Virtual screening of phytochemical compounds as potential inhibitors against SARS-CoV-2 infection

Ram Kothandan,Cashlin Anna Suveetha Gnana Rajan,Rejoe Raymond Michael Raj,Sowfia Syed,Janamitra Arjun

doi:10.1186/s43088-021-00095-x

Ram Kothandan, Cashlin Anna Suveetha Gnana Rajan + Show 3 more

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https://doi.org/10.1186/s43088-021-00095-x

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Abstract

BackgroundThe present pandemic situation due to coronavirus has led to the search for newer prevention, diagnostic, and treatment methods. The onset of the corona infection in a human results in acute respiratory illness followed by death if not diagnosed and treated with suitable antiretroviral drugs. With the unavailability of the targeted drug treatment, several repurposed drugs are being used for treatment. However, the side-effects of the drugs urges us to move to a search for newer synthetic- or phytochemical-based drugs. The present study investigates the use of various phytochemicals virtually screened from various plant sources in Western Ghats, India, and subsequently molecular docking studies were performed to identify the efficacy of the drug in retroviral infection particularly coronavirus infection.ResultsOut of 57 phytochemicals screened initially based on the structural and physicochemical properties, 39 were effectively used for the docking analysis. Finally, 5 lead compounds with highest hydrophobic interaction and number of H-bonds were screened. Results from the interaction analysis suggest Piperolactam A to be pocketed well with good hydrophobic interaction with the residues in the binding region R1. ADME and toxicity profiling also reveals Piperolactam A with higher LogS values indicating higher permeation and hydrophilicity. Toxicity profiling suggests that the 5 screened compounds to be relatively safe.ConclusionThe in silico methods used in this study suggests that the compound Piperolactam A to be the most effective inhibitor of S-protein from binding to the GRP78 receptor. By blocking the binding of the S-protein to the CS-GRP78 cell surface receptor, they can inhibit the binding of the virus to the host.

Highlights

Introduction to methodology and encoding rulesJ Chem Inform Comput Sci. 28(1):31–3637
1 Background COVID-19, an infectious disease caused by Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) has become an unexpected threat to the human population
3 Results In the present study, 57 phytochemicals were initially screened based on their structural and physicochemical properties, later only 39 compounds were utilized for the docking analysis based on the various filters utilized during the course of the study

Summary

Introduction

Introduction to methodology and encoding rulesJ Chem Inform Comput Sci. 28(1):31–3637. Lipinski CA (2004) Lead-and drug-like compounds: the rule-of-five revolution. The onset of the corona infection in a human results in acute respiratory illness followed by death if not diagnosed and treated with suitable antiretroviral drugs. The present study investigates the use of various phytochemicals virtually screened from various plant sources in Western Ghats, India, and subsequently molecular docking studies were performed to identify the efficacy of the drug in retroviral infection coronavirus infection. COVID-19, an infectious disease caused by Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) has become an unexpected threat to the human population. The virion structure contains four parts of protein which are Spike proteins (S-proteins), membrane proteins (M-proteins), envelope proteins (E-proteins), and nucleocapsid proteins (N-proteins) Of these S-proteins play a major role in transfer of virion particles from the virus to the host cells using ACE2 receptor [4].

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