Fisetin 8-C-glucoside as entry inhibitor in SARS CoV-2 infection: molecular modelling study

Abstract

Coronaviruses are RNA viruses that infect varied species including humans. TMPRSS2 is gateway for SARS CoV-2 entry into the host cell. It causes proteolytic activation of spike protein and discharge of the peptide into host cell. The TMPRSS2 inhibition could be one of the approaches to stop the viral entry, therefore, interaction pattern and binding energies for Fisetin and TMPRSS2 have been explored in the present study. TMPRSS2 peptide was used for homology modelling and then for further study. Molecular docking score and MMGBSA Binding energy of Fisetin was better than Nafamostat, a known inhibitor of TMPRSS2. Post docking MM-GBSA free energy for Fisetin and Nafamostat was -42.78 and -21.11 kcal/mol, respectively. Fisetin forms H bond with Val 25, His 41, Lys 42, Lys 45, Glu 44, Ser186. Nafamostat formed H bonds with Lys 85, Asp 90, Asp 203. RMSD plots of TMPRSS2, TMPRSS2-Fisetin and TMPRSS2-Nafamostat complex showed stable profile with very small fluctuation during entire simulation of 150 ns. Significant decrease in TMPRSS2-Fisetin and TMPRSS2-Nafamostat complex fluctuation occurred around His 41, Glu 44, Gly 136, Ser 186 in RMSF study. During simulation Fisetin interaction was observed with residues Val 25, His 41, Glu 44, Lys 45, Lys 87, Gly 136, Gln 183, Ser 186 likewise interaction of Nafamostat with Lys 85, Asp 90, Asn 163, Asp 203 and Ser 205. Post simulation MM-GBSA free energy was found to be -51.87 ± 4.3 and -48.23 ± 4.39 kcal/mol for TMPRSS2 with Fisetin and Nafamostat, respectively.Communicated by Ramaswamy H. Sarma.

Keywords: Fisetin; MD simulation; MMGBSA; TMPRSS2; homology modelling.

Figure 1.

(a) Ramchandran plot of modelled TMPRSS2 protein (target protein) ′. (b) Ramachandran plot of modelled TMPRSS2 protein (target protein) [i-tasser].

Figure 2.

(a) TMPRSS2 with Nafamostat (amino acid 1 corresponds to amino acid 256). (b) TMPRSS2 with Fisetin 8-C-glucoside (amino acid 1 correspond to amino acid 256).

Figure 3.

RMSD profile of TMPRSS2 and during 150 ns MD simulation (blue—TMPRSS2; orange—TMPRSS2-Nafamostat; grey—TMPRSS2-Fisetin).

Figure 4.

Compactness of TMPRSS2 in terms of radius of gyration (Rg) during 150 ns MD simulation (blue—TMPRSS2; orange—TMPRSS2-Nafamostat; grey—TMPRSS2-Fisetin).

Figure 5.

(a) H-bond formation between TMPRSS2 and Nafamostat during 150 ns MD simulation study. (b) H-bond formation between TMPRSS2 and Fisetin during 150 ns MD simulation study.

Figure 6.

RMSF plot to represents local changes around TMPRSS2 chain (blue—TMPRSS2; orange—TMP-Nafamostat; grey—TMP-Fisetin).

Figure 7.

Top panel show specific contact and interaction study of Fisetin and TMPRSS2 during 150 ns simulation.

Figure 8.

(a) Fisetin and TMPRSS2 interaction study during 150 ns simulation (water bridges—blue color; H-bond—green color; hydrophobic contacts—violet). (b) Schematic representation of Fisetin and TMPRSS2 interaction (green—hydrophobic, light blue—polar, red charged—salt bridge; amino acid 1 will correspond to amino acid 256).

Figure 9.

(a) TMPRSS2-Nafamostat interaction during 150 ns simulation (water bridges—blue color; H-bond—green color; hydrophobic contacts—violet). (b) Schematic representation of TMPRSS2 and Fisetin interaction during 150 ns simulation (green—hydrophobic, blue—polar, red charged—salt bridge; amino acid 1 will correspond to amino acid 256).