• residues 1-127 and 133-210 were modeled into the density, and no density was observed for residues 128 to 132.
• residues 7-21, 26-78, and 81-109 were visible and residues 1-6, 22-25, 79, and 80 were disordered.
• residues modeled as smaller residues due to inadequate electron density X-ray experiments see Table 5.
• Zincl was coordinated to Fab light chain residues Glu27 and Glu97, and residues Glul89 and Hisl93 of a symmetry related copy of the light chain (amino acids numbered according to SEQ ED NO:l (FIG. 1A)).
• Zinc2 was coordinated to IL-13 residues His84 and Asp87, and residues Asp98 and Hisl02 of a symmetry related copy of IL- 13.
• Zinc3 was coordinated to IL-13 residues Glul2 and Glul5 with water molecules as other ligands (amino acids numbered according to SEQ ID NO:4 (FIG. 2B)).
• FIG. 3 illustrates the interaction of the C alpha helix of EL-13 with the CDR loops of the antibody. Hydrogen bond interactions were observed to exist between the Fab and EL-13 residues Glu49, Asn53, Gly69, Pro72, His73, Lys74, and Arg86. The N-terminal tip of helix A was within van der Waals distances of the Fab fragment.
• Amino acid residues are numbered according to the processed form of IL-13 (SEQ ID NO:4). "I” indicates amino acid of IL-13.
• Amino acid residues correspond to SEQ ID NO: 1 (for light chain residues, “L”) or SEQ ID NO:2 (for heavy chain residues, “H"), and are numbered according to the Chothia numbering system (Al- Lazikani et al, Jour. Mol. Biol. 273:927-948, 1997).
• Amino acid residues are numbered according to the numbering of SEQ ID NO:l (for light chain residues, "L”) or SEQ ID NO:2 (for heavy chain residues, "H”).
• Amino acid residues are numbered according to the processed form of IL-13 (SEQ ID NO:4). “I” indicates amino acid of IL-13.
• Amino acid residues correspond to SEQ ID NO:l (for light chain residues, “L”) or SEQ ID NO:2 (for heavy chain residues, “H"), and are numbered according to the Chothia numbering system (Al- Lazikani et al., Jour. Mol. Biol. 273:927-948, 1997). See Tables 6 and 7.
• c Amino acid residues are numbered according to the numbering of SEQ ID NO:l (for light chain residues, "L”) or SEQ ID NO:2 (for heavy chain residues, "H”).
• HC heavy chain
• LC light chain
• I IL-13 processed
• Amino acid residues correspond to SEQ ID NO:l (for light chain residues, “LC”) or SEQ ID NO:2 (for heavy chain residues, “HC”), and are numbered according to the Chothia numbering system (Al-Lazikani et al, Jour. Mol. Biol. 273:927-948, 1997). See Tables 6 and 7.
• SEQ ID NO:l for light chain residues, "LC”
• SEQ ID NO:2 for heavy chain residues, "HC”
• SEQ ID NO:4 for residues of the EL-13 processed polypeptide, "I"
• FIG. 3 is a ribbon diagram illustrating the co-crystal structure of mAbl3.2 Fab with human IL-13.
• the light chain of mAbl3.2 Fab is shown in dark shading, and the heavy chain in light shading.
• the IL-13 structure is shown at right.
• the figure depicts the interaction of the C alpha helix of EL-13 with the CDR loops of the antibody.
• the major residues of mAbl3.2 heavy chain that make hydrogen bond contacts with JJL-13 are SER50 (CDR2), SER53 (CDR2), TYR101 (CDR3), and TYR102 (CDR3).
• the major residues of mAbl3.2 heavy chain that make van der Waals contacts with EL-13 are ELE30 (CDRl), SER31 (CDRl), ALA33 (CDRl), TRP47, SER50 (CDR2), SER52 (CDR2), SER53 (CDR2), TYR58 (CDR2), LEU98 (CDR3), ASP99 (CDR3), GLYIOO (CDR3), TYRIOI (CDRS), TYR102 (CDR3), and PHJE103 (CDR3) (see Table 4; amino acids numbered according the numbering of SEQ ID NO:2 (FIG. IB)).
• the major residues of mAbl3.2 light chain that make hydrogen bond contacts with IL-13 are ASN31 (CDRl), TYR32 (CDRl), LYS34 (CDRl), ASN96 (CDR3), and ASP98 (CDR3).
• the major residues of mAbl3.2 light chain that make van der Waals contacts with IL-13 are ASN31 (CDRl), TYR32 (CDRl), LYS34 (CDRl), ARG54 (CDR2), ASN96 (CDR3), ASP98 (CDR3), and TRP100 (CDR3) (see Table 4).
• the Kabat and Chothia schemes number the amino acid residues linearly accept in the defined CDR region of the polypeptide, where insertions are noted.
• the Kabat system (Kabat et al., NIH Publ. No. 91-3242, 5 th ed., vols. 1-3, Dept. of Health and Human Services, 1991) defines the location of the heavy and light chain CDRs by sequence variability, while the Chothia system (Al-Lazikani et al, Jour. Mol. Biol. 273:927-948, 1997) defines the location structurally by loop regions.
• the recombinant protein was purified to homogeneity by affinity chromatography over NiNTA-agarose (Qiagen) followed by anion exchange chromatography over HiTrap Q Sepharose HP (Pharmacia, Amersham Pharmacia Biotech, UK) and gel filtration chromatography over Superdex-75 (Pharmacia).
• the human IL-13 (amino acid residues 1 to 113) (SEQ JD NO:4) was expressed and purified as described in example 5.
• a complex containing IL-13 and EL-13R ⁇ l was was formed by mixing the receptor with a slight excess of IL-13.
• the complex was treated with endoglycosidase Hf (endoHf) (25,000 units/mL) for 90 minutes at 37°C.
• the deglycosylated complexes were applied to a concanavalin A (conA)-Se ⁇ harose column to remove protein with uncleaved oligosaccharides, and the remaining complexes were applied to a NiNTA column to remove EndoHf.
• the purified complexes were purified to homogeneity by gel filtration chromatography over Superdex-200 (GE Healthcare, formerly Amersham Biosciences, Piscatway, NJ).
• mAbl3.2 Fab was purified as described in example 4. Crystals of a complex of EL-13, EL-13R ⁇ l, and mAbl3.2 Fab were grown at
• CCP4 Acta Cryst D50:760-763, 1994.
• the structure was solved by molecular replacement using the coordinates of the mAbl3.2 Fab/IL-13 complex (Table 11).
• Initial phases were improved by solvent flattening using Solomon as implemented in CCP4 ("CCP4,” Acta Cryst D50:760- 763, 1994).
• Rigid body refinement within CCP4 was used to obtain an initial model.
• Experimental maps with continuous density were obtained, and an initial model was constructed using QUANTA (Accelrys, Inc., San Diego, CA) and refined against data from 30 to 2.2 A with CNS (Brunger et al, Acta Cryst. D54:905-921, 1998).
• the final refined model which includes polypeptide chains of IL-13R ⁇ l (residues 6-314), mAbl3.2 Fab (light chain residues 1-213 and heavy chain residues 1-213) and JJL-13 (residues 6-112), as well as 123 water molecules, has a working R-value of 24.4% and a free R-value of 27.2%.
• Statistics for data collection and refinement are shown in Tables 8 and 9. There were no backbone torsion angles outside of the allowed regions of the Ramachandran plot.
• Rfree ⁇ lPobsl -
• the side chain of Met33 of IL-13 extends into a hydrophobic pocket that is created by the side chains of these adjoining strands.
• the predominant feature of the interaction with Ig domain 3 is the insertion of a hydrophobic residue (Phe 107) of JJL-13 into a hydrophobic pocket in Ig domain 3 of the receptor BL-13R ⁇ l.
• the hydrophobic pocket of IL-13R ⁇ l is formed by the side chains of residues Leu319, Cys257, Arg256 and Cys320 (FIG. 17).
• ATOM 104 CD1 LEU L 15 19, .079 31, .484 18, .428 1. .00 50. .28 L c
• ATOM 206 C ASP L 30 6. .050 10. ,052 -10. .314 1. .00 55. .22 L C
• ATOM 213 CA ASN L 30A 3. ,880 10. .701 -11. .174 1. ,00 66. .21 L c
• ATOM 216 CB ASN L 30A 2. ,684 10. ,949 -10. .255 1. ,00 71. .89 L c
• ATOM 231 OH TYR L 30B 0. .224 6. .910 -15. .945 1. .00133, .30 L 0
• ATOM 242 CD LYS L 30D 3, .211 17. .978 -10, .767 1. .00 82, .67 L c
• ATOM 268 CA HIS L 34 5 .930 15 .773 1 .181 1, .00 30, .96 L c
• ATOM 304 CA GLN L 37 7 .419 19, .131 11, .003 1, .00 29. .42 L c
• ATOM 331 CA PRO L 40 7 .732 18, .575 20, .737 1. .00 37. .29 L c
• ATOM 336 CD PRO L 40 9 .222 20, .062 19, .553 1. .00 29. .92 L c
• ATOM 514 CA GLY L 64 12, .563 21, .357 -0, .861 1. .00 30, .22 L c

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