# US 11,896,643 B2 · Fibroblast binding agents and use thereof

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- Number: US 11,896,643 B2
- Document ID: US11896643B2
- Status: Granted
- Kind: B2
- Application number: 16/967,288
- Filed: 2019-02-05
- Published: 2021-01-28
- Granted: 2024-02-13
- Earliest claimed: 2018-02-05
- Assignees: Orionis Biosciences BV
- Applicants: Orionis Biosciences, Inc.; Vib Vzw; Universiteit Gent
- Inventors: Nikolai Kley; Jan Tavernier; Anje Cauwels
- Web page: https://patentgrep.com/patent/US11896643B2

## CPC

- A61K 38/16: Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof {(enzyme inhibitors A61K38/005)}
- A61K 39/395: Antibodies (agglutinins A61K38/36 {; as drug carriers A61K47/50}); Immunoglobulins; Immune serum, e.g. antilymphocytic serum
- A61K 31/704: attached to a condensed carbocyclic ring system, e.g. sennosides, thiocolchicosides, escin, daunorubicin {(digitoxin A61K31/7048)}
- A61K 33/24: Heavy metals; Compounds thereof
- A61P 35/00: Antineoplastic agents
- C07K 14/525: Tumour necrosis factor [TNF]
- C07K 14/555: Interferons [IFN]
- C07K 14/56: IFN-alpha
- C07K 16/244: {Interleukins [IL]}
- C07K 16/2818: {against CD28 or CD152}
- C07K 16/2827: {against B7 molecules, e.g. CD80, CD86}
- C07K 16/2851: {against the lectin superfamily, e.g. CD23, CD72}
- C07K 16/2878: {against the NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95}
- C07K 16/40: against enzymes
- A61K 38/00: Medicinal preparations containing peptides (peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00)
- A61K 2039/505: {comprising antibodies}
- A61K 2039/507: {Comprising a combination of two or more separate antibodies}
- C07K 2317/24: containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
- C07K 2317/31: multispecific
- C07K 2317/565: Complementarity determining region [CDR]
- C07K 2317/569: Single domain, e.g. dAb, sdAb, VHH, VNAR or nanobody®
- C07K 2317/94: Stability, e.g. half-life, pH, temperature or enzyme-resistance
- C07K 2319/00: Fusion polypeptide
- C07K 2319/02: containing a signal sequence
- C07K 2319/33: fusions for targeting to specific cell types, e.g. tissue specific targeting, targeting of a bacterial subspecies
- 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
- 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)

## Abstract

The present invention relates, in part, to agents that bind fibroblast activation protein (FAP) and their use as diagnostic and therapeutic agents. The present invention further relates to pharmaceutical compositions comprising the FAP binding agents and their use in the treatment of various diseases.

## Claims

### Claim 1

A chimeric protein comprising:
(a) at least one recombinant heavy-chain-only antibody (VHH) or a single-chain antibody (scFv) targeting moiety that is a fibroblast activation protein (FAP) binding agent, wherein the FAP binding agent comprises three complementarity determining regions (CDR1, CDR2, and CDR3), wherein:
CDR1 comprises the amino acid sequence of SEQ ID NO: 95; CDR2 comprises the amino acid sequence of SEQ ID NO: 121; CDR3 comprises the amino acid sequence of SEQ ID NO: 152;
CDR1 comprises the amino acid sequence of SEQ ID NO: 87; CDR2 comprises the amino acid sequence of SEQ ID NO: 116; CDR3 comprises the amino acid sequence of SEQ ID NO: 145;
CDR1 comprises the amino acid sequence of SEQ ID NO: 89; CDR2 comprises the amino acid sequence of SEQ ID NO: 117; CDR3 comprises the amino acid sequence of SEQ ID NO: 146;
CDR1 comprises the amino acid sequence of SEQ ID NO: 90; CDR2 comprises the amino acid sequence of SEQ ID NO: 117; CDR3 comprises the amino acid sequence of SEQ ID NO: 147;
CDR1 comprises the amino acid sequence of SEQ ID NO: 91; CDR2 comprises the amino acid sequence of SEQ ID NO: 118; CDR3 comprises the amino acid sequence of SEQ ID NO: 148;
CDR1 comprises the amino acid sequence of SEQ ID NO: 92; CDR2 comprises the amino acid sequence of SEQ ID NO: 118; CDR3 comprises the amino acid sequence of SEQ ID NO: 149;
CDR1 comprises the amino acid sequence of SEQ ID NO: 93; CDR2 comprises the amino acid sequence of SEQ ID NO: 119; CDR3 comprises the amino acid sequence of SEQ ID NO: 146;
CDR1 comprises the amino acid sequence of SEQ ID NO: 94; CDR2 comprises the amino acid sequence of SEQ ID NO: 120; CDR3 comprises the amino acid sequence of SEQ ID NO: 150;
CDR1 comprises the amino acid sequence of SEQ ID NO: 94; CDR2 comprises the amino acid sequence of SEQ ID NO: 120; CDR3 comprises the amino acid sequence of SEQ ID NO: 151;
CDR1 comprises the amino acid sequence of SEQ ID NO: 96; CDR2 comprises the amino acid sequence of SEQ ID NO: 122; CDR3 comprises the amino acid sequence of SEQ ID NO: 153;
CDR1 comprises the amino acid sequence of SEQ ID NO: 97; CDR2 comprises the amino acid sequence of SEQ ID NO: 123; CDR3 comprises the amino acid sequence of SEQ ID NO: 154;
CDR1 comprises the amino acid sequence of SEQ ID NO: 98; CDR2 comprises the amino acid sequence of SEQ ID NO: 124; CDR3 comprises the amino acid sequence of SEQ ID NO:155;
CDR1 comprises the amino acid sequence of SEQ ID NO: 99; CDR2 comprises the amino acid sequence of SEQ ID NO: 125; CDR3 comprises the amino acid sequence of SEQ ID NO: 156;
CDR1 comprises the amino acid sequence of SEQ ID NO: 100; CDR2 comprises the amino acid sequence of SEQ ID NO: 126; CDR3 comprises the amino acid sequence of SEQ ID NO: 157;
CDR1 comprises the amino acid sequence of SEQ ID NO: 101; CDR2 comprises the amino acid sequence of SEQ ID NO: 127; CDR3 comprises the amino acid sequence of SEQ ID NO: 158;
CDR1 comprises the amino acid sequence of SEQ ID NO: 102; CDR2 comprises the amino acid sequence of SEQ ID NO: 128; CDR3 comprises the amino acid sequence of SEQ ID NO: 159;
CDR1 comprises the amino acid sequence of SEQ ID NO: 103; CDR2 comprises the amino acid sequence of SEQ ID NO: 129; CDR3 comprises the amino acid sequence of SEQ ID NO: 160;
CDR1 comprises the amino acid sequence of SEQ ID NO: 104; CDR2 comprises the amino acid sequence of SEQ ID NO: 129; CDR3 comprises the amino acid sequence of SEQ ID NO: 160;
CDR1 comprises the amino acid sequence of SEQ ID NO: 105; CDR2 comprises the amino acid sequence of SEQ ID NO: 130; CDR3 comprises the amino acid sequence of SEQ ID NO: 160;
CDR1 comprises the amino acid sequence of SEQ ID NO: 105; CDR2 comprises the amino acid sequence of SEQ ID NO: 131; CDR3 comprises the amino acid sequence of SEQ ID NO: 161;
CDR1 comprises the amino acid sequence of SEQ ID NO: 106; CDR2 comprises the amino acid sequence of SEQ ID NO: 132; CDR3 comprises the amino acid sequence of SEQ ID NO: 162;
CDR1 comprises the amino acid sequence of SEQ ID NO: 106; CDR2 comprises the amino acid sequence of SEQ ID NO: 132; CDR3 comprises the amino acid sequence of SEQ ID NO: 162;
CDR1 comprises the amino acid sequence of SEQ ID NO: 107; CDR2 comprises the amino acid sequence of SEQ ID NO: 133; CDR3 comprises the amino acid sequence of SEQ ID NO: 163;
CDR1 comprises the amino acid sequence of SEQ ID NO: 108; CDR2 comprises the amino acid sequence of SEQ ID NO: 132; CDR3 comprises the amino acid sequence of SEQ ID NO: 164;
CDR1 comprises the amino acid sequence of SEQ ID NO: 106; CDR2 comprises the amino acid sequence of SEQ ID NO: 134; CDR3 comprises the amino acid sequence of SEQ ID NO: 165;
CDR1 comprises the amino acid sequence of SEQ ID NO: 106; CDR2 comprises the amino acid sequence of SEQ ID NO: 134; CDR3 comprises the amino acid sequence of SEQ ID NO: 165;
CDR1 comprises the amino acid sequence of SEQ ID NO: 106; CDR2 comprises the amino acid sequence of SEQ ID NO: 135; CDR3 comprises the amino acid sequence of SEQ ID NO: 166;
CDR1 comprises the amino acid sequence of SEQ ID NO: 106; CDR2 comprises the amino acid sequence of SEQ ID NO: 135; CDR3 comprises the amino acid sequence of SEQ ID NO: 166;
CDR1 comprises the amino acid sequence of SEQ ID NO: 106; CDR2 comprises the amino acid sequence of SEQ ID NO: 136; CDR3 comprises the amino acid sequence of SEQ ID NO: 167;
CDR1 comprises the amino acid sequence of SEQ ID NO: 109; CDR2 comprises the amino acid sequence of SEQ ID NO: 137; CDR3 comprises the amino acid sequence of SEQ ID NO: 168;
CDR1 comprises the amino acid sequence of SEQ ID NO: 106; CDR2 comprises the amino acid sequence of SEQ ID NO: 138; CDR3 comprises the amino acid sequence of SEQ ID NO: 169;
CDR1 comprises the amino acid sequence of SEQ ID NO: 110; CDR2 comprises the amino acid sequence of SEQ ID NO: 139; CDR3 comprises the amino acid sequence of SEQ ID NO: 170;
CDR1 comprises the amino acid sequence of SEQ ID NO: 111; CDR2 comprises the amino acid sequence of SEQ ID NO: 140; CDR3 comprises the amino acid sequence of SEQ ID NO: 171;
CDR1 comprises the amino acid sequence of SEQ ID NO: 112; CDR2 comprises the amino acid sequence of SEQ ID NO: 141; CDR3 comprises the amino acid sequence of SEQ ID NO: 172;
CDR1 comprises the amino acid sequence of SEQ ID NO: 113; CDR2 comprises the amino acid sequence of SEQ ID NO: 142; CDR3 comprises the amino acid sequence of SEQ ID NO: 173;
CDR1 comprises the amino acid sequence of SEQ ID NO: 114; CDR2 comprises the amino acid sequence of SEQ ID NO: 143; CDR3 comprises the amino acid sequence of SEQ ID NO: 174; or
CDR1 comprises the amino acid sequence of SEQ ID NO: 115; CDR2 comprises the amino acid sequence of SEQ ID NO: 144; CDR3 comprises the amino acid sequence of SEQ ID NO: 175, and
(b) a modified human interferon alpha 2 (IFNα2) signaling agent comprising an amino acid sequence having at least 98% identity with SEQ ID NO: 176 or 177 and having R149A mutation, relative to SEQ ID NO: 176 or 177, that confers reduced affinity or activity for its receptor, as compared to a wild type human IFNα2 having an amino acid sequence of SEQ ID NO: 176 or 177.

### Claim 2 (depends on 1)

The chimeric protein of claim 1, wherein the chimeric protein directly or indirectly polarizes F2 fibroblasts.

### Claim 3 (depends on 1)

The chimeric protein of claim 1, wherein the chimeric protein recruits cytotoxic T cells to tumor cells or to a tumor microenvironment.

### Claim 4 (depends on 1)

The chimeric protein of claim 1, wherein the FAP binding agent recognizes or binds FAP without substantially functionally modulating its activity.

### Claim 5 (depends on 1)

The chimeric protein of claim 1, wherein the targeting moiety comprises an amino acid sequence having at least 95% sequence similarity with SEQ ID NO: 58 or any one of SEQ ID NOS: 2 to 42, 46 to 57, or 59 to 86.

### Claim 6 (depends on 1)

The chimeric protein of claim 1, wherein the chimeric protein comprises one or more additional targeting moieties that recognize or functionally modulate a tumor antigen or an antigen on an immune cell selected from a T cell, a B cell, a dendritic cell, a macrophage, neutrophil, and a NK cell.

### Claim 7 (depends on 6)

The chimeric protein of claim 6, wherein the one or more additional targeting moieties recognize or functionally modulate PD-1, PD-L1, PD-L2, CTLA4, OX40L, OX40, CD8, CD3, CD20, XCR1, and Clec9A.

### Claim 8 (depends on 1)

The chimeric protein of claim 1, wherein the disease-associated fibroblast is associated with a disease selected from cancer, infections, immune disorders, autoimmune disease, fibrotic diseases, and cardiovascular disease.

### Claim 9 (depends on 1)

A recombinant nucleic acid encoding the chimeric protein of claim 1, or a component thereof.

### Claim 10 (depends on 9)

A host cell comprising the nucleic acid of claim 9.

### Claim 11 (depends on 1)

A method for treating cancer, infections, immune disorders, fibrotic diseases, and autoimmune diseases comprising administering to a patient in need thereof an effective amount of the chimeric protein of claim 1.