Table 1.
The result of docking analysis between ligands isolated from plant-originated compounds with the binding sites of an E6 Oncoprotein to E6AP, P53, and Myc
| Row | Compound name |
Docking
Score i (kcal/mol) |
Inhibition constant
(μ M) |
Number of hydrogen bonds | Residues involved in hydrogen bonding | |
|---|---|---|---|---|---|---|
| 1 | Apigenin | E6AP | -5.8 | 57.64 | 2 | Leu67, Cys51 |
| P53 | -6.37 | 21.37 | 2 | Leu67, Cys51 | ||
| Myc | -5.57 | 98.25 | 2 | Arg8, Arg55 | ||
| 2 | Apigetrin | E6AP | -6.37 | 21.27 | 4 | 2i Cys51, Arg55, Pro5 |
| P53 | -7.61 | 2.63 | 6 | Pro5, 3 Cys51, 2 Arg55 | ||
| Myc | -6.13 | 32.2 | 3 | 2 Phe2, Asn58 | ||
| 3 | Aplysin | E6AP | -6.01 | 39.59 | -------- | --------------------- |
| P53 | -6.26 | 32.23 | 1 | Trp132 | ||
| Myc | -5.53 | 89.11 | 1 | Gln3 | ||
| 4 | Curcumin | E6AP | -5.78 | 58.09 | 2 | 2 Cys51 |
| P53 | -6.21 | 28.24 | 2 | 2 Cys51 | ||
| Myc | -6.49 | 17.51 | 3 | Tyr54, Asp56, Gly57 | ||
| 5 | Epicatechin | E6AP | -5.4 | 109.54 | 5 | 2 Pro5, Ile52, Arg55, Tyr54 |
| P53 | -5.95 | 43.64 | 5 | 2 Pro5, Tyr54, Arg55, Ile52 | ||
| Myc | -5.69 | 67.42 | 4 | Tyr54, Arg55, Arg8, Pro5 | ||
| 6 | Eurycomanone | E6AP | -6.13 | 32.25 | 3 | 2 Cys51, Tyr32 |
| P53 | -6.81 | 10.25 | 3 | 2 Cys51, Tyr32 | ||
| Myc | -5.45 | 101,28 | 3 | Pro5, Arg10, Arg8 | ||
| 7 | Genistein | E6AP | -6.68 | 12.74 | 3 | Ser71, Cys51, Tyr32 |
| P53 | -6.66 | 13.03 | 2 | Ser71, Tyr32 | ||
| Myc | -6.26 | 25.74 | 5 | 3 Arg8, Arg55, Tyr54 | ||
| 8 | Gingerol | E6AP | -4.58 | 436.16 | 2 | 2Cys51 |
| P53 | -5.03 | 205.08 | 4 | 2Arg8, Arg55, Tyr54 | ||
| Myc | -4.46 | 534.89 | 3 | Arg8, Arg10, Arg55 | ||
| 9 | Ginkgetin | E6AP | -8.45 | 0.642 | 5 | 2 Arg55, Cys51, Val 53, Tyr 60 |
| P53 | -8.46 | 0.632 | 5 | 2 Arg55, Cys51, Val 53, Tyr 60 | ||
| Myc | -7.22 | 5.11 | 4 | Pro5, 3Arg8 | ||
| 10 | Hypericin | E6AP | -7.15 | 5.7 | 5 | 2 Gln6, Tyr54, Ile52, Pro5 |
| P53 | -7.24 | 4.97 | 5 | Ile52, Tyr54, 2 Gln6, Pro5 | ||
| Myc | -6.67 | 12.99 | 3 | Ile52, Pro5, Arg55 | ||
| 11 | Isonoruon | E6AP | -5.78 | 58.08 | 1 | Cys51 |
| P53 | -5.81 | 55.3 | 1 | Cys51 | ||
| Myc | -5.65 | 72.48 | 1 | Arg8 | ||
| 12 | Klaineanone | E6AP | -6.41 | 20.12 | 3 | 3 Cys51 |
| P53 | -6.8 | 10.44 | 3 | Ile101, Lys115, Ser97 | ||
| Myc | -6.29 | 24.52 | 3 | Ile52, Arg10, Tyr54 | ||
| 13 | L-Ectone | E6AP | -5.12 | 177.32 | 2 | 2 Cys51 |
| P53 | -5.28 | 134.39 | 1 | Leu110 | ||
| Myc | -5.05 | 198.99 | 1 | Arg8 | ||
| 14 | Oleocanthal | E6AP | -3.79 | 1680 | 2 | Leu67, Cys51 |
| P53 | -5.6 | 78.55 | 5 | Tyr54, 2 Arg8, Gln6, Arg55 | ||
| Myc | -5.43 | 105.11 | 4 | Gln6, Arg8, Arg10, Tyr54 | ||
| 15 | Oleuropein | E6AP | -4.36 | 640.94 | 4 | 2 His78, Ser74, Arg131 |
| P53 | -5.02 | 208.38 | 3 | Tyr70, Arg13, Cys51 | ||
| Myc | -5.05 | 198.09 | 8 | 2 Gln6, 2 Arg8, 2 Arg55, Pro5, Arg10 | ||
| 16 | Piceatannol | E6AP | -5.3 | 129.35 | 3 | Ser71, 2 Cys51 |
| P53 | -6.1 | 33.96 | 5 | Lys115, Arg47, 2 Leu99, Ile101 | ||
| Myc | -5.64 | 73.41 | 5 | 2 Glu18, 2 Asp4, Gln7 | ||
| 17 | Pterostilbene | E6AP | -5.74 | 61.921 | 1 | Cys51 |
| P53 | -5.64 | 73.63 | 1 | Cys51 | ||
| Myc | -5.08 | 188.6 | 2 | 2 Asp4 | ||
| 18 | Quercetin | E6AP | -4.33 | 674.16 | 5 | Ser71, Tyr32, Ile104, Ser74, Arg129 |
| P53 | -6.39 | 20.75 | 7 | 2 Leu99, Arg47, Lys108, 2 Asp49, Ile101 | ||
| Myc | -5.29 | 132.96 | 6 | 2 Asn58, 2 Glu18, Gln3, Gly57 | ||
| 19 | Silibinin | E6AP | -6.89 | 8.88 | 4 | 2 Cys51, Arg8, Pro5 |
| P53 | -7 | 7.38 | 5 | Gln14, 2 Arg8, Arg10, Gln6 | ||
| Myc | -6.01 | 39.06 | 4 | 2 Arg55, Arg8, Pro5 | ||
| 20 | Tyrosol | E6AP | -4.33 | 672.1 | 2 | Tyr32, Cys51 |
| P53 | -4.42 | 573.57 | 3 | 2 Asp4, Glu18 | ||
| Myc | -4.63 | 402.47 | 2 | 2 Asp4 | ||
| + | Paclitaxel (Positive control) |
E6AP | -5.99 | 40.87 | 2 | Cys51, Ser74 |
| P53 | -7.59 | 2.73 | 4 | Tyr32, Ile52, Arg8, Arg55 | ||
| Myc | -5.4 | 110.55 | 4 | 2 Arg10, Arg55, Arg8 | ||
(a) Indicates interactions between the binding sites of E6 to E6AP, P53, and Myc with natural inhibitors. (b)The number before the amino acids indicates the number of hydrogen bonds that amino acids of E6 establish with the ligand.