Identification of natural inhibitors against Mpro of SARS-CoV-2 by molecular docking, molecular dynamics simulation, and MM/PBSA methods

Abstract

The recent outbreak of SARS-CoV-2 disease, also known as COVID-19, has emerged as a pandemic. The unavailability of specific therapeutic drugs and vaccines urgently demands sincere efforts for drug discovery against COVID-19. The main protease (Mpro) of SARS-CoV-2 is a critical drug target as it plays an essential role in virus replication. Therefore for the identification of potential inhibitors of SARS-CoV-2 Mpro, we applied a structure-based virtual screening approach followed by molecular dynamics (MD) study. A library of 686 phytochemicals was subjected to virtual screening which resulted in 28 phytochemicals based on binding energy. These phytochemicals were further subjected to drug-likeness and toxicity analysis, which resulted in seven drug-like hits. Out of seven, five phytochemicals viz., Mpro-Dehydrtectol (-10.3 kcal/mol), Epsilon-viniferin (-8.6 kcal/mol), Peimisine (-8.6 kcal/mol), Gmelanone (-8.4 kcal/mol), and Isocolumbin (-8.4 kcal/mol) were non-toxic. Consequently, these phytochemicals are subjected to MD, post MD analysis, and MM/PBSA calculations. The results of 100 ns MD simulation, RMSF, SASA, Rg, and MM/PBSA show that Epsilon-viniferin (-29.240 kJ/mol), Mpro-Peimisine (-43.031 kJ/mol) and Gmelanone (-13.093 kJ/mol) form a stable complex with Mpro and could be used as potential inhibitors of SARS-CoV-2 Mpro. However, further investigation of these inhibitors against Mpro receptor of COVID-19 is needed to validate their candidacy for clinical trials. Communicated by Ramaswamy H. Sarma.

Keywords: COVID-19; Coronavirus; Mpro; molecular docking; molecular dynamic simulation.

Figure 1.

Summary of work used in the present study to identify the phytochemical based inhibitors of SARS-CoV-2 Mpro.

Figure 2.

(A.) 3 D structure of Mpro (6W63) with the co-crystalized ligand. (B.) Superimposition of docked (X77) (Green color) and Experimental reference (X77), (Purple color) by 3 D structure. (C.)Docked reference (X77) of Mpro. (D.) Experimental reference (X77) of Mpro.

Figure 3.

2 D interaction of reference compounds (X77) and screened phytochemicals. In all phytochemicals, dotted green line indicates the hydrogen bond, red sparked arc represents hydrophobic interaction, and red circle and red ellipses represent common protein residue with reference.

Figure 4.

RMSD plot of Mpro protein and screened protein-ligand complexes for 100 ns MD Simulation of protein (Black) protein-reference (X77) (Red), Mpro-Epsilon-vinifein (Cyan), Mpro-Peimisine (Magenta), and Mpro-Gmelanone (Green).

Figure 5.

The RMSF values of the Mpro protein and screened protein-ligand complexes for 100 ns MD Simulation of protein (Black) protein-reference(X77) (Red), Mpro-Epsilon-vinifein (Cyan), Mpro-Peimisine (Magenta), and Mpro-Gmelanone (Green).

Figure 6.

Radius of Gyration plot depicting the changes observed in the conformational behavior of the Mpro protein and all protein-ligand complexes; 100 ns MD Simulation of protein (Black) protein-reference(X77) (Red), Mpro-Epsilon-vinifein (Cyan), Mpro-Peimisine (Magenta), and Mpro-Gmelanone (Green).

Figure 7.

A plot showing hydrogen bonds. The color code for all panels is as follows protein-reference(X77) (Red), Mpro-Epsilon-vinifein (Cyan), Mpro-Peimisine (Magenta), and Mpro-Gmelanone (Green).

Figure 8.

Solvent accessible surface area (SASA). The color code for all panels is as follows protein-reference(X77) (Red), Mpro-Epsilon-vinifein (Cyan), Mpro-Peimisine (Magenta), and Mpro-Gmelanone (Green).

Figure 9.

Interaction energy. The color code for all panels is as follows protein-reference(X77) (Red), Mpro-Epsilon-vinifein (Cyan), Mpro-Peimisine (Magenta), and Mpro-Gmelanone (Green).

Figure 10.

Principal component analysis (A.) Plots of eigenvalues vs. first 40 eigenvectors. (B) First two eigenvector describing the protein motion in phase space for all the complexes. The color code for all panels is as follows protein-reference(X77) (Red), Mpro-Epsilon-vinifein (Cyan), Mpro-Peimisine (Magenta), and Mpro-Gmelanone (Green).

Figure 11.

Gibbs free energy plots (A.) protein-reference(X77), (B.) Mpro-Epsilon-vinifein (C.)Mpro-Peimisine (D) Mpro-Gmelanone.