DRAFT: Targeting SARS-CoV-2 M3CLpro by HCV NS3a/4 Inhibitors: In Silico Modeling and In Vitro Screening. Anjela Manandhar1, Benjamin E Blass2, Dennis J Colussi2, Imane Almi2,3, Magid Abou-Gharbia2, Michael L. Klein1, Khaled M. Elokely1* 1Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States 2 Department of Pharmaceutical Sciences, Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania 19140, United States 3 Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, University of Biskra, BP 145 Biskra, 07000, Algeria Corresponding author: Khaled M. Elokely - Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States Email:
[email protected] ABSTRACT Currently the entire human population is in the midst of a global pandemic caused by SARS-CoV- 2 (Severe Acute Respiratory Syndrome–CoronaVirus-2). This highly pathogenic virus has to date caused >71 million infections and >1.6 million deaths in >180 countries. Several vaccines and drugs are being studied as possible treatment or prophylactics of this viral infection. M3CLpro (coronavirus main cysteine protease) is a promising drug target as it has a significant role in viral replication. Here we use the X-ray crystal structure of M3CLpro in complex with Boceprevir to study the dynamic changes of the protease upon ligand binding. The binding free energy was calculated for water molecules at different locations of the binding site, and molecular dynamics (MD) simulations were carried out for the M3CLpro/Boceprevir complex, to thoroughly understand the chemical environment of the binding site.