WO2016065258A1 - Small antibody-like polypeptides that bind to epha2 receptor - Google Patents

Small antibody-like polypeptides that bind to epha2 receptor Download PDF

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Publication number
WO2016065258A1
WO2016065258A1 PCT/US2015/057111 US2015057111W WO2016065258A1 WO 2016065258 A1 WO2016065258 A1 WO 2016065258A1 US 2015057111 W US2015057111 W US 2015057111W WO 2016065258 A1 WO2016065258 A1 WO 2016065258A1
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domain
amino acid
modified
immunoglobulin
isolated immunoglobulin
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PCT/US2015/057111
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French (fr)
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Kurt R. Gehlsen
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Research Corporation Technologies, Inc.
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Priority to US15/520,573 priority Critical patent/US10829558B2/en
Priority to AU2015335725A priority patent/AU2015335725B2/en
Priority to EP15852472.8A priority patent/EP3209329A4/en
Priority to CA2963556A priority patent/CA2963556C/en
Publication of WO2016065258A1 publication Critical patent/WO2016065258A1/en

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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
    • C07K16/2866—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against receptors for cytokines, lymphokines, interferons
    • 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
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/10—Libraries containing peptides or polypeptides, or derivatives thereof
    • 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
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • 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
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/52—Constant or Fc region; Isotype
    • C07K2317/524—CH2 domain
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2318/00—Antibody mimetics or scaffolds

Definitions

  • Cancer is one disease characterized by the uncontrolled proliferation of cells. While there are a number of causes for such uncontrolled proliferation, one of those causes is aberrant signaling among the cells in a tissue. These aberrant signals, often arising from altered genes or gene products, but also due to viral infection or random mutation, either stimulate or remove inhibitions on the growth of the cell and its neighbors causing rapid and uncontrolled cell division. Other signaling defects may remove usual controls on cell behavior allowing metastasis to develop, spreading the cancer to distant tissues.
  • Eph receptors are a family of transmembrane proteins involved in cell to cell communication. Each Eph receptor has among other components an intracellular domain with tyrosine kinase activity and an extracellular binding domain. In humans, there are 14 types of Eph receptors classified into the Eph A and Eph B families that normally interact with 8 ephrin receptor ligands found on cell surfaces. Binding of an ephrin ligand to the extracellular binding domain of an Eph receptor causes other Eph receptor molecules to cluster with that receptor molecule, activates its intracellular tyrosine kinase activity to phosphorylate certain tyrosine residues in the receptor molecule which creates binding sites for other intracellular signaling proteins.
  • EphA2 receptor is an Eph receptor that is commonly overexpressed (or found in overabundance) on cancer cells. Ovarian, breast, prostate, lung, colon, esophageal, renal, cervical cancers and melanoma have been reported to have a much greater abundance of the receptor than non-cancerous cells in those tissues. Induced expression of the EphA2 receptor in transformed cells converts those cells to a malignant phenotype, enhances experimental metastasis of tumors derived from such cells and increases angiogenesis in those tumors.
  • Antibodies to the EphA2 receptor are well known. Upon binding to the extracellular binding domain of the EphA2 receptor, some act therapeutically to increase tyrosine phosphorylation and turnover of receptor and reduce tumor growth. Others have no effect on tyrosine phosphorylation (that is they do not affect ephrin A2 binding, but still are able to negatively affect tumor growth. Conjugates of these antibodies that deliver cytotoxic moieties to the cells bearing EphA2 receptors have also been described. Once delivered the cytotoxic moieties are released from the antibody to exert their toxic activity.
  • the present disclosure is directed to a modified isolated immunoglobulin CH2 domain that specifically binds to an extracellular region of an EphA2 receptor, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence.
  • the present disclosure also provides a method of treating a disease associated with EphA2 overexpression, such as cancer, the method comprising: administering to a subject in need thereof a therapeutically effective dose of a modified isolated immunoglobulin CH2 domain that specifically binds to an EphA2 receptor, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence.
  • heterologous fusion protein including a toxin fused to a modified isolated immunoglobulin CH2 domain that specifically binds to an EphA2 receptor, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence.
  • the present disclosure provides a pharmaceutical composition including: a modified isolated immunoglobulin CH2 domain that specifically binds to an EphA2 receptor, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence, and a pharmaceutical carrier.
  • Also provided herein is a method for killing a target cell expressing EphA2 receptors in a subject, the method comprising: administering to the subject a fusion protein including a modified isolated immunoglobulin CH2 domain that specifically binds to an EphA2 receptor fused to a toxin, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence; and exposing the target cell to an effective amount of the fusion protein, thereby selectively killing the target cell in the subject.
  • FIG. 1 is a schematic of human wild type immunoglobulin IgG CH2 domain.
  • the numbering refers to the location of the CH2 domain sequence in the human IgG immunoglobulin using EU numbering. See www.imgt.org/IMGTScientificChart/Numbering/Hu_IGHGnber.html, for an explanation of EU numbering and other CH2 domain numbering methodologies, which is herein incorporated by reference in its entirety.
  • FIG. 2 is a diagram of the structure of a modified CH2 domain, Loops 1-3 are indicated at the top of the sequence.
  • FIG. 3 shows the results of a phage ELISA on mouse EphA2, human EphA2, D6-Fc (control) and BSA (control) with individual positives clones B8 (SEQ ID NO: 46), H3 (SEQ ID NO: 48), B l 1 (SEQ ID NO: 47), A5 (SEQ ID NO: 49), D2 (SEQ ID NO: 45), E10 (SEQ ID NO: 44) and H6 (SEQ ID NO: 43).
  • FIG. 4 shows the results of a phage ELISA on HEK293-EphA2 overexpressing cells with individual positives clones A5, B8, B l 1 , D2, E10, H3 and H6.
  • FIG. 5 shows an ELISA on mouse and human EphA2 with the three modified CH2 domains, E10, H3 and H6.
  • FIG. 6A-B show a titration ELISA on mouse (FIG. 6A) and human (FIG. 6B) EphA2.
  • FIG. 7A-C show Surface Plasmon Resonance (SPR) Sensograms of modified CH2 domains binding to human EphrinA2 receptor.
  • FIG. 8 shows binding of CH2 modified domain B6 in decreasing concentrations to cells transfected with human EphA2 or non-transfected cells.
  • FIG 9 shows titration of CH2 modified domains (B l 1 , B6, D2, G7 and parental clones A9 and E10 on transfected cells (top) and non-transfected cells (bottom).
  • FIG. 10 shows the course of product formation over process time as determined by mCE for B6, B 1 1 and shWT.
  • shWT only the last 2 sampling points were analyzed due to the necessity to deglycosylate the protein.
  • FIG. 1 1 shows an electropherogram of filtrate from supernatant of a B 1 1 -modified CH2 domain-producing strain.
  • FIG. 12A-E show the level of radioactivity in tumor or muscle from radiolabeled B6
  • Results are expressed as % injected dose per g (% ID/g) of tumor or muscle.
  • FIG. 13 shows tumor-uptake of 64 CuMeCOSar-B 1 1 and 64 CuMeCOSar-B6 between 4 to 48 hours after tracer injections in mice.
  • T tumor; K: kidney; L: liver
  • FIG. 14 shows tumor uptake of 64 CuMeCOSar-shWTCH2 and 64 Cu MeCOSar-IgG between 4 and 48 hours after tracer injections in mice.
  • T tumor; K: kidney; L: liver
  • FIG. 15 shows the binding and internalization time course of B 1 1 -deimmunized a- sarcin (SEQ ID NO: 73 was used) fusion protein into PC3 cells.
  • FIG. 17 shows the localization of B l 1 modified CH2 domain in early endosome: B l 1 modified CH2 domain was detected with a-Flag that co-localize with EEAl, Early Endosome Marker protein detected with the specific Mab.
  • FIG. 18 shows the binding and internalization time course of B 1 1 -dPEG-biotin in PC3 cells.
  • the B l 1 modified sequences are shown in SEQ ID NOS: 91, 90 and 89.
  • modified CH2 domain(s) that specifically binds to an EphA2 receptor.
  • an "immunoglobulin” (also known as an antibody) is a protein (or complex) having a structural unit that is generally a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light” (about 25 kDa) and one "heavy” (about 50-70 kDa) chain. The N-terminus of each chain defines a variable region of about 100 to 1 10 or more amino acids primarily responsible for antigen recognition.
  • the terms “variable light chain” (VL) and “variable heavy chain” (VH) refer, respectively, to these light and heavy chains. Each light chain contains a single constant domain (CL), while each heavy chain contains three constant domains, CHI, CH2 and CH3 (or four constant domains for IgE and IgM).
  • the modified CH2 domain of the present disclosure is derived from the CH2 constant domain of an immunoglobulin or antibody.
  • "derived from” encompasses actually or theoretically “originating from,” “obtained from,” or “isolated from” a parent substance, e.g., a wild type CH2 domain. Devoid of the VL and VH domains, the modified CH2 domain of the present disclosure is much smaller than a full-length immunoglobulin. Typically, the size of a modified CH2 domain is about 15 kD or less. It is also possible to link one or more modified CH2 domains together to construct a multivalent binding molecule with binding specificity for the same molecule or for different molecules.
  • the CH2 domain of the present disclosure is modified in comparison to a wild type CH2 domain.
  • the wild type CH2 domain may be from any species.
  • the species is a mammalian species, such as a sheep, goat, mouse, rat, human, macaque, camel or baboon.
  • the species is a primate, typically a human or a macaque.
  • the modified CH2 domain of the present invention may be modified in comparison to the amino sequence of the wild type human IgG CH2 domain set forth in SEQ ID NO: 1 or the wild type macaque IgG CH2 domain set forth in SEQ ID NO: 2,
  • the modified CH2 domain of the present disclosure is derived from an IgG, IgA, IgD, IgE or an IgM immunoglobulin. More typically, the modified CH2 domain is derived from an IgG immunoglobulin. In some embodiments, the modified CH2 domain is compared with a wild type CH2 domain having the same isotype or isotype and subclass, e.g., IgG S . IgG2, IgG 3 and IgG4.
  • the CH2 domains of the present disclosure are modified to bind to a receptor, for example, the EphA2 receptor.
  • loop sequences of the CH2 domains of the present disclosure are modified in comparison to loop sequences of wild type CH2 domains.
  • wild type CH2 domains comprise six loop regions: Loop 1 , Loop 2, Loop 3, Loop A-B, Loop C-D and Loop E-F.
  • Wild type CH2 domains also comprise seven ⁇ sheets, A to G, oriented from the N- to C-terminus. Loops A- B, C-D and E-F are located between ⁇ -sheets A and B, C and D, and E and F, respectively.
  • Loops 1 , 2 and 3 are located between ⁇ -sheets B and C, D and E, and F and G, respectively.
  • the amino acid sequences of Loops 1 , 2 and 3 of the CH2 domains of the present disclosure are modified in comparison to LI, L2 and L3 of a wild type CH2 domain.
  • Amino acids 231-341 of FIG. 1 show a CH2 domain of a wild type IgG human antibody.
  • the numbering of the amino acids refers to the location of the CH2 domain in reference to the whole wild type IgG human antibody sequence.
  • the FIG. 1 amino acid sequence is set forth in SEQ ID NO: 1.
  • a diagram of a CH2 domain structure is depicted in FIG. 2.
  • LI corresponds to positions 35-44 of SEQ ID NO: 1 (DVSHEDPEVK, SEQ ID NO: 3) or SEQ ID NO: 2 (DVSQEDPDVK, SEQ ID NO: 6)
  • L2 corresponds to positions 63-67 of SEQ ID NO: 1 (EEQYNS, SEQ ID NO: 4) or SEQ ID NO: 2 (ETQYNS, SEQ ID NO: 7)
  • the L3 corresponds to positions 94- 102 of SEQ ID NO: 1 (SNKALPAPI, SEQ ID NO: 5) or SEQ ID NO: 2 (SNKALPAPI, SEQ ID NO: 8).
  • the loops of wild type CH2 domains can be 1 -2 amino acids longer or shorter than the loop sequences set forth above.
  • the loops may singly or in combination form an antigen binding region, such as an antigen binding region that specifically binds to an EphA2 receptor.
  • the framework regions of the immunoglobulin CH2 domains of the present disclosure are also modified.
  • the term "framework” is conventionally used to refer to amino acid sequences interposed between CDRs (or hypervariable regions) in an intact antibody. Amino acid residues within these framework regions serve to hold the CDRs in an appropriate orientation for antigen binding, and typically form ⁇ -sheet structures.
  • framework region refers to amino acid sequences outside of loops 1 , 2 and 3; i.e.., amino acid sequences interposed between loops 1 -2 and between loops 2-3, as well as amino acid sequences N-terminal to loop 1 and C-terminal to loop 3.
  • Wild type CH2 domains contain four framework regions, referred herein as FR1 , FR2, FR3 and FR4.
  • the framework regions in CH2 serve to hold loops 1 -3 in an appropriate orientation for their usual functions, and also form ⁇ -sheet structures.
  • framework region 1 is composed of amino acids 1 -34 (SEQ ID NO: 9)
  • framework region 2 is composed of 45-62 (SEQ ID NO: 10)
  • framework region 3 is composed of 69-93 (SEQ ID NO: 1 1)
  • framework region 4 is composed of amino acids at positions 103- 1 10 (SEQ ID NO: 13).
  • the framework regions can be 1 -2 amino acids longer or shorter than the framework sequences set forth above.
  • the disclosed CH2 domain is isolated.
  • isolated refers to a biological component, such as a CH2 domain, which has been substantially separated or purified away from other biological components from which the component naturally occurs, for example, other biological components of a cell, other antibodies and other antibody domains.
  • CH2 domains that have been "isolated” include nucleic acids and proteins purified by standard purification methods. The term also embraces CH2 domains prepared by recombinant expression in a host cell, as well as chemically synthesized nucleic acids encoding CH2 domains.
  • One or more loops and/or strands (of the beta sheets, A, B, C, D, E, F, G) of one or more CH2 domains may be modified.
  • the terms "modified” or “modification,” can include one or more mutations, deletions, additions, substitutions, physical alteration (e.g., cross-linking modification, covalent bonding of a component, post- translational modification, e.g., acetylation, glycosylation, tagging, e.g., His-tags or a combination thereof) or a combination thereof.
  • Modification, e.g., mutation is not limited to random modification (e.g., random mutagenesis) but includes rational design as well.
  • LI, L2 and/or L3 may be modified to specifically bind to an EphA2 receptor.
  • an LI, L2 or L3 amino acid sequence of an isolated immunoglobulin CH2 domain of the present disclosure may include at least one amino acid substitution, addition, or deletion of the amino sequence in comparison to an LI, L2 or L3 amino acid sequence of a wild type CH2 domain.
  • loops 1, 2 and/or 3 of the modified CH2 domain of the present disclosure may be modified in comparison to loops 1, 2 and/or 3 of the human wild type IgG CH2 domain set forth in SEQ ID NOS: 3-5, respectively.
  • loops 1, 2 and 3 of the modified CH2 domain of the present disclosure may be modified in comparison to loops 1 , 2 and 3 of the macaque wild type IgG CH2 domain set forth in SEQ ID NOS: 6-8, respectively.
  • the LI amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid substitutions in comparison to a wild type CH2 domain, such as at position 1, position 2, position, 3, position 4, position 5, position 6, position 7, position 8, position 9 and/or position 10.
  • the LI amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid deletions in comparison to a wild type CH2 domain.
  • the LI amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more additional amino acids in comparison to a wild type CH2 domain.
  • the L2 amino acid sequence is modified in comparison to a wild type L2 amino acid sequence.
  • the modification of L2 may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid substitutions in comparison to a wild type CH2 domain, such as at position 1, position 2, position, 3, position 4, position 5, position 6, position 7, position 8, position 9 and/or position 10.
  • the L2 amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid deletions in comparison to a wild type CH2 domain.
  • the L2 amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more additional amino acids in comparison to a wild type CH2 domain.
  • the L3 loop amino acid sequence is modified in comparison to a wild type L3 amino acid sequence.
  • the modification of L3 may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid substitutions in comparison to a wild type CH2 domain.
  • the L3 amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid deletions in comparison to a wild type CH2 domain.
  • the L3 amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more additional amino acids in comparison to a wild type CH2 domain.
  • only the LI amino acid sequence is modified. In other embodiments, only the L2 sequence is modified. In other embodiments, only the L3 amino acid sequence is modified. In various embodiments, the LI or the L2 sequence is modified. In other embodiments, the LI and the L2 amino acid sequences are modified. In yet other embodiments, the LI, L2 and L3 amino acid sequences are modified. In some embodiments, the LI and L3 sequences are modified. In other embodiments, the L2 and L3 sequences are modified.
  • the LI sequence is modified such that it contains 1-6 amino acid substitutions, such as at positions 2-7 of the human wild type LI amino acid sequence or positions 2-7 of the Macaque LI amino acid sequence (SEQ ID NOS: 3 or 6, respectively), e.g., positions 2-7 of LI may be modified with the amino acid sequences described, for example, in SEQ ID NOS: 50-53 or according to residues 2-7 in SEQ ID NOS: 14- 15 and 17- 21 or residues 2-6 of SEQ ID NO: SEQ ID NO: 16.
  • the LI sequence is modified such that it contains 1 deletion, for example, a deletion at position 4 or 5 of the human wild type LI amino acid sequence (SEQ ID NO: 3) or the LI Macaque amino acid sequence (SEQ ID NO: 6).
  • the LI sequences are modified as set forth in any of SEQ ID NOS: 14-21 or SEQ ID NOS: 85-86 and 94-99.
  • the L2 amino acid sequence of the isolated immunoglobulin CH2 domain of the present disclosure is modified to contain 1-6 amino acid substitutions, such as at positions 1-6 of the human wild type L2 amino acid sequence (SEQ ID NO: 4) or the Macaque wild type L2 amino acid sequence (SEQ ID NO: 7).
  • the L2 amino acid sequence of the modified CH2 domain of the present disclosure is the sequence set forth in SEQ ID NOS: 22-28, such as SEQ ID NOS: 22 or 23.
  • FR1, FR2, FR3 and/or FR4 are modified in comparison to wild type FR1, FR2, FR3 or FR4 regions of a wild type CH2 domain.
  • the modified FR1, FR2, FR3 and FR4 may contain at least one, two, three or four or more deletions, substitutions or additions.
  • an amino acid sequence of only one of the FR regions may contain a deletion, substitution or addition.
  • FR3 may be modified to include at least one substitution at position 1, e.g., as set forth in SEQ ID NO: 12 or SEQ ID NO: 101.
  • two or more the FR regions are modified, e.g., FR1 and FR2, FR2, FR3 and FR4, etc.
  • the modified, isolated immunoglobulin CH2 domains disclosed herein retain substantially the structure characteristic of a wild type CH2 domain, such as the beta barrel structure of a naturally occurring CH2 domain, i.e., the 3-stranded sheet containing strands C, F, and G, packed against the 4-stranded sheet containing strands A, B, D, and E.
  • Amino acid residues involved in maintaining the beta barrel structure are known in the art, including the residues that form hydrogen bonding, hydrophobic interactions, and the disulfide bond.
  • the residues critical to maintaining the beta barrel structure are not modified.
  • the framework residues are substantially not modified; for example, not more than 15%, or 10% or 5% of the framework residues are modified in the modified CH2 domains as compared to a wild type CH2 domain. Modifications at or near the terminal regions of a wild type CH2 domain may be more tolerable (i.e., less likely to disrupt the structure or conformation of a wild type CH2 domain) as compared to modifications to other regions.
  • Standard techniques known to those of skill in the art can be used to introduce mutations in the loop and/or framework regions (e.g., deletions, additions, and/or substitutions) in nucleotide sequences encoding the modified CH2 domains of the present disclosure, including, for example, site-directed mutagenesis and PCR-mediated mutagenesis which results in amino acid substitutions.
  • conservative amino acid substitutions are made at one or more predicted non-essential amino acid residues of the loop and/or framework regions of the modified CH2 domains (i.e., amino acid residues that can be modified without abrogating the modified CH2 domain's ability to specifically bind to an EphA2 receptor).
  • a "conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a side chain with a similar charge. Families of amino acid residues having side chains with similar charges have been defined in the art.
  • amino acids with 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
  • beta-branched side chains e.g., threonine, valine, isoleucine
  • aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine
  • a series of variants may be generated that differ by at least one amino acid in their sequence compared with the sequence of the wild type immunoglobulin CH2 domain. Changes may include but are not limited to deletions of an amino acid, additions, and/or substitutions. In generating a library of potential binding molecules, design changes may be focused on the loops. At any one site, variants may be generated that introduce any of the 20 naturally occurring amino acids (or non-natural amino acids), or a more restricted subset of amino acids might be substituted.
  • random mutations may be introduced by mutagenesis of the entire molecule, framework regions and loops.
  • Such mutagenesis can be accomplished either in vivo (in a mutagenic host or by addition of exogenous mutagen) or in vitro (by using mutagenic mixtures of precursors and/or by using a DNA polymerase that exhibits reduced or no proofreading nuclease activity).
  • display methods e.g. phage, CIS, ribosome display
  • a combination of the two approaches may be employed, synthesizing the initial variants to focus changes within the loops and then allowing random mutagenesis at each round of selection-amplification.
  • the libraries made in such a way and displayed by any of the established methods available may be used to isolate individual molecules from that library which bind to a target of interest, e.g., EphA2 receptor.
  • a target molecule such as an EphA2 receptor, is used to contact a display library to screen for modified CH2 domains that are able to bind to the target molecule.
  • the purified target molecules are presented in either 1) a form that is immobilized on a solid surface, or 2) as soluble molecules in solution. If in solution, they are engineered to bear a simple means for subsequent capture, such as biotin.
  • cell surface display e.g.
  • the target molecule is tagged fluorescently to enable cell sorting based upon the fluorescent signal due to bound target by the displayed CH2 domain variant.
  • Various methods may be used for detecting the binding of the modified CH2 domain to the target in the sample. Such methods are well known to one of ordinary skill in the art.
  • the modified immunoglobulin CH2 domain comprises a truncation or deletion of the first seven amino acids of the N-terminus of the wild type CH2 domain from which it is derived.
  • the CH2 domain comprises a deletion of the first amino acid, the first two, the first three, the first four, the first five, the first six, or the first seven amino acids of the N-terminus of the wild type CH2 domain from which it is derived.
  • the modified CH2 domain comprises a deletion of the first eight, the first nine, or the first ten amino acids of the N-terminus of the wild type CH2 domain from which it is derived.
  • the modified CH2 domain comprises a deletion of the last four amino acids of the C-terminus of the wild type CH2 domain from which it is derived. In some embodiments, the modified CH2 domain comprises a deletion of the last amino acid, the last two, the last three, the last four, the last five, the last six, the last seven, the last eight, the last nine, or the last ten amino acids of the C-terminus of the wild type CH2 domain from which it is derived. In some embodiments, the modified CH2 domain comprises a deletion at both the N-terminus and the C-terminus of the wild type CH2 domain from which it is derived.
  • the modified CH2 domain comprises a deletion of the first amino acid, the first two, the first three, the first four, the first five, the first six, or the first seven amino acids of the N-terminus of the wild type CH2 domain from which it is derived and a deletion of the last amino acid, the last two, the last three, the last four, the last five, the last six, the last seven, the last eight, the last nine, or the last ten amino acids of the C-terminus of the wild type CH2 domain from which it is derived.
  • the present disclosure is not limited to the aforementioned examples of deletions.
  • the CH2 domain may comprise other deletions in other regions of the protein. Without wishing to limit the present invention to any theory or mechanism, it is believed that such truncations or deletions (or other modifications) to the molecule may confer a particular property, for example including but not limited to enhanced stability.
  • the modified CH2 domain comprises a one amino acid addition, a two amino acid addition, a three amino acid addition, a four amino acid addition, a five amino acid addition, a six amino acid addition, a seven amino acid addition, an eight amino acid addition, a nine amino acid addition, a ten amino acid addition, an eleven amino acid addition, a twelve amino acid addition, etc. at its N-terminus.
  • the modified CH2 domain comprises a one amino acid addition, a two amino acid addition, a three amino acid addition, a four amino acid addition, a five amino acid addition, a six amino acid addition, a seven amino acid addition, an eight amino acid addition, a nine amino acid addition, a ten amino acid addition, an eleven amino acid addition, a twelve amino acid addition, etc. at its C-terminus, such as set forth in SEQ ID NO: 61 and SEQ ID NOS: 89-93.
  • the modified CH2 domain comprises an addition at the N- terminus and at the C-terminus.
  • the CH2 domain may comprise a one amino acid addition, a two amino acid addition, a three amino acid addition, a four amino acid addition, a five amino acid addition, a six amino acid addition, a seven amino acid addition, an eight amino acid addition, a nine amino acid addition, a ten amino acid addition, an eleven amino acid addition, a twelve amino acid addition, etc.
  • the additions may include for example, adding a serine, tyrosine, cysteine or lysine residue, for example, to facilitate linking to a linker as described herein below, such as set forth in SEQ ID NO: 61 and SEQ ID NOS: 89 and 91-93.
  • one or more portions of the modified CH2 domain or one or more amino acids may be substituted with another peptide or amino acid, respectively. Seeor example SEQ ID NOS: 54 and 55.
  • the modified CH2 domain may comprise a tag, for example including but not limited to a His tag.
  • the modified CH2 domains that bind EphA2 have additional mutations that further increase stability of the molecule.
  • the molecules can comprise mutations that allow for the formation of non-native disulfide bonds, such as by introducing a pair of amino acid substitutions to replace original residues with cysteine residues.
  • a first amino acid substitution is introduced in the N-terminal A strand and the second amino acid substitution is introduced in the C-terminal G strand of the modified CH2 domain of the present disclosure.
  • the modified CH2 domain may comprise a first amino acid substitution of L12 to C12 and a second amino acid substitution of K 104 to CI 04 (numbered with reference to SEQ ID NO: 1).
  • the first amino acid substitution may be V10 to CIO and the second amino acid substitution may be K104 to CI 04 or K102 to CI 02 (numbered with reference to SEQ ID NO: 1). See, for example, SEQ ID NOS: 56-59.
  • the modified CH2 domain of the present disclosure may be modified to enhance or decrease the affinity and/or avidity the modified CH2 domain has to FcRn, e.g. a human FcRn.
  • FcRn e.g. a human FcRn.
  • serum half-life of an immunoglobulin is mediated, in part, by the binding of the F c region to the neonatal receptor FcRn.
  • the alpha domain is the portion of FcRn that interacts with the CH2 domain (and possibly CH3 domain) of IgG, and possibly with IgA, and IgD or with the CH3 domain (and possibly CH4 domain) of IgM and IgE.
  • Modifications to the CH2 domain of the present disclosure to enhance or decrease the affinity and/or avidity to FcRn include mutations (amino acid substitutions, deletions, physical modifications to amino acids) of one or more amino acid residues. Modifications may also include insertion of one or more amino acid residues or one or more binding sites (e.g., insertion of additional binding sites for FcRn). A modification may, for example, increase the affinity for FcRn at a lower pH (or higher pH). See, for example, U.S. Patent Application No. 2007/0135620, which is herein incorporated by reference in its entirety).
  • amino acid substitutions may include but are not limited to M252Y, S254T, T256E, T307A (in reference to FIG. 1), or a combination thereof. Without wishing to limit the present disclosure to any theory or mechanism, it is believed that one or more of the substitutions M252Y, S254T, T256E, T307A may increase serum half life of the modified CH2 domain by increasing FcRn binding.
  • the modified CH2 binding domains such as a modified macaque IgG immunoglobulin CH2 domain
  • deimmunized refers to amino acid sequences carrying one or more amino acid substitutions that (a) reduce an immune response by one to whom a modified CH2 domain, for example, is administered and (b) retains a therapeutically and/or prophylactically effective amount of EphA2 binding activity, for example.
  • Methods for producing deimmunized proteins are known in the art and described, for example, WO2006/082406, WO2004/108158 and WO2004/064724.
  • the method may comprise 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 EphA2.
  • an epitope that occurs within a loop is not mutated unless the mutation is unlikely to reduce epitope binding.
  • Methods for predicting epitopes are known in the art and described, for example, in Saha et ah, BcePred:Prediction of Continuous B-Cell Epitopes in Antigenic Sequences Using Physico-chemical Properties.
  • the modified CH2 domain of the present disclosure specifically binds to an EphA2 receptor.
  • the EphA2 receptor may be from any species.
  • the EphA2 receptor is from a mammal, e.g., a dog, cat, sheep, goat, rat, mouse, macaque, baboon, or a human.
  • the EphA2 receptor is from a mouse, macaque or a human.
  • binding agent such as a modified CH2 domain
  • a binding agent such as a modified CH2 domain
  • specific binding may be distinguished as mediated through specific recognition of an antigen.
  • Specific binding typically results in greater than 2-fold, such as greater than 5-fold, greater than 10-fold, or greater than 100-fold increase in amount of bound molecule (per unit time) to a cell or tissue bearing the target as compared to a cell or tissue lacking the target, respectively.
  • Specific binding to a protein under such conditions requires a molecule that is selected for its specificity for a particular protein.
  • a variety of immunoassay formats are appropriate for selecting molecules specifically reactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used.
  • EphA2 receptor refers to a tyrosine kinase belonging to the Eph receptors family, and comprising, for example, an amino sequence as in Genbank Accession Nos. NM 004431.3, GL296010835 (human EphA2), herein incorporated by reference in its entirety, NM 010139.3, GL342187227 (murine EphA2), herein incorporated by reference in its entirety or NM 001 108977.1 GI: 157822928 (rat EphA2), herein incorporated by reference in its entirety.
  • the modified CH2 domains specifically bind to a human EphA2 receptor.
  • the Eph receptors comprise several distinctive domains required for their signaling capabilities.
  • the extracellular domain contains an ephrin ligand- binding domain in its N-terminal region, followed by a cysteine-rich region and two fibronectin type-Ill repeats.
  • the intracellular region comprises the signaling components which include a tyrosine kinase domain, a SAM (Sterile Alpha Motif) domain, and a PDZ (Postsynaptic density protein, Disks large, Zona occludens)-binding motif. Both SAM and the PDZ domains have been shown to mediate protein-protein interactions.
  • EPHA2 ligands GPI-anchored plasma membrane proteins ephrin-Al to ephrin- A5 are known as EPHA2 ligands.
  • the ligand binding to EPHA2 activates the tyrosine kinase domain and phosphorylates tyrosine residues present in the EPHA2 intracellular region, resulting in signal transduction within the cell. It has also been reported that EPHA2 bound with the ligand is internalized into the cell through endocytosis and is eventually degraded by a proteasome.
  • the modified CH2 domains described herein are capable of inhibiting one or more of the biological activities of a target molecule, such as an EphA2 receptor.
  • a target molecule such as an EphA2 receptor.
  • Such antagonists may act by interfering with the binding of a receptor to a ligand, by decreasing EphA2 phosphorylation that could be induced by a ligand, and/or by inhibiting the intracellular pathways that are induced by the binding of such ligand, and/or by inhibiting the homo/hetero-oligomerization of EphA2 receptors.
  • the antagonist may completely block receptor-ligand interactions or may substantially reduce such interactions.
  • the modified CH2 domains of the present invention may act as antagonists (e.g.
  • the modified CH2 domains of the present disclosure stimulate phosphorylation of the EphA2, thereby triggering degradation of said protein.
  • the modified CH2 domains of the present specifically bind to the EphA2 receptor. In some embodiments, the modified CH2 domains specifically bind to the extracellular domain of the EphA2 receptor.
  • Modified CH2 domains capable of specifically binding the EphA2 receptor, typically, the extracellular domain of the EphA2 receptor, are herein provided, e.g. the modified CH2 domains designated as E10, H6, D2, G7, B6, B l l, F4.1, C5, D9 and E3 set forth as SEQ ID NOS: 29-38.
  • the modified CH2 domains, capable of specifically binding the EphA2 receptor, typically, the extracellular domain of the EphA2 receptor include for example, the modified CH2 domains set forth in SEQ ID NOS: 89-93.
  • isolated modified immunoglobulin CH2 domains that specifically bind to an EphA2 receptor, wherein the modified CH2 domains competitively inhibits binding of an isolated immunoglobulin CH2 domain selected from the group consisting of E10, D2, G7, B6, Bl 1, B4.1, C5, D9, and E3.
  • the disclosure encompasses modified CH2 domains that reduce the binding of E10, H6, D2, G7, B6, B l 1, B4.1, C5, D9 and E3 to an EphA2 receptor by at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or more, 25% to 50%, 45 to 75%, or 75 to 99% relative to a control such as PBS in the competition assays well known in the art.
  • an ELISA competition assay may be performed in the following manner: recombinant EphA2 is prepared in PBS at a concentration of 10 ⁇ g/ml. 100 ⁇ of this solution is added to each well of an ELISA 98-well microtiter plate and incubated overnight at 4-8° C. The ELISA plate is washed with PBS supplemented with 0.1% Tween to remove excess recombinant EphA2. Non-specific protein-protein interactions are blocked by adding 100 ⁇ of bovine serum albumin (BSA) prepared in PBS to a final concentration of 1%. After one hour at room temperature, the ELISA plate is washed.
  • BSA bovine serum albumin
  • Unlabeled competing CH2 domains are prepared in blocking solution at concentrations ranging from 1 ⁇ g/ml to 0.01 ⁇ g/ml.
  • Control wells contain either blocking solution only or control antibodies at concentrations ranging from 1 ⁇ g/ml to 0.01 ⁇ g/ml.
  • Test antibody labeled with horseradish peroxidase is added to competing antibody dilutions at a fixed final concentration of 1 ⁇ g/ml.
  • 100 ⁇ of test and competing CH2 domain mixtures are added to the ELISA wells in triplicate and the plate is incubated for 1 hour at room temperature. Residual unbound CH2 domain is washed away.
  • Bound test CH2 domain is detected by adding 100 ⁇ of horseradish peroxidase substrate to each well. The plate is incubated for 30 min. at room temperature, and absorbance is read using an automated plate reader. The average of triplicate wells is calculated. CH2 domains which compete well with the test antibody reduce the measured absorbance compared with control well
  • the strength of binding between a binding site (X) and a ligand (Y), for example, between a modified CH2 domain of the present disclosure and an EphA2 receptor, may be characterized by the dissociation constant (Kd).
  • Kd is the concentration of Y that is required to occupy half of the binding sites of X present in a solution.
  • a lower (Kd) indicates a stronger or higher-affinity interaction between X and Y and a lower concentration of ligand is needed to occupy the sites.
  • the Kd resulting from binding between a modified CH2 domain and an EphA2 receptor or extracellular domain thereof is less than 1 x 10 2 M, less than l lO ⁇ 3 M, less than l x l0 ⁇ 4 M, less than l x lO ⁇ 5 M, less than l x lO ⁇ 6 M, less than l x lO ⁇ 7 M, less than l x l0 ⁇ 8 M, less than l x lO ⁇ 9 M, less than l x l0 10 M, less than l x l0 ⁇ n M, less than 1 x 10 ⁇ 12 M, less than 1 x 10 ⁇ 13 M, less than 1 x 10 ⁇ 14 M or less than 1 x 10 ⁇ 15 M.
  • the modified CH2 domains described herein may be joined to a second molecule to form an immunoconjugate, wherein the second molecule is, for example, a detectable moiety, a toxin, an epitope binding protein or a small molecule.
  • the terms "linking”, “joining,” or “bonding” refer to making two polypeptides into one continuous polypeptide molecule, or to covalently attaching the modified CH2 domain of the present disclosure to the second molecule.
  • the modified CH2 domains may be joined to a detectable moiety for use in in vivo or in vitro imaging, wherein the labeled, modified CH2 domain is administered to a subject, such as into the bloodstream, and the presence and location of the labeled CH2 domain in the host is assayed.
  • imaging is useful in the staging and treatment of malignancies.
  • the modified CH2 domain of the present disclosure may be labeled with any moiety that is detectable in a host, whether by PET/CT imaging or other detection means known in the art.
  • the label can be any detectable moiety that is capable of producing, either directly or indirectly, a detectable signal.
  • the label may be a detectable radioisotope, e.g., 64 Cu, 67 Cu, 90 Y, m In, 124 I, 125 I 13 T, m Cs, 186 Re, 211 At, 212 Bi, 213 Bi, 223 Ra, 241 Am, 244 Cm and 99m Tc-MDP, a fluorescent compound, e.g., fluorescein phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine); chemiluminescent compound (e.g., fluorescein isothiocyanate, rhodamine), an enzyme label (e.g., luciferase, alkaline phosphatase, beta-galactosidase and horseradish peroxidase), an imaging agent (e.g., Tc
  • the modified isolated immunoglobulin CH2 domain is fused to a toxin to form a heterologous fusion protein.
  • fusion protein refers to a hybrid protein, which consists of two or more proteins, or fragments thereof, linked together covalently.
  • a fusion protein may be "heterologous", i.e., comprising two or more peptides or proteins from different animals, origins, or species.
  • the toxins which may be bound to the modified CH2 domain of the present disclosure include, but are not limited to, abrin, ricin, Pseudomonas exotoxin (PE, such as PE18, PE24, and PE38), diphtheria toxin (DT), botulinum toxin, saporin, restrictocin or gelonin, or modified toxins thereof.
  • Other cytotoxic agents that may be attached to the modified CH2 domain include cytolytic peptides.
  • the toxin is a fungal ribonuclease, for example, a-sarcin or a deimmunized a-sarcin.
  • a deimmunized toxin is one that (a) reduces the anti-toxin immune response by one to whom the toxin is administered, and (b) retains a therapeutically and/or prophylactically effective amount of toxin activity.
  • Methods for preparing deimmunized a- sarcin are well known in the art, as disclosed, for example, in WO 2014/158770, which publication is hereby incorporated by reference in its entirety.
  • the deimmunized ⁇ -sarcin can have an amino acid sequence as set forth in the following table: SEQ ID NO: Variant
  • the modified isolated immunoglobulin CH2 domain is fused to one or more proteins comprising a paratope. Accordingly, the CH2 domain of the present disclosure may be modified to be specific for one, two, three or more targets, e.g.
  • EphA2 and a T cell-specific epitope a T cell-specific epitope, a natural killer (NK) cell-specific epitope (e.g., Fc gammaR llla/CD16A) etc
  • a bispecific modified CH2 domain of the present disclosure recruits an effector cell, such as a T cell, to an aberrant target cell, such as a cell overexpressing EphA2, resulting in the immune effector cell being in close vicinity to the target cell, such that the effector cell can directly kill, or indirectly initiate the killing of the aberrant target cell to which it is recruited.
  • the T cell- specific epitope is CD3.
  • the modified isolated immunoglobulin CH2 domain of the present disclosure is linked to a small molecule.
  • a "small molecule” refers to a beneficial agent, usually synthesized by organic chemistry and having a low molecular weight, e.g. about 500-900 daltons.
  • a small molecule is an effector of a specific protein or nucleic acid, altering the activity of the protein or nucleic acid.
  • small molecules include but are not limited to cytotoxic agents, e.g., compound classes such as the auristatins, maytansinoids and pyrrolobenzodiazepines.
  • the N-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule is linked to the C-terminus of the modified CH2 domain. In some embodiments, the N-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule is linked to the N-terminus of the CH2 domain. In some embodiments, the C-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule is linked to the C-terminus of the CH2 domain. In some embodiments, the N-terminus of the CH2 domain is linked to the C-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule.
  • the N-terminus of the CH2 domain is linked to the N-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule.
  • the C-terminus of the modified CH2 domain is linked to the C-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule.
  • a linker can optionally be inserted between the modified CH2 domain and the detectable moiety, toxin, protein comprising a paratope or small molecule.
  • Linkers and linker technology are well known in the art. Examples of linkers include peptides of various amino acid lengths and/or sequences. In some embodiments, the linker is between 0 to 10 amino acids in length. In some embodiments, the linker is between 0 to 15 amino acids in length. In some embodiments, the linker is between 0 to 20 amino acids in length. In some embodiments, the linker is between 1 to 10 amino acids in length. In some embodiments, the linker is between 1 to 15 amino acids in length.
  • the linker is between 1 to 20 amino acids in length. In some embodiments, the linker is between 2 to 20 amino acids in length. In some embodiments, the linker is between 3 to 20 amino acids in length. In some embodiments, the linker is between 4 to 20 amino acids in length. In some embodiments, the linker is between 5 to 10 amino acids in length. In some embodiments the linker is between 10 to 15 amino acids in length. In some embodiments, the linker is between 15 to 20 amino acids in length. In some embodiments, the linker is more than 20 amino acids in length. The optimal lengths may vary to match the spacing and orientation of the specific target antigen(s), minimizing entropy but allowing effective binding of multiple antigens.
  • the linker can be attached to the individual modified CH2 domain at any appropriate location.
  • Examples of where a linker may attach onto the modified CH2 domain include the following location on the modified CH2 domain: the C-terminus, the N-terminus or a cysteine preceding or following the C-terminus or N-terminus of the modified CH2 domain, such as set forth in SEQ ID NOS: 89-93.
  • the linker may be encoded for in the recombinant nucleic acid that encodes the immunoconjugate, e.g. fusion protein.
  • the linker may be covalently bonded (e.g., cross-linked) to a portion of an immunoconjugate.
  • the linkers may be covalent or very tight non-covalent linkages; chemical conjugation or direct gene fusions of various amino acid sequences, e.g., those (a) rich in Glycine Serine, Proline, Alanine.
  • the linker comprises a non-peptide component (e.g., a sugar residue, a heavy metal ion or a chemical agent such as a therapeutic chemical agent).
  • Classes of commonly used cleavable linkers include hydrazone and hydrazine linkers, disulfide linkers (including N-succinimidyl-4-(2-pyridyldithio)pentanoate (SPP), N-succinimidyl-4-(2- pyridyldithio)butyrate (SPDB), 4-(4"-acetylphenoxy)butanoic acid (AcBut), dipeptides valine-citrulline (Val-Cit), valine-alanine (Val-Ala), and phenylalanine- lysine (Phe-Lys), the dissolving linker technology of Mersana and protease susceptible linkers of CytomX.
  • Non-cleavable linkers include: amide moieties, succinimidyl-4-[N- maleimidomethyl]cyclohexane- l -carboxylate (SMCC), maleimidocaproyl (MC), the dPEG linkers, and pyridinyl-2-disulfanyl linkers.
  • SMCC succinimidyl-4-[N- maleimidomethyl]cyclohexane- l -carboxylate
  • MC maleimidocaproyl
  • dPEG linkers include pyridinyl-2-disulfanyl linkers.
  • the linker comprises polyethylene glycols (PEGs), e.g., discrete PEGs (dPEG), etc.
  • PEGs polyethylene glycols
  • dPEG discrete PEGs
  • a PEG (dPEG) may be bound by a variety of mechanisms, e.g., via chemical treatments and/or modification of the protein structure, sequence, etc. (see, for example, Ashkenazi et al., 1997, Current Opinions in Immunology 9: 195-200; U.S. Patent No. 5,612,034; U.S. Patent No. 6, 103,233).
  • the PEG (dPEG) is between about 200 to 10,000 daltons. In some embodiments, the (dPEG) is between about 600 to 10,000 daltons. In some embodiments, the PEG (dPEG) is between about 700 to 10,000 daltons. In some embodiments, the (dPEG) is between about 800 to 10,000 daltons. In some embodiments, the (dPEG) is between about 900 to 10,000 daltons. In some embodiments, the (dPEG) is between about 200 to 12,000 daltons.
  • the PEG (dPEG) may be linked to a linkage site, such as at least one of a serine, tyrosine, cysteine, or lysine or a glycosylation site of the modified CH2 domain.
  • the PEG (dPEG) may be bound to the immunoconjugate, e.g., a fusion protein (e.g., modified CH2 domain) through a reactive sulfhydryl by incorporating a cysteine at the end of the modified CH2 domain to form, e.g. CH2-dPEG-toxin, detectable moiety, protein comprising a paratope or a small molecule.
  • the linkage site is an N-terminal serine, tyrosine, cysteine, or lysine. In other embodiments, the linkage site is a C-terminal serine, tyrosine, cysteine, or lysine. In some embodiments, the linkage site is a serine, tyrosine, cysteine, or lysine found within the modified CH2 domain, not necessarily a terminal residue. In some embodiments, a tyrosine, cysteine, serine, or lysine is added to the N-terminus and/or C-terminus of the CH2 scaffold for the purpose of the linkage of the PEG (dPEG).
  • dPEG PEG
  • a PEG may be linked to an existing tyrosine, cysteine, serine, or lysine at a terminus or within the modified CH2 domain.
  • the CH2-PEG is then further linked to the detectable moiety, toxin, protein comprising a paratope or small molecule.
  • the PEG (dPEG) is linked to a glycosylation site.
  • the glycosylation site is a natural glycosylation site.
  • the glycosylation site is a new/modified glycosylation site, for example an asparagine N- glycosylation site may be added to the modified CH2 domain.
  • a PEG (dPEG) may be attached at a glycosylation site using methods including enzymatic digestion and expression with an appropriate expression system (e.g., Pichia GlycoSwitch® Man5 strain).
  • the dPEG is attached to a natural Man5 structure or alternatively a GnMan5 structure, a GalGnMan5 structure, a GnMan3 structure, a GalGnMan3 structure, a Gn2Man3 structure, a Gal2Gn2Man3, etc.
  • a natural Man5 structure or alternatively a GnMan5 structure, a GalGnMan5 structure, a GnMan3 structure, a GalGnMan3 structure, a Gn2Man3 structure, a Gal2Gn2Man3, etc.
  • Further methods for using PEG and linkage arrangements of CH2 domains, detectable moieties, toxins, proteins comprising paratopes or small molecules are well known in the art, see, for example, PCT Publication No. WO 2013/1 19903, which is herein incorporated by reference in its entirety.
  • the linker is a hinge component.
  • the hinge component set forth in SEQ ID NO: 60 may be linked to the N-terminus of the FRl region of a modified CH2 domain.
  • Other linkers for fusion proteins are also described in PCT Publication No. WO 2013/1 19903, which is herein incorporated by reference in its entirety.
  • the modified CH2 domains and fusion proteins of the present disclosure are useful as pharmaceutical agents, particularly, as pharmaceutical compositions intended for cancer treatment. Any cancer that expresses the EphA2 receptor can be treated using these pharmaceutical compositions. Examples of cancer types can include, but are not limited to, breast cancer, melanoma, ovarian cancer, lung cancer, gliomas, bladder cancer, prostate cancer, esophageal cancer, renal cancer, colon cancer and vulvar cancer.
  • the compositions comprise a modified CH2 domain or a fusion protein comprising a modified CH2 domain linked to a toxin as discussed above and a pharmaceutical carrier.
  • the pharmaceutical carrier may be conventional, but are not limited to conventional carriers (vehicle).
  • E. W. Martin Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA, 15th Edition (1975) and D. B. Troy, ed. Remington: The Science and Practice of Pharmacy, Lippincott Williams & Wilkins, Baltimore MD and Philadelphia, PA, 21st Edition (2006) describe compositions and formulations suitable for pharmaceutical delivery of one or more therapeutic compounds or molecules and additional pharmaceutical agents.
  • aqueous pharmaceutical compositions suitable for long-term storage of polypeptides containing an Fc domain of an immunoglobulin may be used, such as described in U.S. Patent No. 7,648,702, which is hereby incorporated by reference in its entirety.
  • compositions may comprise buffers (e.g., sodium phosphate, histidine, potassium phosphate, sodium citrate, potassium citrate, maleic acid, ammonium acetate, tris-(hydroxymethyl)-aminomethane (tris), acetate, diethanolamine, etc.), amino acids (e.g., arginine, cysteine, histidine, glycine, serine, lysine, alanine, glutamic acid, proline), sodium chloride, potassium chloride, sodium citrate, sucrose, glucose, mannitol, lactose, glycerol, xylitol, sorbitol, maltose, inositol, trehalose, bovine serum albumin (BSA), albumin (e.g., human serum albumin, recombinant albumin), dextran, PVA, hydroxypropyl methylcellulose (HPMC), polyethyleneimine, gelatin, polyvinylpyrrolidone (ABS-
  • the pharmaceutical compositions may comprise propellants (e.g., hydrofluoroalkane (HFA)) for aerosol delivery.
  • propellants e.g., hydrofluoroalkane (HFA)
  • the pharmaceutical compositions of the present disclosure may be formulated as described in U.S. Patent No. 5,192,743 that form a gel when reconstituted and which can improve stability of a protein of interest (e.g., for storage).
  • compositions may be appropriately constructed for some or all routes of administration, for example topical administration (including inhalation and nasal administration), oral or enteral administration, intravenous or parenteral administration, transdermal administration, epidural administration or the like.
  • parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle.
  • conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate.
  • compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
  • non-toxic auxiliary substances such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
  • a parenteral formulation may comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle.
  • the formulation for injectable trastuzumab includes L-histidine HCI, L- histidine, trehalose dihydrate and polysorbate 20 as a dry powder in a glass vial that is reconstituted with sterile water prior to injection.
  • Other formulations of antibodies and proteins for parenteral or subcutaneous use are well known in the art and may be used with the modified CH2 domains and fusion proteins of the present disclosure.
  • non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate.
  • pharmaceutical compositions to be administered can contain minor amounts of non- toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
  • the present invention is further directed to treating a disease associated with EphA2 overexpression.
  • treatment or “treating” refers to arresting or inhibiting, or attempting to arrest or inhibit, the development or progression of a disease and/or causing, or attempting to cause, the reduction, suppression, regression, or remission of a disease and/or a symptom thereof.
  • various clinical and scientific methodologies and assays may be used to assess the development or progression of a disease, and similarly, various clinical and scientific methodologies and assays may be used to assess the reduction, regression, or remission of a disease or its symptoms.
  • Treatment refers to both therapeutic treatment and prophylactic or preventative measures. Those in need of treatment include those who already have the disease, as well as those with a propensity or predisposition for the disease and those in whom the disease is to be prevented.
  • the disease being treated is cancer, such as described above.
  • a "disease associated with EphA2 overexpression” includes, but is not limited to a variety of cancers, including the cancers described herein.
  • the modified CH2 domains of the present disclosure and the fusion proteins described above may be administered to a subject.
  • the subject is a mammal including a cat, dog, horse, sheep, goat, rat, mouse, baboon, macaque or human.
  • the subject is a human.
  • a therapeutically effective dose of the modified CH2 domains or fusion proteins described herein is administered.
  • a therapeutically effective dose is an amount which eliminates or reduces the patient's tumor burden, or which prevents or reduces the proliferation of metastatic cells.
  • the dosage will depend on many parameters, including the nature of the tumor, patient history, patient condition, the possible co-use of other oncolytic agents, and methods of administration.
  • Methods of administration include injection (e.g., parenteral, subcutaneous, intravenous, intraperitoneal, etc.). Typical dosages may range from about 0.01 to about 20 mg/kg, and more particularly from about 0.1 to about 10 mg/kg. Other methods of administration include oral and transdermal.
  • the modified CH2 domains and fusion proteins can be delivered in a controlled release system.
  • a controlled release system can be placed in the proximity of the therapeutic target, such as a tumor, requiring only a fraction of the dose required if dosed systemically.
  • administration is locally confined to a single cell or tissue and/or is systemically administered in the subject. It may be desirable to administer the modified CH2 domains and fusion proteins described herein locally to the area in need of treatment, such as areas including one or more tumor.
  • This method of administration may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application such as in conjunction with a wound dressing after surgery, injection, catheter, or via an implant or porous membrane.
  • the present invention is directed a method for killing a target cell expressing EphA2 receptors, the method comprising administering to a subject in need thereof a fusion protein as described herein, exposing the target cell to an effective amount of the fusion protein, thereby selectively killing the target cell in the subject.
  • the modified CH2 domain of the fusion protein is capable of being internalized into the cells.
  • the fusion protein preferentially associates in whole or in part with a cell or tissue bearing the EphA2 receptor, such as the extracellular domain of the EphA2 receptor and not to cells or tissues lacking the EphA2 cell receptor.
  • EphA2 has been shown to have little to no appreciable expression in normal tissues, but may be highly expressed in tumors. Accordingly, in some embodiments, the fusion protein selectively kills tumor cells, but does not kill normal cells.
  • the fusion protein is formulated into a pharmaceutical composition.
  • the pharmaceutical composition comprises the fusion protein and a pharmaceutically acceptable carrier, such as described above.
  • the subject may be a mammal or any species of mammal as described herein.
  • the subject is a human.
  • the target cell is a cancer cell, including, for example, a cancer cell selected from the group consisting of lung, colon, rectum, breast, ovary, prostate gland, head, neck, bone, kidney, liver, skin and vulva.
  • Exposure of the target cells to the fusion protein may be carried out by any of a number of routes, including without limitation, intravenous, intraperitoneal, subcutaneous, intramuscular and intralymphatic.
  • the fusion protein may be one in which the modified CH2 domain and the toxin are covalently associated.
  • the term "effective amount” as used herein means that amount of fusion protein or pharmaceutical composition comprising the fusion protein necessary to achieve the desired specific effect, for example killing a target cell and/or in amelioration of a specific disease state.
  • Phagemid vector pIFF6 is derived from the pC89 vector and contains the coding sequence for the capsid protein pill in place of pVIII. After electroporation in TOPI OF' cells, a number of independent clones sufficient to cover the entire diversity of the libraries were collected and 100 clones for each library underwent sequencing to confirm the correct reading frame and the expected sequences pattern. The 4 libraries were individually rescued, purified and titrated, then used in a pool to select against the EphA2 receptor.
  • the phage pool supematants coming from the three rounds of selection were tested in OElisa assay on coated mEphA2 to assess the enrichment for binding ability to the target.
  • the pool of selected clones increased the capability of binding to mEphA2.
  • 192 clones were individually rescued and analyzed by ELISA on coated mEphA2. All 95 clones identified as positives were sequenced and seven variants were identified.
  • the variants' ability to recognize the EphA2 receptor in a native conformation was also tested on a stable HEK293 clone overexpressing the EphA2 receptor. As shown in FIG. 4, all the loop 2 variants retain their binding activity to the human EphA2 receptor expressed on the surface of the cell, and clones H3 and E10 preserve their major intensity signal.
  • EphA2 binders were subcloned into the periplasmic expression vector pJEX404, expressed into E. Coli HB2151 strain, then extracted from periplasm and purified onto a Nickel column, followed by a gel filtration on a Superdex HR75 16/60 column.
  • the proteins were analyzed in an ELISA assay, coated with either mEphA2 and hEphA2 to confirm the binding capability to the target. All the proteins, except A5 whose expression was unsuccessful, preserved their binding capability, even with different strength where E10, H3 and H6 work better.
  • Binding of the E10, H3 and H6 variants to FcRn and to the target mEphA2 was also analyzed by surface plasmon resonance (SPR) to measure the potency of the binding to the receptor.
  • SPR surface plasmon resonance
  • affinity maturation clones E10 and A9 were chosen as representing the 2 different consensus families and they also showed higher expression and binding in the CIS display format.
  • the affinity maturation libraries were built by introducing diversity in loop 1 as it is neighboring loop 2 (compared to loop 3 which is spatially further away). Two loop lengths were designed, a smaller loop where residues Ser267 to Asp270 (as referenced to FIG. 1) were mutated, or a longer loop comprising Val266 to Pro271 (as referenced to FIG. 1).
  • the libraries were built using trinucleotide oligonucleotides using the same 12 residues as in the primary libraries.
  • the affinity maturation was performed using CIS display on mouse EphA2, using increased washing stringency and decreasing target concentration in an attempt to select for the tightest binders.
  • the output from the selection was cloned into a cytoplasmic expression vector, transformed in Shuffle cells and the expressed proteins screened by ELISA. From the ELISA, 21 mouse EphA2 binding clones were sequenced and found to exclusively carry loop 2 from the parental clone E10, none from H3. Moreover, loop 1 sequences are derived only from the longer loop length library, possibly explaining why library #13 failed to yield any binders in the naive selection as the length of the loop is important for structural integrity of the modified CH2 domains or functional binding to EphA2.
  • the affinity was measured using ForteBio's OctetRed.
  • the affinities were generally about 10 times weaker than those measured by ELISA. See Table 6.
  • K D values were also assessed for G7, B6 and B l l clones using Surface Plasmon Resonance (SPR).
  • SPR Surface Plasmon Resonance
  • amine-coupling kit Biacore
  • Biacore 3000 immobilization wizard purified human EphA2 extracellular domain is immobilized at 0.5 ⁇ in acetate pH 5.0 to one of the four flow cells of a CM5 sensorchip (GH Healthcare cat BR- 1000-14) to a level of approx. 2000 RU (resonance units).
  • Purified CH2 domain mutants are dialyzed against 10 mM Hepes (pH 6.0), 150 mM NaCl (running buffer), diluted in the same buffer to a range of concentrations (10 ⁇ -0.625 ⁇ ) and passed over the sensor chip surface at a flow rate of 40 ⁇ /min.
  • Each cycle consists of a 60s analyte injection (the association phase), followed by a 180s dissociation phase. Regeneration is achieved using a 10s injection of Running Buffer with a 300s stabilization period. The data are analyzed using the Biacore 3000 Evaluation software.
  • CHO cells were transfected with human EphA2 and the binding of the affinity matured CH2 domains was assessed by FACS (FIG. 8). Decreasing concentrations of the CH2 domains were tested and the EC50 values against the target expressed on cells were evaluated (see FIG. 9 and Table 8).
  • B6 showed the tightest binding to the cells, with little binding to control CHO cells that did not express human EphA2, whereas Bl l and to a lesser extent D2 show some signal on non-transfected cells, which might be attributable to cross-reactivity with hamster EphA2 expressed in the immortalized ovarian cells and recognition of a different epitope than B6 and G7 (Chinese hamster EphA2 shares 92% and 94% similarity with human and mouse EphA2, respectively).
  • Bioreactor cultivations under controlled conditions were performed using P. pastoris as the expression host.
  • the culture was grown to wet cell weights of approximately 200 g L-l without induction of recombinant protein production.
  • the production phase was initiated by supplementation of methanol, inducing the AOX1 -promoter.
  • the cells were separated by centrifugation, and the supernatant cleared by filtration to obtain the cell-free filtrate containing the secreted target protein.
  • FIG. 10 shows protein production over process time for two modified CH2 domains as measured by microfluidic capillary electrophoresis (mCE).
  • Titers of -900 mg L-l (shWT- CH2D, control), -1,000 mg L-l (B6) and 1,400 mg L-l (Bl l) were obtained after a non- optimized standard 1L bioreactor cultivation. Purities for all 3 target proteins were above 60% in the final filtrate and the filtrates were affinity-purified by IMAC, polishing was performed using CIEX chromatography, and concentration with ultrafiltration (FIG. 1 1).
  • B6 and Bl l Targeting and biodistribution characteristics of 2 modified CH2 domains, B6 and Bl l, engineered to target the EphA2 protein were assessed.
  • MicroPET/CT images were acquired at 3 time points (4, 24 and 48 hours), allowing the identification of the distribution in the whole animal.
  • B6 and B l l showed uptake in the tumors, with B 1 1 providing the highest signal from the PC3 tumors. Uptake was also shown by the B6 product.
  • the negative control shWT_CH2 showed some low level background uptake in the tumor above levels observed in muscle, possibly due to the enhanced permeability and retention (EPR) effect which is known to occur in this xenograft model. Clearance of the CH2 domains was mainly indicated to occur via the liver and the kidneys.
  • EPR enhanced permeability and retention
  • mice were sacrificed and perfused, and a biodistribution study was performed. Several organs including tumor and muscle were removed and the level of radioactivity measured by a gamma-counter. Results are expressed as % injected dose per g (% ID/g) of tissue at 48 hours.
  • the Bl l product showed highest tumor uptake of approximately 6% ID/g compared to muscle of ⁇ 1%.
  • the B6 product showed tumor uptake of approximately 5% ID/g compared to muscle of ⁇ 1%.
  • the negative control shWT product contained slightly more than 2% in the tumor above levels observed in muscle of ⁇ 1%.
  • B6 had much higher liver retention at approximately 17% ID/g than both the B l 1 (9% ID/g) and the shWT_CH2 control (9% ID/g). Kidney retention was similar between B6 and B 1 1 (approx. 17 to 18% ID/g) and also higher than the control at 12% ID/g. Lung and heart showed little difference between products with ⁇ 5% ID/g for all products in both organs. See FIG. 12.
  • tumor-bearing mice injected with the negative control 64 CuMeCOSar-shWTCH2 showed only minor tracer uptake in their tumors, similar to background activity, at any measured time point and a similar lack of tumor uptake was seen for the positive control IgG, 64 CuMeCOSar-IgG, which binds to EphA2 (FIG. 14).
  • the 64 CuMeCOSar-B l 1 modified CH2 domain accumulated in the tumor faster and with a stronger SUV compared to the 64 CuMeCOSar-B6 modified CH2 domain.
  • PC3 cells were incubated at 37°C with Bl l conjugated to deimmunized a-sarcin (Bl l-sarcin) and endosomal or lysosomal vesicles were counted over time.
  • Bl l-sarcin rapidly internalized and was localized into the early endosomes and endosomes up to 60 minutes. After 60 minutes, the Bl 1-sarcin appeared to localize either into lysosomes and is degraded or is found in the cytoplasm.
  • FIG. 15 PC3 cells incubated with Bl l conjugated to deimmunized a-sarcin at 37°C for 72 hours at various concentrations demonstrated cell killing with an IC50 of approximately 2 nM. See FIG 16.
  • Example 1 [153] The results obtained in Example 1 were obtained using the following materials and methods.
  • E. coli standard LB-medium containing 25 ⁇ g/ml Zeocin was used.
  • YPhyD for P. pastoris contained 10 g/1 yeast extract, 20 g/1 phytone peptone and 20 g/1 glucose.
  • For antibiotic selection in Pichia 100 ⁇ g/ml Zeocin (Eubio, Austria) was used. 15 g/1 agar was added for plate media.
  • Buffered minimal media BMD (1%), BMM2 and BMM10 contained per liter: 200 ml 1 M sodium phosphate buffer (pH 6), 13.4 g yeast nitrogen base without amino acids, 0.0004 g/1 biotin and 1 1 g/1 glucose or 1 or 5% (v/v) methanol, respectively.
  • BSM medium contained per liter CaS0 4 2H 2 0 0.47 g, K 2 S0 4 9.1 g, KOH 2.07 g, MgS0 4 7H 2 0 7.5 g, EDTA 0.6 g, H 3 PO 4 (85%) 13.4 ml, Glycerol 40.0 g, NaCl 0.22 g and 4.35 ml PTM1.
  • PTM1 Trace elements solution contained per liter 0.2 g Biotin, 6.0 g CuS0 4 5H 2 0, 0.09 g KI, 3.0 g MnS0 4 H 2 0, 0.2 g Na 2 Mo0 4 2H 2 0, 0.02 g H 3 BO 3 , 0.5 g CoCl 2 , 42,2 g ZnS047H 2 0, 65 g Fe(II)S0 4 7H 2 0 and 5 ml H 2 S0 4 .
  • the fed-batch media were either 60% (w/w) Glycerol or concentrated Methanol and were supplemented with 12 ml/1 PTM1 mineral salts solution.
  • Plasmids were linearized with either Bglll, ethanol-precipitated and desalted.
  • Electro- competent P. pastoris CBS 7435 mutS cells (Naatsaari et al. 2012) were prepared and transformed with 2 ⁇ g of the Bglll- linearized pPpT4 vector constructs according to Lin- Cereghino et al., "Condensed protocol for competent cell preparation and transformation of the methylotrophic yeast Pichia pastoris '' 2005, Biotechniques, 38:44, 46, 48, herein incorporated by reference in its entirety.
  • Transformants were plated on YPD-Zeocin (100 ⁇ g/ml Zeocin) agar plates and grown at 28°C for 48 hours.
  • P. pastoris strains expressing the target genes were cultivated in 96-deep well plates as described by Weiss H.M. et al. "Expression of functional mouse 5-HT 5 A serotonin receptor in the methylotrophic yeast Pichia pastoris: pharmacological characterization and localization," FEBS Lett. 1995, 377:451 ⁇ 156, herein incorporated by reference in its entirety.
  • the fed-batch phase was started upon depletion of initial batch glycerol with 16 g/(l*h) glycerol feed solution followed by methanol induction.
  • the methanol-feed was set to 2 g/(l*h) and was gradually increased within the next 70 h to 6 g/(l*h).
  • the glycerol-feed was phased down during the first hour of methanol induction to 0 g/(l*h). Dissolved oxygen was set to 30% throughout the whole process. After 92 h of methanol induction the bioreactor cultivations were stopped.
  • Microfluidic capillary electrophoresis using the LabChip® GX II (Caliper LS, PerkinElmer, USA) was used to detect and quantify the target proteins. Briefly, several ⁇ of all culture supernatants or bioreactor samples (taken at different time-points throughout the process) are fluorescently labeled and analyzed according to protein size, using an electrophoretic system based on microfluidics. Internal standards enable approximate allocations to size in kDa and approximate concentrations of detected signals. External standards (as e.g. authentic standard material, which was not available; instead, cytochrome c as external standard protein with a similar molecular weight) guarantee more precise allocation of protein signals.
  • Standard deviations of this robust system are usually below 10%, even at high protein loads. More specifically, proteins were quantified by calibrating the integrated areas of the protein-specific peaks in the electropherograms to an external reference protein standard (Cytochrome c) of known concentration. For glycosylated proteins, peak areas of diluted deglycosylated samples were compared to those of untreated samples to compensate for glycosylation-related differences in quantification. Samples were treated with EndoH for deglycosylation according to the manufactures instructions (NEB, USA, catalog# P0702L). The dilutions of samples were in a range to give peak areas of the samples that were comparable to those of the reference protein standard.
  • CIEX Cation exchange
  • Trimer primers were synthesized by Ella Biotech GmbH (Germany). Four first- generation libraries were built by PCR using trinucleotide oligonucleotides and KOD polymerase (Merck Millipore). For each library, 2 PCRs were required to cover the whole gene. For each PCR, lOOpmol primers and lOOng DNA template were used in a 500 ⁇ reactions. 25 cycles were performed, conditions according to KOD manual. [165] lC ⁇ g each PCR fragments were digested with 100 units Bsal (NEB) in 250 ⁇ 1 reaction, and incubated lh at 37°C.
  • NEB Bsal
  • CH2 domain libraries were adapted by PCR to be subcloned into phagemid pIFF6 in frame with pill. Briefly fragments for library #13, #15 and #16 and were digested with HF EcoRI/BamHI restriction enzymes (NEB), purified on Qiaquick columns (Qiagen) and ligated into the EcoRI/BamHI dephosphorylated phagemid O/N at 16°C. Ligations were phenol extracted, EtOH precipitated and transformed into TOPI OF' electro-competent cells. Transformations were plated on 2XTY/Amp/2% glucose big square plates. Each library was ligated, transformed and plated separately and for each one was collected a number of clone equal or 10 fold superior to the theoretical diversity.
  • NEB HF EcoRI/BamHI restriction enzymes
  • Phage rescue was obtained infecting cells at O.D.6oo0.5 with Ml 3 K07 at a MOI of approximately 10. After o/n growth, cells were pelleted and phages in the supernatant purified through a CsCl gradient. After dialysis and titration, libraries were frozen in 10%DMSO and stored at-80°C ready to use.
  • phages were incubated for lhr at RT with the protein in MPBST; after extensive washings with PBST, the bound phages were eluted with Triethylamine (TEA) and used to infect 10ml of a mid-log culture of TGI cells. After 1 hr, a small aliquot was taken, diluted and plated out to titrate the number of selected clones. The remaining cells were centrifuged, resuspended into 1ml of 2XTY and plated onto a 2XTYAG agar bioassay plate.
  • TAA Triethylamine
  • Amplified phages were recovered after o/n growth at 37°C by centrifugation and 900 ⁇ used for the next round of selection, following the procedure described above. During the screening either the phage pool from the different rounds of selection or the individual picked clones were tested in OElisa.
  • a PCR was finally performed with a long primer adding the tac promoter upstream of the libraries (as described in Odegrip et al., 2004;): l . ⁇ g of DNA was amplified in a 1ml PCR reaction, for 15 cycles. Correct library assembly was confirmed by sequencing.
  • Proteins were coated on Nunc maxisorp plates at the desired concentration in the range of ⁇ g/ml in PBS 1X, o/n at 4°C, then blocked with 3%Marvell/PBS for lhr, and incubated with pre-blocked phages in 3%MPBST for lhr at RT. After extensive washing with PBS/0. l%Tween, phage binding was detected by addition of a-M13-HRP mAb (Amersham) diluted 1 :5000 in 3%MPBS incubated for an additional hour at RT. Development with TMB was followed by reading at OD450nm.
  • EphA2 expressing HEK293 were fixed in 4% paraformaldehyde for 20', washed with PBS IX, blocked with 3%MPBS for 1 hr and incubated with phage supernatants for 2 hrs. Binding was revealed with aM13-HRP after 30' of development.
  • PC3 cells were seeded the day before at the density of 18.000 cells/well in 96wells microtiter. The day after the plate were put at 4°C for 10 minutes, then medium was removed and CH2s variants diluted in warm fresh media at 500ng/well added. Binding was allowed at 4°C for 30 min (TO). Then the internalization time course (at time 15 minutes, T15,T30,T60,T180) was started. At each time point media was removed, the cells were fixed with 2% PFA-PBS solution and incubate in the dark for 20 minutes at RT. After 5x washes in 1XPBS, cells were permeabilized with 3%BSA-PBS 0.1% Triton for lhr at RT.
  • the primary antibody was diluted in 3%BSA-PBS 0.1% Triton (aFlag 1 : 1000, aLAMPl 1 :500) and incubated for lhr at RT. After 3 washings in PBS 0.1% Triton and a final wash in lxPBS, the secondary aMouse-AF488 or the aRabbit-AF594 diluted 1 :3000 in 3%BSA-PBS 0.1% Triton were added and incubated for lhr at RT. Washings were repeated as previously described. For the nuclear staining, cells were incubated with DAPI in lxPBS 20min in the dark.
  • the surface of sensor chip was activated for 7 min using a mixture of 0.1 M NHS and 0.4M EDC, 1.2 ⁇ g/ml of hEphA2 in lOmM sodium acetate (pH 4.0) was injected for 7 min at ⁇ /min, and residual activated groups on the surface were blocked by a 7-min injection of 1M ethanolamine (pH 8.5).
  • the binding of CH2-chimeras to the immobilized ligand was evaluated by a multi cycle kinetic procedure in HBS-P running buffer (50 mM Hepes pH 7.4, 150 mM NaCl, 0.005%) surfactant P-20) provided by the manufacturer.
  • the analyte was injected over the ligand for 2.5 min at 40 ⁇ 1/ ⁇ until equilibrium and dissociation was monitored for 5 min.
  • the sensor surface was regenerated with a pulse (30sec) of 0.05M NaOH, 0.5M NaCl, 0.005% SDS, following by extensive washing (6 min, 40 ⁇ 1/ ⁇ ).
  • the collected data and the kinetic parameters were evaluated with BiaEvaluation software v 3.0. The experiments were repeated three times with similar results. All the reagents were purchased from GE Healthcare.
  • Phage selection was performed by coating the recombinant protein targets directly on the Nunc plates (cat#44-2404). Briefly, ⁇ g of mEphA2-Fc (R&D Systems, cat#639-A2) was coated in PBS IX O/N at 4°C. The day after, the well was washed with PBS IX to remove the excess of antigen and blocked for lhr at RT with Milk3% PBS1X (MPBS) to reduce non-specific phages binding to the plastic surface.
  • MPBS Milk3% PBS1X
  • 83nM biotinylated EphA2 was added to the blocked ITT reaction and incubated for lh at room temperature (RT) while mixing on a rotary mixer.
  • ⁇ streptavidin coated magnetic beads M280, Invitrogen
  • the beads were then removed from the selection buffer and washed four times with 1 ml PBS-T (PBS, 0.1% Tween-20) and once with PBS (30sec per wash).
  • Bound DNA was eluted from the beads by incubation in lx ThermoPol buffer (NEB), at 75°C for 10 min. The eluted material was added to a recovery PCR reaction, thereby producing input DNA for the next round of selection.
  • the resulting DNA from the preceding round was added to a fresh ITT mixture and the selection process was repeated.
  • the target concentration was decreased to 20nM for the 2 nd round, 5nM for the 3 rd round, 500pM for the 4 th round and 50pM for the 5 th round; washes were increased to 5 times 5min for round 2 and 7 times 5 min for subsequent round.
  • Enzyme-linked immunosorbent assays were then performed to screen for shCH2 that bound the target ligand. Maxisorp plates were coated with 500ng per well of streptavidin in PBS overnight at 4°C. The plates where then coated with 50ng per well of biotinylated EphA2 in PBS 30min at room temperature. After blocking the plates with blocking buffer (2% BSA in PBS) for lh, the diluted lysate cells were added to the plates and incubated for lh at room temperature.
  • blocking buffer 2% BSA in PBS
  • CH2 domain binders were detected using horseradish peroxidase-conjugated anti-FLAG M2 antibody (Sigma) and TMB peroxidase substrate followed by detection and reading at 450nm in an absorbance plate reader. A selection of positive clones that showed a high signal for EphA2, were sequenced by Sanger sequencing (Cogenics Ltd, UK) to obtain the shCH2 domain sequences.
  • Affinity matured clones were expressed in Shuffle cells, and induced for 22h at 20°C with 0.5mM IPTG. The cells were lysed with BugBuster Master Mix and the Abdurin domains were then purified on a HisTrap HP column using the AKTA Protein Purification Systems (GE Healthcare), followed by further purification through gel filtration Superdex 75 10/300 GL.
  • CHOK1 cells were transfected with transfection-ready huEphA2 cDNA (Origene) according to manufacturer instruction.
  • the CHO-EphA2 cells used in the binding assay were the progeny of a single cell clone, whose expression of EphA2 was verified by fluorescence- activated cell sorter (FACS) using a mouse anti-human EphA2 (R&D Systems). CH2 domains were incubated at different concentrations (InM to 7 ⁇ ) with CHO-EphA2 cells. Binding was then detected with mouse anti histidine tag / Fitc FITC antibody conjugate (AbD Serotec). Cells were washed and resuspended in FACS buffer (PBS, 1% BSA, 0.05% NaN 3 ) and 10,000 events were analyzed on the FACS Jazz instrument (BD Biosciences).
  • FACS buffer PBS, 1% BSA, 0.05% NaN 3
  • MeCOSar a metal ion chelator
  • B6 and Bl l were conjugated onto the B6 and Bl l at a ratio of approximately 1 : 1. Stability of the conjugates was determined by HPLC at 2 weeks for aliquots stored at 2-8°C.
  • the MeCOSar-modified CH2 domains, B6 and Bl l, and MeCOSar-mAb (control) conjugates were radiolabeled with 64 Cu prior to the animal imaging work. 64 Cu synthesis was performed. 500 ⁇ g of each MeCOSar-modified CH2 domains was incubated with 125 MBq at pH 7 and RT for 20 min and cleaned up (EDTA/DIMASAR) via spin columns (3K).
  • MeCOSar-modified CH2 domains and MeCOSar-mAb conjugates were then radiolabelled with 64 Cu. 64 Cu synthesis was performed. 50C ⁇ g of each MeCOSar-modified CH2 domains was incubated with 125 MBq at pH 7 and RT for 20 min and cleaned up (EDTA/DIMASAR) via spin columns (3K).
  • mice Twenty nude mice were inoculated with 2x 10 6 human PC3 prostate cancer cells per animal in 100 ⁇ PBS with 100 ⁇ Matrigel. The inoculation resulted in palpable tumors in the majority of mice by day 4, and the tumors reached a volume of approximately 550mm 3 at Day 1 1. Tumors were very consistent between animals. There was no evidence of ulceration at the time of imaging, and the animals were bright and alert, in good condition apart from the tumors.
  • mice from each treatment group received intravenous 64 Cu-MeCOSar-B6_CH2, 64 Cu-MeCOSar-Bl l_CH2, 64 Cu-MeCOSar-shWT_CH2, 64 CuMeCOSar-shWTCH2 or 64 CuMeCOSar-IgG.
  • animals were perfused, several organs including tumor and muscle were removed and the level of radioactivity measured by a gamma-counter.
  • Radioactivity concentrations in the PET images were recalculated to provide data of Standardized Uptake Value (SUV) by dividing the radioactivity concentration (Bq/ml) by the injected radioactivity (Bq) per body weight (g).
  • SUV Standardized Uptake Value

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Abstract

The present disclosure is directed to a modified isolated immunoglobulin CH2 domain that specifically binds to an extracellular region of an EphA2 receptor, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence, wherein the wild type immunoglobulin CH2 domain amino acid sequence includes SEQ ID NO:1 or SEQ ID NO:2. Heterologous immunoconjugates including fusion proteins and pharmaceutical compositions including the modified isolated immunoglobulin CH2 domain are also disclosed. In addition, methods of treating a disease associated with EphA2 overexpression and methods for killing a target cell expressing EphA2 receptors using the modified isolated immunoglobulin CH2 domain are provided.

Description

SMALL ANTIBODY-LIKE POLYPEPTIDES THAT BIND TO EPHA2 RECEPTOR
CROSS REFERENCE TO RELATED APPLICATIONS
[1] This application claims the benefit of, and relies on the filing date of, U.S. provisional patent application number 62/068,471, filed 24 October 2014, and U.S. provisional patent application number 62/069,781, filed 28 October 2014, the entire disclosures of which are incorporated herein by reference.
SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on October 23, 2015, is named 0185.0002-PCT_SL.txt and is 67,920 bytes in size.
BACKGROUND
[2] Cancer is one disease characterized by the uncontrolled proliferation of cells. While there are a number of causes for such uncontrolled proliferation, one of those causes is aberrant signaling among the cells in a tissue. These aberrant signals, often arising from altered genes or gene products, but also due to viral infection or random mutation, either stimulate or remove inhibitions on the growth of the cell and its neighbors causing rapid and uncontrolled cell division. Other signaling defects may remove usual controls on cell behavior allowing metastasis to develop, spreading the cancer to distant tissues.
[3] Eph receptors are a family of transmembrane proteins involved in cell to cell communication. Each Eph receptor has among other components an intracellular domain with tyrosine kinase activity and an extracellular binding domain. In humans, there are 14 types of Eph receptors classified into the Eph A and Eph B families that normally interact with 8 ephrin receptor ligands found on cell surfaces. Binding of an ephrin ligand to the extracellular binding domain of an Eph receptor causes other Eph receptor molecules to cluster with that receptor molecule, activates its intracellular tyrosine kinase activity to phosphorylate certain tyrosine residues in the receptor molecule which creates binding sites for other intracellular signaling proteins. Phosphorylation also causes internalization of the receptor molecule and marks it for degradation. [4] The EphA2 receptor is an Eph receptor that is commonly overexpressed (or found in overabundance) on cancer cells. Ovarian, breast, prostate, lung, colon, esophageal, renal, cervical cancers and melanoma have been reported to have a much greater abundance of the receptor than non-cancerous cells in those tissues. Induced expression of the EphA2 receptor in transformed cells converts those cells to a malignant phenotype, enhances experimental metastasis of tumors derived from such cells and increases angiogenesis in those tumors.
[5] Antibodies to the EphA2 receptor are well known. Upon binding to the extracellular binding domain of the EphA2 receptor, some act therapeutically to increase tyrosine phosphorylation and turnover of receptor and reduce tumor growth. Others have no effect on tyrosine phosphorylation (that is they do not affect ephrin A2 binding, but still are able to negatively affect tumor growth. Conjugates of these antibodies that deliver cytotoxic moieties to the cells bearing EphA2 receptors have also been described. Once delivered the cytotoxic moieties are released from the antibody to exert their toxic activity.
[6] However, the size of antibodies and their conjugates remains a problem for delivering a sufficient amount of antibody and/or toxin to the cancer cells to effectively shrink or eliminate the tumor. Further, large size can affect the ability of the antibody to bind certain epitopes. Additionally, small antibody-like molecules, such as scFVs, while able to bind their targets, have a very short half-life. Thus, there remains a need for improved EphA2 receptor binding molecules that can affect the activity of the receptor and/or deliver toxic moieties to the cancer cell by targeting the EphA2 receptor.
BRIEF SUMMARY
[7] The present disclosure is directed to a modified isolated immunoglobulin CH2 domain that specifically binds to an extracellular region of an EphA2 receptor, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence.
[8] The present disclosure also provides a method of treating a disease associated with EphA2 overexpression, such as cancer, the method comprising: administering to a subject in need thereof a therapeutically effective dose of a modified isolated immunoglobulin CH2 domain that specifically binds to an EphA2 receptor, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence. [9] Also provided herein is a heterologous fusion protein including a toxin fused to a modified isolated immunoglobulin CH2 domain that specifically binds to an EphA2 receptor, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence.
[10] In addition, the present disclosure provides a pharmaceutical composition including: a modified isolated immunoglobulin CH2 domain that specifically binds to an EphA2 receptor, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence, and a pharmaceutical carrier.
[11] Also provided herein is a method for killing a target cell expressing EphA2 receptors in a subject, the method comprising: administering to the subject a fusion protein including a modified isolated immunoglobulin CH2 domain that specifically binds to an EphA2 receptor fused to a toxin, wherein the amino acid sequence of the modified immunoglobulin CH2 domain includes at least one amino acid substitution, addition or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence; and exposing the target cell to an effective amount of the fusion protein, thereby selectively killing the target cell in the subject.
BRIEF DESCRIPTION OF THE DRAWINGS
[12] The present invention will become more fully understood from the detailed description and the accompanying drawings, wherein:
[13] FIG. 1 is a schematic of human wild type immunoglobulin IgG CH2 domain. The numbering refers to the location of the CH2 domain sequence in the human IgG immunoglobulin using EU numbering. See www.imgt.org/IMGTScientificChart/Numbering/Hu_IGHGnber.html, for an explanation of EU numbering and other CH2 domain numbering methodologies, which is herein incorporated by reference in its entirety.
[14] FIG. 2 is a diagram of the structure of a modified CH2 domain, Loops 1-3 are indicated at the top of the sequence.
[15] FIG. 3 shows the results of a phage ELISA on mouse EphA2, human EphA2, D6-Fc (control) and BSA (control) with individual positives clones B8 (SEQ ID NO: 46), H3 (SEQ ID NO: 48), B l 1 (SEQ ID NO: 47), A5 (SEQ ID NO: 49), D2 (SEQ ID NO: 45), E10 (SEQ ID NO: 44) and H6 (SEQ ID NO: 43).
[16] FIG. 4 shows the results of a phage ELISA on HEK293-EphA2 overexpressing cells with individual positives clones A5, B8, B l 1 , D2, E10, H3 and H6.
[17] FIG. 5 shows an ELISA on mouse and human EphA2 with the three modified CH2 domains, E10, H3 and H6.
[18] FIG. 6A-B show a titration ELISA on mouse (FIG. 6A) and human (FIG. 6B) EphA2.
[19] FIG. 7A-C show Surface Plasmon Resonance (SPR) Sensograms of modified CH2 domains binding to human EphrinA2 receptor.
[20] FIG. 8 shows binding of CH2 modified domain B6 in decreasing concentrations to cells transfected with human EphA2 or non-transfected cells.
[21] FIG 9 shows titration of CH2 modified domains (B l 1 , B6, D2, G7 and parental clones A9 and E10 on transfected cells (top) and non-transfected cells (bottom).
[22] FIG. 10 shows the course of product formation over process time as determined by mCE for B6, B 1 1 and shWT. For shWT, only the last 2 sampling points were analyzed due to the necessity to deglycosylate the protein.
[23] FIG. 1 1 shows an electropherogram of filtrate from supernatant of a B 1 1 -modified CH2 domain-producing strain.
[24] FIG. 12A-E show the level of radioactivity in tumor or muscle from radiolabeled B6
(B6 CH2) or B l l (B 1 1 CH2) modified CH2 domains measured by a gamma-counter.
Results are expressed as % injected dose per g (% ID/g) of tumor or muscle.
[25] FIG. 13 shows tumor-uptake of 64CuMeCOSar-B 1 1 and 64CuMeCOSar-B6 between 4 to 48 hours after tracer injections in mice. T: tumor; K: kidney; L: liver
[26] FIG. 14 shows tumor uptake of 64CuMeCOSar-shWTCH2 and 64Cu MeCOSar-IgG between 4 and 48 hours after tracer injections in mice. T: tumor; K: kidney; L: liver
[27] FIG. 15 shows the binding and internalization time course of B 1 1 -deimmunized a- sarcin (SEQ ID NO: 73 was used) fusion protein into PC3 cells.
[28] FIG. 16 shows the killing of PC3 tumor cells by the B l l -deimmunized a-sarcin fusion protein. Chemiluminescence of viable cells is on Y axis and dose titration on X-axis (0, 1 , 5, 10, 50 nM). WT= native CH2-a-sarcin fusion versus B l l -DI (DI=deimmunized sarcin). [29] FIG. 17 shows the localization of B l 1 modified CH2 domain in early endosome: B l 1 modified CH2 domain was detected with a-Flag that co-localize with EEAl, Early Endosome Marker protein detected with the specific Mab.
[30] FIG. 18 shows the binding and internalization time course of B 1 1 -dPEG-biotin in PC3 cells. The B l 1 modified sequences are shown in SEQ ID NOS: 91, 90 and 89.
DETAILED DESCRIPTION
[31] The following description of the disclosed embodiment(s) is merely exemplary in nature and is in no way intended to limit the invention, its application, or uses.
[32] As used throughout, ranges are used as shorthand for describing each and every value that is within the range. Any value within the range can be selected as the terminus of the range. In addition, all references cited herein are hereby incorporated by referenced in their entireties. In the event of a conflict in a definition in the present disclosure and that of a cited reference, the present disclosure controls.
[33] Unless otherwise specified, all percentages and amounts expressed herein and elsewhere in the specification should be understood to refer to percentages by weight. The amounts given are based on the active weight of the material.
Structure of CH2 Domains
[34] The present disclosure is directed to a modified isolated immunoglobulin CH2 domain ("modified CH2 domain(s)") that specifically binds to an EphA2 receptor.
[35] As used herein an "immunoglobulin" (also known as an antibody) is a protein (or complex) having a structural unit that is generally a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light" (about 25 kDa) and one "heavy" (about 50-70 kDa) chain. The N-terminus of each chain defines a variable region of about 100 to 1 10 or more amino acids primarily responsible for antigen recognition. The terms "variable light chain" (VL) and "variable heavy chain" (VH) refer, respectively, to these light and heavy chains. Each light chain contains a single constant domain (CL), while each heavy chain contains three constant domains, CHI, CH2 and CH3 (or four constant domains for IgE and IgM).
[36] Accordingly, in various embodiments, the modified CH2 domain of the present disclosure is derived from the CH2 constant domain of an immunoglobulin or antibody. As used herein, "derived from" encompasses actually or theoretically "originating from," "obtained from," or "isolated from" a parent substance, e.g., a wild type CH2 domain. Devoid of the VL and VH domains, the modified CH2 domain of the present disclosure is much smaller than a full-length immunoglobulin. Typically, the size of a modified CH2 domain is about 15 kD or less. It is also possible to link one or more modified CH2 domains together to construct a multivalent binding molecule with binding specificity for the same molecule or for different molecules.
[37] In some embodiments, the CH2 domain of the present disclosure is modified in comparison to a wild type CH2 domain. The wild type CH2 domain may be from any species. In some embodiments, the species is a mammalian species, such as a sheep, goat, mouse, rat, human, macaque, camel or baboon. In other embodiments, the species is a primate, typically a human or a macaque. For example, the modified CH2 domain of the present invention may be modified in comparison to the amino sequence of the wild type human IgG CH2 domain set forth in SEQ ID NO: 1 or the wild type macaque IgG CH2 domain set forth in SEQ ID NO: 2,
[38] In various embodiments, the modified CH2 domain of the present disclosure is derived from an IgG, IgA, IgD, IgE or an IgM immunoglobulin. More typically, the modified CH2 domain is derived from an IgG immunoglobulin. In some embodiments, the modified CH2 domain is compared with a wild type CH2 domain having the same isotype or isotype and subclass, e.g., IgG S . IgG2, IgG 3 and IgG4.
[39] In various embodiments, the CH2 domains of the present disclosure are modified to bind to a receptor, for example, the EphA2 receptor. Generally, for binding, loop sequences of the CH2 domains of the present disclosure are modified in comparison to loop sequences of wild type CH2 domains. As shown in FIG. 1 , wild type CH2 domains comprise six loop regions: Loop 1 , Loop 2, Loop 3, Loop A-B, Loop C-D and Loop E-F. Wild type CH2 domains also comprise seven β sheets, A to G, oriented from the N- to C-terminus. Loops A- B, C-D and E-F are located between β-sheets A and B, C and D, and E and F, respectively. Loops 1 , 2 and 3 are located between β-sheets B and C, D and E, and F and G, respectively.
[40] In some embodiments, the amino acid sequences of Loops 1 , 2 and 3 of the CH2 domains of the present disclosure (also interchangeably referred to herein as LI , L2 and L3, respectively) are modified in comparison to LI, L2 and L3 of a wild type CH2 domain. Amino acids 231-341 of FIG. 1 show a CH2 domain of a wild type IgG human antibody. In this figure, the numbering of the amino acids refers to the location of the CH2 domain in reference to the whole wild type IgG human antibody sequence. The FIG. 1 amino acid sequence is set forth in SEQ ID NO: 1. A diagram of a CH2 domain structure is depicted in FIG. 2.
[41] LI corresponds to positions 35-44 of SEQ ID NO: 1 (DVSHEDPEVK, SEQ ID NO: 3) or SEQ ID NO: 2 (DVSQEDPDVK, SEQ ID NO: 6), L2 corresponds to positions 63-67 of SEQ ID NO: 1 (EEQYNS, SEQ ID NO: 4) or SEQ ID NO: 2 (ETQYNS, SEQ ID NO: 7) and the L3 corresponds to positions 94- 102 of SEQ ID NO: 1 (SNKALPAPI, SEQ ID NO: 5) or SEQ ID NO: 2 (SNKALPAPI, SEQ ID NO: 8).
[42] In some embodiments, the loops of wild type CH2 domains can be 1 -2 amino acids longer or shorter than the loop sequences set forth above. The loops may singly or in combination form an antigen binding region, such as an antigen binding region that specifically binds to an EphA2 receptor.
[43] In some embodiments, the framework regions of the immunoglobulin CH2 domains of the present disclosure are also modified. Typically, the term "framework" is conventionally used to refer to amino acid sequences interposed between CDRs (or hypervariable regions) in an intact antibody. Amino acid residues within these framework regions serve to hold the CDRs in an appropriate orientation for antigen binding, and typically form β-sheet structures. As used herein, in the context of a modified immunoglobulin CH2 domain, the term "framework region" refers to amino acid sequences outside of loops 1 , 2 and 3; i.e.., amino acid sequences interposed between loops 1 -2 and between loops 2-3, as well as amino acid sequences N-terminal to loop 1 and C-terminal to loop 3. Wild type CH2 domains contain four framework regions, referred herein as FR1 , FR2, FR3 and FR4. The framework regions in CH2 serve to hold loops 1 -3 in an appropriate orientation for their usual functions, and also form β-sheet structures.
[44] For example, for the wild type human IgG CH2 domain (SEQ ID NO: 1), framework region 1 is composed of amino acids 1 -34 (SEQ ID NO: 9), framework region 2 is composed of 45-62 (SEQ ID NO: 10), framework region 3 is composed of 69-93 (SEQ ID NO: 1 1) and framework region 4 is composed of amino acids at positions 103- 1 10 (SEQ ID NO: 13). In some embodiments, the framework regions can be 1 -2 amino acids longer or shorter than the framework sequences set forth above.
[45] In various embodiments, the disclosed CH2 domain is isolated. As used herein, "isolated" refers to a biological component, such as a CH2 domain, which has been substantially separated or purified away from other biological components from which the component naturally occurs, for example, other biological components of a cell, other antibodies and other antibody domains. CH2 domains that have been "isolated" include nucleic acids and proteins purified by standard purification methods. The term also embraces CH2 domains prepared by recombinant expression in a host cell, as well as chemically synthesized nucleic acids encoding CH2 domains.
Modification of CH2 Domains
[46] One or more loops and/or strands (of the beta sheets, A, B, C, D, E, F, G) of one or more CH2 domains may be modified. As used herein, the terms "modified" or "modification," can include one or more mutations, deletions, additions, substitutions, physical alteration (e.g., cross-linking modification, covalent bonding of a component, post- translational modification, e.g., acetylation, glycosylation, tagging, e.g., His-tags or a combination thereof) or a combination thereof. Modification, e.g., mutation, is not limited to random modification (e.g., random mutagenesis) but includes rational design as well.
Loops
[47] As noted above, in some embodiments, LI, L2 and/or L3 may be modified to specifically bind to an EphA2 receptor. For example, an LI, L2 or L3 amino acid sequence of an isolated immunoglobulin CH2 domain of the present disclosure may include at least one amino acid substitution, addition, or deletion of the amino sequence in comparison to an LI, L2 or L3 amino acid sequence of a wild type CH2 domain. For example, in some embodiments, loops 1, 2 and/or 3 of the modified CH2 domain of the present disclosure may be modified in comparison to loops 1, 2 and/or 3 of the human wild type IgG CH2 domain set forth in SEQ ID NOS: 3-5, respectively. In other embodiments, loops 1, 2 and 3 of the modified CH2 domain of the present disclosure may be modified in comparison to loops 1 , 2 and 3 of the macaque wild type IgG CH2 domain set forth in SEQ ID NOS: 6-8, respectively.
[48] In some embodiments, the LI amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid substitutions in comparison to a wild type CH2 domain, such as at position 1, position 2, position, 3, position 4, position 5, position 6, position 7, position 8, position 9 and/or position 10. In other embodiments, the LI amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid deletions in comparison to a wild type CH2 domain. In other embodiments, the LI amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more additional amino acids in comparison to a wild type CH2 domain.
[49] In other embodiments, the L2 amino acid sequence is modified in comparison to a wild type L2 amino acid sequence. The modification of L2 may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid substitutions in comparison to a wild type CH2 domain, such as at position 1, position 2, position, 3, position 4, position 5, position 6, position 7, position 8, position 9 and/or position 10. In other embodiments, the L2 amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid deletions in comparison to a wild type CH2 domain. In other embodiments, the L2 amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more additional amino acids in comparison to a wild type CH2 domain.
[50] In other embodiments, the L3 loop amino acid sequence is modified in comparison to a wild type L3 amino acid sequence. The modification of L3 may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid substitutions in comparison to a wild type CH2 domain. In other embodiments, the L3 amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more amino acid deletions in comparison to a wild type CH2 domain. In other embodiments, the L3 amino acid sequence may include at least one, two, three, four, five, six, seven, eight, nine or 10 or more additional amino acids in comparison to a wild type CH2 domain.
[51] In some embodiments, only the LI amino acid sequence is modified. In other embodiments, only the L2 sequence is modified. In other embodiments, only the L3 amino acid sequence is modified. In various embodiments, the LI or the L2 sequence is modified. In other embodiments, the LI and the L2 amino acid sequences are modified. In yet other embodiments, the LI, L2 and L3 amino acid sequences are modified. In some embodiments, the LI and L3 sequences are modified. In other embodiments, the L2 and L3 sequences are modified.
[52] In some embodiments, the LI sequence is modified such that it contains 1-6 amino acid substitutions, such as at positions 2-7 of the human wild type LI amino acid sequence or positions 2-7 of the Macaque LI amino acid sequence (SEQ ID NOS: 3 or 6, respectively), e.g., positions 2-7 of LI may be modified with the amino acid sequences described, for example, in SEQ ID NOS: 50-53 or according to residues 2-7 in SEQ ID NOS: 14- 15 and 17- 21 or residues 2-6 of SEQ ID NO: SEQ ID NO: 16. In other embodiments, the LI sequence is modified such that it contains 1 deletion, for example, a deletion at position 4 or 5 of the human wild type LI amino acid sequence (SEQ ID NO: 3) or the LI Macaque amino acid sequence (SEQ ID NO: 6). In some embodiments, the LI sequences are modified as set forth in any of SEQ ID NOS: 14-21 or SEQ ID NOS: 85-86 and 94-99.
[53] In some embodiments, the L2 amino acid sequence of the isolated immunoglobulin CH2 domain of the present disclosure is modified to contain 1-6 amino acid substitutions, such as at positions 1-6 of the human wild type L2 amino acid sequence (SEQ ID NO: 4) or the Macaque wild type L2 amino acid sequence (SEQ ID NO: 7). In some embodiments, the L2 amino acid sequence of the modified CH2 domain of the present disclosure is the sequence set forth in SEQ ID NOS: 22-28, such as SEQ ID NOS: 22 or 23.
Framework
[54] In some embodiments, FR1, FR2, FR3 and/or FR4 are modified in comparison to wild type FR1, FR2, FR3 or FR4 regions of a wild type CH2 domain. The modified FR1, FR2, FR3 and FR4 may contain at least one, two, three or four or more deletions, substitutions or additions. In some embodiments, an amino acid sequence of only one of the FR regions may contain a deletion, substitution or addition. For example, FR3 may be modified to include at least one substitution at position 1, e.g., as set forth in SEQ ID NO: 12 or SEQ ID NO: 101. In other embodiments, two or more the FR regions are modified, e.g., FR1 and FR2, FR2, FR3 and FR4, etc.
[55] In various embodiments, the modified, isolated immunoglobulin CH2 domains disclosed herein retain substantially the structure characteristic of a wild type CH2 domain, such as the beta barrel structure of a naturally occurring CH2 domain, i.e., the 3-stranded sheet containing strands C, F, and G, packed against the 4-stranded sheet containing strands A, B, D, and E. Amino acid residues involved in maintaining the beta barrel structure are known in the art, including the residues that form hydrogen bonding, hydrophobic interactions, and the disulfide bond. In specific embodiments, the residues critical to maintaining the beta barrel structure are not modified. In certain embodiments, the framework residues are substantially not modified; for example, not more than 15%, or 10% or 5% of the framework residues are modified in the modified CH2 domains as compared to a wild type CH2 domain. Modifications at or near the terminal regions of a wild type CH2 domain may be more tolerable (i.e., less likely to disrupt the structure or conformation of a wild type CH2 domain) as compared to modifications to other regions. [56] Standard techniques known to those of skill in the art can be used to introduce mutations in the loop and/or framework regions (e.g., deletions, additions, and/or substitutions) in nucleotide sequences encoding the modified CH2 domains of the present disclosure, including, for example, site-directed mutagenesis and PCR-mediated mutagenesis which results in amino acid substitutions.
[57] In some embodiments, conservative amino acid substitutions are made at one or more predicted non-essential amino acid residues of the loop and/or framework regions of the modified CH2 domains (i.e., amino acid residues that can be modified without abrogating the modified CH2 domain's ability to specifically bind to an EphA2 receptor). A "conservative amino acid substitution" is one in which the amino acid residue is replaced with an amino acid residue having a side chain with a similar charge. Families of amino acid residues having side chains with similar charges have been defined in the art. These families include amino acids with 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), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).
[58] In some embodiments, a series of variants may be generated that differ by at least one amino acid in their sequence compared with the sequence of the wild type immunoglobulin CH2 domain. Changes may include but are not limited to deletions of an amino acid, additions, and/or substitutions. In generating a library of potential binding molecules, design changes may be focused on the loops. At any one site, variants may be generated that introduce any of the 20 naturally occurring amino acids (or non-natural amino acids), or a more restricted subset of amino acids might be substituted.
[59] Alternatively, in some embodiments, random mutations may be introduced by mutagenesis of the entire molecule, framework regions and loops. Such mutagenesis can be accomplished either in vivo (in a mutagenic host or by addition of exogenous mutagen) or in vitro (by using mutagenic mixtures of precursors and/or by using a DNA polymerase that exhibits reduced or no proofreading nuclease activity). In the case of certain display methods (e.g. phage, CIS, ribosome display), a combination of the two approaches may be employed, synthesizing the initial variants to focus changes within the loops and then allowing random mutagenesis at each round of selection-amplification. Such methods of creating a diverse collection of variant nucleotide sequences to produce variant amino acid sequences are well known in the art. See also the methods for making variant CH2 domains and the CH2 domain libraries described in PCT Publication No. WO 2012/109553, which is herein incorporated by reference in its entirety.
[60] The libraries made in such a way and displayed by any of the established methods available, may be used to isolate individual molecules from that library which bind to a target of interest, e.g., EphA2 receptor. A target molecule, such as an EphA2 receptor, is used to contact a display library to screen for modified CH2 domains that are able to bind to the target molecule. The purified target molecules are presented in either 1) a form that is immobilized on a solid surface, or 2) as soluble molecules in solution. If in solution, they are engineered to bear a simple means for subsequent capture, such as biotin. In the case of cell surface display (e.g. on yeast), the target molecule is tagged fluorescently to enable cell sorting based upon the fluorescent signal due to bound target by the displayed CH2 domain variant. Various methods may be used for detecting the binding of the modified CH2 domain to the target in the sample. Such methods are well known to one of ordinary skill in the art.
Other Modifications
[61] In some embodiments, the modified immunoglobulin CH2 domain comprises a truncation or deletion of the first seven amino acids of the N-terminus of the wild type CH2 domain from which it is derived. Or, in some embodiments, the CH2 domain comprises a deletion of the first amino acid, the first two, the first three, the first four, the first five, the first six, or the first seven amino acids of the N-terminus of the wild type CH2 domain from which it is derived. In some embodiments, the modified CH2 domain comprises a deletion of the first eight, the first nine, or the first ten amino acids of the N-terminus of the wild type CH2 domain from which it is derived. In some embodiments, the modified CH2 domain comprises a deletion of the last four amino acids of the C-terminus of the wild type CH2 domain from which it is derived. In some embodiments, the modified CH2 domain comprises a deletion of the last amino acid, the last two, the last three, the last four, the last five, the last six, the last seven, the last eight, the last nine, or the last ten amino acids of the C-terminus of the wild type CH2 domain from which it is derived. In some embodiments, the modified CH2 domain comprises a deletion at both the N-terminus and the C-terminus of the wild type CH2 domain from which it is derived. For example, in some embodiments, the modified CH2 domain comprises a deletion of the first amino acid, the first two, the first three, the first four, the first five, the first six, or the first seven amino acids of the N-terminus of the wild type CH2 domain from which it is derived and a deletion of the last amino acid, the last two, the last three, the last four, the last five, the last six, the last seven, the last eight, the last nine, or the last ten amino acids of the C-terminus of the wild type CH2 domain from which it is derived. The present disclosure is not limited to the aforementioned examples of deletions. The CH2 domain may comprise other deletions in other regions of the protein. Without wishing to limit the present invention to any theory or mechanism, it is believed that such truncations or deletions (or other modifications) to the molecule may confer a particular property, for example including but not limited to enhanced stability.
[62] In some embodiments, the modified CH2 domain comprises a one amino acid addition, a two amino acid addition, a three amino acid addition, a four amino acid addition, a five amino acid addition, a six amino acid addition, a seven amino acid addition, an eight amino acid addition, a nine amino acid addition, a ten amino acid addition, an eleven amino acid addition, a twelve amino acid addition, etc. at its N-terminus.
[63] In some embodiments, the modified CH2 domain comprises a one amino acid addition, a two amino acid addition, a three amino acid addition, a four amino acid addition, a five amino acid addition, a six amino acid addition, a seven amino acid addition, an eight amino acid addition, a nine amino acid addition, a ten amino acid addition, an eleven amino acid addition, a twelve amino acid addition, etc. at its C-terminus, such as set forth in SEQ ID NO: 61 and SEQ ID NOS: 89-93.
[64] In some embodiments, the modified CH2 domain comprises an addition at the N- terminus and at the C-terminus. For example, the CH2 domain may comprise a one amino acid addition, a two amino acid addition, a three amino acid addition, a four amino acid addition, a five amino acid addition, a six amino acid addition, a seven amino acid addition, an eight amino acid addition, a nine amino acid addition, a ten amino acid addition, an eleven amino acid addition, a twelve amino acid addition, etc. at the N-terminus and a one amino acid addition, a two amino acid addition, a three amino acid addition, a four amino acid addition, a five amino acid addition, a six amino acid addition, a seven amino acid addition, an eight amino acid addition, a nine amino acid addition, a ten amino acid addition, an eleven amino acid addition, a twelve amino acid addition, etc. at the C-terminus. The additions may include for example, adding a serine, tyrosine, cysteine or lysine residue, for example, to facilitate linking to a linker as described herein below, such as set forth in SEQ ID NO: 61 and SEQ ID NOS: 89 and 91-93. [65] In some embodiments, one or more portions of the modified CH2 domain or one or more amino acids may be substituted with another peptide or amino acid, respectively. Seeor example SEQ ID NOS: 54 and 55. In some embodiments, the modified CH2 domain may comprise a tag, for example including but not limited to a His tag.
[66] In further embodiments, the modified CH2 domains that bind EphA2 have additional mutations that further increase stability of the molecule. For example, the molecules can comprise mutations that allow for the formation of non-native disulfide bonds, such as by introducing a pair of amino acid substitutions to replace original residues with cysteine residues. In some examples, a first amino acid substitution is introduced in the N-terminal A strand and the second amino acid substitution is introduced in the C-terminal G strand of the modified CH2 domain of the present disclosure.
[67] For example, the modified CH2 domain may comprise a first amino acid substitution of L12 to C12 and a second amino acid substitution of K 104 to CI 04 (numbered with reference to SEQ ID NO: 1). In other examples, the first amino acid substitution may be V10 to CIO and the second amino acid substitution may be K104 to CI 04 or K102 to CI 02 (numbered with reference to SEQ ID NO: 1). See, for example, SEQ ID NOS: 56-59.
[68] in some embodiments, the modified CH2 domain of the present disclosure may be modified to enhance or decrease the affinity and/or avidity the modified CH2 domain has to FcRn, e.g. a human FcRn. As is known in the art, serum half-life of an immunoglobulin is mediated, in part, by the binding of the Fc region to the neonatal receptor FcRn. The alpha domain is the portion of FcRn that interacts with the CH2 domain (and possibly CH3 domain) of IgG, and possibly with IgA, and IgD or with the CH3 domain (and possibly CH4 domain) of IgM and IgE. Several studies support a correlation between the affinity for FcRn binding and the serum half-life of an immunoglobulin.
[69] Modifications to the CH2 domain of the present disclosure to enhance or decrease the affinity and/or avidity to FcRn include mutations (amino acid substitutions, deletions, physical modifications to amino acids) of one or more amino acid residues. Modifications may also include insertion of one or more amino acid residues or one or more binding sites (e.g., insertion of additional binding sites for FcRn). A modification may, for example, increase the affinity for FcRn at a lower pH (or higher pH). See, for example, U.S. Patent Application No. 2007/0135620, which is herein incorporated by reference in its entirety).
[70] Examples of amino acid substitutions may include but are not limited to M252Y, S254T, T256E, T307A (in reference to FIG. 1), or a combination thereof. Without wishing to limit the present disclosure to any theory or mechanism, it is believed that one or more of the substitutions M252Y, S254T, T256E, T307A may increase serum half life of the modified CH2 domain by increasing FcRn binding.
[71] In some embodiments, the modified CH2 binding domains, such as a modified macaque IgG immunoglobulin CH2 domain, are deimmunized. As used herein "deimmunized" refers to amino acid sequences carrying one or more amino acid substitutions that (a) reduce an immune response by one to whom a modified CH2 domain, for example, is administered and (b) retains a therapeutically and/or prophylactically effective amount of EphA2 binding activity, for example. Methods for producing deimmunized proteins are known in the art and described, for example, WO2006/082406, WO2004/108158 and WO2004/064724. For example, the method may comprise 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 EphA2. For example, an epitope that occurs within a loop is not mutated unless the mutation is unlikely to reduce epitope binding. Methods for predicting epitopes are known in the art and described, for example, in Saha et ah, BcePred:Prediction of Continuous B-Cell Epitopes in Antigenic Sequences Using Physico-chemical Properties. In Nicosia, Cutello, Bentley and Timis (Eds.) ICARIS 2004, LNCS 3239, 197-204, Springer, 2004. Also for T cell epitopes: Baker MP and Jones TD. Identification and removal of immunogenicity from therapeutic proteins. Current Opinion Drug Discovery and Development. 2007; 10(2):219-227 and WO2006/082406.
EphA2 receptors
[72] The modified CH2 domain of the present disclosure specifically binds to an EphA2 receptor. The EphA2 receptor may be from any species. In some embodiments, the EphA2 receptor is from a mammal, e.g., a dog, cat, sheep, goat, rat, mouse, macaque, baboon, or a human. Typically, the EphA2 receptor is from a mouse, macaque or a human.
[73] As used herein "specifically binds" refers to the preferential association of a binding agent, such as a modified CH2 domain, in whole or part, with a cell or tissue bearing the target of that binding agent and not to cells or tissues lacking a detectable amount of that target. It is recognized that a certain degree of non-specific interaction may occur between a molecule and a non-target cell or tissue. Nevertheless, specific binding may be distinguished as mediated through specific recognition of an antigen. Specific binding typically results in greater than 2-fold, such as greater than 5-fold, greater than 10-fold, or greater than 100-fold increase in amount of bound molecule (per unit time) to a cell or tissue bearing the target as compared to a cell or tissue lacking the target, respectively. Specific binding to a protein under such conditions requires a molecule that is selected for its specificity for a particular protein. A variety of immunoassay formats are appropriate for selecting molecules specifically reactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used.
[74] As used herein, the term "EphA2 receptor" refers to a tyrosine kinase belonging to the Eph receptors family, and comprising, for example, an amino sequence as in Genbank Accession Nos. NM 004431.3, GL296010835 (human EphA2), herein incorporated by reference in its entirety, NM 010139.3, GL342187227 (murine EphA2), herein incorporated by reference in its entirety or NM 001 108977.1 GI: 157822928 (rat EphA2), herein incorporated by reference in its entirety. In some embodiments, the modified CH2 domains specifically bind to a human EphA2 receptor.
[75] As is known in the art, the Eph receptors comprise several distinctive domains required for their signaling capabilities. The extracellular domain contains an ephrin ligand- binding domain in its N-terminal region, followed by a cysteine-rich region and two fibronectin type-Ill repeats. The intracellular region comprises the signaling components which include a tyrosine kinase domain, a SAM (Sterile Alpha Motif) domain, and a PDZ (Postsynaptic density protein, Disks large, Zona occludens)-binding motif. Both SAM and the PDZ domains have been shown to mediate protein-protein interactions.
[76] GPI-anchored plasma membrane proteins ephrin-Al to ephrin- A5 are known as EPHA2 ligands. The ligand binding to EPHA2 activates the tyrosine kinase domain and phosphorylates tyrosine residues present in the EPHA2 intracellular region, resulting in signal transduction within the cell. It has also been reported that EPHA2 bound with the ligand is internalized into the cell through endocytosis and is eventually degraded by a proteasome.
[77] In some embodiments, the modified CH2 domains described herein are capable of inhibiting one or more of the biological activities of a target molecule, such as an EphA2 receptor. Such antagonists may act by interfering with the binding of a receptor to a ligand, by decreasing EphA2 phosphorylation that could be induced by a ligand, and/or by inhibiting the intracellular pathways that are induced by the binding of such ligand, and/or by inhibiting the homo/hetero-oligomerization of EphA2 receptors. The antagonist may completely block receptor-ligand interactions or may substantially reduce such interactions. Accordingly, the modified CH2 domains of the present invention may act as antagonists (e.g. act as neutralizing antibodies) thai bind to EphA2 receptor, EphA2 liganci or a complex of an EphA2 receptor and EphA2 ligand. In other embodiments, the modified CH2 domains of the present disclosure stimulate phosphorylation of the EphA2, thereby triggering degradation of said protein.
[78] In some embodiments, the modified CH2 domains of the present specifically bind to the EphA2 receptor. In some embodiments, the modified CH2 domains specifically bind to the extracellular domain of the EphA2 receptor.
[79] Modified CH2 domains, capable of specifically binding the EphA2 receptor, typically, the extracellular domain of the EphA2 receptor, are herein provided, e.g. the modified CH2 domains designated as E10, H6, D2, G7, B6, B l l, F4.1, C5, D9 and E3 set forth as SEQ ID NOS: 29-38. In other embodiments, the modified CH2 domains, capable of specifically binding the EphA2 receptor, typically, the extracellular domain of the EphA2 receptor, include for example, the modified CH2 domains set forth in SEQ ID NOS: 89-93.
[80] Also provided herein are isolated modified immunoglobulin CH2 domains that specifically bind to an EphA2 receptor, wherein the modified CH2 domains competitively inhibits binding of an isolated immunoglobulin CH2 domain selected from the group consisting of E10, D2, G7, B6, Bl 1, B4.1, C5, D9, and E3.
[81] In a specific embodiment, the disclosure encompasses modified CH2 domains that reduce the binding of E10, H6, D2, G7, B6, B l 1, B4.1, C5, D9 and E3 to an EphA2 receptor by at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or more, 25% to 50%, 45 to 75%, or 75 to 99% relative to a control such as PBS in the competition assays well known in the art.
[82] For example, an ELISA competition assay may be performed in the following manner: recombinant EphA2 is prepared in PBS at a concentration of 10 μg/ml. 100 μΐ of this solution is added to each well of an ELISA 98-well microtiter plate and incubated overnight at 4-8° C. The ELISA plate is washed with PBS supplemented with 0.1% Tween to remove excess recombinant EphA2. Non-specific protein-protein interactions are blocked by adding 100 μΐ of bovine serum albumin (BSA) prepared in PBS to a final concentration of 1%. After one hour at room temperature, the ELISA plate is washed. Unlabeled competing CH2 domains are prepared in blocking solution at concentrations ranging from 1 μg/ml to 0.01 μg/ml. Control wells contain either blocking solution only or control antibodies at concentrations ranging from 1 μg/ml to 0.01 μg/ml. Test antibody labeled with horseradish peroxidase is added to competing antibody dilutions at a fixed final concentration of 1 μg/ml. 100 μΐ of test and competing CH2 domain mixtures are added to the ELISA wells in triplicate and the plate is incubated for 1 hour at room temperature. Residual unbound CH2 domain is washed away. Bound test CH2 domain is detected by adding 100 μΐ of horseradish peroxidase substrate to each well. The plate is incubated for 30 min. at room temperature, and absorbance is read using an automated plate reader. The average of triplicate wells is calculated. CH2 domains which compete well with the test antibody reduce the measured absorbance compared with control wells.
[83] The strength of binding between a binding site (X) and a ligand (Y), for example, between a modified CH2 domain of the present disclosure and an EphA2 receptor, may be characterized by the dissociation constant (Kd). Kd is the concentration of Y that is required to occupy half of the binding sites of X present in a solution. A lower (Kd) indicates a stronger or higher-affinity interaction between X and Y and a lower concentration of ligand is needed to occupy the sites. Methods for determining binding affinity are well known in the art.
[84] In some embodiments, the Kd resulting from binding between a modified CH2 domain and an EphA2 receptor or extracellular domain thereof, is less than 1 x 10 2M, less than l lO~3M, less than l x l0~4M, less than l x lO~5M, less than l x lO~6M, less than l x lO~7M, less than l x l0~8M, less than l x lO~9M, less than l x l010M, less than l x l0~nM, less than 1 x 10~12M, less than 1 x 10~13M, less than 1 x 10~14M or less than 1 x 10~15M.
Immunoconjugates
[85] In some embodiments, the modified CH2 domains described herein may be joined to a second molecule to form an immunoconjugate, wherein the second molecule is, for example, a detectable moiety, a toxin, an epitope binding protein or a small molecule. The terms "linking", "joining," or "bonding" refer to making two polypeptides into one continuous polypeptide molecule, or to covalently attaching the modified CH2 domain of the present disclosure to the second molecule.
Detectable Moiety
[86] For example, the modified CH2 domains may be joined to a detectable moiety for use in in vivo or in vitro imaging, wherein the labeled, modified CH2 domain is administered to a subject, such as into the bloodstream, and the presence and location of the labeled CH2 domain in the host is assayed. In some embodiments, imaging is useful in the staging and treatment of malignancies. The modified CH2 domain of the present disclosure may be labeled with any moiety that is detectable in a host, whether by PET/CT imaging or other detection means known in the art.
[87] The label can be any detectable moiety that is capable of producing, either directly or indirectly, a detectable signal. For example, the label may be a detectable radioisotope, e.g., 64Cu, 67Cu, 90Y, mIn, 124I, 125I 13T, mCs, 186Re, 211At, 212Bi, 213Bi, 223Ra, 241Am, 244Cm and 99mTc-MDP, a fluorescent compound, e.g., fluorescein phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine); chemiluminescent compound (e.g., fluorescein isothiocyanate, rhodamine), an enzyme label (e.g., luciferase, alkaline phosphatase, beta-galactosidase and horseradish peroxidase), an imaging agent (e.g., Tc-m99 and indium (mIn)) and/or a metal ion (e.g., gallium and europium). In some embodiments, bifunctional chelators e.g., MeCOSar are labeled with radioisotopes, e.g., 64Cu.
Toxins, Epitope Binding Proteins, Small Molecules
[88] In other embodiments, the modified isolated immunoglobulin CH2 domain is fused to a toxin to form a heterologous fusion protein. As used herein, "fusion protein" refers to a hybrid protein, which consists of two or more proteins, or fragments thereof, linked together covalently. A fusion protein may be "heterologous", i.e., comprising two or more peptides or proteins from different animals, origins, or species.
[89] In some embodiments, the toxins, which may be bound to the modified CH2 domain of the present disclosure include, but are not limited to, abrin, ricin, Pseudomonas exotoxin (PE, such as PE18, PE24, and PE38), diphtheria toxin (DT), botulinum toxin, saporin, restrictocin or gelonin, or modified toxins thereof. Other cytotoxic agents that may be attached to the modified CH2 domain include cytolytic peptides.
[90] In some embodiments, the toxin is a fungal ribonuclease, for example, a-sarcin or a deimmunized a-sarcin. A deimmunized toxin is one that (a) reduces the anti-toxin immune response by one to whom the toxin is administered, and (b) retains a therapeutically and/or prophylactically effective amount of toxin activity. Methods for preparing deimmunized a- sarcin are well known in the art, as disclosed, for example, in WO 2014/158770, which publication is hereby incorporated by reference in its entirety. By way of example, the deimmunized α-sarcin can have an amino acid sequence as set forth in the following table: SEQ ID NO: Variant
62 Q10X (X = K or A)
AVTWTCLNDX KNPKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NQGELKLCSH
63 N16X(X= R, K or A)
AVTWTCLNDQ KNPKTXKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NQGELKLCSH
64 Y18X (X= K or R)
AVTWTCLNDQ KNPKTNKXET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NQGELKLCSH
65 K139X(X= D or E)
AVTWTCLNDQ KNPKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTXE NQGELKLCSH
66 E140D
AVTWTCLNDQ KNPKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKD NQGELKLCSH
67 Q142X(X= N, T, or E)
AVTWTCLNDQ KNPKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NXGELKLCSH
68 Q10K + K139X (X = D or E)
AVTWTCLNDK KNPKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTXE NQGELKLCSH SEQ ID NO:
69 N16R + K139X (X = D or E)
AVTWTCLNDQ KNPKTRKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTXE NQGELKLCSH
70 F «¾(Xi = K or R) + K139X2 (X2 = D or E)
AVTWTCLNDQ KNPKTNKXjET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTXjE NQGELKLCSH
71 Q10K + Q142T
AVTWTCLNDK KNPKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NTGELKLCSH
72 Q10K + K139D + Q142T
AVTWTCLNDK KNPKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTDE NTGELKLCSH
73 Q10K + K139E + Q142T
AVTWTCLNDK KNPKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTEE NTGELKLCSH
74 N16R + K139D + Q142T
AVTWTCLNDQ KNPKTRKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTDE NTGELKLCSH
75 N16R + K139E + Q142T
AVTWTCLNDQ KNPKTRKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTEE NTGELKLCSH
76 D9T + Q142T
AVTWTCLNTQ KNPKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NTGELKLCSH SEQ ID NO: Variant
77 Q10A + Q142T
AVTWTCLNDA KNPKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NTGELKLCSH
78 P13I + Q142T
AVTWTCLNDQ KNIKTNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NTGELKLCSH
79 T15G + Q142T
AVTWTCLNDQ KNPKGNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NTGELKLCSH
80 Y18K + Q142T
AVTWTCLNDQ KNPKTNKKET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NTGELKLCSH
81 N16A+ Q142T
AVTWTCLNDQ KNPKTAKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NTGELKLCSH
82 Y18R + Q142T
AVTWTCLNDQ KNPKTNKRET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NTGELKLCSH SEQ ID NO: Variant
83 T15G+ Q142G
AVTWTCLNDQ KNPKGNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKE NGGELKLCSH
84 T15G+ E140D
AVTWTCLNDQ KNPKGNKYET KRLLYNQNKA ESNSHHAPLS DGKTGSSYPH WFTNGYDGDG KLPKGRTPIK FGKSDCDRPP KHSKDGNGKT DHYLLEFPTF PDGHDYKFDS KKPKENPGPA RVIYTYPNKV FCGIIAHTKD NQGELKLCSH
[91] In other embodiments, the modified isolated immunoglobulin CH2 domain is fused to one or more proteins comprising a paratope. Accordingly, the CH2 domain of the present disclosure may be modified to be specific for one, two, three or more targets, e.g. EphA2 and a T cell-specific epitope, a natural killer (NK) cell-specific epitope (e.g., Fc gammaR llla/CD16A) etc In such embodiments, a bispecific modified CH2 domain of the present disclosure, for example, recruits an effector cell, such as a T cell, to an aberrant target cell, such as a cell overexpressing EphA2, resulting in the immune effector cell being in close vicinity to the target cell, such that the effector cell can directly kill, or indirectly initiate the killing of the aberrant target cell to which it is recruited. In some embodiments, the T cell- specific epitope is CD3.
[92] In other embodiments, the modified isolated immunoglobulin CH2 domain of the present disclosure is linked to a small molecule. As used herein a "small molecule" refers to a beneficial agent, usually synthesized by organic chemistry and having a low molecular weight, e.g. about 500-900 daltons. Generally, a small molecule is an effector of a specific protein or nucleic acid, altering the activity of the protein or nucleic acid. Examples of small molecules include but are not limited to cytotoxic agents, e.g., compound classes such as the auristatins, maytansinoids and pyrrolobenzodiazepines. See, for example, Jeffrey et ah, "A potent anti-CD70 antibody-drug conjugate containing a dimeric pyrrolobenzodiazapene drug with site-specific conjugation technology", Bioconjugate Chem., 2013, 24: 1256-1263, which is incorporated herein by reference in its entirety and Smaglo et al., "The development of immunoconjugates for targeted cancer therapy," Nature Reviews Oncology, 2014, 11 :637- 648. Linkage
[93] In some embodiments, the N-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule is linked to the C-terminus of the modified CH2 domain. In some embodiments, the N-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule is linked to the N-terminus of the CH2 domain. In some embodiments, the C-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule is linked to the C-terminus of the CH2 domain. In some embodiments, the N-terminus of the CH2 domain is linked to the C-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule. In some embodiments, the N-terminus of the CH2 domain is linked to the N-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule. In some embodiments, the C-terminus of the modified CH2 domain is linked to the C-terminus of the detectable moiety, toxin, protein comprising a paratope or small molecule.
[94] In some embodiments, a linker can optionally be inserted between the modified CH2 domain and the detectable moiety, toxin, protein comprising a paratope or small molecule. Linkers and linker technology are well known in the art. Examples of linkers include peptides of various amino acid lengths and/or sequences. In some embodiments, the linker is between 0 to 10 amino acids in length. In some embodiments, the linker is between 0 to 15 amino acids in length. In some embodiments, the linker is between 0 to 20 amino acids in length. In some embodiments, the linker is between 1 to 10 amino acids in length. In some embodiments, the linker is between 1 to 15 amino acids in length. In some embodiments, the linker is between 1 to 20 amino acids in length. In some embodiments, the linker is between 2 to 20 amino acids in length. In some embodiments, the linker is between 3 to 20 amino acids in length. In some embodiments, the linker is between 4 to 20 amino acids in length. In some embodiments, the linker is between 5 to 10 amino acids in length. In some embodiments the linker is between 10 to 15 amino acids in length. In some embodiments, the linker is between 15 to 20 amino acids in length. In some embodiments, the linker is more than 20 amino acids in length. The optimal lengths may vary to match the spacing and orientation of the specific target antigen(s), minimizing entropy but allowing effective binding of multiple antigens.
[95] The linker can be attached to the individual modified CH2 domain at any appropriate location. Examples of where a linker may attach onto the modified CH2 domain include the following location on the modified CH2 domain: the C-terminus, the N-terminus or a cysteine preceding or following the C-terminus or N-terminus of the modified CH2 domain, such as set forth in SEQ ID NOS: 89-93.
[96] The linker may be encoded for in the recombinant nucleic acid that encodes the immunoconjugate, e.g. fusion protein. In some embodiments, the linker may be covalently bonded (e.g., cross-linked) to a portion of an immunoconjugate. The linkers may be covalent or very tight non-covalent linkages; chemical conjugation or direct gene fusions of various amino acid sequences, e.g., those (a) rich in Glycine Serine, Proline, Alanine.
[97] In some embodiments, the linker comprises a non-peptide component (e.g., a sugar residue, a heavy metal ion or a chemical agent such as a therapeutic chemical agent). Classes of commonly used cleavable linkers include hydrazone and hydrazine linkers, disulfide linkers (including N-succinimidyl-4-(2-pyridyldithio)pentanoate (SPP), N-succinimidyl-4-(2- pyridyldithio)butyrate (SPDB), 4-(4"-acetylphenoxy)butanoic acid (AcBut), dipeptides valine-citrulline (Val-Cit), valine-alanine (Val-Ala), and phenylalanine- lysine (Phe-Lys), the dissolving linker technology of Mersana and protease susceptible linkers of CytomX. Commonly used non-cleavable linkers include: amide moieties, succinimidyl-4-[N- maleimidomethyl]cyclohexane- l -carboxylate (SMCC), maleimidocaproyl (MC), the dPEG linkers, and pyridinyl-2-disulfanyl linkers.
[98] In other embodiments, the linker comprises polyethylene glycols (PEGs), e.g., discrete PEGs (dPEG), etc. See, for example, Dennis et al., 2002, Journal of Biological Chemistry 33 :238390, discrete PEGs from Quanta BioDesign, Ltd., Powell, Ohio, which is herein incorporated by reference in its entirety. A PEG (dPEG) may be bound by a variety of mechanisms, e.g., via chemical treatments and/or modification of the protein structure, sequence, etc. (see, for example, Ashkenazi et al., 1997, Current Opinions in Immunology 9: 195-200; U.S. Patent No. 5,612,034; U.S. Patent No. 6, 103,233).
[99] In some embodiments, the PEG (dPEG) is between about 200 to 10,000 daltons. In some embodiments, the (dPEG) is between about 600 to 10,000 daltons. In some embodiments, the PEG (dPEG) is between about 700 to 10,000 daltons. In some embodiments, the (dPEG) is between about 800 to 10,000 daltons. In some embodiments, the (dPEG) is between about 900 to 10,000 daltons. In some embodiments, the (dPEG) is between about 200 to 12,000 daltons.
[100] In some embodiments, the PEG (dPEG) may be linked to a linkage site, such as at least one of a serine, tyrosine, cysteine, or lysine or a glycosylation site of the modified CH2 domain. The PEG (dPEG) may be bound to the immunoconjugate, e.g., a fusion protein (e.g., modified CH2 domain) through a reactive sulfhydryl by incorporating a cysteine at the end of the modified CH2 domain to form, e.g. CH2-dPEG-toxin, detectable moiety, protein comprising a paratope or a small molecule.
[101] In some embodiments, the linkage site is an N-terminal serine, tyrosine, cysteine, or lysine. In other embodiments, the linkage site is a C-terminal serine, tyrosine, cysteine, or lysine. In some embodiments, the linkage site is a serine, tyrosine, cysteine, or lysine found within the modified CH2 domain, not necessarily a terminal residue. In some embodiments, a tyrosine, cysteine, serine, or lysine is added to the N-terminus and/or C-terminus of the CH2 scaffold for the purpose of the linkage of the PEG (dPEG). Alternatively, a PEG (dPEG) may be linked to an existing tyrosine, cysteine, serine, or lysine at a terminus or within the modified CH2 domain. In some embodiments, the CH2-PEG (dPEG) is then further linked to the detectable moiety, toxin, protein comprising a paratope or small molecule.
[102] In various embodiments, the PEG (dPEG) is linked to a glycosylation site. In some embodiments, the glycosylation site is a natural glycosylation site. In some embodiments, the glycosylation site is a new/modified glycosylation site, for example an asparagine N- glycosylation site may be added to the modified CH2 domain. A PEG (dPEG) may be attached at a glycosylation site using methods including enzymatic digestion and expression with an appropriate expression system (e.g., Pichia GlycoSwitch® Man5 strain). In some embodiments, the dPEG is attached to a natural Man5 structure or alternatively a GnMan5 structure, a GalGnMan5 structure, a GnMan3 structure, a GalGnMan3 structure, a Gn2Man3 structure, a Gal2Gn2Man3, etc. Further methods for using PEG and linkage arrangements of CH2 domains, detectable moieties, toxins, proteins comprising paratopes or small molecules are well known in the art, see, for example, PCT Publication No. WO 2013/1 19903, which is herein incorporated by reference in its entirety.
[103] In some embodiments, the linker is a hinge component. For example, the hinge component set forth in SEQ ID NO: 60 may be linked to the N-terminus of the FRl region of a modified CH2 domain. Other linkers for fusion proteins are also described in PCT Publication No. WO 2013/1 19903, which is herein incorporated by reference in its entirety. Pharmaceutical Compositions
[104] The modified CH2 domains and fusion proteins of the present disclosure are useful as pharmaceutical agents, particularly, as pharmaceutical compositions intended for cancer treatment. Any cancer that expresses the EphA2 receptor can be treated using these pharmaceutical compositions. Examples of cancer types can include, but are not limited to, breast cancer, melanoma, ovarian cancer, lung cancer, gliomas, bladder cancer, prostate cancer, esophageal cancer, renal cancer, colon cancer and vulvar cancer.
[105] In some embodiments, the compositions comprise a modified CH2 domain or a fusion protein comprising a modified CH2 domain linked to a toxin as discussed above and a pharmaceutical carrier. The pharmaceutical carrier (vehicles) may be conventional, but are not limited to conventional carriers (vehicle). For example, E. W. Martin, Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA, 15th Edition (1975) and D. B. Troy, ed. Remington: The Science and Practice of Pharmacy, Lippincott Williams & Wilkins, Baltimore MD and Philadelphia, PA, 21st Edition (2006) describe compositions and formulations suitable for pharmaceutical delivery of one or more therapeutic compounds or molecules and additional pharmaceutical agents. In some embodiments aqueous pharmaceutical compositions suitable for long-term storage of polypeptides containing an Fc domain of an immunoglobulin may be used, such as described in U.S. Patent No. 7,648,702, which is hereby incorporated by reference in its entirety.
[106] Pharmaceutical compositions may comprise buffers (e.g., sodium phosphate, histidine, potassium phosphate, sodium citrate, potassium citrate, maleic acid, ammonium acetate, tris-(hydroxymethyl)-aminomethane (tris), acetate, diethanolamine, etc.), amino acids (e.g., arginine, cysteine, histidine, glycine, serine, lysine, alanine, glutamic acid, proline), sodium chloride, potassium chloride, sodium citrate, sucrose, glucose, mannitol, lactose, glycerol, xylitol, sorbitol, maltose, inositol, trehalose, bovine serum albumin (BSA), albumin (e.g., human serum albumin, recombinant albumin), dextran, PVA, hydroxypropyl methylcellulose (HPMC), polyethyleneimine, gelatin, polyvinylpyrrolidone (PVP), hydroxyethylcellulose (HEC), polyethylene glycol (PEG), ethylene glycol, dimethylsulfoxide (DMSO), dimethylformamide (DMF), hydrochloride, sacrosine, gamma- aminobutyric acid, Tween-20, Tween-80, sodium dodecyl sulfate (SDS), polysorbate, polyoxyethylene copolymer, sodium acetate, ammonium sulfate, magnesium sulfate, sodium sulfate, trimethylamine N-oxide, betaine, zinc ions, copper ions, calcium ions, manganese ions, magnesium ions, CHAPS, sucrose monolaurate, 2-O-beta-mannoglycerate, the like, or a combination thereof.
[107] In some embodiments, the pharmaceutical compositions may comprise propellants (e.g., hydrofluoroalkane (HFA)) for aerosol delivery. In some embodiments, the pharmaceutical compositions of the present disclosure may be formulated as described in U.S. Patent No. 5,192,743 that form a gel when reconstituted and which can improve stability of a protein of interest (e.g., for storage).
[108] Pharmaceutical compositions may be appropriately constructed for some or all routes of administration, for example topical administration (including inhalation and nasal administration), oral or enteral administration, intravenous or parenteral administration, transdermal administration, epidural administration or the like. For example, parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. For solid compositions (for example, powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically-neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non- toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
[109] In some embodiments, a parenteral formulation may comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. As a non- limiting example, the formulation for injectable trastuzumab includes L-histidine HCI, L- histidine, trehalose dihydrate and polysorbate 20 as a dry powder in a glass vial that is reconstituted with sterile water prior to injection. Other formulations of antibodies and proteins for parenteral or subcutaneous use are well known in the art and may be used with the modified CH2 domains and fusion proteins of the present disclosure.
[110] For solid compositions (for example, powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically-neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non- toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
[Ill] The aforementioned pharmaceutical compositions and protein modifications to increase protein stability can be applied as described in U.S. Patent Application 2009/032692, which is herein incorporated by reference in its entirety.
Therapeutic Methods
[112] The present invention is further directed to treating a disease associated with EphA2 overexpression. As used herein, "treatment" or "treating" refers to arresting or inhibiting, or attempting to arrest or inhibit, the development or progression of a disease and/or causing, or attempting to cause, the reduction, suppression, regression, or remission of a disease and/or a symptom thereof. As would be understood by those skilled in the art, various clinical and scientific methodologies and assays may be used to assess the development or progression of a disease, and similarly, various clinical and scientific methodologies and assays may be used to assess the reduction, regression, or remission of a disease or its symptoms. "Treatment" refers to both therapeutic treatment and prophylactic or preventative measures. Those in need of treatment include those who already have the disease, as well as those with a propensity or predisposition for the disease and those in whom the disease is to be prevented. In at least one embodiment, the disease being treated is cancer, such as described above.
[113] As used herein, a "disease associated with EphA2 overexpression" includes, but is not limited to a variety of cancers, including the cancers described herein.
[114] The modified CH2 domains of the present disclosure and the fusion proteins described above may be administered to a subject. In some embodiments, the subject is a mammal including a cat, dog, horse, sheep, goat, rat, mouse, baboon, macaque or human. Preferably, the subject is a human.
[115] In various embodiments, a therapeutically effective dose of the modified CH2 domains or fusion proteins described herein is administered. As used herein "a therapeutically effective dose" is an amount which eliminates or reduces the patient's tumor burden, or which prevents or reduces the proliferation of metastatic cells. The dosage will depend on many parameters, including the nature of the tumor, patient history, patient condition, the possible co-use of other oncolytic agents, and methods of administration.
[116] Methods of administration include injection (e.g., parenteral, subcutaneous, intravenous, intraperitoneal, etc.). Typical dosages may range from about 0.01 to about 20 mg/kg, and more particularly from about 0.1 to about 10 mg/kg. Other methods of administration include oral and transdermal.
[117] In some embodiments, the modified CH2 domains and fusion proteins can be delivered in a controlled release system. Such methods may include the use of a pump for administration, such as use of an intravenous drip. In another embodiment, a controlled release system can be placed in the proximity of the therapeutic target, such as a tumor, requiring only a fraction of the dose required if dosed systemically.
[118] In various embodiments, administration is locally confined to a single cell or tissue and/or is systemically administered in the subject. It may be desirable to administer the modified CH2 domains and fusion proteins described herein locally to the area in need of treatment, such as areas including one or more tumor. This method of administration may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application such as in conjunction with a wound dressing after surgery, injection, catheter, or via an implant or porous membrane.
[119] In some embodiments, the present invention is directed a method for killing a target cell expressing EphA2 receptors, the method comprising administering to a subject in need thereof a fusion protein as described herein, exposing the target cell to an effective amount of the fusion protein, thereby selectively killing the target cell in the subject. In some embodiments, the modified CH2 domain of the fusion protein is capable of being internalized into the cells.
[120] As used herein, "selectively killing" means that the fusion protein preferentially associates in whole or in part with a cell or tissue bearing the EphA2 receptor, such as the extracellular domain of the EphA2 receptor and not to cells or tissues lacking the EphA2 cell receptor. As noted above, EphA2 has been shown to have little to no appreciable expression in normal tissues, but may be highly expressed in tumors. Accordingly, in some embodiments, the fusion protein selectively kills tumor cells, but does not kill normal cells.
[121] In some embodiments, the fusion protein is formulated into a pharmaceutical composition. The pharmaceutical composition comprises the fusion protein and a pharmaceutically acceptable carrier, such as described above. The subject may be a mammal or any species of mammal as described herein. In some embodiments, the subject is a human. [122] In some embodiments, the target cell is a cancer cell, including, for example, a cancer cell selected from the group consisting of lung, colon, rectum, breast, ovary, prostate gland, head, neck, bone, kidney, liver, skin and vulva.
[123] Exposure of the target cells to the fusion protein may be carried out by any of a number of routes, including without limitation, intravenous, intraperitoneal, subcutaneous, intramuscular and intralymphatic. As described herein, the fusion protein may be one in which the modified CH2 domain and the toxin are covalently associated.
[124] The term "effective amount" as used herein means that amount of fusion protein or pharmaceutical composition comprising the fusion protein necessary to achieve the desired specific effect, for example killing a target cell and/or in amelioration of a specific disease state.
[125] Furthermore, it would be understood by those skilled in the art that the therapeutic methods described would not only apply to treatment in a subject, but could be applied to cell cultures, organs, tissues, or individual cells in vivo, ex vivo or in vitro.
[126] It would also be understood by a skilled artisan how to use the modified CH2 domains and fusion proteins of the present invention for diagnostic purposes without undue experimentation based on the teachings provided throughout the specification.
EXAMPLES
Example 1. Library Construction and Screening
A. First Generation Libraries
[127] Four first generation libraries were designed using three randomized loops of the CH2 domain, Loop 1, Loop 2 and Loop 3. The libraries were built using trinucleotide primers, where each codon was replaced by an equimolar mix of codons encoding the selected amino acids. As shown in Table 1 , selected amino acids in the sequence of the loops were targeted for replacement with alternate amino acids. The numbering of the sequences corresponds to the residues set forth in FIG. 1. Table 1.
First generation libraries showing which residues were randomized in each loop.
Figure imgf000034_0001
[128] The four libraries were cloned in the phagemid vector pIFF6 fused in frame with the minor coat protein pill for the display on the surface of the filamentous phage M13. Phagemid vector pIFF6 is derived from the pC89 vector and contains the coding sequence for the capsid protein pill in place of pVIII. After electroporation in TOPI OF' cells, a number of independent clones sufficient to cover the entire diversity of the libraries were collected and 100 clones for each library underwent sequencing to confirm the correct reading frame and the expected sequences pattern. The 4 libraries were individually rescued, purified and titrated, then used in a pool to select against the EphA2 receptor. After three rounds of selection on coated mEphA2-Fc, the phage pool supematants coming from the three rounds of selection were tested in OElisa assay on coated mEphA2 to assess the enrichment for binding ability to the target. At the third round of selection, the pool of selected clones increased the capability of binding to mEphA2. To identify the single positives, 192 clones were individually rescued and analyzed by ELISA on coated mEphA2. All 95 clones identified as positives were sequenced and seven variants were identified.
[129] Despite all three loops being engineered separately in individual libraries, the selected clones were all isolated from the loop 2 library (library #15). Table 2
Sequences of loop 2 clones selected for EphA2 binding.
Figure imgf000035_0001
[130] Two strong consensus motifs can be observed in the selected binders: the first, x-x-D- P-L-x-G (SEQ ID NO: 39) in clones H6, E10 and D2 and secondly, x-Y-Y-A-L-G-G (SEQ ID NO: 40) in clones B8, Bl l and A9. Clone A5 does not share consensus with the other sequences. The different sequence motifs may reflect binding to alternative epitopes.
[131] Binding capability and specificity of the seven unique clones were confirmed by ELISA assay, coating mEphA2-Fc protein, hEphA2, D6-Fc and BSA. All the isolated clones specifically bind both human and murine EphA2 recombinant protein. None of the isolated clones recognize the Fc domain linked to the selector mEphA2 or unrelated proteins, such as BSA or D6-Fc. The clones H3 and E10 seemed to bind to human EphA2 more strongly than the other variants. See FIG. 3.
[132] The variants' ability to recognize the EphA2 receptor in a native conformation was also tested on a stable HEK293 clone overexpressing the EphA2 receptor. As shown in FIG. 4, all the loop 2 variants retain their binding activity to the human EphA2 receptor expressed on the surface of the cell, and clones H3 and E10 preserve their major intensity signal.
B. Protein production and testing
[133] To analyze the behavior of the isolated proteins, the EphA2 binders were subcloned into the periplasmic expression vector pJEX404, expressed into E. Coli HB2151 strain, then extracted from periplasm and purified onto a Nickel column, followed by a gel filtration on a Superdex HR75 16/60 column. The proteins were analyzed in an ELISA assay, coated with either mEphA2 and hEphA2 to confirm the binding capability to the target. All the proteins, except A5 whose expression was unsuccessful, preserved their binding capability, even with different strength where E10, H3 and H6 work better. Binding of the E10, H3 and H6 variants to FcRn and to the target mEphA2 was also analyzed by surface plasmon resonance (SPR) to measure the potency of the binding to the receptor. The binding properties of the three variants is summarized in FIG. 5 where the ElO variant bound to FcRn with about the same KD (Κ0=3.26μΜ) as the wild type CH2D (Κ0=1.66μΜ), while the KD for mEphA2 for the three variants ranged from 97 to 873 tiM.
Table 3. KB measured with Biacore 3000 on niEphA2
Figure imgf000036_0001
C. Affinity maturation of binders
[134] For the affinity maturation, clones E10 and A9 were chosen as representing the 2 different consensus families and they also showed higher expression and binding in the CIS display format. The affinity maturation libraries were built by introducing diversity in loop 1 as it is neighboring loop 2 (compared to loop 3 which is spatially further away). Two loop lengths were designed, a smaller loop where residues Ser267 to Asp270 (as referenced to FIG. 1) were mutated, or a longer loop comprising Val266 to Pro271 (as referenced to FIG. 1). As before, the libraries were built using trinucleotide oligonucleotides using the same 12 residues as in the primary libraries. The affinity maturation was performed using CIS display on mouse EphA2, using increased washing stringency and decreasing target concentration in an attempt to select for the tightest binders. The output from the selection was cloned into a cytoplasmic expression vector, transformed in Shuffle cells and the expressed proteins screened by ELISA. From the ELISA, 21 mouse EphA2 binding clones were sequenced and found to exclusively carry loop 2 from the parental clone E10, none from H3. Moreover, loop 1 sequences are derived only from the longer loop length library, possibly explaining why library #13 failed to yield any binders in the naive selection as the length of the loop is important for structural integrity of the modified CH2 domains or functional binding to EphA2. [135] The nine clones displaying the highest ELISA signal were expressed and purified. The sequence of loop 1 from the four best expressing clones demonstrates two distinct consensus sequences (Table 4): clones D2 and Bl l shared the motif Y-x-A-x-x-L (SEQ ID NO: 41) and G7 and B6, P-x-L-x-x-D (SEQ ID NO: 42). The expression level was consistent with the motif: clones G7 and B6 showed a better yield in expression than D2 and B l l .
Table 4
Sequences in loop 1 of clones selected from affinity maturation.
Figure imgf000037_0001
[136] In experiments to determine the affinity of the clones, an end-point titration ELISA of the four anti-EphA2 modified CH2 domains was used to establish an EC50 against human and mouse EphA2. See Table 5 and FIGS. 6A and 6B. Binding of parental clones (E10 and H3) could not be detected at the concentrations tested, yet for the affinity matured clones low nanomolar values were calculated, with little difference between human and mouse orthologs, which is consistent with the fact that both proteins share 95% similarity.
Table 5
EC50 of binding to human and mouse EphA2, determined by titration ELISA.
Figure imgf000037_0002
[137] In the second assay, the affinity was measured using ForteBio's OctetRed. The affinities were generally about 10 times weaker than those measured by ELISA. See Table 6.
Table 6
KD measured with OctedRed on mouse and human EphA2
Figure imgf000038_0001
D. Surface Plasmon Resonance (SPR)
[138] KD values were also assessed for G7, B6 and B l l clones using Surface Plasmon Resonance (SPR). Using the amine-coupling kit (Biacore) and the Biacore 3000 immobilization wizard, purified human EphA2 extracellular domain is immobilized at 0.5μΜ in acetate pH 5.0 to one of the four flow cells of a CM5 sensorchip (GH Healthcare cat BR- 1000-14) to a level of approx. 2000 RU (resonance units). Purified CH2 domain mutants are dialyzed against 10 mM Hepes (pH 6.0), 150 mM NaCl (running buffer), diluted in the same buffer to a range of concentrations (10μΜ-0.625μΜ) and passed over the sensor chip surface at a flow rate of 40 μΐ/min.
[139] Each cycle consists of a 60s analyte injection (the association phase), followed by a 180s dissociation phase. Regeneration is achieved using a 10s injection of Running Buffer with a 300s stabilization period. The data are analyzed using the Biacore 3000 Evaluation software.
[140] Baselines are adjusted to zero for all curves and double-referenced by subtracting a sensorgram of buffer injected over the coated surface from the experimental sensograms to give curves representing specific binding. Curves are modeled assuming a simple 1 : 1 interaction to generate the equilibrium and kinetic data. See FIG. 7. KD values ranged from 22 nM (G7) to 56 nM (B6). See Table 7. Table 7.
KDs measured with Biacore 3000 on huEphA2
Figure imgf000039_0001
E. Binding on cells overexpressing EphA2
[141] CHO cells were transfected with human EphA2 and the binding of the affinity matured CH2 domains was assessed by FACS (FIG. 8). Decreasing concentrations of the CH2 domains were tested and the EC50 values against the target expressed on cells were evaluated (see FIG. 9 and Table 8). Of the four clones, B6 showed the tightest binding to the cells, with little binding to control CHO cells that did not express human EphA2, whereas Bl l and to a lesser extent D2 show some signal on non-transfected cells, which might be attributable to cross-reactivity with hamster EphA2 expressed in the immortalized ovarian cells and recognition of a different epitope than B6 and G7 (Chinese hamster EphA2 shares 92% and 94% similarity with human and mouse EphA2, respectively).
Table 8.
EC50 of binding to EphA2 transfected cells. Nd: no binding detected.
Figure imgf000039_0002
F. Expression and purification of proteins
[142] Bioreactor cultivations under controlled conditions were performed using P. pastoris as the expression host. In the initial phase, batch-mode with glycerol feed, the culture was grown to wet cell weights of approximately 200 g L-l without induction of recombinant protein production. The production phase was initiated by supplementation of methanol, inducing the AOX1 -promoter. After a total process time of 108 hours with a methanol- induction/recombinant protein production phase of 92 hours, the cells were separated by centrifugation, and the supernatant cleared by filtration to obtain the cell-free filtrate containing the secreted target protein.
[143] FIG. 10 shows protein production over process time for two modified CH2 domains as measured by microfluidic capillary electrophoresis (mCE). Titers of -900 mg L-l (shWT- CH2D, control), -1,000 mg L-l (B6) and 1,400 mg L-l (Bl l) were obtained after a non- optimized standard 1L bioreactor cultivation. Purities for all 3 target proteins were above 60% in the final filtrate and the filtrates were affinity-purified by IMAC, polishing was performed using CIEX chromatography, and concentration with ultrafiltration (FIG. 1 1).
[144] Purified proteins were tested for EphA2 and hFcRn binding using ELISA and Biacore assays and tested on EphA2-expressing cells lines, PC3 and MBA-245 cells. These data confirmed the Pichia-produced proteins behaved similar to those produced in E. coli.
G. PET/CT imaging
[145] Targeting and biodistribution characteristics of 2 modified CH2 domains, B6 and Bl l, engineered to target the EphA2 protein were assessed. B6 and B l l were conjugated to a bifunctional chelator MeCOSar which allowed for labelling the products with the radioisotope copper-64 (64Cu) and administered to mice with PC3 prostate cancer xenografts (n=3). MicroPET/CT images were acquired at 3 time points (4, 24 and 48 hours), allowing the identification of the distribution in the whole animal. B6 and B l l showed uptake in the tumors, with B 1 1 providing the highest signal from the PC3 tumors. Uptake was also shown by the B6 product. The negative control shWT_CH2 showed some low level background uptake in the tumor above levels observed in muscle, possibly due to the enhanced permeability and retention (EPR) effect which is known to occur in this xenograft model. Clearance of the CH2 domains was mainly indicated to occur via the liver and the kidneys.
[146] Following the final imaging time point at 48 hours, mice were sacrificed and perfused, and a biodistribution study was performed. Several organs including tumor and muscle were removed and the level of radioactivity measured by a gamma-counter. Results are expressed as % injected dose per g (% ID/g) of tissue at 48 hours. The Bl l product showed highest tumor uptake of approximately 6% ID/g compared to muscle of <1%. The B6 product showed tumor uptake of approximately 5% ID/g compared to muscle of <1%. The negative control shWT product contained slightly more than 2% in the tumor above levels observed in muscle of <1%. B6 had much higher liver retention at approximately 17% ID/g than both the B l 1 (9% ID/g) and the shWT_CH2 control (9% ID/g). Kidney retention was similar between B6 and B 1 1 (approx. 17 to 18% ID/g) and also higher than the control at 12% ID/g. Lung and heart showed little difference between products with <5% ID/g for all products in both organs. See FIG. 12.
[147] Small-animal PET imaging and Standard Uptake Value (SUV) analysis (see calculation below) of tumor bearing mice revealed an increasing tumor-uptake from 4.1 1 ± 0.77 at 4 hours, 9.22 ± 0.70 at 24 hours, to 10.89 ± 0.63 at 48 hours after tracer injection for 64CuMeCOSar-Bl l, and an accumulation of 3.95 ± 0.99 at 4 hours, 5.17 ± 1.33 at 24 hours, and 4.42 ± 0.89 at 48 hours after tracer injection for 64CuMeCOSar-B6 (FIG. 13). In contrast, tumor-bearing mice injected with the negative control 64CuMeCOSar-shWTCH2 showed only minor tracer uptake in their tumors, similar to background activity, at any measured time point and a similar lack of tumor uptake was seen for the positive control IgG, 64CuMeCOSar-IgG, which binds to EphA2 (FIG. 14). The 64CuMeCOSar-B l 1 modified CH2 domain accumulated in the tumor faster and with a stronger SUV compared to the 64CuMeCOSar-B6 modified CH2 domain.
H. Localization experiments via immunofluorescence analysis
[148] PC3 cells were incubated at 37°C with Bl l conjugated to deimmunized a-sarcin (Bl l-sarcin) and endosomal or lysosomal vesicles were counted over time. Bl l-sarcin rapidly internalized and was localized into the early endosomes and endosomes up to 60 minutes. After 60 minutes, the Bl 1-sarcin appeared to localize either into lysosomes and is degraded or is found in the cytoplasm. See FIG. 15. PC3 cells incubated with Bl l conjugated to deimmunized a-sarcin at 37°C for 72 hours at various concentrations demonstrated cell killing with an IC50 of approximately 2 nM. See FIG 16.
[149] The Bl l variant was detected with a-Flag antibody and early endosomes were detected with the anti-EEAl antibody. In the merged view it appears that Bl 1 is localized in the early endosome. See FIG. 17. [150] I. Conjugation of Biotin-dPEGll-MAL
[151] Three B l 1 modified CH2 domains, SEQ ID NO: 89 containing a C terminal cysteine and N terminal hinge sequence, SEQ ID NO: 90 containing an N terminal hinge sequence and SEQ ID NO: 91 containing a C terminal cysteine, were conjugated with discrete polyethylene glycol (dPEG) and biotin to assess binding and internalization in PC3 cells. Conjugation of biotin-dPEG was achieved by incubating the modified CH2 domains for 1 hour at room temperature in ImM DTT/lOmM EDTA followed by dialysis against lOmM HEPES pH7.0, 150mM NaCl, 2mM EDTA, 4°C. The modified CH2 domains were then incubated at room temperature overnight with two equivalents of Biotin-dPEG 1 1 -(QUANTA BIODESIGN 10195) dissolved in DMSO (lOmg/ml). Unconjugated Biotin-dPEGl 1 was removed by dialysis against PBSK overnight at 4°C. The reaction was monitored by UPLC on an Acquity BEH300 C4 1.7μηι, 2.1 x 100mm (WATERS 186004496) column and characterized by MALDI-TOF (Applied Biosystem VOYAGER-DE STR) using Sinapic acid (Fluka product No 85429) as a matrix.
[152] Binding and internalization of the modified Bl l CH2 domains to PC-3 cells expressing endogenous EphA2 receptor were evaluated by immunofluorescence. PC-3 cells were incubated with the various proteins at 4°C for 30 minutes to allow binding to the EphA2 receptor on the cell surface and to block internalization (FIG. 18, left column). After binding at 4°C, plates were moved to 37°C to allow internalization, and the cells imaged after 60 minutes and 120 minutes. As shown in FIG. 18, all three of the modified Bl l CH2 domains bound (left column) and internalized (middle and right columns) to PC-3 cells.
Example 2. Materials and Methods
[153] The results obtained in Example 1 were obtained using the following materials and methods.
A. Chemicals and Materials
[154] Synthetic genes were purchased from DNA2.0 (Menlo Park, CA, USA). For plasmid isolation, the PureYield™ Plasmid Miniprep System of Promega (Madison, WI, USA) was used. All DNA-modifying enzymes were obtained from Fermentas GmbH (Burlington, Ontario, Canada). If not stated otherwise, chemicals were purchased from Becton, Dickinson and Company (Franklin Lakes, NJ, USA), Fresenius Kabi Austria (Graz, Austria) and Carl Roth (Karlsruhe, Germany). B. Media
[155] For E. coli standard LB-medium containing 25 μg/ml Zeocin was used. YPhyD for P. pastoris contained 10 g/1 yeast extract, 20 g/1 phytone peptone and 20 g/1 glucose. For antibiotic selection in Pichia 100 μg/ml Zeocin (Eubio, Austria) was used. 15 g/1 agar was added for plate media. Buffered minimal media BMD (1%), BMM2 and BMM10 contained per liter: 200 ml 1 M sodium phosphate buffer (pH 6), 13.4 g yeast nitrogen base without amino acids, 0.0004 g/1 biotin and 1 1 g/1 glucose or 1 or 5% (v/v) methanol, respectively. All pre-cultures were prepared using YPhyD medium containing 20 g/1 phytone peptone, 10 g/1 Bacto-Yeast Extract and 20 g/1 glucose. BSM medium contained per liter CaS042H20 0.47 g, K2S04 9.1 g, KOH 2.07 g, MgS047H20 7.5 g, EDTA 0.6 g, H3PO4 (85%) 13.4 ml, Glycerol 40.0 g, NaCl 0.22 g and 4.35 ml PTM1. PTM1 Trace elements solution contained per liter 0.2 g Biotin, 6.0 g CuS045H20, 0.09 g KI, 3.0 g MnS04 H20, 0.2 g Na2Mo042H20, 0.02 g H3BO3, 0.5 g CoCl2, 42,2 g ZnS047H20, 65 g Fe(II)S047H20 and 5 ml H2S04. The fed-batch media were either 60% (w/w) Glycerol or concentrated Methanol and were supplemented with 12 ml/1 PTM1 mineral salts solution.
C. Construction of expression plasmids and resulting P. pastoris strains
[156] Synthetic genes were cloned into the multiple cloning site of the Zeocin-resistance E. coli/P. pastoris shuttle vector pPpT4 via XhollNotl sites, downstream of the wildtype AOX1 promoter. See Naatsaari, et al. "Deletion of the Pichia Pastoris Ku70 Homologue Facilitates Platform Strain Generation for Gene Expression and Synthetic Biology.".2012, PLoS ONE 7, 7:e39720, herein incorporated by reference in its entirety.
[157] Plasmids were linearized with either Bglll, ethanol-precipitated and desalted. Electro- competent P. pastoris CBS 7435 mutS cells (Naatsaari et al. 2012) were prepared and transformed with 2 μg of the Bglll- linearized pPpT4 vector constructs according to Lin- Cereghino et al., "Condensed protocol for competent cell preparation and transformation of the methylotrophic yeast Pichia pastoris '' 2005, Biotechniques, 38:44, 46, 48, herein incorporated by reference in its entirety. Transformants were plated on YPD-Zeocin (100 μg/ml Zeocin) agar plates and grown at 28°C for 48 hours.
D. Micro-scale cultivation
[158] P. pastoris strains expressing the target genes were cultivated in 96-deep well plates as described by Weiss H.M. et al. "Expression of functional mouse 5-HT5A serotonin receptor in the methylotrophic yeast Pichia pastoris: pharmacological characterization and localization," FEBS Lett. 1995, 377:451^156, herein incorporated by reference in its entirety.
E. Fed-batch bench-scale bioreactor cultivations
[159] Pre-cultures of individual strains were grown in 50 and 200 ml YPhyD medium containing 20 g/1 Bacto-Yeast Extract and 20g/l glucose in wide-necked, baffled shake flasks at 120 rpm at 28°C. Each bioreactor (Infors Multifors system (Infors AG, Bottmingen, Switzerland)) containing 450 ml BSM-media (pH 5.0) was inoculated from the pre-culture to an OD600 of 2.0. During the batch phase P. pastoris was grown on glycerol (4%) at 28°C. At the beginning of the glycerol feeding phase the temperature was decreased to 24°C. For methanol-fed cultures, the fed-batch phase was started upon depletion of initial batch glycerol with 16 g/(l*h) glycerol feed solution followed by methanol induction. In the early stages, the methanol-feed was set to 2 g/(l*h) and was gradually increased within the next 70 h to 6 g/(l*h). Likewise, the glycerol-feed was phased down during the first hour of methanol induction to 0 g/(l*h). Dissolved oxygen was set to 30% throughout the whole process. After 92 h of methanol induction the bioreactor cultivations were stopped.
F. Target protein analysis and quantification
[160] Microfluidic capillary electrophoresis using the LabChip® GX II (Caliper LS, PerkinElmer, USA) was used to detect and quantify the target proteins. Briefly, several μΕ of all culture supernatants or bioreactor samples (taken at different time-points throughout the process) are fluorescently labeled and analyzed according to protein size, using an electrophoretic system based on microfluidics. Internal standards enable approximate allocations to size in kDa and approximate concentrations of detected signals. External standards (as e.g. authentic standard material, which was not available; instead, cytochrome c as external standard protein with a similar molecular weight) guarantee more precise allocation of protein signals. Standard deviations of this robust system are usually below 10%, even at high protein loads. More specifically, proteins were quantified by calibrating the integrated areas of the protein-specific peaks in the electropherograms to an external reference protein standard (Cytochrome c) of known concentration. For glycosylated proteins, peak areas of diluted deglycosylated samples were compared to those of untreated samples to compensate for glycosylation-related differences in quantification. Samples were treated with EndoH for deglycosylation according to the manufactures instructions (NEB, USA, catalog# P0702L). The dilutions of samples were in a range to give peak areas of the samples that were comparable to those of the reference protein standard.
G. Target protein purification
[161] Chromatography was performed using an AKTA Avant 150 system with a HisPrep 16/10 FF Ni-NTA column (both GE Healthcare). Buffers used were 20 mM NaPi, 500 mM NaCl, pH 7.4 (buffer A) and 500 mM Imidazol, 20 mM NaPi, 500 mM NaCl, pH 7.4 (buffer B). For the runs, pH and conductivity of the samples were adjusted to the values of the loading buffer using NaOH and NaCl. Samples were filtered through a 0.2 μηι filter prior to loading. The following protocol was established and applied for all three products: after equilibration at 0% B for 2 column volumes (CV), 200 mg of each sample protein was loaded, followed by a wash step of 0.5 CV at 0% B, a wash step of 3 CV at 8% B (40 mM Imidazole) and an elution step of 3 CV at 60% B (300 mM Imidazole). Samples were collected in 10 mL fractions. The column was washed at 100% B (500 mM Imidazole) for 2 CV and re-equilibrated for the next run at 0% B for 5 CV.
[162] Cation exchange (CIEX) chromatography was selected as polishing step and to exchange buffer to PBS, pH 7.4 (used as elution buffer in CIEX. Samples (pooled IMAC fractions) were diluted to conductivity < 8 mS/cm using MilliQ water and applied to a HiPrep 16/10 SP Sepharose FF column (GE Healthcare). Buffer A used for column equilibration and washing was 20 mM Sodium Phosphate, pH 7.4. Buffer B used for step elution was PBS, pH 7.4 (Gibco). Eluate was collected in 14 mL fractions and pooled after analysis.
[163] After purification via Ni-NTA- and CIEX-chromatography as well as concentration using ultrafiltration (5 kDa cut-off; Vivaspin20 devices, Sartorius), final samples were analyzed by mCE in comparison to cytochrome c. The concentration was determined by spectrophotometrical analysis at 280 nm, and the Endotoxin-content was measured by LAL- assay.
H. Library synthesis
[164] Trimer primers were synthesized by Ella Biotech GmbH (Germany). Four first- generation libraries were built by PCR using trinucleotide oligonucleotides and KOD polymerase (Merck Millipore). For each library, 2 PCRs were required to cover the whole gene. For each PCR, lOOpmol primers and lOOng DNA template were used in a 500 μΐ reactions. 25 cycles were performed, conditions according to KOD manual. [165] lC^g each PCR fragments were digested with 100 units Bsal (NEB) in 250μ1 reaction, and incubated lh at 37°C. Approximately 5.5pmol of each PCR fragment were ligated in 350μ1 reaction with 1400 units T4 DNA ligase (NEB). A PCR was then performed to add the restriction sites required for cloning into the phagemid vector: 800ng template DNA was amplified with both primers below, in 1ml PCR reaction. 15 cycles were performed.
I. Library construction
[166] CH2 domain libraries were adapted by PCR to be subcloned into phagemid pIFF6 in frame with pill. Briefly fragments for library #13, #15 and #16 and were digested with HF EcoRI/BamHI restriction enzymes (NEB), purified on Qiaquick columns (Qiagen) and ligated into the EcoRI/BamHI dephosphorylated phagemid O/N at 16°C. Ligations were phenol extracted, EtOH precipitated and transformed into TOPI OF' electro-competent cells. Transformations were plated on 2XTY/Amp/2% glucose big square plates. Each library was ligated, transformed and plated separately and for each one was collected a number of clone equal or 10 fold superior to the theoretical diversity. Phage rescue was obtained infecting cells at O.D.6oo0.5 with Ml 3 K07 at a MOI of approximately 10. After o/n growth, cells were pelleted and phages in the supernatant purified through a CsCl gradient. After dialysis and titration, libraries were frozen in 10%DMSO and stored at-80°C ready to use.
J. Libraries selections against EphA2
[167] Selection against mEphA2 was carried out directly coating the recombinant protein (Fc chimera, R&D Systems) at 10 μg/well on Nunc Maxisorp ELISA plate. Libraries #13, #15 and #16 were pooled together and 10n phages were pre-blocked in 5%milk/PBS lX/ Tween 0.05% (MPBST) for 1 hr at RT, as well as the coated EphA2 protein. Then for the selection, phages were incubated for lhr at RT with the protein in MPBST; after extensive washings with PBST, the bound phages were eluted with Triethylamine (TEA) and used to infect 10ml of a mid-log culture of TGI cells. After 1 hr, a small aliquot was taken, diluted and plated out to titrate the number of selected clones. The remaining cells were centrifuged, resuspended into 1ml of 2XTY and plated onto a 2XTYAG agar bioassay plate.
[168] After o/n growth at 30°C, cells were harvest from the plate in 2XTY/16%glycerol and frozen at -80°C. For the next round of selection 50ml of 2xTYAG were inoculated with 50μ1 of selected clones, grown at 37°C till OD6oo=0.5 and superinfected with M13K07 at a MOI of 10. After 1 hr of incubation at 37°C the medium was changed, centrifuging the cells and resuspending them in 50 ml of 2XTYAK (ampicillin at 100 μg/ml and kanamycin at 25 μg/ml).
Amplified phages were recovered after o/n growth at 37°C by centrifugation and 900 μΐ used for the next round of selection, following the procedure described above. During the screening either the phage pool from the different rounds of selection or the individual picked clones were tested in OElisa.
K. Affinity maturation libraries
[169] The PCRs to amplify CH2 gene and introduce diversity in loop BC were performed as before. The clones selected from the phage selection, E10 and A9 were used as DNA template. The PCR fragments were digested and ligated together as before. The libraries were then digested with Notl, whereas the gene expressing repA was digested with Bspl20I. 5.5pmol of library DNA and repA were ligated together in 350μ1 reaction, with 1400 units ligase. A PCR was finally performed with a long primer adding the tac promoter upstream of the libraries (as described in Odegrip et al., 2004;): l .^g of DNA was amplified in a 1ml PCR reaction, for 15 cycles. Correct library assembly was confirmed by sequencing.
L. ELISA assays
[170] Proteins were coated on Nunc maxisorp plates at the desired concentration in the range of ^g/ml in PBS 1X, o/n at 4°C, then blocked with 3%Marvell/PBS for lhr, and incubated with pre-blocked phages in 3%MPBST for lhr at RT. After extensive washing with PBS/0. l%Tween, phage binding was detected by addition of a-M13-HRP mAb (Amersham) diluted 1 :5000 in 3%MPBS incubated for an additional hour at RT. Development with TMB was followed by reading at OD450nm.
[171] When phages were tested for binding to cells, upon doxycycline induction EphA2 expressing HEK293 were fixed in 4% paraformaldehyde for 20', washed with PBS IX, blocked with 3%MPBS for 1 hr and incubated with phage supernatants for 2 hrs. Binding was revealed with aM13-HRP after 30' of development.
M. Localization experiments via immunofluorescence analysis
[172] PC3 cells were seeded the day before at the density of 18.000 cells/well in 96wells microtiter. The day after the plate were put at 4°C for 10 minutes, then medium was removed and CH2s variants diluted in warm fresh media at 500ng/well added. Binding was allowed at 4°C for 30 min (TO). Then the internalization time course (at time 15 minutes, T15,T30,T60,T180) was started. At each time point media was removed, the cells were fixed with 2% PFA-PBS solution and incubate in the dark for 20 minutes at RT. After 5x washes in 1XPBS, cells were permeabilized with 3%BSA-PBS 0.1% Triton for lhr at RT.
[173] The primary antibody was diluted in 3%BSA-PBS 0.1% Triton (aFlag 1 : 1000, aLAMPl 1 :500) and incubated for lhr at RT. After 3 washings in PBS 0.1% Triton and a final wash in lxPBS, the secondary aMouse-AF488 or the aRabbit-AF594 diluted 1 :3000 in 3%BSA-PBS 0.1% Triton were added and incubated for lhr at RT. Washings were repeated as previously described. For the nuclear staining, cells were incubated with DAPI in lxPBS 20min in the dark.
Images were acquired at INCELL.
N. Surface Plasmon Resonance assay
[174] All the SPR interaction analyses were performed by a Biacore 3000 instrument (GE Healthcare, Uppsala, Sweden). Human EphA 2 (hEphA2) (12 μg in lOmM sodium acetate buffer pH 4.0) was immobilized on CM5 chip by amine coupling with a ligand density of 500 RU according to the manufacturer instructions. Briefly, the surface of sensor chip was activated for 7 min using a mixture of 0.1 M NHS and 0.4M EDC, 1.2 μg/ml of hEphA2 in lOmM sodium acetate (pH 4.0) was injected for 7 min at ΙΟμΙ/min, and residual activated groups on the surface were blocked by a 7-min injection of 1M ethanolamine (pH 8.5). The binding of CH2-chimeras to the immobilized ligand was evaluated by a multi cycle kinetic procedure in HBS-P running buffer (50 mM Hepes pH 7.4, 150 mM NaCl, 0.005%) surfactant P-20) provided by the manufacturer. The analyte was injected over the ligand for 2.5 min at 40μ1/ηήη until equilibrium and dissociation was monitored for 5 min. The sensor surface was regenerated with a pulse (30sec) of 0.05M NaOH, 0.5M NaCl, 0.005% SDS, following by extensive washing (6 min, 40μ1/ηήη). The collected data and the kinetic parameters were evaluated with BiaEvaluation software v 3.0. The experiments were repeated three times with similar results. All the reagents were purchased from GE Healthcare.
O. Phage Display
[175] Phage selection was performed by coating the recombinant protein targets directly on the Nunc plates (cat#44-2404). Briefly, ^g of mEphA2-Fc (R&D Systems, cat#639-A2) was coated in PBS IX O/N at 4°C. The day after, the well was washed with PBS IX to remove the excess of antigen and blocked for lhr at RT with Milk3% PBS1X (MPBS) to reduce non-specific phages binding to the plastic surface. In parallel, one aliquot of 1012 phages from the pool of libraries (the phage libraries #13, #15 and #16 were mixed respecting the different theoretical diversities) was blocked with ΙΟΟμΙ of MPBS for lhr at RT and then added to the wells. Phages were allowed to bind the antigens for 2hrs at RT, then the solution was taken out, and washings steps with IXPBS/O.05% Tween were performed.
[176] The phases were eluted and bacteria were scraped from the bioassay plates into 10 ml 2XTYAG 50% Glycerol and used to rescue the phages for the next round of selection. 50ml of 2XTYAG were inoculated with 50μ1 of the scraping and grown at 37°C up to OD600=0.5. Bacterial cells containing the phagemids were super- infected with the helper phage M13K07 to produce the selected phages. Cells were incubated with M13K07 30' at 37°C in stationary, then 30' at 37°C in gentle shaking, then cells were recovered by centrifugation to remove the supernatant, the medium was changed with 2XTY Amp 1 OOug/ml Kan 25ug/ml, and grown O/N at 25°C at high shaking.
[177] The day after, the supernatant, after centrifugation, was used for a new round of selection, following the procedure previously described. Starting from the second round, the so-called "input" at each selection round corresponds to the titer of phages amplified from the previous round that, in general, is around 1010-101 1 phages/ml. After four consecutive rounds of selection, the reactivity of the pool of phages from each round was analyzed in phage-ELISA on mEphA2-Fc (^g/well).
P. CIS DNA display
[178] Selections were performed on mouse recombinant EphA2 (Fc chimera, R&D Systems), biotinylated using EZ-Link Sulfo-NHS-LC-Biotin (Pierce). Free biotin removed with Zeba Desalt Spin column (Pierce). Generally, in vitro transcription and translations (ITT) were carried out as previously described (Odegrip et al., 2004; Eldridge et al., 2009). 6μg of DNA (3 1012 molecules) were expressed in 200μ1 ITT reaction. After expression, the samples were diluted 5-fold in selection buffer containing 2% bovine serum albumin (BSA), in phosphate-buffered saline (PBS). 83nM biotinylated EphA2 was added to the blocked ITT reaction and incubated for lh at room temperature (RT) while mixing on a rotary mixer. ΙΟΟμΙ streptavidin coated magnetic beads (M280, Invitrogen) were then added for 15min, to pull down the binders. The beads were then removed from the selection buffer and washed four times with 1 ml PBS-T (PBS, 0.1% Tween-20) and once with PBS (30sec per wash). Bound DNA was eluted from the beads by incubation in lx ThermoPol buffer (NEB), at 75°C for 10 min. The eluted material was added to a recovery PCR reaction, thereby producing input DNA for the next round of selection.
[179] For subsequent rounds of expression, the resulting DNA from the preceding round was added to a fresh ITT mixture and the selection process was repeated. The target concentration was decreased to 20nM for the 2nd round, 5nM for the 3rd round, 500pM for the 4th round and 50pM for the 5th round; washes were increased to 5 times 5min for round 2 and 7 times 5 min for subsequent round.
[180] The DNA outputs from rounds 3, 4 and 5 were cloned in pET33b and transformed in Shuffle cells (NEB) for cytoplasmic expression. After induction overnight at 20°C, the bacterial cells were lysed using BugBuster Master Mix (Merck Millipore), and the cytoplasmic fraction was diluted in blocking buffer (2% BSA in PBS).
[181] Enzyme-linked immunosorbent assays (ELISAs) were then performed to screen for shCH2 that bound the target ligand. Maxisorp plates were coated with 500ng per well of streptavidin in PBS overnight at 4°C. The plates where then coated with 50ng per well of biotinylated EphA2 in PBS 30min at room temperature. After blocking the plates with blocking buffer (2% BSA in PBS) for lh, the diluted lysate cells were added to the plates and incubated for lh at room temperature. CH2 domain binders were detected using horseradish peroxidase-conjugated anti-FLAG M2 antibody (Sigma) and TMB peroxidase substrate followed by detection and reading at 450nm in an absorbance plate reader. A selection of positive clones that showed a high signal for EphA2, were sequenced by Sanger sequencing (Cogenics Ltd, UK) to obtain the shCH2 domain sequences.
Q. Protein expression and affinity measurement
[182] Affinity matured clones were expressed in Shuffle cells, and induced for 22h at 20°C with 0.5mM IPTG. The cells were lysed with BugBuster Master Mix and the Abdurin domains were then purified on a HisTrap HP column using the AKTA Protein Purification Systems (GE Healthcare), followed by further purification through gel filtration Superdex 75 10/300 GL.
[183] Real-time binding assays between the purified CH2 domains and human (R&D Systems) or mouse EphA2 were performed using biolayer interferometry with an Octet Red system (Fortebio, USA). The biotinylated EphA2 was immobilized on streptavidin biosensors at 15μg/ml in Kinetics Buffer (ForteBio). Association curves were obtained by incubating target-coated biosensors with varying concentrations of the respective Abdurin domains (11- 300nM in Kinetics Buffer), and dissociations were detected by incubating in Kinetics Buffer. The data were fitted from steady state equilibrium data using Octet Data Analysis software.
R. Binding on transfected cells
[184] CHOK1 cells were transfected with transfection-ready huEphA2 cDNA (Origene) according to manufacturer instruction. The CHO-EphA2 cells used in the binding assay were the progeny of a single cell clone, whose expression of EphA2 was verified by fluorescence- activated cell sorter (FACS) using a mouse anti-human EphA2 (R&D Systems). CH2 domains were incubated at different concentrations (InM to 7μΜ) with CHO-EphA2 cells. Binding was then detected with mouse anti histidine tag / Fitc FITC antibody conjugate (AbD Serotec). Cells were washed and resuspended in FACS buffer (PBS, 1% BSA, 0.05% NaN3) and 10,000 events were analyzed on the FACS Jazz instrument (BD Biosciences).
S. Protein chelation
[185] MeCOSar, a metal ion chelator, was conjugated onto the B6 and Bl l at a ratio of approximately 1 : 1. Stability of the conjugates was determined by HPLC at 2 weeks for aliquots stored at 2-8°C. The MeCOSar-modified CH2 domains, B6 and Bl l, and MeCOSar-mAb (control) conjugates were radiolabeled with 64Cu prior to the animal imaging work. 64Cu synthesis was performed. 500μg of each MeCOSar-modified CH2 domains was incubated with 125 MBq at pH 7 and RT for 20 min and cleaned up (EDTA/DIMASAR) via spin columns (3K).
[186] Analysis/Quality control was performed using thin layer chromatography (TLC) (silica gel 60, F254; Merck) and lOmM EDTA, 0.1M PBS buffer as the mobile phase. Radiolabeled MeCOSar-modified CH2 domains were spotted at the origin, the strip was allowed to air-dry and was developed. The strip was cut into three pieces and the radioactivity in each section was counted using a gamma counter (Wizard single-detector gamma-counter, Perkin Elmer).
[187] The MeCOSar-modified CH2 domains and MeCOSar-mAb conjugates were radiolabeled with Cobalt-57 and purified. Radio-HPLC was used to determine both conjugation and radiolabeling. Radiolabeling of the products was investigated for reproducibility and stability over 24hrs, with quality control procedures as detailed previously.
[188] The MeCOSar-modified CH2 domains and MeCOSar-mAb conjugates were then radiolabelled with 64Cu. 64Cu synthesis was performed. 50C^g of each MeCOSar-modified CH2 domains was incubated with 125 MBq at pH 7 and RT for 20 min and cleaned up (EDTA/DIMASAR) via spin columns (3K).
[189] Analysis/Quality control was performed using thin layer chromatography (TLC) (silica gel 60, F254; Merck) and lOmM EDTA, 0.1M PBS buffer as the mobile phase. Radiolabelled MeCOSar-modified CH2 domains were spotted at the origin, the strip was allowed to air-dry and was developed. The strip was cut into three pieces and the radioactivity in each section was counted using a gamma counter (Wizard single-detector gamma-counter, Perkin Elmer).
T. Animal model
[190] Twenty nude mice were inoculated with 2x 106 human PC3 prostate cancer cells per animal in 100 μΐ PBS with 100 μΐ Matrigel. The inoculation resulted in palpable tumors in the majority of mice by day 4, and the tumors reached a volume of approximately 550mm3 at Day 1 1. Tumors were very consistent between animals. There was no evidence of ulceration at the time of imaging, and the animals were bright and alert, in good condition apart from the tumors.
[191] The study was performed over a number of weeks according to the following schedule:
Table 9.
Radiolabelling and administration dates
Figure imgf000052_0001
[192] A pilot imaging study was conducted with residual product from the radiolabeling confirmation step with mice that had been used to establish and confirm the suitability of the PC3 model. One mouse each was injected and imaged with 20ug (~3.0 MBq) of B6 and Bl 1. Although uptake was seen in the tumors at 48 hrs in the biodistribution data at sacrifice, no signal could be detected in the images. The dose was therefore increased for the full study, and PET scan time was extended.
[193] Mice were anaesthetized in 2% isoflurane in a closed anesthetic induction chamber. The radiolabelled compounds the conjugated modified CH2 domains, B6 (64Cu-MeCOSar- B6 CH2), and B12 (64Cu-MeCOSar-B l 1 CH2) and the control 64Cu-MeCOSar-shWT_CH2 (total of ~10C^g of each CH2 modified domain— 15.0 MBq) were diluted with normal saline containing 0.9% sodium chloride and injected intravenously via tail vein.
U. PET/CT imaging
[194] The study was conducted using a Bioscan NanoPET-CT small animal imaging system. Post anesthetic, the mice were positioned on the scanner bed and PET scans were acquired using 30-45 minute static acquisitions. Micro-CT scans were subsequently acquired for anatomical co-registration which took approximately 20 minutes. PET scans were obtained at 4 hours, 24 hours and 48hrs after injection of the radiotracer.
[195] Four mice from each treatment group received intravenous 64Cu-MeCOSar-B6_CH2, 64Cu-MeCOSar-Bl l_CH2, 64Cu-MeCOSar-shWT_CH2, 64CuMeCOSar-shWTCH2 or 64CuMeCOSar-IgG. After the last scan (48h time point), animals were perfused, several organs including tumor and muscle were removed and the level of radioactivity measured by a gamma-counter. Radioactivity concentrations in the PET images were recalculated to provide data of Standardized Uptake Value (SUV) by dividing the radioactivity concentration (Bq/ml) by the injected radioactivity (Bq) per body weight (g).

Claims

1. A modified isolated immunoglobulin CH2 domain that specifically binds to an extracellular region of an EphA2 receptor,
wherein the amino acid sequence of the modified immunoglobulin CH2 domain comprises at least one amino acid substitution or deletion in comparison to a wild type immunoglobulin CH2 domain amino acid sequence, wherein the wild type immunoglobulin CH2 domain amino acid sequence comprises a human wild type immunoglobulin CH2 domain amino acid sequence of SEQ ID NO: 1 or a macaque wild type immunoglobulin CH2 domain amino acid sequence of SEQ ID NO: 2,
wherein the modified isolated immunoglobulin CH2 domain comprises: a framework 1 region, a framework 2 region, a framework 3 region, a framework 4 region, a loop 1 amino acid sequence located between the framework 1 region and the framework 2 region, a loop 2 amino acid sequence located between the framework 2 region, wherein the framework 3 region, and a loop 3 located between the framework 3 region and the framework 4 region, and wherein the at least one amino acid substitution or deletion is in the loop 1 amino acid sequence and/or the loop 2 amino acid sequence.
2. The modified isolated immunoglobulin CH2 domain of claim 1, wherein the wild type immunoglobulin CH2 domain amino acid sequence comprises SEQ ID NO: 1.
3. The modified isolated immunoglobulin CH2 domain of claim 1, wherein the wild type immunoglobulin CH2 domain amino acid sequence comprises SEQ ID NO: 2.
4. The modified isolated immunoglobulin CH2 domain of any of the preceding claims, wherein the at least one amino acid substitution is 1-6 amino acid substitutions in the loop 1 amino acid sequence or wherein the at least 1 deletion is in the loop 1 amino acid sequence.
5. The modified isolated immunoglobulin CH2 domain of claim 4, wherein the 1-6 amino acid substitutions are at positions 2-7 of the human wild type loop 1 amino acid sequence of SEQ ID NO: 3 or the macaque wild type loop 1 amino acid sequence of SEQ ID NO: 6.
6. The modified isolated immunoglobulin CH2 domain of claim 4, wherein the at least one deletion is at position 4 of the human wild type loop 1 amino acid sequence of SEQ ID NO: 3 or the macaque wild type loop 1 amino acid sequence of SEQ ID NO: 6.
7. The modified isolated immunoglobulin CH2 domain of any of the preceding claims, wherein the loop 2 amino acid sequence comprises at least one amino acid substitution in comparison to the wild type immunoglobulin CH2 domain amino acid sequence.
8. The modified isolated immunoglobulin CH2 domain of any of the preceding claims, wherein the loop 1 amino acid sequence is selected from the group consisting of SEQ ID NOS: 14-21, SEQ ID NOS: 85-86 and 94-99 and wherein the loop 2 amino acid sequence is selected from the group consisting of SEQ ID NOS: 22-23.
9. The modified isolated immunoglobulin CH2 domain of any of the preceding claims, wherein the framework 3 region is SEQ ID NO: 12 or SEQ ID NO: 101.
10. The modified isolated immunoglobulin CH2 domain of any one of the preceding claims, wherein the modified isolated immunoglobulin CH2 domain is selected from the group consisting of SEQ ID NOS: 29-38 and SEQ ID NOS: 87-88.
1 1. The modified isolated immunoglobulin CH2 domain of any one of the preceding claims, wherein the modified isolated immunoglobulin CH2 domain binds FcRn.
12. The modified isolated immunoglobulin CH2 domain of any one of the preceding claims, wherein the modified isolated immunoglobulin CH2 domain is a deimmunized CH2 domain.
13. The modified isolated immunoglobulin CH2 domain of claim 12, wherein the deimmunized CH2 domain is a modified macaque IgG immunoglobulin CH2 domain.
14. The modified isolated immunoglobulin CH2 domain of any one of the preceding claims, wherein the modified isolated immunoglobulin CH2 domain further comprises at least one amino acid addition or substitution located at the N-terminus, C-terminus or both termini.
15. The modified isolated immunoglobulin CH2 domain of claim 14, wherein the modified isolated immunoglobulin CH2 domain is selected from the group consisting of SEQ ID NOS: 89-93.
16. The modified isolated immunoglobulin CH2 domain of claim 14, wherein the at least one terminal amino acid substitution or addition results in a terminal serine, a terminal tyrosine, a terminal cysteine or a terminal lysine.
17. The modified isolated immunoglobulin CH2 domain of claim 16, wherein the at least one terminal amino acid substitution or addition results in a terminal cysteine.
18. The modified isolated immunoglobulin CH2 domain of claim 17, wherein a linker is joined to the at least one amino acid substitution or addition.
19. The modified isolated immunoglobulin CH2 domain of claim 18, wherein the linker is a peptide or polyethylene glycol.
20. The modified isolated immunoglobulin CH2 domain of claim 19, wherein the modified isolated immunoglobulin CH2 domain is selected from the group consisting of SEQ ID NOS: 89 and 91-93.
21. The modified isolated immunoglobulin CH2 domain of any one of the preceding claims, wherein the at least one amino acid substitution comprises
a first amino acid substitution and a second amino acid substitution,
wherein the first amino acid substitution and the second amino acid substitution are cysteine residues, and wherein the cysteine residues form a disulfide bond.
22. The modified isolated immunoglobulin CH2 domain of claim 21,
wherein the first amino acid substitution is at position 12 and the second amino acid substitution is at position 104 or
wherein the first amino acid substitution is at position 10 and the second amino acid substitution is at position 102 of the human wild type immunoglobulin CH2 domain of SEQ ID NO: 1 or of the macaque wild type immunoglobulin CH2 domain of SEQ ID NO: 2.
23. The modified isolated immunoglobulin CH2 domain of any one of the preceding claims, wherein the modified isolated immunoglobulin CH2 domain further comprises an N- terminal deletion of 6 amino acids.
24. The modified isolated immunoglobulin CH2 domain of any one of the preceding claims, wherein the modified isolated immunoglobulin CH2 domain further comprises an N- terminal deletion of 1-7 amino acids.
25. The modified isolated immunoglobulin CH2 domain of any one of the preceding claims, wherein the modified isolated immunoglobulin CH2 domain further comprises a 1-4 amino acid C-terminal deletion.
26. The modified isolated immunoglobulin CH2 domain of claim 1 1, wherein the FcRn is a human FcRn.
27. The modified isolated immunoglobulin CH2 domain of any of the preceding claims, wherein the modified isolated immunoglobulin CH2 domain is detectably labeled with a radioisotope, a fluorescent compound, a chemiluminescent compound, an enzyme, an imaging agent or a metal ion.
28. An immunoconjugate comprising a modified isolated immunoglobulin CH2 domain that specifically binds to an EphA2 receptor according to any one of the preceding claims and a toxin or a small molecule,
wherein the modified isolated immunoglobulin CH2 domain is fused to the toxin or wherein the modified isolated immunoglobulin CH2 domain is joined to the small molecule.
29. The immunoconjugate of claim 28, wherein the modified isolated immunoglobulin CH2 domain and the toxin or the modified isolated immunoglobulin CH2 domain and the small molecule are joined by a linker.
30. The immunoconjugate of claim 29, wherein the linker is a peptide or polyethylene glycol.
31. The immunoconjugate of any one of claims 28-30, wherein the toxin is a fungal ribonuclease.
32. The immunoconjugate of claim 31, wherein the fungal ribonuclease is a-sarcin or a deimmunized a-sarcin.
33. The modified isolated immunoglobulin CH2 domain or immunoconjugate of any one of the preceding claims, wherein the EphA2 receptor is a human EphA2 receptor.
34. The modified isolated immunoglobulin CH2 domain or immunoconjugate of any one of the preceding claims, wherein the EphA2 receptor is a mouse EphA2 receptor.
35. The modified isolated immunoglobulin CH2 domain or immunoconjugate of any one of the preceding claims, wherein the modified isolated immunoglobulin CH2 domain dissociates from the Eph2A receptor with a K<j of 1.0 xl0~7 M or less.
36. A pharmaceutical composition comprising:
the modified isolated immunoglobulin CH2 domain or the immunoconjugate of any of the preceding claims, and
a pharmaceutical carrier.
37. A method of treating a disease associated with EphA2 overexpression, comprising:
administering to a subject in need thereof a therapeutically effective dose of a modified isolated immunoglobulin CH2 domain, immunoconjugate, or pharmaceutical composition of any one of the preceding claims.
38. The method of claim 37, wherein the modified isolated immunoglobulin CH2 domain is fused to a toxin or linked to a small molecule.
39. The method of claim 37 or 38, wherein the disease associated with EphA2 overexpression is a cancer selected from the group consisting of: breast cancer, melanoma, ovarian cancer, lung cancer, gliomas, bladder cancer, prostate cancer, esophageal cancer, renal cancer, colon cancer and vulvar cancer.
40. A method for killing a target cell comprising EphA2 receptors in a subject in need thereof, which comprises:
providing the immunoconjugate according to any of claims 28-32; and
exposing the target cell to an effective amount of the immunoconjugate, thereby selectively killing the target cell in the subject.
41. The method of claim 40, wherein the modified isolated CH2 domain is capable of being internalized into the target cell.
42. The method of claim 38, wherein the toxin is a cytolytic peptide.
43. The method of claim 38, wherein the small molecule is selected from the group consisting of auristatins, maytansinoids and pyrrolobenzodiazepines.
44. The immunoconjugate of claims 28-32, wherein the small molecule is a compound selected from the group consisting of auristatins, maytansinoids and pyrrolobenzodiazepines.
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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3600394A4 (en) * 2017-03-22 2021-04-14 Research Corporation Technologies, Inc. Engineered stable ch2 polypeptides

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB201810316D0 (en) * 2018-06-22 2018-08-08 Bicyclerd Ltd Peptide ligands for binding to EphA2

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2009099961A2 (en) 2008-01-31 2009-08-13 The Government Of The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Engineered antibody constant domain molecules
US20100143345A1 (en) * 2002-05-10 2010-06-10 Medimmune, Llc Epha2 agonistic monoclonal antibodies and methods of use thereof
WO2011039724A1 (en) 2009-10-02 2011-04-07 Sanofi-Aventis Antibodies that specifically bind to the epha2 receptor
US20120230981A1 (en) 2011-02-11 2012-09-13 David Bramhill CH2 Domain Template Molecules Derived From Rational Grafting Of Donor Loops Onto CH2 Scaffolds
WO2013119903A1 (en) 2012-02-10 2013-08-15 Research Corporation Technologies, Inc. Fusion proteins comprising immunoglobulin constant domain-derived scaffolds

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100143345A1 (en) * 2002-05-10 2010-06-10 Medimmune, Llc Epha2 agonistic monoclonal antibodies and methods of use thereof
WO2009099961A2 (en) 2008-01-31 2009-08-13 The Government Of The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Engineered antibody constant domain molecules
WO2011039724A1 (en) 2009-10-02 2011-04-07 Sanofi-Aventis Antibodies that specifically bind to the epha2 receptor
US20120230981A1 (en) 2011-02-11 2012-09-13 David Bramhill CH2 Domain Template Molecules Derived From Rational Grafting Of Donor Loops Onto CH2 Scaffolds
WO2013119903A1 (en) 2012-02-10 2013-08-15 Research Corporation Technologies, Inc. Fusion proteins comprising immunoglobulin constant domain-derived scaffolds

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
DATABASE UniProtKB/TrEMBL [o] 29 May 2013 (2013-05-29), Database accession no. F7FOD6 *
GEHLSEN ET AL., MABS, vol. 4, no. 4, pages 466 - 474
See also references of EP3209329A4
WEIZAO ET AL., CURRENT DRUG DISCOVERY TECHNOLOGIES, vol. 11, no. 1, pages 1570 - 1638
XIAO ET AL., BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, vol. 387, no. 2, pages 387 - 392
YING ET AL., BIOCHIMICA ET BIOPHYSICA ACTA - PROTEINS AND PROTEOMICS, vol. 1844, no. 11, pages 1977 - 1982

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3600394A4 (en) * 2017-03-22 2021-04-14 Research Corporation Technologies, Inc. Engineered stable ch2 polypeptides
US11542321B2 (en) 2017-03-22 2023-01-03 Research Corporation Technologies, Inc. Engineered stable CH2 polypeptides

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EP3209329A4 (en) 2018-03-28
US20170306032A1 (en) 2017-10-26
CA2963556A1 (en) 2016-04-28
AU2015335725B2 (en) 2021-06-03
EP3209329A1 (en) 2017-08-30
AU2015335725A1 (en) 2017-04-27
CA2963556C (en) 2023-03-14

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