Materials and methods of using engineered ligands

Patent metadata

Field	Value
Publication number	US-2022056104-A1
Application number	US-202117405872-A
Country	US
Kind code	A1
Filing date	Aug 18, 2021
Priority date	Aug 19, 2020
Publication date	Feb 24, 2022
Grant date	—

Abstract

Described herein are compositions and kits that comprise an engineered TL1A ligand that displays high stability, minimal binding to decoy receptor DcR3 while retaining functional activity via binding to its cell surface receptor, DR3, and the ability to activate T cells in vitro and in vivo. Methods of making an engineered TL1A ligand and methods of treating a disease or disorder in a subject by administering an engineered TL1A ligand are also provided.

First claim

1 - 50 . (canceled)

51 . An engineered TL1A ligand, wherein the engineered TL1A ligand comprises a trimeric complex comprising:
a. three TL1A monomers, wherein the three TL1A monomers form a non-covalent TL trimer; or b. three TL1A monomers, wherein the three TL1A monomers are covalently linked to form a single-chain TL1A (scTL1A) trimer.

52 . The engineered TL1A ligand of claim 51 , further comprising a protein stabilizing region, wherein optionally the protein stabilizing region comprises an Fc region, or a human serum albumin (HSA) region.

53 . The engineered TL1A ligand of claim 51 , comprising:
a. the non-covalent TL1A trimer and one or more Fc regions; b. the non-covalent TL1A trimer and one or more HSA regions; c. the scTL1A trimer and one or more Fc regions; or d. the scTL1A trimer and one or more HSA regions.

54 . The engineered TL1A ligand of claim 53 comprising:
a. two non-covalent TL1A trimers and three Fc regions;
b. two scTL1A trimers and one Fc region;
c. one scTL1A trimer and one Fc region;
d. one non-covalent TL1A trimer and three HSA regions; or
e. one scTL1A trimer and one HSA region.

55 . The engineered TL1A ligand of claim 51 , wherein the three TL1A monomers are covalently bound by a linker, wherein optionally the linker is a peptide linker, and wherein optionally the linker has an amino acid sequence of Gly-Ser or multiple repeats thereof.

56 . The engineered TL1A ligand of claim 51 , wherein the Fc region is a human IgG1, IgG2 or IgG4 Fc region, and wherein optionally non-covalent TL1A trimer or the scTL1A trimer is fused to the C-terminus of the Fc region.

57 . The engineered TL1A ligand of claim 51 , wherein:
(i) the engineered TL1A ligand comprises the amino acid residues 72-251 of SEQ ID NO:94; (ii) the engineered TL1A ligand comprises at least one amino acid alteration of residues 72-251 of the amino acid sequence of SEQ ID NO:94, wherein optionally the engineered TL1A ligand has one or more alterations at one or more residue positions of SEQ ID NO:94 selected from the group consisting of R103, K111, N112, F114, E120, L123, G124, R156, M158, Q167, R170, K173, S176, T185, D186, S187, Y188, P189, E190, T192, S206, N207, F209, Y238, T239, K240, and E241, and wherein optionally the one or more alterations at one or more residue positions of SEQ ID NO:94 is an alteration selected from R103A, R103H, R103Q, R103E, R103E, K111A, K111S, K111E, N112E, F114A, E120A, E120K, E120H, L123G, L123S, L123E, L123K, G124S, G124K, G124D, R156A, R156Y, R156K, R156E, M158Y, M158K, M158E, Q167A, R170E, K173S, K173R, S176A, S176L, S176, S176K, T185A, T185L, T185N, T185D, D186Y, S187A, S187L, S187K, S187D, Y188A, Y188S, P189A, P189K, P189F, P189S, E190G, E190F, T192A, T192F, T192K, T192E, S206A, S206F, S206K, S206E, N207A, N207F, N207S, N207K, N207E, F209A, F209W, Y238A, Y238S, Y238K, Y238R, Y238E, T239A, T239E, T239F, T239K, T239W, K240A, K240F, K240S, K240D, E241A, E241L, and E241Q; (iii) the engineered TL1A ligand comprises at least two, three, four, five, six, seven, or more alterations of an amino acid sequence of residues 72-251 of SEQ ID NO:94; (iv) the engineered TL1A ligand comprises one or more amino acid alterations of SEQ ID NO:94 selected from the group consisting of: K111A, L123K, M158Y, Q167A, S187L, E190F, and N207F; (v) the engineered TL1A ligand comprises the amino acid sequence of any one of SEQ ID NO:1-93; (vi) the engineered TL1A ligand comprises:
a. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:79;
b. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:72;
c. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:8;
d. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:65;
e. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:52;
f. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:14;
g. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:36;
h. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:90;
i. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:88;
j. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:91, or
k. an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% identical over its entire length to the amino acid sequence of SEQ ID NO:89.

58 . The engineered TL1A ligand of claim 51 , (i) which comprises a bispecific antibody; (ii) which is fused to a heterologous polypeptide; or (iii) which is conjugated to an agent, wherein optionally the agent is a toxin.

59 . An engineered TL1A ligand comprising: a first means capable of binding DR3 with an affinity comparable to or higher than the affinity of wildtype TL1A and a second means capable of binding DcR3 with an affinity lower than the affinity of wildtype TL1A, wherein optionally:
(i) the engineered TL1A ligand has a longer serum half-life than wildtype TL1A; (ii) the engineered TL1A ligand has a high monodispersity and/or stability compared to wildtype TL1A; (iii) the engineered TL1A ligand co-stimulates T cells in vitro; (iv) the engineered TL1A ligand co-stimulates T cells in a subject; and/or (v) the engineered TL1A ligand increases production of one or more cytokines in a subject, wherein optionally the one or more cytokines comprise IFNγ and TNFα, wherein optionally the subject has an autoimmune disorder or cancer optionally selected from the group consisting of ulcerative colitis, lupus, inflammatory bowel disease (IBD), chronic obstructive pulmonary disease (COPD), arthritis, multiple sclerosis, diabetes, transplant rejection, central nervous system injury, Crohn's disease, psoriasis, leukemia or lymphoma, atherosclerosis, colon cancer, breast cancer, pancreatic cancer, leukemia, lung cancer such as non-small cell lung cancer, glioblastoma, melanoma, prostate cancer, gastric cancer, pituitary adenomas, ovarian cancer, renal cancer, bladder cancer, and a sarcoma, wherein optionally the sarcoma is a rhabdomyosarcoma, and wherein optionally the subject is a subject in need thereof.

60 . A nucleic acid encoding the engineered TL1A ligand of claim 59 .

61 . A pharmaceutical composition, comprising the engineered TL1A ligand of claim 59 or the nucleic acid encoding the engineered TL1A ligand, and a pharmaceutically acceptable excipient.

62 . A method treating a disease or disorder in a subject, comprising administering to the subject an effective amount of an engineered TL1A ligand of

Assignees

• Janssen Biotech Inc

Inventors

• Zwolak Adam
• Chan Szeman
• Ganesan Rajkumar

Classifications

• C07K2319/74

  containing a fusion for binding to a cell surface receptor · CPC title

• A61P37/04 Primary

  Immunostimulants · CPC title

• A61P35/00

  Antineoplastic agents · CPC title

• C07K2319/21

  containing a His-tag · CPC title

• C07K2319/30

  Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto · CPC title