Research Article
In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants
Table 2
Binding interaction analysis of the best-docked coumarins with spike proteins of SARS-CoV-2 variants among the selected top 10 coumarins.
| SARS-CoV-2 variant S-RBDs | Best-dockedcoumarins | Binding energy (kcal/mol) | Interacting residues | Interaction types | Interacting distance (Å) |
| Wild-type variant PDB ID: 6M0J | Inophyllum B | −7.4 | GLN 498 | Conventional H bond | 2.23 | ASN 501 | Conventional H bond | 2.86 | ARG 403 | Pi-cation | 4.91 | TYR 505 | Pi-Pi T-shaped | 4.91 |
| Alpha variant PDB ID: 7EKF | Inophyllum D | −7.5 | SER 494 | Conventional H bond | 2.26 | TYR 449 | Pi-alkyl | 5.17 | TYR 501 | Pi-Pi stacked (Pi-Pi T-shaped) | 5.60, (4.94) | TYR 505 | Pi-Pi stacked | 3.77 |
| Beta variant PDB ID: 7EKG | Soulattrolide | −7.2 | GLN 493 | Conventional H bond | 2.18 | SER 494 | Conventional H bond | 2.82 | PHE 490 | Pi-Pi stacked (Pi-alkyl) | 4.60, 4.90, (4.77) | LYS 484 | Alkyl | 4.81 |
| Gamma variant PDB ID: 7EKC | Inophyllum E | −7.8 | SER 494 | Conventional H bond | 2.32 | GLN 493 | Carbon H bond | 3.51 | LYS 484 | Pi-Pi stacked | 4.18, 5.52 | PHE 490 | Pi-alkyl | 4.99 |
| Delta variant PDB ID: 7WBQ | Soulattrolide | −7.8 | GLN 498 | Conventional H bond | 2.73 | ASN 501 | Conventional H bond | 2.94 | ARG 403 | Pi-cation | 4.03 | TYR 505 | Pi-Pi T-shaped | 5.72 | TYR 449 | Carbon H bond | 3.07 |
|
|