PMC:7544943 / 22807-28937 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7544943","sourcedb":"PMC","sourceid":"7544943","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7544943","text":"3.5. Molecular docking study\n\n3.5.1. Docking study of SARS-CoV-2 receptor-binding domain spike protein\nIn addition to the above investigations, a molecular docking study was performed to estimate the binding affinity and their binding pose of the ligand molecules at the binding site of the SARS-CoV-2 RBD Spro. From the study, it is observed that Piperine has the highest interaction affinity among the screened compounds. The docked poses of the four ligand molecules (Piperine, Capsaicin, Gingerol and Terpinen-4-ol) along with their 2D interaction diagram having the highest binding affinity, among the selected molecules, are presented in descending order in Figure 3. From Table 1, it is observed that these four molecules follow the trend for their binding affinity with Piperine (−6.4 kcal/mol) at the highest, then Capsaicin, Ginerol and Terpinen-4-ol (all having −5.5 kcal/mol) among all the selected molecules. From Figure 3(a), it is observed that Piperine is associated with hydrogen bond interaction with GLY164 and GLY170. TYR173 (TYR505) and SER162 (SER494) are involved with pi–pi T-shaped and carbon-hydrogen bond interactions, respectively. The binding process is also governed by van der Waals interactions with the residues ARG71, TYR121 (TYR453), TYR163 (TYR495) and ASN169 (ASN501) of SARS-CoV-2 RBD Spro. Hence, the interaction of Piperine with SARS-CoV-2 RBD Spro is stabilized by covalent hydrogen bonding, pi–pi T-shaped and van der Waals interactions with a good affinity score. Capsaicin interacts with the residues GLY164 and TYR173 (TYR505) through pi-Donor hydrogen bond and pi–pi T-shaped interactions with the benzene ring, respectively (Figure 3(b)). The residues ARG71 (ARG403), ASP73, GLU74, GLN77, LYS85, TYR121 (TYR453), SER162 (SER494), TYR163 (TYR495) and ASN169 (ASN501) are involved with van der Waals interaction with Capsaicin.\nFigure 3. Lowest energy docked pose of (a) Piperine, (b) Capsaicin, (c) Gingerol and (d) Terpinen-4-ol with SARS-Cov-2 RBD Spro and their 2D interaction diagram. The colour codes represent the nature of interactions.\nOn the other hand, Gingerol is stabilized by various kinds of interactions with the SARS-CoV-2 RBD Spro (Figure 3(c)). The residues GLY164, ASN169 (ASN501) and GLY170 are associated with hydrogen bond interaction with Gingerol. Other than the hydrogen bond interaction TYR173 (TYR505) is having a pi–pi T-shaped interaction with the benzene ring of Gingerol while ARG71 (ARG403), TYR121 (TYR453), TYR163 (TYR495), PHE165 (PHE497) and GLN166 (GLN498) residues are involved in van der Waals interactions. The Terpinen-4-ol is stabilized by hydrophobic interaction with the residues ARG125, LYS126, TYR141 and PRO159 while the residues ARG122, PHE124, ASP135, SER137, GLU139 and ILE140 are involved in van der Waals interactions with Terpinen-4-ol (Figure 3(d)). The lowest energy poses of the rest 26 molecules along with their 2D interaction diagrams are provided in Supplementary Figure S3.\n\n3.5.2. Docking study of SARS-CoV-2 main protease\nThe 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) \u003e Capsaicin (−6.4 kcal/mol) \u003e Carvone (−6.2 kcal/mol) \u003e 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.\nFigure 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. 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