Molecular Dynamics and Free Energy Landscape Study of SARS‐CoV‐2 Omicron M^pro Boswellic acid Compounds of Boswellia Serrata Inhibitors

Abstract

This work sheds light on the effect of boswellic acid compounds (Alpha boswellic acid, Beta boswellic acid, 11-keto beta boswellic acid and 3-Acetyl-11-keto beta boswellic acid) upon inhibiting SARS-CoV-2 M pro and O-M pro (Main protease). A good docking score (À 8.4 kcal/mol) is found in the case of 3-Acetyl-11-keto beta boswellic acid as compared to the reference and three other boswellic acid compounds. ADMET results suggest that all these compounds are nontoxic and their pharmacokinetic properties are satisfactory. Moreover, a stability analysis with M pro /O-M pro through RMSD, RMSF, hydrogen bonds and Rg parameters in MD simulations is made and we found better values than the reference case. Pre and post-MD structures of Ligands-M pro show a similar binding site whereas a drift can be noted for L-O-M pro . 3-Acetyl-11-keto beta boswellic acid shows an average of five hydrogen bonds and it remains stable within the binding pocket of M pro during the simulation period in comparison to other boswellic acids compounds. Various metastable conformations are observed for all compounds in FEL (free energy landscape), however, Acyclovir-M pro , Alpha boswellic acid-M pro and Beta boswellic acid-O-M pro display only one global minimum. The results suggest that these compounds can be used as potential lead molecules for breakthroughs in drug discovery.

A Theoretical Study To Understand the Impact of Mpro of nCoV on the Hormones

“…RMSF is a numeric measurement that is similar to RMSD, however rather than showing how the positions of whole structures change over time, RMSF calculates how flexible each residue is, or how much it moves (varies) during a simulation. [44][45][46][47] Lesser the fluctuation, stable the complex. Also, the development of a ligand-protein complex relies heavily on non-covalent interactions like hydrogen bonding.…”