Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations.

ABSTRACT: The lack of conformational sampling in virtual screening projects can lead to inefficient results because many of the potential drugs may not be able to bind to the target protein during the static docking simulations. Here, we performed ensemble docking for around 2000 United States Food and Drug Administration (FDA)-approved drugs with the RNA-dependent RNA polymerase (RdRp) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a target. The representative protein structures were generated by clustering classical molecular dynamics trajectories, which were evolved using three solvent scenarios, namely, pure water, benzene/water and phenol/water mixtures. The introduction of dynamic effects in the theoretical model showed improvement in docking results in terms of the

SUBMITTER: Szabo PB 

PROVIDER: S-EPMC8659376 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature