Bacterial Cell Wall Formation Research Articles

Penicillin-binding protein (PBP) inhibitor development: A 10-year chemical perspective.

Bacterial cell wall formation is essential for cellular survival and morphogenesis. The peptidoglycan (PG), a heteropolymer that surrounds the bacterial membrane, is a key component of the cell wall, and its multistep biosynthetic process is an attractive antibacterial development target. Penicillin-binding proteins (PBPs) are responsible for cross-linking PG stem peptides, and their central role in bacterial cell wall synthesis has made them the target of successful antibiotics, including β-lactams, that have been used worldwide for decades. Following the discovery of penicillin, several other compounds with antibiotic activity have been discovered and, since then, have saved millions of lives. However, since pathogens inevitably become resistant to antibiotics, the search for new active compounds is continuous. The present review highlights the ongoing development of inhibitors acting mainly in the transpeptidase domain of PBPs with potential therapeutic applications for the development of new antibiotic agents. Both the critical aspects of the strategy, design, and structure-activity relationships (SAR) are discussed, covering the main published articles over the last 10 years. Some of the molecules described display activities against main bacterial pathogens and could open avenues toward the development of new, efficient antibacterial drugs.

Unlocking the Secrets of Streptococcus suis: A peptidomics comparison of virulent and non-virulent serotypes 2, 14, 18, and 19.

Streptococcus suis (S. suis) is an important bacterial pathogen, that causes serious infections in humans and pigs. Although numerous virulence factors have been proposed, their particular role in pathogenesis is still inconclusive. The current study explored putative peptides responsible for the virulence of S. suis serotype 2 (SS2). Thus, the peptidome of highly virulent SS2, less prevalent SS14, and rarely reported serotypes SS18 and SS19 were comparatively analyzed using a high-performance liquid chromatography-mass spectrometry method (LC-MS/MS). Six serotype-specific peptides, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase (DapH), alanine racemase (Alr), CCA-adding enzyme (CCA), peptide chain release factor 3 (RF3), ATP synthase subunit delta (F0F1-ATPases) and aspartate carbamoyltransferase (ATCase), were expressed moderately to highly only in the SS2 peptidome with p-values of less than 0.05. Some of these proteins are responsible for bacterial cellular stability; especially, Alr was highly expressed in the SS2 peptidome and is associated with peptidoglycan biosynthesis and bacterial cell wall formation. This study indicated that these serotype-specific peptides, which were significantly expressed by virulent SS2, could serve as putative virulence factors to promote its competitiveness with other coexistences in a particular condition. Further in vivo studies of these peptides should be performed to confirm the virulence roles of these identified peptides.

Screening Indonesian Pine (Pinus merkusii Jungh at de Vriese) Compound as an Antibacterial Agent: In Vitro and In Silico Study

Pinus merkusii is empirically used as an antibacterial agent and has been found to have secondary metabolites such as alkaloids, terpenoids, and flavonoids. This study aims to investigate the antibacterial effects of pine flower extract on gram-positive and gram-negative bacteria. In addition, molecular docking and molecular dynamics simulations were used to understand the underlying mechanism of its antibacterial activity. The antibacterial screening was performed using the disc diffusion method, compound analysis in the extract was carried out using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS), molecular docking was performed using Autodock Vina integrated into PyRx, and molecular dynamics simulation was run using YASARA Dynamics. The antibacterial test results showed that the pine flower extract had the highest inhibitory effect on Escherichia coli (1.038 ± 0.169 mm) and Staphylococcus aureus (7.154 ± 0.381 mm). Compound analysis of the pine flower extract showed the presence of Myricetin, Epicatechin, Nepetin, Hispidulin, Kaempferol, Luteolin-7-O-rutinoside, and Hesperidin. The molecular docking and molecular dynamics simulation results showed that Epicatechin, Nepetin, and Luteolin-7-O-rutinoside compounds could inhibit bacterial cell wall formation proteins.

D-amino Acids Ameliorate Experimental Colitis and Cholangitis by Inhibiting Growth of Proteobacteria: Potential Therapeutic Role in Inflammatory Bowel Disease

D-amino acids, the chiral counterparts of protein L-amino acids, were primarily produced and utilized by microbes, including those in the human gut. However, little was known about how orally administered or microbe-derived D-amino acids affected the gut microbial community or gut disease progression. The ratio of D- to L-amino acids was analyzed in feces and blood from patients with ulcerative colitis (UC) and healthy controls. Also, composition of microbe was analyzed from patients with UC. Mice were treated with D-amino acid in dextran sulfate sodium colitis model and liver cholangitis model. The ratio of D- to L-amino acids was lower in the feces of patients with UC than that of healthy controls. Supplementation of D-amino acids ameliorated UC-related experimental colitis and liver cholangitis by inhibiting growth of Proteobacteria. Addition of D-alanine, a major building block for bacterial cell wall formation, to culture medium inhibited expression of the ftsZ gene required for cell fission in the Proteobacteria Escherichia coli and Klebsiella pneumoniae, thereby inhibiting growth. Overexpression of ftsZ restored growth of E.coli even when D-alanine was present. We found that D-alanine not only inhibited invasion of pathological K.pneumoniae into the host via pore formation in intestinal epithelial cells but also inhibited growth of E.coli and generation of antibiotic-resistant strains. D-amino acids might have potential for use in novel therapeutic approaches targeting Proteobacteria-associated dysbiosis and antibiotic-resistant bacterial diseases by means of their effects on the intestinal microbiota community.

Antibiotska terapija kod kritično obolelih pacijenata sa sepsom - od koncepta FK/FD do novih lekova

Early detection of sepsis and its severity is critical for initiating proper therapy, including antibiotics, as soon as possible to maximize survival chances. Understanding the pathophysiological changes in septic shock that impact antimicrobial pharmacokinetics and pharmacodynamics (PK/PD), understanding the basics of PK/PD, and knowing PK-PD strategies in septic shock patients are all critical for appropriate therapy. By definition multi-drug resistant (MDR) microorganisms are those with acquired non-susceptibility to at least one agent in three or more antimicrobial categories. In the race between bacteria and novel antibiotics development, unfortunately, the number of new antibiotics/indications is not keeping pace with resistance and needs, especially for MDR Gram-negative microorganisms. When we fast forward to the approved antibiotics in the last five years, the list is rather short. Lefamulin is a novel pleuromutilin antibiotic which manifests activity against most Gram-positive pathogens. Cefiderocol is an injectable siderophore cephalosporin. Like other b-lactam antibiotics, it inhibits Gram-negative bacterial cell wall formation by binding to penicillin-binding proteins. Imipenem/cilastatin/relebactam is a new b-lactam/b-lactamase inhibitor combination with activity against MDR Gram-negative bacteria, including many CRE but excluding Metallo-b-lactamase (MBL)-producing Enterobacterales and CRAB. Those three antibiotics were FDA approved in 2019 and European Medicines Agency (EMA) approved in 2020. Plazomicin is a new semisynthetic aminoglycoside with activity against several MDR Gram-negative organisms, including CRE (FDA-approved in 2018). Meropenem-vaborbactam is a fixed-dose combination product of a carbapenem and a cyclic boronic acid b-lactamase inhibitor with potent activity against resistant Gram-negative bacteria like Klebsiella pneumoniae carbapenemase (KPC)-producing CRE; it is inactive against CRAB (FDA-approved in 2017; EMA-approved in 2018). Eravacycline is a new completely synthesized fluorocycline. It has a high level of effectiveness against Grampositive and Gram-negative bacterial strains that have developed tetracycline-specific resistance mechanisms; it is inactive against Pseudomonas aeruginosa (FDAand EMA-approved in 2018). Concluding this list of recently approved antibiotics is omadacycline, novel aminomethylcycline and a derivative of minocycline, with a chemical structure similar to tigecycline. Like other tetracyclines, omadacycline inhibits bacterial protein synthesis and possesses broad-spectrum antibacterial activity against Gram-positive and Gram-negative aerobic, anaerobic, and atypical bacteria including CRAB. It is inactive against Pseudomonas aeruginosa (FDA-approved in 2018). There are three novel carbapenems sulopenem, tebipenem pivoxil hydrobromide and benapenem. There is a group of antibiotics in phase III clinical trials: the combination aztreonam/ avibactam, sulbactam/durlobactam, cefepime/enmetazobactam, cefepime/zidebactam, cefepime/taniborbactam. An interesting approach to antimicrobial treatment is antimicrobial drug repurposing. Drug combinations could be a strategy to extend the life of antibiotics in the XXI century due to the multi-targeting mechanisms of agents. New active substances are urgently required to stop the spread of antibiotic-resistant bacteria. However, it could be a rather cumbersome and expensive procedure. Antimicrobial misuse and/or overuse contribute greatly to this very important global healthcare problem.

Investigations into the antibacterial effects and potential mechanism of gambogic acid and neogambogic acid.

The growing threat of antibiotic-resistant bacterial infections to public health necessitates the development of novel antibacterial agents. Inhibiting bacterial cell wall synthesis has remained a key focus for antibiotic development. Our search for inhibitors of undecaprenyl diphosphate synthase (UPPS), an essential enzyme required for bacterial cell wall formation, revealed that two primary components of gamboge, gambogic acid (GA) and neogambogic acid (NGA), significantly inhibited the activity of Enterococcus faecalis UPPS (EfaUPPS) with the half maximal inhibitory concentrations (IC50) of 3.08 μM and 3.07 μM, respectively. In the in vitro antibacterial assay, both GA and NGA also exhibited inhibitory activities against E. faecalis with the minimal inhibitory concentrations (MICs) of 2 μg/mL. Using microscale thermophoresis, molecular docking, and enzymatic assays, we further confirmed that GA and NGA occupy the substrate binding pocket of EfaUPPS with micro-molar binding affinity, preventing the natural substrates farnesyl diphosphate (FPP) from entering. Mutagenesis analysis revealed that L91 and L146 are two key residues in the binding between GA/NGA and UPPS. Furthermore, we also demonstrated that GA and NGA can improve E. faecalis-induced undesirable inflammation in a mouse infection model. Taken together, our findings provide a basis for structural optimization of GA/NGA to develop improved antibiotic leads and enhance treatment success rates in clinical practice.

Combined Structural Analysis and Molecular Dynamics Reveal Penicillin-Binding Protein Inhibition Mode with β-Lactones.

β-Lactam antibiotics comprise one of the most widely used therapeutic classes to combat bacterial infections. This general scaffold has long been known to inhibit bacterial cell wall biosynthesis by inactivating penicillin-binding proteins (PBPs); however, bacterial resistance to β-lactams is now widespread, and new strategies are urgently needed to target PBPs and other proteins involved in bacterial cell wall formation. A key requirement in the identification of strategies to overcome resistance is a deeper understanding of the roles of the PBPs and their associated proteins during cell growth and division, such as can be obtained with the use of selective chemical probes. Probe development has typically depended upon known PBP inhibitors, which have historically been thought to require a negatively charged moiety that mimics the C-terminus of the PBP natural peptidoglycan substrate, d-Ala-d-Ala. However, we have identified a new class of β-lactone-containing molecules that interact with PBPs, often in an isoform-specific manner, and do not incorporate this C-terminal mimetic. Here, we report a series of structural biology experiments and molecular dynamics simulations that we utilized to evaluate specific binding modes of this novel PBP inhibitor class. In this work, we obtained <2 Å resolution X-ray structures of four β-lactone probes bound to PBP1b from Streptococcus pneumoniae. Despite their diverging recognition modes beyond the site of covalent modification, these four probes all efficiently labeled PBP1b, as well as other PBPs from S. pneumoniae. From these structures, we analyzed protein-ligand interactions and characterized the β-lactone-bound active sites using in silico mutagenesis and molecular dynamics. Our approach has clarified the dynamic interaction profile in this series of ligands, expanding the understanding of PBP inhibitor binding.

Flap sub-domain dynamics of serine-threonine phosphatase (Stp1) of Staphylococcus aureus: an accelerated molecular dynamics simulation study

Vancomycin and daptomycin are commonly used glycopeptide antibiotics to cure Gram-positive staphylococcal infections. The clinical isolates of mutant Staphylococcus aureus strains, Methicillin-Resistant (MRSA) and Vancomycin-Resistant (VRSA), have developed resistance against these antibiotics. A recently discovered Serine/threonine phosphatase (Stp1) is an Mn+2 containing protein at the active site with a flap sub-domain that participates in the phospho-signaling system of bacterial cell wall formation. The flap sub-domain probably regulates substrates recruitment and release with an extra Mn+2, possibly highly flexible as in the other homologous family of proteins. In this study, the flap sub-domain has been sampled with conventional and accelerated molecular dynamics (cMD and aMD) simulations to get other sub-optimal conformational states of the protein that are nearly impossible to observe through experimental methods. Trajectory analysis has shown that protein remained static in cMD while dynamic in aMD with RMSD of ∼2Å and ∼3Å, respectively. Accelerated MD has shown greater flexibility of ∼4 Å in the flap sub-domain, while cMD only captured a deviation of ∼ 2 Å. Later, the dynamic cross-correlation map (DCCM) confirmed that the flap sub-domain is significantly more flexible than the other part of the structure, indicating its role in substrate regulation. Secondary structure transition in the flap sub-domain, i.e. 3-10 helix and turn (PRO159 - ILE163) region of the flap sub-domain shifted into α-helix, which is a more stable structure. Further, the trajectory has been clustered, and conformational states extracted, which may be exploited in structure-based antibiotics discovery.

Development and characterization of a dry reservoir-hydrogel-forming microneedles composite for minimally invasive delivery of cefazolin

Cefazolin (CFZ) is one of the most extensively used cephalosporins. This antibiotic exerts its bactericidal activity by interfering with bacterial cell wall formation, leading to bacteriolysis. CFZ is highly polar, resulting in the drug having poor oral bioavailability. Accordingly, the antibiotic is administered via intramuscular or intravenous injections, which are both painful and invasive. Due to these limitations, there is an impetus to explore alternative drug delivery platforms which offer a minimally invasive approach to delivery CFZ into and across the skin. The current work presents the development of a composite pharmaceutical system composed of hydrogel-forming microneedles (MNs) in tandem with CFZ dry reservoirs. The hydrogel system was fabricated from Gantrez® S-97 and Carbopol® 974P NF crosslinked with PEG 10,000. Swelling kinetic studies showed that the hydrogel system developed was capable of achieving 4000% swelling in PBS pH 7.4. In addition, results from a solute diffusion study showed that CFZ was able to achieve ≈100% cumulative permeation across the swollen hydrogel film. When formulated into MNs, the hydrogel system was capable of breaching the stratum corneum, resulting in intradermal insertion of the hydrogel forming MNs into ex vivo neonatal porcine skin, as evidenced from optical coherence tomography. In addition, two different CFZ loaded dry reservoirs consisting of directly compressed tablets (DCT) and lyophilised (LYO) wafers were formulated and characterised. These dry reservoir systems showed fast dissolution, dissolving in phosphate buffer saline pH 7.4 in less than one minute. In vitro permeation studies, using full thickness ex vivo neonatal porcine skin were conducted. HPLC analysis demonstrated the dry reservoir combination consisting of DCT with hydrogel-forming MNs was capable of achieving up to 80 µg CFZ delivery into the epidermis within 2 h of application. In addition, DCT reservoir coupled with hydrogel-forming MNs were able to deliver CFZ up to 1.8 mg into and across the skin at 24 h. Should this system be translated into clinical practice, it may provide a minimally invasive strategy to administer CFZ for the treatment of infections such as septic arthritis, osteomyelitis and cellulitis.

Adaptor Molecules Epitranscriptome Reprograms Bacterial Pathogenicity.

The strong decoration of tRNAs with post-transcriptional modifications provides an unprecedented adaptability of this class of non-coding RNAs leading to the regulation of bacterial growth and pathogenicity. Accumulating data indicate that tRNA post-transcriptional modifications possess a central role in both the formation of bacterial cell wall and the modulation of transcription and translation fidelity, but also in the expression of virulence factors. Evolutionary conserved modifications in tRNA nucleosides ensure the proper folding and stability redounding to a totally functional molecule. However, environmental factors including stress conditions can cause various alterations in tRNA modifications, disturbing the pathogen homeostasis. Post-transcriptional modifications adjacent to the anticodon stem-loop, for instance, have been tightly linked to bacterial infectivity. Currently, advances in high throughput methodologies have facilitated the identification and functional investigation of such tRNA modifications offering a broader pool of putative alternative molecular targets and therapeutic avenues against bacterial infections. Herein, we focus on tRNA epitranscriptome shaping regarding modifications with a key role in bacterial infectivity including opportunistic pathogens of the human microbiome.

The MurG glycosyltransferase provides an oligomeric scaffold for the cytoplasmic steps of peptidoglycan biosynthesis in the human pathogen Bordetella pertussis

Peptidoglycan is a major component of the bacterial cell wall and thus a major determinant of cell shape. Its biosynthesis is initiated by several sequential reactions catalyzed by cytoplasmic Mur enzymes. Mur ligases (MurC, -D, -E, and -F) are essential for bacteria, metabolize molecules not present in eukaryotes, and are structurally and biochemically tractable. However, although many Mur inhibitors have been developed, few have shown promising antibacterial activity, prompting the hypothesis that within the cytoplasm, Mur enzymes could exist as a complex whose architecture limits access of small molecules to their active sites. This suggestion is supported by the observation that in many bacteria, mur genes are present in a single operon, and pairs of these genes often are fused to generate a single polypeptide. Here, we explored this genetic arrangement in the human pathogen Bordetella pertussis and show that MurE and MurF are expressed as a single, bifunctional protein. EM, small angle X-ray scattering (SAXS), and analytical centrifugation (AUC) revealed that the MurE–MurF fusion displays an elongated, flexible structure that can dimerize. Moreover, MurE–MurF interacted with the peripheral glycosyltransferase MurG, which formed discrete oligomers resembling 4- or 5-armed stars in EM images. The oligomeric structure of MurG may allow it to play a bona fide scaffolding role for a potential Mur complex, facilitating the efficient conveyance of peptidoglycan-building blocks toward the inner membrane leaflet. Our findings shed light on the structural determinants of a peptidoglycan formation complex involving Mur enzymes in bacterial cell wall formation.

Insight into Elongation Stages of Peptidoglycan Processing in Bacterial Cytoplasmic Membranes

Peptidoglycan (PG) biosynthesis and assembly are needed for bacterial cell wall formation. Lipid II is the precursor in the PG biosynthetic pathway and carries a nascent PG unit that is processed by glycosyltransferases. Despite its immense therapeutic value as a target of several classes of antibiotics, the conformational ensemble of lipid II in bacterial membranes and its interactions with membrane-anchored enzymes remain elusive. In this work, lipid II and its elongated forms (lipid VI and lipid XII) were modeled and simulated in bilayers of POPE (palmitoyl-oleoyl-phosphatidyl-ethanolamine) and POPG (palmitoyl-oleoyl-phosphatidyl-glycerol) that mimic the prototypical composition of Gram-negative cytoplasmic membranes. In addition, penicillin-binding protein 1b (PBP1b) from Escherichia coli was modeled and simulated in the presence of a nascent PG to investigate their interactions. Trajectory analysis reveals that as the glycan chain grows, the non-reducing end of the nascent PG displays much greater fluctuation along the membrane normal and minimally interacts with the membrane surface. In addition, dihedral angles within the pyrophosphate moiety are determined by the length of the PG moiety and its surrounding environment. When a nascent PG is bound to PBP1b, the stem peptide remains in close contact with PBP1b by structural rearrangement of the glycan chain. Most importantly, the number of nascent PG units required to reach the transpeptidase domain are determined to be 7 or 8. Our findings complement experimental results to further understand how the structure of nascent PG can dictate the assembly of the PG scaffold.

Structure-based design of bacterial transglycosylase inhibitors incorporating biphenyl, amine linker and 2-alkoxy-3-phosphorylpropanoate moieties

Transglycosylase (TGase) is essential to biosynthesis of peptidoglycan for formation of bacterial cell wall. Moenomycin is a potent TGase inhibitor, but not used in clinic treatment due to its poor pharmacokinetics. The E−F disaccharide, phosphoglycerate and lipid tail in moenomycin are crucial elements for TGase inhibition and antibacterial activity. Based on this scaffold, a series of truncated mimics comprising biphenyl, amine linker and 2-alkoxy-3-phosphorylpropanoate moieties were designed to test their TGase inhibitory activity. In this design, the phosphorylpropanoate group is a surrogate of phosphoglycerate with improved stability. A library of lipid tails can be constructed by a straightforward approach using Cu(I)-catalyzed (3 + 2) cycloaddition reactions, and the as-synthesized triazole ring can provide additional hydrogen bonds in the TGase active site. Our molecular docking experiments reveal that the biphenyl group provides π–π and π–cation interactions to act as a simplified alternative of the C–E disaccharide in moenomycin. To play the role of the oxonium transition state in transglycosylation, the amine linker exists as a positively charged species in physiological condition to attain electrostatic interactions with acidic residues. In this study, two biphenyl-linked 2-alkoxy-3-phosphorylpropanoate compounds (8 and 10) are found to exhibit modest inhibitory activity (IC50 ≈ 150 μM) against the TGase of Acinetobacter baumannii and good antibacterial activity against Staphylococcus aureus (MIC = 6.3 μM).

Design of live attenuated bacterial vaccines based on D-glutamate auxotrophy

Vaccine development is a priority for global health due to the growing multidrug resistance in bacteria. D-glutamate synthesis is essential for bacterial cell wall formation. Here we present a strategy for generating effective bacterial whole-cell vaccines auxotrophic for D-glutamate. We apply this strategy to generate D-glutamate auxotrophic vaccines for three major pathogens, Acinetobacter baumannii, Pseudomonas aeruginosa and Staphylococcus aureus. These bacterial vaccines show virulence attenuation and self-limited growth in mice, and elicit functional and cross-reactive antibodies, and cellular immunity. These responses correlate with protection against acute lethal infection with other strains of the same species, including multidrug resistant, virulent and/or high-risk clones such as A. baumannii AbH12O-A2 and Ab307-0294, P. aeruginosa PA14, and community-acquired methicillin-resistant S. aureus USA300LAC. This approach can potentially be applied for the development of live-attenuated vaccines for virtually any other bacterial pathogens, and does not require the identification of virulence determinants, which are often pathogen-specific.

Antimicrobial Susceptibility and Molecular Mechanisms of Fosfomycin Resistance in Clinical Escherichia coli Isolates in Mainland China.

Escherichia coli is one of the most common pathogens in nosocomial and community-acquired infections in humans. Fosfomycin is a broad-spectrum antibiotic which inhibits peptidoglycan synthesis responsible for bacterial cell wall formation. Although low, the exact E. coli susceptibility to fosfomycin as well as the mechanisms of resistance in the population from Mainland China are mostly unknown. 1109 non-duplicate clinical E. coli strains isolated from urine, sputum, blood and pus samples in 20 widely dispersed tertiary hospitals from Mainland China were collected from July 2009 to June 2010, followed by determination of minimum inhibitory concentrations of fosfomycin. Detection of the murA, glpT, uhpT, fosA, fosA 3 and fosC genes was performed in fosfomycin non-susceptible E. coli strains and conjugation experiments were employed to determine the mobility of fosA 3 gene. In this study, 7.8% (86/1109) E. coli strains were fosfomycin non-susceptible. Amino acid substitutions in GlpT and MurA were found in six and four E.coli strains, respectively, while the uhpT gene was absent in eighteen E.coli strains. Twenty-nine isolates carried the transferable plasmid with the fosA 3 gene at high frequencies of around 10−6 to 10−7 per donor cell in broth mating. The majority of isolates were susceptible to fosfomycin, showing that the drug is still viable in clinical applications. Also, the main mechanism of E. coli resistance in Mainland China was found to be due to the presence of the fosA 3 gene.

Molecular Dynamics Studies of Lipid I and Lipid II in Various of Lipid Bilayer Environments

The peptidoglycan biosynthesis and assembly is needed for (both gram-negative and positive) bacterial cell wall formation. In the pathway, there are lipid-linked precursors such as lipid I (in the inner leaflet of the cytoplasmic membrane) and lipid II (in its outer leaflet). In addition, by peptidoglycan glycosyltransferase, one peptidoglycan unit from lipid II is transferred to the growing peptidoglycan oligomers attached to lipid II (lipid II-PG(x); x is the number of transferred peptidoglycan units). In this work, lipid I, lipid II-PG(0), lipid II-PG(2), lipid II-PG(5) of both gram-negative and positive bacteria are modeled and simulated in all-atom POPE/POPG (3:1; gram-negative membrane mimetics), POPE/POPG (1:3; gram-positive membrane mimetics), and POPC (neutral) bilayers. Presented and discussed are the structure and dynamics of the lipid-linked precursors and their dependence on bilayer types and vice versa. The preferred structures of these precursors are also discussed in terms of the reactions in (1) glycosyltransferase to add GlcNAc to lipid I, (2) peptidoglycan glycosyltransferase to add peptidoglycan units to lipid II-PG(x), and (3) transpeptidase that cross-links the peptidoglycan units.

A Molecular Dynamics Simulation Study of Lipid-Linked Peptidoglycan Precursors in Lipid Bilayers

The peptidoglycan biosynthesis and assembly is needed for (both Gram negative and positive) bacterial cell wall formation. In the pathway, there are lipid-linked precursors such as lipid I (in the inner leaflet) and lipid II (in the outer leaflet of the cytoplasmic membrane). In addition, by peptidoglycan glycosyltransferase, one peptidoglycan unit from lipid II is transferred to the growing peptidoglycan oligomers attached to lipid II (lipid II-PG(x); x is the number of transferred peptidoglycan units). In this work, lipid I, lipid II-PG(0), lipid II-PG(2), lipid II-PG(5) of both Gram negative and positive bacteria are modeled and simulated in all-atom POPE/POPG (3:1; Gram negative membrane mimetics), POPE/POPG (1:3; Gram positive membrane mimetics), and POPC (neutral) bilayers. Presented are the structure and dynamics of the lipid-linked precursors and their dependence on bilayer types and vice versa. The preferred structures of these precursors are also discussed in terms of the reactions in (1) glycosyltransferase to add GlcNAc to lipid I, (2) peptidoglycan glycosyltransferase to add peptidoglycan units to lipid II-PG(x), and (3) transpeptidase that cross-links the peptidoglycan units.

A 35 kDa antigenic protein from Shigella flexneri: In silico structural and functional studies

Shigella flexneri serotype 2a is a major public health concern in the developing and under-developed countries which contributes to shigellosis endemic and mortality. Thus, there is an urgent need for a rapid diagnostic test for effective therapy and disease management. Previous study showed that a ∼35kDa antigenic protein from S. flexneri is a potential biomarker. We therefore modelled the three-dimensional structure of the antigen to probe its functionality which could aid in the development of an antigen-based diagnostic. Results showed that the antigen is a transmembrane protein consists of OmpA and OmpA-like domains. The OmpA domain is a beta-barrel embedded in the outer membrane with four surface-exposed extracellular loops. The OmpA-like domain is linked to the OmpA domain with a 17 amino acids linker and located in the periplasmic. Docking of peptidoglycan into the groove of OmpA-like domain might help in catalyzing the bacterial cell wall formation. Both domains are expected to be involved in the virulence, structural stability, pathogenesis and survival of Shigella thus made the 35kDa protein a suitable shigellosis diagnostic biomarker. This structural elucidation will also enable a better identification of the epitope regions for the development of specific binders to the 35kDa antigen.

Designing New &amp;#946;-Lactams: Implications from Their Targets, Resistance Factors and Synthesizing Enzymes

Penicillins and cephalosporins are β-lactam antibiotics widely used to treat bacterial infectious diseases. They mainly target the cell wall biosynthesis pathway to inhibit bacterial growth. The targets, known as penicillin-binding proteins, are enzymes involved in the polymerization of glycan chains, cross-linking them during bacterial cell wall formation. However, the dispensation of these antibiotics has been concomitant with increasing incidence of resistance to them. Reportedly, this is due to the evolvement of two resistance mechanisms in the bacterial pathogens. One is the production of β -lactamases that cleave the β -lactam rings of penicillin and cephalosporin antibiotics, rendering them ineffective against the pathogens. Another is the modification of the targets, resulting in their inability to bind β -lactam antibiotics. Nevertheless, β -lactam antibiotics remain clinically relevant due to their high target specificity in bacteria and low toxicity to humans. Thus, to overcome the continuing emergence of resistance in pathogens, more efficacious β -lactams have to be developed and cephalosporins are often preferred over penicillins due to two alkyl sites in the cephalosporin core structure amenable for modification. Transformed β -lactams are expected to have improved antimicrobial spectra and pharmacokinetics. This is illustrated by the development of two cephalosporins, namely ceftobiprole and ceftaroline, which have shown good antimicrobial activities and are currently undergoing clinical trials. This review will discuss computer-aided studies of three enzymes closely related to cephalosporins: (1) its synthesizing enzyme, deacetoxycephalosporin C synthase, (2) its targets, the penicillin-binding proteins, and (3) its degrading enzyme, the β -lactamases, and their implications in the development of new cephalosporins.

Dalbavancin in the treatment of complicated skin and soft-tissue infections: a review

Increasing rates of antimicrobial resistance among strains of Streptococcus, Staphylococcus, and Enterococcus spp. have been widely documented. At least 50% of nosocomial Staphylococcus aureus infections in intensive care units in the US and UK are due methicillin-resistant S. aureus (MRSA). Drug resistance is not confined to hospitals, and community-acquired MRSA (CA-MRSA) strains are now common causes of complicated skin and soft-tissue infections (cSSTIs) in many regions. Dalbavancin is a novel parenterally administered semisynthetic lipoglycopeptide similar to the naturally produced glycopeptides vancomycin and teicoplanin. Dalbavancin features a multifaceted mechanism of action that inhibits bacterial cell wall formation by two different mechanisms that enhances its activity against a wide range of gram-positive bacteria including staphylococci, streptococci, enterococci, and some anaerobes. Additionally, dalbavancin possesses unique pharmacokinetic properties, the most significant of which is a long terminal half-life that allows for once weekly dosing. This attribute may prove to yield clinical and cost benefit. Overall, clinical trials indicate that dalbavancin is a safe, well-tolerated, and effective antimicrobial agent. In the largest investigation evaluating dalbavancin for the treatment of cSSTIs, it appeared to be as effective as linezolid. Dalbavancin, which is expected to receive FDA approval in 2008, appears to be a promising new antimicrobial agent for the treatment of cSSTIs.