Vancomycin Derivative with Damaged d-Ala-d-Ala Binding Cleft Binds to Cross-linked Peptidoglycan in the Cell Wall of Staphylococcus aureus

Abstract

Des-N-methylleucyl-4-(4-fluorophenyl)benzyl-vancomycin (DFPBV) retains activity against vancomycin-resistant pathogens despite its damaged d-Ala-d-Ala binding cleft. Using solid-state nuclear magnetic resonance (NMR), a DFPBV binding site in the cell walls of whole cells of Staphylococcus aureus has been identified. The cell walls were labeled with d-[1-(13)C]alanine, [1-(13)C]glycine, and l-[epsilon-(15)N]lysine. Internuclear distances from (19)F of the DFPBV to the (13)C and (15)N labels of the cell-wall peptidoglycan were determined by rotational-echo double-resonance (REDOR) NMR. The (13)C{(19)F} and (15)N{(19)F} REDOR spectra show that, in situ, DFPBV binds to the peptidoglycan as a monomer with its vancosamine hydrophobic side chain positioned near a pentaglycyl bridge. This result suggests that the antimicrobial activity of other vancosamine-modified glycopeptides depends upon both d-Ala-d-Ala stem-terminus recognition (primary binding site) and stem-bridge recognition (secondary binding site).

In Vivo Studies Suggest that Induction of VanS-Dependent Vancomycin Resistance Requires Binding of the Drug to d -Ala- d -Ala Termini in the Peptidoglycan Cell Wall

“…The two compounds share virtually identical stereochemical structures and would be predicted to present themselves similarly for perception by the sensory domain of VanS. The absence of a leucine residue in the derivative, however, makes complex formation with D-Ala-D-Ala PG precursors impossible (37,39), and according to the model, desleucyl vancomycin is as a consequence not sensed at all by VanS. We cannot, however, exclude the formal possibility that VanS senses vancomycin via interaction with its D-Ala-D-Ala binding pocket, but this seems unlikely given the inability of teicoplanin, which possesses an intact binding pocket, to activate the sensor.…”

Uniformity of Glycyl Bridge Lengths in the Mature Cell Walls of Fem Mutants of Methicillin-Resistant Staphylococcus aureus

“…3 and 4) suggests that the PG units with predominantly triglycyl bridges are not incorporated with monoglycyl-PG units to form a mature cell wall. This may be due to the inability to form mixed cell wall architectures in template-based PG biosynthesis (3,4). The heterogeneous material appears to be localized close to the membrane surface (Fig.…”

“…is an essential component of the bacterial cell wall whose biosynthesis is targeted by several classes of antibiotics, including ␤-lactams (1, 2) and glycopeptides (3)(4)(5). In Staphylococcus aureus (6), a thick cell wall consisting of 20 or more layers of glycan enables the bacteria to withstand fluctuating osmotic pressure (2).…”

Inhibition of Staphylococcus aureus Cell Wall Biosynthesis by Desleucyl-Oritavancin: a Quantitative Peptidoglycan Composition Analysis by Mass Spectrometry

“…1c), which is devoid of any antimicrobial activities, des-Nmethylleucyl-oritavancin (referred to as des-Ori here) retains potent antimicrobial activities against both vancomycin-susceptible and -resistant pathogens (4). Thus, the secondary binding site in des-Ori is responsible for enhanced activities against vancomycin-resistant pathogens by compensating for the damaged D-Ala-D-Ala binding site, enabling it to bind to PG in intact whole cells of S. aureus (4,7). In this study, we investigated the mode of action of the secondary binding site by analyzing changes to the PG composition of S. aureus grown in the presence of des-Ori at a sub-MIC using liquid chromatography-mass spectrometry (LC-MS).…”