Methicillin-Resistant Staphylococcus aureus: Docking-Based Virtual Screening and Molecular Dynamics Simulations to Identify Potential Penicillin-Binding Protein 2a Inhibitors from Natural Flavonoids
Table 1
Details of energies and inhibition constant values between top-ranked flavonoids, control compounds, and SauPBP2a achieved from the AutoDock tool.
(A) Docking results with the active site of the enzyme
Ligand name
Final intermolecular energy (kcal/mol)
Final total internal energy (kcal/mol)
Torsional free energy (kcal/mol)
Unbound system’s energy (kcal/mol)
Estimated free binding energy (kcal/mol)
Ki
Kaempferol 3-rutinoside-7-sophoroside
−12.8
−3.4
2.7
−1.4
−12.1
1.4 nM
Rutin
−8.0
−10.2
4.8
−2.2
−11.1
6.8 nM
Amentoflavone
−9.7
−4.4
2.7
−1.2
−10.2
31.6 nM
Quercetin
−9.9
−6.6
4.5
−1.9
−10.1
36.6 nM
PNM (ctrl ‒)
−7.9
−1.1
1.8
−0.9
−6.4
22.1 uM
Methicillin (ctrl ‒)
−6.8
−1.8
1.8
−1.3
−5.5
91.2 uM
Oxadiazole (ctrl +)
−9.2
−0.9
1.5
−0.7
−7.9
1.7 uM
Ceftobiprole (ctrl +)
−10.6
−2.1
2.7
−1.2
−8.8
362.2 nM
(B) Docking results with the allosteric site of the enzyme
Ligand name
Final intermolecular energy (kcal/mol)
Final total internal energy (kcal/mol)
Torsional free energy (kcal/mol)
Unbound system’s energy (kcal/mol)
Estimated free binding energy (kcal/mol)
Ki
Kaempferol 3-rutinoside-7-sophoroside
−7.3
−17.8
7.5
−3.3
−14.4
30.30 pM
Rutin
−7.4
−9.8
5.1
−2.4
−9.7
79.98 nM
SauPBP2a, Staphylococcus aureus penicillin-binding protein 2a; PNM, penicillin G; Ki, inhibition constant; nM, nanomolar; pM, picomolar.
