The binding mechanism of NHWD-870 to bromodomain-containing protein 4 based on molecular dynamics simulations and free energy calculation

Abstract

Bromodomain and extra-terminal (BET) proteins (BRD2, BRD3, BRD4, and BRDT) are epigenetic readers with tandem bromodomains. Small-molecule inhibitors of BET proteins are a promising treatment strategy against cancer. For example, NHWD-870 can inhibit BRD4 (BD1 + BD2). Presently, structural data on NHWD-870 bound BRD4 remain lacking. Herein, we investigate the interactions between NHWD-870 and BRD4 (BD1 and BD2) via molecular docking, molecular dynamics simulation, and binding free energy calculations. NHWD-870 showed a similar binding affinity for BD1 and BD2 of BRD4. Binding free energy calculations for the R/S conformations of NHWD-870 suggest that the chiral centre of NHWD-870 may confer similar roles upon the R and S conformations for binding with BRD4, facilitating the identification of novel BRD4 inhibitors.