Mapping of a lipoglycopeptide antibiotic binding site on Staphylococcus aureus penicillin-binding protein 2 using a vancomycin photoaffinity analogue

Modification of vancomycin with lipophilic substituents enhances its antibacterial activity against vancomycin-resistant strains. To further improve the activity of the resulting lipoglycopeptides, it is necessary to understand these compounds' molecular modes of action. By developing a photoaffinity probe, we were able to elucidate in this study the binding targets of a novel lipoglycopeptide (Van-M-02) at the cell membrane of Staphylococcus aureus. The probe could be successfully used to identify penicillin-binding protein 2 (PBP2), an indispensable enzyme in bacterial cell-wall synthesis, as a target. LC-MS/MS analysis of affinity-labeled PBP2 enabled us to map the Van-M-02 binding site in the transpeptidase domain. These findings will allow for the rational design of better antibiotics against vancomycin-resistant bacteria.