Methods of identifying a polypeptide target for degradation by a modulator of CRBN

Patent metadata

Field	Value
Publication number	US-11168345-B2
Application number	US-201615759168-A
Country	US
Kind code	B2
Filing date	Sep 9, 2016
Priority date	Sep 11, 2015
Publication date	Nov 9, 2021
Grant date	Nov 9, 2021

Abstract

In one aspect, the invention features a method for identifying a drug-modulated polypeptide substrate of cereblon (CRBN). In another aspect, the invention features a method of identifying a polypeptide target of a modulator of CRBN. In yet another aspect, the invention provides methods of monitoring or characterizing the sensitivity of a subject to a modulator of CRBN.

First claim

What is claimed is:

1. A method of identifying increased polypeptide degradation in a cell, the method comprising:
contacting a cell with a modulator of cereblon (CRBN); and
detecting in a first polypeptide in the cell the presence of a sequence substantially identical to an amino acid sequence FQCNQCGASFTQKGNLLRHIKLH (SEQ ID NO: 1), in an amino terminus (NH 2 ) to carboxy terminus (COOH) orientation, and detecting in a second polypeptide in the cell the presence of at least one amino acid sequence substantially identical to a sequence, in an NH 2 to COOH orientation, selected from:

(SEQ ID NO: 2)

FACPYCGARNLDQQELVKHCVESH;

(SEQ ID NO: 3)

LQCEICGFTCRQKASLNWHQRKH;

or

(SEQ ID NO: 4)

LQCEICGFTCRQKASLNWHMKKH;

wherein detecting the sequences in the first and second polypeptides in the cell indicates increased polypeptide degradation in the cell contacted with the modulator of CRBN.

2. The method of claim 1 , wherein the first or the second polypeptide in the cell is IKZF3, IKZF1, RNF166, ZNF692, or ZFP91.

3. The method of claim 1 , wherein the modulator of CRBN is lenalidomide, thalidomide, or pomalidomide.

4. The method of claim 1 , wherein detecting the presence of the sequence in the first polypeptide and the sequence in the second polypeptide indicates that the first and second polypeptides in the cell are drug-modulated polypeptide substrates of CRBN.

5. The method of claim 1 , wherein detecting the presence of the sequences in the first and second polypeptides in the cell indicates that the polypeptides are drug-modulated polypeptide substrates of CRBN; and wherein detecting the presence of the sequences in the first and second polypeptides in the cell indicates that the polypeptides are polypeptide targets of a modulator of CRBN.

6. The method of claim 1 , wherein the first and the second polypeptides in the cell are degraded by CRBN-mediated degradation when the cell is contacted with the modulator of CRBN.

7. The method of claim 1 , wherein contacting the cell with a modulator of CRBN depletes the polypeptides in the cell.

8. The method of claim 1 , wherein one or both of the first and the second polypeptide sequences comprises a C2H2 zinc finger sequence.

9. The method of claim 8 , wherein amino acid positions in the C2H2 zinc finger sequence corresponding to amino acids 2, 7, and 8 in an amino terminus to carboxy terminus orientation in SEQ ID NO: 1 comprise glutamine (Gln), glycine (Gly), or alanine (Ala).

Assignees

• Mikkelsen Tarjei
• Ebert Benjamin Levine
• Sievers Quinlan
• Broad Inst Inc
• Harvard College
• Brigham & Womens Hospital Inc

Inventors

• Mikkelsen Tarjei
• Ebert Benjamin Levine
• Sievers Quinlan

Classifications

• A61K31/454

  containing a five-membered ring with nitrogen as a ring hetero atom, e.g. pimozide, domperidone · CPC title

• A61K31/4035

  Isoindoles, e.g. phthalimide · CPC title

• A61P35/00

  Antineoplastic agents · CPC title

• C12Q1/6886 Primary

  for cancer (immunoassay for cancer G01N33/575) · CPC title

• C12N5/0635

  B lymphocytes · CPC title