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Patel, Chirag N.; Jani, Siddhi P.; Jaiswal, Dharmesh G.; Kumar, Sivakumar Prasanth; Mangukia, Naman; Parmar, Robin M.; Rawal, Rakesh M.; Pandya, Himanshu A.
Scientific reports, 10/2021, Volume: 11, Issue: 1Journal Article
Abstract 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.
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