Highlights 19 compounds from Neem extract tested against 7 standard anti-COVID drugs for action on PLpro of latter All 19 NEEM molecules show better docking, ADME results vis-a-vis standard drugs Among the 19, desacetylgedunin (DCG) gives highest docking score with PLpro MD simulation of shows binding with DCG induces large structural change on PLpro

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Herein we have made a comprehensive analysis of inhibitory efficacy of 16 RNA virus drugs against RdRp, Mpro and PLpro proteins of SARS-CoV-2. Analysis of docked conformation revealed that Baloxavir marboxil (BMX) corresponds to the highest binding energy. Analysis of residue confirmed that BMX strongly interact with these three proteins involving H-bonding, ionic as well as hydrophobic interactions. Molecular dynamics simulation and analysis of parameters like RMSD, RMSF, binding energy confirmed noticeable conformational alternation with these proteins with makeable effect on RdRp. The potentially inhibitory action of BMX against these three proteins suggests the inhibition of overall transcription process of SARS-CoV-2. These observation along with the recently observed inhibitory action of BMX on influenza with clinically proven no side effects emphasizes to uncover the role of BMX by in-vitro and in-vivo analysis.

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