Docking and Molecular Dynamics Simulations of Flavonoids as Inhibitors of Infectious Agents: Rutin as a Coronavirus Protease Inhibitor
Navvabeh Salarizadeh, Mohammad Reza Aallaei, Ali Zarei, Rahime Eshaghi Malekshah, Elaheh Molaakbari, Amirreza Farajnezhadi · ChemistrySelect · 2022
Abstract 3CL protease as the main protease (M pro ) of coronavirus is investigated as a potential target in medicine. Flavonoid compounds with polyphenolic structures exhibited anti‐viral, anti‐bacterial, immunomodulatory and anti‐inflammatory effects against infectious agents. In this study, the inhibitory effect of flavonoid‐based compounds was evaluated against coronavirus M pro using molecular docking and dynamic simulations. Molegro Virtual Docker 6.0 (MVD) software was used to ensure the accuracy of the docking analysis. Eventually, four compounds including two herbal‐based (Rutin and Quercetin) and two chemical‐based (2‐Iodoadenosine‐5’‐O‐[(phosphonomethyl)phosphonic Acid] and Camostat) are selected based on the interaction energies and docking scores of the investigated structures. The values of MolDock Score for Rutin was −174.355 docked to M pro enzyme. The molecular dynamics was performed by using GROMACS in 100 ns to refine the docking simulation results and evaluated the binding stability of Rutin. Potential energy of Rutin/M pro complex stabilization was measured approximately −1.11×10 6 kcal/mol for 100 ns. As a result, Rutin is suggested as a potent inhibitor for M pro and can be used as an effective drug in the treatment and prevention of covid.