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. 2022 May;29(5):3456-3465.
doi: 10.1016/j.sjbs.2022.02.028. Epub 2022 Feb 25.

Phytocompounds as potential inhibitors of SARS-CoV-2 Mpro and PLpro through computational studies

Mithun Rudrapal  1 , Ismail Celik  2 , Sampath Chinnam  3 , Mohammad Azam Ansari  4 , Johra Khan  5   6 , Saad Alghamdi  7 , Mazen Almehmadi  8 , James H Zothantluanga  9 , Shubham J Khairnar  10
Affiliations

Phytocompounds as potential inhibitors of SARS-CoV-2 Mpro and PLpro through computational studies

Mithun Rudrapal et al. Saudi J Biol Sci. 2022 May.

Abstract

The inhibition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) and papain-like protease (PLpro) prevents viral multiplications; these viral enzymes have been recognized as one of the most favorable targets for drug discovery against SARS-CoV-2. In the present study, we screened 225 phytocompounds present in 28 different Indian spices to identify compounds as potential inhibitors of SARS-CoV-2 Mpro and PLpro. Molecular docking, molecular dynamics simulation, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations, and absorption, distribution, metabolism, excretion and toxicity (ADMET) studies were done. Based on binding affinity, dynamics behavior, and binding free energies, the present study identifies pentaoxahexacyclo-dotriacontanonaen-trihydroxybenzoate derivative (PDT), rutin, and dihyroxy-oxan-phenyl-chromen-4-one derivative (DOC), luteolin-7-glucoside-4'-neohesperidoside as promising inhibitors of SARS-CoV-2 Mpro and PLpro, respectively.

Keywords: Molecular docking; Molecular dynamics; Mpro; PLpro; SARS-CoV-2; Spice phytochemicals.

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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

Fig. 1
Fig. 1
2D and 3D ligand interactions of X77, PDT, and rutin against SARS-COV-2 Mpro.
Fig. 2
Fig. 2
2D and 3D ligand interactions of VYB, DOC, and luteolin-7-Glucoside-4′-Neohesperidoside against SARS-CoV-2 PLpro.
Fig. 3
Fig. 3
RMSD, RMSF, and Rg of co-crystal inhibitor (X77)-Mpro, PDT-Mpro and rutin-Mprocomplexes.
Fig. 4
Fig. 4
RMSD, RMSF, and Rg of co-crystal inhibitor (VBY)-PLpro, luteolin-7-glucoside-4′-neohesperidoside-PLpro and DOC-PLpro complexes.
See this image and copyright information in PMC

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