Structure-based design and molecular simulations identified some quercetin-based drugs as repurposable inhibitors of SARS-CoV-2 main protease: Running title: Natural product drugs as repurposable inhibitors of SARS-CoV-2

Abstract

In this study, virtual screening and molecular dynamics (MD) protocols were applied to screen 2826 FDA-approved natural product drugs from the Selleckchem.com library for prospective inhibitors of the SARS-CoV-2 main protease. From the virtual screening through HTVS, SP and XP docking analysis, hyperoside, rutin hydrate, rutoside and quercitrin displayed a stronger binding affinity with respective XP docking scores of –11.389, –11.340, –11.087 and –10.232 kcal/mol than co-crystallized N-[2-(5-fluoro- 1H-indol-3-yl)ethyl]acetamide (HWH) and positive inhibitors, lopinavir and ritonavir which scored –5.493, –6.463 and –6.221 kcal/mol respectively. Selectively, the binding free energy, MMGB(SA) of hyperoside and rutin hydrate was observed as –21.55 and –25.82 kcal/mol respectively compared to lopinavir and ritonavir with –17.66 and –5.28 kcal/mol respectively. Consistently, the selected drugs displayed good thermodynamics conformational stability, thus, recommended as promising repurposable inhibitors of the SARS-CoV-2 main protease amenable for further studies.