IP Library › Granted Patent US 12,227,591
Granted Patent B2
US 12,227,591 · App. 17/306,241 · Granted Feb 18, 2025

Antigen-binding constructs targeting HER2

Inventors: Eric Escobar-Cabrera (Burnaby, CA); Leonard G. Presta (San Francisco, CA)
Assignee: Zymeworks BC Inc.
C07K16/32A61P35/00G01N33/57415G01N33/57446G01N33/57492C07K2317/24C07K2317/31C07K2317/35C07K2317/526C07K2317/55C07K2317/565C07K2317/567C07K2317/64C07K2317/73C07K2317/77C07K2317/92C07K2317/94G01N2333/71
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Quick Facts
Patent No.
US 12,227,591
App. No.
17/306,241
Granted
Feb 18, 2025
Kind
B2
Abstract

Described herein are high affinity antigen binding constructs, e.g., antibodies, directed to the ECD2 domain of HER2. The antigen-binding constructs comprise at least one antigen-binding polypeptide construct that binds to ECD2 of HER2 (HER2 ECD2) with increased affinity compared to a wild-type 2C4 antibody. Such antigen-binding polypeptide constructs comprise one or more amino acid modifications in the framework region and/or CDRs compared to the amino acid sequence of a wild-type 2C4 antibody that increase affinity of the antigen-binding polypeptide construct for ECD2 by 2-fold or greater. The antigen-binding constructs can inhibit the growth of HER2-expressing breast cancer cells and gastric cancer cells. Antigen-binding constructs in biparatopic format are internalized in HER2-expressing cells.

Claims (84)

1. An antigen-binding construct comprising a variant first antigen-binding polypeptide construct which monovalently binds a first HER2 ECD2 (human epidermal growth factor receptor 2 extracellular domain 2) antigen, the variant first antigen-binding polypeptide construct comprising

a variable heavy (VH) domain comprising a complementary determining region (CDR) 1 (CDR-H1) comprising the sequence as set forth in SEQ ID NO: 956, a CDR-H2 comprising the sequence as set forth in SEQ ID NO: 957, and a CDR-H3 comprising the sequence as set forth in SEQ ID NO: 958; and

a variable light (VL) domain comprising a CDR-L1 comprising the sequence as set forth in SEQ ID NO: 959, a CDR-L2 comprising the sequence as set forth in SEQ ID NO: 960, and a CDR-L3 comprising the sequence as set forth in SEQ ID NO: 609;

and wherein the Glycine at position 56 of CDR-H2 has been substituted with a Tyrosine (H_G56Y) or a Phenylalanine (H_G56F), or the Serine at position 99 of CDR-H3 has been substituted with a Tryptophan (H_S99W), numbering according to Kabat numbering system;

optionally wherein the variant first antigen-binding polypeptide construct comprises H_G56Y and further comprises the following substitution or set of substitutions relative to the VH domain as set forth in SEQ ID NO: 2 and the VL domain as set forth in SEQ ID NO: 11, numbering according to Kabat numbering system;

H_K75W; or

H_T30Q; or

H_T30Y; or

H_S99W; or

L_Y49W; or

L_Y96G; or

H_S99W and L_Y49W; or

L_Y49W and L_Y96G; or

H_T30Q and L_Y49W; or

H_T30Q and H_S99W; or

H_T30Q and L_Y96G; or

H_T30Y and L_Y49W; or

H_T30Q and H_S99W and L_Y49W; or

H_T30Q and L_Y49W and L_Y96G; and

 optionally wherein the variant first antigen-binding polypeptide construct comprises H_S99W and further comprises the following substitution or set of substitutions relative to the VH domain as set forth in SEQ ID NO: 2 and the VL domain as set forth in SEQ ID NO: 11, numbering according to Kabat numbering system;

H_K75W; or

H_T30Q; or

H_K75E; or

H_T30Y; or

H_K75W and L_Y49W; or

H_T30Q and H_K75W; or

H_T30Q and L_Y49W; or

H_T30Q and H_K75W and L_Y49W; or

H_K75W and L Y49W and L_Y96G; or

H_T30Q and H_K75W and L_Y96G; or

H_T30Q and L_Y49W and L_Y96G; or

H_T30Q and H_G56Y and L_Y49W.

2. The antigen-binding construct of claim 1 , wherein the VH domain comprises a sequence having at least 90% identity to the sequence set forth in SEQ ID NO:2 and the VL domain comprises a sequence having at least 90% identity to the sequence set forth in SEQ ID NO:11.

3. The antigen-binding construct of claim 1 , wherein the Glycine at position 56 of CDR-H2 has been substituted with a Tyrosine (H_G56Y), numbering according to Kabat numbering system.

4. The antigen-binding construct of claim 3 , wherein the variant first antigen-binding polypeptide construct further comprises the following substitution or set of substitutions, numbering according to Kabat numbering system:

H_K75W; or

H_T30Q; or

H_T30Y; or

H_S99W; or

L_Y49W; or

L_Y96G; or

H_S99W and L_Y49W; or

L_Y49W and L_Y96G; or

H_T30Q and L_Y49W; or

H_T30Q and H_S99W; or

H_T30Q and L_Y96G; or

H_T30Y and L_Y49W; or

H_T30Q and H_S99W and L_Y49W; or

H_T30Q and L_Y49W and L_Y96G.

5. The antigen-binding construct of claim 1 , wherein the Serine at position 99 of CDR-H3 has been substituted with a Tryptophan (H_S99W), numbering according to Kabat numbering system.

6. The antigen-binding construct of claim 5 , wherein the variant first antigen-binding polypeptide construct further comprises the following substitution or set of substitutions, numbering according to Kabat numbering system:

H_K75W; or

H_T30Q; or

H_K75E; or

H_T30Y; or

H_K75W and L_Y49W; or

H_T30Q and H_K75W; or

H_T30Q and L_Y49W; or

H_T30Q and H_K75W and L_Y49W; or

H_K75W and L_Y49W and L_Y96G; or

H_T30Q and H_K75W and L_Y96G; or

H_T30Q and L_Y49W and L_Y96G; or

H_T30Q and H_G56Y and L_Y49W.

7. The antigen-binding construct of claim 1 , wherein the Glycine at position 56 of CDR-H2 has been substituted with a Tyrosine (H_G56Y) and the Serine at position 99 of CDR-H3 has been substituted with a Tryptophan (H_S99W), numbering according to Kabat numbering system.

8. The antigen-binding construct of claim 1 , wherein the variant first antigen-binding polypeptide construct is a Fab.

9. The antigen binding construct of claim 8 , further comprising a first linker polypeptide operably linked to the variant first antigen-binding polypeptide construct.

10. The antigen-binding construct of claim 9 , wherein the first linker polypeptide is operably linked to a heterodimeric human IgG1 Fc comprising a first Fc polypeptide and a second Fc polypeptide each comprising a different CH3 sequence.

11. The antigen-binding construct of claim 1 , wherein the antigen-binding construct comprises a second antigen-binding polypeptide construct that binds to a second antigen.

12. The antigen-binding construct of claim 11 , further comprising a first linker polypeptide operably linked to the variant first antigen-binding polypeptide construct, and a second linker polypeptide operably linked to the second antigen-binding polypeptide construct.

13. The antigen-binding construct of claim 11 , wherein the second antigen is a HER2 ECD2 antigen and the second antigen-binding polypeptide construct is identical to the variant first antigen-binding polypeptide construct.

14. The antigen-binding construct of claim 11 , wherein the second antigen is a HER2 ECD4 antigen and the second antigen-binding polypeptide construct is an scFv comprising the VH and VL domain of trastuzumab and a glycine-serine linker.

15. The antigen-binding construct according to claim 12 , wherein the first and second linker polypeptides are operably linked to a heterodimeric human IgG1 Fc comprising a first Fc polypeptide and a second Fc polypeptide each comprising a different CH3 sequence.

16. The antigen-binding construct of claim 15 , wherein the CH3 sequence of each Fc polypeptide comprises one or more modifications that promote the formation of a heterodimeric Fc with stability comparable to a wild-type homodimeric Fc, the heterodimeric IgG1 Fc having

a) the modifications L351Y_F405A_Y407V in the first Fc polypeptide, and the modifications T366L_K392M_T394W in the second polypeptide; or

b) the modifications L351Y_F405A_Y407V in the first Fc polypeptide, and the modifications T366L_K392L_T394W in the second Fc polypeptide; or

c) the modifications T350V_L351Y_F405A_Y407V in the first Fc polypeptide, and the modifications T350V_T366L_K392L_T394W in the second Fc polypeptide; or

d) the modifications T350V_L351Y_F405A Y407V in the first Fc polypeptide, and the modifications T350V_T366L_K392M_T394W in the second Fc polypeptide; or

e) the modifications T350V_L351Y_S400E_F405A_Y407V in the first Fc polypeptide, and the modifications T350V_T366L N390R_K392M_T394W in the second Fc polypeptide; or

f) the modifications T350V_L351Y_F405A_Y407V in the first Fc polypeptide, and the modifications T366I_N390R_K392M_T394W in the second Fc polypeptide; or

g) the modifications L351Y_S400E_F405A_Y407V in the first Fc polypeptide, and the modifications T350V_T366L_K392L_T394W in the second Fc polypeptide,

wherein the numbering of amino acid residues in the Fc is according to the EU numbering system.

17. A pharmaceutical composition comprising the antigen-binding construct of claim 1 , and a pharmaceutical carrier, optionally selected from a buffer, an antioxidant, a low molecular weight molecule, a drug, a protein, an amino acid, a carbohydrate, a lipid, a chelating agent, a stabilizer, or an excipient.

18. An isolated polynucleotide or set of isolated polynucleotides comprising at least one nucleic acid sequence that encodes the antigen-binding construct of claim 1 , optionally wherein said polynucleotide or set of polynucleotides is cDNA.

19. An isolated cell comprising a polynucleotide or set of polynucleotides according to claim 18 , the isolated cell optionally selected from a hybridoma, a Chinese Hamster Ovary (CHO) cell, or a HEK293 cell.

Assignments (2)
CHANGE OF NAME Recorded Dec 12, 2022
From: ZYMEWORKS INC.
To: ZYMEWORKS BC INC.
Reel/Frame 062116/0071 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded May 4, 2021
From: ESCOBAR-CABRERA, ERIC; PRESTA, LEONARD G.
To: ZYMEWORKS INC.
Reel/Frame 056132/0788 →
Continuity (4)
Division 15572364
Provisional Application 62161114 · May 13, 2015
Provisional Application 62267247 · Dec 14, 2015
Related Publication 20210395388A1 · Dec 23, 2021
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