In-silico screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 MPro

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F20%3APU137836" target="_blank" >RIV/00216305:26220/20:PU137836 - isvavai.cz</a>

Result on the web

<a href="https://www.tandfonline.com/doi/full/10.1080/07391102.2020.1845980" target="_blank" >https://www.tandfonline.com/doi/full/10.1080/07391102.2020.1845980</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1080/07391102.2020.1845980" target="_blank" >10.1080/07391102.2020.1845980</a>

Result language

angličtina

Original language name

In-silico screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 MPro

Original language description

SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 MPro. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodock Vina. Phytochemicals with binding energy ≥ -8.0 kcal/mol were selected to understand their interaction with MPro. Virtual screening was further validated by performing Molecular docking to generate favorable docked poses and the participation of important amino acid residues. Molecular dynamics simulation for the docked poses was performed to study thermodynamic properties of the protein, ligand and protein-ligand complexes. The finding shows that cinnamtannin B2 and cyanin showed favorable binding affinity values with SARS-CoV-2 MPro. The results are comparable in terms of docked poses, important amino acid participation and thermodynamic properties with the standard control drugs remdesivir, benazepril and hydroxychloroquine. Prime MM-GBSA was employed for end-point binding energy calculation. Binding to domain I and II of MPro were mediated through the OH, SH, NH2 and non-polar side chain of amino acids. Cinnamtannin B2 and cyanin binds to MPro with many sub sites within the active site with RMSD and RMSF within 4 Å. The results computed using Prime MM-GBSA show that Cinnamtannin B2 (-68.54940214 kcal/mol) and Cyanin (-62.1902835 kcal/mol) have better binding affinity in comparison to hydroxychloroquine diphosphate (-54.00912412 kcal/mol) and benazepril (-53.70242369 kcal/mol). The results provide a basis for exploiting the metabolites from spices as a potential candidate for the development of drug against SARS-CoV-2.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10608 - Biochemistry and molecular biology

Project

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Continuities

S - Specificky vyzkum na vysokych skolach

Publication year

2020

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

ISSN

0739-1102

e-ISSN

1538-0254

Volume of the periodical

38

Issue of the periodical within the volume

18

Country of publishing house

US - UNITED STATES

Number of pages

15

Pages from-to

1-15

UT code for WoS article

000589865300001

EID of the result in the Scopus database

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