In silico Molecular Docking Analysis Targeting SARS-CoV-2 Spike Protein and Selected Herbal Constituents

Abstract

In modern drug discovery, molecular docking analysis is routinely used to understand and predict the interaction between a drug molecule and a target protein from a microbe. Drugs identified in this way may inhibit the entry and replication of pathogens in host cells. The SARS-CoV-2 associated coronavirus disease, COVID-19, has become the most contagious and deadly pandemic disease in the world today. In abeyance of any specific vaccine or therapeutic against SARS-CoV-2, the burgeoning situation urges a need for effective drugs to treat the virus-infected patients. Herbal medicines have been used as natural remedies for treating various infectious diseases since ancient times. The spike (S) protein of SARS-CoV-2 is important for the attachment and pathogenesis of the virus. Therefore, this study focused on the search of useful ligands for S protein among active constituents present in common herbs that could serve as efficient remedies for COVID-19. We analysed the binding efficiency of twelve compounds present in common herbs with the S protein of SARS-CoV-2 through molecular docking analysis and also results are validated with two different docking tools. The binding efficiency of ligands was scored based on their predicted pharmacological interactions coupled with binding energy estimates. In docking analysis, compound “I” (Epigallocatechin gallate (EGCG)) was found to have the highest binding affinity with the viral S protein, followed by compounds, “F” (Curcumin),“D” (Apigenin) and “E” (Chrysophanol). The present study corroborates that compound “I” (EGCG) mostly present in the integrants of green tea, shows the highest potentiality for acting as an inhibitor of SARS-CoV-2. Further, characterization of the amino acid residues comprising the viral binding site and the nature of the hydrogen bonding involved in the ligand-receptor interaction revealed significant findings with herbal compound “I” (EGCG) binding to the S protein at eight amino acid residues. The binding sites are situated near to the amino acids which are required for virus pathogenicity. The findings of the present study need in vivo experiments to prove the utility of “I”, “F”,“D” and “E” compounds and their further use in making herb-based anti-SARS-CoV-2 product in near future. This analysis may help to create a new ethno-drug formulation for preventing or curing the COVID-19.

Union is strength: antiviral and anti-inflammatory drugs for COVID-19

“…It has been described that a high intake of turmeric ( Curcuma ) in the diet has beneficial effects against inflammation, apoptosis, and RNA replication. Suppression of pulmonary edema and fibrosis-associated pathways in COVID-19 infection has also been reported [82] . Curcumin derivatives inhibit human A influenza virus in vitro , and docking studies propose curcumin as a potential inhibitor of spike protein binding to ACE-2 [80] , as well as of M pro [81] .…”

Identification of Small Molecule Inhibitors of the Deubiquitinating Activity of the SARS-CoV-2 Papain-Like Protease: in silico Molecular Docking Studies and in vitro Enzymatic Activity Assay

“…The structures of the hits identified from these computational studies could be optimized as part of the drug discovery process (Ojha et al, 2020 ). In addition to synthetic pharmacological compounds, herbal constituents can be screened in the same manner and this method has been described in many papers (Bhowmik et al, 2020 ; Chikhale et al, 2020 ; Ghosh et al, 2020 ; Gupta et al, 2020 ; Jena et al, 2020 ; Krupanidhi et al, 2020 ; Muhseen et al, 2020 ; Sinha et al, 2020 ; Subbaiyan et al, 2020 ). A number of studies that can be found on the World Health Organization's International Clinical Trials Registry Platform also involve plant-based compounds, particularly flavonoids.…”

Breeding Buckwheat for Increased Levels of Rutin, Quercetin and Other Bioactive Compounds with Potential Antiviral Effects

“…It is believed to be a precursor of hypericin [70], and possibly also the precursor of fagopyrin. Emodin isolated from Tartary buckwheat grain [71] has been shown to bind well to all three active sites of the RNA binding domain of the nucleocapsid phosphoprotein of Sars-CoV-2 [70,72,73]. However, the biosynthesis pathways of emodin in Tartary buckwheat remain unclear to date [74].…”