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Exploring the active constituents of Oroxylum indicum in intervention of novel coronavirus (COVID-19) based on molecular docking method - PubMed

Exploring the active constituents of Oroxylum indicum in intervention of novel coronavirus (COVID-19) based on molecular docking method

Sapan Shah et al. Netw Model Anal Health Inform Bioinform. 2021.

Abstract

The severe acute respiratory syndrome COVID-19 declared a global pandemic by WHO has become the present wellbeing worry to the whole world. There is an emergent need to search for possible medications. We report in this study a molecular docking study of eighteen Oroxylum indicum molecules with the main protease (Mpro) responsible for the replication of SARS-CoV-2 virus. The outcome of their molecular simulation and ADMET properties reveal four potential inhibitors of the enzyme (Baicalein-7-O-diglucoside, Chrysin-7-O-glucuronide, Oroxindin and Scutellarein) with preference of ligand Chrysin-7-O-glucuronide that has the second highest binding energy (- 8.6 kcal/mol) and fully obeys the Lipinski's rule of five.

Supplementary information: The online version contains supplementary material available at 10.1007/s13721-020-00279-y.

Keywords: ADMET study; COVID-19; Molecular docking; Molecular dynamics; Oroxylum indicum.

© The Author(s), under exclusive licence to Springer-Verlag GmbH, AT part of Springer Nature 2021.

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Conflict of interest statement

Conflict of interestThe authors have no conflicts of interest to declare that are relevant to the content of this article.

Figures

Fig. 1
Fig. 1

Chemical structure of all selected ligand molecules in docking studies

Fig. 2
Fig. 2

Docked pose of a Baicalein-7-O-diglucoside b Chrysin-7-O-glucuronide and c Oroxindin, d Scutellarein, e N3, f Remdesivir against Mpro protease (PDB ID: 6LU7). The ligand is shown in ball and stick representation whereas residues forming binding pocket of Mpro are shown as colored sticks. Hydrogen bond interactions are shown with black dotted lines

Fig. 3
Fig. 3

Hydrogen-bonds parameters (distances and angles) a Baicalein-7-O-diglucoside, b Chrysin-7-O-glucuronide and c Oroxindin, d Scutellarein, e N3, f Remdesivir

Fig. 4
Fig. 4

Root Mean Square Fluctuations plots of protein structure with compounds. No abrupt fluctuations were observed in any region of the protein with the proposed ligands. a N3, b Baicalein-7-O-diglucoside (10077207), c Chrysin-7-O-glucuronide (14135335), d Oroxindin (3084961) and e Scutellarein (5281697)

Fig. 5
Fig. 5

Stable structures of protein generated after MD Simulation of compound. a N3, b Baicalein-7-O-diglucoside, c Chrysin-7-O-glucuronide, d Oroxindin and e Scutellarein

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