A Time-Resolved FRET Assay Identifies a Small Molecule that Inhibits the Essential Bacterial Cell Wall Polymerase FtsW

The peptidoglycan cell wall is essential for bacterial survival. To form the cell wall, peptidoglycan glycosyltransferases (PGTs) polymerize Lipid II to make glycan strands and then those strands are crosslinked by transpeptidases (TPs). Recently, the SEDS (for shape, elongation, division, and sporulation) proteins were identified as a new class of PGTs. The SEDS protein FtsW, which produces septal peptidoglycan during cell division, is an attractive target for novel antibiotics because it is essential in virtually all bacteria. Here, we developed a time-resolved Förster resonance energy transfer (TR-FRET) assay to monitor PGT activity and screened a Staphylococcus aureus lethal compound library for FtsW inhibitors. We identified a compound that inhibits S. aureus FtsW in vitro. Using a non-polymerizable Lipid II derivative, we showed that this compound competes with Lipid II for binding to FtsW. The assays described here will be useful for discovering and characterizing other PGT inhibitors.     

A new synthetic approach toward bacterial transglycosylase substrates, Lipid II and Lipid IV

A new synthetic approach toward the bacterial transglycosylase substrates, Lipid II (1) and Lipid IV (2), is described. The key disaccharide was synthesized using the concept of relative reactivity value (RRV) and elaborated to Lipid II and Lipid IV by conjugation with the appropriate oligopeptides and pyrophosphate lipids. Interestingly, the results from our HPLC-based functional TGase assay suggested Lipid IV has a higher affinity for the enzyme than Lipid II.     

In Vivo Probe of Lipid II‐Interacting Proteins

β‐Lactams represent one of the most important classes of antibiotics discovered to date. These agents block Lipid II processing and cell wall biosynthesis through inactivation of penicillin‐binding proteins (PBPs). PBPs enzymatically load cell wall building blocks from Lipid II carrier molecules onto the growing cell wall scaffold during growth and division. Lipid II, a bottleneck in cell wall biosynthesis, is the target of some of the most potent antibiotics in clinical use. Despite the immense therapeutic value of this biosynthetic pathway, the PBP–Lipid II association has not been established in live cells. To determine this key interaction, we designed an unnatural d ‐amino acid dipeptide that is metabolically incorporated into Lipid II molecules. By hijacking the peptidoglycan biosynthetic machinery, photoaffinity probes were installed in combination with click partners within Lipid II, thereby allowing, for the first time, demonstration of PBP interactions in vivo with Lipid II.     

Water-soluble substrates of the peptidoglycan-modifying enzyme O-acetylpeptidoglycan esterase (Ape1) from Neisseria gonorrheae

Peptidoglycan is the component of the bacterial cell wall that is essential for maintaining the shape and rigidity of the cell. As such, its polymeric structure, consisting of alternating units of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), is also a target for the action of host defense enzymes, such as lysozymes. Many bacteria have developed methods of masking their cell wall from these environmental dangers through the addition of aglycon moieties that prevent recognition or sterically hinder the degradative action of exogenous enzymes that would otherwise prove detrimental to the cell. Peptidoglycan acetyl-transferases (Pat's) and O-acetylpeptidoglycan esterases (Ape's) are the enzymes responsible for the controlled addition and removal of acetate onto the C-6 hydroxyl group of MurNAc residues in peptidoglycan. Studies on Ape1, an O-acetylpeptidoglycan esterase found in Neisseria gonorrheae, have suggested that this enzyme is essential for bacterial viability and thus presents an attractive target for antibacterial design. Previous studies on Ape1 have been hindered by the fact that Ape1's natural substrate is an insoluble polymer. In this paper we outline the design, synthesis, and testing of the water-soluble di- and monosaccharide substrate analogues 1 and 2. Both 1 and 2 serve as substrates of Ape1 with k(cat)/K(M) values of (5.1 ± 1.7) × 10(3) M(-1) s(-1) and (3.1 ± 0.8) × 10(3) M(-1) s(-1), respectively. It was determined that the substitution of the GlcNAc residue in compound 1 with an O-benzyl group in compound 2 did not significantly decrease the enzyme's affinity for the monosaccharide. These findings are important as they demonstrate that the catalytic prowess of Ape1 is not dependent on its binding to a polymeric substrate. This ensures that small molecule transition state/intermediate analogues can also capture the transition state binding energy of Ape1 and potentially serve as potent inhibitors. The synthetic route to compounds 1 and 2 could readily be modified to allow for the installation of a wide variety of functional groups at the MurNAc C-6 position in both the mono- and disaccharide scaffolds. This will serve as a general method for the construction of Ape1 substrates and inhibitors.     

Synthesis of fluorescently labeled UDP-GlcNAc analogues and their evaluation as chitin synthase substrates

[structure: see text] Chitin synthase (CS) polymerizes UDP-GlcNAc to form chitin (poly-beta(1,4)-GlcNAc), a key component of fungal cell wall biosynthesis. Little is known about the substrate specificity of chitin synthase or the scope of substrate modification the enzyme will tolerate. Following a previous report suggesting that 6-O-dansyl GlcNAc is biosynthetically incorporated into chitin, we became interested in developing an assay for CS activity based on incorporation of a fluorescent substrate. We describe the synthesis of two fluorescent UDP-GlcNAc analogues and their evaluation as chitin synthase substrates.     

The first total synthesis of lipid II: the final monomeric intermediate in bacterial cell wall biosynthesis

Bacterial peptidoglycan is composed of a network of beta-[1,4]-linked glyan strands that are cross-linked through pendant peptide chains. The final product, the murein sacculus, is a single, covalently closed macromolecule that precisely defines the size and shape of the bacterial cell. The recent increase in bacterial resistance to cell wall active agents has led to a resurgence of activity directed toward improving our understanding of the resistance mechanisms at the molecular level. The biosynthetic enzymes and their natural substrates can be invaluable tools in this endeavor. While modern experimental techniques have led to isolation and purification of the biosynthetic enzymes utilized in peptidoglycan biosynthesis, securing useful quantities of their requisite substrates from natural substrates has remained problematic. In an effort to address this issue, we report the first total synthesis of lipid II (4), the final monomeric intermediate utilized by Gram positive bacteria for peptidoglycan biosynthesis.     

Electrophilic RNA for Peptidyl‐RNA Synthesis and Site‐Specific Cross‐Linking with tRNA‐Binding Enzymes

RNA functionalization is challenging due to the instability of RNA and the limited range of available enzymatic reactions. We developed a strategy based on solid phase synthesis and post‐functionalization to introduce an electrophilic site at the 3′ end of tRNA analogues. The squarate diester used as an electrophile enabled sequential amidation and provided asymmetric squaramides with high selectivity. The squaramate‐RNAs specifically reacted with the lysine of UDP‐MurNAc‐pentapeptide, a peptidoglycan precursor used by the aminoacyl‐transferase FemX_Wv for synthesis of the bacterial cell wall. The peptidyl‐RNA obtained with squaramate‐RNA and unprotected UDP‐MurNAc‐pentapeptide efficiently inhibited FemX_Wv. The squaramate unit also promoted specific cross‐linking of RNA to the catalytic Lys of FemX_Wv but not to related transferases recognizing different aminoacyl‐tRNAs. Thus, squaramate‐RNAs provide specificity for cross‐linking with defined groups in complex biomolecules due to its unique reactivity.     

A proteomic approach for the study of Saccharomyces cerevisiae cell wall biogenesis

In fungi, cell shape is determined by the presence of a rigid cell wall which separates the cell from the extracellular medium. This highly dynamic structure is essential for the maintenance of cell integrity and is involved in several phenomena such as flocculation, adherence and pathogenicity. The composition of the fungal cell wall is well known, but issues such as the assembly and remodeling of its components remain poorly understood. In an attempt to study the de novo construction of the yeast cell wall, we have undertaken a large-scale proteomic approach to analyze the proteins secreted by regenerating protoplasts. Upon incubation of protoplasts in regenerating conditions, numerous proteins are secreted into the culture medium. These presumably include proteins destined for the cell wall, comprising both structural proteins as well as enzymes involved in cell wall biogenesis. This work reports the establishment of a reference map of proteins secreted by regenerating protoplasts by means of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and their identification by mass spectrometry. Thirty-two different proteins have been identified, including known cell wall proteins, glycolytic enzymes, heat shock proteins, and proteins involved in several other processes. Using this approach, novel proteins possibly involved in cell wall construction have also been identified. This reference map will allow comparative analyses to be carried out on a selected collection of mutants affected in the cell wall.     

外源铜增强天然铜锌超氧化物歧化酶断裂DNA的活性

铜锌超氧化物歧化酶（CuZnSOD）作为一种抗氧化酶, 最重要的功能是催化超氧阴离子歧化为过氧化氢和氧气。然而最近研究发现CuZnSOD具有过氧化物酶活性,能导致核酸、蛋白质和细胞膜的损伤。本工作采用光谱学和酶学方法研究外源Cu(Ⅱ)与CuZnSOD之间的相互作用,以及H₂O₂存在下外源Cu(Ⅱ)对 CuZnSOD断裂DNA活性的增强效应。比较CuZnSOD + nCu(Ⅱ) (n=0, 1, 2, 4, 6, 8)和单独Cu(Ⅱ)分别断裂DNA的活性,表明外源Cu(Ⅱ)的加入可显著增强CuZnSOD断裂DNA的活性。相对酶活力和稳态动力学的测定证实了这种增强效应。pH依赖性实验表明断裂DNA的最适pH范围为pH3.6-5.6和pH9.0-10,在不同的pH区域CuZnSOD + nCu(Ⅱ)断裂DNA途径可能不同。     

Catalytic inhibition of topoisomerase II by a novel rationally designed ATP-competitive purine analogue

Background

Topoisomerase II poisons are in clinical use as anti-cancer therapy for decades and work by stabilizing the enzyme-induced DNA breaks. In contrast, catalytic inhibitors block the enzyme before DNA scission. Although several catalytic inhibitors of topoisomerase II have been described, preclinical concepts for exploiting their anti-proliferative activity based on molecular characteristics of the tumor cell have only recently started to emerge. Topoisomerase II is an ATPase and uses the energy derived from ATP hydrolysis to orchestrate the movement of the DNA double strands along the enzyme. Thus, interfering with ATPase function with low molecular weight inhibitors that target the nucleotide binding pocket should profoundly affect cells that are committed to undergo mitosis.

Results

Here we describe the discovery and characterization of a novel purine diamine analogue as a potent ATP-competitive catalytic inhibitor of topoisomerase II. Quinoline aminopurine compound 1 (QAP 1) inhibited topoisomerase II ATPase activity and decatenation reaction at sub-micromolar concentrations, targeted both topoisomerase II alpha and beta in cell free assays and, using a quantitative cell-based assay and a chromosome segregation assay, displayed catalytic enzyme inhibition in cells. In agreement with recent hypothesis, we show that BRCA1 mutant breast cancer cells have increased sensitivity to QAP 1.

Conclusion

The results obtained with QAP 1 demonstrate that potent and selective catalytic inhibition of human topoisomerase II function with an ATP-competitive inhibitor is feasible. Our data suggest that further drug discovery efforts on ATP-competitive catalytic inhibitors are warranted and that such drugs could potentially be developed as anti-cancer therapy for tumors that bear the appropriate combination of molecular alterations.     

Bacillus licheniformis peptidoglycan characterization by CZE–MS: Assessment with the benchmark RP‐HPLC‐MS method

Peptidoglycan or murein is an essential polymer found in bacterial cell wall. It is a dynamic structure that is continuously remodeled or modified during bacterial cell growth or in presence of cell wall stresses. These modifications are still poorly understood mainly due to the peptidoglycan, which is rather non‐soluble, and the difficulties to separate the hydrophilic glycopeptides (muropeptides) by reversed phase liquid chromatography, generated by the enzymatic digestion using mutanolysin, an N‐acetyl‐muramidase, cleaving the β_1→4 bound between N‐acetylglucosamine and N‐acetylmuramic acid. Here, we report the use of CZE–MS for an easy and fast screening of muropeptides generated by the action of muramidase on the Bacillus licheniformis cell wall. Electron transfer and CID–MS were also used to unambiguously identify and localize the presence or the absence of amidation and acetylation moieties on muropeptide variants. The reference method to analyse muropeptides by reversed phase chromatography was also tested and the advantages and disadvantages of both methods were evaluated.     

Structure,surface analysis and bioactivity of Mn doped zinc oxide nanoparticles

Undoped zinc oxide nanoparticles and Mn (5 atomic % & 10 atomic %) doped zinc oxide nanoparticles were prepared by soft chemical method. Antibacterial, antioxidant and anticancer activities in breast cancer cell line MDAMB231 of prepared nanoparticles were investigated. The nanoparticles were characterized using XRD, SEM, EDAX, UV–Vis, FT-IR, and room temperature PL Analysis. Antimicrobial activity was tested against both gram positive and gram negative human pathogens. The antioxidant potential of prepared nanoparticles was estimated using Phosphomolybdate and DPPH assay. The MTT assay was used for cytotoxicity evaluation of prepared nanoparticles against breast cancer cell line MDAMB231. XRD patterns confirmed the nanoparticles were crystallized hexagonal wurtzite structure with an average size of 38.95 ?nm. The absorption wavelength was observed at 361 ?nm in UV–Vis spectrum of Mn (10 atomic %) doped ZnO nanoparticles. The Mn (5 atomic %) doped ZnO nanoparticles exhibited significant antibacterial activity against the gram negative bacteria Escherichia coli, Klebsiella pneumonia at all concentrations. Undoped zinc oxide nanoparticles and Mn doped zinc oxide nanoparticles were effective against the breast cancer cell line MDAMB231.     

Loosening of Lipid Packing Promotes Oligoarginine Entry into Cells

Despite extensive use of arginine‐rich cell‐penetrating peptides (CPPs)—including octaarginine (R8)—as intracellular delivery vectors, mechanisms for their internalization are still under debate. Lipid packing in live cell membranes was characterized using a polarity‐sensitive dye (di‐4‐ANEPPDHQ), and evaluated in terms of generalized polarization. Treatment with membrane curvature‐inducing peptides led to significant loosening of the lipid packing, resulting in an enhanced R8 penetration. Pyrenebutyrate (PyB) is known to facilitate R8 membrane translocation by working as a hydrophobic counteranion. Interestingly, PyB also actively induced membrane curvature and perturbed lipid packing. R8 is known to directly cross cell membranes at elevated concentrations. The sites of R8 influx were found to have looser lipid packing than surrounding areas. Lipid packing loosening is proposed as a key factor that governs the membrane translocation of CPPs.     

Lytic transglycosylase MltB of Escherichia coli and its role in recycling of peptidoglycan strands of bacterial cell wall

The cell wall is an indispensable structure for the survival of bacteria and a target for antibiotics. Peptidoglycan is the major constituent of the cell wall, which is comprised of backbone repeats of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). A peptide stem is appended to the NAM unit, which in turn experiences cross-linking with a peptide from another peptidoglycan in the final steps of cell wall assembly. In the normal course of bacterial growth, as much as 60% of the parental cell wall is recycled, a process that is not fully understood. A polymeric cell wall is fragmented by the family of lytic transglycosylases, and certain key fragments are transported to the cytoplasm for recycling. The genes for the six known lytic transglycosylases of Escherichia coli were cloned, and the enzymes were purified in this study. It is shown that MltB is the only lytic transglycosylase to turn over a synthetic peptidoglycan fragment of two NAG-NAM repeats; hence this enzyme is likely to be the lytic transglycosylase responsible for processing of shorter peptidoglycan strands. Lytic transglycosylases have been proposed to go through an oxocarbenium species that would trap the 6-hydroxyl moiety of the glucosamine residue of muramic acid to generate the so-called 1,6-anhydromuramyl moiety. It is documented herein by characterization of the products of turnover that this process takes place to the total exclusion of the entrapment of a water molecule by the reactive intermediary oxocarbenium species. Furthermore, turnover of the E. coli sacculus (whole cell wall) by MltB was characterized. It is documented that each MltB molecule is able to process the cell wall 14000 times in the course of a single doubling time for E. coli.     

Melanosomal damage in normal human melanocytes induced by UVB and metal uptake--a basis for the pro-oxidant state of melanoma

Melanins are ubiquitous catecholic pigments, formed in organelles called melanosomes within melanocytes, the function of which is to protect skin against harmful effects of UV radiation. Melanosomes within melanoma cells are characteristically abnormal, with fragmented melanin and disrupted membranes. We hypothesize that the disruption of melanosomal melanin might be an early event in the etiology and progression of melanoma, leading to increased oxidative stress and mutation. In this report, we examine the effect of a combination of UV treatment and metal ion exposure on melanosomes within melanocytes, as well as their ability to act as pro-oxidants in ex situ experiments, and assay the effects of this treatment on viability and cell cycle progression. UVB exposure causes morphologic changes of the cells and bleaching of melanosomes in normal melanocytes, both significantly enhanced in Cu(II) and Cd(II)-treated cells, as observed by microscopy. The promoted bleaching by Cu(II) is due to its ability to redox cycle under oxidative conditions, generating reactive oxygen species; verified by the observed enhancement of hydroxyl radical generation when isolated melanosomes were treated with both Cu(II) ions and UVB, as assayed by DNA clipping. Single-dose UVB/Cu treatment does not greatly affect cell viability or cell cycle progression in heavily pigmented cells, but did so in an amelanotic early stage melanoma cell line.     

Immobilization of lysozyme-cellulose amide-linked conjugates on cellulose I and II cotton nanocrystalline preparations

Lysozyme was attached through an amide linkage between some of the protein’s aspartate and glutamate residues to amino-glycine-cellulose, which was prepared by esterification of glycine to preparations of cotton nanocrystals. The nanocrystalline preparations were produced through acid hydrolysis and mechanical breakage of the cotton fibers from a scoured and bleached cotton fabric and a scoured and bleached, mercerized fabric, which was shown to produce cellulose I (NCI) and cellulose II (NCII) crystals respectively. A carbodiimide-activation coupling reaction was used to create the lysozyme-amino-glycine-cellulose conjugates using both NCI and NCII in a polar solvent and gave yields of covalently linked lysozyme at 604 mg/gram of cotton nanocrystal. The incorporation of lysozyme conjugated to the NCI and NCII preparations gave very high activity (1,500 U/mg cotton) when assessed using a fluorescence tag assay to measure antimicrobial activity against Micrococcus lysodeikticus. Scanning electron micrographs demonstrated an aggregation of nanoparticles corresponding to lysozyme bound on the surface of larger cotton nanocrystalline sheets. The approach of producing high enzyme activity on cotton nanocrystals is discussed in the context of selectively presenting robust hydrolase activity on nanocrystalline surfaces.     

Characterization of a distinct arabinofuranosyltransferase in Mycobacterium smegmatis

The D-arabinans in Mycobacterium are essential, extraordinarily complex entity comprised of d-arabinofuranose residues which are rarely found in nature. Despite the well-recognized importance of the mycobacterial arabinan, delineation of the arabinosylation process has been severely hampered due to lack of positively identified arabinosyltransferases. Identification of genes involved in arabinan biosynthesis entailed the use of ethambutol (EMB), a first-line antituberculosis agent that is known to inhibit cell wall arabinan synthesis. The three genes (embA, embB, and embC) encode novel membrane proteins, implicated as the only known mycobacterial arabinosyltransferases to this date. We have now adapted a multifaceted approach involving development of convenient arabinosyltransferase assay using novel synthetic acceptors to identify arabinosyltransferase/s that will be distinct from the Emb proteins. In our present work, Mycobacterium smegmatis mc(2) 155 (WTMsm) was used as a model to study the biosynthesis of cell wall arabinan. In an in vitro assay, we demonstrate that transfer of only alpha-Araf had occurred from decaprenylphosphoryl-D-arabinofuranose (DPA) on a newly synthesized branched acceptor [alpha-D-Araf](2)-3,5-alpha-D-Araf-(1-->5)-alpha-d-Araf-(1-->5)-alpha-D-Araf with an octyl aglycon. Higher molecular weight (up to Ara(10)) oligomers were also detected in a parallel reaction using cold phosphoribosepyrophosphate (pRpp). Matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (MALDI-TOF MS/MS) analysis of these products revealed that isomeric products were formed and initiation and elongation of arabinan can occur either on the 5-arm or 3-arm of the branched 3,5-alpha-D-Araf. Individual embA, embB, and embC knockout strains retained this alpha-1,5 arabinosyltransferase activity, and the activity was partially inhibited by ethambutol. This particular enzyme function is distinct from the function of the Emb proteins.     

Development of a microchip capillary electrophoresis method for determination of the purity and integrity of mRNA in lipid nanoparticle vaccines

Messenger RNA (mRNA)-based vaccines are advantageous because they can be relatively quicker and more cost efficient to manufacture compared to other traditional vaccine products. Lipid nanoparticles have three common purposes: delivery, self-adjuvanting properties, and mRNA protection. Faster vaccine development requires an efficient and fast assay to monitor mRNA purity and integrity. Microchip CE is known to be a robust technology that is capable of rapid separation. Here, we describe the development and optimization of a purity and integrity assay for mRNA-based vaccines encapsulated in lipid nanoparticles using commercial microchip-based separation. The analytical parameters of the optimized assay were assessed and the method is a stability indicating assay.     

In vitro pro-oxidant action of Methotrexate in presence of white light

Methotrexate (MTX) an anti-cancer drug as well as a photosensitizer is able to generate reactive oxygen species (ROS). Cu (II) is present associated with chromatin in cancer cells and has been shown to be capable of mediating the action of several anti-cancer drugs through production of ROS. The objective of the present study is to determine Cu (II) mediated anti-cancer mechanism of MTX under photoilluminated condition as well as alone, using alkaline single cell gel electrophoresis (comet assay). We have shown that cellular DNA breakage was enhanced when Cu (II) is used with MTX as compared to MTX alone. It is also shown that MTX alone as well as in combination with Cu (II) is able to generate oxidative stress in lymphocyte which is inhibited by scavengers of ROS but the pattern of inhibition was differential as was also demonstrated by plasmid nicking assay. Thus, we can say that MTX exhibit pro-oxidant action in presence of white light which gets elevated in presence of Cu (II). Hence, we propose that the mobilization of endogenous copper is possibly involved in killing of cancer cells by MTX during chemo-radio therapy besides acting as antifolate.