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Assessing Potential Inhibitors for SARS-CoV-2 Main Protease from Available Drugs using Free Energy Perturbation Simulations

preprint
submitted on 06.08.2020 and posted on 07.08.2020 by Son Tung Ngo, Hung Minh Nguyen, Le Thi Thuy Huong, Pham Minh Quan, Vi Khanh Truong, Nguyen Thanh Tung, Van Vu
A virtual screening approach using docking and free energy pertubation was successfully validated with previously characterized inhibitors of SARS-CoV-2 main protease (Mpro). This approach and then used to estimate the binding affinity to Mpro of more than 6300 compounds in the ZINC15 database. Delamanid, an anti-tuberculosis agent, has a predicted nanomolar binding affinity for SARS-CoV-2 Mpro and is thus a promissing drug candiate for COVID-19. In addition, several compounds including three antibiotics exhibits femtomolar affinity for SARS-CoV-2 Mpro. The residues around positions 24, 45, 143, 165, and 190 were found to be involved in the binding of the strongest inhibitors.

History

Email Address of Submitting Author

vanvu@ntt.edu.vn

Institution

Nguyen Tat Thanh University

Country

Vietnam

ORCID For Submitting Author

0000-0003-0009-6703

Declaration of Conflict of Interest

The authors declare no conflict of interest

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