Issue 2, 2021

Binding selectivity of inhibitors toward the first over the second bromodomain of BRD4: theoretical insights from free energy calculations and multiple short molecular dynamics simulations

Abstract

Bromodomain-containing protein 4 (BRD4) plays an important role in mediating gene transcription involved in cancers and non-cancer diseases such as acute heart failure and inflammatory diseases. In this work, multiple short molecular dynamics (MSMD) simulations are integrated with a molecular mechanics generalized Born surface area (MM-GBSA) approach to decipher binding selectivity of three inhibitors 8NS, 82Y, and 837 toward two domains BD1 and BD2 of BRD4. The results demonstrate that the enthalpy effects play critical roles in selectivity identification of inhibitors toward BD1 and BD2, determining that 8NS has better selectivity toward BD2 than BD1, while 82Y and 837 more favorably bind to BD1 than BD2. A residue-based free-energy decomposition method was used to calculate an inhibitor–residue interaction spectrum and unveil contributions of separate residues to binding selectivity. The results identify six common residues, containing (P82, P375), (V87, V380), (L92, L385), (L94, L387), (N140, N433), and (I146, V439) individually belonging to (BD1, BD2) of BRD4, and yield a considerable binding difference of inhibitors to BD1 and BD2, suggesting that these residues play key roles in binding selectivity of inhibitors toward BD1 and BD2 of BRD4. Therefore, these results provide useful dynamics information and a structure affinity relationship for the development of highly selective inhibitors targeting BD1 and BD2 of BRD4.

Graphical abstract: Binding selectivity of inhibitors toward the first over the second bromodomain of BRD4: theoretical insights from free energy calculations and multiple short molecular dynamics simulations

Supplementary files

Article information

Article type
Paper
Submitted
07 Nov 2020
Accepted
17 Des 2020
First published
24 Des 2020
This article is Open Access
Creative Commons BY-NC license

RSC Adv., 2021,11, 745-759

Binding selectivity of inhibitors toward the first over the second bromodomain of BRD4: theoretical insights from free energy calculations and multiple short molecular dynamics simulations

Y. Wang, S. Wu, L. Wang, Z. Yang, J. Zhao and L. Zhang, RSC Adv., 2021, 11, 745 DOI: 10.1039/D0RA09469B

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