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Original Article

J App Pharm Sci. 2022; 12(5): 104-119

In silico prediction of interactions and Molecular Dynamics Simulation Analysis of Main Protease of SARS – CoV2 with the FDA approved Non-Protein Antiviral Drugs

Subramaniam Sivakumar, Sugumar Mohanasundaram, Narasimhan Rangarajan, Venkatesan Sampath, Maderi Velayutham Dass Prakash.

Cited by 13 Articles

In the current scenario of the SARS-CoV-2 pandemic, the repurposing of the FDA approved antiviral drugs for the possibility to treat SARS-CoV-2 is an unavoidable scientific method. It further exemplifies the physical interactions between the target protein and the chosen drugs. In this study, the main protease (Mpro) structure of SARS-CoV-2 (PDB ID: 7BUY) with 42 FDA approved antiviral drugs were analysed by Molecular Docking using PyRx-Vina, and the amino acids involved in docking are analysed using Discovery Studio visualiser. The protein-drug complex stability was analysed by Molecular Dynamics Simulation using GROMACS. In results, Ledipasvir showed the maximum binding affinity (-10.4 kcal/mol) with Mpro of SARS-CoV-2 followed by Paritaprevir (-9.1 kcal/mol) and Velpatasvir (-8.8 kcal/mol). These three compounds are found to have a significant number of interactions. Moreover, Ledipasvir and Velpatasvir showed similar interactions at GLU240, PRO241, ILE249, PRO293 and VAL202. Molecular dynamics simulations showed that the top ligands had formed stable complexes with Mpro. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculation revealed thermodynamically stable binding energies of -195.370±1.119 kJ/mol and -180.778±0.868 kJ/mol for Ledipasvir and Velpatasvir, respectively. Paritaprevir showed stable binding energy of -75.679±0.922 kJ/mol with Mpro of SARS-CoV-2.

Key words: SARS-CoV-2; Main Protease; In silico; Docking; Repurposing; Molecular dynamic simulation

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