Table 2.
Molecular docking analysis showing estimated binding energy, interacting residues, and molecular interactions of potential compounds in the binding site of HCV-NS5B
| Ligand name | Binding energy (kcal/mol) | VdW interacting residues | Number of H-bonds | H-bonds interacting residues | Number of direct contact (all polar, nonpolar interactions) |
|---|---|---|---|---|---|
| Naringenin | −9.7 | His428A, Val494, Leu392, Leu492, Ala395 | 3 | Thr399, Arg503 | 36 |
| Tryphanthrine | −9.7 | His428, Leu392, Leu492 | 3 | Ala396, Ala395, Arg503 | 27 |
| Dicoumarin | −9.3 | Ala395, Leu392, Val494 | 2 | His428, Leu396 | 37 |
| Swertianin | −9.3 | His428, Ala395, Leu392, Leu492 | 3 | Cys146, Arg503, Ala396 | 26 |
| Diosmetin | −9.3 | His428, Leu392, Val494 | 3 | Ala396, Val37, Leu492 | 32 |
| Apigenin | −9.3 | Leu492, Leu392, His428, Ala395 | 1 | Cys146 | 35 |
| Honokiol | −9.3 | Ala396, Ala395, His428, Val494, Leu392, Leu492 | 2 | Leu492, Arg503 | 34 |
| Luteolin | −9.3 | Val494, Leu392, Leu492 | 3 | His428, Val37, Arg503 | 35 |
| Thaliporphine | −9.1 | Ala395, His428, Leu392, Leu492, Pro495 | 3 | Cys146, Ala396, Arg503 | 30 |
| Oxymatrine | −9 | His428, Val494, Leu392, Ala396, Ala395, Pro495 | 1 | Cys146, Arg503 | 31 |
| Wedelolactone | −8.9 | Leu492, Leu392, His428 | 2 | Ala396, Cys146 | 22 |
| Desmethylwedelolactone | −8.9 | His428, Leu392, Leu492 | 3 | Ala396, Cys146 | 27 |
| Berberine | −8.9 | Ala396, His428, Leu392, Val494, Leu492 | 1 | Thr399 | 30 |
| Andrographolide | −8.9 | Ala395, His428, Leu392, Val494, Leu492 | 2 | Cys146, Ala396 | 29 |
| Ladanein | −8.9 | Ala396, Leu392, Val494, Leu492 | 2 | His428, Cys146 | 33 |
| Curcumin | −8.8 | Leu492, Ala396, Leu392, Leu492, Pro495 | 2 | His428, Cys146 | 41 |
| Genistein | −8.8 | Leu492, Ala396, Ala395, Leu392, Val494 | 2 | His428, Arg503 | 29 |
| Loganin | −8.7 | His428, Leu392 | 2 | Ala396 | 25 |
| Epicatechin | −8.6 | His428, Leu392, Ala396 | 2 | Cys146, Arg503 | 34 |
| Hypophyllanthin | −8.6 | Leu492, Leu392 | 2 | Arg503 | 32 |
| Quercetin | −8.5 | Val494, Leu492 | 1 | Ala396 | 29 |
| Silymarin/silibinin | −8.5 | Pro495, Ala396, Arg503, Ala395 | 4 | His428, Arg503 | 40 |
| Phyllanthin | −8.4 | His428, Arg503, Leu392, Pro495, Val494, Leu492, Ala396, Ala395 | 0 | n/a | 42 |
| Lucidone | −8.3 | His428, Leu392, Val494, Leu492 | 3 | Cys146, Ala395, Ala396 | 35 |
| Jatrorrhizine | −8.3 | Ala396, Leu392, Val494, Leu492 | 2 | Cys146, His428 | 21 |
| Caruilignan C | −8.1 | Ala396, His428, Leu392, Val494, Leu492 | 1 | Cys146, Arg503 | 34 |
| Verbenalin | −8.1 | His428, Pro495, Val494, Leu492 | 4 | Cys146, Arg503, Ala396 | 33 |
| Geranyl acetone | −8.1 | His428, Leu392, Leu492, Val494, Ala396, Ala395 | 0 | n/a | 36 |
| Nobiletin | −7.8 | Ala396 | 2 | Leu492 | 29 |
| Tetradecanoic acid | −7.4 | Ala396, His428, Leu392, Val494, Leu492 | 1 | Arg503 | 24 |
| Sofosbuvir | −6.2 | Ala395, Ile424, Ala396, Val494, Leu492, His428 | 2 | Arg503, Thr399 | 26 |
Abbreviations: HCV, hepatitis C virus; NS5B, nonstructural protein 5B; n/a, not available.