Innovative discovery of therapeutic, diagnostic, and antibody compositions related to protein fragments of threonyl-tRNA synthetases

Patent metadata

Field	Value
Publication number	US-10563192-B2
Application number	US-201816171087-A
Country	US
Kind code	B2
Filing date	Oct 25, 2018
Priority date	Apr 27, 2010
Publication date	Feb 18, 2020
Grant date	Feb 18, 2020

Abstract

Provided are compositions comprising newly identified protein fragments of aminoacyl-tRNA synthetases, polynucleotides that encode them and complements thereof, related agents, and methods of use thereof in diagnostic, drug discovery, research, and therapeutic applications.

First claim

We claim:

1. A therapeutic composition, comprising an isolated aminoacyl-tRNA synthetase (AARS) polypeptide that is at least 95%, 98%, or 100% identical to a sequence selected from:
(a) SEQ ID NO: 14 or 26 or a fragment thereof which is 100 or more contiguous amino acids of SEQ ID NO: 14 or 26;
(b) SEQ ID NO: 12 or 24 or a fragment thereof which is 300 or more contiguous amino acids of SEQ ID NO: 12 or 24; and
(c) SEQ ID NO: 50 or 58 or a fragment thereof which is 400 or more contiguous amino acids of SEQ ID NO: 50 or 58,
wherein the AARS polypeptide has an extracellular signaling activity and a solubility of at least about 5 mg/mL, and wherein the composition has a purity of at least about 95% on a protein basis and less than about 10 EU endotoxin/mg protein.

2. The therapeutic composition of claim 1 , wherein the AARS polypeptide consists of an amino acid sequence selected from SEQ ID NOs: 12, 14, 24, 26, 50 and 58 or differs from the amino acid sequence selected from SEQ ID NOs: 12, 14, 24, 26, 50 and 58 by substitution, deletion, and/or addition of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 amino acids.

3. The therapeutic composition of claim 1 , wherein the AARS polypeptide is fused to a heterologous polypeptide.

4. The therapeutic composition of claim 1 , wherein at least one moiety or a solid substrate is covalently or non-covalently attached to said polypeptide.

5. An isolated aminoacyl-tRNA synthetase (AARS) polypeptide that is at least 95%, 98%, or 100% identical to an amino acid sequence selected from:
(a) SEQ ID NO: 14 or 26 or a fragment thereof which is 100 or more contiguous amino acids of SEQ ID NO: 14 or 26;
(b) SEQ ID NO: 12 or 24 or a fragment thereof which is 300 or more contiguous amino acids of SEQ ID NO: 12 or 24; and
(c) SEQ ID NO: 50 or 58 or a fragment thereof which is 400 or more contiguous amino acids of SEQ ID NO: 50 or 58,
wherein the AARS polypeptide has an extracellular signaling activity.

6. The isolated AARS polypeptide of claim 5 , wherein the AARS polypeptide is fused to a heterologous polypeptide.

7. The isolated AARS polypeptide of claim 5 , further comprising an element selected from the group consisting of:
(i) a binding partner that binds to the AARS polypeptide;
(ii) an engineered population of cells in which at least one cell comprises a polynucleotide encoding said AARS polypeptide, wherein the cells are capable of growing in a serum-free medium;
(iii) a cell that comprises a cell-surface receptor or an extracellular portion thereof that binds to the polypeptide, and a molecule of less than about 2000 daltons, or a second polypeptide, which modulates binding or interaction of the AARS polypeptide and the extracellular receptor;
(iv) a cell that comprises a cell-surface receptor or an extracellular portion thereof that specifically binds to the AARS polypeptide, wherein the cell comprises an indicator molecule that allows detection of a change in the levels or activity of the cell-surface receptor or extracellular portion thereof; and
(v) an engineered population of cells in which at least one cell comprises a polynucleotide encoding said AARS polypeptide, at least about 10 liters of a serum-free growth medium, and a sterile container.

8. A method of determining presence or levels of an AARS polypeptide or a polynucleotide that encodes the AARS polypeptide in a sample, comprising:
(a) contacting the sample with one or more binding agents or antibodies or antigen-binding fragments thereof that specifically bind to an AARS polypeptide of claim 5 , detecting the presence or absence of the binding agent, and thereby determining the presence or levels of the AARS polypeptide;
(b) analyzing the sample with a detector that is capable of specifically identifying an AARS polypeptide of claim 5 , and thereby determining the presence or levels of the AARS polypeptide;
(c) contacting the sample with one or more oligonucleotides that specifically hybridize to polynucleotide that encodes an AARS polypeptide of claim 5 , detecting the presence or absence of the oligonucleotides in the sample, and thereby determining the presence or levels of the polynucleotide; or
(d) contacting the sample with at least two oligonucleotides that specifically amplify a polynucleotide that encodes an AARS polypeptide of claim 5 , performing an amplification reaction, detecting the presence or absence of an amplified product, and thereby determining presence or levels of the polynucleotide.

9. A method of modulating a cellular activity of a cell, or protein, comprising contacting the cell or protein with an AARS polypeptide claim 5 , or a composition comprising a pharmaceutically-acceptable carrier and said AARS polypeptide.

10. The method of claim 9 , wherein the cell or protein is in a subject having a disease or disorder optionally mediated by the dysregulation of the expression, activity or spatiotemporal location of a tRNA synthetase, comprising administering the AARS polypeptide or the composition to the subject.

11. A composition, comprising (a) an antibody or antigen binding fragment thereof that exhibits binding specificity for an AARS polypeptide of claim 5 , or (b) an isolated polynucleotide that encodes an AARS polypeptide of claim 5 .

12. A method of identifying a compound that specifically binds to an AARS polypeptide of claim 5 , comprising a) combining the AARS polypeptide with at least one test compound under suitable conditions, and b) detecting binding of the AARS polypeptide to the test compound, thereby identifying a compound that specifically binds to the AARS polypeptide.

Assignees

• Atyr Pharma Inc
• Pangu Biopharma Ltd

Inventors

• Greene Leslie Ann
• Chiang Kyle P
• Hong Fei
• Vasserot Alain P
• Lo Wing-Sze
• Watkins Jeffry D
• Quinn Cheryl L
• Mendlein John D

Classifications

• A61P43/00

  Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00 · CPC title

• A61P37/02

  Immunomodulators · CPC title

• A61P9/14

  Vasoprotectives; Antihaemorrhoidals; Drugs for varicose therapy; Capillary stabilisers · CPC title

• A61P9/10

  for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis · CPC title

• A61P9/00

  Drugs for disorders of the cardiovascular system · CPC title