Penicillin-binding Protein 1b Research Articles

FengycinA-M3 Inhibits Listeria monocytogenes by Binding to Penicillin-Binding Protein 2B Targets to Disrupt Cell Structure.

The contamination of food with Listeria monocytogenes threatens food safety and human health, and developing a novel, green, and safe antimicrobial substance will offer a new food preservation strategy. FengycinA-M3 is a novel lipid peptide with low cytotoxicity and resistance and has effective antibacterial activity against L. monocytogenes with a minimum inhibitory concentration (MIC) of 4 µg/mL. Further combined transcriptomics and proteomics analysis yielded 20 differentially expressed genes (DEGs). The MICs of the combined use of FengycinA-M3 and Cefalexin on L. monocytogenes were further determined as FengycinA-M3 (2 µg/mL) and Cefalexin (8 µg/mL) using the checkerboard method. In addition, FengycinA-M3 was found to play a role in delaying pork deterioration. This study explored the inhibitory effect of FengycinA-M3 on L. monocytogenes and its mechanism of action. FengycinA-M3 interacted with penicillin-binding protein 2B on the cell membrane of L. monocytogenes, destroying the permeability of the membrane, causing cell membrane rupture, thereby inhibiting the growth of L. monocytogenes. Overall, FengycinA-M3 is a promising candidate for preventing the emergence and spread of L. monocytogenes with potential applications in food processing.

Molecular Docking and Dynamic Simulation Approach to Target Penicillin-Binding Protein 1B (LpoB) of Salmonella typhimurium with Flavonoids

Background and Objective: Lipopolysaccharide (LPS) is an essential constituent of the outer membrane of gram-negative bacteria, such as Salmonella typhimurium, and it plays a crucial role by inducing disease in the host. Penicillin-binding protein 1B (LpoB) is a key enzyme in the production of peptidoglycans, making it a potential target for the development of new antimicrobials. Flavonoids are naturally occurring plant-derived chemicals with a wide range of pharmacological properties, including antibacterial capabilities. The goal of this study was to identify the potential flavonoid that inhibits the protein LpoB using computational approaches and compare it with the standard antibiotic ciprofloxacin. Methods: The study was carried out by selecting fifty flavonoids based on Lipinski’s rule of five. Molecular docking was carried out for selected flavonoids and ciprofloxacin against the LpoB protein using AutoDock 4. A 100 nanosecond molecular dynamic simulation was performed for apoprotein, LopB-fisetin, and LpoB-ciprofloxacin complexes, followed by free energy calculation by Molecular Mechanics Generalized Born Surface Area (MMGBSA) solvation analysis. Results: The docking results revealed that fisetin displayed five hydrogen bonds with a binding affinity of -4.67 kcal/mol, and ciprofloxacin exhibited a binding affinity of -4.36 kcal/mol with two hydrogen bonds. The apoprotein and fisetin complex remained stable throughout the 100 ns molecular dynamic simulation, while the ciprofloxacin complex lost its stability. The MMGBSA analysis with fisetin showed better binding free energy compared to ciprofloxacin. Conclusion: The present study has emphasized the potential of flavonoids as probable candidates that can inhibit the protein LpoB. The integration of molecular docking, dynamic simulations, and MMGBSA analysis has provided significant insight into the thermodynamics and binding interactions of the LpoB- fisetin complex, and it has enabled further experimental validations.

Boronic acid inhibitors of penicillin-binding protein 1b: serine and lysine labelling agents

Penicillin-binding proteins (PBPs) contribute to bacterial cell wall biosynthesis and are targets of antibacterial agents. Here, we investigated PBP1b inhibition by boronic acid derivatives. Chemical starting points were identified by structure-based virtual screening and aliphatic boronic acids were selected for further investigations. Structure–activity relationship studies focusing on the branching of the boron-connecting carbon and quantum mechanical/molecular mechanical simulations showed that reaction barrier free energies are compatible with fast reversible covalent binding and small or missing reaction free energies limit the inhibitory activity of the investigated boronic acid derivatives. Therefore, covalent labelling of the lysine residue of the catalytic dyad was also investigated. Compounds with a carbonyl warhead and an appropriately positioned boronic acid moiety were shown to inhibit and covalently label PBP1b. Reversible covalent labelling of the catalytic lysine by imine formation and the stabilisation of the imine by dative N–B bond is a new strategy for PBP1b inhibition.

Phytochemical Profiling and Pharmacological Evaluation of Leaf Extracts of Ruellia tuberosa L.: An In Vitro and In Silico Approach.

The present study was designed to appraise the photoprotective, antioxidant, and antibacterial bioactivities of Ruellia tuberosa leaves extracts (RtPE, RtChl, RtEA, RtAc, RtMe, and RtHMe). The results showed that, RtHMe extracts of R. tuberosa was rich in total phenolic content, i. e., 1.60 mgGAE/g dry extract, while highest total flavonoid content was found in RtAc extract, i. e., 0.40 mgQE/g. RtMe showed effective antioxidant activity (%RSA: 58.16) at the concentration of 120 μL. RtMe, RtEA and RtHMe exhibited effective in vitro antibacterial activity against Gram-negative bacteria (E. coli). In silico docking studies revealed that paucifloside (-11.743 kcal/mol), indole-3-carboxaldehyde (-7.519 kcal/mol), nuomioside (-7.275 kcal/mol), isocassifolioside (-6.992 kcal/mol) showed best docking score against PDB ID 2EX8 [penicillin binding protein 4 (dacB) from Escherichia coli, complexed with penicillin-G], PDB ID 6CQA (E. coli dihydrofolate reductase protein complexed with inhibitor AMPQD), PDB ID 2Y2I [Penicillin-binding protein 1B in complex with an alkyl boronate (ZA3)] and PDB ID 2OLV (from S. aureus), respectively. Docked phytochemicals also showed good drug likeness properties.

In silico Studies on Potential Inhibitors of the Penicillin Binding Protein 2B (PBP2B) of the Resistant G54 and Intermediate-resistant Hungary 19A-6 and SP195 Strains of Streptococcus Pneumoniae

Background: Mutations in Penicillin Binding Protein 2B (PBP2B) lead to resistance against commercial β-lactam antibiotics among some strains of Streptococcus pneumoniae. In this study, the molecular mechanism of resistance and the alternate strategy for controlling the Penicillin Binding Protein 2B (PBP2B) of resistant G54 and the two intermediate-resistant Hungary19A-6 and SP195 strains of Streptococcus pneumoniae are determined using an in silico approach. Methods: In this study, we considered four ligand compounds, namely ZINC59376795, ZINC36922620, ZINC39550705, and ZINC36953975 of the ZINC database, identified through high-throughput screening (HTS) study for the resistant strain (5204-PBP2B). Glide XP docking and molecular dynamic simulation studies were performed on the PBP2B of the three resistant strains chosen for this study. The stability analysis was performed with prime-MM/GBSA, and the binding free energy, RMSD, and RMSF were also evaluated. Results: Out of the four ligands, the ZINC39550705 ligand was found to form a stable complex with PBP2B of all three strains. Furthermore, this ZINC39550705 ligand was observed to form four hydrogen bonds with the PBP2B of all three strains. Molecular dynamics simulations were performed with these four selected ligands and targets. The resulting binding pattern, RMSD, RMSF, and hydrogen bond calculation analyses provide deeper insight into the molecular interactions of these four selected ligands with the PBP2B of the three resistance strains of S. pneumoniae. Conclusion: The interaction of the selected ligand molecules and PBP2B of the resistant strains of S. pneumoniae revealed that hydroxyl amino acid Thr at position 224, acidic amino acids including Glu at positions 301, 245, and 240, amidic amino acids, Asn at positions 265 and 260, and aliphatic amino acid Gly at the 302 position had a crucial role in the formation of hydrogen bonds with most of the selected ligands that contributed to the stability of the complexes. The molecular dynamics simulation further confirmed that the stability of ligand ZINC39550705–PBP2B of all mutant strains was higher compared to other ligand-protein complexes evaluated in the present study. Selected ligand molecules showed significant properties of the inhibitor to be used against the resistant strains of S. pneumoniae, and the ligand ZINC39550705, in particular, is a potential alternative to commercial β-lactam antibiotics.

A global genomic perspective on the multidrug-resistant Streptococcus pneumoniae 15A-CC63 sub-lineage following pneumococcal conjugate vaccine introduction.

The introduction of pneumococcal conjugate vaccines (PCV7, PCV10, PCV13) around the world has proved successful in preventing invasive pneumococcal disease. However, immunization against Streptococcus pneumoniae has led to serotype replacement by non-vaccine serotypes, including serotype 15A. Clonal complex 63 (CC63) is associated with many serotypes and has been reported in association with 15A after introduction of PCVs. A total of 865 CC63 isolates were included in this study, from the USA (n=391) and a global collection (n=474) from 1998-2019 and 1995-2018, respectively. We analysed the genomic sequences to identify serotypes and penicillin-binding protein (PBP) genes 1A, 2B and 2X, and other resistance determinants, to predict minimum inhibitory concentrations (MICs) against penicillin, erythromycin, clindamycin, co-trimoxazole and tetracycline. We conducted phylogenetic and spatiotemporal analyses to understand the evolutionary history of the 15A-CC63 sub-lineage. Overall, most (89.5 %, n=247) pre-PCV isolates in the CC63 cluster belonged to serotype 14, with 15A representing 6.5 % of isolates. Conversely, serotype 14 isolates represented 28.2 % of post-PCV CC63 isolates (n=618), whilst serotype 15A isolates represented 65.4 %. Dating of the CC63 lineage determined the most recent common ancestor emerged in the 1980s, suggesting the 15A-CC63 sub-lineage emerged from its closest serotype 14 ancestor prior to the development of pneumococcal vaccines. This sub-lineage was predominant in the USA, Israel and China. Multidrug resistance (to three or more drug classes) was widespread among isolates in this sub-lineage. We show that the CC63 lineage is globally distributed and most of the isolates are penicillin non-susceptible, and thus should be monitored.

Penicillin-binding protein 1b encoded by mrcB gene mediates the enhancement of biofilm formation by subinhibitory concentrations of cefotaxime in monophasic Salmonella Typhimurium strain SH16SP46.

Development of cefotaxime-resistance and biofilm formation increase the difficulty to prevent and control the infection and contamination of Salmonella, one of the most important foodborne and zoonotic bacterial pathogen. Our previous study observed that 1/8 minimum inhibitory concentration (MIC) of cefotaxime induced the enhancement of biofilm formation and filamentous morphological change by a monophasic Salmonella Typhimurium strain SH16SP46. This study was designed to explore the role of three penicillin-binding proteins (PBPs) in mediating the induction effect of cefotaxime. Three deletion mutants of the genes mrcA, mrcB, and ftsI, encoding the proteins PBP1a, PBP1b, and PBP3, respectively, were constructed using the parental Salmonella strain SH16SP46. Gram staining and scanning electron microscopy showed that these mutants showed normal morphology comparable to the parental strain without cefotaxime treatment. However, under the stress of 1/8 MIC of cefotaxime, the strains WT, ΔmrcA, and ΔftsI, rather than ΔmrcB, exhibited filamentous morphological change. Moreover, cefotaxime treatment significantly enhanced biofilm formation by the strains WT, ΔmrcA, and ΔftsI, but not by the ΔmrcB strain. The complement of mrcB gene in the ΔmrcB strain recovered the enhanced biofilm formation and filamentous morphological change induced by cefotaxime. Our results suggest that PBP1b encoded by mrcB gene may be a binding target of cefotaxime for initiating the effect on Salmonella morphology and biofilm formation. The study will contribute to further understanding of the regulatory mechanism of cefotaxime on Salmonella biofilm formation.

Integrative Reverse Genetic Analysis Identifies Polymorphisms Contributing to Decreased Antimicrobial Agent Susceptibility in Streptococcus pyogenes.

ABSTRACTIdentification of genetic polymorphisms causing increased antibiotic resistance in bacterial pathogens traditionally has proceeded from observed phenotype to defined mutant genotype. The availability of large collections of microbial genome sequences that lack antibiotic susceptibility metadata provides an important resource and opportunity to obtain new information about increased antimicrobial resistance by a reverse genotype-to-phenotype bioinformatic and experimental workflow. We analyzed 26,465 genome sequences of Streptococcus pyogenes, a human pathogen causing 700 million infections annually. The population genomic data identified amino acid changes in penicillin-binding proteins 1A, 1B, 2A, and 2X with signatures of evolution under positive selection as potential candidates for causing decreased susceptibility to β-lactam antibiotics. Construction and analysis of isogenic mutant strains containing individual amino acid replacements in penicillin-binding protein 2X (PBP2X) confirmed that the identified residues produced decreased susceptibility to penicillin. We also discovered the first chimeric PBP2X in S. pyogenes and show that strains containing it have significantly decreased β-lactam susceptibility. The novel integrative reverse genotype-to-phenotype strategy presented is broadly applicable to other pathogens and likely will lead to new knowledge about antimicrobial agent resistance, a massive public health problem worldwide.

Comparative genomics of invasive Streptococcus pneumoniae CC320/271 serotype 19F/19A before the introduction of pneumococcal vaccine in India.

The emergence of multi drug resistant clone CC320 serotype19F/19A and their capsular (cps) antigenic variants due to selective pressures such as vaccine had been reported worldwide. Hence, it is important to identify the prevalent clones, sequence types and cps variants of serotype 19F/19A in India, where PCV13 has been recently introduced. Multi-locus sequence typing (MLST) was performed for all (n = 21) invasive S. pneumoniae isolates of serotype 19A (n = 5) and 19F (n = 16) collected between the years 2012 and 2018 from children less than 5years. The genome characterization by whole genome sequencing for the Sequence types (STs) 320 and 271(n = 7) were performed and compared with another six Indian WGSs of similar STs available from the GPS platform. The predominant STs in the serotype 19F/19A study isolates were of CC320: ST 320, 236 and 271, associated with PMEN clone Taiwan19F-14. The WGSs of CC320 study isolates showed high genomic similarity to the Taiwan19F-14 clone, and the penicillin binding protein (PBP) amino acid sequence similarity was 100% for PBP1A, 93% for PBP 2B and 2X. Whilst PBP comparison with other global MDR ST320 strains revealed that the ST320 clones in India are of low-level penicillin resistance. The presence of a few ST320/19A/19F invasive isolates with high similarity to the Taiwan clone suggests slow and gradual expansion of Taiwan19F-14 associated CC320 clones in India. Since serotype 19F/19A is covered by PCV13 vaccine, the expansion of 19F/19A cones with non-PCV13 vaccine serotype in India should be monitored.

Analysis of Amino Acid Sequences of Penicillin-Binding Proteins 1a, 2b, and 2x in Invasive Streptococcus pneumoniae Nonsusceptible to Penicillin Isolated from Children in India.

Penicillin-binding proteins are the primary targets for beta lactam drugs, which are main stay of treatment for Streptococcus pneumoniae. The emergence of increased penicillin resistance in meningeal isolates of S. pneumoniae in India is alarming. With this background, we aimed to analyze the pbp gene mutations of penicillin nonsusceptible pneumococcal (PNSP) isolates from within India and their association with international clones. A total of 32 PNSP invasive isolates with a penicillin minimal inhibitory concentrations (MIC) of ≥0.12 μg/mL were subjected to PCR and sequencing for multilocus sequence typing and the pbp genes (pbp2b, pbp2x, and pbp1a). The S. pneumoniae R6 susceptible strain was used as the reference for the comparison analyses. In the majority of the present study isolates, amino acid substitutions were only seen in one of the three active sites of one of the three pbp genes. Thus, pbp genes in the absence of the major substitutions usually associated with penicillin resistance combined with mosaicism in pbp1a resulted in a slight increase in the penicillin MIC to between 0.06 and 2.0 μg/mL, which according to meningeal break point denote resistance. Clonal analyses revealed that the emergence of PNSP in India is due to the gradual expansion of the resistant clones CC320, CC230, and CC63.

Genomic Insight into the Spread of Meropenem-Resistant Streptococcus pneumoniae Spain23F-ST81, Taiwan.

Incidence of invasive pneumococcal disease caused by antimicrobial-resistant Streptococcus pneumoniae types not included in pneumococcal conjugate vaccines has increased, including a penicillin- and meropenem-resistant serotype 15A-ST63 clone in Japan. During 2013–2017, we collected 206 invasive pneumococcal isolates in Taiwan for penicillin and meropenem susceptibility testing. We found serotypes 15B/C-ST83 and 15A-ST63 were the most prevalent penicillin- and meropenem-resistant clones. A transformation study confirmed that penicillin-binding protein (PBP) 2b was the primary meropenem resistance determinant, and PBP1a was essential for high-level resistance. The rate of serotype 15B/C-ST83 increased during the study. All 15B/C-ST83 isolates showed an ermB macrolide resistance genotype. Prediction analysis of recombination sites revealed 12 recombination regions in 15B/C-ST83 compared with the S. pneumoniae Spain23F-ST81 genome. Pneumococcal clones rapidly recombine to acquire survival advantages and undergo local expansion under the selective pressure exerted by vaccines and antimicrobial drugs. The spread of 15B/C-ST83 is alarming for countries with high antimicrobial pressure.

PBP1a glycosyltransferase and transpeptidase activities are both required for maintaining cell morphology and envelope integrity in Shewanella oneidensis.

In rod-shaped Gram-negative bacteria, penicillin binding protein 1a (PBP1a) and 1b (PBP1b) form peptidoglycan-synthesizing complexes with the outer membrane lipoprotein LpoA and LpoB, respectively. Escherichia coli mutants lacking PBP1b/LpoB are sicker than those lacking PBP1a/LpoA. However, we previously found that mutants lacking PBP1a/LpoA but not PBP1b/LpoB are deleterious in Shewanella oneidensis. Here, we show that S. oneidensis PBP1a (SoPBP1a) contains conserved signature motifs with its E. coli counterpart, EcPBP1a. Although EcPBP1a play a less prominent role in E. coli, it is capable of substituting for the SoPBP1a in a manner dependent on SoLpoA. In S. oneidensis, expression of PBP1b is lower than PBP1a, and therefore the additional expression of SoPBP1b at low levels can functionally compensate for the absence of SoPBP1a. Importantly, S. oneidensis PBP1a variants lacking either glycosyltransferase (GTase) or transpeptidase (TPase) activity fail to maintain normal morphology and cell envelope integrity. Similarly, SoPBP1b variants also fail to compensate for the loss of SoPBP1a. Furthermore, overproduction of variants of SoPBP1a, but not SoPBP1b, has detrimental effects on cell morphology in S. oneidensis wild type cells. Overall, our results indicate that the combined enzymatic activities of SoPBP1a are essential for cell wall homeostasis.

Simultaneously inhibiting undecaprenyl phosphate production and peptidoglycan synthases promotes rapid lysis in Escherichia coli.

Peptidoglycan (PG) is a highly cross-linked polysaccharide that encases bacteria, resists the effects of turgor and confers cell shape. PG precursors are translocated across the cytoplasmic membrane by the lipid carrier undecaprenyl phosphate (Und-P) where they are incorporated into the PG superstructure. Previously, we found that one of our Escherichia coli laboratory strains (CS109) harbors a missense mutation in uppS, which encodes an enzymatically defective Und-P(P) synthase. Here, we show that CS109 cells lacking the bifunctional aPBP PBP1B (penicillin binding protein 1B) lyse during exponential growth at elevated temperature. PBP1B lysis was reversed by: (i) reintroducing wild-type uppS, (ii) increasing the availability of PG precursors or (iii) overproducing PBP1A, a related bifunctional PG synthase. In addition, inhibiting the catalytic activity of PBP2 or PBP3, two monofunctional bPBPs, caused CS109 cells to lyse. Limiting the precursors required for Und-P synthesis in MG1655, which harbors a wild-type allele of uppS, also promoted lysis in mutants lacking PBP1B or bPBP activity. Thus, simultaneous inhibition of Und-P production and PG synthases provokes a synergistic response that leads to cell lysis. These findings suggest a biological connection that could be exploited in combination therapies.

The detection of altered penicillin-binding protein 2b, autolysin, and pneumolysin genes in Streptococcus pneumoniae colonizing the upper respiratory tract of healthy schoolchildren in Puducherry

Background: Infections due to Streptococcus pneumoniae are responsible for morbidity and mortality in a large proportion of children in developing countries where childhood vaccination has not been widely implemented. S. pneumoniae colonizing the upper respiratory tract of children as a normal commensal is a potential pathogen when it crosses the mucosal barrier and enters the bloodstream. Aims and Objectives: The aim of the study was to analyze the carriage rate of pneumococci among healthy school children and in doing so to analyze the presence of penicillin-binding protein 2b (pbp2b) gene which is responsible for penicillin resistance using polymerase chain reaction. Methods: Nasopharyngeal swabs were collected from school children and processed according to standard microbiological procedures. The genes for penicillin resistance were detected using PCR. Results: The carriage rate was 32.2% and about 14 strains had the pbp2b gene. Conclusion: Pneumococcal carriage among children is important as they can cross the mucosal barrier and cause infection. Constant follow up of the carriage rate have to be performed to prevent further spread.

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.

Transcriptional Modulation of Penicillin-Binding Protein 1b, Outer Membrane Protein P2 and Efflux Pump (AcrAB-TolC) during Heat Stress Is Correlated to Enhanced Bactericidal Action of Imipenem on Non-typeable Haemophilus influenzae.

Objective: The purpose of the present study was to investigate the penicillin binding proteins (PBPs), drug influx and efflux modulations during heat stress and their effects on the bactericidal action of imipenem on non-typeable Haemophilus influenzae (NTHi).Methods: The two NTHi clinical isolates (GE47 and GE88, imipenem MICs by E-test > 32 μg/mL) examined in this study were collected at Geneva University Hospitals. The imipenem killing activity was assessed after incubation of the NTHi strains at either 37 or 42°C for 3 h with increasing concentrations of imipenem. The detection of PBPs was carried out by Bocillin-FL. Global transcriptional changes were monitored by RNA-seq after pre-incubation of bacterial cells at either 37 or 42°C, and the expression levels of relevant target genes were confirmed by qRT-PCR.Results: Quantitation of NTHi viable cells after incubation with 0.25 μg/mL of imipenem for 3 h revealed more than a twofold decrease in GE47 and GE88 viable cells at 42°C as compared to 37°C. Transcriptome analysis showed that under heat stress conditions, there were 141 differentially expressed genes with a | log2(fold change)| > 1, including 67 up-regulated and 74 down-regulated genes. The expression levels of ponB (encoding PBP1b) and acrR (regulator of AcrAB-TolC efflux pump) were significantly increased at 42°C. In contrast, the transcript levels of ompP2 (encoding the outer membrane protein P2) and acrB gene (encoding AcrB) were significantly lower under heat stress condition.Conclusion: This study shows that the transcriptional modulation of ponB, ompP2, acrR, and acrB in the heat stress response is correlated to enhanced antimicrobial effects of imipenem on non-typeable H. influenzae.

Molecular Dynamics Simulations of Novel Potential Inhibitors for Penicillin Binding Protein 2B of the Resistant 5204 Strain of Streptococcus Pneumoniae.

Top five best hit compounds (ZINC59376795, ZINC60175365, ZINC36922620, ZINC39550705 and ZINC36953975) were obtained through our high throughput virtual screening (HTVS) analysis with resistant 5204-PBP2B (5204 Penicillin Binding Protein 2B) and sensitive R6-PBP2B (R6 Penicillin Binding Protein 2B) proteins of Streptococcus pneumoniae. To gain insight in molecular docking and dynamics simulations of these top five best hit compounds with both resistant 5204-PBP2B and sensitive R6-PBP2B targets. We have employed Glide XP docking and molecular dynamics simulations of these five best hit compounds with 5204-PBP2B and R6-PBP2B targets. The stability analysis has been carried out through DFT, prime-MM/GBSA binding free energy, RMSD, RMSF and Principal Component Analysis. The reference drug, penicillin G forms stable complex with sensitive R6-PBP2B protein. Similar stability is observed for the mutant resistant 5204-PBP2B with the top scoring compound ZINC592376795 which implies that this compound may act as an effective potential inhibitor. The compound ZINC59376795 forms a total of five hydrogen bonds with resistant 5204-PBP2B protein of which three are with mutated residues. Similarly, the other four compounds including penicillin G also form hydrogen bonds with mutated residue. The MD simulations and stability analysis of the complexes of wild and mutant forms are evaluated for a trajectory period of 16ns and further MD simulations of ZINC59376795 with resistant 5204-PBP2B and sensitive R6-PBP2B confirmed the stability for 50 ns. These results suggest that the top five best hit compounds are found to be a promising gateway for the further development of anti-pneumococcal therapeutics.

PBP1B Glycosyltransferase and Transpeptidase Activities Play Different Essential Roles during the De Novo Regeneration of Rod Morphology in Escherichia coli.

Peptidoglycan is a vital component of nearly all cell wall-bearing bacteria and is a valuable target for antibacterial therapy. However, despite decades of work, there remain important gaps in understanding how this macromolecule is synthesized and molded into a three-dimensional structure that imparts specific morphologies to individual cells. Here, we investigated the particularly enigmatic area of how peptidoglycan is synthesized and shaped during the first stages of creating cell shape de novo, that is, in the absence of a preexisting template. We found that when lysozyme-induced (LI) spheroplasts of Escherichia coli were allowed to resynthesize peptidoglycan, the cells divided first and then elongated to recreate a normal rod-shaped morphology. Penicillin binding protein 1B (PBP1B) was critical for the first stage of this recovery process. PBP1B synthesized peptidoglycan de novo, and this synthesis required that PBP1B interact with the outer membrane lipoprotein LpoB. Surprisingly, when LpoB was localized improperly to the inner membrane, recovering spheroplasts synthesized peptidoglycan and divided but then propagated as amorphous spheroidal cells, suggesting that the regeneration of a normal rod shape depends on a particular spatial interaction. Similarly, spheroplasts carrying a PBP1B variant lacking transpeptidase activity or those in which PBP1A was overproduced could synthesize new peptidoglycan and divide but then grew as oddly shaped spheroids. We conclude that de novo cell wall synthesis requires the glycosyltransferase activity of PBP1B but that PBP1B transpeptidase activity is needed to assemble cell walls with wild-type morphology.IMPORTANCE Bacterial cell wall peptidoglycan is synthesized and modified by penicillin binding proteins (PBPs), which are targeted by about half of all currently prescribed antibiotics, including penicillin and its derivatives. Because antibiotic resistance is rising, it has become increasingly urgent that we fill the gaps in our knowledge about how PBPs create and assemble this protective wall. We report here that PBP1B plays an essential role in synthesizing peptidoglycan in the absence of a preexisting template: its glycosyltransferase activity is responsible for de novo synthesis, while its transpeptidase activity is required to construct cell walls of a specific shape. These results highlight the importance of this enzyme and distinguish its biological roles from those of other PBPs and peptidoglycan synthases.

Pentapeptide-rich peptidoglycan at the Bacillus subtilis cell-division site.

Peptidoglycan (PG), the major component of the bacterial cell wall, is one large macromolecule. To allow for the different curvatures of PG at cell poles and division sites, there must be local differences in PG architecture and eventually also chemistry. Here we report such local differences in the Gram-positive rod-shaped model organism Bacillus subtilis. Single-cell analysis after antibiotic treatment and labeling of the cell wall with a fluorescent analogue of vancomycin or the fluorescent D-amino acid analogue (FDAA) HCC-amino-D-alanine revealed that PG at the septum contains muropeptides with unprocessed stem peptides (pentapeptides). Whereas these pentapeptides are normally shortened after incorporation into PG, this activity is reduced at division sites indicating either a lower local degree of PG crosslinking or a difference in PG composition, which could be a topological marker for other proteins. The pentapeptides remain partially unprocessed after division when they form the new pole of a cell. The accumulation of unprocessed PG at the division site is not caused by the activity of the cell division specific penicillin-binding protein 2B. To our knowledge, this is the first indication of local differences in the chemical composition of PG in Gram-positive bacteria.

Structural Insights into Inhibition of Escherichia coli Penicillin-binding Protein 1B

In Escherichia coli, the peptidoglycan cell wall is synthesized by bifunctional penicillin-binding proteins such as PBP1b that have both transpeptidase and transglycosylase activities. The PBP1b transpeptidase domain is a major target of β-lactams, and therefore it is important to attain a detailed understanding of its inhibition. The peptidoglycan glycosyltransferase domain of PBP1b is also considered an excellent antibiotic target yet is not exploited by any clinically approved antibacterials. Herein, we adapt a pyrophosphate sensor assay to monitor PBP1b-catalyzed glycosyltransfer and present an improved crystallographic model for inhibition of the PBP1b glycosyltransferase domain by the potent substrate analog moenomycin. We elucidate the structure of a previously disordered region in the glycosyltransferase active site and discuss its implications with regards to peptidoglycan polymerization. Furthermore, we solve the crystal structures of E. coli PBP1b bound to multiple different β-lactams in the transpeptidase active site and complement these data with gel-based competition assays to provide a detailed structural understanding of its inhibition. Taken together, these biochemical and structural data allow us to propose new insights into inhibition of both enzymatic domains in PBP1b.