Identification of antiviral phytochemicals as a potential SARS-CoV-2 main protease (M(pro)) inhibitor using docking and molecular dynamics simulations

Patel, Chirag N.; Jani, Siddhi P.; Jaiswal, Dharmesh G.; Kumar, Sivakumar Prasanth; Mangukia, Naman; Parmar, Robin M.; Rawal, Rakesh M.; Pandya, Himanshu A.

Novel SARS-CoV-2, an etiological factor of Coronavirus disease 2019 (COVID-19), poses a great challenge to the public health care system. Among other druggable targets of SARS-Cov-2, the main protease (M(pro)) is regarded as a prominent enzyme target for drug developments owing to its crucial role in virus replication and transcription. We pursued a computational investigation to identify M(pro) inhibitors from a compiled library of natural compounds with proven antiviral activities using a hierarchical workflow of molecular docking, ADMET assessment, dynamic simulations and binding free-energy calculations. Five natural compounds, Withanosides V and VI, Racemosides A and B, and Shatavarin IX, obtained better binding affinity and attained stable interactions with M(pro) key pocket residues. These intermolecular key interactions were also retained profoundly in the simulation trajectory of 100 ns time scale indicating tight receptor binding. Free energy calculations prioritized Withanosides V and VI as the top candidates that can act as effective SARS-CoV-2 M(pro) inhibitors.