Thermodynamic analysis of the interaction of the antibiotic teicoplanin and its aglycone with cell-wall peptides

Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach

Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a D-alanine-containing peptide. A carrier-protein strategy was used to crystallize the complex of teicoplanin and its target peptide by fusing the cell-wall peptide to either MBP or ubiquitin via native chemical ligation and subsequently crystallizing the protein-peptide-antibiotic complex. The 2.05 Å resolution MBP-peptide-teicoplanin structure shows that teicoplanin recognizes its ligand through a combination of five hydrogen bonds and multiple van der Waals interactions. Comparison of this teicoplanin structure with that of unliganded teicoplanin reveals a flexibility in the antibiotic peptide backbone that has significant implications for ligand recognition. Diffraction experiments revealed an X-ray-induced dechlorination of the sixth amino acid of the antibiotic; it is shown that teicoplanin is significantly more radiation-sensitive than other similar antibiotics and that ligand binding increases radiosensitivity. Insights derived from this new teicoplanin structure may contribute to the development of next-generation antibacterials designed to overcome bacterial resistance.

A carrier protein strategy yields the structure of dalbavancin

Many large natural product antibiotics act by specifically binding and sequestering target molecules found on bacterial cells. We have developed a new strategy to expedite the structural analysis of such antibiotic-target complexes, in which we covalently link the target molecules to carrier proteins, and then crystallize the entire carrier-target-antibiotic complex. Using native chemical ligation, we have linked the Lys-D-Ala-D-Ala binding epitope for glycopeptide antibiotics to three different carrier proteins. We show that recognition of this peptide by multiple antibiotics is not compromised by the presence of the carrier protein partner, and use this approach to determine the first-ever crystal structure for the new therapeutic dalbavancin. We also report the first crystal structure of an asymmetric ristocetin antibiotic dimer, as well as the structure of vancomycin bound to a carrier-target fusion. The dalbavancin structure reveals an antibiotic molecule that has closed around its binding partner; it also suggests mechanisms by which the drug can enhance its half-life by binding to serum proteins, and be targeted to bacterial membranes. Notably, the carrier protein approach is not limited to peptide ligands such as Lys-D-Ala-D-Ala, but is applicable to a diverse range of targets. This strategy is likely to yield structural insights that accelerate new therapeutic development.

Direct affinity screening chromatography-mass spectrometry assay for identification of antibacterial agents from natural product sources

A direct affinity screening-mass spectrometry assay, coupled to liquid chromatography, is presented as a tool for natural product drug discovery. Using the assay, fractionated extracts from a Caribbean gorgonian coral were shown to contain a new chemical entity (NCE) which binds to a mimic of the Gram positive bacterial cell wall (lysine-D-alanine-D-alanine). Conditions for observation of a specific noncovalent complex between the NCE and the target mimic using electrospray ionization-mass spectrometry were validated in a series of positive and negative control experiments, which featured flow injection analysis-based titrations. While the structural identity of the NCE could not be determined due to limited sample quantities, this work provides proof-of-principle for such an approach to potentially accelerate drug discovery from natural product sources.

Thermodynamic origin of the chiral recognition of tryptophan on teicoplanin and teicoplanin aglycone stationary phases

The D-, L-tryptophan binding and the chiral recognition properties of the teicoplanin and teicoplanin aglycone (TAG) chiral stationary phase (CSPs) were compared at various column temperatures. The solute adsorption isotherms (bi-Langmuir model) were determined for both the two CSPs using the perturbation method. It was demonstrated that the sugar units were involved in the reduction of the apparent enantioselectivity through two phenomena: (i) the inhibition of some enantioselective contacts with low-affinity binding regions of the aglycone and (ii) a decrease in the stereoselective properties of the aglycone high-affinity binding pocket. The phenomenon (ii) was governed by both a decrease in the ratio of the enantiomer adsorption constant and a strong reduction of the site accessibility for D- and L-tryptophan. In addition, a temperature effect study was performed to investigate the chiral recognition mechanism at the aglycone high-affinity pocket. An enthalpy-entropy compensation analysis derived from the Grunwald model as well as the comparison with the literature data demonstrated that the enantioselective binding mode was dependent on an interface dehydration process. The change in the enantioselective process observed between the TAG and teicoplanin CSP was characterized by a difference of ca. 2-3 ordered water molecules released from the species interface.

Microcalorimetry and the molecular recognition of peptides and proteins

Isothermal titration (ITC) and differential scanning calorimetry (DSC) techniques are now routinely applicable to the study of non-covalent interactions in biomolecular recognition. Examples from our own current work on peptide antibiotic interactions and protein folding illustrate what may be achieved, ITC binding studies of vancomycin antibiotics with model peptides give information about the thermodynamics of group interactions, and also demonstrate possible complexities due to ligand-induced aggregation processes. The thermal stability of proteins in mixed aqueous solvents, studied by DSC, shows how the balance of forces responsible for folding stability may switch, without markedly perturbing the native structure. Separate experiments on the molecular recognition of unfolded polypeptide chains by cyclodextrins are consistent with simple binding of these cyclic polysaccharides to exposed aromatic groups on the therm ally denatured protein.

Facile liquid chromatographic enantioresolution of native amino acids and peptides using a teicoplanin chiral stationary phase

The glycopeptide antibiotic teicoplanin is shown to be a highly effective stationary phase chiral selector for the resolution of underivatized amino-acid and imino-acid enantiomers. Fifty four of these compounds (including all chiral protein amino acids) as well as a number of dipeptides were resolved. Hydro-organic mobile phases are used and no buffers or added salts are needed in most cases. Hence the purified analytes are easily isolated in pure form, if needed, by evaporating of the solvent. The effect of pH, organic modifier type and amount are discussed. The enantioselective separation mechanism is examined using both molecular modeling and retention data. The strongest stereoselective interaction is for carboxy-terminated D-amino-acids. In case of peptides, it is not necessary for these to be a D-, D-, terminal sequence for strong interactions. In some cases, including Ala-Ala, the L-, D-, terminal sequence showed greater interaction with the teicoplanin chiral stationary phase.

In vitro activity of vancomycin against the spirochete Borrelia burgdorferi

Borrelia burgdorferi, a spirochete and the causative agent of Lyme disease, has been reported to be susceptible to a variety of antimicrobial agents. In this investigation, the action of vancomycin, a glycopeptide antibiotic not previously known to have activity against spirochetes, against borrelias was examined. The in vitro activity of vancomycin against a variety of strains of B. burgdorferi and one strain of Borrelia hermsii was determined by use of a microdilution MIC method (L.L. Dever, J.H. Jorgensen, and A.G. Barbour, J. Clin. Microbiol. 30:2692-2697, 1992). MICs ranged from 0.5 to 2 micrograms/ml. MICs of the glycopeptides ristocetin and teicoplanin and the lipopeptide daptomycin against strain B31 of B. burgdorferi were all > or = 8 micrograms/ml. Subsurface plating, time-kill studies, synergy studies, and electron microscopy were used to investigate further the activity of vancomycin against B31. The MBC of vancomycin was 2 micrograms/ml. Time-kill curves demonstrated > or = 3-log10-unit (99.9%) killing of the final inoculum after 72 h by vancomycin concentrations twice the MIC. Synergy between vancomycin and penicillin was demonstrated at concentrations one-fourth the MIC of each drug. In electron microscopy, B31 cells exposed to vancomycin showed a disruption of cellular integrity and were indistinguishable from those exposed to penicillin. These studies demonstrate another class of microorganisms susceptible in vitro to vancomycin.