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Identification of Potential Binders of the SARS-Cov-2 Spike Protein via Molecular Docking, Dynamics Simulation and Binding Free Energy Calculation

preprint
submitted on 10.05.2020 and posted on 12.05.2020 by Dr. Chirag N. Patel, Dr. Prasanth Kumar S., Dr. Himanshu A. Pandya, Dr. Rakesh M. Rawal

The pandemic outbreak of COVID-19 virus (SARS-CoV-2) has become critical global health issue. The biophysical and structural evidence shows that SARS-CoV-2 spike protein possesses higher binding affinity towards angiotensin-converting enzyme 2 (ACE2) and hemagglutinin-acetylesterase (HE) glycoprotein receptor. Hence, it was selected as a target to generate the potential candidates for the inhibition of HE glycoprotein. The present study focuses on extensive computational approaches which contains molecular docking, ADMET prediction followed by molecular dynamics simulations and free energy calculations. Furthermore, virtual screening of NPACT compounds identified 3,4,5-Trihydroxy-1,8-bis[(2R,3R)-3,5,7-trihydroxy-3,4-dihydro-2H-chromen-2-yl]benzo[7]annulen-6-one, Silymarin, Withanolide D, Spirosolane and Oridonin were interact with high affinity. The ADMET prediction revealed pharmacokinetics and drug-likeness properties of top-ranked compounds. Molecular dynamics simulations and binding free energy calculations affirmed that these five NPACT compounds were robust HE inhibitor.

Funding

Department of Science and Technology [Grant number GSBTM/MD/JDR/1409/2017-18], India.

Gujarat Council on Science and Technology [GUJCOST/Supercomputer/2019-20/1359], India.

History

Email Address of Submitting Author

rakeshmrawal@gmail.com

Institution

Gujarat University

Country

India

ORCID For Submitting Author

0000-0002-7985-1187

Declaration of Conflict of Interest

The authors declare that there are no conflicts of interest.

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