Table 2.
Molecular docking analysis of studied compounds against SARS-Cov-2 RdRp (6M71).
| Ligand No | Ligands | Free Energy of Binding (kcal/mol) | H-bond | Salt Bridge | Hydrophobic |
|---|---|---|---|---|---|
| 1 | Nicotinamide | -4.4 | PHE442, ALA547, SER549, ARG553 | - | GLN444, ARG555 |
| 2 | NR | -5.9 | ASP845, ARG858 | - | PHE441, VAL844 |
| 3 | NMN | -6.7 | ARG553, ARG555, THR556, THR680, SER682, THR687, ASN691 | ARG624 | ASP623 |
| 4 | ATP | -7.5 | ASP452, THR556, TYR619, CYS622, ASP623, ASP760 | ARG553, ARG555, ARG624 | - |
| 5 | GTP | -7.9 | ARG553, THR556, TYR619, LYS621, CYS622, ASP623 | ARG553, ARG555, ARG55, ASP623, ARG624 | - |
| 6 | Favipiravir | -5.2 | ARG553, THR556, ARG624 | - | - |
| 7 | Favipiravir riboside | -7.1 | ARG553, THR556, TYR619, LYS621, CYS622, ASP623, ARG624 | - | - |
| 8 | Favipiravir-RMP | -7.2 | ARG553, THR556, TYR619, LYS621, CYS622, ASP623, ARG624 | LYS621 | - |
| 9 | Favipiravir-RTP | -7.2 | ARG553, THR556, LYS621, CYS622, ASP623 | ARG553, ARG555, ARG624 | - |
| 10 | Ribavirin | -6.1 | ARG553, THR556, LYS621, CYS622, ASP623, ARG624 | ARG553, ARG624 | - |
| 11 | Ribavirin monophosphate | -6.4 | ARG553, THR556, LYS621, CYS622, ASP623, ARG624 | ARG553, ARG624 | - |
| 12 | Ribavirin triphosphate | -7.2 | ASP452, ARG553, THR556, ASP623, SER682, ASN691, SER759 | ARG553, ARG555, ARG624 | - |
| 13 | DMB220 | -6.6 | ASP452, ARG553, THR556, LYS621, ARG624 | - | - |