Table 1.
Table showing binding energy values and interactions of the top two ligands (protease inhibitors) with the key residues of 3CLpro and PLpro of the SARS-CoV-2 evaluated by PyRx docking.
| Target protein | Inhibitors | Binding energy (kcal/mol) | Key residues interaction | Chain | H-bonds | Bond length (Å) |
|---|---|---|---|---|---|---|
| 3CLpro | Nafamostat | −9.0 | Ser1 | – | N-N4 | 3.04 |
| Thr26 | – | O-N2 | 2.93 | |||
| N-N2 | 3.14 | |||||
| Glu166 | – | OE2-N3 | 2.93 | |||
| VR23 | −9.1 | Ser1 | – | N-O3 | 2.65 | |
| Ser144 | – | OG-O5 | 3.24 | |||
| Glu166 | – | N-O1 | 2.90 | |||
| PLpro | Nafamostat | −9.2 | Trp106 | C | N2-N | 3.21 |
| Tyr273 | B | N5-OH | 2.91 | |||
| Asp286 | C | N1-O | 3.13 | |||
| Ala288 | C | N2-N | 3.10 | |||
| Asp302 | B | N4-OD1 | 3.26 | |||
| VR23 | −9.1 | Trp106 | C | O3-N | 2.80 | |
| Asn267 | A | O5-ND2 | 3.13 | |||
| Tyr273 | A | N5-OH | 2.97 | |||
| Ala288 | C | O3-N | 2.93 |