A theoretical study of binding mode of vancomycin

The binding mode and the complex ability of vancomycin against the analogue of peptidogylcons, N-Ac-D-Ala-D-Ala, and N-Ac-D-Ala and acetate were studied by molecular dynamic calculations and MM-PBSA. The calculations produce similar binding mode and recognition cites for the complexes of vancomycin with ligands compared to the experimental results in literatures. The binding free energies (?Gbind) obtained from MM-PBSA calculations are -24.68 kcal mol-1, -17.10 kcal mol-1 and -17.70 kcal mol-1 for N-Ac-D-Ala-D-Ala, and N-Ac-D-Ala and acatate, respectively. These are quite comparable to experimental ones if one ignores the overestimation of binding energies of charged species by MM-PBSA since the method utilizes the continuum solvation model and ignores solute-solvent interactions . So the results prove that the method is reliable for predictions of binding energies of similar systems.