Table 2.
Scoring energies and critical interactions for the re-docking of each ligand in its active site.
| Ligand | Vina Docking score (kcal mol–1) | Vina re-docking score (kcal mol–1) | Critical ligand interactions after re-docking process |
|---|---|---|---|
| 3-Dihydrocadambinea | –7.1 | –7.5 | ASN501 (H-bond), GLY496 (three H-bond), TYR453 (H-bond), TYR505 (π-cation), and hydrophobic interactions: PHE497, TYR495, TYR449, GLN493, GLN498, GLU406. |
| Proanthocyanidin B2a | –7.2 | –6.5 | ARG403 (H-bond), SER494 (H-bond), LYS417 (H-bond), ARG403 (π-cation), GLU406 (π-anion) TYR505 (π–π stacked) and hydrophobic interactions: PHE497, TYR453, TIR495, GLN409. |
| Proanthocyanidin C1b | –8.6 | –9.0 | GLN388 (H-bond), ASP30 (two H-bond), TYR505 (H-bond), ASP405 (H-bond), ARG408 (H-bond), ARG403 (H-bond), ALA387 (amide-π stacking interaction) and hydrophobic interactions: HIS34, PHE390, GLU37, LYS353, GLY354, LYS417. |
| QAG-2b | –8.2 | –8.1 | TYR505 (H-bond), GLY354 (H-bond) and hydrophobic interactions: GLU37, GLN388, LYS353 and ASP355. |
a
Re-docking inside the SARS-CoV-2 RBD active site.
b
Re-docking at RBD/ACE-2 interface.