Table 1
Best docking scores (lowest binding energy) of selected compounds of grapefruit seed extract (GSE) as well as of the positive controls and their distance from best mode
| Distance from best mode | |||
|---|---|---|---|
| Ligands | Affinity (kcal/mol§) | rmsd l.b.† | rmsd u.b‡ |
| Narirutin | -10.5 | 0.000 | 0.000 |
| Naringin | -10.1 | 0.000 | 0.000 |
| Naringenin | -8.2 | 0.000 | 0.000 |
| Limonin | -9.9 | 0.000 | 0.000 |
| Ascorbic acid | -6.7 | 0.000 | 0.000 |
| Citric acid | -6.4 | 0.000 | 0.000 |
| Acetoside | -10.0 | 0.000 | 0.000 |
| Remdesivir | -9.6 | 0.000 | 0.000 |
| Gallic acid | -6.4 | 0.000 | 0.000 |
Figure 1
A-B. Visualisation of the SARS-CoV-2 main protease (A) (PDB ID: 6Y84) with ligand narirutin and their best mode binding interactions (B) via PyMOL 2.4.
Figure 2
A-B. Visualisation of the SARS-CoV-2 main protease (A) (PDB ID: 6Y84) with ligand naringin and their best mode binding interactions (B) via PyMOL 2.4.
Figure 3
A-B. Visualisation of the SARS-CoV-2 main protease (A) (PDB ID:6Y84) with ligand limonin and their best mode binding interactions (B) via PyMOL 2.4.
Figure 4
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand naringenin and their best mode binding interactions (b) via PyMOL 2.4
Figure 5
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand ascorbic acid and their best mode binding interactions (b) via PyMOL 2.4.
Figure 6
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand citric acid and their best mode binding interactions (b) via PyMOL 2.4.
Figure 7
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand acetoside and their best mode binding interactions (b) via PyMOL 2.4.
Figure 8
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand remdesivir and their best mode binding interactions (b) via PyMOL 2.4.
Figure 9
A-B. Visualisation of the SARS-CoV-2 main protease (a) (PDB ID:6Y84) with ligand gallic acid and their best mode binding interactions (b) via PyMOL 2.4.