Methicillin-Resistant Staphylococcus aureus: Docking-Based Virtual Screening and Molecular Dynamics Simulations to Identify Potential Penicillin-Binding Protein 2a Inhibitors from Natural Flavonoids

Table 4

The relative binding-free energies (kcal/mol) obtained by prime MM-GBSA.

Compound name	MM-GBSA-dG binding energy	MM-GBSA-dG binding, coulomb	MM-GBSA-dG bind (NS)	MM-GBSA-dG bind (NS), coulomb
Kaempferol 3-rutinoside-7-sophoroside	−19.6	−57.4	−43.2	−60.4
Rutin	−27.9	−32.6	−41.6	−27.9
Amentoflavone	−28.9	−32.9	−36.0	−29.5
Quercetin	267.9	−57.9	−29.5	−35.8

MM-GBSA dG bind = complex–receptor–ligand; MM-GBSA dG bind (NS) = complex−receptor (from optimized complex)−ligand (from optimized complex) = MM-GBSA dG bind−receptor strain−ligand strain. NS in the table is the binding energy without considering for the receptor and ligand conformational changes needed for the formation of complex.