Heterodimeric bispecific antibodies
Provided herein are heterodimeric bispecific antibodies that can mediate cytolysis of a target cell by an immune effector cell, nucleic acids encoding such antibodies, methods of making such antibodies, and methods of using such antibodies. These antibodies comprise two different polypeptide chains, each comprising two immunoglobulin variable regions and, optionally, a half life-extending moiety.
1. A heterodimeric bispecific antibody comprising
(a) a first polypeptide chain comprising an amino acid sequence having the formula V1-L1-V2-L2-CH1, wherein V1 and V2 are immunoglobulin variable regions, L1 and L2 are linkers, L2 can be present or absent, and CH1 is a first immunoglobulin heavy chain constant region comprising SEQ ID NO: 70; and
(b) a second polypeptide chain comprising an amino acid sequence having the formula V3-L3-V4-L4-CL, wherein V3 and V4 are immunoglobulin variable regions, L3 and L4 are linkers, L4 can be present or absent, and CL is an immunoglobulin light chain constant region comprising SEQ ID NO: 71 or 73;
wherein either or both of the first polypeptide chain and the second polypeptide chain further comprise(s) an in vivo half life-extending moiety positioned C-terminally to the first polypeptide chain and/or the second polypeptide chain;
wherein the half life-extending moiety is
(i) an Fc polypeptide comprising any one of the amino acid sequences of SEQ ID NOS: 2-5 or a variant thereof containing no more than 10 amino acid substitutions, insertions, and/or deletions of a single amino acid per 100 amino acids;
(ii) albumin or a fragment thereof;
(iii) a fibronectin derivative comprising SEQ ID NO: 1, or a variant thereof containing no more than 10 amino acid substitutions, insertions, and/or deletions of a single amino acid per 100 amino acids, or a fragment thereof; or
(iiii) polyethylene glycol (PEG);
wherein the heterodimeric bispecific antibody binds to a cancer antigen on a target cell and a cluster of differentiation 3 (CD3) epsilon protein on a T cell and mediates cytolysis of the target cell by the T cell in vivo;
wherein V1, V2, V3, and V4 are selected from the group consisting of:
(a) V1 and V2 are each heavy chain variable regions and V3 and V4 are each light chain variable regions, and V1 and V3 create a complete VH/VL antigen binding pair binding the cancer antigen on the target cell and V2 and V4 create a complete VH/VL antigen binding pair binding the CD3 epsilon protein on the T cell;
(b) V1 and V2 are each light chain variable regions and V3 and V4 are each heavy chain variable regions, and V1 and V3 create a complete VH/VL antigen binding pair binding the CD3 epsilon protein on the T cell and V2 and V4 create a complete VH/VL antigen binding pair binding the cancer antigen on the target cell;
(c) V1 and V3 are each heavy chain variable regions and V2 and V4 are each light chain variable regions, and V1 and V4 create a complete VH/VL antigen binding pair binding the cancer antigen on the target cell and V2 and V3 create a complete VH/VL antigen binding pair binding the CD3 epsilon protein on the T cell; and
(d) V1 and V3 are each light chain variable regions and V2 and V4 are each heavy chain variable regions, and V1 and V4 create a complete VH/VL antigen binding pair binding the CD3 epsilon protein on the T cell and V2 and V3 create a complete VH/VL antigen binding pair binding the cancer antigen on the target cell; and
wherein L1 and L3 are each no more than 10 amino acids long;
wherein when L2 and/or L4 are present, L2 and L4 are each no more than 10 amino acids long;
wherein the VH region binding the CD3 epsilon protein comprises the heavy chain CDR1, CDR2, and CDR3 sequences in SEQ ID NO: 42, 44, or 82; and
wherein the VL region binding the CD3 epsilon protein comprises the light chain CDR1, CDR2, and CDR3 sequences in SEQ ID NO: 43, 45, or 83.
2. The heterodimeric bispecific antibody of claim 1 , wherein L2 and L4 are absent.
3. The heterodimeric bispecific antibody of claim 1 , wherein both the first polypeptide chain and the second polypeptide chain comprise the half life-extending moiety.
4. The heterodimeric bispecific antibody of claim 1 , wherein the target cell is a cancer cell.
5. The heterodimeric bispecific antibody of claim 1 , wherein the heterodimeric bispecific antibody can mediate increased expression of CD25 and CD69 on the T cell in the presence of the target cell, but not in the absence of the target cell.
6. The heterodimeric bispecific antibody of claim 3 , wherein the Fc polypeptide of the first polypeptide and the second polypeptide chains is human IgG Fc polypeptide.
7. The heterodimeric bispecific antibody of claim 6 , wherein the human IgG Fc polypeptide is human IgG1 Fc polypeptide, human IgG2 Fc polypeptide, or human IgG4 Fc polypeptide.
8. The heterodimeric bispecific antibody of claim 1 ,
wherein the first polypeptide chain and the second polypeptide chain each comprise an Fc polypeptide, and
wherein each Fc polypeptide comprises at least one charge pair substitution.
9. The heterodimeric bispecific antibody of claim 8 , wherein
(a) the Fc polypeptide of the first polypeptide chain comprises the charge pair substitutions E356K, E356R, D356R, or D356K and D399K or D399R, and the Fc polypeptide of the second polypeptide chain comprises the charge pair substitutions R409D, R409E, K409E, or K409D and N392D, N392E, K392E, or K392D; or
(b) the Fc polypeptide of the second polypeptide chain-comprises the charge pair substitutions E356K, E356R, D356R, or D356K and D399K or D399R, and the Fc polypeptide of the first polypeptide chain comprises the charge pair substitutions R409D, R409E, K409E, or K409D and N392D, N392E, K392E, or K392D;
(c) the Fc polypeptide of the first and/or second polypeptide chains comprises one or more alteration(s) that inhibit(s) Fc gamma receptor (FcγR) binding;
(d) the Fc polypeptide of the first and/or second polypeptide chains comprises an alteration that extends half life; or
(e) the Fc polypeptide of the first and/or second polypeptides comprises an alteration that enhances antibody-dependent cell-mediated cytotoxicity (ADCC).
10. The heterodimeric bispecific antibody of claim 9 , wherein the one or more alteration(s) that inhibit(s) Fc gamma receptor (FcγR) binding comprise the alterations L234A, L235A, and/or any substitution at position 297.
11. The heterodimeric bispecific antibody of claim 9 , wherein the Fc alteration that extends half life comprises an insertion between residues 384 and 385 according to the EU numbering system, and wherein the insertion comprises the amino acid sequence of any one of SEQ ID NOs: 54-65.
12. The heterodimeric bispecific antibody of claim 1 , wherein V1, V2, V3, and V4 comprise the amino acid sequences of:
(a) SEQ ID NO:46 or 49, SEQ ID NO:43, SEQ ID NO:42, and SEQ ID NO:48, respectively;
(b) SEQ ID NO:43, SEQ ID NO:46 or 49, SEQ ID NO:48, and SEQ ID NO:42, respectively;
(c) SEQ ID NO:50, SEQ ID NO:46 or 49, SEQ ID NO:48, and SEQ ID NO:51, respectively; or
(d) SEQ ID NO:44, SEQ ID NO:52, SEQ ID NO:53, and SEQ ID NO:45, respectively.
13. The heterodimeric bispecific antibody of claim 1 , wherein the heterodimeric bispecific antibody comprises the amino acid sequence set forth in SEQ ID NO: 82 or 83.
14. The heterodimeric bispecific antibody of claim 1 , wherein the fibronectin derivative comprises the amino acid sequence set forth in SEQ ID NO: 1.
15. The antibody of claim 1 , wherein L1 and L3 are 5-10 amino acids long.
16. A composition comprising the heterodimeric bispecific antibody of claim 1 and a pharmaceutically acceptable carrier.
17. A nucleic acid encoding the first polypeptide chain or the second polypeptide chain of the heterodimeric bispecific antibody of claim 1 .
18. A vector comprising the nucleic acid of claim 17 .
19. A host cell containing the nucleic acid of claim 17 .
20. A method of making a first polypeptide chain and a second polypeptide chain of a heterodimeric bispecific antibody comprising
culturing the host cell of claim 19 under conditions to express the nucleic acid encoding the first polypeptide chain and the second polypeptide chain of the heterodimeric bispecific antibody, and
recovering the first polypeptide chain or the second polypeptide chain of the antibody from the cell culture.
21. A heterodimeric bispecific antibody comprising
(a) a first polypeptide chain comprising an amino acid sequence having the formula V1-L1-V2-L2-CH1, wherein V1 and V2 are immunoglobulin variable regions, L1 and L2 are linkers, L2 can be present or absent, and CH1 is a first immunoglobulin heavy chain constant region comprising SEQ ID NO: 70; and
(b) a second polypeptide chain comprising an amino acid sequence having the formula V3-L3-V4-L4-CL, wherein V3 and V4 are immunoglobulin variable regions, L3 and L4 are linkers, L4 can be present or absent, and CL is an immunoglobulin light chain constant region comprising SEQ ID NO: 71 or 73;
wherein one of V1 and V4 is an immunoglobulin heavy chain variable (VH) region and the other is an immunoglobulin light chain variable (VL) region, and V1 and V4 can bind to a cancer antigen on a target cell or a cluster of differentiation 3 (CD3) epsilon protein on a T cell when they are part of an IgG and/or an scFv antibody;
wherein one of V2 and V3 is a VH region and the other is a VL region, and V2 and V3 can bind to the cancer antigen on the target cell or the CD3 epsilon protein on the T cell when they are part of an IgG and/or an scFv antibody;
wherein when V1 and V4 bind the cancer antigen V2 and V3 bind the CD3 epsilon protein, and when V1 and V4 bind the CD3 epsilon protein V2 and V3 bind the cancer antigen;
wherein either or both of the first polypeptide chain and the second polypeptide chain further comprise(s) an in vivo half life-extending moiety positioned C-terminally to the first polypeptide chain and/or the second polypeptide-chain;
wherein the half life-extending moiety is
(i) an Fc polypeptide comprising any one of the amino acid sequences of SEQ ID NOS: 2-5 or a variant thereof containing no more than 10 amino acid substitutions, insertions, and/or deletions of a single amino acid per 100 amino acids;
(ii) albumin or a fragment thereof;
(iii) a fibronectin derivative comprising SEQ ID NO: 1, or a variant thereof containing no more than 10 amino acid substitutions, insertions, and/or deletions of a single amino acid per 100 amino acids, or a fragment thereof; or
(iiii) polyethylene glycol (PEG);
wherein the heterodimeric bispecific antibody binds to the cancer antigen and the CD3 epsilon protein and mediates cytolysis of the target cell by the T cell in vivo;
wherein L1 and L3 are each no more than 10 amino acids long;
wherein when L2 and/or L4 are present, L2 and L4 are each no more than 10 amino acids long;
wherein the VH region binding the CD3 epsilon protein comprises the heavy chain CDR1, CDR2, and CDR3 sequences in SEQ ID NO: 42, 44, or 82; and
wherein the VL region binding the CD3 epsilon protein comprises the light chain CDR1, CDR2, and CDR3 sequences in SEQ ID NO: 43, 45, or 83.
22. The antibody of claim 21 , wherein L1 and L3 are 5-10 amino acids long.
23. A heterodimeric bispecific antibody comprising
(a) a first polypeptide chain comprising an amino acid sequence having the formula V1-L1-V2-CH1, wherein V1 and V2 are immunoglobulin variable regions, L1 is a linker no more than 10 amino acids long, and CH1 is a first immunoglobulin heavy chain constant region comprising SEQ ID NO: 70; and
(b) a second polypeptide chain comprising an amino acid sequence having the formula V3-L3-V4-CL, wherein V3 and V4 are immunoglobulin variable regions, L3 is a linker no more than 10 amino acids long, and CL is an immunoglobulin light chain constant region comprising SEQ ID NO: 71 or 73;
wherein either or both of the first polypeptide chain and the second polypeptide chain further comprise(s) an in vivo half life-extending moiety positioned C-terminally to the first polypeptide chain and/or the second polypeptide chain;
wherein the half life-extending moiety is
(i) an Fc polypeptide comprising any one of the amino acid sequences of SEQ ID NOS: 2-5 or a variant thereof containing no more than 10 amino acid substitutions, insertions, and/or deletions of a single amino acid per 100 amino acids;
(ii) albumin or a fragment thereof;
(iii) a fibronectin derivative comprising SEQ ID NO: 1, or a variant thereof containing no more than 10 amino acid substitutions, insertions, and/or deletions of a single amino acid per 100 amino acids, or a fragment thereof; or
(iiii) polyethylene glycol (PEG);
wherein the heterodimeric bispecific antibody binds to a cancer antigen on a target cell and a cluster of differentiation 3 (CD3) epsilon protein on a T cell and mediates cytolysis of the target cell by the T cell in vivo;
wherein V1, V2, V3, and V4 are selected from the group consisting of:
(a) V1 and V2 are each heavy chain variable regions and V3 and V4 are each light chain variable regions, and V1 and V3 create a complete VH/VL antigen binding pair binding the cancer antigen on the target cell and V2 and V4 create a complete VH/VL antigen binding pair binding the CD3 epsilon protein on the T cell;
(b) V1 and V2 are each light chain variable regions and V3 and V4 are each heavy chain variable regions, and V1 and V3 create a complete VH/VL antigen binding pair binding the CD3 epsilon protein on the T cell and V2 and V4 create a complete VH/VL antigen binding pair binding the cancer antigen on the target cell;
(c) V1 and V3 are each heavy chain variable regions and V2 and V4 are each light chain variable regions, and V1 and V4 create a complete VH/VL antigen binding pair binding the cancer antigen on the target cell and V2 and V3 create a complete VH/VL antigen binding pair binding the CD3 epsilon protein on the T cell; and
(d) V1 and V3 are each light chain variable regions and V2 and V4 are each heavy chain variable regions, and V1 and V4 create a complete VH/VL antigen binding pair binding the CD3 epsilon protein on the T cell and V2 and V3 create a complete VH/VL antigen binding pair binding the cancer antigen on the target cell; and
wherein the VH region binding the CD3 epsilon protein comprises the heavy chain CDR1, CDR2, and CDR3 sequences in SEQ ID NO: 42, 44, or 82; and
wherein the VL region binding the CD3 epsilon protein comprises the light chain CDR1, CDR2, and CDR3 sequences in SEQ ID NO: 43, 45, or 83.
24. The antibody of claim 23 , wherein L1 and L3 are 5-10 amino acids long.