WO2015112822A1 - Antibody-drug conjugates targeting kit receptor and uses thereof - Google Patents

Antibody-drug conjugates targeting kit receptor and uses thereof Download PDF

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Publication number
WO2015112822A1
WO2015112822A1 PCT/US2015/012621 US2015012621W WO2015112822A1 WO 2015112822 A1 WO2015112822 A1 WO 2015112822A1 US 2015012621 W US2015012621 W US 2015012621W WO 2015112822 A1 WO2015112822 A1 WO 2015112822A1
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Prior art keywords
amino acid
seq
acid sequence
antibody
kit
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PCT/US2015/012621
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French (fr)
Inventor
Yaron Hadari
Elizabeth M. MANDEL-BAUSCH
Vivien A. WARREN
Christine K. LUBESKI
Philip Wilson Howard
Christina Louisa VON BULOW
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Kolltan Pharmaceuticals, Inc.
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Publication of WO2015112822A1 publication Critical patent/WO2015112822A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
    • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
    • C07D487/04—Ortho-condensed systems
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/54—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
    • A61K47/55—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug, i.e. a dimer, oligomer or polymer of pharmacologically or therapeutically active compounds
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6801—Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent
    • A61K47/6803—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates
    • A61K47/68035—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates the drug being a pyrrolobenzodiazepine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6801—Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent
    • A61K47/6803—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates
    • A61K47/6807—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates the drug or compound being a sugar, nucleoside, nucleotide, nucleic acid, e.g. RNA antisense
    • A61K47/6809—Antibiotics, e.g. antitumor antibiotics anthracyclins, adriamycin, doxorubicin or daunomycin
    • 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
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • 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
    • 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
    • A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
    • A61K2039/55511—Organic adjuvants
    • A61K2039/55516—Proteins; Peptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation

Definitions

  • ADCs antibody-drug conjugates
  • D4 Ig-like domain 4
  • ECD extracellular domain
  • Antibody-drug conjugates are a class of drug designed as a targeted therapy, for example, therapy for treating cancer by targeting cancer cells.
  • ADCs contain an antibody or an antigen-binding antibody fragment such as a single-chain variable fragment (scFv) linked, usually via a linker, to a biological active cytotoxic moiety.
  • scFv single-chain variable fragment
  • ADC efficacy of particular ADCs depends on selectivity of the antibodies, drug mechanism of action, compatible drug linker, drug-antibody ratio (DAR), and drug release properties, as well as appropriate synthesis processes.
  • DAR drug-antibody ratio
  • Challenges in developing ADCs involve identifying the appropriate balance of these factors, among others.
  • Abnormal KIT (or c-Kit) receptor expression and/or activity has been implicated in connection with a number of cancers.
  • gain-of-function KIT mutations resulting in SCF-independent, constitutive activation of KIT are found in certain cancer cells and are associated with certain cancers such as leukemia (e.g., chronic myelogenous leukemia) and gastrointestinal stromal tumors (see, e.g., Mol et al., J. Biol. Chem., 2003, 278:31461-31464).
  • KIT Abnormal KIT expression and/or activity also has been implicated in other disorders such as fibrosis and certain inflammatory disorders.
  • Expression of KIT has been detected in various cell types, such as mast cells, stem cells, brain cells, melanoblasts, ovary cells, and cancer cells (e.g., leukemia cells).
  • cancer cells e.g., leukemia cells.
  • loss-of-function KIT mutations indicate that KIT is important for the normal growth of hematopoietic progenitor cells, mast cells, melanocytes, primordial germ cells, and the interstitial cells of Cajal (see, e.g., Besmer, P., Curr. Opin.
  • Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, comprising:
  • VL light chain variable region
  • VL a light chain variable region
  • VL CDR1, VL CDR2, and VL CDR3 comprising the amino acid sequences KASQNVRTNVA (SEQ ID NO: 19), SASYRYS (SEQ ID NO: 20), and QQYNSYPRT (SEQ ID NO: 21), respectively;
  • VH heavy chain variable region
  • VH CDR1, VH CDR2, and VH CDR3 comprising the amino acid sequences DYYIN (SEQ ID NO: 16), RIYPGSGNTYYNEKFKG (SEQ ID NO: 17), and GVYYFDY (SEQ ID NO: 18), respectively;
  • n 1 to 20;
  • q 1 to 3;
  • R is independently selected from hydrogen, Ci-C 6 alkyl, C3-C6 cycloalkyl, C 2 -C6
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to D4 of a human KIT receptor, comprising:
  • VL light chain variable region
  • ⁇ is an amino acid with an aromatic or aliphatic hydroxyl side chain
  • ⁇ 2 is an amino acid with an aromatic or aliphatic hydroxyl side chain
  • ⁇ 3 is an amino acid with an aliphatic hydroxyl side chain
  • X K4 is an amino acid with an aliphatic hydroxyl side chain or is P
  • X KS is an amino acid with a charged or acidic side chain
  • ⁇ is an amino acid with an aromatic side chain
  • VH heavy chain variable region
  • VL comprising a VL CDR1 , VL CDR2, and VL CDR3 having the amino acid sequences of SEQ ID NO: 19, SEQ ID NO: 20, and SEQ ID NO: 21 , respectively;
  • X M is an amino acid with an aliphatic side chain
  • X H2 is an amino acid with an aliphatic side chain
  • X H3 is an amino acid with a polar or basic side chain
  • X R4 is an amino acid with an aliphatic side chain
  • X HS is an amino acid with an aliphatic side chain
  • X H6 is an amino acid with an acidic side chain
  • X H7 is an amino acid with an acidic or amide derivative side chain
  • X HS is an amino acid with an aliphatic hydroxyl side chain.
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein m is 1 to 3, or m is 2. In a certain embodiment, the PBD dimer conjugates of Formula Ab(X) m are those, wherein m is 1 to 3.
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein
  • the PBD dimer conjugates of Formula Ab(X) m are those,
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein q is 1 or 3. In another embodiment, the PBD dimer conjugates of Formula Ab(X) m are those, wherein q is 1.
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein R is methyl or (E)-prop-l-en-l-yl. In another embodiment, the PBD dimer conjugates of Formula Ab(X) m are those, wherein
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein n is 4 or 8. In another embodiment, the PBD dimer conjugates of Formula Ab(X) m are those, wherein n is 8.
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein p is 5.
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, comprising:
  • VL light chain variable region
  • VH heavy chain variable region
  • X M is an amino acid with an aliphatic side chain
  • X H2 is an amino acid with an aliphatic side chain
  • X H3 is an amino acid with a polar or basic side chain
  • X H4 is an amino acid with an aliphatic side chain
  • X HS is an amino acid with an aliphatic side chain
  • X H6 is an amino acid with an acidic side chain
  • X R7 is an amino acid with an acidic or amide derivative side chain
  • X HS is an amino acid with an aliphatic
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, comprising:
  • VL light chain variable region
  • VH heavy chain variable region
  • X M is an amino acid with an aliphatic side chain
  • X H2 is an amino acid with an aliphatic side chain
  • X H3 is an amino acid with a polar or basic side chain
  • X R4 is an amino acid with an aliphatic side chain
  • X HS is an amino acid with an aliphatic side chain
  • X H6 is an amino acid with an acidic side chain
  • X H7 is an amino acid with an acidic or amide derivative side chain
  • X HS is an amino acid with an aliphatic aliphatic side chain
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein X is
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein Ab is an antibody or an antigen-binding fragment thereof, which immunospecifically binds to D4 of a human KIT receptor, comprising a light chain variable region ("VL”) and a heavy chain variable region (“VH”), wherein:
  • VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
  • VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
  • VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
  • VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
  • the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
  • the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
  • VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
  • VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
  • VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
  • the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
  • the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
  • the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
  • the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
  • the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
  • the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
  • the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
  • VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
  • the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
  • the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
  • the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 6.
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein m is 1 to 3.
  • the PBD dimer conjugates of Formula Ab(X) m are those, wherein m is 2.
  • composition comprising a PBD dimer conjugate described herein of Formula Ab(X) m or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable excipient.
  • a method of treating cancer comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate described herein of Formula Ab(X) m or a pharmaceutically acceptable salt thereof.
  • the cancer is leukemia, lung cancer, melanoma, sarcoma, or gastrointestinal stromal tumors.
  • the cancer is acute myeloid leukemia (AML) or small cell lung cancer.
  • the methods of treating cancer are those, wherein the cancer is refractory to treatment by a tyrosine kinase inhibitor.
  • the tyrosine kinase inhibitor is imatinib mesylate or SU11248.
  • the methods of treating cancer are those, wherein the method further comprises administering a second therapeutic agent.
  • the second therapeutic agent is a chemotherapeutic agent, a tyrosine kinase inhibitor, a histone deacetylase inhibitor, an antibody, or a cytokine.
  • the tyrosine kinase inhibitor is imatinib mesylate or SU11248.
  • a method of treating fibrosis or an inflammatory disorder comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate described herein of Formula Ab(X) m or a pharmaceutically acceptable salt thereof.
  • a method of treating a mast cell associated disorder comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate described herein of Formula Ab(X) m or a pharmaceutically acceptable salt thereof.
  • a method of treating neurofibromatosis comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate of Formula Ab(X) m or a pharmaceutically acceptable salt thereof.
  • a method of treating systemic mastocytosis comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate described herein of Formula Ab(X) m or a pharmaceutically acceptable salt thereof.
  • a method of treating cancer comprising
  • fibrosis In a certain aspect, provided herein is a method of treating fibrosis or an
  • inflammatory disorder comprising administering to a subject in need thereof a therapeutically effective amount of a plurality of PBD dimer conjugates described herein of Formula Ab(X) m , wherein the average drug-per-antibody ratio (“DAR”) is 1.5 to 3.
  • DAR average drug-per-antibody ratio
  • a method of treating a mast cell associated disorder comprising administering to a subject in need thereof a therapeutically effective amount of a plurality of PBD dimer conjugates described herein of Formula Ab(X) m , wherein the average drug-per-antibody ratio (“DAR”) is 1.5 to 3.
  • DAR average drug-per-antibody ratio
  • a method of treating neurofibromatosis comprising administering to a subject in need thereof a therapeutically effective amount of a plurality of PBD dimer conjugates described herein of Formula Ab(X) m , wherein the average drug-per-antibody ratio (“DAR”) is 1.5 to 3.
  • DAR average drug-per-antibody ratio
  • a method of treating systemic mastocytosis comprising administering to a subject in need thereof a therapeutically effective amount of a plurality of PBD dimer conjugates described herein of Formula Ab(X) m , wherein the average drug-per-antibody ratio (“DAR”) is 1.5 to 3.
  • DAR average drug-per-antibody ratio
  • a method of making a PBD dimer conjugate or a pharmaceutically acceptable salt thereof comprising conjugating an anti-KIT antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, wherein the anti-KIT antibody or antigen- binding fragment thereof comprises:
  • VL light chain variable region
  • VL a light chain variable region
  • VL CDR1, VL CDR2, and VL CDR3 comprising the amino acid sequences KASQNVRTNVA (SEQ ID NO: 19), SASYRYS (SEQ ID NO: 20), and QQYNSYPRT (SEQ ID NO: 21), respectively;
  • VH heavy chain variable region
  • the method comprising conjugating the anti-KIT antibody to a PBD dimer with a linker, such as any one of compounds 42, 43, 44, 45, 46, or 47.
  • Fig. 1A depicts pyrrolobenzodiazepine ("PBD") dimers attached to reactive linkers (compounds 42, 43, 44, 45, 46 and 47) for conjugation with anti-KIT antibodies to generate ADCs, specifically, PBD dimer conjugates.
  • PBD pyrrolobenzodiazepine
  • Fig. IB depicts the amino acid sequence of a full length human KIT receptor (SEQ ID NO: 1), GenBankTM accession number AAC50969.
  • the first through fifth extracellular Ig- like domains i.e., Dl, D2, D3, D4, and D5 are indicated; " ⁇ ” depicts the amino-terminal residue of each domain and " ⁇ ” depicts the carboxyl-terminal residue of each domain.
  • the Dl domain is depicted at P34 to Rl 12
  • the D2 domain is depicted at Dl 13 to P206
  • the D3 domain is depicted at A207 to D309
  • the D4 domain is depicted at K310 to N410 (SEQ ID NO: 15)
  • the hinge region between D4 and D5 is located at V409 to N410
  • the D5 domain is depicted at T411 to K509.
  • the D1/D2 hinge region is located at Dl 13 to LI 17
  • the D2/D3 hinge region is located at P206 to A210
  • the D3/D4 hinge region is located at D309 to G311.
  • the D4/D5 region comprises K310 to K509.
  • the transmembrane domain comprises residues F525 to Q545, and the kinase domain comprises residues K589 to S933.
  • Fig. 2 A depicts the amino acid sequence (SEQ ID NO: 2) of the HI VH domain, and a DNA (SEQ ID NO:22) encoding the amino acid sequence.
  • the framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
  • Fig. 2B depicts the amino acid sequence (SEQ ID NO: 3) of the H2 VH domain and a DNA (SEQ ID NO:23) encoding the amino acid sequence.
  • the framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
  • Fig. 2C depicts the amino acid sequence (SEQ ID NO: 4) of the H3 VH domain and a DNA (SEQ ID NO:24) encoding the amino acid sequence.
  • the framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
  • Fig. 2D depicts the amino acid sequence (SEQ ID NO: 5) of the H4 VH domain and a DNA (SEQ ID NO:25) encoding the amino acid sequence.
  • the framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
  • Fig. 2E depicts the amino acid sequence (SEQ ID NO: 6) of the H5 VH domain and a DNA (SEQ ID NO:26) encoding the amino acid sequence.
  • the framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
  • Fig. 2F depicts the amino acid sequence (SEQ ID NO: 7) of the LI VL domain and a DNA (SEQ ID NO:27) encoding the amino acid sequence.
  • the framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
  • Fig. 2G depicts the amino acid sequence (SEQ ID NO: 8) of the K2 VL domain and a DNA (SEQ ID NO:28) encoding the amino acid sequence.
  • the framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
  • Fig. 2H depicts the amino acid sequence (SEQ ID NO: 9) of the L3 VL domain and a DNA (SEQ ID NO:29) encoding the amino acid sequence.
  • the framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
  • Fig. 21 depicts the amino acid sequence (SEQ ID NO: 10) of the L4 VL domain and a DNA (SEQ ID NO:30) encoding the amino acid sequence.
  • the framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
  • Fig. 2J depicts the consensus sequence of a VH domain (SEQ ID NO: 11).
  • X HI - HS indicate amino acids which can be any amino acid.
  • Fig. 2K depicts the consensus sequence of a VL domain (SEQ ID NO: 12).
  • ⁇ - ⁇ 6 indicate amino acids which can be any amino acid.
  • Fig. 3 depicts the binding activity of PBD dimer conjugates comprising anti-KIT antibodies, to a recombinant polypeptide of the D4/D5 region of human KIT as determined by solid phase ELISA.
  • the results for PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2) are provided, with control PBD dimer conjugates comprising an anti-keyhole limpet hemocyanin ("KLH") antibody conjugated to compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), as well as controls of unconjugated anti-KIT antibody (KIT-Ab) and unconjugated anti-KLH antibody (KLH-Ab).
  • KLH anti-keyhole limpet hemocyanin
  • Fig. 4 depicts a graph of results of KIT phosphorylation inhibition assays performed by ELISA with CHO cells recombinantly expressing wild-type KIT to characterize the phosphorylation blocking activity of PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), relative to an unconjugated form of the anti-KIT antibody (KIT-Ab).
  • KIT-PBDl compound 42
  • KIT-PBD2 compound 45
  • KIT-Ab unconjugated form of the anti-KIT antibody
  • Fig. 5 presents results of cell proliferation assays with PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), relative to control PBD dimer conjugates comprising an anti-KLH antibody conjugated to compound 42 (KLH-PBDl) or compound 45 (KLH-PBD2).
  • IC50 (nM) values are provided.
  • Cells with detectable KIT expression on the cell surface are labelled with "+”; cells with no detectable KIT expression on the cell surface are labelled and "ND" indicates that KIT expression was not determined.
  • FIG. 6 depicts results of xenograft mouse model studies of RD-ES Ewing's Sarcoma with a PBD dimer conjugate comprising an anti-KIT antibody conjugated to compound 42 (KIT- PBD1) at three different concentrations (i.e., 0.3 mg/kg, 1 mg/kg, and 3 mg/kg), a control PBD dimer conjugate comprising an anti-KLH antibody conjugated to compound 42 (KLH-PBD1), and a control unconjugated anti-KIT antibody (KIT-Ab).
  • the graph is a plot of median tumor volume for each group over time (days after start of treatment).
  • Fig. 7A-B depict results of xenograft mouse model studies of erythroid leukemia with PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT- PBD1) or compound 45 (KIT-PBD2), control PBD dimer conjugates comprising an anti-KLH antibody conjugated to compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), and a control unconjugated anti-KIT antibody (KIT-Ab).
  • the graphs are plots of mean tumor volume for each group over time (days after start of treatment).
  • Fig. 8A-B depict results of xenograft mouse model studies of small cell lung cancer (SCLC) with PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT-PBDl) (Fig. 8 A) or compound 45 (KIT-PBD2) (Fig. 8B), control PBD dimer conjugates comprising an anti-KLH antibody conjugated to compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), and a control unconjugated anti-KIT antibody (KIT-Ab).
  • the graphs are plots of mean tumor volume for each group over time (days after start of treatment).
  • Fig. 9A-C presents results of colony formation assays with PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), relative to the naked anti-KIT antibody (KIT) and PBD dimer conjugates comprising an anti-KLH antibody conjugated to compound 42 (KLH-PBDl) or compound 45 (KLH-PBD2), which served as controls.
  • ADCs antibody-drug conjugates
  • D4 Ig-like domain 4
  • ECD human KIT
  • PBD dimer conjugate comprising an antibody (anti-KIT antibody) described herein (e.g., section 5.1.2) or antigen-binding fragment thereof which specifically binds to a KIT receptor, e.g. , a human KIT receptor, wherein the antibody or antigen-binding fragment thereof is conjugated to one or more PBD dimers described herein (e.g, section 5.1.1), and optionally comprises one or more linkers (e.g., N10 or C2 linker), such as reactive linkers, linking the antibody or antigen-binding fragment thereof to the one or more PBD dimers.
  • kits and pharmaceutical compositions comprising such ADCs or PBD dimer conjugates, as well as uses and methods for treating or managing disorders such as cancer or inflammatory disorders, and methods of making such ADCs or PBD dimer conjugates.
  • PBDs Pyrrolobenzodiazepines
  • PBD dimers can be synthesized by joining two PBD units together through their C8/C 8 '-hydroxy 1 functionalities via a flexible alkylene linker (Bose, D. S., et al., J. Am. Chem. Soc, 114, 4939-4941 (1992); Thurston, D. E., et al, J. Org. Chem., 61, 8141-8147 (1996)).
  • a PBD dimer is:
  • PBD dimers can be symmetrical, such as the above, or unsymmetrical, wherein the PBD units comprised in the dimer are not identical. Some PBDs can recognize and bind to specific sequences of DNA, such as PuGPu.
  • D4/D5 region refers to a region within a KIT polypeptide spanning the fourth Ig-like extracellular (“D4") domain, the fifth Ig-like extracellular (“D5") domain, and the hinge region in between the D4 and D5 domains ("D4-D5 hinge region"), of KIT, in the following order from the amino terminus to the carboxyl terminus: D4, D4-D5 hinge region, and D5.
  • amino acids V308 to H515 of a human KIT e.g., GenBank No. AAC50969; see also Figure IB
  • D4 region or D4 domain in the context of a KIT receptor refer to a region within a KIT receptor polypeptide spanning the fourth Ig-like extracellular ("D4") domain of KIT.
  • amino acids K310 to N410 of a human KIT e.g., GenBank No. AAC50969; see also Figure IB
  • K4 region or domain of human KIT is considered an example of a D4 region or domain of human KIT.
  • KIT or "KIT receptor” or “KIT polypeptide” refer to any form of full-length KIT including, but not limited to, native KIT, an isoform of KIT, an interspecies KIT homolog, or a KIT variant, e.g., naturally occurring (for example, allelic or splice variant, or mutant, e.g., somatic mutant) or artificially constructed variant (for example, a recombinant or chemically modified variant).
  • native KIT for example, an isoform of KIT
  • an interspecies KIT homolog or a KIT variant, e.g., naturally occurring (for example, allelic or splice variant, or mutant, e.g., somatic mutant) or artificially constructed variant (for example, a recombinant or chemically modified variant).
  • KIT is a type III receptor tyrosine kinase encoded by the c-kit gene (see, e.g., Yarden et al, Nature, 1986, 323:226-232; Ullrich and Schlessinger, Cell, 1990, 61 :203-212; Clifford et al, J. Biol. Chem., 2003, 278:31461-31464; Yarden et al, EMBO J., 1987, 6:3341-3351; Mol et al, J. Biol. Chem., 2003, 278:31461-31464).
  • GenBankTM accession number NM 000222 provides an exemplary human KIT nucleic acid sequence.
  • GenBankTM accession numbers NP 001087241, PI 0721, and AAC50969 provide exemplary human KIT amino acid sequences.
  • GenBankTM accession number AAH75716 provides an exemplary murine KIT amino acid sequence.
  • Native KIT comprises five extracellular immunoglobulin (Ig)-like domains (Dl, D2, D3, D4, D5), a single transmembrane region, an inhibitory cytoplasmic juxtamembrane domain, and a split cytoplasmic kinase domain separated by a kinase insert segment (see, e.g., Yarden et al, Nature, 1986, 323:226-232; Ullrich and Schlessinger, Cell, 1990, 61 :203-212; Clifford et al, J.
  • Ig immunoglobulin
  • KIT is human KIT.
  • KIT can exist as a monomer, dimer, multimer, native form, or denatured form.
  • KIT-PBD-ADC or "KIT-PBD ADC” refers to an ADC comprising an antibody or antigen-binding fragment thereof which specifically binds to KIT receptor (anti-KIT antibody), such as a human KIT receptor, wherein the antibody or antigen- binding fragment thereof is conjugated to one or more pyrrolobenzodiazepmes (PBDs), such as PBD dimers ("KIT-PBD dimer-ADC” or "KIT-PBD dimer ADC”).
  • PBDs pyrrolobenzodiazepmes
  • ADCs antibody-drug conjugates
  • a D4 of a KIT receptor e.g., a human KIT receptor
  • a pyrrolobenzodiazepine (PBD) conjugate which is an ADC comprising an antibody described herein (e.g., Section 5.1.2) or an antigen-binding fragment thereof which specifically binds to a D4 of a human KIT receptor, wherein the antibody or antigen-binding fragment thereof is conjugated to one or more pyrrolobenzodiazepmes (PBDs), for example PBDs described herein (e.g., Section 5.1.1).
  • PBDs pyrrolobenzodiazepmes
  • a PBD dimer conjugate which is an ADC comprising an antibody described herein (e.g., Section 5.1.2) or an antigen-binding fragment thereof which specifically binds to a D4 of a human KIT receptor, wherein the antibody or antigen-binding fragment thereof is conjugated to one or more PBD dimers, for example PBDs described herein (e.g., Section 5.1.1).
  • a PBD dimer conjugate of Formula Ab(X) m or a pharmaceutically acceptable salt thereof wherein Ab is an antibody described herein (e.g., Section 5.1.2), or an antigen-binding fragment thereof, which specifically binds to a D4 of a human KIT receptor, X is a PBD dimer attached to a linker (e.g., reactive linker) , for example as described herein (e.g., Section 5.1.1), and m is at least 1 , for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 3, and refers to the number of X moieties conjugated to Ab.
  • a linker e.g., reactive linker
  • ADCs which are PBD dimer conjugates comprising an anti-KIT antibody described herein (e.g., any one of antibodies Huml -Hum20), for example an anti-KIT antibody described in Section 5.1.2, conjugated to one or more PBD dimers (KIT-PBD dimer ADCs).
  • a KIT-PBD dimer ADC provided herein comprises an N10 linked PBD dimer or a C2 linked PBD dimer, for example, as described in more details in the sections below.
  • the specified link between the PBD dimer and an anti-KIT antibody described herein is generally stable extracellularly, such that, extracellularly, the antibody generally remains linked to the drug moiety.
  • the linkers are stable extracellularly (e.g., outside a target cell expressing KIT) and may be cleaved or otherwise processed inside the cell to release an active PBD compound.
  • an effective linker can: (i) maintain the specific binding properties of the conjugated antibody (e.g, anti-KIT antibody); (ii) allow intracellular delivery of a conjugate or drug moiety; (iii) remain stable and intact, i.e., not cleaved, until the conjugate has been delivered or transported to its targeted site (e.g., target site with KIT receptor); and (iv) maintain a cytotoxic, cell-killing effect or a cytostatic effect of a PBD dimer drug moiety.
  • Stability of an ADC such as a PBD dimer conjugate (e.g. , KIT-PBD dimer ADC) may be measured by standard analytical techniques such as mass spectroscopy, HPLC, and the separation/analysis technique LC/MS.
  • a PBD dimer with a linker e.g. , reactive linker
  • a linker e.g., reactive linker
  • the PBD dimer is conjugated via the linker to an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)).
  • PBD dimer-linked ADCs e.g. , PBD dimer conjugates, such as KIT-PBD dimer ADCs
  • PBD dimer conjugates such as KIT-PBD dimer ADCs
  • KIT-PBD dimer ADCs KIT-PBD dimer ADCs
  • a PBD dimer conjugate provided herein is of the following Formula Ab(X) m :
  • Ab is an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, see Table 4), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)); and wherein m is the number of X moieties conjugated to Ab.
  • m is at least 1 , for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 4, or 1 to 3.
  • m is about 1 to 3 or about 1 or 4.
  • a PBD dimer conjugate provided herein is of the following Formula Ab(
  • Ab is an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, see Table 4), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)); and wherein m is the number of X moieties conjugated to Ab.
  • m is at least 1, for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 4, or 1 to 3.
  • m is about 1 to 3 or about 1 or 4.
  • a PBD dimer with a linker e.g., reactive linker
  • a linker e.g., reactive linker
  • the PBD dimer is conjugated via the linker to an anti-KIT antibody described herein (e.g., any one of antibodies Huml- Hum20), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)).
  • PBD dimer-linked ADCs e.g., PBD dimer conjugates, such as KIT-PBD dimer ADCs
  • PBD dimer conjugates such as KIT-PBD dimer ADCs
  • a PBD dimer conjugate provided herein is of the following Formula Ab(X) m : herein X is
  • Ab is an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, see Table 4), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)); and wherein m is the number of X moieties conjugated to Ab.
  • m is at least 1 , for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 4, or 1 to 3.
  • m is about 1 to 3 or about 1 or 4.
  • a PBD dimer conjugate provided herein is of the following Formula Ab(X) m :
  • Ab is an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, see Table 4), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)); and wherein m is the number of X moieties conjugated to Ab.
  • m is at least 1 , for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 4, or 1 to 3.
  • m is about 1 to 3 or about 1 or 4.
  • a PBD dimer conjugate provided herein is of the following Formula Ab(X) m :
  • Ab is an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, see Table 4), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)); and wherein m is the number of X moieties conjugated to Ab.
  • m is at least 1 , for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 4, or 1 to 3.
  • m is about 1 to 3 or about 1 or 4.
  • Drug loading is the average number of PBD dimer drugs per antibody, e.g. such as an anti-KIT antibody.
  • drug loading may, for example, range from 1 to 80, 1 to 50, 1 to 40, 1 to 20, 1 to 10, or 1 to 8 drugs per antibody ⁇ e.g., such as an anti-KIT antibody), e.g., where 1, 2, 3, 4, 5, 6, 7, or 8 drug moieties are covalently attached to an antibody ⁇ e.g., such as an anti-KIT antibody).
  • PBD dimer conjugates provided herein comprise an anti-KIT antibody described herein ⁇ e.g., any one of antibodies Huml-Hum20), for example an anti-KIT antibody described in Section 5.1.2 ⁇ e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)), conjugated with from 1 to 8 PBD dimers, 2 to 6 PBD dimers, or 1 to 3 PBD dimers, bound to thiol groups, e.g., cysteine thiol groups.
  • compositions of ADCs provided herein include collections of antibodies, e.g., such as anti-KIT antibodies, conjugated with a range of drugs ⁇ e.g., PBD dimers), from 1 to 80, 1 to 50, 1 to 40, 1 to 20, 1 to 10, or 1 to 8.
  • drugs e.g., PBD dimers
  • drug loading may, for example, range from 1 to 80 drugs per antibody, e.g., such as an anti-KIT antibody, although in certain embodiments, there is an upper limit of 50, 40, 20, 10 or 8 drugs per antibody.
  • Compositions of ADCs provided herein include collections of antibodies, e.g. such as anti-KIT antibodies, conjugated with a range of drugs, from 1 to 80, 1 to 40, 1 to 20, 1 to 10, or 1 to 8.
  • PBD dimer conjugates provided herein comprise an anti-KIT antibody described herein ⁇ e.g., any one of antibodies Huml-Hum20), for example an anti-KIT antibody described in Section 5.1.2 ⁇ e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)), conjugated with from 1 to 80, 1 to 40, 1 to 20, 1 to 10, 1 to 8, 2 to 6, 1 to 4, or 1 to 3 PBDs bound to lysines.
  • compositions comprising a plurality of ADCs exhibiting an average number of drugs, e.g., PBD dimers, per antibody.
  • such compositions can comprise a plurality of ADCs exhibiting an average of 1 to 8 PBD dimers, e.g., from 2 to 6 or 1 to 3 PBD dimers, bound to cysteines, and/or from 1 to 80, 1 to 40, 1 to 20, 1 to 10, 1 to 8, 2 to 6, 1 to 4, or 1 to 3 PBD dimers bound to lysines.
  • an average number of drugs per antibody in a collection or plurality of ADCs is described in terms of a ratio, drug per antibody ratio ("DAR").
  • a composition of ADCs such as PBD dimer conjugates ⁇ e.g., KIT-PBD dimer ADCs, such as KIT-PBDl or KIT-PBD2), described herein has a DAR of about 1 to 5, or about 1 to 4, or about 1 to 3, or about 1.5 to 3 or 4.
  • the average number of drugs per antibody, or DAR, in preparations of ADC from conjugation reactions may be characterized by conventional means such as UV, reverse phase HPLC, HIC, mass spectroscopy, ELISA assay, and electrophoresis.
  • the quantitative distribution of ADCs in terms of drug loading may also be determined.
  • ELISA the average drug loading value in a particular preparation of ADC may be determined (see, e.g. , Hamblett et al (2004) Clin. Cancer Res. 10:7063-7070; Sanderson et al (2005) Clin. Cancer Res. 11 :843-852).
  • separation, purification, and characterization of homogeneous ADC with a certain drug loading value may be achieved via, for example, reverse phase HPLC or electrophoresis.
  • drug loading may be limited by the number of attachment sites on an antibody or antigen-binding fragment thereof.
  • an antibody may have only one or several cysteine thiol groups, or may have only one or several sufficiently reactive thiol groups through which a linker may be attached.
  • fewer than the theoretical maximum of drug moieties are conjugated to an antibody or an antigen-binding fragment thereof during a conjugation reaction.
  • many cysteine thiol residues in antibodies for conjugation exist as disulfide bridges and must be reduced with a reducing agent such as dithiothreitol (DTT) or TCEP, under partial or total reducing conditions.
  • DTT dithiothreitol
  • TCEP reducing agent
  • the loading (drug/antibody ratio, or DAR) of an ADC may be controlled in several different manners, including, but not limited to: (i) limiting the molar excess of drug-linker intermediate or linker reagent relative to antibody, (ii) limiting the conjugation reaction time or temperature, and (iii) partial or limiting reductive conditions for cysteine thiol modification.
  • certain antibodies have reducible interchain disulfides, e.g., cysteine bridges.
  • antibodies ⁇ e.g., anti-KIT antibodies may be made reactive for conjugation with linker reagents by treatment with a reducing agent such as DTT (dithiothreitol).
  • DTT dithiothreitol
  • Each cysteine bridge will thus form, theoretically, two reactive thiol nucleophiles.
  • Additional nucleophilic groups can be introduced into antibodies ⁇ e.g., anti-KIT antibodies), e.g., through the reaction of lysines with 2-iminothiolane (Traut's reagent) resulting in conversion of an amine into a thiol.
  • reactive thiol groups may be introduced into an antibody, e.g., anti-KIT antibody, (or fragment thereof) by engineering one, two, three, four, or more cysteine residues ⁇ e.g., preparing mutant antibodies comprising one or more non-native cysteine amino acid residues). See, e.g., US 7521541.
  • cysteine amino acids may be engineered at reactive sites in an antibody ⁇ e.g., anti-KIT antibody) and which do not form intrachain or intermolecular disulfide linkages (Junutula, et ah, 2008, Nature Biotech., 26(8):925-932; Dornan et al (2009) Blood 114(13):2721-2729; US 7521541; US 7723485; WO2009/052249).
  • the engineered cysteine thiols may react with linker reagents or the drug-linker reagents of the compounds provided herein which have thiol-reactive, electrophilic groups such as maleimide or alpha-halo amides to form ADC with cysteine engineered antibodies and the PBD drug moieties.
  • the location of the drug moiety can thus be designed, controlled, and known.
  • the drug loading can be controlled since the engineered cysteine thiol groups typically react with thiol-reactive linker reagents or drug-linker reagents in high yield.
  • Engineering an IgG antibody to introduce a cysteine amino acid by substitution at a single site on the heavy or light chain gives two new cysteines on the symmetrical antibody.
  • nucleophilic or electrophilic group of an antibody reacts with a drug linker intermediate, or linker reagent followed by drug moiety reagent
  • the resulting product is a mixture of ADC compounds with a distribution of drug moieties attached to an antibody, e.g., 1, 2, 3, etc.
  • Liquid chromatography methods such as polymeric reverse phase (“PLRP") and hydrophobic interaction (“HIC”) may separate compounds in the mixture by drug loading value.
  • Preparations of ADC with a single drug loading value may be isolated. For example, in particular aspects, a drug loading value near 2 can be achieved with near homogeneity of the ADC.
  • ADC such as PBD dimer conjugate
  • compositions provided herein include mixtures of ADC compounds where the antibody (e.g. , anti-KIT antibody) has one or more PBD drug moieties and where the drug moieties may be attached to the antibody at various amino acid residues.
  • the average number of dimer PBD groups per antibody (e.g., anti-KIT antibody) or antigen-binding fragment thereof is in the range 1 to 20. In some embodiments, the range is selected from 1 to 8, 1 to 4, 1 to 3, 2 to 8, 2 to 6, 2 to 4, and 4 to 8.
  • isotopic variations of the PBD dimers and PBD dimer conjugates provided herein.
  • An isotopic variation of a PBD dimer or PBD dimer conjugate is one in which at least one atom is replaced by an atom having the same atomic number but an atomic mass different from the atomic mass usually found in nature.
  • isotopes that can be incorporated into the PBD dimers or PBD dimer conjugates provided herein include, but are not limited to, isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorus, sulphur, fluorine and chlorine such as 2 H, 3 H, 13 C, 14 C, 15 N, 17 0, 18 0, 31 P, 32 P, 35 S, 18 F and 36 C1, respectively.
  • certain isotopic variations of the PBD dimers or PBD dimer conjugates provided herein are those in which a radioactive isotope such as 3 H or 14 C is incorporated. These isotopic variations of PBD dimers or PBD dimer conjugates are useful in drug and/or substrate tissue distribution studies.
  • the PDB compounds or conjugates are tritiated, i.e., 3 H, or incorporate carbon- 14, i.e., 14 C, isotopes.
  • substitution of a PDB dimer compound or PBD dimer conjugate with isotopes may afford certain therapeutic advantages resulting from greater metabolic stability, for example, increased in vivo half-life or reduced dosage
  • the isotopic variations of the PBD dimer compounds or PBD dimer conjugates provided herein can generally be prepared by conventional procedures such as by the general methods or by the preparations described in the Examples hereafter, using appropriate isotopic variations of suitable reagents.
  • a pharmaceutically acceptable salt is a salt prepared from a pharmaceutically acceptable non-toxic acid or base including an inorganic acid and base and an organic acid and base.
  • Suitable non-toxic acids include, but are not limited to, inorganic and organic acids such as acetic, alginic, anthranilic, benzenesulfonic, benzoic, camphorsulfonic, citric, ethenesulfonic, formic, fumaric, furoic, galacturonic, gluconic, glucuronic, glutamic, glycolic, hydrobromic, hydrochloric, isethionic, lactic, maleic, malic, mandelic, methanesulfonic, mucic, nitric, pamoic, pantothenic, phenylacetic, phosphoric, propionic, salicylic, stearic, succinic, sulfanilic, sulfuric, tartaric acid, and p-toluenesulfonic acid.
  • Specific non-toxic acids include hydrochloric, hydrobromic, phosphoric, sulfuric, and
  • Tautomers of a PBD dimer or PBD dimer conjugate are isomeric forms of a PBD dimer or PBD dimer conjugate that are in equilibrium with each other.
  • concentrations of the isomeric forms will depend on the environment the compound is found in and may be different depending upon, for example, whether the compound is a solid or is in an organic or aqueous solution.
  • pyrazoles may exhibit the following isomeric forms, which are referred to as tautomers of each other: [00116] Also disclosed herein are all stereoisomers of ADCs, e.g., PBD dimer conjugates, provided herein.
  • a stereoisomer or a stereoisomeric form of a PBD dimer or PBD dimer conjugate is a stereoisomer of a PBD dimer or PBD dimer conjugate that is substantially free of other stereoisomers of that compound or conjugate.
  • a stereoisomerically pure PBD dimer having one chiral center will be substantially free of the opposite enantiomer of the compound.
  • a stereoisomerically pure PBD dimer or PBD dimer conjugate having two or more chiral centers will be substantially free of other diastereomers of the compound or conjugate.
  • a typical stereoisomerically pure compound or conjugate comprises greater than about 80% by weight of one stereoisomer of the compound or conjugate and less than about 20%> by weight of other stereoisomers of the compound or conjugate, greater than about 90%> by weight of one stereoisomer of the compound or conjugate and less than about 10%) by weight of the other stereoisomers of the compound or conjugate, greater than about 95% by weight of one stereoisomer of the compound or conjugate and less than about 5% by weight of the other stereoisomers of the compound or conjugate, or greater than about 97% by weight of one stereoisomer of the compound and less than about 3% by weight of the other stereoisomers of the compound or conjugate.
  • the PBD dimers or PBD dimer conjugates provided herein have chiral centers and can occur as racemates, individual enantiomers or diastereomers, and mixtures thereof. All such isomeric forms are included within the embodiments disclosed herein, including mixtures thereof.
  • the use of stereoisomerically pure forms of such PBD dimers or PBD dimer conjugates, as well as the use of mixtures of those forms, are encompassed by the embodiments disclosed herein.
  • mixtures comprising equal or unequal amounts of the enantiomers of a particular PBD dimer or PBD dimer conjugate may be used in methods and compositions disclosed herein.
  • isomers may be asymmetrically synthesized or resolved using standard techniques such as chiral columns or chiral resolving agents. See, e.g., Jacques, J., et al., Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981);
  • an "alkyl” group is a saturated straight chain or branched non-cyclic hydrocarbon having, for example, from 1 to 12 carbon atoms, 1 to 9 carbon atoms, 1 to 6 carbon atoms, 1 to 4 carbon atoms, or 2 to 6 carbon atoms.
  • alkyl groups include -methyl, -ethyl, -n-propyl, -n-butyl, -n-pentyl and -n-hexyl; while branched alkyls include -isopropyl, - sec-butyl, -z ' so-butyl, -tert-butyl, -z ' so-pentyl, 2-methylpentyl, 3-methylpentyl, 4-methylpentyl, 2,3-dimethylbutyl and the like.
  • alkenyl is a partially unsaturated straight chain or branched non-cyclic hydrocarbon having, for example, from 2 to 6 carbon atoms, 3 to 4 carbon atoms, or 3 carbon atoms.
  • Representative alkenyl groups include propenyl and the like.
  • an "alkynyl” group is a partially unsaturated straight chain or branched non-cyclic hydrocarbon having, for example, from 2 to 6 carbon atoms, 3 to 6 carbon atoms, or 3 carbon atoms.
  • Representative alkynyl groups include propynyl, butynyl and the like.
  • an "cycloalkyl” group is a saturated cyclic alkyl group of from 3 to 6 carbon atoms having a single cyclic ring. In some embodiments, the cycloalkyl group has 3 ring members. Such cycloalkyl groups include, by way of example, single ring structures such as cyclopropyl, cyclobutyl, and cyclopentyl.
  • Scheme 1 In one embodiment, compounds of Formula V can be synthesized by the route depicted in Scheme 1. Amide coupling of acids of Formula II with a pyrrolidine of Formula I through reactive acid derivatives such as an acid chloride formed via reaction with oxalyl chloride, affords bis-amides of Formula III. Bis-ketones of Formula IV are produced via oxidation, such as TEMPO catalyzed oxidation, of bis-alcohols of Formula III.
  • peptide-PBD dimers of Formula XIV can be prepared as shown in Scheme 2.
  • Bis-enol-triflates of Formula V can be substituted with R groups via metal mediated coupling, such as a palladium mediated cross-coupling with a boronic acid derivative in the presence of a base, such as potassium phosphate to form compounds of Formula VI.
  • metal mediated coupling such as a palladium mediated cross-coupling with a boronic acid derivative in the presence of a base, such as potassium phosphate to form compounds of Formula VI.
  • Reduction of bis-esters of Formula VI with a metal hydride such as lithium borohydride followed by acylation of the resulting bis-alcohols of Formula VII with an acylating agent such as acetyl chloride in the presence of a base such as triethylamine provides bis-acetates of Formula VIII.
  • Scheme 3 In one embodiment, compounds of Formula XX can be synthesized by the route depicted in Scheme 3. Amide coupling of acids of Formula II with a pyrrolidine of Formula I through a reactive acid derivative such as an acid chloride formed via reaction with oxalyl chloride, affords bis-amides of Formula III. Catalytic reduction of the nitro moiety, such as with hydrazine and a catalyst such as Raney Nickel, and cyclization produces PBD dimer intermediates of Formula XV.
  • a reactive acid derivative such as an acid chloride formed via reaction with oxalyl chloride
  • Bis-alcohols of Formula XVIII are produced via selective alcohol deprotection of intermediates of Formula XVII, for example, via fluoride mediated removal of a silyl protecting group, such as TBAF deprotection of a TBS moiety.
  • peptide-PBD dimers of Formula XXV can be prepared as shown in Scheme 4.
  • Bis-enol-triflates of Formula XX can be mono-substituted with aniline via metal mediated coupling, such as palladium mediated cross coupling with an aniline boronic acid derivative in the presence of a base, such as sodium carbonate to form compounds of Formula XXI.
  • Mono-triflates of Formula XXI can be substituted via coupling mediated by a metal, such as palladium, with a boronic acid derivative in the presence of a base, such as potassium phosphate tribasic, and optional additives such as silver(I)oxide and triphenylarsine, to form compounds of Formula XXII.
  • a metal such as palladium
  • a boronic acid derivative in the presence of a base, such as potassium phosphate tribasic
  • optional additives such as silver(I)oxide and triphenylarsine
  • peptide-PBD dimers of Formula XXV can be prepared as shown in Scheme 5.
  • Bis-enol-triflates of Formula XX can be mono-substituted with an aniline/protected peptide moiety, such as /?ara-aminoPh-Ala-Val-Fmoc, via metal mediated coupling, such as palladium mediated cross coupling with an aniline boronic acid derivative in the presence of a base, such as sodium carbonate to form compounds of Formula XXVI.
  • Mono- triflates of Formula XXVI can be substituted via coupling mediated by a metal, such as palladium, with a boronic acid derivative in the presence of a base, such as potassium phosphate tribasic, and optional additives such as silver(I)oxide and triphenylarsine, to form compounds of Formula XXVII.
  • a metal such as palladium
  • a boronic acid derivative in the presence of a base, such as potassium phosphate tribasic
  • optional additives such as silver(I)oxide and triphenylarsine
  • LiTEBH LiTEBH
  • subsequent peptide deprotection such as basic removal of a carbamate, such as removal of an Fmoc group with piperidine, affords the peptide-PBD dimers of Formula XXV.
  • Scheme 6 In one embodiment, compounds of Formula XXX and XXXI can be synthesized via the reaction depicted in Scheme 6. Peptide coupling, such as through acid activation via EDCI, of compounds of Formula XIV or XXV with acids of Formula XXIX (an acid attached to an electrophile E, such as a maleimide or an alkyl iodide, through a linker L', such as an amide containing alkyl chain or amide containing polyethyleneoxide chain), affords the final products of Formula XXX or XXI, respectively.
  • Peptide coupling such as through acid activation via EDCI
  • acids of Formula XXIX an acid attached to an electrophile E, such as a maleimide or an alkyl iodide
  • L' such as an amide containing alkyl chain or amide containing polyethyleneoxide chain
  • Antibody drug conjugates of Formula XXX or XXXI may be prepared by several routes, employing organic chemistry reactions, conditions, and reagents known to those skilled in the art, including reaction of a nucleophilic group (Nu) of an antibody (Ab) with a drug-linker reagent of Formula XXX or Formula XXXI.
  • antibody drug conjugates of Formula XXX or XXXI may be prepared by several routes, employing organic chemistry reactions, conditions, and reagents known to those skilled in the art, including reaction of two or more nucleophilic groups (Nu) of the same antibody (Ab) with two or more drug-linker reagents of Formula XXX or Formula XXI.
  • Nucleophilic groups on antibodies include, but are not limited to side chain thiol groups, e.g., cysteine.
  • Thiol groups are nucleophilic and capable of reacting to form covalent bonds with electrophilic groups on linker moieties such as a maleimide or an alkyl iodide.
  • Certain antibodies have reducible interchain disulfides, i.e., cysteine bridges.
  • Antibodies may be made reactive for conjugation with linker reagents by treatment with a reducing agent such as DTT (Cleland's reagent, dithiothreitol) or TCEP (tris(2-carboxyethyl)phosphine hydrochloride; Getz et al (1999) Anal. Biochem. Vol 273:73-80; Soltec Ventures, Beverly, MA).
  • a reducing agent such as DTT (Cleland's reagent, dithiothreitol) or TCEP (tris(2-carboxyethyl)phosphine hydrochloride; Getz et al (1999) Anal. Biochem. Vol 273:73-80; Soltec Ventures, Beverly, MA).
  • a reducing agent such as DTT (Cleland's reagent, dithiothreitol) or TCEP (tris(2-carboxyethyl)phosphine hydrochloride; Get
  • anti-KIT antibodies or antigen-binding fragments thereof which specifically bind to a D4 of human KIT and are conjugated to one or more drug moieties, such as one or more PBDs, e.g., PBD dimers, forming ADCs, such as PBD dimer conjugates.
  • PBDs e.g., PBD dimers
  • ADCs such as PBD dimer conjugates
  • target cells expressing KIT target cells expressing KIT
  • antibody and “immunoglobulin” and “Ig” are terms of art and can be used interchangeably herein and refer to a molecule with an antigen binding site that immunospecifically binds an antigen.
  • an "antigen" is a moiety or molecule that contains an epitope, and, as such, also is specifically bound by antibody.
  • the antigen, to which an antibody described herein binds is KIT ⁇ e.g., human KIT), or a fragment thereof, for example, an extracellular domain of KIT ⁇ e.g., human KIT) or a D4 region of KIT ⁇ e.g., human KIT).
  • an epitope is a term in the art and refers to a localized region of an antigen to which an antibody can specifically bind.
  • a region or a polypeptide contributing to an epitope can be contiguous amino acids of the polypeptide or an epitope can come together from two or more non-contiguous regions of the polypeptide.
  • the terms "antigen binding domain,” “antigen binding region,” “antigen binding fragment,” and similar terms refer to a portion of an antibody molecule which comprises the amino acid residues that interact with an antigen and confer on the antibody molecule its specificity for the antigen ⁇ e.g., the complementarity determining regions (CDR)).
  • the antigen binding region can be derived from any animal species, such as rodents ⁇ e.g., mouse, rat or hamster) and humans.
  • the CDRs of an antibody molecule can be determined by any method well known to one of skill in the art. In particular, the CDRs can be determined according to the Kabat numbering system ⁇ see Kabat et al.
  • the CDRs of an antibody can be determined according to (i) the Chothia numbering scheme, which will be referred to herein as the "Chothia CDRs" (see, e.g., Chothia and Lesk, 1987, J. Mol. Biol, 196:901-917; Al-Lazikani et al, 1997, J. Mol. Biol, 273:927-948; and U.S. Patent No.
  • a “conformational epitope” or “non-linear epitope” or “discontinuous epitope” refers to one comprised of at least two amino acids which are not consecutive amino acids in a single protein chain.
  • a conformational epitope can be comprised of two or more amino acids which are separated by a stretch of intervening amino acids but which are close enough to be recognized by an antibody (e.g., an anti-KIT antibody) described herein as a single epitope.
  • amino acids which are separated by intervening amino acids on a single protein chain, or amino acids which exist on separate protein chains can be brought into proximity due to the conformational shape of a protein structure or complex to become a conformational epitope which can be bound by an anti-KIT antibody described herein.
  • a linear epitope bound by an anti- KIT antibody described herein may or may not be dependent on the secondary, tertiary, or quaternary structure of the KIT receptor.
  • an anti-KIT antibody described herein binds to a group of amino acids regardless of whether they are folded in a natural three dimensional protein structure.
  • an anti-KIT antibody described herein does not recognize the individual amino acid residues making up the epitope, and require a particular conformation (bend, twist, turn or fold) in order to recognize and bind the epitope.
  • the term “constant region” or “constant domain” refers to an antibody portion, e.g., a carboxyl terminal portion of a light and/or heavy chain which is not directly involved in binding of an antibody to antigen but which exhibits various effector functions, such as interaction with the Fc receptor.
  • the terms refer to a portion of an immunoglobulin molecule having a generally more conserved amino acid sequence relative to an immunoglobulin variable domain.
  • the term "heavy chain” when used in reference to an antibody refers to any distinct types, e.g., alpha (a), delta ( ⁇ ), epsilon ( ⁇ ), gamma ( ⁇ ) and mu ( ⁇ ), based on the amino acid sequence of the constant domain, which give rise to IgA, IgD, IgE, IgG and IgM classes of antibodies, respectively, including subclasses of IgG, e.g., IgGi, IgG 2 , IgG 3 and IgG 4 .
  • the heavy chain is a human heavy chain.
  • the terms “immunospecifically binds,” “immunospecifically recognizes,” “specifically binds,” and “specifically recognizes” are analogous terms in the context of antibodies and refer to molecules that bind to an antigen (e.g., epitope or immune complex) as such binding is understood by one skilled in the art.
  • a molecule that specifically binds to an antigen may bind to other peptides or polypeptides, generally with lower affinity as determined by, e.g., immunoassays, BiacoreTM, KinExA 3000 instrument (Sapidyne Instruments, Boise, ID), or other assays known in the art.
  • molecules that immunospecifically bind to an antigen bind to the antigen with a K a that is at least 2 logs, 2.5 logs, 3 logs, 4 logs or greater than the Ka when the molecules bind to another antigen.
  • molecules that immunospecifically bind to an antigen do not cross react with other proteins.
  • molecules that immunospecifically bind to an antigen do not cross react with other non-KIT proteins.
  • an “isolated” or “purified” antibody is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the antibody is derived, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • Kabat numbering and like terms are recognized in the art and refer to a system of numbering amino acid residues in the heavy and light chain variable regions of an antibody, or an antigen binding portion thereof (Kabat et al. (1971) Ann. NY Acad. Sci. 190:382- 391 and, Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242).
  • CDRs within an antibody heavy chain molecule are typically present at amino acid positions 31 to 35 (“CDR1"), amino acid positions 50 to 65 (“CDR2”), and amino acid positions 95 to 102 (“CDR3").
  • CDRs within an antibody light chain molecule are typically present at amino acid positions 24 to 34 (CDR1), amino acid positions 50 to 56 (CDR2), and amino acid positions 89 to 97 (CDR3).
  • the term "light chain” when used in reference to an antibody refers to any distinct types, e.g., kappa ( ⁇ ) of lambda ( ⁇ ) based on the amino acid sequence of the constant domains. Light chain amino acid sequences are well known in the art. In specific embodiments, the light chain is a human light chain.
  • the term "monoclonal antibody” refers to an antibody obtained from a population of homogenous or substantially homogeneous antibodies. The term “monoclonal” is not limited to any particular method for making the antibody. Generally, a population of monoclonal antibodies can be generated by cells, a population of cells, or a cell line.
  • a "monoclonal antibody,” as used herein, is an antibody produced by a single hybridoma or other cell (e.g. , host cell producing a recombinant antibody), wherein the antibody immunospecifically binds to a KIT epitope (e.g., an epitope of a D4 of human KIT) as determined, e.g., by ELISA or other antigen-binding or competitive binding assay known in the art or in the Examples provided herein.
  • a KIT epitope e.g., an epitope of a D4 of human KIT
  • Monoclonal antibodies described herein can, for example, be made by the hybridoma method as described in Kohler et ah; Nature, 256:495 (1975) or can be isolated from phage libraries using the techniques as described herein, for example. Other methods for the preparation of clonal cell lines and of monoclonal antibodies expressed thereby are well known in the art (see, for example, Chapter 11 in: Short Protocols in Molecular Biology, (2002) 5th Ed., Ausubel et ah, eds., John Wiley and Sons, New York).
  • polyclonal antibodies refers to an antibody population that includes a variety of different antibodies directed to the same and to different epitopes within an antigen or antigens. Methods for producing polyclonal antibodies are known in the art (See, e.g., see, for example, Chapter 11 in: Short Protocols in Molecular Biology, (2002) 5th Ed., Ausubel et ah, eds., John Wiley and Sons, New York).
  • variable region refers to a portion of an antibody, generally, a portion of a light or heavy chain, typically about the amino-terminal 110 to 120 amino acids in the mature heavy chain and about 90 to 100 amino acids in the mature light chain, which differ extensively in sequence among antibodies and are used in the binding and specificity of a particular antibody for its particular antigen.
  • the variability in sequence is concentrated in those regions called complementarity determining regions (CDRs) while the more highly conserved regions in the variable domain are called framework regions (FR).
  • CDRs complementarity determining regions
  • FR framework regions
  • the CDRs of an antibody can be determined according to (i) the Chothia numbering scheme, which will be referred to herein as the "Chothia CDRs" (see, e.g., Chothia and Lesk, 1987, J. Mol. Biol, 196:901-917; Al-Lazikani et al, 1997, J. Mol. Biol, 273:927-948; Chothia et al, 1992, J. Mol. Biol, 227:799-817;
  • variable region is a human variable region.
  • variable region comprises rodent or murine CDRs and human framework regions (FRs).
  • variable region is a primate (e.g., non-human primate) variable region.
  • variable region comprises rodent or murine CDRs and primate (e.g., non-human primate) framework regions (FRs).
  • primate e.g., non-human primate
  • FRs framework regions
  • a variable region described herein is obtained from assembling two or more fragments of human sequences into a composite human sequence.
  • antibodies e.g., human, composite human, or humanized antibodies
  • an ADC or PBC conjugate wherein the antibodies or antigen-binding fragments thereof specifically binds to a D4 region of human KIT and comprises:
  • VH CDRs of a VH domain comprising the amino acid sequence of SEQ ID NO: 31 (QVQLKQSGAELVRPGASVKLSCKASGYTFTDYYINWVKQRPGQGLEWIARIYPGS GNTYYNEKFKGKATLTAEKSSSTAYMQLSSLTSEDSAVYFCARGVYYFDYWGQG TTLTVSS) or SEQ ID NO: 69
  • VL CDRs of a VL domain comprising the amino acid sequence of SEQ ID NO: 32 (DIVMTQSQKFMSTSVGDRVSVTCKASQNVRTNVAWYQQKPGQSPKALIYSASYR YSGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYNSYPRTFGGGTKLEIKR).
  • an antibody e.g., a human, composite human, or humanized antibody
  • an ADC or PBC conjugate which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT)
  • a KIT polypeptide e.g., the D4 region of human KIT
  • VH CDRs SEQ ID NOs: 16-18
  • VL CDRs SEQ ID NOs: 19-21
  • an antibody e.g., a human, composite human, or humanized antibody
  • an ADC or PBC conjugate which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT)
  • a KIT polypeptide e.g., the D4 region of human KIT
  • Table 2 e.g., set 1 or set 2.
  • an antibody e.g., a human, composite human, or humanized antibody
  • an ADC or PBC conjugate which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT)
  • a KIT polypeptide e.g., the D4 region of human KIT
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the CDRs of an antibody described herein is determined according to the method of Chothia, for example Chothia and Lesk, 1987, J. Mol. Biol, 196:901-917, which will be referred to herein as the "Chothia CDRs" (see also, e.g., Al-Lazikani et al., 1997, J. Mol. Biol, 273:927-948; Chothia et al, 1992, J. Mol. Biol, 227:799-817; Tramontano A et al, 1990, J. Mol. Biol. 215(1): 175-82; and U.S. Patent No. 7,709,226).
  • Chothia CDRs within an antibody heavy chain molecule are typically present at amino acid positions 26 to 32 (“CDR1"), amino acid positions 53 to 55 (“CDR2”), and amino acid positions 96 to 101 (“CDR3").
  • CDR1 amino acid positions 26 to 32
  • CDR2 amino acid positions 53 to 55
  • CDR3 amino acid positions 96 to 101
  • Chothia CDRs within an antibody light chain molecule are typically present at amino acid positions 26 to 33 (CDR1), amino acid positions 50 to 52 (CDR2), and amino acid positions 91 to 96 (CDR3).
  • the position of a CDR along the VH and/or VL region of an antibody described herein may vary by one, two, three or four amino acid positions so long as immunospecific binding to KIT (e.g., the D4 region of human KIT) is maintained (e.g., substantially maintained, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%).
  • KIT e.g., the D4 region of human KIT
  • the position defining a CDR of an antibody described herein may vary by shifting the N-terminal and/or C-terminal boundary of the CDR by one, two, three, or four, amino acids, relative to the CDR position depicted in Figures 2A-2I, so long as immunospecific binding to KIT (e.g., the D4 region) is maintained (e.g., substantially maintained, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%).
  • KIT e.g., the D4 region
  • VH domains e.g., HI, H2, H3, H4 and H5 comprising SEQ ID NOs: 2-6, respectively
  • VL domains e.g., LI, L2, L3, and L4 comprising SEQ ID NOs: 7-10, respectively
  • an antibody e.g., a human, composite human, or humanized antibody
  • ADC or PBC conjugate described herein which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT).
  • antibodies which specifically binds to a D4 region of human KIT, of an ADC such as a PBD dimer conjugate described herein comprising such VH and VL domains, as set forth, for example, in Table 4 (i.e., antibodies Huml-Hum20).
  • these antibodies of an ADC such as a PBD dimer conjugate describe herein comprise VH CDRsl-3 and VL CDRs 1-3 comprising SEQ ID NOs: 16-18 and 19-21, respectively.
  • an antibody described herein which immunospecifically binds to a D4 region of a KIT polypeptide may be described by its VL chain region (e.g., any one of SEQ ID NOs: 7-10) or VH chain region (e.g., any one of SEQ ID NOs: 2-6), or by its 3 VL CDRs or its 3 VH CDRs. See, for example, Rader et ⁇ , 1998, Proc. Natl. Acad. Sci.
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody described herein, or an antigen-binding fragment thereof, comprising a variable light (VL) chain region comprising an amino acid sequence described herein, for example, any one of SEQ ID NOs: 7-10 (e.g., see Figures 2A-2K) or SEQ ID NO: 12.
  • VL variable light
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody described herein, or an antigen-binding fragment thereof, comprising a variable heavy (VH) chain region comprising an amino acid sequence described herein, for example any one of SEQ ID NOs: 2-6 (e.g., see Figures 2A-2K) or SEQ ID NO: 1 1.
  • VH variable heavy chain region comprising an amino acid sequence described herein, for example any one of SEQ ID NOs: 2-6 (e.g., see Figures 2A-2K) or SEQ ID NO: 1 1.
  • an ADC such as a PBD dimer conjugate provided herein comprising an antibody that immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT) and comprises (i) the VH domain HI (SEQ ID NO: 2), H2 (SEQ ID NO: 3), H3 (SEQ ID NO: 4), H4 (SEQ ID NO: 5), or H5 (SEQ ID NO: 6) and/or (ii) the VL domain LI (SEQ ID NO: 7), L2 (SEQ ID NO: 8), L3 (SEQ ID NO: 9), or L4 (SEQ ID NO: 10).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • a KIT polypeptide e.g., the D4 region of human KIT
  • a KIT polypeptide e.g., the D4 region of human KIT
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, or an antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT and comprises a VH domain and/or a VL domain of any one of antibodies Hum4, Hum8, HumlO, or Huml7.
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which immunospecifically binds to a D4 region of human KIT and comprises VH domain HI (SEQ ID NO: 2) and VL domain LI (SEQ ID NO: 7).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain HI (SEQ ID NO: 2) and VL domain L2 (SEQ ID NO: 8).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain HI (SEQ ID NO: 2) and VL domain L3 (SEQ ID NO: 9).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain HI (SEQ ID NO: 2) and VL domain L4 (SEQ ID NO: 10).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H2 (SEQ ID NO: 3) and VL domain LI (SEQ ID NO: 7).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H2 (SEQ ID NO: 3) and VL domain L2 (SEQ ID NO: 8).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H2 (SEQ ID NO: 3) and VL domain L3 (SEQ ID NO: 9).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H2 (SEQ ID NO: 3) and VL domain L4 (SEQ ID NO: 10).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H3 (SEQ ID NO: 4) and VL domain LI (SEQ ID NO: 7).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H3 (SEQ ID NO: 4) and VL domain L2 (SEQ ID NO: 8).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H3 (SEQ ID NO: 4) and VL domain L3 (SEQ ID NO: 9).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H3 (SEQ ID NO: 4) and VL domain L4 (SEQ ID NO: 10).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H4 (SEQ ID NO: 5) and VL domain LI (SEQ ID NO: 7).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H4 (SEQ ID NO: 5) and VL domain L2 (SEQ ID NO: 8).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H4 (SEQ ID NO: 5) and VL domain L3 (SEQ ID NO: 9).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H4 (SEQ ID NO: 5) and VL domain L4 (SEQ ID NO: 10).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H5 (SEQ ID NO: 6) and VL domain LI (SEQ ID NO: 7).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H5 (SEQ ID NO: 6) and VL domain L2 (SEQ ID NO: 8).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H5 (SEQ ID NO: 6) and VL domain L3 (SEQ ID NO: 9).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H5 (SEQ ID NO: 6) and VL domain L4 (SEQ ID NO: 10).
  • an anti-KIT antibody, or an antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein is non-immunogenic in a human.
  • a non-immunogenic amino acid sequence is devoid of epitopes identified to be binders to human MHC class II, e.g., epitopes that are non-human germline binders to human MHC class II.
  • amino acid sequences substantially devoid of epitopes identified to be binders to human MHC class II e.g. , epitopes that are non-human germline binders to human MHC class II.
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody described herein which specifically binds to a D4 region of human KIT, and comprises a VH domain and a VL domain that are not
  • immunogenic e.g., not immunogenic in a human
  • in vitro assay described in the art, see, e.g., Wang et al, 2008, PLoS Computational Biology, 2008, 4(4):el000048; and Arnold et al, 2002, J. Immunol, 169:739-749.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), and comprises a VH domain that has at least 93% sequence identity to HI (SEQ ID NO: 2).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which immunospecifically binds to a KIT polypeptide (e.g.
  • the D4 region of human KIT comprising a VH domain that has at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to HI (SEQ ID NO: 2).
  • the VH domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VH domain that has at least 92% sequence identity to H2 (SEQ ID NO: 3).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an antibody which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises a VH domain that has at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to H2 (SEQ ID NO: 3).
  • the VH domain is non-immunogenic (e.g.
  • such antibody, or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VH domain that has at least 90% sequence identity to H3 (SEQ ID NO: 4).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VH domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to H3 (SEQ ID NO: 4).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VH domain is non-immunogenic (e.g., non- immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VH domain that has at least 87% sequence identity to H4 (SEQ ID NO: 5).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide e.g.
  • the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein comprises a VH domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to H4 (SEQ ID NO: 5).
  • the VH domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VH domain that has at least 86% sequence identity to H5 (SEQ ID NO: 6).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide e.g.
  • the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein comprises a VH domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to H5 (SEQ ID NO: 6) .
  • the VH domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VL domain that has at least 90% sequence identity to LI (SEQ ID NO: 7).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide e.g.
  • the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein comprises a VL domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to LI (SEQ ID NO:
  • the VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21 , respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VL domain that has at least 88% sequence identity to L2 (SEQ ID NO: 8).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an antibody which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein, comprises a VL domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to L2 (SEQ ID NO: 8).
  • the VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof comprises a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21 , respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VL domain that has at least 87% sequence identity to L3 (SEQ ID NO: 9).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide e.g.
  • the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein comprises a VL domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to L3 (SEQ ID NO:
  • the VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21 , respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VL domain that has at least 84% sequence identity to L4 (SEQ ID NO: 10).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide e.g.
  • the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein comprises a VL domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to L4 (SEQ ID NO:
  • the VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21 , respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 93% or at least 95% sequence identity to HI (SEQ ID NO: 2); and (ii) a VL domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to LI (SEQ ID NO: 7).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 92% or at least 94% sequence identity to H2 (SEQ ID NO: 3); and (ii) a VL domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to LI (SEQ ID NO: 7).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to H3 (SEQ ID NO: 4); and (ii) a VL domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to LI (SEQ ID NO: 7).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to H4 (SEQ ID NO: 5); and (ii) a VL domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to LI (SEQ ID NO: 7).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 86%> or at least 88%> sequence identity to H5 (SEQ ID NO: 6); and (ii) a VL domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to LI (SEQ ID NO: 7).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 93% or at least 95% sequence identity to HI (SEQ ID NO: 2); and (ii) a VL domain comprising an amino acid sequence that has at least 88% or at least 90% sequence identity to L2 (SEQ ID NO: 8).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 92% or at least 94% sequence identity to H2 (SEQ ID NO: 3); and (ii) a VL domain comprising an amino acid sequence that has at least 88% or at least 90% sequence identity to L2 (SEQ ID NO: 8).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to H3 (SEQ ID NO: 4); and (ii) a VL domain comprising an amino acid sequence that has at least 88% or at least 90% sequence identity to L2 (SEQ ID NO: 8).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to H4 (SEQ ID NO: 5); and (ii) a VL domain comprising an amino acid sequence that has at least 88% or at least 90% sequence identity to L2 (SEQ ID NO: 8).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • VL and VH domains are non-immunogenic, for example as determined by the absence of epitopes that binds to MHC class II, e.g., non- human germline binders to MHC class II.
  • such antibody or antigen- binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 86%> or at least 88%> sequence identity to H5 (SEQ ID NO: 6); and (ii) a VL domain comprising an amino acid sequence that has at least 88% or at least 90% sequence identity to L2 (SEQ ID NO: 8).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 93% or at least 95% sequence identity to HI (SEQ ID NO: 2); and (ii) a VL domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to L3 (SEQ ID NO: 9).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 92% or at least 94% sequence identity to H2 (SEQ ID NO: 3); and (ii) a VL domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to L3 (SEQ ID NO: 9).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to H3 (SEQ ID NO: 4); and (ii) a VL domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to L3 (SEQ ID NO: 9).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to H4 (SEQ ID NO: 5); and (ii) a VL domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to L3 (SEQ ID NO: 9).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 86%> or at least 88%> sequence identity to H5 (SEQ ID NO: 6); and (ii) a VL domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to L3 (SEQ ID NO: 9).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 93% or at least 95% sequence identity to HI (SEQ ID NO: 2); and (ii) a VL domain comprising an amino acid sequence that has at least 84% or at least 86% sequence identity to L4 (SEQ ID NO: 10).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 92% or at least 94% sequence identity to H2 (SEQ ID NO: 3); and (ii) a VL domain comprising an amino acid sequence that has at least 84% or at least 86% sequence identity to L4 (SEQ ID NO: 10).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to H3 (SEQ ID NO: 4); and (ii) a VL domain comprising an amino acid sequence that has at least 84% or at least 86% sequence identity to L4 (SEQ ID NO: 10).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to H4 (SEQ ID NO: 5); and (ii) a VL domain comprising an amino acid sequence that has at least 84% or at least 86% sequence identity to L4 (SEQ ID NO: 10).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 86%> or at least 88%> sequence identity to H5 (SEQ ID NO: 6); and (ii) a VL domain comprising an amino acid sequence that has at least 84% or at least 86% sequence identity to L4 (SEQ ID NO: 10).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21, respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
  • the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence).
  • the amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the
  • the molecules are identical at that position.
  • the two sequences are the same length.
  • the percent identity is determined over the entire length of an amino acid sequence or nucleotide sequence.
  • Gapped BLAST can be utilized as described in Altschul et al, 1997, Nucleic Acids Res. 25:3389 3402.
  • PSI BLAST can be used to perform an iterated search which detects distant relationships between molecules ⁇ Id.).
  • a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CABIOS 4: 11 17. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package.
  • ALIGN program version 2.0
  • a PAM120 weight residue table a gap length penalty of 12, and a gap penalty of 4 can be used.
  • the percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide ⁇ e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising VH CDRl, VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and one, two, three or four framework regions of HI, H2, H3, H4 or H5 (see Table 5 A); and/or (ii) a VL domain comprising VL CDRl, VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21, respectively, and one, two, three or four framework regions of LI, L2, L3, or L4 (see Table 5B).
  • a VH domain comprising VH CDRl, VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18,
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl, VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework region FR1 of HI, H2, H3, H4 or H5 ⁇ e.g., Table 5 A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl, VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework region FR2 of HI, H2, H3, H4 or H5 ⁇ e.g., Table 5 A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework region FR3 of HI , H2, H3, H4 or H5 (e.g., Table 5 A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework region FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl and FR2 of HI , H2, H3, H4 or H5 (e.g., Table 5 A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl , FR2, and FR3 of HI , H2, H3, H4 or H5 (e.g., Table 5A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl , FR2, FR3, and FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5A).
  • an antibody which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl , FR2, FR3, and FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl and FR3 of HI , H2, H3, H4 or H5 (e.g., Table 5 A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl , FR3, and FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl and FR4 of HI , H2, H3, H4 or H5 (e.g. , Table 5 A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl , FR2, and FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5 A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FR2 and FR3 of HI , H2, H3, H4 or H5 (e.g., Table 5A).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g.
  • human, composite human, or humanized antibody or antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FR2, FR3, and FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5 A).
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FR3 and FR4 of HI , H2, H3, H4 or H5 (
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework region FRl of LI , L2, L3, or L4 (e.g., Table 5B).
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework region FR2 of LI , L2, L3, or L4 (e.g., Table 5B).
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework region FR3 of LI , L2, L3, or L4.
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen-binding fragment thereof which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework region FR4 of LI , L2, L3, or L4 (e.g., Table 5B).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g.
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g.
  • human, composite human, or humanized antibody or antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl , FR2, FR3, and FR4 of LI , L2, L3, or L4 (e.g., Table 5B).
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g.
  • human, composite human, or humanized antibody or antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl , FR3, and FR4 of LI , L2, L3, or L4 (e.g., Table 5B).
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl and FR4 of LI , L2, L3, or L4 (e.g
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl , FR2, and FR4 of LI , L2,
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g.
  • human, composite human, or humanized antibody or antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FR2, FR3, and FR4 of LI , L2, L3, or L4 (e.g., Table 5B).
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FR3 and FR4 of LI , L2, L3, or L4 (e.g
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FR1-FR4 of any one of VH domains HH257-HH281 (see Table 5C); and (ii) a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21 , respectively, and FR1-FR4 of any one of VL domains LL65- LL76 (see Table 5D).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising a combination of amino acid sequences set forth in Table 2 or 3, and framework regions FR1-FR4 of any one of VH domains H1-H5 (Table 5A) and HH257-HH281 (see Table 5C); and (ii) a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising a combination of amino acid sequences set forth in either Table 2 (set 1 or set 2) or 3 (AbM or Contact CDRs), respectively, and FR1-FR4 of any one of VL domains L1-L4 (Table 5B) and LL65
  • a KIT polypeptide e.g
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising VH CDRl, VH CDR2, and VH CDR3 comprising a combination of amino acid sequences set forth in Table 2 or 3, and corresponding framework regions FR1-FR4 comprising sequences flanking the VH CDRs for example, as depicted in any one of Figures 2A-2I; and (ii) a VL domain comprising VL CDRl, VL CDR2, and VL CDR3 comprising a combination of amino acid sequences set forth in in either Table 2 (set 1 or set 2) or 3 (AbM or Contact CDRs), respectively, and corresponding framework regions FR1-FR4 comprising sequences flanking the VL CDRs, for example as depicted in
  • Table 5C Framework region sequences of VH domains HH257 to HH281
  • Table 5D Framework region sequences of VL domains LL65 to LL76
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising the amino acid sequence: QVQLVQSGAEX HI KKPGASVKX HI SCKASGYTFTDYYINWVX HS QAPGKGLEWIARIYPG SGNTYYNEKFKGRX H4 TX H5 TAX H6 KSTSTAYMX H7 LSSLRSEDX H8 AVYFCARGVYYFDY WGQGTT VTVS S (SEQ ID NO: 1 1), wherein X M at Kabat position 1 1 , X H2 at Kabat position 20, X H3 at Kabat position 38, X H4 at Kabat position 67,
  • the VH and/or VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising the amino acid sequence:
  • DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILIYSASYRYS GVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK 5 YXK6CQQYNSYPRTFGGGTKVEIK (SEQ ID NO: 12), wherein ⁇ at Kabat position 10, ⁇ 2 at Kabat position 46, ⁇ 3 at Kabat position 63, XK4 at Kabat position 80, XKS at Kabat position 85, and ⁇ 6 at Kabat position 87 are selected from the combination of amino acids set forth in Table 6A.
  • the VH and/or VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
  • XRI at Kabat position 1 1 is an amino acid with an aliphatic side chain (e.g., hydrophobic side chain, or nonpolar side chain branched-chain amino acid (BCAA)), such as L or V.
  • XR 2 at Kabat position 20 is an amino acid with an aliphatic side chain (e.g. , hydrophobic side chain, or nonpolar side chain branched-chain amino acid (BCAA)), such as L or V.
  • XR3 at Kabat position 38 is an amino acid with a polar side chain (e.g., hydrophilic side chain, basic side chain, or charged side chain, e.g., positively charged side chain or negatively charged side chain), such as K or R.
  • XR 4 at Kabat position 67 is an amino acid with an aliphatic side chain (e.g., hydrophobic side chain, or nonpolar side chain branched-chain amino acid (BCAA)), such as V or A.
  • X H5 at Kabat position 69 is an amino acid with an aliphatic side chain (e.g., hydrophobic side chain, or nonpolar side chain branched-chain amino acid (BCAA)), such as L or I.
  • X H6 at Kabat position 72 is an amino acid with an acidic side chain, such as E or D.
  • XR7 at Kabat position 81 is an amino acid with an acidic side chain or its amide derivative, such as Q (uncharged/amide derivative of E) or E.
  • XRS at Kabat position 87 is an amino acid with an aliphatic hydroxyl group or a hydrophilic side chain, such as S or T.
  • XRI at Kabat position 1 1 is an aliphatic amino acid, such as a branched-chain amino acid (BCAA), for example V;
  • XH 2 at Kabat position 20 is an aliphatic amino acid, such as a branched-chain amino acid (BCAA), for example L;
  • XR3 at Kabat position 38 is an amino acid with a polar side chain, such as R;
  • XR 4 at Kabat position 67 is an amino acid with an aliphatic side chain, such as A;
  • XRS at Kabat position 69 is an amino acid with an aliphatic side chain, such as L;
  • XR6 at Kabat position 72 is an amino acid with a polar side chain, such as D;
  • XR7 at Kabat position 81 is an amino acid with an amide derivative of an acidic amino acid, such as Q; and
  • XRS at Kabat position 87 is an amino acid with an aliphatic hydroxyl side chain, such as T.
  • XRI at Kabat position 1 1 is an aliphatic amino acid, such as a branched-chain amino acid (BCAA), for example V
  • XH 2 at Kabat position 20 is an aliphatic amino acid, such as a branched-chain amino acid (BCAA), for example V
  • XR3 at Kabat position 38 is an amino acid with a polar side chain, such as R
  • XR 4 at Kabat position 67 is an amino acid with an aliphatic side chain, such as A
  • XRS at Kabat position 69 is an amino acid with an aliphatic side chain, such as I
  • XH 6 at Kabat position 72 is an amino acid with a polar side chain, such as D
  • XR7 at Kabat position 81 is an acidic amino acid, such as E
  • XHS at Kabat position 87 is an amino acid with an aliphatic hydroxyl side chain, such as T.
  • ⁇ at Kabat position 10 is an aromatic amino acid such as F or an amino acid with an aliphatic hydroxyl side chain such as S.
  • XK2 at Kabat position 46 is an amino acid with an aliphatic side chain (e.g., hydrophobic amino acid) such as A or an amino acid with an aliphatic hydroxyl side chain such as S.
  • ⁇ 3 at Kabat position 63 is an amino acid with an aliphatic hydroxyl side chain such as T or S.
  • XK 4 at Kabat position 80 is an amino acid with an aliphatic hydroxyl side chain such as S or an aromatic amino acid such as P.
  • X K5 at Kabat position 85 is an acidic amino acid such as D or an amino acid with an aliphatic hydroxyl side chain such as T.
  • ⁇ 6 at Kabat position 87 is an aromatic amino acid such as F or Y.
  • ⁇ at Kabat position 10 is an amino acid with an aliphatic hydroxyl side chain such as S; ⁇ 2 at Kabat position 46 is an amino acid with an aliphatic side chain (e.g. , hydrophobic amino acid) such as A; X at Kabat position 63 is an amino acid with an aliphatic hydroxyl side chain such as T; X K4 at Kabat position 80 is an aromatic amino acid such as P; XKS at Kabat position 85 is an acidic amino acid such as D; and ⁇ 6 at Kabat position 87 is an aromatic amino acid such as F.
  • S amino acid with an aliphatic hydroxyl side chain
  • ⁇ 2 at Kabat position 46 is an amino acid with an aliphatic side chain (e.g. , hydrophobic amino acid) such as A
  • X at Kabat position 63 is an amino acid with an aliphatic hydroxyl side chain such as T
  • X K4 at Kabat position 80 is an aromatic amino acid such as P
  • ⁇ at Kabat position 10 is an aromatic amino acid such as F
  • X K 2 at Kabat position 46 is an amino acid with an aliphatic side chain (e.g., hydrophobic amino acid) such as A
  • ⁇ 3 at Kabat position 63 is an amino acid with an aliphatic hydroxyl side chain such as T
  • ⁇ 4 at Kabat position 80 is an aliphatic hydroxyl side chain such as S
  • XKS at Kabat position 85 is an acidic amino acid such as D
  • ⁇ 6 at Kabat position 87 is an aromatic amino acid such as F.
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising the amino acid sequence:
  • X m at Kabat position 1 1 is an amino acid with an aliphatic side chain such as V
  • XH 2 at Kabat position 20 is an amino acid with an aliphatic side chain such as L
  • X H3 at Kabat position 38 is an amino acid with a polar side chain such as K
  • X H4 at Kabat position 67 is an amino acid with an aliphatic side chain such as A
  • XRS at Kabat position 69 is an amino acid with an aliphatic side chain such as L
  • XR6 at Kabat position 72 is an acidic amino acid such as D
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising the amino acid sequence:
  • X M at Kabat position 1 1 is an amino acid with an aliphatic side chain such as V
  • XH 2 at Kabat position 20 is an amino acid with an aliphatic side chain such as V
  • XH 3 at Kabat position 38 is an amino acid with a polar side chain such as R
  • XH 4 at Kabat position 67 is an amino acid with an aliphatic side chain such as A
  • X H5 at Kabat position 69 is an amino acid with an aliphatic side chain such as I
  • XH 6 at Kabat position 72 is an acidic amino acid such as D
  • DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILIYSASYRYS GVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK 5 YXK6CQYNSYPRTFGGGTKVEIK (SEQ ID NO: 12), wherein ⁇ at Kabat position 10 is an aromatic amino acid such as F, ⁇ 2 at Kabat position 46 is an amino acid with an aliphatic side chain such as A, ⁇ 3 at Kabat position 63 is an amino acid with an aliphatic hydroxyl side chain such as T, X K4 at Kabat position 80 is an amino acid with an aliphatic hydroxyl side chain such as S, XKS at Kabat position 85 is an acidic amino acid such as D, and ⁇ 6 at Kabat position 87 is an aromatic amino acid such as F.
  • ⁇ at Kabat position 10 is an aromatic amino acid such as F
  • ⁇ 2 at Kabat position 46 is an amino acid with
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively; and (ii) a VL domain comprising SEQ ID NO: 7, 8, 9, or 10.
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively; and (ii) a VL domain comprising the amino acid sequence
  • DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILIYSASYRYS GVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK 5 YXK6CQQYNSYPRTFGGGTKVEIK (SEQ ID NO: 12), wherein ⁇ at Kabat position 10, ⁇ 2 at Kabat position 46, ⁇ 3 at Kabat position 63, X K 4 at Kabat position 80, X K5 at Kabat position 85, and X K6 at Kabat position 87 are selected from the combination of amino acids set forth in Table 6A.
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising the amino acid sequence of SEQ ID NO: 2, 3, 4, or 5; and (ii) a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising the amino acid sequence:
  • the position (i.e., boundary) of a VL chain region described herein relative to the constant region may change by one, two, three, or four amino acid positions so long as immunospecific binding to KIT (e.g., the D4 region of human KIT) is maintained (e.g., substantially maintained, for example, at least 50%, at least 60%, at least 70%, at least 80%), at least 90%, at least 95%).
  • the position (i.e., boundary) of a VH chain region described herein relative to the constant region may change by one, two, three, or four amino acid positions so long as immunospecific binding to KIT (e.g. , the D4 region of human KIT) is maintained (e.g., substantially maintained, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%).
  • an ADC such as a PBD dimer conjugate comprising a moiety comprising VH CDRs and/or VL CDRs described herein, for example as set forth in Tables 1-3 and 10-15, wherein the VH CDRs and VL CDRs are arranged in a spatial orientation that confers specific binding to a D4 region of human KIT.
  • an ADC such as a PBD dimer conjugate comprising a moiety comprising VH CDRs comprising the amino acid sequences of SEQ ID NOs: 16-18 and VL CDRs comprising the amino acid sequences of SEQ ID NOs: 19-21, VH CDRs comprising the amino acid sequences of SEQ ID NOs: 56, 62 and 63 and VL CDRs comprising the amino acid sequences of SEQ ID NOs: 59-61, VH CDRs comprising the amino acid sequences of SEQ ID NOs: 70-72 and VL CDRs comprising the amino acid sequences of SEQ ID NOs: 66-68, wherein the VH CDRs and VL CDRs are arranged in a spatial orientation that confers specific binding to a D4 region of human KIT.
  • the moiety is an antibody or an antigen-binding fragment thereof.
  • the moiety is a protein, such as a fusion protein
  • an ADC such as a PBD dimer conjugate comprising a moiety comprising VH CDRs selected from Tables 13-15 and/or VL CDRs selected from Tables 10-12, wherein the VH CDRs and VL CDRs are arranged in a spatial orientation that confers specific binding to a D4 region of human KIT.
  • the moiety is an antibody or an antigen-binding fragment thereof.
  • the moiety is a protein, such as a fusion protein comprising an Fc region.
  • an ADC such as a PBD dimer conjugate comprising a moiety, such as an antibody or an antigen-binding fragment thereof, comprising VH CDRs 1-3 and VL CDRs 1-3 selected from the ones presented in Tables 10-15, wherein the VH CDRs and VL CDRs are arranged in a spatial orientation that confers specific binding to a D4 region of human KIT.
  • a moiety described herein comprises linkers, such as peptide linkers, that link the VH CDRs 1-3 and/or VL CDRs 1-3 in the spatial orientation that confers specific binding to a D4 region of human KIT.
  • an ADC such as a PBD dimer conjugate provided herein comprises a moiety described herein comprising linkers, such as peptide linkers, that links the VH CDRs and/or VL CDRs in a spatial orientation that confers specific binding to a D4 region of human KIT.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof comprising VL CDRs 1-3 and VH CDRs 1-3 selected from the ones presented in Tables 10-15, wherein the antibody or antigen-binding fragment thereof immunospecifically binds a D4 region of KIT, such as human KIT.
  • the "X" amino acid of a CDR in any one of Tables 10-15 is any naturally occurring amino acid that maintains specific binding affinity to a D4 region of human KIT.
  • the "X" amino acid of a CDR in any one of Tables 10-15 is a non-natural amino acid that maintains specific binding affinity to a D4 region of human KIT.
  • the "X" amino acid of a CDR in any one of Tables 10-15 is a conservative substitution of the corresponding amino acid of the CDRs having the amino acid sequences of SEQ ID NOs: 16-21 , wherein specific binding affinity to a D4 region of human KIT is maintained.
  • the "X" amino acid of a CDR in any one of Tables 10-15 is, independently, amino acid A, G, T, K, or L.
  • the "X" amino acid of a CDR in any one of Tables 10-15 is amino acid A, G, T, Y, C, or S. In certain aspects of these embodiments, specific binding affinity to a D4 region of human KIT is maintained.
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising VH CDRs and/or VL CDRs selected from those presented in Tables 10-15.
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising VH CDRs and/or VL CDRs selected from those presented in Tables 10-15.
  • a CDR such as any one of VL CDRs 1-3 and VH CDRs 1-3 depicted in Tables 10-15, comprises one or more (e.g., two, three, four, or five) "X" amino acids, wherein each "X" amino acid can be any amino acid which can maintain specific binding of the antibody or fragment thereof to a D4 region of human KIT.
  • an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof comprising VL FRs 1-4 selected from the ones presented in Tables 20-23 and/or VH FRs 1-4 selected from the ones presented in Tables 16-19, wherein the antibody or antigen-binding fragment thereof immunospecifically binds a D4 region of KIT, such as human KIT.
  • the "X" amino acid of an FR in any one of Tables 16-23 is any naturally occurring amino acid that maintains specific binding affinity to a D4 region of human KIT.
  • the "X" amino acid of a CDR in any one of Tables 16-23 is a non-natural amino acid that maintains specific binding affinity to a D4 region of human KIT.
  • the "X" amino acid of a CDR in any one of Tables 16-23 is a conservative substitution of the corresponding amino acid of the CDRs having the amino acid sequences of SEQ ID NOs: 16-21 , wherein specific binding affinity to a D4 region of human KIT is maintained.
  • the "X" amino acid of a CDR in any one of Tables 16-23 is amino acid A, G, T, K, or L.
  • the "X" amino acid of a CDR in any one of Tables 16-23 is amino acid A, G, T, Y, C, or S. In certain aspects of these embodiments, specific binding affinity to a D4 region of human KIT is maintained.
  • an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising VH CDRs and/or VL CDRs selected from those presented in Tables 16-23.
  • an antibody e.g., human, composite human, or humanized antibody
  • antigen- binding fragment thereof which specifically binds to a D4 region of human KIT, comprising VH CDRs and/or VL CDRs selected from those presented in Tables 16-23.
  • an FR such as any one of VL FRs 1-4 and VH FRs 1-4 depicted in Tables 16-23, comprises one or more (e.g., two, three, four, or five) "X" amino acids, wherein each "X" amino acid can be any amino acid which can maintain specific binding of the antibody or fragment thereof to a D4 region of human KIT.
  • DIVMXQSPS F/S LSASVGDRVTITC 258
  • an ADC such as a PBD dimer conjugate comprising an antibody comprising an antibody light chain and heavy chain, e.g. , a separate light chain and heavy chain.
  • the light chain of an antibody described herein is a kappa light chain.
  • the light chain of an antibody described herein is a lambda light chain.
  • the light chain of an antibody described herein is a human kappa light chain or a human lambda light chain.
  • an antibody described herein, which immunospecifically binds to a KIT polypeptide e.g. , a KIT polypeptide comprising a D4 region of KIT, for example human KIT (e.g., SEQ ID NO: 15)
  • a KIT polypeptide e.g. , a KIT polypeptide comprising a D4 region of KIT, for example human KIT (e.g., SEQ ID NO: 15)
  • the amino acid sequence of the VL chain region comprises any amino acid sequence described herein (e.g., SEQ ID NO: 7, 8, 9, or 10)
  • the constant region of the light chain comprises the amino acid sequence of a human kappa light chain constant region.
  • Non-limiting examples of human light chain constant region sequences have been described in the art, e.g., see U.S. Patent No. 5,693,780 and Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91- 3242.
  • the heavy chain of an antibody described herein can be an alpha (a), delta ( ⁇ ), epsilon ( ⁇ ), gamma ( ⁇ ) or mu ( ⁇ ) heavy chain.
  • the heavy chain of an antibody described can comprise a human alpha (a), delta ( ⁇ ), epsilon ( ⁇ ), gamma ( ⁇ ) or mu ( ⁇ ) heavy chain.
  • an antibody described herein, which immunospecifically binds to a KIT an antibody described herein, which immunospecifically binds to a KIT
  • polypeptide e.g., a KIT polypeptide comprising a KIT polypeptide comprising a D4 region of KIT, for example human KIT (e.g., SEQ ID NO: 15)
  • the amino acid sequence of the VH chain region can comprise any amino acid sequence described herein (e.g., any of SEQ ID NOs: 2-6)
  • the constant region of the heavy chain comprises the amino acid sequence of a human gamma ( ⁇ ) heavy chain constant region.
  • Non- limiting examples of human heavy chain constant region sequences have been described in the art, e.g., see U.S. Patent No. 5,693,780 and Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242.
  • an antibody of an ADC such as a PBD dimer conjugate described herein which immunospecifically binds to a KIT polypeptide (e.g. , a D4 region of KIT, for example human KIT) comprises a VL chain region and a VH chain region comprising any amino acid sequences described herein, and wherein the constant regions comprise the amino acid sequences of the constant regions of an IgG, IgE, IgM, IgD, IgA or IgY
  • immunoglobulin molecule or a human IgG, IgE, IgM, IgD, IgA or IgY immunoglobulin molecule.
  • an antibody described herein which
  • a KIT polypeptide e.g., a D4 region of KIT, for example human KIT
  • a KIT polypeptide comprises a VL chain region and a VH chain region comprising any amino acid sequences described herein
  • the constant regions comprise the amino acid sequences of the constant regions of an IgG, IgE, IgM, IgD, IgA or IgY immunoglobulin molecule, any class (e.g., IgGl, IgG2, IgG3, IgG4, IgAl and IgA2), or any subclass (e.g., IgG2a and IgG2b) of immunoglobulin molecule.
  • the constant regions comprise the amino acid sequences of the constant regions of a human IgG, IgE, IgM, IgD, IgA or IgY
  • immunoglobulin molecule any class (e.g., IgGl, IgG2, IgG3, IgG4, IgAl and IgA2), or any subclass (e.g., IgG2a and IgG2b) of immunoglobulin molecule.
  • class e.g., IgGl, IgG2, IgG3, IgG4, IgAl and IgA2
  • subclass e.g., IgG2a and IgG2b
  • a KIT polypeptide e.g., a D4 region of KIT, for example human KIT
  • VL chain region and a VH chain region comprising any amino acid sequences described herein (e.g. , any one of SEQ ID NOs: 2-6 and/or any one of SEQ ID NOs: 7-10)
  • the constant regions comprise the amino acid sequences of the constant regions of a human IgGl or
  • a KIT polypeptide e.g., a D4 region of KIT, for example human KIT
  • VL chain region and a VH chain region comprising any amino acid sequences described herein
  • an antibody of an ADC such as a PBD dimer conjugate described herein, which immunospecifically binds to a KIT polypeptide, e.g., a human KIT polypeptide, for example, a D4 region of KIT ⁇ e.g., human KIT, for example SEQ ID NO: 15
  • a KIT polypeptide e.g., a human KIT polypeptide, for example, a D4 region of KIT ⁇ e.g., human KIT, for example SEQ ID NO: 15
  • framework regions ⁇ e.g., framework regions of the VL domain and/or VH domain
  • Non-limiting examples of human framework regions are described in the art, e.g., see Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No.
  • an antibody described herein comprises framework regions ⁇ e.g., framework regions of the VL domain and/or VH domain) that are primate ⁇ e.g., non-human primate) framework regions or derived from primate ⁇ e.g., non-human primate) framework regions.
  • an antibody of an ADC such as a PBD dimer conjugate described herein comprises framework regions ⁇ e.g., framework regions of the VL domain and/or VH domain) that are not primate ⁇ e.g., non-human primate, for example, ape such as Old World ape) framework regions or derived from primate ⁇ e.g. , non-human primate) framework regions.
  • the VL chain region does not comprise non-human primate ⁇ e.g. , ape such as Old World ape) framework regions or is derived from non-human primate ⁇ e.g., ape such as Old World ape) framework regions.
  • the VH chain region does not comprise non-human primate ⁇ e.g. , ape such as Old World ape) framework regions or is derived from non-human primate ⁇ e.g., ape such as Old World ape) framework regions.
  • Non-limiting examples of non-human primate framework regions include those from Old World apes, e.g., Pan troglodytes, Pan paniscus or Gorilla gorilla; chimpanzee Pan troglodytes; Old World monkey such as Old World monkey from the genus Macaca; and cynomolgus monkey Macaca cynomolgus.
  • Non-limiting examples of non-human primate framework sequences are described in U.S. Patent Application Publication No. US
  • ADCs such as PBD dimer conjugates comprising antibodies, which immunospecifically bind to a KIT polypeptide (e.g., a D4 region of KIT, for example human KIT), comprising one or more amino acid residue substitutions, e.g., in the VL chain region or VH chain region, for example, the CDRs or FRs.
  • a KIT polypeptide e.g., a D4 region of KIT, for example human KIT
  • amino acid residue substitutions e.g., in the VL chain region or VH chain region, for example, the CDRs or FRs.
  • none of the amino acid residue substitutions are located within the CDRs. In specific embodiments, all of the amino acid substitutions are in the FRs (see, e.g., Tables 5A- 6B). In a certain embodiment, an amino acid substitution is a conservative amino acid substitution.
  • 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
  • the glycosylation of antibodies of an ADC such as a PBD dimer conjugate described herein is modified.
  • an aglycoslated antibody can be made (i.e. , the antibody lacks glycosylation) or an antibody comprising a mutation or substitution at one or more glycosylation sites to eliminate glycosylation at the one or more glycosylation sites can be made.
  • Glycosylation can be altered to, for example, increase the affinity of the antibody for a target antigen (e.g., human KIT, for example, a D4 region of human KIT).
  • target antigen e.g., human KIT, for example, a D4 region of human KIT.
  • Such carbohydrate modifications can be accomplished by, for example, altering one or more sites of glycosylation within the antibody sequence.
  • one or more amino acid substitutions can be made that result in elimination of one or more variable region (e.g., VL and/or VH CDRs or VL and/or VH FRs) glycosylation sites to thereby eliminate glycosylation at that site.
  • variable region e.g., VL and/or VH CDRs or VL and/or VH FRs
  • Such aglycosylation can increase the affinity of the antibody for antigen (e.g., human KIT, for example, a D4 region of human KIT).
  • antigen e.g., human KIT, for example, a D4 region of human KIT.
  • Glycosylation can occur via N-linked (or asparagine-linked) glycosylation or O- linked glycosylation.
  • N-linked glycosylation involves carbohydrate modification at the side- chain NH2 group of an asparagine amino acid in a polypeptide.
  • O-linked glycosylation involves carbohydrate modification at the hydroxyl group on the side chain of a serine, threonine, or hydroxylysine amino acid.
  • an asparagine (N) residue within a VH (e.g., SEQ ID NO: 2, 3, 4, 5, or 6) or VL region (e.g., SEQ ID NO: 7, 8, 9, or 10) of an antibody described herein is substituted with a serine (S) or another amino acid (e.g., alanine, glycine, glutamine, threonine, tyrosine, cysteine).
  • S serine
  • another amino acid e.g., alanine, glycine, glutamine, threonine, tyrosine, cysteine
  • an asparagine (N) residue within a VH CDR e.g., VH CDR1, VH CDR2, and/or VH CDR3 comprising the sequences of SEQ ID NOs: 16- 18, respectively
  • a VL CDR e.g., VL CDR1, VL CDR2, and/or VL CDR3 comprising the sequences of SEQ ID NOs: 19-21, respectively
  • S serine
  • another amino acid e.g., alanine, glycine, glutamine, threonine, tyrosine, cysteine
  • an asparagine (N) residue within a VH FR e.g., VH FRl, VH FR2, VH FR3 and/or VH FR4 as set forth in Tables 5 A, 5C, and 6B
  • a VL FR e.g., VL FRl, VL FR2, VL FR3, and/or VL FR4 as set forth in Table 5B, 5D, and 6A
  • S serine
  • another amino acid e.g. , alanine, glycine, glutamine, threonine, tyrosine, cysteine
  • aglycosylated antibodies can be produced in bacterial cells which lack the necessary glycosylation machinery.
  • Cells with altered glycosylation machinery have been described in the art and can be used as host cells in which to express recombinant antibodies described herein to thereby produce an antibody with altered glycosylation. See, for example, Shields, R.L. et al. (2002) J. Biol. Chem. 277:26733-26740; Umana et al. (1999) Nat. Biotech. 17: 176-1, as well as, European Patent No: EP 1,176,195; PCT Publications WO
  • one or more modifications can be made to the Fc region of an antibody described here, generally, to alter one or more functional properties of the antibody, such as serum half-life, complement fixation, Fc receptor binding, and/or antibody-dependent cellular cytotoxicity. These modifications are described, for example, in International Patent Application Publication No. WO 2008/153926 A2.
  • an asparagine (N) residue within the constant region of a heavy chain and/or the constant region of a light region of an antibody described herein is substituted with a serine (S) or another amino acid (e.g., alanine, glycine, glutamine, threonine, tyrosine, cysteine).
  • an antibody or an antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate described herein, specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT) with an EC 50 (half maximal effective concentration) value of about 50 nM or less as determined by ELISA.
  • a KIT polypeptide e.g., the D4 region of human KIT
  • EC 50 half maximal effective concentration
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or an antigen-binding fragment thereof specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT) with an EC 50 value of about 150 pM or less as determined by FACs with CHO-WT-KIT cells (CHO cells engineered to recombinantly express wild-type human KIT).
  • a KIT polypeptide e.g., the D4 region of human KIT
  • FACs with CHO-WT-KIT cells (CHO cells engineered to recombinantly express wild-type human KIT).
  • an ADC such as a PBD dimer conjugate comprises an anti-KIT antibody which immunospecifically binds to human KIT or a fragment thereof.
  • a non-human KIT e.g. , monkey, mouse, goat, donkey, dog, cat, rabbit, pig, rat, or bird
  • an ADC such as a PBD dimer conjugate (e.g., KIT-PBD- ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to an extracellular domain of human KIT having a mutation, for example a somatic mutation associated with cancer (e.g., GIST), such as a mutation in exon 9 of human KIT wherein the Ala and Tyr residues at positions 502 and 503 are duplicated.
  • a somatic mutation associated with cancer e.g., GIST
  • an ADC such as a PBD dimer conjugate (e.g., KIT-PBD-ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to an extracellular domain of wild-type human KIT and an extracellular domain of human KIT with a mutation, for example a somatic mutation associated with cancer (e.g., GIST), such as a mutation in exon 9 of human KIT wherein the Ala and Tyr residues at positions 502 and 503 are duplicated (see, e.g., Marcia et ah, (2000) Am. J. Pathol. 156(3):791-795; and Debiec-Rychter et al, (2004) European Journal of Cancer. 40:689- 695, which are both incorporated herein by reference in their entireties, describing KIT mutations).
  • a somatic mutation associated with cancer e.g., GIST
  • an ADC such as a PBD dimer conjugate (e.g., KIT-PBD- ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to an extracellular domain of human KIT which is glycosylated.
  • an ADC such as a PBD dimer conjugate (e.g. , KIT-PBD-ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to two different glycosylated forms of an extracellular domain of human KIT. For example, two forms of human KIT with different molecular weights, indicating different glycosylation patterns, have been observed by immunoblotting.
  • an ADC such as a PBD dimer conjugate (e.g., KIT-PBD-ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to both of these forms of human KIT which have different glycosylation patterns, e.g., one form is more glycosylated than the other.
  • an ADC such as a PBD dimer conjugate (e.g., KIT-PBD- ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to an extracellular domain of human KIT which is not glycosylated.
  • an antibody of an ADC such as a PBD dimer conjugate described herein or an antigen-binding fragment thereof, which specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), and can be recombinantly expressed in CHO cells at an average titer of at least 0.5 ⁇ g/mL.
  • a KIT polypeptide e.g., the D4 region of human KIT
  • an antibody of an ADC such as a PBD dimer conjugate described herein or an antigen-binding fragment thereof, which specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), can be recombinantly expressed in CHO cells at an average titer of at least 1.0 ⁇ g/mL.
  • an antibody of an ADC such as a PBD dimer conjugate described herein or an antigen-binding fragment thereof, which specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprises a VH domain and a VL domain that are non-immunogenic (e.g., non-immunogenic in a human), for example, the VH domain and VL domain do not contain T cell epitopes.
  • antibodies of ADC such as a PBD dimer conjugates provided herein include, but are not limited to, monoclonal antibodies, recombinantly produced antibodies, multispecific antibodies (including bi-specific antibodies), human antibodies, humanized antibodies, chimeric antibodies, synthetic antibodies, tetrameric antibodies comprising two heavy chain and two light chain molecule, an antibody light chain monomer, an antibody heavy chain monomer, an antibody light chain dimer, an antibody heavy chain dimer, an antibody light chain-antibody heavy chain pair, intrabodies, heteroconjugate antibodies, single domain antibodies, monovalent antibodies, single chain antibodies or single-chain Fvs (scFv) (e.g., including monospecific, bispecific, etc.), camelized antibodies, affybodies, Fab fragments, F(ab') fragments, disulfide-linked Fvs (sdFv), anti-idiotypic (anti-Id) antibodies (including, e.g., anti-anti-Id antibodies), and epitope-
  • antibodies described herein refer to polyclonal antibody populations.
  • Antibodies can be of any type (e.g., IgG, IgE, IgM, IgD, IgA or IgY), any class, (e.g., IgGl , IgG2, IgG3, IgG4, IgAl or IgA2), or any subclass (e.g., IgG2a or IgG2b) of immunoglobulin molecule.
  • antibodies of an ADC such as a PBD dimer conjugate described herein are IgG antibodies, or a class (e.g., human IgGl or IgG4) or subclass thereof.
  • a monoclonal antibody is an antibody produced by a single hybridoma or other cell, wherein the antibody immunospecifically binds to a D4 region of human KIT epitope as determined, e.g., by ELISA or other antigen-binding or competitive binding assay known in the art or in the Examples provided herein.
  • the term "monoclonal" is not limited to any particular method for making the antibody.
  • an anti-KIT antibody of an ADC such as a PBD dimer conjugate provided herein is a Fab fragment that immunospecifically binds to a KIT polypeptide, such as the D4 region of human KIT.
  • antibodies of an ADC such as a PBD dimer conjugate described herein are monoclonal antibodies or isolated monoclonal antibodies.
  • an antibody of an ADC such as a PBD dimer conjugate described herein is a humanized monoclonal antibody.
  • an antibody of an ADC such as a PBD dimer conjugate described herein is a recombinant antibody, for example, a recombinant human antibody, recombinant humanized antibody or a recombinant monoclonal antibody.
  • an antibody of an ADC such as a PBD dimer conjugate described herein contains non-human amino acid sequences, e.g., non-human CDRs or non-human (e.g., non-human primate) framework residues.
  • recombinant antibodies of an ADC such as a PBD dimer conjugate can be isolated, prepared, expressed, or created by recombinant means, such as antibodies expressed using a recombinant expression vector transfected into a host cell, antibodies isolated from a recombinant, combinatorial antibody library, or antibodies prepared, expressed, created or isolated by any other means that involves creation, e.g., via synthesis, genetic engineering of DNA sequences that encode human immunoglobulin sequences, or splicing of sequences that encode human immunoglobulins, e.g., human immunoglobulin gene sequences, to other such sequences.
  • recombinant means such as antibodies expressed using a recombinant expression vector transfected into a host cell, antibodies isolated from a recombinant, combinatorial antibody library, or antibodies prepared, expressed, created or isolated by any other means that involves creation, e.g., via synthesis, genetic engineering of DNA sequences that encode human immunoglobulin sequences, or splic
  • the amino acid sequences of such recombinant antibodies have been modified such thus the amino acid sequences of such antibodies, e.g., VH and/or VL regions, are sequences that do not naturally exist within an organism's antibody germline repertoire in vivo, for example a murine or human germline repertoire.
  • a recombinant antibody of an ADC such as a PBD dimer conjugate can be obtained by assembling several sequence fragments that naturally exist in an organism (e.g., primate, such as human) into a composite sequence of a recombinant antibody, wherein the composite sequence does not naturally exist within an organism (e.g. , primate such as human).
  • Antibodies of an ADC such as a PBD dimer conjugate provided herein include immunoglobulin molecules of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgGl, IgG2, IgG3, IgG4, IgAl and IgA2) or subclass of immunoglobulin molecule.
  • an antibody provided herein is an IgG antibody (e.g., human IgG antibody), or a class (e.g., human IgGl or IgG4) or subclass thereof.
  • an antibody described herein is an IgGl (e.g., human IgGl (isotype a, z, or f)) or IgG4 antibody.
  • an antibody described herein is a whole or entire antibody, e.g., a whole or entire humanized, human, or composite human antibody.
  • Antibodies of an ADC such as a PBD dimer conjugate provided herein can include antibody fragments that retain the ability to specifically bind to an antigen, e.g. , KIT epitope (e.g., a KIT epitope within a KIT polypeptide containing a D4 region of human KIT).
  • fragments include Fab fragments (an antibody fragment that contains the antigen-binding domain and comprises a light chain and part of a heavy chain (i.e., the VH and CHI domains of a heavy chain) bridged by a disulfide bond); Fab' (an antibody fragment containing a single antigen-binding domain comprising an Fab and an additional portion of the heavy chain through the hinge region); F(ab') 2 (two Fab' molecules joined by interchain disulfide bonds in the hinge regions of the heavy chains; the Fab' molecules can be directed toward the same or different epitopes); a bispecific Fab (a Fab molecule having two antigen binding domains, each of which can be directed to a different epitope); a single chain Fab chain comprising a variable region, also known as a sFv (the variable, antigen-binding determinative region of a single light and heavy chain of an antibody linked together by a chain of 10-25 amino acids); a disulfide-linked
  • Antibodies of an ADC such as a PBD dimer conjugate provided herein can also include one or more CDR sequences of an antibody.
  • the CDR sequences can be linked together on a scaffold when two or more CDR sequences are present.
  • an antibody of an ADC such as a PBD dimer conjugate comprises a single-chain Fv ("scFv").
  • scFvs are antibody fragments comprising the VH and VL domains of an antibody, wherein these domains are present in a single polypeptide chain.
  • the scFv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the scFv to form the desired structure for antigen binding.
  • a polypeptide linker between the VH and VL domains which enables the scFv to form the desired structure for antigen binding.
  • antibodies of ADCs such as PBD dimer conjugates described herein are human, composite human, or humanized monoclonal antibodies.
  • an antibody described herein is an engineered antibody, for example, antibody produced by recombinant methods.
  • an antibody of an ADC such as a PBD dimer conjugate described herein is a humanized antibody comprising one or more non- human (e.g., rodent or murine) CDRs and one or more human framework regions (FR), and optionally human heavy chain constant region and/or light chain constant region.
  • an antibody of an ADC such as a PBD dimer conjugate described herein comprises one or more primate (or non-human primate) framework regions. In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate described herein does not comprise non- human primate framework regions.
  • Antibodies of ADCs such as PBD dimer conjugates provided herein can include antibodies comprising chemical modifications, for example, antibodies which have been chemically modified, e.g., by covalent attachment of any type of molecule to the antibody.
  • an anti-KIT antibody of an ADC such as a PBD dimer conjugate can be glycosylated, acetylated, pegylated, phosphorylated, or amidated, can be derivitized via protective/blocking groups, or can further comprise a cellular ligand and or other protein or peptide, etc.
  • an antibody of an ADC such as a PBD dimer conjugate provided herein can be chemically modified, e.g.
  • an anti-KIT antibody of an ADC such as a PBD dimer conjugate described herein can contain one or more non-classical amino acids.
  • Antibodies e.g., human, composite human, or humanized antibodies
  • an antigen- binding fragment thereof described herein that immunospecifically bind to a KIT antigen, for conjugation to produce ADCs such as PBD dimer conjugates provided herein can be produced by any method known in the art for the synthesis of antibodies, for example, by chemical synthesis or by recombinant expression techniques.
  • the methods described herein employs, unless otherwise indicated, conventional techniques in molecular biology, microbiology, genetic analysis, recombinant DNA, organic chemistry, biochemistry, PCR, oligonucleotide synthesis and modification, nucleic acid hybridization, and related fields within the skill of the art.
  • humanized antibodies can be produced using a variety of techniques known in the art, including but not limited to, CDR-grafting (European Patent No. EP 239,400; International publication No. WO 91/09967; and U.S. Patent Nos. 5,225,539, 5,530,101, and 5,585,089), veneering or resurfacing (European Patent Nos. EP 592,106 and EP 519,596; Padlan, 1991, Molecular Immunology 28(4/5):489-498; Studnicka et al, 1994, Protein Engineering 7(6):805-814; and Roguska et al, 1994, PNAS 91 :969-973), chain shuffling (U.S. Patent No.
  • a humanized antibody is capable of binding to a predetermined antigen and which comprises a framework region having substantially the amino acid sequence of a human immunoglobulin and CDRs having substantially the amino acid sequence of a non- human immunoglobulin (e.g., a murine immunoglobulin).
  • a humanized antibody also comprises at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
  • the antibody also can include the CHI, hinge, CH2, CH3, and CH4 regions of the heavy chain.
  • a humanized antibody can be selected from any class of immunoglobulins, including IgM, IgG, IgD, IgA and IgE, and any isotype, including IgGi, IgG 2 , IgG 3 and IgG 4 .
  • Monoclonal antibodies can be prepared using a wide variety of techniques known in the art including the use of hybridoma, recombinant, and phage display technologies, or a combination thereof.
  • monoclonal antibodies can be produced using hybridoma techniques including those known in the art and taught, for example, in Harlow et al.,
  • monoclonal antibody as used herein is not limited to antibodies produced through hybridoma technology.
  • monoclonal antibodies can be produced by recombinant technology, e.g. , recombinant monoclonal antibodies expressed by a host cell, such as a mammalian host cell.
  • Antibodies of ADCs such as PBD dimer conjugates described herein include antibody fragments which recognize specific KIT antigens and can be generated by any technique known to those of skill in the art.
  • Fab and F(ab') 2 fragments described herein can be produced by proteolytic cleavage of immunoglobulin molecules, using enzymes such as papain (to produce Fab fragments) or pepsin (to produce F(ab') 2 fragments).
  • a Fab fragment corresponds to one of the two identical arms of an antibody molecule and contains the complete light chain paired with the VH and CHI domains of the heavy chain.
  • a F(ab') 2 fragment contains the two antigen-binding arms of an antibody molecule linked by disulfide bonds in the hinge region.
  • PCR primers including VH or VL nucleotide sequences, a restriction site, and a flanking sequence to protect the restriction site can be used to amplify the VH or VL sequences from a template, e.g., scFv clones.
  • the PCR amplified VH domains can be cloned into vectors expressing a VH constant region
  • the PCR amplified VL domains can be cloned into vectors expressing a VL constant region, e.g., human kappa or lambda constant regions.
  • the VH and VL domains can also be cloned into one vector expressing the necessary constant regions.
  • the heavy chain conversion vectors and light chain conversion vectors are then co-transfected into cell lines to generate stable or transient cell lines that express full-length antibodies, e.g., IgG, using techniques known to those of skill in the art.
  • Single domain antibodies for example, antibodies lacking the light chains, can be produced by methods well-known in the art. See Riechmann et al. , 1999, J. Immunol. 231 :25- 38; Nuttall et al, 2000, Curr. Pharm. Biotechnol. l(3):253-263; Muylderman, 2001, J.
  • antibodies of ADCs such as PBD dimer conjugates described herein, such as heteroconjugate antibodies, single chain antibodies, and bispecific antibodies, can be produced through recombinant technology known in the art.
  • mammalian host cells comprising vectors expressing an antibody described herein are cultured under conditions suitable for antibody production.
  • Recombinant expression of an antibody of an ADC such as a PBD dimer conjugate described herein ⁇ e.g., a full-length antibody, heavy and/or light chain of an antibody, or a single chain antibody described herein) that immunospecifically binds to a KIT antigen involves construction of an expression vector containing a polynucleotide that encodes the antibody. Once a polynucleotide encoding an antibody molecule, heavy and/or light chain of an antibody, or fragment thereof (preferably, but not necessarily, containing the heavy and/or light chain variable domain) described herein has been obtained, the vector for the production of the antibody molecule can be produced by recombinant DNA technology using techniques well- known in the art.
  • a protein by expressing a polynucleotide containing an antibody encoding nucleotide sequence are described herein. Methods which are well known to those skilled in the art can be used to construct expression vectors containing antibody coding sequences and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Also provided are replicable vectors comprising a nucleotide sequence encoding an antibody molecule described herein, a heavy or light chain of an antibody, a heavy or light chain variable domain of an antibody or a fragment thereof, or a heavy or light chain CDR, operably linked to a promoter.
  • Such vectors can, for example, include the nucleotide sequence encoding the constant region of the antibody molecule (see, e.g., International Publication Nos. WO 86/05807 and WO 89/01036; and U.S. Patent No. 5,122,464) and the variable domain of the antibody can be cloned into such a vector for expression of the entire heavy, the entire light chain, or both the entire heavy and light chains.
  • An expression vector can be transferred to a cell ⁇ e.g., host cell) by conventional techniques and the resulting cells can then be cultured by conventional techniques to produce an antibody described herein or a fragment thereof.
  • host cells containing a polynucleotide encoding an antibody described herein or fragments thereof, or a heavy or light chain thereof, or fragment thereof, or a single chain antibody described herein, operably linked to a promoter for expression of such sequences in the host cell.
  • vectors encoding both the heavy and light chains, individually can be co-expressed in the host cell for expression of the entire immunoglobulin molecule, as detailed below.
  • a host cell contains a vector comprising a polynucleotide encoding both the heavy chain and light chain of an antibody described herein, or a fragment thereof.
  • a host cell contains two different vectors, a first vector comprising a polynucleotide encoding a heavy chain of an antibody described herein, or a fragment thereof, and a second vector comprising a polynucleotide encoding a light chain of an antibody described herein, or a fragment thereof.
  • a first host cell comprises a first vector comprising a polynucleotide encoding a heavy chain of an antibody described herein, or a fragment thereof
  • a second host cell comprises a second vector comprising a polynucleotide encoding a light chain of an antibody described herein.
  • host-expression vector systems can be utilized to express antibody molecules described herein (see, e.g., U.S. Patent No. 5,807,715).
  • host-expression systems represent vehicles by which the coding sequences of interest can be produced and subsequently purified, but also represent cells which can, when transformed or transfected with the appropriate nucleotide coding sequences, express an antibody molecule described herein in situ.
  • These include but are not limited to microorganisms such as bacteria ⁇ e.g., E. coli and B.
  • subtilis transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing antibody coding sequences; yeast ⁇ e.g., Saccharomyces Pichia) transformed with recombinant yeast expression vectors containing antibody coding sequences; insect cell systems infected with recombinant virus expression vectors ⁇ e.g., baculovirus) containing antibody coding sequences; plant cell systems (e.g., green algae such as Chlamydomonas reinhardtii) infected with recombinant virus expression vectors ⁇ e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors ⁇ e.g., Ti plasmid) containing antibody coding sequences; or mammalian cell systems ⁇ e.g., COS, CHO, BHK, MDCK, HEK 293, NSO, PER.C6, VERO, CRL7030,
  • cells for expressing antibodies described herein ⁇ e.g., Huml-Hum20) or an antigen- binding fragment thereof are CHO cells, for example CHO cells from the CHO GS SystemTM (Lonza).
  • a mammalian expression vector is pOptiVECTM or pcDNA3.3.
  • bacterial cells such as Escherichia coli, and more preferably, eukaryotic cells, especially for the expression of whole recombinant antibody molecule, are used for the expression of a recombinant antibody molecule.
  • mammalian cells such as Chinese hamster ovary (CHO) cells
  • CHO Chinese hamster ovary
  • a vector such as the major intermediate early gene promoter element from human cytomegalovirus
  • antibodies described herein are produced by CHO cells or NSO cells.
  • the expression of nucleotide sequences encoding antibodies described herein which immunospecifically bind to a KIT antigen is regulated by a constitutive promoter, inducible promoter or tissue specific promoter.
  • a number of expression vectors can be advantageously selected depending upon the use intended for the antibody molecule being expressed.
  • vectors which direct the expression of high levels of fusion protein products that are readily purified can be desirable.
  • Such vectors include, but are not limited to, the E. coli expression vector pUR278 (Ruther et ah, 1983, EMBO 12: 1791), in which the antibody coding sequence can be ligated individually into the vector in frame with the lac Z coding region so that a fusion protein is produced; pIN vectors (Inouye & Inouye, 1985, Nucleic Acids Res.
  • pGEX vectors can also be used to express foreign polypeptides as fusion proteins with glutathione 5-transferase (GST).
  • GST glutathione 5-transferase
  • fusion proteins are soluble and can easily be purified from lysed cells by adsorption and binding to matrix glutathione agarose beads followed by elution in the presence of free glutathione.
  • the pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene product can be released from the GST moiety.
  • Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes.
  • the virus grows in Spodoptera frugiperda cells.
  • the antibody coding sequence can be cloned individually into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter).
  • a number of viral-based expression systems can be utilized.
  • the antibody coding sequence of interest can be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and tripartite leader sequence. This chimeric gene can then be inserted in the adenovirus genome by in vitro or in vivo recombination.
  • Insertion in a non-essential region of the viral genome ⁇ e.g., region El or E3) will result in a recombinant virus that is viable and capable of expressing the antibody molecule in infected hosts ⁇ e.g., see Logan & Shenk, 1984, Proc. Natl. Acad. Sci. USA 8 1 :355-359).
  • Specific initiation signals can also be required for efficient translation of inserted antibody coding sequences. These signals include the ATG initiation codon and adjacent sequences. Furthermore, the initiation codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert.
  • These exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic.
  • a host cell strain can be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products can be important for the function of the protein.
  • Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins and gene products. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed. To this end, eukaryotic host cells which possess the cellular machinery for proper processing of the primary transcript, glycosylation, and
  • Such mammalian host cells include but are not limited to CHO, VERO, BHK, Hela, COS, MDCK, HEK 293, NIH 3T3, W138, BT483,
  • humanized monoclonal anti-KIT antibodies described herein are produced in mammalian cells, such as CHO cells.
  • cell lines which stably express the antibody molecule can be engineered.
  • host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker.
  • appropriate expression control elements e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.
  • engineered cells can be allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media.
  • the selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn can be cloned and expanded into cell lines.
  • This method can advantageously be used to engineer cell lines which express the antibody molecule.
  • Such engineered cell lines can be particularly useful in screening and evaluation of compositions that interact directly or indirectly with the antibody molecule.
  • a number of selection systems can be used, including but not limited to, the herpes simplex virus thymidine kinase (Wigler et ah, 1977, Cell 11 :223), hypoxanthineguanine phosphoribosyltransferase (Szybalska & Szybalski, 1992, Proc. Natl. Acad. Sci. USA 48:202), and adenine phosphoribosyltransferase (Lowy et ah, 1980, Cell 22:8-17) genes can be employed in tk-, hgprt- or aprt-cells, respectively.
  • antimetabolite resistance can be used as the basis of selection for the following genes: dhfr, which confers resistance to methotrexate (Wigler et al, 1980, Natl. Acad. Sci. USA 77:357; O'Hare et al, 1981, Proc. Natl. Acad. Sci. USA
  • the expression levels of an antibody molecule can be increased by vector
  • the host cell can be co-trans fected with two or more expression vectors described herein, the first vector encoding a heavy chain derived polypeptide and the second vector encoding a light chain derived polypeptide.
  • the two vectors can contain identical selectable markers which enable equal expression of heavy and light chain polypeptides.
  • the host cells can be co-trans fected with different amounts of the two or more expression vectors.
  • host cells can be transfected with any one of the following ratios of a first expression vector and a second expression vector: 1 : 1, 1 :2, 1 :3, 1 :4, 1 :5, 1 :6, 1 :7, 1 :8, 1 :9, 1 :10, 1 : 12, 1 : 15, 1 :20, 1 :25, 1 :30, 1 :35, 1 :40, 1 :45, or 1 :50.
  • a single vector can be used which encodes, and is capable of expressing, both heavy and light chain polypeptides.
  • the coding sequences for the heavy and light chains can comprise cDNA or genomic DNA.
  • the expression vector can be monocistronic or multicistronic.
  • a multicistronic nucleic acid construct can encode 2, 3, 4, 5, 6, 7, 8, 9, 10 or more, or in the range of 2-5, 5-10 or 10-20 genes/nucleotide sequences.
  • a bicistronic nucleic acid construct can comprise in the following order a promoter, a first gene (e.g., heavy chain of an antibody described herein), and a second gene and (e.g., light chain of an antibody described herein).
  • a promoter e.g., a promoter
  • a first gene e.g., heavy chain of an antibody described herein
  • a second gene and e.g., light chain of an antibody described herein.
  • the transcription of both genes can be driven by the promoter, whereas the translation of the mRNA from the first gene can be by a cap-dependent scanning mechanism and the translation of the mRNA from the second gene can be by a cap-independent mechanism, e.g., by an IRES.
  • an antibody molecule described herein has been produced by recombinant expression, it can be purified by any method known in the art for purification of an
  • immunoglobulin molecule for example, by chromatography (e.g., ion exchange, affinity, particularly by affinity for the specific antigen after Protein A, and sizing column
  • chromatography e.g., ion exchange, affinity, particularly by affinity for the specific antigen after Protein A, and sizing column
  • antibodies described herein can be fused to heterologous polypeptide sequences described herein or otherwise known in the art to facilitate purification.
  • an antibody described herein is isolated or purified.
  • an isolated antibody is one that is substantially free of other antibodies with different antigenic specificities than the isolated antibody.
  • a preparation of an antibody described herein is substantially free of cellular material and/or chemical precursors.
  • substantially free of cellular material includes preparations of an antibody in which the antibody is separated from cellular components of the cells from which it is isolated or recombinantly produced.
  • an antibody that is substantially free of cellular material includes preparations of antibody having less than about 30%, 20%, 10%>, 5%, 2%>, 1%, 0.5%, or 0.1%) (by dry weight) of heterologous protein (also referred to herein as a "contaminating protein") and/or variants of an antibody, for example, different post-translational modified forms of an antibody or other different versions of an antibody (e.g. , antibody fragments).
  • heterologous protein also referred to herein as a "contaminating protein”
  • variants of an antibody for example, different post-translational modified forms of an antibody or other different versions of an antibody (e.g. , antibody fragments).
  • the antibody is recombinantly produced, it is also generally substantially free of culture medium, i.e., culture medium represents less than about 20%, 10%>, 2%, 1%, 0.5%>, or 0.1% of the volume of the protein preparation.
  • the antibody When the antibody is produced by chemical synthesis, it is generally substantially free of chemical precursors or other chemicals, i.e., it is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein. Accordingly, such preparations of the antibody have less than about 30%>, 20%>, 10%>, or 5% (by dry weight) of chemical precursors or compounds other than the antibody of interest.
  • antibodies described herein are isolated or purified
  • ADCs such as PBD dimer conjugates comprising an anti-KIT antibody or an antigen binding fragment thereof which can modulate a KIT activity.
  • antibodies ⁇ e.g., human, composite human, or humanized antibodies) of ADCs such as PBD dimer conjugates described herein are inhibitory antibodies, that is, antibodies that inhibit ⁇ e.g., partially inhibit) KIT activity, i.e., one or more KIT activities.
  • partial inhibition of a KIT activity results in, for example, about 25% to about 65% or 75% inhibition.
  • partial inhibition of a KIT activity results in, for example, about 35% to about 85% or 95% inhibition.
  • KIT activities include KIT dimerization, KIT
  • phosphorylation ⁇ e.g., tyrosine phosphorylation
  • signaling downstream of KIT ⁇ e.g., AKT, MAPK/ERK, Ras, Statl, Stat3, or Stat5 signaling
  • transcription ⁇ e.g., SCF-induced transcriptional activation of c-Myc), induction or enhancement of cell proliferation or cell survival.
  • KIT activity is induced by KIT ligand ⁇ e.g., SCF) binding to KIT receptor.
  • KIT activity can be induced or enhanced by gain-of-function mutations which can result, for example, in dimerization and constitutively active KIT signaling (see, e.g., Mol et al, J. Biol. Chem., 2003, 278:31461-31464; Hirota et al., J. Pathology, 2001, 193:505-510).
  • gain-of-function can allow for KIT receptor dimerization and KIT signaling to occur in the absence of KIT ligand ⁇ e.g., SCF) binding to KIT receptor.
  • an increase in KIT activity or signaling can occur, in the absence of KIT ligand ⁇ e.g., SCF) binding KIT receptor, due to high (or overexpression) expression of KIT receptors.
  • High or overexpression of KIT in a cell refers to an expression level which is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% more than the expression level of a reference cell known to have normal KIT expression or KIT activity or more than the average expression level of KIT in a population of cells or samples known to have normal KIT expression or KIT activity.
  • Expression levels of KIT can be assessed by methods described herein or known to one of skill in the art (e.g., Western blotting or immunohistochemistry).
  • KIT activity that is higher than normal KIT activity can lead to cellular transformation, neoplasia, and tumorogenesis.
  • KIT activity that is higher than normal KIT activity can lead to other KIT-associated disorders or diseases.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting KIT phosphorylation (e.g. , ligand- induced phosphorylation).
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting KIT tyrosine phosphorylation in the KIT cytoplasmic domain.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting cell proliferation (e.g., cancer cell proliferation).
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting cell survival (e.g., cancer cell survival).
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inducing apoptosis (e.g., cancer cell apoptosis).
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inducing cell differentiation, e.g., cell differentiation in a cell expressing KIT, e.g., human KIT.
  • an antibody described herein inhibits KIT activity but does not inhibit KIT dimerization.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting KIT activity and does not inhibit ligand binding to KIT, e.g., does not inhibit KIT ligand (e.g., SCF) binding to KIT, but does inhibit KIT dimerization.
  • KIT ligand e.g., SCF
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting a KIT activity, such as ligand- induced tyrosine phosphorylation of a KIT cytoplasmic domain, by at least about 25%, 35%, 45%, 55%, 65%), 75%o, 85%, or 95% as determined by a cell-based phosphorylation assay well known in the art, for example, the cell-based phosphorylation assay described herein.
  • a KIT activity such as ligand- induced tyrosine phosphorylation of a KIT cytoplasmic domain
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting a KIT activity, such as ligand-induced tyrosine phosphorylation of a KIT cytoplasmic domain, by at least about 25%, 35%, 45%, 55%, 65%, 75%), 85%), or 95%, as determined by a cell-based phosphorylation assay well known in the art, for example, the cell-based phosphorylation assay described herein.
  • a KIT activity such as ligand-induced tyrosine phosphorylation of a KIT cytoplasmic domain
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting a KIT activity, such as ligand- induced tyrosine phosphorylation of a KIT cytoplasmic domain, with a 50% inhibition concentration (IC 50 ) of less than about 600 pM, or less than about 500 pM, or less than about 250 pM, or less than about 100 pM, as determined by a cell-based phosphorylation assay well known in the art, for example, the cell-based phosphorylation assay described herein. In a specific embodiment, the IC 50 is less than about 550 pM or 200 pM.
  • the IC 50 is in the range of about 50 pM to about 225 pM, or about 50 pM to about 100 pM, or in the range of 100 pM to about 600 pM. In a specific embodiment, the IC 50 is in the range of about 50 pM to about 550 pM, or about 50 pM to about 600 pM, or about 150 pM to about 550 pM. In a certain embodiment, the IC 50 is determined as described in Section 6.23, below.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or an antigen-binding fragment thereof, which specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), is capable of blocking KIT phosphorylation with IC 50 (50% inhibition concentration) value of about 600 pM or less, or about 200 pM or less, or about 100 pM or less, as determined by methods known in the art, for example, KIT receptor phosphorylation as described herein in Section 6.23.
  • IC 50 50% inhibition concentration
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody described herein, or an antigen-binding fragment thereof, (i) immunospecifically binds to a KIT polypeptide comprising the D4 region of human KIT, (ii) inhibits KIT phosphorylation (e.g., tyrosine phosphorylation), and (iii) does not inhibit KIT ligand (e.g., SCF) binding to KIT.
  • KIT phosphorylation e.g., tyrosine phosphorylation
  • KIT ligand e.g., SCF binding to KIT.
  • such an antibody does not inhibit KIT dimerization.
  • such an antibody can be recombinantly expressed by CHO cells at an average titer of at least 0.5 ⁇ / ⁇ ⁇ ., for example at least 1.0 ⁇ g/mL.
  • such an antibody of an ADC such as PBD dimer conjugate comprises a VH domain and a VL domain that are non-immunogenic (e.g., non- immunogenic in a human), for example, the VH domain and VL domain do not contain T cell epitopes.
  • ADCs such as PBD dimer conjugates provided herein comprise anti-KIT antibodies or an antigen-binding fragment thereof which specifically bind to a D4 region of KIT and block or inhibit tyrosine phosphorylation in the cytoplasmic domain of KIT by at least about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art, e.g., ELISA assay as described in Section 6 (e.g., Section 6.23) or immunob lotting assay, relative to phosphorylation in the presence of KIT ligand stimulation without any antibody or with an unrelated antibody (e.g. , an antibody that does not
  • ADCs such as PBD dimer conjugates provided herein comprise anti-KIT antibodies or an antigen-binding fragment thereof which specifically bind to KIT and block or inhibit tyrosine phosphorylation of the cytoplasmic domain of KIT with an IC 50 of less than about 600 pM, or less than about 550 pM, or less than about 500 pM, or less than about 400 pM, or less than about 300 pM, or less than about 100 pM as assessed by methods described herein (e.g., phosphorylation inhibition assay with CHO cells expressing wild-type KIT as described in Section 6 below, such as Section 6.23) or known to one of skill in the art.
  • IC 50 of less than about 600 pM, or less than about 550 pM, or less than about 500 pM, or less than about 400 pM, or less than about 300 pM, or less than about 100 pM as assessed by methods described herein (e.g., phosphorylation inhibition assay with CHO
  • antibodies of ADCs such as PBD dimer conjugates described herein specifically bind to KIT and block or inhibit tyrosine phosphorylation of the cytoplasmic domain of KIT with an IC 50 of less than about 600 pM, or less than about 100 pM. In specific embodiments, antibodies of ADCs such as PBD dimer conjugates described herein specifically bind to KIT and block or inhibit tyrosine phosphorylation of the cytoplasmic domain of KIT with an IC 50 of less than about 550 pM.
  • antibodies of ADCs such as PBD dimer conjugates described herein specifically bind to KIT and block or inhibit tyrosine phosphorylation of the cytoplasmic domain of KIT with an IC 50 in the range of about 50 pM to about 100 M, about 100 pM to about 500 pM, about 25 pM to about 550 pM, or about 40 pM to about 600 pM, or about 50 pM to about 350 pM.
  • an IC 50 for inhibition of tyrosine phosphorylation can be determined by assaying lysates from cells, e.g., CHO cells,
  • cells e.g., CHO cells, recombinantly expressing KIT, are sorted, e.g., sorted to select for cells highly expressing KIT, prior to use in the phosphorylation inhibition assays. In some embodiments, the cells are not sorted prior to use in the phosphorylation inhibition assays.
  • ADCs such as PBD dimer conjugates comprise antibodies described herein or an antigen-binding fragment thereof which specifically bind to KIT and induce or enhance KIT receptor internalization by at least about 5%, 10%, 15%, 20%>, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art, relative to
  • ADCs such as PBD dimer conjugates comprise anti-KIT antibodies described herein or an antigen-binding fragment thereof which specifically bind to KIT and induce or enhance KIT receptor internalization by at least about 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art, relative to internalization in the presence of an unrelated antibody ⁇ e.g., an antibody that does not immunospecifically bind to KIT).
  • Techniques for the quantitation or visualization of cell surface receptors include a variety of fluorescent and radioactive techniques. For example, one method involves incubating the cells with a radiolabeled anti-receptor antibody. Alternatively, the natural ligand of the receptor can be conjugated to a fluorescent molecule or radioactive-label and incubated with the cells.
  • antibodies described herein specifically bind to KIT and induce or enhance KIT receptor turnover by at least about 5%>, 10%>, 15%>, 20%>, 25%>, 30%>, 35%>, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art (e.g., pulse-chase assay), relative to turnover in the presence of an unrelated antibody (e.g., an antibody that does not
  • ADCs such as PBD dimer conjugates comprising anti-KIT antibodies described herein (or an antigen-binding fragment thereof) specifically bind to KIT and induce or enhance KIT receptor turnover by at least about 25%o or 35%), optionally to about 75%, as assessed by methods described herein or known to one of skill in the art (e.g., pulse-chase assay), relative to turnover in the presence of an unrelated antibody (e.g., an antibody that does not immunospecifically bind to KIT).
  • an unrelated antibody e.g., an antibody that does not immunospecifically bind to KIT.
  • antibodies described herein specifically bind to KIT and induce or enhance KIT receptor turnover by at least about 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art (e.g., pulse-chase assay), relative to turnover in the presence of an unrelated antibody (e.g. , an antibody that does not immunospecifically bind to KIT).
  • pulse-chase assay e.g., pulse-chase assay
  • cells expressing KIT can be pulse-labeled using 35 S-EXPRESS Protein Labeling mix (NEG772, NEN Life Science Products), washed and chased with unlabeled medium for a period of time before protein lysates from the labeled cells are immunoprecipitated using an anti-KIT antibody and resolved by SDS-PAGE and visualized (e.g., exposed to a Phospholmager screen (Molecular Dynamics), scanned using the Typhoon8600 scanner (Amersham), and analyzed using 35 S-EXPRESS Protein Labeling mix (NEG772, NEN Life Science Products), washed and chased with unlabeled medium for a period of time before protein lysates from the labeled cells are immunoprecipitated using an anti-KIT antibody and resolved by SDS-PAGE and visualized (e.g., exposed to a Phospholmager screen (Molecular Dynamics), scanned using the Typhoon8600 scanner (Amersham), and analyzed using
  • ImageQuant software (Molecular Dynamics)) (see, e.g., Chan et al, Development, 2004, 131 :5551-5560).
  • ADCs such as PBD dimer conjugates comprise antibodies described herein or an antigen-binding fragment thereof which specifically bind to KIT and induce or enhance KIT receptor degradation by at least about 5%, 10%>, 15%, 20%>, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art (e.g. , pulse-chase assays), relative to degradation in the presence of an unrelated antibody (e.g., an antibody that does not immunospecifically bind to KIT).
  • an unrelated antibody e.g., an antibody that does not immunospecifically bind to KIT.
  • ADCs such as PBD dimer conjugates comprise antibodies described herein or an antigen-binding fragment thereof which specifically bind to KIT and induce or enhance KIT receptor degradation by at least about 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art (e.g., pulse-chase assays), relative to degradation in the presence of an unrelated antibody (e.g., an antibody that does not immunospecifically bind to KIT).
  • an unrelated antibody e.g., an antibody that does not immunospecifically bind to KIT
  • KIT ligand e.g., SCF
  • PI phosphatidylinositol
  • MAPK Ras mitogen-activated protein kinase
  • Phosphorylated tyrosines in the cytoplasmic domain of KIT can provide for binding sites for SH2 domain- containing proteins, which include, but are not limited to, proteins of the p21Ras-mitogen activated protein kinase (MAPK) pathway, the p85 subunit of PI 3-kinase, phospholipase C- gammai, the Grb2 adaptor protein, the Src family kinases (SFKs), Cbl, CRKL, p62Dok-l, SHPl, and SHP2 (see Ueda et al, Blood, 2002, 99:3342-3349).
  • MAPK p21Ras-mitogen activated protein kinase
  • SFKs Src family kinases
  • Cbl Cbl
  • CRKL CRKL
  • p62Dok-l p62Dok-l
  • SHPl SHP2
  • ADCs such as PBD dimer conjugates comprising anti-KIT antibodies or an antigen-binding fragment thereof which act as inhibitors of KIT activity and can inhibit signaling of a member of the Src family kinases, PI 3-kinases, or Ras-MAPK.
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody which acts as inhibitors of KIT activity can inhibit binding (or inhibit interaction), to the cytoplasmic domain of KIT, of one or more SH2 domain- containing proteins, such as proteins of the p21Ras-MAPK pathway, the p85 subunit of PI 3- kinase, phospholipase C-gammal, the Grb2 adaptor protein, a member of the SFK, Cbl, CRKL, p62Dok-l, SHPl, and SHP2.
  • SH2 domain- containing proteins such as proteins of the p21Ras-MAPK pathway, the p85 subunit of PI 3- kinase, phospholipase C-gammal, the Grb2 adaptor protein, a member of the SFK, Cbl, CRKL, p62Dok-l, SHPl, and SHP2.
  • an ADC such as a PBD dimer conjugate described herein which act as inhibitors of KIT activity can inhibit activation by KIT of one or more SH2 domain-containing proteins, such as proteins of the p21Ras-MAPK pathway, the p85 subunit of PI 3-kinase, phospholipase C-gammal, the Grb2 adaptor protein, a member of the SFK, Cbl, CPvKL, p62Dok-l, SHP1, and SHP2.
  • SH2 domain-containing proteins such as proteins of the p21Ras-MAPK pathway, the p85 subunit of PI 3-kinase, phospholipase C-gammal, the Grb2 adaptor protein, a member of the SFK, Cbl, CPvKL, p62Dok-l, SHP1, and SHP2.
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, can inhibit downstream signaling such as phosphorylation of MAPK,
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, can inhibit cellular proliferation of cells (e.g., cancer cells such as RD-ES or HEL cells) that express KIT.
  • cells e.g., cancer cells such as RD-ES or HEL cells
  • Cell proliferation assays are described in the art and can be readily carried out by one of skill in the art. For example, cell proliferation can be assayed by measuring Bromodeoxyuridine (BrdU) incorporation (see, e.g., Hoshino et ah, 1986, Int. J. Cancer 38, 369; Campana et ah, 1988, J. Immunol. Meth.
  • immunodiagnostic methods such as ELISA, Western blotting or immunoprecipitation using antibodies, including commercially available antibodies.
  • mRNA can be quantitated using methods that are well known and routine in the art, for example, using northern analysis, RNase protection, or polymerase chain reaction in connection with reverse transcription.
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, can inhibit cell proliferation by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art ⁇ e.g. , BrdU
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, can reduce or inhibit survival of cells (e.g., cancer cells such as RD-ES or HEL cells) that express KIT.
  • Cell survival assays are described in the art and can be readily carried out by one of skill in the art. For example, cell viability can be assessed by using trypan-blue staining or other cell death or viability markers known in the art. In a specific embodiment, the level of cellular ATP is measured to determined cell viability.
  • cell viability is measured in three-day and seven-day periods using an assay standard in the art, such as the CellTiter-Glo Assay Kit (Promega) which measures levels of intracellular ATP. A reduction in cellular ATP is indicative of a cytotoxic effect.
  • cell viability can be measured in the neutral red uptake assay.
  • visual observation for morphological changes can include enlargement, granularity, cells with ragged edges, a filmy appearance, rounding, detachment from the surface of the well, or other changes.
  • T 50% toxic
  • PVH partially toxic-very heavy- 80%
  • PH partially toxic-heavy-60%
  • P partially toxic-40%
  • Ps partially toxic-slight-20%)
  • 0 no toxicity-0%
  • a 50% cell inhibitory (cytotoxic) concentration (IC 50 ) is determined by regression analysis of these data.
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, is capable of inducing cell death such as apoptosis (i.e., programmed cell death) of cells (e.g., cancer cells, such as RD-ES cells) that express KIT.
  • apoptosis i.e., programmed cell death
  • cells e.g., cancer cells, such as RD-ES cells
  • Apoptosis is described in the art and can be readily carried out by one of skill in the art.
  • flow cytometry can be used to detect activated caspase 3, an apoptosis-mediating enzyme, in cells undergoing apoptosis, or Western blotting can be used to detect cleavage of poly(ADP-ribose) polymerase (PARP) (see, e.g., Smolich et ah, Blood, 2001, 97:1413-1421). Cleavage of PARP is an indicator of apoptosis.
  • PARP poly(ADP-ribose) polymerase
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, can induce or enhance apoptosis by at least about 0.25 fold, 0.5 fold, 0.75 fold, 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art (e.g., flow cytometry to detect activated caspase 3).
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, is capable of inhibiting or decreasing anchorage independent cell growth (e.g. , colony formation) by cells (e.g., H526 cells or CHO cells expressing exogenous KIT) that express KIT, as measured by methods commonly known in the art, e.g., soft agar assay.
  • anchorage independent cell growth e.g., colony formation
  • cells e.g., H526 cells or CHO cells expressing exogenous KIT
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, can inhibit or decrease anchorage independent cell growth by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99%) as assessed by methods described herein or known to one of skill in the art (e.g. , soft agar assay).
  • Cells and cell lines which are appropriate for use in the assays described herein relating to KIT activity are readily available (e.g., ATCC) or can be readily identified using methods known in the art.
  • ATCC e.g., ATCC
  • cells and/or cell lines that express KIT endogenously or that possess KIT signaling or activity are known to one of skill in the art.
  • cells or cell lines that are appropriate for use in the assays described herein can express KIT, either endogenously or recombinantly.
  • cells or cell lines for use in cell proliferation assays can express KIT, endogenously or recombinantly, and proliferate or increase proliferation in response to KIT ligand (e.g., SCF) stimulation.
  • KIT ligand e.g., SCF
  • Cells or cell lines for use in cell viability assays can express KIT, endogenously or recombinantly, and exert changes in cell viability in response to KIT ligand (e.g., SCF) stimulation.
  • Cells or cell lines for use in apoptosis assays can express KIT, endogenously or recombinantly, and exert changes in apoptosis in response to KIT ligand (e.g., SCF) stimulation.
  • Non- limiting examples of cells that can be used in the methods and assays described herein include primary cells, cancer cells, transformed cells, stem cells, mast cells, primordial germ cells, oocytes, spermatocytes, embryonic stem cells, hematopoietic cells, leukemia cells (e.g., HEL or Kasumi-1 cells) such as erythroleukemia cells (e.g., F36P and TF-1 cell lines) or human myeloid leukemia cell lines (e.g., M07E cells); gastrointestinal stromal tumor cell lines such as ST-882, GIST-Tl , GIST48, GIST48B, GIST430, and GIST882; neuroblastoma cell lines such as SK-N-SH, SK-SY5Y, H-EP1 , SK-N-BE(2), SK-N-BE(ZkM17), SK-N-BE(2)C, LA-N-1, or LA-N-1 -5 s; neuroectoderma
  • cells and cell lines that express KIT can routinely be generated recombinantly.
  • KIT e.g., human KIT
  • Non-limiting examples of cells that can be engineered to express KIT recombinantly include COS cells, HEK 293 cells, CHO cells, fibroblasts (e.g., human
  • fibroblasts such as NIH3T3 cells, and MEFS.
  • cells for use in the methods described herein are CHO cells, for example CHO cells from the CHO GS SystemTM (Lonza).
  • these engineered cells exogenously expressing full-length human KIT (e.g., SEQ ID NO: 1).
  • an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof is capable of inhibiting tumor growth or inducing tumor regression in mouse model studies.
  • tumor cell lines can be introduced into nude mice, and the mice can be administered with anti-KIT antibodies described herein one or more times, and tumor progression of the injected tumor cells can be monitored over a period of weeks and/or months.
  • administration of an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof to the nude mice can occur prior to introduction of the tumor cell lines.
  • tumor cell line e.g., tumor cell line expressing KIT
  • tumor cell lines for use in these xenograft mouse models include megakaryoblastic leukemia cell lines such as M07e; gastrointestinal stromal tumor cell lines such as ST-882, GIST-T1 , GIST430, GIST48, GIST48B and GIST882; acute myeloblastic leukemia cell line Kasumi-1 ; human erythroleukemic cell lines such as HEL and TF-1 ; human promyelocytic leukemia cell line, HL60; neuroblastoma cell lines such as SK-N-SH, SK-SY5Y, H-EP1 , SK-N-BE(2), SK-N-BE(ZkM17), SK-N-BE(2)C, LA-N-1, or LA-N-l-5s; Ewing's sarcoma cell lines such as TC
  • an ADC such as a PBD dimer conjugate provided herein comprises an anti-KIT antibody or antigen-binding fragment thereof which specifically bind to KIT and inhibits tumor grow, delays tumor growth, or induces tumor regression in a mouse model by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art.
  • Determining tumor growth inhibition or tumor regression can be assessed by monitoring tumor size over a period of time, such as by physical measurement of palpable tumors, or other visual detection methods.
  • tumor cell lines can be generated to recombinantly express a visualization agent, such as green fluorescent protein (GFP) or luciferase, then in vivo visualization of GFP can be carried out by microscopy, and in vivo visualization of luciferase can be carried out by administering luciferase substrate to the xenograft mice and detecting luminescent due to the luciferase enzyme processing the luciferase substrate. The degree or level of detection of GFP or luciferase correlates to the size of the tumor in the xenograft mice.
  • a visualization agent such as green fluorescent protein (GFP) or luciferase
  • an ADC such as a PBD dimer conjugate provided herein comprises an anti-KIT antibody or antigen- binding fragment thereof which specifically bind to KIT and can increase survival of mice in tumor xenograft models by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art.
  • an ADC such as a PBD dimer conjugate provided herein comprises an anti-KIT antibody or antigen-binding fragment thereof which specifically bind to KIT and can increase survival of mice in tumor xenograft models by at least about 0.5 fold, 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art. Survival can be determined by plotting a survival curve of number of surviving mice against time (e.g. , days or weeks) after tumor cell line injection.
  • compositions, pharmaceutical compositions, and kits comprising one or more PBD dimer ADCs.
  • compositions described herein can be for in vitro, in vivo, or ex vivo uses.
  • a pharmaceutical composition comprising a PBD dimer ADC (e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT- PBD2) described herein and a pharmaceutically acceptable carrier or excipient.
  • a PBD dimer ADC e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT- PBD2
  • Pharmaceutically acceptable carriers or pharmaceutically acceptable excipients refer to carriers or excipients approved by a regulatory agency of the Federal or a state government, or listed in the U.S. Pharmacopeia, European Pharmacopeia or other generally recognized
  • Pharmacopeia for use in animals, and more particularly in humans.
  • Therapeutic formulations containing one or more PBD dimer ADCs can, for example, be prepared for storage by mixing the PBD dimer ADCs having the desired degree of purity with optional pharmaceutically acceptable carriers or excipients (Remington's Pharmaceutical Sciences (1990) Mack Publishing Co., Easton, PA; Remington: The Science and Practice of Pharmacy, 21st ed. (2006) Lippincott Williams & Wilkins, Baltimore, MD), in the form of lyophilized formulations or aqueous solutions.
  • Acceptable carriers or excipients are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; and/or non-ionic surfactants such as TWEENTM, PLURONICSTM or polyethylene glycol (PEG).
  • Pharmaceutical carriers suitable for administration of PBD dimer ADCs e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2
  • KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2
  • Formulations can also contain more than one active compounds (for example, molecules, e.g., PBD dimer ADCs described herein) as necessary for the particular indication being treated.
  • formulations comprise a PBD dimer ADC (e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2) provided herein and one or more active compounds with complementary activities that do not adversely affect each other.
  • PBD dimer ADC e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2
  • a PBD dimer ADC e.g., KIT-PBD ADC such as KIT-PBD 1 or ⁇ - PBD2
  • KIT-PBD ADC such as KIT-PBD 1 or ⁇ - PBD2
  • other therapeutic agents e.g. , a tyrosine kinase inhibitor such as imatinib mesylated or sunitinib, or a histone deacetylase inhibitor such as vorinostat.
  • Such combination therapy can be administered to the patient serially or simultaneously or in sequence.
  • the formulations to be used for in vivo administration can be sterile. This can readily accomplished by filtration through, e.g., sterile filtration membranes.
  • the pharmaceutical compositions provided herein contain therapeutically effective amounts of one or more of the PBD dimer ADCs (e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2) provided herein, and optionally one or more additional prophylactic of therapeutic agents, in a pharmaceutically acceptable carrier.
  • PBD dimer ADCs e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2
  • additional prophylactic of therapeutic agents in a pharmaceutically acceptable carrier.
  • Such pharmaceutical compositions are useful in the prevention, treatment, management or amelioration of a disorder or disease such as cancer (e.g., Ewings' sarcoma, small cell lung cancer, leukemia, or GIST) or an inflammatory disorder (e.g., inflammatory bowel disease), or one or more of the symptoms thereof.
  • cancer e.g., Ewings' sarcoma, small cell lung cancer, leukemia, or GIST
  • an inflammatory disorder e
  • compositions containing one or more PBD dimer ADCs provided herein.
  • the PBD dimer ADCs are formulated into suitable pharmaceutical preparations, such as solutions, suspensions, tablets, dispersible tablets, pills, capsules, powders, sustained release formulations or elixirs, for oral administration or in sterile solutions or suspensions for parenteral administration, as well as transdermal patch preparation and dry powder inhalers.
  • one or more ADCs such as PBD dimer ADCs is mixed with a suitable pharmaceutical carrier.
  • concentrations of a PBD dimer ADC or PBD dimer ADCs in the compositions can, for example, be effective for delivery of an amount of a drug(s), upon administration, that treats, prevents, or ameliorates a disorder or disease described herein such as cancer or a symptom thereof.
  • compositions are formulated for single dosage
  • a PBD dimer ADC e.g., KIT-PBD ADC such as KIT-PBD1 or KIT-PBD2
  • KIT-PBD ADC such as KIT-PBD1 or KIT-PBD2
  • Concentration of a PBD dimer ADC e.g. , KIT-PBD dimer ADC such as KIT-PBD 1 or KIT-PBD2 in a pharmaceutical composition will depend on, e.g., the physicochemical characteristics of the antibody and/or the PBD dimer, the dosage schedule, and amount administered as well as other factors known to those of skill in the art.
  • compositions provide a dosage of about 50 mg of PBD dimer ADC per kilogram of body weight for administration over a period of time, e.g., twice daily, every day, every week, every 2 weeks, or every 3 weeks.
  • Pharmaceutical dosage unit forms can be prepared to provide 500 mg, and in one embodiment about 400 mg of a PBD dimer ADC and/or a combination of other optional essential ingredients per dosage unit form.
  • a PBD dimer ADC (e.g., KIT-PBD ADC such as KIT- PBD 1 or KIT-PBD2)described herein is administered at an effective dosage of about 50 mg of PBD dimer ADC per kilogram of body weight for administration over a period of time, e.g., twice daily, every day, every week, every 2 weeks, or every 3 weeks.
  • the resulting mixture can be a solution, suspension, emulsion or the like.
  • the form of the resulting mixture depends upon a number of factors, including the intended mode of administration and the solubility of the compound in the selected carrier or vehicle.
  • the effective concentration is sufficient for ameliorating the symptoms of the disease, disorder or condition treated and can be empirically determined.
  • compositions are provided for:
  • sterile parenteral e.g., intravenous
  • suitable quantities of PBD dimer ADCs e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2
  • KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2
  • compositions are also provided for administration to humans and animals in unit dosage form, such as tablets, capsules, pills, powders, granules, and oral solutions or suspensions, and oil-water emulsions containing suitable quantities of the compounds or pharmaceutically acceptable derivatives thereof.
  • a PBD dimer ADC described herein is, in one embodiment, formulated and administered in unit-dosage forms or multiple-dosage forms.
  • Unit- dose forms as used herein refers to physically discrete units suitable for human and animal subjects and packaged individually as is known in the art. Each unit-dose contains a
  • unit-dose forms include ampoules and syringes and individually packaged tablets or capsules. Unit-dose forms can be administered in fractions or multiples thereof.
  • a multiple-dose form is a plurality of identical unit-dosage forms packaged in a single container to be administered in segregated unit-dose form. Examples of multiple-dose forms include vials, bottles of tablets or capsules or bottles of pints or gallons. Hence, multiple dose form is a multiple of unit-doses which are not segregated in packaging.
  • one or more PBD dimer ADCs described herein are in a liquid pharmaceutical formulation.
  • Liquid pharmaceutically administrable compositions can, for example, be prepared by dissolving, dispersing, or otherwise mixing an active compound as defined above and optional pharmaceutical adjuvants in a carrier, such as, for example, water, saline, aqueous dextrose, glycerol, glycols, ethanol, and the like, to thereby form a solution or suspension.
  • a carrier such as, for example, water, saline, aqueous dextrose, glycerol, glycols, ethanol, and the like.
  • the pharmaceutical composition to be administered can also contain minor amounts of nontoxic auxiliary substances such as wetting agents, emulsifying agents, solubilizing agents, and pH buffering agents and the like.
  • Parenteral administration in one embodiment, is characterized by injection, either subcutaneously, intramuscularly or intravenously is also contemplated herein.
  • injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions.
  • the injectables, solutions and emulsions also contain one or more excipients. Suitable excipients are, for example, water, saline, dextrose, glycerol or ethanol.
  • compositions to be administered can also contain minor amounts of non-toxic auxiliary substances such as wetting or emulsifying agents, pH buffering agents, stabilizers, solubility enhancers, and other such agents.
  • auxiliary substances such as wetting or emulsifying agents, pH buffering agents, stabilizers, solubility enhancers, and other such agents.
  • Other routes of administration may include, enteric administration, intracerebral administration, nasal administration, intraarterial administration, intracardiac administration, intraosseous infusion, intrathecal administration, and intraperitoneal administration.
  • Preparations for parenteral administration include sterile solutions ready for injection, sterile dry soluble products, such as lyophilized powders, ready to be combined with a solvent just prior to use, including hypodermic tablets, sterile suspensions ready for injection, sterile dry insoluble products ready to be combined with a vehicle just prior to use and sterile emulsions.
  • the solutions can be either aqueous or nonaqueous.
  • suitable carriers include physiological saline or phosphate buffered saline (PBS), and solutions containing thickening and solubilizing agents, such as glucose, polyethylene glycol, and polypropylene glycol and mixtures thereof.
  • PBS physiological saline or phosphate buffered saline
  • pharmaceutically acceptable carriers used in parenteral preparations include aqueous vehicles, nonaqueous vehicles, antimicrobial agents, isotonic agents, buffers, antioxidants, local anesthetics, suspending and dispersing agents, emulsifying agents, sequestering or chelating agents and other pharmaceutically acceptable substances.
  • pharmaceutical carriers also include ethyl alcohol, polyethylene glycol and propylene glycol for water miscible vehicles; and sodium hydroxide, hydrochloric acid, citric acid or lactic acid for pH adjustment.
  • intravenous or intraarterial infusion of a sterile aqueous solution containing a PBD dimer ADC can be an effective mode of administration.
  • Another embodiment is a sterile aqueous or oily solution or suspension containing a PBD dimer ADC injected as necessary to produce the desired pharmacological effect.
  • the PBD dimer ADC can be suspended in micronized or other suitable form.
  • the form of the resulting mixture depends upon a number of factors, including the intended mode of administration and the solubility of the compound in the selected carrier or vehicle.
  • the effective concentration is sufficient for ameliorating one or more symptoms of a disorder or condition described herein and can be empirically determined.
  • the pharmaceutical formulations are lyophilized powders, which can be reconstituted for administration as solutions, emulsions and other mixtures. They can also be reconstituted and formulated as solids or gels.
  • the lyophilized powder is prepared by dissolving a PBD dimer ADC provided herein, in a suitable solvent.
  • the lyophilized powder is sterile.
  • the solvent can contain an excipient which improves the stability or other
  • pharmacological component of the powder or reconstituted solution, prepared from the powder Excipients that can be used include, but are not limited to, dextrose, sorbital, fructose, corn syrup, xylitol, glycerin, glucose, sucrose or other suitable agent.
  • the solvent can also contain a buffer, such as citrate, sodium or potassium phosphate or other such buffer known to those of skill in the art at, in one embodiment, about neutral pH.
  • Subsequent sterile filtration of the solution followed by lyophilization under standard conditions known to those of skill in the art provides the desired formulation.
  • the resulting solution will be apportioned into vials for lyophilization. Each vial will contain a single dosage or multiple dosages of the compound.
  • the lyophilized powder can be stored under appropriate conditions, such as at about 4 °C to room temperature.
  • Reconstitution of this lyophilized powder with water for injection provides a formulation for use in parenteral administration.
  • the lyophilized powder is added to sterile water or other suitable carrier. The precise amount depends upon the selected compound. Such amount can be empirically determined.
  • PBD dimer ADCs e.g. , KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2
  • KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2
  • Topical administration is contemplated for transdermal delivery and also for administration to the eyes or mucosa, or for inhalation therapies. Nasal solutions of the active compound alone or in combination with other pharmaceutically acceptable excipients can also be administered.
  • PBD dimer ADCs e.g. , KIT-PBD ADCs such as KIT-PBD 1 or KIT-PBD2
  • KIT-PBD ADCs such as KIT-PBD 1 or KIT-PBD2
  • other compositions provided herein can also be formulated to be targeted to a particular cell or tissue, receptor, or other area of the body of the subject to be treated.
  • Many such targeting methods are well known to those of skill in the art. All such targeting methods are contemplated herein for use in the instant compositions.
  • targeting methods see, e.g., U.S. Patent Nos.
  • the PBD dimer ADCs described herein are targeted (or otherwise administered) to the bone marrow, such as in a patient having or at risk of having leukemia.
  • PBD dimer ADCs e.g., KIT-PBD ADC such as KIT-PBDl or KIT-PBD2
  • KIT-PBD ADC such as KIT-PBDl or KIT-PBD2
  • PBD dimer ADCs described herein are targeted (or otherwise administered) to the gastrointestinal tract, such as in a patient having or at risk of having gastrointestinal stromal tumors.
  • PBD dimer ADCs described herein are targeted (or otherwise administered) to the lungs, such as in a patient having or at risk of lung cancer (e.g., small cell lung cancer).
  • lung cancer e.g., small cell lung cancer
  • PBD dimer ADCs e.g., KIT-PBD ADC such as KIT-PBDl or KIT-PBD2
  • KIT-PBD ADC such as KIT-PBDl or KIT-PBD2
  • a PBD dimer ADC described herein is capable of crossing the blood-brain barrier.
  • a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions described herein, such as one or more PBD dimer ADCs provided herein.
  • Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration.
  • kits for impeding, preventing, treating and/or managing disorders or diseases such as KIT-associated disorders or diseases comprise administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate (e.g. , KIT-PBD ADC) comprising an anti-KIT antibody described herein (e.g., humanized antibodies, and antigen-binding fragments thereof, or conjugates thereof).
  • an ADC such as a PBD dimer conjugate (e.g. , KIT-PBD ADC) comprising an anti-KIT antibody described herein (e.g., humanized antibodies, and antigen-binding fragments thereof, or conjugates thereof).
  • KIT-PBD ADC e.g., humanized antibodies, and antigen-binding fragments thereof, or conjugates thereof.
  • methods for preventing, impeding, treating or managing one or more symptoms of a disorder or disease such as a KIT- associated disorder or disease.
  • Non-limiting examples of such disorder or disease include cancer, mast cell or eosinophil related disorder (e.g., mastocytosis, neurofibromatosis or neuromyelitis optica), or an inflammatory disorder.
  • administer or “administration” refers to the act of injecting or otherwise physically delivering a substance (e.g.
  • an ADC such as a PBD dimer conjugate comprising a humanized anti-KIT antibody provided herein or an antigen-binding fragment thereof
  • a subject or a patient e.g., human
  • the terms "effective amount” or “therapeutically effective amount” refer to an amount of a therapy (e.g., a humanized antibody or pharmaceutical composition provided herein) which is sufficient to reduce and/or ameliorate the severity and/or duration of a given disease and/or a symptom related thereto. These terms also encompass an amount necessary for the reduction or amelioration of the advancement or progression of a given disease, reduction or amelioration of the recurrence, development or onset of a given disease, and/or to improve or enhance the prophylactic or therapeutic effect(s) of another therapy (e.g., a therapy other than an anti-KIT antibody provided herein).
  • a therapy e.g., a humanized antibody or pharmaceutical composition provided herein
  • "effective amount” as used herein also refers to the amount of an antibody described herein to achieve a specified result (e.g. , inhibition (e.g. , partial inhibition) of a KIT biological activity of a cell, such as inhibition of cell proliferation or cell survival, or enhancement or induction of apoptosis or cell
  • the term "in combination” in the context of the administration of other therapies refers to the use of more than one therapy.
  • the use of the term “in combination” does not restrict the order in which therapies are administered.
  • the therapies may be
  • the terms “manage,” “managing,” and “management” refer to the beneficial effects that a subject derives from a therapy (e.g., a prophylactic or therapeutic agent), which does not result in a cure of a KIT-associated disease or disorder.
  • a subject is administered one or more therapies (e.g., prophylactic or therapeutic agents, such as an antibody described herein) to "manage” a KIT-associated disease (e.g., cancer, inflammatory condition, or fibrosis), one or more symptoms thereof, so as to prevent the progression or worsening of the disease.
  • a KIT-associated disease e.g., cancer, inflammatory condition, or fibrosis
  • the terms "impede” or “impeding” in the context of a KIT- associated disorder or disease refer to the total or partial inhibition (e.g., less than 100%, 95%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, or 5%) or blockage of the development, recurrence, onset or spread of a KIT-associated disease and/or symptom related thereto, resulting from the administration of a therapy or combination of therapies provided herein (e.g., a combination of prophylactic or therapeutic agents, such as an antibody described herein).
  • a therapy or combination of therapies provided herein (e.g., a combination of prophylactic or therapeutic agents, such as an antibody described herein).
  • the term “prophylactic agent” refers to any agent that can totally or partially inhibit the development, recurrence, onset or spread of a KIT-associated disease and/or symptom related thereto in a subject.
  • the term “prophylactic agent” refers to an antibody described herein.
  • the term “prophylactic agent” refers to an agent other than an antibody described herein.
  • a prophylactic agent is an agent which is known to be useful to or has been or is currently being used to prevent a KIT-associated disease and/or a symptom related thereto or impede the onset, development, progression and/or severity of a KIT-associated disease and/or a symptom related thereto.
  • the prophylactic agent is a human anti-KIT antibody, such as a humanized or a fully human anti-KIT monoclonal antibody.
  • side effects encompasses unwanted and adverse effects of a therapy (e.g., a prophylactic or therapeutic agent). Unwanted effects are not necessarily adverse. An adverse effect from a therapy (e.g., a prophylactic or therapeutic agent) can be harmful or uncomfortable or risky.
  • side effects include, diarrhea, cough, gastroenteritis, wheezing, nausea, vomiting, anorexia, abdominal cramping, fever, pain, loss of body weight, dehydration, alopecia, dyspenea, insomnia, dizziness, mucositis, nerve and muscle effects, fatigue, dry mouth, and loss of appetite, rashes or swellings at the site of administration, flu-like symptoms such as fever, chills and fatigue, digestive tract problems and allergic reactions. Additional undesired effects experienced by patients are numerous and known in the art. Many are described in the Physician's Desk Reference (63 rd ed., 2009).
  • a subject is a mammal such as a non-primate (e.g., cows, pigs, horses, cats, dogs, goats, rabbits, rats, mice, etc.) or a primate (e.g., monkey and human), e.g., a human.
  • the subject is a mammal, such as a human, having a KIT-associated disorder or disease.
  • the subject is a mammal, such as a human, at risk of developing a KIT-associated disorder or disease.
  • the subject is a non- human primate.
  • the subject is an adult human subject at least 18 years old.
  • therapies can refer to any protocol(s), method(s), compositions, formulations, and/or agent(s) that can be used in the prevention, treatment, management, or amelioration of a condition or disorder or symptom thereof (e.g., cancer or one or more symptoms or condition associated therewith; inflammatory condition or one or more symptoms or condition associated therewith; fibrosis or one or more symptoms or condition associated therewith).
  • a condition or disorder or symptom thereof e.g., cancer or one or more symptoms or condition associated therewith; inflammatory condition or one or more symptoms or condition associated therewith; fibrosis or one or more symptoms or condition associated therewith.
  • the terms “therapies” and “therapy” refer to drug therapy, adjuvant therapy, radiation, surgery, biological therapy, supportive therapy, and/or other therapies useful in treatment, management, prevention, or amelioration of a condition or disorder or one or more symptoms thereof (e.g., cancer or one or more symptoms or condition associated therewith; inflammatory condition or one or more symptoms or condition associated therewith; fibrosis or one or more symptoms or condition associated therewith).
  • the term “therapy” refers to a therapy other than an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or pharmaceutical
  • an “additional therapy” and “additional therapies” refer to a therapy other than a treatment using an anti-KIT antibody described herein or pharmaceutical composition.
  • a therapy includes the use of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein as an adjuvant therapy.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein in conjunction with a drug therapy, biological therapy, surgery, and/or supportive therapy.
  • the term “therapeutic agent” refers to any agent that can be used in the treatment, management or amelioration of a KIT-associated disease and/or a symptom related thereto.
  • the term “therapeutic agent” refers to an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g. , any one of antibodies Huml-Hum20), an antigen-binding fragment thereof.
  • the term “therapeutic agent” refers to an agent other than a PBD dimer conjugate comprising an anti-KIT antibody described herein.
  • a therapeutic agent is an agent which is known to be useful for, or has been or is currently being used for the treatment, management or amelioration of a KIT-associated disease or one or more symptoms related thereto.
  • KIT-associated disorder or “KIT-associated disease” are used interchangeably and refer to any disorder or disease involving KIT expression and/or KIT activity, or to any disorder or disease that is completely or partially caused by, associated with, or is the result of, KIT expression and/or activity or lack thereof.
  • a KIT-associated disorder or disease can be known to one of skill in the art or can be ascertained by one of skill in the art.
  • a KIT-associated disease or disorder is associated with KIT expression and/or activity.
  • KIT expression and/or activity may be present in cells and/or tissue associated or related to a disease or disorder, and may or may not contribute to development and/or progression of a KIT-associated disease or disorder.
  • KIT expression and/or activity may contribute, in combination with one or more other factors (e.g., mutation or expression and/or activity of another gene), to development and/or progression of a KIT-associated disease or disorder.
  • a KIT-associated disease or disorder is associated with one or more mutations of KIT.
  • a KIT-associated disease is fibrosis or an inflammatory disorder, e.g., asthma, arthritis, inflammatory bowel disease (IBD), such as Crohn's disease (CD) or ulcerative colitis (UC).
  • IBD inflammatory bowel disease
  • UC ulcerative colitis
  • a KIT-associated disease is cancer, such as lung cancer (e.g., small cell lung cancer), leukemia, neuroblastoma, melanoma, sarcoma (e.g., Ewing's sarcoma) or gastrointestinal stromal tumor (GIST).
  • lung cancer e.g., small cell lung cancer
  • leukemia e.g., neuroblastoma, melanoma
  • sarcoma e.g., Ewing's sarcoma
  • GIST gastrointestinal stromal tumor
  • a KIT- associated disease is a mast cell or eosinophil related disorder, such as neuromyelitis optica (NMO) or NMO spectrum disorder (NMOSD), multiple sclerosis (MS), and neurofibromatosis (NF).
  • NMO neuromyelitis optica
  • NMO spectrum disorder NMO spectrum disorder
  • MS multiple sclerosis
  • NF neurofibromatosis
  • the terms “treat,” “treatment” and “treating” refer to the reduction or amelioration of the progression, severity, and/or duration of a KIT-associated disease (e.g., cancer, inflammatory disorder, or fibrosis) resulting from the administration of one or more therapies (including, but not limited to, the administration of one or more prophylactic or therapeutic agents, such as an antibody provided herein).
  • a KIT-associated disease e.g., cancer, inflammatory disorder, or fibrosis
  • therapies including, but not limited to, the administration of one or more prophylactic or therapeutic agents, such as an antibody provided herein.
  • methods described herein for treating a KIT-associated disorder or disease provide for the reduction or amelioration of the progression, severity, and/or duration of a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, or fibrosis) resulting from the administration of one or more therapies (including, but not limited to, the administration of one or more prophylactic or therapeutic agents, such as an ADC, e.g., PBD dimer conjugate, comprising an anti-KIT antibody described herein).
  • methods described herein for treating a KIT-associated disorder or disease relate to reducing one or more symptoms of a KIT-associated disorder or disease.
  • an ADC such as a PBD dimer conjugate provided herein comprising any one of anti-KIT antibodies Huml-Hum20, e.g., antibody Hum8 or Hum4 or Huml7 or HumlO, or an antigen-binding fragment thereof, is for use in treating or managing a KIT-associated disorder (e.g., cancer).
  • a KIT-associated disorder e.g., cancer
  • a KIT-associated disease or disorder being treated or managed with an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein, or an antigen-binding fragment thereof, is associated with KIT expression and/or activity, e.g., involves cells expressing KIT and/or exhibiting KIT activity, but is not caused by or the result of KIT expression or activity.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody (e.g., a humanized anti-KIT antibody), for example any one of antibodies Huml-Hum20, or Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof, for use in treating or managing a KIT-associated disorder (e.g., cancer), wherein the antibody comprises (i) a VL chain region having the amino acid sequence of SEQ ID NO: 7, 8, 9, or 10, and/or (ii) a VH chain region having the amino acid sequence of SEQ ID NO: 2, 3, 4, 5, or 6.
  • an anti-KIT antibody e.g., a humanized anti-KIT antibody
  • the antibody comprises (i) a VL chain region having the amino acid sequence of SEQ ID NO: 7, 8, 9, or 10, and/or (ii) a VH chain region having the amino acid sequence of SEQ ID NO: 2, 3, 4, 5, or 6.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody, or an antigen-binding fragment thereof, for use in treating or managing a KIT-associated disorder (e.g., cancer), wherein the antibody comprises a combination of a VH domain (e.g., H1-H5, SEQ ID NOs: 2-6) and a VL domain (L1-L4, SEQ ID NOs: 7-10) selected from the group presented in Table 4.
  • a VH domain e.g., H1-H5, SEQ ID NOs: 2-6
  • VL domain L1-L4, SEQ ID NOs: 7-10
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody (e.g. , a humanized anti-KIT antibody) for example, any one of anti-KIT antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof, for use in treating or managing a KIT-associated disorder (e.g., cancer), wherein the antibody comprises (i) a VL chain region comprising the amino acid sequence of SEQ ID NO: 12 (see, e.g., Figure 2K), and/or (ii) a VH chain region comprising the consensus amino acid sequence of SEQ ID NO: 11 (see, e.g., Figure 2J).
  • an anti-KIT antibody e.g. , a humanized anti-KIT antibody
  • Huml-Hum20 such as Huml7, HumlO, Hum8 or Hum4
  • an antigen-binding fragment thereof for use in treating or managing a KIT-associated disorder (e
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen- binding fragment thereof, for use in treating or managing a KIT-associated disorder (e.g.
  • the antibody comprises (i) a VL chain region comprising an amino acid sequence set forth in Table 6A (e.g., L1-L4 and LL1-LL62), and/or (ii) a VH chain region comprising the amino acid sequence set forth in Table 6B (e.g., H1-H5 and HH1-HH256).
  • Table 6A e.g., L1-L4 and LL1-LL62
  • VH chain region comprising the amino acid sequence set forth in Table 6B (e.g., H1-H5 and HH1-HH256).
  • the ADC such as a PBD dimer conjugate provided herein comprises an anti-KIT antibody used in the methods described herein is internalized by the cell to which it binds.
  • KIT is aberrantly (e.g., highly) expressed by cells, for example, KIT is overexpressed.
  • KIT expression e.g., on the cell surface
  • a control cell e.g., a cell expressing normal levels of KIT, for example, a normal, e.g., human, mast cell, stem cell, brain cell, melanoblast, or ovary cell.
  • KIT expression yields at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 250%, or 500% higher cell surface KIT expression than the average KIT expression on the surface of a control cell population (e.g., a cell population expressing normal levels of KIT, for example, a normal, e.g., human, mast cell population, stem cell population, brain cell population, melanoblast population, or ovary cell population).
  • a control cell population e.g., a cell population expressing normal levels of KIT, for example, a normal, e.g., human, mast cell population, stem cell population, brain cell population, melanoblast population, or ovary cell population.
  • control cells can be obtained or derived from a healthy individual (e.g., healthy human).
  • KIT can be aberrantly upregulated in a particular cell type, whether or not KIT is aberrantly expressed on the cell surface.
  • KIT signaling or activity can be aberrantly upregulated in a particular cell type, whether or not KIT is aberrantly expressed on the cell surface.
  • KIT signaling is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 250%, or 500% higher than KIT signaling of a control cell (e.g., a cell containing normal KIT signaling, for example, a mast cell, stem cell, brain cell, melanoblast, or ovary cell).
  • KIT signaling is at least about 10%>, 20%>, 30%>, 40%>, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 250%, or 500% higher than average KIT signaling of a control cell population (e.g. , a cell population exhibiting normal KIT signaling, for example, a normal, e.g. , human, mast cell population, stem cell population, brain cell population, melanoblast population, or ovary cell population).
  • normal, aberrant or excessive cell signaling is caused by binding of KIT to a KIT ligand.
  • aberrant or excessive cell signaling occurs independent of binding of KIT to a KIT ligand.
  • a KIT-associated disorder or disease can be characterized by gain- of-function KIT activity, increase in KIT activity, or overexpression of KIT.
  • a KIT-associated disorder or disease is completely or partially caused by or is the result of gain-of-function KIT activity or expression, e.g., overexpression, of KIT.
  • the gain-of-function KIT activity can occur independent of KIT ligand (e.g., SCF) binding KIT receptor.
  • high or overexpression of KIT in a cell refers to an expression level which is at least about 35%, 45%, 55%, or 65% more than the expression level of a reference cell known to have normal KIT expression or KIT activity or more than the average expression level of KIT in a population of cells or samples known to have normal KIT expression or KIT activity.
  • KIT-associated disorder or disease is characterized by KIT activity which is higher than normal KIT activity and contributes to cellular transformation, neoplasia, and tumorogenesis.
  • high or increase of KIT activity in a cell refers to a KIT activity level which is at least about 35%, 45%, 55%, or 65% more than the expression level of a reference cell known to have normal KIT activity or more than the average level of KIT activity in a population of cells or samples known to have normal KIT activity.
  • a KIT activity includes tyrosine phosphorylation of the cytoplasmic domain of KIT, and signaling downstream of KIT, such as Stat or Akt signaling.
  • Non-limiting examples of disorders or KIT-associated disorders or diseases include cancers such as breast cancer, leukemia (e.g., chronic myelogenous leukemia, acute myeloid leukemia (AML), mast cell leukemia), lung cancer (e.g., small cell lung cancer), neuroblastoma, gastrointestinal stromal tumors (GIST), melanoma, colorectal cancer, sarcoma (e.g., Ewing's sarcoma), and germ cell tumors (e.g., seminoma).
  • a cancer which is treated or managed by the methods provided herein is characterized by a gain-of-function KIT mutation or overexpression of KIT.
  • a method described herein is for treating cancer (e.g., GIST, leukemia (e.g., erythroid leukemia), lung cancer (e.g., small cell lung cancer), or sarcoma (e.g., Ewing's sarcoma)), wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate (e.g.
  • PBD dimer conjugate comprising compound 42 or 45
  • an anti-KIT antibody described herein e.g., a humanized anti-KIT antibody
  • kits for preventing, treating or managing one or more symptoms of cancer comprising administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti- KIT antibody described herein (e.g., a humanized anti-KIT antibody), for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an ADC such as a PBD dimer conjugate comprising an anti- KIT antibody described herein (e.g., a humanized anti-KIT antibody), for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating cancer described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3).
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating cancer described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
  • a method described herein is for treating leukemia (e.g. , erythroid leukemia) or lung cancer (e.g., small cell lung cancer), wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising (i) an anti-KIT antibody described herein (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, Huml O, Hum8 or Hum4, or an antigen-binding fragment thereof, (ii) a PBD dimer, and optionally, a linker, such as in compound 45.
  • an ADC such as a PBD dimer conjugate comprising (i) an anti-KIT antibody described herein (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, Huml O, Hum8 or Hum4, or an antigen-binding fragment
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating leukemia (e.g., erythroid leukemia) or lung cancer (e.g. , small cell lung cancer) described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3).
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating leukemia (e.g., erythroid leukemia) or lung cancer (e.g., small cell lung cancer) described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
  • leukemia e.g., erythroid leukemia
  • lung cancer e.g., small cell lung cancer
  • a method described herein is for treating sarcoma (e.g., Ewing's sarcoma) or lung cancer (e.g., small cell lung cancer), wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising (i) an anti-KIT antibody described herein (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, Huml O, Hum8 or Hum4, or an antigen-binding fragment thereof and (ii) a PBD dimer and optionally, a linker, such as in compound 42.
  • an ADC such as a PBD dimer conjugate comprising (i) an anti-KIT antibody described herein (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, Huml O, Hum8 or Hum4, or an antigen-bind
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating sarcoma (e.g., Ewing's sarcoma) or lung cancer (e.g. , small cell lung cancer) described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3).
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating sarcoma (e.g.
  • Ewing's sarcoma or lung cancer (e.g., small cell lung cancer) described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
  • VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI)
  • VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
  • a method described herein is for treating GIST, wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • kits for preventing, treating or managing one or more symptoms of GIST comprising administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti- KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an ADC such as a PBD dimer conjugate comprising an anti- KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating GIST described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3).
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating GIST described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
  • a method described herein is for treating lung cancer (e.g., small cell lung carcinoma), wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml 7, HumlO, Hum8 or Hum4, or an antigen- binding fragment thereof conjugated to a PBD dimer, such as in compound 42 or 45, optionally comprising a linker (e.g., reactive linker) as in compound 42 or 45.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml 7, HumlO, Hum8 or Hum4, or an antigen- binding fragment thereof conjugated to a PBD dimer, such as
  • kits for preventing, treating or managing one or more symptoms of lung cancer comprising administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof conjugated to a PBD such as compound 42 or 45.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof conjugated to a PBD such as compound 42 or 45.
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating lung cancer comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3).
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating lung cancer comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
  • a method described herein is for treating melanoma, wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • kits for preventing, treating or managing one or more symptoms of melanoma comprising administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating melanoma described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3).
  • an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating melanoma described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
  • a cancer treated in accordance with the methods described herein can be any type of cancer which comprises cancer or tumor cells expressing cell surface KIT or a mutated form thereof, which can be confirmed by any histologically or cytologically method known to one of skill in the art.
  • a cancer is metastatic. In certain embodiments, a cancer is an advanced cancer which has spread outside the site or organ of origin, either by local invasion or metastasis.
  • a cancer is a recurrent cancer which has regrown, either at the initial site or at a distant site, after a response to initial therapy (e.g., after surgery to remove the tumor and adjuvant therapy following surgery).
  • a cancer is a refractory cancer which progresses even though an anti-tumor agent, such as a chemotherapeutic agent, is being administered, or has been administered, to the cancer patient.
  • a non-limiting example of a refractory cancer is one which is refractory to a tyrosine kinase inhibitor, such as GLEEVEC® (imatinib mesylate), SUTENT® (SU1 1248 or sunitinib), IRESSATM (gefitinib), TARCEVA® (erlotinib), NEXAVAR® (sorafenib), or VOTRIENTTM (pazopanib).
  • a cancer is a refractory cancer which progresses even though radiation or chemotherapy is being administered, or has been administered, to the cancer patient.
  • tyrosine kinase inhibitors include 706 and AMNI07 (nilotinib). RADOOI, PKC412, gefitinib (IRESSATM), erlotinib
  • TARCEVA ® sorafenib
  • NEXAVAR ® sorafenib
  • YAVAR ® sorafenib
  • VOTRIENTTM axitinib
  • bosutinib cediranib
  • SPRYCEL ® dasatinib
  • lapatinib TYKERB ®
  • lestaurtinib neratinib
  • nilotinib TASIGNA ®
  • semaxanib toceranib
  • PALLADIATM vandetanib
  • ZACTIMATM vandetanib
  • the refractory cancer was initially responsive to an anticancer agent, such as a tyrosine kinase inhibitor (e.g., GLEEVEC ® or SU11248 (i.e., sunitinib)), but has developed resistance the anti-cancer agent.
  • a subject has one or more mutations in KIT that confers resistance to an anti-cancer agent such as a tyrosine kinase inhibitor.
  • an antibody described herein is administered to a patient who has previously received, or is currently receiving, one or more anti-cancer therapies, for example, a chemotherapeutic agent, or a tyrosine kinase inhibitor (e.g.
  • GLEEVEC ® imatinib mesylate
  • SUTENT ® SU11248 or sunitinib
  • IRESSATM gefitinib
  • TARCEVA TARCEVA
  • NEXAVAR ® sorafenib
  • VOTRIENTTM pazopanib
  • a histone deacetylase inhibitor e.g., vorinostat (suberoylanilide hydroxamic acid (SAHA)
  • SAHA suberoylanilide hydroxamic acid
  • an antibody described herein is administered to a patient who is, or is suspected of being, resistant or refractory to an anti-cancer therapy, for example, a tyrosine kinase inhibitor, e.g.
  • GLEEVEC ® imatinib mesylate
  • SUTENT ® SU11248 or sunitinib
  • IRESSATM gefitinib
  • TARCEVA erlotinib
  • NEXAVAR ® sorafenib
  • VOTRIENTTM pazopanib
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, or an antigen binding fragment thereof (e.g., KIT-binding fragment thereof)) is administered to a patient who has previously received, or is currently receiving, one or more anti-cancer therapies, for example, an anti-growth factor receptor antibody (e.g., anti-HER2 antibody, anti-EGFR antibody, anti- VEGFR antibody, or anti-KIT antibody), or anti-growth factor antibody (e.g., anti-EGF antibody, anti-VEGF antibody).
  • an anti-growth factor receptor antibody e.g., anti-HER2 antibody, anti-EGFR antibody, anti- VEGFR antibody, or anti-KIT antibody
  • anti-growth factor antibody e.g., anti-EGF antibody, anti-VEGF antibody
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is administered to a patient who is, or is suspected of being, resistant or refractory to an anti-cancer therapy, for example, an anti- growth factor receptor antibody (e.g. , anti-HER2 antibody, anti-EGFR antibody, anti-VEGFR antibody, or anti-KIT antibody) or anti-growth factor antibody (e.g., anti-EGF antibody, anti- VEGF antibody).
  • an anti- growth factor receptor antibody e.g. , anti-HER2 antibody, anti-EGFR antibody, anti-VEGFR antibody, or anti-KIT antibody
  • anti-growth factor antibody e.g., anti-EGF antibody, anti- VEGF antibody
  • a method described herein for treating or managing cancer in a subject in need thereof can achieve at least one, two, three, four or more of the following effects due to administration of a therapeutically effective amount of an anti-KIT antibody described herein: (i) the reduction or amelioration of the severity of cancer (e.g., leukemia, lung cancer, or gastrointestinal stromal cancer) and/or one or more symptoms associated therewith; (ii) the reduction in the duration of one or more symptoms associated with a cancer (e.g., leukemia, lung cancer, or gastrointestinal stromal cancer); (iii) the prevention in the recurrence of a tumor (e.g.
  • a cancer e.g., leukemia, lung cancer, or gastrointestinal stromal tumor
  • the regression of a cancer e.g., leukemia, lung cancer, or gastrointestinal stromal tumor
  • the reduction in hospitalization of a subject e.g., the reduction in hospitalization length
  • the increase in the survival of a subject e.g. , the inhibition of the progression of a cancer (e.g. , leukemia, lung cancer, or gastrointestinal stromal tumor) and/or one or more symptoms associated therewith
  • cancer cell population e.g. , leukemia cell population, lung cancer cell population, gastrointestinal stromal tumor cell population
  • a reduction in the growth of a tumor or neoplasm e.g., leukemia cell population, lung cancer cell population, gastrointestinal stromal tumor cell population
  • a decrease in tumor size e.g., volume or diameter
  • a reduction in the formation of a newly formed tumors e.g., eradication, removal, or control of primary, regional and/or metastatic cancer
  • xv ease in removal of a tumor by reducing tumor and/or edema-related vascularization prior to surgery
  • a decrease in the number or size of metastases a reduction in mortality
  • xviii an increase in tumor- free survival rate of patients
  • an increase or elimination in the cancer cell population e.g. , leukemia cell population, lung cancer cell population, gastrointestinal stromal tumor cell population
  • a decrease in tumor size
  • kits for killing cancer cells in an individual comprising administering to an individual in need thereof an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • kits for inhibiting growth or proliferation of cancer cells in an individual comprising administering to an individual in need thereof an effective amount of an ADC such as a PBD dimer conjugate comprising an anti- KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an ADC such as a PBD dimer conjugate comprising an anti- KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • ADC such as a PBD dimer conjugate comprising an anti- KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8
  • kits for delaying tumor growth or for reducing tumor size or load in an individual in need thereof comprising administering to said individual an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof.
  • KIT-associated disorders or diseases include systemic mast cell disorders (e.g., mastocytosis), hematologic disorders, fibrosis (e.g., idiopathic pulmonary fibrosis (TPF), scleroderma, or myelofibrosis) and inflammatory conditions such as asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation.
  • systemic mast cell disorders e.g., mastocytosis
  • fibrosis e.g., idiopathic pulmonary fibrosis (TPF), scleroderma, or myelofibrosis
  • inflammatory conditions such as asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation.
  • a method described herein for treating or managing a KIT-associated disorder e.g., fibrosis or an inflammatory condition (e.g., asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation), in a subject in need thereof, can achieve at least one, two, three, four or more of the following effects due to administration of a therapeutically effective amount of an anti-KIT antibody described herein: (i) the reduction or amelioration of the severity of fibrosis or an inflammatory condition (e.g., asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation) and/or one or more symptoms associated therewith; (ii) the reduction in the duration of one or more symptoms associated with fibrosis or an inflammatory condition (e.g., asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation); (iii) the prevention in the recurrence of fibrosis or an inflammatory condition
  • fibrosis or an inflammatory condition e.g. , asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation
  • inflammatory condition e.g. , asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation
  • the enhancement or improvement of the therapeutic effect of another therapy e.g. , anti-inflammatory therapy such as steroids
  • an increase in the number of patients in remission i.e., a time period characterized by no or minimal symptoms associated with the inflammatory condition
  • an increase in the length of remission in patients i.e., a decrease in hospitalization rate
  • fibrosis or an inflammatory condition e.g.
  • a decrease in the concentration of one or more inflammatory mediators e.g., cytokines or interleukins
  • biological specimens e.g. , plasma, serum, cerebral spinal fluid, urine, or any other biofluids
  • an inflammatory condition e.g., asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation
  • improvement in the quality of life as assessed by methods well known in the art, e.g., questionnaires.
  • an anti-KIT antibody described herein may be administered by any suitable method to a subject in need thereof.
  • administration methods include mucosal, intradermal, intravenous, intratumoral, subcutaneous, intramuscular delivery and/or any other method of physical delivery described herein or known in the art.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody or a pharmaceutical composition thereof is administered systemically (e.g., parenterally) to a subject in need thereof.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody or a pharmaceutical composition thereof is administered locally (e.g. , intratumorally) to a subject in need thereof.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein can be administered via multiple routes of administration simultaneously or subsequently to other doses of the same or a different ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein.
  • ADCs such as PBD dimer conjugates, comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof, useful in therapeutic methods to prevent, manage or treat an eosinophil or mast cell related disorder, such as an eosinophil or mast cell related disorder of the central nervous system or nervous system.
  • an anti-KIT antibody e.g., any one of antibodies Huml-Hum20
  • an anti-KIT antibody e.g., any one of antibodies Huml-Hum20
  • antigen binding fragment thereof useful in therapeutic methods to prevent, manage or treat an eosinophil or mast cell related disorder, such as an eosinophil or mast cell related disorder of the central nervous system or nervous system.
  • eosinophil or mast cell related disorder such as an eosinophil or mast cell related disorder of the central nervous system or nervous system.
  • disorders include neuromyelitis optica (NMO) or NMO spectrum disorder (NMOSD), multiple s
  • a method of protecting against, treating, or managing an eosinophil or mast cell related disorder of the central nervous system or nervous system in a subject comprising administering to a subject in need thereof a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
  • an ADC such as a PBD dimer conjugate
  • an anti-KIT antibody e.g., any one of antibodies Huml-Hum20
  • an antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
  • a method of protecting against, treating, or managing neuromyelitis optica (NMO) in a subject comprising administering to a subject in need thereof a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
  • an ADC such as a PBD dimer conjugate
  • an anti-KIT antibody e.g., any one of antibodies Huml-Hum20
  • an antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
  • a method of protecting against, treating, or managing a NMO spectrum disorder in a subject comprising administering to a subject in need thereof a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g. , human KIT, such as a D4 domain of human KIT.
  • an ADC such as a PBD dimer conjugate
  • an anti-KIT antibody e.g., any one of antibodies Huml-Hum20
  • an antigen binding fragment thereof which specifically binds to KIT, e.g. , human KIT, such as a D4 domain of human KIT.
  • a method of protecting against, treating, or managing multiple sclerosis (MS) in a subject comprising administering to a subject in need thereof a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g. , human KIT, such as a D4 domain of human KIT.
  • an ADC such as a PBD dimer conjugate
  • an anti-KIT antibody e.g., any one of antibodies Huml-Hum20
  • human KIT such as a D4 domain of human KIT.
  • NF neurofibromatosis
  • a method of protecting against, treating, or managing neurofibromatosis (NF) in a subject comprising administering to a subject in need thereof a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g. , human KIT, such as a D4 domain of human KIT.
  • an ADC such as a PBD dimer conjugate
  • an anti-KIT antibody e.g., any one of antibodies Huml-Hum20
  • an antigen binding fragment thereof which specifically binds to KIT, e.g. , human KIT, such as a D4 domain of human KIT.
  • a method of inhibiting growth of neurofibromas in a subject comprising administering to a subject diagnosed with NF a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
  • an ADC such as a PBD dimer conjugate
  • an anti-KIT antibody e.g., any one of antibodies Huml-Hum20
  • an antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
  • a method of reducing inflammation for example, inflammation of the nervous system, e.g., central nervous system, in a subject, comprising administering to a subject diagnosed with a mast cell related disorder of the central nervous system or nervous system a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
  • an ADC such as a PBD dimer conjugate
  • a method of inhibiting mast cell activation in a subject comprising administering to a subject diagnosed with a mast cell related disorder of the central nervous system or nervous system a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g. , any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
  • an ADC such as a PBD dimer conjugate
  • the mast cell related disorder of the central nervous system or nervous system is NMO, NMO spectrum disorder, multiple sclerosis (MS), or NF.
  • MS multiple sclerosis
  • NF the type of NF is NF1 , NF2, or Schwannomatosis.
  • the anti-KIT antibody of an ADC such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), described herein for use in the methods provided herein is a bivalent monospecific antibody.
  • the anti-KIT antibody antibody of an ADC such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), described herein for use in the methods provided herein is a humanized antibody.
  • the anti-KIT antibody of an ADC such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), described herein for use in the methods provided herein is not a bispecific antibody.
  • the anti-KIT antibody of an ADC such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), described herein for use in the methods provided herein comprises a light chain variable region (“VL”) comprising VL CDRs 1-3 comprising SEQ ID NOs: 19-21 , respectively, and a heavy chain variable region (“VH”) comprising VH CDRs 1- 3 comprising SEQ ID NOs: 16-18, respectively.
  • VL light chain variable region
  • VH heavy chain variable region
  • mast cell related disorder refers to disorders where mast cell activity contributes to the pathology and/or mast cells are found in abnormal amounts, such as above-normal amounts or below-normal amounts, in various parts of the body.
  • mast cell related disorders can exhibit accumulation of pathological mast cells in potentially any or all organs and tissues and/or aberrant release of one or more mast cell mediators such as inflammatory mediators.
  • Non- limiting examples of inflammatory mediators released by mast cells include any of: (i) granule-associated mediators, including histamine, serotonin (5-hydroxytryptamine), and a variety of proteases and peptidases; (ii) eicosanoids such as prostaglandin D 2 (PGD 2 ) and leukotriene C 4 (LTC 4 ); and (iii) cytokines including interleukin-2 (IL-2), IL-3, IL-4, IL-5, IL-6, IL-10, IL-13, granulocyte-macrophage colony-stimulating factor (GM-CSF), and tumor necrosis factor a (TNFa), and chemokines including CCL-2, CCL-3, CCL-5, and CXCL8.
  • granule-associated mediators including histamine, serotonin (5-hydroxytryptamine), and a variety of proteases and peptidases
  • PGD 2 prostaglandin D 2
  • a mast cell related disorder is a mast cell related disorder of the central nervous system or nervous system, such as neuromyelitis optica (NMO), neuromyelitis optica spectrum disorder (NMOSD), multiple sclerosis (MS), or neurofibromatosis (e.g., NF type 1 (NF1), NF type 2 (NF2), or Schwannomatosis).
  • NMO neuromyelitis optica
  • NOSD neuromyelitis optica spectrum disorder
  • MS multiple sclerosis
  • neurofibromatosis e.g., NF type 1 (NF1), NF type 2 (NF2), or Schwannomatosis.
  • MS Multiple sclerosis
  • brain and spinal cord a chronic inflammatory demyelinating disorder of the central nervous system (brain and spinal cord) involving episodes where white matter within the brain or spinal cord becomes inflamed and then damaged by the individual's own immune system. These inflamed areas become scarred within the brain and spinal cord. The damage disrupts the ability of parts of the nervous system to communicate, resulting in a variety of symptoms, including physical, mental, and/or psychiatric problems.
  • Forms of MS include, but are not limited to, relapsing forms, with symptoms either occurring in isolated attacks, and progressive forms, with symptoms building up over time. Symptoms of MS can manifest as any neurological symptom or sign such as autonomic, visual, motor, and sensory problems.
  • Non- limiting examples of symptoms of MS include loss of sensitivity or changes in sensation such as tingling, pins and needles or numbness, muscle weakness, very pronounced reflexes, muscle spasms, or difficulty in moving, difficulties with coordination and balance (ataxia), problems with speech or swallowing, visual problems (nystagmus, optic neuritis or double vision), fatigue, acute or chronic pain, bladder and bowel difficulties, emotional problems such as depression or unstable mood, Uhthoff s phenomenon (a worsening of symptoms due to exposure to higher than usual temperatures), and Lhermitte's sign (an electrical sensation that runs down the back when bending the neck).
  • an ADC provided herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen-binding fragment thereof.
  • a PBD dimer conjugate e.g., KIT-PBD1 or KIT-PBD2
  • an anti-KIT antibody e.g., any one of antibodies Huml-Hum20
  • mast cell related disorders include, for example, anaphylaxis, atopic disease, and mast cell activation syndrome.
  • Eosinophils are white blood cells activated by the lymphocytes of the adaptive immune response and are important in defense against parasitic infections. The level of eosinophils in the blood is normally low, and it can increase markedly in certain situations, such as atopy, which can result in eosinophilia, an abnormally large number of eosinophils in the blood.
  • an eosinophil related disorder refers to disorders that arise when eosinophils are found in abnormal amounts, such as above -normal amounts or below-normal amounts, in various parts of the body. For example, when the body produces too many eosinophils, they can cause chronic inflammation resulting in tissue damage.
  • an eosinophil disorder may be associated with an abnormal amount of eosinophil in a tissue for a prolonged period of time in response to a trigger.
  • eosinophils may be produced in response to a trigger, such as an infection or allergen, but the high amounts of eosinophils do not decrease at a normal rate and thus are maintained at a high amount for a longer period of time than expected.
  • a trigger such as an infection or allergen
  • Eosinophil related disorders can be diagnosed according to the location where the levels of eosinophils are elevated.
  • eosinophil related disorders include allergic disorders, infectious diseases, blood disorders, immunologic disorders and reactions, endocrine disorders, pulmonary conditions, gastrointestinal disorders, neurologic disorders, rheumatologic disorders, cardiac conditions, and renal diseases.
  • eosinophilia is an eosinophil related disorder characterized by a peripheral blood eosinophil count greater than a normal level, for example, greater than 450/ ⁇ .
  • Eosinophilia can be induced or triggered by a variety of conditions, such as allergy or infection.
  • elevated levels of eosinophils are observed locally, for example, in the lung, heart, spinal cord, or brain.
  • Non-limiting examples of neurologic disorders involving eosinophils include central nervous system infections, ventriculoperitoneal shunts, and drug-induced adverse reactions.
  • an increase in eosinophil count or activity can be detected in cerebrospinal fluid (CSF) or in other samples obtained from tissue of fluid of the central nervous system.
  • CSF cerebrospinal fluid
  • Non-limiting examples of eosinophil or mast cell related indications include upper airway diseases such as allergic rhinitis and sinusitis, foreign body aspiration, glottic stenosis, tracheal stenosis, laryngotracheomalacia, vascular rings, chronic obstructive pulmonary disease (COPD), and congestive heart failure, eosinophilic bronchitis, polychondritis, sarcoidosis, papillomatosis, arthritis (e,g., rheumatoid arthritis) and Wegener's granulomatosis.
  • upper airway diseases such as allergic rhinitis and sinusitis, foreign body aspiration, glottic stenosis, tracheal stenosis, laryngotracheomalacia, vascular rings, chronic obstructive pulmonary disease (COPD), and congestive heart failure
  • eosinophilic bronchitis polychond
  • NMO Neuromyelitis optica
  • Devic's disease is an autoimmune inflammatory disorder of the central nervous system that predominantly affects the optic nerves and spinal cord, and also the brain in some cases. NMO can lead to paralysis and blindness. A majority of patients with NMO are seropositive for immunoglobulin autoantibodies (AQP4-IgG or NMO- IgG) against aquaporin-4 (AQP4), a water channel widely expressed in optic nerves, spinal cord, and periventricular regions. A small percentage of NMO patients are NMO-IgG negative.
  • NMO spectrum disorders refer to a variety of disorders related to NMO but may not quite meet the clinical diagnostic criteria for definite NMO.
  • disorders that are typically included in this classification of NMO spectrum disorders include NMO-IgG seropositive limited forms of NMO (e.g., single or recurrent longitudinally extensive transverse myelitis (LETM) [for example, >3 vertebral segment spinal cord lesions seen on MRI), recurrent or simultaneous bilateral optic neuritis (ON)], Asian opticospinal MS (OSMS), optic neuritis or LETM associated with systemic autoimmune disease, and optic neuritis or myelitis associated with brain lesions typical of NMO (e.g., hypothalamic or brainstem lesions) (see, e.g., Oh et ah, Neurology Research International, vol. 2012, Article ID 460825, 13 pages, 2012).
  • diagnosis criteria for NMO include, but are not limited to, the presence of myelitis and optic neuritis, and any two of the following: (i) extended myelitis on spinal cord MRI, (ii) normal brain MRI at onset, and (iii) positive anti-AQP4 antibodies (see, e.g., Collongues et al, Ther. Adv. Neurol. Disord., 2011, 4: 111-121).
  • kits for alleviating one or more symptoms (e.g., myelitis) of NMO in a subject comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
  • an ADC described herein such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
  • NMO spectrum disorder NMO spectrum disorder
  • a method for alleviating one or more symptoms of NMO spectrum disorder (NMOSD) in a subject comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT- PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml- Hum20) or antigen-binding fragment thereof.
  • a PBD dimer conjugate e.g., KIT- PBD1 or KIT-PBD2
  • an anti-KIT antibody e.g., any one of antibodies Huml- Hum20 or antigen-binding fragment thereof.
  • Non-limiting examples of symptoms of NMO or NMOSD include acute optic neuritis (e.g., bilateral), transverse myelitis (e.g., longitudinally extensive), unilateral or bilateral loss of visual acuity, ocular pain, severe paraplegia, asymmetric sensory level, bladder dysfunction, paroxysmal tonic spasms of the trunk and limbs, and Lhermitte's phenomenon.
  • rostral extension of cervical cord lesions into the cervicomedullary junction can cause symptoms such as acute respiratory decompensation, nausea, intractable vomiting, and hiccups.
  • hypothalamic-pituitary axis dysfunction associated with NMO can manifest as hypersomnolence, hyponatremia, hypothermia, hypothyroidism, and hyperprolactinemia.
  • confusion, abrupt changes in level of consciousness, cortical blindness, and imaging findings suggestive of posterior reversible encephalopathy syndrome (PRES) also can be associated with NMO.
  • methods described herein for preventing, treating or managing NMO or NMO spectrum disorder or for alleviating one or more symptoms of NMO or NMO spectrum disorder can achieve one or more of the following:
  • a patient with NMO has recurring episodes/attacks wherein one or more symptoms of NMO manifest for a period of time and then subside.
  • a patient with NMO may be affected by only one episode.
  • a patient with NMO may be affected by more than one episodes (e.g., at least 2, 3, 4, or 5) over a period of time (e.g., at least 1 year, 2 years, 3 years, 4, years, 5, years, 10 years, 15 years, 20 years, 25 years, 30 years or more).
  • ambulatory difficulties and/or residual visual deficits are observed in NMO patients following an episode.
  • kits for reducing the number of episodes that manifest in a patient with NMO comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
  • an ADC described herein such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
  • kits for reducing the duration of an episode that manifests in a patient with NMO comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
  • an ADC described herein such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
  • kits for increase the period of time between episodes in a patient with NMO comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
  • an ADC described herein such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
  • NF Neurofibromatosis
  • neural neural
  • neurofibromas to grow along nerves in the body.
  • NF generally is an inherited disorder, new cases can arise spontaneously through gene mutation. NF is commonly diagnosed in childhood, approximately around 3-16 years of age, and sometimes in infancy (in children with severe cases).
  • Non-limiting types of NF include NF type 1 (NF1), NF type 2 (NF2), and
  • NF1 is also known as von Recklinghausen disease. Phenotypic
  • NF1 gastrointestinal stromal tumor
  • NF2 is an autosomal dominant genetic disorder associated with neurologic, ophthalmologic, and cutaneous abnormalities.
  • Non-limiting examples of NF2 symptoms include hearing loss, tinnitus, visual impairment, imbalance, and painful skin lesions.
  • skull-base tumors including vestibular schwannomas (VS) and meningiomas) in NF2 patients because they can lead to lower cranial nerve dysfunction and death.
  • NF2 can be established by the presence of bilateral vestibular schwannoma (VS) or unilateral VS in conjunction with the presence of NF2-associated tumors (e.g., meningiomas, schwannomas, ependymomas, glioma, or neurofibroma), posterior cataracts, or a family history of other NF2-related tumors.
  • NF2-associated tumors e.g., meningiomas, schwannomas, ependymomas, glioma, or neurofibroma
  • posterior cataracts e.g., posterior cataracts
  • NF2-associated tumors e.g., meningiomas, schwannomas, ependymomas, glioma, or neurofibroma
  • posterior cataracts e.g., posterior cataracts
  • a family history of other NF2-related tumors e.g., a family history of other NF2-related tumors.
  • patients may experience other neurologic dysfunction
  • Schwannomatosis shares many features with the better-known forms of NF. Multiple schwannomas, or tumors of nerve sheaths, are seen in schwannomatosis, but not the
  • schwannomatosis develop tumors on the sheaths, or coverings, of their nerves (see, e.g., MacCollin et al. , Neurology, 2005, 64: 1838-1845).
  • NF e.g., NF1, NF2 or Schwannomatosis
  • methods of alleviating one or more symptoms of NF comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
  • a PBD dimer conjugate e.g., KIT-PBD1 or KIT- PBD2
  • an anti-KIT antibody e.g., any one of antibodies Huml-Hum20
  • a method of treating neurofibromas in a subject diagnosed with NF comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT- PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml- Hum20) or antigen-binding fragment thereof.
  • NF e.g., NF1, NF2 or Schwannomatosis
  • a method of inhibiting growth of neurofibromas in a subject diagnosed with NF comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT- PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml- Hum20) or antigen-binding fragment thereof.
  • NF e.g., NF1, NF2 or Schwannomatosis
  • a method of protecting against neurofibromas in a subject diagnosed with NF comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT- PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml- Hum20) or antigen-binding fragment thereof.
  • NF e.g., NF1, NF2 or Schwannomatosis
  • an anti-KIT antibody or antigen binding fragment thereof described herein or a pharmaceutical composition thereof is administered to a subject in need thereof in accordance with the methods provided herein for treating NF (e.g., NF1 , NF2 or
  • Schwannomatosis provided herein at a dosage and a frequency of administration that achieves one or more of the following: reduces or ameliorates the severity of NF and/or a symptom associated therewith in a subject with NF; reduces the number symptoms and/or the duration of a symptom(s) associated with NF in a subject with NF; prevents the onset, progression or recurrence of one or more symptoms associated with NF in a subject with NF; prevents the recurrence of a tumor associated with NF; reduces hearing loss, tinnitus, visual impairment, imbalance, and/or painful skin lesions associated with NF in a subject with NF; improves hearing, hearing function and/or word recognition in a subject with NF; enhances or improves the therapeutic effect of another therapy in a subject with NF or an animal model; reduction or inhibition in the growth of a tumor or neoplasm associated with NF and/or decrease in the tumor size (e.g., volume or diameter) of a tumor
  • an ADC described herein such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml- Hum20) or antigen-binding fragment thereof or a pharmaceutical composition thereof is administered to a subject in need thereof in accordance with the methods provided herein at a dosage and a frequency of administration that achieves one or more of the following in a subject diagnosed with NF, NMO or NMO spectrum disorder: reduction in the number and/or activity of eosinophils, reduction in mast cell proliferation, reduction in mast cell number or amount, inhibition or reduction in mast cell activity, and promotion of mast cell death.
  • methods provided herein can reduce the severity of one or more symptoms of a condition or disorder described herein in a subject by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, or 80%.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is administered
  • An ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein can be prophylactically or therapeutically administered to a subject so as to prevent, lessen or ameliorate a KIT-associated disorder or disease (e.g. , cancer, inflammatory condition, fibrosis) or symptom thereof.
  • a KIT-associated disorder or disease e.g. , cancer, inflammatory condition, fibrosis
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or a pharmaceutical composition thereof is administered to a subject in need thereof in accordance with the methods for treating a KIT-associated disorder or disease provided herein will be efficacious while minimizing side effects.
  • the exact dosage of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein to be administered to a particular subject or a pharmaceutical composition thereof can be determined by a practitioner, in light of factors related to the subject that requires treatment.
  • Factors which can be taken into account include the severity of the disease state, general health of the subject, age, and weight of the subject, diet, time and frequency of administration, combination(s) with other therapeutic agents or drugs, reaction sensitivities, and tolerance/response to therapy.
  • the dosage and frequency of administration of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or a pharmaceutical composition thereof can be adjusted over time to provide sufficient levels of the ADC such as a PBD dimer conjugate comprising an anti-KIT antibody or to maintain the desired effect.
  • the dosage administered to a patient, to manage a KIT-associated disorder or disease is typically about 50 mg/kg of the patient's body weight.
  • a KIT-associated disorder or disease e.g., cancer, inflammatory condition, fibrosis
  • human antibodies have a longer half-life within the human body than antibodies from other species due to the immune response to the foreign polypeptides.
  • the dosage and frequency of administration of the antibodies described herein can be reduced by enhancing uptake and tissue penetration of the antibodies by modifications such as, for example, lipidation.
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is administered to manage a KIT- associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis).
  • a KIT- associated disorder or disease e.g., cancer, inflammatory condition, fibrosis.
  • an "effective amount" of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein refers to an amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein which is sufficient to achieve at least one, two, three, four or more of the following effects: (i) the reduction or amelioration of the severity of a KIT-associated disorder or disease (e.g. , cancer, inflammatory condition, fibrosis) and/or one or more symptoms associated therewith; (ii) the reduction in the duration of one or more symptoms associated with a KIT-associated disorder or disease (e.g.
  • a tumor e.g., gastrointestinal stromal tumor
  • a KIT-associated disorder or disease e.g. , cancer, inflammatory condition, fibrosis
  • the reduction in hospitalization of a subject e.g., cancer, inflammatory condition, fibrosis
  • the reduction in hospitalization of a subject e.g., cancer, inflammatory condition, fibrosis
  • the reduction in hospitalization length e.g., the increase in the survival of a subject
  • the inhibition e.g., partial inhibition of the progression of a KIT-associated disorder or disease (e.g. , cancer, inflammatory condition, fibrosis) and/or one or more symptoms associated therewith
  • cancer cell population e.g. , leukemia cell population, lung cancer cell population,
  • gastrointestinal stromal cancer cell population (xi) a reduction in the growth of a tumor or neoplasm; (xii) a decrease in tumor size (e.g., volume or diameter); (xiii) a reduction in the formation of a newly formed tumors; (xiv) eradication, removal, or control of primary, regional and/or metastatic cancer; (xv) ease in removal of a tumor by reducing tumor and/or edema- related vascularization prior to surgery; (xvi) a decrease in the number or size of metastases; (xvii) a reduction in mortality; (xviii) an increase in tumor-free survival rate of patients; (xvix) an increase in relapse-free survival; (xx) an increase in the number of patients in remission; (xxi) a decrease in hospitalization rate; (xxii) the size of the tumor is maintained and does not increase or increases by less than the increase of a tumor after administration of a standard therapy as measured by conventional methods available to one of skill
  • cytokines or interleukins in biological specimens (e.g., plasma, serum, cerebral spinal fluid, urine, or any other bio fluids) of a subject with a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis); (xxviii) a decrease in circulating tumor cells (CTCs) in the blood of a subject with cancer; (xxix) inhibition (e.g., partial inhibition) or decrease in tumor metabolism or perfusion; and (xxx) improvement in the quality of life as assessed by methods well known in the art, e.g. , questionnaires.
  • "effective amount” as used herein also refers to the amount of an antibody described herein to achieve a specified result (e.g., inhibition of one or more KIT biological activities of a cell, such as inhibition of cell proliferation).
  • a single dose of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is administered one or more times to a patient to impede, prevent, manage, treat and/or ameliorate a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis).
  • a KIT-associated disorder or disease e.g., cancer, inflammatory condition, fibrosis
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody or pharmaceutical composition thereof is administered to a subject in accordance with the methods for treating a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis) presented herein in cycles, wherein the anti-KIT antibody or pharmaceutical composition is administered for a period of time, followed by a period of rest (i.e., the anti-KIT antibody or pharmaceutical composition is not administered for a period of time).
  • a KIT-associated disorder or disease e.g., cancer, inflammatory condition, fibrosis
  • combination therapies for the treatment of a KIT- associated disorder or disease which involve the administration of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT-binding fragment thereof), in combination with one or more additional therapies (e.g., chemotherapeutic agent, tyrosine kinase inhibitor, PGP inhibitors, HSP-90 inhibitors, proteosome inhibitors, or histone deacetylase inhibitor) to a subject in need thereof.
  • additional therapies e.g., chemotherapeutic agent, tyrosine kinase inhibitor, PGP inhibitors, HSP-90 inhibitors, proteosome inhibitors, or histone deacetylase inhibitor
  • combination therapies for the treatment of a KIT-associated disorder or disease
  • an amount e.g. , a therapeutically effective amount or a sub-optimal amount
  • an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein in combination with an amount (e.g., a therapeutically effective amount or a sub-optimal amount) of another therapy (e.g., chemotherapeutic agent, tyrosine kinase inhibitor, or histone deacetylase inhibitor) to a subject in need thereof.
  • another therapy e.g., chemotherapeutic agent, tyrosine kinase inhibitor, or histone deacetylase inhibitor
  • one or more ADCs such as PBD dimer conjugates comprising anti-KIT antibodies provided herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT-binding fragment thereof), can be administered prior to, concurrently with, or subsequent to the administration of one or more additional therapies (e.g., agents, surgery, or radiation) for use in treating, managing, and/or ameoliorating a KIT- associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis).
  • additional therapies e.g., agents, surgery, or radiation
  • a KIT-associated disorder or disease e.g., cancer, inflammatory condition, fibrosis
  • the therapies can be administered serially or sequentially.
  • one or more ACDs such as PBD dimer conjugates comprising anti-KIT antibodies provided herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT-binding fragment thereof), can be administered prior to, concurrently with, or subsequent to the administration of one or more additional therapies such as anticancer agents, for example, tyrosine kinase inhibitors (e.g., imatinib myselyate (Gleevec®) or sunitinib (SUTENT), or histone deacetylase inhibitors (e.g., vorinostat
  • tyrosine kinase inhibitors e.g., imatinib myselyate (Gleevec®) or sunitinib (SUTENT
  • histone deacetylase inhibitors e.g.
  • SAHA suberoylanilide hydroxamic acid
  • combination therapies for the treatment of a KIT-associated disorder or disease which involve the administration of an amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT-binding fragment thereof), in combination with an amount of another therapy (e.g., chemotherapeutic agent, tyrosine kinase inhibitor, or histone deacetylase inhibitor) to a subject in need thereof.
  • the combination therapies result in a synergistic effect.
  • the combination therapies result in an additive effect.

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Abstract

Provided herein are antibody-drug conjugates ("ADCs") wherein the antibody portion of the ADCs specifically binds to an Ig-like domain 4 ("D4") of the extracellular domain ("ECD") of human KIT and is conjugated to pyrrolobenzodiazepme ("PBD"). Also provided herein are kits and pharmaceutical compositions comprising such ADCs, and uses and methods for treating or managing disorders such as cancer.

Description

ANTIBODY-DRUG CONJUGATES TARGETING KIT RECEPTOR
AND USES THEREOF
[0001] This application claims the benefit of U.S. Provisional Application No.
61/931,551, filed on January 24, 2014, which is hereby incorporated by reference in its entirety.
[0002] The instant application contains a Sequence Listing, which is being concurrently submitted as an ASCII text file named "Sequence_Listing_12638-73-228.TXT", created January 22, 2015, and being 151,635 bytes in size. The Sequence Listing is hereby incorporated by reference in its entirety.
1. FIELD
[0003] Provided herein are antibody-drug conjugates ("ADCs") wherein the antibody portion of the ADCs specifically binds to an Ig-like domain 4 ("D4") of the extracellular domain ("ECD") of human KIT. Also provided herein are kits and pharmaceutical compositions comprising such ADCs, and uses and methods for treating or managing a disorder such as cancer.
2. BACKGROUND
[0004] Antibody-drug conjugates, or ADCs, are a class of drug designed as a targeted therapy, for example, therapy for treating cancer by targeting cancer cells. ADCs contain an antibody or an antigen-binding antibody fragment such as a single-chain variable fragment (scFv) linked, usually via a linker, to a biological active cytotoxic moiety.
[0005] The efficacy of particular ADCs depends on selectivity of the antibodies, drug mechanism of action, compatible drug linker, drug-antibody ratio (DAR), and drug release properties, as well as appropriate synthesis processes. Challenges in developing ADCs involve identifying the appropriate balance of these factors, among others.
[0006] Abnormal KIT (or c-Kit) receptor expression and/or activity has been implicated in connection with a number of cancers. For example, gain-of-function KIT mutations resulting in SCF-independent, constitutive activation of KIT are found in certain cancer cells and are associated with certain cancers such as leukemia (e.g., chronic myelogenous leukemia) and gastrointestinal stromal tumors (see, e.g., Mol et al., J. Biol. Chem., 2003, 278:31461-31464).
[0007] Abnormal KIT expression and/or activity also has been implicated in other disorders such as fibrosis and certain inflammatory disorders. [0008] Expression of KIT has been detected in various cell types, such as mast cells, stem cells, brain cells, melanoblasts, ovary cells, and cancer cells (e.g., leukemia cells). Studies of loss-of-function KIT mutations indicate that KIT is important for the normal growth of hematopoietic progenitor cells, mast cells, melanocytes, primordial germ cells, and the interstitial cells of Cajal (see, e.g., Besmer, P., Curr. Opin. Cell Biol, 1991, 3:939-946; Lyman et al., Blood, 1998, 91 : 1101-1134; Ashman, L. K., Int. J. Biochem. Cell BioL, 1999, 31 : 1037-1051; Kitamura et al, Mutat. Res., 2001, 477: 165-171; Mol et al, J. Biol. Chem., 2003, 278:31461-
31464).
[0009] There is a need for more effective and better targeted therapies targeting cells expressing KIT for treating disorders, such as cancer.
3. SUMMARY
[0010] Provided herein is a PBD dimer conjugate of Formula Ab(X)m or a pharmaceutically acceptable salt thereof, wherein
Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, comprising:
(i) a light chain variable region ("VL") comprising a VL CDR1, VL CDR2, and VL CDR3 comprising the amino acid sequences KASQNVRTNVA (SEQ ID NO: 19), SASYRYS (SEQ ID NO: 20), and QQYNSYPRT (SEQ ID NO: 21), respectively; and
(ii) a heavy chain variable region ("VH") comprising VH CDR1, VH CDR2, and VH CDR3 comprising the amino acid sequences DYYIN (SEQ ID NO: 16), RIYPGSGNTYYNEKFKG (SEQ ID NO: 17), and GVYYFDY (SEQ ID NO: 18), respectively;
Figure imgf000004_0001
m is 1 to 20;
Figure imgf000005_0001
Figure imgf000005_0002
q is 1 to 3;
R is independently selected from hydrogen, Ci-C6 alkyl, C3-C6 cycloalkyl, C2-C6
alkenyl, C2-C6 alkynyl,
Figure imgf000005_0003
[0011] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to D4 of a human KIT receptor, comprising:
(a) (i) a light chain variable region ("VL") comprising the amino acid sequence:
DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKI LIYSASYRYSGVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQY NSYPRTFGGGTKVEIK, wherein Χκι is an amino acid with an aromatic or aliphatic hydroxyl side chain, Χκ2 is an amino acid with an aromatic or aliphatic hydroxyl side chain Χκ3 is an amino acid with an aliphatic hydroxyl side chain XK4 is an amino acid with an aliphatic hydroxyl side chain or is P, XKS is an amino acid with a charged or acidic side chain, and Χκβ is an amino acid with an aromatic side chain; and
(ii) a heavy chain variable region ("VH") comprising a VH CDR1 , VH CDR2, and VH CDR3 having the amino acid sequences of SEQ ID NO: 16, SEQ ID NO: 17, and SEQ ID NO: 18, respectively; or
(b)(i) a VL comprising a VL CDR1 , VL CDR2, and VL CDR3 having the amino acid sequences of SEQ ID NO: 19, SEQ ID NO: 20, and SEQ ID NO: 21 , respectively; and
(ii) a VH comprising the amino acid sequence:
QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKG LEWIARIYPGSGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSE DXH8AVYFCARGVYYFDYWGQGTTVTVSS, wherein XM is an amino acid with an aliphatic side chain, XH2 is an amino acid with an aliphatic side chain XH3 is an amino acid with a polar or basic side chain XR4 is an amino acid with an aliphatic side chain XHS is an amino acid with an aliphatic side chain XH6 is an amino acid with an acidic side chain, XH7 is an amino acid with an acidic or amide derivative side chain, and XHS is an amino acid with an aliphatic hydroxyl side chain.
[0012] In ne embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein
Figure imgf000006_0001
[0013] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein m is 1 to 3, or m is 2. In a certain embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein m is 1 to 3.
[0014] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein
Figure imgf000007_0001
In another embodiment, the PBD dimer conjugates of Formula Ab(X)m are those,
Figure imgf000007_0002
[0016] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein q is 1 or 3. In another embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein q is 1.
[0017] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein R is methyl or (E)-prop-l-en-l-yl. In another embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein
Figure imgf000007_0003
[0018] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein
Figure imgf000007_0004
[0019] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein
Figure imgf000007_0005
[0020] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein
Figure imgf000008_0001
[0021] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein n is 4 or 8. In another embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein n is 8.
[0022] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein p is 5.
[0023] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein
Figure imgf000008_0002
[0025] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein
Figure imgf000009_0001
-7- [0028] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein
Figure imgf000010_0001
[0029] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, comprising:
(i) a light chain variable region ("VL") comprising the amino acid sequence:
DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILI YSASYRYSGVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQYNSY PRTFGGGTKVEIK, wherein Χκι is an amino acid with an aromatic or aliphatic hydroxyl side chain, Χκ2 is an amino acid with an aromatic or aliphatic hydroxyl side chain Χκ3 is an amino acid with an aliphatic hydroxyl side chain, Χ 4 is an amino acid with an aliphatic hydroxyl side chain or is P, XKS is an amino acid with a charged or acidic side chain and Χκβ is an amino acid with an aromatic side chain; and
(ii) a heavy chain variable region ("VH") comprising the amino acid sequence: QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKGLE WIARIYPGSGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSEDXH sAVYFC ARGVY YFD Y WGQGTT VT VS S , wherein XM is an amino acid with an aliphatic side chain, XH2 is an amino acid with an aliphatic side chain XH3 is an amino acid with a polar or basic side chain XH4 is an amino acid with an aliphatic side chain XHS is an amino acid with an aliphatic side chain XH6 is an amino acid with an acidic side chain, XR7 is an amino acid with an acidic or amide derivative side chain, and XHS is an amino acid with an aliphatic hydroxyl side chain; and wherein X is
Figure imgf000011_0001
and wherein m is 1 to 8.
[0030] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, comprising:
(i) a light chain variable region ("VL") comprising the amino acid sequence:
DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILI YSASYRYSGVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQYNSY PRTFGGGTKVEIK, wherein Χκι is an amino acid with an aromatic or aliphatic hydroxyl side chain, Χκ2 is an amino acid with an aromatic or aliphatic hydroxyl side chain Χ 3 is an amino acid with an aliphatic hydroxyl side chain, XK4 is an amino acid with an aliphatic hydroxyl side chain or is P, XKS is an amino acid with a charged or acidic side chain and Χκβ is an amino acid with an aromatic side chain; and
(ii) a heavy chain variable region ("VH") comprising the amino acid sequence: QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKGLE WIARIYPGSGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSEDXH 8AVYFC ARGVY YFD Y WGQGTT VT VS S , wherein XM is an amino acid with an aliphatic side chain, XH2 is an amino acid with an aliphatic side chain XH3 is an amino acid with a polar or basic side chain XR4 is an amino acid with an aliphatic side chain XHS is an amino acid with an aliphatic side chain XH6 is an amino acid with an acidic side chain, XH7 is an amino acid with an acidic or amide derivative side chain, and XHS is an amino acid with an aliphatic hydroxyl side chain; and
Figure imgf000012_0001
s
Figure imgf000013_0001
-11- 0032] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein
Figure imgf000014_0001
[0035] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein X is
Figure imgf000015_0001
Figure imgf000015_0002
[0037] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein Ab is an antibody or an antigen-binding fragment thereof, which immunospecifically binds to D4 of a human KIT receptor, comprising a light chain variable region ("VL") and a heavy chain variable region ("VH"), wherein:
(i) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(ii) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(iii) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
(iv) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
(v) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 2; (vi) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(vii) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(viii) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
(ix) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(x) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(xi) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
(xii) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(xiii) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(xiv) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(xv) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
(xvi) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
(xvii) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(xviii) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(xix) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 5; or
(xx) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 6. [0038] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein m is 1 to 3.
[0039] In one embodiment, the PBD dimer conjugates of Formula Ab(X)m are those, wherein m is 2.
[0040] Provided herein is a pharmaceutical composition comprising a PBD dimer conjugate described herein of Formula Ab(X)m or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable excipient.
[0041] Provided herein is a plurality of PBD dimer conjugates of Formula Ab(X)m, wherein the average drug-per-antibody ratio ("DAR") is 1.5 to 3.
[0042] Provided herein is a method of treating cancer comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate described herein of Formula Ab(X)m or a pharmaceutically acceptable salt thereof. In certain embodiments the cancer is leukemia, lung cancer, melanoma, sarcoma, or gastrointestinal stromal tumors. In particular embodiments the cancer is acute myeloid leukemia (AML) or small cell lung cancer.
[0043] In one embodiment the methods of treating cancer are those, wherein the cancer is refractory to treatment by a tyrosine kinase inhibitor. In certain embodiments the tyrosine kinase inhibitor is imatinib mesylate or SU11248.
[0044] In one embodiment the methods of treating cancer are those, wherein the method further comprises administering a second therapeutic agent. In certain embodiments the second therapeutic agent is a chemotherapeutic agent, a tyrosine kinase inhibitor, a histone deacetylase inhibitor, an antibody, or a cytokine. In particular embodiments, the tyrosine kinase inhibitor is imatinib mesylate or SU11248.
[0045] In one aspect, provided herein is a method of treating fibrosis or an inflammatory disorder, comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate described herein of Formula Ab(X)m or a pharmaceutically acceptable salt thereof.
[0046] In a particular aspect, provided herein is a method of treating a mast cell associated disorder, comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate described herein of Formula Ab(X)m or a pharmaceutically acceptable salt thereof. [0047] In a certain aspect, provided herein is a method of treating neurofibromatosis, comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate of Formula Ab(X)m or a pharmaceutically acceptable salt thereof.
[0048] In a specific aspect, provided herein is a method of treating systemic mastocytosis, comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate described herein of Formula Ab(X)m or a pharmaceutically acceptable salt thereof.
[0049] In one aspect, provided herein is a method of treating cancer comprising
administering to a subject in need thereof a therapeutically effective amount of a plurality of PBD dimer conjugates described herein of Formula Ab(X)m, wherein the average drug-per- antibody ratio ("DAR") is 1.5 to 3.
[0050] In a certain aspect, provided herein is a method of treating fibrosis or an
inflammatory disorder, comprising administering to a subject in need thereof a therapeutically effective amount of a plurality of PBD dimer conjugates described herein of Formula Ab(X)m, wherein the average drug-per-antibody ratio ("DAR") is 1.5 to 3.
[0051] In one aspect, provided herein is a method of treating a mast cell associated disorder, comprising administering to a subject in need thereof a therapeutically effective amount of a plurality of PBD dimer conjugates described herein of Formula Ab(X)m, wherein the average drug-per-antibody ratio ("DAR") is 1.5 to 3.
[0052] In a particular aspect, provided herein is a method of treating neurofibromatosis, comprising administering to a subject in need thereof a therapeutically effective amount of a plurality of PBD dimer conjugates described herein of Formula Ab(X)m, wherein the average drug-per-antibody ratio ("DAR") is 1.5 to 3.
[0053] In a specific aspect, provided herein is a method of treating systemic mastocytosis, comprising administering to a subject in need thereof a therapeutically effective amount of a plurality of PBD dimer conjugates described herein of Formula Ab(X)m, wherein the average drug-per-antibody ratio ("DAR") is 1.5 to 3.
[0054] In a certain aspect, provided herein is a method of making a PBD dimer conjugate or a pharmaceutically acceptable salt thereof, comprising conjugating an anti-KIT antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, wherein the anti-KIT antibody or antigen- binding fragment thereof comprises:
(i) a light chain variable region ("VL") comprising a VL CDR1, VL CDR2, and VL CDR3 comprising the amino acid sequences KASQNVRTNVA (SEQ ID NO: 19), SASYRYS (SEQ ID NO: 20), and QQYNSYPRT (SEQ ID NO: 21), respectively; and
(ii) a heavy chain variable region ("VH") comprising VH CDR1, VH CDR2, and VH CDR3 comprising the amino acid sequences DYYIN (SEQ ID NO: 16),
RIYPGSGNTYYNEKFKG (SEQ ID NO: 17), and GVYYFDY (SEQ ID NO: 18), respectively;
to a PBD dimer described herein (e.g., PBD dimer described in section 5.1.1), wherein the PBD dimer optional is linked to the antibody via a linker (e.g., reactive linker). In a specific embodiment, the method comprising conjugating the anti-KIT antibody to a PBD dimer with a linker, such as any one of compounds 42, 43, 44, 45, 46, or 47.
4. BRIEF DESCRIPTION OF THE FIGURES
[0055] Fig. 1A depicts pyrrolobenzodiazepine ("PBD") dimers attached to reactive linkers (compounds 42, 43, 44, 45, 46 and 47) for conjugation with anti-KIT antibodies to generate ADCs, specifically, PBD dimer conjugates.
[0056] Fig. IB depicts the amino acid sequence of a full length human KIT receptor (SEQ ID NO: 1), GenBank™ accession number AAC50969. The first through fifth extracellular Ig- like domains (i.e., Dl, D2, D3, D4, and D5) are indicated; "{" depicts the amino-terminal residue of each domain and "}" depicts the carboxyl-terminal residue of each domain. The Dl domain is depicted at P34 to Rl 12, the D2 domain is depicted at Dl 13 to P206, the D3 domain is depicted at A207 to D309, the D4 domain is depicted at K310 to N410 (SEQ ID NO: 15), the hinge region between D4 and D5 is located at V409 to N410, and the D5 domain is depicted at T411 to K509. Also, the D1/D2 hinge region is located at Dl 13 to LI 17; the D2/D3 hinge region is located at P206 to A210; and the D3/D4 hinge region is located at D309 to G311. The D4/D5 region comprises K310 to K509. The transmembrane domain comprises residues F525 to Q545, and the kinase domain comprises residues K589 to S933. [0057] Fig. 2 A depicts the amino acid sequence (SEQ ID NO: 2) of the HI VH domain, and a DNA (SEQ ID NO:22) encoding the amino acid sequence. The framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
[0058] Fig. 2B depicts the amino acid sequence (SEQ ID NO: 3) of the H2 VH domain and a DNA (SEQ ID NO:23) encoding the amino acid sequence. The framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
[0059] Fig. 2C depicts the amino acid sequence (SEQ ID NO: 4) of the H3 VH domain and a DNA (SEQ ID NO:24) encoding the amino acid sequence. The framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
[0060] Fig. 2D depicts the amino acid sequence (SEQ ID NO: 5) of the H4 VH domain and a DNA (SEQ ID NO:25) encoding the amino acid sequence. The framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
[0061] Fig. 2E depicts the amino acid sequence (SEQ ID NO: 6) of the H5 VH domain and a DNA (SEQ ID NO:26) encoding the amino acid sequence. The framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
[0062] Fig. 2F depicts the amino acid sequence (SEQ ID NO: 7) of the LI VL domain and a DNA (SEQ ID NO:27) encoding the amino acid sequence. The framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
[0063] Fig. 2G depicts the amino acid sequence (SEQ ID NO: 8) of the K2 VL domain and a DNA (SEQ ID NO:28) encoding the amino acid sequence. The framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
[0064] Fig. 2H depicts the amino acid sequence (SEQ ID NO: 9) of the L3 VL domain and a DNA (SEQ ID NO:29) encoding the amino acid sequence. The framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
[0065] Fig. 21 depicts the amino acid sequence (SEQ ID NO: 10) of the L4 VL domain and a DNA (SEQ ID NO:30) encoding the amino acid sequence. The framework regions (FR1, FR2, FR3, and FR4), and CDRs (CDRl, CDR2, and CDR3) are indicated. Both Kabat numbering and numerical numbering of the amino acid residues are indicated.
[0066] Fig. 2J depicts the consensus sequence of a VH domain (SEQ ID NO: 11). XHI-HS indicate amino acids which can be any amino acid.
[0067] Fig. 2K depicts the consensus sequence of a VL domain (SEQ ID NO: 12). Χκι-Κ6 indicate amino acids which can be any amino acid.
[0068] Fig. 3 depicts the binding activity of PBD dimer conjugates comprising anti-KIT antibodies, to a recombinant polypeptide of the D4/D5 region of human KIT as determined by solid phase ELISA. The results for PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2) are provided, with control PBD dimer conjugates comprising an anti-keyhole limpet hemocyanin ("KLH") antibody conjugated to compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), as well as controls of unconjugated anti-KIT antibody (KIT-Ab) and unconjugated anti-KLH antibody (KLH-Ab). The EC50 value for each PBD dimer conjugate is indicated.
[0069] Fig. 4 depicts a graph of results of KIT phosphorylation inhibition assays performed by ELISA with CHO cells recombinantly expressing wild-type KIT to characterize the phosphorylation blocking activity of PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), relative to an unconjugated form of the anti-KIT antibody (KIT-Ab). The IC50 values for each ADC or unconjugated antibody control are indicated.
[0070] Fig. 5 presents results of cell proliferation assays with PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), relative to control PBD dimer conjugates comprising an anti-KLH antibody conjugated to compound 42 (KLH-PBDl) or compound 45 (KLH-PBD2). IC50 (nM) values are provided. Cells with detectable KIT expression on the cell surface are labelled with "+"; cells with no detectable KIT expression on the cell surface are labelled and "ND" indicates that KIT expression was not determined. [0071] Fig. 6 depicts results of xenograft mouse model studies of RD-ES Ewing's Sarcoma with a PBD dimer conjugate comprising an anti-KIT antibody conjugated to compound 42 (KIT- PBD1) at three different concentrations (i.e., 0.3 mg/kg, 1 mg/kg, and 3 mg/kg), a control PBD dimer conjugate comprising an anti-KLH antibody conjugated to compound 42 (KLH-PBD1), and a control unconjugated anti-KIT antibody (KIT-Ab). The graph is a plot of median tumor volume for each group over time (days after start of treatment).
[0072] Fig. 7A-B depict results of xenograft mouse model studies of erythroid leukemia with PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT- PBD1) or compound 45 (KIT-PBD2), control PBD dimer conjugates comprising an anti-KLH antibody conjugated to compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), and a control unconjugated anti-KIT antibody (KIT-Ab). The graphs are plots of mean tumor volume for each group over time (days after start of treatment).
[0073] Fig. 8A-B depict results of xenograft mouse model studies of small cell lung cancer (SCLC) with PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT-PBDl) (Fig. 8 A) or compound 45 (KIT-PBD2) (Fig. 8B), control PBD dimer conjugates comprising an anti-KLH antibody conjugated to compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), and a control unconjugated anti-KIT antibody (KIT-Ab). The graphs are plots of mean tumor volume for each group over time (days after start of treatment).
[0074] Fig. 9A-C presents results of colony formation assays with PBD dimer conjugates comprising an anti-KIT antibody conjugated to either compound 42 (KIT-PBDl) or compound 45 (KIT-PBD2), relative to the naked anti-KIT antibody (KIT) and PBD dimer conjugates comprising an anti-KLH antibody conjugated to compound 42 (KLH-PBDl) or compound 45 (KLH-PBD2), which served as controls.
5. DETAILED DESCRIPTION
[0075] Provided herein are antibody-drug conjugates ("ADCs") wherein the antibody portion of the ADCs specifically binds to an Ig-like domain 4 ("D4") of the extracellular domain
("ECD") of human KIT. In specific aspects, provided herein is an ADC which is a
pyrrolobenzodiazepine ("PBD") dimer conjugate comprising an antibody (anti-KIT antibody) described herein (e.g., section 5.1.2) or antigen-binding fragment thereof which specifically binds to a KIT receptor, e.g. , a human KIT receptor, wherein the antibody or antigen-binding fragment thereof is conjugated to one or more PBD dimers described herein (e.g, section 5.1.1), and optionally comprises one or more linkers (e.g., N10 or C2 linker), such as reactive linkers, linking the antibody or antigen-binding fragment thereof to the one or more PBD dimers. Also provided herein are kits and pharmaceutical compositions comprising such ADCs or PBD dimer conjugates, as well as uses and methods for treating or managing disorders such as cancer or inflammatory disorders, and methods of making such ADCs or PBD dimer conjugates.
[0076] Pyrrolobenzodiazepines ("PBDs") have the following general structure:
Figure imgf000023_0001
and can differ in the number, type and position of substituents, in both their aromatic A rings and pyrrolo C rings, and in the degree of saturation of the C ring. In the B-ring there is either an imine (N=C), a carbinolamine (NH-CH(OH)), or a carbinolamine methyl ether (NH-CH(OMe)) at the N10-C1 1 position which, without wishing to be bound by any particular theory, is considered the electrophilic center responsible for alkylating DNA.
[0077] PBD dimers can be synthesized by joining two PBD units together through their C8/C 8 '-hydroxy 1 functionalities via a flexible alkylene linker (Bose, D. S., et al., J. Am. Chem. Soc, 114, 4939-4941 (1992); Thurston, D. E., et al, J. Org. Chem., 61, 8141-8147 (1996)). One example of a PBD dimer is:
Figure imgf000023_0002
PBD dimers can be symmetrical, such as the above, or unsymmetrical, wherein the PBD units comprised in the dimer are not identical. Some PBDs can recognize and bind to specific sequences of DNA, such as PuGPu.
[0078] As used herein, the terms "D4/D5 region" or "D4/D5 domain" refer to a region within a KIT polypeptide spanning the fourth Ig-like extracellular ("D4") domain, the fifth Ig-like extracellular ("D5") domain, and the hinge region in between the D4 and D5 domains ("D4-D5 hinge region"), of KIT, in the following order from the amino terminus to the carboxyl terminus: D4, D4-D5 hinge region, and D5. As used herein, amino acids V308 to H515 of a human KIT (e.g., GenBank No. AAC50969; see also Figure IB) are considered examples of a D4/D5 region or domain of human KIT.
[0079] As used herein, the terms "D4" or "D4 region" or "D4 domain" in the context of a KIT receptor refer to a region within a KIT receptor polypeptide spanning the fourth Ig-like extracellular ("D4") domain of KIT. As used herein, amino acids K310 to N410 of a human KIT (e.g., GenBank No. AAC50969; see also Figure IB) is considered an example of a D4 region or domain of human KIT.
[0080] As used herein, the terms "KIT" or "KIT receptor" or "KIT polypeptide" refer to any form of full-length KIT including, but not limited to, native KIT, an isoform of KIT, an interspecies KIT homolog, or a KIT variant, e.g., naturally occurring (for example, allelic or splice variant, or mutant, e.g., somatic mutant) or artificially constructed variant (for example, a recombinant or chemically modified variant). KIT is a type III receptor tyrosine kinase encoded by the c-kit gene (see, e.g., Yarden et al, Nature, 1986, 323:226-232; Ullrich and Schlessinger, Cell, 1990, 61 :203-212; Clifford et al, J. Biol. Chem., 2003, 278:31461-31464; Yarden et al, EMBO J., 1987, 6:3341-3351; Mol et al, J. Biol. Chem., 2003, 278:31461-31464). GenBank™ accession number NM 000222 provides an exemplary human KIT nucleic acid sequence.
GenBank™ accession numbers NP 001087241, PI 0721, and AAC50969 provide exemplary human KIT amino acid sequences. GenBank™ accession number AAH75716 provides an exemplary murine KIT amino acid sequence. Native KIT comprises five extracellular immunoglobulin (Ig)-like domains (Dl, D2, D3, D4, D5), a single transmembrane region, an inhibitory cytoplasmic juxtamembrane domain, and a split cytoplasmic kinase domain separated by a kinase insert segment (see, e.g., Yarden et al, Nature, 1986, 323:226-232; Ullrich and Schlessinger, Cell, 1990, 61 :203-212; Clifford et al, J. Biol. Chem., 2003, 278:31461-31464). An exemplary amino acid sequence of the D4/D5 region of human KIT is provided in Figure IB, at amino acid residues V308 to H515. In a specific embodiment, KIT is human KIT. In a particular embodiment, KIT can exist as a monomer, dimer, multimer, native form, or denatured form. [0081] As used herein the term "KIT-PBD-ADC" or "KIT-PBD ADC" refers to an ADC comprising an antibody or antigen-binding fragment thereof which specifically binds to KIT receptor (anti-KIT antibody), such as a human KIT receptor, wherein the antibody or antigen- binding fragment thereof is conjugated to one or more pyrrolobenzodiazepmes (PBDs), such as PBD dimers ("KIT-PBD dimer-ADC" or "KIT-PBD dimer ADC").
5.1 Antibody-Drug Conjugates
[0082] In a particular aspect, provided herein are antibody-drug conjugates ("ADCs") wherein the antibody portion of the ADCs specifically binds to a D4 of a KIT receptor (e.g., a human KIT receptor). In a specific aspect, provided herein is a pyrrolobenzodiazepine (PBD) conjugate which is an ADC comprising an antibody described herein (e.g., Section 5.1.2) or an antigen-binding fragment thereof which specifically binds to a D4 of a human KIT receptor, wherein the antibody or antigen-binding fragment thereof is conjugated to one or more pyrrolobenzodiazepmes (PBDs), for example PBDs described herein (e.g., Section 5.1.1). In a particular aspect, provided herein is a PBD dimer conjugate which is an ADC comprising an antibody described herein (e.g., Section 5.1.2) or an antigen-binding fragment thereof which specifically binds to a D4 of a human KIT receptor, wherein the antibody or antigen-binding fragment thereof is conjugated to one or more PBD dimers, for example PBDs described herein (e.g., Section 5.1.1).
[0083] In a specific embodiment, provided herein is a PBD dimer conjugate of Formula Ab(X)m or a pharmaceutically acceptable salt thereof, wherein Ab is an antibody described herein (e.g., Section 5.1.2), or an antigen-binding fragment thereof, which specifically binds to a D4 of a human KIT receptor, X is a PBD dimer attached to a linker (e.g., reactive linker) , for example as described herein (e.g., Section 5.1.1), and m is at least 1 , for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 3, and refers to the number of X moieties conjugated to Ab.
5.1.1. PBD Dimer ADCs
[0084] In specific aspects, provided herein are ADCs which are PBD dimer conjugates comprising an anti-KIT antibody described herein (e.g., any one of antibodies Huml -Hum20), for example an anti-KIT antibody described in Section 5.1.2, conjugated to one or more PBD dimers (KIT-PBD dimer ADCs). In particular embodiments, a KIT-PBD dimer ADC provided herein comprises an N10 linked PBD dimer or a C2 linked PBD dimer, for example, as described in more details in the sections below. [0085] The specified link between the PBD dimer and an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)) is generally stable extracellularly, such that, extracellularly, the antibody generally remains linked to the drug moiety. In a specific embodiment, the linkers are stable extracellularly (e.g., outside a target cell expressing KIT) and may be cleaved or otherwise processed inside the cell to release an active PBD compound. In a certain embodiment, an effective linker can: (i) maintain the specific binding properties of the conjugated antibody (e.g, anti-KIT antibody); (ii) allow intracellular delivery of a conjugate or drug moiety; (iii) remain stable and intact, i.e., not cleaved, until the conjugate has been delivered or transported to its targeted site (e.g., target site with KIT receptor); and (iv) maintain a cytotoxic, cell-killing effect or a cytostatic effect of a PBD dimer drug moiety. Stability of an ADC, such as a PBD dimer conjugate (e.g. , KIT-PBD dimer ADC) may be measured by standard analytical techniques such as mass spectroscopy, HPLC, and the separation/analysis technique LC/MS.
N10 Linked PBD Dimer ADCs
[0086] In a particular aspect, provided herein is a PBD dimer with a linker (e.g. , reactive linker) connected through the N10 position on one of the PBD dimer moieties wherein the PBD dimer is conjugated via the linker to an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)).
[0087] The PBD dimer-linked ADCs (e.g. , PBD dimer conjugates, such as KIT-PBD dimer ADCs) provided herein are suitable for use in providing PBD dimers to a target site (e.g., a target site with KIT receptors) in a subject.
[0088] In a specific embodiment, a PBD dimer conjugate provided herein is of the following Formula Ab(X)m:
wherein X is
Figure imgf000027_0001
wherein the bond intersected by the wavy line signifies the attachment point of X to Ab;
wherein Ab is an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, see Table 4), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)); and wherein m is the number of X moieties conjugated to Ab. In a particular embodiment, m is at least 1 , for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 4, or 1 to 3. In a specific embodiment, m is about 1 to 3 or about 1 or 4.
[0089] Intracellularly, this PBD dimer conjugate Ab(X)m releases PBD dimer A:
Figure imgf000027_0002
[0090] In specific embodiments, a PBD dimer conjugate provided herein is of the following Formula Ab(
wherein X is
Figure imgf000027_0003
or
Figure imgf000028_0001
wherein the bond intersected by the wavy line signifies the attachment point of X to Ab;
wherein Ab is an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, see Table 4), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)); and wherein m is the number of X moieties conjugated to Ab. In a particular embodiment, m is at least 1, for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 4, or 1 to 3. In a specific embodiment, m is about 1 to 3 or about 1 or 4.
[0091] Intracellularly, this PBD dimer conjugate Ab(X)m releases PBD dimer B:
Figure imgf000028_0002
C2 Linked PBD Dimer ADCs
[0092] Also provided herein is a PBD dimer with a linker (e.g., reactive linker) connected through the C2 position on one of the PBD dimer moieties wherein the PBD dimer is conjugated via the linker to an anti-KIT antibody described herein (e.g., any one of antibodies Huml- Hum20), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)).
[0093] PBD dimer-linked ADCs (e.g., PBD dimer conjugates, such as KIT-PBD dimer ADCs) provided herein are suitable for use in providing PBD dimers to a target site (e.g., a target site with KIT receptors) in a subject. In a specific embodiment, a PBD dimer conjugate provided herein is of the following Formula Ab(X)m: herein X is
Figure imgf000029_0001
wherein the bond intersected by the wavy line signifies the attachment point of X to Ab;
wherein Ab is an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, see Table 4), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)); and wherein m is the number of X moieties conjugated to Ab. In a particular embodiment, m is at least 1 , for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 4, or 1 to 3. In a specific embodiment, m is about 1 to 3 or about 1 or 4.
[0094] Intracellularly, this PBD dimer conjugate Ab(X)m releases PDB dimer C:
Figure imgf000029_0002
[0095] In specific embodiments, a PBD dimer conjugate provided herein is of the following Formula Ab(X)m:
wherein X is
Figure imgf000029_0003
wherein the bond intersected by the wavy line signifies the attachment point of X to Ab;
wherein Ab is an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, see Table 4), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)); and wherein m is the number of X moieties conjugated to Ab. In a particular embodiment, m is at least 1 , for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 4, or 1 to 3. In a specific embodiment, m is about 1 to 3 or about 1 or 4.
[0096] Intracellularly, this PBD dimer conjugate Ab(X)m releases active PBD dimer D:
Figure imgf000030_0001
[0097] In specific embodiments, a PBD dimer conjugate provided herein is of the following Formula Ab(X)m:
wherein X is
Figure imgf000030_0002
wherein the bond intersected by the wavy line signifies the attachment point of X to Ab;
wherein Ab is an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, see Table 4), for example an anti-KIT antibody described in Section 5.1.2 (e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)); and wherein m is the number of X moieties conjugated to Ab. In a particular embodiment, m is at least 1 , for example m is 1 to 20, or 1 to 10, or 1 to 5, or 1 to 4, or 1 to 3. In a specific embodiment, m is about 1 to 3 or about 1 or 4. [0098] Intracellularly, this PBD dimer conjugate Ab(X)m releases PBD dimer E:
Figure imgf000031_0001
Drug loading of PBD Dimer ADCs
[0099] Drug loading is the average number of PBD dimer drugs per antibody, e.g. such as an anti-KIT antibody. In particular aspects where the compounds {e.g., PBD dimers attached to linkers) provided herein are bound to thiol groups, e.g., cysteine thiol groups, drug loading may, for example, range from 1 to 80, 1 to 50, 1 to 40, 1 to 20, 1 to 10, or 1 to 8 drugs per antibody {e.g., such as an anti-KIT antibody), e.g., where 1, 2, 3, 4, 5, 6, 7, or 8 drug moieties are covalently attached to an antibody {e.g., such as an anti-KIT antibody). In a particular embodiment, PBD dimer conjugates provided herein comprise an anti-KIT antibody described herein {e.g., any one of antibodies Huml-Hum20), for example an anti-KIT antibody described in Section 5.1.2 {e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)), conjugated with from 1 to 8 PBD dimers, 2 to 6 PBD dimers, or 1 to 3 PBD dimers, bound to thiol groups, e.g., cysteine thiol groups.
[00100] In specific aspects, compositions of ADCs provided herein include collections of antibodies, e.g., such as anti-KIT antibodies, conjugated with a range of drugs {e.g., PBD dimers), from 1 to 80, 1 to 50, 1 to 40, 1 to 20, 1 to 10, or 1 to 8.
[00101] In certain aspects, where the compounds {e.g., PBD dimers attached to linkers) provided herein are bound to lysines, drug loading may, for example, range from 1 to 80 drugs per antibody, e.g., such as an anti-KIT antibody, although in certain embodiments, there is an upper limit of 50, 40, 20, 10 or 8 drugs per antibody. Compositions of ADCs provided herein include collections of antibodies, e.g. such as anti-KIT antibodies, conjugated with a range of drugs, from 1 to 80, 1 to 40, 1 to 20, 1 to 10, or 1 to 8. In a particular embodiment, PBD dimer conjugates provided herein comprise an anti-KIT antibody described herein {e.g., any one of antibodies Huml-Hum20), for example an anti-KIT antibody described in Section 5.1.2 {e.g., an anti-KIT antibody comprising VH CDRs and VL CDRs as set forth in Table 1 (SEQ ID NOs: 16-21)), conjugated with from 1 to 80, 1 to 40, 1 to 20, 1 to 10, 1 to 8, 2 to 6, 1 to 4, or 1 to 3 PBDs bound to lysines.
[00102] In particular embodiments, provided herein are compositions comprising a plurality of ADCs exhibiting an average number of drugs, e.g., PBD dimers, per antibody. For example, such compositions can comprise a plurality of ADCs exhibiting an average of 1 to 8 PBD dimers, e.g., from 2 to 6 or 1 to 3 PBD dimers, bound to cysteines, and/or from 1 to 80, 1 to 40, 1 to 20, 1 to 10, 1 to 8, 2 to 6, 1 to 4, or 1 to 3 PBD dimers bound to lysines.
[00103] In specific embodiments, an average number of drugs per antibody in a collection or plurality of ADCs, such as PBD dimer conjugates, is described in terms of a ratio, drug per antibody ratio ("DAR"). In specific embodiments, a composition of ADCs, such as PBD dimer conjugates {e.g., KIT-PBD dimer ADCs, such as KIT-PBDl or KIT-PBD2), described herein has a DAR of about 1 to 5, or about 1 to 4, or about 1 to 3, or about 1.5 to 3 or 4.
[00104] The average number of drugs per antibody, or DAR, in preparations of ADC from conjugation reactions may be characterized by conventional means such as UV, reverse phase HPLC, HIC, mass spectroscopy, ELISA assay, and electrophoresis. The quantitative distribution of ADCs in terms of drug loading may also be determined. By ELISA, the average drug loading value in a particular preparation of ADC may be determined (see, e.g. , Hamblett et al (2004) Clin. Cancer Res. 10:7063-7070; Sanderson et al (2005) Clin. Cancer Res. 11 :843-852). In some instances, separation, purification, and characterization of homogeneous ADC with a certain drug loading value may be achieved via, for example, reverse phase HPLC or electrophoresis.
[00105] For some ADCs, drug loading may be limited by the number of attachment sites on an antibody or antigen-binding fragment thereof. For example, an antibody may have only one or several cysteine thiol groups, or may have only one or several sufficiently reactive thiol groups through which a linker may be attached.
[00106] In specific embodiments, typically, fewer than the theoretical maximum of drug moieties are conjugated to an antibody or an antigen-binding fragment thereof during a conjugation reaction. In specific aspects, many cysteine thiol residues in antibodies for conjugation exist as disulfide bridges and must be reduced with a reducing agent such as dithiothreitol (DTT) or TCEP, under partial or total reducing conditions. In particular embodiments, the loading (drug/antibody ratio, or DAR) of an ADC may be controlled in several different manners, including, but not limited to: (i) limiting the molar excess of drug-linker intermediate or linker reagent relative to antibody, (ii) limiting the conjugation reaction time or temperature, and (iii) partial or limiting reductive conditions for cysteine thiol modification.
[00107] In particular embodiments, certain antibodies have reducible interchain disulfides, e.g., cysteine bridges. In certain embodiments, antibodies {e.g., anti-KIT antibodies) may be made reactive for conjugation with linker reagents by treatment with a reducing agent such as DTT (dithiothreitol). Each cysteine bridge will thus form, theoretically, two reactive thiol nucleophiles. Additional nucleophilic groups can be introduced into antibodies {e.g., anti-KIT antibodies), e.g., through the reaction of lysines with 2-iminothiolane (Traut's reagent) resulting in conversion of an amine into a thiol. In specific embodiments, reactive thiol groups may be introduced into an antibody, e.g., anti-KIT antibody, (or fragment thereof) by engineering one, two, three, four, or more cysteine residues {e.g., preparing mutant antibodies comprising one or more non-native cysteine amino acid residues). See, e.g., US 7521541.
[00108] In particular embodiments, cysteine amino acids may be engineered at reactive sites in an antibody {e.g., anti-KIT antibody) and which do not form intrachain or intermolecular disulfide linkages (Junutula, et ah, 2008, Nature Biotech., 26(8):925-932; Dornan et al (2009) Blood 114(13):2721-2729; US 7521541; US 7723485; WO2009/052249). The engineered cysteine thiols may react with linker reagents or the drug-linker reagents of the compounds provided herein which have thiol-reactive, electrophilic groups such as maleimide or alpha-halo amides to form ADC with cysteine engineered antibodies and the PBD drug moieties. The location of the drug moiety can thus be designed, controlled, and known. The drug loading can be controlled since the engineered cysteine thiol groups typically react with thiol-reactive linker reagents or drug-linker reagents in high yield. Engineering an IgG antibody to introduce a cysteine amino acid by substitution at a single site on the heavy or light chain gives two new cysteines on the symmetrical antibody.
[00109] Where more than one nucleophilic or electrophilic group of an antibody reacts with a drug linker intermediate, or linker reagent followed by drug moiety reagent, then the resulting product is a mixture of ADC compounds with a distribution of drug moieties attached to an antibody, e.g., 1, 2, 3, etc. Liquid chromatography methods such as polymeric reverse phase ("PLRP") and hydrophobic interaction ("HIC") may separate compounds in the mixture by drug loading value. Preparations of ADC with a single drug loading value may be isolated. For example, in particular aspects, a drug loading value near 2 can be achieved with near homogeneity of the ADC.
[00110] In specific embodiments, ADC, such as PBD dimer conjugate, compositions provided herein include mixtures of ADC compounds where the antibody (e.g. , anti-KIT antibody) has one or more PBD drug moieties and where the drug moieties may be attached to the antibody at various amino acid residues.
[00111] In one embodiment, the average number of dimer PBD groups per antibody (e.g., anti-KIT antibody) or antigen-binding fragment thereof is in the range 1 to 20. In some embodiments, the range is selected from 1 to 8, 1 to 4, 1 to 3, 2 to 8, 2 to 6, 2 to 4, and 4 to 8.
[00112] In some embodiments, there is one PBD dimer group per antibody (e.g., anti-KIT antibody) or antigen-binding fragment thereof. In some embodiments, there are two PBD dimer groups per antibody (e.g., anti-KIT antibody) or antigen-binding fragment thereof. In some embodiments, there are three PBD dimer groups per antibody (e.g., anti-KIT antibody) or antigen-binding fragment thereof.
[00113] Also disclosed herein are all suitable isotopic variations of the PBD dimers and PBD dimer conjugates provided herein. An isotopic variation of a PBD dimer or PBD dimer conjugate is one in which at least one atom is replaced by an atom having the same atomic number but an atomic mass different from the atomic mass usually found in nature. Examples of isotopes that can be incorporated into the PBD dimers or PBD dimer conjugates provided herein include, but are not limited to, isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorus, sulphur, fluorine and chlorine such as 2H, 3H, 13C, 14C, 15N, 170, 180, 31P, 32P, 35S, 18F and 36C1, respectively. In one embodiment, certain isotopic variations of the PBD dimers or PBD dimer conjugates provided herein, for example, are those in which a radioactive isotope such as 3H or 14C is incorporated. These isotopic variations of PBD dimers or PBD dimer conjugates are useful in drug and/or substrate tissue distribution studies. In a particular embodiment the PDB compounds or conjugates are tritiated, i.e., 3H, or incorporate carbon- 14, i.e., 14C, isotopes. In a further embodiment substitution of a PDB dimer compound or PBD dimer conjugate with isotopes, such as deuterium, i.e., 2H, may afford certain therapeutic advantages resulting from greater metabolic stability, for example, increased in vivo half-life or reduced dosage
requirements. In certain embodiments, the isotopic variations of the PBD dimer compounds or PBD dimer conjugates provided herein can generally be prepared by conventional procedures such as by the general methods or by the preparations described in the Examples hereafter, using appropriate isotopic variations of suitable reagents.
[00114] Also disclosed herein are all salts, e.g., pharmaceutically acceptable salts of ADCs, e.g., PBD dimer conjugates provided herein. A pharmaceutically acceptable salt is a salt prepared from a pharmaceutically acceptable non-toxic acid or base including an inorganic acid and base and an organic acid and base. Suitable pharmaceutically acceptable base addition salts of the ADCs, e.g., PBD dimer conjugates, provided herein include, but are not limited to, metallic salts made from aluminum, calcium, lithium, magnesium, potassium, sodium and zinc or organic salts made from ammonium, alkyl substituted ammonium {e.g., N(alkyl)4_nHn; n=l, 2, or 3, wherein each alkyl substituent is selected independently), lysine, Ν,Ν'- dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, meglumine (N-methylglucamine) and procaine. Suitable non-toxic acids include, but are not limited to, inorganic and organic acids such as acetic, alginic, anthranilic, benzenesulfonic, benzoic, camphorsulfonic, citric, ethenesulfonic, formic, fumaric, furoic, galacturonic, gluconic, glucuronic, glutamic, glycolic, hydrobromic, hydrochloric, isethionic, lactic, maleic, malic, mandelic, methanesulfonic, mucic, nitric, pamoic, pantothenic, phenylacetic, phosphoric, propionic, salicylic, stearic, succinic, sulfanilic, sulfuric, tartaric acid, and p-toluenesulfonic acid. Specific non-toxic acids include hydrochloric, hydrobromic, phosphoric, sulfuric, and
methanesulfonic acids. Others are well known in the art, see for example, Berge, et al., J.
Pharm. Sci. 66, 1-19 (1977), Remington 's Pharmaceutical Sciences, 18th eds., Mack Publishing, Easton PA (1990) or Remington: The Science and Practice of Pharmacy, 19th eds., Mack Publishing, Easton PA (1995).
[00115] Also disclosed herein are all tautomers of ADCs, e.g., PBD dimer conjugates provided herein. Tautomers of a PBD dimer or PBD dimer conjugate, are isomeric forms of a PBD dimer or PBD dimer conjugate that are in equilibrium with each other. The concentrations of the isomeric forms will depend on the environment the compound is found in and may be different depending upon, for example, whether the compound is a solid or is in an organic or aqueous solution. For example, in aqueous solution, pyrazoles may exhibit the following isomeric forms, which are referred to as tautomers of each other:
Figure imgf000035_0001
[00116] Also disclosed herein are all stereoisomers of ADCs, e.g., PBD dimer conjugates, provided herein. A stereoisomer or a stereoisomeric form of a PBD dimer or PBD dimer conjugate, is a stereoisomer of a PBD dimer or PBD dimer conjugate that is substantially free of other stereoisomers of that compound or conjugate. For example, a stereoisomerically pure PBD dimer having one chiral center will be substantially free of the opposite enantiomer of the compound. A stereoisomerically pure PBD dimer or PBD dimer conjugate having two or more chiral centers will be substantially free of other diastereomers of the compound or conjugate.
[00117] In one embodiment, a typical stereoisomerically pure compound or conjugate comprises greater than about 80% by weight of one stereoisomer of the compound or conjugate and less than about 20%> by weight of other stereoisomers of the compound or conjugate, greater than about 90%> by weight of one stereoisomer of the compound or conjugate and less than about 10%) by weight of the other stereoisomers of the compound or conjugate, greater than about 95% by weight of one stereoisomer of the compound or conjugate and less than about 5% by weight of the other stereoisomers of the compound or conjugate, or greater than about 97% by weight of one stereoisomer of the compound and less than about 3% by weight of the other stereoisomers of the compound or conjugate.
[00118] Typically the PBD dimers or PBD dimer conjugates provided herein have chiral centers and can occur as racemates, individual enantiomers or diastereomers, and mixtures thereof. All such isomeric forms are included within the embodiments disclosed herein, including mixtures thereof. The use of stereoisomerically pure forms of such PBD dimers or PBD dimer conjugates, as well as the use of mixtures of those forms, are encompassed by the embodiments disclosed herein. For example, mixtures comprising equal or unequal amounts of the enantiomers of a particular PBD dimer or PBD dimer conjugate may be used in methods and compositions disclosed herein. These isomers may be asymmetrically synthesized or resolved using standard techniques such as chiral columns or chiral resolving agents. See, e.g., Jacques, J., et al., Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981);
Wilen, S. H., et al, Tetrahedron 33:2725 (1977); Eliel, E. L., Stereochemistry of Carbon Compounds (McGraw Hill, NY, 1962); and Wilen, S. H., Tables of Resolving Agents and Optical Resolutions p. 268 (E.L. Eliel, Ed., Univ. of Notre Dame Press, Notre Dame, IN, 1972).
[00119] As used herein, an "alkyl" group is a saturated straight chain or branched non-cyclic hydrocarbon having, for example, from 1 to 12 carbon atoms, 1 to 9 carbon atoms, 1 to 6 carbon atoms, 1 to 4 carbon atoms, or 2 to 6 carbon atoms. Representative alkyl groups include -methyl, -ethyl, -n-propyl, -n-butyl, -n-pentyl and -n-hexyl; while branched alkyls include -isopropyl, - sec-butyl, -z'so-butyl, -tert-butyl, -z'so-pentyl, 2-methylpentyl, 3-methylpentyl, 4-methylpentyl, 2,3-dimethylbutyl and the like.
[00120] As used herein, an "alkenyl" group is a partially unsaturated straight chain or branched non-cyclic hydrocarbon having, for example, from 2 to 6 carbon atoms, 3 to 4 carbon atoms, or 3 carbon atoms. Representative alkenyl groups include propenyl and the like.
[00121] As used herein, an "alkynyl" group is a partially unsaturated straight chain or branched non-cyclic hydrocarbon having, for example, from 2 to 6 carbon atoms, 3 to 6 carbon atoms, or 3 carbon atoms. Representative alkynyl groups include propynyl, butynyl and the like.
[00122] As used herein, an "cycloalkyl" group is a saturated cyclic alkyl group of from 3 to 6 carbon atoms having a single cyclic ring. In some embodiments, the cycloalkyl group has 3 ring members. Such cycloalkyl groups include, by way of example, single ring structures such as cyclopropyl, cyclobutyl, and cyclopentyl.
5.1.1.1 Synthesis of PBD Dimer ADCs
Scheme 1
Figure imgf000037_0001
[00123] Scheme 1 : In one embodiment, compounds of Formula V can be synthesized by the route depicted in Scheme 1. Amide coupling of acids of Formula II with a pyrrolidine of Formula I through reactive acid derivatives such as an acid chloride formed via reaction with oxalyl chloride, affords bis-amides of Formula III. Bis-ketones of Formula IV are produced via oxidation, such as TEMPO catalyzed oxidation, of bis-alcohols of Formula III. Finally, conversion of bis-ketones of Formula IV to bis-enol-triflates via base mediated enolate formation, with a base such as 2,6-lutidine, and trapping with a triflating agent such as triflic anhydride, yields the intermediate compounds of Formula V.
Scheme 2
Figure imgf000038_0001
[00124] Scheme 2: In one embodiment, peptide-PBD dimers of Formula XIV can be prepared as shown in Scheme 2. Bis-enol-triflates of Formula V can be substituted with R groups via metal mediated coupling, such as a palladium mediated cross-coupling with a boronic acid derivative in the presence of a base, such as potassium phosphate to form compounds of Formula VI. Reduction of bis-esters of Formula VI with a metal hydride such as lithium borohydride followed by acylation of the resulting bis-alcohols of Formula VII with an acylating agent such as acetyl chloride in the presence of a base such as triethylamine, provides bis-acetates of Formula VIII. Reduction of bis-nitro compounds of Formula IX with a reducing agent, such as zinc in the presence of formic acid, followed by monoprotection with a protecting group P, such as Alloc, using a reactive allyloxycarbonyl agent, such as allyl chloroformate, in the presence of a base, such as pyridine, produces primary amines of Formula X. Conversion of anilines of Formula X to carbamates of P' -protected peptide -benzyl alcohols, such as Alloc- VAL-ALA- para-NHBnOH, for example via isocyanate formation, such as through reaction with triphosgene in the presence of triethylamine, followed by nuclophilic attack by a P' -protected peptide -benzyl alcohol in the presence of a base such as triethylamine yields carbamates of Formula XI. Basic removal of the acetate groups, such as in the presence of potassium carbonate, from compounds of Formula XI followed by cyclization via oxidation, such as with Dess-Martin periodinane, results in protected PBD derivatives of Formula XIII. Deprotection of the PBD dimer and peptide groups, such as through palladium mediated removal of Alloc groups, provides the N10 PBD dimer-carbamate-peptides of Formula XIV.
[00125] Scheme 3: In one embodiment, compounds of Formula XX can be synthesized by the route depicted in Scheme 3. Amide coupling of acids of Formula II with a pyrrolidine of Formula I through a reactive acid derivative such as an acid chloride formed via reaction with oxalyl chloride, affords bis-amides of Formula III. Catalytic reduction of the nitro moiety, such as with hydrazine and a catalyst such as Raney Nickel, and cyclization produces PBD dimer intermediates of Formula XV. Protection of the alcohols in Formula XV with a protecting group P, such as TBS, using a reactive silylating agent, such as TBS chloride, in the presence of a base, such as imidazole, followed by protection of the free nitrogens of Formula XVI with a protecting group P', such as SEM, via addition of a base, such as n-butyl lithium, followed by addition of a reactive alkyl chloride, such as SEM chloride, yields the fully protected intermediates of Formula XVII. Bis-alcohols of Formula XVIII are produced via selective alcohol deprotection of intermediates of Formula XVII, for example, via fluoride mediated removal of a silyl protecting group, such as TBAF deprotection of a TBS moiety. Calalyzed oxidation of the bis- alcohols of Formula XVIII, such as via TEMPO catalyzed oxidation, to the bis-ketones of Formula XIX followed by conversion to bis-enol-triflates via base mediated enolate formation, with a base such as 2,6-lutidine, and trapping with a triflating agent such as triflic anhydride, yields the bis-enol-triflate intermediates of Formula XX.
Scheme 3
Figure imgf000040_0001
[00126] Scheme 4: In one embodiment, peptide-PBD dimers of Formula XXV can be prepared as shown in Scheme 4. Bis-enol-triflates of Formula XX can be mono-substituted with aniline via metal mediated coupling, such as palladium mediated cross coupling with an aniline boronic acid derivative in the presence of a base, such as sodium carbonate to form compounds of Formula XXI. Mono-triflates of Formula XXI can be substituted via coupling mediated by a metal, such as palladium, with a boronic acid derivative in the presence of a base, such as potassium phosphate tribasic, and optional additives such as silver(I)oxide and triphenylarsine, to form compounds of Formula XXII. Deprotection of bis-protected compounds of Formula XXII, such as through removal of SEM groups with LiTEBH, affords the PBD dimer intermediates of Formula XXIII. Acylation of the anilines of Formula XXIII with a protected peptide reagent such as Alloc yields the intermediates of Formula XXIV, and subsequent deprotection, such as through palladium mediated removal of an Alloc group, affords the peptide-PBD dimers of Formula XXV.
Scheme 4
Figure imgf000041_0001
[00127] Scheme 5: In one embodiment, peptide-PBD dimers of Formula XXV can be prepared as shown in Scheme 5. Bis-enol-triflates of Formula XX can be mono-substituted with an aniline/protected peptide moiety, such as /?ara-aminoPh-Ala-Val-Fmoc, via metal mediated coupling, such as palladium mediated cross coupling with an aniline boronic acid derivative in the presence of a base, such as sodium carbonate to form compounds of Formula XXVI. Mono- triflates of Formula XXVI can be substituted via coupling mediated by a metal, such as palladium, with a boronic acid derivative in the presence of a base, such as potassium phosphate tribasic, and optional additives such as silver(I)oxide and triphenylarsine, to form compounds of Formula XXVII. Deprotection of the bis-protected PBD dimers of Formula XXVII affords the PBD dimer intermediates of Formula XXIV, such as through removal of SEM groups with
LiTEBH, and subsequent peptide deprotection, such as basic removal of a carbamate, such as removal of an Fmoc group with piperidine, affords the peptide-PBD dimers of Formula XXV.
Scheme 5
Figure imgf000042_0001
General Conditions for Attachment of Linker/Electrophile Moieties
[00128] Scheme 6: In one embodiment, compounds of Formula XXX and XXXI can be synthesized via the reaction depicted in Scheme 6. Peptide coupling, such as through acid activation via EDCI, of compounds of Formula XIV or XXV with acids of Formula XXIX (an acid attached to an electrophile E, such as a maleimide or an alkyl iodide, through a linker L', such as an amide containing alkyl chain or amide containing polyethyleneoxide chain), affords the final products of Formula XXX or XXXI, respectively.
Scheme 6
Figure imgf000043_0001
General Conditions for Conjugate Formation
[00129] Scheme 7: In one embodiment, antibody drug conjugates derivatives of Formula XXXII and XXXIII can be synthesized via the reaction depicted in Scheme 7.
[00130] Antibody drug conjugates of Formula XXX or XXXI, may be prepared by several routes, employing organic chemistry reactions, conditions, and reagents known to those skilled in the art, including reaction of a nucleophilic group (Nu) of an antibody (Ab) with a drug-linker reagent of Formula XXX or Formula XXXI. In certain embodiments, antibody drug conjugates of Formula XXX or XXXI, may be prepared by several routes, employing organic chemistry reactions, conditions, and reagents known to those skilled in the art, including reaction of two or more nucleophilic groups (Nu) of the same antibody (Ab) with two or more drug-linker reagents of Formula XXX or Formula XXXI. [00131] Nucleophilic groups on antibodies include, but are not limited to side chain thiol groups, e.g., cysteine. Thiol groups are nucleophilic and capable of reacting to form covalent bonds with electrophilic groups on linker moieties such as a maleimide or an alkyl iodide. Certain antibodies have reducible interchain disulfides, i.e., cysteine bridges. Antibodies may be made reactive for conjugation with linker reagents by treatment with a reducing agent such as DTT (Cleland's reagent, dithiothreitol) or TCEP (tris(2-carboxyethyl)phosphine hydrochloride; Getz et al (1999) Anal. Biochem. Vol 273:73-80; Soltec Ventures, Beverly, MA). Each cysteine disulfide bridge will thus form, theoretically, two reactive thiol nucleophiles.
Scheme 7
Figure imgf000044_0001
5.1.2. Anti-KIT Antibodies
[00132] In particular aspects, provided herein are anti-KIT antibodies or antigen-binding fragments thereof which specifically bind to a D4 of human KIT and are conjugated to one or more drug moieties, such as one or more PBDs, e.g., PBD dimers, forming ADCs, such as PBD dimer conjugates. These ADCs, such as PBD dimer conjugates, target cells expressing KIT, and are useful for managing and treating disorders such as cancer.
[00133] As used herein, the terms "antibody" and "immunoglobulin" and "Ig" are terms of art and can be used interchangeably herein and refer to a molecule with an antigen binding site that immunospecifically binds an antigen.
[00134] As used herein, an "antigen" is a moiety or molecule that contains an epitope, and, as such, also is specifically bound by antibody. In a specific embodiment, the antigen, to which an antibody described herein binds, is KIT {e.g., human KIT), or a fragment thereof, for example, an extracellular domain of KIT {e.g., human KIT) or a D4 region of KIT {e.g., human KIT).
[00135] As used herein, an "epitope" is a term in the art and refers to a localized region of an antigen to which an antibody can specifically bind. A region or a polypeptide contributing to an epitope can be contiguous amino acids of the polypeptide or an epitope can come together from two or more non-contiguous regions of the polypeptide.
[00136] As used herein, the terms "antigen binding domain," "antigen binding region," "antigen binding fragment," and similar terms refer to a portion of an antibody molecule which comprises the amino acid residues that interact with an antigen and confer on the antibody molecule its specificity for the antigen {e.g., the complementarity determining regions (CDR)). The antigen binding region can be derived from any animal species, such as rodents {e.g., mouse, rat or hamster) and humans. The CDRs of an antibody molecule can be determined by any method well known to one of skill in the art. In particular, the CDRs can be determined according to the Kabat numbering system {see Kabat et al. (1991) Sequences of Proteins of Immunological Interest. (U.S. Department of Health and Human Services, Washington, D.C.) 5th ed.). In certain aspects, the CDRs of an antibody can be determined according to (i) the Chothia numbering scheme, which will be referred to herein as the "Chothia CDRs" (see, e.g., Chothia and Lesk, 1987, J. Mol. Biol, 196:901-917; Al-Lazikani et al, 1997, J. Mol. Biol, 273:927-948; and U.S. Patent No. 7,709,226); or (ii) the IMGT numbering system, for example, as described in Lefranc, M.-P., 1999, The Immunologist, 7: 132-136 and Lefranc, M.-P. et al., 1999, Nucleic Acids Res., 27:209-212.
[00137] As used herein, a "conformational epitope" or "non-linear epitope" or "discontinuous epitope" refers to one comprised of at least two amino acids which are not consecutive amino acids in a single protein chain. For example, a conformational epitope can be comprised of two or more amino acids which are separated by a stretch of intervening amino acids but which are close enough to be recognized by an antibody (e.g., an anti-KIT antibody) described herein as a single epitope. As a further example, amino acids which are separated by intervening amino acids on a single protein chain, or amino acids which exist on separate protein chains, can be brought into proximity due to the conformational shape of a protein structure or complex to become a conformational epitope which can be bound by an anti-KIT antibody described herein. It will be appreciated by one of skill in the art that, in general, a linear epitope bound by an anti- KIT antibody described herein may or may not be dependent on the secondary, tertiary, or quaternary structure of the KIT receptor. For example, in some embodiments, an anti-KIT antibody described herein binds to a group of amino acids regardless of whether they are folded in a natural three dimensional protein structure. In other embodiments, an anti-KIT antibody described herein does not recognize the individual amino acid residues making up the epitope, and require a particular conformation (bend, twist, turn or fold) in order to recognize and bind the epitope.
[00138] As used herein, the term "constant region" or "constant domain" refers to an antibody portion, e.g., a carboxyl terminal portion of a light and/or heavy chain which is not directly involved in binding of an antibody to antigen but which exhibits various effector functions, such as interaction with the Fc receptor. The terms refer to a portion of an immunoglobulin molecule having a generally more conserved amino acid sequence relative to an immunoglobulin variable domain.
[00139] As used herein, the term "heavy chain" when used in reference to an antibody refers to any distinct types, e.g., alpha (a), delta (δ), epsilon (ε), gamma (γ) and mu (μ), based on the amino acid sequence of the constant domain, which give rise to IgA, IgD, IgE, IgG and IgM classes of antibodies, respectively, including subclasses of IgG, e.g., IgGi, IgG2, IgG3 and IgG4. In a specific embodiment, the heavy chain is a human heavy chain. [00140] As used herein, the terms "immunospecifically binds," "immunospecifically recognizes," "specifically binds," and "specifically recognizes" are analogous terms in the context of antibodies and refer to molecules that bind to an antigen (e.g., epitope or immune complex) as such binding is understood by one skilled in the art. For example, a molecule that specifically binds to an antigen may bind to other peptides or polypeptides, generally with lower affinity as determined by, e.g., immunoassays, Biacore™, KinExA 3000 instrument (Sapidyne Instruments, Boise, ID), or other assays known in the art. In a specific embodiment, molecules that immunospecifically bind to an antigen bind to the antigen with a Ka that is at least 2 logs, 2.5 logs, 3 logs, 4 logs or greater than the Ka when the molecules bind to another antigen. In another specific embodiment, molecules that immunospecifically bind to an antigen do not cross react with other proteins. In another specific embodiment, molecules that immunospecifically bind to an antigen do not cross react with other non-KIT proteins.
[00141] As used herein, an "isolated" or "purified" antibody is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the antibody is derived, or substantially free of chemical precursors or other chemicals when chemically synthesized.
[00142] The terms "Kabat numbering," and like terms are recognized in the art and refer to a system of numbering amino acid residues in the heavy and light chain variable regions of an antibody, or an antigen binding portion thereof (Kabat et al. (1971) Ann. NY Acad. Sci. 190:382- 391 and, Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242). Using the Kabat numbering system, CDRs within an antibody heavy chain molecule are typically present at amino acid positions 31 to 35 ("CDR1"), amino acid positions 50 to 65 ("CDR2"), and amino acid positions 95 to 102 ("CDR3"). Using the Kabat numbering system, CDRs within an antibody light chain molecule are typically present at amino acid positions 24 to 34 (CDR1), amino acid positions 50 to 56 (CDR2), and amino acid positions 89 to 97 (CDR3).
[00143] As used herein, the term "light chain" when used in reference to an antibody refers to any distinct types, e.g., kappa (κ) of lambda (λ) based on the amino acid sequence of the constant domains. Light chain amino acid sequences are well known in the art. In specific embodiments, the light chain is a human light chain. [00144] As used herein, the term "monoclonal antibody" refers to an antibody obtained from a population of homogenous or substantially homogeneous antibodies. The term "monoclonal" is not limited to any particular method for making the antibody. Generally, a population of monoclonal antibodies can be generated by cells, a population of cells, or a cell line. In specific embodiments, a "monoclonal antibody," as used herein, is an antibody produced by a single hybridoma or other cell (e.g. , host cell producing a recombinant antibody), wherein the antibody immunospecifically binds to a KIT epitope (e.g., an epitope of a D4 of human KIT) as determined, e.g., by ELISA or other antigen-binding or competitive binding assay known in the art or in the Examples provided herein. Monoclonal antibodies described herein can, for example, be made by the hybridoma method as described in Kohler et ah; Nature, 256:495 (1975) or can be isolated from phage libraries using the techniques as described herein, for example. Other methods for the preparation of clonal cell lines and of monoclonal antibodies expressed thereby are well known in the art (see, for example, Chapter 11 in: Short Protocols in Molecular Biology, (2002) 5th Ed., Ausubel et ah, eds., John Wiley and Sons, New York).
[00145] As used herein, the term "polyclonal antibodies" refers to an antibody population that includes a variety of different antibodies directed to the same and to different epitopes within an antigen or antigens. Methods for producing polyclonal antibodies are known in the art (See, e.g., see, for example, Chapter 11 in: Short Protocols in Molecular Biology, (2002) 5th Ed., Ausubel et ah, eds., John Wiley and Sons, New York).
[00146] As used herein, the terms "variable region" or "variable domain" refer to a portion of an antibody, generally, a portion of a light or heavy chain, typically about the amino-terminal 110 to 120 amino acids in the mature heavy chain and about 90 to 100 amino acids in the mature light chain, which differ extensively in sequence among antibodies and are used in the binding and specificity of a particular antibody for its particular antigen. The variability in sequence is concentrated in those regions called complementarity determining regions (CDRs) while the more highly conserved regions in the variable domain are called framework regions (FR).
Without wishing to be bound by any particular mechanism or theory, it is believed that the CDRs of the light and heavy chains are primarily responsible for the interaction of the antibody with antigen. In a specific embodiment, numbering of amino acid positions of antibodies described herein is according to the EU Index, as in Kabat et al. (1991) Sequences of Proteins of
Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242 ("Kabat et a/."). In certain aspects, the CDRs of an antibody can be determined according to (i) the Chothia numbering scheme, which will be referred to herein as the "Chothia CDRs" (see, e.g., Chothia and Lesk, 1987, J. Mol. Biol, 196:901-917; Al-Lazikani et al, 1997, J. Mol. Biol, 273:927-948; Chothia et al, 1992, J. Mol. Biol, 227:799-817;
Tramontano A et al, 1990, J. Mol. Biol. 215(1): 175-82; and U.S. Patent No. 7,709,226); or (ii) the IMGT numbering system, for example, as described in Lefranc, M.-P., 1999, The
Immunologist, 7: 132-136 and Lefranc, M.-P. et al, 1999, Nucleic Acids Res., 27:209-212; or (iii) MacCallum et al, 1996, J. Mol. Biol, 262:732-745. See also, e.g., Martin, A., "Protein Sequence and Structure Analysis of Antibody Variable Domains," in Antibody Engineering, Kontermann and Diibel, eds., Chapter 31, pp. 422-439, Springer- Verlag, Berlin (2001). In certain embodiments, the variable region is a human variable region. In certain embodiments, the variable region comprises rodent or murine CDRs and human framework regions (FRs). In particular embodiments, the variable region is a primate (e.g., non-human primate) variable region. In certain embodiments, the variable region comprises rodent or murine CDRs and primate (e.g., non-human primate) framework regions (FRs). As a non-limiting example, a variable region described herein is obtained from assembling two or more fragments of human sequences into a composite human sequence.
[00147] In specific aspects, provided herein are antibodies (e.g., human, composite human, or humanized antibodies), including antigen-binding fragments thereof, of an ADC or PBC conjugate, wherein the antibodies or antigen-binding fragments thereof specifically binds to a D4 region of human KIT and comprises:
(i) VH CDRs of a VH domain comprising the amino acid sequence of SEQ ID NO: 31 (QVQLKQSGAELVRPGASVKLSCKASGYTFTDYYINWVKQRPGQGLEWIARIYPGS GNTYYNEKFKGKATLTAEKSSSTAYMQLSSLTSEDSAVYFCARGVYYFDYWGQG TTLTVSS) or SEQ ID NO: 69
(QVQLKQSGAELVRPGASVKLSCKASGYTFTDYYINWVKQRPGQGLEWIARIYPGS GNTYYNEKFKGKATLTAEKSSSTAYMQLSSLTSEDSAVYFCARGVYYFDYWGQG TTLTVSA), and
(ii) VL CDRs of a VL domain comprising the amino acid sequence of SEQ ID NO: 32 (DIVMTQSQKFMSTSVGDRVSVTCKASQNVRTNVAWYQQKPGQSPKALIYSASYR YSGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYNSYPRTFGGGTKLEIKR). [00148] In a specific embodiment, an antibody (e.g., a human, composite human, or humanized antibody) described herein of an ADC or PBC conjugate, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprises the VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) described in Table 1.
[00149] In a specific embodiment, an antibody (e.g., a human, composite human, or humanized antibody) described herein of an ADC or PBC conjugate, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprises the VH CDRs and VL CDRs described in Table 2 (e.g., set 1 or set 2). In a certain embodiment, an antibody (e.g., a human, composite human, or humanized antibody) described herein of an ADC or PBC conjugate, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprises the VH CDRs and VL CDRs described in Table 3 (AbM CDRs or Contact CDRs).
[00150] In certain aspects, the CDRs of an antibody described herein is determined according to the method of Chothia, for example Chothia and Lesk, 1987, J. Mol. Biol, 196:901-917, which will be referred to herein as the "Chothia CDRs" (see also, e.g., Al-Lazikani et al., 1997, J. Mol. Biol, 273:927-948; Chothia et al, 1992, J. Mol. Biol, 227:799-817; Tramontano A et al, 1990, J. Mol. Biol. 215(1): 175-82; and U.S. Patent No. 7,709,226). Using the Kabat numbering system of numbering amino acid residues in the VH chain region and VL chain region, Chothia CDRs within an antibody heavy chain molecule are typically present at amino acid positions 26 to 32 ("CDR1"), amino acid positions 53 to 55 ("CDR2"), and amino acid positions 96 to 101 ("CDR3"). Using the Kabat numbering system of numbering amino acid residues in the VH chain region and VL chain region, Chothia CDRs within an antibody light chain molecule are typically present at amino acid positions 26 to 33 (CDR1), amino acid positions 50 to 52 (CDR2), and amino acid positions 91 to 96 (CDR3).
[00151] In a specific embodiment, the position of a CDR along the VH and/or VL region of an antibody described herein may vary by one, two, three or four amino acid positions so long as immunospecific binding to KIT (e.g., the D4 region of human KIT) is maintained (e.g., substantially maintained, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%). For example, in one embodiment, the position defining a CDR of an antibody described herein may vary by shifting the N-terminal and/or C-terminal boundary of the CDR by one, two, three, or four, amino acids, relative to the CDR position depicted in Figures 2A-2I, so long as immunospecific binding to KIT (e.g., the D4 region) is maintained (e.g., substantially maintained, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%).
Figure imgf000051_0001
[00153] Table 2: CDR Amino Acid Sequences
Figure imgf000051_0002
[00155] Table 4: VL and VH domains of Antibodies Huml-20
Figure imgf000052_0001
[00156] In certain aspects, provided herein are VH domains (e.g., HI, H2, H3, H4 and H5 comprising SEQ ID NOs: 2-6, respectively) and VL domains (e.g., LI, L2, L3, and L4 comprising SEQ ID NOs: 7-10, respectively) of an antibody (e.g., a human, composite human, or humanized antibody) of an ADC or PBC conjugate described herein, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT). In certain embodiments, provided herein are antibodies, which specifically binds to a D4 region of human KIT, of an ADC such as a PBD dimer conjugate described herein comprising such VH and VL domains, as set forth, for example, in Table 4 (i.e., antibodies Huml-Hum20). In particular embodiments, these antibodies of an ADC such as a PBD dimer conjugate describe herein comprise VH CDRsl-3 and VL CDRs 1-3 comprising SEQ ID NOs: 16-18 and 19-21, respectively.
[00157] In certain aspects, an antibody described herein which immunospecifically binds to a D4 region of a KIT polypeptide (e.g., human KIT polypeptide) may be described by its VL chain region (e.g., any one of SEQ ID NOs: 7-10) or VH chain region (e.g., any one of SEQ ID NOs: 2-6), or by its 3 VL CDRs or its 3 VH CDRs. See, for example, Rader et αί, 1998, Proc. Natl. Acad. Sci. USA, 95 : 8910-8915, which is incorporated herein by reference in its entirety, which describes the humanization of the mouse anti-avP3 antibody by identifying a complementing light chain or heavy chain from a human light chain or heavy chain library, respectively, resulting in humanized antibody variants having affinities as high or higher than the affinity of the original antibody. See also, Clackson et αί, 1991, Nature, 352:624-628, which is
incorporated herein by reference in its entirety, describing methods of producing antibodies that bind a specific antigen by using a specific VL (or VH) domain and screening a library for the complimentary variable domains. The screen produced 14 new partners for a specific VH domains and 13 new partners for a specific VL domain, which were strong binders as determined by ELISA.
[00158] In certain embodiments, an ADC such as a PBD dimer conjugate provided herein comprises an antibody described herein, or an antigen-binding fragment thereof, comprising a variable light (VL) chain region comprising an amino acid sequence described herein, for example, any one of SEQ ID NOs: 7-10 (e.g., see Figures 2A-2K) or SEQ ID NO: 12.
[00159] In certain embodiments, an ADC such as a PBD dimer conjugate provided herein comprises an antibody described herein, or an antigen-binding fragment thereof, comprising a variable heavy (VH) chain region comprising an amino acid sequence described herein, for example any one of SEQ ID NOs: 2-6 (e.g., see Figures 2A-2K) or SEQ ID NO: 1 1.
[00160] For example, described herein is an ADC such as a PBD dimer conjugate provided herein comprising an antibody that immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT) and comprises (i) the VH domain HI (SEQ ID NO: 2), H2 (SEQ ID NO: 3), H3 (SEQ ID NO: 4), H4 (SEQ ID NO: 5), or H5 (SEQ ID NO: 6) and/or (ii) the VL domain LI (SEQ ID NO: 7), L2 (SEQ ID NO: 8), L3 (SEQ ID NO: 9), or L4 (SEQ ID NO: 10). In a particular example, an ADC such as a PBD dimer conjugate provided herein comprises an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT) and comprises a VH domain and/or a VL domain of any one of antibodies Huml-Hum20 (see Table 4). In a particular example, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, or an antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT and comprises a VH domain and/or a VL domain of any one of antibodies Hum4, Hum8, HumlO, or Huml7.
[00161] In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which immunospecifically binds to a D4 region of human KIT and comprises VH domain HI (SEQ ID NO: 2) and VL domain LI (SEQ ID NO: 7). In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain HI (SEQ ID NO: 2) and VL domain L2 (SEQ ID NO: 8). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain HI (SEQ ID NO: 2) and VL domain L3 (SEQ ID NO: 9). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain HI (SEQ ID NO: 2) and VL domain L4 (SEQ ID NO: 10). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H2 (SEQ ID NO: 3) and VL domain LI (SEQ ID NO: 7). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H2 (SEQ ID NO: 3) and VL domain L2 (SEQ ID NO: 8). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H2 (SEQ ID NO: 3) and VL domain L3 (SEQ ID NO: 9). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H2 (SEQ ID NO: 3) and VL domain L4 (SEQ ID NO: 10). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H3 (SEQ ID NO: 4) and VL domain LI (SEQ ID NO: 7). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H3 (SEQ ID NO: 4) and VL domain L2 (SEQ ID NO: 8). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H3 (SEQ ID NO: 4) and VL domain L3 (SEQ ID NO: 9). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H3 (SEQ ID NO: 4) and VL domain L4 (SEQ ID NO: 10). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H4 (SEQ ID NO: 5) and VL domain LI (SEQ ID NO: 7). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H4 (SEQ ID NO: 5) and VL domain L2 (SEQ ID NO: 8). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H4 (SEQ ID NO: 5) and VL domain L3 (SEQ ID NO: 9). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H4 (SEQ ID NO: 5) and VL domain L4 (SEQ ID NO: 10). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H5 (SEQ ID NO: 6) and VL domain LI (SEQ ID NO: 7). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H5 (SEQ ID NO: 6) and VL domain L2 (SEQ ID NO: 8). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H5 (SEQ ID NO: 6) and VL domain L3 (SEQ ID NO: 9). In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT and comprises VH domain H5 (SEQ ID NO: 6) and VL domain L4 (SEQ ID NO: 10).
[00162] In certain aspects, an anti-KIT antibody, or an antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein is non-immunogenic in a human. In a particular embodiment, a non-immunogenic amino acid sequence is devoid of epitopes identified to be binders to human MHC class II, e.g., epitopes that are non-human germline binders to human MHC class II. In a particular embodiment, amino acid sequences substantially devoid of epitopes identified to be binders to human MHC class II, e.g. , epitopes that are non-human germline binders to human MHC class II. In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody described herein which specifically binds to a D4 region of human KIT and comprises a VH domain and a VL domain that are not immunogenic (e.g., not immunogenic in a human), as determined, for example, by the T Cell Epitope Database™ (TCED™). In a certain embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody described herein which specifically binds to a D4 region of human KIT, and comprises a VH domain and a VL domain that are not
immunogenic (e.g., not immunogenic in a human), as determined by an in vitro assay described in the art, see, e.g., Wang et al, 2008, PLoS Computational Biology, 2008, 4(4):el000048; and Arnold et al, 2002, J. Immunol, 169:739-749.
[00163] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), and comprises a VH domain that has at least 93% sequence identity to HI (SEQ ID NO: 2). In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which immunospecifically binds to a KIT polypeptide (e.g. , the D4 region of human KIT), comprising a VH domain that has at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to HI (SEQ ID NO: 2). In a particular embodiment, the VH domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00164] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VH domain that has at least 92% sequence identity to H2 (SEQ ID NO: 3). In a particular embodiment, an antibody, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises a VH domain that has at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to H2 (SEQ ID NO: 3). In a particular embodiment, the VH domain is non-immunogenic (e.g. , non-immunogenic in a human), for example as determined by the absence of epitopes that bind to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody, or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00165] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VH domain that has at least 90% sequence identity to H3 (SEQ ID NO: 4). In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VH domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to H3 (SEQ ID NO: 4). In a particular embodiment, the VH domain is non-immunogenic (e.g., non- immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00166] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VH domain that has at least 87% sequence identity to H4 (SEQ ID NO: 5). In a particular embodiment, an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g. , the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein, comprises a VH domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to H4 (SEQ ID NO: 5). In a particular embodiment, the VH domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00167] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VH domain that has at least 86% sequence identity to H5 (SEQ ID NO: 6). In a particular embodiment, an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g. , the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein, comprises a VH domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to H5 (SEQ ID NO: 6) . In a particular embodiment, the VH domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00168] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VL domain that has at least 90% sequence identity to LI (SEQ ID NO: 7). In a particular embodiment, an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g. , the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein, comprises a VL domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to LI (SEQ ID NO:
7) . In a particular embodiment, the VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21 , respectively.
[00169] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VL domain that has at least 88% sequence identity to L2 (SEQ ID NO: 8). In a particular embodiment, an antibody, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein, comprises a VL domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to L2 (SEQ ID NO: 8). In a particular embodiment, the VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof comprises a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21 , respectively.
[00170] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VL domain that has at least 87% sequence identity to L3 (SEQ ID NO: 9). In a particular embodiment, an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g. , the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein, comprises a VL domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to L3 (SEQ ID NO:
9) . In a particular embodiment, the VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21 , respectively.
[00171] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising a VL domain that has at least 84% sequence identity to L4 (SEQ ID NO: 10). In a particular embodiment, an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g. , the D4 region of human KIT), of an ADC such as a PBD dimer conjugate provided herein, comprises a VL domain that has at least 92%, at least 93%, at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99% sequence identity to L4 (SEQ ID NO:
10) . In a particular embodiment, the VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21 , respectively. [00172] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 93% or at least 95% sequence identity to HI (SEQ ID NO: 2); and (ii) a VL domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to LI (SEQ ID NO: 7). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00173] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 92% or at least 94% sequence identity to H2 (SEQ ID NO: 3); and (ii) a VL domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to LI (SEQ ID NO: 7). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00174] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to H3 (SEQ ID NO: 4); and (ii) a VL domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to LI (SEQ ID NO: 7). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00175] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to H4 (SEQ ID NO: 5); and (ii) a VL domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to LI (SEQ ID NO: 7). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00176] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 86%> or at least 88%> sequence identity to H5 (SEQ ID NO: 6); and (ii) a VL domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to LI (SEQ ID NO: 7). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00177] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 93% or at least 95% sequence identity to HI (SEQ ID NO: 2); and (ii) a VL domain comprising an amino acid sequence that has at least 88% or at least 90% sequence identity to L2 (SEQ ID NO: 8). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00178] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 92% or at least 94% sequence identity to H2 (SEQ ID NO: 3); and (ii) a VL domain comprising an amino acid sequence that has at least 88% or at least 90% sequence identity to L2 (SEQ ID NO: 8). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate provided herein comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00179] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to H3 (SEQ ID NO: 4); and (ii) a VL domain comprising an amino acid sequence that has at least 88% or at least 90% sequence identity to L2 (SEQ ID NO: 8). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00180] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to H4 (SEQ ID NO: 5); and (ii) a VL domain comprising an amino acid sequence that has at least 88% or at least 90% sequence identity to L2 (SEQ ID NO: 8). In a particular embodiment, the VL and VH domains are non-immunogenic, for example as determined by the absence of epitopes that binds to MHC class II, e.g., non- human germline binders to MHC class II. In a certain embodiment, such antibody or antigen- binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00181] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 86%> or at least 88%> sequence identity to H5 (SEQ ID NO: 6); and (ii) a VL domain comprising an amino acid sequence that has at least 88% or at least 90% sequence identity to L2 (SEQ ID NO: 8). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00182] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 93% or at least 95% sequence identity to HI (SEQ ID NO: 2); and (ii) a VL domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to L3 (SEQ ID NO: 9). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00183] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 92% or at least 94% sequence identity to H2 (SEQ ID NO: 3); and (ii) a VL domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to L3 (SEQ ID NO: 9). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00184] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to H3 (SEQ ID NO: 4); and (ii) a VL domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to L3 (SEQ ID NO: 9). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00185] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to H4 (SEQ ID NO: 5); and (ii) a VL domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to L3 (SEQ ID NO: 9). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00186] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 86%> or at least 88%> sequence identity to H5 (SEQ ID NO: 6); and (ii) a VL domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to L3 (SEQ ID NO: 9). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00187] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 93% or at least 95% sequence identity to HI (SEQ ID NO: 2); and (ii) a VL domain comprising an amino acid sequence that has at least 84% or at least 86% sequence identity to L4 (SEQ ID NO: 10). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00188] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 92% or at least 94% sequence identity to H2 (SEQ ID NO: 3); and (ii) a VL domain comprising an amino acid sequence that has at least 84% or at least 86% sequence identity to L4 (SEQ ID NO: 10). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof, of an ADC such as a PBD dimer conjugate provided herein, comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00189] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 90% or at least 92% sequence identity to H3 (SEQ ID NO: 4); and (ii) a VL domain comprising an amino acid sequence that has at least 84% or at least 86% sequence identity to L4 (SEQ ID NO: 10). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00190] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 87% or at least 90% sequence identity to H4 (SEQ ID NO: 5); and (ii) a VL domain comprising an amino acid sequence that has at least 84% or at least 86% sequence identity to L4 (SEQ ID NO: 10). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00191] In specific embodiments, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising (i) a VH domain comprising an amino acid sequence that has at least 86%> or at least 88%> sequence identity to H5 (SEQ ID NO: 6); and (ii) a VL domain comprising an amino acid sequence that has at least 84% or at least 86% sequence identity to L4 (SEQ ID NO: 10). In a particular embodiment, the VL and VH domains are non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II. In a certain embodiment, such antibody or antigen-binding fragment thereof comprises VL CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 19-21, respectively, and VH CDRs 1-3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively.
[00192] To determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the
corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity = number of identical overlapping positions/total number of positions X 100%). In one embodiment, the two sequences are the same length. In a certain embodiment, the percent identity is determined over the entire length of an amino acid sequence or nucleotide sequence.
[00193] The determination of percent identity between two sequences (e.g., amino acid sequences or nucleic acid sequences) can also be accomplished using a mathematical algorithm. A preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. U.S.A.
87:2264 2268, modified as in Karlin and Altschul, 1993, Proc. Natl. Acad. Sci. U.S.A. 90:5873 5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et ah, 1990, J. Mol. Biol. 215:403. BLAST nucleotide searches can be performed with the NBLAST nucleotide program parameters set, e.g., for score=100, wordlength=12 to obtain nucleotide sequences homologous to a nucleic acid molecules described herein. BLAST protein searches can be performed with the XBLAST program parameters set, e.g., to score 50, wordlength=3 to obtain amino acid sequences homologous to a protein molecule described herein. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al, 1997, Nucleic Acids Res. 25:3389 3402. Alternatively, PSI BLAST can be used to perform an iterated search which detects distant relationships between molecules {Id.). When utilizing BLAST, Gapped BLAST, and PSI Blast programs, the default parameters of the respective programs {e.g., of XBLAST and NBLAST) can be used (see, e.g., National Center for Biotechnology Information (NCBI) on the worldwide web,
ncbi.nlm.nih.gov). Another preferred, non limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CABIOS 4: 11 17. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used.
[00194] The percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.
[00195] In a particular aspect, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide {e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising VH CDRl, VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and one, two, three or four framework regions of HI, H2, H3, H4 or H5 (see Table 5 A); and/or (ii) a VL domain comprising VL CDRl, VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21, respectively, and one, two, three or four framework regions of LI, L2, L3, or L4 (see Table 5B).
[00196] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl, VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework region FR1 of HI, H2, H3, H4 or H5 {e.g., Table 5 A). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl, VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework region FR2 of HI, H2, H3, H4 or H5 {e.g., Table 5 A). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework region FR3 of HI , H2, H3, H4 or H5 (e.g., Table 5 A). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework region FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5A).
[00197] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl and FR2 of HI , H2, H3, H4 or H5 (e.g., Table 5 A). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl , FR2, and FR3 of HI , H2, H3, H4 or H5 (e.g., Table 5A). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl , FR2, FR3, and FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5A).
[00198] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl and FR3 of HI , H2, H3, H4 or H5 (e.g., Table 5 A). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl , FR3, and FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5A). [00199] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl and FR4 of HI , H2, H3, H4 or H5 (e.g. , Table 5 A).
[00200] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FRl , FR2, and FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5 A).
[00201] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FR2 and FR3 of HI , H2, H3, H4 or H5 (e.g., Table 5A). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g. , human, composite human, or humanized antibody) or antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FR2, FR3, and FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5 A).
[00202] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FR3 and FR4 of HI , H2, H3, H4 or H5 (e.g., Table 5A).
[00203] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework region FRl of LI , L2, L3, or L4 (e.g., Table 5B). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework region FR2 of LI , L2, L3, or L4 (e.g., Table 5B). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework region FR3 of LI , L2, L3, or L4. In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework region FR4 of LI , L2, L3, or L4 (e.g., Table 5B).
[00204] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl and FR2 of LI , L2, L3, or L4 (e.g., Table 5B). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g. , human, composite human, or humanized antibody) or antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl , FR2, and FR3 of LI , L2, L3, or L4 (e.g., Table 5B). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g. , human, composite human, or humanized antibody) or antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl , FR2, FR3, and FR4 of LI , L2, L3, or L4 (e.g., Table 5B).
[00205] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl and FR3 of LI , L2, L3, or L4 (e.g., Table 5B). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g. , human, composite human, or humanized antibody) or antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl , FR3, and FR4 of LI , L2, L3, or L4 (e.g., Table 5B).
[00206] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl and FR4 of LI , L2, L3, or L4 (e.g. , Table 5B).
[00207] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FRl , FR2, and FR4 of LI , L2, L3, or L4 (e.g., Table 5B).
[00208] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FR2 and FR3 of LI , L2, L3, or L4 (e.g., Table 5B). In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g. , human, composite human, or humanized antibody) or antigen-binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FR2, FR3, and FR4 of LI , L2, L3, or L4 (e.g., Table 5B).
[00209] In one embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively, and framework regions FR3 and FR4 of LI , L2, L3, or L4 (e.g. , Table 5B).
[00210] In a particular aspect, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively, and framework regions FR1-FR4 of any one of VH domains HH257-HH281 (see Table 5C); and (ii) a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NO: 19-21 , respectively, and FR1-FR4 of any one of VL domains LL65- LL76 (see Table 5D).
[00211] In a particular aspect, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising VH CDRl , VH CDR2, and VH CDR3 comprising a combination of amino acid sequences set forth in Table 2 or 3, and framework regions FR1-FR4 of any one of VH domains H1-H5 (Table 5A) and HH257-HH281 (see Table 5C); and (ii) a VL domain comprising VL CDRl , VL CDR2, and VL CDR3 comprising a combination of amino acid sequences set forth in either Table 2 (set 1 or set 2) or 3 (AbM or Contact CDRs), respectively, and FR1-FR4 of any one of VL domains L1-L4 (Table 5B) and LL65-LL76 (see Table 5D).
[00212] In a particular aspect, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising VH CDRl, VH CDR2, and VH CDR3 comprising a combination of amino acid sequences set forth in Table 2 or 3, and corresponding framework regions FR1-FR4 comprising sequences flanking the VH CDRs for example, as depicted in any one of Figures 2A-2I; and (ii) a VL domain comprising VL CDRl, VL CDR2, and VL CDR3 comprising a combination of amino acid sequences set forth in in either Table 2 (set 1 or set 2) or 3 (AbM or Contact CDRs), respectively, and corresponding framework regions FR1-FR4 comprising sequences flanking the VL CDRs, for example as depicted in any one of Figures 2A-2I.
[00213] Table 5A: VH domain Framework Regions (FRs)
Figure imgf000075_0001
[00214] Table 5B: VL domain Framework Regions (FRs)
Figure imgf000075_0002
[00215] Table 5C: Framework region sequences of VH domains HH257 to HH281
Figure imgf000076_0001
[00216] Table 5D: Framework region sequences of VL domains LL65 to LL76
Figure imgf000077_0001
[00217] In a particular aspect, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising the amino acid sequence: QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKGLEWIARIYPG SGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSEDXH8AVYFCARGVYYFDY WGQGTT VTVS S (SEQ ID NO: 1 1), wherein XM at Kabat position 1 1 , XH2 at Kabat position 20, XH3 at Kabat position 38, XH4 at Kabat position 67, XHS at Kabat position 69, XH6 at Kabat position 72, XH7 at Kabat position 81 , and XHS at Kabat position 87 are independently selected from any amino acid; and/or (ii) a VL domain comprising the amino acid sequence
DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILIYSASYRYS GVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQYNSYPRTFGGGTKVEIK (SEQ ID NO: 12), wherein Χκι at Kabat position 10, Χκ2 at Kabat position 46, Χκ3 at Kabat position 63, XK4 at Kabat position 80, XKS at Kabat position 85, and Χκ6 at Kabat position 87 are independently selected from any amino acid. In a particular embodiment, the VH and/or VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
[00218] In a particular aspect, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody (e.g. , human, composite human, or humanized antibody) or an antigen- binding fragment thereof, which immunospecifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprising: (i) a VH domain comprising the amino acid sequence:
QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKGLEWIARIYPG SGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSEDXH8AVYFCARGVYYFDY WGQGTT VTVS S (SEQ ID NO: 1 1), wherein XM at Kabat position 1 1 , XH2 at Kabat position 20, XR3 at Kabat position 38, XR4 at Kabat position 67, XRS at Kabat position 69, XR6 at Kabat position 72, XR7 at Kabat position 81 , and XHS at Kabat position 87 are selected from the combination of amino acids set forth in Table 6B; and/or (ii) a VL domain comprising the amino acid sequence:
DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILIYSASYRYS GVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQYNSYPRTFGGGTKVEIK (SEQ ID NO: 12), wherein Χκι at Kabat position 10, Χκ2 at Kabat position 46, Χκ3 at Kabat position 63, XK4 at Kabat position 80, XKS at Kabat position 85, and Χκ6 at Kabat position 87 are selected from the combination of amino acids set forth in Table 6A. In a particular embodiment, the VH and/or VL domain is non-immunogenic (e.g., non-immunogenic in a human), for example as determined by the absence of epitopes that binds to MHC class II, e.g., non-human germline binders to MHC class II.
[00219] In one embodiment, XRI at Kabat position 1 1 is an amino acid with an aliphatic side chain (e.g., hydrophobic side chain, or nonpolar side chain branched-chain amino acid (BCAA)), such as L or V. In one embodiment, XR2 at Kabat position 20 is an amino acid with an aliphatic side chain (e.g. , hydrophobic side chain, or nonpolar side chain branched-chain amino acid (BCAA)), such as L or V. In one embodiment, XR3 at Kabat position 38 is an amino acid with a polar side chain (e.g., hydrophilic side chain, basic side chain, or charged side chain, e.g., positively charged side chain or negatively charged side chain), such as K or R. In one embodiment, XR4 at Kabat position 67 is an amino acid with an aliphatic side chain (e.g., hydrophobic side chain, or nonpolar side chain branched-chain amino acid (BCAA)), such as V or A. In one embodiment, XH5 at Kabat position 69 is an amino acid with an aliphatic side chain (e.g., hydrophobic side chain, or nonpolar side chain branched-chain amino acid (BCAA)), such as L or I. In one embodiment, XH6 at Kabat position 72 is an amino acid with an acidic side chain, such as E or D. In one embodiment, XR7 at Kabat position 81 is an amino acid with an acidic side chain or its amide derivative, such as Q (uncharged/amide derivative of E) or E. In one embodiment, XRS at Kabat position 87 is an amino acid with an aliphatic hydroxyl group or a hydrophilic side chain, such as S or T.
[00220] In one embodiment, XRI at Kabat position 1 1 is an aliphatic amino acid, such as a branched-chain amino acid (BCAA), for example V; XH2 at Kabat position 20 is an aliphatic amino acid, such as a branched-chain amino acid (BCAA), for example L; XR3 at Kabat position 38 is an amino acid with a polar side chain, such as R; XR4 at Kabat position 67 is an amino acid with an aliphatic side chain, such as A; XRS at Kabat position 69 is an amino acid with an aliphatic side chain, such as L; XR6 at Kabat position 72 is an amino acid with a polar side chain, such as D; XR7 at Kabat position 81 is an amino acid with an amide derivative of an acidic amino acid, such as Q; and XRS at Kabat position 87 is an amino acid with an aliphatic hydroxyl side chain, such as T.
[00221] In one embodiment, XRI at Kabat position 1 1 is an aliphatic amino acid, such as a branched-chain amino acid (BCAA), for example V; XH2 at Kabat position 20 is an aliphatic amino acid, such as a branched-chain amino acid (BCAA), for example V; XR3 at Kabat position 38 is an amino acid with a polar side chain, such as R; XR4 at Kabat position 67 is an amino acid with an aliphatic side chain, such as A; XRS at Kabat position 69 is an amino acid with an aliphatic side chain, such as I; XH6 at Kabat position 72 is an amino acid with a polar side chain, such as D; XR7 at Kabat position 81 is an acidic amino acid, such as E; and XHS at Kabat position 87 is an amino acid with an aliphatic hydroxyl side chain, such as T.
[00222] In a specific embodiment, Χκι at Kabat position 10 is an aromatic amino acid such as F or an amino acid with an aliphatic hydroxyl side chain such as S. In a certain embodiment, XK2 at Kabat position 46 is an amino acid with an aliphatic side chain (e.g., hydrophobic amino acid) such as A or an amino acid with an aliphatic hydroxyl side chain such as S. In one embodiment, Χκ3 at Kabat position 63 is an amino acid with an aliphatic hydroxyl side chain such as T or S. In a specific embodiment, XK4 at Kabat position 80 is an amino acid with an aliphatic hydroxyl side chain such as S or an aromatic amino acid such as P. In a certain embodiment, XK5 at Kabat position 85 is an acidic amino acid such as D or an amino acid with an aliphatic hydroxyl side chain such as T. In one embodiment, Χκ6 at Kabat position 87 is an aromatic amino acid such as F or Y.
[00223] In a specific embodiment, Χκι at Kabat position 10 is an amino acid with an aliphatic hydroxyl side chain such as S; Χκ2 at Kabat position 46 is an amino acid with an aliphatic side chain (e.g. , hydrophobic amino acid) such as A; X at Kabat position 63 is an amino acid with an aliphatic hydroxyl side chain such as T; XK4 at Kabat position 80 is an aromatic amino acid such as P; XKS at Kabat position 85 is an acidic amino acid such as D; and Χκ6 at Kabat position 87 is an aromatic amino acid such as F.
[00224] In a specific embodiment, Χκι at Kabat position 10 is an aromatic amino acid such as F; XK2 at Kabat position 46 is an amino acid with an aliphatic side chain (e.g., hydrophobic amino acid) such as A; Χκ3 at Kabat position 63 is an amino acid with an aliphatic hydroxyl side chain such as T; Χκ4 at Kabat position 80 is an aliphatic hydroxyl side chain such as S; XKS at Kabat position 85 is an acidic amino acid such as D; and Χκ6 at Kabat position 87 is an aromatic amino acid such as F.
[00225] In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising the amino acid sequence:
QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKGLEWIARIYPG SGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSEDXH8AVYFCARGVYYFDY WGQGTT VTVS S (SEQ ID NO: 1 1), wherein Xm at Kabat position 1 1 is an amino acid with an aliphatic side chain such as V, XH2 at Kabat position 20 is an amino acid with an aliphatic side chain such as L, XH3 at Kabat position 38 is an amino acid with a polar side chain such as K, XH4 at Kabat position 67 is an amino acid with an aliphatic side chain such as A, XRS at Kabat position 69 is an amino acid with an aliphatic side chain such as L, XR6 at Kabat position 72 is an acidic amino acid such as D, XR7 at Kabat position 81 is an acidic amino acid or an amide derivative thereof such as Q, and XRS at Kabat position 87 is an amino acid with an aliphatic hydroxyl side chain such as T; and (ii) a VL domain comprising the amino acid sequence DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILIYSASYRYS GVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQYNSYPRTFGGGTKVEIK (SEQ ID NO: 12), wherein XKi at Kabat position 10 is an amino acid with an aliphatic hydroxyl side chain such as S, Χκ2 at Kabat position 46 is an amino acid with an aliphatic side chain such as A, XK3 at Kabat position 63 is an amino acid with an aliphatic hydroxyl side chain such as T, XK4 at Kabat position 80 is an aromatic amino acid such as P, XKS at Kabat position 85 is an acidic amino acid such as D, and Χκ6 at Kabat position 87 is an aromatic amino acid such as F.
[00226] In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising the amino acid sequence:
QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKGLEWIARIYPG SGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSEDXH8AVYFCARGVYYFDY WGQGTT VTVS S (SEQ ID NO: 1 1), wherein XM at Kabat position 1 1 is an amino acid with an aliphatic side chain such as V, XH2 at Kabat position 20 is an amino acid with an aliphatic side chain such as V, XH3 at Kabat position 38 is an amino acid with a polar side chain such as R, XH4 at Kabat position 67 is an amino acid with an aliphatic side chain such as A, XH5 at Kabat position 69 is an amino acid with an aliphatic side chain such as I, XH6 at Kabat position 72 is an acidic amino acid such as D, XR7 at Kabat position 81 is an acidic amino acid such as E, and XHS at Kabat position 87 is an amino acid with an aliphatic hydroxyl side chain such as T; and (ii) a VL domain comprising the amino acid sequence
DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILIYSASYRYS GVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQYNSYPRTFGGGTKVEIK (SEQ ID NO: 12), wherein Χκι at Kabat position 10 is an aromatic amino acid such as F, Χκ2 at Kabat position 46 is an amino acid with an aliphatic side chain such as A, Χκ3 at Kabat position 63 is an amino acid with an aliphatic hydroxyl side chain such as T, XK4 at Kabat position 80 is an amino acid with an aliphatic hydroxyl side chain such as S, XKS at Kabat position 85 is an acidic amino acid such as D, and Χκ6 at Kabat position 87 is an aromatic amino acid such as F.
[00227] In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively; and (ii) a VL domain comprising SEQ ID NO: 7, 8, 9, or 10. [00228] In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising VH CDR1 , VH CDR2, and VH CDR3 comprising the amino acid sequences of SEQ ID NOs: 16-18, respectively; and (ii) a VL domain comprising the amino acid sequence
DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILIYSASYRYS GVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQYNSYPRTFGGGTKVEIK (SEQ ID NO: 12), wherein Χκι at Kabat position 10, Χκ2 at Kabat position 46, Χκ3 at Kabat position 63, XK4 at Kabat position 80, XK5 at Kabat position 85, and XK6 at Kabat position 87 are selected from the combination of amino acids set forth in Table 6A.
[00229] In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising the amino acid sequence of SEQ ID NO: 2, 3, 4, or 5; and (ii) a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively.
[00230] In a particular embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising: (i) a VH domain comprising the amino acid sequence:
QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKGLEWIARIYPG SGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSEDXH8AVYFCARGVYYFDY WGQGTT VTVS S (SEQ ID NO: 1 1), wherein XM at Kabat position 1 1 , XH2 at Kabat position 20, XH3 at Kabat position 38, XH4 at Kabat position 67, XHS at Kabat position 69, XH6 at Kabat position 72, XR7 at Kabat position 81 , and XHS at Kabat position 87 are selected from the combination of amino acids set forth in Table 6B; and (ii) a VL domain comprising VL CDR1 , VL CDR2, and VL CDR3 comprising the amino acid sequences of SEQ ID NOs: 19-21 , respectively. [00231] Table 6 A: VK domain Amino Acid Substitutions
Figure imgf000083_0001
Figure imgf000084_0001
[00232] Table 6B: VH domain Amino Acid Substitutions
Figure imgf000085_0001
Figure imgf000086_0001
Figure imgf000087_0001
Figure imgf000088_0001
Figure imgf000089_0001
Figure imgf000090_0001
Xm XH2 XH3 XH4 XH5 XH6 XH7 XH8
Kabat 11 20 38 67 69 72 81 87 position
Numerical 11 20 38 68 70 73 82 91 position of
SEQ ID
NO: 11
HH210 V L K A I E E T
HH211 L V K A I E E T
HH212 V V K A I E E T
HH213 L L R A I E E T
HH214 V L R A I E E T
HH215 L V R A I E E T
HH216 V V R A I E E T
HH217 L L K V I E E T
HH218 V L K V I E E T
HH219 L V K V I E E T
HH220 V V K V I E E T
HH221 L L R V I E E T
HH222 V L R V I E E T
HH223 L V R V I E E T
HH224 V V R V I E E T
HH225 L L K A L D E T
HH226 V L K A L D E T
HH227 L V K A L D E T
HH228 V V K A L D E T
HH229 L L R A L D E T
HH230 V L R A L D E T
HH231 L V R A L D E T
HH232 V V R A L D E T
HH233 L L K V L D E T
HH234 V L K V L D E T
HH235 L V K V L D E T
HH236 V V K V L D E T
HH237 L L R V L D E T
HH238 V L R V L D E T
HH239 L V R V L D E T
HH240 V V R V L D E T
HH241 L L K A I D E T
HH242 V L K A I D E T
HH243 L V K A I D E T
HH244 V V K A I D E T
HH245 L L R A I D E T
HH246 V L R A I D E T XHI XH2 XH3 XH4 XH5 XH6 XH7 XH8
Kabat 11 20 38 67 69 72 81 87 position
Numerical 11 20 38 68 70 73 82 91 position of
SEQ ID
NO: 11
HH247 L V R A I D E T
HH248 V V R A I D E T
HH249 L L K V I D E T
HH250 V L K V I D E T
HH251 L V K V I D E T
HH252 V V K V I D E T
HH253 L L R V I D E T
HH254 V L R V I D E T
HH255 L V R V I D E T
HH256 V V R V I D E T
[00233] In a specific embodiment, the position (i.e., boundary) of a VL chain region described herein relative to the constant region may change by one, two, three, or four amino acid positions so long as immunospecific binding to KIT (e.g., the D4 region of human KIT) is maintained (e.g., substantially maintained, for example, at least 50%, at least 60%, at least 70%, at least 80%), at least 90%, at least 95%). In a specific embodiment, the position (i.e., boundary) of a VH chain region described herein relative to the constant region may change by one, two, three, or four amino acid positions so long as immunospecific binding to KIT (e.g. , the D4 region of human KIT) is maintained (e.g., substantially maintained, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%).
[00234] In specific aspects, provided herein is an ADC such as a PBD dimer conjugate comprising a moiety comprising VH CDRs and/or VL CDRs described herein, for example as set forth in Tables 1-3 and 10-15, wherein the VH CDRs and VL CDRs are arranged in a spatial orientation that confers specific binding to a D4 region of human KIT.
[00235] In specific aspects, provided herein is an ADC such as a PBD dimer conjugate comprising a moiety comprising VH CDRs comprising the amino acid sequences of SEQ ID NOs: 16-18 and VL CDRs comprising the amino acid sequences of SEQ ID NOs: 19-21, VH CDRs comprising the amino acid sequences of SEQ ID NOs: 56, 62 and 63 and VL CDRs comprising the amino acid sequences of SEQ ID NOs: 59-61, VH CDRs comprising the amino acid sequences of SEQ ID NOs: 70-72 and VL CDRs comprising the amino acid sequences of SEQ ID NOs: 66-68, wherein the VH CDRs and VL CDRs are arranged in a spatial orientation that confers specific binding to a D4 region of human KIT. In certain embodiments, the moiety is an antibody or an antigen-binding fragment thereof. In a particular embodiment, the moiety is a protein, such as a fusion protein comprising an Fc region.
[00236] In specific aspects, provided herein is an ADC such as a PBD dimer conjugate comprising a moiety comprising VH CDRs selected from Tables 13-15 and/or VL CDRs selected from Tables 10-12, wherein the VH CDRs and VL CDRs are arranged in a spatial orientation that confers specific binding to a D4 region of human KIT. In certain embodiments, the moiety is an antibody or an antigen-binding fragment thereof. In a particular embodiment, the moiety is a protein, such as a fusion protein comprising an Fc region.
[00237] In specific aspects, provided herein is an ADC such as a PBD dimer conjugate comprising a moiety, such as an antibody or an antigen-binding fragment thereof, comprising VH CDRs 1-3 and VL CDRs 1-3 selected from the ones presented in Tables 10-15, wherein the VH CDRs and VL CDRs are arranged in a spatial orientation that confers specific binding to a D4 region of human KIT. In particular aspects, a moiety described herein comprises linkers, such as peptide linkers, that link the VH CDRs 1-3 and/or VL CDRs 1-3 in the spatial orientation that confers specific binding to a D4 region of human KIT.
[00238] In particular aspects, an ADC such as a PBD dimer conjugate provided herein comprises a moiety described herein comprising linkers, such as peptide linkers, that links the VH CDRs and/or VL CDRs in a spatial orientation that confers specific binding to a D4 region of human KIT.
[00239] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof comprising VL CDRs 1-3 and VH CDRs 1-3 selected from the ones presented in Tables 10-15, wherein the antibody or antigen-binding fragment thereof immunospecifically binds a D4 region of KIT, such as human KIT.
[00240] In a specific embodiment, the "X" amino acid of a CDR in any one of Tables 10-15 is any naturally occurring amino acid that maintains specific binding affinity to a D4 region of human KIT. In a specific embodiment, the "X" amino acid of a CDR in any one of Tables 10-15 is a non-natural amino acid that maintains specific binding affinity to a D4 region of human KIT. In a specific embodiment, the "X" amino acid of a CDR in any one of Tables 10-15 is a conservative substitution of the corresponding amino acid of the CDRs having the amino acid sequences of SEQ ID NOs: 16-21 , wherein specific binding affinity to a D4 region of human KIT is maintained.
[00241] In a specific embodiment, the "X" amino acid of a CDR in any one of Tables 10-15 is, independently, amino acid A, G, T, K, or L. In a particular embodiment, the "X" amino acid of a CDR in any one of Tables 10-15 is amino acid A, G, T, Y, C, or S. In certain aspects of these embodiments, specific binding affinity to a D4 region of human KIT is maintained.
[00242] In a certain embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising VH CDRs and/or VL CDRs selected from those presented in Tables 10-15.
[00243] In a particular embodiment, a CDR, such as any one of VL CDRs 1-3 and VH CDRs 1-3 depicted in Tables 10-15, comprises one or more (e.g., two, three, four, or five) "X" amino acids, wherein each "X" amino acid can be any amino acid which can maintain specific binding of the antibody or fragment thereof to a D4 region of human KIT.
[00244] Table 10: VL CDR1
Figure imgf000094_0001
[00245] Table 11 : VL CDR2
Figure imgf000095_0001
[00247] Table 13: VH CDRl
Figure imgf000096_0001
[00248] Table 14: VH CDR2
Figure imgf000096_0002
[00249] Table 15: VH CDR3
Figure imgf000097_0001
[00250] In certain aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody or an antigen-binding fragment thereof comprising VL FRs 1-4 selected from the ones presented in Tables 20-23 and/or VH FRs 1-4 selected from the ones presented in Tables 16-19, wherein the antibody or antigen-binding fragment thereof immunospecifically binds a D4 region of KIT, such as human KIT.
[00251] In a specific embodiment, the "X" amino acid of an FR in any one of Tables 16-23 is any naturally occurring amino acid that maintains specific binding affinity to a D4 region of human KIT. In a specific embodiment, the "X" amino acid of a CDR in any one of Tables 16-23 is a non-natural amino acid that maintains specific binding affinity to a D4 region of human KIT. In a specific embodiment, the "X" amino acid of a CDR in any one of Tables 16-23 is a conservative substitution of the corresponding amino acid of the CDRs having the amino acid sequences of SEQ ID NOs: 16-21 , wherein specific binding affinity to a D4 region of human KIT is maintained.
[00252] In a specific embodiment, the "X" amino acid of a CDR in any one of Tables 16-23 is amino acid A, G, T, K, or L. In a particular embodiment, the "X" amino acid of a CDR in any one of Tables 16-23 is amino acid A, G, T, Y, C, or S. In certain aspects of these embodiments, specific binding affinity to a D4 region of human KIT is maintained.
[00253] In a certain embodiment, an ADC such as a PBD dimer conjugate provided herein comprises an antibody (e.g., human, composite human, or humanized antibody) or antigen- binding fragment thereof, which specifically binds to a D4 region of human KIT, comprising VH CDRs and/or VL CDRs selected from those presented in Tables 16-23.
[00254] In a particular embodiment, an FR, such as any one of VL FRs 1-4 and VH FRs 1-4 depicted in Tables 16-23, comprises one or more (e.g., two, three, four, or five) "X" amino acids, wherein each "X" amino acid can be any amino acid which can maintain specific binding of the antibody or fragment thereof to a D4 region of human KIT.
[00255] Table 16: VH FR1
Figure imgf000098_0001
[00256] Table 17: VH FR2
Figure imgf000099_0001
[00257] Table 18: VH FR3
Figure imgf000099_0002
VH FR3 SEQ ID
NO:
R (A/V) (I/L) TADKSTSTAYM (E/Q) XSSLRSED (S/T) AVYFCAR 227
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LXSLRSED ( S /T ) AVYFCAR 228
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSXLRSED ( S /T ) AVYFCAR 229
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSXRSED (S/T) AVYFCAR 230
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLXSED (S/T) AVYFCAR 231
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRXED (S/T) AVYFCAR 232
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRSXD (S/T) AVYFCAR 233
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRSEX (S/T) AVYFCAR 234
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRSEDXAVYFCAR 235
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRSED (S/T) XVYFCAR 236
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRSED (S/T) AXYFCAR 237
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRSED (S/T) AVXFCAR 238
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRSED (S/T) AVYXCAR 239
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRSED (S/T) AVYFXAR 240
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRSED (S/T) AVYFCXR 241
R (A/V) T (I/L) TADKSTSTAYM (E/Q) LSSLRSED (S/T) AVYFCAX 242
[00258] Table 19: VH FR4
Figure imgf000100_0001
[00259] Table 20: VL FR1
Figure imgf000100_0002
DIXMTQSPS (F/S) LSASVGDRVTITC 256
DIVXTQSPS (F/S) LSASVGDRVTITC 257
DIVMXQSPS (F/S) LSASVGDRVTITC 258
DIVMTXSPS (F/S) LSASVGDRVTITC 259
DIVMTQXPS (F/S) LSASVGDRVTITC 260
DIVMTQSXS (F/S) LSASVGDRVTITC 261
DIVMTQSPX (F/S) LSASVGDRVTITC 262
DIVMTQSPSXLSASVGDRVTITC 263
DIVMTQSPS (F/S) XSASVGDRVTITC 264
DIVMTQSPS (F/S) LXASVGDRVTITC 265
DIVMTQSPS (F/S) LSXSVGDRVTITC 266
DIVMTQSPS (F/S) LSAXVGDRVTITC 267
DIVMTQSPS (F/S) LSASXGDRVTITC 268
DIVMTQSPS (F/S) LSASVXDRVTITC 269
DIVMTQSPS (F/S) LSASVGXRVTITC 270
DIVMTQSPS (F/S) LSASVGDXVTITC 271
DIVMTQSPS (F/S) LSASVGDRXTITC 272
DIVMTQSPS (F/S) LSASVGDRVXITC 273
DIVMTQSPS (F/S) LSASVGDRVTXTC 274
DIVMTQSPS (F/S) LSASVGDRVTIXC 275
DIVMTQSPS (F/S) LSASVGDRVTITX 276
[00260] Table 21: VL FR2
Figure imgf000101_0001
[00261] Table 22: VL FR3
Figure imgf000101_0002
VL FR3 SEQ ID
NO:
LI GVPDRFTGSGSGTDFTL I SSLQSEDFADYFC 46
L2 GVPDRFTGSGSGTDFTL I SSLQPEDFADYFC 49
L3 GVPDRFSGSGSGTDFTL I SSLQPEDFADYFC 50
L4 GVPDRFSGSGSGTDFTL I SSLQPEDFATYYC 52
XVPDRF (S/T) GSGSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 292
GXPDRF (S/T) GSGSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 293
GVXDRF (S/T) GSGSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 294
GVPXRF (S/T) GSGSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 295
GVPDXF (S/T) GSGSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 296
GVPDRX (S/T) GSGSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 297
GVPDRFXGSGSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 298
GVPDRF (S/T) XSGSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 299
GVPDRF (S/T) GXGSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 300
GVPDRF (S/T) GSXSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 301
GVPDRF (S/T) GSGXGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 302
GVPDRF (S/T) GSGSXTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 303
GVPDRF (S/T) GSGSGXDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 304
GVPDRF (S/T) GSGSGTXFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 305
GVPDRF (S/T) GSGSGTDXTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 306
GVPDRF (S/T) GSGSGTDFXLTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 307
GVPDRF (S/T) GSGSGTDFTXTISSLQ (P/S) EDFA (D/T) Y (F/Y) C 308
GVPDRF (S/T) GSGSGTDFTLXISSLQ (P/S) EDFA (D/T) Y (F/Y) C 309
GVPDRF (S/T) GSGSGTDFTLTXSSLQ (P/S) EDFA (D/T) Y (F/Y) C 310
GVPDRF (S/T) GSGSGTDFTLTIXSLQ (P/S) EDFA (D/T) Y (F/Y) C 311
GVPDRF (S/T) GSGSGTDFTLTISXLQ (P/S) EDFA (D/T) Y (F/Y) C 312
GVPDRF (S/T) GSGSGTDFTLTISSXQ (P/S) EDFA (D/T) Y (F/Y) C 313
GVPDRF (S/T) GSGSGTDFTLTISSLX (P/S) EDFA (D/T) Y (F/Y) C 314
GVPDRF (S/T) GSGSGTDFTLTISSLQXEDFA (D/T) Y (F/Y) C 315
GVPDRF (S/T) GSGSGTDFTLTISSLQ (P/S) XDFA (D/T) Y (F/Y) C 316
GVPDRF (S/T) GSGSGTDFTLTISSLQ (P/S) EXFA (D/T) Y (F/Y) C 317
GVPDRF (S/T) GSGSGTDFTLTISSLQ (P/S) EDXA (D/T) Y (F/Y) C 318
GVPDRF (S/T) GSGSGTDFTLTISSLQ (P/S) EDFX (D/T) Y (F/Y) C 319
GVPDRF (S/T) GSGSGTDFTLTISSLQ (P/S) EDFAXY (F/Y) C 320
GVPDRF (S/T) GSGSGTDFTLTISSLQ (P/S) EDFA (D/T) X (F/Y) C 321
GVPDRF (S/T) GSGSGTDFTLTISSLQ (P/S) EDFA (D/T) YXC 322
GVPDRF (S/T) GSGSGTDFTLTISSLQ (P/S) EDFA (D/T) Y (F/Y) X 323
[00262] Table 23: VL FR4
Figure imgf000102_0001
FGXGTKVE IK 326
FGGXTKVE IK 327
FGGGXKVE IK 328
FGGGTXVE IK 329
FGGGTKXE IK 330
FGGGTKVXIK 331
FGGGTKVEXK 332
FGGGTKVE IX 333
[00263] In specific aspects, provided herein is an ADC such as a PBD dimer conjugate comprising an antibody comprising an antibody light chain and heavy chain, e.g. , a separate light chain and heavy chain. With respect to the light chain, in a specific embodiment, the light chain of an antibody described herein is a kappa light chain. In another specific embodiment, the light chain of an antibody described herein is a lambda light chain. In yet another specific
embodiment, the light chain of an antibody described herein is a human kappa light chain or a human lambda light chain. In a particular embodiment, an antibody described herein, which immunospecifically binds to a KIT polypeptide (e.g. , a KIT polypeptide comprising a D4 region of KIT, for example human KIT (e.g., SEQ ID NO: 15)) comprises a light chain wherein the amino acid sequence of the VL chain region comprises any amino acid sequence described herein (e.g., SEQ ID NO: 7, 8, 9, or 10), and wherein the constant region of the light chain comprises the amino acid sequence of a human kappa light chain constant region. Non-limiting examples of human light chain constant region sequences have been described in the art, e.g., see U.S. Patent No. 5,693,780 and Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91- 3242.
[00264] With respect to the heavy chain, in a specific embodiment, the heavy chain of an antibody described herein can be an alpha (a), delta (δ), epsilon (ε), gamma (γ) or mu (μ) heavy chain. In another specific embodiment, the heavy chain of an antibody described can comprise a human alpha (a), delta (δ), epsilon (ε), gamma (γ) or mu (μ) heavy chain. In a particular embodiment, an antibody described herein, which immunospecifically binds to a KIT
polypeptide (e.g., a KIT polypeptide comprising a KIT polypeptide comprising a D4 region of KIT, for example human KIT (e.g., SEQ ID NO: 15)), comprises a heavy chain wherein the amino acid sequence of the VH chain region can comprise any amino acid sequence described herein (e.g., any of SEQ ID NOs: 2-6), and wherein the constant region of the heavy chain comprises the amino acid sequence of a human gamma (γ) heavy chain constant region. Non- limiting examples of human heavy chain constant region sequences have been described in the art, e.g., see U.S. Patent No. 5,693,780 and Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242.
[00265] In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate described herein, which immunospecifically binds to a KIT polypeptide (e.g. , a D4 region of KIT, for example human KIT) comprises a VL chain region and a VH chain region comprising any amino acid sequences described herein, and wherein the constant regions comprise the amino acid sequences of the constant regions of an IgG, IgE, IgM, IgD, IgA or IgY
immunoglobulin molecule, or a human IgG, IgE, IgM, IgD, IgA or IgY immunoglobulin molecule. In another specific embodiment, an antibody described herein, which
immunospecifically binds to a KIT polypeptide (e.g., a D4 region of KIT, for example human KIT) comprises a VL chain region and a VH chain region comprising any amino acid sequences described herein, and wherein the constant regions comprise the amino acid sequences of the constant regions of an IgG, IgE, IgM, IgD, IgA or IgY immunoglobulin molecule, any class (e.g., IgGl, IgG2, IgG3, IgG4, IgAl and IgA2), or any subclass (e.g., IgG2a and IgG2b) of immunoglobulin molecule. In a particular embodiment, the constant regions comprise the amino acid sequences of the constant regions of a human IgG, IgE, IgM, IgD, IgA or IgY
immunoglobulin molecule, any class (e.g., IgGl, IgG2, IgG3, IgG4, IgAl and IgA2), or any subclass (e.g., IgG2a and IgG2b) of immunoglobulin molecule.
[00266] In yet another specific embodiment, an ADC such as a PBD dimer conjugate comprises an antibody described herein, which immunospecifically binds to a KIT polypeptide (e.g., a D4 region of KIT, for example human KIT), comprising a VL chain region and a VH chain region comprising any amino acid sequences described herein (e.g. , any one of SEQ ID NOs: 2-6 and/or any one of SEQ ID NOs: 7-10), and wherein the constant regions comprise the amino acid sequences of the constant regions of a human IgGl or human IgG4. In a particular embodiment, an ADC such as a PBD dimer conjugate comprises an antibody described herein, which immunospecifically binds to a KIT polypeptide (e.g., a D4 region of KIT, for example human KIT) and comprises a VL chain region and a VH chain region comprising any amino acid sequences described herein, and wherein the constant regions comprise the amino acid sequences of the constant region of a human IgGl .
[00267] In specific embodiments, an antibody of an ADC such as a PBD dimer conjugate described herein, which immunospecifically binds to a KIT polypeptide, e.g., a human KIT polypeptide, for example, a D4 region of KIT {e.g., human KIT, for example SEQ ID NO: 15), comprises framework regions {e.g., framework regions of the VL domain and/or VH domain) that are human framework regions or derived from human framework regions. Non-limiting examples of human framework regions are described in the art, e.g., see Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242). In a certain embodiment, an antibody described herein comprises framework regions {e.g., framework regions of the VL domain and/or VH domain) that are primate {e.g., non-human primate) framework regions or derived from primate {e.g., non-human primate) framework regions.
[00268] In certain examples, an antibody of an ADC such as a PBD dimer conjugate described herein comprises framework regions {e.g., framework regions of the VL domain and/or VH domain) that are not primate {e.g., non-human primate, for example, ape such as Old World ape) framework regions or derived from primate {e.g. , non-human primate) framework regions.
[00269] In certain examples, with respect to any of these antibodies of an ADC such as a PBD dimer conjugate described herein, the VL chain region does not comprise non-human primate {e.g. , ape such as Old World ape) framework regions or is derived from non-human primate {e.g., ape such as Old World ape) framework regions. In certain other embodiments, the VH chain region does not comprise non-human primate {e.g. , ape such as Old World ape) framework regions or is derived from non-human primate {e.g., ape such as Old World ape) framework regions.
[00270] Non-limiting examples of non-human primate framework regions include those from Old World apes, e.g., Pan troglodytes, Pan paniscus or Gorilla gorilla; chimpanzee Pan troglodytes; Old World monkey such as Old World monkey from the genus Macaca; and cynomolgus monkey Macaca cynomolgus. Non-limiting examples of non-human primate framework sequences are described in U.S. Patent Application Publication No. US
2005/0208625. [00271] In certain aspects, also provided herein are ADCs such as PBD dimer conjugates comprising antibodies, which immunospecifically bind to a KIT polypeptide (e.g., a D4 region of KIT, for example human KIT), comprising one or more amino acid residue substitutions, e.g., in the VL chain region or VH chain region, for example, the CDRs or FRs. In specific
embodiments, none of the amino acid residue substitutions are located within the CDRs. In specific embodiments, all of the amino acid substitutions are in the FRs (see, e.g., Tables 5A- 6B). In a certain embodiment, an amino acid substitution is a conservative amino acid substitution.
[00272] As used herein, 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).
[00273] In particular embodiments, the glycosylation of antibodies of an ADC such as a PBD dimer conjugate described herein is modified. For example, an aglycoslated antibody can be made (i.e. , the antibody lacks glycosylation) or an antibody comprising a mutation or substitution at one or more glycosylation sites to eliminate glycosylation at the one or more glycosylation sites can be made. Glycosylation can be altered to, for example, increase the affinity of the antibody for a target antigen (e.g., human KIT, for example, a D4 region of human KIT). Such carbohydrate modifications can be accomplished by, for example, altering one or more sites of glycosylation within the antibody sequence. For example, one or more amino acid substitutions can be made that result in elimination of one or more variable region (e.g., VL and/or VH CDRs or VL and/or VH FRs) glycosylation sites to thereby eliminate glycosylation at that site. Such aglycosylation can increase the affinity of the antibody for antigen (e.g., human KIT, for example, a D4 region of human KIT). Such an approach is described in further detail in U.S. Patent Nos. 5,714,350 and 6,350,861. [00274] Glycosylation can occur via N-linked (or asparagine-linked) glycosylation or O- linked glycosylation. N-linked glycosylation involves carbohydrate modification at the side- chain NH2 group of an asparagine amino acid in a polypeptide. O-linked glycosylation involves carbohydrate modification at the hydroxyl group on the side chain of a serine, threonine, or hydroxylysine amino acid.
[00275] In specific embodiments, an asparagine (N) residue within a VH (e.g., SEQ ID NO: 2, 3, 4, 5, or 6) or VL region (e.g., SEQ ID NO: 7, 8, 9, or 10) of an antibody described herein is substituted with a serine (S) or another amino acid (e.g., alanine, glycine, glutamine, threonine, tyrosine, cysteine). In other specific embodiments, an asparagine (N) residue within a VH CDR (e.g., VH CDR1, VH CDR2, and/or VH CDR3 comprising the sequences of SEQ ID NOs: 16- 18, respectively) and/or a VL CDR (e.g., VL CDR1, VL CDR2, and/or VL CDR3 comprising the sequences of SEQ ID NOs: 19-21, respectively) of an antibody described herein is substituted with a serine (S) or another amino acid (e.g., alanine, glycine, glutamine, threonine, tyrosine, cysteine). In other specific embodiments, an asparagine (N) residue within a VH FR (e.g., VH FRl, VH FR2, VH FR3 and/or VH FR4 as set forth in Tables 5 A, 5C, and 6B) and/or a VL FR (e.g., VL FRl, VL FR2, VL FR3, and/or VL FR4 as set forth in Table 5B, 5D, and 6A) of an antibody described herein is substituted with a serine (S) or another amino acid (e.g. , alanine, glycine, glutamine, threonine, tyrosine, cysteine).
[00276] In certain embodiments, aglycosylated antibodies can be produced in bacterial cells which lack the necessary glycosylation machinery. Cells with altered glycosylation machinery have been described in the art and can be used as host cells in which to express recombinant antibodies described herein to thereby produce an antibody with altered glycosylation. See, for example, Shields, R.L. et al. (2002) J. Biol. Chem. 277:26733-26740; Umana et al. (1999) Nat. Biotech. 17: 176-1, as well as, European Patent No: EP 1,176,195; PCT Publications WO
03/035835; WO 99/54342.
[00277] In certain embodiments, one or more modifications can be made to the Fc region of an antibody described here, generally, to alter one or more functional properties of the antibody, such as serum half-life, complement fixation, Fc receptor binding, and/or antibody-dependent cellular cytotoxicity. These modifications are described, for example, in International Patent Application Publication No. WO 2008/153926 A2. [00278] In specific embodiments, an asparagine (N) residue within the constant region of a heavy chain and/or the constant region of a light region of an antibody described herein is substituted with a serine (S) or another amino acid (e.g., alanine, glycine, glutamine, threonine, tyrosine, cysteine).
[00279] In a particular embodiment, an antibody or an antigen-binding fragment thereof of an ADC such as a PBD dimer conjugate described herein, specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT) with an EC50 (half maximal effective concentration) value of about 50 nM or less as determined by ELISA.
[00280] In a particular embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or an antigen-binding fragment thereof specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT) with an EC50 value of about 150 pM or less as determined by FACs with CHO-WT-KIT cells (CHO cells engineered to recombinantly express wild-type human KIT).
[00281] In specific embodiments, an ADC such as a PBD dimer conjugate comprises an anti- KIT antibody or an antigen-binding fragment thereof which specifically binds to a native isoform or native variant of KIT (that is a naturally occurring isoform or variant of KIT in an animal (e.g. , monkey, mouse, goat, donkey, dog, cat, rabbit, pig, rat, human, frog, or bird) that can be isolated from an animal, preferably a human). In particular embodiments, an ADC such as a PBD dimer conjugate comprises an anti-KIT antibody which immunospecifically binds to human KIT or a fragment thereof. In specific embodiments, an ADC such as a PBD dimer conjugate comprises an anti-KIT antibody (or an antigen-binding fragment thereof) which specifically binds to human KIT or a fragment thereof and does not specifically bind to a non-human KIT (e.g. , monkey, mouse, goat, donkey, dog, cat, rabbit, pig, rat, or bird) or a fragment thereof. In certain embodiments, an ADC such as a PBD dimer conjugate comprises an anti-KIT antibody or antigen-binding fragment thereof which specifically binds to human KIT or a fragment thereof (e.g., a D4 region of human KIT) and to canine (dog) and non-human primate (e.g., monkey) KIT, but does not specifically bind to murine KIT or a fragment thereof (e.g. , a D4 region of murine KIT).
[00282] In certain embodiments, an ADC such as a PBD dimer conjugate (e.g., KIT-PBD- ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to an extracellular domain of human KIT having a mutation, for example a somatic mutation associated with cancer (e.g., GIST), such as a mutation in exon 9 of human KIT wherein the Ala and Tyr residues at positions 502 and 503 are duplicated. In certain embodiments, an ADC such as a PBD dimer conjugate (e.g., KIT-PBD-ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to an extracellular domain of wild-type human KIT and an extracellular domain of human KIT with a mutation, for example a somatic mutation associated with cancer (e.g., GIST), such as a mutation in exon 9 of human KIT wherein the Ala and Tyr residues at positions 502 and 503 are duplicated (see, e.g., Marcia et ah, (2000) Am. J. Pathol. 156(3):791-795; and Debiec-Rychter et al, (2004) European Journal of Cancer. 40:689- 695, which are both incorporated herein by reference in their entireties, describing KIT mutations).
[00283] In certain embodiments, an ADC such as a PBD dimer conjugate (e.g., KIT-PBD- ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to an extracellular domain of human KIT which is glycosylated. In certain embodiments, an ADC such as a PBD dimer conjugate (e.g. , KIT-PBD-ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to two different glycosylated forms of an extracellular domain of human KIT. For example, two forms of human KIT with different molecular weights, indicating different glycosylation patterns, have been observed by immunoblotting. In certain embodiments, an ADC such as a PBD dimer conjugate (e.g., KIT-PBD-ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to both of these forms of human KIT which have different glycosylation patterns, e.g., one form is more glycosylated than the other. In certain embodiments, an ADC such as a PBD dimer conjugate (e.g., KIT-PBD- ADC) comprises an antibody or antigen-binding fragment thereof which specifically binds to an extracellular domain of human KIT which is not glycosylated.
[00284] In a particular embodiment, an antibody of an ADC such as a PBD dimer conjugate described herein or an antigen-binding fragment thereof, which specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), and can be recombinantly expressed in CHO cells at an average titer of at least 0.5 μg/mL. In a particular embodiment, an antibody of an ADC such as a PBD dimer conjugate described herein or an antigen-binding fragment thereof, which specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), can be recombinantly expressed in CHO cells at an average titer of at least 1.0 μg/mL. [00285] In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate described herein or an antigen-binding fragment thereof, which specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), comprises a VH domain and a VL domain that are non-immunogenic (e.g., non-immunogenic in a human), for example, the VH domain and VL domain do not contain T cell epitopes.
[00286] In particular aspects, antibodies of ADC such as a PBD dimer conjugates provided herein include, but are not limited to, monoclonal antibodies, recombinantly produced antibodies, multispecific antibodies (including bi-specific antibodies), human antibodies, humanized antibodies, chimeric antibodies, synthetic antibodies, tetrameric antibodies comprising two heavy chain and two light chain molecule, an antibody light chain monomer, an antibody heavy chain monomer, an antibody light chain dimer, an antibody heavy chain dimer, an antibody light chain-antibody heavy chain pair, intrabodies, heteroconjugate antibodies, single domain antibodies, monovalent antibodies, single chain antibodies or single-chain Fvs (scFv) (e.g., including monospecific, bispecific, etc.), camelized antibodies, affybodies, Fab fragments, F(ab') fragments, disulfide-linked Fvs (sdFv), anti-idiotypic (anti-Id) antibodies (including, e.g., anti-anti-Id antibodies), and epitope-binding fragments of any of the above. In certain embodiments, antibodies described herein refer to polyclonal antibody populations. Antibodies can be of any type (e.g., IgG, IgE, IgM, IgD, IgA or IgY), any class, (e.g., IgGl , IgG2, IgG3, IgG4, IgAl or IgA2), or any subclass (e.g., IgG2a or IgG2b) of immunoglobulin molecule. In certain embodiments, antibodies of an ADC such as a PBD dimer conjugate described herein are IgG antibodies, or a class (e.g., human IgGl or IgG4) or subclass thereof. In specific
embodiments, a monoclonal antibody is an antibody produced by a single hybridoma or other cell, wherein the antibody immunospecifically binds to a D4 region of human KIT epitope as determined, e.g., by ELISA or other antigen-binding or competitive binding assay known in the art or in the Examples provided herein. The term "monoclonal" is not limited to any particular method for making the antibody.
[00287] In a particular embodiment, an anti-KIT antibody of an ADC such as a PBD dimer conjugate provided herein is a Fab fragment that immunospecifically binds to a KIT polypeptide, such as the D4 region of human KIT. In a specific embodiment, antibodies of an ADC such as a PBD dimer conjugate described herein are monoclonal antibodies or isolated monoclonal antibodies. In another specific embodiment, an antibody of an ADC such as a PBD dimer conjugate described herein is a humanized monoclonal antibody. In a particular embodiment, an antibody of an ADC such as a PBD dimer conjugate described herein is a recombinant antibody, for example, a recombinant human antibody, recombinant humanized antibody or a recombinant monoclonal antibody. In certain embodiments, an antibody of an ADC such as a PBD dimer conjugate described herein contains non-human amino acid sequences, e.g., non-human CDRs or non-human (e.g., non-human primate) framework residues.
[00288] In particular embodiments provided herein, recombinant antibodies of an ADC such as a PBD dimer conjugate can be isolated, prepared, expressed, or created by recombinant means, such as antibodies expressed using a recombinant expression vector transfected into a host cell, antibodies isolated from a recombinant, combinatorial antibody library, or antibodies prepared, expressed, created or isolated by any other means that involves creation, e.g., via synthesis, genetic engineering of DNA sequences that encode human immunoglobulin sequences, or splicing of sequences that encode human immunoglobulins, e.g., human immunoglobulin gene sequences, to other such sequences. In certain embodiments, the amino acid sequences of such recombinant antibodies have been modified such thus the amino acid sequences of such antibodies, e.g., VH and/or VL regions, are sequences that do not naturally exist within an organism's antibody germline repertoire in vivo, for example a murine or human germline repertoire. In a particular embodiment, a recombinant antibody of an ADC such as a PBD dimer conjugate can be obtained by assembling several sequence fragments that naturally exist in an organism (e.g., primate, such as human) into a composite sequence of a recombinant antibody, wherein the composite sequence does not naturally exist within an organism (e.g. , primate such as human).
[00289] Antibodies of an ADC such as a PBD dimer conjugate provided herein include immunoglobulin molecules of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgGl, IgG2, IgG3, IgG4, IgAl and IgA2) or subclass of immunoglobulin molecule. In a specific embodiment, an antibody provided herein is an IgG antibody (e.g., human IgG antibody), or a class (e.g., human IgGl or IgG4) or subclass thereof. In another specific embodiment, an antibody described herein is an IgGl (e.g., human IgGl (isotype a, z, or f)) or IgG4 antibody. In certain embodiments, an antibody described herein is a whole or entire antibody, e.g., a whole or entire humanized, human, or composite human antibody. [00290] Antibodies of an ADC such as a PBD dimer conjugate provided herein can include antibody fragments that retain the ability to specifically bind to an antigen, e.g. , KIT epitope (e.g., a KIT epitope within a KIT polypeptide containing a D4 region of human KIT). In a specific embodiment, fragments include Fab fragments (an antibody fragment that contains the antigen-binding domain and comprises a light chain and part of a heavy chain (i.e., the VH and CHI domains of a heavy chain) bridged by a disulfide bond); Fab' (an antibody fragment containing a single antigen-binding domain comprising an Fab and an additional portion of the heavy chain through the hinge region); F(ab')2 (two Fab' molecules joined by interchain disulfide bonds in the hinge regions of the heavy chains; the Fab' molecules can be directed toward the same or different epitopes); a bispecific Fab (a Fab molecule having two antigen binding domains, each of which can be directed to a different epitope); a single chain Fab chain comprising a variable region, also known as a sFv (the variable, antigen-binding determinative region of a single light and heavy chain of an antibody linked together by a chain of 10-25 amino acids); a disulfide-linked Fv, or dsFv (the variable, antigen-binding determinative region of a single light and heavy chain of an antibody linked together by a disulfide bond); a camelized VH (the variable, antigen-binding determinative region of a single heavy chain of an antibody in which some amino acids at the VH interface are those found in the heavy chain of naturally occurring camel antibodies); a bispecific sFv (a sFv or a dsFv molecule having two antigen- binding domains, each of which can be directed to a different epitope); a diabody (a dimerized sFv formed when the VH domain of a first sFv assembles with the VL domain of a second sFv and the VL domain of the first sFv assembles with the VH domain of the second sFv; the two antigen-binding regions of the diabody can be directed towards the same or different epitopes); and a triabody (a trimerized sFv, formed in a manner similar to a diabody, but in which three antigen-binding domains are created in a single complex; the three antigen binding domains can be directed towards the same or different epitopes). Antibodies of an ADC such as a PBD dimer conjugate provided herein can also include one or more CDR sequences of an antibody. The CDR sequences can be linked together on a scaffold when two or more CDR sequences are present. In certain embodiments, an antibody of an ADC such as a PBD dimer conjugate comprises a single-chain Fv ("scFv"). scFvs are antibody fragments comprising the VH and VL domains of an antibody, wherein these domains are present in a single polypeptide chain.
Generally, the scFv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the scFv to form the desired structure for antigen binding. For a review of scFvs, see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds. Springer- Verlag, New York, pp. 269-315 (1994). Without being bound by any particular theories, Fv molecules can be able to penetrate tissues because of their small size. A whole antibody can be enzymatically cleaved by pepsin to produce a F(ab')2 fragment, or can be enzymatically cleaved by papain to produce two Fab fragments.
[00291] In certain embodiments, antibodies of ADCs such as PBD dimer conjugates described herein are human, composite human, or humanized monoclonal antibodies. In a particular embodiment, an antibody described herein is an engineered antibody, for example, antibody produced by recombinant methods. In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate described herein is a humanized antibody comprising one or more non- human (e.g., rodent or murine) CDRs and one or more human framework regions (FR), and optionally human heavy chain constant region and/or light chain constant region. In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate described herein comprises one or more primate (or non-human primate) framework regions. In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate described herein does not comprise non- human primate framework regions.
[00292] Antibodies of ADCs such as PBD dimer conjugates provided herein can include antibodies comprising chemical modifications, for example, antibodies which have been chemically modified, e.g., by covalent attachment of any type of molecule to the antibody. For example, but not by way of limitation, an anti-KIT antibody of an ADC such as a PBD dimer conjugate can be glycosylated, acetylated, pegylated, phosphorylated, or amidated, can be derivitized via protective/blocking groups, or can further comprise a cellular ligand and or other protein or peptide, etc. For example, an antibody of an ADC such as a PBD dimer conjugate provided herein can be chemically modified, e.g. , by glycosylation, acetylation, pegylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein, etc. Further, an anti-KIT antibody of an ADC such as a PBD dimer conjugate described herein can contain one or more non-classical amino acids.
5.1.2.1 Antibody Production [00293] Antibodies (e.g., human, composite human, or humanized antibodies) or an antigen- binding fragment thereof described herein that immunospecifically bind to a KIT antigen, for conjugation to produce ADCs such as PBD dimer conjugates provided herein, can be produced by any method known in the art for the synthesis of antibodies, for example, by chemical synthesis or by recombinant expression techniques. The methods described herein employs, unless otherwise indicated, conventional techniques in molecular biology, microbiology, genetic analysis, recombinant DNA, organic chemistry, biochemistry, PCR, oligonucleotide synthesis and modification, nucleic acid hybridization, and related fields within the skill of the art. These techniques are described in the references cited herein and are fully explained in the literature. See, e.g.,, Maniatis et al. (1982) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press; Sambrook et al. (1989), Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press; Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; Ausubel et al, Current Protocols in Molecular Biology, John Wiley & Sons (1987 and annual updates); Current Protocols in Immunology, John Wiley & Sons (1987 and annual updates) Gait (ed.) (1984) Oligonucleotide Synthesis: A Practical Approach, IRL Press; Eckstein (ed.) (1991)
Oligonucleotides and Analogues: A Practical Approach, IRL Press; Birren et al. (eds.) (1999) Genome Analysis: A Laboratory Manual, Cold Spring Harbor Laboratory Press.
[00294] For example, humanized antibodies can be produced using a variety of techniques known in the art, including but not limited to, CDR-grafting (European Patent No. EP 239,400; International publication No. WO 91/09967; and U.S. Patent Nos. 5,225,539, 5,530,101, and 5,585,089), veneering or resurfacing (European Patent Nos. EP 592,106 and EP 519,596; Padlan, 1991, Molecular Immunology 28(4/5):489-498; Studnicka et al, 1994, Protein Engineering 7(6):805-814; and Roguska et al, 1994, PNAS 91 :969-973), chain shuffling (U.S. Patent No. 5,565,332), and techniques disclosed in, e.g., U.S. Pat. No. 6,407,213, U.S. Pat. No. 5,766,886, WO 9317105, Tan et al, J. Immunol. 169: 1119 25 (2002), Caldas et al, Protein Eng. 13(5):353- 60 (2000), Morea et al, Methods 20(3):267 79 (2000), Baca et al, J. Biol. Chem.
272(16): 10678-84 (1997), Roguska et al, Protein Eng. 9(10):895 904 (1996), Couto et al, Cancer Res. 55 (23 Supp):5973s- 5977s (1995), Couto et al, Cancer Res. 55(8): 1717-22 (1995), Sandhu JS, Gene 150(2):409-10 (1994), and Pedersen et al, J. Mol. Biol. 235(3):959-73 (1994). See also U.S. Patent Pub. No. US 2005/0042664 Al (Feb. 24, 2005), which is incorporated herein by reference.
[00295] In specific aspects, a humanized antibody is capable of binding to a predetermined antigen and which comprises a framework region having substantially the amino acid sequence of a human immunoglobulin and CDRs having substantially the amino acid sequence of a non- human immunoglobulin (e.g., a murine immunoglobulin). In particular embodiments, a humanized antibody also comprises at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. The antibody also can include the CHI, hinge, CH2, CH3, and CH4 regions of the heavy chain. A humanized antibody can be selected from any class of immunoglobulins, including IgM, IgG, IgD, IgA and IgE, and any isotype, including IgGi, IgG2, IgG3 and IgG4.
[00296] Monoclonal antibodies can be prepared using a wide variety of techniques known in the art including the use of hybridoma, recombinant, and phage display technologies, or a combination thereof. For example, monoclonal antibodies can be produced using hybridoma techniques including those known in the art and taught, for example, in Harlow et al.,
Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988);
Hammerling et al., in: Monoclonal Antibodies and T-Cell Hybridomas 563 681 (Elsevier, N.Y., 1981). The term "monoclonal antibody" as used herein is not limited to antibodies produced through hybridoma technology. For example, monoclonal antibodies can be produced by recombinant technology, e.g. , recombinant monoclonal antibodies expressed by a host cell, such as a mammalian host cell.
[00297] Antibodies of ADCs such as PBD dimer conjugates described herein include antibody fragments which recognize specific KIT antigens and can be generated by any technique known to those of skill in the art. For example, Fab and F(ab')2 fragments described herein can be produced by proteolytic cleavage of immunoglobulin molecules, using enzymes such as papain (to produce Fab fragments) or pepsin (to produce F(ab')2 fragments). A Fab fragment corresponds to one of the two identical arms of an antibody molecule and contains the complete light chain paired with the VH and CHI domains of the heavy chain. A F(ab')2 fragment contains the two antigen-binding arms of an antibody molecule linked by disulfide bonds in the hinge region. [00298] In one aspect, to generate whole antibodies, PCR primers including VH or VL nucleotide sequences, a restriction site, and a flanking sequence to protect the restriction site can be used to amplify the VH or VL sequences from a template, e.g., scFv clones. Utilizing cloning techniques known to those of skill in the art, the PCR amplified VH domains can be cloned into vectors expressing a VH constant region, and the PCR amplified VL domains can be cloned into vectors expressing a VL constant region, e.g., human kappa or lambda constant regions. The VH and VL domains can also be cloned into one vector expressing the necessary constant regions. The heavy chain conversion vectors and light chain conversion vectors are then co-transfected into cell lines to generate stable or transient cell lines that express full-length antibodies, e.g., IgG, using techniques known to those of skill in the art.
[00299] Single domain antibodies, for example, antibodies lacking the light chains, can be produced by methods well-known in the art. See Riechmann et al. , 1999, J. Immunol. 231 :25- 38; Nuttall et al, 2000, Curr. Pharm. Biotechnol. l(3):253-263; Muylderman, 2001, J.
Biotechnol. 74(4):277302; U.S. Patent No. 6,005,079; and International Publication Nos. WO 94/04678, WO 94/25591, and WO 01/44301.
[00300] In certain aspects, antibodies of ADCs such as PBD dimer conjugates described herein, such as heteroconjugate antibodies, single chain antibodies, and bispecific antibodies, can be produced through recombinant technology known in the art. For example, mammalian host cells comprising vectors expressing an antibody described herein are cultured under conditions suitable for antibody production.
[00301] Recombinant expression of an antibody of an ADC such as a PBD dimer conjugate described herein {e.g., a full-length antibody, heavy and/or light chain of an antibody, or a single chain antibody described herein) that immunospecifically binds to a KIT antigen involves construction of an expression vector containing a polynucleotide that encodes the antibody. Once a polynucleotide encoding an antibody molecule, heavy and/or light chain of an antibody, or fragment thereof (preferably, but not necessarily, containing the heavy and/or light chain variable domain) described herein has been obtained, the vector for the production of the antibody molecule can be produced by recombinant DNA technology using techniques well- known in the art. Thus, methods for preparing a protein by expressing a polynucleotide containing an antibody encoding nucleotide sequence are described herein. Methods which are well known to those skilled in the art can be used to construct expression vectors containing antibody coding sequences and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Also provided are replicable vectors comprising a nucleotide sequence encoding an antibody molecule described herein, a heavy or light chain of an antibody, a heavy or light chain variable domain of an antibody or a fragment thereof, or a heavy or light chain CDR, operably linked to a promoter. Such vectors can, for example, include the nucleotide sequence encoding the constant region of the antibody molecule (see, e.g., International Publication Nos. WO 86/05807 and WO 89/01036; and U.S. Patent No. 5,122,464) and the variable domain of the antibody can be cloned into such a vector for expression of the entire heavy, the entire light chain, or both the entire heavy and light chains.
[00302] An expression vector can be transferred to a cell {e.g., host cell) by conventional techniques and the resulting cells can then be cultured by conventional techniques to produce an antibody described herein or a fragment thereof. Thus, provided herein are host cells containing a polynucleotide encoding an antibody described herein or fragments thereof, or a heavy or light chain thereof, or fragment thereof, or a single chain antibody described herein, operably linked to a promoter for expression of such sequences in the host cell. In certain embodiments, for the expression of double-chained antibodies, vectors encoding both the heavy and light chains, individually, can be co-expressed in the host cell for expression of the entire immunoglobulin molecule, as detailed below. In certain embodiments, a host cell contains a vector comprising a polynucleotide encoding both the heavy chain and light chain of an antibody described herein, or a fragment thereof. In specific embodiments, a host cell contains two different vectors, a first vector comprising a polynucleotide encoding a heavy chain of an antibody described herein, or a fragment thereof, and a second vector comprising a polynucleotide encoding a light chain of an antibody described herein, or a fragment thereof. In other embodiments, a first host cell comprises a first vector comprising a polynucleotide encoding a heavy chain of an antibody described herein, or a fragment thereof, and a second host cell comprises a second vector comprising a polynucleotide encoding a light chain of an antibody described herein.
[00303] A variety of host-expression vector systems can be utilized to express antibody molecules described herein (see, e.g., U.S. Patent No. 5,807,715). Such host-expression systems represent vehicles by which the coding sequences of interest can be produced and subsequently purified, but also represent cells which can, when transformed or transfected with the appropriate nucleotide coding sequences, express an antibody molecule described herein in situ. These include but are not limited to microorganisms such as bacteria {e.g., E. coli and B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing antibody coding sequences; yeast {e.g., Saccharomyces Pichia) transformed with recombinant yeast expression vectors containing antibody coding sequences; insect cell systems infected with recombinant virus expression vectors {e.g., baculovirus) containing antibody coding sequences; plant cell systems (e.g., green algae such as Chlamydomonas reinhardtii) infected with recombinant virus expression vectors {e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors {e.g., Ti plasmid) containing antibody coding sequences; or mammalian cell systems {e.g., COS, CHO, BHK, MDCK, HEK 293, NSO, PER.C6, VERO, CRL7030, HsS78Bst, HeLa, and NIH 3T3 cells) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells {e.g., metallothionein promoter) or from mammalian viruses {e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter). In a specific embodiment, cells for expressing antibodies described herein {e.g., Huml-Hum20) or an antigen- binding fragment thereof are CHO cells, for example CHO cells from the CHO GS System™ (Lonza). In a specific embodiment, a mammalian expression vector is pOptiVEC™ or pcDNA3.3. Preferably, bacterial cells such as Escherichia coli, and more preferably, eukaryotic cells, especially for the expression of whole recombinant antibody molecule, are used for the expression of a recombinant antibody molecule. For example, mammalian cells such as Chinese hamster ovary (CHO) cells, in conjunction with a vector such as the major intermediate early gene promoter element from human cytomegalovirus is an effective expression system for antibodies (Foecking et al., 1986, Gene 45: 101; and Cockett et al., 1990, Bio/Technology 8:2). In certain embodiments, antibodies described herein are produced by CHO cells or NSO cells. In a specific embodiment, the expression of nucleotide sequences encoding antibodies described herein which immunospecifically bind to a KIT antigen is regulated by a constitutive promoter, inducible promoter or tissue specific promoter.
[00304] In bacterial systems, a number of expression vectors can be advantageously selected depending upon the use intended for the antibody molecule being expressed. For example, when a large quantity of such an antibody is to be produced, for the generation of pharmaceutical compositions of an antibody molecule, vectors which direct the expression of high levels of fusion protein products that are readily purified can be desirable. Such vectors include, but are not limited to, the E. coli expression vector pUR278 (Ruther et ah, 1983, EMBO 12: 1791), in which the antibody coding sequence can be ligated individually into the vector in frame with the lac Z coding region so that a fusion protein is produced; pIN vectors (Inouye & Inouye, 1985, Nucleic Acids Res. 13:3101-3109; Van Heeke & Schuster, 1989, J. Biol. Chem. 24:5503-5509); and the like. pGEX vectors can also be used to express foreign polypeptides as fusion proteins with glutathione 5-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption and binding to matrix glutathione agarose beads followed by elution in the presence of free glutathione. The pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene product can be released from the GST moiety.
[00305] In an insect system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The antibody coding sequence can be cloned individually into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter).
[00306] In mammalian host cells, a number of viral-based expression systems can be utilized. In cases where an adenovirus is used as an expression vector, the antibody coding sequence of interest can be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and tripartite leader sequence. This chimeric gene can then be inserted in the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome {e.g., region El or E3) will result in a recombinant virus that is viable and capable of expressing the antibody molecule in infected hosts {e.g., see Logan & Shenk, 1984, Proc. Natl. Acad. Sci. USA 8 1 :355-359). Specific initiation signals can also be required for efficient translation of inserted antibody coding sequences. These signals include the ATG initiation codon and adjacent sequences. Furthermore, the initiation codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert. These exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc. (see, e.g., Bittner et al, 1987, Methods in Enzymol. 153:51-544). [00307] In addition, a host cell strain can be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products can be important for the function of the protein. Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins and gene products. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed. To this end, eukaryotic host cells which possess the cellular machinery for proper processing of the primary transcript, glycosylation, and
phosphorylation of the gene product can be used. Such mammalian host cells include but are not limited to CHO, VERO, BHK, Hela, COS, MDCK, HEK 293, NIH 3T3, W138, BT483,
Hs578T, HTB2, BT20 and T47D, NSO (a murine myeloma cell line that does not endogenously produce any immunoglobulin chains), CRL7030 and HsS78Bst cells. In certain embodiments, humanized monoclonal anti-KIT antibodies described herein are produced in mammalian cells, such as CHO cells.
[00308] For long-term, high-yield production of recombinant proteins, stable expression is preferred. For example, cell lines which stably express the antibody molecule can be engineered. Rather than using expression vectors which contain viral origins of replication, host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker. Following the introduction of the foreign DNA, engineered cells can be allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media. The selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn can be cloned and expanded into cell lines. This method can advantageously be used to engineer cell lines which express the antibody molecule. Such engineered cell lines can be particularly useful in screening and evaluation of compositions that interact directly or indirectly with the antibody molecule.
[00309] A number of selection systems can be used, including but not limited to, the herpes simplex virus thymidine kinase (Wigler et ah, 1977, Cell 11 :223), hypoxanthineguanine phosphoribosyltransferase (Szybalska & Szybalski, 1992, Proc. Natl. Acad. Sci. USA 48:202), and adenine phosphoribosyltransferase (Lowy et ah, 1980, Cell 22:8-17) genes can be employed in tk-, hgprt- or aprt-cells, respectively. Also, antimetabolite resistance can be used as the basis of selection for the following genes: dhfr, which confers resistance to methotrexate (Wigler et al, 1980, Natl. Acad. Sci. USA 77:357; O'Hare et al, 1981, Proc. Natl. Acad. Sci. USA
78: 1527); gpt, which confers resistance to mycophenolic acid (Mulligan & Berg, 1981, Proc. Natl. Acad. Sci. USA 78:2072); neo, which confers resistance to the aminoglycoside G-418 (Wu and Wu, 1991, Biotherapy 3:87-95; Tolstoshev, 1993, Ann. Rev. Pharmacol. Toxicol. 32:573- 596; Mulligan, 1993, Science 260:926-932; and Morgan and Anderson, 1993, Ann. Rev.
Biochem. 62: 191-217; May, 1993, TIB TECH l l(5):155-2 15); and hygro, which confers resistance to hygromycin (Santerre et al, 1984, Gene 30: 147). Methods commonly known in the art of recombinant DNA technology can be routinely applied to select the desired recombinant clone, and such methods are described, for example, in Ausubel et al (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, NY (1993); Kriegler, Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY (1990); and in Chapters 12 and 13, Dracopoli et al. (eds.), Current Protocols in Human Genetics, John Wiley & Sons, NY (1994); Colberre-Garapin et al, 1981, J. Mol. Biol. 150: 1, which are incorporated by reference herein in their entireties.
[00310] The expression levels of an antibody molecule can be increased by vector
amplification (for a review, see Bebbington and Hentschel, The use of vectors based on gene amplification for the expression of cloned genes in mammalian cells in DNA cloning, Vol. 3 (Academic Press, New York, 1987)). When a marker in the vector system expressing antibody is amplifiable, increase in the level of inhibitor present in culture of host cell will increase the number of copies of the marker gene. Since the amplified region is associated with the antibody gene, production of the antibody will also increase (Crouse et al, 1983, Mol. Cell. Biol. 3:257).
[00311] The host cell can be co-trans fected with two or more expression vectors described herein, the first vector encoding a heavy chain derived polypeptide and the second vector encoding a light chain derived polypeptide. The two vectors can contain identical selectable markers which enable equal expression of heavy and light chain polypeptides. The host cells can be co-trans fected with different amounts of the two or more expression vectors. For example, host cells can be transfected with any one of the following ratios of a first expression vector and a second expression vector: 1 : 1, 1 :2, 1 :3, 1 :4, 1 :5, 1 :6, 1 :7, 1 :8, 1 :9, 1 :10, 1 : 12, 1 : 15, 1 :20, 1 :25, 1 :30, 1 :35, 1 :40, 1 :45, or 1 :50. [00312] Alternatively, a single vector can be used which encodes, and is capable of expressing, both heavy and light chain polypeptides. In such situations, the light chain should be placed before the heavy chain to avoid an excess of toxic free heavy chain (Proudfoot, 1986, Nature 322:52; and Kohler, 1980, Proc. Natl. Acad. Sci. USA 77:2197-2199). The coding sequences for the heavy and light chains can comprise cDNA or genomic DNA. The expression vector can be monocistronic or multicistronic. A multicistronic nucleic acid construct can encode 2, 3, 4, 5, 6, 7, 8, 9, 10 or more, or in the range of 2-5, 5-10 or 10-20 genes/nucleotide sequences. For example, a bicistronic nucleic acid construct can comprise in the following order a promoter, a first gene (e.g., heavy chain of an antibody described herein), and a second gene and (e.g., light chain of an antibody described herein). In such an expression vector, the transcription of both genes can be driven by the promoter, whereas the translation of the mRNA from the first gene can be by a cap-dependent scanning mechanism and the translation of the mRNA from the second gene can be by a cap-independent mechanism, e.g., by an IRES.
[00313] Once an antibody molecule described herein has been produced by recombinant expression, it can be purified by any method known in the art for purification of an
immunoglobulin molecule, for example, by chromatography (e.g., ion exchange, affinity, particularly by affinity for the specific antigen after Protein A, and sizing column
chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins. Further, the antibodies described herein can be fused to heterologous polypeptide sequences described herein or otherwise known in the art to facilitate purification.
[00314] In specific embodiments, an antibody described herein is isolated or purified.
Generally, an isolated antibody is one that is substantially free of other antibodies with different antigenic specificities than the isolated antibody. For example, in a particular embodiment, a preparation of an antibody described herein is substantially free of cellular material and/or chemical precursors. The language "substantially free of cellular material" includes preparations of an antibody in which the antibody is separated from cellular components of the cells from which it is isolated or recombinantly produced. Thus, an antibody that is substantially free of cellular material includes preparations of antibody having less than about 30%, 20%, 10%>, 5%, 2%>, 1%, 0.5%, or 0.1%) (by dry weight) of heterologous protein (also referred to herein as a "contaminating protein") and/or variants of an antibody, for example, different post-translational modified forms of an antibody or other different versions of an antibody (e.g. , antibody fragments). When the antibody is recombinantly produced, it is also generally substantially free of culture medium, i.e., culture medium represents less than about 20%, 10%>, 2%, 1%, 0.5%>, or 0.1% of the volume of the protein preparation. When the antibody is produced by chemical synthesis, it is generally substantially free of chemical precursors or other chemicals, i.e., it is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein. Accordingly, such preparations of the antibody have less than about 30%>, 20%>, 10%>, or 5% (by dry weight) of chemical precursors or compounds other than the antibody of interest. In a specific embodiment, antibodies described herein are isolated or purified
5.1.2.2 Activity
[00315] In certain aspects, provided herein are ADCs such as PBD dimer conjugates comprising an anti-KIT antibody or an antigen binding fragment thereof which can modulate a KIT activity.
[00316] In specific aspects, antibodies {e.g., human, composite human, or humanized antibodies) of ADCs such as PBD dimer conjugates described herein are inhibitory antibodies, that is, antibodies that inhibit {e.g., partially inhibit) KIT activity, i.e., one or more KIT activities. In a specific embodiment, partial inhibition of a KIT activity results in, for example, about 25% to about 65% or 75% inhibition. In a specific embodiment, partial inhibition of a KIT activity results in, for example, about 35% to about 85% or 95% inhibition.
[00317] Non-limiting examples of KIT activities include KIT dimerization, KIT
phosphorylation {e.g., tyrosine phosphorylation), signaling downstream of KIT {e.g., AKT, MAPK/ERK, Ras, Statl, Stat3, or Stat5 signaling), induction or enhancement of gene
transcription {e.g., SCF-induced transcriptional activation of c-Myc), induction or enhancement of cell proliferation or cell survival.
[00318] In certain aspects, KIT activity is induced by KIT ligand {e.g., SCF) binding to KIT receptor. In particular aspects, KIT activity can be induced or enhanced by gain-of-function mutations which can result, for example, in dimerization and constitutively active KIT signaling (see, e.g., Mol et al, J. Biol. Chem., 2003, 278:31461-31464; Hirota et al., J. Pathology, 2001, 193:505-510). Such gain-of-function can allow for KIT receptor dimerization and KIT signaling to occur in the absence of KIT ligand {e.g., SCF) binding to KIT receptor. In certain
embodiments, an increase in KIT activity or signaling can occur, in the absence of KIT ligand {e.g., SCF) binding KIT receptor, due to high (or overexpression) expression of KIT receptors. High or overexpression of KIT in a cell refers to an expression level which is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% more than the expression level of a reference cell known to have normal KIT expression or KIT activity or more than the average expression level of KIT in a population of cells or samples known to have normal KIT expression or KIT activity. Expression levels of KIT can be assessed by methods described herein or known to one of skill in the art (e.g., Western blotting or immunohistochemistry). In particular embodiments, KIT activity that is higher than normal KIT activity can lead to cellular transformation, neoplasia, and tumorogenesis. In particular embodiments, KIT activity that is higher than normal KIT activity can lead to other KIT-associated disorders or diseases.
[00319] In a particular embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting KIT phosphorylation (e.g. , ligand- induced phosphorylation).
[00320] In a specific embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting KIT tyrosine phosphorylation in the KIT cytoplasmic domain. In another particular embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting cell proliferation (e.g., cancer cell proliferation). In yet another particular embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting cell survival (e.g., cancer cell survival). In a specific embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inducing apoptosis (e.g., cancer cell apoptosis). In another specific embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inducing cell differentiation, e.g., cell differentiation in a cell expressing KIT, e.g., human KIT. In a particular embodiment, an antibody described herein inhibits KIT activity but does not inhibit KIT dimerization. In another particular embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting KIT activity and does not inhibit ligand binding to KIT, e.g., does not inhibit KIT ligand (e.g., SCF) binding to KIT, but does inhibit KIT dimerization.
[00321] In a particular embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting a KIT activity, such as ligand- induced tyrosine phosphorylation of a KIT cytoplasmic domain, by at least about 25%, 35%, 45%, 55%, 65%), 75%o, 85%, or 95% as determined by a cell-based phosphorylation assay well known in the art, for example, the cell-based phosphorylation assay described herein. In a certain embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting a KIT activity, such as ligand-induced tyrosine phosphorylation of a KIT cytoplasmic domain, by at least about 25%, 35%, 45%, 55%, 65%, 75%), 85%), or 95%, as determined by a cell-based phosphorylation assay well known in the art, for example, the cell-based phosphorylation assay described herein.
[00322] In a particular embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is capable of inhibiting a KIT activity, such as ligand- induced tyrosine phosphorylation of a KIT cytoplasmic domain, with a 50% inhibition concentration (IC50) of less than about 600 pM, or less than about 500 pM, or less than about 250 pM, or less than about 100 pM, as determined by a cell-based phosphorylation assay well known in the art, for example, the cell-based phosphorylation assay described herein. In a specific embodiment, the IC50 is less than about 550 pM or 200 pM. In a specific embodiment, the IC50 is in the range of about 50 pM to about 225 pM, or about 50 pM to about 100 pM, or in the range of 100 pM to about 600 pM. In a specific embodiment, the IC50 is in the range of about 50 pM to about 550 pM, or about 50 pM to about 600 pM, or about 150 pM to about 550 pM. In a certain embodiment, the IC50 is determined as described in Section 6.23, below.
[00323] In a particular embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or an antigen-binding fragment thereof, which specifically binds to a KIT polypeptide (e.g., the D4 region of human KIT), is capable of blocking KIT phosphorylation with IC50 (50% inhibition concentration) value of about 600 pM or less, or about 200 pM or less, or about 100 pM or less, as determined by methods known in the art, for example, KIT receptor phosphorylation as described herein in Section 6.23.
[00324] In a specific embodiment, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody described herein, or an antigen-binding fragment thereof, (i) immunospecifically binds to a KIT polypeptide comprising the D4 region of human KIT, (ii) inhibits KIT phosphorylation (e.g., tyrosine phosphorylation), and (iii) does not inhibit KIT ligand (e.g., SCF) binding to KIT. [00325] In yet another specific embodiment, such an antibody does not inhibit KIT dimerization. In yet another specific embodiment, such an antibody can be recombinantly expressed by CHO cells at an average titer of at least 0.5 μ§/ι Ι., for example at least 1.0 μg/mL.
[00326] In a further specific embodiment, such an antibody of an ADC such as PBD dimer conjugate comprises a VH domain and a VL domain that are non-immunogenic (e.g., non- immunogenic in a human), for example, the VH domain and VL domain do not contain T cell epitopes.
[00327] In specific embodiments, ADCs such as PBD dimer conjugates provided herein comprise anti-KIT antibodies or an antigen-binding fragment thereof which specifically bind to a D4 region of KIT and block or inhibit tyrosine phosphorylation in the cytoplasmic domain of KIT by at least about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art, e.g., ELISA assay as described in Section 6 (e.g., Section 6.23) or immunob lotting assay, relative to phosphorylation in the presence of KIT ligand stimulation without any antibody or with an unrelated antibody (e.g. , an antibody that does not
immunospecifically bind to KIT).
[00328] In specific embodiments, ADCs such as PBD dimer conjugates provided herein comprise anti-KIT antibodies or an antigen-binding fragment thereof which specifically bind to KIT and block or inhibit tyrosine phosphorylation of the cytoplasmic domain of KIT with an IC50 of less than about 600 pM, or less than about 550 pM, or less than about 500 pM, or less than about 400 pM, or less than about 300 pM, or less than about 100 pM as assessed by methods described herein (e.g., phosphorylation inhibition assay with CHO cells expressing wild-type KIT as described in Section 6 below, such as Section 6.23) or known to one of skill in the art. In specific embodiments, antibodies of ADCs such as PBD dimer conjugates described herein specifically bind to KIT and block or inhibit tyrosine phosphorylation of the cytoplasmic domain of KIT with an IC50 of less than about 600 pM, or less than about 100 pM. In specific embodiments, antibodies of ADCs such as PBD dimer conjugates described herein specifically bind to KIT and block or inhibit tyrosine phosphorylation of the cytoplasmic domain of KIT with an IC50 of less than about 550 pM. In specific embodiments, antibodies of ADCs such as PBD dimer conjugates described herein specifically bind to KIT and block or inhibit tyrosine phosphorylation of the cytoplasmic domain of KIT with an IC50 in the range of about 50 pM to about 100 M, about 100 pM to about 500 pM, about 25 pM to about 550 pM, or about 40 pM to about 600 pM, or about 50 pM to about 350 pM. For example, an IC50 for inhibition of tyrosine phosphorylation can be determined by assaying lysates from cells, e.g., CHO cells,
recombinantly expressing KIT, in ELISA which detects tyrosine phosphorylation, for example, as described in Section 6 below (e.g,. Section 6.23). In certain embodiments, cells, e.g., CHO cells, recombinantly expressing KIT, are sorted, e.g., sorted to select for cells highly expressing KIT, prior to use in the phosphorylation inhibition assays. In some embodiments, the cells are not sorted prior to use in the phosphorylation inhibition assays.
[00329] In specific embodiments, ADCs such as PBD dimer conjugates comprise antibodies described herein or an antigen-binding fragment thereof which specifically bind to KIT and induce or enhance KIT receptor internalization by at least about 5%, 10%, 15%, 20%>, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art, relative to
internalization in the presence of an unrelated antibody {e.g., an antibody that does not immunospecifically bind to KIT). In specific embodiments, ADCs such as PBD dimer conjugates comprise anti-KIT antibodies described herein or an antigen-binding fragment thereof which specifically bind to KIT and induce or enhance KIT receptor internalization by at least about 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art, relative to internalization in the presence of an unrelated antibody {e.g., an antibody that does not immunospecifically bind to KIT). Techniques for the quantitation or visualization of cell surface receptors are well known in the art and include a variety of fluorescent and radioactive techniques. For example, one method involves incubating the cells with a radiolabeled anti-receptor antibody. Alternatively, the natural ligand of the receptor can be conjugated to a fluorescent molecule or radioactive-label and incubated with the cells.
Additional receptor internalization assays are well known in the art and are described in, for example, Jimenez et al., Biochemical Pharmacology, 1999, 57: 1125-1131; Bernhagen et al, Nature Medicine, 2007, 13:587-596; and Conway et al, J. Cell Physiol, 2001, 189:341-55.
[00330] In specific embodiments, antibodies described herein specifically bind to KIT and induce or enhance KIT receptor turnover by at least about 5%>, 10%>, 15%>, 20%>, 25%>, 30%>, 35%>, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art (e.g., pulse-chase assay), relative to turnover in the presence of an unrelated antibody (e.g., an antibody that does not
immunospecifically bind to KIT). In specific embodiments, ADCs such as PBD dimer conjugates comprising anti-KIT antibodies described herein (or an antigen-binding fragment thereof) specifically bind to KIT and induce or enhance KIT receptor turnover by at least about 25%o or 35%), optionally to about 75%, as assessed by methods described herein or known to one of skill in the art (e.g., pulse-chase assay), relative to turnover in the presence of an unrelated antibody (e.g., an antibody that does not immunospecifically bind to KIT). In specific embodiments, antibodies described herein specifically bind to KIT and induce or enhance KIT receptor turnover by at least about 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art (e.g., pulse-chase assay), relative to turnover in the presence of an unrelated antibody (e.g. , an antibody that does not immunospecifically bind to KIT). Methods for the determining receptor turnover are well known in the art. For example, cells expressing KIT can be pulse-labeled using 35S-EXPRESS Protein Labeling mix (NEG772, NEN Life Science Products), washed and chased with unlabeled medium for a period of time before protein lysates from the labeled cells are immunoprecipitated using an anti-KIT antibody and resolved by SDS-PAGE and visualized (e.g., exposed to a Phospholmager screen (Molecular Dynamics), scanned using the Typhoon8600 scanner (Amersham), and analyzed using
ImageQuant software (Molecular Dynamics)) (see, e.g., Chan et al, Development, 2004, 131 :5551-5560).
[00331] In specific embodiments, ADCs such as PBD dimer conjugates comprise antibodies described herein or an antigen-binding fragment thereof which specifically bind to KIT and induce or enhance KIT receptor degradation by at least about 5%, 10%>, 15%, 20%>, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art (e.g. , pulse-chase assays), relative to degradation in the presence of an unrelated antibody (e.g., an antibody that does not immunospecifically bind to KIT). In specific embodiments, ADCs such as PBD dimer conjugates comprise antibodies described herein or an antigen-binding fragment thereof which specifically bind to KIT and induce or enhance KIT receptor degradation by at least about 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art (e.g., pulse-chase assays), relative to degradation in the presence of an unrelated antibody (e.g., an antibody that does not immunospecifically bind to KIT). Techniques for quantitating or monitoring ubiquitination and/or degradation (e.g., kinetics or rate of degradation) of cell surface receptors are well known in the art and involve a variety of fluorescent and radioactive techniques (see, e.g., International Patent Application Publication No. WO 2008/153926 A2). For example, pulse chase experiments or experiments using radiolabeled ligands such as 125I- SCF can be carried out to quantitatively measure degradation of KIT.
[00332] In particular aspects, signaling events downstream of KIT receptor phosphorylation can serve as indicators of KIT activity. For example, KIT ligand (e.g., SCF) binding to its receptor KIT stimulates several distinct signaling pathways, including for example members of Src family kinases, phosphatidylinositol (PI) 3-kinases, and Ras mitogen-activated protein kinase (MAPK) (see Munugalavadla et al., Mol. Cell. Biol, 2005, 25:6747-6759). Phosphorylated tyrosines in the cytoplasmic domain of KIT can provide for binding sites for SH2 domain- containing proteins, which include, but are not limited to, proteins of the p21Ras-mitogen activated protein kinase (MAPK) pathway, the p85 subunit of PI 3-kinase, phospholipase C- gammai, the Grb2 adaptor protein, the Src family kinases (SFKs), Cbl, CRKL, p62Dok-l, SHPl, and SHP2 (see Ueda et al, Blood, 2002, 99:3342-3349).
[00333] Thus, in certain aspects, provided herein are ADCs such as PBD dimer conjugates comprising anti-KIT antibodies or an antigen-binding fragment thereof which act as inhibitors of KIT activity and can inhibit signaling of a member of the Src family kinases, PI 3-kinases, or Ras-MAPK. In particular embodiments, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody which acts as inhibitors of KIT activity can inhibit binding (or inhibit interaction), to the cytoplasmic domain of KIT, of one or more SH2 domain- containing proteins, such as proteins of the p21Ras-MAPK pathway, the p85 subunit of PI 3- kinase, phospholipase C-gammal, the Grb2 adaptor protein, a member of the SFK, Cbl, CRKL, p62Dok-l, SHPl, and SHP2. In certain embodiments, an ADC such as a PBD dimer conjugate described herein which act as inhibitors of KIT activity can inhibit activation by KIT of one or more SH2 domain-containing proteins, such as proteins of the p21Ras-MAPK pathway, the p85 subunit of PI 3-kinase, phospholipase C-gammal, the Grb2 adaptor protein, a member of the SFK, Cbl, CPvKL, p62Dok-l, SHP1, and SHP2.
[00334] In particular embodiments, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, can inhibit downstream signaling such as phosphorylation of MAPK,
phosphorylation of AKT, or phosphorylation of Statl, Stat3, or Stat5.
[00335] In certain aspects, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, can inhibit cellular proliferation of cells (e.g., cancer cells such as RD-ES or HEL cells) that express KIT. Cell proliferation assays are described in the art and can be readily carried out by one of skill in the art. For example, cell proliferation can be assayed by measuring Bromodeoxyuridine (BrdU) incorporation (see, e.g., Hoshino et ah, 1986, Int. J. Cancer 38, 369; Campana et ah, 1988, J. Immunol. Meth. 107:79) or (3H) thymidine incorporation (see, e.g., Blechman et a/., Cell, 1995, 80:103-113; Chen, J., 1996, Oncogene 13: 1395-403; Jeoung, J., 1995, J. Biol. Chem. 270: 18367 73), by direct cell count at various time intervals {e.g., 12-hour or 24-hour intervals), or by detecting changes in transcription, translation or activity of known genes such as proto-oncogenes {e.g., fos, myc) or cell cycle markers (Rb, cdc2, cyclin A, Dl, D2, D3, E, etc). The levels of such protein and mRNA and activity can be determined by any method well known in the art. For example, protein can be quantitated by known
immunodiagnostic methods such as ELISA, Western blotting or immunoprecipitation using antibodies, including commercially available antibodies. mRNA can be quantitated using methods that are well known and routine in the art, for example, using northern analysis, RNase protection, or polymerase chain reaction in connection with reverse transcription.
[00336] In specific embodiments, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, can inhibit cell proliferation by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art {e.g. , BrdU
incorporation assay). [00337] In certain aspects, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, can reduce or inhibit survival of cells (e.g., cancer cells such as RD-ES or HEL cells) that express KIT. Cell survival assays are described in the art and can be readily carried out by one of skill in the art. For example, cell viability can be assessed by using trypan-blue staining or other cell death or viability markers known in the art. In a specific embodiment, the level of cellular ATP is measured to determined cell viability. In specific embodiments, cell viability is measured in three-day and seven-day periods using an assay standard in the art, such as the CellTiter-Glo Assay Kit (Promega) which measures levels of intracellular ATP. A reduction in cellular ATP is indicative of a cytotoxic effect. In another specific embodiment, cell viability can be measured in the neutral red uptake assay. In other embodiments, visual observation for morphological changes can include enlargement, granularity, cells with ragged edges, a filmy appearance, rounding, detachment from the surface of the well, or other changes. These changes are given a designation of T (100% toxic), PVH (partially toxic-very heavy- 80%), PH (partially toxic-heavy-60%), P (partially toxic-40%), Ps (partially toxic-slight-20%), or 0 (no toxicity-0%), conforming to the degree of cytotoxicity seen. A 50% cell inhibitory (cytotoxic) concentration (IC50) is determined by regression analysis of these data.
[00338] In certain aspects, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, is capable of inducing cell death such as apoptosis (i.e., programmed cell death) of cells (e.g., cancer cells, such as RD-ES cells) that express KIT. Apoptosis is described in the art and can be readily carried out by one of skill in the art. For example, flow cytometry can be used to detect activated caspase 3, an apoptosis-mediating enzyme, in cells undergoing apoptosis, or Western blotting can be used to detect cleavage of poly(ADP-ribose) polymerase (PARP) (see, e.g., Smolich et ah, Blood, 2001, 97:1413-1421). Cleavage of PARP is an indicator of apoptosis. In specific embodiments, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, can induce or enhance apoptosis by at least about 0.25 fold, 0.5 fold, 0.75 fold, 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art (e.g., flow cytometry to detect activated caspase 3).
[00339] In certain aspects, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, is capable of inhibiting or decreasing anchorage independent cell growth (e.g. , colony formation) by cells (e.g., H526 cells or CHO cells expressing exogenous KIT) that express KIT, as measured by methods commonly known in the art, e.g., soft agar assay. In specific embodiments, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof, which acts as inhibitors of KIT activity, can inhibit or decrease anchorage independent cell growth by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99%) as assessed by methods described herein or known to one of skill in the art (e.g. , soft agar assay).
[00340] Cells and cell lines which are appropriate for use in the assays described herein relating to KIT activity are readily available (e.g., ATCC) or can be readily identified using methods known in the art. For example, cells and/or cell lines that express KIT endogenously or that possess KIT signaling or activity are known to one of skill in the art. In certain
embodiments, cells or cell lines that are appropriate for use in the assays described herein can express KIT, either endogenously or recombinantly. In particular embodiments, cells or cell lines for use in cell proliferation assays can express KIT, endogenously or recombinantly, and proliferate or increase proliferation in response to KIT ligand (e.g., SCF) stimulation. Cells or cell lines for use in cell viability assays can express KIT, endogenously or recombinantly, and exert changes in cell viability in response to KIT ligand (e.g., SCF) stimulation. Cells or cell lines for use in apoptosis assays can express KIT, endogenously or recombinantly, and exert changes in apoptosis in response to KIT ligand (e.g., SCF) stimulation.
[00341] Non- limiting examples of cells that can be used in the methods and assays described herein include primary cells, cancer cells, transformed cells, stem cells, mast cells, primordial germ cells, oocytes, spermatocytes, embryonic stem cells, hematopoietic cells, leukemia cells (e.g., HEL or Kasumi-1 cells) such as erythroleukemia cells (e.g., F36P and TF-1 cell lines) or human myeloid leukemia cell lines (e.g., M07E cells); gastrointestinal stromal tumor cell lines such as ST-882, GIST-Tl , GIST48, GIST48B, GIST430, and GIST882; neuroblastoma cell lines such as SK-N-SH, SK-SY5Y, H-EP1 , SK-N-BE(2), SK-N-BE(ZkM17), SK-N-BE(2)C, LA-N-1, or LA-N-1 -5 s; neuroectodermal tumor (PNET) cell line SK-PN-DW; Ewing's sarcoma cell lines such as TC71 , TC32, RD-ES, 5838, A4573, EWS-925, NCI-EWS-94, SK-N-MC, and NCI- EWS-95; and small cell lung carcinoma cell lines such as H526, H524, H69, ECC12, TMK1 , MKN7, GCIY, and HGC27.
[00342] Alternatively, cells and cell lines that express KIT, e.g., human KIT, can routinely be generated recombinantly. Non-limiting examples of cells that can be engineered to express KIT recombinantly include COS cells, HEK 293 cells, CHO cells, fibroblasts (e.g., human
fibroblasts) such as NIH3T3 cells, and MEFS. In a specific embodiment, cells for use in the methods described herein are CHO cells, for example CHO cells from the CHO GS System™ (Lonza). In a particular embodiment, these engineered cells exogenously expressing full-length human KIT (e.g., SEQ ID NO: 1).
[00343] In certain aspects, an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof is capable of inhibiting tumor growth or inducing tumor regression in mouse model studies. For example, tumor cell lines can be introduced into nude mice, and the mice can be administered with anti-KIT antibodies described herein one or more times, and tumor progression of the injected tumor cells can be monitored over a period of weeks and/or months. In some cases, administration of an ADC such as a PBD dimer conjugate provided herein comprising an anti-KIT antibody or antigen-binding fragment thereof to the nude mice can occur prior to introduction of the tumor cell lines. Any appropriate tumor cell line (e.g., tumor cell line expressing KIT) can be used in the mouse xenograft models described herein. Non-limiting examples of tumor cell lines for use in these xenograft mouse models include megakaryoblastic leukemia cell lines such as M07e; gastrointestinal stromal tumor cell lines such as ST-882, GIST-T1 , GIST430, GIST48, GIST48B and GIST882; acute myeloblastic leukemia cell line Kasumi-1 ; human erythroleukemic cell lines such as HEL and TF-1 ; human promyelocytic leukemia cell line, HL60; neuroblastoma cell lines such as SK-N-SH, SK-SY5Y, H-EP1 , SK-N-BE(2), SK-N-BE(ZkM17), SK-N-BE(2)C, LA-N-1, or LA-N-l-5s; Ewing's sarcoma cell lines such as TC71 , TC32, RD-ES, 5838, A4573, EWS- 925, NCI-EWS-94, SK-N-MC, RD-ES, and NCI-EWS-95; primitive neuroectodermal tumour (PNET) cell line SK-PN-DW; and small cell lung carcinoma cell lines such as H526, H524, H69, DMS153, DMS79, ECC12, TMK1 , MKN7, GCIY, and HGC27. In a specific embodiments, a tumor cell line for use in a xenograft mouse model is the GIST882, GIST430, GIST48,
GIST48B, HEL, HL60, H526, DMS153, or DMS79 cell line. In certain embodiments, suitable cell lines for use in xenograft tumor models can be generated by recombinantly expressing KIT in cell. In specific embodiments, an ADC such as a PBD dimer conjugate provided herein comprises an anti-KIT antibody or antigen-binding fragment thereof which specifically bind to KIT and inhibits tumor grow, delays tumor growth, or induces tumor regression in a mouse model by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art. Determining tumor growth inhibition or tumor regression can be assessed by monitoring tumor size over a period of time, such as by physical measurement of palpable tumors, or other visual detection methods. For example, tumor cell lines can be generated to recombinantly express a visualization agent, such as green fluorescent protein (GFP) or luciferase, then in vivo visualization of GFP can be carried out by microscopy, and in vivo visualization of luciferase can be carried out by administering luciferase substrate to the xenograft mice and detecting luminescent due to the luciferase enzyme processing the luciferase substrate. The degree or level of detection of GFP or luciferase correlates to the size of the tumor in the xenograft mice.
[00344] In certain aspects, an ADC such as a PBD dimer conjugate provided herein comprises an anti-KIT antibody or antigen-binding fragment thereof which specifically bind to KIT and can increase survival of animals in tumor xenograft models. In specific embodiments, an ADC such as a PBD dimer conjugate provided herein comprises an anti-KIT antibody or antigen- binding fragment thereof which specifically bind to KIT and can increase survival of mice in tumor xenograft models by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art. In specific embodiments, an ADC such as a PBD dimer conjugate provided herein comprises an anti-KIT antibody or antigen-binding fragment thereof which specifically bind to KIT and can increase survival of mice in tumor xenograft models by at least about 0.5 fold, 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art. Survival can be determined by plotting a survival curve of number of surviving mice against time (e.g. , days or weeks) after tumor cell line injection.
5.2 Pharmaceutical Compositions and Kits
[00345] Provided herein are compositions, pharmaceutical compositions, and kits comprising one or more PBD dimer ADCs. In particular aspects, compositions described herein can be for in vitro, in vivo, or ex vivo uses. In specific embodiments, provided herein is a pharmaceutical composition comprising a PBD dimer ADC (e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT- PBD2) described herein and a pharmaceutically acceptable carrier or excipient.
[00346] Pharmaceutically acceptable carriers or pharmaceutically acceptable excipients refer to carriers or excipients approved by a regulatory agency of the Federal or a state government, or listed in the U.S. Pharmacopeia, European Pharmacopeia or other generally recognized
Pharmacopeia for use in animals, and more particularly in humans.
[00347] Therapeutic formulations containing one or more PBD dimer ADCs (e.g. , KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2) provided herein can, for example, be prepared for storage by mixing the PBD dimer ADCs having the desired degree of purity with optional pharmaceutically acceptable carriers or excipients (Remington's Pharmaceutical Sciences (1990) Mack Publishing Co., Easton, PA; Remington: The Science and Practice of Pharmacy, 21st ed. (2006) Lippincott Williams & Wilkins, Baltimore, MD), in the form of lyophilized formulations or aqueous solutions. Acceptable carriers or excipients are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; and/or non-ionic surfactants such as TWEEN™, PLURONICS™ or polyethylene glycol (PEG). Pharmaceutical carriers suitable for administration of PBD dimer ADCs (e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2) provided herein include any such carriers known to those skilled in the art to be suitable for the particular mode of administration.
[00348] Formulations, such as those described herein, can also contain more than one active compounds (for example, molecules, e.g., PBD dimer ADCs described herein) as necessary for the particular indication being treated. In certain embodiments, formulations comprise a PBD dimer ADC (e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2) provided herein and one or more active compounds with complementary activities that do not adversely affect each other. Such molecules are suitably present in combination in amounts that are effective for the purpose intended. For example, a PBD dimer ADC (e.g., KIT-PBD ADC such as KIT-PBD 1 or ΚΓΓ- PBD2) described herein can be combined with one or more other therapeutic agents (e.g. , a tyrosine kinase inhibitor such as imatinib mesylated or sunitinib, or a histone deacetylase inhibitor such as vorinostat). Such combination therapy can be administered to the patient serially or simultaneously or in sequence.
[00349] The formulations to be used for in vivo administration can be sterile. This can readily accomplished by filtration through, e.g., sterile filtration membranes.
[00350] In specific aspects, the pharmaceutical compositions provided herein contain therapeutically effective amounts of one or more of the PBD dimer ADCs (e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2) provided herein, and optionally one or more additional prophylactic of therapeutic agents, in a pharmaceutically acceptable carrier. Such pharmaceutical compositions are useful in the prevention, treatment, management or amelioration of a disorder or disease such as cancer (e.g., Ewings' sarcoma, small cell lung cancer, leukemia, or GIST) or an inflammatory disorder (e.g., inflammatory bowel disease), or one or more of the symptoms thereof.
[00351] In particular aspects, provided herein are pharmaceutical compositions containing one or more PBD dimer ADCs provided herein. In one embodiment, the PBD dimer ADCs are formulated into suitable pharmaceutical preparations, such as solutions, suspensions, tablets, dispersible tablets, pills, capsules, powders, sustained release formulations or elixirs, for oral administration or in sterile solutions or suspensions for parenteral administration, as well as transdermal patch preparation and dry powder inhalers.
[00352] In certain compositions provided herein, one or more ADCs such as PBD dimer ADCs is mixed with a suitable pharmaceutical carrier. The concentrations of a PBD dimer ADC or PBD dimer ADCs in the compositions can, for example, be effective for delivery of an amount of a drug(s), upon administration, that treats, prevents, or ameliorates a disorder or disease described herein such as cancer or a symptom thereof.
[00353] In one embodiment, the compositions are formulated for single dosage
administration. In certain embodiments, to formulate a composition, the weight fraction of compound is dissolved, suspended, dispersed or otherwise mixed in a selected carrier at an effective concentration such that the treated condition is relieved, prevented, or one or more symptoms are ameliorated. [00354] In certain aspects, a PBD dimer ADC (e.g., KIT-PBD ADC such as KIT-PBD1 or KIT-PBD2) is included in the pharmaceutically acceptable carrier in an effective amount sufficient to exert a therapeutically useful effect in the absence of, or with minimal or negligible, undesirable side effects on the patient treated.
[00355] Concentration of a PBD dimer ADC (e.g. , KIT-PBD dimer ADC such as KIT-PBD 1 or KIT-PBD2) in a pharmaceutical composition will depend on, e.g., the physicochemical characteristics of the antibody and/or the PBD dimer, the dosage schedule, and amount administered as well as other factors known to those of skill in the art.
[00356] In one embodiment, pharmaceutical compositions provide a dosage of about 50 mg of PBD dimer ADC per kilogram of body weight for administration over a period of time, e.g., twice daily, every day, every week, every 2 weeks, or every 3 weeks. Pharmaceutical dosage unit forms can be prepared to provide 500 mg, and in one embodiment about 400 mg of a PBD dimer ADC and/or a combination of other optional essential ingredients per dosage unit form.
[00357] In a particular embodiment, a PBD dimer ADC (e.g., KIT-PBD ADC such as KIT- PBD 1 or KIT-PBD2)described herein is administered at an effective dosage of about 50 mg of PBD dimer ADC per kilogram of body weight for administration over a period of time, e.g., twice daily, every day, every week, every 2 weeks, or every 3 weeks.
[00358] Upon mixing or addition of an PBD dimer ADC (e.g. , KIT-PBD ADC such as KIT- PBD 1 or KIT-PBD2) described herein, the resulting mixture can be a solution, suspension, emulsion or the like. The form of the resulting mixture depends upon a number of factors, including the intended mode of administration and the solubility of the compound in the selected carrier or vehicle. The effective concentration is sufficient for ameliorating the symptoms of the disease, disorder or condition treated and can be empirically determined.
[00359] In particular embodiments, pharmaceutical compositions are provided for
administration to humans and animals in unit dosage forms, such as sterile parenteral (e.g., intravenous) solutions or suspensions containing suitable quantities of PBD dimer ADCs (e.g., KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2) or pharmaceutically acceptable derivatives thereof.
[00360] Methods of preparing such dosage forms are known, or will be apparent, to those skilled in this art; for example, see, e.g., Remington's Pharmaceutical Sciences (1990) Mack Publishing Co., Easton, PA; Remington: The Science and Practice of Pharmacy, 21st ed. (2006) Lippincott Williams & Wilkins, Baltimore, MD.
[00361] Pharmaceutical compositions are also provided for administration to humans and animals in unit dosage form, such as tablets, capsules, pills, powders, granules, and oral solutions or suspensions, and oil-water emulsions containing suitable quantities of the compounds or pharmaceutically acceptable derivatives thereof. A PBD dimer ADC described herein is, in one embodiment, formulated and administered in unit-dosage forms or multiple-dosage forms. Unit- dose forms as used herein refers to physically discrete units suitable for human and animal subjects and packaged individually as is known in the art. Each unit-dose contains a
predetermined quantity of the PBD dimer ADC sufficient to produce the desired therapeutic effect, in association with the required pharmaceutical carrier, vehicle or diluent. Examples of unit-dose forms include ampoules and syringes and individually packaged tablets or capsules. Unit-dose forms can be administered in fractions or multiples thereof. A multiple-dose form is a plurality of identical unit-dosage forms packaged in a single container to be administered in segregated unit-dose form. Examples of multiple-dose forms include vials, bottles of tablets or capsules or bottles of pints or gallons. Hence, multiple dose form is a multiple of unit-doses which are not segregated in packaging.
[00362] In certain embodiments, one or more PBD dimer ADCs described herein are in a liquid pharmaceutical formulation. Liquid pharmaceutically administrable compositions can, for example, be prepared by dissolving, dispersing, or otherwise mixing an active compound as defined above and optional pharmaceutical adjuvants in a carrier, such as, for example, water, saline, aqueous dextrose, glycerol, glycols, ethanol, and the like, to thereby form a solution or suspension. If desired, the pharmaceutical composition to be administered can also contain minor amounts of nontoxic auxiliary substances such as wetting agents, emulsifying agents, solubilizing agents, and pH buffering agents and the like.
[00363] Parenteral administration, in one embodiment, is characterized by injection, either subcutaneously, intramuscularly or intravenously is also contemplated herein. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions. The injectables, solutions and emulsions also contain one or more excipients. Suitable excipients are, for example, water, saline, dextrose, glycerol or ethanol. In addition, if desired, the pharmaceutical compositions to be administered can also contain minor amounts of non-toxic auxiliary substances such as wetting or emulsifying agents, pH buffering agents, stabilizers, solubility enhancers, and other such agents. Other routes of administration may include, enteric administration, intracerebral administration, nasal administration, intraarterial administration, intracardiac administration, intraosseous infusion, intrathecal administration, and intraperitoneal administration.
[00364] Preparations for parenteral administration include sterile solutions ready for injection, sterile dry soluble products, such as lyophilized powders, ready to be combined with a solvent just prior to use, including hypodermic tablets, sterile suspensions ready for injection, sterile dry insoluble products ready to be combined with a vehicle just prior to use and sterile emulsions. The solutions can be either aqueous or nonaqueous.
[00365] If administered intravenously, suitable carriers include physiological saline or phosphate buffered saline (PBS), and solutions containing thickening and solubilizing agents, such as glucose, polyethylene glycol, and polypropylene glycol and mixtures thereof.
[00366] In specific embodiments, pharmaceutically acceptable carriers used in parenteral preparations include aqueous vehicles, nonaqueous vehicles, antimicrobial agents, isotonic agents, buffers, antioxidants, local anesthetics, suspending and dispersing agents, emulsifying agents, sequestering or chelating agents and other pharmaceutically acceptable substances.
[00367] In certain embodiments, pharmaceutical carriers also include ethyl alcohol, polyethylene glycol and propylene glycol for water miscible vehicles; and sodium hydroxide, hydrochloric acid, citric acid or lactic acid for pH adjustment.
[00368] Illustratively, intravenous or intraarterial infusion of a sterile aqueous solution containing a PBD dimer ADC can be an effective mode of administration. Another embodiment is a sterile aqueous or oily solution or suspension containing a PBD dimer ADC injected as necessary to produce the desired pharmacological effect.
[00369] The PBD dimer ADC can be suspended in micronized or other suitable form. The form of the resulting mixture depends upon a number of factors, including the intended mode of administration and the solubility of the compound in the selected carrier or vehicle. The effective concentration is sufficient for ameliorating one or more symptoms of a disorder or condition described herein and can be empirically determined. [00370] In other embodiments, the pharmaceutical formulations are lyophilized powders, which can be reconstituted for administration as solutions, emulsions and other mixtures. They can also be reconstituted and formulated as solids or gels.
[00371] In certain aspects, The lyophilized powder is prepared by dissolving a PBD dimer ADC provided herein, in a suitable solvent. In some embodiments, the lyophilized powder is sterile. The solvent can contain an excipient which improves the stability or other
pharmacological component of the powder or reconstituted solution, prepared from the powder. Excipients that can be used include, but are not limited to, dextrose, sorbital, fructose, corn syrup, xylitol, glycerin, glucose, sucrose or other suitable agent. The solvent can also contain a buffer, such as citrate, sodium or potassium phosphate or other such buffer known to those of skill in the art at, in one embodiment, about neutral pH. Subsequent sterile filtration of the solution followed by lyophilization under standard conditions known to those of skill in the art provides the desired formulation. In one embodiment, the resulting solution will be apportioned into vials for lyophilization. Each vial will contain a single dosage or multiple dosages of the compound. The lyophilized powder can be stored under appropriate conditions, such as at about 4 °C to room temperature.
[00372] Reconstitution of this lyophilized powder with water for injection provides a formulation for use in parenteral administration. For reconstitution, the lyophilized powder is added to sterile water or other suitable carrier. The precise amount depends upon the selected compound. Such amount can be empirically determined.
[00373] PBD dimer ADCs (e.g. , KIT-PBD ADC such as KIT-PBD 1 or KIT-PBD2) provided herein can be formulated for local or topical application, such as for topical application to the skin and mucous membranes, such as in the eye, in the form of gels, creams, and lotions and for application to the eye or for intracisternal or intraspinal application. Topical administration is contemplated for transdermal delivery and also for administration to the eyes or mucosa, or for inhalation therapies. Nasal solutions of the active compound alone or in combination with other pharmaceutically acceptable excipients can also be administered.
[00374] PBD dimer ADCs (e.g. , KIT-PBD ADCs such as KIT-PBD 1 or KIT-PBD2) and other compositions provided herein can also be formulated to be targeted to a particular cell or tissue, receptor, or other area of the body of the subject to be treated. Many such targeting methods are well known to those of skill in the art. All such targeting methods are contemplated herein for use in the instant compositions. For non-limiting examples of targeting methods, see, e.g., U.S. Patent Nos. 6,316,652, 6,274,552, 6,271 ,359, 6,253,872, 6,139,865, 6,131 ,570, 6,120,751 , 6,071 ,495, 6,060,082, 6,048,736, 6,039,975, 6,004,534, 5,985,307, 5,972,366, 5,900,252, 5,840,674, 5,759,542 and 5,709,874. In some embodiments, the PBD dimer ADCs described herein are targeted (or otherwise administered) to the bone marrow, such as in a patient having or at risk of having leukemia. In some embodiments, PBD dimer ADCs (e.g., KIT-PBD ADC such as KIT-PBDl or KIT-PBD2) described herein are targeted (or otherwise administered) to the gastrointestinal tract, such as in a patient having or at risk of having gastrointestinal stromal tumors. In some embodiments, PBD dimer ADCs described herein are targeted (or otherwise administered) to the lungs, such as in a patient having or at risk of lung cancer (e.g., small cell lung cancer). In some embodiments, PBD dimer ADCs (e.g., KIT-PBD ADC such as KIT-PBDl or KIT-PBD2) described herein are targeted (or otherwise administered) to the brain, such as in a patient having or at risk of having neuroblastoma. In specific embodiments, a PBD dimer ADC described herein is capable of crossing the blood-brain barrier.
[00375] Provided herein is a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions described herein, such as one or more PBD dimer ADCs provided herein. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration.
5.3 Methods and Uses
[00376] Provided herein are methods for impeding, preventing, treating and/or managing disorders or diseases such as KIT-associated disorders or diseases (e.g., cancer). Such methods comprise administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate (e.g. , KIT-PBD ADC) comprising an anti-KIT antibody described herein (e.g., humanized antibodies, and antigen-binding fragments thereof, or conjugates thereof). In certain aspects, also provided herein are methods for preventing, impeding, treating or managing one or more symptoms of a disorder or disease such as a KIT- associated disorder or disease. Non-limiting examples of such disorder or disease include cancer, mast cell or eosinophil related disorder (e.g., mastocytosis, neurofibromatosis or neuromyelitis optica), or an inflammatory disorder. [00377] As used herein, "administer" or "administration" refers to the act of injecting or otherwise physically delivering a substance (e.g. , an ADC such as a PBD dimer conjugate comprising a humanized anti-KIT antibody provided herein or an antigen-binding fragment thereof) to a subject or a patient (e.g., human) , such as by mucosal, topical, intradermal, intravenous, intramuscular delivery and/or any other method of physical delivery described herein or known in the art.
[00378] As used herein, the terms "effective amount" or "therapeutically effective amount" refer to an amount of a therapy (e.g., a humanized antibody or pharmaceutical composition provided herein) which is sufficient to reduce and/or ameliorate the severity and/or duration of a given disease and/or a symptom related thereto. These terms also encompass an amount necessary for the reduction or amelioration of the advancement or progression of a given disease, reduction or amelioration of the recurrence, development or onset of a given disease, and/or to improve or enhance the prophylactic or therapeutic effect(s) of another therapy (e.g., a therapy other than an anti-KIT antibody provided herein). In some embodiments, "effective amount" as used herein also refers to the amount of an antibody described herein to achieve a specified result (e.g. , inhibition (e.g. , partial inhibition) of a KIT biological activity of a cell, such as inhibition of cell proliferation or cell survival, or enhancement or induction of apoptosis or cell
differentiation).
[00379] As used herein, the term "in combination" in the context of the administration of other therapies refers to the use of more than one therapy. The use of the term "in combination" does not restrict the order in which therapies are administered. The therapies may be
administered, e.g., serially, sequentially, concurrently, or concomitantly.
[00380] As used herein, the terms "manage," "managing," and "management" refer to the beneficial effects that a subject derives from a therapy (e.g., a prophylactic or therapeutic agent), which does not result in a cure of a KIT-associated disease or disorder. In certain embodiments, a subject is administered one or more therapies (e.g., prophylactic or therapeutic agents, such as an antibody described herein) to "manage" a KIT-associated disease (e.g., cancer, inflammatory condition, or fibrosis), one or more symptoms thereof, so as to prevent the progression or worsening of the disease.
[00381] As used herein, the terms "impede" or "impeding" in the context of a KIT- associated disorder or disease refer to the total or partial inhibition (e.g., less than 100%, 95%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, or 5%) or blockage of the development, recurrence, onset or spread of a KIT-associated disease and/or symptom related thereto, resulting from the administration of a therapy or combination of therapies provided herein (e.g., a combination of prophylactic or therapeutic agents, such as an antibody described herein).
[00382] As used herein, the term "prophylactic agent" refers to any agent that can totally or partially inhibit the development, recurrence, onset or spread of a KIT-associated disease and/or symptom related thereto in a subject. In certain embodiments, the term "prophylactic agent" refers to an antibody described herein. In certain other embodiments, the term "prophylactic agent" refers to an agent other than an antibody described herein. Generally, a prophylactic agent is an agent which is known to be useful to or has been or is currently being used to prevent a KIT-associated disease and/or a symptom related thereto or impede the onset, development, progression and/or severity of a KIT-associated disease and/or a symptom related thereto. In specific embodiments, the prophylactic agent is a human anti-KIT antibody, such as a humanized or a fully human anti-KIT monoclonal antibody.
[00383] As used herein, the term "side effects" encompasses unwanted and adverse effects of a therapy (e.g., a prophylactic or therapeutic agent). Unwanted effects are not necessarily adverse. An adverse effect from a therapy (e.g., a prophylactic or therapeutic agent) can be harmful or uncomfortable or risky. Examples of side effects include, diarrhea, cough, gastroenteritis, wheezing, nausea, vomiting, anorexia, abdominal cramping, fever, pain, loss of body weight, dehydration, alopecia, dyspenea, insomnia, dizziness, mucositis, nerve and muscle effects, fatigue, dry mouth, and loss of appetite, rashes or swellings at the site of administration, flu-like symptoms such as fever, chills and fatigue, digestive tract problems and allergic reactions. Additional undesired effects experienced by patients are numerous and known in the art. Many are described in the Physician's Desk Reference (63rd ed., 2009).
[00384] As used herein, the terms "subject" and "patient" are used interchangeably. As used herein, in one embodiment, a subject is a mammal such as a non-primate (e.g., cows, pigs, horses, cats, dogs, goats, rabbits, rats, mice, etc.) or a primate (e.g., monkey and human), e.g., a human. In one embodiment, the subject is a mammal, such as a human, having a KIT-associated disorder or disease. In another embodiment, the subject is a mammal, such as a human, at risk of developing a KIT-associated disorder or disease. In another embodiment, the subject is a non- human primate. In a specific embodiment, the subject is an adult human subject at least 18 years old.
[00385] As used herein, the terms "therapies" and "therapy" can refer to any protocol(s), method(s), compositions, formulations, and/or agent(s) that can be used in the prevention, treatment, management, or amelioration of a condition or disorder or symptom thereof (e.g., cancer or one or more symptoms or condition associated therewith; inflammatory condition or one or more symptoms or condition associated therewith; fibrosis or one or more symptoms or condition associated therewith). In certain embodiments, the terms "therapies" and "therapy" refer to drug therapy, adjuvant therapy, radiation, surgery, biological therapy, supportive therapy, and/or other therapies useful in treatment, management, prevention, or amelioration of a condition or disorder or one or more symptoms thereof (e.g., cancer or one or more symptoms or condition associated therewith; inflammatory condition or one or more symptoms or condition associated therewith; fibrosis or one or more symptoms or condition associated therewith). In certain embodiments, the term "therapy" refers to a therapy other than an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or pharmaceutical
composition thereof. In specific embodiments, an "additional therapy" and "additional therapies" refer to a therapy other than a treatment using an anti-KIT antibody described herein or pharmaceutical composition. In a specific embodiment, a therapy includes the use of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein as an adjuvant therapy. For example, using an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein in conjunction with a drug therapy, biological therapy, surgery, and/or supportive therapy.
[00386] As used herein, the term "therapeutic agent" refers to any agent that can be used in the treatment, management or amelioration of a KIT-associated disease and/or a symptom related thereto. In certain embodiments, the term "therapeutic agent" refers to an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g. , any one of antibodies Huml-Hum20), an antigen-binding fragment thereof. In certain other embodiments, the term "therapeutic agent" refers to an agent other than a PBD dimer conjugate comprising an anti-KIT antibody described herein. In a specific embodiment, a therapeutic agent is an agent which is known to be useful for, or has been or is currently being used for the treatment, management or amelioration of a KIT-associated disease or one or more symptoms related thereto. [00387] As used herein, the terms "KIT-associated disorder" or "KIT-associated disease" are used interchangeably and refer to any disorder or disease involving KIT expression and/or KIT activity, or to any disorder or disease that is completely or partially caused by, associated with, or is the result of, KIT expression and/or activity or lack thereof. In one aspect, a KIT-associated disorder or disease can be known to one of skill in the art or can be ascertained by one of skill in the art. In a certain embodiment, a KIT-associated disease or disorder is associated with KIT expression and/or activity. For example, KIT expression and/or activity may be present in cells and/or tissue associated or related to a disease or disorder, and may or may not contribute to development and/or progression of a KIT-associated disease or disorder. As another example, KIT expression and/or activity may contribute, in combination with one or more other factors (e.g., mutation or expression and/or activity of another gene), to development and/or progression of a KIT-associated disease or disorder. In a certain embodiment, a KIT-associated disease or disorder is associated with one or more mutations of KIT.
[00388] In certain embodiments, a KIT-associated disease is fibrosis or an inflammatory disorder, e.g., asthma, arthritis, inflammatory bowel disease (IBD), such as Crohn's disease (CD) or ulcerative colitis (UC). In other embodiments, a KIT-associated disease is cancer, such as lung cancer (e.g., small cell lung cancer), leukemia, neuroblastoma, melanoma, sarcoma (e.g., Ewing's sarcoma) or gastrointestinal stromal tumor (GIST). In other embodiments, a KIT- associated disease is a mast cell or eosinophil related disorder, such as neuromyelitis optica (NMO) or NMO spectrum disorder (NMOSD), multiple sclerosis (MS), and neurofibromatosis (NF).
[00389] As used herein, the terms "treat," "treatment" and "treating" refer to the reduction or amelioration of the progression, severity, and/or duration of a KIT-associated disease (e.g., cancer, inflammatory disorder, or fibrosis) resulting from the administration of one or more therapies (including, but not limited to, the administration of one or more prophylactic or therapeutic agents, such as an antibody provided herein).
[00390] In specific embodiments, methods described herein for treating a KIT-associated disorder or disease provide for the reduction or amelioration of the progression, severity, and/or duration of a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, or fibrosis) resulting from the administration of one or more therapies (including, but not limited to, the administration of one or more prophylactic or therapeutic agents, such as an ADC, e.g., PBD dimer conjugate, comprising an anti-KIT antibody described herein). In further specific embodiments, methods described herein for treating a KIT-associated disorder or disease relate to reducing one or more symptoms of a KIT-associated disorder or disease. In specific embodiments, an ADC such as a PBD dimer conjugate provided herein comprising any one of anti-KIT antibodies Huml-Hum20, e.g., antibody Hum8 or Hum4 or Huml7 or HumlO, or an antigen-binding fragment thereof, is for use in treating or managing a KIT-associated disorder (e.g., cancer). In a particular embodiment, a KIT-associated disease or disorder being treated or managed with an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein, or an antigen-binding fragment thereof, is associated with KIT expression and/or activity, e.g., involves cells expressing KIT and/or exhibiting KIT activity, but is not caused by or the result of KIT expression or activity.
[00391] In a particular embodiment, provided herein is an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody (e.g., a humanized anti-KIT antibody), for example any one of antibodies Huml-Hum20, or Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof, for use in treating or managing a KIT-associated disorder (e.g., cancer), wherein the antibody comprises (i) a VL chain region having the amino acid sequence of SEQ ID NO: 7, 8, 9, or 10, and/or (ii) a VH chain region having the amino acid sequence of SEQ ID NO: 2, 3, 4, 5, or 6.
[00392] In another particular embodiment, provided herein is an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody, or an antigen-binding fragment thereof, for use in treating or managing a KIT-associated disorder (e.g., cancer), wherein the antibody comprises a combination of a VH domain (e.g., H1-H5, SEQ ID NOs: 2-6) and a VL domain (L1-L4, SEQ ID NOs: 7-10) selected from the group presented in Table 4.
[00393] In a particular embodiment, provided herein is an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody (e.g. , a humanized anti-KIT antibody) for example, any one of anti-KIT antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof, for use in treating or managing a KIT-associated disorder (e.g., cancer), wherein the antibody comprises (i) a VL chain region comprising the amino acid sequence of SEQ ID NO: 12 (see, e.g., Figure 2K), and/or (ii) a VH chain region comprising the consensus amino acid sequence of SEQ ID NO: 11 (see, e.g., Figure 2J). [00394] In a particular embodiment, provided herein is an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen- binding fragment thereof, for use in treating or managing a KIT-associated disorder (e.g. , cancer), wherein the antibody comprises (i) a VL chain region comprising an amino acid sequence set forth in Table 6A (e.g., L1-L4 and LL1-LL62), and/or (ii) a VH chain region comprising the amino acid sequence set forth in Table 6B (e.g., H1-H5 and HH1-HH256).
[00395] In a specific embodiment, the ADC such as a PBD dimer conjugate provided herein comprises an anti-KIT antibody used in the methods described herein is internalized by the cell to which it binds.
[00396] In certain embodiments, KIT is aberrantly (e.g., highly) expressed by cells, for example, KIT is overexpressed. In particular embodiments, KIT expression (e.g., on the cell surface) is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%), 250%), or 500% higher than KIT expression on the surface of a control cell (e.g., a cell expressing normal levels of KIT, for example, a normal, e.g., human, mast cell, stem cell, brain cell, melanoblast, or ovary cell). In particular embodiments, KIT expression yields at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 250%, or 500% higher cell surface KIT expression than the average KIT expression on the surface of a control cell population (e.g., a cell population expressing normal levels of KIT, for example, a normal, e.g., human, mast cell population, stem cell population, brain cell population, melanoblast population, or ovary cell population). In specific embodiments, such control cells can be obtained or derived from a healthy individual (e.g., healthy human). In some embodiments, KIT can be aberrantly upregulated in a particular cell type, whether or not KIT is aberrantly expressed on the cell surface. In particular embodiments, KIT signaling or activity can be aberrantly upregulated in a particular cell type, whether or not KIT is aberrantly expressed on the cell surface. In particular embodiments, KIT signaling is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 250%, or 500% higher than KIT signaling of a control cell (e.g., a cell containing normal KIT signaling, for example, a mast cell, stem cell, brain cell, melanoblast, or ovary cell). In particular embodiments, KIT signaling is at least about 10%>, 20%>, 30%>, 40%>, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 250%, or 500% higher than average KIT signaling of a control cell population (e.g. , a cell population exhibiting normal KIT signaling, for example, a normal, e.g. , human, mast cell population, stem cell population, brain cell population, melanoblast population, or ovary cell population). In certain embodiments, normal, aberrant or excessive cell signaling is caused by binding of KIT to a KIT ligand. In other embodiments, aberrant or excessive cell signaling occurs independent of binding of KIT to a KIT ligand.
[00397] In certain aspects, a KIT-associated disorder or disease can be characterized by gain- of-function KIT activity, increase in KIT activity, or overexpression of KIT. In one
embodiment, a KIT-associated disorder or disease is completely or partially caused by or is the result of gain-of-function KIT activity or expression, e.g., overexpression, of KIT. In certain embodiments, the gain-of-function KIT activity can occur independent of KIT ligand (e.g., SCF) binding KIT receptor. In particular aspects, high or overexpression of KIT in a cell refers to an expression level which is at least about 35%, 45%, 55%, or 65% more than the expression level of a reference cell known to have normal KIT expression or KIT activity or more than the average expression level of KIT in a population of cells or samples known to have normal KIT expression or KIT activity. Expression levels of KIT can be assessed by methods described herein or known to one of skill in the art (e.g., Western blotting or immunohistory chemistry). In particular embodiments, a KIT-associated disorder or disease is characterized by KIT activity which is higher than normal KIT activity and contributes to cellular transformation, neoplasia, and tumorogenesis. In particular aspects, high or increase of KIT activity in a cell refers to a KIT activity level which is at least about 35%, 45%, 55%, or 65% more than the expression level of a reference cell known to have normal KIT activity or more than the average level of KIT activity in a population of cells or samples known to have normal KIT activity. Non-limiting examples of a KIT activity includes tyrosine phosphorylation of the cytoplasmic domain of KIT, and signaling downstream of KIT, such as Stat or Akt signaling.
[00398] Non-limiting examples of disorders or KIT-associated disorders or diseases include cancers such as breast cancer, leukemia (e.g., chronic myelogenous leukemia, acute myeloid leukemia (AML), mast cell leukemia), lung cancer (e.g., small cell lung cancer), neuroblastoma, gastrointestinal stromal tumors (GIST), melanoma, colorectal cancer, sarcoma (e.g., Ewing's sarcoma), and germ cell tumors (e.g., seminoma). In a particular embodiment, a cancer which is treated or managed by the methods provided herein is characterized by a gain-of-function KIT mutation or overexpression of KIT. [00399] In a specific embodiment, a method described herein is for treating cancer (e.g., GIST, leukemia (e.g., erythroid leukemia), lung cancer (e.g., small cell lung cancer), or sarcoma (e.g., Ewing's sarcoma)), wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate (e.g. , PBD dimer conjugate comprising compound 42 or 45) comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof. In certain aspects, also provided herein are methods for preventing, treating or managing one or more symptoms of cancer, wherein said methods comprise administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti- KIT antibody described herein (e.g., a humanized anti-KIT antibody), for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof. In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating cancer described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3). In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating cancer described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
[00400] In a specific embodiment, a method described herein is for treating leukemia (e.g. , erythroid leukemia) or lung cancer (e.g., small cell lung cancer), wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising (i) an anti-KIT antibody described herein (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, Huml O, Hum8 or Hum4, or an antigen-binding fragment thereof, (ii) a PBD dimer, and optionally, a linker, such as in compound 45. In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating leukemia (e.g., erythroid leukemia) or lung cancer (e.g. , small cell lung cancer) described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3). In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating leukemia (e.g., erythroid leukemia) or lung cancer (e.g., small cell lung cancer) described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
[00401] In a specific embodiment, a method described herein is for treating sarcoma (e.g., Ewing's sarcoma) or lung cancer (e.g., small cell lung cancer), wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising (i) an anti-KIT antibody described herein (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, Huml O, Hum8 or Hum4, or an antigen-binding fragment thereof and (ii) a PBD dimer and optionally, a linker, such as in compound 42. In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating sarcoma (e.g., Ewing's sarcoma) or lung cancer (e.g. , small cell lung cancer) described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3). In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating sarcoma (e.g. , Ewing's sarcoma) or lung cancer (e.g., small cell lung cancer) described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
[00402] In a specific embodiment, a method described herein is for treating GIST, wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof. In certain aspects, also provided herein are methods for preventing, treating or managing one or more symptoms of GIST, wherein said methods comprise administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti- KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof. In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating GIST described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3). In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating GIST described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
[00403] In a specific embodiment, a method described herein is for treating lung cancer (e.g., small cell lung carcinoma), wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml 7, HumlO, Hum8 or Hum4, or an antigen- binding fragment thereof conjugated to a PBD dimer, such as in compound 42 or 45, optionally comprising a linker (e.g., reactive linker) as in compound 42 or 45. In certain aspects, also provided herein are methods for preventing, treating or managing one or more symptoms of lung cancer (e.g., small cell lung carcinoma), wherein said methods comprise administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof conjugated to a PBD such as compound 42 or 45. In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating lung cancer (e.g., small cell lung cancer) comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3). In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating lung cancer (e.g., small cell lung cancer) comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
[00404] In a specific embodiment, a method described herein is for treating melanoma, wherein said method comprises administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof. In certain aspects, also provided herein are methods for preventing, treating or managing one or more symptoms of melanoma, wherein said methods comprise administering to a subject in need thereof a therapeutically effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof. In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating melanoma described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 8 (L2), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 4 (H3). In a specific embodiment, an antibody of an ADC such as a PBD dimer conjugate provided herein for use in the methods of treating melanoma described herein comprises a VL domain comprising the amino acid sequence of SEQ ID NO: 7 (LI), and/or a VH domain comprising the amino acid sequence of SEQ ID NO: 5 (H4).
[00405] In specific embodiments, a cancer treated in accordance with the methods described herein can be any type of cancer which comprises cancer or tumor cells expressing cell surface KIT or a mutated form thereof, which can be confirmed by any histologically or cytologically method known to one of skill in the art.
[00406] In certain embodiments, a cancer is metastatic. In certain embodiments, a cancer is an advanced cancer which has spread outside the site or organ of origin, either by local invasion or metastasis.
[00407] In particular embodiments, a cancer is a recurrent cancer which has regrown, either at the initial site or at a distant site, after a response to initial therapy (e.g., after surgery to remove the tumor and adjuvant therapy following surgery). In some embodiments, a cancer is a refractory cancer which progresses even though an anti-tumor agent, such as a chemotherapeutic agent, is being administered, or has been administered, to the cancer patient. A non-limiting example of a refractory cancer is one which is refractory to a tyrosine kinase inhibitor, such as GLEEVEC® (imatinib mesylate), SUTENT® (SU1 1248 or sunitinib), IRESSA™ (gefitinib), TARCEVA® (erlotinib), NEXAVAR® (sorafenib), or VOTRIENT™ (pazopanib). In some embodiments, a cancer is a refractory cancer which progresses even though radiation or chemotherapy is being administered, or has been administered, to the cancer patient. [00408] In specific embodiments, provided herein are methods for treating a refractory cancer in a patient in need thereof comprising administering to the patient a therapeutically effective amount of an antibody described herein, wherein the refractory cancer is refractory or resistant to an anti-cancer agent such as a tyrosine kinase inhibitor (e.g. , GLEEVEC® (imatinib mesylate) or SUTENT® (SU11248 or Sunitinib)). Other non-limiting examples of tyrosine kinase inhibitors include 706 and AMNI07 (nilotinib). RADOOI, PKC412, gefitinib (IRESSA™), erlotinib
(TARCEVA®), sorafenib (NEXAVAR®), pazopanib (VOTRIENT™), axitinib, bosutinib, cediranib (RECENTIN®), SPRYCEL® (dasatinib), lapatinib (TYKERB®), lestaurtinib, neratinib, nilotinib (TASIGNA®), semaxanib, toceranib (PALLADIA™), vandetanib (ZACTIMA™), and vatalanib. In certain embodiments, the refractory cancer was initially responsive to an anticancer agent, such as a tyrosine kinase inhibitor (e.g., GLEEVEC® or SU11248 (i.e., sunitinib)), but has developed resistance the anti-cancer agent. In certain embodiments, a subject has one or more mutations in KIT that confers resistance to an anti-cancer agent such as a tyrosine kinase inhibitor.
[00409] In particular embodiments, an antibody described herein is administered to a patient who has previously received, or is currently receiving, one or more anti-cancer therapies, for example, a chemotherapeutic agent, or a tyrosine kinase inhibitor (e.g. , GLEEVEC® (imatinib mesylate), SUTENT® (SU11248 or sunitinib), IRESSA™ (gefitinib), TARCEVA® (erlotinib), NEXAVAR® (sorafenib), or VOTRIENT™ (pazopanib)) or a histone deacetylase inhibitor (e.g., vorinostat (suberoylanilide hydroxamic acid (SAHA))). In other particular embodiments, an antibody described herein is administered to a patient who is, or is suspected of being, resistant or refractory to an anti-cancer therapy, for example, a tyrosine kinase inhibitor, e.g. , GLEEVEC® (imatinib mesylate), SUTENT® (SU11248 or sunitinib), IRESSA™ (gefitinib), TARCEVA® (erlotinib), NEXAVAR® (sorafenib), or VOTRIENT™ (pazopanib).
[00410] In particular embodiments, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., any one of antibodies Huml-Hum20, or an antigen binding fragment thereof (e.g., KIT-binding fragment thereof)) is administered to a patient who has previously received, or is currently receiving, one or more anti-cancer therapies, for example, an anti-growth factor receptor antibody (e.g., anti-HER2 antibody, anti-EGFR antibody, anti- VEGFR antibody, or anti-KIT antibody), or anti-growth factor antibody (e.g., anti-EGF antibody, anti-VEGF antibody). In other particular embodiments, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is administered to a patient who is, or is suspected of being, resistant or refractory to an anti-cancer therapy, for example, an anti- growth factor receptor antibody (e.g. , anti-HER2 antibody, anti-EGFR antibody, anti-VEGFR antibody, or anti-KIT antibody) or anti-growth factor antibody (e.g., anti-EGF antibody, anti- VEGF antibody).
[00411] In a particular embodiment, a method described herein for treating or managing cancer in a subject in need thereof, can achieve at least one, two, three, four or more of the following effects due to administration of a therapeutically effective amount of an anti-KIT antibody described herein: (i) the reduction or amelioration of the severity of cancer (e.g., leukemia, lung cancer, or gastrointestinal stromal cancer) and/or one or more symptoms associated therewith; (ii) the reduction in the duration of one or more symptoms associated with a cancer (e.g., leukemia, lung cancer, or gastrointestinal stromal cancer); (iii) the prevention in the recurrence of a tumor (e.g. , lung tumor or gastrointestinal stromal tumor); (iv) the regression of a cancer (e.g., leukemia, lung cancer, or gastrointestinal stromal tumor) and/or one or more symptoms associated therewith; (v) the reduction in hospitalization of a subject; (vi) the reduction in hospitalization length; (vii) the increase in the survival of a subject; (viii) the inhibition of the progression of a cancer (e.g. , leukemia, lung cancer, or gastrointestinal stromal tumor) and/or one or more symptoms associated therewith; (ix) the enhancement or
improvement of the therapeutic effect of another therapy (e.g. , surgery, radiation, chemotherapy, or another tyrosine kinase inhibitor); (x) a reduction or elimination in the cancer cell population (e.g. , leukemia cell population, lung cancer cell population, gastrointestinal stromal tumor cell population); (xi) a reduction in the growth of a tumor or neoplasm; (xii) a decrease in tumor size (e.g., volume or diameter); (xiii) a reduction in the formation of a newly formed tumors; (xiv) eradication, removal, or control of primary, regional and/or metastatic cancer; (xv) ease in removal of a tumor by reducing tumor and/or edema-related vascularization prior to surgery; (xvi) a decrease in the number or size of metastases; (xvii) a reduction in mortality; (xviii) an increase in tumor- free survival rate of patients; (xvix) an increase in relapse-free survival; (xx) an increase in the number of patients in remission; (xxi) a decrease in hospitalization rate; (xxii) the size of the tumor is maintained and does not increase or increases by less than the increase of a tumor after administration of a standard therapy as measured by conventional methods available to one of skill in the art, such as computed tomography (CT) scan, magnetic resonance imaging (MRI), dynamic contrast-enhanced MRI (DCE-MRI), or a positron emission tomography (PET) scan; (xxiii) the prevention of the development or onset of one or more symptoms associated cancer; (xxiv) an increase in the length of remission in patients; (xxv) the reduction in the number of symptoms associated with cancer; (xxvi) an increase in symptom-free survival of cancer patients; (xxvii) a decrease in the concentration of one or more inflammatory mediators (e.g., cytokines or interleukins) in biological specimens (e.g., plasma, serum, cerebral spinal fluid, urine, or any other bio fluids) of a subject with a cancer (e.g., leukemia, lung cancer, or gastrointestinal stromal cancer); (xxviii) a decrease in circulating tumor cells (CTCs) in the blood of a subject with cancer (e.g., leukemia, lung cancer, or gastrointestinal stromal cancer); (xxix) inhibition (e.g., partial inhibition) or decrease in tumor metabolism or perfusion; and (xxx) improvement in the quality of life as assessed by methods well known in the art, e.g.,
questionnaires.
[00412] In certain aspects, provided herein are methods for killing cancer cells in an individual, wherein said method comprises administering to an individual in need thereof an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof. In certain aspects, provided herein are methods for inhibiting growth or proliferation of cancer cells in an individual, wherein said method comprises administering to an individual in need thereof an effective amount of an ADC such as a PBD dimer conjugate comprising an anti- KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof. In certain embodiments, partial inhibition of growth or proliferation of cancer cells is achieved, for example, inhibition of at least about 20% to about 55% of growth or proliferation of cancer cells.
[00413] In certain aspects, provided herein are methods for delaying tumor growth or for reducing tumor size or load in an individual in need thereof, wherein said method comprises administering to said individual an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as Huml7, HumlO, Hum8 or Hum4, or an antigen-binding fragment thereof. [00414] Other non-limiting examples of KIT-associated disorders or diseases include systemic mast cell disorders (e.g., mastocytosis), hematologic disorders, fibrosis (e.g., idiopathic pulmonary fibrosis (TPF), scleroderma, or myelofibrosis) and inflammatory conditions such as asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation.
[00415] In a particular embodiment, a method described herein for treating or managing a KIT-associated disorder, e.g., fibrosis or an inflammatory condition (e.g., asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation), in a subject in need thereof, can achieve at least one, two, three, four or more of the following effects due to administration of a therapeutically effective amount of an anti-KIT antibody described herein: (i) the reduction or amelioration of the severity of fibrosis or an inflammatory condition (e.g., asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation) and/or one or more symptoms associated therewith; (ii) the reduction in the duration of one or more symptoms associated with fibrosis or an inflammatory condition (e.g., asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation); (iii) the prevention in the recurrence of fibrosis or an inflammatory condition (e.g., asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation); (iv) the reduction in hospitalization of a subject; (v) the reduction in hospitalization length; (vi) the inhibition (e.g. , partial inhibition) of the progression of fibrosis or an inflammatory condition (e.g. , asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation) and/or one or more symptoms associated therewith; (vii) the enhancement or improvement of the therapeutic effect of another therapy (e.g. , anti-inflammatory therapy such as steroids); (viii) an increase in the number of patients in remission (i.e., a time period characterized by no or minimal symptoms associated with the inflammatory condition); (ix) an increase in the length of remission in patients; (x) a decrease in hospitalization rate; (xi) the reduction in the number of symptoms associated with fibrosis or an inflammatory condition (e.g. , asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation); (xii) a decrease in the concentration of one or more inflammatory mediators (e.g., cytokines or interleukins) in biological specimens (e.g. , plasma, serum, cerebral spinal fluid, urine, or any other biofluids) of a subject with fibrosis or an inflammatory condition (e.g., asthma, rheumatoid arthritis, inflammatory bowel disease, and allergic inflammation); and (xiii) improvement in the quality of life as assessed by methods well known in the art, e.g., questionnaires. [00416] In certain embodiments, an anti-KIT antibody described herein may be administered by any suitable method to a subject in need thereof. Non- limiting examples of administration methods include mucosal, intradermal, intravenous, intratumoral, subcutaneous, intramuscular delivery and/or any other method of physical delivery described herein or known in the art. In one embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody or a pharmaceutical composition thereof is administered systemically (e.g., parenterally) to a subject in need thereof. In another embodiment, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody or a pharmaceutical composition thereof is administered locally (e.g. , intratumorally) to a subject in need thereof. Each dose may or may not be administered by an identical route of administration. In some embodiments, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein can be administered via multiple routes of administration simultaneously or subsequently to other doses of the same or a different ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein.
[00417] In one aspect, provided herein are ADCs, such as PBD dimer conjugates, comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof, useful in therapeutic methods to prevent, manage or treat an eosinophil or mast cell related disorder, such as an eosinophil or mast cell related disorder of the central nervous system or nervous system. Non-limiting examples of such disorders include neuromyelitis optica (NMO) or NMO spectrum disorder (NMOSD), multiple sclerosis (MS), and neurofibromatosis (NF).
[00418] In one aspect, provided herein is a method of protecting against, treating, or managing an eosinophil or mast cell related disorder of the central nervous system or nervous system in a subject, comprising administering to a subject in need thereof a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
[00419] In another aspect, provided herein is a method of protecting against, treating, or managing neuromyelitis optica (NMO) in a subject, comprising administering to a subject in need thereof a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
[00420] In a particular aspect, provided herein is a method of protecting against, treating, or managing a NMO spectrum disorder in a subject, comprising administering to a subject in need thereof a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g. , human KIT, such as a D4 domain of human KIT.
[00421] In another aspect, provided herein is a method of protecting against, treating, or managing multiple sclerosis (MS) in a subject, comprising administering to a subject in need thereof a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g. , human KIT, such as a D4 domain of human KIT.
[00422] In a specific aspect, provided herein is a method of protecting against, treating, or managing neurofibromatosis (NF) in a subject, comprising administering to a subject in need thereof a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g. , human KIT, such as a D4 domain of human KIT.
[00423] In one aspect, provided herein is a method of inhibiting growth of neurofibromas in a subject, comprising administering to a subject diagnosed with NF a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
[00424] In another aspect, provided herein is a method of reducing inflammation, for example, inflammation of the nervous system, e.g., central nervous system, in a subject, comprising administering to a subject diagnosed with a mast cell related disorder of the central nervous system or nervous system a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
[00425] In a particular aspect, provided herein is a method of inhibiting mast cell activation in a subject, comprising administering to a subject diagnosed with a mast cell related disorder of the central nervous system or nervous system a therapeutically effective amount of an ADC, such as a PBD dimer conjugate, provided herein comprising an anti-KIT antibody (e.g. , any one of antibodies Huml-Hum20) or antigen binding fragment thereof which specifically binds to KIT, e.g., human KIT, such as a D4 domain of human KIT.
[00426] In a specific aspect, the mast cell related disorder of the central nervous system or nervous system is NMO, NMO spectrum disorder, multiple sclerosis (MS), or NF. In a particular aspect, the type of NF is NF1 , NF2, or Schwannomatosis.
[00427] In one aspect, the anti-KIT antibody of an ADC, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), described herein for use in the methods provided herein is a bivalent monospecific antibody. In certain aspects, the anti-KIT antibody antibody of an ADC, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), described herein for use in the methods provided herein is a humanized antibody. In one aspect, the anti-KIT antibody of an ADC, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), described herein for use in the methods provided herein is not a bispecific antibody.
[00428] In particular aspects, the anti-KIT antibody of an ADC, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), described herein for use in the methods provided herein comprises a light chain variable region ("VL") comprising VL CDRs 1-3 comprising SEQ ID NOs: 19-21 , respectively, and a heavy chain variable region ("VH") comprising VH CDRs 1- 3 comprising SEQ ID NOs: 16-18, respectively.
[00429] As used herein, the term "mast cell related disorder" or "mast cell related disorders" refers to disorders where mast cell activity contributes to the pathology and/or mast cells are found in abnormal amounts, such as above-normal amounts or below-normal amounts, in various parts of the body. For example, mast cell related disorders can exhibit accumulation of pathological mast cells in potentially any or all organs and tissues and/or aberrant release of one or more mast cell mediators such as inflammatory mediators. Non- limiting examples of inflammatory mediators released by mast cells include any of: (i) granule-associated mediators, including histamine, serotonin (5-hydroxytryptamine), and a variety of proteases and peptidases; (ii) eicosanoids such as prostaglandin D2 (PGD2) and leukotriene C4 (LTC4); and (iii) cytokines including interleukin-2 (IL-2), IL-3, IL-4, IL-5, IL-6, IL-10, IL-13, granulocyte-macrophage colony-stimulating factor (GM-CSF), and tumor necrosis factor a (TNFa), and chemokines including CCL-2, CCL-3, CCL-5, and CXCL8.
[00430] In a specific aspect, a mast cell related disorder is a mast cell related disorder of the central nervous system or nervous system, such as neuromyelitis optica (NMO), neuromyelitis optica spectrum disorder (NMOSD), multiple sclerosis (MS), or neurofibromatosis (e.g., NF type 1 (NF1), NF type 2 (NF2), or Schwannomatosis).
[00431] Multiple sclerosis (MS), is a chronic inflammatory demyelinating disorder of the central nervous system (brain and spinal cord) involving episodes where white matter within the brain or spinal cord becomes inflamed and then damaged by the individual's own immune system. These inflamed areas become scarred within the brain and spinal cord. The damage disrupts the ability of parts of the nervous system to communicate, resulting in a variety of symptoms, including physical, mental, and/or psychiatric problems. Forms of MS include, but are not limited to, relapsing forms, with symptoms either occurring in isolated attacks, and progressive forms, with symptoms building up over time. Symptoms of MS can manifest as any neurological symptom or sign such as autonomic, visual, motor, and sensory problems. Non- limiting examples of symptoms of MS include loss of sensitivity or changes in sensation such as tingling, pins and needles or numbness, muscle weakness, very pronounced reflexes, muscle spasms, or difficulty in moving, difficulties with coordination and balance (ataxia), problems with speech or swallowing, visual problems (nystagmus, optic neuritis or double vision), fatigue, acute or chronic pain, bladder and bowel difficulties, emotional problems such as depression or unstable mood, Uhthoff s phenomenon (a worsening of symptoms due to exposure to higher than usual temperatures), and Lhermitte's sign (an electrical sensation that runs down the back when bending the neck). In specific aspects, provided herein are methods for protecting against, treating, alleviating, or managing one or more of these symptoms of MS by administering to a subject in need thereof a therapeutically effective amount of an ADC provided herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen-binding fragment thereof.
[00432] Other non-limiting examples of mast cell related disorders include, for example, anaphylaxis, atopic disease, and mast cell activation syndrome. [00433] Eosinophils are white blood cells activated by the lymphocytes of the adaptive immune response and are important in defense against parasitic infections. The level of eosinophils in the blood is normally low, and it can increase markedly in certain situations, such as atopy, which can result in eosinophilia, an abnormally large number of eosinophils in the blood.
[00434] As used herein, the term "eosinophil related disorder" or "eosinophil related disorders" refers to disorders that arise when eosinophils are found in abnormal amounts, such as above -normal amounts or below-normal amounts, in various parts of the body. For example, when the body produces too many eosinophils, they can cause chronic inflammation resulting in tissue damage. In certain aspects, an eosinophil disorder may be associated with an abnormal amount of eosinophil in a tissue for a prolonged period of time in response to a trigger. For example, higher amounts of eosinophils may be produced in response to a trigger, such as an infection or allergen, but the high amounts of eosinophils do not decrease at a normal rate and thus are maintained at a high amount for a longer period of time than expected.
[00435] Eosinophil related disorders can be diagnosed according to the location where the levels of eosinophils are elevated. Non-limiting examples of eosinophil related disorders include allergic disorders, infectious diseases, blood disorders, immunologic disorders and reactions, endocrine disorders, pulmonary conditions, gastrointestinal disorders, neurologic disorders, rheumatologic disorders, cardiac conditions, and renal diseases. In certain aspects, eosinophilia is an eosinophil related disorder characterized by a peripheral blood eosinophil count greater than a normal level, for example, greater than 450/ μί. Eosinophilia can be induced or triggered by a variety of conditions, such as allergy or infection. In particular aspects, elevated levels of eosinophils are observed locally, for example, in the lung, heart, spinal cord, or brain.
[00436] Non-limiting examples of neurologic disorders involving eosinophils include central nervous system infections, ventriculoperitoneal shunts, and drug-induced adverse reactions. In certain aspects, an increase in eosinophil count or activity can be detected in cerebrospinal fluid (CSF) or in other samples obtained from tissue of fluid of the central nervous system.
[00437] Non-limiting examples of eosinophil or mast cell related indications include upper airway diseases such as allergic rhinitis and sinusitis, foreign body aspiration, glottic stenosis, tracheal stenosis, laryngotracheomalacia, vascular rings, chronic obstructive pulmonary disease (COPD), and congestive heart failure, eosinophilic bronchitis, polychondritis, sarcoidosis, papillomatosis, arthritis (e,g., rheumatoid arthritis) and Wegener's granulomatosis.
[00438] Neuromyelitis optica (NMO), or Devic's disease, is an autoimmune inflammatory disorder of the central nervous system that predominantly affects the optic nerves and spinal cord, and also the brain in some cases. NMO can lead to paralysis and blindness. A majority of patients with NMO are seropositive for immunoglobulin autoantibodies (AQP4-IgG or NMO- IgG) against aquaporin-4 (AQP4), a water channel widely expressed in optic nerves, spinal cord, and periventricular regions. A small percentage of NMO patients are NMO-IgG negative.
[00439] NMO spectrum disorders (NMOSD) refer to a variety of disorders related to NMO but may not quite meet the clinical diagnostic criteria for definite NMO. Non-limiting examples of disorders that are typically included in this classification of NMO spectrum disorders include NMO-IgG seropositive limited forms of NMO (e.g., single or recurrent longitudinally extensive transverse myelitis (LETM) [for example, >3 vertebral segment spinal cord lesions seen on MRI), recurrent or simultaneous bilateral optic neuritis (ON)], Asian opticospinal MS (OSMS), optic neuritis or LETM associated with systemic autoimmune disease, and optic neuritis or myelitis associated with brain lesions typical of NMO (e.g., hypothalamic or brainstem lesions) (see, e.g., Oh et ah, Neurology Research International, vol. 2012, Article ID 460825, 13 pages, 2012).
[00440] In particular aspects, diagnosis criteria for NMO include, but are not limited to, the presence of myelitis and optic neuritis, and any two of the following: (i) extended myelitis on spinal cord MRI, (ii) normal brain MRI at onset, and (iii) positive anti-AQP4 antibodies (see, e.g., Collongues et al, Ther. Adv. Neurol. Disord., 2011, 4: 111-121).
[00441] In particular aspects, provided herein are methods for alleviating one or more symptoms (e.g., myelitis) of NMO in a subject, comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof. In a specific aspect, provided herein is a method for alleviating one or more symptoms of NMO spectrum disorder (NMOSD) in a subject, comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT- PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml- Hum20) or antigen-binding fragment thereof. [00442] Non-limiting examples of symptoms of NMO or NMOSD include acute optic neuritis (e.g., bilateral), transverse myelitis (e.g., longitudinally extensive), unilateral or bilateral loss of visual acuity, ocular pain, severe paraplegia, asymmetric sensory level, bladder dysfunction, paroxysmal tonic spasms of the trunk and limbs, and Lhermitte's phenomenon. In certain aspects, rostral extension of cervical cord lesions into the cervicomedullary junction can cause symptoms such as acute respiratory decompensation, nausea, intractable vomiting, and hiccups. In some aspects, hypothalamic-pituitary axis dysfunction associated with NMO can manifest as hypersomnolence, hyponatremia, hypothermia, hypothyroidism, and hyperprolactinemia. In addition, confusion, abrupt changes in level of consciousness, cortical blindness, and imaging findings suggestive of posterior reversible encephalopathy syndrome (PRES) also can be associated with NMO.
[00443] In particular aspects, methods described herein for preventing, treating or managing NMO or NMO spectrum disorder or for alleviating one or more symptoms of NMO or NMO spectrum disorder can achieve one or more of the following:
(i) reduction in pain in the eye;
(ii) improved vision;
(iii) inhibition of vision loss or inhibition of further vision loss;
(iv) reduction in weakness or numbness in the arm or leg;
(v) inhibition of further weakness or numbness in the arm or leg;
(vi) improvement in bladder and/or bowel control;
(vii) reduction in sensory disturbances;
(viii) reduction in, or inhibition of, paralysis.
[00444] In certain aspects, a patient with NMO has recurring episodes/attacks wherein one or more symptoms of NMO manifest for a period of time and then subside. In certain aspects, a patient with NMO may be affected by only one episode. In certain aspects, a patient with NMO may be affected by more than one episodes (e.g., at least 2, 3, 4, or 5) over a period of time (e.g., at least 1 year, 2 years, 3 years, 4, years, 5, years, 10 years, 15 years, 20 years, 25 years, 30 years or more). In certain cases, ambulatory difficulties and/or residual visual deficits are observed in NMO patients following an episode. [00445] Therefore, in certain aspects, provided herein are methods of reducing the number of episodes that manifest in a patient with NMO, comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof. In some aspects, provided herein are methods of reducing the duration of an episode that manifests in a patient with NMO, comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof. In a particular aspect, provided herein are methods of increase the period of time between episodes in a patient with NMO, comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
[00446] Neurofibromatosis (NF) is a genetic disorder of the nervous system that primarily affects the development and growth of neural (nerve) tissues, and that causes tumors called neurofibromas to grow along nerves in the body. Although NF generally is an inherited disorder, new cases can arise spontaneously through gene mutation. NF is commonly diagnosed in childhood, approximately around 3-16 years of age, and sometimes in infancy (in children with severe cases).
[00447] Non-limiting types of NF include NF type 1 (NF1), NF type 2 (NF2), and
Schwannomatosis. NF1 is also known as von Recklinghausen disease. Phenotypic
manifestations of NF1 include presence of light brown skin spots at birth or during childhood, neurofibromas (tumors that grow along nerves under the skin), plexiform neurofibromas (tumors involving multiple nerves), spinal cord and optic nerve tumors, and learning disabilities. In certain aspects, an individual affected by NF1 may have a greater probability of developing gastrointestinal stromal tumor (GIST) than the general population.
[00448] NF2 is an autosomal dominant genetic disorder associated with neurologic, ophthalmologic, and cutaneous abnormalities. Non-limiting examples of NF2 symptoms include hearing loss, tinnitus, visual impairment, imbalance, and painful skin lesions. In certain aspects, skull-base tumors (including vestibular schwannomas (VS) and meningiomas) in NF2 patients because they can lead to lower cranial nerve dysfunction and death. [00449] Diagnosis of NF2 can be established by the presence of bilateral vestibular schwannoma (VS) or unilateral VS in conjunction with the presence of NF2-associated tumors (e.g., meningiomas, schwannomas, ependymomas, glioma, or neurofibroma), posterior cataracts, or a family history of other NF2-related tumors. In addition to the morbidity associated with auditory and vestibular deficits, patients may experience other neurologic dysfunction related to VS growth (e.g., due to compression of other cranial nerves).
[00450] Schwannomatosis shares many features with the better-known forms of NF. Multiple schwannomas, or tumors of nerve sheaths, are seen in schwannomatosis, but not the
characteristic vestibular (ear nerve) tumors seen in NF2. In certain aspects, patients with schwannomatosis develop tumors on the sheaths, or coverings, of their nerves (see, e.g., MacCollin et al. , Neurology, 2005, 64: 1838-1845).
[00451] Also provided herein are methods of alleviating one or more symptoms of NF (e.g., NF1, NF2 or Schwannomatosis) in a subject, comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT- PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml-Hum20) or antigen- binding fragment thereof.
[00452] In particular aspects, provided herein is a method of treating neurofibromas in a subject diagnosed with NF (e.g., NF1, NF2 or Schwannomatosis), comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT- PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml- Hum20) or antigen-binding fragment thereof.
[00453] In specific aspects, provided herein is a method of inhibiting growth of neurofibromas in a subject diagnosed with NF (e.g., NF1, NF2 or Schwannomatosis), comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT- PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml- Hum20) or antigen-binding fragment thereof.
[00454] In specific aspects, provided herein is a method of protecting against neurofibromas in a subject diagnosed with NF (e.g., NF1, NF2 or Schwannomatosis), comprising administering to a subject in need thereof an ADC described herein, such as a PBD dimer conjugate (e.g., KIT- PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml- Hum20) or antigen-binding fragment thereof. [00455] In certain aspect, an anti-KIT antibody or antigen binding fragment thereof described herein or a pharmaceutical composition thereof is administered to a subject in need thereof in accordance with the methods provided herein for treating NF (e.g., NF1 , NF2 or
Schwannomatosis) provided herein at a dosage and a frequency of administration that achieves one or more of the following: reduces or ameliorates the severity of NF and/or a symptom associated therewith in a subject with NF; reduces the number symptoms and/or the duration of a symptom(s) associated with NF in a subject with NF; prevents the onset, progression or recurrence of one or more symptoms associated with NF in a subject with NF; prevents the recurrence of a tumor associated with NF; reduces hearing loss, tinnitus, visual impairment, imbalance, and/or painful skin lesions associated with NF in a subject with NF; improves hearing, hearing function and/or word recognition in a subject with NF; enhances or improves the therapeutic effect of another therapy in a subject with NF or an animal model; reduction or inhibition in the growth of a tumor or neoplasm associated with NF and/or decrease in the tumor size (e.g., volume or diameter) of a tumor associated with NF (e.g., neurofibromas, plexiform neurofibromas, meningiomas, schwannomas, gliomas, or ependymomas) in a subject with NF or an animal model; improvement in neural function, e.g., hearing, balance, tinnitus, or vision; stabilization or reduction of peritumoral inflammation or edema in a subject; and/or
improvement in quality of life as assessed by methods well known in the art, e.g., questionnaires.
[00456] In a certain aspect, an ADC described herein, such as a PBD dimer conjugate (e.g., KIT-PBD1 or KIT-PBD2), comprising an anti-KIT antibody (e.g., any one of antibodies Huml- Hum20) or antigen-binding fragment thereof or a pharmaceutical composition thereof is administered to a subject in need thereof in accordance with the methods provided herein at a dosage and a frequency of administration that achieves one or more of the following in a subject diagnosed with NF, NMO or NMO spectrum disorder: reduction in the number and/or activity of eosinophils, reduction in mast cell proliferation, reduction in mast cell number or amount, inhibition or reduction in mast cell activity, and promotion of mast cell death.
[00457] In specific aspects, methods provided herein can reduce the severity of one or more symptoms of a condition or disorder described herein in a subject by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, or 80%.
[00458] When a disease, or a symptom thereof, is being treated, administration of the substance typically occurs after the onset of the disease or symptoms thereof. When a disease, or symptoms thereof, are being prevented, administration of the substance typically occurs before the onset of the disease or symptoms thereof. In certain embodiments, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is administered
prophylactically or therapeutically to a subject. An ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein can be prophylactically or therapeutically administered to a subject so as to prevent, lessen or ameliorate a KIT-associated disorder or disease (e.g. , cancer, inflammatory condition, fibrosis) or symptom thereof.
[00459] The dosage and frequency of administration of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or a pharmaceutical composition thereof is administered to a subject in need thereof in accordance with the methods for treating a KIT-associated disorder or disease provided herein will be efficacious while minimizing side effects. The exact dosage of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein to be administered to a particular subject or a pharmaceutical composition thereof can be determined by a practitioner, in light of factors related to the subject that requires treatment. Factors which can be taken into account include the severity of the disease state, general health of the subject, age, and weight of the subject, diet, time and frequency of administration, combination(s) with other therapeutic agents or drugs, reaction sensitivities, and tolerance/response to therapy. The dosage and frequency of administration of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or a pharmaceutical composition thereof can be adjusted over time to provide sufficient levels of the ADC such as a PBD dimer conjugate comprising an anti-KIT antibody or to maintain the desired effect.
[00460] In one embodiment, for ADCs such as PBD dimer conjugates comprising anti-KIT antibodies described herein, the dosage administered to a patient, to manage a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis) is typically about 50 mg/kg of the patient's body weight. Generally, human antibodies have a longer half-life within the human body than antibodies from other species due to the immune response to the foreign polypeptides. Thus, lower dosages of human antibodies and less frequent administration is often possible. Further, the dosage and frequency of administration of the antibodies described herein can be reduced by enhancing uptake and tissue penetration of the antibodies by modifications such as, for example, lipidation. [00461] In one embodiment, approximately 50 mg/kg of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is administered to manage a KIT- associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis).
[00462] In specific embodiments, an "effective amount" of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein refers to an amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein which is sufficient to achieve at least one, two, three, four or more of the following effects: (i) the reduction or amelioration of the severity of a KIT-associated disorder or disease (e.g. , cancer, inflammatory condition, fibrosis) and/or one or more symptoms associated therewith; (ii) the reduction in the duration of one or more symptoms associated with a KIT-associated disorder or disease (e.g. , cancer, inflammatory condition, fibrosis); (iii) the prevention in the recurrence of a tumor (e.g., gastrointestinal stromal tumor); (iv) the regression of a KIT-associated disorder or disease (e.g. , cancer, inflammatory condition, fibrosis) and/or one or more symptoms associated therewith; (v) the reduction in hospitalization of a subject; (vi) the reduction in hospitalization length; (vii) the increase in the survival of a subject; (viii) the inhibition (e.g., partial inhibition) of the progression of a KIT-associated disorder or disease (e.g. , cancer, inflammatory condition, fibrosis) and/or one or more symptoms associated therewith; (ix) the enhancement or
improvement of the therapeutic effect of another therapy; (x) a reduction or elimination in the cancer cell population (e.g. , leukemia cell population, lung cancer cell population,
gastrointestinal stromal cancer cell population); (xi) a reduction in the growth of a tumor or neoplasm; (xii) a decrease in tumor size (e.g., volume or diameter); (xiii) a reduction in the formation of a newly formed tumors; (xiv) eradication, removal, or control of primary, regional and/or metastatic cancer; (xv) ease in removal of a tumor by reducing tumor and/or edema- related vascularization prior to surgery; (xvi) a decrease in the number or size of metastases; (xvii) a reduction in mortality; (xviii) an increase in tumor-free survival rate of patients; (xvix) an increase in relapse-free survival; (xx) an increase in the number of patients in remission; (xxi) a decrease in hospitalization rate; (xxii) the size of the tumor is maintained and does not increase or increases by less than the increase of a tumor after administration of a standard therapy as measured by conventional methods available to one of skill in the art, such as computed tomography (CT) scan, magnetic resonance imaging (MRI), dynamic contrast-enhanced MRI (DCE-MRI), or a positron emission tomography (PET) scan; (xxiii) the prevention of the development or onset of one or more symptoms associated cancer; (xxiv) an increase in the length of remission in patients; (xxv) the reduction in the number of symptoms associated with cancer; (xxvi) an increase in symptom-free survival of cancer patients; (xxvii) a decrease in the concentration of one or more inflammatory mediators (e.g. , cytokines or interleukins) in biological specimens (e.g., plasma, serum, cerebral spinal fluid, urine, or any other bio fluids) of a subject with a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis); (xxviii) a decrease in circulating tumor cells (CTCs) in the blood of a subject with cancer; (xxix) inhibition (e.g., partial inhibition) or decrease in tumor metabolism or perfusion; and (xxx) improvement in the quality of life as assessed by methods well known in the art, e.g. , questionnaires. In some embodiments, "effective amount" as used herein also refers to the amount of an antibody described herein to achieve a specified result (e.g., inhibition of one or more KIT biological activities of a cell, such as inhibition of cell proliferation).
[00463] In some embodiments, a single dose of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein is administered one or more times to a patient to impede, prevent, manage, treat and/or ameliorate a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis).
[00464] In particular embodiments, an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody or pharmaceutical composition thereof is administered to a subject in accordance with the methods for treating a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis) presented herein in cycles, wherein the anti-KIT antibody or pharmaceutical composition is administered for a period of time, followed by a period of rest (i.e., the anti-KIT antibody or pharmaceutical composition is not administered for a period of time).
[00465] Also, presented herein are combination therapies for the treatment of a KIT- associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis) which involve the administration of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT-binding fragment thereof), in combination with one or more additional therapies (e.g., chemotherapeutic agent, tyrosine kinase inhibitor, PGP inhibitors, HSP-90 inhibitors, proteosome inhibitors, or histone deacetylase inhibitor) to a subject in need thereof. In a specific embodiment, presented herein are combination therapies for the treatment of a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis) which involve the
administration of an amount (e.g. , a therapeutically effective amount or a sub-optimal amount) of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein in combination with an amount (e.g., a therapeutically effective amount or a sub-optimal amount) of another therapy (e.g., chemotherapeutic agent, tyrosine kinase inhibitor, or histone deacetylase inhibitor) to a subject in need thereof.
[00466] In combination therapies, one or more ADCs such as PBD dimer conjugates comprising anti-KIT antibodies provided herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT-binding fragment thereof), can be administered prior to, concurrently with, or subsequent to the administration of one or more additional therapies (e.g., agents, surgery, or radiation) for use in treating, managing, and/or ameoliorating a KIT- associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis). The use of the term "in combination" does not restrict the order in which one or more ADC such as a PBD dimer conjugates and one or more additional therapies are administered to a subject. In specific embodiments, the therapies can be administered serially or sequentially.
[00467] In specific embodiments, one or more ACDs such as PBD dimer conjugates comprising anti-KIT antibodies provided herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT-binding fragment thereof), can be administered prior to, concurrently with, or subsequent to the administration of one or more additional therapies such as anticancer agents, for example, tyrosine kinase inhibitors (e.g., imatinib myselyate (Gleevec®) or sunitinib (SUTENT), or histone deacetylase inhibitors (e.g., vorinostat
(suberoylanilide hydroxamic acid (SAHA))), for treating, managing, and/or ameoliorating a KIT- associated disorder or disease (e.g., cancer, for example, GIST, melanoma, or lung cancer).
[00468] In another specific embodiment, presented herein are combination therapies for the treatment of a KIT-associated disorder or disease (e.g., cancer, inflammatory condition, fibrosis) which involve the administration of an amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT-binding fragment thereof), in combination with an amount of another therapy (e.g., chemotherapeutic agent, tyrosine kinase inhibitor, or histone deacetylase inhibitor) to a subject in need thereof. In a specific embodiment, the combination therapies result in a synergistic effect. In certain embodiments, the combination therapies result in an additive effect.
[00469] In a specific embodiment, presented herein are combination therapies for the treatment of cancer which involve the administration of an amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein in combination with an amount of another therapy (e.g., surgery, radiation, stem cell transplantation, or chemotherapy) to a subject in need thereof. In a specific embodiment, the combination therapies result in a synergistic effect. In another specific embodiment, the combination therapies result in an additive effect.
[00470] In a specific embodiment, presented herein are combination therapies for the treatment of an inflammatory condition which involve the administration of an amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein in combination with an amount of another therapy (e.g., anti-inflammatory therapy, for example, steroid therapy) to a subject in need thereof. In a specific embodiment, the combination therapies result in a synergistic effect. In another specific embodiment, the combination therapies result in an additive effect.
[00471] Non-limiting examples of another therapy for use in combination with antibodies described herein include, another anti-KIT antibody that immunospecifically binds to a different epitope of KIT, one or more other antibodies (e.g., anti-HER2 antibody, anti-EGFR antibody, anti-VEGF antibody), anti-inflammatory therapy, chemotherapy (e.g., microtubule disassembly blocker, antimetabolite, topisomerase inhibitor, and DNA crosslinker or damaging agent), radiation, surgery, PGP inhibitors (e.g., cyclosporine A, Verapamil), HSP-90 inhibitors (e.g., 17- AAG, STA-9090), proteosome inhibitors (e.g., Bortezomib), and tyrosine kinase inhibitors (e.g., imatinib mesylate (GLEEVEC®), sunitinib (SUTENT® or SU1 1248), gefitinib (IRESSA™), erlotinib (TARCEVA®), sorafenib (NEXAVAR®), pazopanib (VOTRIENT™), axitinib, bosutinib, cediranib (RECENTIN®), SPRYCEL® (dasatinib), lapatinib (TYKERB®), lestaurtinib, neratinib, nilotinib (TASIGNA®), semaxanib, toceranib (PALLADIA™), vandetanib (ZACTIMA™), and vatalanib). In a specific embodiment, another therapy for use in combination with antibodies described herein is imatinib mesylate.
[00472] Other non-limiting examples of another therapy for use in combination with an ADCs such as PBD dimer conjugates comprising anti-KIT antibodies described herein (e.g. , a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT -binding fragment thereof), include a histone deacetylase inhibitor, such as vorinostat (suberoylanilide hydroxamic acid (SAHA)) or a compound having the chemical formula (i), (ii), or (iii) as set forth below. In a specific embodiment, provided herein is a method for treating cancer (e.g. , GIST or lung cancer) comprising (i) administering an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT-binding fragment thereof); and (ii) a histone deacetylase inhibitor, for example, vorinostat (suberoylanilide hydroxamic acid (SAHA)) or a compound having the chemical formula (i), (ii), or (iii) as set forth below.
[00473] In one embodiment, provided herein for use in the methods described herein in combination with ADCs such PBD dimer conjugates comprising anti-KIT antibodies are compounds of Formula (i)
Figure imgf000172_0001
Formula (i) or a pharmaceutically acceptable salt, hydrate, or solvate thereof, wherein
Ri is hydroxylamino;
each of R2 and R3 are independently the same as or different from each other, substituted or unsubstituted, branched or unbranched, and are hydrogen, hydroxyl, alkyl, alkenyl, cycloalkyl, aryl, alkyloxy, aryloxy, arylalkyloxy or pyridine; or R2 and R3 are bonded together to form a piperidine; and
n is an integer from 5 to 7. [00474] In one embodiment, R2 is hydrogen atom and R3 is substituted or unsubstituted phenyl. In a certain embodiment, R3 is phenyl substituted with methyl, cyano, nitro,
trifluoromethyl, amino, aminocarbonyl, methylcyano, chloro, fluoro, bromo, iodo, 2,3-difiuoro, 2,4-difiuoro, 2,5-difiuoro, 3,4-difluoro, 3,5-difluoro, 2,6-difluoro, 1,2,3-trifluoro, 2,3,6-trifluoro, 2,4,6-trifluoro, 3,4,5-trifluoro, 2,3,5,6-tetrafluoro, 2,3,4,5,6-pentafluoro, azido, hexyl, t-butyl, phenyl, carboxyl, hydroxyl, methoxy, phenyloxy, benzyloxy, phenylaminooxy,
phenylaminocarbonyl, methoxycarbonyl, methylaminocarbonyl, dimethylamino,
dimethylaminocarbonyl, or hydroxylaminocarbonyl. In another embodiment, R3 is unsubstituted phenyl. In a further embodiment, n is 6.
[00475] In one embodiment, provided herein for use in the methods described herein in combination with ADCs such as PBD dimer conjugates comprising anti-KIT antibodies are compounds of Formula (ii)
Figure imgf000173_0001
Formula (ii)
or a pharmaceutically acceptable salt, or solvate thereof, wherein n is an integer from 5 to 8. In one embodiment n is 6.
[00476] In one embodiment, provided herein for use in the methods described herein in combination with ADCs such as PBD dimer conjugates comprising anti-KIT antibodies is a compound of Formula (iii) (SAHA
Figure imgf000173_0002
Formula (iii) (SAHA)
or a pharmaceutically acceptable salt, hydrate or solvate thereof.
[00477] Compounds of Formulae i-iii can be synthesized according to the methods described in U.S. Reissued Patent No. RE38,506 and U.S. Patent No. 6,087,367, each of which is herewith incorporated by reference in its entirety. [00478] In one embodiment, provided herein for use in the methods described herein in combination with ADCs such as PBD dimer conjugates comprising anti-KIT antibodies is a Form I polymorph of SAHA characterized by an X-ray diffraction pattern substantially similar to that set forth in Figure 13A of U.S. Patent No. 7,456,219, which is herewith incorporated by reference in its entirety. In one embodiment the Form I polymorph of SAHA is characterized by an X-ray diffraction pattern including characteristic peaks at about 9.0, 9.4, 17.5, 19.4, 20.0, 24.0, 24.4, 24.8, 25.0, 28.0, and 43.3 degrees 2Θ, as measured with a Siemens D500 Automated Powder Diffractometer (range: 4-40 degrees 2Θ ; source: Cu; λ=1.54 Angstrom, 50kV, 40mA).
[00479] In a certain embodiment, the Form I polymorph of SAHA is characterized by a Differential Scanning Calorimetry (DSC) thermogram having a single maximum value at about 164.4±2.0°C, as measured by a Perkins Elmer DSC 6 Instrument at a heating rate of 10°C/min from 50°C to at least 30°C above the observed melting temperature.
[00480] The Form I polymorph of SAHA can be synthesized according to the methods described in U.S. Patent No. 7,456,219.
[00481] In one embodiment, provided herein is a crystalline composition comprising Lysine and SAHA characterized by an X-ray diffraction pattern substantially similar to that set forth in Figure 1 of International Patent Application Publication No. WO2008/042146, which is herewith incorporated by reference in its entirety. In another embodiment, the crystalline composition is characterized by an X-ray diffraction pattern including characteristic peaks at about 6.8, 20.1 and 23.2 degrees 2Θ, as measured with a PANanalytical X'Pert Pro X-ray powder diffractometer (range: 2-40 degrees 2Θ; source: Cu Kal and Ka2). In another embodiment, the crystalline composition is characterized by an X-ray diffraction pattern including characteristic peaks at about 6.8, 12.6, 18.7, 20.1 23.2, and 24.0 degrees 2Θ, as measured with a PANanalytical X'Pert Pro X-ray powder diffractometer (range: 2-40 degrees 2Θ; source: Cu Kal and Ka2). In another embodiment, the crystalline composition is characterized by an X-ray diffraction pattern including characteristic peaks at about 6.8, 12.0, 12.6, 16.4, 18.7, 20.1 23.2, 24.0, 29.3 degrees 2Θ, as measured with a PANanalytical X'Pert Pro X-ray powder diffractometer (range: 2-40 degrees 2Θ; source: Cu Kal and Ka2).
[00482] In a certain embodiment, the crystalline composition comprising Lysine and SAHA is characterized by a Differential Scanning Calorimetry (DSC) thermogram, wherein the endotherm of the crystalline composition exhibits an extrapolated onset temperature of approximately 182°C, as measured by a TA Instruments Q1000 differential scanning calorimeter at a heating rate of 10°C/min from room temperature to 300°C.
[00483] The crystalline composition comprising Lysine and SAHA can be synthesized according to the methods described in International Patent Application Publication No.
WO2008/042146.
[00484] In certain embodiments, combination therapies described herein result in synergy or a synergistic effect. In a specific embodiment, a synergistic effect of a combination therapy permits the use of lower dosages (e.g. , sub-optimal doses) of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein and/or an additional therapy and/or less frequent administration of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein or an additional therapy to a subject. In certain embodiments, the ability to utilize lower dosages of an ADC such as a PBD dimer conjugate comprising an anti- KIT antibody and/or of an additional therapy and/or to administer an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody or said additional therapy less frequently reduces the toxicity associated with the administration of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody or of said additional therapy, respectively, to a subject without reducing the efficacy of an anti-KIT antibody or of said additional therapy, respectively, in the treatment of a KIT-associated disorder or disease. In some embodiments, a synergistic effect results in improved efficacy of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein and/or of said additional therapies in treating a KIT-associated disorder or disease. In some embodiments, a synergistic effect of a combination of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein and one or more additional therapies avoids or reduces adverse or unwanted side effects associated with the use of any single therapy.
[00485] Provided herein are methods for inhibiting KIT activity in a cell expressing KIT comprising contacting the cell with an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein (e.g., a humanized anti-KIT antibody) for example, any one of antibodies Huml-Hum20, such as HumlO, Huml7, Hum8 or Hum4, or an antigen-binding fragment thereof (e.g., KIT -binding fragment thereof). Also provided herein are methods for inducing or enhancing cell death such as apoptosis in a cell expressing KIT comprising contacting the cell with an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein.
[00486] In specific embodiments, a method for inhibiting (e.g., partially inhibiting) KIT activity in cells (e.g. , cancer cells) expressing KIT comprises contacting the cells with an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein sufficient to inhibit cell proliferation by at least about 5%, 10%, 15%, 20%>, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%) or 100%), as assessed by methods described herein or known to one of skill in the art (e.g., BrdU incorporation assay). In specific embodiments, a method for inhibiting (e.g., partially inhibiting) KIT activity in cells expressing KIT comprises contacting the cells with an effective amount of an antibody described herein sufficient to inhibit cell proliferation by at least about 25%), 35%), 45%), 55%), or 65%, as assessed by methods described herein or known to one of skill in the art (e.g., BrdU incorporation assay).
[00487] In certain aspects, a method provided herein for inhibiting KIT activity in a cell (e.g. , cancer cell) expressing KIT comprises contacting the cell with an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein sufficient to reduce or to inhibit survival of the cell. Cell survival assays are described in the art and can be readily carried out by one of skill in the art. For example, cell viability can be assessed by using trypan-blue staining or other cell death or viability markers known in the art. In a specific embodiment, the level of cellular ATP is measured to determined cell viability. In specific embodiments, cell viability is measured in three-day and seven-day periods using an assay standard in the art, such as the CellTiter-Glo Assay Kit (Promega) which measures levels of intracellular ATP. A reduction in cellular ATP is indicative of a cytotoxic effect. In another specific embodiment, cell viability can be measured in the neutral red uptake assay. In other embodiments, visual observation for morphological changes can include enlargement, granularity, cells with ragged edges, a filmy appearance, rounding, detachment from the surface of the well, or other changes. These changes are given a designation of T (100%) toxic), PVH (partially toxic-very heavy-80%), PH (partially toxic-heavy-60%), P (partially toxic-40%), Ps (partially toxic-slight-20%), or 0 (no toxicity-0%), conforming to the degree of cytotoxicity seen. A 50%> cell inhibitory (cytotoxic) concentration (IC50) is determined by regression analysis of these data. [00488] In specific embodiments, a method provided herein for inhibiting (e.g., partially inhibiting) KIT activity in cells expressing KIT comprises contacting the cells with an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein sufficient to reduce or to inhibit survival of the cells by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%o, or 99%o as assessed by methods described herein or known to one of skill in the art (e.g., trypan blue exclusion assay). In specific embodiments, a method provided herein for inhibiting (e.g. , partially inhibiting) KIT activity in cells expressing KIT comprises contacting the cells with an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein sufficient to reduce or to inhibit survival of the cells by at least about 25%o, 35%o, 45%o, 55%o, or 65%, as assessed by methods described herein or known to one of skill in the art (e.g., trypan blue exclusion assay.
[00489] In a specific embodiment, a method provided herein for inhibiting (e.g., partially inhibiting) KIT activity in cells expressing KIT comprises contacting the cells with an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein sufficient to induce cell death such as apoptosis (i.e., programmed cell death). Methods for detecting cell death such as apoptosis are described in the art and can be readily carried out by one of skill in the art. For example, flow cytometry can be used to detect activated caspase 3, an apoptosis-mediating enzyme, in cells undergoing apoptosis, or Western blotting can be used to detect cleavage of poly(ADP-ribose) polymerase (PARP (see, e.g., Smolich et ah, Blood, 2001, 97: 1413-1421). Cleavage of PARP is an indicator of apoptosis. In specific embodiments, a method provided herein for an inhibiting or antagonizing KIT activity in cells expressing KIT comprises contacting the cells with an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein sufficient to induce or enhance cell death such as apoptosis by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% as assessed by methods described herein or known to one of skill in the art (e.g., flow cytometry to detect activated caspases 3). In specific embodiments, a method provided herein for an inhibiting or
antagonizing KIT activity in cells expressing KIT comprises contacting the cells with an effective amount of an antibody described herein sufficient to induce or enhance apoptosis by at least about 25%, 35%, 45%, 55%, or 65%, as assessed by methods described herein or known to one of skill in the art (e.g. , flow cytometry to detect activated caspases 3). In specific embodiments, a method provided herein for inhibiting KIT activity in cells expressing KIT comprises contacting the cells with an effective amount of an ADC such as a PBD dimer conjugate comprising an anti-KIT antibody described herein sufficient to induce or enhance cell death such as apoptosis by at least about 1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold as assessed by methods described herein or known to one of skill in the art (e.g., flow cytometry to detect activated caspase 3).
6. EXAMPLES
[00490] The examples in this section (i.e. , section 6) are offered by way of illustration, and not by way of limitation.
[00491] ADCs, in particular PBD dimer conjugates, were produced as described in more detail below by conjugating anti-KIT antibodies which specifically bind to a D4 region of human KIT comprising human (e.g. , composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set in Table 1 provided herein. For example, VH domain (HI , H2, H3, H4 and H5) and VL domain (LI , L2, L3 and L4) sequences of anti-KIT antibodies produced using Composite Human Antibody™ technology (Antitope Ltd., Cambridge, United Kingdom) are provided in Figures 2A-2I (e.g. , anti-KIT antibodies Huml-Hum20). Figures 2 J and 2K provide consensus sequences for the VH domain and VL domain, respectively, of anti-KIT antibodies Huml-Hum20. These anti-KIT antibodies were expressed in mammalian cells (e.g. , CHO cells), purified, and confirmed to specifically bind to a D4 region of human KIT and to block KIT receptor activity (e.g. , block KIT receptor
phosphorylation induced by stem cell factor (SCF)).
General Experimental Methods
[00492] Optical rotations were measured on an ADP 220 polarimeter (Bellingham Stanley Ltd.) and concentrations (c) are given in g/lOOmL. Melting points were measured using a digital melting point apparatus (Electrothermal). IR spectra were recorded on a Perkin-Elmer Spectrum 1000 FT IR Spectrometer. 1H and 13C NMR spectra were acquired at 300 K using a Bruker Avance NMR spectrometer at 400 and 100 MHz, respectively. Chemical shifts are reported relative to TMS (δ = 0.0 ppm), and signals are designated as s (singlet), d (doublet), t (triplet), dt (double triplet), dd (doublet of doublets), ddd (double doublet of doublets) or m (multiplet), with coupling constants given in Hertz (Hz). Mass spectroscopy (MS) data were collected using a Waters Micromass ZQ instrument coupled to a Waters 2695 HPLC with a Waters 2996 PDA. Waters Micromass ZQ parameters used were: Capillary (kV), 3.38; Cone (V), 35; Extractor (V), 3.0; Source temperature (°C), 100; Desolvation Temperature (°C), 200; Cone flow rate (L/h), 50; De-solvation flow rate (L/h), 250. High-resolution mass spectroscopy (HRMS) data were recorded on a Waters Micromass QTOF Global in positive W-mode using metal-coated borosilicate glass tips to introduce the samples into the instrument. Thin Layer Chromatography (TLC) was performed on silica gel aluminium plates (Merck 60, F254), and flash
chromatography utilised silica gel (Merck 60, 230-400 mesh ASTM). Except for the HOBt (NovaBiochem) and solid-supported reagents (Argonaut), all other chemicals and solvents were purchased from Sigma- Aldrich and were used as supplied without further purification.
Anhydrous solvents were prepared by distillation under a dry nitrogen atmosphere in the presence of an appropriate drying agent, and were stored over 4A molecular sieves or sodium wire. Petroleum ether refers to the fraction boiling at 40-60°C.
General LC/MS conditions:
Method 1 (default method, used unless stated otherwise)
[00493] The HPLC (Waters Alliance 2695) was run using a mobile phase of water (A) (formic acid 0.1%) and acetonitrile (B) (formic acid 0.1%). Gradient: initial composition 5% B held over 1.0 min, then increase from 5% B to 95% B over a 3 min period. The composition was held for 0.1 min at 95% B, then returned to 5% B in 0.03 minutes and hold there for 0.87 min. Total gradient run time equals 5 minutes.
Method 2
[00494] The HPLC (Waters Alliance 2695) was run using a mobile phase of water (A) (formic acid 0.1%) and acetonitrile (B) (formic acid 0.1%). Gradient: initial composition 5% B held over 1.0 minute, then increase from 5% B to 95% B over a 2.5 minute period. The composition was held for 0.5 minutes at 95% B, then returned to 5% 5 B in 0.1 minutes and hold there for 0.9 min. Total gradient run time equals 5 minutes.
For both methods
-111- [00495] Flow rate 3.0 mL/min, 400μί was split via a zero dead volume tee piece which passes into the mass spectrometer. Wavelength detection range: 220 to 400 nm. Function type: diode array (535 scans). Column: Phenomenex Onyx Monolithic CI 8 50 x 4.60 mm.
[00496] Abbreviations:
Ac acetyl
Acm acetamidomethyl
ADC antibody-drug conjugate
Alloc allyloxycarbonyl
Bn benzyl
Boc di-tert-butyl dicarbonate
t-Bu tert-butyl
Bzl benzyl, where Bzl-OMe is methoxybenzyl and Bzl-Me is methylbenzene
Cbz or Z benzyloxy-carbonyl, where Z-Cl and Z-Br are chloro- and bromobenzyloxy
carbonyl respectively
DCC N,N'-dicyclhexylcarbodiimide
DCM dichloromethane
DMAP 4-dimethylaminopyridine
DMF N,N-dimethylformamide
DMSO dimethylsulfoxide
Dnp dinitrophenyl
DTT dithiothreitol
EDCI 1 -ethyl-3 -(3 -dimethylaminopropyl)carbodiimide
EDTA ethylenediaminetetraacetic acid
EEDQ N-ethoxycarbonyl-2-ethoxy- 1 ,2-dihydroquinoline
ELISA enzyme-linked immunosorbent assay
Fmoc 9H-fluoren-9-ylmethoxycarbonyl
HIC hydrophobic interaction chromatography
HOBt hydroxybenzotriazole
HPLC high-performance liquid chromatography
imp N-10 imine protecting group: 3-(2-methoxyethoxy)propanoate-Val-Ala-PAB
LC/MS liquid chromatography/mass spectrometry LiTEBH lithium triethylborohydride (Super Hydride)
MC-OSu maleimidocaproyl-O-N-succinimide
Moc methoxycarbonyl
MP maleimidoprop anamide
Mtr 4-methoxy-2,3,6-trimethtylbenzenesulfonyl
NAC N-acetylcysteine
NMR nuclear magnetic resonance
PAB para-aminobenzyloxycarbonyl
PBD pyrrolobenzodiazepine
PBS-P phosphate buffered saline + 0.05% Tween 20/Polysorbate 20
PEG ethyleneoxy
PNZ p-nitrobenzyl carbamate
Psec 2-(phenylsulfonyl)ethoxycarbonyl
SEC size exclusion chromatography with ultraviolet detection
SEM 2-(trimethylsilyl)ethoxymethyl
TBDMS tert-butyldimethylsilyl
TBDPS tert-butyldiphenylsilyl
TCEP tris(2-carboxyethyl)phosphine hydrochloride
TEA triethylamine
TEMPO 2,2, 6 ,6-tetramethy lpiperidiny loxy
Teoc 2-(trimethylsilyl)ethoxycarbonyl
Tf triflate
THF tetrahydrofuran
TLC thin layer chromatography
TMS trimethylsilane
Tos tosyl
Troc 2,2,2-trichlorethoxycarbonyl chloride
Trt trityl
Xan xanthyl 6.1 Example 1
(llS,llaS)-4-((S)-2-((S)-2-amino-3-methylbutanamido)propanamido)benzyl 1 l-hydroxy-7 - methoxy-8-(3-(((S)-7-methoxy-5-oxo-2-((E)-prop-l-en-l-yl)-5,lla-dihydro-lH- benzo[ ejpyrrolof 1, 2-aJf 1, 4]diazepin-8-yl)oxy)propoxy)-5-oxo-2-((E)-prop-l-en-l-yl)-ll, 11a- dihydro- lH-benzo [ ejpyrrolof 1, 2-aJf 1, 4]diazepine-10( 5H)-carboxylate (8)
Figure imgf000182_0001
[00497] The synthesis of compound 8 was described previously (compound 79 of
US2011/0256157), and the above route was employed starting from the bis-aryl compound 2 (compound 39a of US2011/0256157). 6.2 Example 2
(llS,llaS)-4-((S)-2-((S)-2-amino-3-methylbutanamido)propanamido)benzyl 1 l-hydroxy-7 - methoxy-8-((5-(( (S)- 7-methoxy-2-methyl-5-oxo-5,l la-dihydro-lH-benzof ejpyrrolof 1,2- a] [1,4] diazepin-8-yl)oxy)pentyl)oxy)-2-methyl-5-oxo- 11,1 la-dihydro-lH-benzo[e]pyrrolo [1,2- a] [1 ,4] diazepine-10(5H)-carboxylate (15)
Figure imgf000183_0001
[00498] Compound 15 can be synthesized by the route shown above, which employs the same conditions as those described in Example 1 with the following exceptions: 1) the synthesis of 15 starts with a pentane-linked bis-ether 9 (compound 3 of US2011/0256157), instead of the propane-linked bis-ether 2; and 2) in step B of Example 2, triphenylarsine is added to a mixture of triflate 12, methylboronic acid, silver oxide and potassium phosphate tribasic in dry dioxane under an argon atmosphere. The reaction is flushed with argon 3 times and bis(benzonitrile)palladium(II) chloride is added, then the reaction is warmed instantaneously to 110°C. After approximately 10 mins the reaction is cooled to room temperature and filtered through celite. Removal of excess solvent under reduced pressure and purification via flash silica gel chromatography yields the intermediate 11.
6.3 Example 3
Figure imgf000184_0001
(S)-2-amino-N-((S)-l-((4-((S)-8-(3-(( (S)-2-cyclopropyl- 7-methoxy-5-oxo-5 , 11 a-dihydro-l Ή- benzo[ ejpyrrolof 1,2-aJf 1, 4] diazepin-8-yl)oxy)propoxy)- 7-methoxy-5-oxo-5, 11 a-dihydro-l Ή- benzo [e] pyrrolo [ 1 ,2-a] [1 ,4] diazepin-2-yl)phenyl)amino)- l-oxopropan-2-yl)-3- methylbutanamide (21)
[00499] The synthesis of compound 19 was described previously (compound 26 of
US2013/0059800), and the above route was employed starting from the bis-aryl compound 16
(compound 8a of US2013/0059800).
Step D: Allyl ((2S)-l-(((2S)-l-((4-(8-(3-((2-cyclopropyl-7-methoxy-5-oxo-5,lla-dihydro- IHbenzof e] pyrrolo [ 1, 2-aJf 1, 4] diazepin-8-yl)oxy)propoxy)- 7-methoxy-5-oxo-5, 11a- dihydro lHbenzo [ ejpyrrolof 1,2-aJ [ 1, 4]diazepin-2-yl)phenyl)amino)-l-oxopropan-2-yl)amino)-3- methy I- l-oxobutan-2-y I) carbamate (20)
[00500] Under inert atmosphere, an equimolar ratio of HO-Ala-Val-alloc and EEDQ were dissolved in a 9: 1 mixture of CE^Cb/MeOH and allowed to stir for 1 hour in the dark.
Compound 19 was added and the reaction mixture was stirred for 40 hours, isolated under vacuum and purified by flash silica gel chromatography to afford the pure product. Method 2 LC/MS (2.70 min (ES+) m/z (relative intensity) 914.73 ([M+H]+, 60), 660.43 (60), 184.31 (100)). Step E: ( 2S) -2-amino-N- ( ( 2S)-1 -((4-(8-(3-(( 2-cyclopropyl- 7-methoxy-5-oxo-5, 11 a-dihydro- IHbenzof ejpyrrolof 1,2-aJf 1, 4] diazepin-8-yl)oxy)propoxy)- 7-methoxy-5-oxo-5,l la-dihydro- IHbenzof ejpyrrolof 1,2-aJf 1, 4]diazepin-2-yl)phenyl)amino)-l-oxopropan-2-yl)-3- methylbutanamide (21)
[00501] The starting material 20 was dissolved in dry CH2C12 under argon, and pyrrolidine was added. Pd(PPh3)4 was added and the reaction was allowed to stir for approximately 1 hour. A standard workup afforded the product 21. LC/MS method 2 (2.70 min (ES ) m/z (relative intensity) 830.27 ([M+H]+, 50), 660.13 (80), 171.15 (100)).
6.4 Example 4
Figure imgf000185_0001
(S)-2-amino-N-((S)-l-((4-((S)- 7-methoxy-8-(3-(( (S)- 7-methoxy-2-(4-(4-methylpiperazin-l- yl)phenyl)-5-oxo-5, 1 la-dihydro-lH-benzof ejpyrrolof 1, 2-aJf 1, 4] diazepin-8-yl)oxy)propoxy)-5- oxo-5, 1 la-dihydro-lH-benzof ejpyrrolof 1, 2-aJf 1, 4] diazepin-2-yl)phenyl)amino)-l -oxopropan-2- yl)-3-methylbutanamide (25)
[00502] Compound 25 can be synthesized by the route shown above, which employs the same conditions as those described in Example 3 with the following exception. In step B, Pd(PPh3)4 is added to a stirred mixture of the triflate 17, N-methyl piperazine boronic ester and Na2C03 in a 1 :2: 1 mixture of MeOH, toluene and water. The reaction mixture is allowed to stir at 30°C under a nitrogen atmosphere for 24 hours after which time all the boronic ester should be consumed. A standard workup and purification by flash silica gel chromatography yields the intermediate 22.
6.5 Example 5
Figure imgf000186_0001
(S)-2-amino-N-((S)-l-((4-((S)-8-(3-(((S)-2-(benzo[d] [l,3]dioxol-5-yl)-7-methoxy-5-oxo-5,l la- dihydro-lH-benzofeJpyrrolofl,2-aJfl,4Jdiazepin-8-yl)oxy)propoxy)-7-methoxy-5-oxo-5,lla- dihydro- lH-benzo [e] pyrrolo [1 ,2-a] [1 ] diazepin-2-yl)phenyl)amino)- l-oxopropan-2-yl)-3- methylbutanamide (29)
[00503] Compound 29 can be synthesized by the route shown above, which employs the same conditions as those described in Example 3 with the following exception. In step B, 3,4- (methylenedioxy)phenyl boronic acid, TEA, and trifiate/aniline 17 are dissolved in a mixture of ethanol, toluene and water under an Ar atmosphere. The reaction mixture is evacuated and flushed with argon, before addition of tetrakis(triphenylphosphine)palladium(0). The reaction is heated in a microwave at 80°C for approximately 10 minutes with 30 seconds pre-stirring time. A standard workup and purification by flash silica gel chromatography yields the intermediate 26.
6.6 Example 6
Figure imgf000187_0001
(S)-2-amino-N-((S)-l-((4-((S)-8-(3-(( (S)-2-cyclopropyl- 7-methoxy-5-oxo-5 , 11 a-dihydro-1 Ή- benzo[ ejpyrrolof 1,2-a] [ 1, 4] diazepin-8-yl)oxy)propoxy)- 7-methoxy-5-oxo-5, 11 a-dihydro-1 H- benzo [e] pyrrolo [ 1 ,2-a] [1 ,4] diazepin-2-yl)phenyl)amino)- l-oxopropan-2-yl)-3- methylbutanamide (21)
[00504] Step A: (R)-2-((R)-2-((((9H-fluoren-9-yl)methoxy)carbonyl)amino)-3- methylbutanamido) propanoic acid (31)
[00505] HO-Ala-Val-H 30 and Na2C03 were dissolved in distilled H20 and the mixture was cooled to 0°C before dioxane was added. A solution of Fmoc-Cl in dioxane was added dropwise with vigorous stirring over 10 minutes. The resulting mixture was stirred at 0°C for 2 hours before warming to room temperature and stirring for 16 hours. The solvent was removed by rotary evaporation under reduced pressure and a standard work up afforded HO-Ala-Val-Fmoc 31 (746 mg, 97% yield). LC/MS 2.85 min (ES+) m/z (relative intensity) 410.60 ; 1HNMR (400 MHz, CDCls) δ 7.79 (d, J=7.77 Hz, 2H), 7.60(d, J=7.77 Hz, 2H), 7.43(d, J=7.5 Hz, 2H), 7.34 (d, J=7.5 Hz, 2H), 6.30 (bs, 1H), 5.30 (bs, 1H), 4.71-7.56 (m, 1H), 4.54-4.36 (m, 2H), 4.08-3.91 (m, 1H), 2.21-2.07 (m, 1H), 1.50 (d, J=7.1 Hz, 3H), 1.06-0.90 (m, 6H).
[00506] Step B: (9H-fluoren-9-yl)methyl ((S)-3-methyl-l-oxo-l-(((S)-l-oxo-l-((4-(4,4,5,5- tetramethyl-l,3,2-dioxaborolan-2-yl)phenyl)amino)propan-2-yl)amino)butan-2-yl)
(32)
[00507] 4-Aminophenylboronic acid pinacol ester was added to a solution of HO-Ala-Val- Fmoc 31, DCC and catalytic DMAP in dry DCM under an argon atmosphere. The reaction mixture was then allowed to stir at room temperature overnight. The reaction was followed by LCMS and TLC. Standard work up and purification by silica gel chromatography yielded the product 32.
[00508] Step C: 8-(3-((2-(4-((S)-2-((S)-2-((((9H-fluoren-9-yl)methoxy)carbony
methylbutanamido)propanamido)phenyl)-7-methoxy-5, 11-dioxo-l 0-((2-
( trimethylsilyl)ethoxy)methyl)-5, 10,11, 1 la-tetrahydro-lH-benzof e] pyrrolo [ 1,2-aJf 1 ,4] diazepin- 8-yl)oxy)propoxy)-7 -methoxy-5 ,1 l-dioxo-10-((2-
( trimethylsilyl)ethoxy)methyl)5, 10,11, 1 latetrahydro-lH-benzof e] pyrrolo [ 1, 2-aJf 1, 4] diazepin-2- yl trifluoromethanesulfonate (33)
[00509] Bis-triflate 16, boronic pinacol ester and Na2C03 were dissolved in a mixture of toluene/MeOH/H20, 2: 1 :1. The reaction flask was purged and filled with argon three times before tetra^z'5(triphenylphosphine)palladium(0) was added and the reaction mixture heated to 30°C overnight. Standard work up and purification by silica gel chromatography yielded the product 32. LC/MS 3.85 min (ES+) m/z (relative intensity) 1452.90 ; 1H NMR (400 MHz, CDCI3) δ 7.78 - 7.16 (m, 17H), 7.13 (s, 1H), 6.51 - 6.24 (m, 1H), 5.51 (dd, J= 10.0, 5.1 Hz, 2H), 5.36 - 5.11 (m, 1H), 4.74 (dd, J= 10.1, 4.4 Hz, 2H), 4.70 - 4.53 (m, 2H), 4.47 (d, J= 6.4 Hz, 1H), 4.37 (d, J= 7.2 Hz, 1H), 4.27 (m, 4H), 4.20 - 4.14 (m, 1H), 3.90 (s, 3H), 3.89 (s, 3H), 3.77 (ddd, J= 16.7, 9.0, 6.4 Hz, 3H), 3.71 - 3.61 (m, 2H), 3.24 - 2.91 (m, 3H), 2.55 - 2.33 (m, 2H), 2.22 - 2.07 (m, 1H), 1.52 - 1.37 (m, 3H), 1.04 - 0.86 (m, 10H), 0.00 (s, 18H).
[00510] Step D: (9H-fluoren-9-yl)methyl((2S)-l-(((2S)-l-((4-(8-(3-((2-cyclopropyl-7- methoxy-5,1 l-dioxo-10-((2-(trimethylsilyl)ethoxy)methyl)-5, 10,11,1 la-tetrahydro-lH- benzof ejpyrrolof 1,2-aJf l,4Jdiazepin-8-yl)oxy)propoxy)- 7-methoxy-5, ll-dioxo-10-((2- ( trimethylsilyl)ethoxy)methyl)-5, 10,11, 1 la-tetrahydro-lH-benzof ejpyrrolof 1,2-aJf 1 ,4] diazepin- 2-yl)phenyl)amino)-l-oxopropan-2-yl)amino)-3-methyl-l-oxobutan-2-yl)carbamate (34)
[00511] Triphenylarsine was added to a mixture of PBD dimer-triflate 33, cyclopropylboronic acid, silver oxide and potassium phosphate tribasic in dry dioxane under an argon atmosphere. The reaction was flushed with argon 3 times and ¾z's(benzonitrile)palladium(II) chloride was added and the reaction was flushed with Argon 3 more times before being warmed to 75°C and stirred for 10 minutes. Standard work up and purification by flash silica gel chromatography yielded the product 34. LC/MS 3.83 min (ES+) m/z (relative intensity) 1345.91 ; 1H NMR (400 MHz, CDCI3) δ 7.88 - 7.14 (m, 17H), 6.69 (s, 1H), 6.45 - 6.25 (m, 1H), 5.57 - 5.41 (m, 2H), 5.34 - 5.14 (m, 1H), 4.78 - 4.67 (m, 2H), 4.62 - 4.55 (m, 1H), 4.50 - 4.45 (m, 2H), 4.51 - 4.44 (m, 1H), 4.31 - 4.21 (m, 4H), 4.16 (m, 1H), 3.92 (s, 3H), 3.86 (s, 3H), 3.82 - 3.71 (m, 2H), 3.66 (m, 3H), 3.40 - 3.28 (m, 1H), 3.07 (m, 1H), 2.70 - 2.57 (m, 1H), 2.47 - 2.36 (m, 2H), 2.15 (m, 1H), 1.51 - 1.40 (m, 3H), 1.03 - 0.87 (m, 11H), 0.77 - 0.71 (m, 2H), 0.60 - 0.54 (m, 2H), 0.00 (t, J= 3.0 Hz, 18H).
[00512] Step E: (9H-fluoren-9-yl)methyl((2S)-l-(((2S)-l-((4-(8-(3-((2-cyclopm
5-oxo-5, 1 la-dihydro-lH-benzof ejpyrrolof 1,2-aJf 1 ,4] diazepin-8-yl)oxy)propoxy)- 7-methoxy-5- oxo- 5, 1 la-dihydro-lH-benzof ejpyrrolof 1, 2-aJf 1, 4] diazepin-2-yl)phenyl) amino) -1 -oxopropan-2- yl)amino)-3-methyl-l-oxobutan-2-yl)carbamate (35)
[00513] A solution of Super-Hydride® was added dropwise to a solution of SEM dilactam 34 in THF at -78°C under an argon atmosphere. The addition was completed over 5 minutes in order to maintain the internal temperature of the reaction mixture. After 20 minutes, the reaction was complete. Standard work up produced a crude product which was dissolved in MeOH, CH2CI2, water and enough silica gel to form a thick stirring suspension. After 5 days, the suspension was filtered through a sintered funnel and washed with CH2Cl2/MeOH (9: 1) until the elution of the product was complete. Standard work up of the product and purification by silica gel chromatography yielded compound 35. LC/MS 3.02 min (ES+) m/z (relative intensity) 1052.37.
[00514] Step F: (2S)-2-amino-N-((2S)-l-((4-(8-(3-((2-cyclopropyl-7-methoxy-5-oxo-5,lla- dihydro-lH-benzofeJpyrrolofl,2-aJfl,4Jdiazepin-8-yl)oxy)propoxy)-7-methoxy-5-oxo-5,lla- dihydro- lH-benzo [e] pyrrolo [1 ,2-a] [1 ,4] diazepin-2-yl)phenyl)amino)- l-oxopropan-2-yl)-3- methylbutanamide (21)
[00515] Excess piperidine was added to a solution of SEM-dilactam 35 in DMF. The mixture was allowed to stir at room temperature for 20 min, at which point the reaction had gone to completion. Standard work up produced the crude product 21. LC/MS 2.32 min (ES+) m/z (relative intensity) 830.00.
6.7 Example 7
Figure imgf000190_0001
(S)-2-amino-N-((S)-l-((4-((S)- 7-methoxy-8-(3-(( (S)- 7-methoxy-2-(4-(4-methylpiperazin-l- yl)phenyl)-5-oxo-5, 1 la-dihydro-lH-benzof ejpyrrolof 1, 2-aJf 1, 4] diazepin-8-yl)oxy)propoxy)-5- oxo-5, 11 a-dihydro- lH-benzo [ ejpyrrolof 1, 2-aJ [ 1, 4] diazepin-2-yl)phenyl)amino)-l -oxopropan-2- yl)-3-methylbutanamide (25)
[00516] Step A: (9H-fluoren-9-yl)methyl ((S)-l-(((S)-l-((4-((S)-7-methoxy-8-(3-(((S)-7- methoxy-2-(4-(4-methylpiperazin-l-yl)phenyl)-5,ll-dioxo-10-((2-(trimethylsilyl)ethoxy)methyl)- 5,10,11, 1 latetrahydro-lH-pyrrolo[2, l-cjf l,4]benzodiazepin-8-yl)oxy)5 propoxy)-5, ll-dioxo- 10-((2-( trimethylsilyl) ethoxy)methyl)-5, 10,11, 1 la-tetrahydro-lH- pyrrolof 2,1c] [ 1, 4Jbenzodiazepin-2-yl)phenyl)amino)-l-oxopropan-2-yl)amino)-3-methyl- loxobutan-2-yl) carbamate (37)
[00517] PBD dimer-trifiate 33, N-methyl piperazine boronic pinacol ester and Na2C03 (157 mg, 1.48 mmol) were dissolved in a mixture of toluene/MeOH/H20, 2: 1 :1. The reaction flask was purged with argon three times before tetrakis(triphenylphosphine)palladium(0) was added and the reaction mixture heated to 30°C overnight. Standard work up and purification by silica gel chromatography yielded compound 37. LC/MS 3.27 min (ES+) m/z (relative intensity) 1478 ([M + H]+, 100%).
[00518] Step B: (9H-fluoren-9-yl)methyl ((S)-l-(((S)-l-((4-((S)-7-methoxy-8-(3-(((S)-7- methoxy-2-(4-(4-methylpiperazin-l-yl)phenyl)-5-oxo-5,lla-dihydro-lH-pyrrolo[2,l- c] [l,4]benzodiazepin-8-yl)oxy)propoxy)-5-oxo-5,lla-dihydro-lH-pyrrolo[2,l- c] [1 ,4] benzodiazepin-2-yl)phenyl)amino)-l -oxopropan-2-yl)amino)-3-methyl-l -oxobutan-2- yl)carbamate (38)
[00519] A solution of Super-Hydride® (LiTEBH) was added dropwise to a solution of SEM- dilactam 37 in THF at -78°C under an argon atmosphere. The addition was completed over 5 minutes in order to maintain the internal temperature of the reaction mixture. After 20 minutes, the reaction was complete. Standard work up produced a crude product which was dissolved in MeOH, CH2C12, water and enough silica gel to form a thick stirring suspension. After 5 days, the suspension was filtered through a sintered funnel and washed with CH2Cl2/MeOH (9: 1) until the elution of the product was complete. Standard work up of the product and purification by silica gel chromatography yielded compound 38. LC/MS 2.67 min (ES+) m/z (relative intensity) 1186 ([M + H]+, 5%).
[00520] Step C: (S)-2-amino-N-((S)-l-((4-((R)-7-methoxy-8-(3-(((R)-7-methoxy-2-(4-^ methylpiperazin-l-yl)phenyl)-5-oxo-5, 11 a-dihydro- IH-pyrrolof 2, l-cjf 1, 4] benzodiazepin-5 8- yl)oxy)propoxy)-5-oxo-5 ,11 a-dihydro- lH-pyrrolo [2 ,1-cJ / 1 ,4] }benzodiazepin-2-yl)phenyl)amino)- l-oxopropan-2-yl)-3-methylbutanamide (25)
[00521] Excess piperidine was added to a solution of PBD dimer 38 in DMF. The mixture was allowed to stir at room temperature for 20 min. Standard work up produced the crude product 25. LC/MS 2.20 min (ES+) m/z (relative intensity) 964 ([M + H]+, 5).
6.8 Example 8
Figure imgf000192_0001
(S)-2-amino-N-((S)-l-((4-((S)-8-(3-(((S)-2-(benzo[d] [l,3]dioxol-5-yl)-7-methoxy-5-oxo-5,l la- dihydro-lH-benzofeJpyrrolofl,2-aJfl,4Jdiazepin-8-yl)oxy)propoxy)-7-methoxy-5-oxo-5,lla- dihydro- lH-benzo [e] pyrrolo [1 ,2-a] [1 ,4] diazepin-2-yl)phenyl)amino)- l-oxopropan-2-yl)-3- methylbutanamide (29)
[00522] Step A: 9H-Fluoren-9-yl)methyl ((S)-l-(((S)-l-((4-((S)-8-(3-(((S)-2- (benzof d] [ 1, 3]dioxol-5-yl)- 7-methoxy-5, 11 -dioxo-l 0-((2-(trimethylsilyl)ethoxy)methyl)- 5,10,11, 1 la-tetrahydro-lH-pyrrolof 2, l-cjf 1, 4]benzodiazepin-8-yl)oxy)propoxy)- 7-methoxy- 5,11 -dioxo-l 0-((2-(trimethylsilyl)ethoxy)methyl)-5, 10,11,1 la-tetrahydro-lH-pyrrolo[2,l- cJ[l,4Jbenzodiazepin-2-yl)phenyl)amino)-l-oxopropan-2-yl)amino)-3-methyl-l-oxobutan-2- yl)carbamate (40)
[00523] The triflate 33, 3,4-(methylenedioxy)phenyl boronic acid and Na2C03 were dissolved in toluene, EtOH and water under an argon atmosphere. Pd(PPh3)4 was added and the flask was heated to 30°C and left stirred overnight. Standard work up and purification by column chromatography afforded the product 40. LC/MS (1.44 min (ES~) m/z (relative intensity) 1423.35 ([M - H]-, 79).
[00524] Step B: (9H-Fluoren-9-yl)methyl ((S)-l-(((S)-l-((4-((S)-8-(3-(((S)-2-
(benzo[ d] [ 1, 3]dioxol-5-yl)- 7-methoxy-5-oxo-5, 1 la-dihydro-lH-pyrrolo[2, 1- c][ 1, 4]benzodiazepin-8-yl)oxy)propoxy)-7-methoxy-5-oxo-5, 1 la-dihydro-lH-pyrrolo[2, 1- c] [1 ,4] benzodiazepin-2-yl)phenyl)amino)-l -oxopropan-2-yl)amino)-3-methyl-l -oxobutan-2- yl)carbamate (41)
[00525] A solution of Super-Hydride® (LiTEBH) was added dropwise to a solution of SEM- dilactam 40 in THF at -78°C under an argon atmosphere. The addition was completed over 5 minutes in order to maintain the internal temperature of the reaction mixture. After 30 minutes, the reaction was complete. Standard work up produced a crude product which was dissolved in MeOH, CH2C12, water and enough silica gel to form a thick stirring suspension. After 5 days, the suspension was filtered through a sintered funnel and washed with CH2Cl2/MeOH (9: 1) until the elution of the product was complete. Standard work up of the product and purification by silica gel column chromatography yielded compound 41. LC/MS (1.70 min (ES ) m/z (relative intensity) 1132.85 ([M + H]+ , 60).
[00526] Step C: (S)-2-Amino-N-((S)-l-((4-((S)-8-(3-(((S)-2-(benzo[d] ' [l,3]dioxol-5-yl)-7- methoxy-5-oxo-5, 1 la-dihydro-lH-pyrrolo[2, l-cjf 1, 4]benzodiazepin-8-yl)oxy)propoxy)- 7- methoxy-5-oxo-5 la-dihydro-lH-pyrrolo[2,l-c] [l,4]benzodiazepin-2-yl)phenyl)amino)-l- oxopropan-2-yl)-3-methylbutanamide (29)
[00527] Excess piperidine was added to a solution of PBD dimer 41 in DMF. The mixture was allowed to stir at room temperature for 20 min. Standard work up produced the crude product 29. LC/MS (1.15 min (ES+) m/z (relative intensity) 910.60 ([M + H]+, 58). 6.9 Example 9
Figure imgf000194_0001
(11 S,l 1 aS)-4-((20S,23S)-l -iodo-20-isopropyl-23-methyl-2, 18,21 -trioxo-6,9, 12, 15-tetraoxa- 3, 19,22-triazatetracosanamido)benzyl 11 -hydroxy- 7-methoxy-8-(3-(( (S)- 7-methoxy-5-oxo-2-((E)- prop-l-en-l-yl)-5, 1 la-dihydro-lH-benzof ejpyrrolof 1,2-aJf 1, 4] diazepin-8-yl)oxy)propoxy)-5- oxo-2-((E)-prop-l-en-l-yl)-ll, 1 la-dihydro-lH-benzof ejpyrrolof 1, 2-aJf l,4]diazepine-10( 5H)- carboxylate (42)
[00528] EDCI was added to a solution of amine 8 and iodoacetamide-PEG4-acid in dry dichloromethane and the reaction was stirred in the dark. After 50 minutes, a further amount of iodoacetamide-PEG4-acid was added along with a further amount of EDCI. After a total of 2.5 hours, standard work up and purification by flash silica gel chromatography followed by preparative TLC purification yielded the product 42. LC/MS (2.689 min (ES+)), m/z: 681.0 1/2[M+2H]+.
6.10 Example 10
Figure imgf000194_0002
(1 IS, llaS)-4-((32S, 35S)-l-iodo-32-isopropyl-35-methyl-2,30, 33-trioxo-6, 9, 12,15,18,21,24, 27- octaoxa-3,31, 34-triazahexatriacontanamido)benzyl 11 -hydroxy- 7-methoxy-8-(( 5-(( (S)- 7- methoxy-2-methyl-5-oxo-5 , 11 a-dihydro- lH-benzo [ ejpyrrolof 1, 2-aJ [ 1 ,4] diazepin-8- yl)oxy)pentyl)oxy)-2-methyl-5-oxo-l 1 , 11 a-dihydro- lH-benzo[ ejpyrrolof 1,2-aJf 1 ,4] diazepine- 10(5H)-carboxylate (43)
[00529] Compound 43 can be synthesized using the same procedure as Example 9 starting from compound 15 instead of compound 8, and substituting iodoacetamide-PEG4-acid with iodoacetamide-PEGg-acid.
6.11 Example 11
Figure imgf000195_0001
( I IS, 1 laS)-4-((2S, 5S)-37-(2, 5-dioxo-2, 5-dihydro-lH-pyrrol-l-yl)-5-isopropyl-2-methyl-4, 7, 35- trioxo-10,13 ,16,19 22 ',25 ' ,28,3l-octaoxa-3 ,6,34-triazaheptatriacontanamido)benzyl 11-hydroxy- 7-methoxy-8-( (5-(( (S)-7-methoxy-2-methyl-5-oxo-5, 11 a-dihydro- lH-benzo[ ejpyrrolof 1, 2- a] [1 ,4]diazepin-8-yl)oxy)pentyl)oxy)-2-methyl-5-oxo-l 1 ,11 a-dihydro- lH-benzo[ ejpyrrolof 1 ,2- a ][ 1, 4]diazepine-l 0( 5H)-carboxylate ( 44)
[00530] Compound 44 can be synthesized using the same procedure as Example 9 starting from compound 15 instead of compound 8, and substituting iodoacetamide-PEG4-acid with maleimide-PEG8-acid.
6.12 Example 12
Figure imgf000196_0001
N-((S)-l-(((S)-l-((4-((S)-8-(3-(((S)-2-cyclopropyl-7-methoxy-5-ox^
benzo[ ejpyrrolof 1,2-a] [ 1, 4] diazepin-8-yl)oxy)propoxy)- 7-methoxy-5-oxo-5, lla-dihydro-lH- benzo [ej 'pyrrolo [ 1 ,2-aJ [1 ,4] diazepin-2-yl)phenyl) amino)- l-oxopropan-2-yl)amino)-3-methyl-l- oxobutan-2-yl)-l-(3-(2,5-dioxo-2,5-dihydro-lH-pyrrol-l-yl)propanamido)-3,6,9,12,15,18,21,24- octaoxaheptacosan-27 -amide (45)
[00531] EDCI hydrochloride was added to a suspension of maleimide-PEGg-acid in dry CH2CI2 under argon atmosphere. The mixture was stirred for 1 hour at room temperature before PBD dimer 21 was added. Stirring was maintained for about 5 hours. Standard work up and purification by flash silica gel chromatography followed by preparative TLC purification yielded the product 45. LC/MS 2.57 min (ES+) m/z (relative intensity) 1405.30 ; 1H NMR (400 MHz, CDCI3) δ 7.91 (t, J= 3.5 Hz, 1H), 7.80 (d, J= 4.0 Hz, 1H), 7.75 (d, J = 8.8 Hz, 1H), 7.69 (d, J = 8.7 Hz, 1H), 7.54 - 7.50 (m, 2H), 7.45 (s, 1H), 7.39 - 7.31 (m, 2H), 6.87 (d, J = 10.5 Hz, 2H), 6.76 (s, 1H), 6.72 - 6.68 (m, 2H), 4.74 - 4.62 (m, 1H), 4.45 - 4.17 (m, 7H), 3.95 (s, 3H), 3.94 (s, 3H), 3.67 - 3.58 (m, 34H), 3.54 (m, 2H), 3.42 (dd, J= 10.2, 5.2 Hz, 2H), 3.16 - 3.07 (m, 1H), 2.92 (dd, J= 16.1, 4.1 Hz, 1H), 2.62 - 2.49 (m, 4H), 2.48 - 2.39 (m, 2H), 2.37 - 2.25 (m, 1H), 1.92 (s, 1H), 1.52 - 1.44 (m, 3H), 1.10 - 0.93 (m, 6H), 0.79 (dd, J= 9.2, 5.3 Hz, 2H), 0.57 (dd, J = 9.2, 5.3 Hz, 2H), NH were not observed. 6.13 Example 13
Figure imgf000197_0001
6-(2,5-dioxo-2,5-dihydro-lH^yrrol-l-yl)-N-((S)-l-(((S)-l-((4-^^
methoxy-2-(4-(4-methylpiperazin-l-yl)phenyl)-5-oxo-5, 1 la-dihydro-lH-benzof ejpyrrolof 1, 2- ajf 1, 4]diazepin-8-yl)oxy)propoxy)-5-oxo-5, 1 la-dihydro-lH-benzof ejpyrrolof 1, 2- a] [1 ,4] diazepin-2-yl)phenyl)amino)-l -oxopropan-2-yl)amino)-3-methyl-l -oxobutan-2- yl)hexanamide (46)
[00532] EDCI hydrochloride was added to a suspension of 6-maleimidohexanoic acid in dry CH2CI2 under argon atmosphere. The mixture was stirred for 1 hour at room temperature before PBD dimer 25 was added. Stirring was maintained for approximately 6 hours. Standard work up and purification by flash silica gel chromatography followed by reverse phase chromatography yielded the product 46. LC/MS 2.40 min (ES+) m/z (relative intensity) 1157 ([M + H]+, 5)
6.14 Example 14
Figure imgf000197_0002
N-((S)-l-(((S)-l-((4-((S)-8-(3-(((S)-2-(benzo[d][l,3]dioxo
dihydro-lH-benzofeJpyrrolofl ,2-aj ' [1 ,4j 1 diazepin-8-yl)oxy)propoxy)-7-methoxy-5-oxo-5,l la- dihydro-lH-benzo[e]pyrrolo[l,2-a] ' [1 ,4] diazepin-2-yl)phenyl)amino)-l-oxopropan-2-yl)amino)- 3-methyl-l-oxobutan-2-yl)-l-(3-(2,5-dioxo-2,5-dihydro-lH-pyrrol-l-yl)propanamido)- 3, 6,9, 12,15, 18,21 ,24-octaoxaheptacosan-27 -amide (47)
[00533] The amine 29 was dissolved in CHCI3 with one drop of anhydrous MeOH to aid dissolution. Maleimide-PEGg-acid was added followed by EEDQ. The reaction was stirred vigorously for 4 days. Standard work up and purification by flash silica gel chromatography followed by preparative HPLC purification yielded the product 47. Fast Formic run: LC/MS (1.39 min (ES+) m/z (relative intensity) 1485.00 ([M + H]+, 64).
6.15 Example 15: General antibody conjugation procedure
[00534] Antibodies {e.g. , anti-KIT antibodies) are diluted to 1-5 mg/mL in a reduction buffer (examples: phosphate buffered saline PBS, histidine buffer, sodium borate buffer, TRIS buffer). A freshly prepared solution of TCEP (tris(2-carboxyethyl)phosphine hydrochloride) is added to selectively reduce cysteine disulfide bridges. The amount of TCEP is proportional to the target level of reduction, within 1 to 4 molar equivalents per antibody, generating 2 to 8 reactive thiols. After reduction for several hours at 37°C, the mixture is cooled down to room temperature and excess drug linker (e.g, any one of compounds 42-47) added as a diluted DMSO solution (final DMSO content of up to 10% volume/volume of reaction mixture). The mixture is gently shaken at either 4°C or room temperature for the appropriate time, generally between 1-3 hours and 10- 30 hours. Excess reactive thiols can be reacted with a 'thiol capping reagent' like Nethyl maleimide (NEM) at the end of the conjugation. Antibody-drug conjugates are concentrated using centrifugal spin- filters with a molecular weight cut-off of 10 kDa or higher, then purified by tangential flow filtration (TFF) or Fast Protein Liquid Chromatography (FPLC).
Corresponding antibody-drug conjugates can be determined by analysis by High Performance Liquid Chromatography (HPLC) or Ultra-High-Performance Liquid Chromatography (UHPLC) to assess drug-per-antibody ratio (DAR) using reverse-phase chromatography (RP) or
Hydrophobic-Interaction Chromatography (HIC), coupled with UVVisible, Fluorescence or Mass-Spectrometer detection; aggregate level and monomer purity can be analysed by HPLC or UHPLC using size-exclusion chromatography coupled with UVVisible, Fluorescence or Mass- Spectrometer detection. Final conjugate concentration is determined by a combination of spectroscopic (absorbance at 280, 214 and 330 nm) and biochemical assay (bicinchonic acid assay BCA; Smith, P.K., et al. (1985) Anal. Biochem. 150 (1): 76-85; using a known- concentration IgG antibody as reference). Antibody-drug conjugates are generally sterile filtered using 0.2 μιη filters under aseptic conditions, and stored at +4°C, -20°C or -80°C.
[00535] Examples of particular conjugations are described below.
6.16 Example 16: Conjugation Procedure for Compound 42 with an Anti-KIT
Antibody
Figure imgf000199_0001
KIT-PBD1
[00536] PBD dimer A conjugate KIT-PBD1 was generated by conjugating compound 42 to an anti-KIT antibody, which specifically binds to a D4 region of human KIT, comprising human (e.g composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set in Table 1 provided herein. Briefly, the anti-KIT antibody was diluted in a reduction buffer (sodium phosphate buffer/EDTA). Approximately 3 {e.g., 2.8-3.4) equivalents of a freshly prepared solution of TCEP (tris(2-carboxyethyl)phosphine
hydrochloride) was added to selectively reduce cysteine disulfide bridges. After reduction at 37°C, the mixture was cooled down to room temperature and an excess of compound 42 was added as a diluted DMSO solution. The mixture was gently shaken at room temperature for appropriately 14 hours, followed by quenching with either excess 42 or NAC. Antibody-drug conjugates were purified by tangential flow filtration (TFF) and SEC purification, if necessary.
Reverse-phase HPLC analysis was performed to characterize the DAR (drug-per-antibody ratio) of the batch of KIT-PBDl generated from this protocol, and a DAR of about 2.5 was determined.
In one embodiment, the PBD dimer A conjugate KIT-PBDl is a PBD dimer A conjugate as represented in the scheme above.
6.17 Example 17: Conjugation Procedure for Compound 45 with an Anti-KIT Antibody
Figure imgf000200_0001
KIT-PBD2
[00537] PBD dimer C conjugate KIT-PBD2 was generated by conjugating compound 45 to an anti-KIT antibody, which specifically binds to a D4 region of human KIT, comprising human (e.g., composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set in Table 1 provided herein. Briefly, the anti-KIT antibody was diluted in a reduction buffer (PBS-P buffer/EDTA). Approximately 3 (e.g., 2.6-3.2) equivalents of a freshly prepared solution of TCEP (tris(2-carboxyethyl)phosphine hydrochloride) was added to selectively reduce cysteine disulfide bridges. After reduction at 37°C, the mixture was cooled down to room temperature and an excess of compound 45 was added as a diluted DMSO solution. The mixture was gently shaken at room temperature for appropriately 2 hours, followed by quenching with either excess 45 or NAC. Antibody-drug conjugates were purified by tangential flow filtration (TFF) and SEC purification, if necessary. Reverse-phase HPLC analysis was performed to characterize the DAR (drug-per-antibody ratio) of the batch of KIT- PBD2 generated from this protocol, and a DAR of about 2.2 was determined. In one
embodiment, the PBD dimer C conjugate KIT-PBD2 is a PBD dimer C conjugate as represented in the scheme above.
6.18 Example 18: Conjugation Procedure for Compound 43 with an Anti-KIT Antibody
Figure imgf000201_0001
KIT-PBD3
[00538] PBD dimer B conjugate KIT-PBD3 can be generated using the method set forth in Example 15 to conjugate compound 43 to an anti-KIT antibody, which specifically binds to a D4 region of human KIT, comprising human (e.g. , composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set in Table 1 provided herein. In one embodiment, the PBD dimer B conjugate KIT-PBD3 is a PBD dimer B conjugate as represented in the scheme above. 6.19 Example 19: Conjugation Procedure for Compound 44 with an Anti-KIT Antibody
Figure imgf000202_0001
[00539] PBD dimer B conjugate KIT-PBD4 can be generated using the method set forth in Example 15 to conjugate compound 44 to an anti-KIT antibody, which specifically binds to a D4 region of human KIT, comprising human (e.g. , composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set in Table 1 provided herein. In one embodiment, the PBD dimer B conjugate KIT-PBD4 is a PBD dimer B conjugate as represented in the scheme above.
6.20 Example 20: Conjugation Procedure for Compound 46 with an Anti-KIT Antibody
Figure imgf000203_0001
[00540] PBD dimer D conjugate KIT-PBD5 can be generated using the method set forth in Example 15 to conjugate compound 46 to an anti-KIT antibody, which specifically binds to a D4 region of human KIT, comprising human (e.g. , composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set in Table 1 provided herein. In one embodiment, the PBD dimer D conjugate KIT-PBD5 is a PBD dimer D conjugate as represented in the scheme above.
6.21 Example 21: Conjugation Procedure for Compound 47 with an Anti-KIT
Antibody
Figure imgf000203_0002
[00541] PBD dimer E conjugate KIT-PBD6 can be generated using the method set forth in Example 15 to conjugate compound 47 to an anti-KIT antibody, which specifically binds to a D4 region of human KIT, comprising human (e.g. , composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set in Table 1 provided herein. In one embodiment, the PBD dimer E conjugate KIT-PBD6 is a PBD dimer E conjugate as represented in the scheme above.
6.22 Example 22: KIT Binding Assays by ELISA
[00542] The binding affinity of KIT-PBD 1 and KIT-PBD2 to the target antigen, a polypeptide containing human KIT Ig-like domains D4 and D5 (D4/D5 region), was assessed by solid phase ELISA. The general protocol used for the solid phase ELISA experiments is described below.
[00543] Materials:
• Recombinant antigen: Recombinant Ig-like domain four and five of the extracellular region of human KIT
• Controls: anti-keyhole limpet hemocyanin ("KLH") antibody in naked form (KLH-Ab) and in ADC form with compound 42 (KLH-PBDl) and compound 45 (KLH-PBD2) and anti-KIT antibody in naked form (KIT-Ab)
• TBS-T: 50 mM Tris pH 7.4, 150 mM NaCl, 0.1% Tween 20
• TBS: 50 mM Tris pH 7.4, 150 mM NaCl
• Blocking solution: 1% bovine serum albumin (BSA) in TBS
• Dilution buffer: 1 % BSA in TBS-T
• Detection antibody solution: goat anti-human IgG F(ab')2 specific antibody conjugated to HRP
• Detection Substrate: TMB (3,3',5,5' - tetramethylbenzidine) Substrate kit (e.g., Thermo scientific #34021)
[00544] Recombinant antigen corresponding to the D4/D5 region in the extracellular domain (ECD) of human KIT was absorbed onto 96-well microtiter plates. In particular, recombinant antigen (5 μg) were diluted into 10 mL of Borate Buffer (50 mM borate), and 100 of the antigen solution were added to each well of a 96 well plate and were incubated at 4°C overnight.
[00545] Serial dilutions of ADC samples (KIT-PBD 1 and KIT-PBD2) and controls were prepared with dilution buffer for ELISA. [00546] ELISA: Following one rinse with TBS-T, blocking buffer (200 μί) was added to each well of the plate with the adsorbed antigen and was incubate at room temperature for one hour. Then, the blocking buffer was removed, and the serially diluted solutions of test ADCs and controls were added to the plate in a volume of 50 μΐ^ and incubated at room temperature for one hour. The antibody solutions were removed, and the plate was washed three times with 100 μΐ, of wash buffer on a plate washer. After the last wash, the plate was blotted dry. Secondary antibody solution was diluted 1 :8000 and was added to each well in a volume of 100 μΐ, and allowed to incubate for one hour at room temperature. The diluted secondary antibody solution was removed, and the plate was washed three times with 100 μΐ, of wash buffer on a plate washer. Then, freshly mixed TMB substrate solution was added to each well in a volume of 100 μΐ, and was allowed to incubate at room temperature for 30 minutes. Subsequently, 100 μΐ, of 2N H2SO4 were added to each well and immediately read on the plate reader. Irrelevant anti- KLH antibody in naked and ADC forms served as the negative control, and an anti-KIT antibody which is the unconjugated version of KIT-PBD1 and KIT-PBD2 served as the positive control. OD values for each sample were obtained at a wavelength of 450 nm.
[00547] Results were analyzed using Graph Pad Prism and Excel to obtain the effective concentration at 50% binding (EC50) to antigen.
[00548] Figure 3 depicts a graph plotting OD450 versus log concentration (M) of antibody or ADCs. The results show that KIT-PBD1 and KIT-PBD2 exhibit comparable binding to the D4/D5 region of KIT as their unconjugated anti-KIT antibody (KIT-Ab).
[00549] The EC50 for the binding affinity of KIT-Ab, KIT-PBD 1 and KIT-PBD2 to the D4/D5 region of human KIT was calculated to be approximately 9pM, 4 pM, and 9 pM, respectively. These results demonstrate that transformation of the anti-KIT antibody into the KIT-PBD 1 and KIT-PBD2 ADCs did not compromise the KIT binding property of the anti-KIT antibody.
6.23 Example 23: KIT Phosphorylation Blocking Assays
[00550] To characterize the effect of KIT-PBD 1 and KIT-PBD2 on KIT activity, specifically, SCF-induced tyrosine phosphorylation of the cytoplasmic domain of KIT, cell-based phospho- KIT assays were carried out as follows.
[00551] Materials: • CHO/KIT-WT cells: CHO cells stably trans fected with a plasmid encoding full-length human KIT, which was cloned from a human ovary cDNA library (OriGene, Rockville, Maryland)
• Cell culture media:
o Basic medium: Gibco F12 Nutrient Mixture (Ham) IX
o Penicillin/Streptomycin: 50 IU/mL penicillin and 50 μg/mL streptomycin o IX GlutaMAX™ (Gibco® 35050)
o 1 mg/mL Geneticin (for selection of transfected cells only)
• Complete cell culture media: cell culture media with FBS (fetal bovine serum)
• Starving media: complete cell culture media without FBS
• Trypsin-EDTA
• PBS
• SCF solution: rhSCF (RD Systems 255-SC/CF); final concentration 30 ng/niL
• Lysis buffer: 50 mM Tris pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100,
protease inhibitor cocktail tables EDTA free, 1 mM NaV04
• TBS-T: 50 mM Tris pH 7.4, 150 mM NaCl, 0.1% Tween 20
• Blocking solution: 5% bovine serum albumin (BSA) in TBS-T
• Dilution buffer: 1% BSA in TBS-T containing 1 mM NaV04
• Detection antibody solution: anti-phospho-tyrosine antibody conjugated with horse radish peroxidase (Millipore, 4G10); dilution factor 1 :500
• Capture antibody: anti-KIT antibody Ab3 from Thermo Scientific (MS-289-PABX)
[00552] Passaging of CHO/KIT-WT cells: Confluent cells were washed once with sterile PBS, incubated with 0.25% Trypsin-EDTA at room temperature until cells detached from the plastic tissue culture plates. Complete culture medium, which contains FBS, was added to the plate to end the tryptic digestion.
[00553] Cell Treatment: Cells (25,000 per well) were transferred into a 96-well cell culture plate, and were cultivated in complete medium for 24 hours under normal cell culture conditions (e.g., humidified 95% air and 5% C02 atmosphere at 37°C). After the cells were plated in the 96-well plates and cultured overnight, the medium was removed, and the cell monolayer was washed once with starvation medium. The cells were then cultured for 24 hours in starvation medium under normal cell culture conditions. Then the cells were treated with KIT-Ab (naked), KIT-PBD1, or KIT-PBD2 for 2 hours under normal cell culture conditions. The final concentration for the antibody solution was 100 nM (5 μg/mL) or less. Subsequently, SCF solution was added to the cells pretreated with anti-KIT antibodies or ADCs at a final concentration of 30 ng/mL for 10 minutes under normal cell culture conditions.
[00554] Preparation of cell lysates: After stimulation, cells in the 96-well plate were placed on ice immediately, the cells were washed once with cold PBS, and lysed with 70 μΐ, of cold lysis buffer.
[00555] Preparation of 96-well ELISA plate with capture antibody: Capture antibody (5 i ) was diluted in 10 mL 50 mM Borate buffer, and the capture antibody solution (100 μί or 50 ng/well) was added to each well of the 96-well ELISA plate. The 96-well plate was incubated at room temperature for 5-6 hours or overnight at 4°C. The capture antibody solution was removed prior to the blocking step. Blocking was carried out by adding 100 iL of blocking solution to each well and allowed to incubate at room temperature for 1 hour. The blocking solution was removed, the wells were washed once with dilution buffer, and 50 of dilution buffer were added to each well.
[00556] Phospho-KIT assay: 50
Figure imgf000207_0001
of the cell lysates of each sample from a well of the 96- well plate were transferred into 1 well of the prepared 96-well plate containing 50
Figure imgf000207_0002
dilution buffer, and the 96-well plate was incubated overnight at 4°C. Following the overnight incubation, the supernatant was removed, and the plate was washed 3 times (5 minute incubation each time) with TBS-T. Detection antibody dilution (100
Figure imgf000207_0003
was added to each well and incubated for 1 hour at room temperature in the dark. The plate was washed 3 times with TBS- T, washed once with TBS, and the TBS was removed. The "SuperSignal West Dura Extended Duration Substrate" reagents (Thermo Scientific) were mixed (1 : 1), and 100
Figure imgf000207_0004
of the mix were added to each well.
[00557] Luminescence was detected in the ELISA plate reader using the GEN5™ protocol "Luminescence Glow" and the data were analyzed using Microsoft Excel.
[00558] Figure 4 depicts a graph plotting the data from these experiments. The graph is a plot of arbitrary luminescence units versus log concentration (M) of KIT-Ab, KIT-PBD1, and KIT- PBD2. The 50% inhibition concentrations (IC50) of KIT-Ab, KIT-PBD1, and KIT-PBD2 were calculated to be approximately 88 pM, 55 pM, and 70pM, respectively. The results indicate that KIT-PBD1 and KIT-PBD2 exhibit comparable KIT blocking activity as KIT-Ab, and are effective inhibitors of ligand (SCF)-induced tyrosine phosphorylation of the cytoplasmic domain of KIT.
6.24 Example 24: Cell Proliferation Assays
[00559] Cell proliferation experiments with various cancer cell lines were performed to assess the effectiveness of KIT-PBD ADCs for use as an anti-cancer therapeutic. H526, H69, RD-ES, SK-N-MC, GIST Tl , GIST 430, GIST 882, HEL, and Kasumi-1 cells were confirmed to exhibit detectable KIT expression levels on the cell surface, while H524 did not exhibit detectable KIT expression levels on the cell surface; and KIT expression was not characterized for SK-PN-DW cells.
[00560] Briefly, cancer cells were plated onto 96-well plates, and then were treated with various doses of KIT-PBD l and KIT-PBD2 in 2% FBS medium. Following 96 hours in culture, CellTiter-Glo® reagent (Promega Madison, WI) was used to determine ATP content in each well (an indirect measurement of cell proliferation).
[00561] Figure 5 depicts a table summarizing the results, reported as IC50 values (nM), of representative cell proliferation assays. Specifically, KIT-PBDl and KIT-PBD2 ADCs exhibited inhibition of cell proliferation distinguishable from negative controls (KLH-PBD 1 and KLH- PBD2) with the following cell lines: SCLC cell line H526, Ewing's sarcoma cell lines RD-ES and SK-N-MC, GIST cell line GIST882, primitive neuroectodermal tumour (PNET) cell line SK-PN-DW, and leukemia cell line HEL.
[00562] KIT-PBD 1 and KIT-PBD2 ADCs did not exhibit inhibition of cell proliferation distinguishable from a negative control (KLH-PBD 1 and KLH-PBD2) in certain cancer cell lines, such as small cell lung cancer (SCLC) cell lines H524 and H69, and Gastrointestinal stromal tumor (GIST) cell line GIST430. This result is expected for H524 cells, as KIT expression on the cell surface was not detectable in these cells.
[00563] Inhibition of cell proliferation of the tested cancer cell lines described above was not observed with certain ADCs comprising a different toxin conjugated to the same anti-KIT antibodies which specifically bind to a D4 region of human KIT comprising human (e.g., composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set forth in Table 1 provided herein. 6.25 Example 25: In Vivo Xenograft Mouse Models
[00564] Anti-tumor efficacy of KIT-PBD ADCs in vivo was evaluated in various xenograft mouse models. In particular, studies with xenograft mouse models of Ewing's sarcoma, erythroid leukemia, and small cell lung cancer are described in the sections below.
6.25.1. RD-ES Ewing's Sarcoma Model
[00565] Studies were carried out to evaluate KIT-Ab, KIT-PBD 1 ADC, and KLH-PBD 1 ADC for efficacy in the RD-ES Ewing's sarcoma SCID mouse xenograft model. KIT-PBD2 ADC was not tested in this particular study. These studies were performed as follows.
[00566] Mice: Female severe combined immunodeficient mice (Fox Chase SCID®, C.B- \1 llcv-Prkdc cld , Charles River Laboratories) were eight weeks old with a body weight (BW) range of 16.2 to 21.7 grams on Day 1 of the study.
[00567] In Vivo Implantation: On the day of tumor implant, RD-ES cells were harvested and resuspended in 50% Matrigel (BD Biosciences) and 50% phosphate buffered saline (PBS) at a concentration of 2.5 x 107 cells/mL. Xenografts were initiated by subcutaneously injecting 5 x 106 RD-ES cells (0.2 mL cell suspension) into the right flank of each test animal and tumors were monitored as their volumes approached the target range of 200 to 300 mm3. Tumors were measured in two dimensions using calipers, and volume was calculated using the formula:
Tumor Volume (mm3) = w2 x 1
2
where w = width and 1 = length, in mm, of the tumor. Tumor weight may be estimated with the assumption that 1 mg is equivalent to 1 mm3 of tumor volume.
[00568] Twenty-one days after tumor implantation, the animals were sorted into six groups each consisting of ten mice with individual tumor volumes ranging from 172 to 352 mm3 and group mean tumor volumes from 258 to 260 mm3. This was designated as Day 1 of the study.
[00569] Treatment: On Day 1 of the study, mice bearing upstaged RD-ES xenografts were sorted into six groups (n = 10). Group 1 served as the control group for the study, and received PBS vehicle administered once on Day 1. Groups 2 and 3 received KLH-PBDl and KIT-Ab, respectively, each administered at 3 mg/kg once on Day 1. Group 4 received KIT-PBDl at 0.3 mg/kg once on Day 1. Groups 5 and 6 received KIT-PBDl at 1 and 3 mg/kg, respectively, each given on Days 1 and 43. All doses were administered intraperitoneally (i.p.). [00570] Endpoint and Tumor Growth Delay (TGD) Analysis: Tumors were measured using calipers twice per week, and each animal was euthanized when its tumor reached a volume of
2000 mm3 or at the end of the study, whichever came first. Animals that exited the study for tumor volume endpoint were documented as euthanized for tumor progression (TP), with the date of euthanasia. The time to endpoint (TTE) for analysis was calculated for each mouse by the following equation:
TTE = login (endpoint volume) - b
m
where TTE is expressed in days, endpoint volume is expressed in mm3, b is the intercept, and m is the slope of the line obtained by linear regression of a log-transformed tumor growth data set. The data set consisted of the first observation that exceeded the endpoint volume used in analysis and the three consecutive observations that immediately preceded the attainment of this endpoint volume. The calculated TTE is usually less than the TP date, the day on which the animal was euthanized for tumor size. Animals with tumors that did not reach the endpoint volume were assigned a TTE value equal to the last day of the study. Any animal classified as having died from NTR (non-treatment related) causes due to accident (NTRa) or due to unknown etiology (NTRu) were excluded from TTE calculations (and all further analyses). Animals classified as TR (treatment-related) deaths or NTRm (non-treatment-related death due to metastasis) were assigned a TTE value equal to the day of death.
[00571] Treatment outcome was evaluated from tumor growth delay (TGD), which is defined as the increase in the median time to endpoint (TTE) in a treatment group compared to the control group:
TGD = T - C
expressed in days, or as a percentage of the median TTE of the control group:
%TGD = T - C x 100
C
where:
T = median TTE for a treatment group, and
C = median TTE for the designated control group.
[00572] MTV and Criteria for Regression Responses: Treatment outcome may be determined from the tumor volumes of animals remaining in the study on the last day. The MTV (n) was defined as the median tumor volume on the last day of the study in the number of animals remaining (n) whose tumors had not attained the endpoint volume. Treatment outcome may also be determined from the incidence and magnitude of regression responses observed during the study. Treatment may cause partial regression (PR) or complete regression (CR) of the tumor in an animal. In a PR response, the tumor volume was 50% or less of its Day 1 volume for three consecutive measurements during the course of the study, and equal to or greater than 13.5 mm3 for one or more of these three measurements. In a CR response, the tumor volume was less than 13.5 mm3 for three consecutive measurements during the course of the study. An animal with a CR response at the termination of a study is additionally classified as a tumor-free survivor (TFS). Animals were monitored for regression responses.
[00573] Toxicity: Animals were weighed daily on Days 1-5, then twice per week until the completion of the study. The mice were observed frequently for overt signs of any adverse, treatment related side effects, and clinical signs of toxicity were recorded when observed.
Individual body weight loss was monitored, and any animal that exceeded the limits for acceptable body weight loss was euthanized. Group mean body weight loss also was monitored. Acceptable toxicity was defined as a group mean body- weight loss of less than 20% during the study and not more than 10% treatment-related (TR) deaths. Any dosing regimen resulting in greater toxicity was considered above the maximum tolerated dose (MTD). A death is classified as TR if attributable to treatment side effects as evidenced by clinical signs and/or necropsy, or may also be classified as TR if due to unknown causes during the dosing period or within 14 days of the last dose. A death is classified as non-treatment-related (NTR) if there is no evidence that death was related to treatment side effects. NTR deaths may be further characterized based on cause of death. A death may be classified as NTRa if it resulted from an accident or human error. A death may be classified as NTRm if necropsy indicated that it might have resulted from tumor dissemination by invasion and/or metastasis. A death may be classified as NTRu if the cause of death is unknown and there is no available evidence of death related to treatment side effects, metastasis, accident or human error, although death due to treatment side effects cannot be excluded.
[00574] Statistical and Graphical Analyses: Prism (GraphPad) for Windows 3.03 was used for graphical presentations and statistical analyses. The logrank test was employed to assess the significance of the difference between the overall survival experiences of two groups. The logrank test analyzes the individual TTEs for all animals in a group, except those lost to the study due to NTR death. For statistical analyses, two-tailed tests were conducted at significance level P = 0.05.
[00575] Prism summarizes test results as not significant (ns) at P > 0.05, significant
(symbolized by "*") at 0.01 < P < 0.05, very significant ("**") at 0.001 < P < 0.01 , and extremely significant ("***") at P < 0.001.
[00576] Results: There were no mean BW losses in Groups 1-5, and an acceptable mean BW nadir of -5.3% on Day 57 in Group 6.
[00577] Figure 6 presents plots of median tumor growth for each group in the study. The median TTE for PBS-treated control mice was 26.2 days, establishing a maximum possible TGD of 41.8 days (160%) for the 68-day study. KLH-PBDl and KIT-Ab (3 mg/kg i.p.) were negligibly active in this model, yielding TGDs of 4.9 days (19%>) and 3.7 days (14%>), respectively, with no regressions.
[00578] KIT-PBDl at 0.3 mg/kg i.p. on Day 1 produced TGD of 12.6 days (48%), no regressions, and a significant survival difference compared to controls (P < 0.001). The mean tumor growth plot for this group suggested measureable delay, given the single dose on Day 1. KIT-PBDl at 1 and 3 mg/kg i.p. on Days 1 and 43 resulted in TGD of 34.4 days (131%) and the maximum TGD (41.8 days, 160%), respectively, with 100% regressions (after the first dose) in the 3 mg/kg group. KIT-PBDl at 3 mg/kg i.p. Days 1 and 43 produced important activity with a notable advantage in regression responses compared to all other regimens in the study.
[00579] In summary, all three doses of KIT-PBD 1 ADC exhibited better TGD efficacy than KLH-PBDl and KIT-Ab. KIT-PBDl ADC produced dose-related efficacy and noteworthy TGD and regressions at the highest dosage tested.
[00580] In contrast, delay of tumor growth was not observed in this xenograph mouse model of Ewing's sarcoma with certain ADCs comprising a different toxin conjugated to the same anti- KIT antibodies which specifically bind to a D4 region of human KIT comprising human (e.g., composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set forth in Table 1 provided herein. 6.25.2. Erythroid Leukemia Model
[00581] Studies were conducted to evaluate the in vivo efficacy of KIT-PBD ADCs in xenograft mouse models of leukemia.
[00582] Animals: BALB/c nude, female, 6-8 weeks, weighing approximately 18-22g were used in these studies.
[00583] Tumor Inoculation and treatment protocol: Each mouse was inoculated
subcutaneously at the right flank with HEL92.1.7 tumor cells (3 x 106) in 0.1 ml of PBS for tumor development. The animals were randomized and treatment with KIT-PBD ADCs started when the average tumor volume reached approximately 150-200 mm3. The animals were divided into the following groups with 16 animals each:
• Group 1 : PBS control (10 μΐ/g), administered i.p.
• Group 2: 3 mg/kg KLH-PBD2 administered i.p. (1 dose)
• Group 3 : 3 mg/kg KLH-PBD1 administered i.p. (1 dose)
• Group 4: 3 mg/kg KIT-PBD2 administered i.p. (1 dose)
• Group 5 : 3 mg/kg KIT-PBD 1 administered i.p. (1 dose)
• Group 6: 3 mg/kg KIT-Ab administered i.p. (ldose)
[00584] Two animals in each group were harvested for serum collection at 6 hours post dose. An additional two animals in each group were sacrificed for both serum collection and tumor excision at Day 6. The remaining animals in each group was harvested for both serum collection and tumor collection at the end of the study.
[00585] Tumor sizes was measured twice weekly in two dimensions using a caliper, and tumor volume was expressed in mm3 using the formula: V = 0.5 a x b2 where a and b are the long and short diameters of the tumor, respectively. The tumor sizes are then used for the calculations of both T-C and T/C values. T-C is calculated with T as the median time (in days) required for the treatment group tumors to reach a predetermined size (e.g., 1 ,000 mm3), and C is the median time (in days) for the control group tumors to reach the same size. The T/C value (in percent) is an indication of antitumor effectiveness, T and C are the mean volume of the treated and control groups, respectively, on a given day. [00586] TGI is calculated for each group using the formula: TGI (%) = [ 1 -(Ti-T0)/ (Vi-V0)] x 100; Ti is the average tumor volume of a treatment group on a given day, TO is the average tumor volume of the treatment group on the first day of treatment, Vi is the average tumor volume of the vehicle control group on the same day with Ti, and V0 is the average tumor volume of the vehicle group on the first day of treatment. All animals were sacrificed when the mean tumor volume of the vehicle treated control group reaches a value of 2,000 mm3.
[00587] Statistical Analysis: For comparison among three or more groups, a one-way ANOVA was performed. If a significant F-statistics (a ratio of treatment variance to the error variance) is obtained, multiple comparison procedures were applied after ANOVA. All data were analyzed using SPSS 17.0. p < 0.05 is considered to be statistically significant.
[00588] Results: No effects on body weight were observed in any treatment group. Figures 7A-B present plots of mean tumor growth for each group in the study. Specifically, KIT-PBD2 ADC was more effective than KIT-Ab and KLH-PBD2, in delaying tumor growth in this erythroid leukemia model. In this model, KIT-PBD l was slightly more effective than KIT-Ab, but was comparable to the negative control KLH-PBDl , in delaying tumor growth.
[00589] Delay of tumor growth was not observed in this xenograft mouse model of erythroid leukemia with certain ADCs comprising a different toxin conjugated to the same anti-KIT antibodies which specifically bind to a D4 region of human KIT comprising human (e.g., composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set forth in Table 1 provided herein.
6.25.3. SCLC Model
[00590] Studies were conducted to evaluate the in vivo efficacy of KIT-PBD ADCs in xenograft mouse models of small cell lung cancer (SCLC).
[00591] Animals: BALB/c nude, female, 6-8 weeks, weighing approximately 18-22g were used in these studies.
[00592] Tumor Inoculation and treatment protocol: Each mouse was inoculated
subcutaneously at the right flank with H526 tumor cells (5 x 106) in 0.1 ml of PBS
(supplemented with Matrigel in a ratio of 1 : 1 with PBS) for tumor development. The animals were randomized and treatment with KIT-PBD ADCs and controls started when the average tumor volume reached approximately 150-200 mm3. The animals were divided into the following groups with 10 animals each: • Group 1 : PBS control (10 μΐ/g), administered i.p.
• Group 2: 1 mg/kg KIT -PBDl administered i.p. (1 dose)
• Group 3 : 3 mg/kg KIT -PBDl administered i.p. (1 dose)
• Group 4: 1 mg/kg KIT-PBD2 administered i.p. (1 dose)
• Group 5 : 3 mg/kg KIT-PBD2 administered i.p. (1 dose)
• Group 6: 3 mg/kg KLH-PBDl administered i.p. (ldose)
• Group 7: 3mg/kg KLH-PBD2 administered i.p. (ldose)
[00593] Tumor sizes was measured twice weekly in two dimensions using a caliper, and tumor volume was expressed in mm3 using the formula: V = 0.5 a x b2 where a and b are the long and short diameters of the tumor, respectively. The tumor sizes are then used for the calculations of both T-C and T/C values. T-C is calculated with T as the median time (in days) required for the treatment group tumors to reach a predetermined size (e.g., 1 ,000 mm3), and C is the median time (in days) for the control group tumors to reach the same size. The T/C value (in percent) is an indication of antitumor effectiveness, T and C are the mean volume of the treated and control groups, respectively, on a given day.
[00594] TGI is calculated for each group using the formula: TGI (%) = [ 1 -(Ti-T0)/ (Vi-V0)] x 100; Ti is the average tumor volume of a treatment group on a given day, TO is the average tumor volume of the treatment group on the first day of treatment, Vi is the average tumor volume of the vehicle control group on the same day with Ti, and V0 is the average tumor volume of the vehicle group on the first day of treatment. All animals were sacrificed when the mean tumor volume of the vehicle treated control group reaches a value of 2,000 mm3.
[00595] Statistical Analysis: For comparison among three or more groups, a one-way
ANOVA was performed. If a significant F-statistics (a ratio of treatment variance to the error variance) is obtained, multiple comparison procedures were applied after ANOVA. All data were analyzed using SPSS 17.0. p < 0.05 is considered to be statistically significant.
[00596] Results: No effect on body weight were observed in any treatment group. Figures 8 A (PBDl ADCs) and 8B (PBD2 ADCs) present graphs plotting of mean tumor growth for each treatment group in the study. In particular, both KIT-PBDl and KIT-PBD2 (at the 1 mg/kg and 3mg/kg doses) exhibited activity, relative to their respective ADC negative controls (KLH-PBDl and KLH-PBD2), in delaying and/or inhibiting tumor growth in this SCLC model.
[00597] Delay of tumor growth was not observed in these xenograft mouse models of SCLC with certain ADCs comprising a different toxin conjugated to the same anti-KIT antibodies which specifically bind to a D4 region of human KIT comprising human (e.g., composite human) framework regions and VH CDRs (SEQ ID NOs: 16-18) and VL CDRs (SEQ ID NOs: 19-21) as set forth in Table 1 provided herein.
6.26 Example 26: Colony Formation Assays
[00598] Colony formation assays with various acute myeloid leukemia (AML) cell lines were performed to further assess the effectiveness of KIT-PBD ADCs for use as an anti-cancer therapeutic. Kasumi-1 , UKE-1 , and OCI Ml AML cell lines were incubated with different concentrations of anti-KIT antibody, anti-KIT ADCs, or control ADCs, and cultured in triplicate in methylcellulose-based semi-solid media without or supplemented with growth factors
(Methocult H4230 and Methocult H4435 Enriched) (Stem Cell Technologies, Vancouver, Canada). After seven to twelve days, the number of colonies was counted using an inverted microscope (Axiovert 25, Zeiss, Jena, Germany).
[00599] Figures 9A, 9B, and 9C depict the results for the colony formation assays for Kasumi- 1 , UKE-1 , and OCI Ml cell lines, respectively. Specifically, KIT-PBDl and KIT-PBD2 ADCs exhibited inhibition of colony formation distinguishable from their ADC negative controls (KLH-PBDl and KLH-PBD2, respectively) and the naked anti-KIT antibody for all three cell lines.
[00600] The invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described will become apparent to those skilled in the art from the foregoing description and accompanying figures. Such modifications are intended to fall within the scope of the appended claims.
[00601] All references (e.g., publications or patents or patent applications) cited herein are incorporated herein by reference in their entirety and for all purposes to the same extent as if each individual reference (e.g. , publication or patent or patent application) was specifically and individually indicated to be incorporated by reference in its entirety for all purposes.

Claims

CLAIMS:
1. A PBD dimer conjugate of Formula Ab(X)m or a pharmaceutically acceptable salt
thereof, wherein
Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, comprising:
(i) a light chain variable region ("VL") comprising the amino acid sequence:
DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILI YSASYRYSGVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQYNSY PRTFGGGTKVEIK, wherein Χκι is an amino acid with an aromatic or aliphatic hydroxyl side chain, Χκ2 is an amino acid with an aromatic or aliphatic hydroxyl side chain Χ 3 is an amino acid with an aliphatic hydroxyl side chain, XK4 is an amino acid with an aliphatic hydroxyl side chain or is P, XKS is an amino acid with a charged or acidic side chain and Χκβ is an amino acid with an aromatic side chain; and
(ii) a heavy chain variable region ("VH") comprising the amino acid sequence: QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKGLE WIARIYPGSGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSEDXH sAVYFC ARGVY YFD Y WGQGTT VT VS S , wherein XM is an amino acid with an aliphatic side chain, XH2 is an amino acid with an aliphatic side chain XH3 is an amino acid with a polar or basic side chain XH4 is an amino acid with an aliphatic side chain XHS is an amino acid with an aliphatic side chain XH6 is an amino acid with an acidic side chain, XR7 is an amino acid with an acidic or amide derivative side chain, and XHS is an amino acid with an aliphatic hydroxyl side chain; and wherein X is
Figure imgf000218_0001
or X is
Figure imgf000218_0002
and wherein m is 1 to 8.
2. A PBD dimer conjugate of Formula Ab(X)m or a pharmaceutically acceptable salt
thereof, wherein
Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, comprising:
(i) a light chain variable region ("VL") comprising the amino acid sequence:
DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXK2LI YSASYRYSGVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQYNSY PRTFGGGTKVEIK, wherein Χκι is an amino acid with an aromatic or aliphatic hydroxyl side chain, Χ 2 is an amino acid with an aromatic or aliphatic hydroxyl side chain Χκ3 is an amino acid with an aliphatic hydroxyl side chain, Χ 4 is an amino acid with an aliphatic hydroxyl side chain or is P, XKS is an amino acid with a charged or acidic side chain and Χκβ is an amino acid with an aromatic side chain; and
(ii) a heavy chain variable region ("VH") comprising the amino acid sequence: QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKGLE WIARIYPGSGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSEDXH sAVYFC ARGVY YFD Y WGQGTT VT VS S , wherein XM is an amino acid with an aliphatic side chain, XH2 is an amino acid with an aliphatic side chain XH3 is an amino acid with a polar or basic side chain XH4 is an amino acid with an aliphatic side chain XHS is an amino acid with an aliphatic side chain XH6 is an amino acid with an acidic side chain, XR7 is an amino acid with an acidic or amide derivative side chain, and XHS is an amino acid with an aliphatic hydroxyl side chain; and
wher
Figure imgf000219_0001
Figure imgf000219_0002
Figure imgf000220_0001
and wherein m is 1 to 8.
3. The PBD dimer conjugate of claim 1, wherein X is
Figure imgf000220_0002
Figure imgf000221_0001
Figure imgf000221_0002
Figure imgf000221_0003
-219- The PBD dimer conjugate of claim 2, wherein X
Figure imgf000222_0001
The PBD dimer conjugate of claim 2, wherein X
Figure imgf000222_0002
9. The PBD dimer conjugate of any one of claims 1 to 8, wherein Ab is an antibody or an antigen-binding fragment thereof, which immunospecifically binds to D4 of a human KIT receptor, comprising: a light chain variable region ("VL") and a heavy chain variable region ("VH"), wherein:
(i) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(ii) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(iii) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
(iv) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 5; (v) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(vi) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(vii) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(viii) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
(ix) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(x) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(xi) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
(xii) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(xiii) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(xiv) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(xv) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
(xvi) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
(xvii) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(xviii) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(xix) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 5; or (xx) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 6.
10. The PBD dimer conjugate of any one of claims 1 to 8, wherein m is 1 to 3.
11. The PBD dimer conjugate of any one of claims 1 to 8, wherein m is 2.
12. The PBD dimer conjugate of claim 9, wherein m is 1 to 3.
13. The PBD dimer conjugate of claim 9, wherein m is 2.
14. A PBD dimer conjugate of Formula Ab(X)m or a pharmaceutically acceptable salt
thereof, wherein
Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to an Ig-like domain 4 (D4) of a human KIT receptor, comprising:
(i) a light chain variable region ("VL") comprising a VL CDRl, VL CDR2, and VL CDR3 comprising the amino acid sequences KASQNVRTNVA (SEQ ID NO: 19), SASYRYS (SEQ ID NO: 20), and QQYNSYPRT (SEQ ID NO: 21), respectively; and
(ii) a heavy chain variable region ("VH") comprising VH CDRl, VH CDR2, and VH CDR3 comprising the amino acid sequences DYYIN (SEQ ID NO: 16), RIYPGSGNTYYNEKFKG (SEQ ID NO: 17), and GVYYFDY (SEQ ID NO: 18), res ectively;
Figure imgf000224_0001
1 to 20
Figure imgf000224_0002
n is 2 to 12;
p is 2 to 36;
Figure imgf000225_0001
q is 1 to 3;
C6 cycloalkyl, C2-C6 alkenyl,
Figure imgf000225_0002
The PBD dimer conjugate of claim 14, wherein Ab is an antibody, or an antigen-binding fragment thereof, which immunospecifically binds to D4 of a human KIT receptor, comprising:
(a) (i) a light chain variable region ("VL") comprising the amino acid sequence:
DIVMTQSPSXKILSASVGDRVTITCKASQNVRTNVAWYQQKPGKAPKXKILIY SASYRYSGVPDRFXK3GSGSGTDFTLTISSLQXK4EDFAXK5YXK6CQQYNSYPR TFGGGTKVEIK, wherein Χκι is an amino acid with an aromatic or aliphatic hydroxyl side chain, Χκ2 is an amino acid with an aromatic or aliphatic hydroxyl side chain XK3 is an amino acid with an aliphatic hydroxyl side chain XK4 is an amino acid with an aliphatic hydroxyl side chain or is P, XKS is an amino acid with a charged or acidic side chain, and Χκβ is an amino acid with an aromatic side chain; and (ii) a heavy chain variable region ("VH") comprising a VH CDR1 , VH CDR2, and VH CDR3 having the amino acid sequences of SEQ ID NO: 16, SEQ ID NO: 17, and SEQ ID NO: 18, respectively; or (b)(i) a VL comprising a VL CDR1 , VL CDR2, and VL CDR3 having the amino acid sequences of SEQ ID NO: 19, SEQ ID NO: 20, and SEQ ID NO: 21 , respectively; and
(ii) a VH comprising the amino acid sequence:
QVQLVQSGAEXHIKKPGASVKXHISCKASGYTFTDYYINWVXHSQAPGKGLE WIARIYPGSGNTYYNEKFKGRXH4TXH5TAXH6KSTSTAYMXH7LSSLRSEDXH8 AVYFC ARGVYYFD YWGQGTT VT VS S , wherein XM is an amino acid with an aliphatic side chain, XH2 is an amino acid with an aliphatic side chain XH3 is an amino acid with a polar or basic side chain, XR4 is an amino acid with an aliphatic side chain XHs is an amino acid with an aliphatic side chain XH6 is an amino acid with an acidic side chain, XR7 is an amino acid with an acidic or amide derivative side chain, and XHS is an amino acid with an aliphatic hydroxyl side chain.
The PBD dimer con ugate of claim 14 or 15, wherein
Figure imgf000226_0001
17. The PBD dimer conjugate of any one of claims 14 to 16, wherein m is 1 to 3, or m is 2.
18. The PBD dimer conjugate of any one of claims 14 to 17, wherein
Figure imgf000226_0002
19. The PBD dimer conjugate of any one of claims 14 to 18, wherein q is 1 or 3.
20. The PBD dimer conjugate of any one of claims 14 to 19, wherein R is methyl or E-prop- 1-en-l-yl. The PBD dimer conjugate of any one of claims 14 to 20, wherein
Figure imgf000227_0001
The PBD dimer conjugate of any one of claims 14 to 20 wherein
Figure imgf000227_0002
23. The PBD dimer conjugate of any one of claims 14 to 22, wherein n is 4 or 8.
24. The PBD dimer conjugate of claim 14, wherein
Figure imgf000227_0003
Figure imgf000228_0001
Figure imgf000228_0002
27. The PBD dimer conjugate of any one of claims 24 to 26, wherein m is 1 to 3.
The PBD dimer conjugate of any one of claims 14 to 17, wherein
Z is
Figure imgf000228_0003
29. The PBD dimer conjugate of any one of claims 14 to 17 and 2727, wherein q is 1. The PBD dimer c 17, 27, and 29, wherein
R is cyclopropyl,
Figure imgf000229_0001
31. The PBD dimer conjugate of any one of claims 14 to 17 and 27 to 30, wherein
Figure imgf000229_0002
32. The PBD dimer conjugate of any one of claims 14 to 17 and 27 to 30, wherein
-L-NH- is
Figure imgf000229_0003
33. The PBD dimer conjugate of any one of claims 14 to 31, wherein n is 8.
34. The PBD dimer conjugate of any one of claims 14 to 30 and 32, wherein p is 5.
35. The PBD dimer conjugate of claim 14, wherein
Figure imgf000229_0004
The PBD dimer conjugate of claim 14, wherein
X is
Figure imgf000230_0001
The PBD dimer conjugate of claim 14, wherein
X is
Figure imgf000230_0002
38. The PBD dimer conjugate of any one of claims 35 to 37, wherein m is 1 to 3.
39. The PBD dimer conjugate of any one of claims 14, 24, 25, 26, 27, 35, 36, 37, and 38, wherein Ab is an antibody or an antigen-binding fragment thereof, which
immunospecifically binds to D4 of a human KIT receptor, comprising ) a light chain variable region ("VL") and a heavy chain variable region ("VH"), wherein:
(i) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(ii) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(iii) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 6; (iv) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
(v) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(vi) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(vii) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(viii) the VL comprises the amino acid sequence of SEQ ID NO: 7 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
(ix) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(x) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(xi) the VL comprises the amino acid sequence of SEQ ID NO: 8 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
(xii) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(xiii) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 3;
(xiv) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 4;
(xv) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 5;
(xvi) the VL comprises the amino acid sequence of SEQ ID NO: 9 and the VH comprises the amino acid sequence of SEQ ID NO: 6;
(xvii) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 2;
(xviii) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 4; (xix) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 5; or
(xx) the VL comprises the amino acid sequence of SEQ ID NO: 10 and the VH comprises the amino acid sequence of SEQ ID NO: 6.
40. A pharmaceutical composition comprising the PBD dimer conjugate of any one of claims 1 to 39 or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable excipient.
41. A plurality of PBD dimer conjugates of any one of claims 1 to 39, wherein the average drug-per-antibody ratio ("DAR") is 1.5 to 3.
42. A method of treating cancer comprising administering to a subject in need thereof a
therapeutically effective amount of a PBD dimer conjugate of any one of claims 1 to 39 or a pharmaceutically acceptable salt thereof.
43. The method of claim 42, wherein the cancer is leukemia, lung cancer, melanoma,
sarcoma, or gastrointestinal stromal tumors.
44. The method of claim 42, wherein the cancer is acute myeloid leukemia (AML) or small cell lung cancer.
45. The method of claim 42, wherein the cancer is refractory to treatment by a tyrosine
kinase inhibitor.
46. The method of claim 45, wherein the tyrosine kinase inhibitor is imatinib mesylate or SU11248.
47. The method of claim 42, wherein the method further comprises administering a second therapeutic agent.
48. The method of claim 47, wherein the second therapeutic agent is a chemotherapeutic agent, a tyrosine kinase inhibitor, a histone deacetylase inhibitor, an antibody, or a cytokine.
49. The method of claim 48, wherein the tyrosine kinase inhibitor is imatinib mesylate or SU11248.
50. A method of treating fibrosis or an inflammatory disorder, comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate of any one of claims 1 to 39 or a pharmaceutically acceptable salt thereof.
51. A method of treating a mast cell associated disorder, comprising administering to a
subject in need thereof a therapeutically effective amount of a PBD dimer conjugate of any one of claims 1 to 39 or a pharmaceutically acceptable salt thereof.
52. A method of treating neurofibromatosis, comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate of any one of claims 1 to 39 or a pharmaceutically acceptable salt thereof.
53. A method of treating systemic mastocytosis, comprising administering to a subject in need thereof a therapeutically effective amount of a PBD dimer conjugate of any one of claims 1 to 39 or a pharmaceutically acceptable salt thereof.
54. A method of treating cancer comprising administering to a subject in need thereof a therapeutically effective amount of the plurality of PBD dimer conjugates of claim 41.
55. A method of treating fibrosis or an inflammatory disorder, comprising administering to a subject in need thereof a therapeutically effective amount of the plurality of PBD dimer conjugates of claim 41.
56. A method of treating a mast cell associated disorder, comprising administering to a
subject in need thereof a therapeutically effective amount of the plurality of PBD dimer conjugates of claim 41.
57. A method of treating neurofibromatosis, comprising administering to a subject in need thereof a therapeutically effective amount of the plurality of PBD dimer conjugates of claim 41. A method of treating systemic mastocytosis, comprising administering to a subject in need thereof a therapeutically effective amount of the plurality of PBD dimer conjugates of claim 41.
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