Table 2. The 40 best molecule hits of COVID-19 main protease inhibitor candidates from a dataset of 50,000 natural compounds from the ZINC Database.
| Known Drug | Ligand | Energ.
Binding (Kcal/Mol) |
Classification | RMSD
Å |
Pred.
IC50 (uM) |
Exp. IC50
(uM) |
Tanimoto
combo |
|---|---|---|---|---|---|---|---|
| OEW | OEW * | -8.86 | Peptide-like | 1.97 | 0.320 | 0.670 | - |
| ZINC1845382 | -10.2 | β-carboline Alkaloid | 1.12 | ||||
| ZINC1875405 ** | -10.1 | β-carboline Alkaloid | 1.00 | ||||
| ZINC2092396 | -9.8 | β-carboline Alkaloid | 1.20 | ||||
| ZINC1900463 | -9.8 | β-carboline Alkaloid | 1.00 | ||||
| ZINC2149492 | -9.8 | β-carboline Alkaloid | 1.12 | ||||
| ZINC2112405 | -9.7 | β-carboline Alkaloid | 1.10 | ||||
| ZINC2095426 | -9.7 | β-carboline Alkaloid | 1.00 | ||||
| ZINC2094306 | -9.6 | β-carboline Alkaloid | 1.00 | ||||
| ZINC2144677 | -9.6 | Anthracene | 1.10 | ||||
| ZINC1095868 | -9.5 | Harmala Alkaloids | 1.13 | ||||
| N3 * | -9,77 | Peptide-like | 1.94 | 0.07 | 4.67 | - | |
| N3 | ZINC2104482 | -10.1 | β-carboline Alkaloid | 1.10 | |||
| ZINC3984030 | -9.9 | Polyflavonoid | 1.20 | ||||
| ZINC1531664 | -9.8 | Polyflavonoid | 1.10 | ||||
| ZINC2152199 | -9.8 | β-carboline Alkaloid | 1.00 | ||||
| ZINC4096847 | -9.6 | Flavonoid-3-O-
glycoside |
1.20 | ||||
| ZINC3947428 | -9.6 | Flavonoid-3-O-
glycoside |
1.20 | ||||
| ZINC2092587 | -9.6 | β-carboline Alkaloid | 1.14 | ||||
| ZINC2115924 | -9.5 | β-carboline Alkaloid | 1.00 | ||||
| ZINC2110081 | -9.5 | Lupin Alkaloid | 1.00 | ||||
| ZINC1898165 | -9.5 | Benzofuran | 1.00 | ||||
| HCQ | -7.90 | 4-aminoquinoline | - | ||||
| Hydroxychloroquine
(HCQ) |
ZINC2101723 | -10.2 | β-carboline Alkaloid | 1.10 | |||
| ZINC2094526 | -9.8 | β-carboline Alkaloid | 1.14 | ||||
| ZINC2094304 | -9.6 | β-carboline Alkaloid | 1.16 | ||||
| ZINC2091604 | -9.4 | β-carboline Alkaloid | 1.00 | ||||
| ZINC2113496 | -9.4 | β-carboline Alkaloid | 1.10 | ||||
| ZINC1460216 | -9.3 | Angular
Pyranocoumarin |
1.12 | ||||
| ZINC2123008 | -9.2 | β-carboline Alkaloid | 1.10 | ||||
| ZINC682759 | -9.2 | Harmala Alkaloids | 1.00 | ||||
| ZINC2105243 | -9.2 | β-carboline Alkaloid | 1.00 | ||||
| ZINC2111696 | -9.1 | β-carboline Alkaloid | 1.20 | ||||
| REMD | -8.28 | Nucleoside | - | ||||
| Remdesivir (REMD) | ZINC2104424 | -10.6 | β-carboline Alkaloid | 1.15 | |||
| ZINC1875405 ** | -10.1 | β-carboline Alkaloid | 1.22 | ||||
| ZINC44018332 | -10.0 | Polyflavonoid | 1.20 | ||||
| ZINC2148932 | -9.9 | β-carboline Alkaloid | 1.00 | ||||
| ZINC2156531 | -9.9 | Indoles Alkaloid | 1.00 | ||||
| ZINC3197535 | -9.9 | Polyflavonoid | 1.00 | ||||
| ZINC2102620 | -9.9 | Indoles Alkaloid | 1.00 | ||||
| ZINC2123402 | -9.9 | β-carboline Alkaloid | 1.00 | ||||
| ZINC2149488 | -9.9 | β-carboline Alkaloid | 1.10 | ||||
| ZINC1531664 | -9.9 | Polyflavonoid | 1.00 |
*Re-docked crystallographic structures.
**Repeated ligand between OEW and Remdesivir pharmacophores.