Table 1.
Binding affinity of the top-five phenolics against the active site of PBP2a and their ADMET properties.
| Ligands Zinc Code | Popular Name | B A (kcal/mol) | MW < 500 (g/mol) | HB-A ≤ 10 | HB-D ≤ 5 | Log Po/w ≤ 5 |
RT-B ≤ 9 | LV < 2 | WS | GI -A |
BS | pgp | Inhibitor of CYP 450s | H | C | IM | M | CY | TC | SA | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CYP 1A2 |
CYP 2C19 |
CYP 2C9 |
CYP 2D6 |
CYP 3A4 |
||||||||||||||||||||
| Amoxicillin | Amoxicillin | −6.2 | 365.40 | 6 | 4 | −0.39 | 5 | N | VS | L | 0.55 | N | N | N | N | N | N | I | I | I | I | I | 6 | 4.17 |
| ZINC34953149 | Silicristin | −7.5 | 482.44 | 10 | 6 | 1.49 | 4 | N | S | L | 0.55 | N | N | N | N | N | Y | I | I | A | I | I | 4 | 4.88 |
| ZINC71621503 | Propan-2-one | −7.1 | 458.46 | 7 | 6 | 3.3 | 6 | N | MS | L | 0.55 | N | N | N | Y | N | Y | I | I | I | I | I | 4 | 3.67 |
| ZINC38337968 | Epigallocatechin 4-benzylthioether | −7.1 | 428.46 | 7 | 6 | 2.23 | 4 | N | MS | L | 0.55 | N | N | N | N | N | Y | I | I | I | I | I | 5 | 4.57 |
| ZINC95486076 | Chroman-4-one | −7.0 | 356.37 | 6 | 3 | 3.09 | 3 | N | MS | H | 0.55 | N | Y | N | Y | N | Y | I | I | A | I | I | 4 | 3.83 |
| ZINC03978503 | Epicatechin gallate | −6.8 | 442.37 | 10 | 7 | 1.3 | 4 | N | S | L | 0.55 | N | N | N | N | N | N | I | I | I | I | I | 4 | 4.16 |
Keywords: BA: Binding affinity; MW: Molecular weight; HB-A: Hydrogen bond acceptor; HB-D: Hydrogen bond donor; Log Po/w: Partition coefficient; RT-B: rotatable bond; WS: Water solubility; GI- A: Gastrointestinal absorption; Pgp: Permeability glycoprotein substrate; CYP: Cytochrome; VS: very soluble; MS: Moderately soluble; S: Soluble; N: No; Y: Yes; L: low; I: Inactive; A: Active; LV: Lipinski violations; BS: Bioavailability score; H: Hepatotoxicity; C: Carcinogenicity; IM: Immunotoxicity; M: Mutagenicity; CY: Cytotoxicity; LD: Lethal dose; TC: Toxicity class; SA: Synthetic accessibility; and BA: binding affinity.