Membrane Disruption and Enhanced Inhibition of Cell‐Wall Biosynthesis: A Synergistic Approach to Tackle Vancomycin‐Resistant Bacteria

Resistance to glycopeptide antibiotics, the drugs of choice for life‐threatening bacterial infections, is on the rise. In order to counter the threat of glycopeptide‐resistant bacteria, we report development of a new class of semi‐synthetic glycopeptide antibiotics, which not only target the bacterial membrane but also display enhanced inhibition of cell‐wall biosynthesis through increased binding affinity to their target peptides. The combined effect of these two mechanisms resulted in improved in vitro activity of two to three orders of magnitude over vancomycin and no propensity to trigger drug resistance in bacteria. In murine model of kidney infection, the optimized compound was able to bring bacterial burden down by about 6 logs at 12 mg kg^?1 with no observed toxicity. The results furnished in this report emphasize the potential of this class of compounds as future antibiotics for drug‐resistant Gram‐positive infections.     

19F NMR in the measurement of binding affinities of chloroeremomycin to model bacterial cell-wall surfaces that mimic VanA and VanB resistance

Background: The emergence of bacteria that are resistant to vancomycin, the drug of choice against methicillin-resistant Staphylococcus aureus, has made the study of the binding characteristics of glycopeptides to biologically relevant depsipeptides important. These depsipeptides, terminating in -d-alanyl-d-lactate, mimic the cell-wall precursors of resistant bacteria.Results: The use of ¹⁹F-labelled ligands in the study of the therapeutically important vancomycin series of antibiotics is demonstrated. The substantial simplification of spectra that occurs when such labelled ligands are employed is used in the measurement of binding affinities of depsipeptides to chloroeremomycin (CE). Large enhancements of binding affinities are found at a model bacterial cell-wall surface (constituted from depsipetides that are anchored into vesicles) relative to those measured in free solution.Conclusions: Surface-enhanced binding, previously shown for strongly dimerising glycopeptide antibiotics to normal -d-alanyl-d-alanine-terminating cell-wall precursors, is now demonstrated for CE to the surface of models of VanA- and VanB-resistant bacteria. The effect of depsipeptide chain length is shown to be critically important in producing and maximising this enhancement.     

Paving the way to conformationally unravel complex glycopeptide antibiotics by means of Raman optical activity

It is crucial for fundamental physical chemistry techniques to find their application in tackling real-world challenges. Hitherto, Raman optical activity (ROA) spectroscopy is one of the examples where a promising future within the pharmaceutical sector is foreseen, but has not yet been established. Namely, the technique is believed to be able to contribute in investigating the conformational behaviour of drug candidates. We, herein, strive towards the alignment of the ROA analysis outcome and the pharmaceutical expectations by proposing a fresh strategy that ensures a more complete, reliable, and transferable ROA study. The strategy consists of the treatment of the conformational space by means of a principal component analysis (PCA) and a clustering algorithm, succeeded by a thorough ROA spectral analysis and a novel way of estimating the contributions of the different chemical fragments to the total ROA spectral intensities. Here, vancomycin, an antibiotic glycopeptide, has been treated; it is the first antibiotic glycopeptide studied by means of ROA and is a challenging compound in ROA terms. By applying our approach we discover that ROA is capable of independently identifying the correct conformation of vancomycin in aqueous solution. In addition, we have a clear idea of what ROA can and cannot tell us regarding glycopeptides. Finally, the glycopeptide class turns out to be a spectroscopically curious case, as its spectral responses are unlike the typical ROA spectral responses of peptides and carbohydrates. This preludes future ROA studies of this intriguing molecular class.

Raman optical activity tackles the complex conformational space of glycopeptide antibiotics.     

Design,synthesis and biological activity of novel demethylvancomycin dimers against vancomycin-resistant enterococcus faecalis

The emergence of resistance to vancomycin and other glycopeptide antibiotics is a serious concern in clinical practice and has prompted intensive efforts to develop analogues that may overcome the resistance. One of major strategies to enhancing anti-vancomycin-resistant enterococci (VRE) activity emerged in recent years was connecting two vancomycin molecules by covalent linkers. Herein, we reported the design and synthesis of three different covalently linked demethylvancomycin dimers 7a-c by applying click chemistry. Interestingly, these dimers restored their activities against VRE. Furthermore, the interactions of molecules with peptidoglycan were also investigated via computer modelling.     

Synthesis,conformational analysis and in vivo assays of an anti-cancer vaccine that features an unnatural antigen based on an sp2-iminosugar fragment

The Tn antigen (GalNAc-α-1-O-Thr/Ser) is a well-known tumor-associated carbohydrate determinant. The use of glycopeptides that incorporate this structure has become a significant and promising niche of research owing to their potential use as anticancer vaccines. Herein, the conformational preferences of a glycopeptide with an unnatural Tn antigen, characterized by a threonine decorated with an sp²-iminosugar-type α-GalNAc mimic, have been studied both in solution, by combining NMR spectroscopy and molecular dynamics simulations, and in the solid state bound to an anti-mucin-1 (MUC1) antibody, by X-ray crystallography. The Tn surrogate can mimic the main conformer sampled by the natural antigen in solution and exhibits high affinity towards anti-MUC1 antibodies. Encouraged by these data, a cancer vaccine candidate based on this unnatural glycopeptide and conjugated to the carrier protein Keyhole Limpet Hemocyanin (KLH) has been prepared and tested in mice. Significantly, the experiments in vivo have proved that this vaccine elicits higher levels of specific anti-MUC1 IgG antibodies than the analog that bears the natural Tn antigen and that the elicited antibodies recognize human breast cancer cells with high selectivity. Altogether, we compile evidence to confirm that the presentation of the antigen, both in solution and in the bound state, plays a critical role in the efficacy of the designed cancer vaccines. Moreover, the outcomes derived from this vaccine prove that there is room for exploring further adjustments at the carbohydrate level that could contribute to designing more efficient cancer vaccines.

An anti-cancer vaccine based on an unnatural antigen with an sp²-iminosugar fragment.     

Binding of glycopeptide antibiotics to a model of a vancomycin-resistant bacterium

BACKGROUND: The vancomycin group of glycopeptide antibiotics is active against a wide range of gram-positive bacteria. The increasing resistance to vancomycin is the result of a change of an amide linkage (D-Ala-D-Ala) to an ester linkage (D-Ala-D-Lactate) in the bacterial cell-wall precursors. RESULTS: We have used a peptide terminating in the sequence -Lys-D-Ala-D-Lactate linked by its amino terminus to a docosanoyl (C22) acyl chain and anchored in a supported lipid monolayer to mimic the surface of vancomycin-resistant enterococci. Surface plasmon resonance analysis was then used to investigate the binding of glycopeptide group antibiotics to this surface. Vancomycin, which dimerises weakly, bound with low affinity, whereas strongly dimerising antibiotics, such as chloroeremomycin, bound with higher affinities. Antibiotics that have attached hydrophobic groups, such as teicoplanin and biphenylchloroeremomycin (LY307599), bound to the lipid monolayer. This resulted in an enhanced affinity for the lipid-anchored peptide at the surface relative to affinities for an analogous non-anchored peptide in solution. CONCLUSIONS: We have shown that the affinities of glycopeptide antibiotics for a model of the surface of a vancomycin-resistant bacterium are enhanced relative to affinities determined in free solution. We have also shown that antibiotics that have membrane anchors bind tightly to the model surface and that this feature is an important determinant of the ability of an antibiotic to kill vancomycin-resistant enterococci.     

Synthesis of new ribosylated Asn building blocks as useful tools for glycopeptide and glycoprotein synthesis

We performed the first synthesis of new Asn derivatives bearing α- or β-ribose as pure anomers, linked by an N-glycosidic bond, on the side chain of the Asn residue orthogonally protected for Fmoc/^tBu SPPS, by an efficient five-step strategy with a global yield of 73% starting from d-ribose. These building blocks are obtained in a large scale and can be useful tools for glycopeptide and glycoproteins synthesis.     

Low-cost and versatile analytical tool with purpose-made capillary electrophoresis coupled to contactless conductivity detection: Application to antibiotics quality control in Vietnam

In this study, the development of our purpose-made capacitively coupled contactless conductivity detection (C⁴D) for CE is reported. These systems have been employed as a simple, versatile, and cost-effective analytical tool. CE-C⁴D devices, whose principle is based on the control of the ion movements under an electrical field, can be constructed even with a modest financial budget and limited infrastructure. A featured application was developed for quality control of antimicrobial drugs using CE-C⁴D, with most recent work on determination of aminoglycoside and glycopeptide antibiotics being communicated. For aminoglycosides, the development of CE-C⁴D methods was adapted to two categories. The first one includes drugs (liquid or powder form) for intravenous injection, containing either amikacin, streptomycin, kanamycin A, or kanamycin B. The second one covers drugs for eye drops (liquid or ointment form), containing either neomycin, tobramycin, or polymyxin. The CE-C⁴D method development was also made for determination of some popular glycopeptide antibiotics in Vietnam, including vancomycin and teicoplanin. The best detection limit achieved using the developed CE-C⁴D methods was 0.5 mg/L. Good agreement between results from CE-C⁴D and the confirmation method (HPLC- Photometric Diode Array ) was achieved, with their result deviations less than 8% and 13% for aminoglycoside and glycopeptide antibiotics, respectively.     

Total synthesis and evaluation of [Psi[CH2NH]Tpg4]vancomycin aglycon: reengineering vancomycin for dual D-Ala-D-Ala and D-Ala-D-Lac binding

An effective synthesis of [Psi[CH(2)NH]Tpg(4)]vancomycin aglycon (5) is detailed in which the residue 4 amide carbonyl of vancomycin aglycon has been replaced with a methylene. This removal of a single atom was conducted to enhance binding to D-Ala-D-Lac, countering resistance endowed to bacteria that remodel their D-Ala-D-Ala peptidoglycan cell wall precursor by a similar single atom change (ester O for amide NH). Key elements of the approach include a synthesis of the modified vancomycin ABCD ring system featuring a reductive amination coupling of residues 4 and 5 for installation of the deep-seated amide modification, the first of two diaryl ether closures for formation of the modified CD ring system (76%, 2.5-3:1 kinetic atropodiastereoselectivity), a Suzuki coupling for installation of the hindered AB biaryl bond (90%) on which the atropisomer stereochemistry could be thermally adjusted, and a macrolactamization closure of the AB ring system (70%). Subsequent DE ring system introduction enlisted a room-temperature aromatic nucleophilic substitution reaction for formation of the remaining diaryl ether (86%, 6-7:1 kinetic atropodiastereoselectivity), completing the carbon skeleton of 5. Consistent with expectations and relative to the vancomycin aglycon, 5 exhibited a 40-fold increase in affinity for D-Ala-D-Lac (K(a) = 5.2 x 10(3) M(-1)) and a 35-fold reduction in affinity for D-Ala-D-Ala (K(a) = 4.8 x 10(3) M(-1)), providing a glycopeptide analogue with balanced, dual binding characteristics. Beautifully, 5 exhibited antimicrobial activity (MIC = 31 microg/mL) against a VanA-resistant organism that remodels its D-Ala-D-Ala cell wall precursor to d-Ala-d-Lac upon glycopeptide antibiotic challenge, displaying a potency that reflects these binding characteristics.     

Cooperativity and anti-cooperativity between ligand binding and the dimerization of ristocetin A: asymmetry of a homodimer complex and implications for signal transduction

Background: Recent work has indicated that dimerization is important in the mode of action of the vancomycin group of glycopeptide antibiotics. NMR studies have shown that one member of this group, ristocetin A₁ forms an asymmetric dimer with two physically different binding sites for cell wall peptides. Ligand binding by ristocetin A and dimerization are slightly anti-cooperative. In contrast, for the other glycopeptide antibiotics of the vancomycin group that have been examined so far, binding of cell wall peptides and dimerization are cooperative.Results: Here we show that the two halves of the asymmetric homodimer formed by ristocetin A have different affinities for ligand binding. One of these sites is preferentially filled before the other, and binding to this site is cooperative with dimerization. Ligand binding to the other, less favored half of the dimer, is anti-cooperative with dimerization.Conclusions: In dinner complexes, anti-cooperativity of dimerization upon ligand binding can be a result of asymmetry, in which two binding sites have different affinities for ligands. Such a system, in which one binding site is filled preferentially, may be a mechanism by which the cooperativity between ligand binding and dimerization is fine tuned and may thus have relevance to the control of signal transduction in biological systems.     

Synthesis and characterization of D-Alanyl-D-Alanine-Agarose

A new affinity adsorbent, using D-alanyl-D-alanine as ligand, has been prepared. The dipeptide immobilized on Activated CH-Sepharose 4B (D-Ala-D-Ala-AGA) bioselectively binds the glycopeptide antibiotics teicoplanin, vancomycin, ristocetin A (vancomycinlike group of antibiotics) while it does not bind other antibiotics equally active on cell wall biosynthesis but with different target sites, such as penicillin G, cephalosporin C, gardimycin, and bacitracin. Teicoplanin, vancomycin, and ristocetin A have similar binding characteristics for the immobilized dipeptide, as indicated by equilibrium binding experiments. The affinity constants of the three antibiotics for D-Ala-D-Ala-AGA is of the same order of magnitude (10⁵ L mol^-1) and the number of effective binding sites is similar for each antibiotic (6–7 μEq/mL of gel). The adsorption is biospecific as no binding has been observed to immobilized L-alanyl-L -alanine. D-Ala-D-Ala-AGA has been successfully used to purify teicoplanin from mixtures of different complexity and for concomitant extraction and purification from fermentation liquors by both batch adsorption and column chromatography. The antibiotic can be recovered from the resin in high yields by elution at pH 11.     

Enkephalin-based drug design: conformational analysis of O-linked glycopeptides by NMR and molecular modeling

Glycosylation provides an effective means of enhancing penetration of the blood–brain barrier by pharmacologically active peptides. Glycosylated enkephalin analogues demonstrate much greater analgesic effects than their unglycosylated counterparts when administered peripherally. The solution conformations of glycopeptide enkephalin analogues with the sequences H-Tyr-c-[d-Cys-Gly-Phe-d-Cys]-Ser(β-O-Glcp)-Gly-NH₂, 2, and H-Tyr-c-[d-Cys-Gly-Phe-d-Cys]-Ser(α-O-Glcp)-Gly-NH₂, 3, have been determined by NMR and molecular modeling, and were compared to the unglycosylated peptide H-Tyr-c-[d-Cys-Gly-Phe-d-Cys]-Ser-Gly-NH₂, 1, to determine the impact of glycosylation on peptide conformation. The only observed conformational effects were on the residue of attachment, Ser⁶, and on the adjacent Gly⁷-amide. This has important implications in peptide-based drug design in that strategically placed glycosylation can improve transport without destruction of the receptor selectivity of a pre-existing non-glycosylated peptide pharmacophore.     

Synthesis and reaction with metal ions of a new thionocarbamate

The synthesis and research of a novel thionocarbamate N,N??-diethoxycarbonyl-O,O??-(1,4-butylidene) dithionocarbamate which contains two ester and two thioamide groups are reported. This compound was characterized by elemental analysis, UV spectrum, infrared spectrum, mass spectrum, and ¹H NMR and ¹³C NMR spectroscopy. Additionally, the metal ion?Ccollector interaction in organic solution was put into practice. The results of UV spectroscopic analysis showed that this dithionocarbamate with a new structure exhibited a stronger complex ability with Cu²⁺ than with Ni²⁺ or Fe³⁺. Furthermore, infrared spectroscopic analysis implicated that this dithionocarbamate binds to Cu²⁺ through both the C=O and C=S groups. Bench-scale flotation tests were also carried out, verifying that it has a higher copper flotation recovery and better selectivity to sulfide ores containing Cu compared with universal collectors.     

Characterization of structural variations in the peptidoglycan of vancomycin-susceptible <Emphasis Type="Italic">Enterococcus faecium</Emphasis>: Understanding glycopeptide-antibiotic binding sites using mass spectrometry

Enterococcus faecium, an opportunistic pathogen that causes a significant number of hospital-acquired infections each year, presents a serious clinical challenge because an increasing number of infections are resistant to the so-called antibiotic of last resort, vancomycin. Vancomycin and other new glycopeptide derivatives target the bacterial cell wall, thereby perturbing its biosynthesis. To help determine the modes of action of glycopeptide antibiotics, we have developed a bottom-up mass spectrometry approach complemented by solid-state nuclear magnetic resonance (NMR) to elucidate important structural characteristics of vancomycin-susceptible E. faecium peptidoglycan. Using accurate-mass measurements and integrating ion-current chromatographic peaks of digested peptidoglycan, we identified individual muropeptide species and approximated the relative amount of each. Even though the organism investigated is susceptible to vancomycin, only 3% of the digested peptidoglycan has the well-known d-Ala-d-Ala vancomycin-binding site. The data are consistent with a previously proposed template model of cell-wall biosynthesis where d-Ala-d-Ala stems that are not cross-linked are cleaved in mature peptidoglycan. Additionally, our mass-spectrometry approach allowed differentiation and quantification of muropeptide species seen as unresolved chromatographic peaks. Our method provides an estimate of the extent of muropeptides containing O-acetylation, amidation, hydroxylation, and the number of species forming cyclic imides. The varieties of muropeptides on which the modifications are detected suggest that significant processing occurs in mature peptidoglycan where several enzymes are active in editing cell-wall structure.     

Thermal racemization of biaryl atropisomers

Many biaryl compounds possess atropisomerism due to the steric hindrance of substituents at the ortho-position of the two aromatic moieties. Upon heating, atropisomers may have enough energy to surpass the rotational energy barrier and racemize. The thermal stability of five atropisomers was studied using chiral chromatography by following the change in enantiomeric excess ratio at different temperatures. The first order racemization reaction rate was obtained at a given temperature as the slope of the change in enantiomeric excess ratio versus time. For each atropisomer, the racemization rates at different temperatures led to the value of the rotational energy barrier for racemization, ΔG³, and to the racemization half lifetime, t_1/2, indicating the atropisomer thermal stability. Binaphthol started to racemize significantly at temperature of 190 °C and above while binaphthyldiamine was much more stable showing little or very minor racemization up to 210 °C. A chloro-substituted phenylamino-naphthol was very sensitive to thermal racemization starting at a low 40 °C.     

Conformational studies of resin-bound vancomycin and the complex of vancomycin and Ac2-L-Lys-D-Ala-D-Ala

The molecular target of vancomycin, a commonly used glycopeptide antibiotic, is the D-Ala-D-Ala dipeptide subunit on the bacterial cell wall. The molecular basis of interaction between vancomycin and D-Ala-D-Ala in solution is well-known. However, there is no structural data on vancomycin, and its interaction with D-Ala-D-Ala when the drug is tethered to a solid support. In this Article, vancomycin was directly coupled onto TentaGel or PEGA resin through its C terminus. High-resolution magic angle spinning NMR studies indicated that conformation of PEGA bead-bound vancomycin is identical to that of the free drug. Broadening and shifts of the same proton resonances were observed in solution-phase vancomycin or PEGA-bound vancomycin when complexed with Ac(2)-L-Lys-D-Ala-D-Ala. This study demonstrates that bead-bound molecules can behave the same as solution-phase molecules in terms of molecular interaction with its target molecule, thus validating the on-bead screening approach of the "one-bead-one-compound" combinatorial library method.     

Atropselective macrocyclization of diaryl ether ring systems: application to the synthesis of vancomycin model systems

Vancomycin is the last line of defense available in the clinic for treating multidrug-resistant bacterial infections. Vancomycin contains two 16-membered diaryl ether macrocycles, each of which contains a stereogenic axis across the diaryl ether linkage. Since an effective total synthesis of vancomycin requires that these stereogenic axes be formed in a stereoselective manner, we have developed an atropselective variation of the triazene mediated diaryl ether forming reaction. This variation introduced an energetic penalty into the transition state of the undesired atropisomer. This reaction is used to synthesize the C-O-D diaryl ether macrocycle found in vancomycin with high diastereoselectivity (de > 90%), providing the naturally occurring atropisomeric configuration.     

A visual test paper for extremely strong concentrated acidity with a new synthesized isoindole reagent

A visual test paper by taking common filter paper as solid support for extremely strong concentrated acidity has been developed in this contribution with a new synthesized isoindole compound starting from p-phenylenediamine and the coupled fluorogenic reagent of o-phthaldialdehyde-β-mercaptoethanol. It was very easy for semiquantitative detection of acidity in the range of 0.2-18 M ([H⁺]) in extreme acidic solution based on the color changes of the solution or the visual test paper prepared by immerging filter paper slides into the solution of the new synthesized reagent. Quantitative detection of concentrated strong acids could be successfully constructed through the linear relationship exists between the absorbance of the chromogenic reagent at 510 nm and the acid concentrations.     

Synthesis of a new chiral cyclic aminal derived from rac-1,2-propanediamine

The cyclic aminal 4,9-dimethyl-1,3,6,8-tetraazatricyclo[4.4.1.1^3,8]dodecane 4c was synthesized by the reaction of commercial rac-1,2-propanediamine with paraformaldehyde in an aqueous solution. ¹H NMR analysis clearly revealed that the compound is chiral and racemic with an axis of chirality. To our knowledge, this is the first example of an azaadamantane derivative having axial chirality. This aminal was used in a Mannich type reaction with p-chlorophenol yielding 2,2′-[(4-methylimidazolidine-1,3-diyl)dimethanediyl]bis(4-chlorophenol) 7 as a racemic mixture. The crystal structure of 7 was determined by single X-ray diffraction analysis.     

Elucidation of the Active Conformation of Vancomycin Dimers with Antibacterial Activity against Vancomycin‐Resistant Bacteria

Covalently linked vancomycin dimers have attracted a great deal of attention among researchers because of their enhanced antibacterial activity against vancomycin‐resistant strains. However, the lack of a clear insight into the mechanisms of action of these dimers hampers rational optimization of their antibacterial potency. Here, we describe the synthesis and antibacterial activity of novel vancomycin dimers with a constrained molecular conformation achieved by two tethers between vancomycin units. Conformational restriction is a useful strategy for studying the relationship between the molecular topology and biological activity of compounds. In this study, two vancomycin units were linked at three distinct positions of the glycopeptide (vancosamine residue (V), C terminus (C), and N terminus (N)) to form two types of novel vancomycin cyclic dimers. Active NC‐VV‐linked dimers with a stable conformation as indicated by molecular mechanics calculations selectively suppressed the peptidoglycan polymerization reaction of vancomycin‐resistant Staphylococcus aureus in vitro. In addition, double‐disk diffusion tests indicated that the antibacterial activity of these dimers against vancomycin‐resistant enterococci might arise from the inhibition of enzymes responsible for peptidoglycan polymerization. These findings provide a new insight into the biological targets of vancomycin dimers and the conformational requirements for efficient antibacterial activity against vancomycin‐resistant strains.