Table 1.
The binding affinities and noncovalent (hydrogen bonds and hydrophobic) interactions of the ligands with top-docking scores against each protein.
| Target protein | Ligand | Binding affinity (kcal/mol) | Noncovalent interactions | |
|---|---|---|---|---|
| Hydrogen bonds | Hydrophobic | |||
| Spike protein | Dithymoquinone | −7.5 | — | PHE342, LEU368 |
| Kaempferol | −7.6 | SER349, LEU441, ASP442, TYR451, ARG509 | ARG346 | |
| Nigelladine A | −7.8 | LEU368 | PHE342, PHE374, PHE375, TRP436 | |
| Nigelladine B | −7.3 | LEU368 | PHE342, LEU371, PHE374, PHE375, TRP436 | |
| Nigellidine | −7.5 | — | PHE342, LEU368, LEU371, ALA372, PHE374, PHE375, TRP436 | |
| Nigellidine sulphate | −7.4 | LEU368 | PHE342, PHE374, PHE375, TRP436 | |
|
| ||||
| Mpro | Dithymoquinone | −7.2 | THR292 | PHE294 |
| Kaempferol | −7.2 | HIS41, PHE140, ASN142 | LEU141 | |
| Nigelladine A | −7.8 | — | PRO293, PHE294 | |
| Nigelladine B | −7.2 | — | PHE8, PHE294 | |
| Nigellidine | −7.6 | THR25, HIS164 | HIS41, CYS145 | |
| Nigellidine sulphate | −7.8 | HIS41, ASN142, GLY143 | CYS44, MET49, CYS145 | |