The Interactions between Polyphenols and COVID-19 Proteins

Although scientists around the world put lots of efforts into the development of new treatments for COVID-19 since the outbreak, no drugs except Veklury (Remdesivir) have been approved by FDA. There is an urgent need to discover some alternative antiviral treatment for COVID-19. Because polyphenols have been shown to possess antiviral activities, in this project, we plan to conduct a large-scale virtual screening for more than 500 polyphenols against several target proteins of SARS-CoV-2, such as main protease (Mpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp) and spike protein. After the binding affinities and binding poses are predicted by molecular docking, we propose to perform molecular dynamics (MD) simulations with GROMACS and CHARMM36 force field on Bridges-2 PSC. It will assist us in further analyzing the stability of complexes of polyphenols and target proteins. Analyzing the docking results will shed light on the potential efficacy of the top-ranked drug candidates and pinpoints the key residues on the target proteins for the drug development.