Variant CD3-Binding Domains and Their Use in Combination Therapies for the Treatment of Disease

Abstract

The present invention is directed to DA×CD3 Binding Molecules comprising a vCD3-Binding Domain, which comprises a CDR H 1 Domain, a CDR H 2 Domain, a CDR H 3 Domain, a CDR L 1 Domain, a CDR L 2 Domain, and a CDR L 3 Domain, at least one of which differs in amino acid sequence from the amino acid sequence of the corresponding CDR of a rCD3-Binding Domain, wherein the DA×CD3 Binding Molecule comprising such vCD3-Binding Domain exhibits an altered affinity for CD3, relative to a DA×CD3 Binding Molecule comprising such rCD3-Binding Domain. The invention particularly concerns to such DA×CD3 Binding Molecules comprising a vCD3-Binding Domain which exhibit reduced affinity for CD3 and are capable of mediating redirected killing of target cells expressing a DA and exhibit lower levels of cytokine release relative to a DA×CD3 Binding Molecule comprising a rCD3-Binding Domain. The invention particularly concerns the use of DA×CD3 Binding Molecules comprising a vCD3-Binding Domain in the treatment of cancer and pathogen-associated diseases. The present invention is also directed to pharmaceutical compositions that comprise such molecule(s).

1 . A DA×CD3 Binding Molecule comprising a CD3-Binding Domain capable of binding an epitope of CD3 and a Disease Antigen-Binding Domain capable of binding an epitope of 5T4, CD19 or the env protein of HIV, wherein said CD3-Binding Domain comprises:
 (I) (A) a CDR H 1 Domain comprising the amino acid sequence of SEQ ID NO:99;
 (B) a CDR H 2 Domain comprising the amino acid sequence of SEQ ID NO:58; 
 (C) a CDR H 3 Domain comprising the amino acid sequence of SEQ ID NO:59; 
 (D) a CDR L 1 Domain comprising the amino acid sequence of SEQ ID NO:60; 
 (E) a CDR L 2 Domain comprising the amino acid sequence of SEQ ID NO:61; and 
 (F) a CDR L 3 Domain comprising the amino acid sequence of SEQ ID NO:62; or. 
 
 
     
     
         2 . The DA×CD3 Binding Molecule of  claim 1 , wherein said CD3-Binding Domain comprises:
 (I) (A) a VL Domain comprising the amino acid sequence of SEQ ID NO:56;
 (B) a VH Domain comprising the amino acid sequence of SEQ ID NO:98. 
 
 
     
     
         3 . The DA×CD3 Binding Molecule of  claim 1 , wherein said DA×CD3 Binding Molecule is a bispecific antibody, a bispecific diabody, a bispecific scFv, a bispecific TandAb, or a trivalent binding molecule. 
     
     
         4 - 10 . (canceled) 
     
     
         11 . The DA×CD3 Binding Molecule of  claim 1 , wherein said DA×CD3 Binding Molecule comprises: a first polypeptide chain and a second polypeptide chain, covalently bonded to one another, wherein:
 (A) the first polypeptide chain comprises, in the N-terminal to C-terminal direction:
 (i) a Domain 1, comprising:
 (1) (a) sub-Domain (1A), which comprises a VL Domain of a monoclonal antibody capable of binding to said epitope of 5T4 (VL 5T4 ); or
 (b) a sub-Domain (1A), which comprises a VL Domain of a monoclonal antibody capable of binding to said epitope of CD19 (VL CD19 ); or 
 (c) a sub-Domain (1A), which comprises a VL Domain of a monoclonal antibody capable of binding to said epitope of the env protein of HIV (VL HIV ); and 
 
 (2) a sub-Domain (1B), which comprises a VH Domain of a monoclonal antibody capable of binding to said epitope of CD3 (VH CD3 ); 
 wherein said sub-Domains 1A and 1B are separated from one another by a peptide Linker; and 
 
 (ii) a Domain 2, wherein said Domain 2 is a Heterodimer-Promoting Domain; 
 
 (B) the second polypeptide chain comprises, in the N-terminal to C-terminal direction:
 (i) a Domain 1, comprising:
 (1) a sub-Domain (1A), which comprises a VL Domain of said monoclonal antibody capable of binding to said epitope of CD3 (VL CD3 ); and 
 (2) (a) sub-Domain (1B), which comprises a VH Domain of said monoclonal antibody capable of binding to said epitope of 5T4 (VH 5T4 ); or
 (b) a sub-Domain (1B), which comprises a VH Domain of said monoclonal antibody capable of binding to said epitope of CD19 (VH CD19 ): or 
 (c) a sub-Domain (1B), which comprises a VH Domain of said monoclonal antibody capable of binding to said epitope of the env protein of HIV (VH HIV ): 
 
 wherein said sub-Domains 1A and 1B are separated from one another by a peptide Linker; 
 
 (ii) a Domain 2, wherein said Domain 2 is a Heterodimer-Promoting Domain, wherein said Heterodimer-Promoting Domain of said first and said second polypeptide chains are different; 
 
 and wherein: 
 (a) the VL Domain of the first polypeptide chain and the VH Domain of the second polypeptide chain associate to form the 5T4, CD19 or the env protein of HIV binding domain, and the VH Domain of the first polypeptide chain and the VL Domain of the second polypeptide chain associate to form the CD3-Binding Domain; or 
 (b) the VL Domain of the first polypeptide chain and the VH Domain of the second polypeptide chain associate to form the CD3-Binding Domain, and the VH Domain of the first polypeptide chain and the VL Domain of the second polypeptide chain associate to form the 5T4, CD19 or the env protein of HIV binding domain. 
 
     
     
         12 . The DA×CD3 Binding Molecule of  claim 11 , wherein:
 (a) said Heterodimer-Promoting Domain of said first polypeptide chain is an E-coil Domain, and said Heterodimer-Promoting Domain of said second polypeptide chain is a K-coil Domain; or 
 (b) said Heterodimer-Promoting Domain of said first polypeptide chain is a K-coil Domain, and said Heterodimer-Promoting Domain of said second polypeptide chain is an E-coil Domain. 
 
     
     
         13 . The DA×CD3 Binding Molecule of  claim 11 , wherein the first or second polypeptide chain additionally comprises a Domain 3 comprising a CH2 and CH3 Domain of an immunoglobulin Fc Domain. 
     
     
         14 . The DA×CD3 Binding Molecule of  claim 13 , wherein said DA×CD3 Binding Molecule further comprises a third polypeptide chain comprising a CH2 and CH3 Domain of an immunoglobulin Fc Domain. 
     
     
         15 - 16 . (canceled) 
     
     
         17 . A pharmaceutical composition that comprises the DA×CD3 Binding Molecule of  claim 1  and a pharmaceutically acceptable carrier. 
     
     
         18 . A method for the treatment of a disease, comprising administering to a subject in need thereof a therapeutically effective amount of the pharmaceutical composition of  claim 17 . 
     
     
         19 - 27 . (canceled) 
     
     
         28 . The DA×CD3 Binding Molecule of  claim 1 , wherein said Disease Antigen-Binding Domain Comprises:
 (I) (A) the CDR H 1 Domain, CDR H 2 Domain, and the CDR H 3 Domain of SEQ ID NO:156; and
 (B) the CDR L 1 Domain, the CDR L 2 Domain, and the CDR L 3 Domain of SEQ ID NO:157; or 
 
 (II) (A) the CDR H 1 Domain, CDR H 2 Domain, and the CDR H 3 Domain of SEQ ID NO:164; and
 (B) the CDR L 1 Domain, the CDR L 2 Domain, and the CDR L 3 Domain of SEQ ID NO:165; or 
 
 (III) (A) the CDR H 1 Domain, CDR H 2 Domain, and the CDR H 3 Domain of SEQ ID NO:164; and
 (B) the CDR L 1 Domain, the CDR L 2 Domain, and the CDR L 3 Domain of SEQ ID NO:195; or 
 
 (IV) (A) the CDR H 1 Domain, CDR H 2 Domain, and the CDR H 3 Domain of SEQ ID NO:168; and
 (B) the CDR L 1 Domain, the CDR L 2 Domain, and the CDR L 3 Domain of SEQ ID NO:169. 
 
 
     
     
         29 . The DA×CD3 Binding Molecule of  claim 1 , wherein said Disease Antigen-Binding Domain Comprises:
 (I) (A) a VH Domain comprising the amino acid sequence of SEQ ID NO:156; and
 (B) a VL Domain comprising the amino acid sequence of SEQ ID NO:157; or 
 
 (II) (A) a VH Domain comprising the amino acid sequence of SEQ ID NO:164; and
 (B) a VL Domain comprising the amino acid sequence of SEQ ID NO:165; or 
 
 (III) (A) a VH Domain comprising the amino acid sequence of SEQ ID NO:164; and
 (B) a VL Domain comprising the amino acid sequence of SEQ ID NO:195; or 
 
 (IV) (A) a VH Domain comprising the amino acid sequence of SEQ ID NO:168; and
 (B) a VL Domain comprising the amino acid sequence of SEQ ID NO:169. 
 
 
     
     
         30 . The DA×CD3 Binding Molecule of  claim 2 , wherein said Disease Antigen-Binding Domain Comprises:
 (I) (A) a VH Domain comprising the amino acid sequence of SEQ ID NO:156; and
 (B) a VL Domain comprising the amino acid sequence of SEQ ID NO:157; or 
 
 (II) (A) a VH Domain comprising the amino acid sequence of SEQ ID NO:164; and
 (B) a VL Domain comprising the amino acid sequence of SEQ ID NO:165; or 
 
 (III) (A) a VH Domain comprising the amino acid sequence of SEQ ID NO:164; and
 (B) a VL Domain comprising the amino acid sequence of SEQ ID NO:195; or 
 
 (IV) (A) a VH Domain comprising the amino acid sequence of SEQ ID NO:168; and
 (B) a VL Domain comprising the amino acid sequence of SEQ ID NO:169. 
 
 
     
     
         31 . The DA×CD3 Binding Molecule of  claim 11 , wherein:
 (I) (A) said VH5T4 comprises the amino acid sequence of SEQ ID NO:156; and
 (B) said VL5T4 comprises the amino acid sequence of SEQ ID NO:157; or 
 (A) said VH CD19  comprises the amino acid sequence of SEQ ID NO:164; and 
 (B) said VL CD19  comprises the amino acid sequence of SEQ ID NO:165; or 
 (A) said VH CD19  comprises the amino acid sequence of SEQ ID NO:164; and 
 (B) said VL CD19  comprises the amino acid sequence of SEQ ID NO:195; or 
 (A) said VH HIV  comprises the amino acid sequence of SEQ ID NO:168; and 
 (B) said VL HIV  comprises the amino acid sequence of SEQ ID NO:169; and 
 
 (II) (C) said VH CD3  comprises the amino acid sequence of SEQ ID NO:98; and
 (D) said VL CD3  comprises the amino acid sequence of SEQ ID NO:56. 
 
 
     
     
         32 . The DA×CD3 Binding Molecule of  claim 12 , wherein:
 (I) (A) said VH5T4 comprises the amino acid sequence of SEQ ID NO:156; and
 (B) said VL5T4 comprises the amino acid sequence of SEQ ID NO:157; or 
 (A) said VH CD19  comprises the amino acid sequence of SEQ ID NO:164; and 
 (B) said VL CD19  comprises the amino acid sequence of SEQ ID NO:165; or 
 (A) said VH CD19  comprises the amino acid sequence of SEQ ID NO:164; and 
 (B) said VL CD19  comprises the amino acid sequence of SEQ ID NO:195; or 
 (A) said VH HIV  comprises the amino acid sequence of SEQ ID NO:168; and 
 (B) said VL HIV  comprises the amino acid sequence of SEQ ID NO:169; and 
 
 (II) (C) said VH CD3  comprises the amino acid sequence of SEQ ID NO:98; and
 (D) said VL CD3  comprises the amino acid sequence of SEQ ID NO:56. 
 
 
     
     
         33 . The DA×CD3 Binding Molecule of  claim 13 , wherein:
 (I) (A) said VH5T4 comprises the amino acid sequence of SEQ ID NO:156; and
 (B) said VL5T4 comprises the amino acid sequence of SEQ ID NO:157; or 
 (A) said VH CD19  comprises the amino acid sequence of SEQ ID NO:164; and 
 (B) said VL CD19  comprises the amino acid sequence of SEQ ID NO:165; or 
 (A) said VH CD19  comprises the amino acid sequence of SEQ ID NO:164; and 
 (B) said VL CD19  comprises the amino acid sequence of SEQ ID NO:195; or 
 (A) said VH HIV  comprises the amino acid sequence of SEQ ID NO:168; and 
 (B) said VL HIV  comprises the amino acid sequence of SEQ ID NO:169; and 
 
 (II) (C) said VH CD3  comprises the amino acid sequence of SEQ ID NO:98; and
 (D) said VL CD3  comprises the amino acid sequence of SEQ ID NO:56. 
 
 
     
     
         34 . The DA×CD3 Binding Molecule of  claim 14 , wherein:
 (I) (A) said VH5T4 comprises the amino acid sequence of SEQ ID NO:156; and
 (B) said VL5T4 comprises the amino acid sequence of SEQ ID NO:157; or 
 (A) said VH CD19  comprises the amino acid sequence of SEQ ID NO:164; and 
 (B) said VL CD19  comprises the amino acid sequence of SEQ ID NO:165; or 
 (A) said VH CD19  comprises the amino acid sequence of SEQ ID NO:164; and 
 (B) said VL CD19  comprises the amino acid sequence of SEQ ID NO:195; or 
 (A) said VH HIV  comprises the amino acid sequence of SEQ ID NO:168; and 
 (B) said VL HIV  comprises the amino acid sequence of SEQ ID NO:169; and 
 
 (II) (C) said VH CD3  comprises the amino acid sequence of SEQ ID NO:98; and
 (D) said VL CD3  comprises the amino acid sequence of SEQ ID NO:56. 
 
 
     
     
         35 . A DA×CD3 Binding Molecule, wherein said DA×CD3 Binding Molecule comprises:
 (I) (A) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO:184;
 (B) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO:181; and 
 (C) a third polypeptide chain comprising the amino acid sequence of SEQ ID NO:176; or 
 
 (II) (A) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO:193;
 (B) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO:194; and 
 (C) a third polypeptide chain comprising the amino acid sequence of SEQ ID NO:176; or 
 
 (III) (A) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO:197;
 (B) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO:192; and 
 (C) a third polypeptide chain comprising the amino acid sequence of SEQ ID NO:176; or 
 
 (IV) (A) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO:196;
 (B) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO:186; and 
 (C) a third polypeptide chain comprising the amino acid sequence of SEQ ID NO:176. 
 
 
     
     
         36 . A pharmaceutical composition that comprises the DA×CD3 Binding Molecule of  claim 35  and a pharmaceutically acceptable carrier. 
     
     
         37 . A method for the treatment of a hematological cancer or for the treatment of HIV infection, comprising administering to a subject in need thereof a therapeutically effective amount of the pharmaceutical composition of  claim 36 . 
     
     
         38 . The method of  claim 37 , wherein said hematological cancer is selected from the group consisting of: acute myeloid leukemia (AML), chronic myelogenous leukemia (CML), myelodysplastic syndrome (MDS), acute B lymphoblastic leukemia (B-ALL), chronic lymphocytic leukemia (CLL), Richter's syndrome, hairy cell leukemia (HCL), blastic plasmacytoid dendritic cell neoplasm (BPDCN), non-Hodgkin's lymphoma (NHL), including mantle cell lymphoma (MCL) and small lymphocytic lymphoma (SLL), Hodgkin's lymphoma, systemic mastocytosis, and Burkitt's lymphoma. 
     
     
         39 . The method of  claim 38 , wherein the pharmaceutical composition is administered intravenously. 
     
     
         40 . The method of  claim 39 , wherein said intravenous administration is by infusion. 
     
     
         41 . The method of  claim 40 , wherein the DA×CD3 Binding Molecule of the pharmaceutical composition is administered at a dosage of about 0.01 μg/kg to about 30 mg/kg of said subject's body weight. 
     
     
         42 . The method of  claim 40 , wherein the pharmaceutical composition is administered once a week, once every two weeks, or once a month. 
     
     
         43 . A host cell comprising:
 (I) (A) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:184;
 (B) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:181; and 
 (C) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:176; or 
   (II) (A) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:193;
 (B) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:194; and 
 (C) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:176; or 
   (III) (A) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:197;
 (B) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:192; and 
 (C) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:176; or 
   (IV) (A) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:196;
 (B) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:186; and 
 (C) a polynucleotide encoding a polypeptide chain comprising the amino acid sequence of SEQ ID NO:176.