The Inhibitory Effect of Some Natural Bioactive D-Glucopyranoside Derivatives against SARS-CoV-2 Main Protease (Mpro) and Spike Protease (Spro)

Abstract

Outbreak of coronavirus seems to have exacerbated across the globe, but drugs have not been discovered till now. Due to having the antiviral activity of D-glucopyranoside derivatives, this study was designed to examine as the inhibitor by in sillico study against the main protease (Mpro) and Spike protease (Spro) of SARS-CoV-2. First, these derivatives were optimised by Density Functional Theory (DFT). The observation of this study was monitored by molecular docking tools calculating the binding affinities. Afterwards, the ligand interaction with protein was accounted for selecting the how to bind of active sites of the protein. Next, the root means square deviation (RMSD) and root mean square fluctuation (RMSF) were illustrated for determining the stability of the docked complex. Finally, AMDET properties were calculated as well as the Lipisinki rule. All of the derivates showed a binding affinity more than -6.0 kcal/mol while derivatives 2, 3, and 9 were the best-bonded scoring inhibitor against Mpro and Spro. In addition, the chemical descriptors were more supportive tools as an inhibitor, and the Lipisinki rule was satisfied for maximum molecules as a drug. Besides, D-glucopyranoside derivatives may be predicted that they are non-carcinogenic and low toxic for both aquatic and non-aquatic species.

Keywords

• glucopyranoside
• sars-cov-2
• docking
• molecular dynamic
• admet