Computational assessment of select antiviral phytochemicals as potential SARS-Cov-2 main protease inhibitors: molecular dynamics guided ensemble docking and extended molecular dynamics.

ABSTRACT: Covid-19 caused by novel coronavirus, 2019-nCoV or SARS-CoV-2 has become most severe pandemic of this century. No specific therapies are available to treat Covid-19 so far. Recently, main protease (M^pro), a potential drug target from SARS-CoV-2 has been successfully crystallised. The present study is aimed at assessment of bioactive antiviral phytochemicals as potential SARS-COV-2 M^pro inhibitors, using ensemble docking, molecular dynamics and MM-PBSA calculations. Ensemble docking studies were performed with Autodock vina program. The top 5 compounds having highest binding free energy were subjected to 100 ns molecular dynamics simulations with Gromacs. The resulting trajectories of converged period of MD were further exploited in MM-PBSA calculations to derive accur

SUBMITTER: Sawant S 

PROVIDER: S-EPMC8288410 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature