5O3E

Human Brd2(BD2) mutant in complex with Me-Am1

Summary for 5O3E

• Entry DOI: 10.2210/pdb5o3e/pdb
• Descriptor: Bromodomain-containing protein 2, (2~{R})-2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-~{N}-ethyl-propanamide, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: the bromodomain and extra-terminal domain (bet) family chromatin binding protein, transcription
• Biological source: Homo sapiens (Human)
• Cellular location: Nucleus : P25440
• Total number of polymer chains: 1
• Total formula weight: 13968.93

Authors

Chan, K.-H.,Runcie, A.C.,Ciulli, A. (deposition date: 2017-05-23, release date: 2018-02-14, Last modification date: 2024-01-17)

Primary citation

Runcie, A.C.,Zengerle, M.,Chan, K.H.,Testa, A.,van Beurden, L.,Baud, M.G.J.,Epemolu, O.,Ellis, L.C.J.,Read, K.D.,Coulthard, V.,Brien, A.,Ciulli, A.
Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition.
Chem Sci, 9:2452-2468, 2018

PubMed 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 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 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 target validation studies.

PubMed: 29732121
DOI: 10.1039/c7sc02536j

Experimental method

X-RAY DIFFRACTION (1.4 Å)