Bacterial Targets Research Articles

Multi-Target Effect of Aloeresin-A against Bacterial and Host Inflammatory Targets Benefits Contact Lens-Related Keratitis: A Multi-Omics and Quantum Chemical Investigation.

Contact lens-mediated microbial keratitis caused by Pseudomonas aeruginosa and Streptococcus pneumoniae provokes corneal damage and vision loss. Recently, natural phytochemicals have become complementary medicines for corneal destruction. Herein, we aimed to identify multi-targeting Aloe vera-derived phytochemicals capable of inhibiting bacterial and host targets of keratitis through ADME (absorption, distribution, metabolism, and excretion), docking, molecular dynamics (MD) simulation, MMGBSA (molecular mechanics generalized Born surface area) and density functional theory (DFT) investigations. An extensive literature search revealed ExoU, ExoS, ExoT, ExoY, and PLY as virulent bacterial targets. Simultaneously, differential gene expression (DGE) and pathway enrichment analysis-specified host transcription factor (SPI1) influences keratitis pathogenesis. Molecular docking analysis uncovered aloeresin-A as a promising inhibitor against bacterial and host targets, demonstrating strong binding energies ranging from -7.59 to -6.20 kcal/mol. Further, MMGBSA and MD simulation analysis reflect higher binding free energies and stable interactions of aloeresin-A with the targets. In addition, DFT studies reveal the chemical reactiveness of aloeresin-A through quantum chemical calculations. Hence, our findings show aloeresin-A to be a promising candidate for effectively inhibiting keratitis. However, additional research is imperative for potential integration into lens care solutions.

Regioselective synthesis, structural and bioactivity of acetylated 1,5-benzodiazepin-2-one derivatives — X-ray crystallography, DFT and molecular docking approaches

Benzodiazepines, a well-studied class of seven-membered aromatic heterocycles containing two nitrogen atoms, have shown great promise as therapeutic agents. Efficient protocols have been developed to synthesize a variety of functionalized benzodiazepines. This study focuses on the synthesis of three derivatives of 1,5-benzodiazepin-2-one through regioselective acetylation using acetyl chloride under various conditions. One of the derivatives was characterized for its molecular and crystal structure using X-ray crystallography, Hirshfeld surfaces, and density functional theory computations (at wB97X-D/aug-cc-pVTZ level). The synthesized compounds were then subjected to in vitro evaluation to assess their antibacterial and antifungal activities against multiple strains. Additionally, their antioxidant and anti-inflammatory properties were examined. The results showed different levels of inhibitory effects on the growth of microorganisms, with all compounds displaying moderate to significant biological activities. Furthermore, molecular docking simulations were conducted to investigate the binding interactions of the compounds with bacterial and fungal targets. This research enhances our understanding of the chemistry of benzodiazepine derivatives and further highlights their therapeutic potential.

Essential Oils – Anti-Microbial and Pharmacological Properties of Essential Oils

The oils that are essential are highly concentrated herbal extracts from extremely significant botanicals. Popularly these oils are used in complementary and substitute medicine. The oil is usually extracted from flowers, leaves, roots, and added parts of plants. The antimicrobial activity of essential oils and their components has been studied for a very long time. Essential oils are produced from a complex combination of unstable atoms that are delivered by the optional digestion of sweet-smelling and medicinal plants and can be produced by various techniques, including distillation or microwaves. The huge number of studies on the antimicrobial action of essential oils has permitted the logical acknowledgment of these mixtures on the control of a wide scope of microbial microorganisms. The advances made on the examination of the method of activity of essential oils against bacterial cell targets give us new points of view to battle constant and antimicrobial safe bacterial microorganisms.

Boswellia Essential Oil: Natural Antioxidant as an Effective Antimicrobial and Anti-Inflammatory Agent.

The research aimed to determine the chemical composition, the antioxidant and anti-inflammatory activity as well as the antimicrobial activity against Gram-positive, Gram-negative and two fungal Candida ATCC strains of a commercial Boswellia essential oil (BEO) containing Boswellia carteri, Boswellia sacra, Boswellia papryfera, and Boswellia frereana. Additionally, molecular docking was carried out to show the molecular dynamics of the compounds identified from the essential oil against three bacterial protein targets and one fungal protein target. The major components identified by GC-MS (Gas Chromatography-Mass Spectrometry) were represented by α-pinene, followed by limonene. Evaluation of antioxidant activity using the DPPH (2,2-Diphenyl-1-Picrylhydrazyl) method showed high inhibition comparable to the synthetic antioxidant used as a control. Oxidative stability evaluation showed that BEO has the potential to inhibit primary and secondary oxidation products with almost the same efficacy as butylated hydroxyanisole (BHA). The use of BEO at a concentration of 500 ppm provided the best protection against secondary oxidation during 30 days of storage at room temperature, which was also evident in the peroxide value. Regarding the in vitro anti-inflammatory activity, the membrane lysis assay and the protein denaturation test revealed that even if the value of protection was lower than the value registered in the case of dexamethasone, the recommendation of using BEO as a protective agent stands, considering the lower side effects. Gram-positive bacteria proved more sensitive, while Pseudomonas aeruginosa presented different sensitivity, with higher MICs (minimal inhibitory concentration). Haemophilus influenzae demonstrated a MIC at 2% but with consecutive inhibitory values in a negative correlation with the increase in concentration, in contrast to E. coli, which demonstrated low inhibitory rates at high concentrations of BEO. The computational tools employed revealed interesting binding energies with compounds having low abundance. The interaction of these compounds and the proteins (tyrosyl-tRNA synthetase, DNA gyrase, peptide deformylase, 1,3-β-glucan synthase) predicts hydrogen bonds with amino acid residues, which are reported in the active sites of the proteins. Even so, compounds with low abundance in BEO could render the desired bioactive properties to the overall function of the oil sustained by physical factors such as storage and temperature. Interestingly, the findings from this study demonstrated the antioxidant and antimicrobial potential of Boswellia essential oil against food-related pathogens, thus making the oil a good candidate for usage in food, feed or food-safety-related products.

Biogeographical patterns of the soil fungal:bacterial ratio across France.

Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.

Identification of a novel transcriptional regulator, CorR, for copper stress response in Edwardsiella piscicida.

Copper plays a vital role in the host-pathogen interface, potentially making components of the bacterial copper response suitable targets for the development of innovative antimicrobial strategies. The anti-copper arsenal of intracellular pathogens has expanded as an adaptation to survive copper toxicity in order to escape intracellular killing by the host immune system. Herein, we employed transposon insertion sequencing to investigate the genetic mechanisms underlying the survival of Edwardsiella piscicida under copper stress. A novel transcriptional regulator, ETAE_2324 (named CorR), was identified to participate in the response to copper ions by controlling the expression of copA, the core component of cytoplasmic copper homeostasis. Furthermore, CorR regulated the expression of virulent determinant eseB, influencing the in vivo colonization of E. piscicida. Collectively, our results contribute to the comprehension of the underlying mechanism of the adaption of intracellular pathogens to copper stress during bacterial infections. IMPORTANCE Copper ions play a pivotal role in the interaction between bacteria and the host during infection. The host's innate immune system employs copper ions for their bactericidal properties, thereby making bacterial copper tolerance a crucial determinant of virulence. Edwardsiella piscicida, a significant marine pathogen, has caused substantial losses in the global aquaculture industry. To comprehensively investigate how E. piscicida responds to copper stress, we utilized transposon insertion sequencing to explore genes associated with copper tolerance in culture media containing different concentrations of copper ions. A novel transcriptional regulator, CorR, was identified to respond to copper ions and regulates the expression of crucial components of copper homeostasis CopA, along with the essential virulence factor EseB. These findings offer valuable insights into the underlying mechanisms that govern bacterial copper tolerance and present novel perspectives for the development of vaccines and therapeutic strategies targeting E. piscicida.

Recent Progress in Synthesis of Sulfonamides and N‐Acylsulfonamides, Biological Applications and Their Structure‐Activity Relationship (SAR) Studies

AbstractIn recent years, sulfonamide and N‐acylsulfonamide have emerged as prominent areas of scientific research across multiple fields, including chemistry, biology, and medicine. The large number of drugs and lead compounds reported in recent literature evidences the growing interest in these derivatives. Chemists are increasingly intrigued by these molecules owing to their seemingly limitless potential to serve as preferred molecules for numerous applications. Consequently, powerful activities are needed to think of new efficacious therapeutic agents, and it is imperative to discover novel synthetic analogs towards bacterial targets. Advancements in medicinal chemistry have focused on the development of novel sulfonamide and NAS‐bearing analogs that are less harmful, exhibit minimum side‐effort and enhanced dynamic properties. These advanced research areas are currently at the forefront of scientific inquiry. This present review elucidates the contemporary advancements in sulfonamide and N‐acylsulfonamide derivatives, which exhibit diverse and promising pharmacological activities. The different aspects of structure‐activity relationship (SAR) were discussed.

Evaluation of the QIAstat-Dx Meningitis/Encephalitis Panel, a multiplex PCR platform for the detection of community-acquired meningoencephalitis.

Rapid identification of the causative pathogens of central nervous system infections is essential for providing appropriate management and improving patient outcomes. The performance of QIAstat-Dx Meningitis/Encephalitis (ME) Panel-a multiplex PCR testing platform-in detecting pathogens implicated in meningitis and/or encephalitis was evaluated using BioFire FilmArray ME Panel as a comparator method. This multicenter study analyzed 585 retrospective residual cerebrospinal fluid specimens and 367 contrived specimens. The QIAstat-Dx ME Panel showed positive percent agreement (PPA) values of 100% for Neisseria meningitidis, Streptococcus agalactiae, Escherichia coli K1, Listeria monocytogenes, and Cryptococcus gattii/neoformans on clinical samples compared to the BioFire FilmArray ME Panel. The PPA values observed for Haemophilus influenzae and Streptococcus pneumoniae were 80% and 88.24%, respectively. Negative percent agreement (NPA) values were >99.0% for each of the six bacterial targets and one fungal target tested with clinical samples. One viral target, herpes simplex virus 1, exhibited a PPA value of 100.0%, while the remaining viral targets-human parechovirus, herpes simplex virus 2, human herpes virus 6, and varicella zoster virus-were >90.0%, with the exception of enterovirus, which had a PPA value of 77.8%. The QIAstat-Dx ME Panel detected five true-positive and four true-negative cases compared to BioFire FilmArray ME Panel. The NPA values for all viral pathogens were >99.0%. Overall, the QIAstat-Dx ME Panel showed comparable performance to the BioFire FilmArray ME Panel as a rapid diagnostic tool for community-acquired meningitis and encephalitis.

Antibiotic Potential of the Ambigol Cyanobacterial Natural Product Class and Simplified Synthetic Analogs.

The ambigols are cyanobacterial natural products characterized by three polychlorinated aromatic building blocks connected by biaryl and biaryl ether bridges. All ambigols known to date possess promising biological activities. Most significantly, ambigol A was reported to have antibacterial activity against Gram-positive bacteria, such as Bacillus megaterium and B. subtilis. We established a diverse compound library for in-depth biological evaluation building on our previous bio- and total synthetic research on this natural product family. To explore the antimicrobial potential in detail and to determine initial structure-activity relationships of this product class, a large set of dimeric and trimeric compounds were screened against selected bacterial and Candida target strains. Our results reveal exceptional antibiotic activity of the ambigols, especially against challenging clinical isolates.

Synergy between polypyrrol and benzoic acid against antibiotic-resistant Salmonella spp.

The purpose was to characterize Salmonella Heidelberg (SH) and Minnesota (SM) isolates in terms of their resistance and persistence profile and to assess the antimicrobial effect of benzoic acid (BA) and polypyrrole (PPy). The 20 isolates from broiler litter drag swabs were submitted to antibiogram and efflux pump expression. The minimum inhibitory/bactericidal concentration (MIC/MBC) of the compounds, synergistic activity, time kill, biofilm production, presence of related genes, and molecular docking between compounds and bacterial target sites were evaluated. All isolates showed multidrug resistance (MDR) and BA and PPy showed mean MIC (1750 and 342 µg ml-1) and MBC (3167 and 1000 µg ml-1), respectively. None of the isolates expressed an efflux pump. The compounds showed synergism against an SH isolate and reduced the count by 3 logs in the presence of the compounds after 4 h. Most isolates (16/20) produced weak to moderate biofilm and 17 showed genes related to biofilm. The compounds interacted with two essential proteins, 3,4-dihydroxy-2-butanone 4-phosphate synthase proteins and ferritin-like domain-containing protein, in bacterial metabolism at different target sites. It can be concluded that BA and PPy showed activity on SH and SM, MDR, and biofilm producers, with a potential synergistic effect.

Integration of Photoelectrochemical Signal Transduction with RNA-Cleaving Dnazymes for Culture-Free Detection of Bacteria

There is a growing interest in developing ultrasensitive biological sensors that can be used for rapid testing at the point-of-need.1 A major hurdle in developing such sensors for detecting pathogens such as bacteria is that they require target enrichment or amplification to deliver the required limit-of-detection.2 Among signal transduction strategies, photoelectrochemical (PEC) signal readout, built on the use of light for enhancing electrochemical reactions, is emerging as an ultrasensitive signal transduction mechanism.3 However, the existing PEC platforms fail to deliver single step testing due to the existence of multiple manual steps, including the addition of biological materials labelled with inorganic photoactive nanoparticles, for signal transduction.3 RNA-cleaving DNAzymes (RCDs), a class of synthetic nucleic acids, have been selected for precisely identifying specific bacterial species without the need for sample processing.4 RCDs are molecular switches that cleave a segment of themselves in response to a particular bacterial target, combining biological recognition with signal transduction.4 We developed photoactive RCDs by tagging them with TiO2 nanomaterials for combining these molecular switches with PEC signal readout. We designed these molecular switches to make and then break semiconductive heterostructures in response to bacterial targets. These photoactive RCDs were the foundational basis for the design novel and highly sensitive PEC bacterial sensor.We developed two photoactive materials for use in the PEC bacterial assay: TiO2 nanorod clusters (rutile) that form high surface area photoelectrodes and sub-nanometer sized TiO2-nanoparticles (anatase) that link to RCDs to create photoactive reporter probes. Combining TiO2-assemblies and TiO2-nanoparticles gives rise to a semiconductor heterostructure that massively improves the photoexcitation efficiency of the combined material system and improves photocurrent generation. Our PEC bacterial sensor makes use of this phenomenon for bacterial detection by utilizing photoactive RCDs to modulate photocurrent by breaking and then rebuilding the TiO2 heterostructures, as a signaling mechanism. The assay consists of a release electrode – modified with photoactive RCDs and a capture electrode – modified with single-stranded DNA probes. Upon target interaction, RCDs release photoactive reporters which are captured by the probes, decreasing the release electrode signal while raising the capture electrode signal.The resulting biosensor can detect E. coli bacterial contamination with high specificity and has achieved a very low limit of detection of 21 CFU/mL in buffer and 18 CFU/mL in lake water samples. These results have set a new record for amplification-free detection of bacteria, that does not rely on target enrichment, reagent addition, or sample processing. This presents a new tool for rapid and in-field water testing.References Nat. Microbiol., 1, 16089 (2016).L. Castillo-Henríquez et al., Sensors, 20, 6926 (2020).A. Victorious, S. Saha, R. Pandey, T. F. Didar, and L. Soleymani, Front. Chem., 7, 617 (2019).I. Cozma, E. M. McConnell, J. D. Brennan, and Y. Li, Biosens. Bioelectron., 177, 112972 (2021).

Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study

BackgroundCompared to their healthy counterparts, patients with type 2 diabetes (T2D) can exhibit an altered gut microbiota composition, correlated with detrimental outcomes, including reduced insulin sensitivity, dyslipidemia, and increased markers of inflammation. However, a typical T2D microbiota profile is not established. The aim of this pilot study was to explore the gut microbiota and bacteria associated with prediabetes (pre-T2D) patients, and treatment naïve T2D patients, compared to healthy subjects.MethodsFecal samples were collected from patients and healthy subjects (from Norway). The bacterial genomic DNA was extracted, and the microbiota analyzed utilizing the bacterial 16S rRNA gene. To secure a broad coverage of potential T2D associated bacteria, two technologies were used: The GA-map® 131-plex, utilizing 131 DNA probes complementary to pre-selected bacterial targets (covering the 16S regions V3-V9), and the LUMI-Seq™ platform, a full-length 16S sequencing technology (V1-V9). Variations in the gut microbiota between groups were explored using multivariate methods, differential bacterial abundance was estimated, and microbiota signatures discriminating the groups were assessed using classification models.ResultsIn total, 24 pre-T2D patients, 18 T2D patients, and 52 healthy subjects were recruited. From the LUMI-Seq™ analysis, 10 and 9 bacterial taxa were differentially abundant between pre-T2D and healthy, and T2D and healthy, respectively. From the GA-map® 131-plex analysis, 10 bacterial markers were differentially abundant when comparing pre-T2D and healthy. Several of the bacteria were short-chain fatty acid (SCFA) producers or typical opportunistic bacteria. Bacteria with similar function or associated properties also contributed to the separation of pre-T2D and T2D from healthy as found by classification models. However, limited overlap was found for specific bacterial genera and species.ConclusionsThis pilot study revealed that differences in the abundance of SCFA producing bacteria, and an increase in typical opportunistic bacteria, may contribute to the variations in the microbiota separating the pre-T2D and T2D patients from healthy subjects. However, further efforts in investigating the relationship between gut microbiota, diabetes, and associated factors such as BMI, are needed for developing specific diabetes microbiota signatures.

Schlesinger Nailed It! Assessing a Key Primary Pharmacodynamic Property of Phages for Phage Therapy: Virion Encounter Rates with Motionless Bacterial Targets.

Bacteriophages (phages) are viruses of bacteria and have been used as antibacterial agents now for over one-hundred years. The primary pharmacodynamics of therapeutic phages can be summed up as follows: phages at a certain concentration can reach bacteria at a certain rate, attach to bacteria that display appropriate receptors on their surfaces, infect, and (ideally) kill those now-adsorbed bacteria. Here, I consider the rate at which phages reach bacteria, during what can be dubbed as an 'extracellular search'. This search is driven by diffusion and can be described by what is known as the phage adsorption rate constant. That constant in turn is thought to be derivable from knowledge of bacterial size, virion diffusion rates, and the likelihood of phage adsorption given this diffusion-driven encounter with a bacterium. Here, I consider only the role of bacterial size in encounter rates. In 1932, Schlesinger hypothesized that bacterial size can be described as a function of cell radius (, or ), as based on the non-phage-based theorizing of Smoluchowski (1917). The surface area of a cell-what is actually encountered-varies however instead as a function . Here, I both provide and review evidence indicating that Schlesinger's assertion seems to have been correct.

Bacterial network construction and molecular docking approach to study interaction of Myristica fragrans on Acne infections

Acne vulgaris is a very common bacterial infection caused. Herbal remedies have always give a positive response in treatment of various disease in disorders. The present study works on predicting the probable interactions between the Myristica fragrans bioactives with the bacterial targets via network pharmacology and docking techniques. The bio-actives and disease targets were obtained from open databases and literature review. Protein and pathway enrichment analysis was done by utilizing metascape and STRING tool. Cytoscape tool were utilized for construction of network. The compounds were further assessed using molsoft tools and docking was done using auto-dock tools. The potential bio-actives were selected further the network construction gave insights on the highest degree values. The targets with highest interactions were docked and the complex which showed good binding was selected. It was found that Stigmasterol and Campesterol have the highest potential and can be considered as hit compounds for further studies too. 

Development of an mRNA-lipid nanoparticle vaccine against Lyme disease

Lyme disease is the most common vector-borne infectious disease in the United States, in part because a vaccine against it is not currently available for humans. We propose utilizing the lipid nanoparticle-encapsulated nucleoside-modified mRNA (mRNA-LNP) platform to generate a Lyme disease vaccine like the successful clinical vaccines against SARS-CoV-2. Of the antigens expressed by Borrelia burgdorferi, the causative agent of Lyme disease, outer surface protein A (OspA) is the most promising candidate for vaccine development. We have designed and synthesized an OspA-encoding mRNA-LNP vaccine and compared its immunogenicity and protective efficacy to an alum-adjuvanted OspA protein subunit vaccine. OspA mRNA-LNP induced superior humoral and cell-mediated immune responses in mice after a single immunization. These potent immune responses resulted in protection against bacterial infection. Our study demonstrates that highly efficient mRNA vaccines can be developed against bacterial targets.

Detection of Escherichia coli by capillary electrophoresis assisted by large volume sample stacking and nicking endonuclease signal amplification

Efficient, accurate and economical detection of pathogenic bacteria is crucial in ensuring food safety and preventing foodborne illnesses. In this study, a capillary electrophoresis coupled laser-induced fluorescence assay (CE-LIF) was developed for the detection of Escherichia coli (E. coli) by detecting its specific DNA. The CE-LIF was assisted by both online enrichment and offline amplification to improve the detection sensitivity of bacterial DNA. Here the online amplification was performed by large volume sample stacking (LVSS), while the offline amplification was nicking endonuclease signal amplification (NESA). Under the optimal experimental conditions, the detection limit of bacterial target DNA was 2.5 fM, and the conversion concentration of E. coli was 3 CFU · mL−1. The method had been applied to the detection of commercially available skim milk samples with good results, which proved that it could be used as an effective tool for food and environmental bacteria monitoring.

Functional characterization of VirB/VirD4 and Icm/Dot type IV secretion systems from the plant-pathogenic bacterium Xanthomonas euvesicatoria.

Many Gram-negative plant- and animal-pathogenic bacteria employ type IV secretion (T4S) systems to transport proteins or DNA/protein complexes into eukaryotic or bacterial target cells. T4S systems have been divided into minimized and expanded T4S systems and resemble the VirB/VirD4 T4S system from the plant pathogen Agrobacterium tumefaciens and the Icm/Dot T4S system from the human pathogen Legionella pneumophila, respectively. The only known plant pathogen with both types of T4S systems is Xanthomonas euvesicatoria which is the causal agent of bacterial spot disease on pepper and tomato plants. In the present study, we show that virB/virD4 and icm/dot T4S genes are expressed and encode components of oligomeric complexes corresponding to known assemblies of VirB/VirD4 and Icm/Dot proteins. Both T4S systems are dispensable for the interaction of X. euvesicatoria with its host plants and do not seem to confer contact-dependent lysis of other bacteria, which was previously shown for the chromosomally encoded VirB/VirD4 T4S system from Xanthomonas axonopodis pv. citri. The corresponding chromosomal T4S gene cluster from X. euvesicatoria is incomplete, however, the second plasmid-localized vir gene cluster encodes a functional VirB/VirD4 T4S system which contributes to plasmid transfer. In agreement with this finding, we identified the predicted relaxase TraI as substrate of the T4S systems from X. euvesicatoria. TraI and additional candidate T4S substrates with homology to T4S effectors from X. axonopodis pv. citri interact with the T4S coupling protein VirD4. Interestingly, however, the predicted C-terminal VirD4-binding sites are not sufficient for T4S, suggesting the contribution of additional yet unknown mechanisms to the targeting of T4S substrates from X. euvesicatoria to both VirB/VirD4 and Icm/Dot T4S systems.

Small Molecules Incorporating Privileged Amidine Moiety as Potential Hits Combating Antibiotic-Resistant Bacteria.

The continuing need for the discovery of potent antibacterial agents against antibiotic-resistant pathogens is the driving force for many researchers to design and develop such agents. Herein, we report the design, synthesis, and biological evaluation of amidine derivatives as new antibacterial agents. Compound 13d was the most active in this study against a wide range of antibiotic-resistant, and susceptible, Gram-positive, and Gram-negative bacterial strains. Time-kill assay experiments indicated that compound 13d was an effective bactericidal compound against the tested organisms at the log-phase of bacterial growth. Docking simulations were performed to assess in silico its mode of action regarding UPPS, KARI, and DNA as potential bacterial targets. Results unveiled the importance of structural features of compound 13d in its biological activity including central thiophene ring equipped with left and right pyrrolo[2,3-b]pyridine and phenyl moieties and two terminal amidines cyclized into 4,5-dihydro-1H-imidazol-2-yl functionalities. Collectively, compound 13d represents a possible hit for future development of potent antibacterial agents.

Suppression of NLR-mediated plant immune detection by bacterial pathogens.

The plant immune system is constituted of two functionally interdependent branches that provide the plant with an effective defense against microbial pathogens. They can be considered separate since one detects extracellular pathogen-associated molecular patterns by means of receptors on the plant surface, while the other detects pathogen-secreted virulence effectors via intracellular receptors. Plant defense depending on both branches can be effectively suppressed by host-adapted microbial pathogens. In this review we focus on bacterially driven suppression of the latter, known as effector-triggered immunity (ETI) and dependent on diverse NOD-like receptors (NLRs). We examine how some effectors secreted by pathogenic bacteria carrying type III secretion systems can be subject to specific NLR-mediated detection, which can be evaded by the action of additional co-secreted effectors (suppressors), implying that virulence depends on the coordinated action of the whole repertoire of effectors of any given bacterium and their complex epistatic interactions within the plant. We consider how ETI activation can be avoided by using suppressors to directly alter compromised co-secreted effectors, modify plant defense-associated proteins, or occasionally both. We also comment on the potential assembly within the plant cell of multi-protein complexes comprising both bacterial effectors and defense protein targets.

Computational Insight into Substrate-Induced Conformational Changes in Methionyl-tRNA Synthetase of Mycobacterium Tuberculosis.

Tuberculosis caused by Mycobacterium tuberculosis (M.tb) has killed millions worldwide. Antibiotic resistance leads to the ineffectiveness of the current therapies. Aminoacyl tRNA synthetase (aaRS) class of proteins involved in protein synthesis are promising bacterial targets for developing new therapies. Here, we carried out a systematic comparative study on the aaRS sequences from M.tb and human. We listed important M.tb aaRS that could be explored as potential M.tb targets alongside the detailed conformational space analysis of methionyl-tRNA synthetase (MetRS) in apo- and substrate-bound form, which is among the proposed targets. Understanding the conformational dynamics is central to the mechanistic understanding of MetRS, as the substrate binding leads to the conformational changes causing the reaction to proceed. We performed the most complete simulation study of M.tb MetRS for 6 microseconds (2 systems × 3 runs × 1 microsecond) in the apo and substrate-bound states. Interestingly, we observed differential features, showing comparatively large dynamics for the holo simulations, whereas the apo structures became slightly compact with reduced solvent exposed area. In contrast, the ligand size decreased significantly in holo structures possibly to relax ligand conformation. Our findings correlate with experimental studies, thus validating our protocol. Adenosine monophosphate moiety of the substrate exhibited quite higher fluctuations than the methionine. His21 and Lys54 were found to be the important residues forming prominent hydrogen bond and salt-bridge interactions with the ligand. The ligand-protein affinity decreased during simulations as computed by MMGBSA analysis over the last 500 ns trajectories, which indicates the conformational changes upon ligand binding. These differential features could be further explored for designing new M.tb inhibitors.