ANTI-ITGA3 ANTIBODIES, ACTIVATABLE ANTI-ITGA3 ANTIBODIES, AND METHODS OF USE THEREOF

• US 20190309072A1
• Filed: 01/18/2019
• Published: 10/10/2019
• Est. Priority Date: 05/04/2015
• Status: Abandoned Application

• Current Assignee: CytomX Therapeutics, Inc
• Original Assignee: CytomX Therapeutics, Inc
• Inventors: SAGERT, Jason Gary, Terrett, Jonathan Alexander, Desnoyers, Luc Roland, Singh, Shweta, Weaver, Annie Yang
• Application Number:
  US16/251,919
• Publication Number:
  US 20190309072A1
• Time in Patent Office: Days
• CPC Class Codes: A61K 2039/505 comprising antibodies
• CPC Class Codes: A61K 47/68031 the drug being an auristatin
• CPC Class Codes: A61K 47/68033 the drug being a maytansine
• CPC Class Codes: A61K 47/6809 Antibiotics, e.g. antitumor antibiotics anthracyclins, adriamycin, doxorubicin or daunomycin
• CPC Class Codes: A61K 47/6849 the antibody targeting a receptor, a cell surface antigen or a cell surface determinant
• CPC Class Codes: A61K 47/6851 the antibody targeting a determinant of a tumour cell
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/02 specific for leukemia
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07K 16/2839 against the integrin superfamily
• CPC Class Codes: C07K 16/2842 against integrin beta1-subunit-containing molecules, e.g. CD29, CD49
• CPC Class Codes: C07K 16/30 from tumour cells
• CPC Class Codes: C07K 2317/24 containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
• CPC Class Codes: C07K 2317/33 Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
• CPC Class Codes: C07K 2317/732 Antibody-dependent cellular cytotoxicity [ADCC]
• CPC Class Codes: C07K 2317/92 Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C07K 2319/50 containing protease site
• CPC Class Codes: C07K 7/08 having 12 to 20 amino acids gastrins C07K14/595; somatostatins C07K14/655; melanotropins C07K14/68

Abstract

The invention relates generally to antibodies that bind ITGa3, activatable antibodies that specifically bind to ITGa3 and methods of making and using these anti-ITGa3 antibodies and anti-ITGa3 activatable antibodies in a variety of therapeutic, diagnostic and prophylactic indications.

Claims

1-91. -91. (canceled)

92. A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease in which diseased cells express ITGa3 comprising administering a therapeutically effective amount of a conjugated activatable antibody that, in an activated state, binds ITGa3 to a subject in need thereof, the conjugated activatable antibody comprising:

(a) an activatable antibody, wherein the activatable antibody comprises;

(i) an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian ITGa3, wherein the AB specifically binds human ITGa3 and cynomolgus monkey ITGa3;

(ii) a masking moiety (MM) coupled to the AB, wherein the MM inhibits the binding of the AB to ITGa3 when the activatable antibody is in an uncleaved state; and

(iii) a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease; and

(b) an agent conjugated to the AB.

93. The method of claim 92, wherein the disorder or disease is cancer.

96. The method of claim 93, wherein the cancer is an adenocarcinoma, a bile duct (biliary) cancer, a bladder cancer, a bone cancer, a breast cancer, a Her2-negative breast cancer, a triple-negative breast cancer, an endometrial cancer, an estrogen receptor-positive breast cancer, a carcinoid, a cervical cancer, a cholangiocarcinoma, a colorectal cancer, a colon cancer, an endometrial cancer, a glioma, a head and neck cancer, a head and neck squamous cell cancer, a leukemia, a liver cancer, a lung cancer, a non-small cell lung cancer, a small cell lung cancer, a lymphoma, a melanoma, an oropharyngeal cancer, an ovarian cancer, a pancreatic cancer, a prostate cancer, a metastatic castration-resistant prostate carcinoma, a renal cancer, a sarcoma, a skin cancer, a squamous cell cancer, a stomach cancer, a testis cancer, a thyroid cancer, a urogenital cancer, or a urothelial cancer.

99. The method of claim 92, wherein the method comprises administering an additional agent.

100. The method of claim 99, wherein the additional agent is a therapeutic agent.

101. The method of claim 92, wherein the agent has one or more of the characteristics selected from the group consisting of:

(a) the agent is a toxin or fragment thereof;

(b) the agent is a microtubule inhibitor;

(c) the agent is a nucleic acid damaging agent;

(d) the agent is a dolastatin or a derivative thereof;

(e) the agent is an auristatin or a derivative thereof;

(f) the agent is a maytansinoid or a derivative thereof;

(g) the agent is a duocarmycin or a derivative thereof;

(h) the agent is a calicheamicin or a derivative thereof;

(i) the agent is a pyrrolobenzodiazepine or a derivative thereof;

(j) the agent is auristatin E or a derivative thereof;

(k) the agent is monomethyl auristatin E (MMAE);

(l) the agent is monomethyl auristatin D (MMAD);

(m) the agent is monomethyl auristatin F (MMAF);

(m) the agent is the maytansinoid DM1;

(n) the agent is the maytansinoid DM4;

(o) the agent is a pyrrolobenzodiazepine dimer;

(p) the agent is a detectable moiety; and

(q) the agent is a diagnostic agent.

102. The method of claim 92, wherein the agent is conjugated to the AB via a linker.

103. The method of claim 102, wherein the linker with which the agent is conjugated to the AB comprises an SPDB moiety, a vc moiety, or a PEG2-vc moiety,

104. The method of claim 92, wherein the agent is a toxin conjugated to the AB via a linker, and wherein the linker and the toxin conjugated to the AB comprise a moiety selected from the group consisting of:

an SPDB-DM4 moiety, a vc-MMAD moiety, a vc-MMAE moiety, a vc-duocarmycin moiety, or a PEG2-vc-MMAD moiety.

105. The method of claim 102, wherein the linker is a cleavable linker.

106. The method of claim 102, wherein the linker is a non-cleavable linker.

107. The method of claim 92, wherein the activatable antibody of the conjugated activatable antibody has one or more of the characteristics selected from the group consisting of:

(i) the activatable antibody comprises a VH CDR1 comprising the amino acid sequence EYIIH (SEQ ID NO;

     13);

a VH CDR2 comprising the amino acid sequence WFYPESGSVKYNETFKG (SEQ ID NO;

     14) or WFYPESGSVKYSETFKG (SEQ ID NO;

     15) or WFYPESGSVKYNEAFKG (SEQ ID NO;

     16) or WFYPESGSVKYNEGFKG (SEQ ID NO;

     17);

a VH CDR3 comprising the amino acid sequence HEERDYYGYYAMDY (SEQ ID NO;

     18);

a VL CDR1 comprising the amino acid sequence SASSSISSNYLH (SEQ ID NO;

     19);

a VL CDR2 comprising the amino acid sequence RTSNLA (SEQ ID NO;

     20); and

a VL CDR3 comprising the amino acid sequence QQGSSIPRFT (SEQ ID NO;

     21);

(ii) the activatable antibody comprises a heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

3-10, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

11, 12, 396, 398, 400, 402, 404-431, 436, 438, 440, 442, and 444-471; and

(iii) the activatable antibody comprises a heavy chain comprising an amino acid sequence of SEQ ID NO;

320; and

a light chain sequence comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

255, 257, 259, 261, 322, 324, 326, 328, 330, 332-359, and 364-391.

108. The method of claim 92, wherein the MM comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:

22-54.

109. The method of claim 92, wherein the CM comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:

182-249 and 276-316.

110. The method of claim 92, wherein the conjugated activatable antibody has one or more of the following characteristics selected from the group consisting of:

(i) the activatable antibody of the conjugated activatable antibody comprises a combination of amino acid sequences, wherein the combination of amino acid sequences is selected from a single row in Table D,

wherein for a given combination,

(a) the heavy chain of the AB comprises the amino acid sequences of the VH CDR sequences corresponding to the given combination in the single row listed in Table D,

(b) the light chain of the AB comprises the amino acid sequences of the VL CDR sequences corresponding to the given combination in the single row listed in Table D,

(c) the MM comprises the amino acid sequence of the mask sequence (MM) corresponding to the given combination in the single row listed in Table D, and

(d) the CM comprises the amino acid sequence of the substrate sequence (CM) corresponding to the given combination in the single row listed in Table D;

(ii) the activatable antibody of the conjugated activatable antibody comprises a combination of amino acid sequences, wherein for a given combination of amino acid sequences,

(a) the heavy chain of the AB comprises the amino acid sequences of the VH sequence or VH CDR sequences selected from the group consisting of;

the VH sequence or VH CDR sequences listed in the corresponding column of Table E,

(b) the light chain of the AB comprises the amino acid sequences of the VL sequence or VL CDR sequences selected from the group consisting of;

the VL sequence or VL CDR sequences listed in the corresponding column of Table E,

(c) the MM comprises the amino acid sequence of the mask sequence (MM) selected from the group consisting of;

the MM sequences listed in the corresponding column of Table E, and

(d) the CM comprises the amino acid sequence of the substrate sequence (CM) selected from the group consisting of;

the CM sequences listed in the corresponding column of Table E; and

(iii) the conjugated activatable antibody comprises a combination of amino acid sequences, a linker, and a toxin selected from a single row in Table F, wherein for the given combination;

(a) the AB comprises a heavy chain comprising the amino acid sequence of the heavy chain sequence or heavy chain variable domain sequence corresponding to the given combination in the single row listed in Table F,

(b) the AB comprises a light chain comprising the amino acid sequence of the light chain sequence or light chain variable domain sequence corresponding to the given combination in the single row listed in Table F, and

(c) the linker and the toxin comprise the linker and the toxin corresponding to the given combination in the single row listed in Table F.

94. A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease associated with cells expressing ITGa3 comprising administering a therapeutically effective amount of a conjugated activatable antibody that, in an activated state, binds ITGa3 to a subject in need thereof, the conjugated activatable antibody comprising:

(a) an activatable antibody, wherein the activatable antibody comprises;

(i) an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian ITGa3, wherein the AB specifically binds human ITGa3 and cynomolgus monkey ITGa3;

(ii) a masking moiety (MM) coupled to the AB, wherein the MM inhibits the binding of the AB to ITGa3 when the activatable antibody is in an uncleaved state; and

(iii) a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease; and

(b) an agent conjugated to the AB.

95. The method of claim 94, wherein the disorder or disease associated with cells expressing ITGa3 is cancer.

97. A method of inhibiting or reducing the growth, proliferation, or metastasis of cells expressing mammalian ITGa3 comprising administering a therapeutically effective amount of a conjugated activatable antibody that, in an activated state, binds ITGa3 to a subject in need thereof, conjugated activatable antibody comprising:

(a) an activatable antibody, wherein the activatable antibody comprises;

(i) an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian ITGa3, wherein the AB specifically binds human ITGa3 and cynomolgus monkey ITGa3;

(ii) a masking moiety (MM) coupled to the AB, wherein the MM inhibits the binding of the AB to ITGa3 when the activatable antibody is in an uncleaved state; and

(iii) a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease; and

(b) an agent conjugated to the AB.

98. A method of inhibiting, blocking, or preventing the binding of a natural ligand or receptor to mammalian ITGa3, comprising administering a therapeutically effective amount of a conjugated activatable antibody that, in an activated state, binds ITGa3 to a subject in need thereof, w the conjugated activatable antibody comprising:

(a) an activatable antibody, wherein the activatable antibody comprises;

(i) an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian ITGa3, wherein the AB specifically binds human ITGa3 and cynomolgus monkey ITGa3;

(ii) a masking moiety (MM) coupled to the AB, wherein the MM inhibits the binding of the AB to ITGa3 when the activatable antibody is in an uncleaved state; and

(iii) a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease; and

(b) an agent conjugated to the AB.

111. A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease, wherein the diseased cells express ITGa3 or wherein the disorder or the disease is associated with cells expressing ITGa3, or a method of inhibiting or reducing the growth, proliferation, or metastasis of cells expressing mammalian ITGa3, wherein the method comprises

administering a therapeutically effective amount of conjugated activatable antibody that, in an activated state, binds ITGa3 to a subject in need thereof, the conjugated activatable antibody comprising:

(a) an activatable antibody comprising;

(i) an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian ITGa3, wherein the AB specifically binds human ITGa3 and cynomolgus monkey ITGa3;

(ii) a masking moiety (MM) coupled to the AB that inhibits the binding of the AB to ITGa3 when the activatable antibody is in an uncleaved state;

(iii) a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease; and

(b) an agent conjugated to the AB,

wherein the activatable antibody comprises;

(i) a VH CDR1 comprising the amino acid sequence EYIIH (SEQ ID NO;

     13);

a VH CDR2 comprising the amino acid sequence WFYPESGSVKYNETFKG (SEQ ID NO;

     14) or WFYPESGSVKYSETFKG (SEQ ID NO;

     15) or WFYPESGSVKYNEAFKG (SEQ ID NO;

     16) or WFYPESGSVKYNEGFKG (SEQ ID NO;

     17);

a VH CDR3 comprising the amino acid sequence HEERDYYGYYAMDY (SEQ ID NO;

     18);

a VL CDR1 comprising the amino acid sequence SASSSISSNYLH (SEQ ID NO;

     19);

a VL CDR2 comprising the amino acid sequence RTSNLA (SEQ ID NO;

     20); and

a VL CDR3 comprising the amino acid sequence QQGSSIPRFT (SEQ ID NO;

     21), or

(ii) a heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

3-10, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

11, 12, 396, 398, 400, 402, 404-431, 436, 438, 440, 442, and 444-471;

or

(iii) a heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO;

320, and a light chain comprising an amino acid sequence selected from the group consisting of SEQ ID NOS;

255, 257, 259, 261, 322, 324, 326, 328, 330, 332-359, and 364-391; and

wherein the agent is selected from the group consisting of auristatin E, monomethyl auristatin F (MMAF), monomethyl auristatin E (MMAE), monomethyl auristatin D (MMAD), maytansinoid DM4, maytansinoid DM1, a calicheamicin, a pyrrolobenzodiazepine, a pyrrolobenzodiazepine dimer, and a duocarmycin.

112. The method of claim 111, wherein the MM comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:

22-54.

113. The method of claim 111, wherein the CM comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:

182-249 and 276-316.

114. A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease, wherein the diseased cells express ITGa3 or wherein the disorder or the disease is associated with cells expressing ITGa3, or a method of inhibiting or reducing the growth, proliferation, or metastasis of cells expressing mammalian ITGa3, wherein the method comprises

administering a therapeutically effective amount of an isolated antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian ITGa3 to a subject in need thereof,

wherein the AB specifically binds human ITGa3 and cynomolgus monkey ITGa3.

115. The method of claim 114, wherein the AB has one or more of the characteristics selected from the group consisting of:

(i) the AB is humanized;

(ii) the AB comprises a VH CDR1 comprising the amino acid sequence EYIIH (SEQ ID NO;

     13);

a VH CDR2 comprising the amino acid sequence WFYPESGSVKYNETFKG (SEQ ID NO;

     14) or WFYPESGSVKYSETFKG (SEQ ID NO;

     15) or WFYPESGSVKYNEAFKG (SEQ ID NO;

     16) or WFYPESGSVKYNEGFKG (SEQ ID NO;

     17);

a VH CDR3 comprising the amino acid sequence HEERDYYGYYAMDY (SEQ ID NO;

     18);

a VL CDR1 comprising the amino acid sequence SASSSISSNYLH (SEQ ID NO;

     19);

a VL CDR2 comprising the amino acid sequence RTSNLA (SEQ ID NO;

     20); and

a VL CDR3 comprising the amino acid sequence QQGSSIPRFT (SEQ ID NO;

     21), and

(iii) the AB comprises a heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

3-10, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

11 and 12.

116. A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease, wherein the diseased cells express ITGa3 or wherein the disorder or the disease is associated with cells expressing ITGa3, or a method of inhibiting or reducing the growth, proliferation, or metastasis of cells expressing mammalian ITGa3, wherein the method comprises

administering a therapeutically effective amount of an activatable antibody that, in an activated state, binds ITGa3 to a subject in need thereof, wherein the activatable antibody comprises:

(i) an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian ITGa3, wherein the AB specifically binds human ITGa3 and cynomolgus monkey ITGa3;

(ii) a masking moiety (MM) coupled to the AB that inhibits the binding of the AB to ITGa3 when the activatable antibody is in an uncleaved state;

(iii) a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease.

117. The method of claim 116, wherein the AB has one or more of the characteristics selected from the group consisting of:

(i) the AB comprises a VH CDR1 comprising the amino acid sequence EYIIH (SEQ ID NO;

     13);

a VH CDR2 comprising the amino acid sequence WFYPESGSVKYNETFKG (SEQ ID NO;

     14) or WFYPESGSVKYSETFKG (SEQ ID NO;

     15) or WFYPESGSVKYNEAFKG (SEQ ID NO;

     16) or WFYPESGSVKYNEGFKG (SEQ ID NO;

     17);

a VH CDR3 comprising the amino acid sequence HEERDYYGYYAMDY (SEQ ID NO;

     18);

a VL CDR1 comprising the amino acid sequence SASSSISSNYLH (SEQ ID NO;

     19);

a VL CDR2 comprising the amino acid sequence RTSNLA (SEQ ID NO;

     20); and

a VL CDR3 comprising the amino acid sequence QQGSSIPRFT (SEQ ID NO;

     21);

(ii) the AB comprises a heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

3-10, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

11 and 12;

(iii) the AB comprises a heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

3-10, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

11, 12, 396, 398, 400, 402, 404-431, 436, 438, 440, 442, and 444-471; and

(iv) the AB comprises a heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO;

320, and a light chain comprising an amino acid sequence selected from the group consisting of SEQ ID NOS;

255, 257, 259, 261, 322, 324, 326, 328, 330, 332-359, and 364-391.

118. A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease, wherein the diseased cells express ITGa3 or wherein the disorder or the disease is associated with cells expressing ITGa3, or a method of inhibiting or reducing the growth, proliferation, or metastasis of cells expressing mammalian ITGa3, wherein the method comprises

administering a therapeutically effective amount of a conjugated antibody to a subject in need thereof, wherein the conjugated antibody comprises:

(i) an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian ITGa3, wherein the AB specifically binds human ITGa3 and cynomolgus monkey ITGa3;

(ii) an agent conjugated to the AB.

119. The method of claim 118,

wherein the AB has one or more of the characteristics selected from the group consisting of:

(i) the AB is humanized;

(ii) the AB comprises a VH CDR1 comprising the amino acid sequence EYIIH (SEQ ID NO;

     13);

a VH CDR2 comprising the amino acid sequence WFYPESGSVKYNETFKG (SEQ ID NO;

     14) or WFYPESGSVKYSETFKG (SEQ ID NO;

     15) or WFYPESGSVKYNEAFKG (SEQ ID NO;

     16) or WFYPESGSVKYNEGFKG (SEQ ID NO;

     17);

a VH CDR3 comprising the amino acid sequence HEERDYYGYYAMDY (SEQ ID NO;

     18);

a VL CDR1 comprising the amino acid sequence SASSSISSNYLH (SEQ ID NO;

     19);

a VL CDR2 comprising the amino acid sequence RTSNLA (SEQ ID NO;

     20); and

a VL CDR3 comprising the amino acid sequence QQGSSIPRFT (SEQ ID NO;

     21); and

(iii) the AB comprises a heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

3-10, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs;

11 and 12, and

wherein the agent is selected from the group consisting of auristatin E, monomethyl auristatin F (MMAF), monomethyl auristatin E (MMAE), monomethyl auristatin D (MMAD), maytansinoid DM4, maytansinoid DM1, a calicheamicin, a pyrrolobenzodiazepine, a pyrrolobenzodiazepine dimer, and a duocarmycin.