Compositions and methods for inducing conformational changes in cereblon and other E3 ubiquitin ligases

Patent metadata

Field	Value
Publication number	US-10830762-B2
Application number	US-201616066288-A
Country	US
Kind code	B2
Filing date	Dec 27, 2016
Priority date	Dec 28, 2015
Publication date	Nov 10, 2020
Grant date	Nov 10, 2020

Abstract

Provided herein are compositions, therapeutic methods, screening methods, computational methods and biomarkers based upon the elucidation of the interaction among cereblon, its substrates and certain compounds or agents, including small molecules, peptides, and proteins.

First claim

What is claimed is:

1. A method of identifying a CRBN-associated protein (CAP), or identifying a target of a compound, comprising:
(I) (a) searching a protein database for a protein comprising an amino acid sequence of a degron in a CAP;
(b) testing the protein in a CRBN-binding assay; and
(c) identifying the protein as a CAP if the protein specifically binds to CRBN in the CRBN-binding assay;

or
(II) (a) searching a protein database for a protein comprising an amino acid sequence of a degron in a CAP;
(b) testing the protein in a CRBN-mediated degradation assay; and
(c) identifying the protein as a CAP if the protein level decreases in the CRBN-mediated degradation assay;

or
(III) (a) searching a protein database for a protein comprising an amino acid sequence of a degron in a CAP;
(b) testing the protein in a CRBN-binding assay in the presence of the compound; and
(c) identifying the protein as the target of the compound if the protein specifically binds to CRBN in the CRBN-binding assay;

or
(IV) (a) searching a protein database for a protein comprising an amino acid sequence of a degron in a CAP;
(b) testing the protein in a CRBN-mediated degradation assay in the presence of the compound; and
(c) identifying the protein as the target of the compound if the protein level decreases in the CRBN-mediated degradation assay;

and wherein the amino acid sequence of the degron is [D/N]XX[S/T]G (SEQ ID NO:11), CXXCG (SEQ ID NO:16), or NXXNG (SEQ ID NO:17), wherein X can be any amino acid residue.

2. The method of claim 1 , wherein the CAP is a substrate of CRBN.

3. The method of claim 1 , wherein the amino acid sequence of the degron is [D/N]XX[S/T]G (SEQ ID NO:11), wherein X can be any amino acid residue.

4. The method of claim 1 , wherein the amino acid sequence of the degron is CXXCG (SEQ ID NO:16) or NXXNG (SEQ ID NO:17), wherein X can be any amino acid residue.

5. The method of claim 1 , wherein the CRBN-binding assay is performed in the presence of a compound.

6. The method of claim 5 , wherein the compound is a cereblon modifying agent (CMA).

7. The method of claim 5 , wherein the compound is an immunomodulatory compound.

8. The method of claim 5 , wherein the compound is selected from the group consisting of thalidomide, lenalidomide, pomalidomide, Compound A (3-(5-amino-2-methyl-4-oxo-4H-quinazolin-3-yl)-piperidine-2,6-dione), Compound B (3-(4-((4-(morpholinomethyl)benzyl)oxy)-1-oxoisoindolin-2-yl)piperidine-2,6-dione), Compound C (1-(3-chloro-4-methylphenyl)-3-42-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-5-yl)methyl)urea), Compound D (2-(4-chlorophenyl)-N-42-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-5-yl)methyl)-2,2-difluoroacetamide), and Compound E (2-(4-flurophenyl)-N-42-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-5-yl)methyl)-2,2-difluoroacetamide).

Assignees

• Celgene Corp

Inventors

• Cathers Brian E
• Chamberlain Philip
• Lopez-Girona Antonia
• Lu Gang

Classifications

• A61K31/4035 Primary

  Isoindoles, e.g. phthalimide · CPC title

• C07K2319/95

  containing a motif/fusion for degradation (ubiquitin fusions, PEST sequence) · CPC title

• G01N33/566

  using specific carrier or receptor proteins as ligand binding reagents {where possible specific carrier or receptor proteins are classified with their target compounds} · CPC title

• A61K38/00

  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) · CPC title

• C07D401/04

  directly linked by a ring-member-to-ring-member bond · CPC title