Table 2.
Interaction modes between top-ranked SauPBP2a inhibitors and active site of the enzyme.
| (A) Molecular dockings performed using the AutoDock tool, and subsequently, the interactions between ligands and residues studied before MD simulations. | ||||
|---|---|---|---|---|
| Ligand name | Hydrogen bond (distance Å, subtype) | Hydrophobic interaction (distance Å, subtype) | Electrostatic (distance Å, subtype) | Miscellaneous (distance Å, subtype) |
| Kaempferol 3-rutinoside-7-sophoroside | Thr444 (3.54 classical, 3.95 classical); Glu602 (3.18 classical); Ser643 (4.66 classical); Val448 (3.12 classical); Lys430 (3.57 classical) | Thr600 (5.83 pi-alkyl) | Glu602 (6.55 pi-anion) | NA |
| Rutin | Thr600 (3.19 classical); Tyr446 (4.62 classical); Lys430 (4.59 classical) | Tyr446 (4.41 pi-pi stacked) | NA | NA |
| Amentoflavone | Thr600 (2.99 classical); Asn464 (4.91 classical); Thr444 (3.03 classical) | Tyr446 (4.46 pi-pi stacked); Val448 (5.97 pi-alkyl); Met641 (7.53 pi-alkyl); Lys430 (4.18 pi-alkyl) | Lys430 (4.18 pi-cation); Glu602 (6.26 pi-anion) | Tyr446 (5.28 lone pairs); Met641 (7.47 sulfur) |
| Quercetin | Lys430 (3.84 classical) | Tyr446 (4.02 pi-alkyl, 4.06 alkyl); Met641 (5.32 alkyl, 6.44 alkyl); Val443 (4.65 alkyl); Tyr519 (5.66 pi-alkyl) | NA | NA |
|
| ||||
| (B) Molecular dockings executed using the AutoDock tool, and subsequently, the interactions between ligands and residues studied after 10 ns MD simulations. | ||||
| Ligand name | Hydrogen bond (distance Å, subtype) | Hydrophobic interaction (distance Å, subtype) | Electrostatic (distance Å, subtype) | Miscellaneous (distance Å, subtype) |
|
| ||||
| Kaempferol 3-rutinoside-7-sophoroside | Val443 (3.70 nonclassical); Val448 (3.86 classical); Glu447 (4.84 classical, 3.87 nonclassical); Ser643 (4.87 classical); Ser403 (4.06 classical); Gln521 (4.06 classical); Thr444 (4.02 classical, 3.03 classical, 3.78 nonclassical); Asn464 (4.65 classical); Gly640 (3.90 nonclassical) | Tyr446 (4.62 pi-pi T-shape, 5.07 pi-pi T-shape, 4.62 pi-alkyl) | NA | NA |
| Rutin | Ser643 (4.11 classical); Thr444 (3.75) | Tyr444 (4.66 pi-pi T-shape); Arg445 (8.57 amid-pi stacked, 9.08 amid-pi stacked) | NA | NA |
|
| ||||
| (C) Molecular dockings performed using the Schrödinger software, and subsequently, the interactions between ligands and residues studied. | ||||
| Ligand name | Hydrogen bond (distance Å, subtype) | Hydrophobic interaction (distance Å, subtype) | Electrostatic (distance Å, subtype) | Miscellaneous (distance Å, subtype) |
|
| ||||
| Kaempferol 3-rutinoside-7-sophoroside | Glu262 (3.25 classical, 4.57 nonclassical); Asn260 (4.02 classical); Met375 (4.37 classical, 4.53 classical); Glu263 (4.44 classical, 4.94 classical); Lys285 (4.97 classical); Lys280 (4.13 nonclassical) | NA | NA | NA |
| Rutin | Asn260 (4.73 classical); Glu263 (4.71 classical, 4.59 classical); Pro258 (3.52 classical); Lys280 (4.59 classical); Lys285 (4.94 classical, 4.72 nonclassical); Gln266 (4.90 classical) | Pro258 (4.78 alkyl, 4.24 alkyl); Tyr380 (5.31 pi-alkyl) | NA | NA |
SauPBP2a, Staphylococcus aureus penicillin-binding protein 2a.