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Molecular docking analysis of selected phytochemicals against SARS-CoV-2 Mpro receptor.

ABSTRACT: Presently world is on a war with the novel coronavirus and with no immediate treatments available the scourge caused by the SARS-CoV-2 is increasing day by day. A lot of researches are going on for the potential drug candidate that could help the healthcare system in this fight. Plants are a natural data bank of bioactive compounds. Many phytochemicals are being studied for various ailments including cancer, bacterial and viral infections, etc. The present study aims to screen 38 bioactive compounds from 5 selected plants viz., Azadirachta indica, Curcuma longa, Zingiber officinale, Ocimum basilicum and Panax ginseng against SARS-CoV-2. Lipinski's rule was taken as the foundation for initial screening. Shortlisted compounds were subjected to molecular docking study with Mpro receptor present in SARS-CoV-2. The study identified that gedunin, epoxyazadiradione, nimbin and ginsenosides have potential to inhibit Mpro activity and their binding energies are - 9.51 kcal/mol, - 8.47 kcal/mol, - 8.66 kcal/mol and - 9.63 kcal/mol respectively. Based on bioavailability radar studies gedunin and epoxyazadiradione are the two most potent compounds which are used for molecular dynamics simulation studies. Molecular dynamics studies showed that gedunin is more potent than epoxyazadiradione. To find the effectiveness and to propose the exact mechanism, in-vitro studies can be further performed on gedunin.

SUBMITTER: Garg S

PROVIDER: S-EPMC7567421 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Molecular docking analysis of selected phytochemicals against SARS-CoV-2 M<sup>pro</sup> receptor.

Garg Saksham S Anand Ashutosh A Lamba Yash Y Roy Arpita A

Vegetos (Bareilly, India) 20201016 4

Presently world is on a war with the novel coronavirus and with no immediate treatments available the scourge caused by the SARS-CoV-2 is increasing day by day. A lot of researches are going on for the potential drug candidate that could help the healthcare system in this fight. Plants are a natural data bank of bioactive compounds. Many phytochemicals are being studied for various ailments including cancer, bacterial and viral infections, etc. The present study aims to screen 38 bioactive compo ...[more]

PMID: 33100613

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Project description:The SARS-Cov-2 virus, which is evolving continuously and causing adverse effects throughout the world, needs an effective drug molecule for its treatment. There are several receptors of SARS Cov-2 which are targeted for its inhibition by many lead molecules both in-vitro and in-vivo. Papain like Protease (PLpro) is one of the two SARS-Cov-2 proteases that can be used as a drug target for SARS Cov-2. It is a coronavirus enzyme that plays a role in the cleavage and maturation of viral polyproteins, assembly of the replicase-transcriptase complex and disruption of host responses. PLpro has also been linked to the cleavage of proteinaceous post translational modifications on host proteins as a means of evading antiviral immune responses. Structure-based drug discovery can be one of the effective methods to screen for various molecules against the target receptors. In this study, PLpro of SARS CoV-2 was chosen as the target for docking. Forty phytochemicals from various plant sources and four synthetic drugs have been screened for their inhibitory potential against PLpro using AutoDock Vina. Phytochemicals such as Tinosponone, Rhoifolin, Rosmanol, Berberin, Nimbin and two other existing drugs Elbasvir and Declatasvir showed higher inhibitory potential in terms of higher binding affinities. ADME and toxicity analysis were also performed to predict the pharmacokinetics and drug likeliness properties. It was concluded from the study that Tinosponone possesss potential inhibitor property of papain-like proteases (PLpro) of SARS CoV-2. Tinosponone from the plant Tinospora cordifolia had a binding affinity of - 9.3 kcal/mol and obeyed the Lipinski rules, making it an effective lead molecule for treating SARS CoV-2. Molecular Dynamics simulation of Tinosponone with PLpro has proved the stability and validity of the binding with RMSD value in range of 0.2 nm when it was run for 50 ns using GROMACS. Therefore, Tinosponone could be considered as a potential inhibitor of PLpro of SARS CoV-2.

Dataset Information

Molecular docking analysis of selected phytochemicals against SARS-CoV-2 Mpro receptor.

Publications

Molecular docking analysis of selected phytochemicals against SARS-CoV-2 M<sup>pro</sup> receptor.

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