Research Article
In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants
Table 1
Binding interaction analysis of the top 10 best-docked coumarins and reference ligands with SARS-CoV-2 Omicron S-RBD.
| S.N. | Compounds | Binding energy (kcal/mol) | Interacting residues | Interaction types | Interacting distance (Å) |
| 1 | Inophyllum C | −7.6 | SER 494 | Conventional H bond | 1.95 | PHE 490 | Pi-Pi stacked | 4.87 | ARG 493 | Pi-alkyl | 4.38 |
| 2 | (+)-Rutamarin | −7.5 | TRP 436 | Pi-Pi T-shaped | 5.46, 5.74 | LYS 440 | Alkyl | 4.69 | PRO 373 | Pi-alkyl | 5.27, 5.33 |
| 3 | Cordatolide A | −7.5 | SER 494 | Conventional H bond | 2.07 | ARG 493 | Pi-alkyl | 3.77, 4.12 |
| 4 | Soulattrolide | −7.5 | SER 494 | Conventional H bond | 2.26 | PHE 490 | Pi-Pi stacked | 3.90, 5.27 | ARG 493 | Pi-alkyl | 5.21, 5.34 |
| 5 | Wedelolactone | −7.4 | TYR 449 | Conventional H bond | 2.31 | SER 494 | Conventional H bond | 2.35 | ARG 493 | Pi-sigma, Pi-alkyl | 3.73, (5.35) | LEU 452 | Pi-sigma | 3.80, 5.14 | PHE 490 | Pi-Pi stacked | 5.33 |
| 6 | Inophyllum A | −7.4 | ASP 339 | Pi-anion | 4.03, 4.25 | LEU 371 | Pi-alkyl | 5.36 | LEU 368 | Pi-alkyl | 5.47 |
| 7 | Inophyllum E | −7.4 | SER 494 | Conventional H bond | 1.89 | PHE 490 | Pi-Pi stacked | 4.41, 5.84 | ARG 493 | Pi-alkyl | 4.75 |
| 8 | (+)-Calanolide C | −7.3 | SER 494 | Conventional H bond | 2.03, 2.51 | PHE 490 | Pi-sigma | 3.96 | ARG 493 | Pi-alkyl | 3.78, 4.13 |
| 9 | Inophyllum B | −7.3 | SER 494 | Conventional H bond | 2.43 | PHE 490 | Pi-Pi stacked | 3.85, 5.18 | ARG 493 | Pi-alkyl | 5.25, 5.28 |
| 10 | Inophyllum D | −7.3 | SER 494 | Conventional H bond | 1.88 | PHE 490 | Pi-Pi stacked | 4.27, 5.79 | ARG 493 | Pi-alkyl | 4.72 |
| Reference ligands | Ceftazidime | −6.5 | TYR 453 | Conventional H bond | 1.90 | ARG 403 | Conventional H bond | 2.45, 6.00 | SER 496 | Conventional H bond | 2.00 | HIS 505 | Pi-cation, (C-H bond) | 3.46, (4.08) | Molnupiravir | −6.1 | TYR 453 | Conventional H bond | 2.05 | ARG 403 | Conventional H bond | 2.20 | SER 496 | C-H bond | 3.33, 3.45 | ARG 493 | C-H bond | 3.46 | HIS 505 | Pi-sigma | 3.87 |
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