Reprogramming effector protein interactions to correct epigenetic defects in cancer

• US 9,552,457 B2
• Filed: 02/27/2013
• Issued: 01/24/2017
• Est. Priority Date: 02/27/2012
• Status: Active Grant

• Current Assignee: British Columbia Cancer Agency Branch (Province of British Columbia)
• Original Assignee: British Columbia Cancer Agency Branch (Province of British Columbia)
• Inventors: Jones, Steven J. M., Yakovenko, Oleksandr, Thoene, Silvia, Cheung, Pierre Yulmin, An, Jianghong
• Primary Examiner(s): BORIN, MICHAEL L
• Application Number:
  US14/381,588
• Publication Number:
  US 20150154345A1
• Time in Patent Office: 1,427 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: A61K 31/10 Sulfides; Sulfoxides; Sulfones
• CPC Class Codes: A61K 31/135 having aromatic rings , e.g. ketamine, nortriptyline methadone A61K31/137
• CPC Class Codes: A61K 31/137 Arylalkylamines, e.g. amphetamine, epinephrine, salbutamol, ephedrine or methadone
• CPC Class Codes: A61K 31/167 having the nitrogen of a carboxamide group directly attached to the aromatic ring, e.g. lidocaine, paracetamol
• CPC Class Codes: A61K 31/245 Amino benzoic acid types, e.g. procaine, novocaine salicylic acid esters A61K31/60
• CPC Class Codes: A61K 31/343 condensed with a carbocyclic ring, e.g. coumaran, bufuralol, befunolol, clobenfurol, amiodarone
• CPC Class Codes: A61K 31/36 Compounds containing methylenedioxyphenyl groups, e.g. sesamin
• CPC Class Codes: A61K 31/407 condensed with other heterocyclic ring systems, e.g. ketorolac, physostigmine
• CPC Class Codes: A61K 31/47 Quinolines; Isoquinolines
• CPC Class Codes: A61K 31/4709 Non-condensed quinolines and containing further heterocyclic rings
• CPC Class Codes: A61K 31/5375 1,4-Oxazines, e.g. morpholine
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16C 20/50 Molecular design, e.g. of drugs
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry
• CPC Class Codes: G16C 20/64 Screening of libraries
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

Methods of “reprogramming” epigenetic mark readers or erasers to recognize epigenetic marks other than their cognate (or natural) marks are provided. Reprogramming the reader or eraser can offset the effects of aberrant writer activity (for example, loss of function or overactivity) that can contribute to certain diseases states, such as cancer. The use of the reprogramming compounds identified by these methods in the treatment of such disease states is also provided. Exemplary mark readers that can be targeted by these methods include BPTF and CBX2.

Claims

1. A method for identifying a candidate compound that increases binding of a histone mark reader protein to a target histone tail mark, the method comprising:

(a) computationally generating a structural model of the active site of the reader protein in complex with the target histone tail mark, the structural model based on a computational model of the active site of the reader protein complexed with its cognate histone tail mark;

(b) identifying one or more functional features required for binding of the target histone tail mark in the active site of the reader protein;

(c) modeling into the active site a virtual probe structure that, together with residues in the active site and the target histone tail mark, substantially reproduces the functional features identified in step (b) to form a stable complex comprising the target histone tail mark, the residues of the active site and the virtual probe structure;

(d) modeling candidate compounds in place of the virtual probe structure to identify a candidate compound which forms a stable complex comprising the target histone tail mark, the residues of the active site and the identified candidate compound;

(e) providing the candidate compound identified in step (d) for use in one or more in vitro assays to assess increased binding of the histone mark reader protein to the histone tail mark; and

(f) testing the candidate compound provided in step (e) in the one or more in vitro assays to assess increased binding of the reader protein to the target histone tail mark.

2. The method according to claim 1, wherein step (c) comprises conducting an iterative molecular dynamics simulation of a series of virtual probe structures in the active site with the target histone tail mark to identify an optimal probe structure that provides the stable complex comprising the target histone tail mark, the residues of the active site and the virtual probe structure.

3. The method according to claim 2, wherein step (d) comprises docking the candidate compounds into an average protein structure based on the stable complex comprising the target histone tail mark, the residues of the active site and the virtual probe structure.

4. The method according to claim 1, wherein step (d) comprises performing molecular dynamics simulations, in silico docking methods, structural similarity searching, or a combination thereof.

5. The method according to claim 1, wherein the target histone tail mark and the cognate histone tail mark are methylated lysine marks.

6. The method according to claim 5, wherein the cognate histone tail mark is a trimethylated lysine and the target histone tail mark is a di-, mono- or un-methylated lysine.

7. The method according to claim 6, wherein the one or more functional features include an aromatic cage formed by 3 or more aromatic residues in the active site.

8. The method according to claim 6, wherein the one or more functional features comprise a hydrogen bond.

9. The method according to claim 1, wherein the cognate histone tail mark is a trimethylated lysine and the target histone tail mark is a di-, mono- or un-methylated lysine, and wherein the virtual probe structure comprises a hydrogen acceptor.

10. The method according to claim 9, wherein the virtual probe structure further comprises a 6-membered aliphatic or aromatic ring structure.

11. The method according to claim 1, wherein the candidate compounds are selected from a virtual small molecule library.

12. The method according to claim 1, wherein the histone mark reader protein is CBX2 or BPTF.

13. The method according to claim 12, wherein the candidate compound identified in step (d) is a candidate for treatment of a cancer characterized by increased methylation activity of EZH2, or a cancer characterized by decreased methylation activity of MLL2.