Bispecific antibodies with alternatively matched interchain cysteines and uses thereof
Engineered bispecific antibodies with shifted interchain disulfide bond on one arm while maintaining the native interchain disulfide bond on the second arm are described. Also described are anti-CD47/FRα bispecific antibodies and antigen-binding fragments thereof. Also described are nucleic acids encoding the antibodies, compositions comprising the antibodies, and methods of producing the antibodies and using the antibodies for treating or preventing diseases, such as cancer and/or associated complications.
1 . An isolated bispecific antibody or antigen-binding fragment thereof comprising:
a. a first heavy chain, H1;
b. a second heavy chain, H2;
c. a first light chain, L1; and
d. a second light chain, L2;
wherein H1 and L1 form a first arm comprising a first antigen-binding domain that specifically binds a first antigen, wherein the first antigen-binding domain comprises a VH region and a VL region, and
wherein H2 and L2 form a second arm comprising a second antigen-binding domain that specifically binds a second antigen, wherein the second antigen-binding domain comprises a VH region and a VL region, wherein
(a) H1 comprises a CH1 region of human IgG1, IgG2, IgG3, or IgG4; and
(b) L1 comprises a CL region of a human kappa light chain or a human lambda light chain;
wherein the CH1 region sequence of H1 is selected from the group consisting of SEQ ID NO:15, 21, 22, and 23; the CL region sequence of L1 is selected from SEQ ID NO:19 or 24; and wherein the CH1 and CL regions further comprise amino acid substitutions selected from:
(1) K133C and C220X in CH1, and F209C and C214X in CL;
(2) K133C and C220X in CH1, and K207C and C214X in CL;
(3) R133C and C131X in CH1, and K207C and C214X in CL;
(4) R133C and C131X in CH1, and F209C and C214X in CL;
(5) R133C and C131X in CH1, and V209C and C214X in CL; or
(6) K133C and C220X in CH1, and V209C and C214X in CL;
wherein X is selected from S, A or G;
wherein the second arm comprising H2 and L2 does not comprise the amino acid substitutions of the first arm comprising H1 and L1, maintaining its native interchain disulfide bond, and wherein EU numbering is used for the CH1 and CL regions.
2 . An isolated bispecific antibody or antigen-binding fragment thereof comprising:
a. a first heavy chain, H1;
b. a second heavy chain, H2;
c. a first light chain, L1; and
d. a second light chain, L2;
wherein H1 and L1 form a first arm comprising a first antigen-binding domain that specifically binds a first antigen, wherein the first antigen-binding domain comprises a VH region and a VL region, and
wherein H2 and L2 form a second arm comprising a second antigen-binding domain that specifically binds a second antigen, wherein the second antigen-binding domain comprises a VH region and a VL region, wherein
(a) H1 comprises a CH1 region of human IgG1, IgG2, IgG3, or IgG4 and a heavy chain variable region (VH region); and
(b) L1 comprises a CL region of a human kappa light chain or a human lambda light chain and a light chain variable region (VL region);
wherein the CH1 region sequence of H1 is selected from the group consisting of SEQ ID NO: 15, 21, 22, and 23, the VH region sequence of H1 is SEQ ID NO:13, the CL region sequence of L1 is selected from SEQ ID NO:19 or 24, and the VL region sequence of L1 is SEQ ID NO:17; and
wherein the CH1, VH1, CL, and VL regions further comprise amino acid substitutions selected from:
(1) C220X in CH1, G44C in VH, C214X in CL, and G101C in VL; or
(2) C131X in CH1, G44C in VH, C214X in CL, and G101C in VL;
wherein X is selected from S, A or G;
wherein the second arm comprising H2 and L2 does not comprise the amino acid substitutions of the first arm comprising H1 and L1, maintaining its native interchain disulfide bond, and wherein EU numbering is used for the CH1, VH, CL, and VL regions.
3 . The isolated bispecific antibody or antigen-binding fragment thereof of claim 1 , wherein the first antigen-binding domain is a CD47 binding domain.
4 . The isolated bispecific antibody or antigen-binding fragment thereof of claim 3 , wherein the VH region comprises the amino acid sequence of SEQ ID NO: 1, and the VL region comprises the amino acid sequence of SEQ ID NO: 3.
5 . The isolated bispecific antibody or antigen-binding fragment thereof of claim 1 , wherein
(a) the two heavy chains H1 and H2 each comprise a VH region, a CH1 region, and a Fc region (containing CH2 and CH3 regions), wherein the VH regions have different amino acid sequences;
(b) the two heavy chains H1 and H2 each comprise a VH region, a CH1 region, and a Fc region (containing CH2 and CH3 regions), wherein the CH1 regions have different amino acid sequences;
(c) the two heavy chains H1 and H2 each comprise a VH region, a CH1 region, and a Fc region (containing CH2 and CH3 regions), wherein the Fc regions have different amino acid sequences;
(d) the two light chains L1 and L2 each comprise a VL region and a CL region, wherein the VL regions have different amino acid sequences; and/or
(e) the two light chains L1 and L2 each comprise a VL region and a CL region, wherein the CL regions have different amino acid sequences.
6 . The isolated bispecific antibody or antigen-binding fragment thereof of claim 5 , wherein H1 and H2 form a heterodimer.
7 . The isolated bispecific antibody or antigen-binding fragment thereof of claim 1 , wherein
(a) the VH region of H1 and the VL region of L1 have a Q39E and a Q38K substitution mutation, respectively, and the VH region of H2 and the VL region of L2 have a Q39K and a Q38E substitution mutation, respectively; or
(b) the VH region of H1 and the VL region of L1 have a Q39K and a Q38E substitution mutation, respectively, and the VH region of H2 and the VL region of L2 have a Q39E and a Q38K substitution mutation, respectively.
8 . The isolated bispecific antibody or antigen-binding fragment thereof of claim 1 , wherein the isolated bispecific antibody or antigen-binding fragment is an anti-CD47/anti-FRα bispecific antibody or antigen-binding fragment thereof, wherein the first antigen-binding domain specifically binds CD47, and the second antigen-binding domain specifically binds folate receptor α (FRα).
9 . The isolated bispecific antibody or antigen-binding fragment thereof of claim 1 , wherein
(a) the first antigen-binding domain has the VH sequence of SEQ ID: 13 and VL sequence of SEQ ID: 17, and the second antigen-binding domain has the VH sequence of SEQ ID: 33 and VL sequence of SEQ ID: 35; or
(b) the first antigen-binding domain has the VH sequence of SEQ ID: 13 and VL sequence of SEQ ID: 17, and the second antigen-binding domain has the VH sequence of SEQ ID: 14 and VL sequence of SEQ ID: 18.
10 . The isolated bispecific antibody or antigen-binding fragment thereof of claim 8 , wherein the anti-CD47/anti-FRα bispecific antibody or antigen-binding fragment thereof is capable of blocking binding of signal regulatory protein alpha (SIRPα) to CD47 on cancer cells that express both FRα and CD47, inducing macrophage-mediated phagocytosis of cancer cells that express both FRα and CD47, and/or binding cancer cells that express both FRα and CD47 with minimal to undetectable binding to human red blood cells (RBCs).
11 . An isolated nucleic acid encoding the bispecific antibody or antigen-binding fragment of claim 1 .
12 . A vector comprising the isolated nucleic acid of claim 11 .
13 . A host cell comprising the vector of claim 12 .
14 . A pharmaceutical composition, comprising the isolated bispecific antibody or antigen-binding fragment thereof of claim 1 and a pharmaceutically acceptable carrier.
15 . A method of targeting FRα and CD47 that are both expressed on a cancer cell surface in a subject in need thereof, blocking the binding of SIRPα to CD47 on cancer cells that express both FRα and CD47 in a subject in need thereof, inducing macrophage-mediated phagocytosis of cancer cells that express both FRα and CD47 in a subject in need thereof, binding cancer cells that express both FRα and CD47 with minimal to undetectable binding to human red blood cells (RBCs) in a subject in need thereof, and/or treating cancer in a subject in need thereof, comprising administering to the subject a pharmaceutical composition comprising the isolated anti-CD47/anti-FRα bispecific antibody or antigen-binding fragment thereof of claim 8 and a pharmaceutically acceptable carrier, optionally the cancer is selected from the group consisting of a lung cancer, a gastric cancer, an esophageal cancer, a bile duct cancer, a cholangiocarcinoma, a colon cancer, a hepatocellular carcinoma, a renal cell carcinoma, a bladder urothelial carcinoma, a metastatic melanoma, a breast cancer, an ovarian cancer, a cervical cancer, a head and neck cancer, a pancreatic cancer, a glioma, a glioblastoma, and other solid tumors, and a non-Hodgkin's lymphoma (NHL), an acute lymphocytic leukemia (ALL), a chronic lymphocytic leukemia (CLL), a chronic myelogenous leukemia (CML), a multiple myeloma (MM), an acute myeloid leukemia (AML), and other liquid tumors.
16 . A method of producing the bispecific antibody or antigen-binding fragment thereof of claim 1 , comprising culturing a cell comprising a vector comprising a nucleic acid encoding the bispecific antibody or antigen-binding fragment thereof under conditions to produce the bispecific antibody or antigen-binding fragment thereof, and recovering the bispecific antibody or antigen-binding fragment thereof from the cell or culture.
17 . A method of producing a pharmaceutical composition comprising the bispecific antibody or antigen-binding fragment thereof of claim 1 , comprising combining the bispecific antibody or antigen-binding fragment thereof with a pharmaceutically acceptable carrier to obtain the pharmaceutical composition.
18 . The isolated bispecific antibody or antigen-binding fragment thereof of claim 1 , wherein H1 and H2 comprise one or more mutations in CH3 region to promoter heterodimer formation.
19 . The isolated bispecific antibody or antigen-binding fragment thereof of claim 1 , wherein the amino acid substitutions allow the formation of a single disulfide bond between H1 and L1.