In Silico Study of Selected Natural Products as SARS-CoV-2 M^Pro Binder: Molecular Docking and Molecular Dynamics Simulation

Abstract

The SARS-CoV-2 virus is the causative agent of COVID-19 still pose significant threat to humanity. Discovery of an effective medication regime against this infection still under development. In the present study the potentiality of selected naturally occurring compounds as a SARS-CoV-2 M^Pro binder were investigated employing molecular docking and dynamics simulation. The Quantum chemical calculations were used to optimize the 3 D geometry of hits. Known inhibitor profiles were used for comparison purposes. The values of Binding Energy showed that the majority of natural ligands have better affinity to M^Pro, compared to drugs used to cure SARS-CoV-2. The biological and pharmacological properties of these ligands were on the same side as the docking and molecular dynamic results.

Keywords:

• SARS-CoV-2 M^Pro
• inhibition
• molecular docking
• molecular dynamic simulations