Table 2.
Molecular interactions between the best ligands and the receptor main protease (6LU7).
| Ligand | Interacting Residues | Category | Type of Interaction |
|---|---|---|---|
| Lopinavir | Glu:A166 | H-bond | Conventional |
| Asn:A142 | H-bond | Conventional | |
| Gln:A189 | H-bond | Conventional | |
| Gly:A143 | H-bond | Conventional | |
| Asn:A142 | H-bond | Carbon | |
| Met:A49 | Hydrophobic | Pi-sigma | |
| Pro:A168 | Hydrophobic | Alkyl/pi-alkyl | |
| His:A163 | Hydrophobic | Alkyl/pi-alkyl | |
| Cys:A145 | Hydrophobic | Alkyl/pi-alkyl | |
| His:A163 | Hydrophobic | Pi-sulfur | |
| Cys:A145 | Hydrophobic | Pi-sulfur | |
| Chelidimerine | Cys:A145 | H-bond | Pi-donor/carbon |
| Phe:A140 | H-bond | Pi-donor/carbon | |
| His:A41 (2) | Hydrophobic | Pi-pi T-shaped | |
| Met:A49 | Hydrophobic | Alkyl/pi-alkyl | |
| Cys:A145 | Hydrophobic | Alkyl/pi-alkyl | |
| Met:A165 (3) | Hydrophobic | Alkyl/pi-alkyl | |
| Pro:A168 (2) | Hydrophobic | Alkyl/pi-alkyl | |
| Asn:A142 | Hydrophobic | Pi-sigma | |
| Catechin gallate | Glu:A166 | H-bond | Conventional |
| Asp:A187 | H-bond | Conventional | |
| Gln:A192 | H-bond | Conventional | |
| Cys:A145 | H-bond | Conventional | |
| Leu:A141 | H-bond | Conventional | |
| His:A163 | H-bond | Conventional | |
| Phe:A140 | H-bond | Conventional | |
| Met:A165 (3) | Hydrophobic | Alkyl/pi-alkyl | |
| Pro:A168 | Hydrophobic | Alkyl/pi-alkyl | |
| His:A41 | Hydrophobic | Pi-pi T-shaped | |
| Cys:A145 | Hydrophobic | Pi-sulfur | |
| Badrakemin acetate | His:A41 | H-bond | Conventional |
| Gln:A192 | H-bond | Conventional | |
| Cys:A145 (3) | Hydrophobic | Alkyl/pi-alkyl | |
| His:A163 (2) | Hydrophobic | Alkyl/pi-alkyl | |
| His:A41 | Hydrophobic | Alkyl/pi-alkyl | |
| Met:A165 (2) | Hydrophobic | Pi-sulfur | |
| His:A41 | Hydrophobic | Pi-sigma | |
| Withanolide G | Asn:A142 | H-bond | Conventional |
| Gly:A143 | H-bond | Conventional | |
| Glu:A166 | H-bond | Conventional | |
| Asn:A142 | H-bond | Carbon | |
| Cys:A145 (3) | Hydrophobic | Alkyl/pi-alkyl | |
| His:A163 | Hydrophobic | Alkyl/pi-alkyl | |
| Pro:A168 (2) | Hydrophobic | Alkyl/pi-alkyl | |
| Met:A165 | Hydrophobic | Alkyl/pi-alkyl | |
| Samarcandin | Cys:A145 | H-bond | Conventional |
| Gly:A143 | H-bond | Conventional | |
| Glu:A166 (2) | H-bond | Conventional | |
| Cys:A145 | H-bond | Pi-donor | |
| Leu:A167 | Hydrophobic | Alkyl | |
| Pro:A168 (2) | Hydrophobic | Alkyl | |
| Somniferine | Gln:A189 | H-bond | Conventional |
| Glu:A166 (2) | H-bond | Conventional | |
| Met:A165 | H-bond | Carbon | |
| His:A41 | Hydrophobic | Alkyl/pi-alkyl | |
| Cys:A145 | Hydrophobic | Alkyl/pi-alkyl | |
| Pro:A168 | Hydrophobic | Alkyl/pi-alkyl | |
| Adlumidine | Glu:A166 | H-bond | Conventional |
| Cys:A145 | H-bond | Conventional | |
| Glu:A166 | H-bond | Carbon | |
| Leu:A167 | H-bond | Carbon | |
| Phe:A140 | H-bond | Carbon | |
| Glu:A166 (2) | Hydrophobic | Pi-anion | |
| Cys:A145) | Hydrophobic | Pi-alkyl | |
| Withanone | Glu:A166 | H-bond | Conventional |
| Cys:A145 | H-bond | Conventional | |
| Gly:A143 | H-bond | Conventional | |
| Ser:A144 | H-bond | Conventional | |
| His:A41 (2) | Hydrophobic | Alkyl/pi-alkyl | |
| Met:A49 | Hydrophobic | Alkyl/pi-alkyl | |
| Cys:A145 (2) | Hydrophobic | Alkyl/pi-alkyl | |
| Pelargonidin-3 glucoside | His:A163 | H-bond | Conventional |
| His:A164 | H-bond | Conventional | |
| Glu:A166 (2) | H-bond | Conventional | |
| Thr:A190 | H-bond | Conventional | |
| Gln:A189 | Hydrophobic | Pi-sigma | |
| His:A41 | Hydrophobic | Pi-pi T-shaped | |
| Pro:A168 | Hydrophobic | Pi-alkyl | |
| Met:A165 | Hydrophobic | Pi-alkyl | |
| Met:A165 (2) | Hydrophobic | Pi-sulfur | |
| Astragalin | Gln:A189 (2) | H-bond | Conventional |
| Tyr:A54 | H-bond | Conventional | |
| Glu:A166 (2) | H-bond | Conventional | |
| Thr:A190 | H-bond | Conventional | |
| Met:A165 (3) | Hydrophobic | Pi-alkyl | |
| Met:A49 | Hydrophobic | Pi-alkyl | |
| His:A41 | Hydrophobic | Pi-pi T-shaped | |
| Fumariline | Glu:A166 | H-bond | Conventional |
| Glu:A166 | H-bond | Carbon | |
| Gln:A192 | H-bond | Carbon | |
| Leu:A167 | H-bond | Carbon | |
| Gln:A189 | Hydrophobic | Amide-pi stacked | |
| Pro:A168 | Hydrophobic | Pi-sigma | |
| Leu:A167 | Hydrophobic | Pi-alkyl | |
| Pro:A168 | Hydrophobic | Pi-alkyl | |
| Met:A165 | Hydrophobic | Pi-alkyl | |
| Sanguinarine | Tyr:A54 | H-bond | Conventional |
| Met:A49 | H-bond | Carbon | |
| Asp:A187 | H-bond | Carbon | |
| Cys:A145 | H-bond | Carbon | |
| Glu:A166 | H-bond | Carbon | |
| Met:A49 (2) | Hydrophobic | Alkyl/pi-alkyl | |
| Cys:A145 (2) | Hydrophobic | Alkyl/pi-alkyl | |
| His:A163 | Hydrophobic | Pi-cation | |
| Norsanguinarine | His:A163 | H-bond | Conventional |
| Leu:A141 | H-bond | Carbon | |
| Ser:A144 | H-bond | Carbon | |
| Met:A49 (2) | Hydrophobic | Pi-alkyl | |
| Cys:A145 | Hydrophobic | Pi-alkyl | |
| Met:A165 | Hydrophobic | Pi-alkyl | |
| His:A41 (2) | Hydrophobic | Pi-pi T-shaped | |
| Met:A165 | Hydrophobic | Pi-sigma | |
| Rutin | Asp:A187 | H-bond | Conventional |
| His:A41 | H-bond | Conventional | |
| Arg:A188 | H-bond | Conventional | |
| Thr(A190) | H-bond | Conventional | |
| Glu:A166 (2) | H-bond | Conventional | |
| Glu:A166 | H-bond | Carbon | |
| Pro:A168 | H-bond | Carbon | |
| Cys:A145 (2) | Hydrophobic | Pi-cation/pi-sulfur | |
| Met:A49 | Hydrophobic | Pi-cation/pi-sulfur | |
| His:A49 | Hydrophobic | Pi-cation/pi-sulfur | |
| Met:A165 | Hydrophobic | Pi-alkyl | |
| Cyanidin 3,5-di-O-glucoside | Gln:A192 | H-bond | Conventional |
| Glu:A166 (2) | H-bond | Conventional | |
| Gly:A143 | H-bond | Conventional | |
| Leu:A141 | H-bond | Conventional | |
| Glu:A166 | H-bond | Carbon | |
| His:A41 | Hydrophobic | Pi-pi T-shaped | |
| Gln:A189 | Hydrophobic | Pi-sigma | |
| Met:A165 (2) | Hydrophobic | Pi-alkyl | |
| Pro:A168 | Hydrophobic | Pi-alkyl | |
| Met:A165 (2) | Hydrophobic | Pi-sulfur | |
| His:A164 | Unfavorable | Donor-donor | |
| Cyanidin 3-O-rutinoside | Asn:A142 (2) | H-bond | Conventional |
| Cys:A145 | H-bond | Conventional | |
| His:A164 | H-bond | Conventional | |
| Asp:A187 | H-bond | Conventional | |
| Met:A49 | H-bond | Conventional | |
| Thr:A190 | H-bond | Conventional | |
| Gln:A189 | H-bond | Carbon | |
| Met:A165 (2) | Hydrophobic | Pi-alkyl | |
| His:A41 | Hydrophobic | Pi-pi T-shaped | |
| His:A163 | Unfavorable | Donor-donor | |
| Gln:A192 | Unfavorable | Donor-donor | |
| Kaempferitrin | Ser:A144 | H-bond | Conventional |
| Cys:A145 | H-bond | Conventional | |
| Leu:A141 | H-bond | Conventional | |
| Glu:A166 | H-bond | Conventional | |
| Asn:A142 | H-bond | Conventional | |
| Glu:A166 | H-bond | Pi-donor | |
| Met:A49 | Hydrophobic | Alkyl/pi-alkyl | |
| Ala:A191 | Hydrophobic | Alkyl/pi-alkyl | |
| Met:A165 | Hydrophobic | Pi-sulfur | |
| Glu:A166 | Hydrophobic | Pi-lone pair | |
| Harpagoside | Glu:A166 (3) | H-bond | Conventional |
| Asn:A142 | H-bond | Conventional | |
| Leu:A141 | H-bond | Carbon | |
| Met:A49 | Hydrophobic | Pi-sulfur | |
| Met:A165 | Hydrophobic | Pi-sulfur | |
| His:A41 | Hydrophobic | Pi-pi T-shaped |