Structures of <i>Staphylococcus aureus</i> Cell-Wall Complexes with Vancomycin, Eremomycin, and Chloroeremomycin Derivatives by ¹³C{¹⁹F} and ¹⁵N{¹⁹F} Rotational-Echo Double Resonance

Solid-state NMR has been used to examine isolated cell walls and intact whole cells of Staphylococcus aureus complexed to five different vancomycin, eremomycin, and chloroeremomycin derivatives. The cell walls and whole cells were specifically labeled with d-[1-(13)C]alanine, or a combination of [1-(13)C]glycine and [epsilon-(15)N]lysine. Each of the bound glycopeptides had a (19)F-labeled substituent at either its C-terminus or its disaccharide position. The (13)C{(19)F} rotational-echo double-resonance (REDOR) dephasing for the cell-wall (13)C-labeled bridging pentaglycyl segment connecting a glycopeptide-complexed peptidoglycan stem with its neighboring stem indicates that the fluorine labels for all bound glycopeptides are positioned at one or the other end of the bridge. An exception is N'-(p-trifluoromethoxybenzyl)chloroeremomycin, whose hydrophobic substituent differs in length by one phenyl group compared to that of oritavancin, N'-4-[(4-chlorophenyl)benzyl)]chloroeremomycin. For this drug, the fluorine label is near the middle of the pentaglycyl segment. (15)N{(19)F} REDOR dephasing shows the proximity of the fluorine to the bridge-link site of the pentaglycyl bridge for C-terminus-substituted moieties and the cross-link site for disaccharide-substituted moieties. Full-echo REDOR spectra of cell-wall complexes from cells labeled by d-[1-(13)C]alanine (in the presence of an alanine racemase inhibitor) reveal three different carbonyl carbon chemical-shift environments, arising from the d-Ala-d-Ala binding site and the d-Ala-Gly-1 cross-link site. The REDOR results indicate a single fluorine dephasing center in each peptidoglycan complex. Molecular models of the mature cell-wall complexes that are consistent with internuclear distances obtained from (13)C{(19)F} and (15)N{(19)F} REDOR dephasing allow a correlation of structure and antimicrobial activity of the glycopeptides.