WO2011075786A1 - Immuno-conjugates and methods for producing them 2 - Google Patents

Immuno-conjugates and methods for producing them 2 Download PDF

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Publication number
WO2011075786A1
WO2011075786A1 PCT/AU2010/001737 AU2010001737W WO2011075786A1 WO 2011075786 A1 WO2011075786 A1 WO 2011075786A1 AU 2010001737 W AU2010001737 W AU 2010001737W WO 2011075786 A1 WO2011075786 A1 WO 2011075786A1
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protein
cysteine residues
residues
seq
compound
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English (en)
French (fr)
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Peter John Hudson
Debra Tamvakis
Michael Paul Wheatcroft
Fabio Turatti
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Avipep Pty Ltd
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Avipep Pty Ltd
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Priority to AU2010336029A priority Critical patent/AU2010336029B2/en
Priority to SG2012045241A priority patent/SG181814A1/en
Priority to US13/383,836 priority patent/US9315581B2/en
Priority to EP20100838426 priority patent/EP2516462B1/en
Priority to CA2784610A priority patent/CA2784610C/en
Priority to KR1020127018914A priority patent/KR101961495B1/ko
Priority to JP2012545018A priority patent/JP2013514788A/ja
Publication of WO2011075786A1 publication Critical patent/WO2011075786A1/en
Anticipated expiration legal-status Critical
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/18—Growth factors; Growth regulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/56—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule
    • A61K47/59—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
    • A61K47/60—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes the organic macromolecular compound being a polyoxyalkylene oligomer, polymer or dendrimer, e.g. PEG, PPG, PEO or polyglycerol
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/0002—General or multifunctional contrast agents, e.g. chelated agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/06—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations
    • A61K49/08—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations characterised by the carrier
    • A61K49/10—Organic compounds
    • A61K49/14—Peptides, e.g. proteins
    • A61K49/16—Antibodies; Immunoglobulins; Fragments thereof
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/475—Growth factors; Growth regulators
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/22—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against growth factors ; against growth regulators
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/24—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • C07K16/3076—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells against structure-related tumour-associated moieties
    • C07K16/3092—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells against structure-related tumour-associated moieties against tumour-associated mucins
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/32—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against translation products of oncogenes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K19/00—Hybrid peptides, i.e. peptides covalently bound to nucleic acids, or non-covalently bound protein-protein complexes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • 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
    • C07K2317/565—Complementarity determining region [CDR]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • 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
    • C07K2317/567—Framework region [FR]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/624—Disulfide-stabilized antibody (dsFv)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/626—Diabody or triabody
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/20—Fusion polypeptide containing a tag with affinity for a non-protein ligand
    • C07K2319/21—Fusion polypeptide containing a tag with affinity for a non-protein ligand containing a His-tag

Definitions

  • the present invention relates to proteins comprising immunoglobulin variable regions modified to facilitate conjugation of a compound thereto or having a compound conjugated thereto.
  • immunoglobulins e.g., antibodies and antibody-like molecules (e.g., camelid immunoglobulin or immunoglobulin new antigen receptors (IgNARs) from cartilaginous fish) or proteins comprising antigen binding domains thereof makes them particularly suitable for delivering molecules to specific targets in a subject.
  • immunoglobulins or proteins comprising antigen binding domains thereof can be conjugated to cytotoxic or cytostatic compounds e.g., drugs, to kill or inhibit growth of cells, such as tumour cells (Lambert, 2005).
  • Such a conjugate facilitates targeted delivery of the cytotoxic or cytostatic compounds to cells expressing the antigen to which the immunoglobulin or fragment binds, rather than non-specifically throughout a subject.
  • Such conjugates can permit use of compounds that are generally toxic to a subject by ensuring the delivery of toxic levels of the compound to the site at which it is required rather than systemically within a subject.
  • conjugation of antibodies or proteins comprising antigen binding domains thereof to detectable compounds, such as fluorophores or radioisotopes facilitates detection of target molecules within a subject, for example to facilitate detection of diseased cells such as cancer cells, e.g., using in vivo, imaging- based methods.
  • non-specific conjugation of a compound to an antibody or protein comprising an antigen binding domain thereof may reduce or completely prevent binding of the antibody/protein to an antigen, for example, if the compound is conjugated to a region required for antigen binding.
  • This risk is increased in proteins that comprise antigen binding domains that are far smaller than an intact antibody in which there may be few residues suitable for conjugation that are not important for antigen binding.
  • proteins comprising little more than antigen binding domains of an antibody have few sites to which a compound can be conjugated without reducing or preventing antigen binding.
  • Carbohydrate(s) on the Fc region of an antibody is a natural site for attaching compounds.
  • the carbohydrate is modified by periodate oxidation to generate reactive aldehydes, which can then be used to attach reactive amine containing compounds by Schiff base formation.
  • the aldehydes can react with amine groups, reactions are carried out at low pH so that lysine residues in the antibody or antigen binding domain are protonated and unreactive. Hydrazide groups are most suitable for attachment to the aldehydes generated since they are reactive at low pH to form a hydrazone linkage. The linkage can then be further stabilised by reduction with sodium cyanoborohydride to form a hydrazine linkage (Rodwell et al, 1986).
  • Disadvantages of this approach include the harsh conditions required for linkage which can damage and aggregate some antibody molecules.
  • methionine residues present in some antibody variable regions may be particularly susceptible to oxidation by periodate which can lead to loss of antigen binding avidity.
  • Histidine and/or tryptophan residues are also susceptible to oxidation.
  • proteins comprising antigen binding domains of an antibody do not necessarily comprise a Fc region, meaning that they cannot be conjugated to a compound using the foregoing process.
  • Cysteine thiols are reactive at neutral pH, unlike most amines which are protonated and less nucleophilic near pH 7. Since free thiol groups are relatively reactive, proteins with cysteine residues often exist in their oxidized form as disulfide- linked oligomers or have internally bridged disulfide groups. Extracellular proteins generally do not have free thiols (Garman, 1997). Cysteine residues have been introduced into proteins by genetic engineering techniques to form covalent attachments to ligands or to form new intramolecular disulfide bonds.
  • cysteine thiol groups are potentially problematic, particularly in the case of those which are relatively accessible for reaction or oxidation, i.e., positioned at sites useful for conjugation of a compound. This is because, in concentrated solutions of the protein, whether in the periplasm of Escherichia coli, culture supernatants, or partially or completely purified protein, cysteine residues on the surface of the protein can pair and oxidize to form intermolecular disulfides, and hence protein aggregates. Such protein aggregation often leads to poor yields of isolated protein that is in a useful form, e.g., having a desired biological activity.
  • the protein oxidatively can form an intramolecular disulfide bond between the newly engineered cysteine and an existing cysteine residue, which can render the protein inactive or non-specific by misfolding or loss of tertiary structure.
  • proteins comprising antigen binding domains of immunoglobulins that are modified so as to permit simple conjugation of a compound thereto.
  • Preferred proteins will facilitate recombinant production in a variety of systems, preferably without resulting in considerably levels of multimeric aggregates linked by intermolecular bonds.
  • the inventors sought to identify sites within a variable region of an immunoglobulin, e.g., an antibody that permit conjugation of a compound thereto without preventing binding of the variable region to an antigen.
  • an immunoglobulin e.g., an antibody that permit conjugation of a compound thereto without preventing binding of the variable region to an antigen.
  • the inventors have determined that numerous sites within framework region 2 (FR2) and/or freamework region 3 (FR3) of a variable region that are accessible for conjugation, and are sufficiently removed from the antigen binding site of the variable region that a compound conjugated thereto is unlikely to interfere with or prevent antigen binding. These sites are conserved in both heavy chain variable regions (V H ) and light chain variable regions (V L ).
  • the inventors produced various proteins comprising mutated variable regions in which two cysteine residues are inserted into FR2 and/or FR3. These cysteine residues are positioned such that a disulfide bond can also form between them if they are not conjugated to a compound.
  • the cysteine residues are linked by a disulphide bond thereby reducing or preventing those residues bonding with other cysteine residues either within the same protein or in another protein. This reduces the likelihood of production of linked multimers and/or an aberrantly folded variable region, and permits production and/or isolation of functional protein. Following isolation, the cysteine residues are reduced or otherwise broken permitting conjugation of a compound to the protein.
  • the inventors have also demonstrated that conjugation of numerous compounds to these proteins, including bulky compounds such as polyethylene glycol (PEG) does not prevent binding of the variable region to an antigen.
  • PEG polyethylene glycol
  • the present invention provides an isolated protein comprising an immunoglobulin variable region comprising:
  • the present invention provides an isolated protein comprising an immunoglobulin variable region comprising:
  • the present invention provides an isolated protein comprising an immunoglobulin heavy chain variable region (V H ) and an immunoglobulin light chain variable region (V L ), wherein at least one of the variable regions comprises: (i) at least two cysteine residues positioned within framework region (FR) 2, wherein if at least two of the cysteine residues in FR2 are not conjugated to a compound then a disulphide bond is capable of forming between the cysteine residues in FR2; and/or
  • the present invention provides an isolated protein comprising an immunoglobulin heavy chain variable region (V H ) and an immunoglobulin light chain variable region (V L ), wherein at least one of the variable regions comprises:
  • the cysteine residues in FR3 are additional to the conserved cysteine residue in FR3, e.g., are additional to a cysteine residue at position 88 of a V L according to the Kabat numbering system or position 92 of a V H according to the Kabat numbering system.
  • the cysteine residues do not form a disulphide bond with the conserved cysteine residue.
  • the protein comprises at least one of V L and at least one of V H in a single polypeptide chain.
  • the cysteine residues are positioned such that the disulphide bond is present under non-reducing conditions.
  • the cysteine residues are positioned such that a compound can be conjugated to at least one of the residues if they are not linked by a disulphide bond.
  • cysteine residues within FR2 are positioned between CDRl and CDR2, and/or the cysteine residues FR3 are positioned between CDR2 and CDR3.
  • the cysteine residues are positioned within one or more loop regions of FR2 and/or FR3.
  • the cysteine residues are within a V H .
  • the cysteine residues within FR2 are positioned between residues 36 to 49 numbered according to the Kabat numbering system, and/or the cysteine residues within FR3 are positioned between residues 66 to 94 according to the Kabat numbering system .
  • the cysteine residues within FR2 are positioned between residues 39 to 45 numbered according to the Kabat numbering system, and/or the cysteine residues in FR3 are positioned between residues 68 to 86 numbered according to the Kabat numbering system.
  • the cysteine residues within FR2 are positioned between residues 39 to 45 numbered according to the Kabat numbering system, and/or the cysteine residues within FR3 are positioned between residues 68 to 81 numbered according to the Kabat numbering system. In one example, the cysteine residues within FR3 are positioned between residues 82C to 86 numbered according to the Kabat numbering system. In one example, the cysteine residues are positioned within FR3 between residues 68 to 81 numbered according to the Kabat numbering system.
  • FR3 are positioned between residues 59 to 86 numbered according to the Kabat numbering system.
  • the cysteine residues within the region are positioned between residues 59 to 63 and/or 65 to 68 and/or 82C to 86 numbered according to the Kabat numbering system.
  • the cysteine residues are within a V L .
  • the cysteine residues within FR2 are positioned between residues 35 to 49 numbered according to the Kabat numbering system, and/or the cysteine residues positioned within FR3 are positioned between residues 57 to 88 numbered according to the Kabat numbering system.
  • the cysteine residues within FR2 are positioned between residues 38 to 44 numbered according to the Kabat numbering system, and/or the cysteine residues within FR3 are positioned between residues 63 to 82 numbered according to the Kabat numbering system.
  • cysteine residues within FR3 are positioned between residues 63 to 74 numbered according to the Kabat numbering system In one example, the cysteine residues within FR3 are positioned between residues 78 to 82 numbered according to the Kabat numbering system.
  • cysteine residues are positioned within FR3 between residues 63 to 74 numbered according to the Kabat numbering system.
  • FR3 are positioned between residues 54 to 82 numbered according to the Kabat numbering system.
  • the cysteine residues within the region are positioned between residues 54 to 58 and/or 60 to 63 and/or 78 to 82 numbered according to the Kabat numbering system.
  • the present invention clearly contemplates modifying additional residues within the variable region or protein comprising same.
  • the invention additionally contemplates substituting residues positioned between cysteine residues or even replacing cysteine residues naturally occurring within CDRs.
  • a protein as described herein specifically binds to human epidermal growth factor HER2, tumor associated glycoprotein TAG72, MUC1 or prostate specific membrane antigen (PSMA).
  • Other proteins bind to a plurality of antigens, e.g. the previously listed antigens, by virtue of cross-reactivity or the protein being multi-specific.
  • the protein comprises a V H and a V L comprising sequences at least about 80% identical to a V H and a V L sequence set forth in any one or more of
  • SEQ ID NOs: 59, 61, 63 or 65 modified to include the two or more cysteine residues positioned within FR2 and/or FR3.
  • the protein comprises a sequence at least about 80% identical to a sequence set forth in any one or more of SEQ ID NO: 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145,
  • the present invention also provides an isolated protein comprising a Fv comprising at least one protein of the invention in which at least one V L binds to at least one V H to form an antigen binding site.
  • the protein comprises the V L and the V H which form the antigen binding site being in a single polypeptide chain.
  • the protein is: (i) a single chain Fv fragment (scFv);
  • the protein comprises the V L and the V H which form the antigen binding site being in different polypeptide chains.
  • each polypeptide chain in the protein comprises a V L and a V H -
  • such a protein is:
  • Avibody or Avibodies includes any form of AvibodyTM products which include any diabody (diabodies), triabody (triabodies) and tetrabody (tetrabodies), such as those described in WO98/044001 and/or WO94/007921.
  • the protein of the present invention is an immunoglobulin, preferably an antibody.
  • immunoglobulins are described herein and are to be taken to apply mutatis mutandis to the present example of the invention.
  • the protein of the invention comprises the cysteine residues being linked by a disulphide bond.
  • the protein of the invention comprises a compound conjugated to at least one of the cysteine residues, wherein conjugation of the compound does not prevent binding of the protein to an antigen.
  • exemplary compounds include a compound selected from the group consisting of a radioisotope, a detectable label, a therapeutic compound, a colloid, a toxin, a nucleic acid, a peptide, a protein, a compound that increases the half life of the protein in a subject and mixtures thereof.
  • protein encompasses proteins comprising one or more immunoglobulin variable regions, for example, an antibody or fragment thereof including an Fv containing protein such as is described herein.
  • a protein of the present invention further comprises at least two cysteine residues positioned within framework region (FR) 1, wherein if at least two of the cysteine residues are not conjugated to a compound a disulphide bond is capable of forming between the cysteine residues in FR1.
  • FR framework region
  • Exemplary variable region containing proteins comprising cysteine residues in FR1 that are adapatable to the present invention are disclosed in co-pending International Application No. PCT/AU2010/000847, the entire contents of which are incorporated by reference.
  • the cysteine residues are positioned such that the disulphide bond is present under non-reducing conditions.
  • cysteine residues in FR1 are positioned between residue 2 numbered according to the Kabat numbering system and CDR1.
  • cysteine residues are positioned within one or more loop regions of FR1.
  • the cysteine residues are within the V H and are positioned between residues 2 to 30 numbered according to the Kabat numbering system.
  • the cysteine residues are positioned between residues 7- 20 and/or residues 24-30 numbered according to the Kabat numbering system, and more preferably positioned between residues 7-20.
  • the residues are positioned between residues 6-16 numbered according to the Kabat numbering system.
  • the residues are positioned between residues 7-16 numbered according to the Kabat numbering system.
  • the cysteine residues are within the V L and are positioned between residues 2 to 22 numbered according to the Kabat numbering system.
  • the cysteine residues are positioned between residues 7- 20 numbered according to the Kabat numbering system.
  • the residues are positioned between residues 7-19 numbered according to the Kabat numbering system.
  • the residues are positioned between residues 7-17 numbered according to the Kabat numbering system.
  • cysteine residues are additional to a conserved cysteine residue in the V H and/or V L .
  • conserved cysteine residue is at residue 23 in the V L and/or residue 22 in the V H numbered according to the Kabat numbering system in at least a majority of naturally occurring antibodies.
  • cysteine residues are positioned N- terminal to the conserved cysteine residue.
  • the cysteine residues are positioned at one or more of the following:
  • cysteine residues are positioned at one or more of the following:
  • the protein described herein according to any example can comprise one or more and preferably less than 10 or 5 or 4 or 3 or 2 substitutions, preferably conservative amino acid substitutions or deletions or insertions.
  • Exemplary changes to the recited sequence include deleting a N-terminal serine or substituting the serine for another amino acid residue (preferably a conservative amino acid substitution) and/or deleting or substituting a C terminal lysine and/or arginine.
  • the inventors have also modified proteins comprising variable regions to include a serine or threonine residue at the N-terminus. This residue permits site- specific conjugation of a compound thereto.
  • the inventors have produced proteins to which they can site-specifically conjugate at least two different compounds.
  • an example of the invention provides a protein of the invention additionally comprises at least one N-terminal threonine or serine residue.
  • the serine or threonine residue may be added to the N-terminus of the protein (i.e., is additional to the sequence of the protein).
  • the serine or threonine residue replaces a naturally occurring amino acid residue at the N-terminus of the protein, i.e., is the result of a substitutional mutation.
  • the threonine or serine residue is linked to a compound such as a compound described above, wherein conjugation of the compound does not prevent binding of the protein to an antigen.
  • a protein of the invention comprises a first compound conjugated to at least one of the cysteine residues and a second compound conjugated to the threonine or serine residue, wherein the second compound is different to the first compound.
  • a protein as described herein according to any example is conjugated to polyethylene glycol (PEG).
  • PEG polyethylene glycol
  • the PEG is monodispersed PEG.
  • the monodispersed PEG has no more than 48 ethylene glycol units, such as about 24 ethylene glycol units.
  • proteins of the invention comprise a sequence 80% or 90% or 95% or 96%) or 97% or 98%> or 99% or 100% identical to the sequence set forth in any one of SEQ ID NOs: 59, 61, 63 or 65, modified to include the two or more positioned within FR2 and/or FR3. Suitable sites for modification are described herein and are to be taken to apply mutatis mutandis to this example of the invention.
  • the protein comprises a sequence at least about 80%> or 90%> or 95% or 96% or 97% or 98% or 99% or 100% identical to the sequence set forth in SEQ ID NO: 83, 85, 87 or 89, optionally comprising a N-terminal serine residue.
  • the protein TAG72 and comprises a V H and a V L comprising sequences at least about 80% identical to a sequence set forth in SEQ ID NO: 101, 103, 105, 107, 109, 111, 113, 115, 117 or 119.
  • the protein binds to Her2 and comprises a V H and a V L comprising sequences at least about 80% identical to a sequence set forth in one or more of SEQ ID NO: 127, 129, 141, 143, 145, 147 or 149.
  • the protein binds to MUC1 and comprises a V H and a V L comprising sequences at least about 80% identical to a sequence set forth in one or more of SEQ ID NO: 131, 133, 135, 137 or 139.
  • a protein of the invention is human, humanized, deimmunized or chimeric.
  • the present invention also provides a composition comprising a protein of the invention and a pharmaceutically acceptable carrier.
  • the present invention also encompasses an isolated nucleic acid encoding a protein of the invention.
  • Exemplary nucleic acids include those having a sequence at least about 80% or 90% or 95% or 96% or 97% or 98% or 99% or 100% identical to the sequence set forth in any one or more of SEQ ID NOs: 58, 60, 62 or 64 altered to include codons encoding at least two cysteine residues in FR2 and/or FR3 of the encoded protein, optionally including a N-terminal serine or threonine residue.
  • a nucleic acid of the invention comprises a sequence at least about 80% or 90% or 95% or 96% or 97% or 98% or 99% or 100% identical to the sequence set forth in any one or more of SEQ ID NO: 82, 84, 86 or 88.
  • SEQ ID NO: 82, 84, 86 or 88 The skilled artisan will be aware that due to the degeneracy of codon usage, numerous nucleotide sequences can encode a protein of the invention. All such nucleotide sequences are encompassed by the present invention.
  • a codon optimized nucleic acid can be produced to facilitate expression in a specific cell type or organism.
  • a nucleic acid of the invention can be operably linked to a promoter to thereby produce an expression construct.
  • Such an expression construct or the nucleic acid is preferably included in a vector, preferably a vector replicable in a cell, e.g., a plasmid or phagemid or cosmid or artificial chromosome.
  • the present invention also provides an isolated cell comprising an exogenous nucleic acid or expression construct of the invention, preferably wherein the cell expresses a protein of the invention.
  • exemplary cells include, but are not limited to, bacterial cells, yeast cells, mammalian cells or insect cells.
  • the nucleic acids and/or expression constructs and/or cells provided by the invention also provide a basis for methods for producing proteins of the invention. Accordingly, the present invention also provides a method for producing a protein of the invention, the method comprising maintaining an expression construct of the invention under conditions sufficient for the encoded protein to be produced. For example, the method comprises culturing a cell of the invention under conditions sufficient the encoded for the protein to be produced. In one example, the method additionally comprises isolating the protein. The method can additionally comprise testing the protein, e.g., for binding activity or affinity. The method can additionally comprise formulating the protein into a pharmaceutical composition.
  • the present invention also provides a method for producing a conjugate comprising a protein of the invention, the method comprising:
  • the cysteine residues in the protein obtained at (i) are linked by a disulphide bond and the method additionally comprises reducing or otherwise breaking the disulphide bond prior to linking the compound to the cysteine residue(s).
  • reducing or otherwise breaking the disulphide bond generates a free thiol group in the protein and the compound has a thiol reactive group. By reacting the compound with the thiol reactive group, the conjugate is produced.
  • the compound is conjugated to the protein using a maleimide.
  • the protein is contacted with a compound comprising a maleimide functional group such that conjugation occurs.
  • the protein additionally comprises at least one N-terminal serine or threonine residue and the method additionally comprises conjugating a compound to the serine or threonine residue.
  • the compound conjugated to the serine or threonine residue is different to the compound conjugated to the cysteine residue(s).
  • the present invention provides an alternative method for producing a conjugate comprising a protein of the invention, the method comprising:
  • a method of the invention for producing a conjugate additionally comprises isolating the conjugate and/or formulating the conjugate into a pharmaceutical composition.
  • reagents that are useful in a variety of applications, including, delivery of a toxic compound or a radioisotope to a diseased cell, tissue or organ (e.g., a cancer) and/or in vivo imaging and/or for increasing the stability of a protein.
  • the present invention also provides for use of a protein or a composition of the invention in medicine.
  • the present invention provides for use of a protein of the invention in the manufacture of a medicament for treating or preventing a condition.
  • the present invention also provides a method of treating or preventing a condition in a subject, the method comprising administering a protein or composition of the invention to a subject in need thereof.
  • Exemplary conditions are described herein and are to be taken to apply mutatis mutandis to the present example of the invention.
  • exemplary conjugated forms of a protein of the invention are described herein and shall be taken to apply mutatis mutandis to the present example of the invention.
  • the present invention additionally provides a method for delivering a compound to a cell, the method comprising contacting the cell with a protein of the invention that is conjugated to the compound or a composition comprising same.
  • the cell is contacted by administering the protein or composition to a subject.
  • the present invention also provides imaging methods, such as a method for localising or detecting an antigen in a subject, said method comprising:
  • the present invention also provides a method for diagnosing or prognosing a condition in a subject, the method comprising contacting a sample from the subject with a protein or composition of the invention for a time and under conditions sufficient for the protein to bind to an antigen and form a complex and detecting the complex, wherein detection of the complex is diagnostic or prognostic of the condition.
  • the protein is conjugated to a detectable label and detection of the label is indicative of the complex.
  • the method comprises determining the level of the complex, wherein an enhanced or reduced level of said complex compared to a control sample is diagnostic or prognostic of the condition.
  • the present invention additionally provides a library comprising a plurality of proteins of the invention.
  • the proteins are displayed on the surface of a particle (e.g., a phage or a ribosome) or a cell.
  • a particle e.g., a phage or a ribosome
  • the present invention also provides a library of nucleic acids encoding said library comprising a plurality of proteins of the invention.
  • the present invention additionally provides a method for isolating a protein of the invention, the method comprising contacting a library of the invention with an antigen for a time and under conditions sufficient for (or such that) a protein binds to the antigen and isolating the protein.
  • the present invention additionally provides a method for producing a library comprising a plurality of proteins of the invention, the method comprising:
  • variable regions comprising at least two cysteine residues positioned within FR2 and/or FR3 and, optionally a N-terminal threonine or serine residue;
  • nucleic acid encoding a polypeptide that facilitates display of the variable region containing protein in/on the cells or particles
  • Suitable sites for positioning the cysteine residues and/or threonine or serine residue are described herein and are to be taken to apply mutatis mutandis to the present example of invention.
  • the amino acids in the CDRs of the protein are random or semi- random or are derived from a human antibody.
  • the method additionally comprises isolating nucleic acid encoding the protein.
  • nucleic acid can be introduced into an expression construct.
  • the protein can be expressed.
  • Figure 1A is a diagrammatic representation showing a molecular model generated for AVP04-50 in which the amino acids in V L framework 1 at Kabat residues 8 and 11 (black space fill) have been converted to cysteines (in silico).
  • Figure IB is a diagrammatic representation showing the antigen binding domains (shaded) and the cysteine replacement mutations in V L framework 1 Kabat residues 8 and 11 (black space fill) of the diabody AVP04-50 are distant from each other in space.
  • Figure 2A is a graphical representation showing the 280nm chromatograph of AVP04-50 His-Tag affinity chromatography purification. Arrow indicates elution peak of interest.
  • Figure 2B is a graphical representation showing results of cation purification of AVP04-50. Arrow indicates elution peak of interest.
  • Figure 2C is a graphical representation showing results of size exclusion chromatography of AVP04-50. Arrow indicates elution peak of interest. Dotted lines outline fractions of interest.
  • Figure 2D is a graphical representation showing results of post purification size exclusion chromatography of AVP04-50. Arrow indicates elution peak of interest.
  • Figure 2E is a copy of a photographic representation showing results of a reducing SDS-PAGE showing the purity of AVP04-50 post purification. MW. Marker. Arrow indicates AVP04-07 protein band.
  • Figure 3A is a graphical representation showing results of a column shift assay of AVP04-07 (dotted line) and AVP04-07 complexed with its antigen bovine submaxillary mucin (BSM) (containing TAG72) (Black line).
  • BSM antigen bovine submaxillary mucin
  • Figure 3B is a graphical representation showing results of a column shift assay of AVP04-50 (dotted line) and AVP04-50 complexed with its antigen BSM (containing TAG72) (Black line).
  • Figure 3C is a graphical representation showing results of a column shift assay of AVP07-17 (dotted line) and AVP07-17 complexed with its antigen HER2 (Recombinant HER2 ectodomain) (Black line).
  • Figure 3D is a graphical representation showing results of a column shift assay of AVP07-63 (dotted line) and AVP07-63 complexed with its antigen HER2 (Recombinant HER2 ectodomain) (Black line).
  • Figure 4 is a graphical representation showing results of a column shift assay of site-specifically europium labelled AVP04-50 and AVP04-50 complexed with its antigen BSM (containing TAG72). Europium was tracked in each fraction to determine peak shifts, where Eu-AVP04-50/TAG72 complexes elute at 14 min.
  • Figure 5A is a copy of a photographic representation showing PEGylated AVP04-50 resolved using SDS-PAGE. MW. marker, 1. naked AVP04-50, 2. AVP04- 50-PEG2000-NH2.
  • Figure 5B is a graphical representation showing results of a gel filtration elution of AVP04-50-PEG2000 (Black line).
  • Figure 5C is a graphical representation showing results of a column shift assay of AVP04-50-PEG2000 (dotted line) and AVP04-50-PEG2000 complexed with its antigen BSM (containing TAG72) (Black line).
  • Figure 6A is a diagrammatic representation of the positioning of cysteine residues in framework region FR2 according some examples of the invention.
  • the circled “S” represents the conserved cysteine residue(s) present in most mammalian antibody variable (V)-domains whilst the uncircled “S” represents the cysteine residues of the invention in FR2.
  • Figure 6B is a diagrammatic representation showng some modifications and insertions of cysteine residues into FR3 according to some examples of the present invention.
  • the circled “S” represents the conserved cysteine residue(s) present in most mammalian antibody V-domains whilst the uncircled “S” represents the cysteine residues of the invention.
  • the situation depicted at C2 is not encompassed by the invention.
  • Figure 7 is a diagrammatic representation showing the in silico homology modelled, un-mutated AVP04-07 diabody (comprising a polypeptide comprising a sequence set forth in SEQ ID NO: 59). Potential disulphide insertion residues identified for mutation are indicated with an arrow.
  • Figure 8 is a diagrammatic representation showing the in silico homology modelled, un-mutated AVP07-17 diabody (comprising a polypeptide comprising a sequence set forth in SEQ ID NO: 61). Potential disulphide insertion residues identified for mutation are indicated with an arrow.
  • Figure 9 is a diagrammatic representation showing the in silico homology modelled, un-mutated AVP02-60 diabody (comprising a polypeptide comprising a sequence set forth in SEQ ID NO: 63). Potential disulphide insertion residues identified for mutation are indicated with an arrow.
  • Figure 10A is a series of diagrammatic representations showing a) an Fv from each of the AVP04-xx diabody models (AVP04-07, AVP04-xx with modelling mutation c5 and AVP04-xx with modelling mutation c6), shown least squares aligned by the framework regions. All the FR2 cysteine mutant side chains are shown as ball and stick, b) represents only the FR2 regions for the Avibodies modelled in A. c) represents the V H FR2 regions and their mutations side by side for comparison, d) represents the V L FR2 regions and their mutations side by side for comparison, c) and d) are also labelled with the Kabat residue numbers and modelling mutation numbers (c5, c6) for reference purposes.
  • Figure 1 OB is a series of diagrammatic representations showing an Fv from each of the AVP04-xx diabody models (AVP04-07, AVP04-xx with modelling mutation c4, AVP04-xx with modelling mutation c8 and AVP04-xx with modelling mutation c9), shown least squares aligned by the framework regions and cysteine mutant side chains shown as ball and stick, b) represents the FR3 regions only for the Avibodies modelled in a.
  • c) represents the V H FR3 regions and their mutations side by side for comparison
  • d) represents the V L FR3 regions and their mutations side by side for comparison
  • c) and d) are also labelled with the Kabat residue numbers and modelling mutation numbers (c4, c8, c9) for reference purposes.
  • Figure 11 is a graphical representation of the Accessible Surface Areas (ASA) values for each individual candidate cysteine replacement has been plotted in the context of models of an AVP04-xx diabody in the V H -V L orientation (first column in each series), an AVP04-xx triabody in the V H -V L orientation with a -1 residue linker (second column in each series), an AVP04-xx triabody in the V H -V L orientation with a zero-residue linker (third column in each series), an AVP04-xx diabody in the V L -V H orientation with Fv spatial orientation modeled on the ILMK diabody (fourth column in each series), an AVP04-xx diabody in the V L -V H orientation with Fv spatial orientation modeled on the 1MOE diabody (fifth column in each series), an AVP04-xx triabody in the V L -V H orientation with a 1 residue linker (sixth column in each series) and an AVP04
  • the modeling mutation designated by c6 contain the H39-H43 and L38-L42 disulphide mutations and similarly for c5 H39-H45/L38-L44, c8 H70-H79/L65-L72, c9 H72-H75 and c4 H82C-H86/L78-L82.
  • Figure 12A is a series of diagrammatic representations showing A) an Fv from each of the AVP02-xx diabody models (AVP02-60, AVP02-xx with modeling mutation c5 and AVP02-xx with modeling mutation c6), shown least squares aligned by the framework regions. All the FR2 cysteine mutant side chains are shown as ball and stick.
  • B) represents only the FR2 regions for the Avibodies modeled in A.
  • C) represents the V H FR2 regions and their mutations side by side for comparison.
  • D) represents the V L FR2 regions and their mutations side by side for comparison.
  • C) and D) are also labeled with the Kabat residue numbers and modeling mutation numbers (c5, c6) for reference purposes.
  • Figure 12B is a series of diagrammatic representations showing an Fv from each of the AVP02-XX diabody models (AVP02-60, AVP02-xx with modeling mutation c4, AVP02-xx with modeling mutation c8 and AVP02-xx with modeling mutation c9), shown least squares aligned by the framework regions and cysteine mutant side chains shown as ball and stick.
  • B) represents the FR3 regions only for the Avibodies modeled in A.
  • C) represents the V H FR3 regions and their mutations side by side for comparison.
  • D) represents the V L FR3 regions and their mutations side by side for comparison.
  • C) and D) are also labeled with the Kabat residue numbers and modeling mutation numbers (c4, c8, c9) for reference purposes.
  • Figure 13 A is a series of diagrammatic representations showing A) an Fv from each of the AVP07-xx diabody models (AVP07-17, AVP07-xx with modeling mutation c5 and AVP07-xx with modeling mutation c6), shown least squares aligned by the framework regions. All the FR2 cysteine mutant side chains are shown as ball and stick.
  • B) represents only the FR2 regions for the Avibodies modeled in A.
  • C) represents the V H FR2 regions and their mutations side by side for comparison.
  • D) represents the V L FR2 regions and their mutations side by side for comparison.
  • C) and D) are also labeled with the Kabat residue numbers and modeling mutation numbers (c5, c6) for reference purposes.
  • Figure 13B is a series of diagrammatic representations showing an Fv from each of the AVP07-xx diabody models (AVP07-17, AVP07-xx with modeling mutation c4, AVP07-xx with modeling mutation c8 and AVP07-xx with modeling mutation c9), shown least squares aligned by the framework regions and cysteine mutant side chains shown as ball and stick.
  • B) represents the FR3 regions only for the Avibodies modeled in A.
  • C) represents the V H FR3 regions and their mutations side by side for comparison.
  • D) represents the V L FR3 regions and their mutations side by side for comparison.
  • C) and D) are also labeled with the Kabat residue numbers and modeling mutation numbers (c4, c8, c9) for reference purposes.
  • Figure 14 is a graphical representation showing the Accessible Surface Areas
  • ASA ASA values for each individual candidate cysteine replacement has been plotted in the context of models of an AVP02-xx diabody in the V H -V L orientation (first column in each series), an AVP02-xx triabody in the V H -V L orientation with a -1 residue linker (second column in each series), an AVP02-xx triabody in the V H -V L orientation with a zero-residue linker (third column in each series), an AVP02-xx diabody in the V L -V H orientation with Fv spatial orientation modeled on the ILMK diabody (fourth column in each series), an AVP02-xx diabody in the V L -V H orientation with Fv spatial orientation modeled on the 1MOE diabody (fifth column in each series), an AVP02-xx triabody in the V L -V H orientation with a 1 residue linker (sixth column in each series) and an AVP02-xx triabody in the V L -V H orientation
  • the modeling mutation designated by c6 contain the H39-H43 and L38-L42 disulphide mutations and similarly for c5 H39-H45/L38-L44, c8 H70-H79/L65-L72, c9 H72-H75 and c4 H82C-H86/L78-L82.
  • Figure 15 is a graphical representation showing the Accessible Surface Areas (ASA) values for each individual candidate cysteine replacement has been plotted in the context of models of an AVP07-xx diabody in the V H -V L orientation (first column in each series), an AVP07-xx triabody in the V H -V L orientation with a -1 residue linker (second column in each series), an AVP07-xx triabody in the V H -V L orientation with a zero-residue linker (third column in each series), an AVP07-xx diabody in the V L -V H orientation with Fv spatial orientation modeled on the ILMK diabody (fourth column in each series), an AVP07-xx diabody in the V L -V H orientation with Fv spatial orientation modeled on the 1MOE diabody (fifth column in each series), an AVP07-xx triabody in the V L -V H orientation with a 1 residue linker (sixth column in each series) and an AVP07
  • the modeling mutation designated by c6 contain the H39-H43 and L38-L42 disulphide mutations and similarly for c5 H39-H45/L38-L44, c8 H70-H79/L65-L72, c9 H72-H75 and c4 H82C-H86/L78-L82.
  • Figure 16 is a graphical representation of the Root Mean Squared Deviations (RMSDs) for the native and cysteine mutated V domains from Avibody models, where H or L-VHVLD 5, H or L-VHVLT -1, H or L-VHVLT 0, H or L-VLVHD lmk5, H or L-VLVHD moe5, H or L-VLVHT 1 and H or L-VLVHT 2 are the VH or VL domains from the construct group models defined described in Example 9.8.
  • RMSDs Root Mean Squared Deviations
  • All Avibody models were compared to all other native (non-thiolated) Avibody models (first column in each construct group) and subsequently compared to all models generated of modeling mutation c6 (H39-H43/L38-L42, second bar in each construct group), modeling mutation c5 (H39-H45/L38-L44, third bar in each construct group), modeling mutation c8 (H70-H79/L65-L72, fourth bar in each construct group), modeling mutation c9 (H72-H75, fifth bar in each construct group) and modeling mutation c4 (H82C-H86/L78-L82, sixth and final bar in each construct group).
  • Figure 17A is a graphical representation showing the 280nm chromatograph of the His-tag immobilized metal affinity chromatography purification of AVP04-111
  • Figure 17B is a graphical representation showing the 280nm chromatograph of the His-tag immobilized metal affinity chromatography purification of AVP04-120
  • Figure 17C is a graphical representation showing the 280nm chromatograph of the His-tag immobilized metal affinity chromatography purification of AVP04-121 (SEQ ID NO: 115). Arrow indicates elution peak of interest. Dotted line indicates proportion of elution buffer.
  • Figure 18A is a graphical representation showing the 280nm chromatograph of the anion exchange chromatography purification of AVP04-111 (SEQ ID NO: 107). Arrow indicates elution peak of interest. Dotted line indicates proportion of elution buffer.
  • Figure 18B is a graphical representation showing the 280nm chromatograph of the anion exchange chromatography purification of AVP04-120 (SEQ ID NO: 113). Arrow indicates elution peak of interest. Dotted line indicates proportion of elution buffer.
  • Figure 18C is a graphical representation showing the 280nm chromatograph of the anion exchange chromatography purification of AVP04-121 (SEQ ID NO: 115). Arrow indicates elution peak of interest. Dotted line indicates proportion of elution buffer.
  • Figure 19A is a graphical representation showing the 280nm chromatograph of the Gel filtration chromatography purification of AVP04-111 (SEQ ID NO: 107). Arrow indicates elution peak of interest.
  • Figure 19B is a graphical representation showing the 280nm chromatograph of the Gel filtration chromatography purification of AVP04-120 (SEQ ID NO: 113). Arrow indicates elution peak of interest.
  • Figure 19C is a graphical representation showing the 280nm chromatograph of the Gel filtration chromatography purification of AVP04-121 (SEQ ID NO: 115). Arrow indicates elution peak of interest.
  • Figure 20A is a graphical representation showing the 280nm chromatograph of the size exclusion chromatography analysis of AVP04-111 (SEQ ID NO: 107). Arrow indicates elution peak of interest.
  • Figure 20B is a graphical representation showing the 280nm chromatograph of the size exclusion chromatography analysis of AVP04-120 (SEQ ID NO: 113). Arrow indicates elution peak of interest.
  • Figure 20C is a graphical representation showing the 280nm chromatograph of the size exclusion chromatography analysis of AVP04-121 (SEQ ID NO: 115). Arrow indicates elution peak of interest.
  • Figures 21 A and B include a series of graphical representations of the purified Avibodies mentioned herein (as indicated, nomenclature corresponds to that used throughout the text and in the sequence listing) following size exclusion chromatography.
  • Figures 22A and B include a series of graphical representations of a column shift assay used to determine immunoreactivity of Avibodies mentioned herein (as indicated, nomenclature corresponds to that used throughout the text and in the sequence listing). Each graph comprises two overlaid size exclusion chromatography profiles; of the Avibody incubated either in the presence (solid line) or absence (dotted line) of antigen.
  • Figures 23A and B are a series of graphical representations of thiol reactivity of proteins by Ellman's assay for A) control Avibody proteins and intact IgG and B) Avibody proteins carrying engineered cysteine replacement mutations.
  • the black horizontal line represents 1 : 1 ratio of thiol reactivity before and after reduction with TCEP.
  • Figure 24 is a graphical representation of example MS spectra following electrospray ionization mass spectrometry of PEGylated samples (AVP04-111 (SEQ ID NO: 107), AVP04-120 (SEQ ID NO: 113) and AVP04-121 (SEQ ID NO: 115)).
  • Figures 25A and B are a series of a graphical representations showing a column shift assay used to determine immunoreactivity of PEGylated Avibody proteins mentioned herein (as indicated, nomenclature corresponds to that used throughout the text and in the sequence listing).
  • Each graph comprises two overlaid size exclusion chromatography profiles; of the Avibody-PEG conjugate incubated either in the presence (solid line) or absence (dotted line) of antigen.
  • SEQ ID NO 1166 amino acid sequence of FR2 of a human antibody ⁇ light chain
  • SEQ ID NO: 17 amino acid sequence of FR2 of a human antibody ⁇ light chain
  • SEQ ID NO: 18 amino acid sequence of FR2 of a human antibody ⁇ light chain
  • SEQ ID NO: 19 amino acid sequence of FR2 of a human antibody ⁇ light chain
  • SEQ ID NO: 20 amino acid sequence of FR2 of a human antibody ⁇ light chain
  • SEQ ID NO: 21 amino acid sequence of FR2 of a human antibody ⁇ light chain
  • SEQ ID NO: 22 amino acid sequence of FR3 of a human antibody heavy chain
  • SEQ ID NO: 23 amino acid sequence of FR3 of a human antibody heavy chain
  • SEQ ID NO: 24 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 25 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 26 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 27 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 28 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 29 amino acid sequence of FR3 of a human antibody heavy chain
  • SEQ ID NO: 30 amino acid sequence of FR3 of a human antibody heavy chain
  • SEQ ID NO: 31 amino acid sequence of FR3 of a human antibody heavy chain
  • SEQ ID NO: 32 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 33 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 34 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 35 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 36 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 37 amino acid sequence of FR3 of a human antibody heavy chain
  • SEQ ID NO: 38 amino acid sequence of FR3 of a human antibody heavy chain
  • SEQ ID NO: 39 amino acid sequence of FR3 of a human antibody heavy chain
  • SEQ ID NO: 40 amino acid sequence of FR3of a human antibody heavy chain
  • SEQ ID NO: 41 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 42 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 43 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 44 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 45 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 46 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 47 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 48 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 49 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 50 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 51 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 52 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 53 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 54 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 55 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 56 amino acid sequence of FR3 of a human antibody ⁇ light chain
  • SEQ ID NO: 58 nucleotide sequence encoding AVP04-07 anti-TAG72 diabody
  • SEQ ID NO: 60 nucleotide sequence encoding AVP07-17 anti-Her2 diabody
  • SEQ ID NO: 62 nucleotide sequence encoding AVP02-60 anti-Mud diabody
  • SEQ ID NO: 64 nucleotide sequence encoding a modified AVP07-17 anti-HER2 diabody replacing CDR3H Cysteine residues Cysl04 (Kabat numbering HI 00) and
  • Cysl09 (H100E) with Alanines and comprising a N-terminal serine designated AVP07- 86;
  • SEQ ID NO: 65 amino acid sequence of modified AVP07-17 anti-HER2 diabody replacing CDR3H Cysteine residues Cysl04 (Kabat numbering HI 00) and Cysl09 (H100E) with Alanines and comprising a N-terminal serine designated AVP07-86;
  • SEQ ID NO: 66 nucleotide sequence of mutagenic primer for substituting the N- terminal Gin residue with a Ser residue in AVP04-07;
  • SEQ ID NO: 67 nucleotide sequence of mutagenic primer for substituting the N- terminal Gin residue with a Ser residue in AVP04-07;
  • SEQ ID NO: 68 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 38 and 42 in the V L FR2 of AVP04-07
  • SEQ ID NO: 69 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 38 and 42 in the V L FR2 of AVP04-07
  • SEQ ID NO: 70 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 38 and 44 in the V L FR2 of AVP04-07
  • SEQ ID NO: 71 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 38 and 44 in the V L FR2 of AVP04-07
  • SEQ ID NO: 72 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 78 and 82 in the V L FR3 of AVP04-07
  • SEQ ID NO: 73 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 78 and 82 in the V L FR3 of AVP04-07
  • SEQ ID NO: 74 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 39 and 43 in the V H FR2 of AVP04-07
  • SEQ ID NO: 75 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 39 and 43 in the V H FR2 of AVP04-07
  • SEQ ID NO: 76 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 39 and 45 in the V H FR2 of AVP04-07
  • SEQ ID NO: 77 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 39 and 45 in the V H FR2 of AVP04-07
  • SEQ ID NO: 78 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 82C and 86 in the V H FR3 of AVP04-07
  • SEQ ID NO: 79 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 82C and 86 in the V H FR3 of AVP04-07
  • SEQ ID NO: 80 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 70 and 79 in the V H FR3 of AVP04-07
  • SEQ ID NO: 81 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 70 and 79 in the V H FR3 of AVP04-07
  • SEQ ID NO: 82 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 72 and 75 in the V H FR3 of AVP04-07
  • SEQ ID NO: 83 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 72 and 75 in the V H FR3 of AVP04-07
  • SEQ ID NO: 84 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 65 and 72 in the V L FR3 of AVP04-07
  • SEQ ID NO: 85 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 65 and 72 in the V L FR3 of AVP04-07
  • SEQ ID NO: 86 nucleotide sequence of mutagenic primer for modification of linker residues of AVP04-79 for scFv expression
  • SEQ ID NO: 87 nucleotide sequence of mutagenic primer for modification of linker residues of AVP04-79 for scFv expression
  • SEQ ID NO: 88 nucleotide sequence of mutagenic primer for modification of linker residues of AVP04-79 for triabody expression.
  • SEQ ID NO: 89 nucleotide sequence of mutagenic primer for modification of linker residues of AVP04-79 for triabody expression.
  • SEQ ID NO: 90 nucleotide sequence of mutagenic primer for AVP07-17 anti-HER2 diabody replacing CDR3H Cysteine residues with alanines designated AVP07-86 SEQ ID NO: 91 - nucleotide sequence of mutagenic primer for AVP07-17 anti-HER2 diabody replacing CDR3H Cysteine residues with alanines designated AVP07-86 SEQ ID NO: 92 - nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 38 and 42 in the V L FR2 of AVP02-60 SEQ ID NO: 93 - nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 38 and 42 in the V L FR2 of AVP02-60
  • SEQ ID NO: 94 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 39 and 43 in the V H FR2 of AVP02-60
  • SEQ ID NO: 95 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 39 and 43 in the V H FR2 of AVP02-60
  • SEQ ID NO: 96 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 38 and 42 in the V L FR2 of AVP07-86
  • SEQ ID NO: 97 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 38 and 42 in the V L FR2 of AVP07-86
  • SEQ ID NO: 98 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 39 and 43 in the V H FR2 of AVP07-86
  • SEQ ID NO: 99 nucleotide sequence of mutagenic primer for introducing cysteine residue substitutions at positions 39 and 43 in the V H FR2 of AVP07-86
  • SEQ ID NO: 100 nucleotide sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 42 designated AVP04-79.
  • SEQ ID NO: 101 amino acid sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 42 designated AVP04-79.
  • SEQ ID NO: 102 - nucleotide sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 44 is designated AVP04- 80.
  • SEQ ID NO: 103 - amino acid sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 44 is designated AVP04-80.
  • SEQ ID NO: 104 nucleotide sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V L FR3 Kabat positions 78 and 82 designated AVP04-83.
  • SEQ ID NO: 105 amino acid sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V L FR3 Kabat positions 78 and 82 designated AVP04-83.
  • SEQ ID NO: 106 nucleotide sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 43 designated AVP04- 1 1 1.
  • SEQ ID NO: 107 amino acid sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 43 designated AVP04-1 1 1.
  • SEQ ID NO: 108 nucleotide sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 45 designated AVP04- 112.
  • SEQ ID NO: 109 amino acid sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 45 designated AVP04-112.
  • SEQ ID NO: 110 nucleotide sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 82C and 86 designated AVP04- 114.
  • SEQ ID NO: 111 amino acid sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 82C and 86 designated AVP04-114.
  • SEQ ID NO: 112 nucleotide sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 70 and 79 designated AVP04- 120.
  • SEQ ID NO: 113 amino acid sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 70 and 79 designated AVP04-120.
  • SEQ ID NO: 114 nucleotide sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 72 and 75 designated AVP04- 121.
  • SEQ ID NO: 115 amino acid sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 72 and 75 designated AVP04-121.
  • SEQ ID NO: 116 nucleotide sequence of an anti-TAG72 diabody comprising cysteine replacement mutations in the V L FR3 Kabat positions 65 and 72 designated AVP04- 123.
  • SEQ ID NO: 118 nucleotide sequence of an anti-TAG72 scFv comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 42 designated AVP04- 124.
  • SEQ ID NO: 119 amino acid sequence of an anti-TAG72 scFv comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 42 designated AVP04- 124.
  • SEQ ID NO: 120 nucleotide sequence of an anti-TAG72 triabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 42 designated AVP04-125.
  • SEQ ID NO: 121 amino acid sequence of an anti-TAG72 triabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 42 designated AVP04-125.
  • SEQ ID NO: 122 nucleotide sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 42 designated AVP02- 115.
  • SEQ ID NO: 123 amino acid sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 42 designated AVP02- 115.
  • SEQ ID NO: 124 nucleotide sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 43 designated AVP02- 116.
  • SEQ ID NO: 125 amino acid sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 43 designated AVP02- 116.
  • SEQ ID NO: 126 nucleotide sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 42 designated AVP07- 117.
  • SEQ ID NO: 127 amino acid sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 42 designated AVP07- 117.
  • SEQ ID NO: 128 nucleotide sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 43 designated AVP07- 118.
  • SEQ ID NO: 129 amino acid sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 43 designated AVP07- 118.
  • SEQ ID NO: 130 nucleotide sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 44 designated AVP02- 126.
  • SEQ ID NO: 131 amino acid sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 44 designated AVP02- 126.
  • SEQ ID NO: 132 nucleotide sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 45 designated AVP02- 127.
  • SEQ ID NO: 133 amino acid sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 45 designated AVP02- 127.
  • SEQ ID NO: 134 nucleotide sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V L FR3 Kabat positions 65 and 72 designated AVP02- 128.
  • SEQ ID NO: 135 amino acid sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V L FR3 Kabat positions 65 and 72 designated AVP02- 128.
  • SEQ ID NO: 136 nucleotide sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 70 and 79 designated AVP02- 129.
  • SEQ ID NO: 137 amino acid sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 70 and 79 designated AVP02- 129.
  • SEQ ID NO: 138 nucleotide sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 72 and 75 designated AVP02- 130.
  • SEQ ID NO: 139 amino acid sequence of an anti-Mud diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 72 and 75 designated AVP02- 130.
  • SEQ ID NO: 140 nucleotide sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 44 designated AVP07- 131.
  • SEQ ID NO: 141 amino acid sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V L FR2 Kabat positions 38 and 44 designated AVP07- 131.
  • SEQ ID NO: 142 nucleotide sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 45 designated AVP07- 132.
  • SEQ ID NO: 143 amino acid sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V H FR2 Kabat positions 39 and 45 designated AVP07- 132.
  • SEQ ID NO: 144 nucleotide sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V L FR3 Kabat positions 65 and 72 designated AVP07- 133.
  • SEQ ID NO: 145 amino acid sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V L FR3 Kabat positions 65 and 72 designated AVP07- 133.
  • SEQ ID NO: 146 nucleotide sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 70 and 79 designated AVP07- 134.
  • SEQ ID NO: 147 amino acid sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 70 and 79 designated AVP07- 134.
  • SEQ ID NO: 148 nucleotide sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 72 and 75 designated AVP07- 135.
  • SEQ ID NO: 149 amino acid sequence of an anti-Her2 diabody comprising cysteine replacement mutations in the V H FR3 Kabat positions 72 and 75 designated AVP07- 135.
  • SEQ ID NO: 152 amino acid sequence of an isoform of human MUC1;
  • SEQ ID NO: 153 amino acid sequence of an isoform of human MUC1 expressed in several forms of cancer
  • variable regions and parts thereof, immunoglobulins, antibodies and fragments thereof herein may be further clarified by the discussion in, for example, Kabat (1987 and/or 1991), Bork et al (1994) and/or Chothia and Lesk (1987 and 1989) or Al-Lazikani et al (1997).
  • the term "and/or”, e.g., "X and/or Y” shall be understood to mean either "X and Y" or "X or Y” and shall be taken to provide explicit support for both meanings or for either meaning.
  • the term "between” in the context of defining the positioning of an amino acid residue or nucleotide residue based on a specific position number shall be taken to mean any residues located between the two recited residues and the two recited residues.
  • the term “between residues 38-42” shall be understood to include residues 38, 39, 40, 41 and 42.
  • derived from shall be taken to indicate that a specified integer may be obtained from a particular source albeit not necessarily directly from that source.
  • an antibody is generally considered to be a protein that comprises a variable region made up of a plurality of polypeptide chains, e.g., a light chain variable region (V L ) and a heavy chain variable region (V H ).
  • An antibody also generally comprises constant domains, which can be arranged into a constant region or constant fragment or fragment crystallisable (Fc).
  • Antibodies can bind specifically to one or a few closely related antigens. Generally, antibodies comprise a four-chain structure as their basic unit.
  • Full- length antibodies comprise two heavy chains (-50-70 kD) covalently linked and two light chains ( ⁇ 23 kD each).
  • a light chain generally comprises a variable region and a constant domain and in mammals is either a ⁇ light chain or a ⁇ light chain.
  • a heavy chain generally comprises a variable region and one or two constant domain(s) linked by a hinge region to additional constant domain(s).
  • Heavy chains of mammals are of one of the following types ⁇ , ⁇ , ⁇ , ⁇ , or ⁇ .
  • Each light chain is also covalently linked to one of the heavy chains.
  • the two heavy chains and the heavy and light chains are held together by inter-chain disulfide bonds and by non-covalent interactions. The number of inter-chain disulfide bonds can vary among different types of antibodies.
  • Each chain has an N-terminal variable region (V H or V L wherein each are -1 10 amino acids in length) and one or more constant domains at the C- terminus.
  • the constant domain of the light chain (C L which is—110 amino acids in length) is aligned with and disulfide bonded to the first constant domain of the heavy chain (C H which is -330-440 amino acids in length).
  • the light chain variable region is aligned with the variable region of the heavy chain.
  • the antibody heavy chain can comprise 2 or more additional C H domains (such as, C H 2, C H 3 and the like) and can comprise a hinge region can be identified between the C H I and Cm constant domains.
  • Antibodies can be of any type (e.g., IgG, IgE, IgM, IgD, IgA, and IgY), class (e.g., Igd, IgG 2 , IgG 3 , IgG 4 , IgAi and IgA 2 ) or subclass.
  • the antibody is a murine (mouse or rat) antibody or a primate (preferably human) antibody.
  • the term "antibody” also encompasses humanized antibodies, primatized antibodies, human antibodies and chimeric antibodies.
  • immunoglobulin Proteins related to antibodies, and thus encompassed by the term "immunoglobulin: include domain antibodies, camelid antibodies and antibodies from cartilaginous fish (i.e., immunoglobulin new antigen receptors (IgNARs)). Generally, camelid antibodies and IgNARs comprise a V3 ⁇ 4 however lack a V L and are often referred to as heavy chain immunoglobulins. As used herein, the term “immunoglobulin” does not encompass T cell receptors and other immunoglobulin-like domain containing proteins that are not capable of binding to an antigen, e.g., by virtue of an antigen binding site comprising a variable region. Furthermore, the term “immunoglobulin” does not encompass a protein comprising an immunoglobulin domain that does not comprise a FR2 and/or FR3, since the invention cannot be performed with such a protein.
  • IgNARs immunoglobulin new antigen receptors
  • variable region refers to the portions of the light and heavy chains of an antibody or immunoglobulin as defined herein that includes amino acid sequences of CDRs; i.e., CDR1, CDR2, and CDR3, and FRs. In the case of IgNARs the term “variable region” does not require the presence of a CDR2.
  • V H refers to the variable region of the heavy chain.
  • V L refers to the variable region of the light chain. According to the methods used in this invention, the amino acid positions assigned to CDRs and FRs are defined according to Kabat (1987 and 1991).
  • the term "heavy chain variable region” or "V H" shall be taken to mean a protein capable of binding to one or more antigens, preferably specifically binding to one or more antigens and at least comprising a FR2 and/or FR3. Sequences of exemplary FR2 and/or FR3 from a heavy chain are provided herein (see, for example, SEQ ID NOs 1 to 8 or 22 to 40).
  • the heavy chain comprises three or four FRs (e.g., FR1, FR2, FR3 and optionally FR4) together with three CDRs.
  • a heavy chain comprises FRs and CDRs positioned as follows residues 1-30 (FR1 ), 31-25 (CDR1), 36-49 (FR2), 50-65 (CDR2), 66-94 (FR3), 95-102 (CDR3) and 103- 113 (FR4), numbered according to the Kabat numbering system.
  • the heavy chain is derived from an immunoglobulin comprising said heavy chain and a plurality of (preferably 3 or 4) constant domains or linked to a constant fragment (Fc).
  • the term "light chain variable region" or "V L " shall be taken to mean a protein capable of binding to one or more antigens, preferably specifically binding to one or more antigens and at least comprising a FR2 and/or FR3. Sequences of exemplary FR2 and/or FR3 from a light chain are provided herein (see, for example, SEQ ID NO's 9 to 21 or 41 to 56).
  • the light chain comprises three or four FRs (e.g., FR1, FR2, FR3 and optionally FR4) together with three CDRs.
  • a light chain comprises FRs and CDRs positioned as follows residues 1-23 (FR1), 24-34 (CDR1), 35-49 (FR2), 50-56 (CDR2), 57-88 (FR3), 89-97 (CDR3) and 98-107 (FR4), numbered according to the Kabat numbering system.
  • the light chain is derived from an immunoglobulin comprising said light chain linked to one constant domain and/or not linked to a constant fragment (Fc).
  • variable region residues are other than the CDR residues.
  • Each variable region of a naturally-occurring immunoglobulin typically has four FRs identified as FR1, FR2, FR3 and FR4.
  • exemplary light chain FR (LCFR) residues are positioned at about residues 1-23 (LCFR1 ), 35-49 (LCFR2), 57-88 (LCFR3), and 98-107 (LCFR4).
  • LCFRl does not comprise residue 10, which is included in KLCFRI .
  • Exemplary heavy chain FR (HCFR) residues are positioned at about residues 1-30 (HCFR1), 36-49 (HCFR2), 66-94 (HCFR3), and 103- 113 (HCFR4).
  • FR2 framework region 2
  • CDR1 and CDR2 residues between CDR1 and CDR2.
  • These residues have been numbered by at least two nomenclatures being 1) Kabat (1987 and/or 2001) and 2) Chothia and Lesk (1987, 1989 and Al-Lazikani et al 1997).
  • the Chothia and Lesk numbering system was based on the well established Kabat system and attempted to correct the numbering of light chain CDR1 and heavy chain CDR1 sequence length variability in the immunoglobulin variable regions to better fit their actual position in the three-dimensional structure.
  • the CDR-specific numbering adopted by Chothia and Lesk was later modified in 1989 but then reverted in 1997. There are subtle differences between these numbering systems when dealing with residues found within CDR loops.
  • FR2 is positioned between residues 36 to 49 in a V H and 35 to 49 in a V L .
  • FR3 framework region 3
  • residues 66 to 94 residues 66 to 94 in a V H and 57 to 88 in a V L .
  • framework region 1 is defined as the residues between the natural N-terminal residue and the start of the complementarity determining region No. 1 (CDRl).
  • CDRl complementarity determining region No. 1
  • these residues have been numbered by at least two nomenclatures being 1) Kabat (1987 and/or 2001) and 2) Chothia and Lesk (1987, 1989 and Al-Lazikani et al 1997).
  • Cys cysteine residue
  • this conserved cysteine is invariantly in Kabat position 23 and forms a disulphide bond with another highly conserved cysteine residue, invariantly in Kabat position 88, within the region defined as framework region 3, between CDR2 and CDR3.
  • the present invention contemplates indels, generally man made indels of one, two or three amino acids, which may alter the position of the conserved cysteine relative to other amino acids of FRl .
  • CDRs complementarity determining regions
  • CDRl complementarity determining regions
  • CDR2 complementarity determining regions
  • CDR3 hypervariable region
  • Each CDR may comprise amino acid residues from a "complementarity determining region” as defined by Kabat (1987 and/or 1991).
  • CDRHl is between residues 31-35
  • CDRH2 is between residues 50-65
  • CDRH3 is between residues 95-102.
  • CDRL1 is between residues 24-34
  • CDRL2 is between residues 50-56
  • CDRL3 is between residues 89-97.
  • CDRs can also comprise numerous insertions, e.g., as described in Kabat (1987 and/or 1991).
  • constant region refers to a portion of an immunoglobulin comprising at least one constant domain and which is generally (though not necessarily) glycosylated and which binds to one or more F receptors and/or components of the complement cascade (e.g., confers effector functions).
  • the heavy chain constant region can be selected from any of the five isotypes: ⁇ , ⁇ , ⁇ , ⁇ , or ⁇ .
  • heavy chains of various subclasses are responsible for different effector functions and thus, by choosing the desired heavy chain constant region, proteins with desired effector function can be produced.
  • Preferred heavy chain constant regions are gamma 1 (IgGl), gamma 2 (IgG2) and gamma 3 (IgG3).
  • a “constant domain” is a domain in an immunoglobulin the sequence of which is highly similar in immunoglobulins/antibodies of the same type, e.g., IgG or IgM or IgE.
  • a constant region of an immunoglobulin generally comprises a plurality of constant domains, e.g., the constant region of ⁇ , a and ⁇ heavy chains comprise three constant domains and the Fc of ⁇ , a and ⁇ heavy chains comprise two constant domains.
  • a constant region of ⁇ and ⁇ heavy chains comprises four constant domains and the Fc region comprises two constant domains.
  • the term "Fv” shall be taken to mean any protein, whether comprised of multiple polypeptides or a single polypeptide, in which a VL and a VH associate and form a complex having an antigen binding site, i.e., capable of specifically binding to an antigen.
  • the VH and the VL which form the antigen binding site can be in a single polypeptide chain or in different polypeptide chains.
  • an Fv of the invention (as well as any protein of the invention) may have multiple antigen binding sites which may or may not bind the same antigen. This term shall be understood to encompass fragments directly derived from an immunoglobulin as well as proteins corresponding to such a fragment produced using recombinant means.
  • the VH is not linked to a heavy chain constant domain (CH) 1 and/or the VL is not linked to a light chain constant domain (CL).
  • exemplary Fv containing polypeptides or proteins include a Fab fragment, a Fab' fragment, a F(ab') fragment, a scFv, a diabody, a triabody, a tetrabody or higher order complex, or any of the foregoing linked to a constant region or domain thereof, e.g., CH2 or CH3 domain.
  • a "Fab fragment” consists of a monovalent antigen-binding fragment of an immunoglobulin, and can be produced by digestion of a whole immunoglobulin with the enzyme papain, to yield a fragment consisting of an intact light chain and a portion of a heavy chain or can be produced using recombinant means.
  • a "Fab' fragment” of an immunoglobulin can be obtained by treating a whole immunoglobulin with pepsin, followed by reduction, to yield a molecule consisting of an intact light chain and a portion of a heavy chain. Two Fab' fragments are obtained per immunoglobulin treated in this manner.
  • a Fab' fragment can also be produced by recombinant means.
  • a "F(ab')2 fragment” of an immunoglobulin consists of a dimer of two Fab' fragments held together by two disulfide bonds, and is obtained by treating a whole immunoglobulin molecule with the enzyme pepsin, without subsequent reduction.
  • a "Fab 2 " fragment is a recombinant fragment comprising two Fab fragments linked using, for example a leucine zipper or a C H 3 domain.
  • a "single chain Fv” or “scFv” is a recombinant molecule containing the variable region fragment (Fv) of an immunoglobulin in which the variable region of the light chain and the variable region of the heavy chain are covalently linked by a suitable, flexible polypeptide linker.
  • the term "antigen binding site” shall be taken to mean a structure formed by a protein that is capable of specifically binding to an antigen.
  • the antigen binding site need not be a series of contiguous amino acids, or even amino acids in a single polypeptide chain.
  • the antigen binding site is made up of a series of regions of a V L and a V H that interact with the antigen and that are generally, however not always in the one or more of the CDRs in each variable region.
  • Kabat numbering system is meant the numbering system to determining the position of FRs and CDRs in a variable region of an immunoglobulin as set out in Kabat (1987 and/or 1991).
  • protein shall be taken to include a single polypeptide chain, i.e., a series of contiguous amino acids linked by peptide bonds or a series of polypeptide chains covalently or non-covalently linked to one another (i.e., a polypeptide complex).
  • the series of polypeptide chains can be covalently linked using a suitable chemical or a disulphide bond.
  • non-covalent bonds include hydrogen bonds, ionic bonds, Van der Waals forces, and hydrophobic interactions.
  • a non- covalent bond contemplated by the present invention is the interaction between a V H and a V L , e.g., in some forms of diabody or a triabody or a tetrabody.
  • polypeptide chain will be understood to mean from the foregoing paragraph to mean a series of contiguous amino acids linked by peptide bonds.
  • a "disulphide bond” is a covalent bond formed by coupling of thiol groups. The bond is also called an SS-bond or disulfide bridge. In proteins, a disulphide bond generally occurs between the thiol groups of two cysteine residues to produce cystine.
  • non-reducing conditions includes conditions sufficient for oxidation of sulfhydryl (-SH) groups in a protein, e.g., permissive for disulphide bond formation.
  • antigen shall be understood to mean any composition of matter against which an immunoglobulin response (e.g., an antibody response) can be raised.
  • exemplary antigens include proteins, peptides, polypeptides, carbohydrates, phosphate groups, phosphor-peptides or polypeptides, glyscosylated peptides or peptides, etc.
  • the term "specifically binds" shall be taken to mean a protein of the invention reacts or associates more frequently, more rapidly, with greater duration and/or with greater affinity with a particular antigen or antigens or cell expressing same than it does with alternative antigens or cells.
  • a protein that specifically binds to an antigen binds that antigen with greater affinity, avidity, more readily, and/or with greater duration than it binds to other antigens. It is also understood by reading this definition that, for example, a protein that specifically binds to a first antigen may or may not specifically bind to a second antigen.
  • binding does not necessarily require exclusive binding or non-detectable binding of another antigen, this is meant by the term “selective binding”.
  • binding means specific binding, and each term shall be understood to provide explicit support for the other term.
  • preventing in the context of binding of a protein of the invention to an antigen shall be taken to mean complete abrogation or complete inhibition of binding to the antigen.
  • the present invention contemplates any protein that comprises an immunoglobulin variable region that specifically or selectively binds to one or more antigens and that is modified as described herein according to any embodiment.
  • Preferred proteins comprise at least one V H and at least one V L .
  • Exemplary immunoglobulin variable regions are variable regions from antibodies and modified forms thereof (e.g., humanized antibodies) and heavy chain antibodies, such as, camelid immunoglobulin and IgNAR.
  • the proteins of the invention can comprise one or more variable regions from an antibody modified to comprise at least two cysteine residues in FR2 and/or FR3 as described herein.
  • the present invention also provides antibody molecules. Such antibodies may be produced by first producing an antibody against an antigen of interest and modifying that antibody (e.g., using recombinant means) or by modifying a previously produced antibody.
  • Methods for producing antibodies are known in the art. For example, methods for producing monoclonal antibodies, such as the hybridoma technique, are by Kohler and Milstein, (1975).
  • a hybridoma method a mouse, hamster, or other appropriate host animal, is typically immunized with an immunogen or antigen or cell expressing same to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunogen or antigen. Lymphocytes or spleen cells from the immunized animals are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, 1986).
  • a suitable fusing agent such as polyethylene glycol
  • the resulting hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells.
  • a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells.
  • the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine ("HAT medium"), which substances prevent the growth of HGPRT-deficient cells.
  • HGPRT medium hypoxanthine, aminopterin, and thymidine
  • Other methods for producing antibodies are also contemplated by the present invention, e.g., using ABL-MYC technology described generically in detail in Largaespada (1990) or Weissinger et al. (1991).
  • the antibody, or sequence encoding same is generated from a previously produced cell expressing an antibody of interest, e.g., a hybridoma or transfectoma.
  • an antibody of interest e.g., a hybridoma or transfectoma.
  • Various sources of such hybridomas and/or transfectomas will be apparent to the skilled artisan and include, for example, American Type Culture Collection (ATCC) and/or European Collection of Cell Cultures (ECACC). Methods for isolating and/or modifying sequences encoding variable regions from antibodies will be apparent to the skilled artisan and/or described herein.
  • the antibody is modified to include cysteine residues in FR2 and/or FR3 as described herein at sites as described herein according to any embodiment.
  • this involves isolating the nucleic acid encoding the antibody, modifying the sequence thereof to include codons encoding cysteine residues (i.e., TGT or TGC) at the requisite sites in a FR2 and/or FR3 as described herein encoding region and expressing the modified antibody.
  • Exemplary human antibody heavy chain FR2 sequences comprise a sequence selected from the group consisting of WVRQAPGKGLEWVS (SEQ ID NO: 1);
  • WVRQAPGKGLEWVG SEQ ID NO: 2
  • WVRQAPGQLEWMG SEQ ID NO: 3
  • WVRQAPGKGLEWMG SEQ ID NO: 4
  • WIRQPPGKGLEWIG SEQ ID NO: 5
  • WIRQPPGKALEWLG SEQ ID NO: 6
  • WVRQMPGKGLEWMG SEQ ID NO: 7
  • WIRQSPSRGLEWLG SEQ ID NO: 8
  • Exemplary human antibody ⁇ light chain FR2 sequences comprise a sequence selected from the group consisting of WYQQKPGKAPKLLIY (SEQ ID NO: 9);
  • WYQQKPGQAPRLLIY (SEQ ID NO: 10); WYQQKPGQPPKLLIY (SEQ ID NO: 11); WYLQKPGQSPQLLIY (SEQ ID NO: 12); WYQQKPCQAPRLLIY (SEQ ID NO: 10); WYQQKPGQPPKLLIY (SEQ ID NO: 11); WYLQKPGQSPQLLIY (SEQ ID NO: 12); WYQQKPCQAPRLLIY (SEQ ID NO: 10); WYQQKPGQPPKLLIY (SEQ ID NO: 11); WYLQKPGQSPQLLIY (SEQ ID NO: 12); WYQQKPCQAPRLLIY (SEQ ID NO: 12); WYQQKPCQAPRLLIY (SEQ ID NO: 12);
  • Exemplary human antibody ⁇ light chain FR2 sequences comprise a sequence selected from the group consisting of WYQQLPGTAPKLLIY (SEQ ID NO: 17);
  • WYQQHPGKAPKLMIY SEQ ID NO: 18
  • WYQQKPGQAPVLVIY SEQ ID NO: 18
  • WYQQKPGQSPVLVIY SEQ ID NO: 19
  • WHQQQPEKGPRYLMY SEQ ID NO: 20
  • Exemplary human antibody heavy chain FR3 sequences comprise a sequence selected from the group consisting of
  • RVTISVDTSKNQFSLKLSSVTAADTAVYYCAR SEQ ID NO: 25
  • RVTISADKSISTAYLQWSSLKASDTAMYYCAR SEQ ID NO: 28
  • RVTITADKSTSTAYMELSSLRSEDTAVYYCAR SEQ ID NO: 29
  • RVTITADESTSTAYMELSSLRSEDTAVYYCAR SEQ ID NO: 31
  • RVTMTRNTSISTAYMELSSLRSEDTAVYYCAR SEQ ID NO: 32
  • RFTISRDNSKNTLHLQMNSLRAEDTAVYYCK SEQ ID NO: 33
  • RFTISRDNSKNSLYLQMNSLRTEDTALYYCAKD SEQ ID NO: 34
  • RVTMTRDTSTSTAYMELSSLRSEDTAVYYCAR SEQ ID NO: 40.
  • Exemplary human antibody ⁇ light chain FR3 sequences comprise a sequence selected from the group consisting of GVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 41); GVPSRFSGSGSGTDFTFTISSLQPEDIATYYC (SEQ ID NO: 42);
  • GIPARFSGSGSGTEFTLTISSLQSEDFAVYYC (SEQ ID NO: 44);
  • GIPARFSGSGSGTDFTLTISSLEPEDFAVYYC SEQ ID NO: 45
  • GIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC SEQ ID NO: 46
  • Exemplary human antibody ⁇ light chain FR3 sequences comprise a sequence selected from the group consisting of
  • GIPARFSGSGPGTDFTLTISSLEPEDFAVYYC SEQ ID NO: 51
  • GIPARFSGSGSGTDFTLTISSLQPEDFAVYYC SEQ ID NO: 53
  • GVPSRFSGSGSGTDFTLTISSLQPEDVATYYC SEQ ID NO: 56.
  • FR2 and/or FR3 regions are readily modified to include two or more cysteine residues at positions as described herein in any example or embodiment.
  • the skilled artisan will be readily able to determine the sequence of nucleic acid encoding a FR2 and/or FR3 based on knowledge in the art and/or sequences set forth herein.
  • the proteins of the present invention may be derived from or may be humanized antibodies or human antibodies or variable regions derived therefrom.
  • humanized antibody shall be understood to refer to a chimeric molecule, generally prepared using recombinant techniques, having an antigen binding site derived from an antibody from a non-human species and the remaining antibody structure of the molecule based upon the structure and/or sequence of a human antibody.
  • the antigen- binding site preferably comprises CDRs from the non-human antibody grafted onto appropriate FRs in the variable regions of a human antibody and the remaining regions from a human antibody.
  • Antigen binding sites may be wild type or modified by one or more amino acid substitutions. In some instances, framework residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • Humanized antibodies may also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable regions, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence.
  • Methods for humanizing non-human antibodies are known in the art. Humanization can be essentially performed following the method of US5225539, US6054297 or US5585089. Other methods for humanizing an antibody are not excluded.
  • a protein of the invention that is not a complete antibody can also be humanized, e.g., a variable domain can be humanized.
  • human antibody as used herein in connection with antibody molecules and binding proteins refers to antibodies having variable and, optionally, constant antibody regions derived from or corresponding to sequences found in humans, e.g. in the human germline or somatic cells.
  • the "human” antibodies can include amino acid residues not encoded by human sequences, e.g. mutations introduced by random or site directed mutations in vitro (in particular mutations which involve conservative substitutions or mutations in a small number of residues of the antibody, e.g. in 1, 2, 3, 4 or 5 of the residues of the antibody, preferably e.g. in 1, 2, 3, 4 or 5 of the residues making up one or more of the CDRs of the antibody).
  • Human antibodies do not actually need to be produced by a human, rather, they can be produced using recombinant means and/or isolated from a transgenic animal (e.g., a mouse) comprising nucleic acid encoding human antibody constant and/or variable regions.
  • Human antibodies or fragments thereof can be produced using various techniques known in the art, including phage display libraries (e.g., as described in US6300064; US5885793; US6204023; US6291158; or US6248516), or using transgenic animals expressing human immunoglobulin genes (e.g., as described in WO2002/066630; Lonberg et al. (1994)or Jakobovits et al. (2007)).
  • a protein of the invention is a chimeric antibody or part thereof, e.g., a Fab fragment.
  • the term '"chimeric antibody refers to antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species (e.g., murine, such as mouse) or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species (e.g., primate, such as human) or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (US4,816,567).
  • chimeric antibodies utilize rodent or rabbit variable regions and human constant regions, in order to produce an antibody with predominantly human domains.
  • a chimeric antibody comprises a variable region from a mouse antibody modified according to the present invention any embodiment fused to a human constant domain and/or a human constant region.
  • the production of such chimeric antibodies is known in the art, and may be achieved by standard means (as described, e.g., in US5, 807,715; US4,816,567 and US4,816,397).
  • the present invention also contemplates a deimmunized protein.
  • De-immunized proteins have one or more epitopes, e.g., B cell epitopes or T cell epitopes removed (i.e., mutated) to thereby reduce the likelihood that a subject will raise an immune response against the protein.
  • epitopes e.g., B cell epitopes or T cell epitopes removed (i.e., mutated) to thereby reduce the likelihood that a subject will raise an immune response against the protein.
  • Methods for producing deimmunized proteins are known in the art and described, for example, in WO00/34317, WO2004/108158 and WO2004/064724.
  • the method comprises performing an in silico analysis to predict an epitope in a protein and mutating one or more residues in the predicted epitope to thereby reduce its immunogenicity.
  • the protein is then analyzed, e.g., in silico or in vitro or in vivo to ensure that it retains its ability to bind to an antigen.
  • an epitope that occurs within a CDR is not mutated unless the mutation is unlikely to reduce antigen binding.
  • Methods for predicting antigens are known in the art and described, for example, in Saha (2004).
  • Exemplary epitopes in AVP04-07 occur at the following positions 35-41; 68-77; 84-90; 109-119; 122-128; 160-169; and 185-194 of SEQ ID NO: 59.
  • Residues that may be mutated to potentially reduce immunogenicity include K38, T71, A72, K74, T87, T112, VI 13, SI 14, SI 15, G116, T125, Q163, Q164, P166, F188, T189, G190 or S191.
  • Heavy chain immunoglobulins differ structurally from many other forms of immunoglobulin (e.g., antibodies,), in so far as they comprise a heavy chain, but do not comprise a light chain. Accordingly, these immunoglobulins are also referred to as "heavy chain only antibodies”. Heavy chain immunoglobulins are found in, for example, camelids and cartilaginous fish (also called IgNAR).
  • variable regions present in naturally occurring heavy chain immunoglobulins are generally referred to as "V HH domains" in camelid Ig and V-NAR in IgNAR, in order to distinguish them from the heavy chain variable regions that are present in conventional 4-chain antibodies (which are referred to as "V H domains”) and from the light chain variable regions that are present in conventional 4-chain antibodies
  • V L domains (which are referred to as "V L domains").
  • Heavy chain immunoglobulins do not require the presence of light chains to bind with high affinity and with high specificity to a relevant antigen. This feature distinguishes heavy chain immunoglobulins from some conventional 4-chain antibodies, which comprise both V H and V L domains. This means that single domain binding fragments can be derived from heavy chain immunoglobulins, which are easy to express and are generally stable and soluble. Heavy chain immunoglobulins and variable regions domains thereof domains derived therefrom can also comprise long surface loops (particularly CDR3), which facilitate penetration of and binding to cavities often found in antigens such as enzymes and on the surface of proteins of viruses and agents causative of infectious diseases.
  • CDR3 long surface loops
  • Exemplary preferred proteins comprising an immunoglobulin variable region are diabodies, triabodies, tetrabodies and higher order protein complexes such as those described in WO98/044001 and WO94/007921.
  • the term "Avibody” or “Avibodies” includes any form of AvibodyTM products which include any diabody (diabodies), triabody (triabodies) and tetrabody (tetrabodies), such as those described in WO98/044001 and/or WO94/007921.
  • the term "diabody” shall be taken to mean a protein comprising two associated polypeptide chains, each polypeptide chain comprising the structure V L - X-V H or V H -X-V L , wherein V L is an immunoglobulin light chain variable region, V H is an immunoglobulin heavy chain variable region, X is a linker comprising insufficient residues to permit the V H and V L in a single polypeptide chain to associate (or form an Fv) or is absent, and wherein the V H of one polypeptide chain binds to a V L of the other polypeptide chain to form an antigen binding site, i.e., to form a Fv molecule capable of specifically binding to one or more antigens.
  • the V L and V H can be the same in each polypeptide chain so as to form a bivalent diabody (i.e., comprising two Fvs of the same specificity) or the V L and V H can be different in each polypeptide chain so as to form a bispecific diabody (i.e., comprising two Fvs having different specificity).
  • the term "triabody” shall be taken to mean a protein comprising three associated polypeptide chains, each polypeptide chain comprising the structure V L -X-V H or V H -X-V L , wherein V L is an immunoglobulin light chain variable region, V H is an immunoglobulin heavy chain variable region, X is a linker comprising insufficient residues to permit the V H and V L in a single polypeptide chain to associate (or form an Fv) or is absent, and wherein the V H of one polypeptide chain is associated with the V L of another polypeptide chain to thereby form a trimeric protein (a triabody).
  • a V H of a first polypeptide chain is associated with the V L of a second polypeptide chain
  • the V H of the second polypeptide chain is associated with the V L of a third polypeptide chain
  • the V H of the third polypeptide is associated with the V L of the first polypeptide chain.
  • the V L and V H associate so as to form an antigen binding site, i.e., a Fv capable of specifically binding to one or more antigens.
  • the V L and V H can be the same in each polypeptide chain (i.e., to produce a monospecific triabody) or two of the V L and two of the V H can be the same and the third of each different in the third polypeptide chain to produce a bispecific protein or the V L and V H can be different in each polypeptide chain so as to form a trivalent protein.
  • tetrabody shall be taken to mean a protein comprising four associated polypeptide chains, each polypeptide chain comprising the structure V L -X-V H or V H -X-V L , wherein V L is an immunoglobulin light chain variable region, V H is an immunoglobulin heavy chain variable region, X is a linker comprising insufficient residues to permit the V H and V L in a single polypeptide chain to associate (or form an Fv) or is absent, and wherein the V H of one polypeptide chain is associated with the V L of another polypeptide chain to thereby form a tetrameric protein (a tetrabody).
  • the V L and V H associate so as to form an antigen binding site, i.e., a Fv capable of specifically binding to one or more antigens.
  • a Fv capable of specifically binding to one or more antigens.
  • the V H of a first polypeptide chain is associated with the V L of a second polypeptide chain
  • the V H of the second polypeptide chain is associated with the V L of a third polypeptide chain
  • the V H of the third polypeptide chain is associated with the V L of a fourth polypeptide chain
  • the V H of the fourth polypeptide chain is associated with the V L of the first polypeptide chain.
  • the V L and V H can be the same in each polypeptide chain (i.e., to produce a monospecific tetrabody) or the V L and V H can be of one type in two polypeptide chains and a different type in the other two polypeptide chains to produce a bispecific tetrabody or the V L and V H can be different in each polypeptide chain so as to form a tetraspecific tetrabody.
  • these proteins comprise a polypeptide chain in which a V H and a V L are linked directly or using a linker that is of insufficient length to permit the V H and V L to associate.
  • the V H and V L can be positioned in any order, i.e., V L -V H or V H -V L .
  • V H and V L are readily obtained, e.g., by isolating nucleic acid encoding these polypeptide chains from a cell expressing an immunoglobulin comprising one or more variable region(s) of interest (including an antibody or a chimeric antibody or a humanized antibody or a human antibody) or from a recombinant library expressing V H and V L polypeptide chains (e.g., a scFv library, e.g., as described in EP0239400 or US4946778).
  • the V H and/or V L can then readily be modified to include the requisite cysteine residues as described herein according to any embodiment.
  • Proteins comprising V H and V L associate to form diabodies, triabodies and/or tetrabodies depending on the length of the linker (if present) and/or the order of the V H and V L domains.
  • the linker comprises 12 or fewer amino acids.
  • X is a linker
  • a linker having 3-12 residues generally results in formation of diabodies
  • a linker having 1 or 2 residues or where a linker is absent generally results in formation of triabodies.
  • Linkers for use in fusion proteins are known in the art. Linker sequence composition could affect the folding stability of a fusion protein. By indirect fusion of proteins through a linker not related to the fused proteins, the steric hindrance between the two proteins is avoided and the freedom degree for the linking is achieved.
  • linker sequences with high propensity to adopt a- helix or ⁇ -strand structures, which could limit the flexibility of the protein and consequently its functional activity. Rather, a more desirable linker is a sequence with a preference to adopt extended conformation.
  • most currently designed linker sequences have a high content of glycine residues that force the linker to adopt loop conformation. Glycine is generally used in designed linkers because the absence of a ⁇ - carbon permits the polypeptide backbone to access dihedral angles that are energetically forbidden for other amino acids.
  • the linker is a glycine rich linker.
  • the linker is a glycine linker that additionally comprises alanine and/or serine.
  • Such linkers provide flexibility, enhance hydrophilicity and are relatively protease resistant, see, e.g., Kortt et a., 2001.
  • the conformational flexibility imparted by glycine may be important at the junction between C terminus of the protein and the N terminus of the linker. Accordingly, linkers that comprise glycine in the region adjacent to the C terminus of the protein are preferred. In this regard, this does not impart a requirement that the first amino acid residue of the linker need be a glycine.
  • a linker comprises the sequence Gly n -Pro-Gly n where n is a number between about 1 and about 5.
  • Preferred linkers include a sequence selected from the group consisting of G;
  • Diabodies and higher order multimers can also comprise proteins that are covalently linked, e.g., by virtue of a disulphide bond between the proteins, e.g., as described in WO2006/113665.
  • Multispecific diabodies and higher order multimers can be produced through the noncovalent association of two single chain fusion products comprising V H domain from one immunoglobulin connected by a short linker to the V L domain of another immunoglobulin, thereby forming two Fvs, each from a different immunoglobulin, see, for example, Hudson and Kortt (1999).
  • multispecific triabodies can be produced by noncovalent association of three single chain fusion proteins as follows: (i) a first protein comprising a V H domain from a first immunoglobulin connected by a short linker to the V L domain of a second immunoglobulin;
  • a third protein comprising a V H domain from the third immunoglobulin connected by a short linker to the V L domain of the first immunoglobulin.
  • the present invention contemplates a diabody, triabody, tetrabody or higher order multimer against any antigen or combination thereof, and is not to be construed to be limited to those that bind to a specific antigen. Exemplary antigens are described herein for the purposes of illustration and not limitation.
  • Exemplary publications describing diabodies, triabodies and/or tetrabodies include WO94/07921; WO98/44001; HoUiger et al (1993); Kortt et al (1997); Hudson and Kortt (1999); Le Gall et al (1999); Todorovska et al, (2001); Hollinger and Hudson (2005); and references cited therein.
  • Exemplary diabodies, triabodies and/or tetrabodies comprise a V H sequence set forth in amino acids 1-115 of SEQ ID NO: 59 or amino acids 1-129 of SEQ ID NO: 61 or amino acids 1-129 of SEQ ID NO: 63 or amino acids 1-129 of SEQ ID NO: 65, which are modified to include two or more cysteine residues in FR2 and/or FR3 as described herein, optionally with a N-terminal threonine/serine residue. .
  • Exemplary diabodies, triabodies and/or tetrabodies comprise a V L sequence set forth in amino acids 121-239 of SEQ ID NO: 59 or amino acids 135-262 of SEQ ID NO: 61 or amino acids 126-237 of SEQ ID NO: 63 or amino acids 135-262 of SEQ ID NO: 65, which are modified to include two or more cysteine residues in FR2 and/or FR3, optionally with a N-terminal threonine/serine residue.
  • the V L comprises a sequence set forth in :
  • Exemplary diabodies, triabodies and/or tetrabodies comprise a V H sequence set forth in amino acids 1-115 of SEQ ID NO: 59 or amino acids 1-129 of SEQ ID NO: 61 or amino acids 1-120 of SEQ ID NO: 63 or amino acids 1-129 of SEQ ID NO: 65, which are modified to include two or more cysteine residues in FR2 and/or FR3 as described herein, optionally with a N-terminal threonine/serine residue.
  • the V H comprises a sequence set forth in:
  • the V H and V L described in the foregoing paragraphs can be arranged in any order and linked by a suitable linker as described herein.
  • the linker preferably comprises the sequence GGGGS (SEQ ID NO: 57).
  • the linker preferably there is no linker or a single glycine residue.
  • a diabody binds to TAG72 and comprises at least one polypeptide chain comprising (and preferably two polypeptide chains each comprising) a sequence set forth in SEQ ID NO: 59 which are modified to include two or more cysteine residues in FR2 and/or FR3, optionally with a N-terminal threonine/serine residue.
  • a diabody comprises at least one polypeptide chain comprising (and preferably two polypeptide chains each comprising) a sequence set forth in SEQ ID NO: 101, 103, 105, 107, 109, 111, 113, 115, 117 or 119.
  • a triabody binds to TAG72 and comprises at least one polypeptide chain comprising (and preferably two or three polypeptide chains each comprising) a sequence set forth in SEQ ID NO: 121.
  • a diabody binds to Her2 and comprises at least one polypeptide chain comprising (and preferably two polypeptide chains each comprising) a sequence set forth in SEQ ID NO: 61 or 64 which are modified to include two or more cysteine residues in FR2 and/or FR3 and optionally a N-terminal threonine/serine residue.
  • a diabody comprises at least one polypeptide chain comprising (and preferably two polypeptide chains each comprising) a sequence set forth in one or more of SEQ ID NO: 127, 129, 141, 143, 145, 147 or 149.
  • a diabody binds to MUC1 and comprises at least one polypeptide chain comprising (and preferably two polypeptide chains each comprising) a sequence set forth in SEQ ID NO: 63 which are modified to include two or more cysteine residues in FR1 and/or FR2 and, optionally a N-terminal threonine/serine residue.
  • a diabody comprises at least one polypeptide chain comprising (and preferably two polypeptide chains each comprising) a sequence set forth in one or more of SEQ ID NO: 131, 133, 135, 137 or 139.
  • scFvs comprise V H and V L regions in a single polypeptide chain.
  • the polypeptide chain further comprises a polypeptide linker between the V H and V L which enables the scFv to form the desired structure for antigen binding (i.e., for the V H and V L of the single polypeptide chain to associate with one another to form a Fv).
  • the linker comprises in excess of 12 amino acid residues with (Gly 4 Ser) 3 being one of the more favored linkers for a scFv.
  • Exemplary scFvs comprise a VH and a VL as described above in relation to diabodies, triabodies and tetrabodies.
  • the scfv binds to TAG72.
  • the scFv comprises a sequence set forth in SEQ ID NO: 119.
  • the present invention also contemplates a disulfide stabilized Fv (or diFv or dsFv), in which a single cysteine residue is introduced into a FR of V H and a FR of V L and the cysteine residues linked by a disulfide bond to yield a stable Fv (see, for example, Brinkmann et al., 1993).
  • the present invention provides a dimeric scFv, i.e., a protein comprising two scFv molecules linked by a non-covalent or covalent linkage.
  • dimeric scFv examples include, for example, two scFvs linked to a leucine zipper domain (e.g., derived from Fos or Jun) whereby the leucine zipper domains associate to form the dimeric compound (see, for example, Kostelny 1992 or Kruif and Logtenberg, 1996).
  • two scFvs are linked by a peptide linker of sufficient length to permit both scFvs to form and to bind to an antigen, e.g., as described in US20060263367.
  • each scFv is modified to include a cysteine residue, e.g., in the linker region or at a terminus, and the scFvs are linked by a disulfide bond, e.g., as described in Albrecht et ah, (2004).
  • scFv Modified forms of scFv are also contemplated by the present invention, e.g., scFv comprising a linker modified to permit glycosylation, e.g., as described in US623322.
  • a minibody comprises the V H and V L domains of an immunoglobulin fused to the C H 2 and/or C H 3 domain of an immunoglobulin.
  • the minibody comprises a hinge region between the V H and a V L , sometimes this conformation is referred to as a Flex Minibody (Hu et al., 1996).
  • a minibody does not comprise a C H I or a CL.
  • the V H and V L domains are fused to the hinge region and the C H 3 domain of an immunoglobulin. Each of the regions may be derived from the same immunoglobulin.
  • the V H and V L domains can be derived from one immunoglobulin and the hinge and C H 2/C H 3 from another, or the hinge and C H 2/C H 3 can also be derived from different immunoglobulins.
  • the present invention also contemplates a multispecific minibody comprising a V H and V L from one immunoglobulin and a V H and a V L from another immunoglobulin. At least one of the variable regions of said minibody comprises cysteine residues in FR2 and/or FR3 as described herein. The skilled artisan will be readily able to produce a minibody of the invention using methods known in the art together with the teaching provided herein.
  • minibodies are small versions of whole immunoglobulins encoded in a single protein chain which retain the antigen binding region, the C H 3 domain (or a C H 2 domain) to permit assembly into a bivalent molecule and the immunoglobulin hinge to accommodate dimerization by disulfide linkages.
  • Exemplary minibodies and methods for their production are described, for example, in WO94/09817.
  • US5, 731,168 describes molecules in which the interface between a pair of Fv is engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture to thereby produce bi-specific proteins.
  • the preferred interface comprises at least a part of a C H 3 domain.
  • one or more small amino acid side chains from the interface of the first protein are replaced with larger side chains ⁇ e.g., tyrosine or tryptophan).
  • Compensatory "cavities" of identical or similar size to the large side chain(s) are created on the interface of the second protein by replacing large amino acid side chains with smaller ones (e.g., alanine or threonine).
  • Bispecific proteins comprising variable regions include cross-linked or
  • heteroconjugate proteins For example, one of the proteins in the heteroconjugate can be coupled to avidin, the other to biotin. Such proteins have, for example, been proposed to target immune system cells to unwanted cells (US4,676,980). Heteroconjugate proteins comprising variable regions may be made using any convenient cross-linking methods. Suitable cross-linking agents are known in the art, and are disclosed in US4,676,980, along with a number of cross-linking techniques.
  • Bispecific proteins comprising variable regions can also be prepared using chemical linkage.
  • Brennan (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab')2 fragments. These fragments are reduced in the presence of the dithiol complexing agent, sodium arsenite, to stabilize vicinal dithiols and prevent intermolecular disulfide formation.
  • the Fab' fragments generated are then converted to thionitrobenzoate (TNB) derivatives.
  • TAB thionitrobenzoate
  • One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB derivative to form the bispecific protein.
  • Additional variable region containing proteins include, for example, domain antibodies (dAbs) and fusions thereof (e.g., as described in US6248516), single chain Fab (e.g., Hust et al, 2007) or a Fab 3 (e.g., as described in EP19930302894).
  • dAbs domain antibodies
  • fusions thereof e.g., as described in US62485166
  • single chain Fab e.g., Hust et al, 2007
  • a Fab 3 e.g., as described in EP19930302894.
  • the present invention encompasses proteins comprising a variable region and a constant region (e.g., Fc) or a domain thereof, e.g., C H 2 and/or C H 3 domain.
  • the present invention provides a minibody (as discussed above) or a scFv-Fc fusion or a diabody-Fc fusion or a triabody-Fc fusion or a tetrabody-Fc fusion or a SCFC-C H 2 fusion or a diabody-Cii2 fusion or a triabody-Cn2 fusion or a tetrabody-Cn2 fusion or a SCFV-C H 3 fusion or a diabody-Cii3 fusion or a triabody-Cn3 fusion or a tetrabody-Cn3 fusion.
  • Any of these proteins may comprise a linker, preferably an immunoglobulin hinge region, between the variable region and the constant region or constant domain.
  • Hinge region includes the portion of a heavy chain molecule that joins the C H I domain to the C H 2 domain. This hinge region comprises approximately 25 residues and is flexible, thus allowing the two N-terminal antigen binding regions to move independently. Hinge regions can be subdivided into three distinct domains: upper, middle, and lower hinge domains (Roux et al. 1998).
  • C H 2 domain includes the portion of a heavy chain immunoglobulin molecule that extends, e.g., from between about positions 231-340 according to the Kabat EU numbering system. Two N-linked branched carbohydrate chains are generally interposed between the two CH 2 domains of an intact native IgG molecule.
  • a protein of the invention comprises a C H 2 domain derived from an IgGl molecule (e.g. a human IgGl molecule).
  • a protein of the invention comprises a C H 2 domain derived from an IgG4 molecule (e.g., a human IgG4 molecule).
  • C H 3 domain includes the portion of a heavy chain immunoglobulin molecule that extends approximately 110 residues from N-terminus of the C H 2 domain, e.g., from about position 341-446b (Kabat EU numbering system).
  • the C H 3 domain typically forms the C-terminal portion of the immunoglobulin.
  • additional domains may extend from C H 3 domain to form the C-terminal portion of the molecule (e.g. the C H 4 domain in the ⁇ chain of IgM and the e chain of IgE).
  • a protein of the invention comprises a C H 3 domain derived from an IgGl molecule (e.g., a human IgGl molecule).
  • a protein of the invention comprises a C H 3 domain derived from an IgG4 molecule (e.g., a human IgG4 molecule).
  • Constant domain sequences useful for producing the proteins of the present invention may be obtained from a number of different sources.
  • the constant region domain or portion thereof of the protein is derived from a human immunoglobulin. It is understood, however, that the constant region domain or portion thereof may be derived from an immunoglobulin of another mammalian species, including for example, a rodent (e.g. a mouse, rat, rabbit, guinea pig) or non-human primate (e.g. chimpanzee, macaque) species.
  • rodent e.g. a mouse, rat, rabbit, guinea pig
  • non-human primate e.g. chimpanzee, macaque
  • the constant region domain or portion thereof may be derived from any immunoglobulin class, including IgM, IgG, IgD, IgA and IgE, and any immunoglobulin isotype, including IgGl, IgG2, IgG3 and IgG4.
  • immunoglobulin class including IgM, IgG, IgD, IgA and IgE
  • immunoglobulin isotype including IgGl, IgG2, IgG3 and IgG4.
  • the human isotype IgGl is used.
  • constant region gene sequences e.g. human constant region gene sequences
  • Constant region domains can be selected having a particular effector function (or lacking a particular effector function) or with a particular modification to reduce immunogenicity.
  • effector function refers to the functional ability of the Fc region or portion thereof (e.g., C H 2 domain) to bind proteins and/or cells of the immune system and mediate various biological effects. Effector functions may be antigen-dependent or antigen-independent.
  • Antigen-dependent effector function refers to an effector function which is normally induced following the binding of an immunoglobulin to a corresponding antigen. Typical antigen-dependent effector functions include the ability to bind a complement protein (e.g. Clq). For example, binding of the C 1 component of complement to the Fc region can activate the classical complement system leading to the opsonisation and lysis of cell pathogens, a process referred to as complement-dependent cytotoxicity (CDC).
  • complement-dependent cytotoxicity CDC
  • FcRs Fc receptors
  • IgG gamma receptors, or Ig Rs
  • IgE epsilon receptors, or IgsRs
  • IgA alpha receptors, or IgaRs
  • IgM mu receptors, or ⁇ Rs
  • binding of immunoglobulin to Fc receptors on cell surfaces triggers a number of important and diverse biological responses including endocytosis of immune complexes, engulfment and destruction of immunoglobulin-coated particles or microorganisms (also called antibody-dependent phagocytosis, or ADCP), clearance of immune complexes, lysis of antibody-coated target cells by killer cells (called antibody-dependent cell-mediated cytotoxicity, or ADCC), release of inflammatory mediators, regulation of immune system cell activation, placental transfer and control of immunoglobulin production.
  • endocytosis of immune complexes also called antibody-dependent phagocytosis, or ADCP
  • ADCP antibody-dependent phagocytosis
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • the term "antigen-independent effector function” refers to an effector function which may be induced by an immunoglobulin, regardless of whether it has bound its corresponding antigen.
  • Typical antigen-independent effector functions include cellular transport, circulating half-life and clearance rates of immunoglobulins, and facilitation of purification.
  • a structurally unique Fc receptor the "neonatal Fc receptor” or “FcRn”, also known as the salvage receptor, plays a critical role in regulating half-life and cellular transport.
  • Other Fc receptors purified from microbial cells e.g. Staphylococcal Protein A or G are capable of binding to the Fc region with high affinity and can be used to facilitate the purification of the Fc-containing protein.
  • Constant region domains can be cloned, e.g., using the polymerase chain reaction and primers which are selected to amplify the domain of interest.
  • the cloning of immunoglobulin sequences is described in for example, in US5,658,570.
  • the protein of the invention may comprise any number of constant region domains of different types.
  • the constant region domains or portions thereof making up the constant region of a protein may be derived from different immunoglobulin molecules.
  • a protein may comprise a C H 2 domain or portion thereof derived from an IgGl molecule and a C H 3 region or portion thereof derived from an IgG3 molecule.
  • the protein of the invention comprises at least a region of an Fc sufficient to confer FcRn binding.
  • the portion of the Fc region that binds to FcRn comprises from about amino acids 282-438 of IgGl , according to Kabat numbering.
  • a protein of the invention comprises an altered synthetic constant region wherein or more constant region domains therein are partially or entirely deleted ("domain-deleted constant regions").
  • domain-deleted constant regions The present invention also encompasses modified Fc regions or parts there having altered, e.g., improved or reduced effector function.
  • mutant polypeptide comprises one or more conservative amino acid substitutions compared to a sequence set forth herein.
  • the polypeptide comprises 10 or fewer, e.g., 9 or 8 or 7 or 6 or 5 or 4 or 3 or 2 conservative amino acid substitutions.
  • a "conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain and/or hydropathicity and/or hydrophilicity.
  • a mutant protein has only, or not more than, one or two or three or four conservative amino acid changes when compared to a naturally occurring protein. Details of conservative amino acid changes are provided below. As the skilled person would be aware, such minor changes can reasonably be predicted not to alter the activity of the polypeptide when expressed in a recombinant cell
  • Families of amino acid residues having similar side chains have been defined in the art, including basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), ⁇ - branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).
  • basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g., aspart
  • the present invention also contemplates one or more insertions or deletions compared to a sequence set forth herein.
  • the polypeptide comprises 10 or fewer, e.g., 9 or 8 or 7 or 6 or 5 or 4 or 3 or 2 insertions and/or deletions.
  • the present invention contemplates positioning of cysteine residues in FR2 and/or FR3 at any site as described herein in any embodiment or example.
  • Exemplary cysteine residues contemplated by the present invention are depicted in Figures 6A and 6B.
  • the present invention provides an isolated protein comprising an immunoglobulin variable region comprising at least two cysteine residues positioned within framework region (FR) 1 , wherein the cysteine residues are positioned such that at least one of the residues is capable of being conjugated to a compound and wherein if at least one of the cysteine residues is not conjugated to a compound a disulphide bond is capable of forming between the cysteine residues.
  • FR framework region
  • the present invention provides an isolated protein comprising an immunoglobulin variable region comprising at least two cysteine residues positioned within framework region (FR) 1 , wherein the cysteine residues are positioned such that at least one of the residues is capable of being conjugated to a compound and wherein if at least two of the cysteine residues are not conjugated to a compound a disulphide bond is capable of forming between the cysteine residues.
  • FR framework region
  • the present invention provides an isolated protein comprising an immunoglobulin heavy chain variable region (V H ) and an immunoglobulin light chain variable region (V L ), wherein at least one of the variable regions comprises at least two cysteine residues positioned within framework region (FR) 1, wherein the cysteine residues are positioned such that at least one of the residues is capable of being conjugated to a compound and wherein if at least one of the cysteine residues is not conjugated to another compound a disulphide bond is capable of forming between the cysteine residues.
  • V H immunoglobulin heavy chain variable region
  • V L immunoglobulin light chain variable region
  • the present invention provides an isolated protein comprising an immunoglobulin heavy chain variable region (V H ) and an immunoglobulin light chain variable region (V L ), wherein at least one of the variable regions comprises at least two cysteine residues positioned within framework region (FR) 1, wherein the cysteine residues are positioned such that at least one of the residues is capable of being conjugated to a compound and wherein if at least two of the cysteine residues are not conjugated to another compound a disulphide bond is capable of forming between the cysteine residues.
  • V H immunoglobulin heavy chain variable region
  • V L immunoglobulin light chain variable region
  • At least two or the at least two cysteine residues are positioned such that they are capable of being conjugated to a compound.
  • the cysteine residues are positioned within a loop region of FR2 and/or FR3.
  • the term "loop region” shall be taken to mean a sequence of amino acids within FR2 or FR3 that provides flexibility for two regions and/or two amino acids of FR2 or FR3 to associate with or bind to one another (e.g., by virtue of a hydrogen bond), e.g., that provides sufficient flexibility for two amino acids in a beta sheet to associate with or bind to one another.
  • a loop region of FR2 and/or FR3 is not part of the CDR1 or CDR3.
  • cysteine residues in a FR2 and/or FR3 are positioned so as to permit formation of a disulfide bond between the residues.
  • positioned so as to permit formation of a disulphide bond shall be understood to mean that two cysteine residues are positioned within a protein such that when the protein folds they are sufficiently close for a disulphide bond to be formed between the residues.
  • the distance between two carbon atoms in two cysteine residues may be within about 6-7 A of one another or 2-9A of one another, such as about 6-7 A of one another or 3.5-6.8A of one another, e.g., about 4A of one another.
  • a protein of the invention comprises at least two cysteine residues positioned within FR2 and/or FR3, wherein the cysteine residues are within about 2-9A of one another, preferably, within about 6-7 A of one another.
  • cysteine residues are positioned at residues in a protein at which their side chains will be exposed to solvent.
  • Methods for determining solvent exposure or solvent accessible surface area include, for example, the Shrake-Rupley algorithm or the LCPO method.
  • a protein of the invention comprises at least two cysteine residues positioned within FR2 and/or FR3, wherein the cysteine residues are positioned such that their side chains (preferably their thiol groups) are exposed to solvent.
  • Exposed to solvent shall be understood to mean that the side chains of the cysteine residues are on the surface of a protein when folded such that they are capable of being in contact with a solvent in which the protein is present or suspended.
  • at least one (or one or both) of the side chains are sufficiently exposed to solvent such that a compound can be conjugated thereto.
  • the protein of the invention comprises at least two cysteine residues positioned at one or more of, preferably two or more of, preferably all of:
  • proteins of the present invention thus provide at least two cysteine residues positioned within FR2 and/or FR3 that can form a disulphide bond within FR2 and/or FR3 and which can alternatively be reduced for stoichiometric conjugation of compounds.
  • threading is a process of assigning the folding of the protein by threading (or comparing) its sequence to a library of potential structural templates (e.g., known structures of Fv or Fabs or FR2 and/or FR3 as described herein) by using a scoring function that incorporates the sequence as well as the local parameters such as secondary structure and solvent exposure (Rost et al.
  • the threading process starts from prediction of the secondary structure of the amino acid sequence and solvent accessibility for each residue of the query sequence.
  • the resulting one-dimensional (ID) profile of the predicted structure is threaded into each member of a library of known 3D structures.
  • the optimal threading for each sequence-structure pair is obtained using dynamic programming.
  • the overall best sequence-structure pair constitutes the predicted 3D structure for the query sequence. Threading is made relatively simple in the present case because of the number of Fv and Fab fragments of immunoglobulins for which the secondary structure has been solved.
  • cysteine residues are paired, i.e., combinations of two residues are arranged such that a disulphide bond can form between them.
  • a protein of the invention does not comprise a free thiol in FR2 and/or FR3 under non-reducing conditions and/or does not comprise a cysteine residue that is not linked to another cysteine residue or to a compound under non-reducing conditions.
  • the cysteine residues are positioned such that an intra-framework disulphide bond can form between them when they are not conjugated to a compound.
  • intra-framework disulphide bond shall be taken to mean that a disulphide bond is formed within a single framework region. For example, if two cysteine residues are positioned within FR2, an intrachain disulphide bond forms within FR2.
  • DNA encoding a protein comprising a variable region is isolated using standard methods in the art. For example, primers are designed to anneal to conserved regions within a variable region that flank the region of interest, and those primers are then used to amplify the intervening nucleic acid, e.g., by PCR. Suitable methods and/or primers are known in the art and/or described, for example, in Borrebaeck (ed), 1995 and/or Froyen et al., 1995. Suitable sources of template DNA for such amplification methods is derived from, for example, hybridomas, transfectomas and/or cells expressing proteins comprising a variable region, e.g., as described herein.
  • the DNA is modified to include cysteine residues at the requisite locations by any of a variety of methods known in the art. These methods include, but are not limited to, preparation by site-directed (or oligonucleotide- mediated) mutagenesis, PCR mutagenesis, and cassette mutagenesis of an earlier prepared DNA encoding the protein. Variants of recombinant proteins may be constructed also by restriction fragment manipulation or by overlap extension PCR with synthetic oligonucleotides. Mutagenic primers encode the cysteine codon replacement(s), for example include residues that make up a codon encoding cysteine (i.e., TGT or TGC). Standard mutagenesis techniques can be employed to generate DNA encoding such mutant DNA. General guidance can be found in Sambrook et al 1989; and/or Ausubel et al 1993.
  • Site-directed mutagenesis is one method for preparing substitution variants, i.e. mutant proteins. This technique is known in the art (see for example, Carter et al 1985; Ho et al 1989; and Kunkel 1987). Briefly, in carrying out site-directed mutagenesis of DNA, the starting DNA is altered by first hybridizing an oligonucleotide encoding the desired mutation (e.g., insertion of one or more cysteine encoding codons) to a single strand of such starting DNA. After hybridization, a DNA polymerase is used to synthesize an entire second strand, using the hybridized oligonucleotide as a primer, and using the single strand of the starting DNA as a template.
  • an oligonucleotide encoding the desired mutation e.g., insertion of one or more cysteine encoding codons
  • the oligonucleotide encoding the desired mutation is incorporated in the resulting double-stranded DNA.
  • Site-directed mutagenesis may be carried out within the gene expressing the protein to be mutagenized in an expression plasmid and the resulting plasmid may be sequenced to confirm the introduction of the desired cysteine replacement mutations.
  • Site-directed protocols and formats include commercially available kits, e.g. QuikChange® Multi Site-Directed Mutagenesis Kit (Stratagene, La Jolla, CA).
  • PCR mutagenesis is also suitable for making amino acid sequence variants of the starting protein. See Higuchi, 1990; Ito et al 1991; Bernhard et al 1994; and Vallette et al 1989. Briefly, when small amounts of template DNA are used as starting material in a PCR, primers that differ slightly in sequence from the corresponding region in a template DNA can be used to generate relatively large quantities of a specific DNA fragment that differs from the template sequence only at the positions where the primers differ from the template.
  • the starting material is the plasmid (or other vector) comprising the starting protein DNA to be mutated.
  • the codon(s) in the starting DNA to be mutated are identified.
  • the plasmid DNA is cut at these sites to linearize it.
  • a double-stranded oligonucleotide encoding the sequence of the DNA between the restriction sites but containing the desired mutation(s) is synthesized using standard procedures, wherein the two strands of the oligonucleotide are synthesized separately and then hybridized together using standard techniques.
  • This double-stranded oligonucleotide is referred to as the cassette.
  • This cassette is designed to have 5' and 3' ends that are compatible with the ends of the linearized plasmid, such that it can be directly ligated to the plasmid.
  • This plasmid now contains the mutated DNA sequence. Mutant DNA containing the encoded cysteine replacements can be confirmed by DNA sequencing.
  • Single mutations are also generated by oligonucleotide directed mutagenesis using double stranded plasmid DNA as template by PCR based mutagenesis (Sambrook and Russel, 2001; Zoller et al 1983; Zoller and Smith, 1982). Recombinant Expression
  • nucleic acid encoding same is preferably placed into expression vectors, which are then transfected into host cells, preferably cells that can produce a disulphide bridge or bond, such as E. coli cells, yeast cells, insect cells, or mammalian cells, such as simian COS cells, Chinese Hamster Ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of proteins in the recombinant host cells.
  • host cells preferably cells that can produce a disulphide bridge or bond, such as E. coli cells, yeast cells, insect cells, or mammalian cells, such as simian COS cells, Chinese Hamster Ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of proteins in the recombinant host cells.
  • host cells preferably cells that can produce a disulphide bridge or bond
  • E. coli cells preferably cells that can produce a disulphide bridge
  • nucleic acid encoding a protein of the invention is preferably inserted into an expression construct or replicable vector for further cloning (amplification of the DNA) or for expression in a cell-free system or in cells.
  • the nucleic acid is operably linked to a promoter,
  • promoter is to be taken in its broadest context and includes the transcriptional regulatory sequences of a genomic gene, including the TATA box or initiator element, which is required for accurate transcription initiation, with or without additional regulatory elements (e.g., upstream activating sequences, transcription factor binding sites, enhancers and silencers) that alter expression of a nucleic acid, e.g., in response to a developmental and/or external stimulus, or in a tissue specific manner.
  • promoter is also used to describe a recombinant, synthetic or fusion nucleic acid, or derivative which confers, activates or enhances the expression of a nucleic acid to which it is operably linked.
  • Preferred promoters can contain additional copies of one or more specific regulatory elements to further enhance expression and/or alter the spatial expression and/or temporal expression of said nucleic acid.
  • operably linked to means positioning a promoter relative to a nucleic acid such that expression of the nucleic acid is controlled by the promoter.
  • a nucleic acid encoding a protein of the invention is operably linked to a suitable promoter, e.g., a T7 promoter, and the resulting expression construct exposed to conditions sufficient for transcription and translation.
  • a suitable promoter e.g., a T7 promoter
  • Typical expression vectors for in vitro expression or cell-free expression have been described and include, but are not limited to the TNT T7 and TNT T3 systems (Promega), the pEXPl-DEST and pEXP2- DEST vectors (Invitrogen).
  • the vector components generally include, but are not limited to, one or more of the following: a signal sequence, a sequence encoding protein of the present invention (e.g., derived from the information provided herein), an enhancer element, a promoter, and a transcription termination sequence.
  • a signal sequence e.g., a sequence encoding protein of the present invention (e.g., derived from the information provided herein), an enhancer element, a promoter, and a transcription termination sequence.
  • exemplary signal sequences include prokaryotic secretion signals (e.g., pelB, alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II), yeast secretion signals (e.g., invertase leader, a factor leader, or acid phosphatase leader) or mammalian secretion signals (e.g., herpes simplex gD signal).
  • prokaryotic secretion signals e.g., pelB, alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II
  • yeast secretion signals e.g., invertase leader, a factor leader, or acid phosphatase leader
  • mammalian secretion signals e.g., herpes simplex gD signal.
  • promoters include those active in prokaryotes (e.g., phoA promoter , ⁇ -lactamase and lactose promoter systems, alkaline phosphatase, a tryptophan (trp) promoter system, and hybrid promoters such as the tac promoter). These promoter are useful for expression in prokaryotes including eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as Escherichia, e.g., E.
  • eubacteria such as Gram-negative or Gram-positive organisms
  • Enterobacteriaceae such as Escherichia, e.g., E.
  • the host is E. coli.
  • E. coli cloning host is E. coli 294 (ATCC 31,446), although other strains such as E. coli B, E. coli X 1776 (ATCC 31,537), and E. coli W3110 (ATCC 27,325), DH5a or DH10B are suitable.
  • Exemplary promoters active in mammalian cells include cytomegalovirus immediate early promoter (CMV-IE), human elongation factor 1-cc promoter (EF1), small nuclear RNA promoters (Ula and Ulb), cc-myosin heavy chain promoter, Simian virus 40 promoter (SV40), Rous sarcoma virus promoter (RSV), Adenovirus major late promoter, ⁇ -actin promoter; hybrid regulatory element comprising a CMV enhancer/ ⁇ - actin promoter or an immunoglobulin promoter or active fragment thereof.
  • CMV-IE cytomegalovirus immediate early promoter
  • EF1 human elongation factor 1-cc promoter
  • EF1 small nuclear RNA promoters
  • Ula and Ulb small nuclear RNA promoters
  • cc-myosin heavy chain promoter Simian virus 40 promoter (SV40), Rous sarcoma virus promoter (RSV), Adenovirus major late promoter, ⁇ -
  • Examples of useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture; baby hamster kidney cells (BHK, ATCC CCL 10); or Chinese hamster ovary cells (CHO).
  • COS-7 monkey kidney CV1 line transformed by SV40
  • human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture
  • baby hamster kidney cells BHK, ATCC CCL 10
  • Chinese hamster ovary cells CHO
  • Typical promoters suitable for expression in yeast cells such as for example a yeast cell selected from the group comprising Pichia pastoris, Saccharomyces cerevisiae and S. pombe, include, but are not limited to, the ADH1 promoter, the GAL1 promoter, the GAL4 promoter, the CUPl promoter, the PH05 promoter, the nmt promoter, the RPR1 promoter, or the TEF1 promoter.
  • Typical promoters suitable for expression in insect cells include, but are not limited to, the OPEI2 promoter, the insect actin promoter isolated from Bombyx muri, the Drosophila sp. dsh promoter (Marsh et al 2000) and the inducible metallothionein promoter.
  • Preferred insect cells for expression of recombinant proteins include an insect cell selected from the group comprising, BT1-TN-5B1-4 cells, and Spodoptera frugiperda cells (e.g., sfl9 cells, sf21 cells).
  • Suitable insects for the expression of the nucleic acid fragments include but are not limited to Drosophila sp. The use of S. frugiperda is also contemplated.
  • Means for introducing the isolated nucleic acid molecule or a gene construct comprising same into a cell for expression are known to those skilled in the art. The technique used for a given cell depends on the known successful techniques. Means for introducing recombinant DNA into cells include microinjection, trans fection mediated by DEAE-dextran, transfection mediated by liposomes such as by using lipofectamine (Gibco, MD, USA) and/or cellfectin (Gibco, MD, USA), PEG-mediated DNA uptake, electroporation and microparticle bombardment such as by using DNA-coated tungsten or gold particles (Agracetus Inc., WI, USA) amongst others.
  • the host cells used to produce the protein of this invention may be cultured in a variety of media, depending on the cell type used.
  • Commercially available media such as Ham's F10 (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPM1-1640 (Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma) are suitable for culturing mammalian cells.
  • Media for culturing other cell types discussed herein are known in the art.
  • a protein of the present invention is preferably isolated.
  • isolated is meant that the protein is substantially purified or is removed from its naturally-occurring environment, e.g., is in a heterologous environment.
  • substantially purified is meant the protein is substantially free of contaminating agents, e.g., at least about 70% or 75% or 80% or 85% or 90% or 95% or 96% or 97% or 98% or 99% free of contaminating agents.
  • the protein of the invention can be produced intracellularly, in the periplasmic space, or directly secreted into the medium. If the protein is produced intracellularly, as a first step, the particulate debris, either host cells or lysed fragments, is removed, for example, by centrifugation or ultrafiltration. Carter et al. (1992) describe a procedure for isolating antibodies which are secreted to the periplasmic space of E. coli.
  • cell paste is thawed in the presence of sodium acetate (pH 3.5), EDTA, and phenylmethylsulfonylfluoride (PMSF) over about 30 min.
  • PMSF phenylmethylsulfonylfluoride
  • Cell debris can be removed by centrifugation.
  • supernatants from such expression systems are generally first concentrated using a commercially available protein concentration filter, for example, an Amicon or Millipore Pellicon ultrafiltration unit.
  • a protease inhibitor such as PMSF may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.
  • the protein prepared from the cells can be purified using, for example, hydroxyl apatite chromatography, gel electrophoresis, dialysis, and affinity chromatography, with affinity chromatography being the preferred purification technique.
  • affinity chromatography is the preferred purification technique.
  • the suitability of protein A as an affinity ligand depends on the species and isotype of any immunoglobulin Fc domain that is present in the protein (if present at all). Protein A can be used to purify immunoglobulins that are based on human ⁇ , ⁇ 2, or ⁇ 4 heavy chains (Lindmark et al. 1983). Protein G is recommended for all mouse isotypes and for human ⁇ 3 (Guss et al. 1986).
  • affinity purification can be performed using the antigen or epitopic determinant to which a variable region in a protein of the invention binds or was raised.
  • the matrix to which the affinity ligand is attached is most often agarose, but other matrices are available.
  • Mechanically stable matrices such as controlled pore glass or poly(styrenedivinyl)benzene allow for faster flow rates and shorter processing times than can be achieved with agarose.
  • a protein of the invention can be modified to include a tag to facilitate purification or detection, e.g., a poly-histidine tag, e.g., a hexa-histidine tag, or a influenza virus hemagglutinin (HA) tag, or a Simian Virus 5 (V5) tag, or a FLAG tag, or a glutathione S-transferase (GST) tag.
  • the tag is a hexa-his tag.
  • the resulting protein is then purified using methods known in the art, such as, affinity purification.
  • a protein comprising a hexa-his tag is purified by contacting a sample comprising the protein with nickel-nitrilotriacetic acid (Ni-NTA) that specifically binds a hexa-his tag immobilized on a solid or semisolid support, washing the sample to remove unbound protein, and subsequently eluting the bound protein.
  • Ni-NTA nickel-nitrilotriacetic acid
  • a ligand or antibody that binds to a tag is used in an affinity purification method.
  • the mixture comprising the protein of the invention and contaminants may be subjected to low pH hydrophobic interaction chromatography.
  • a protein of the present invention is readily synthesized from its determined amino acid sequence using standard techniques, e.g., using BOC or FMOC chemistry.
  • Synthetic peptides are prepared using known techniques of solid phase, liquid phase, or peptide condensation, or any combination thereof, and can include natural and/or unnatural amino acids.
  • Amino acids used for peptide synthesis may be standard Boc (Na-amino protected Na-t-butyloxycarbonyl) amino acid resin with the deprotecting, neutralization, coupling and wash protocols of the original solid phase procedure of Merrifield, 1963, or the base-labile Na-amino protected 9-fluorenylmethoxycarbonyl (Fmoc) amino acids described by Carpino and Han, 1972.
  • Boc Na- amino protected amino acids can be obtained from various commercial sources, such as, for example, Fluka, Bachem, Advanced Chemtech, Sigma, Cambridge Research Biochemical, Bachem, or Peninsula Labs. Conjugates
  • the present invention also provides conjugates of proteins described herein according to any embodiment.
  • compounds to which a protein can be conjugated are the compound is selected from the group consisting of a radioisotope, a detectable label, a therapeutic compound, a colloid, a toxin, a nucleic acid, a peptide, a protein, a compound that increases the half life of the protein in a subject and mixtures thereof .
  • exemplary therapeutic agents include, but are not limited to an anti- angiogenic agent, an anti-neovascularization and/or other vascularization agent, an antiproliferative agent, a pro-apoptotic agent, a chemotherapeutic agent or a therapeutic nucleic acid.
  • a toxin includes any agent that is detrimental to (e.g., kills) cells.
  • kills any agent that is detrimental to (e.g., kills) cells.
  • these classes of drugs which are known in the art, and their mechanisms of action, see Goodman et al., Goodman and Gilman's The Pharmacological Basis of Therapeutics, 8th Ed., Macmillan Publishing Co., 1990. Additional techniques relevant to the preparation of immunoglobulin-immunotoxin conjugates are provided in for instance Vitetta (1993) and US 5,194,594.
  • Exemplary toxins include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha- sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin and the tricothecenes. See, for example, WO 93/21232.
  • Suitable chemotherapeutic agents for forming immunoconjugates of the present invention include auristatins and maytansines, taxol, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1-de-hydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and puromycin, antimetabolites (such as methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, fludarabin, 5-fluorouracil, decarbazine, hydroxyurea, asparaginase, gemcitabine, cladribine), alky
  • angiogenesis inhibitors include, but are not limited to, urokinase inhibitors, matrix metalloprotease inhibitors (such as marimastat, neovastat, BAY 12-9566, AG 3340, BMS-275291 and similar agents), inhibitors of endothelial cell migration and proliferation (such as TNP-470, squalamine, 2-methoxyestradiol, combretastatins, endostatin, angiostatin, penicillamine, SCH66336 (Schering-Plough Corp, Madison, NJ), Rl 15777 (Janssen Pharmaceutica, Inc, Titusville, NJ) and similar agents), antagonists of angiogenic growth factors (such as such as ZD6474, SU6668, antibodies against angiogenic agents and/or their receptors (such as VEGF, bFGF, and angiopoietin-1), thalidomide, thalidomide analogs (such as
  • inhibitors of angiogenesis, neovascularization, and/or other vascularization are anti- angiogenic heparin derivatives and related molecules (e.g., heperinase III), temozolomide, NK4, macrophage migration inhibitory factor (MIF), cyclooxygenase-2 inhibitors, inhibitors of hypoxia-inducible factor 1, anti-angiogenic soy isoflavones, oltipraz, fumagillin and analogs thereof, somatostatin analogues, pentosan polysulfate, tecogalan sodium, dalteparin, tumstatin, thrombospondin, NM-3, combrestatin, canstatin, avastatin, antibodies against other relevant targets (such as anti-alpha-v/beta- 3 integrin and anti-kininostatin mAbs) and similar agents.
  • heperinase III anti-angiogenic heparin derivatives and related molecules
  • a protein as described herein is conjugated or linked to another protein, including another protein of the invention or a protein comprising an immunoglobulin variable region, such as an immunoglobulin or a protein derived therefrom, e.g., as described herein.
  • Other proteins are not excluded. Additional proteins will be apparent to the skilled artisan and include, for example, an immunomodulator or a half-life extending protein or a peptide or other protein that binds to serum albumin amongst others.
  • immunomodulators include cytokines and chemokines.
  • cytokine is a generic term for proteins or peptides released by one cell population which act on another cell as intercellular mediators.
  • cytokines include lymphokines, monokines, growth factors and traditional polypeptide hormones.
  • cytokines include growth hormones such as human growth hormone, N-methionyl human growth hormone, and bovine growth hormone; parathyroid hormone, thyroxine, insulin, proinsulin, relaxin, prorelaxin, glycoprotein hormones such as follicle stimulating hormone (FSH), thyroid stimulating hormone (TSH) and luteinizing hormone (LH), hepatic growth factor; prostaglandin, fibroblast growth factor, prolactin, placental lactogen, OB protein, tumor necrosis factor-a and - ⁇ ; mullerian-inhibiting substance, gonadotropin-associated peptide, inhibin, activin, vascular endothelial growth factor, integrin, thrombopoietin (TPO), nerve growth factors such as NGF-B, platelet-growth factor, transforming growth factors (TGFs) such as TGF-a and TGF- ⁇ , insulin-like growth factor-I or -II, erythropoietin (IL)
  • Chemokines generally act as chemoattractants to recruit immune effector cells to the site of chemokine expression.
  • Chemokines include, but are not limited to, RANTES, MCAF, MlPl-alpha or MIPl-Beta. The skilled artisan will recognize that certain cytokines are also known to have chemoattractant effects and could also be classified under the term chemokines.
  • radionuclides are available for the production of radioconjugated proteins. Examples include, but are not limited to, low energy radioactive nuclei (e.g., suitable for diagnostic purposes), such as 13 C, 15 N, 2 H, 125 1, 123 1 , "Tc, 43 K, 52 Fe, 67 Ga, 68 Ga, l u In and the like.
  • the radionuclide is a gamma, photon, or positron- emitting radionuclide with a half-life suitable to permit activity or detection after the elapsed time between administration and localization to the imaging site.
  • the present invention also encompasses high energy radioactive nuclei (e.g., for therapeutic purposes), such as 125 1 , 131 1, 123 1, m In, 105 Rh, 153 Sm, 67 Cu, 67 Ga, 166 Ho, 177 Lu, 186 Re and 188 Re.
  • high energy radioactive nuclei e.g., for therapeutic purposes
  • isotopes typically produce high energy a- or ⁇ -particles which have a short path length.
  • Such radionuclides kill cells to which they are in close proximity, for example neoplastic cells to which the conjugate has attached or has entered. They have little or no effect on non-localized cells and are essentially non-immunogenic.
  • high-energy isotopes may be generated by thermal irradiation of an otherwise stable isotope, for example as in boron neutron -capture therapy (Guan et ah, 1998).
  • the protein is conjugated to a "receptor” (such as streptavidin) for utilization in cell pretargeting wherein the conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand” (e.g., avidin) that is conjugated to a therapeutic agent (e.g., a radionucleotide).
  • a "receptor” such as streptavidin
  • a "ligand” e.g., avidin
  • a therapeutic agent e.g., a radionucleotide
  • the proteins of the present invention can be modified to contain additional nonproteinaceous moieties that are known in the art and readily available.
  • the moieties suitable for derivatization of the protein are water soluble polymers.
  • water soluble polymers include, but are not limited to, polyethylene glycol (PEG), polyvinyl alcohol (PVA), copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly-1, 3-dioxolane, poly-1, 3, 6-trioxane, ethyl ene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)polyethylene glycol, propropylene glycol (PPG) homopolymers, prolypropylene oxide/ethylene oxide co-polymers, polyoxyethylated
  • the polymer molecules are typically characterized as having for example from about 2 to about 1000, or from about 2 to about 300 repeating units.
  • water-soluble polymers including but not limited to PEG, poly(ethylene oxide) (PEO), polyoxyethylene (POE), polyvinyl alcohols, hydroxyethyl celluloses, or dextrans, are commonly conjugated to proteins to increase stability or size, etc., of the protein.
  • PEG, PEO or POE refers to an oligomer or polymer of ethylene oxide.
  • these oligomers or polymers are produced by, e.g., anionic ring opening polymerization of ethylene oxide initiated by nucleophilic attack of a hydroxide ion on the epoxide ring.
  • PEG polymethoxy PEG
  • Preferred PEGs are monodisperse or polydisperse, preferably monodisperse.
  • PEG can be polydisperse or monodisperse.
  • Polydisperse PEG comprises a mixture of PEGs having different molecular weights.
  • reference to a specific molecular weight will be understood to refer to the number average molecular weight of PEGs in the mixture.
  • the size distribution is characterized statistically by its weight average molecular weight (MW) and its number average molecular weight (Mn), the ratio of which is called the polydispersity index (Mw/Mn). MW and Mn are measured, in certain aspects, by mass spectroscopy.
  • PEG-protein conjugates particularly those conjugated to PEG larger than 1 KD, exhibit a range of molecular weights due to a polydisperse nature of the parent PEG molecule.
  • mPEG2K Small ME-020HS, NOF
  • actual molecular masses are distributed over a range of 1.5— 3.0 KD with a polydispersity index of 1.036.
  • monodisperse PEG comprises a mixture of PEGs comprising substantially the same molecular weight.
  • Monodisperse PEGs are commercially available, e.g., from Polypure AS, Norway.
  • the average or preferred molecular weight of the PEG will range from about 500 Da to about 200 kDa.
  • the molecular weight of the PEG is from about 1 to about 100 kDa, from about 1.5 to about 50 kDa, from about 1.5 to about 10 kDa, from about 1.5 kDa to about 5 kDa, from about 1.5 kDa to about 4 kDa, from about 1.5 to about 2 kDa.
  • the PEG is monodisperse and has a molecular weight of about 500 Da.
  • the PEG has a molecular weight of about 1.5 kDa.
  • the PEG has a molecular weight of about 2 kDa.
  • the PEG comprises a reactive group, such as a maleimide group.
  • the PEG is PEG 24 -maleimide.
  • the physiologically acceptable polymer molecule is not limited to a particular structure and is, in various aspects, linear (e.g. alkoxy PEG or bifunctional PEG), branched or multi-armed (e.g. forked PEG or PEG attached to a polyol core), dentritic, or with degradable linkages.
  • the internal structure of the polymer molecule is organized in any number of different patterns and is selected from the group consisting of homopolymer, alternating copolymer, random copolymer, block copolymer, alternating tripolymer, random tripolymer, and block tripolymer.
  • the number of polymers attached to the protein may vary, and if more than one polymer is attached, they can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the protein to be improved, whether the protein derivative will be used in a therapy under defined conditions, etc.
  • the polymer is PEG.
  • a polymer e.g., PEG
  • PEG polymer having a functional group at one or both termini
  • a spacer moiety is included between the compound and the protein to which it is conjugated.
  • the spacer moieties of the invention may be cleavable or non-cleavable.
  • the cleavable spacer moiety is a redox-cleavable spacer moiety, such that the spacer moiety is cleavable in environments with a lower redox potential, such the cytoplasm and other regions with higher concentrations of molecules with free sulfliydryl groups.
  • Examples of spacer moieties that may be cleaved due to a change in redox potential include those containing disulfides.
  • the cleaving stimulus can be provided upon intracellular uptake of the conjugated protein where the lower redox potential of the cytoplasm facilitates cleavage of the spacer moiety.
  • a decrease in pH causes cleavage of the spacer to thereby release of the compound into a target cell.
  • a decrease in pH is implicated in many physiological and pathological processes, such as endosome trafficking, tumor growth, inflammation, and myocardial ischemia. The pH drops from a physiological 7.4 to 5-6 in endosomes or 4-5 in lysosomes.
  • acid sensitive spacer moieties which may be used to target lysosomes or endosomes of cancer cells, include those with acid- cleavable bonds such as those found in acetals, ketals, orthoesters, hydrazones, trityls, cis-aconityls, or thiocarbamoyls (see for example, US Pat. Nos. 4,569,789, 4,631,190, 5,306,809, and 5,665,358).
  • Other exemplary acid-sensitive spacer moieties comprise dipeptide sequences Phe-Lys and Val-Lys.
  • Cleavable spacer moieties may be sensitive to biologically supplied cleaving agents that are associated with a particular target cell, for example, lysosomal or tumor- associated enzymes.
  • linking moieties that can be cleaved enzymatically include, but are not limited to, peptides and esters.
  • Exemplary enzyme cleavable linking moieties include those that are sensitive to tumor-associated proteases such as Cathepsin B or plasmin.
  • Cathepsin B cleavable sites include the dipeptide sequences valine-citrulline, phenylalanine-lysine and/or valine-alanine.
  • Reagents for such conjugation typically bear reactive functionality which may react (i) directly with a cysteine thiol of a cysteine to form the labeled protein, (ii) with a linker reagent to form a linker-label intermediate, or (iii) with a linker protein to form the labeled protein.
  • the bifunctional linker comprises a thiol modification group for covalent linkage to the cysteine residue(s) and at least one attachment moiety (e.g., a second thiol modification moiety) for covalent or non-covalent linkage to the compound.
  • Cysteine thiol groups are nucleophilic and capable of reacting to form covalent bonds with electrophilic groups on linker reagents or compound-linker intermediates or drugs including: (i) active esters such as NHS esters, HOBt esters, haloformates, and acid halides; (ii) alkyl and benzyl halides, such as haloacetamides; (iii) aldehydes, ketones, carboxyl, and maleimide groups; and (iv) disulfides, including pyridyl disulfides, via sulfide exchange.
  • active esters such as NHS esters, HOBt esters, haloformates, and acid halides
  • alkyl and benzyl halides such as haloacetamides
  • aldehydes ketones, carboxyl, and maleimide groups
  • disulfides including pyridyl disulfides, via sulfide exchange.
  • Nucleophilic groups on a compound or linker include, but are not limited to amine, thiol, hydroxyl, hydrazide, oxime, hydrazine, thiosemicarbazone, hydrazine carboxylate, and arylhydrazide groups capable of reacting to form covalent bonds with electrophilic groups on linker moieties and linker reagents.
  • Preferred labelling reagents include maleimide, haloacetyl, iodoacetamide succinimidyl ester, isothiocyanate, sulfonyl chloride, 2,6-dichlorotriazinyl, pentafluorophenyl ester, and phosphoramidite, although other functional groups can also be used.
  • Maytansine may, for example, be converted to May-SSCH3, which can be reduced to the free thiol, May-SH, and reacted with a protein of the invention (Chari et al, 1992) to generate a maytansinoid-immunoconjugate with a disulfide linker.
  • Maytansinoid conjugates with disulfide linkers have been reported (WO 04/016801; US 6884874; and WO 03/068144).
  • the disulfide linker SPP is constructed with linker reagent N-succinimidyl 4-(2-pyridylthio) pentanoate.
  • N-hydroxysuccinimidyl ester of a carboxyl group substituent of a compound, e.g. biotin or a fluorescent dye or a toxin or a protein.
  • the NHS ester of the compound may be preformed, isolated, purified, and/or characterized, or it may be formed in situ and reacted with a nucleophilic group of the protein.
  • the carboxyl form of the compound is activated by reacting with some combination of a carbodiimide reagent, e.g. dicyclohexylcarbodiimide, diisopropylcarbodiimide, or a uranium reagent, e.g.
  • TSTU (0-(N-Succinimidyl)-N,N,N',N'-tetramethyluronium tetrafluoroborate
  • HBTU O- benzotriazol-l-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate
  • HATU O- (7-azabenzotriazol-l-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate
  • an activator such as 1 -hydroxy benzotriazole (HOBt)
  • HOBt 1 -hydroxy benzotriazole
  • the compound and the protein may be coupled by in situ activation of the compound and reaction with the protein to form the conjugate in one step.
  • Other activating and coupling reagents include TBTU (2-(lH- benzotriazo-l-yl)-l-l,3,3-tetramethyluronium hexafluorophosphate), TFFH ( ⁇ , ⁇ ', ⁇ ', ⁇ '- tetramethyluronium 2-fluoro- hexafluorophosphate), PyBOP (benzotriazole- 1-yl-oxy- tris-pyrrolidino-phosphonium hexafluorophosphate, EEDQ (2-ethoxy- 1- ethoxycarbonyl-l,2-dihydro-quinoline), DCC (dicyclohexylcarbodiimide); DIPCDI (diisopropylcarbodiimide), MSNT (l-(mesitylene-2-sulfonyl)-3-nitro-lH-l
  • Additional conjugation methods include, for example, the use of maleimides, iodoacetimides or haloacetyl/alkyl halides, aziridne, acryloyl derivatives to react with the thiol of a cysteine to produce a thioeter that is reactive with a compound (e.g., Schelte et al., 2000 (use of maleimides); Reddy et al., 1988 (use of maleimide derivatives); Ramseier and Chang, 1994 (use of iodacetamide); Eisen et al., 1953 (use of 2,4-dinitrobenzeneulfonic acid); Grossman et al., 1981 (use of aziridine); or Yem et al., 1992 (use of acryloyl derivatives).
  • a compound e.g., Schelte et al., 2000 (use of maleimides); Reddy et al., 1988 (use of maleimide derivatives); Ramseier and Chang
  • Disulphide exchange of a free thiol with an activated piridyldisulphide is also useful for producing a conjugate (King et al., 1978 and references cited therein, e.g., use of 5-thio-2-nitrobenzoic (TNB) acid).
  • a maleimide is used.
  • proteins of the invention may be directly labeled (such as through iodination) or may be labeled indirectly through the use of a chelating agent.
  • a chelating agent is covalently attached to a protein and at least one radionuclide is associated with the chelating agent.
  • Such chelating agents are typically referred to as bifunctional chelating agents as they bind both the protein and the radioisotope.
  • Exemplary chelating agents comprise 1- isothiocycmatobenzyl- 3-methyldiothelene triaminepentaacetic acid ("MX-DTPA",) and cyclohexyl diethylenetriamine pentaacetic acid (“CHX-DTPA”) derivatives, or DOTA.
  • Linker reagents such as DOTA-maleimide (4-maleimidobutyramidobenzyl- DOTA) can be prepared by the reaction of aminobenzyl-DOTA with A- maleimidobutyric acid (Fluka) activated with isopropylchloroformate (Aldrich), following the procedure of Axworthy et al, (2000).
  • DOTA-maleimide reagents react with free cysteine amino acids of the proteins of the invention and provide a metal complexing ligand thereon (Lewis et al, 1998).
  • Chelating linker labelling reagents such as DOTA-NHS (l,4,7,10-tetraazacyclododecane-l,4,7,10-tetraacetic acid mono (N- hydroxysuccinimide ester) are commercially available (Macrocyclics, Dallas, TX).
  • the protein of the invention Prior to linkage it is preferred that the protein of the invention is made reactive for conjugation with linker reagents by treatment with a reducing agent such as DTT (Cleland's reagent, dithiothreitol) or TCEP (tris(2-carboxyethyl)phosphine hydrochloride; Getz et al, 1999; Soltec Ventures, Beverly, MA). Disulfide bonds can be re-established between cysteine residues that are not required for linkage with dilute (200 nM) aqueous copper sulfate (CuS0 4 ) at room temperature. Other oxidants, i.e. oxidizing agents, and oxidizing conditions, which are known in the art may be used. Ambient air oxidation is also effective. This mild, partial reoxidation step forms intrachain disulfides efficiently with high fidelity. Conjugation to Threonine/Serine
  • a reducing agent such as DTT (Cleland'
  • a spacer moiety is included between the compound and the protein to which it is conjugated.
  • the spacer moieties of the invention may be cleavable or non-cleavable.
  • the cleavable spacer moiety is a redox-cleavable spacer moiety, such that the spacer moiety is cleavable in environments with a lower redox potential, such the cytoplasm and other regions with higher concentrations of molecules with free sulfliydryl groups.
  • Examples of spacer moieties that may be cleaved due to a change in redox potential include those containing disulfides.
  • the cleaving stimulus can be provided upon intracellular uptake of the conjugated protein where the lower redox potential of the cytoplasm facilitates cleavage of the spacer moiety.
  • a decrease in pH causes cleavage of the spacer to thereby release of the compound into a target cell.
  • a decrease in pH is implicated in many physiological and pathological processes, such as endosome trafficking, tumour growth, inflammation, and myocardial ischemia. The pH drops from a physiological 7.4 to 5-6 in endosomes or 4-5 in lysosomes.
  • acid sensitive spacer moieties which may be used to target lysosomes or endosomes of cancer cells, include those with acid-cleavable bonds such as those found in acetals, ketals, orthoesters, hydrazones, trityls, cis-aconityls, or thiocarbamoyls (see for example, US Pat. No's. 4,569,789, 4,631,190, 5,306,809, and 5,665,358).
  • Other exemplary acid-sensitive spacer moieties comprise dipeptide sequences Phe-Lys and Val-Lys.
  • Cleavable spacer moieties may be sensitive to biologically supplied cleaving agents that are associated with a particular target cell, for example, lysosomal or tumor- associated enzymes.
  • linking moieties that can be cleaved enzymatically include, but are not limited to, peptides and esters.
  • Exemplary enzyme cleavable linking moieties include those that are sensitive to tumor-associated proteases such as Cathepsin B or plasmin.
  • Cathepsin B cleavable sites include the dipeptide sequences valine-citrulline and phenylalanine-lysine.
  • the spacer moieties of the invention may be cleavable or non-cleavable.
  • the cleavable spacer moiety is a redox- cleavable spacer moiety, such that the spacer moiety is cleavable in environments with a lower redox potential, such the cytoplasm and other regions with higher concentrations of molecules with free sulfhydryl groups.
  • Examples of spacer moieties that may be cleaved due to a change in redox potential include those containing disulfides.
  • the cleaving stimulus can be provided upon intracellular uptake of the conjugated protein where the lower redox potential of the cytoplasm facilitates cleavage of the spacer moiety.
  • the molecule can be activated to facilitate its binding to amines or imidazoles, a carboxylic group, a hydroxyl group or a sulfhydryl group.
  • a decrease in pH causes cleavage of the spacer to thereby release of the compound into a target cell.
  • a decrease in pH is implicated in many physiological and pathological processes, such as endosome trafficking, tumour growth, inflammation, and myocardial ischemia. The pH drops from a physiological 7.4 to 5-6 in endosomes or 4-5 in lysosomes.
  • acid sensitive spacer moieties which may be used to target lysosomes or endosomes of cancer cells, include those with acid-cleavable bonds such as those found in acetals, ketals, orthoesters, hydrazones, trityls, cis-aconityls, or thiocarbamoyls (see for example, US Pat. No's. 4,569,789, 4,631,190, 5,306,809, and 5,665,358).
  • Other exemplary acid-sensitive spacer moieties comprise dipeptide sequences Phe-Lys and Val-Lys.
  • Cleavable spacer moieties may be sensitive to biologically supplied cleaving agents that are associated with a particular target cell, for example, lysosomal or tumor- associated enzymes.
  • linking moieties that can be cleaved enzymatically include, but are not limited to, peptides and esters.
  • Exemplary enzyme cleavable linking moieties include those that are sensitive to tumor-associated proteases such as Cathepsin B or plasmin.
  • Cathepsin B cleavable sites include the dipeptide sequences valine-citrulline and phenylalanine-lysine.
  • Abuchowski et al (1977) activated PEG using cyanuric chloride to produce a PEG dichlorotriazine derivative.
  • This derivative can react with multiple functional nucleophilic functional groups, such as lysine, serine, tyrosine, cysteine and histidine.
  • a modified form of this protocol produced PEG-chlorotriazine, which has lower reactivity and conjugates more selectively with lysine or cysteine residues (Mutsushima et al, 1980).
  • succinimidyl carbonate PEG S-PEG; Zalipsky et al, 1992
  • benzotriazole carbonate PEG BTC-PEG; US 5,560,234. Both of these compounds react preferentially with lysine residues to form carbamate linkages, however are also known to react with hystidine and tyrosine. SC-PEG is slightly more resistant to hydrolysis than BTC-PEG.
  • PEG-propionaldehyde US 5,252,714
  • PEG-propionaldehyde i.e., PEG- acetalaldehyde provides an additional benefit in so far as it provides for longer storage than PEG-propionaldehyde (US 5,990,237).
  • Active esters of PEG carboxylic acids are probably one of the most used acylating agents for protein conjugation. Active esters react with primary amines near physiological conditions to form stable amides. Activation of PEG-carboxylic acids to succinimidyl active esters is accomplished by reacting the PEG-carboxylic acid with N- hydroxysuccinimide (NHS or HOSu) and a carbodiimide.
  • exemplary carboxylic acid derivatives of PEG include carboxymethylated PEG (CM-PEG; Zalipsky et ah, 1990), butanoic acid derivatives and propionic acid derivatives (US 5,672,662).
  • Changing the distance between the active ester and the PEG backbone by the addition of methylene units can dramatically influence reactivity towards water and amines (e.g., by reducing hydrolysis).
  • hydrolysis can be reduced by introducing an a-branching moiety to the carboxylic acid.
  • PEGylation of free cysteine residues in a protein is useful for site-specific conjugation (e.g., using a protein modified to include cysteine residues as described herein).
  • Exemplary PEG derivatives for cysteine conjugation include PEG-maleimide, PEG-vinylsulfone, PEG-iodoacetamide and PEG-orthopyridyl disulfide.
  • Exemplary methods for conjugating PEG to cysteine residues are described in Goodson and Katre (1990) and/or above.
  • Exemplary methods for conjugation using PEG-vinylsulfone are described, for example, in Li et al. (2006).
  • US 5985263 describes methods for conjugating PEG to the secondary amine group of histidine, which has a lower pKa than the primary amine.
  • An advantage of this approach is that the acyl-histidne bond is not stable meaning that the protein is slowly released (i.e., the conjugate behaves as a slow release formulation or a prodrug).
  • PEGylation is to take advantage of a N-terminal serine or threonine, which can be converted to periodate as discussed above. Using this approach, PEG has been conjugated to bioactive proteins (e.g., Gaertner and Offord, 1996).
  • PEG can also be conjugated to carbohydrate groups.
  • the present invention also encompasses the use of reversible PEGylation strategies. Uses
  • the proteins of the present invention are useful in a variety of applications, including research, diagnostic and therapeutic applications. Depending on the antigen to which the protein binds it may be useful for delivering a compound to a cell, e.g., to kill the cell or prevent growth and/or for imaging and/or for in vitro assays. In one example, the protein is useful for both imaging and delivering a cytotoxic agent to a cell, i.e., it is conjugated to a detectable label and a cytotoxic agent or a composition comprises a mixture of proteins some of which are conjugated to a cytotoxic agent and some of which are conjugated to a detectable label.
  • the proteins described herein can also act as inhibitors to inhibit (which can be reducing or preventing) (a) binding (e.g., of a ligand, an inhibitor) to a receptor, (b) a receptor signalling function, and/or (c) a stimulatory function. Proteins which act as inhibitors of receptor function can block ligand binding directly or indirectly (e.g., by causing a conformational change).
  • the present invention contemplates a protein comprising at least one variable region comprising at least two cysteine residues in FR2 and/or FR3 capable of specifically binding to any antigen(s), i.e., an example of the invention is generic as opposed to requiring a specific antigen.
  • Examples of the present invention contemplate a protein that specifically binds to an antigen associated with a disease or disorder (i.e., a condition) e.g., associated with or expressed by a cancer or cancerous/transformed cell and/or associated with an autoimmune disease and/or associated with an inflammatory disease or condition and/or associated with a neurodegenerative disease and/or associated with an immune- deficiency disorder.
  • a disease or disorder i.e., a condition
  • Exemplary antigens against which a protein of the invention can be produced include BMPR1B (bone morphogenetic protein receptor-type IB, Dijke. et al 1994, WO2004063362); E16 (LAT1 , SLC7A5, Gaugitsch et al 1992; WO2004048938); STEAP1 (six transmembrane epithelial antigen of prostate, Hubert, et al, 1999);,; WO2004065577); CA125 (MUC16, WO2004045553); MPF (MSLN, SMR, megakaryocyte potentiating factor, mesothelin, Yamaguchi et al, 1994, WO2003101283); Napi3b (NAPI-3B, NPTIIb, SLC34A2, solute carrier family 34; Feild et al, 1999; WO2004022778); Sema 5b (FLJ10372, KIAA1445, SEMA5B, SEMAG, Semaphorin 5
  • the protein of the invention specifically binds to HER2 (e.g., comprising a sequence set forth in SEQ ID NO: 150), MUCl (e.g., comprising a sequence set forth in SEQ ID NO: 152 or 153), TAG72 (a high molecular weight mucin like protein e.g., as described in Johnson et al., 1986) or PSMA (e.g., comprising a sequence set forth in SEQ ID NO: 151).
  • the protein of the invention specifically binds to Her2.
  • the protein of the invention specifically binds to MUCl .
  • the protein of the invention specifically binds to TAG72.
  • the protein of the invention specifically binds to PSMA.
  • exemplary antibodies from which a protein of the invention can be derived will be apparent to the skilled artisan and include, for example, rituximab (C2B8; W094/11026); or bevacizumab (humanized A.4.6.1; Presta et al, 1997)).
  • Exemplary bispecific proteins may bind to two different epitopes of the antigen of interest. Other such proteins may combine one antigen binding site with a binding site for another protein. Alternatively, an anti-antigen of interest region may be combined with a region which binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g., CD3), or Fc receptors for IgG (FcyR), such as FcyRI (CD64), FcyRII (CD32) and/or FcyRIII (CD16), so as to focus and localize cellular defence mechanisms to the cells expressing the antigen of interest. Bispecific proteins may also be used to localize cytotoxic agents to cells which express the antigen of interest.
  • a triggering molecule such as a T-cell receptor molecule (e.g., CD3), or Fc receptors for IgG (FcyR), such as FcyRI (CD64), FcyRII (CD32) and/or Fcy
  • WO 96/16673 describes a bispecific anti-ErbB2/anti-FcYRIII antibody and U.S. Pat. No. 5,837,234 discloses a bispecific anti-ErbB2/anti-FcyRI antibody.
  • a bispecific anti- ErbB2/Fca antibody is shown in WO98/02463.
  • US5,821 ,337 teaches a bispecific anti-ErbB2/anti-CD3 antibody.
  • the proteins of the present invention are useful for parenteral, topical, oral, or local administration, aerosol administration, or transdermal administration for prophylactic or for therapeutic treatment.
  • the pharmaceutical compositions can be administered in a variety of unit dosage forms depending upon the method of administration.
  • unit dosage forms suitable for oral administration include powder, tablets, pills, capsules and lozenges or by parenteral administration.
  • the pharmaceutical compositions of this invention when administered orally, should be protected from digestion. This is typically accomplished either by complexing the proteins with a composition to render it resistant to acidic and enzymatic hydrolysis or by packaging the compound in an appropriately resistant carrier such as a liposome. Means of protecting proteins from digestion are known in the art.
  • a therapeutically effective amount of the protein will be formulated into a composition for administration to a subject.
  • the phrase "a therapeutically effective amount" refers to an amount sufficient to promote, induce, and/or enhance treatment or other therapeutic effect in a subject.
  • concentration of proteins of the present invention in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight and the like in accordance with the particular mode of administration selected and the patient's needs.
  • a therapeutically effective amount may be about 1 ⁇ g/kg to 15 mg/kg (e.g. 0.1-20 mg/kg) of molecule, whether, for example, by one or more separate administrations, or by continuous infusion.
  • a typical daily dosage might range from about 1 ⁇ g/kg to 100 mg/kg or more.
  • An exemplary dosage of the protein to be administered to a patient is in the range of about 0.1 to about 10 mg/kg of patient weight.
  • An exemplary dosing regimen comprises administering an initial loading dose of about 4mg/kg, followed by a weekly maintenance dose of about 2 mg/kg of the protein.
  • Other dosage regimens may be useful. The progress of this therapy is easily monitored by conventional techniques and assays.
  • the protein of the invention is formulated at a concentrated does that is diluted to a therapeutically effective dose prior to administration to a subject.
  • compositions of this invention are particularly useful for parenteral administration, e.g., formulated for injection via the intravenous, intramuscular, sub-cutaneous, transdermal, or other such routes, including peristaltic administration and direct instillation into a tumour or disease site (intracavity administration).
  • the compositions for administration will commonly comprise a solution of the proteins of the present invention dissolved in a pharmaceutically acceptable carrier, preferably an aqueous carrier.
  • a pharmaceutically acceptable carrier preferably an aqueous carrier.
  • aqueous carriers can be used, e.g., buffered saline and the like.
  • Other exemplary carriers include water, saline, Ringer's solution, dextrose solution, and 5% human serum albumin.
  • Nonaqueous vehicles such as mixed oils and ethyl oleate may also be used. Liposomes may also be used as carriers.
  • the vehicles may contain minor amounts of additives that enhance isotonicity and chemical stability, e.g., buffers and preservatives.
  • the compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like.
  • WO2002/080967 describes compositions and methods for administering aerosolized compositions comprising proteins for the treatment of, e.g., asthma, which are also suitable for administration of protein of the present invention.
  • Suitable dosages of compounds of the present invention will vary depending on the specific protein, the condition to be diagnosed/treated/prevented and/or the subject being treated. It is within the ability of a skilled physician to determine a suitable dosage, e.g., by commencing with a sub-optimal dosage and incrementally modifying the dosage to determine an optimal or useful dosage. Alternatively, to determine an appropriate dosage for treatment/prophylaxis, data from cell culture assays or animal studies are used, wherein a suitable dose is within a range of circulating concentrations that include the ED50 of the active compound with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. A therapeutically/prophylactically effective dose can be estimated initially from cell culture assays.
  • a dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma maybe measured, for example, by high performance liquid chromatography.
  • a protein of the invention may be combined in a pharmaceutical combination formulation, or dosing regimen as combination therapy, with a second compound.
  • the second compound of the pharmaceutical combination formulation or dosing regimen preferably has complementary activities to the protein of the combination such that they do not adversely affect each other.
  • the second compound may be a chemotherapeutic agent, cytotoxic agent, cytokine, growth inhibitory agent, anti-hormonal agent, and/or cardioprotectant.
  • chemotherapeutic agent such as a tubulin- forming inhibitor, a topoisomerase inhibitor, or a DNA binder.
  • Slow release capsules or compositions may also be used. Slow release formulations are generally designed to give a constant drug level over an extended period and may be used to deliver compounds of the present invention.
  • the present invention also provides a method of treating or preventing a condition in a subject, the method comprsing administering a therapeutically effective amount of a protein of the invention to a subject in need thereof.
  • preventing in the context of preventing a condition include administering an amount of a protein described herein sufficient to stop or hinder the development of at least one symptom of a specified disease or condition.
  • treating include administering a therapeutically effective amount of an inhibitor(s) and/or agent(s) described herein sufficient to reduce or eliminate at least one symptom of a specified disease or condition.
  • the term "subject” shall be taken to mean any animal including humans, preferably a mammal.
  • exemplary subjects include but are not limited to humans, primates, livestock (e.g. sheep, cows, horses, donkeys, pigs), companion animals (e.g. dogs, cats), laboratory test animals (e.g. mice, rabbits, rats, guinea pigs, hamsters), captive wild animals (e.g. fox, deer).
  • livestock e.g. sheep, cows, horses, donkeys, pigs
  • companion animals e.g. dogs, cats
  • laboratory test animals e.g. mice, rabbits, rats, guinea pigs, hamsters
  • captive wild animals e.g. fox, deer.
  • the mammal is a human or primate. More preferably the mammal is a human.
  • a "condition” is a disruption of or interference with normal function, and is not to be limited to any specific condition, and will include diseases or disorders.
  • the condition is a cancer or an immunopatho logical disorder.
  • Exemplary cancers include, but are not limited to, carcinoma, lymphoma, blastoma, sarcoma, and leukemia or lymphoid malignancies. More particular examples of such cancers include squamous cell cancer (e.g. epithelial squamous cell cancer), lung cancer including small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung and squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, rectal cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, as well as head and neck cancer.
  • a cancer is breast cancer or ovarian cancer or
  • the cancer expresses Her2.
  • Exemplary cancers include breast cancer, ovarian cancer, stomach cancer or uterine cancer, preferably breast cancer.
  • Such a cancer can be treated, for example, with a protein of the invention that binds to Her2.
  • the cancer expresses PSMA.
  • exemplary cancers include prostate cancer.
  • Such a cancer can be treated, for example, with a protein of the invention that binds to PSMA.
  • the cancer expresses Tag72.
  • Exemplary cancers include carcinomas, such as colorectal cancer, gastric cancer, pancreatic cancer, ovarian cancer, endometrial cancer, breast cancer, non-small cell lung cancer, and prostate cancer.
  • carcinomas such as colorectal cancer, gastric cancer, pancreatic cancer, ovarian cancer, endometrial cancer, breast cancer, non-small cell lung cancer, and prostate cancer.
  • Such a cancer can be treated, for example, with a protein of the invention that binds to Tag72.
  • the cancer expresses MUC1, preferably a glycoform of MUC1 associated with cancer.
  • MUC1 preferably a glycoform of MUC1 associated with cancer.
  • Exemplary cancers include carcinomas, such as colorectal cancer, gastric cancer, pancreatic cancer, breast cancer, lung cancer, and bladder cancer.
  • Such a cancer can be treated, for example, with a protein of the invention that binds to MUC 1.
  • Immunopathology is the study of disease having an immunological cause and immunologic disease is any condition caused by the reactions of immunoglobulins to antigens.
  • an "immunopathological disorder” can be defined as a disorder arising from reaction of a subject's immune system to antigens.
  • Immunopathological disorders include autoimmune diseases and hypersensitivity responses (e.g. Type I: anaphylaxis, hives, food allergies, asthma; Type II: autoimmune haemo lytic anaemia, blood transfusion reactions; Type III: serum sickness, necrotizing vasculitis, glomerulonephritis, rheumatoid arthritis, lupus; Type IV: contact dermatitis, graft rejection).
  • Autoimmune diseases include rheumatologic disorders (such as, for example, rheumatoid arthritis, Sjogren's syndrome, scleroderma, lupus such as SLE and lupus nephritis, polymyositis/dermatomyositis, cryoglobulinemia, anti-phospholipid antibody syndrome, and psoriatic arthritis), osteoarthritis, autoimmune gastrointestinal and liver disorders (such as, for example, inflammatory bowel diseases (e.g., ulcerative colitis and Crohn's disease), autoimmune gastritis and pernicious anemia, autoimmune hepatitis, primary biliary cirrhosis, primary sclerosing cholangitis, and celiac disease), vasculitis (such as, for example, ANCA-associated vasculitis, including Churg-Strauss vasculitis, Wegener's granulomatosis, and polyarteriitis), autoimmune neurological disorders (such as,
  • More preferred such diseases include, for example, rheumatoid arthritis, ulcerative colitis, ANCA-associated vasculitis, lupus, multiple sclerosis, Sjogren's syndrome, Graves' disease, IDDM, pernicious anemia, thyroiditis, and glomerulonephritis.
  • the disorder is an inflammatory disease.
  • Inflammation is a protective response of body tissues to irritation or injury- and can be acute or chronic.
  • inflammatory disorders include diseases involving neutrophils, monocytes, mast cells, basophils, eosinophils, macrophages where cytokine release, histamine release, oxidative burst, phagocytosis, release of other granule enzymes and chemotaxis occur.
  • Hypersensitivity responses (defined above under immunopathological disorders) can also be regarded as inflammatory diseases (acute or chronic) since they often involve complement activation and recruitment/infiltration of various leukocytes such as neutrophils, mast cells, basophils, etc.
  • compositions of the present invention will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically/prophylactically effective.
  • Formulations are easily administered in a variety of manners, e.g., by ingestion or injection or inhalation.
  • the combination therapy may be administered as a simultaneous or sequential regimen.
  • the combination may be administered in two or more administrations.
  • the combined administration includes co-administration, using separate formulations or a single pharmaceutical formulation, and consecutive administration in either order, wherein preferably there is a time period while both (or all) active agents simultaneously exert their biological activities.
  • a protein of the invention is preferably tested in vitro and/or in vivo, e.g., as described below. In Vitro Testing
  • a protein of the invention binds to an antigen, even if conjugated to a compound.
  • the protein may bind to the antigen at least as well as the protein from which it is derived.
  • the protein or conjugate comprising same binds to the antigen with at least about 10% or 20% or 30% or 40% or 50% or 60% or 70% or 80% or 90% of the affinity or avidity of the protein from which it is derived or a form of the protein lacking the cysteine residues and/or not conjugated to the compound.
  • Exemplary methods for determining binding affinity of a protein include a simple immunoassay showing the ability of the protein to block the binding of the unmodified protein or unconjugated protein to a target antigen, e.g., a competitive binding assay.
  • Competitive binding is determined in an assay in which the protein under test inhibits specific binding of a reference protein to a common antigen.
  • RIA solid phase direct or indirect radioimmunoassay
  • EIA solid phase direct or indirect enzyme immunoassay
  • sandwich competition assay see Stahli et ah, 1983; Kim, et ah, 1989
  • solid phase direct biotin-avidin EIA see Kirkland et ah, 1986
  • solid phase direct labelled assay solid phase direct labelled sandwich assay (see Harlow and Lane,
  • solid phase direct label RIA using I label see Morel et al., 1988
  • solid phase direct biotin-avidin EIA Cheung et al., 1990
  • direct labelled RIA Mimetic et al, 1990
  • such an assay involves the use of purified antigen bound to a solid surface or cells bearing either of these, an unlabeled test protein and a labelled reference protein.
  • Competitive inhibition is measured by determining the amount of label bound to the solid surface or cells in the presence of the test protein
  • the present invention also encompasses methods for testing the activity of a protein of the invention.
  • Various assays are available to assess the activity of a protein of the present invention in vitro.
  • a protein of the present invention is administered to a cell or population thereof to determine whether or not it can bind to said cell and/or be internalized by said cell.
  • Such an assay is facilitated by labelling the protein of the present invention with a detectable label (i.e., producing a conjugate), however this is not essential since the protein of the present invention can also be detected with a labelled protein.
  • Such an assay is useful for assessing the ability of a protein of the present invention to deliver a compound (i.e., a payload) to a cell and/or its utility in imaging.
  • the cell expresses an antigen to which the protein of the present invention binds and more preferably is a cell line or primary cell culture of a cell type that it desired to be detected or treated.
  • the cytotoxic or cytostatic activity of a protein of the present invention is measured by: exposing cells expressing an antigen to which the protein of the present invention binds to the protein of the present invention; culturing the cells for a suitable period for the protein to exert a biological effect, e.g., from about 6 hours to about 5 days; and measuring cell viability, cytotoxicity and/or cell death.
  • a biological effect e.g., from about 6 hours to about 5 days
  • cell viability, cytotoxicity and/or cell death are known in the art.
  • the CellTiter-Glo® Luminescent Cell Viability Assay is a commercially available (Promega Corp., Madison, WI), homogeneous assay method based on the recombinant expression of Coleoptera luciferase (US Patent Nos. 5583024; 5674713 and 5700670).
  • This cell proliferation assay determines the number of viable cells in culture based on quantitation of the ATP present in a cell, an indicator of metabolically active cells (Crouch et al 1993; US 6602677).
  • cell viability is assayed using non-fluorescent resazurin, which is added to cells cultured in the presence of a protein of the present invention.
  • Viable cells reduce resazurin to red- fluorescent resorufm, easily detectable, using, for example microscopy or a fluorescent plate reader.
  • Kits for analysis of cell viability are available, for example, from Molecular Probes, Eugene, OR, USA.
  • Other assays for cell viability include determining incorporation of 3 H-thymidine or 14 C-thymidine into DNA as it is synthesized is an assay for DNA synthesis associated with cell division. In such an assay, a cell is incubated in the presence of labeled thymidine for a time sufficient for cell division to occur. Following washing to remove any unincorporated thymidine, the label (e.g.
  • Radioactive label is detected, e.g., using a scintilation counter.
  • Alternative assays for determining cellular proliferation include, for example, measurement of DNA synthesis by BrdU incorporation (by ELISA or immunohistochemistry, kits available from Amersham Pharmacia Biotech).
  • Exemplary assays for detecting cell death include APOPTEST (available from Immunotech) stains cells early in apoptosis, and does not require fixation of the cell sample. This method utilizes an annexin V antibody to detect cell membrane re-configuration that is characteristic of cells undergoing apoptosis.
  • Apoptotic cells stained in this manner can then be sorted either by fluorescence activated cell sorting (FACS), ELISA or by adhesion and panning using immobilized annexin V antibodies.
  • FACS fluorescence activated cell sorting
  • ELISA ELISA
  • adhesion and panning using immobilized annexin V antibodies Alternatively, a terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end-labeling (TUNEL) assay is used to determine the level of cell death.
  • the TUNEL assay uses the enzyme terminal deoxynucleotidyl transferase to label 3' -OH DNA ends, generated during apoptosis, with biotinylated nucleotides. The biotinylated nucleotides are then detected by using streptavidin conjugated to a detectable marker. Kits for TUNEL staining are available from, for example, Intergen Company, Purchase, NY
  • Stability of a protein of the present invention can also be assessed by exposing a protein of the present invention to serum and/or cells and subsequently isolating the protein of the present invention using, for example, immunoaffinity purification. A reduced amount of recovered protein of the present invention indicates that the protein of the present invention is degraded in serum or when exposed to cells.
  • the ability of the protein of the present invention to block binding of a ligand to a receptor is assessed using a standard radio-immunoassay or fiuorescent-immunoassay.
  • a protein of the present invention can also be tested for its stability and/or efficacy in vivo.
  • the protein of the present invention is administered to a subject and the serum levels of the protein is detected over time, e.g., using an ELISA or by detecting a detectable label conjugated to the protein. This permits determination of the in vivo stability of the protein of the present invention.
  • a protein of the present invention can also be administered to an animal model of a human disease.
  • the skilled artisan will be readily able to determine a suitable model based on the antigen to which the protein of the present invention binds.
  • Exemplary models of, for example, human cancer are known in the art.
  • mouse models of breast cancer include mice overexpressing fibroblast growth factor 3 (Muller et al, 1990); TGF-alpha (Matsui et al, 1990); erbB2 (Guy, et al, 1992); RET-1 (Iwamoto et al., 1990) or transplantation of human breast cancer cells into SCID mice.
  • Models of ovarian cancer include transplantation of ovarian cancer cells into mice (e.g., as described in Roby et al., 2000); transgenic mice chronically secreting luteinising hormone (Risma et al., 1995); or Wx/Wv mice.
  • Mouse models of prostate cancer are also known in the art and include, for example, models resulting from enforced expression of SV40 early genes (e.g., the TRAMP model that utilizes the minimal rat probasin promoter to express the SV40 early genes or transgenic mice using the long probasin promoter to express large T antigen, collectively termed the 'LADY' model or mice expressing c-myc or Bcl-2 or Fgf8b or expressing dominant negative TGFB (see, Matusik et al., 2001, for a review of transgenic models of prostate cancer).
  • the TRAMP model that utilizes the minimal rat probasin promoter to express the SV40 early genes or transgenic mice using the long probasin promoter to express large T antigen
  • mice expressing c-myc or Bcl-2 or Fgf8b or expressing dominant negative TGFB see, Matusik et al., 2001, for a review of transgenic models of prostate cancer.
  • a protein of the present invention can also be administered to an animal model of a disease other than cancer, e.g., NOD mice to test their ability to suppress, prevent, treat or delay diabetes (e.g., as described in Tang et al. (2004)) and/or to a mouse model of GVHD (e.g., as described in Trenado (2002)) and/or to a mouse model of psoriasis (e.g., Wang et al.
  • a disease other than cancer e.g., NOD mice to test their ability to suppress, prevent, treat or delay diabetes (e.g., as described in Tang et al. (2004)) and/or to a mouse model of GVHD (e.g., as described in Trenado (2002)) and/or to a mouse model of psoriasis (e.g., Wang et al.
  • rheumatoid arthritis e.g., a SKG strain of mouse (Sakaguchi et al.), rat type II collagen arthritis model, mouse type II collagen arthritis model or antigen induced arthritis models in several species (Bendele, 2001)) and/or a model of multiple sclerosis (for example, experimental autoimmune encephalomyelitis (EAE; Bradl and Linington, 1996)) and/or inflammatory airway disease (for example, OVA challenge or cockroach antigen challenge (Chen et al. 2007; Lukacs et al. 2001) and/or models of inflammatory bowel disease (e.g., dextran sodium sulphate (DSS)-induced colitis or Muc2 deficient mouse model of colitis (Van der Sluis et al. 2006).
  • a model of rheumatoid arthritis e.g., a SKG strain of mouse (Sakaguchi et al.), rat type II collagen arthritis model, mouse type II collagen
  • the present invention provides methods for diagnosing or prognosing a condition.
  • diagnosis and variants thereof such as, but not limited to, “diagnose”, “diagnosed” or “diagnosing” includes any primary diagnosis of a clinical state or diagnosis of recurrent disease.
  • Prognosis refers to the likely outcome or course of a disease, including the chance of recovery or recurrence.
  • the method comprises determining the amount of an antigen in a sample.
  • the proteins of the invention have utility in applications such as cell sorting (e.g., flow cytometry, fluorescence activated cell sorting), for diagnostic or research purposes.
  • a sample is contacted with a protein of the invention for a time and under conditions sufficient for it to bind to an antigen and form a complex and the complex is then detected or the level of complex is determined.
  • the proteins can be labelled or unlabeled.
  • the proteins can be directly labelled, e.g., using a method described herein. When unlabeled, the proteins can be detected using suitable means, as in agglutination assays, for example.
  • Unlabeled antibodies or fragments can also be used in combination with another (i.e., one or more) suitable reagent which can be used to detect a protein, such as a labelled antibody (e.g., a second antibody) reactive with the protein or other suitable reagent (e.g., labelled protein A).
  • a suitable reagent which can be used to detect a protein, such as a labelled antibody (e.g., a second antibody) reactive with the protein or other suitable reagent (e.g., labelled protein A).
  • a protein of the invention is used in an immunoassay.
  • an assay selected from the group consisting of, immunohistochemistry, immunofluorescence, enzyme linked immunosorbent assay (ELISA), fluorescence linked immunosorbent assay (FLISA) Western blotting, RIA, a biosensor assay, a protein chip assay and an immunostaining assay (e.g. immunofluorescence).
  • Standard solid-phase ELISA or FLISA formats are particularly useful in determining the concentration of a protein from a variety of samples.
  • such an assay involves immobilizing a biological sample onto a solid matrix, such as, for example a polystyrene or polycarbonate microwell or dipstick, a membrane, or a glass support (e.g. a glass slide).
  • a protein of the invention that specifically binds to an antigen of interest is brought into direct contact with the immobilized sample, and forms a direct bond with any of its target antigen present in said sample.
  • This protein of the invention is generally labelled with a detectable reporter molecule, such as for example, a fluorescent label (e.g. FITC or Texas Red) or a fluorescent semiconductor nanocrystal (as described in US 6,306,610) in the case of a FLISA or an enzyme (e.g.
  • HRP horseradish peroxidase
  • AP alkaline phosphatase
  • ⁇ -galactosidase ⁇ -galactosidase
  • a labelled antibody can be used that binds to the protein of the invention.
  • the label is detected either directly, in the case of a fluorescent label, or through the addition of a substrate, such as for example hydrogen peroxide, TMB, or toluidine, or 5-bromo-4-chloro-3-indol-beta-D-galaotopyranoside (x-gal) in the case of an enzymatic label.
  • a substrate such as for example hydrogen peroxide, TMB, or toluidine, or 5-bromo-4-chloro-3-indol-beta-D-galaotopyranoside (x-gal) in the case of an enzymatic label.
  • Such ELISA or FLISA based systems are particularly suitable for quantification of the amount of a protein in a sample, by calibrating the detection system against known amounts of a protein standard to which the protein binds, such as for example, an isolated and/or recombinant protein or immunogenic fragment thereof or epitope thereof.
  • an ELISA or FLISA comprises of immobilizing a protein of the invention or an antibody that binds to an antigen of interest on a solid matrix, such as, for example, a membrane, a polystyrene or polycarbonate microwell, a polystyrene or polycarbonate dipstick or a glass support.
  • a sample is then brought into physical relation with said protein of the invention, and the protein to which said compound binds is bound or 'captured'.
  • the bound protein is then detected using a labelled protein of the invention that binds to a different protein or a different site in the same protein.
  • a third labelled antibody can be used that binds the second (detecting) antibody.
  • the present invention also contemplates imaging methods using a protein of the invention.
  • protein of the invention is conjugated to a detectable label, which can be any molecule or agent that can emit a signal that is detectable by imaging.
  • the detectable label may be a protein, a radioisotope, a fluorophore, a visible light emitting fluorophore, infrared light emitting fluorophore, a metal, a ferromagnetic substance, an electromagnetic emitting substance a substance with a specific MR spectroscopic signature, an X-ray absorbing or reflecting substance, or a sound altering substance.
  • the protein of the present invention can be administered either systemically or locally to the tumour, organ, or tissue to be imaged, prior to the imaging procedure.
  • the protein is administered in doses effective to achieve the desired optical image of a tumour, tissue, or organ.
  • doses may vary widely, depending upon the particular protein employed, the tumour, tissue, or organ subjected to the imaging procedure, the imaging equipment being used, and the like.
  • the protein of the invention is used as in vivo optical imaging agents of tissues and organs in various biomedical applications including, but not limited to, imaging of tumours, tomographic imaging of organs, monitoring of organ functions, coronary angiography, fluorescence endoscopy, laser guided surgery, photoacoustic and sonofluorescence methods, and the like.
  • Exemplary diseases, e.g., cancers, in which a protein of the invention is useful for imaging are described herein and shall be taken to apply mutatis mutandis to the present embodiment of the invention.
  • the protein conjugates of the invention are useful for the detection of the presence of tumours and other abnormalities by monitoring where a particular protein of the invention is concentrated in a subject.
  • the protein of the invention is useful for laser-assisted guided surgery for the detection of micro-metastases of tumours upon laparoscopy. In yet another embodiment, the protein of the invention is useful in the diagnosis of atherosclerotic plaques and blood clots.
  • imaging methods include magnetic resonance imaging (MRI), MR spectroscopy, radiography, CT, ultrasound, planar gamma camera imaging, single- photon emission computed tomography (SPECT), positron emission tomography (PET), other nuclear medicine-based imaging, optical imaging using visible light, optical imaging using luciferase, optical imaging using a fluorophore, other optical imaging, imaging using near infrared light, or imaging using infrared light.
  • MRI magnetic resonance imaging
  • MR spectroscopy radiography
  • CT coronary gamma camera imaging
  • SPECT single- photon emission computed tomography
  • PET positron emission tomography
  • other nuclear medicine-based imaging optical imaging using visible light
  • optical imaging using luciferase optical imaging using a fluorophore
  • other optical imaging imaging using near infrared light, or imaging using infrared light.
  • Certain examples of the methods of the present invention further include imaging a tissue during a surgical procedure on a subject.
  • optical imaging is one imaging modality that has gained widespread acceptance in particular areas of medicine. Examples include optical labeling of cellular components, and angiography such as fluorescein angiography and indocyanine green angiography.
  • optical imaging agents include, for example, fluorescein, a fluorescein derivative, indocyanine green, Oregon green, a derivative of Oregon green derivative, rhodamine green, a derivative of rhodamine green, an eosin, an erytlirosin, Texas red, a derivative of Texas red, malachite green, nanogold sulfosuccinimidyl ester, cascade blue, a coumarin derivative, a naphthalene, a pyridyloxazole derivative, cascade yellow dye, dapoxyl dye.
  • Gamma camera imaging is contemplated as a method of imaging that can be utilized for measuring a signal derived from the detectable label.
  • One of ordinary skill in the art would be familiar with techniques for application of gamma camera imaging.
  • measuring a signal can involve use of gamma-camera imaging of an U1 ln or 99m Tc conjugate, in particular lu In- octreotide or 99m Tc-somatostatin analogue.
  • CT Computerized tomography
  • a computer is programmed to display two- dimensional slices from any angle and at any depth. The slices may be combined to build three-dimensional representations.
  • contrast agents aid in assessing the vascularity of a soft tissue lesion.
  • the use of contrast agents may aid the delineation of the relationship of a tumor and adjacent vascular structures.
  • CT contrast agents include, for example, iodinated contrast media. Examples of these agents include iothalamate, iohexol, diatrizoate, iopamidol, ethiodol, and iopanoate. Gadolinium agents have also been reported to be of use as a CT contrast agent, for example, gadopentate.
  • Magnetic resonance imaging is an imaging modality that uses a high- strength magnet and radio-frequency signals to produce images.
  • the sample to be imaged is placed in a strong static magnetic field and excited with a pulse of radio frequency (RF) radiation to produce a net magnetization in the sample.
  • RF radio frequency
  • Various magnetic field gradients and other RF pulses then act to code spatial information into the recorded signals.
  • By collecting and analyzing these signals it is possible to compute a three-dimensional image which, like a CT image, is normally displayed in two-dimensional slices. The slices may be combined to build three-dimensional representations.
  • Contrast agents used in MRI or MR spectroscopy imaging differ from those used in other imaging techniques.
  • MRI contrast agents include gadolinium chelates, manganese chelates, chromium chelates, and iron particles.
  • a protein of the invention is conjugated to a compound comprising a chelate of a paramagnetic metal selected from the group consisting of scandium, titanium, vanadium, chromium, manganese, iron, cobalt, nickel, copper, molybdenum, ruthenium, cerium, indium, praseodymium, neodymium, promethium, samarium, europium, gadolinium, terbium, dysprosium, holmium, erbium, thulium, and ytterbium.
  • imaging agents useful for the present invention is halocarbon- based nanoparticle such as PFOB or other fluorine-based MRl agents. Both CT and MRl provide
  • Imaging modalities that provide information pertaining to information at the cellular level, such as cellular viability, include positron emission tomography (PET) and single- photon emission computed tomography (SPECT).
  • PET positron emission tomography
  • SPECT single- photon emission computed tomography
  • PET a patient ingests or is injected with a radioactive substance that emits positrons, which can be monitored as the substance moves through the body.
  • SPECT single-photon emission computed tomography
  • the major difference between the two is that instead of a positron-emitting substance, SPECT uses a radioactive tracer that emits high-energy photons.
  • SPECT is valuable for diagnosing multiple illnesses including coronary artery disease, and already some 2.5 million SPECT heart studies are done in the United States each year.
  • a protein of the invention is commonly labeled with positron-emitters such as U C, 13 N, 15 0, 18 F, 82 Rb, 62 Cu, and 68 Ga. Proteins of the invention are labelled with positron emitters such as 99mTc, 201 T1, and 67 Ga, lu In for SPECT.
  • Non-invasive fluorescence imaging of animals and humans can also provide in vivo diagnostic information and be used in a wide variety of clinical specialties. For instance, techniques have been developed over the years including simple observations following UV excitation of fluorophores up to sophisticated spectroscopic imaging using advanced equipment (see, e.g., Andersson-Engels et al, 1997).
  • fluorescence e.g., from fluorophores or fluorescent proteins
  • specific devices or methods known in the art for the in vivo detection of fluorescence include, but are not limited to, in vivo near- infrared fluorescence (see, e.g., Frangioni, 2003), the MaestroTM in vivo fluorescence imaging system (Cambridge Research & Instrumentation, Inc.; Woburn, MA), in vivo fluorescence imaging using a flying-spot scanner (see, e.g., Ramanujam et al, 2001), and the like.
  • Other methods or devices for detecting an optical response include, without limitation, visual inspection, CCD cameras, video cameras, photographic film, laser- scanning devices, fluorometers, photodiodes, quantum counters, epifluorescence microscopes, scanning microscopes, flow cytometers, fluorescence microplate readers, or signal amplification using photomultiplier tubes.
  • an imaging agent is tested using an in vitro or in vivo assay prior to use in humans, e.g., using a model described herein.
  • the present invention also provides an article of manufacture, or "kit", containing a protein of the invention.
  • the article of manufacture optionally comprises a container and a label or package insert on or associated with the container, e.g., providing instructions to use the protein of the invention in a method described herein according to any embodiment.
  • Suitable containers include, for example, bottles, vials, syringes, blister pack, etc.
  • the containers may be formed from a variety of materials such as glass or plastic.
  • the container holds a protein of the invention composition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • the article of manufacture may further comprise a second (or third) container comprising a pharmaceutically-acceptable buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes.
  • BWFI bacteriostatic water for injection
  • phosphate-buffered saline such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution.
  • BWFI bacteriostatic water for injection
  • phosphate-buffered saline such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution.
  • BWFI bacteriostatic water for injection
  • Ringer's solution such as phosphate
  • Examples 1-8 describe production of proteins comprising an antibody variable region, comprising two or more cysteine residues within FR1 and conjugation of compounds thereto. These experiments are used as a model to demonstrate that the inventors have produced methods for predicting positions of cysteine residues that can form disulphide bonds or provide positions for conjugation without preventing binding of the protein to an antigen. Using these methods, the inventors also identified positions within FR2 and/or a region comprising FR3 and CDR2 in which cysteine residues can be introduced. Examples 9-15 describe experiments in relation to positioning cysteine residues within FR2 and/or FR3 and conjugating compounds thereto.
  • V H /V L interfaces of numerous diabody sequences were modelled and residues meeting the following criteria were identified: • Not involved in the structural integrity of the domains and the domain-domain interfaces;
  • Antibody residues are numbered according to Kabat (1987 and/or 1991).
  • DNA constructs encoding diabodies comprising the V regions of a mouse mAb specific for TAG72 (SEQ ID NO: 58) and a human mAb specific for HER2 (SEQ ID NO: 60) were synthesised with the appropriate restriction sites and cloned into pUC57 by GenScript. V regions were arranged as V H -Gly 4 Ser-V L or V L -Gly 4 Ser-V H .
  • the clone containing the V regions of the anti-TAG72 mAb in the VH-Gly 4 Ser-VL orientation was designated AVP04-07 (SEQ ID NO: 58).
  • the clone containing the V regions of the anti-HER2 mAb in the Vn-Gly 4 Ser-V L orientation was designated AVP07-17 (SEQ ID NO: 60).
  • This method of cloning allowed for the insertion of a carboxy terminal 6xHIS tag. This tag was routinely used to streamline downstream purification processes and is known to be neutral in activity.
  • the amino acid sequence ProsSerpSerioLeun is found in the FRl sequence of the V L region of the AVP04-07.
  • the Proline residue at position 8 is encoded by the sequence CCG and the Leucine residue at position 11 is encoded by the sequence CTG. Mutagenesis technique was used to alter these nucleotide sequences to TGC, which encodes Cysteine.
  • the QuikChange ® site-directed mutagenesis method (Stratagene) was used to introduce the cysteine residues and modify the N-terminus.
  • This PCR-based method uses two complementary synthetic oligonucleotides that contain the desired mutations as primers and plasmid DNA as the template to synthesise the double-stranded mutant PCR product. Dpnl digestion is then applied to remove the template plasmid to increase the mutagenesis efficiency. Briefly, a PCR is performed using a 50 ⁇ 1 reaction mixture containing 15ng of template and 125ng each of the forward and reverse mutagenic primers, according to the manufacturer's instructions.
  • AVP04-07 (SEQ ID NO: 58) was used as the template, with 5' - CC CAG CCG GCC ATG GCG AGC GTG CAG CTG CAG CAG AGC G - 3' (SEQ ID NO: 66) as the forward primer and 5' - C GCT CTG CTG CAG CTG CAC GCT CGC CAT GGC CGG CTG GG - 3' (SEQ ID NO: 67) (Geneworks, Sydney, SA) as the reverse primer.
  • the resulting construct was used as the template to introduce Cysteine residues at positions 8 and 11 of the FRl region of the V L chain using site directed mutagenesis.
  • Amplification was performed using the following conditions in sequence: 95°C for 30 sec; 18 cycles consisting of 95°C for 30 sec, 55°C for 30 sec and 68°C for 13 min; a final extension of 68°C for 7 min.
  • the template was digested with Dpnl at 37°C for 1 hour. Trans formants were obtained using the protocol supplied by Stratagene, miniprep DNA extracted and the DNA sequence confirmed as above. Similar mutagenesis approaches were utilized to generate all the diabodies exemplified here.
  • the anti-TAG72 diabody comprising cysteine replacement mutations in the V L FR1 and an engineered N-terminal serine residue was designated AVP04-50.
  • the anti- HER2 diabody comprising cysteine replacement mutations in the V L FRl and an engineered N-terminal serine residue was designated AVP07-63.
  • Diabody encoding DNA were transformed into chemically competent E. coli BL21 cells using the standard protocol.
  • a single transformant was inoculated into 500ml 2xYT containing 1% D-glucose and 100 ⁇ g/ml ampicillin and incubated at 37°C overnight, shaking at 220rpm.
  • 18L of the same media was seeded with the overnight culture to a final OD 6 oo of 0.1 and incubated at 30°C until the OD 6 oo was between about 0.6 - 0.8.
  • the cultures were transferred to 12°C and shaking continued until the induction temperature was reached.
  • Protein expression was induced with the addition of 0.2mM IPTG and the cultures incubated at 12°C for 15 hours.
  • Bacterial pellets were prepared by centrifugation at 10,000g, harvested, weighed and stored at -20°C overnight. 1.7 Purification of Diabodies Expressed in E. coli
  • Bacterial pellets (of approximately 150-300g) were lysed, protein extracted and subsequently purified. 5mL of His-Tag affinity chromatography extraction buffer (20mM phosphate, 500mM NaCl, 20mM Imidazole, 0.025% Lysozyme (w/v), lmM PMSF, 250 ⁇ / ⁇ Benzonase, pH 7.4) for every gram of bacterial pellet was employed in the lysis protocol. Bacterial pellets were resuspended in lysis buffer by mechanical homogenisation then sonicated (6 x 30 second pulses on ice). Bacterial lysate was subsequently incubated at 37°C for 30 minutes prior to centrifugation (10,000g, 30min) and filtration (0.45 ⁇ filter membrane).
  • His-Tag affinity chromatography purification using the AKTA Purifier 10 was then used to purify diabodies from filtered bacterial lysate. Between two and four 5mL HisTrapTM (GE LifeSciences) Crude FF columns were employed in series for purification. Lysate was passed through the nickel column via an external P960 pump. HisTrapTM columns were washed with 10 column volumes of His-Tag affinity chromatography extraction buffer (20mM phosphate, 500mM NaCl, 20mM Imidazole).
  • Purified protein was eluted in 50% His-Tag affinity chromatography elution buffer (500mM phosphate, 500mM NaCl, 20mM Imidazole) and 50% His-Tag affinity chromatography extraction buffer (260mM Imidazole final concentration). Fractions containing eluted proteins (as determined by 280mM absorbance on AKTA Unicorn program) were collected, pooled, protein concentration determined and dialysed in the appropriate ion exchange buffer.
  • Proteins were dialysed in a buffer 1.0 - 1.5 pH units higher than the pi of the protein (for cation exchange) or 1.0 - 1.5 pH units lower that the pi of the protein (for anion exchange).
  • diabodies with a pi of 7.0 - 8.0 are dialysed in MES buffer (50mM MES, pH 6.0 for cation exchange)
  • those with a pi of 8.0 - 9.0 are dialysed in phosphate buffer (50mM phosphate, pH 7.0 for cation exchange)
  • those with a pi of 5.0 - 6.5 are dialysed in Tris buffer (20mM, pH 7.5 for anion exchange).
  • Most diabody pis fall within the aforementioned ranges.
  • Diabodies were dialysed into 200x volume of buffer with three identical buffer exchanges no less than 4 hours apart. Dialysis was performed using 10K cut-off dialysis tubing at 4°C.
  • the protein sample was centrifuged at 3220 x g for 10 minutes to pellet denatured insoluble material prior to ion exchange.
  • Ion exchange was performed using the AKTA purifier 10, employing 2 x 5mL HiTrapTM SP HP column run in series, passing the cleared dialysed material through the column via the P960 external pump.
  • the column was washed with 10 column volumes of ion-exchange buffer prior to commencement of a linear buffer gradient (salt gradient) for elution of the protein from the column.
  • the ion exchange buffer was replaced over a linear gradient with the identical buffer with the addition of NaCl to 1M final concentration.
  • the elution gradient was performed over 300mL with a final concentration of 600mM NaCl.
  • Fractions corresponding to the eluted diabody were pooled and quantified.
  • the major protein species eluted from the ion exchange column is typically the dimeric form of the diabody.
  • eluted protein material was placed in dialysis membrane (10K cut off) and concentrated to approximately 3mg/mL at 4°C by exposing the membrane to a polyethylene glycol product (Aquacide II, Calbiochem). Concentrated protein was subsequently dialysed once in phosphate buffered saline (PBS) (200x volume at 4°C for 4hrs minimum) prior to size exclusion chromatography (gel filtration).
  • PBS phosphate buffered saline
  • Binding activity to soluble antigen was established by a column shift.
  • Soluble antigen for the AVP04-07 and AVP04-50 diabodies is TAG72, available in soluble form from bovine submaxillary mucin (BSM) (Sigma).
  • BSM bovine submaxillary mucin
  • the soluble antigen is recombinant HER2 ectodomain.
  • Binding activity was determined by comparing the resulting diabody/antigen complex peak to the free diabody peak.
  • the elution profiles of the diabody or diabody/antigen complex was monitored either directly though absorbance at 280nm or, in cases where the diabody was Europium labelled, elution fractions were measured in a Victor time -resolved fluorometer using the Europium mode in the Victor multilabel program wizard.
  • Diabody at approximately 3mg/mL was labelled with Europium (DELFIA Eu- Nl ITC Chelate, Perkin Elmer) to free amino groups for dissociation-enhanced time- resolved fluorometric assays.
  • Diabody was labelled with the Europium reagent at a ratio of 20nmol Europium to lnmol protein. This was achieved by adding 100 ⁇ g of protein to 40nmol Europium reagent in the presence of lOOmM sodium bicarbonate buffer pH 9.0 - 9.3, in a final volume of 48.5 ⁇ .
  • the reaction was performed in a Reacti Vial (Pierce) containing a small magnetic stirring flea. The reaction was performed at 4°C overnight in the dark.
  • Tris-buffered saline (TBS, 50 mmol/L Tris- HC1, pH 7.8) was added to the reaction after incubation (200 ⁇ ) to quench excess Europium reagent by means of introducing an abundance of free amino groups.
  • the Europium reaction was purified by gel filtration using a Superdex ® 200 10/300 column (GE Healthcare Life Sciences) and collecting 0.5ml fractions that correspond to the purified diabody. The Eu concentration of the fractions was measured by making a 1 : 100 dilution in DELFIA enhancement solution on a LumiTrac 600 96 well plate. Fractions were measured in a Victor time-resolved fluorometer using the Europium mode in the Victor multilabel program wizard.
  • the fluorescence profile was plotted against the gel filtration 280nm chromatogram and fractions that correlate to the diabody elution profile (as determined by 280nm absorbance) and a peak in 3+ fluorescence were collected and pooled. Protein was quantified and the Eu concentration in the labelled protein was calculated using the Europium standards provided with the kit according to the manufacturer's instructions, whereby the molar absorptivity of reacted Eu-Nl ITC chelate is 8000 at 280nm (1 ⁇ /L reacted chelate gives an absorbance of 0.008 at 280nm). Prior to storage, 7.5% BSA in Tris-HCl (highly pure, supplied with the DELFIA Europium labelling kit) was added to the Europium labelled diabody to a final concentration of 0.1% (w/v).
  • TCEP Tris (2-carboxyethyl) phosphine hydrochloride
  • Eu-DTPA was added at 30 times (Eu-DTPA: protein) molar excess to reduced AVP04-50. The reaction was completed following 3-16hrs at 4°C. Unreacted Eu-DTPA was separated from the protein by gel filtration on a Superdex ® 200 10/300 column, pre-equilibrated with Tris- buffered saline, pH 7.4. Each resulting fraction was diluted in Enhancement Solution (PerkinElmer, Turku, Finland) and assayed for Europium counts using a Victor time resolved flurometer. Peak Europium counts corresponding with peak protein fractions were pooled and stabilised with 0.1 % of highly pure BSA, and stored at 4°C, protected from light. Concentration of incorporated Eu-DTPA was determined by calculating Eu counts of the sample relative to a ⁇ Eu standard supplied with the kit. 1.12 Quantification of Free Sulphydryls
  • Reduced thiolated diabodies were concentrated to at least 2mg/ml using Microcon centrifugal concentrator (Millipore, MA).
  • 25 ⁇ of reduced protein was mixed with 250 ⁇ 1 of lOOmM phosphate buffer + ImM EDTA, pH 8.0 and 5 ⁇ 1 of 4mg/mL Ellman's reagent (DTNB) (Pierce, Rockford, II). The reaction was allowed to proceed at ambient temperature for 15min. Free sulphydryl concentration was quantified by molar absorptivity, assuming the molar extinction coefficient of TNB in this buffer system, at 412nm, is 14,150 M "1 cm "1 . Estimation of sulphydryl groups per diabody was obtained by dividing the molar concentration of sulphydryls by the molar concentration of diabody.
  • Heterobifunctional, monodispersed Maleimide-PEG2000-NH2 was purchased from JenKem Technology, USA (polydispersity Q-values ⁇ 1.04). Prior to use, a small amount of PEG was reconstituted in water, and added to reduced thiolated diabody at 20-fold mole excess in lOOmM phosphate buffer + ImM EDTA pH 7.0. The reaction was allowed to proceed for 3-16 hrs at 4°C with constant stirring. Following incubation, the entire sample was applied to a Superdex ® 200 10/300 column.
  • Example 2 - Molecular Modelling and Identification of Framework 1 as a Suitable Position to Engineer Cysteine Replacement Mutations.
  • FIG. 2B represents a typical cationic exchange elution profile tracing absorbance at 280nm in which the major dimeric isoform (arrow) of AVP04-50 could be easily separated from other unwanted AVP04-50 iso forms or proteins.
  • the elution fractions containing the major isoform of interest were pooled for downstream purification.
  • AVP04-50 dimer was concentrated and passed through a Superdex ® 75 26/60 prep-grade column. Under the elution settings outlined in Example 1, the AVP04-50 diabody eluted at approximately 53.5 minutes post injection (Figure 2C). Fractions within the margins outlined in Figure 2C, corresponding to the eluted AVP04-50 dimer, were pooled and concentrated to between 1.5-3 mg/ml. The final purity of the purified product was assessed by gel filtration chromatography on a Superdex ® 200 10/300 column and SDS-PAGE electrophoresis.
  • AVP04-07, AVP04-50, AVP07-17 and AVP07-63 The immunoreactivity of purified diabodies (AVP04-07, AVP04-50, AVP07-17 and AVP07-63) was tested in vitro by column shift assay following core methods outlined in Example 1.
  • AVP04-07 and AVP04-50 were allowed to pre-complex with their antigen BSM (containing TAG72) prior to gel filtration, a significant shortening of elution times were observed when compared to diabody alone ( Figures 3 A, 3B).
  • AVP07-17 and AVP07-63 also showed complex formation with their antigen as evidenced by a significant shortening of elution times in gel filtration ( Figures 3C, 3D).
  • thiolated diabody (AVP04-50) was reduced with TCEP and reactive thiols quantified using Ellman's reagent. Intact IgG and a diabody not containing cysteine replacement mutations in V L framework 1 (e.g., either AVP04-07) were used as standardizing controls. Under reduction conditions outlined in Example 1, native and intact IgG have 8 reactive thiols available for reduction and diabodies such as AVP04-07 have no free reactive thiols.
  • Free sulphhydryl quantification indicated that the correct number of cysteines in intact IgG and diabody-controls not containing cysteine replacement mutations, respectively 8 and zero, were reactive (Table 2).
  • AVP04-50 a diabody consisting of two identical monomeric chains, each with 2 cysteine replacement mutations in V L framework 1, an average of 4 cysteines were freely accessable to reduction by TCEP, forming at least 4 free and reactive thiols (Table 2). The data shown is representative of three individual experiments.
  • the cysteine replacement mutations in V L framework 1 of AVP04-50 were labelled with a Europium loaded DTPA chelate followed by immunoreactivity assays as outlined in Example 1.
  • Europium- AVP04-50 was shown able to form complexes with with its antigen BSM (which contains TAG72), evidenced by a shortening of protein elution times in gel filtration chromatography on a Superdex ® 200 10/300 column. The elution times were shortened from an approximate 27 minutes (Eu- AVP04-50) ( Figure 4) to an approximate 14 minutes (Eu-AVP04-50-TAG72 complex) ( Figure 4).
  • PEGylated protein (AVP04-50-PEG2000) was resolved on a non-reducing SDS-PAGE ( Figure 5A) and an average shift in molecular weight of 10 kDa was observed per AVP04-50 monomeric chain. This shift in molecular weight was also confirmed by a change in protein elution times in gel filtration chromatography on a Superdex ® 200 10/300 column. Under gel filtration conditions outlined in Example 1, AVP04-50 in its native state eluted from this coulmn at approximately 30 minutes.
  • Example 2 To confirm that AVP04-50-PEG2000 was still able to bind antigen, a column shift binding assay was performed as outlined in Example 1. Under standard conditions, AVP04-50-PEG2000 eluted from the Superdex ® 200 10/300 column at approximately 24 min ( Figure 5C dotted line). When AVP04-50-PEG2000 was allowed to complex with it's antigen BSM (containing TAG72), a shortening of elution time to 15 min was observed by tracing the absorbance at 280nm, clearly indicating an AVP04-50-PEG2000/TAG72 complex formation (Figure 5C).
  • Avibodies are recombinant proteins comprising variable domains of antibodies.
  • Avibodies utilize the variable domains of monoclonal antibodies by fusing them into a single polypeptide chain interspersed by a short linker region in either VH-to-VL or VL- to-VH orientation. Depending on the linker length, these Avibodies are designed to form stable, biologically active monobodies (scFv), diabodies, triabodies or tetrabodies containing one, two, three or four functional binding sites respectively.
  • the V H and V L domain sequences of the Avibodies modeled were used to search the RCSB PDB Data bank (www.pdb.org) using both BLAST and/or FASTA searches. The structure hits with the highest sequence identity, resolution and completeness were selected for use as templates for the Fv domains of the modeled Avibodies. If the asymmetric unit in a pdb file contained more than one template model all templates were used and treated identically.
  • Molecular models of Avibodies were generated using Discovery Studio (DS) Software (v2.5, Accelrys, CA, USA) using the MODELLER algorithm (Sali and Blundell, 1993) embedded in the software and evaluated using the scoring functions contained in the software. The best model was selected on the basis of the presence of a high ranking score in each of the MODELLER generated Probability Density Function (PDF) for total and physical energy and the Discrete Optimized Protein Energy (DOPE) score, (Shen et. al, 2006). The selected model was written out to a pdb file for further analysis. Images of the resulting models were also generated using DS.
  • PDF Probability Density Function
  • DOPE Discrete Optimized Protein Energy
  • the ASA was used here as an assessment of the modeled disulphide mutant's ability to be available for conjugation. For each construct 10 models were generated and the average ASA determined for each mutated residue in each modeled V domain, then a standard deviation calculated. In this analysis, a large standard deviation indicates that the surface exposure of a particular residue varies depending on the model indicating variability in the modeled disulphide and hence potentially less accessible for reduction and/or conjugation.
  • AVP04-07 Avibody (SEQ ID NO. 59) is a recombinant diabody with a theoretical pI/Mw: 8.0 / 51 kDa, a V L K light chain and a subgroup I V H chain.
  • AVP04- 07 recognizes the tumor associated antigen TAG72.
  • Modified versions of this Avibody are referred to herein as AVP04-xx, in which "xx" is a number designating different forms of the Avibody.
  • This Avibody utilizes the variable regions of the murine monoclonal antibody CC49, fusing them in sequence to form a stable, biologically active diabody containing two functional binding sites.
  • the variable domains of CC49 have been modified (Roberge, et al, 2006) in amino acid sequence in order to achieve a high-expressing and highly stable recombinant molecule with exceptional in vitro and in vivo properties.
  • the 1ZA6 template encodes the structure of an anti-tumor CH2-domain-deleted humanized antibody. This recombinant humanized antibody also recognizes the TAG72 antigen.
  • the Fv structure in the 1ZA6 pdb file was used to model the Fv domains of the AVP04-07 diabody.
  • the ILMK described above was used for the quaternary spatial alignment of the templates to form an AVP04-07 diabody in the method described above.
  • the selected highest scoring model of the AVP04-07 diabody is shown in Figure 7 with the positions targeted for thiol mutations (section 9.6) and represents the "un-mutated" configuration of this Avibody dimer.
  • AVP07-17 Avibody (SEQ ID NO: 61) is a recombinant diabody with a theoretical pI/Mw: 6.4 / 55 kDa, an exceptionally long CDRH3 loop a ViA light chain and a subgroup I V H chain.
  • AVP07-17 recognizes the tumor associated antigen HER2.
  • Modified versions of this Avibody are referred to herein as AVP07-xx, in which "xx" is a number designating different forms of the Avibody.
  • AVP07-17 has lower identity with the structures available in the RCSB pdb when using standard FASTA and BLAST searches compared to the AVP04-07. No Fv pair of V L and V H showed as high an identity with AVP07-17 when compared with the results obtained for AVP04-07.
  • the MATRAS server uses a standard sequence homology search against the current PDB using the BLAST program with a graphical representation of the aligned regions to assist in template selection. This method revealed two good templates, both with greater than 64% sequence identity in both the V L and V H domains.
  • the selected Fv templates were contained in the pdb files of a) 2B1H (Stanfield et. al, 2006) which had 80.6% identity to AVP07-17 excluding the linker residues and CDRH3 and b) 3G04 (Sanders et. al, 2007) which had 73.5% identity to AVP07-17 excluding the linker residues and CDRH3.
  • the 1LMK diabody described above was used for the quaternary spatial alignment of the template Fvs to form an AVP07-17 ("un-mutated") diabody in the method described above.
  • the long CDRH3 loop length of AVP07-17 was also problematic for modeling as no homologous structures could be found for use as templates. These were modeled as loops with no template constraints (essentially ab initio) and assessed for structural violations after modeling. In all cases presented here, the CDR3 loops are modeled with low confidence levels and are not included in some analyses as they were not considered to affect the overall structure or framework regions of the Avibodies.
  • the AVP02-60 Avibody (SEQ ID NO: 63) is a recombinant diabody with a theoretical pI/Mw: 8.47 / 50.1 kDa, a V L chain kappa and a subgroup III V H chain. It is based on the primary mouse monoclonal C595 antibody that recognizes a breast cancer associated mucin encoded by the MUC1 gene, CD227 (Gendler et. al, 1990). It recognizes the epitope RPAP within the protein core of the mucin, a motif repeated some 40 times in the sequence. Modified versions of this Avibody are referred to herein as AVP02-xx, in which "xx" is a number designating different forms of the Avibody.
  • BLAST and FASTA searching with the V L or V H revealed several templates with high identity scores that contained both the V L and V H domains. However, only one template had a V H with sufficient identity in sequence and length to model the CDRH3. Hence two templates were selected for V H and V L modeling while one extra template was selected for V H only modeling.
  • the templates selected were: a) 1MHP V H and V L (86.9% identity, 89.6% homology; Karpusas, et. al, 2003), b) 2B2X V H and V L (85.7% identity, 88.3% homology; Clark, et. al, 2006) and c) 2ADG V H : (86.8% identity, 96.5%> homology; Zhou et. al, 2005) which was the only template with an un- gapped alignment for CDRH3, the V L domain of this Fv was not used in the modeling.
  • the templates and AVP02-60 have 88.4% and identity and 91.1% homology.
  • the 1LMK diabody described above was used for the quaternary spatial alignment of the template Fvs to form an AVP02-60 ("un-mutated") diabody in the method described above.
  • the selected highest scoring model of the AVP02-60 diabody is shown in Figure 9 with the positions targeted for thiol mutations (section 9.6) and represents the "un-mutated" configuration of this Avibody dimer.
  • V L and V H domains of antibodies are firstly members of the Immunoglobulin superfamily classically containing 7-10 ⁇ strands in two sheets with a typical topology and connectivity. These domains are secondly members of the V-type immmunoglobulins showing symmetry of the / ⁇ -sheets within the domain axis (Halaby, et. al, 1999).
  • the antibody V-type or V-set domains are divided into V H (type 1-4), V L K and V L ⁇ domains in online databases such as SCOP (http://scop.mrc- lmb.cam.ac.uk/scop/data/scop.b.c.b.b.b.html, Murzin, et.
  • V H type 1-4
  • V L K type 1-4
  • ViA domains Well defined structural similarities exist between V H (type 1-4), V L K and ViA domains. Due to these known and accepted structural similarities, it is reasonable to assume that the majority of intra-framework cysteine replacement mutations identified in any V L domain should also be transferable to the same structural position in any other V H domain. This assumption is shown to be true below, with one notable exception in the FR3 V H that could not be structurally matched with high confidence to the same position in the V L (see modeling mutation c9 below).
  • Preferred residues for engineered cysteine replacement were selected by visual inspection of the V L domain of the AVP04-07 diabody. Preferred residues were identified if they met specific structural requirements including having side chains generally angled towards each other, side chains atoms generally exposed to solvent and distances between Ca carbon atoms of approximately 6-7A. Engineered cysteine replacements meeting such criteria were considered good candidates for mutation to form intra-framework disulphide bridges replacements which could be selectively broken on controlled reduction and used to conjugate a payload. These positions in silico were then transferred by least squares alignment to the V H domain of the same Fv and this domain inspected for any further potential sites.
  • All identified sites in the AVP04-07 V L and V H domains could then be transferred to the AVP02-xx and AVP07-xx family Fvs by least squares alignment and modeling of the same.
  • FR2 Framework 2 in the architecture of an immunoglobulin V domain is a candidate for engineering cysteine replacements.
  • FR2 is defined by Kabat as V L residues 35 to 49 inclusive and V H residues 36 to 49 inclusive. It comprises C and C strands of the immunoglobulin ⁇ -sheet which extends from CDR1 to a loop/turn then back to CDR2.
  • the C strand is part of the CDC'FG sheet and has interactions with both the C and the F strand.
  • the C strand is on the edge of the sheet and is partly involved in the interface between the V H and V L domains of the Fv via interaction with opposing domain buried C-terminal section of Kabat CDR3 and FR4.
  • modeling mutation c5 and modeling mutation c6 in the V H were Kabat residues H39-H45 (modeling mutation c5) and H39-H43 (modeling mutation c6).
  • FR3 Framework 3 in the architecture of an immunoglobulin V domain is also a good candidate for engineering cysteine replacements.
  • FR3 is defined by Kabat as V L residues 57 to 88 inclusive and V H residues 66 to 94 inclusive. It comprises C", D, E and F strands and their connecting loops/turns.
  • regions between Kabat positions 63-74 of VL and between Kabat positions 68-81 VH were identified as good regions for engineering cysteine replacements.
  • Two positions within each region were identified as good candidates for engineering cysteine replacements.
  • These candidates were V H Kabat residues H70-L79 (labeled as modeling mutation c8) and H72-H75 (labeled as modeling mutation c9).
  • modeling mutation c8 in FR3 region could be easily mapped to the same structural position in the V L domain at residues L65-L72.
  • no structural homologue for modeling mutation c9 i.e. Kabat residues V H H72-H75
  • V H H72-H75 the structural homologue for modeling mutation c9
  • Mutants containing modeling mutation c4 (Kabat L78-L82, AVP04-83, SEQ ID NO: 105 and Kabat H82C-H86, AVP04-114, SEQ ID NO: 111) were designed, expressed, tested and used to demonstrate that the introduction of engineering cysteine replacements did not abrogate stability and/or immunoreactivity, but subsequent controlled disulphide-bond reduction and payload conjugation relied on high accessible surface areas.
  • the un-mutated AVP04-07 model was the starting point for mapping the framework 2 (FR2) and framework 3 (FR3) engineered cysteine replacements described above that are capable of forming intra-framework disulphide bonds.
  • the identified positions are indicated in Figure 7 on the native AVP04-07 diabody model.
  • AVP04-79 Diabody nucleic acid sequence (SEQ ID NO: 100), forming the Avibody mutated in Kabat residues L38 and L42 (SEQ ID NO: 101) and also referred to herein as modeling mutation number c6.
  • AVP04-80 Diabody nucleic acid sequence (SEQ ID NO: 102), forming the Avibody mutated in Kabat residues L38 and L44 (SEQ ID NO: 103) and also referred to herein as modeling mutation number c5.
  • AVP04-111 Diabody nucleic acid sequence (SEQ ID NO: 106), forming the Avibody mutated in Kabat residues H39 and H43 (SEQ ID NO: 107) and also referred to herein as modeling mutation number c6.
  • AVP04-112 Diabody nucleic acid sequence (SEQ ID NO: 108), forming the Avibody mutated in Kabat residues H39 and H45 (SEQ ID NO: 109) and also referred to herein as modeling mutation number c5.
  • AVP04-124 scFv nucleic acid sequence (SEQ ID NO: 118), forming the Avibody mutated in Kabat residues L38 and L42 (SEQ ID NO: 119) and also referred to herein as modeling mutation number c6.
  • AVP04-125 Triabody nucleic acid sequence (SEQ ID NO: 120), forming the Avibody mutated in Kabat residues L38 and L42 (SEQ ID NO: 121) and also referred to herein as modeling mutation number c6.
  • AVP04-120 Diabody nucleic acid sequence (SEQ ID NO: 112), forming the Avibody mutated in Kabat residues H70 and H79 (SEQ ID NO: 113) and also referred to herein as modeling mutation number c8.
  • AVP04-123 Diabody nucleic acid sequence (SEQ ID NO: 116), forming the Avibody mutated in Kabat residues L65 and L72 (SEQ ID NO: 117) and also referred to herein as modeling mutation number c8.
  • AVP04-121 Diabody nucleic acid sequence (SEQ ID NO: 114), forming the Avibody mutated in Kabat residues H72 and H75 (SEQ ID NO: 115) and also referred to herein as modeling mutation number c9.
  • mapping engineered cysteine replacements within the V L domain could be easily mapped to identical structural positions within the V H domain.
  • Modeling of the above mutants was repeated using the method outlined for the AVP04-07 model (Example 9.2) using the same input parameters except for the sequence input and designation of disulphide linkages which reflected the desired mutations above. Model assessment was also carried out as for the AVP04-07 models.
  • Each candidate engineered cysteine replacement was subjected to modeling with one V L cysteine pair mutant and its analogous V H cysteine pair mutant included in each modeling run.
  • the results of cysteine replacement modeling onto the AVP04-07 FR2/FR3 structure are shown in Figures 10A-B.
  • Figure 10A-B shows that there was little structural change in the vicinity of the engineered FR2/FR3 cysteine mutations, even when an intra-framework disulphide bond between the cysteine replacements was prescribed in silico.
  • ASA solvent accessible surface area
  • diabody in the V H -V L orientation (first column in each series), an AVP04-xx triabody in the V H -V L orientation with a -1 residue linker (second column in each series), an AVP04-xx triabody in the V H -V L orientation with a zero-residue linker (third column in each series), an AVP04-xx diabody in the V L -V H orientation with Fv spatial orientation modeled on the 1LMK diabody (fourth column in each series), an AVP04-xx diabody in the V L -V H orientation with Fv spatial orientation modeled on the 1MOE diabody (fifth column in each series), an AVP04-xx triabody in the V L -V H orientation with a 1 residue linker (sixth column in each series) and an AVP04-xx triabody in the V L -V H orientation with a 2 residue linker (seventh and last column in each series).
  • the modeling mutation designated by c6 contain the H39-H43 and L38- L42 disulphide mutations and similarly for c5 H39-H45/L38-L44, c8 H70-H79/L65- L72, c9 H72-H75 and c4 H82C-H86/L78-L82.
  • the ASA values for candidate cysteine replacement pairs was significantly higher than the ASA values of the highly conserved, yet structurally buried, cysteine pairs H22-H92 and L23-L88, which averaged an ASA value of 0.025.
  • the ASA values of candidate cysteine replacement pairs were more similar to the ASA values of the structurally exposed CDR residues.
  • AVP04-83 Diabody nucleic acid sequence (SEQ ID NO: 104), forming the Avibody mutated in Kabat residues L78 and L82 (SEQ ID NO: 105) and also referred to herein as modeling mutation number c4.
  • AVP04-114 Diabody nucleic acid sequence (SEQ ID NO: 110), forming the Avibody mutated in Kabat residues H82C and H86 (SEQ ID NO: 111) and also referred to herein as modeling mutation number c4.
  • Mutants containing modeling mutation c4 met all the structural requirements for engineering cysteine replacements, however, the mutated residues displayed very low accessible surface areas (refer to Figure 11). Mutants containing modeling mutation c4 were used to clearly demonstrate that the introduction of engineered cysteine replacements does not abrogate stability and immunoreactivity, but it is preferable for subsequent controlled disulphide-bond reduction and payload conjugation that the residues are "surface exposure" to solvent; a characteristic lacking in the mutants of modeling mutation c4. 9.7 Framework 2 and 3 Cysteine Insertion Positions Identified for Engineering Cysteine Replacement Mutations and Molecular Modeling in AVP02-xx and AVP07- xx Avibody Diabodies.
  • AVP02-115 Diabody nucleic acid sequence (SEQ ID NO: 122), forming the Avibody mutated in Kabat residues L38 and L42 (SEQ ID NO: 123) and also referred to herein as modeling mutation number c6.
  • AVP02-116 Diabody nucleic acid sequence (SEQ ID NO: 124), forming the Avibody mutated in Kabat residues H39 and H43 (SEQ ID NO: 125) and also referred to herein as modeling mutation number c6.
  • AVP02-126 Diabody nucleic acid sequence (SEQ ID NO: 130), forming the Avibody mutated in Kabat residues L38 and L44 (SEQ ID NO: 131) and also referred to herein as modeling mutation number c5.
  • AVP02-127 Diabody nucleic acid sequence (SEQ ID NO: 132), forming the Avibody mutated in Kabat residues H39 and H45 (SEQ ID NO: 133) and also referred to herein as modeling mutation number c5.
  • AVP02-128 Diabody nucleic acid sequence (SEQ ID NO: 134), forming the Avibody mutated in Kabat residues L65 and L72 (SEQ ID NO: 135) and also referred to herein as modeling mutation number c8.
  • AVP02-129 Diabody nucleic acid sequence (SEQ ID NO: 136), forming the Avibody mutated in Kabat residues H70 and H79 (SEQ ID NO: 137) and also referred to herein as modeling mutation number c8.
  • AVP02-130 Diabody nucleic acid sequence (SEQ ID NO: 138), forming the Avibody mutated in Kabat residues H72 and H75 (SEQ ID NO: 139) and also referred to herein as modeling mutation number c9.
  • AVP07-117 Diabody nucleic acid sequence (SEQ ID NO: 126), forming the Avibody mutated in Kabat residues L38 and L42 (SEQ ID NO: 127) and also referred to herein as modeling mutation number c6.
  • AVP07-118 Diabody nucleic acid sequence (SEQ ID NO: 128), forming the Avibody mutated in Kabat residues H39 and H43 (SEQ ID NO: 129) and also referred to herein as modeling mutation number c6.
  • AVP07-131 Diabody nucleic acid sequence SEQ ID NO: 140
  • AVP07-132 Diabody nucleic acid sequence SEQ ID NO: 142
  • AVP07-132 Diabody nucleic acid sequence SEQ ID NO: 143
  • AVP07-133 Diabody nucleic acid sequence (SEQ ID NO: 144), forming the Avibody mutated in Kabat residues L65 and L72 (SEQ ID NO: 145) and also referred to herein as modeling mutation number c8.
  • AVP07-134 Diabody nucleic acid sequence (SEQ ID NO: 146), forming the Avibody mutated in Kabat residues H70 and H79 (SEQ ID NO: 147) and also referred to herein as modeling mutation number c8.
  • AVP07-135 Diabody nucleic acid sequence (SEQ ID NO: 148), forming the Avibody mutated in Kabat residues H72 and H75 (SEQ ID NO: 149) and also referred to herein as modeling mutation number c9.
  • AVP04 the solvent accessible surface area (ASA) values for candidate cysteine replacements in AVP02-xx and AVP07-xx was calculated from the models generated above.
  • Figure 14 outlines the calculated ASA values for AVP02-xx models
  • Figure 15 outlines the calculated ASA values for AVP07-xx model.
  • the model mutations designated by c6 contain the H39-H43 and L38-L42 disulphide mutations and similarly for c5 H39-H45/L38-L44, c8 H70-H79/L65-L72, c9 H72-H75 and c4 H82C-H86/L78- L82.
  • an exception was modeling mutation c4 (H82C-H86/L78-L82) which again showed low ASA values in both the AVP02-XX and AVP07-xx.
  • Figure 16 shows the Root Mean Squared Deviations (RMSDs) for the native and cysteine-mutated V domains from Avibody construct models.
  • the RMSD values were used to gauge the perturbation of the V domain caused by the in silico insertion of engineered cysteine disulphide mutations.
  • the RMSDs were obtained by alignment of the mutated modeled V domains against the best scoring modeled native structure for the respective construct group.
  • Figure 16 shows fourteen construct groups which have been labeled as:
  • H-VHVLD 5 V H domains from diabodies in the V H -V L orientation with a 5 residue linker containing a V H engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • H-VHVLT - 1 V H domains from triabodies in the V H -V L orientation with a - 1 residue linker containing a V H engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • H-VHVLT 0 V H domains from triabodies in the V H -V L orientation with a zero residue linker containing a V H engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • H-VLVHD lmk5 V H domains from diabodies in the V L -V H orientation with Fv spatial orientation modeled on the 1LMK diabody and with a 5 residue linker containing a V H engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • H-VLVHD moe5 V H domains from diabodies in the V L -V H orientation with Fv spatial orientation modeled on the 1MOE diabody and with a 5 residue linker containing a V H engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • H-VLVHT 1 V H domains from triabodies in the V L -V H orientation with a one residue linker containing a V H engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • H-VLVHT 2 V H domains from diabodies triabodies in the V L -V H orientation with a two residue linker containing a V H engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • L-VHVLD 5 V L domains from diabodies in the V H -V L orientation with a 5 residue linker containing a V L engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • L-VHVLT - 1 V L domains from triabodies in the V H -V L orientation with a -1 residue linker containing a V L engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • L-VHVLT 0 V L domains from triabodies in the V H -V L orientation with a zero residue linker containing a V L engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • L-VLVHD lmk5 V L domains from diabodies in the V L -V H orientation with Fv spatial orientation modeled on the 1LMK diabody and with a 5 residue linker containing a V L engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • L-VLVHD moe5 V L domains from diabodies in the V L -V H orientation with Fv spatial orientation modeled on the 1MOE diabody and with a 5 residue linker containing a V L engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • L-VLVHT 1 V L domains from triabodies in the V L -V H orientation with a one residue linker containing a V L engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • L-VLVHT 2 V L domains from triabodies in the V L -V H orientation with a two residue linker containing a V L engineered cysteine replacement pair prescribed to form a disulphide-bond in silico.
  • the above construct groups were modeled in order to cover all possible Fv permutations of orientation, Fv number and spatial orientation.
  • the best native (non-thiolated) Avibody model was compared to all other native (non-thiolated) Avibody models (first column in each construct group) and subsequently compared to all models generated of modeling mutation c6 (H39- H43/L38-L42, second bar in each construct group), modeling mutation c5 (H39- H45/L38-L44, third bar in each construct group), modeling mutation c8 (H70- H79/L65-L72, fourth bar in each construct group), modeling mutation c9 (H72-H75, fifth bar in each construct group) and modeling mutation c4 (H82C-H86/L78-L82, sixth and final bar in each construct group).
  • VH-Linker-VL DNA constructs encoding the VH and VL regions of a mouse mAb specific for TAG72 (SEQ ID NO: 58), a human mAb specific for HER2 (SEQ ID NO: 60) and a murine mAb specific for MUC1 (SEQ ID NO: 62) were synthesized with the appropriate restriction sites and cloned into pUC57 by GenScript (Piscataway, NJ, USA). Although Avibodies have been isolated in either orientation of V region i.e. VH- Linker-VL and VL-Linker-VH (Carmichael et al., 2003), all constructs described herein were arranged as VH-Linker-VL.
  • Miniprep DNA was extracted from transformants using the Qiagen miniprep spin kit and recombinant clones identified by sequencing with T7 promoter and terminator primers using Dye Terminator Cycle Sequencing kits with AmpliTaq.
  • the clone containing the V regions of the anti-TAG72 mAb in the V H -Gly 4 Ser-V L orientation was designated AVP04-07 (SEQ ID NO: 58).
  • the clone containing the V regions of the anti-HER2 mAb in the VH-Gly 4 Ser-VL orientation was designated AVP07-17 (SEQ ID NO: 60).
  • the clone containing the V regions of the anti-MUCl mAb in the VH-Gly 4 Ser-VL orientation was designated AVP02-60 (SEQ ID NO: 62). These three clones formed the base parental sequences from which all other Avibody mutants and thiolated Avibodies were derived.
  • This method of cloning allowed for the insertion of an amino-terminal pelB leader sequence for periplasmic expression of the target protein and either a carboxy- terminal (His) 6 tag or a carboxy-terminal Myc+(His)6 tag.
  • an affinity tags such as (His) 6 , was routinely used to streamline downstream purification processes and is known to be neutral in biological activity.
  • AVP07-86 SEQ ID NO: 64.
  • All AVP07-xx Thiolated Avibodies contain this extra modification of V H CDR3, rendering the AVP07-xx family compatible with the intra- framework 2 or intra-framework 3 engineered cysteine replacement strategy.
  • Thiolated Avibodies were also generated with modified linker lengths in order to generate thiolated versions of scFv or Triabodies. It is well known from published literature in the antibody field that modification of linker composition and length can affect formation of Avibody multimers (Kortt et al. 1997). Promotion of scFv formation was engineered by modifying the linker length of the diabody parent from five residues, typically GGGGS (SEQ ID NO: 57) to fifteen, GGGGSGGGGSGGGGS or twenty, GGGGSGGGGSGGGGSGGGGS using a mutagenic primer encoding the extra residues and sequencing the DNA resultant clones for the correct sequence. For example, the nucleic acid encoding the AVP04-124 Avibody (SEQ ID NO: 118), encodes an scFv.
  • the nucleic acid encoding the AVP04-125 Avibody (SEQ ID NO: 120), encodes a triabody with the residues 'VTVS-DIVM' instead of the linker region.
  • This clone was engineered from the parent AVP04-07 by deletion mutagenesis using mutagenic primers encoding the desired sequence above.
  • Intra-Framework 2 or Intra-Framework 3 Engineered Cysteines and N-terminal Serine substitution by site-directed mutagenesis.
  • the intra-framework 2 or intra-framework 3 engineered cysteine insertion mutations were introduced into the Avibody sequences of AVP04-xx, AVP07-xx and AVP02-xx families to form the following thiolated Avibodies: AVP04-XX Family Template Sequences (TAG72-specific):
  • AVP04-79 Diabody nucleic acid sequence (SEQ ID NO: 100), forming the Avibody mutated in Kabat residues L38 and L42 (SEQ ID NO: 101) and also referred to herein as modeling mutation number c6.
  • AVP04-80 Diabody nucleic acid sequence (SEQ ID NO: 102), forming the Avibody mutated in Kabat residues L38 and L44 (SEQ ID NO: 103) and also referred to herein as modeling mutation number c5.
  • AVP04-83 Diabody nucleic acid sequence (SEQ ID NO: 104), forming the Avibody mutated in Kabat residues L78 and L82 (SEQ ID NO: 105) and also referred to herein as modeling mutation number c4.
  • AVP04-111 Diabody nucleic acid sequence (SEQ ID NO: 106), forming the Avibody mutated in Kabat residues H39 and H43 (SEQ ID NO: 107) and also referred to herein as modeling mutation number c6.
  • AVP04-112 Diabody nucleic acid sequence (SEQ ID NO: 108), forming the Avibody mutated in Kabat residues H39 and H45 (SEQ ID NO: 109) and also referred to herein as modeling mutation number c5.
  • AVP04-114 Diabody nucleic acid sequence (SEQ ID NO: 110), forming the Avibody mutated in Kabat residues H82C and H86 (SEQ ID NO: 111) and also referred to herein as modeling mutation number c4.
  • AVP04-120 Diabody nucleic acid sequence (SEQ ID NO: 112), forming the Avibody mutated in Kabat residues H70 and H79 (SEQ ID NO: 113) and also referred to herein as modeling mutation number c8.
  • AVP04-121 Diabody nucleic acid sequence (SEQ ID NO: 114), forming the Avibody mutated in Kabat residues H72 and H75 (SEQ ID NO: 115) and also referred to herein as modeling mutation number c9.
  • AVP04-123 Diabody nucleic acid sequence (SEQ ID NO: 116), forming the Avibody mutated in Kabat residues L65 and L72 (SEQ ID NO: 117) and also referred to herein as modeling mutation number c8.
  • AVP04-124 scFv nucleic acid sequence (SEQ ID NO: 118), forming the Avibody mutated in Kabat residues L38 and L42 (SEQ ID NO: 119) and also referred to herein as modeling mutation number c6.
  • AVP04-125 Triabody nucleic acid sequence (SEQ ID NO: 120), forming the Avibody mutated in Kabat residues L38 and L42 (SEQ ID NO: 121) and also referred to herein as modeling mutation number c6.
  • AVP02-XX Family Template Sequences (MUC1 -specific):
  • AVP02-115 Diabody nucleic acid sequence (SEQ ID NO: 122), forming the Avibody mutated in Kabat residues L38 and L42 (SEQ ID NO: 123) and also referred to herein as modeling mutation number c6.
  • AVP02-116 Diabody nucleic acid sequence (SEQ ID NO: 124), forming the Avibody mutated in Kabat residues H39 and H43 (SEQ ID NO: 125) and also referred to herein as modeling mutation number c6.
  • AVP02-126 Diabody nucleic acid sequence (SEQ ID NO: 130), forming the Avibody mutated in Kabat residues L38 and L44 (SEQ ID NO: 131) and also referred to herein as modeling mutation number c5.
  • AVP02-127 Diabody nucleic acid sequence (SEQ ID NO: 132), forming the Avibody mutated in Kabat residues H39 and H45 (SEQ ID NO: 133) and also referred to herein as modeling mutation number c5.
  • AVP07-XX Family Template Sequences (HER2-specific):
  • AVP07-117 Diabody nucleic acid sequence (SEQ ID NO: 126), forming the Avibody mutated in Kabat residues L38 and L42 (SEQ ID NO: 127) and also referred to herein as modeling mutation number c6.
  • AVP07-118 Diabody nucleic acid sequence (SEQ ID NO: 128), forming the Avibody mutated in Kabat residues H39 and H43 (SEQ ID NO: 129) and also referred to herein as modeling mutation number c6.
  • AVP07-131 Diabody nucleic acid sequence (SEQ ID NO: 140), forming the Avibody mutated in Kabat residues L38 and L44 (SEQ ID NO: 141) and also referred to herein as modeling mutation number c5.
  • AVP07-132 Diabody nucleic acid sequence (SEQ ID NO: 142), forming the Avibody mutated in Kabat residues H39 and H45 (SEQ ID NO: 143) and also referred to herein as modeling mutation number c5.
  • cysteine residues were introduced by altering the nucleotide sequences encoding for the specific amino acid of interest using a QuikChange ® site- directed mutagenesis method (Stratagene) as per instructions.
  • a QuikChange ® site- directed mutagenesis method (Stratagene) as per instructions.
  • AVP04-07 Avibody the glutamine residues at Kabat positions L38 and L42 (FR2 V L region) are both encoded by the nucleotide sequence CAG.
  • the QuikChange ® site- directed mutagenesis technique in context of DNA primers described in SEQ ID NO: 68 and SEQ ID NO: 69, was used to alter both of these nucleotide sequence codons to TGC, which encodes Cysteine.
  • These modifications formed the nucleic acid sequence of the thiolated Avibody AVP04-79 (SEQ ID NO: 100).
  • the QuikChange ® site-directed mutagenesis PCR-based method uses two complementary synthetic oligonucleotides that contain the desired mutations as primers and plasmid DNA as the template to synthesise the double-stranded mutant PCR product.
  • Amplification was performed using the following conditions in sequence: 95°C for 30 sec; 18 cycles consisting of 95°C for 30 sec, 55°C for 30 sec and 68°C for 13 min; a final extension of 68°C for 7 min.
  • the template was digested with Dpnl at 37°C for 1 hour.
  • Trans formants were obtained following the manufacturer's instructions and identified by DNA sequencing as described above.
  • Example 11 Expression and Purification of "un-mutated” and Thiolated Avibodies Using Bacterial Expression
  • the DNA of individual Avibody constructs was transformed into chemically competent E. coli BL21 cells using the manufacturer's standard protocol (Stratagene).
  • the E. coli BL21 expression strain served as the major expression strain for all Avibodies exemplified. Expression was by means of two interchangeable approaches depending on expected yield requirements; either bacterial shake-flask expression or bacterial fed-batch fermentation. Quality assessment on Avibody protein from either method indicated that the two methods were interchangeable and protein quality and properties were comparable.
  • Bacterial pellets containing expressed protein from this expression system averaged approximately 6 g/L of culture media.
  • Seed cultures were grown in 2L baffled Erlenmeyer flasks containing 500 mL of a complex medium and incubated at 37°C shaking at 200 rpm for 16 h; the complex medium contained (per L): Tryptone, 16 g; Yeast Extract, 5 g; NaCl, 5 g; ampicillin, 200 mg. Defined medium was used for protein expression and contained (per L): KH2PO4, 10.64 g; ( ⁇ 4) 2 ⁇ 04, 4.0 g; and citric acid monohydrate, 1.7 g; glucose 25 g; MgS0 4 .7H 2 0, 1.25 g; PTM4 trace salts, 5 mL; ampicillin, 200 mg; thiamine-HCl, 4.4 mg.
  • the complex medium contained (per L): Tryptone, 16 g; Yeast Extract, 5 g; NaCl, 5 g; ampicillin, 200 mg. Defined medium was used for protein expression and contained (per L): KH2PO4, 10.
  • PTM4 trace salts contained (per L): CuS0 4 .5H 2 0, 2.0 g; Nal, 0.08 g; MnS0 4 .H 2 0, 3.0 g; NaMo0 4 .2H 2 0, 0.2 g; H3BO3, 0.02 g; CoCl 2 .6H 2 0, 0.5 g; ZnCl 2 , 7.0 g; FeS0 4 .7H 2 0, 22.0 g; CaS0 4 .2H 2 0, 0.5 g; H 2 S0 4 , 1 mL. All media and additives were sterilized by autoclaving at 121°C for 30 minutes except PTM4 trace salts, thiamine hydrochloride and ampicillin which were filter sterilized.
  • Protein expression was completed in 2 L glass Biostat B bioreactors (Sartorius Stedim Biotech, Germany) containing 1.6 L of defined medium.
  • the dissolved oxygen concentration was maintained at 20% by automatically varying the agitation rate between 500 and 1,200 rpm and the aeration rate (air supplemented with 5% oxygen) between 0.3 and 1.5 L min "1 .
  • Oxygen supplementation of the air flow was manually increased as required.
  • the pH of the culture was controlled at 7.0 via automatic addition of 10% (v/v) H 3 P0 4 or 10%> (v/v) NH 3 solution and foam was controlled by the automatic addition of antifoaming agent [10% (v/v) polypropylene 2025)].
  • the vessel temperature was maintained at 37°C. Bioreactors were inoculated with seed culture to attain a starting optical density (measured at 600 nm) of 0.25.
  • nutrient solution containing (per L): glucose, 600 g; and MgS0 4 .7H 2 0 22.4 g, was pumped into the bioreactor at a flow rate of 40 mL h "1 .
  • feed containing (per L): glucose, 600 g; and MgS0 4 .7H 2 0 22.4 g
  • a flow rate 40 mL h "1 .
  • Two hours after initiation of the feed the vessel temperature was slowly reduced to 20°C over a 2.5 hour period (6.8°C h "1 ) after which protein expression was induced by the addition of 0.2 mM IPTG and the feed rate was decreased to 6 mL h "1 .
  • Cultures were harvested 12 hours after induction and typically optical densities (measured at 600 nm) reached 110 and approximately 330g of wet cell paste was recovered from each 2 L culture.
  • Bacterial pellets harvested from expression culture were lysed, protein extracted and subsequently purified by standard chromatographic techniques.
  • HisTrapTM GE LifeSciences
  • HisTrapTM GE LifeSciences
  • HisTrapTM GE LifeSciences
  • Lysate was passed through the HisTrapTM column via an external P960 pump.
  • HisTrapTM columns were washed with 10 column volumes of His-Tag affinity chromatography extraction buffer (20mM sodium phosphate, 500mM NaCl, 20mM Imidazole, pH7.4).
  • Purified protein was eluted in 50% His-Tag affinity chromatography elution buffer (20mM sodium phosphate, 500mM NaCl, 500mM Imidazole, pH7.4) and 50% His-Tag affinity chromatography extraction buffer (a final concentration of 260mM Imidazole). Fractions containing eluted proteins (as determined by 280mM absorbance on AKTA Unicorn software) were collected, pooled, protein concentration determined and dialyzed in the appropriate ion exchange buffer.

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