Vancomycin Forms Ligand-Mediated Supramolecular Complexes

Abstract

SummaryThe emergence of resistance to vancomycin and related glycopeptide antibiotics is spurring efforts to develop new antimicrobial therapeutics. High resolution structural information about antibioticligand recognition should prove valuable in the rational design of improved drugs. We have determined the X-ray crystal structure of the complex of vancomycin with N-acetyl-D-Ala-D-Ala, a mimic of the natural muramyl peptide target, and refined this structure at a resolution of 1.3 Å to R and R free values of 0.172 and 0.195, respectively. The crystal asymmetric unit contains three backback vancomycin dimers; two of these dimers participate in ligand-mediated face-face interactions that produce an infinite chain of molecules running throughout the crystal. The third dimer packs against the side of a face-face interface in a tight "side-side" interaction that involves both polar contacts and burial of hydrophobic surface. The trimer of dimers found in the asymmetric unit is essentially identical to complexes seen in three other crystal structures of glycopeptide antibiotics complexed with peptide ligands. These four structures are derived from crystals belonging to different space groups, suggesting that the trimer of dimers may not be simply a crystal packing artifact, and prompting us to ask if ligand-mediated oligomerization could be observed in solution. Using size exclusion chromatography, dynamic light scattering, and small-angle X-ray scattering, we demonstrate that vancomycin forms discrete supramolecular complexes in the presence of tripeptide ligands. Size estimates for these complexes are consistent with assemblies containing 4-6 vancomycin monomers.

Functionalized arrays of Raman-enhancing nanoparticles for capture and culture-free analysis of bacteria in human blood

“…1e,f). Such observation is consistent with the results obtained from the size analyses of concentrated Van in aqueous solution with sizeexclusion chromatography, dynamic light scattering and smallangle X-ray scattering 35 . The formation of the nanometer-sized Van aggregates is a result of the fact that Van easily forms noncovalent, asymmetric dimmers-mostly through multiple hydrogen bondwhere the dimerization surface is on the opposite side (back) of the molecule from the ligand binding pocket 36 .…”

“…The formation of the nanometer-sized Van aggregates is a result of the fact that Van easily forms noncovalent, asymmetric dimmers-mostly through multiple hydrogen bondwhere the dimerization surface is on the opposite side (back) of the molecule from the ligand binding pocket 36 . Loll and co-workers 35 further asserted that collective back-back and side-side interactions between Van monomers facilitate the self-association formation of large supramolecular complex (more than six Van monomers). Their calculation also showed that the multiple noncovalent interactions engender variation in molecular conformation.…”

Vancomycin: ligand recognition, dimerization and super‐complex formation

“…Lipid II is insoluble in water and thus most investigations of the recognition of lipid II by vancomycin have involved either chemically modified or truncated fragments of lipid II [10]. NMR and X-ray crystallographic studies [11][12][13][14][15][16][17] showed that the ligand bound to the concave (front face) of vancomycin, the C-terminal carboxylic acid group of D-Ala-D-Ala interacting with the backbone amide groups of resides NLEU1, HDPY2 and ASN3. In addition, the amide group of Ala1 forms a stable hydrogen bond with the carbonyl oxygen of DPYG4.…”

“…In the presence of ligand, the extent of the association increases by one to two orders of magnitude [23]. In addition to back-to-back dimers, crystallographic studies suggest that vancomycin also forms stable face-to-face and side-to-side interactions [12,17]. In the face-to-face dimer, the N-and C-termini of vancomycin are in close proximity, with potentially two ligand molecules sandwiched within the interface.…”

Chiral electromigration techniques in pharmaceutical and biomedical analysis

“…However, so far there is no clear understanding about the chiral recognition mechanism. Only X-ray crystallographic studies have been conducted, for example, in the case of vancomycin with the tripeptide N α , N ω -diacetyl-L-Lys-D-Ala-D-Ala [50,51] or small ligands such as N-acetyl glycine [52]. NMR Studies illustrating the interaction between solute and selector have not been published.…”