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. 2021 Mar 5:1227:129390.
doi: 10.1016/j.molstruc.2020.129390. Epub 2020 Oct 3.

Screening of potential drug from Azadirachta Indica (Neem) extracts for SARS-CoV-2: An insight from molecular docking and MD-simulation studies

Nabajyoti Baildya  1 , Abdul Ashik Khan  2 , Narendra Nath Ghosh  2 , Tanmoy Dutta  3 , Asoke P Chattopadhyay  1
Affiliations

Screening of potential drug from Azadirachta Indica (Neem) extracts for SARS-CoV-2: An insight from molecular docking and MD-simulation studies

Nabajyoti Baildya et al. J Mol Struct. .

Abstract

Azadirachta Indica (Neem) extracts have been known for their anti-bacterial and other effects since ancient times. The present work examines the inhibitory activity of Neem extracts on Papain like protease (PLpro) of the novel coronavirus SARS-CoV-2. The activity is analysed by molecular docking study along with molecular dynamics simulation. All the studied Neem compounds showed decent level of inhibitory activity against PLpro of SARS-CoV-2. Among them, desacetylgedunin (DCG) found in Neem seed showed the highest binding affinity towards PLpro. Furthermore, MD-simulation studies supported by standard analysis (e.g. root mean square deviation and fluctuation (RMSD, RMSF), radius of gyration, solvent accessible surface area (SASA)) showed large impact on the structure of PLpro by DCG. We believe that the significant effect of DCG on PLpro may help in therapeutic efforts against SARS-CoV-2.

Keywords: MD simulation; Molecular docking; Neem extracts; PLpro.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Image, graphical abstract
Graphical abstract
Fig 1
Fig. 1
Docked structures of some Neem compounds with PLpro having high binding affinity.
Fig 2
Fig. 2
Docked structure of DCG with PLpro.
Fig 3
Fig. 3
Root mean square deviation (RMSD) plot of PLpro, DCG and PLpro+DCG.
Fig 4
Fig. 4
Root mean square fluctuation (RMSF) of PLpro in docked and undocked state.
Fig 5
Fig. 5
Radius of Gyration of undocked and docked PLpro (a) and solvent accessible surface area (SASA) plot for undocked and docked PLpro (b).
Fig 6
Fig. 6
Structural changes during MD-simulation of undocked (brown) and docked (sky blue) PLpro.
See this image and copyright information in PMC

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