Issue 9, 2018

Optimization of a “bump-and-hole” approach to allele-selective BET bromodomain inhibition

Abstract

Allele-specific chemical genetics enables selective inhibition within families of highly-conserved proteins. The four BET (bromodomain & extra-terminal domain) proteins – BRD2, BRD3, BRD4 and BRDT bind acetylated chromatin via their bromodomains and regulate processes such as cell proliferation and inflammation. BET bromodomains are of particular interest, as they are attractive therapeutic targets but existing inhibitors are pan-selective. We previously established a bump-&-hole system for the BET bromodomains, pairing a leucine/alanine mutation with an ethyl-derived analogue of an established benzodiazepine scaffold. Here we optimize upon this system with the introduction of a more conservative and less disruptive leucine/valine mutation. Extensive structure–activity-relationships of diverse benzodiazepine analogues guided the development of potent, mutant-selective inhibitors with desirable physiochemical properties. The active enantiomer of our best compound – 9-ME-1 – shows ∼200 nM potency, >100-fold selectivity for the L/V mutant over wild-type and excellent DMPK properties. Through a variety of in vitro and cellular assays we validate the capabilities of our optimized system, and then utilize it to compare the relative importance of the first and second bromodomains to chromatin binding. These experiments confirm the primacy of the first bromodomain in all BET proteins, but also significant variation in the importance of the second bromodomain. We also show that, despite having a minor role in chromatin recognition, BRD4 BD2 is still essential for gene expression, likely through the recruitment of non-histone proteins. The disclosed inhibitor:mutant pair provides a powerful tool for future cellular and in vivo target validation studies.

Graphical abstract: Optimization of a “bump-and-hole” approach to allele-selective BET bromodomain inhibition

Supplementary files

Article information

Article type
Edge Article
Submitted
07 Jun 2017
Accepted
23 Jan 2018
First published
24 Jan 2018
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY license

Chem. Sci., 2018,9, 2452-2468

Optimization of a “bump-and-hole” approach to allele-selective BET bromodomain inhibition

A. C. Runcie, M. Zengerle, K.-H. Chan, A. Testa, L. van Beurden, M. G. J. Baud, O. Epemolu, L. C. J. Ellis, K. D. Read, V. Coulthard, A. Brien and A. Ciulli, Chem. Sci., 2018, 9, 2452 DOI: 10.1039/C7SC02536J

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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