Table 3.
Molecular docking analysis for natural compounds
| RdRp of DENV-1
|
RdRp of DENV-2
|
RdRp of DENV-4
|
|||
|---|---|---|---|---|---|
| Ligand name | ΔG (kcal/mol) mean ± SD | Ligand name | ΔG (kcal/mol) mean ± SD | Ligand name | ΔG (kcal/mol) mean ± SD |
| SN00091933 | −10.8±0.7 | SN00151425 | −11.1±0.8 | SN00016053 | −11.2±1.0 |
| SN00074091 | −10.7±0.7 | SN00010280 | −10.9±0.8 | SN00057073 | −11.1±1.1 |
| SN00091667 | −10.7±0.8 | SN00023794 | −10.9±0.7 | SN00063622 | −11.1±1.2 |
| SN00306679 | −10.6±1.0 | SN00372243 | −10.9±0.9 | SN00058424 | −11.1±1.1 |
| SN00151425 | −10.6±0.9 | SN00115885 | −10.8±1.1 | SN00058828 | −11.1±1.1 |
| SN00366028 | −10.5±1.0 | SN00018927 | −10.8±0.5 | SN00057669 | −11.1±1.1 |
| SN00372243 | −10.5±1.0 | SN00016053 | −10.8±0.5 | SN00230471 | −11.1±1.3 |
| SN00074088 | −10.5±0.9 | SN00057073 | −10.7±1.1 | SN00057220 | −11.0±1.2 |
| SN00010280 | −10.5±0.6 | SN00081933 | −10.6±1.1 | SN00057061 | −11.0±1.2 |
| SN00127203 | −10.5±1.1 | SN00127203 | −10.6±1.3 | SN00303561 | −11.0±1.2 |
| SN00016053 | −10.5±0.6 | SN00058424 | −10.6±1.1 | SN00058587 | −10.9±1.1 |
| SN00230471 | −10.5±0.9 | SN00063622 | −10.6±1.0 | SN00366028 | −10.9±0.8 |
| SN00245001 | −10.5±0.7 | SN00379696 | −10.6±0.6 | SN00127203 | −10.8±0.8 |
| SN00396968 | −10.6±0.8 | SN00303525 | −10.8±1.0 | ||
| SN00014343 | −10.6±0.9 | SN00016042 | −10.7±1.4 | ||
| SN00057669 | −10.5±1.0 | SN00010280 | −10.7±0.6 | ||
| SN00282274 | −10.5±0.9 | SN00111882 | −10.6±1.0 | ||
| SN00381633 | −10.5±1.2 | SN00282274 | −10.6±1.0 | ||
| SN00004095 | −10.5±0.6 | SN00317979 | −10.6±1.0 | ||
| SN00245001 | −10.5±0.4 | SN00018896 | −10.6±0.9 | ||
| SN00058828 | −10.5±1.0 | SN00026414 | −10.6±1.2 | ||
| SN00397486 | −10.5±0.9 | SN00151956 | −10.6±0.6 | ||
| SN00282224 | −10.5±0.9 | SN00282224 | −10.6±1.2 | ||
| SN00009726 | −10.5±0.9 | SN00004146 | −10.6±0.9 | ||
| SN00151425 | −10.6±1.1 | ||||
| SN00379696 | −10.6±1.0 | ||||
| SN00012056 | −10.5±0.7 | ||||
| SN00381633 | −10.5±0.7 | ||||
| SN00115885 | −10.5±0.8 | ||||
| SN00148919 | −10.5±0.6 | ||||
| SN00276030 | −10.5±0.8 | ||||
| SN00249137 | −10.5±0.7 | ||||
| SN00091933 | −10.5±0.9 | ||||
Notes: The maps of the interacting residues of the protein with the best ligands and ΔG values among the candidate compounds are available at http://docking.umh.es/. The name of each ligand was obtained from the SuperNatural database (http://bioinf-applied.charite.de/supernatural_new/index.php?site=home). The table shows estimated binding free energy variation31 (mean ± SD) of potential inhibitors at the binding site of NS5 RdRp located in the RNA template tunnel.
Abbreviations: NS5, nonstructural protein 5; RdRp, RNA-dependent RNA polymerase; SD, standard deviation.