Synthesis of modified peptidoglycan precursor analogues for the inhibition of glycosyltransferase

The peptidoglycan glycosyltransferases (GTs) are essential enzymes that catalyze the polymerization of glycan chains of the bacterial cell wall from lipid II and thus constitute a validated antibacterial target. Their enzymatic cavity is composed of a donor site for the growing glycan chain (where the inhibitor moenomycin binds) and an acceptor site for lipid II substrate. In order to find lead inhibitors able to fill this large active site, we have synthesized a series of substrate analogues of lipid I and lipid II with variations in the lipid, the pyrophosphate, and the peptide moieties and evaluated their biological effect on the GT activity of E. coli PBP1b and their antibacterial potential. We found several compounds able to inhibit the GT activity in vitro and cause growth defect in Bacillus subtilis . The more active was C16-phosphoglycerate-MurNAc-(L-Ala-D-Glu)-GlcNAc, which also showed antibacterial activity. These molecules are promising leads for the design of new antibacterial GT inhibitors.     

Oxazolidinone structure-activity relationships leading to linezolid

The development of bacterial resistance to currently available antibacterial agents is a growing global health problem. Of particular concern are infections caused by multidrug-resistant Gram-positive pathogens which are responsible for significant morbidity and mortality in both the hospital and community settings. A number of solutions to the problem of bacterial resistance are possible. The most common approach is to continue modifying existing classes of antibacterial agents to provide new analogues with improved attributes. Other successful strategies are to combine existing antibacterial agents with other drugs as well as the development of improved diagnostic procedures that may lead to rapid identification of the causative pathogen and permit the use of antibacterial agents with a narrow spectrum of activity. Finally, and most importantly, the discovery of novel classes of antibacterial agents employing new mechanisms of action has considerable promise. Such agents would exhibit a lack of cross-resistance with existing antimicrobial drugs. This review describes the work leading to the discovery of linezolid, the first clinically useful oxazolidinone antibacterial agent.     

Traffic jam at the bacterial sec translocase: targeting the SecA nanomotor by small-molecule inhibitors

The rapid rise of drug-resistant bacteria is one of the most serious unmet medical needs facing the world. Despite this increasing problem of antibiotic resistance, the number of different antibiotics available for the treatment of serious infections is dwindling. Therefore, there is an urgent need for new antibacterial drugs, preferably with novel modes of action to potentially avoid cross-resistance with existing antibacterial agents. In recent years, increasing attention has been paid to bacterial protein secretion as a potential antibacterial target. Among the different protein secretion pathways that are present in bacterial pathogens, the general protein secretory (Sec) pathway is widely considered as an attractive target for antibacterial therapy. One of the key components of the Sec pathway is the peripheral membrane ATPase SecA, which provides the energy for the translocation of preproteins across the bacterial cytoplasmic membrane. In this review, we will provide an overview of research efforts on the discovery and development of small-molecule SecA inhibitors. Furthermore, recent advances on the structure and function of SecA and their potential impact on antibacterial drug discovery will be discussed.     

Discovery of kibdelomycin, a potent new class of bacterial type II topoisomerase inhibitor by chemical-genetic profiling in Staphylococcus aureus

Bacterial resistance to known therapeutics has led to an urgent need for new chemical classes of antibacterial agents. To address this we have applied?a Staphylococcus aureus fitness test strategy to natural products screening. Here we report the discovery of kibdelomycin, a novel class of antibiotics produced by a new member of the genus Kibdelosporangium. Kibdelomycin exhibits broad-spectrum, gram-positive antibacterial activity and is a potent inhibitor of DNA synthesis. We demonstrate through chemical genetic fitness test profiling and biochemical enzyme assays that kibdelomycin is a structurally new class of bacterial type II topoisomerase inhibitor preferentially inhibiting the ATPase activity of DNA gyrase and topoisomerase IV. Kibdelomycin is thus the first truly novel bacterial type II topoisomerase inhibitor with potent antibacterial activity discovered from natural product sources in more than six decades.     

Enzymatic Synthesis of Lipid II and Analogues

The emergence of antibiotic resistance has prompted active research in the development of antibiotics with new modes of action. Among all essential bacterial proteins, transglycosylase polymerizes lipid II into peptidoglycan and is one of the most favorable targets because of its vital role in peptidoglycan synthesis. Described in this study is a practical enzymatic method for the synthesis of lipid II, coupled with cofactor regeneration, to give the product in a 50–70 % yield. This development depends on two key steps: the overexpression of MraY for the synthesis of lipid I and the use of undecaprenol kinase for the preparation of polyprenol phosphates. This method was further applied to the synthesis of lipid II analogues. It was found that MraY and undecaprenol kinase can accept a wide range of lipids containing various lengths and configurations. The activity of lipid II analogues for bacterial transglycolase was also evaluated.     

Identification of Mtb GlmU Uridyltransferase Domain Inhibitors by Ligand-Based and Structure-Based Drug Design Approaches

Targeting enzymes that play a role in the biosynthesis of the bacterial cell wall has long been a strategy for antibacterial discovery. In particular, the cell wall of Mycobacterium tuberculosis (Mtb) is a complex of three layers, one of which is Peptidoglycan, an essential component providing rigidity and strength. UDP-GlcNAc, a precursor for the synthesis of peptidoglycan, is formed by GlmU, a bi-functional enzyme. Inhibiting GlmU Uridyltransferase activity has been proven to be an effective anti-bacterial, but its similarity with human enzymes has been a deterrent to drug development. To develop Mtb selective hits, the Mtb GlmU substrate binding pocket was compared with structurally similar human enzymes to identify selectivity determining factors. Substrate binding pockets and conformational changes upon substrate binding were analyzed and MD simulations with substrates were performed to quantify crucial interactions to develop critical pharmacophore features. Thereafter, two strategies were applied to propose potent and selective bacterial GlmU Uridyltransferase domain inhibitors: (i) optimization of existing inhibitors, and (ii) identification by virtual screening. The binding modes of hits identified from virtual screening and ligand growing approaches were evaluated further for their ability to retain stable contacts within the pocket during 20 ns MD simulations. Hits that are predicted to be more potent than existing inhibitors and selective against human homologues could be of great interest for rejuvenating drug discovery efforts towards targeting the Mtb cell wall for antibacterial discovery.     

表面抗菌功能涂层的构建及在生物医用材料中的应用研究

近年来,生物医用材料在使用过程中产生的医源性感染问题层出不穷,对人们健康和生命造成严重威胁.表面抗菌涂层构建是解决该类医源性感染问题最有效的策略之一.目前,按照作用机制和功能不同将表面抗菌涂层分为接触式抗菌涂层、抗黏附抑菌涂层、抗黏附杀菌涂层以及智能抗菌涂层.表面抗菌涂层的构建不仅赋予了生物医用材料抗菌性能,有效解决了...     

A revised pathway proposed for Staphylococcus aureus wall teichoic acid biosynthesis based on in vitro reconstitution of the intracellular steps

Resistance to every family of clinically used antibiotics has emerged, and there is a pressing need to explore unique antibacterial targets. Wall teichoic acids (WTAs) are anionic polymers that coat the cell walls of many Gram-positive bacteria. Because WTAs play an essential role in Staphylococcus aureus colonization and infection, the enzymes involved in WTA biosynthesis are proposed to be targets for antibiotic development. To facilitate the discovery of WTA inhibitors, we have reconstituted the intracellular steps of S. aureus WTA biosynthesis. We show that two intracellular steps in the biosynthetic pathway are different from what was proposed. The work reported here lays the foundation for the discovery and characterization of inhibitors of WTA biosynthetic enzymes to assess their potential for treating bacterial infections.     

Suppressing Alpha-Hemolysin as Potential Target to Screen of Flavonoids to Combat Bacterial Coinfection

The rapid emergence of bacterial coinfection caused by cytosolic bacteria has become a huge threat to public health worldwide. Past efforts have been devoted to discover the broad-spectrum antibiotics, while the emergence of antibiotic resistance encourages the development of antibacterial agents. In essence, bacterial virulence is a factor in antibiotic tolerance. However, the discovery and development of new antibacterial drugs and special antitoxin drugs is much more difficult in the antibiotic resistance era. Herein, we hypothesize that antitoxin hemolytic activity can serve as a screening principle to select antibacterial drugs to combat coinfection from natural products. Being the most abundant natural drug of plant origins, flavonoids were selected to assess the ability of antibacterial coinfections in this paper. Firstly, we note that four flavonoids, namely, baicalin, catechin, kaempferol, and quercetin, have previously exhibited antibacterial abilities. Then, we found that baicalin, kaempferol, and quercetin have better inhibitions of hemolytic activity of Hla than catechin. In addition, kaempferol and quercetin, have therapeutic effectivity for the coinfections of Staphylococcus aureus and Pseudomonas aeruginosa in vitro and in vivo. Finally, our results indicated that kaempferol and quercetin therapied the bacterial coinfection by inhibiting S. aureus α-hemolysin (Hla) and reduced the host inflammatory response. These results suggest that antitoxins may play a promising role as a potential target for screening flavonoids to combat bacterial coinfection.     

Antibacterial Mechanisms of Zinc Oxide Nanoparticle against Bacterial Food Pathogens Resistant to Beta-Lactam Antibiotics

The increase in β-lactam-resistant Gram-negative bacteria is a severe recurrent problem in the food industry for both producers and consumers. The development of nanotechnology and nanomaterial applications has transformed many features in food science. The antibacterial activity of zinc oxide nanoparticles (ZnO NPs) and their mechanism of action on β-lactam-resistant Gram-negative food pathogens, such as Escherichia coli, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Klebsiella pneumoniae, and Proteus mirabilis, are investigated in the present paper. The study results demonstrate that ZnO NPs possesses broad-spectrum action against these β-lactamase-producing strains. The minimal inhibitory and minimal bactericidal concentrations vary from 0.04 to 0.08 and 0.12 to 0.24 mg/mL, respectively. The ZnO NPs elevate the level of reactive oxygen species (ROS) and malondialdehyde in the bacterial cells as membrane lipid peroxidation. It has been confirmed from the transmission electron microscopy image of the treated bacterial cells that ZnO NPs diminish the permeable membrane, denature the intracellular proteins, cause DNA damage, and cause membrane leakage. Based on these findings, the action of ZnO NPs has been attributed to the fact that broad-spectrum antibacterial action against β-lactam-resistant Gram-negative food pathogens is mediated by Zn²⁺ ion-induced oxidative stress, actions via lipid peroxidation and membrane damage, subsequently resulting in depletion, leading to β-lactamase enzyme inhibition, intracellular protein inactivation, DNA damage, and eventually cell death. Based on the findings of the present study, ZnO NPs can be recommended as potent broad-spectrum antibacterial agents against β-lactam-resistant Gram-negative pathogenic strains.     

A Chemical Biology Approach to Understanding Molecular Recognition of Lipid II by Nisin(1–12): Synthesis and NMR Ensemble Analysis of Nisin(1–12) and Analogues

Natural products that target lipid II, such as the lantibiotic nisin, are strategically important in the development of new antibacterial agents to combat the rise of antimicrobial resistance. Understanding the structural factors that govern the highly selective molecular recognition of lipid II by the N-terminal region of nisin, nisin(1–12), is a crucial step in exploiting the potential of such compounds. In order to elucidate the relationships between amino acid sequence and conformation of this bicyclic peptide fragment, we have used solid-phase peptide synthesis to prepare two novel analogues of nisin(1–12) in which the dehydro residues have been replaced. We have carried out an NMR ensemble analysis of one of these analogues and of the wild-type nisin(1–12) peptide in order to compare the conformations of these two bicyclic peptides. Our analysis has shown the effects of residue mutation on ring conformation. We have also demonstrated that the individual rings of nisin(1–12) are pre-organised to an extent for binding to the pyrophosphate group of lipid II, with a high degree of flexibility exhibited in the central amide bond joining the two rings.     

A conformationally constrained fused tricyclic nisin AB-ring system mimic toward an improved pyrophosphate binder of lipid II

The bacteria-specific membrane component lipid II is essential for bacterial cell wall synthesis. A tricyclic nisin mimic was designed and synthesized in which both thioether moieties were mimicked by an alkane-bridge, as well as the introduction of a third conformational constraint consisting of a macrocyclic lactam-bridge between the N-terminus and the B-ring. The newly designed tricyclic AB-ring mimic was found to bind lipid II since it was able to inhibit nisin-induced membrane leakage in a dose-dependent manner. These results imply that the tricyclic AB-ring mimic may form a novel class of lead structures for the development of nisin-based peptide antibiotics.     

Cell-wall engineering of living bacteria

The cell walls of living bacteria were chemically modified by adding cell-wall precursors. As the precursors to be incorporated into the cell wall, UDP-MurNAc pentapeptide, lipid I, and lipid II derivatives were synthesized. The aimed compounds were attached to the amine residue of lysine at the pentapeptide moiety. Fluorescein-attached UDP-MurNAc pentapeptide was efficiently incorporated into both Gram-positive and Gram-negative bacteria. In the case of Gram-negative bacteria, such as Escherichia coli, the permeability of the outer membrane (lipopolysaccharide layer) was enhanced by EDTA treatment before the incorporation. For Gram-positive bacteria, UDP-MurNAc derivatives were incorporated in the cell wall without EDTA treatment due to the lack of the lipopolysaccharide layer. Furthermore, instead of dyes, a ketone group was attached to the UDP-MurNAc pentapeptide. The ketone group was also delivered to the bacterial cell wall of lactic acid bacteria, giving a platform to attach large molecules on the surface.     

Ligand directed synthesis of a unprecedented tetragonalbipyramidal copper (II) complex and its antibacterial activity and catalytic role in oxidative dimerisation of 2-aminophenol

In pursuit of the significant contribution of copper ion in different biological processes, this research work describes the synthesis, X-ray structure, Hirshfeld surface analysis, oxidative dimerization of 2-aminophenol and antibacterial activity of a newly designed copper (II)-Schiff base complex, [Cu( L )₂] (1), [Schiff base (H L ) = 2-(2-methoxybenzylideneamino)phenol]. X- ray structural analysis of 1 reveals that the Cu (II) complex crystallizes in a cubic crystal system with Ia-3d space group. The Cu (II) centre adopts an unprecedented tetragonal bipyramidal geometry in its crystalline phase. The Schiff base behaves as a tridentate chelator and forms an innermetallic chelate of first order with Cu (II) ion. The copper (II) complex has been tested in the bio-mimics of phenaxozinone synthase activity in acetonitrile and exhibits good catalytic activity as evident from high turnover number, 536.4 h⁻¹. Electrochemical analysis exhibits the appearance of two additional peaks at −0.15 and 0.46 V for Cu (II) complex in presence of 2-AP and suggests the development of AP⁻/AP^•− and AP^•−/IQ redox couples in solution, respectively. The presence of iminobenzosemiquinone radical at g = 2.057 in the reaction mixture was confirmed by electron paramagnetic resonance and may be considered the driving force for the oxidative dimerisation of 2-AP. The existence of a peak at m/z 624.81 for Cu (II) complex in presence of 2-AP in electrospray ionization mass spectrum ensures that the catalytic oxidation proceeds through enzyme-substrate adduct formation. The copper (II) complex exhibits potential antibacterial properties against few pathogenic bacterial species like Staphylococcus aureus, Enterococcus and Klebsiella pneumonia and scanning electron microscope studies consolidates that destruction of bacterial cell membrane accounts on the development of antibacterial activity.     

Molecular mechanisms of membrane perturbation by antimicrobial peptides and the use of biophysical studies in the design of novel peptide antibiotics

Antibiotic resistant bacterial strains represent a global health problem with a strong social and economic impact. Thus, there is an urgent need for the development of antibiotics with novel mechanisms of action. There is currently an extensive effort to understand the mode of action of antimicrobial peptides which are considered as one alternative to classical antibiotics. The main advantage of this class of substances, when considering bacterial resistance, is that they rapidly, within minutes, kill bacteria. Antimicrobial peptides can be found in every organism and display a wide spectrum of activity. Hence, the goal is to engineer peptides with an improved therapeutic index, i.e. high efficacy and target specificity. For the rational design of such novel antibiotics it is essential to elucidate the molecular mechanism of action. Biophysical studies have been performed using to a large extent membrane model systems demonstrating that there are distinctive different mechanisms of bacterial killing by antimicrobial peptides. One can distinguish between peptides that permeabilize and/or disrupt the bacterial cell membrane and peptides that translocate through the cell membrane and interact with a cytosolic target. Lantibiotics exhibit specific mechanisms, e.g. binding to lipid II, a precursor of the peptidoglycan layer, either resulting in membrane rupture by pore formation or preventing cell wall biosynthesis. The classical models of membrane perturbation, pore formation and carpet mechanism, are discussed and related to other mechanisms that may lead to membrane dysfunction such as formation of lipid-peptide domains or membrane disruption by formation of non-lamellar phases. Emphasis is on the role of membrane lipid composition in these processes and in the translocation of antimicrobial peptides.     

Examination of a synthetic benzophenone membrane-targeted antibiotic

The enormous success of antibiotics is seriously threatened by the development of resistance to most of the drugs available on the market. Thus, novel antibiotics are needed that are less prone to bacterial resistance and are directed toward novel biological targets. Antimicrobial peptides (AMPs) have attracted considerable attention due to their unique mode of action and broad spectrum activity. However, these agents suffer from liability to proteases and the high cost of manufacturing has impeded their development. Previously, we have reported on a novel class of benzophenone-based antibiotics and early studies suggested that these agents might target the bacterial membrane. In this study, we present our work on the mechanism of action of these novel membrane targeted antibiotics. These compounds have good affinities to polyanionic components of the cell wall such as lipoteichoic acid (LTA) and lipopolysaccharide (LPS). We found that these agents release potassium ions from treated bacteria; thus, resulting in disruption of the bacterial membrane potential. Benzophenone-based membrane targeted antibiotics (BPMTAs) cause membrane disruption in synthetic lipid vesicles that mimic Gram-positive or Gram-negative bacteria. The compounds display no hemolytic activity up to a concentration that is 100 times the MIC values and they are capable of curing mice of a lethal MRSA infection. Repeated attempts to develop a mutant resistant to these agents has failed. Taken together, BPMTAs represent a promising new class of membrane-targeted antibacterial agents.     

The natural and synthetic indole weaponry against bacteria

The emergence of drug resistant bacterial infections leading to high mortality rates has posed a formidable challenge to organic synthesis and medicinal chemists to deliver potent and novel antibacterial drug candidates. In particular, antibacterial agents based on novel chemotypes and first-in-class drug candidates with novel mode of actions are highly desired. Indole scaffold has found a consistent presence in the bioactive molecules of synthetic and natural origin. The potential of indole based small molecules as antibacterial agents has not been as much explored as in other areas of medicine, like cancer therapy. In this review, we present a brief account of indole based antibacterial small molecules which have been either synthesized in the laboratory or isolated from natural sources and provide intriguing potential leads in the antibiotic drug discovery research.     

Immobilization of cationic rifampicin-loaded liposomes on polystyrene for drug-delivery applications

Polymer-associated infections are a major problem in implanted or intravascular devices. Among others, microorganisms of the staphylococcal family have been identified as the most important culprit. Prevention of bacterial adhesion and colonization of polymeric surfaces by release of antimicrobial agents incorporated into the polymers itself are currently under study. We have developed a novel method for the functionalization of a polymeric surface which is based on the deposition of covalently coupled lipid structures from antibiotic loaded vesicles. We have found that such process significantly reduces the bacterial growth on polystyrene material. In this work, lipid coverage obtained from multilamellar (MLVs) and extruded unilamellar (LUVs) vesicles were analyzed with respect to their adhesion efficiency on three types of polystyrene (PS) well-plates. Two methods of lipid deposition were characterized and compared in terms of surface lipid density and time stability: deposition of cationic vesicles on negatively charged surfaces and formation of covalent linkages between functionalized lipids and amines enriched surfaces. In order to study the antibiotic encapsulation efficiency we measured how the rifampicin (RIF) loading was affected by changes of liposome charge upon introduction of various amounts of stearylamine (SA), distearoyl-trimethylammonium propane (DSTAP) or dioleoyloxypropyl-trimethylammonium chloride (DOTAP) into the liposomal formulation. RIF-coated polymeric surfaces were also tested against a Staphylococcus epidermidis strain to evaluate their efficacy in vitro, showing that only approximately 2% of such bacteria inoculated on MLV-treated PS substrate were able to proliferate. Covalently immobilized lipid films showed about a tenfold increase in time stability compared to electrostatically bonded lipid films. Furthermore, substrates covalently modified with RIF-loaded MLVs retained an antibacterial activity for up to 12 days when aged in buffer at 37 degrees C. Such antimicrobial polymer coatings show promise for their use as antibacterial barrier for the prevention of catheter-related infections.     

Synthesis of cobalt(II) and nickel(II) complexes of Ceclor (cefaclor) and preliminary experiments on their antibacterial character

Cobalt(II) and nickel(II) complexes of the antibacterial drug Ceclor have been synthesized and characterized on the basis of their elemental analysis, molar conductance, magnetic moment and electronic and infrared spectral data. These complex have been, then subjected to screening for their antibacterial properties against bacterial species such as Streptococcus pyogenes, Streptococcus pneumoniae, Staphylococcus aureus and Escherichia coli. In comparison to uncomplexed Ceclor, the metal complexes have been shown to be more antibacterial.