Molecular basis of the activity of antibiotics of the vancomycin group

Robust Chemoenzymatic Synthesis of Keratinimicin Aglycone Analogues Facilitated by the Structure and Selectivity of OxyB

The emergence of multidrug-resistant pathogens poses a threat to public health and requires new antimicrobial agents. As the archetypal glycopeptide antibiotic (GPA) used against drug-resistant Gram-positive pathogens, vancomycin provides a promising starting point. Peripheral alterations to the vancomycin scaffold have enabled the development of new GPAs. However, modifying the core remains challenging due to the size and complexity of this compound family. The recent successful chemoenzymatic synthesis of vancomycin suggests that such an approach can be broadly applied. Herein, we describe the expansion of chemoenzymatic strategies to encompass type II GPAs bearing all aromatic amino acids through the production of the aglycone analogue of keratinimicin A, a GPA that is 5-fold more potent than vancomycin against Clostridioides difficile. In the course of these studies, we found that the cytochrome P450 enzyme OxyB_ker boasts both broad substrate tolerance and remarkable selectivity in the formation of the first aryl ether cross-link on the linear peptide precursors. The X-ray crystal structure of OxyB_ker, determined to 2.8 Å, points to structural features that may contribute to these properties. Our results set the stage for using OxyB_ker broadly as a biocatalyst toward the chemoenzymatic synthesis of diverse GPA analogues.

An extensively validated whole-cell biosensor for specific, sensitive and high-throughput detection of antibacterial inhibitors targeting cell-wall biosynthesis

BACKGROUND

Whole-cell biosensor strains are powerful tools for antibacterial drug discovery, in principle allowing the identification of inhibitors acting on specific, high-value target pathways. Whilst a variety of biosensors have been described for detecting cell-wall biosynthesis inhibitors (CWBIs), these strains typically lack specificity and/or sensitivity, and have for the most part not been rigorously evaluated as primary screening tools. Here, we describe several Staphylococcus aureus CWBI biosensors and show that specific and sensitive biosensor-based discovery of CWBIs is achievable.

METHODS

Biosensors comprised lacZ reporter fusions with S. aureus promoters (PgltB, PilvD, PmurZ, PoppB, PORF2768, PsgtB) that are subject to up-regulation following inhibition of cell-wall biosynthesis. Induction of biosensors was detected by measuring expression of β-galactosidase using fluorogenic or luminogenic substrates.

RESULTS

Three of the six biosensors tested (those based on PgltB, PmurZ, PsgtB) exhibited apparently specific induction of β-galactosidase expression in the presence of CWBIs. Further validation of one of these (PmurZ) using an extensive array of positive and negative control compounds and conditional mutants established that it responded appropriately and uniquely to inhibition of cell-wall biosynthesis. Using this biosensor, we established, validated and deployed a high-throughput assay that identified a potentially novel CWBI from a screen of >9000 natural product extracts.

CONCLUSIONS

Our extensively validated PmurZ biosensor strain offers specific and sensitive detection of CWBIs, and is well-suited for high-throughput screening; it therefore represents a valuable tool for antibacterial drug discovery.

Vancomycin mimicry: towards new supramolecular antibiotics

Vancomycin is the best-known of the glycopeptide group antibiotics (GPAs), a family of agents which operate by binding the C-terminal deptide D-Ala-D-Ala. This anionic epitope is an interesting target because it plays a central role in bacterial cell wall synthesis, and is not readily modified by evolution. Accordingly, vancomycin has been in use for >60 years but has only provoked limited resistance. Agents which mimic vancomycin but are easier to synthesise and modify could serve as valuable weapons against pathogenic bacteria, broadening the scope of the GPAs and addressing the resistance that does exist. This article gives an overview of vancomycin's structure and action, surveys past work on vancomycin mimicry, and makes the case for renewed effort in the future.

The Lasso Peptide Siamycin-I Targets Lipid II at the Gram-Positive Cell Surface

Ribosomally synthesized post-translationally modified peptides (RiPPs) are a diverse class of biologically active molecules produced by many environmental bacteria. While thousands of these compounds have been identified, mostly through genome mining, a relatively small number has been investigated at the molecular level. One less understood class of RiPPs is the lasso peptides. These are 20-25 amino acid residue compounds bearing an N-terminal macrocyclic ring and a C-terminal tail that is threaded through the ring. We have carried out a detailed investigation on the mechanism of action of the siamycin-I lasso peptide. We demonstrate that siamycin-I interacts with lipid II, the central building block of the major cell wall component peptidoglycan, which is readily accessible on the outside of the cell. This interaction compromises cell wall biosynthesis in a manner that activates the liaI stress response. Additionally, resistance to siamycin-I can be brought about by mutations in the essential WalKR two-component system that causes thickening of the cell wall. Siamycin-I is the first lasso peptide that has been shown to inhibit cell wall biosynthesis.

Natural Products as Platforms To Overcome Antibiotic Resistance

Natural products have served as powerful therapeutics against pathogenic bacteria since the golden age of antibiotics of the mid-20th century. However, the increasing frequency of antibiotic-resistant infections clearly demonstrates that new antibiotics are critical for modern medicine. Because combinatorial approaches have not yielded effective drugs, we propose that the development of new antibiotics around proven natural scaffolds is the best short-term solution to the rising crisis of antibiotic resistance. We analyze herein synthetic approaches aiming to reengineer natural products into potent antibiotics. Furthermore, we discuss approaches in modulating quorum sensing and biofilm formation as a nonlethal method, as well as narrow-spectrum pathogen-specific antibiotics, which are of interest given new insights into the implications of disrupting the microbiome.

Hollow mesoporous carbon nanocarriers for vancomycin delivery: understanding the structure-release relationship for prolonged antibacterial performance

Mono-dispersed mesoporous hollow carbon (MHC) nanospheres with comparable structures have been designed as nanocarriers for the delivery of vancomycin (Van) to inhibit bacterial growth. It is demonstrated that MHC materials possess a Van loading capacity of 861 mg g^-1, much higher than that of any Van nanocarrier in previous reports. By comparing the drug loading, release and antibacterial performance of MHC nanospheres with controllable structures, it is shown that MHC with a pore size of 5.8 nm and a wall thickness of 25 nm exhibits compromising storage-release behaviour and achieves extended bactericidal activity of Van towards E. coli and S. epidermidis compared to free Van and other MHC nanocarriers. This study provides new knowledge about the rational design of carbon based nanocarriers to enhance the therapeutic efficacy of antibiotics.

Palladium-Catalyzed Enantioselective Three-Component Synthesis of α-Arylglycines

A general Pd-catalyzed, enantioselective three-component synthesis of α-arylglycines starting from sulfonamides, glyoxylic acid derivatives, and boronic acids was developed. This operationally straightforward procedure enables the preparation of a wide variety of α-arylglycines in high yields and excellent levels of enantioselectivity from a simple set of readily available starting materials. Incorporation of Pbf-amides gives a racemization-free access to N-unprotected α-arylglycines.

Vancomycin: ligand recognition, dimerization and super-complex formation

The antibiotic vancomycin targets lipid II, blocking cell wall synthesis in Gram-positive bacteria. Despite extensive study, questions remain regarding how it recognizes its primary ligand and what is the most biologically relevant form of vancomycin. In this study, molecular dynamics simulation techniques have been used to examine the process of ligand binding and dimerization of vancomycin. Starting from one or more vancomycin monomers in solution, together with different peptide ligands derived from lipid II, the simulations predict the structures of the ligated monomeric and dimeric complexes to within 0.1 nm rmsd of the structures determined experimentally. The simulations reproduce the conformation transitions observed by NMR and suggest that proposed differences between the crystal structure and the solution structure are an artifact of the way the NMR data has been interpreted in terms of a structural model. The spontaneous formation of both back-to-back and face-to-face dimers was observed in the simulations. This has allowed a detailed analysis of the origin of the cooperatively between ligand binding and dimerization and suggests that the formation of face-to-face dimers could be functionally significant. The work also highlights the possible role of structural water in stabilizing the vancomycin ligand complex and its role in the manifestation of vancomycin resistance.

Catalytic site-selective thiocarbonylations and deoxygenations of vancomycin reveal hydroxyl-dependent conformational effects

We have examined peptide-based catalysts for the site-selective thiocarbonylation of a protected form of vancomycin. Several catalysts were identified that either enhanced or altered the inherent selectivity profile exhibited by the substrate. Two catalysts, one identified through screening and another through rational design, were demonstrated to be effective on 0.50-g scale. Deoxygenations led ultimately to two new deoxy-vancomycin derivatives, and surprising conformational consequences of deoxygenation were revealed for one of the new compounds. These effects were mirrored in the biological activities of the new analogues and support a structural role for certain hydroxyls in the native structure.

Vancomycin forms ligand-mediated supramolecular complexes

The emergence of resistance to vancomycin and related glycopeptide antibiotics is spurring efforts to develop new antimicrobial therapeutics. High-resolution structural information about antibiotic-ligand 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 A to R and R(free) values of 0.172 and 0.195, respectively. The crystal asymmetric unit contains three back-back 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 four to six vancomycin monomers.

Why are secondary metabolites biosynthesized? Sophistication in the inhibition of cell wall biosynthesis by vancomycin group antibiotics

The evidence that secondary metabolites serve sophisticated roles in the survival strategy of the producer is briefly reviewed. This evidence stems from the common involvement of tens of kilobases of DNA in the programming of their synthesis, of up to several tens of discrete enzymic conversions in their biosynthesis, and of the existence of sophisticated mechanisms in the producers for resistance against their physiological effects. It also stems from a study of the molecular basis for these physiological effects. The molecular basis for the antibacterial action of the vancomycin group antibiotics is presented, and demonstrates that essentially every portion of these molecules appears to be finely honed to promote efficient antibacterial action.

The natural design of vancomycin family antibiotics to bind their target peptides

The vancomycin family of antibiotics provide a rare opportunity among natural systems to study a molecular recognition process in which both the 'receptor' and the 'ligand' are relatively small molecules. Unlike the vast majority of antibiotics, in the vancomycin family the antibiotic performs the role of the receptor. All members of the family are covalently cross-linked heptapeptides that contain a variety of glycosidic modifications. Their site of action in bacterial cell walls is modelled by simple dipeptides and tripeptides. NMR experiments have been used to characterize the binding of these species through the study of both the complex and the free components. In unbound antibiotics conformational freedom is observed in regions of the molecule not severely restricted by covalent linkages. On binding of the ligand much of this conformational freedom is lost and the hydrophobic side chains of the antibiotics reside close to the intermolecular hydrogen-bonding interactions, thus shielding these interactions from the solvent. The charged amino groups of the N-terminus and disaccharide region of vancomycin are orientated not to optimize intermolecular electrostatic interactions but rather to retain solvation. This causes further hydrophobic faces to be presented to the ligand. Removal of saccharide units from the antibiotics leads to small losses in binding energy but may have considerable influence on the selectivity of the antibiotics. Specific dimerization through the non-ligand-binding faces of ristocetin is observed at millimolar concentrations. The geometry of the dimeric complex enables a close approach of the ligand carboxylate anion and the charged amino group of the novel sugar, ristosamine.

Telavancin, a multifunctional lipoglycopeptide, disrupts both cell wall synthesis and cell membrane integrity in methicillin-resistant Staphylococcus aureus

The emergence and spread of multidrug-resistant gram-positive bacteria represent a serious clinical problem. Telavancin is a novel lipoglycopeptide antibiotic that possesses rapid in vitro bactericidal activity against a broad spectrum of clinically relevant gram-positive pathogens. Here we demonstrate that telavancin's antibacterial activity derives from at least two mechanisms. As observed with vancomycin, telavancin inhibited late-stage peptidoglycan biosynthesis in a substrate-dependent fashion and bound the cell wall, as it did the lipid II surrogate tripeptide N,N'-diacetyl-L-lysinyl-D-alanyl-D-alanine, with high affinity. Telavancin also perturbed bacterial cell membrane potential and permeability. In methicillin-resistant Staphylococcus aureus, telavancin caused rapid, concentration-dependent depolarization of the plasma membrane, increases in permeability, and leakage of cellular ATP and K(+). The timing of these changes correlated with rapid , concentration-dependent loss of bacterial viability, suggesting that the early bactericidal activity of telavancin results from dissipation of cell membrane potential and an increase in membrane permeability. Binding and cell fractionation studies provided direct evidence for an interaction of telavancin with the bacterial cell membrane; stronger binding interactions were observed with the bacterial cell wall and cell membrane relative to vancomycin. We suggest that this multifunctional mechanism of action confers advantageous antibacterial properties.

Solid-phase synthesis and antibacterial evaluations of N-demethylvancomycin derivatives

Twenty-five N-demethylvancomycin derivatives were synthesized on solid-support and their structures were determined by LC-MS/MS. Biological evaluation of these compounds indicated that bulky hydrophobic substituent on vancosamine of N-demethylvancomycin can increase antibacterial activity against vancomycin-resistant Enterococcus faecalis.

Study of mechanisms of chiral discrimination of amino acids and their derivatives on a teicoplanin-based chiral stationary phase

The behavior of a series of amino acids and some of their methyl ester hydrochloride, N-acetyl and N-tert-butyloxycarbonyl derivatives has been investigated on a teicoplanin-based chiral stationary phase by changing the chromatographic conditions, namely, the type and amount of mobile phase organic modifier and the ionic strength of the solutions. By using species with significantly different characteristics and chemical reactivity, some general conclusions regarding the chiral recognition process on this kind of stationary phase have been formulated. The importance of the carboxylic moiety for the formation of the complex between enantiomers and the aglycone basket of teicoplanin has been demonstrated via chromatography. Additionally, the increased possibility to make an hydrogen bond between the amidic hydrogen of the acetylated compounds and an amidic group on the stationary phase has been proposed to be pivotal for the stability of the complex aglycone D-enantiomer. Phenomena leading to the exclusion from the chiral stationary phase of one or both enantiomers have been rationalized by considering the ionic interactions between stationary phase, molecules to be separated and the surrounding medium and/or steric hindrance effects. The understanding of some of the observed phenomena may be important for optimizing the performance of the separation on aglycone-based media.

Glycopeptide Antibiotics

Vancomycin and teicoplanin are still the only glycopeptide antibiotics available for use in humans. Emergence of resistance in enterococci and staphylococci has led to restriction of their use to severe infections caused by Gram-positive bacteria for which no other alternative is acceptable (because of resistance or allergy). In parallel, considerable efforts have been made to produce semisynthetic glycopeptides with improved pharmacokinetic and pharmacodynamic properties, and with activity towards resistant strains. Several molecules have now been obtained, helping to better delineate structure-activity relationships. Two are being currently evaluated for skin and soft tissue infections and are in phases II/III. The first, oritavancin (LY333328), is the 4'-chlorobiphenylmethyl derivative of chloroeremomycin, an analogue to vancomycin. It is characterised by: i) a spectrum covering vancomycin-resistant enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA) and to some extent glycopeptide-intermediate S. aureus (GISA); ii) rapid bactericidal activity including against the intracellular forms of enterococci and staphylococci; and iii) a prolonged half-life, allowing for daily administration. The second molecule is dalbavancin (BI397), a derivative of the teicoplanin analogue A40926. Dalbavancin has a spectrum of activity similar to that of oritavancin against vancomycin-sensitive strains, but is not active against VRE. It can be administered once a week, based on its prolonged retention in the organism. Despite these remarkable properties, the use of these potent agents should be restricted to severe infections, as should the older glycopeptides, with an extension towards resistant or poorly sensitive bacteria, to limit the risk of potential selection of resistance.

A Synthesis of l-Vancosamine Derivatives from Non-Carbohydrate Precursors by a Short Sequence Based on the Marshall, McDonald, and Du Bois Reactions

[reaction: see text] The carbamate-protected l-vancosamine glycal, viewed as a universal precursor for vancosamine derivatives, was prepared by a short scheme based on diastereoselective addition of an allenyl stannane to a lactaldehyde ether, the tungsten-catalyzed alkynol cycloisomerization, and the rhodium-catalyzed C-H insertion of a carbamate nitrogen. This sequence is a prototype for a new and efficient strategy for the synthesis of 3-amino sugar derivatives. The key intermediate was elaborated to the silyl ether of N,N-dimethyl vancosamine glycal.

Mechanism of action of oritavancin and related glycopeptide antibiotics

Oritavancin (LY333328) is a semisynthetic glycopeptide antibiotic having excellent bactericidal activity against glycopeptide-susceptible and -resistant Gram-positive bacteria. Oritavancin is the N-alkyl-p-chlorophenylbenzyl derivative of chloroeremomycin (LY264826) and is currently in phase III clinical trials for use in Gram-positive infections. Studies show that oritavancin and related alkyl glycopeptides inhibit bacterial cell wall formation by blocking the transglycosylation step in peptidoglycan biosynthesis in a substrate-dependent manner. As with other glycopeptide antibiotics, including vancomycin, the effects of oritavancin on cell wall synthesis are attributable to interactions with dipeptidyl residues of peptidoglycan precursors. Unlike vancomycin, however, oritavancin is strongly dimerized and can anchor to the cytoplasmic membrane, the latter facilitated by its alkyl side chain. Cooperative interactions derived from dimerization and membrane anchoring in situ can be of sufficient strength to enable binding to either dipeptidyl or didepsipeptidyl peptidoglycan residues of vancomycin-susceptible and -resistant enterococci, respectively. This review describes the antibacterial activity of oritavancin, and examines the evidence supporting the proposed mechanism of action for this agent and related analogs.

Molecular interactions of glycopeptide antibiotics investigated by affinity capillary electrophoresis and bioaffinity electrospray ionization-mass spectrometry

Many analytical approaches are available to evaluate (bio)molecular interactions, all of which have their particular advantages and disadvantages. In recent years, two relatively new techniques have emerged that may be used by the bioanalytical community to evaluate such interactions, namely affinity capillary electrophoresis (ACE) and bioaffinity electrospray ionization-mass spectrometry (ESI-MS). In this paper, we describe and evaluate the use of both these techniques for the investigation of the interactions of glycopeptide antibiotics with peptides that mimic the bacterial cell wall binding site. We focus particularly on the effect of the sugar moieties attached to the antibiotic peptide backbone and on the noncovalent dimerization of these glycopeptide antibiotics.

The role of sugar residues in molecular recognition by vancomycin

The sugar residues of the glycopeptide antibiotic vancomycin contribute to the cooperativity of ligand binding, thereby increasing ligand affinity and enhancing antimicrobial activity. To assess the structural basis for these effects, we determined a 0.98 A X-ray crystal structure of the vancomycin aglycon and compared it to structures of several intact vancomycin:ligand complexes. The crystal structure reveals that the aglycon binds acetate anions and forms back-to-back dimeric complexes in a manner similar to that of intact vancomycin. However, the four independent copies of the aglycon in each asymmetric unit of the crystal exhibit a high degree of conformational heterogeneity. These results suggest that the sugar residues, in addition to enlarging and strengthening the dimer interface, provide steric constraints that limit the vancomycin molecule to a relatively small number of productive conformations.

The structural biology of molecular recognition by vancomycin

Vancomycin is the archetype among naturally occurring compounds known as glycopeptide antibiotics. Because it is a vital therapeutic agent used world-wide for the treatment of infections with gram-positive bacteria, emerging bacterial resistance to vancomycin is a major public health threat. Recent investigations into the mechanisms of action of glycopeptide antibiotics are driven by a need to understand their detailed mechanism of action so that new agents can be developed to overcome resistance. These investigations have revealed that glycopeptide antibiotics exhibit a rich array of complex cooperative phenomena when they bind target ligands, making them valuable model systems for the study of molecular recognition.

Use of the cell wall precursor lipid II by a pore-forming peptide antibiotic

Resistance to antibiotics is increasing in some groups of clinically important pathogens. For instance, high vancomycin resistance has emerged in enterococci. Promising alternative antibiotics are the peptide antibiotics, abundant in host defense systems, which kill their targets by permeabilizing the plasma membrane. These peptides generally do not act via specific receptors and are active in the micromolar range. Here it is shown that vancomycin and the antibacterial peptide nisin Z use the same target: the membrane-anchored cell wall precursor Lipid II. Nisin combines high affinity for Lipid II with its pore-forming ability, thus causing the peptide to be highly active (in the nanomolar range).

Considerations concerning interaction characterization of oligopeptide mixtures with vancomycin using affinity capillary electrophoresis-electrospray mass spectrometry

In the past few years affinity capillary electrophoresis (ACE) has proven to be a powerful tool to study molecular interactions. In ACE the change in electrophoretic mobility between a free and a complexed ligand with a receptor dissolved in the background electrolyte is observed. It provides an accurate way to calculate binding or dissociation constants and, when coupled to mass spectrometry, it forms a promising method to analyze solution-based combinatorial libraries. We report a model study on the macrocyclic antibiotic vancomycin using a 36-component library of tetrapeptides of the type 9-fluorenylmethoxycarbonyl (Fmoc)-L-Asp-L-Asp-D-Xaa-D-Xaa. The mass spectrometry conditions were optimized by fine-tuning the background electrolyte and sheath flow composition to achieve optimal sensitivity in the negative ionization mode. Different types of capillaries were also evaluated on their potential to screen combinatorial libraries. The library components that show the strongest interaction were identified. The dissociation constants of a mixture of six compounds with a broad affinity range were simultaneously established by Scatchard analysis on ACE-MS.

Vancomycin: conformational consequences of the sugar substituent

High-resolution, three-dimensional structures of vancomycin and aglyco-vancomycin in DMSO were determined by nuclear magnetic resonance, metric matrix distance geometry, and molecular dynamics calculations. Conformational flexibility fast on the NMR time scale was examined by ensemble-based calculations which apply the experimentally derived restraints as an ensemble average. Two families of conformations of vancomycin, differing in the positioning of the vancosamine substituent, were observed. In contrast, the aglyco-vancomycin adopts only one conformation in solution. The conformations of vancomycin and the aglyco-vancomycin differ in the alignment of the amide protons which participate in the hydrogen-bonding network with the cell-wall precursor and orientation of the aromatic rings relative to the backbone. Therefore, the high-resolution structural characterization provides insight into a possible role of glycosylation on the activity of this important family of antibiotics.

Affinity capillary electrophoresis: a physical-organic tool for studying interactions in biomolecular recognition

Affinity capillary electrophoresis (ACE) is a technique that is used to measure the binding affinity of receptors to neutral and charged ligands. ACE experiments are based on differences in the values of electrophoretic mobility of free and bound receptor. Scatchard analysis of the fraction of bound receptor, at equilibrium, as a function of the concentration of free ligand yields the dissociation constant of the receptor-ligand complex. ACE experiments are most conveniently performed on fused silica capillaries using a negatively charged receptor (molecular mass < 50 kDa) and increasing concentrations of a low molecular weight, charged ligand in the running buffer. ACE experiments that involve high molecular weight receptors may require the use of running buffers containing zwitterionic additives to prevent the receptors from adsorbing appreciably to the wall of the capillary. This review emphasizes ACE experiments performed with two model systems: bovine carbonic anhydrase II (BCA II) with arylsulfonamide ligands and vancomycin (Van), a glycopeptide antibiotic, with D-Ala-D-Ala (DADA)-based peptidyl ligands. Dissociation constants determined from ACE experiments performed with charged receptors and ligands can often be rationalized using electrostatic arguments. The combination of differently charged derivatives of proteins - protein charge ladders - and ACE is a physical-organic tool that is used to investigate electrostatic effects. Variations of ACE experiments have been used to estimate the charge of Van and of proteins in solution, and to determine the effect of the association of Van to Ac2KDADA on the value of pKa of its N-terminal amino group.

Synthesis of 2"-oxidized derivatives of 5-deoxy-5-epi-5-fluoro-dibekacin and -arbekacin, and study on structure-chemical shift relationships of urethane(or amide)-type NH protons in synthetic intermediates

Three 2"-modified dibekacin-analogs have been prepared as potential compounds active against resistant bacteria producing 2"-O-phosphotransferases; one is 5-deoxy-5,2"-diepi-5-fluorodibekacin (9) prepared from a suitably protected 2"-O-triflyl derivative through the 2" 3"-cyclic carbamate, and the others are 2"-oxo derivatives (12 and 22, both as the hydrate) of 5-deoxy-5-epi-5-fluoro-dibekacin and -arbekacin prepared through oxidation at C-2" of suitably protected derivatives. Relationships between the t-butoxycarbonyl(= Boc)-NH-shifts of per-N-Boc synthetic intermediates and their structures were studied. It was found that the shifts, measured in pyridine-d5 at 80 degrees C, which spread over a close range (delta 6-7 ppm), are sensitively influenced by nearby and surrounding groups around the BocNH group in respect of electron-withdrawing character, hydrogen bonding (BocNH ... acceptor), and also solvent effects (BocNH ... NC5H5).

Use of capillary electrophoresis to measure dimerization of glycopeptide antibiotics

Capillary electrophoretic methods were used to examine dimerization and estimate dimerization constants (Kdim) for the glycopeptide antibiotics vancomycin, ristocetin A, and LY264826 (A82846B). The Kdim for LY264826 was 60- and 200-fold higher than the Kdim for ristocetin A and vancomycin, respectively. Dimerization of vancomycin measured in the presence of the cell wall analog N, N'-diacetyl-L-Lys-D-Ala-D-Ala was enhanced 200-fold; however, dimerization of ristocetin A was antagonized by the presence of N, N'-diacetyl-L-Lys-D-Ala-D-Ala. The relative differences in Kdim determined by capillary electrophoresis in general follow the same trend as those observed using nuclear magnetic resonance spectroscopy and sedimentation equilibrium.

Simulated dipeptide recognition by vancomycin

The antimicrobial activity of vancomycin and related glycopeptide antibiotics is due to stereospecific recognition of polypeptide components in bacterial cell walls. To better understand how these antibiotics recognize polypeptide determinants, we have developed dynamic models of the complexes formed by the vancomycin aglycon and two different dipeptide ligands, Ac-D-ala-D-ala and Ac-D-ala-gly. Molecular dynamics simulations of the two complexes, initially conditioned with distance constraints derived from two-dimensional nuclear magnetic resonance (NMR) studies, are conformationally stable and propagate in a manner consistent with the NMR-derived constraints after the constraints are removed. Free energy calculations accurately predict the relative binding affinity of these two complexes and help validate the simulation models for detailed structural analysis. Although the two ligands adopt similar conformations when bound to the antibiotic, there are clear differences in the configuration of intermolecular hydrogen bonds, the overall shape of the antibiotic, and other structural features of the two complexes. This analysis illustrates how complex structural and dynamic factors interrelate and contribute to differences in binding affinity.

Inhibition of peptidoglycan biosynthesis in vancomycin-susceptible and -resistant bacteria by a semisynthetic glycopeptide antibiotic

LY191145 is a p-chlorobenzyl derivative of LY264826 (A82846B) with activity against both vancomycin-susceptible and -resistant enterococci. Incorporation of L-[14C]lysine into peptidoglycan of intact vancomycin-susceptible and -resistant Enterococcus faecium was inhibited by LY191145 (50% inhibitory concentrations of 1 and 5 microgram/ml, respectively). Inhibition was accompanied by accumulation of UDP-muramyl-peptide precursors in the cytoplasm. This agent inhibited late-stage steps in peptidoglycan biosynthesis in permeabilized E. faecium when either the UDP-muramyl-pentapeptide precursor from vancomycin-susceptible E. faecium or the UDP-muramyl-pentadepsipeptide precursor from vancomycin-resistant E. faecium was used as a substrate. Inhibition of late-stage steps led to accumulation of an N-acetyl-[14C]glucosamine-labeled lipid intermediate indicative of inhibition of the transglycosylation step. Inhibition of peptidoglycan polymerization without affecting cross-linking in a particulate membrane-plus-wall-fragment assay from Aerococcus viridans was consistent with this explanation. The fact that inhibition of peptidoglycan biosynthesis by LY191145 was not readily antagonized by an excess of free acyl-D-alanyl-D-alanine or acyl-D-alanyl-D-lactate ligands indicates that the manner in which this compound inhibits transglycosylation may not be identical to that of vancomycin.

Semisynthetic glycopeptide antibiotics derived from LY264826 active against vancomycin-resistant enterococci

Certain derivatives of the glycopeptide antibiotic LY264826 with N-alkyl-linked substitutions on the epivancosamine sugar are active against glycopeptide-resistant enterococci. Six compounds representing our most active series were evaluated for activity against antibiotic-resistant, gram-positive pathogens. For Enterococcus faecium and E. faecalis resistant to both vancomycin and teicoplanin, the MICs of the six semisynthetic compounds for 90% of the strains tested were 1 to 4 micrograms/ml, compared with 2,048 micrograms/ml for vancomycin and 256 micrograms/ml for LY264826. For E. faecium and E. faecalis resistant to vancomycin but not teicoplanin, the MICs were 0.016 to 1 micrograms/ml, compared with 64 to 1,024 micrograms/ml for vancomycin. The compounds were highly active against vancomycin-susceptible enterococci and against E. gallinarum and E. casseliflavus and showed some activity against isolates of highly vancomycin-resistant leuconostocs and pediococci. The MICs for 90% of the strains of methicillin-resistant Staphylococcus aureus tested were typically 0.25 to 1 micrograms/ml, compared with 1 microgram/ml for vancomycin. Against methicillin-resistant S. epidermidis MICs ranged from 0.25 to 2 micrograms/ml, compared with 1 to 4 micrograms/ml for vancomycin and 4 to 16 micrograms/ml for teicoplanin. The spectrum of these new compounds included activity against teicoplanin-resistant, coagulase-negative staphylococci. The compounds exhibited exceptional potency against pathogenic streptococci, with MICs of < or = 0.008 microgram/ml against Streptococcus pneumoniae, including penicillin-resistant isolates. In in vivo studies with a mouse infection model, the median effective doses against a challenge by S. aureus, S. pneumoniae, or S. pyogenes were typically 4 to 20 times lower than those of vancomycin. Overall, these new glycopeptides, such as LY307599 and LY333328, show promise for use as agents against resistant enterococci, methicillin-resistant S. aureus, and penicillin-resistant pneumococci.

Mechanism-based screens in the discovery of chemotherapeutic antibacterials

Numerous assays have been developed over the last 40 years for the detection of novel antibacterial metabolites. I have discussed many of the successful strategies and suggested some potential targets. Although the trend toward mechanism-based assays is relatively recent, it is clear that they have had a profound impact on screening in drug discovery. Often a mechanism-based assay requires construction of specific strains and verification of the antibacterial role of the selected target. Since the conception and development of a mechanism-based screen depends upon knowledge of the specific target and perhaps a compound that affects that target, it is implicit that mode of action studies on compounds discovered through random screening may subsequently lead to new mechanistic assays. While serendipity continues to play a crucial role in any screen, target-directed assays appear to be a worthwhile approach in antibacterial screening.

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.