Natural inhibitors of SARS-CoV-2 main protease: structure based pharmacophore modeling, molecular docking and molecular dynamic simulation studies

Abstract

Main protease (M^pro) plays a key role in replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study was designed for finding natural inhibitors of SARS-CoV-2 M^pro by in silico methods. To this end, the co-crystal structure of M^pro with telaprevir was explored and receptor-ligand pharmacophore models were developed and validated using pharmit. The database of "ZINC Natural Products" was screened, and 288 compounds were filtered according to pharmacophore features. In the next step, Lipinski's rule of five was applied and absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the filtered compounds were calculated using in silico methods. The resulted 15 compounds were docked into the active site of M^pro and those with the highest binding scores and better interaction including ZINC61991204, ZINC67910260, ZINC61991203, and ZINC08790293 were selected. Further analysis by molecular dynamic simulation studies showed that ZINC61991203 and ZINC08790293 dissociated from M^pro active site, while ZINC426421106 and ZINC5481346 were stable. Root mean square deviation (RMSD), radius of gyration (Rg), number of hydrogen bonds between ligand and protein during the time of simulation, and root mean square fluctuations (RMSF) of protein and ligands were calculated, and components of binding free energy were calculated using the molecular mechanic/Poisson-Boltzmann surface area (MM/PBSA) method. The result of all the analysis indicated that ZINC61991204 and ZINC67910260 are drug-like and nontoxic and have a high potential for inhibiting M^pro.

Keywords: Docking; Molecular dynamic simulation; Mpro; Natural inhibitor; Pharmacophore modelling.

Fig. 1

Overall process and the result of pharmacophore validation

Fig. 2

Orientation of telaprevir in complex with M^pro. His41 and Cys145, residues of the catalytic dyad, are depicted as green and yellow, respectively (A). Non-bond interactions of telaprevir in binding site of M^pro. Green, hydrogen bond; pink, amide-Pi stacked; light pink, Pi-alkyl; blue halo, solvent accessible surface (B)

Fig. 3

List of 27 known active inhibitors of M^pro and their binding energy towards M^pro obtained by molecular docking method. The number in parenthesis shows the estimated binding energy (kcal/mol)

Fig. 4

The structure of Pharm_A. HBA. hydrogen acceptor; HBD, hydrogen donor; HYD, hydrophobic. Protein (M^pro) is depicted as yellow ribbon. Molecule description: blue, carbon; purple, nitrogen; red, oxygen. Numbers in parentheses show x, y, z coordinates of the pharmacophoric feature

Fig. 5

Compounds with the best binding energies including ZINC61991204 (yellow), ZINC67910260 (purple), ZINC61991203 (red), and ZINC08790293 (green) in M^pro active site. Protein is depicted as cyan

Fig. 6

The best binding pose of the selected compounds in the active site of M^pro resulting from the docking studies. His41 and Cys145, residues of the catalytic dyad, are depicted as green and yellow, respectively

Fig. 7

Non-bond interactions of the selected compounds in the active site of M^pro. Green, hydrogen bond; pink, amide-Pi stacked; light pink, Pi-alkyl; orange, Pi-sulfur

Fig. 8

Superimposed RMSD of the C_α atoms of M^pro in complex with ZINC61991204 (green), ZINC67910260 (orange), and telaprevir (blue)

Fig. 9

Superimposed RMSD of ZINC61991204 (green), ZINC67910260 (orange), and telaprevir (blue) in complex with M^pro

Fig. 10

RMSF graph of the Cα atoms of M^pro in complex with ZINC61991204 (green), ZINC67910260 (orange), and telaprevir (blue)

Fig. 11

RMSF graph of the heavy atoms of ZINC61991204 and ZINC67910260 in complex with M^pro. Structure of these compounds and parts of these molecules with highest and lowest fluctuations are illustrated

Fig. 12

Time dependence of the radius of gyration (Rg) graph of M^pro in complex with ZINC61991204 (green), ZINC67910260 (orange), and telaprevir (blue)

Fig. 13

Numbers of hydrogen bonds formed between M^pro and ZINC61991204 (green) and ZINC67910260 (orange)

Fig. 14

Diagram of binding energy changes during the last 20 ns of simulation time. M^pro in complex with ZINC61991204 (green), ZINC67910260 (orange), and telaprevir (blue)

Fig. 15

Contribution of M^pro residues to the binding energy (KJ/mol). M^pro-ZINC61991204 complex (A) and M^pro-ZINC67910260 complex (B)

Fig. 16

Residues with the largest and smallest contribution to the binding energy (KJ/mol) of M^pro-ZINC61991204 complex (A) and M^pro- ZINC67910260 complex (B)