Table 2.
The resulting data (free energies and binding modes) from the docking studies of the best-tested ligands onSARS-CoV-2 RdRp (PDB ID: 6M71)
| Entry | Compounds | Free energy of binding (kcal/mol) | Hydrogen bands | Hydrophobic interactions | Other interactions |
|---|---|---|---|---|---|
| 7 | Famotidine | − 6.2 | ASP452, ARG553, THR556, ARG624, THR680, THR687, ASN691 | – | ASP623 |
| 8 | Chlorproguanil | − 6.0 | ARG553, THR556, ARG624 | TYR455, LYS545, ARG555, ARG624 | ASP452, ASP623 |
| 9 | CHS 828 | − 6.4 | ARG553, THR556, ARG624, SER682 | LYS621, ASP623, ARG624 | ARG624 |
| 11 | cycloguanil | − 6.0 | ARG553, THR556, ARG624 | LYS621,ARG624, TYR455 | ASP452, ASP623 |
| 16 | KR 31,378 | − 7.2 | ARG553, THR556, ARG624 | TYR455, ARG555, ARG624 | ASP452, ASP623 |
| 17 | Proguanil | − 6.1 | ARG553, THR556, ARG624 | TYR455, ARG555, ARG624 | ASP452, ASP623 |
| 20 | Rosuvastatin | − 6.3 | ARG553, ARG555, THR556, LYS621, ASP623, ARG624 | TYR455, LYS621, ARG624 | ARG553, LYS545, ARG555 |
| 21 | TP201565 | − 7.3 | ARG553, THR556, LYS621, ARG624, SER682 | ASP618, PRO620, LYS621, ASP623, LYS798 | ARG624 |
| 24 | Imatinib | − 8.3 | ARG553, LYS621, ASP623, ASN691, SER759 | TYR455, PRO620, ASP623, LYS798 | ARG553, ASP760 |
| 25 | Terbogrel | − 7.4 | GLN408, LEU544, TYR546 | TYR546, LYS545, LYS411, VAL410 | – |
| 26 | Benznidazole | − 6.1 | ARG553, THR556, ASP623 | TYR455, LYS621, ARG624 | ARG553 |
| 27 | Phenformin | − 6.2 | GLY413, TYR546 | LYS411, TYR546 | TYR546, ASP846 |
| 28 | CGP 48664A | − 6.5 | ILE548, ARG555, PHE843, ASP845, ARG858 | ILE548, ARG836, ALA840 | ASP845 |
| 29 | Berenil | − 6.4 | ILE548, ASP845, ARG858 | PHE441, ILE548, ARG836, VAL844 | ARG858 |
| 30 | CGP 40215A | − 8.0 | ASP164, ARG553, THR556, LYS621, ARG624, PHE793 | – | PRO620, LYS798 |
| 32 | CGP-35753 | − 6.6 | ASP452, TYR455, ARG553, THR556, LYS621 | TYR455, LYS621, ARG624 | ASP623 |
| 33 | CGP39937 | − 6.6 | ILE548, ASP845, ARG858 | ILE548, VAL844, ARG858 | ARG858, PHE441 |
| 34 | GBPA | − 7.5 | LYS545, ILE548 | PHE441, ILE548, VAL844 | ARG858 |
| 35 | Camostat | − 7.7 | THR556, TYR619, LYS621, ARG624, ASP760 | ASP618, LYS621, ARG624 | ARG553, LYS621, ARG624, ASP760 |
| Ref1* | ATP | − 7.5 | ASP452, THR556, TYR619, CYS622, ASP623, ASP760 | – | ARG553, ARG555, ARG624 |
| Ref2* | GTP | − 7.9 | ARG553, THR556, TYR619, LYS621, CYS622, ASP623 | – | ARG553, ARG555, ARG55, ASP623, ARG624 |
| Ref3* | Ribavirin triphosphate | − 7.2 | ASP452, ARG553, THR556, ASP623, SER682, ASN691, SER759 | – | ARG553, ARG555, ARG624 |
In addition to the best-investigated ligands, the docking results of the rest tested ligands against 6M71 are summarized in Table S1
*Reference molecules 1, 2, and 3 in docking study against SARS-CoV-2 RdRp