Computational molecular interaction between SARS-CoV-2 main protease and theaflavin digallate using free energy perturbation and molecular dynamics.

ABSTRACT: Our objective was to identify the molecule which can inhibit SARS-CoV-2 main protease and can be easily procured. Natural products may provide such molecules and can supplement the current custom chemical synthesis-based drug discovery for this objective. A combination of docking approaches, scoring functions, classical molecular dynamic simulation, binding pose metadynamics, and free energy perturbation calculations have been employed in this study. Theaflavin digallate has been observed in top-scoring compounds after the three independent virtual screening simulations of 598435 compounds (unique 27256 chemical entities). The main protease-theaflavin digallate complex interacts with critical active site residues of the main protease in molecular dynamics simulation independent of the expl

SUBMITTER: Manish M 

PROVIDER: S-EPMC9507791 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature