The molecular interactions of the glycopeptide antibiotic vancomycin (Van) with bacterial cell wall analogues N,N'-diacetyl-L-Lys-D-Ala-D-Ala (Ac(2) KdAdA) and N,N'-diacetyl-L-Lys-D-Ala-D-Lac (Ac(2) KdAdL) were investigated in neat water, phosphate buffer and HEPES buffer by using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. The FCS determined dissociation constants (k(d)) show that the intrinsic binding affinity between Van and the drug-sensitive peptide ligand Ac(2)KdAdA remains invariant when the solvent is changed from neat water to either PBS or HEPES buffer; this demonstrates that there are no obvious solvent effects on the association between Van and Ac(2)KdAdA due to the strong intermolecular interaction between the two moieties. When compared to Ac(2)KdAdA, a significantly larger k(d) value was observed for the binding between the drug-resistant peptide ligand Ac(2)KdAdL and Van. Furthermore, the k(d) increased by about 8- to 11-times when the solvent was changed from neat water to 10 mM phosphate/HEPES buffer. The stability of the Ac(2)KdAdL-Van complex was dependent on the concentration of the buffer and k(d) increases as the concentration of either phosphate ions or HEPES increased until an equilibrium was attained. Both FCS and MD simulation studies clearly showed that the components constituting the buffer solution (e.g., phosphate ions and HEPES) are involved in molecular interactions with the binding pocket of Van and they profoundly affect the intrinsic stability of the complex formed between the low-affinity Ac(2)KdAdL and Van. These results could help us to better understand the detailed structure and activity of glycopeptide antibiotic derivatives toward bacterial cell wall peptide analogues, and can further facilitate the development of new drug candidates against drug-resistant bacterial strains.
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