# US 12,600,783 B2 · Anti-New York esophageal squamous cell carcinoma 1 (NY-ESO-1) antigen-binding proteins and methods of use thereof

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- Number: US 12,600,783 B2
- Document ID: US12600783B2
- Status: Granted
- Kind: B2
- Application number: 17/622,307
- Filed: 2020-07-02
- Published: 2022-08-11
- Granted: 2026-04-14
- Earliest claimed: 2019-07-03
- Assignees: Regeneron Pharmaceuticals, Inc.
- Applicants: Regeneron Pharmaceuticals, Inc.
- Inventors: Kevin A. Bray; Frank Delfino; David Dilillo; Matthew C. Franklin; Jessica Kirshner; Douglas MacDonald
- Web page: https://patentgrep.com/patent/US12600783B2

## CPC

- C07K 16/2833: {against MHC-molecules, e.g. HLA-molecules}
- A61K 31/7088: Compounds having three or more nucleosides or nucleotides
- A61K 40/11: T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
- A61K 40/31: Chimeric antigen receptors [CAR]
- A61K 40/4269: {NY-ESO}
- A61P 35/00: Antineoplastic agents
- C07K 16/3076: {against structure-related tumour-associated moieties}
- A61K 2239/31: characterized by the route of administration
- A61K 2239/38: characterised by the dose, timing or administration schedule
- A61K 2239/57: Skin; melanoma
- C07K 2317/24: containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
- C07K 2317/32: specific for a neo-epitope on a complex, e.g. antibody-antigen or ligand-receptor
- C07K 2317/34: Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
- C07K 2317/622: Single chain antibody (scFv)
- C07K 2317/71: Decreased effector function due to an Fc-modification
- C07K 2317/92: Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
- C07K 2319/03: containing a transmembrane segment
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS

## Abstract

The present disclosure provides antigen-binding proteins that specifically bind to an H LA-displayed New York esophageal squamous cell carcinoma 1 (NY-ESO-1) peptide, and therapeutic and diagnostic methods of using those binding proteins. The antigen-binding proteins of the present disclosure bind with a high degree of specificity to HLA-displayed NY-ESO-1 and do not bind to HLA-displayed peptides that differ by 2, 3, 4, 5 or more amino acids.

## Claims

### Claim 1

An antibody, or antigen-binding portion thereof, that binds specifically to at least one amino acid of an HLA-A2: New York esophageal squamous cell carcinoma 1 peptide (NY-ESO-1 peptide) complex,
wherein the antibody, or antigen-binding portion thereof, comprises a heavy chain variable region (HCVR) comprising a heavy chain complementarity determining region (HCDR) 1 of SEQ ID NO: 4, an HCDR2 of SEQ ID NO: 6, an HCDR3 of SEQ ID NO: 8, and a light chain variable region (LCVR) comprising a light chain complementarity determining region (LCDR) 1 of SEQ ID NO: 12, an LCDR2 of SEQ ID NO: 14, and an LCDR3 of SEQ ID NO: 16.

### Claim 2 (depends on 1)

The antibody, or antigen-binding portion thereof, of claim 1 that binds specifically to an HLA-A2: NY-ESO-1 157-165 peptide complex, wherein said antibody, or antigen-binding portion thereof, interacts with amino acids M160, W161, and Q164 of said NY-ESO-1 157-165 peptide as determined by X-ray crystallography at a resolution of 4.0 Å or higher.

### Claim 3 (depends on 1)

The antibody, or antigen-binding portion thereof, of claim 1 that specifically binds to an HLA-A2: NY-ESO-1 157-165 peptide complex but does not specifically bind to one or more off-target peptides selected from the group consisting of BCL9L 1351-1359 (SEQ ID NO: 273), GRID1 7-15 (SEQ ID NO: 274), ZDHHC1 376-384 (SEQ ID NO: 276), ITCH 807-815 (SEQ ID NO: 277), and URB1 1853-1861 (SEQ ID NO: 280), wherein the ratio of i) said antibody, or antigen-binding portion thereof, binding to cells pulsed with said one or more off-target peptides to ii) unpulsed cells is less than about nine.

### Claim 4 (depends on 1)

The antibody, or antigen-binding portion thereof, of claim 1, wherein said NY-ESO-1 peptide comprises the amino acid sequence of SLLMWITQC (SEQ ID NO: 269) or SLLMWITQV (SEQ ID NO: 291).

### Claim 5 (depends on 1)

The antibody, or antigen-binding portion thereof, of claim 1, wherein the antibody, or antigen-binding portion thereof, is, a Fab, a Fab′, a (Fab′)2, an Fv, a single chain Fv (scFv), or a T-body construct.

### Claim 6 (depends on 1)

The antibody, or antigen-binding portion thereof, of claim 1, further comprising a detectable moiety.

### Claim 7 (depends on 1)

A pharmaceutical composition comprising the antibody, or antigen-binding portion thereof, that binds to HLA-A2: NY-ESO-1 according to claim 1 and a pharmaceutically acceptable carrier or diluent.

### Claim 8 (depends on 1)

An isolated polynucleotide molecule comprising a polynucleotide sequence that encodes the HCVR of the antibody, or antigen-binding portion thereof, as set forth in claim 1 and the LCVR of the antibody, or antigen-binding portion thereof, as set forth in claim 1.

### Claim 9 (depends on 8)

A vector comprising the polynucleotide molecule of claim 8.

### Claim 10 (depends on 8)

A cell expressing the polynucleotide molecule of claim 8.

### Claim 11 (depends on 1)

A method of treating a subject having an NY-ESO-1-associated disease or disorder, comprising administering to the subject a therapeutically effective amount of the antibody, or antigen-binding portion thereof, as set forth in claim 1, thereby treating the subject.

### Claim 12 (depends on 11)

The method of claim 11, wherein the NY-ESO-1-associated disease or disorder is an NY-ESO-1-associated cancer.

### Claim 13

An isolated nucleic acid molecule encoding a chimeric antigen receptor (CAR), wherein the CAR comprises an extracellular binding domain that specifically binds to a conformational epitope of an HLA-A2 presented New York esophageal squamous cell carcinoma 1 peptide (NY-ESO-1 peptide), a transmembrane domain, and an intracellular signaling domain,
wherein the extracellular binding domain is an antibody, or antigen-binding portion thereof, comprising a heavy chain variable region (HCVR) comprising a heavy chain complementarity determining region (HCDR) 1 of SEQ ID NO: 4, an HCDR2 of SEQ ID NO: 6, an HCDR3 of SEQ ID NO: 8, and a light chain variable region (LCVR) comprising a light chain complementarity determining region (LCDR) 1 of SEQ ID NO: 12, an LCDR2 of SEQ ID NO: 14, and an LCDR3 of SEQ ID NO: 16.

### Claim 14 (depends on 13)

A vector comprising the isolated nucleic acid molecule of claim 13.

### Claim 15 (depends on 13)

An isolated immune effector cell comprising the isolated nucleic acid molecule of claim 13.

### Claim 16 (depends on 15)

A method of treating a subject having an NY-ESO-1-associated disease or disorder, comprising administering to the subject the immune effector cell of claim 15.

### Claim 17 (depends on 16)

The method of claim 16, wherein the NY-ESO-1-associated disease or disorder is NY-ESO-1-associated cancer.

### Claim 18 (depends on 1)

The antibody, or antigen-binding portion thereof, of claim 1, wherein:
(a) the amino acid sequence of the HCVR comprises at least 90% or at least 95% sequence identity to SEQ ID NO: 2; and
(b) the amino acid sequence of the LCVR comprises at least 90% or at least 95% sequence identity to SEQ ID NO: 10.

### Claim 19 (depends on 18)

The human monoclonal antibody, or antigen-binding portion thereof, of claim 18, wherein the amino acid sequence of the HCVR comprises SEQ ID NO:2 and the amino acid sequence of the LCVR comprises SEQ ID NO: 10.

### Claim 20 (depends on 5)

The antibody, or antigen-binding portion thereof, of claim 5, wherein the antibody, or antigen-binding portion thereof, is a scFv.

### Claim 21 (depends on 1)

A Chimeric Antigen Receptor (CAR), comprising the antibody, or antigen-binding portion thereof, of claim 1.

### Claim 22 (depends on 8)

The isolated polynucleotide molecule of claim 8, wherein the antibody, or antigen-binding portion thereof, is an scFv.

### Claim 23 (depends on 12)

The method of claim 12, wherein the NY-ESO-associated cancer is a liposarcoma, a neuroblastoma, a myeloma, a metastatic melanoma, a synovial sarcoma, a bladder cancer, an esophageal cancer, a hepatocellular cancer, a head and neck cancer, a non-small cell lung cancer, an ovarian cancer, a prostate cancer, a breast cancer, astrocytic tumor, glioblastoma multiforme, anaplastic astrocytoma, brain tumor, fallopian tube cancer, ovarian epithelial cancer, primary peritoneal cavity cancer, advanced solid tumors, soft tissue sarcoma, melanoma, a sarcoma, myelodysplastic syndrome, acute myeloid leukemia, Hodgkin lymphoma, non-Hodgkin lymphoma, Hodgkin disease, multiple myeloma, synovial sarcoma, metastatic solid tumors, esophageal cancer, rhabdomyosarcoma, advanced myxoid, round cell liposarcoma, metastatic melanoma, or recurrent non-small cell lung cancer.

### Claim 24 (depends on 11)

The method of claim 11, further comprising administering a second therapeutic agent.

### Claim 25 (depends on 24)

The method of claim 24, wherein the second therapeutic agent is a PD-1 inhibitor, a CTLA-4 inhibitor, an antibody to a tumor specific antigen, an antibody to a virally-infected-cell antigen, a PD-L1 inhibitor, a CD20 inhibitor, a bispecific antibody against CD20 and CD3, a dietary supplement such as an antioxidant, a VEGF antagonist, a chemotherapeutic agent, a cytotoxic agent, surgery, radiation, a NSAID, a corticosteroid, or any other therapy useful for ameliorating at least one symptom associated with the disease or disorder.

### Claim 26 (depends on 11)

The method of claim 11, wherein the antibody, or antigen-binding portion thereof, is for subcutaneous, intravenous, intradermal, intraperitoneal, oral, intramuscular or intracranial administration.

### Claim 27 (depends on 11)

The method of claim 11, wherein the antibody, or antigen-binding portion thereof, is for administration at a dose of about 0.1 mg/kg of body weight to about 100 mg/kg of body weight of the subject.

### Claim 28 (depends on 13)

The isolated nucleic acid molecule of claim 13, wherein the antibody, or antigen-binding portion thereof, is an scFv.

### Claim 29 (depends on 13)

The isolated nucleic acid molecule of claim 13, wherein the costimulatory domain is a 4-1BB costimulatory domain.

### Claim 30 (depends on 13)

The isolated nucleic acid molecule of claim 13, wherein the costimulatory domain is a CD28 costimulatory domain.

### Claim 31 (depends on 15)

The isolated immune effector cell of claim 15, which is a T-body.

### Claim 32 (depends on 15)

A method of treating a subject having an NY-ESO-1-associated disease or disorder, comprising administering to the subject the immune effector cell of claim 15.

### Claim 33 (depends on 32)

The method of claim 32, wherein the NY-ESO-1-associated disease or disorder is NY-ESO-1-associated cancer.

### Claim 34 (depends on 33)

The method of claim 33, wherein the NY-ESO-associated cancer is a liposarcoma, a neuroblastoma, a myeloma, a metastatic melanoma, a synovial sarcoma, a bladder cancer, an esophageal cancer, a hepatocellular cancer, a head and neck cancer, a non-small cell lung cancer, an ovarian cancer, a prostate cancer, a breast cancer, astrocytic tumor, glioblastoma multiforme, anaplastic astrocytoma, brain tumor, fallopian tube cancer, ovarian epithelial cancer, primary peritoneal cavity cancer, advanced solid tumors, soft tissue sarcoma, melanoma, a sarcoma, myelodysplastic syndrome, acute myeloid leukemia, Hodgkin lymphoma, non-Hodgkin lymphoma, Hodgkin disease, multiple myeloma, synovial sarcoma, metastatic solid tumors, esophageal cancer, rhabdomyosarcoma, advanced myxoid, round cell liposarcoma, metastatic melanoma, or recurrent non-small cell lung cancer.

### Claim 35 (depends on 32)

The method of claim 32, further comprising a second therapeutic agent.

### Claim 36 (depends on 35)

The method of claim 35, wherein the second therapeutic agent is a PD-1 inhibitor, a CTLA-4 inhibitor, an antibody to a tumor specific antigen, an antibody to a virally-infected-cell antigen, a PD-L1 inhibitor, a CD20 inhibitor, a bispecific antibody against CD20 and CD3, a dietary supplement such as an antioxidant, a VEGF antagonist, a chemotherapeutic agent, a cytotoxic agent, surgery, radiation, a NSAID, a corticosteroid, or any other therapy useful for ameliorating at least one symptom associated with the disease or disorder.

### Claim 37 (depends on 8)

The isolated polynucleotide molecule of claim 8, wherein the polynucleotide sequence that encodes the HCVR comprises the nucleotide sequence of SEQ ID NO: 1.

### Claim 38 (depends on 8)

The isolated polynucleotide molecule of claim 8, wherein the polynucleotide sequence that encodes the LCVR comprises the nucleotide sequence of SEQ ID NO: 9.

### Claim 39 (depends on 1)

A cell comprising
a first polynucleotide molecule, wherein the first polynucleotide molecule comprises a polynucleotide sequence that encodes the HCVR as set forth in claim 1; and
a second polynucleotide molecule, wherein the second polynucleotide molecule comprises a polynucleotide sequence that encodes the LCVR as set forth in claim 1.

### Claim 40 (depends on 39)

The cell of claim 39, wherein the polynucleotide sequence that encodes the HCVR comprises the nucleotide sequence of SEQ ID NO: 1, and wherein the polynucleotide sequence that encodes the LCVR comprises the nucleotide sequence of SEQ ID NO: 9.

### Claim 41 (depends on 39)

The cell of claim 39, wherein the first polynucleotide molecule is contained within a vector.

### Claim 42 (depends on 39)

The cell of claim 39, wherein the second polynucleotide molecule is contained within a vector.

### Claim 43 (depends on 39)

The cell of claim 39, wherein the first polynucleotide molecule and the second polynucleotide molecule are contained within a vector.

### Claim 44 (depends on 9)

A cell expressing the vector of claim 9.

### Claim 45 (depends on 14)

An isolated immune effector cell comprising the vector of claim 14.

### Claim 46 (depends on 15)

A pharmaceutical composition comprising the isolated immune effector cell of claim 15.