# US 11,440,967 B2 · Therapeutic antibodies

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- Number: US 11,440,967 B2
- Document ID: US11440967B2
- Status: Granted
- Kind: B2
- Application number: 16/427,146
- Filed: 2019-05-30
- Published: 2019-12-05
- Granted: 2022-09-13
- Earliest claimed: 2018-05-31
- Assignees: GlycoNex Inc.
- Applicants: GlycoNex Inc.
- Inventors: Tong-Hsuan Chang; Mei-Chun Yang; Liahng-Yim Liu; Jerry Ting; Shu-Yen Chang; Yen-Ying Chen; Yu-Yu Lin; Shu-Lun Tang
- Web page: https://patentgrep.com/patent/US11440967B2

## CPC

- C07K 16/2896: {against molecules with a "CD"-designation, not provided for elsewhere}
- A61K 47/65: Peptidic linkers, binders or spacers, e.g. peptidic enzyme-labile linkers
- A61K 47/6801: {Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent}
- A61K 49/0058: {Antibodies}
- A61K 51/1048: {the tumor cell determinant being a carcino embryonic antigen}
- A61P 35/00: Antineoplastic agents
- C07K 16/30: from tumour cells
- C07K 16/34: against blood group antigens
- C07K 16/44: against material not provided for elsewhere {, e.g. haptens, metals, DNA, RNA, amino acids}
- C12N 15/85: for animal cells
- G01N 33/5753: of the stomach or small intestine
- G01N 33/57535: of the large intestine, e.g. colon, rectum or anus
- G01N 33/57557: {of other specific parts of the body, e.g. brain}
- A61K 2039/505: {comprising antibodies}
- C07K 2317/33: Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
- C07K 2317/41: Glycosylation, sialylation, or fucosylation
- C07K 2317/565: Complementarity determining region [CDR]
- C07K 2317/73: Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
- C07K 2317/77: Internalization into the cell
- C07K 2317/92: Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
- C12N 2015/8518: {expressing industrially exogenous proteins, e.g. for pharmaceutical use, human insulin, blood factors, immunoglobulins, pseudoparticles}
- 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
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)

## Abstract

Disclosed herein are humanized antibodies, antigen-binding fragments thereof, and antibody conjugates, that are capable of specifically binding to certain biantennary Lewis antigens, which antigens are expressed in a variety of cancers. The presently disclosed antibodies are useful to target antigen-expressing cells for treatment or detection of disease, including various cancers. Also provided are polynucleotides, vectors, and host cells for producing the disclosed antibodies and antigen-binding fragments thereof. Pharmaceutical compositions, methods of treatment and detection, and uses of the antibodies, antigen-binding fragments, antibody conjugates, and compositions are also provided.

## Claims

### Claim 1

An isolated antibody or an antigen-binding fragment thereof, comprising an immunoglobulin heavy chain variable region that comprises an amino acid sequence that has at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 percent identity to the amino acid sequence set forth in SEQ ID NO: 35; and an immunoglobulin light chain variable region that comprises an amino acid sequence that has at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 percent identity to the amino acid sequence set forth in SEQ ID NO: 5, wherein the antibody or antigen-binding fragment thereof is capable of binding specifically:
to a biantennary LeB/LeB antigen comprising Fuc4(Galβ1→3GlcNAc)2 [I] or [Fucα1-2Galβ1-3(Fucα1-4)GlcNAc]2[II],
to a biantennary LeY/LeY antigen comprising Fuc4(Galβ1→4GlcNAc)2 [III] or [Fucα1-2Galβ1-4(Fucα1-3)GlcNAc]2 [IV],
to a biantennary LeB/LeY antigen comprising Fuc2(Galβ1→3GlcNAc)[Fuc2(Galβ1→4GlcNAc)] [V], or [Fucα1-2Galβ1-3(Fucα1-4)GlcNAc][Fucα1-2Galβ1-4(Fucα1-3)GlcNAc] [VI],
and to a biantennary LeY/LeB antigen comprising Fuc2(Galβ1-4GlcNAc)[Fuc2(Galβ1-3GlcNAc)] [VII] or [Fucα1-2Galβ1-4(Fucα1-3)GlcNAc][Fucα1-2Galβ1-3(Fucα1-4)GlcNAc] [VIII],
and wherein the antibody or antigen-binding fragment thereof does not bind specifically to a monoantennary Lex antigen that comprises Galβ1→4(Fucα1→3)GlcNAc [IX], or to a biantennary Lex antigen that comprises [Galβ1→4(Fucα1→3)GlcNAc]2 [X], or to a monoantennary LeA antigen that comprises Galβ1-3(Fucα1-4)GlcNAc [XI], or to a monoantennary H antigen type 2 that comprises Fucα1-2Galβ1-4GlcNAc [XII], or to a biantennary H antigen type 2 that comprises (Fucα1-2Galβ1-4GlcNAc)2 [XIII] or to a monoantennary H antigen type 1 that comprises Fucα1-2Galβ1-3GlcNAc [XIV].

### Claim 2 (depends on 1)

The isolated antibody or an antigen-binding fragment thereof of claim 1, comprising:
(a) an immunoglobulin heavy chain variable region that comprises a heavy chain complementarity determining region 1 (VH CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 2 or an amino acid sequence that has at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 percent identity to the amino acid sequence set forth in SEQ ID NO:2; a heavy chain complementarity determining region 2 (VH CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 3 or an amino acid sequence that has at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 percent identity to the amino acid sequence set forth in SEQ ID NO:3; and a heavy chain complementarity determining region 3 (VH CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 4 or an amino acid sequence that has at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 percent identity to the amino acid sequence set forth in SEQ ID NO:4; and
(b) an immunoglobulin light chain variable region that comprises a light chain complementarity determining region 1 (VL CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 6 or an amino acid sequence that has at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 percent identity to the amino acid sequence set forth in SEQ ID NO:6; a light chain complementarity determining region 2 (VL CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 7 or an amino acid sequence that has at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 percent identity to the amino acid sequence set forth in SEQ ID NO: 7; and a light chain complementarity determining region 3 (VL CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 8 or an amino acid sequence that has at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 percent identity to the amino acid sequence set forth in SEQ ID NO: 8.

### Claim 3 (depends on 1)

The isolated antibody or an antigen-binding fragment thereof of claim 1, comprising (i), (ii), (iii), (iv), (v), or (vi), as follows, or a combination thereof:
(i) a VH CDR1 comprising a variant of the amino acid sequence set forth in SEQ ID NO: 2, wherein the variant consists of a Y→A substitution at position 33 of SEQ ID NO: 35; and/or
(ii) a VH CDR3 comprising a variant of the amino acid sequence set forth in SEQ ID NO: 4, wherein the variant consists of a Y→A substitution at position 104 of SEQ ID NO: 35;
(iii) a VH CDR3 comprising a variant of the amino acid sequence set forth in SEQ ID NO: 4, wherein the variant consists of a A→substitution at position 106 of SEQ ID NO: 35;
(iv) a VL CDR1 comprising a variant of the amino acid sequence set forth in SEQ ID NO: 6, wherein the variant consists of a Y→A substitution at position 30 of SEQ ID NO: 5;
(v) a VL CDR2 comprising a variant of the amino acid sequence set forth in SEQ ID NO: 7, wherein the variant consists of a G→A substitution at position 50 of SEQ ID NO: 5; or
(vi) a VL CDR3 comprising a variant of the amino acid sequence set forth in SEQ ID NO: 8, wherein the variant consists of a T→S substitution at position 93 of SEQ ID NO: 5.

### Claim 4

An isolated antibody or antigen-binding fragment thereof, comprising: (a) an immunoglobulin heavy chain variable region that comprises a heavy chain complementarity determining region 1 (VH CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 2; and a heavy chain complementarity determining region 2 (VH CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 3; a heavy chain complementarity determining region 3 (VH CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 4; and (b) an immunoglobulin light chain variable region that comprises a light chain complementarity determining region 1 (VL CDR1) comprising the amino acid sequence set forth in SEQ ID NO: 6; a light chain complementarity determining region 2 (VL CDR2) comprising the amino acid sequence set forth in SEQ ID NO: 7; and a light chain complementarity determining region 3 (VL CDR3) comprising the amino acid sequence set forth in SEQ ID NO: 8; wherein the antibody or antigen-binding fragment thereof is capable of binding specifically:
to a biantennary LeB/LeB antigen comprising Fuc4(Galβ1→3GlcNAc)2 [I] or A [Fucα1-2Galβ1-3(Fucα1-4)GlcNAc]2 [II],
to a biantennary LeY/LeY antigen comprising Fuc4(Galβ1→4GlcNAc)2 [III] or [Fucα1-2Galβ1-4(Fucα1-3)GlcNAc]2 [IV],
to a biantennary LeB/LeY antigen comprising Fuc2(Galβ1→3GlcNAc)[Fuc2(Galβ1→4GlcNAc)] [V], or [Fucα1-2Galβ1-3(Fucα1-4)GlcNAc][Fucα1-2Galβ1-4(Fucα1-3)GlcNAc] [VI],
and to a biantennary LeY/LeB antigen comprising Fuc2(Galβ1l-4GlcNAc)[Fuc2(Galβ1-3GlcNAc)] [VII] or [Fucα1-2Galβ1-4(Fucα1-3)GlcNAc][Fucα1-2Galβ1-3(Fucα1-4)GlcNAc] [VIII],
and wherein the antibody or antigen-binding fragment thereof does not bind specifically to a monoantennary Lex antigen that comprises Galβ1→4(Fucα1→3)GlcNAc [IX], or to a biantennary Lex antigen that comprises [Galβ1→4(Fucα1→3)GlcNAc]2 [X], or to a monoantennary LeA antigen that comprises Galβ1-3(Fucα1-4)GlcNAc [XI], or to a monoantennary H antigen type 2 that comprises Fucα1-2Galβ1-4GlcNAc [XII], or to a biantennary H antigen type 2 that comprises (Fucα1-2Galβ1-4GlcNAc)2 [XIII] or to a monoantennary H antigen type 1 that comprises Fucα1-2Galβ1-3GlcNAc [XIV].

### Claim 5

An isolated antibody or antigen-binding fragment thereof, comprising: an immunoglobulin heavy chain variable region that comprises the amino acid sequence set forth in SEQ ID NO: 35; and an immunoglobulin light chain variable region that comprises the amino acid sequence set forth in SEQ ID NO: 5, wherein the antibody or antigen-binding fragment thereof is capable of binding specifically:
to a biantennary LeB/LeB antigen comprising Fuc4(Galβ1→3GlcNAc)2 [I] or [Fucα1-2Galβ1-3(Fucα1-4)GlcNAc]2, [II],
to a biantennary LeY/LeY antigen comprising Fuc4(Galβ1→4GlcNAc)2 [III] or [Fucα1-2Galβ1-4(Fucα1-3)GlcNAc]2 [IV],
to a biantennary LeB/LeY antigen comprising Fuc2(Galβ1→3GlcNAc)[Fuc2(Galβ1→4GlcNAc)] [V], or [Fucα1-2Galβ1-3(Fucα1-4)GlcNAc][Fucα1-2Galβ1-4(Fucα1-3)GlcNAc] [VI],
and to a biantennary LeY/LeB antigen comprising Fuc2(Galβ1-4GlcNAc)[Fuc2(Galβ1-3GlcNAc)] [VII] or [Fucα1-2Galβ1-4(Fucα1-3)GlcNAc][Fucα1-2Galβ1-3(Fucα1-4)GlcNAc] [VIII],
and wherein the antibody or antigen-binding fragment thereof does not bind specifically to a monoantennary Lex antigen that comprises Galβ1→4(Fucα1→3)GlcNAc [IX], or to a biantennary Lex antigen that comprises [Galβ1→4(Fucα1→3)GlcNAc]2 [X], or to a monoantennary LeA antigen that comprises Galβ1-3(Fucα1-4)GlcNAc [XI], or to a monoantennary H antigen type 2 that comprises Fucα1-2Galβ1-4GlcNAc [XII], or to a biantennary H antigen type 2 that comprises (Fucα1-2Galβ1-4GlcNAc)2 [XIII] or to a monoantennary H antigen type 1 that comprises Fucα1-2Galβ1-3GlcNAc [XIV].

### Claim 6

An isolated antibody comprising an immunoglobulin heavy chain having the amino acid sequence set forth in SEQ ID NO: 10 and an immunoglobulin light chain having the amino acid sequence set forth in SEQ ID NO: 11.

### Claim 7 (depends on 6)

The isolated antibody of claim 6, which is monoclonal.

### Claim 8 (depends on 4)

The isolated antibody or antigen-binding fragment thereof of claim 4, wherein the antibody is monoclonal.

### Claim 9 (depends on 4)

The isolated antibody or antigen-binding fragment thereof of claim 4, wherein the antibody is a humanized antibody.

### Claim 10 (depends on 4)

The isolated antibody or antigen-binding fragment thereof of claim 4, wherein the antigen-binding fragment is selected from a Fab fragment, an F(ab′)2 fragment, an Fv fragment, a single chain Fv (ScFv) antibody, and a diabody.

### Claim 11 (depends on 4)

A pharmaceutical composition comprising: the isolated antibody or an antigen-binding fragment thereof of claim 4; and a pharmaceutical carrier.

### Claim 12 (depends on 11)

A method of treating a cancer that expresses one or more biantennary Lewis antigens selected from the group consisting of biantennary LeB/LeB, biantennary LeY/LeY, biantennary LeB/LeY, and biantennary LeY/LeB, comprising administering the pharmaceutical composition of claim 11 a subject in need thereof.

### Claim 13 (depends on 4)

The antibody or antigen-binding fragment of claim 4, wherein the heavy chain variable region comprises an amino acid sequence that has at least 90 percent identity to the amino acid sequence set forth in SEQ ID NO: 35, and the immunoglobulin light chain variable region comprises an amino acid sequence that has at least 90 percent identity to the amino acid sequence set forth in SEQ ID NO: 5.

### Claim 14 (depends on 4)

The antibody or antigen-binding fragment of claim 4, wherein the heavy chain variable region comprises an amino acid sequence that has at least 95 percent identity to the amino acid sequence set forth in SEQ ID NO: 35, and the immunoglobulin light chain variable region comprises an amino acid sequence that has at least 95 percent identity to the amino acid sequence set forth in SEQ ID NO: 5.

### Claim 15 (depends on 4)

The antibody or antigen-binding fragment of claim 4, wherein the heavy chain variable region comprises an amino acid sequence that has at least 97 percent identity to the amino acid sequence set forth in SEQ ID NO: 35, and the immunoglobulin light chain variable region comprises an amino acid sequence that has at least 97 percent identity to the amino acid sequence set forth in SEQ ID NO: 5.

### Claim 16 (depends on 11)

A method of treating colorectal adenocarcinoma, gastric adenocarcinoma or lung cancer that expresses one or more biantennary Lewis antigens selected from the group consisting of biantennary LeB/LeB, biantennary LeY/LeY, biantennary LeB/LeY, and biantennary LeY/LeB, comprising administering to a subject in need thereof the pharmaceutical composition of claim 11.