Molecular docking and simulation investigation: effect of beta-sesquiphellandrene with ionic integration on SARS-CoV2 and SFTS viruses

Amit Joshi,G Sunil Krishnan,Vikas Kaushik

doi:10.1186/s43141-020-00095-x

Amit Joshi, G Sunil Krishnan + Show 1 more

Open Access

https://doi.org/10.1186/s43141-020-00095-x

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Abstract

BackgroundAt present, viral diseases become major concern for the world. SARS-CoV2 and SFTS viruses are deadly in nature, and there is a need for developing best treatments for them. Modern in silico approaches were found to be very handy in determining putative drug molecules. In this study, we analyze interaction of beta-sesquiphellandrene (compound belongs to ginger) with spike protein (Sp) and membrane glycoprotein polyprotein (MPp). ResultsOur molecular docking and simulation study reveals the perfect binding pocket of Sp and MPp holding beta-sesquiphellandrene (bS). Binding energies for MPp-bS and Sp-bS were found to be − 9.5 kcal/mol and − 10.3 kcal/mol respectively. RMSD and RMSF values for docked complexes were found to be in selectable range, i.e., 1 to 3 Å and 1 to 8 Å respectively. Modern computational tools were used here to make this investigation fast and effective. Further, ADME analysis reveals the therapeutic validations for beta-sesquiphellandrene to act as a useful pharmacoactive compound. Beta-sesquiphellandrene provides not only inhibitory effect on spike protein of SARS-CoV2 but also similar inhibitory effects on membrane glycoprotein polyprotein complex of SFTS virus, which hampers the pathological initiation of the diseases caused by both the viruses, i.e., COVID-19 and severe fever with thrombocytopenia syndrome. ConclusionThis method of computational analysis was found to be rapid and effective, and opens new doors in the domain of in silico drug discovery. Beta-sesquiphellandrene can be used as effective medicine to control these harmful pathogens after wet lab validations.

Highlights

IntroductionViral diseases become major concern for the world. SARS-CoV2 and SFTS viruses are deadly in nature, and there is a need for developing best treatments for them
At present, viral diseases become major concern for the world
Beta-sesquiphellandrene: ADME analysis Beta-sesquiphellandrene ((3R)-3-[(2S)-6-methylhept-5en-2-yl]-6-methylidenecyclohexene) was found to have a molecular weight of 204.35 g/mol; it does not have hydrogen bond donors and acceptors; it consists of 4 rotatable bonds, topological surface area 0Å2, and single Lipinski violation

Summary

Introduction

Viral diseases become major concern for the world. SARS-CoV2 and SFTS viruses are deadly in nature, and there is a need for developing best treatments for them. Traditional therapy for controlling cough-cold problems with fast recovery includes mixture of ginger and jaggery. Latest studies supported such treatment strategies or home remedies for antiviral effects; it was observed that the Chinese used same contemporary medications, like Ge Gen Tang (consist of ginger and a sweet kudzu roots) [1, 2]. Latest reports have explored the current proof on a few properties of ginger in wellbeing and physical movement, including its anti-malignancy properties [4]. Ginger (Zingiber officinale) contains a very crucial anti-viral compound beta-sesquiphellandrene [6]. Prior work by Denyer and collaborators extracted compound called beta-sesquiphellandrene from ginger which holds antiviral capacity and defeats the infection caused by common cold virus [3]. Jaggery a nutritive product obtained from sugarcane holds nutritive elements sugar, calcium, iron, phosphorus, and magnesium [7]

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