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

• Published in: Antibiotics (Basel) Vol. 10; no. 8; p. 1011
• Main Authors: Rehman, Muhammad Fayyaz ur, Akhter, Shahzaib, Batool, Aima Iram, Selamoglu, Zeliha, Sevindik, Mustafa, Eman, Rida, Mustaqeem, Muhammad, Akram, Muhammad Safwan, Kanwal, Fariha, Lu, Changrui, Aslam, Mehwish
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 20.08.2021; MDPI
• Subjects: Amino acids; Antioxidants; antioxidants for COVID-19; Antiviral agents; Baicalin; Binding sites; Coronaviruses; COVID-19 vaccines; DNA helicase; DNA-directed RNA polymerase; Drug development; Enzymes; FDA approval; Flavonoids; Genetic algorithms; Glycoproteins; Glycyrrhizin; Hesperidin; Immunization; Infections; Ligands; Metabolites; Molecular docking; natural antivirals; Pandemics; Papain; Phytochemicals; Plants; Protease; Protein interaction; Proteinase; Proteins; Ribonucleic acid; RNA; RNA polymerase; RNA-directed RNA polymerase; SARS CoV-2; Secondary metabolites; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Spike glycoprotein; Steroid hormones; Viral infections
• ISSN: 2079-6382; 2079-6382
• DOI: 10.3390/antibiotics10081011

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.