3.5.2.  Docking study of SARS-CoV-2 main protease
The above-selected molecules were also docked with the SARS-CoV-2 Mpro to observe the inhibitory effect of these molecules. The docking study reveals that all the molecules are interacting with the SARS-CoV-2 Mpro with certain binding affinity. The docking data are also presented in Table 1. From Table 1, it is seen that Piperine has the highest affinity at the binding site of SARS-CoV-2 Mpro among all the selected molecules, which is similar to the case of SARS-CoV-2 RBD Spro. The ΔG value, known as binding free energy, for the four molecules having the highest affinity among all the selected molecules, along with their 2D interaction diagram, is given in Figure 4. The four molecules have followed the binding affinity trend as Piperine (−7.3 kcal/mol) > Capsaicin (−6.4 kcal/mol) > Carvone (−6.2 kcal/mol) > Gingerol (−6.1 kcal/mol). From Figure 4(a), it is observed that the interaction of Piperine at the binding site of the SARS-CoV-2 Mpro is stabilized by hydrogen bonding, electrostatics and van der Waals interactions. The residues GLN299 and VAL303 are associated with hydrogen bonding interaction; ASP295 and ARG298 with charged interactions while MET6 and PRO9 are associated with hydrophobic interactions with Piperine. The molecule is also stabilized through van der Waals interactions with residues PHE8, GLY127, ILE152, PHE291 and THR304 at the binding site of the SARS-CoV-2 Mpro. The molecule Capsaicin is stabilized in the binding pocket through van der Waals and hydrophobic interactions (Figure 4(b)). The residues MET6, PHE8, PRO9 and ILE152 are interacting through hydrophobic interactions such as alkyl and pi–alkyl with the Capsaicin. Capsaicin is interacting with residues ALA7, GLY11, LYS12, GLN127, TYR154, PHE291, ASP295, ARG298, GLN299, VAL303 and THR304 through van der Waals interaction. The interaction of Carvone with the SARS-CoV-2 Mpro is stabilized through hydrophobic and van der Walls interactions (Figure 4(c)). Carvone interacts with the residues MET6, PHE8 and ARG298 of SARS-CoV-2 Mpro through hydrophobic contacts. The residues ALA7, PRO9, GLN127, ASP295, GLN299, GLY302 and VAL303 are in van der Waals interactions with Carvone. Gingerol is stabilized by hydrogen bond, hydrophobic and van der Waals interactions in the binding pocket of the SARS-Cov-2 Mpro (Figure 4(d)). VAL303 is interacting through hydrogen bond interaction with Gingerol. The residues LYS12 and THR304 are involved in carbon-hydrogen bond interactions while MET6, ALA7, PHE8, GLN127, TYR154, ASP295 and ARG298 are associated with van der Waals interactions with Gingerol. The interaction of Gingerol with the residues PRO9 and ILE152 is stabilized through pi–alkyl interactions. The lowest energy binding poses of the rest 26 molecules along with the ligand interaction diagram at the binding sites of the SARS-CoV-2 Mpro are provided in Supplementary Figure S4.
Figure 4.  Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Carvone and (d) Gingerol with SARS-CoV-2 Mpro and their 2D interaction diagram. The colour codes represent the nature of interactions.