Effectiveness of Natural Antioxidants against SARS-CoV-2? Insights from the In-Silico World

Muhammad Fayyaz Ur Rehman,Shahzaib Akhter,Changrui Lu,Muhammad Mustaqeem,Mustafa Sevindik,Zeliha Selamoglu,Mehwish Aslam,Muhammad Safwan Akram,Rida Eman,Aima Iram Batool,Fariha Kanwal

doi:10.3390/antibiotics10081011

Abstract

The SARS CoV-2 pandemic has affected millions of people around the globe. Despite many efforts to find some effective medicines against SARS CoV-2, no established therapeutics are available yet. The use of phytochemicals as antiviral agents provides hope against the proliferation of SARS-CoV-2. Several natural compounds were analyzed by virtual screening against six SARS CoV-2 protein targets using molecular docking simulations in the present study. More than a hundred plant-derived secondary metabolites have been docked, including alkaloids, flavonoids, coumarins, and steroids. SARS CoV-2 protein targets include Main protease (MPro), Papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), Spike glycoprotein (S), Helicase (Nsp13), and E-Channel protein. Phytochemicals were evaluated by molecular docking, and MD simulations were performed using the YASARA structure using a modified genetic algorithm and AMBER03 force field. Binding energies and dissociation constants allowed the identification of potentially active compounds. Ligand-protein interactions provide an insight into the mechanism and potential of identified compounds. Glycyrrhizin and its metabolite 18-β-glycyrrhetinic acid have shown a strong binding affinity for MPro, helicase, RdRp, spike, and E-channel proteins, while a flavonoid Baicalin also strongly binds against PLpro and RdRp. The use of identified phytochemicals may help to speed up the drug development and provide natural protection against SARS-CoV-2.

Highlights

IntroductionWuhan province of Central China in December 2019 [1] and its disease, COVID-19, was declared as a pandemic on 11 March 2020, after the infection spread globally [2]
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) originated in theWuhan province of Central China in December 2019 [1] and its disease, COVID-19, was declared as a pandemic on 11 March 2020, after the infection spread globally [2]
Our study has examined and screened more than a hundred natural compounds from plants against six SARS CoV-2 proteins by using molecular docking and molecular dynamics simulations to identify potential bioactive compounds

Summary

Introduction

Wuhan province of Central China in December 2019 [1] and its disease, COVID-19, was declared as a pandemic on 11 March 2020, after the infection spread globally [2]. This disease has affected more than 204 million people and claimed more than 4.31 million lives around the globe [3]. The rise of the SARS-CoV-2 delta variant requires better disease management as vaccinated people, including adults and children, seem to be susceptible to infection. Many of these phytochemicals provide antiviral activity and act as antioxidants to tame interleukin storm and ROS damage during COVID-19

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Results

Discussion

Conclusion