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In Silico Pathway Analysis Predicts Metabolites that are Potential Antimicrobial Targets
Abstract
Antibiotic discovery aimed at conventional targets such as proteins and nucleic acids faces challenges from mutations and antibiotic resistance. Small molecule metabolites, however, can be considered resistant to change, as they do not undergo rapid mutations. Developing analogs or scavengers of essential microbial metabolites as antibiotics is a promising strategy that can delay drug resistance. The objective of this work was to identify microbial metabolites that are most suitable targets for antimicrobial discovery. We performed extensive literature mining and systems level pathway analysis to identify bacterial metabolites that fulfill the criteria for drug targets. The BioCyc interactive metabolic pathway maps and Pathway Tools software were used to corroborate our finding. We identified ten metabolites as potential candidates for developing novel antibiotics. These metabolites are Lipid II, meso-diaminopimelate, pantothenate, shikimate, biotin, L-aspartyl-4-phosphate, dTDP-?-L-rhamnose, UDP-Dgalacto- 1,4-furanose, des-N-acetyl mycothiol, and Siroheme. The article describes the selection criteria, analysis of metabolic pathways, and the potential role of each of the ten metabolites in therapeutic intervention as broadspectrum antibiotics with emphasis on M. tuberculosis. Our study revealed previously unexplored targets along with metabolites that are well established in antibiotic discovery. Identification of established metabolites strengthen our analyses while the newly discovered metabolites could lead to novel antimicrobials.
... One of the research has been focused on metabolites that these are essential for the growth and survival of the relevant bacteria. To identify potential drug targets, they have to be further screened these metabolites to eliminate any found in the human host [22]. Short interfering RNAs (siRNAs) can be used to suppress gene expression and have a lot of potential applications in therapy, yet how to design an effective siRNA is still under consideration [23]. ...
... DNA Micro arrays, In Vivo Expression Technology (IVET), Signature-Tagged Mutagenesis (STM), Differential Fluorescence Induction (DFI), etc., are some of the metabolomics applications [27]. Pathway Tools software were used to corroborate finding ten metabolites as potential candidates for developing novel antibiotics [22]. Molecular docking has been used for lead discovery in pharmaceutical industries for virtual screening [28] which will be helpful for further metabolomics studies in future. ...
The collection of global metabolic data and their interpretation (both spectral and biochemical) using modern spectroscopic techniques and appropriate statistical approaches, are known as `metabolomics’. This review covers research on metabolomics, ranging from the development of specialized chemical analytical techniques to the construction of databases and methods for metabolic simulation. Furthermore we have also outlined the recent developments in elucidating the system-level functions of the bioconstituents of living organisms. Metabolomics has the potential to serve an important role in diagnosis and management of human conditions. As such the purpose of this systematic review is to summarize existing literature on metabolomics and its various techniques in terms of diagnostic accuracies and distinguishing metabolites. This article has also highlighted the novelty of the field of metabolomics with various detection methods. Here metabolomic methodologies are discussed briefly followed by a more detailed review of the use of metabolomics in integrated applications where metabolomics information has been combined with other “omic” data sets (proteomics, transcriptomics) to enable greater understanding of a biological system.
... Identification of dominant environmental species by microbiota profiling of the rhizosphere and phyllosphere of economically important plant species allows us to rapidly identify numerous BCA candidates that successfully colonize plants, and colonization tests can be targeted and specific to confirm such potential. Whole-genome [152] and RNA sequencing [158], pathway analysis [159], and metabolomic analysis [160,161] is a fast way to identify the production of secondary metabolite microbicidal function under real environmental conditions [162] rather than optimal in vitro growth. ...
Bacterial biological control agents (BCAs) have been increasingly used against plant diseases. The traditional approach to manufacturing such commercial products was based on the selection of bacterial species able to produce secondary metabolites that inhibit mainly fungal growth in optimal media. Such species are required to be massively produced and sustain long-term self-storage. The endpoint of this pipeline is large-scale field tests in which BCAs are handled as any other pesticide. Despite recent knowledge of the importance of BCA-host-microbiome interactions to trigger plant defenses and allow colonization, holistic approaches to maximize their potential are still in their infancy. There is a gap in scientific knowledge between experiments in controlled conditions for optimal BCA and pathogen growth and the nutrient-limited field conditions in which they face niche microbiota competition. Moreover, BCAs are considered to be safe by competent authorities and the public, with no side effects to the environment; the OneHealth impact of their application is understudied. This review summarizes the state of the art in BCA research and how current knowledge and new biotechnological tools have impacted BCA development and application. Future challenges, such as their combinational use and ability to ameliorate plant stress are also discussed. Addressing such challenges would establish their long-term use as centerfold agricultural pesticides and plant growth promoters.
... These metabolites are Lipid II, meso-diaminopimelate, pantothenate, shikimate, biotin, L-aspartyl-4-phosphate, dTDP-α-L-rhamnose, UDP Dgalacto-1,4-furanose, des-N-acetyl mycothiol, and Siroheme. The selection criteria, analysis of metabolic pathways, and the potential role of each of the ten metabolites in therapeutic intervention as broadspectrum antibiotics with emphasis on M. tuberculosis is made [26]. Damage analysis in metabolic pathways is one of the most highlighted fields in systems biology area. ...
Systems biology explains how higher level properties of complex biological systems arise from the interactions among their parts. This requires a combination of concepts from many disciplines, including biology, computer science, applied mathematics, physics and engineering. The importance and its various implementations in various fields like proteomics, genomics, metabolomics, docking studies etc., recent works and advancements are portrayed in this review article.
... One study has revealed previously unexplored targets along with metabolites that are well established in antibiotic discovery. Identification of established metabolites strengthen our analyses while the newly discovered metabolites could lead to novel antimicrobials [52,60]. ...
Metabolomics is the newly emerging field of ‘omics’ research.Its Comprehensive and simultaneous systematic determination of metabolite levels in the metabolome and their changes over time.This review outlines how metabolomics is emerging in today’s life. It presents metabolomics methodology and focuses on the current and potential applications of metabolomics in different diseases with particular attention to its use as a biomarker in diagnosis, prognosis, and therapeutic evaluation. We think this review will appeal to both translational researchers and clinicians as it reviews up-to-date evidence on the utility of metabolomics, an often poorly understood topic. The report also highlights the use of metabolomics in maximizing and sustaining revenues post-marketing and in the development of clinical diagnostics.
... These metabolites are Lipid II, meso-diaminopimelate, pantothenate, shikimate, biotin, L-aspartyl-4-phosphate, dTDP-α-L-rhamnose, UDP Dgalacto-1,4-furanose, des-N-acetyl mycothiol, and Siroheme. The selection criteria, analysis of metabolic pathways, and the potential role of each of the ten metabolites in therapeutic intervention as broadspectrum antibiotics with emphasis on M. tuberculosis is made [26]. Damage analysis in metabolic pathways is one of the most highlighted fields in systems biology area. ...
Systems biology explains how higher level properties of complex biological systems arise from the interactions among their parts. This requires a combination of concepts from many disciplines, including biology, computer science, applied mathematics, physics and engineering. The importance and its various implementations in various fields like proteomics, genomics, metabolomics, docking studies etc., recent works and advancements are portrayed in this review article.
... The functions depicted here are the main functions of the nano particles on to the fabric. The use of the silver and gold particles [73] enables the odour resistance and anti bacterial and antifungal properties [74,75]. The titanium dioxide is for the uv-protection and nano whiskers for the water repellent property. ...
Nano Technology means optimizing performance and providing smart solutions for the future. It means configuring molecules to change in size and properties for enhancement as in the case of smart fabrics. Smart fabrics can help manufacturers and designers with the increased emphasis on lifestyle, aesthetic appeal and form demanded for technological products. Nanosize particles can exhibit unexpected properties different from those of the bulk material. The basic premise is that properties can dramatically change when a substance's size is reduced to the nanometer range. Nanotechnology has versatile applications in Textile Chemicals industry in manufacturing garments with stain resistance, flame retardant finishes, wrinkle resistance finishes, moisture management, antimicrobial qualities, UV protection, and soil release properties. Incorporating nanomaterials into a textile can affect a host of properties, including shrinkage, strength, electrical conductivity and flammability. Nanotechnology has also made a tremendous impact on functionality and performance. Nano-treated textiles may lead to many inventions as the science develops in future. & copy 2011 Jeevani T.
Classical antibiotic discovery efforts have relied mainly on molecular library screening coupled with target-based lead optimization. The conventional approaches are unable to tackle the emergence of antibiotic resistance and are failing to provide understanding of multiple mechanisms behind drug actions and the off-target effects. These insufficiencies have prompted researchers to focus on a multidisciplinary approach of systems biology-based antibiotic discovery. Systems biology is capable of providing a big-picture view for therapeutic targets through interconnected networks of biochemical reactions derived from both experimental and computational techniques. In this chapter, we have compiled software tools and databases that are typically used for target identification through in silico analyses. We have also identified enzyme- and broad-spectrum metabolite-based drug targets that have emerged through in silico systems microbiology.
The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism.
Mycothiol ligase (MshC) is a key enzyme in the biosynthesis of mycothiol, a small molecular weight thiol that is unique to actinomycetes and whose primary role is to maintain intracellular redox balance and remove toxins. MshC catalyzes the adenosine triphosphate (ATP)-dependent condensation of cysteine and glucosamine-inositol (GI) to produce cysteine-glucosamine-inositol (CGI). MshC is essential to Mycobacterium tuberculosis and therefore represents an attractive target for chemotherapeutic intervention. A screening protocol was developed to identify MshC inhibitors based on quantification of residual ATP using a coupled luminescent assay. The protocol was used to screen a library of 3100 compounds in a 384-well plate format (Z'>or=0.65). Fifteen hits (0.48%) were identified from the screen, and 2 hits were confirmed in a secondary assay that measures production of CGI. The structures of both hits contain N-substituted quinolinium moieties, and the more potent of the 2-namely, dequalinium chloride-inhibits MshC with an IC50 value of 24+/-1 microM. Further studies showed dequalinium to be an ATP-competitive inhibitor of MshC, to bind MshC with a KD of 0.22 microM, and to inhibit the growth of M. tuberculosis under aerobic and anaerobic conditions with minimum inhibitory and anaerobic bactericidal concentrations of 1.2 and 0.3 microg/mL, respectively. The screening protocol described is robust and has enabled the identification of new MshC inhibitors.
Mycolic acids are essential for the survival, virulence and antibiotic resistance of the human pathogen Mycobacterium tuberculosis. Inhibitors of mycolic acid biosynthesis, such as isoniazid and ethionamide, have been used as efficient drugs for the treatment of tuberculosis. However, the increase in cases of multidrug-resistant tuberculosis has prompted a search for new targets and agents that could also affect synthesis of mycolic acids. In mycobacteria, the acyl-CoA carboxylases (ACCases) provide the building blocks for de novo fatty acid biosynthesis by fatty acid synthase (FAS) I and for the elongation of FAS I products by the FAS II complex to produce meromycolic acids. By generating a conditional mutant in the accD6 gene of Mycobacterium smegmatis, we demonstrated that AccD6 is the essential carboxyltransferase component of the ACCase 6 enzyme complex implicated in the biosynthesis of malonyl-CoA, the substrate of the two FAS enzymes of Mycobacterium species. Based on the conserved structure of the AccD5 and AccD6 active sites we screened several inhibitors of AccD5 as potential inhibitors of AccD6 and found that the ligand NCI-172033 was capable of inhibiting AccD6 with an IC(50) of 8 microM. The compound showed bactericidal activity against several pathogenic Mycobacterium species by producing a strong inhibition of both fatty acid and mycolic acid biosynthesis at minimal inhibitory concentrations. Overexpression of accD6 in M. smegmatis conferred resistance to NCI-172033, confirming AccD6 as the main target of the inhibitor. These results define the biological role of a key ACCase in the biosynthesis of membrane and cell envelope fatty acids, and provide a new target, AccD6, for rational development of novel anti-mycobacterial drugs.
The aspartate pathway is responsible for the biosynthesis of lysine, threonine, isoleucine, and methionine in most plants and micro-organisms. The absence of this pathway in humans and animals makes the central enzymes potential targets for inhibition, with the aim of developing new herbicides and biocides, and also for enhancement, to improve the nutritional value of crops. Our current state of knowledge of these enzymes is reviewed, including recently determined structural information and newly constructed bifunctional fusion enzymes.
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Abstract Pathway Tools is a production-quality software environment for creating a type of model- organism database (MOD) called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network, and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, and prediction of operons. It enables interactive editing of PGDBs by database curators. It supports Web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated databases for important model organisms. Those PGDBs can be exchanged using a peer-to-peer database sharing system called the PGDB Registry. Biographical Note
The ring contraction of readily available δ-lactones provides a short route to the synthesis of both epimers of C-L-rhamnofuranosides, radical bromination of which give access to an α-azidocarboxylate as a divergent intermediate for applying combinatorial methodology for the preparation of a wide range of mimics of L-rhamnofuranose; such materials may provide an approach to the study of the biosynthesis of the cells walls of mycobacteria such as Mycobacterium tuberculosis and M. leprae.
Spontaneous mutants of Mycobacterium tuberculosis that were resistant to the anti-tuberculosis drugs ethionamide and isoniazid were isolated and found to map to mshA, a gene encoding the first enzyme involved in the biosynthesis of mycothiol, a major low-molecular-weight thiol in M. tuberculosis. Seven independent missense or frameshift mutations within mshA were identified and characterized. Precise null deletion mutations of the mshA gene were generated by specialized transduction in three different strains of M. tuberculosis. The mshA deletion mutants were defective in mycothiol biosynthesis, were only ethionamide-resistant and required catalase to grow. Biochemical studies suggested that the mechanism of ethionamide resistance in mshA mutants was likely due to a defect in ethionamide activation. In vivo, a mycothiol-deficient strain grew normally in immunodeficient mice, but was slightly defective for growth in immunocompetent mice. Mutations in mshA demonstrate the non-essentiality of mycothiol for growth in vitro and in vivo, and provide a novel mechanism of ethionamide resistance in M. tuberculosis.
The galactofuran region of the mycobacterial cell wall consists of alternating 5- and 6-linked beta-d-galactofuranose (beta-D-Galf) residues, essential for viability. UDP-galactofuranose (UDP-Galf), the donor for Galf, is synthesised from UDP-galactopyranose (UDP-Galp) by the enzyme UDP-galactopyranose mutase (UGM), which is not found in humans, rendering it a therapeutic target. The in vitro properties, i.e. enzymatic activity, antimycobacterial activity, cellular toxicity, activity in mycobacterial-infected macrophages and activity against non-replicating persistent mycobacteria, of (4-chlorophenyl)-[1-(4-chlorophenyl)-3-hydroxy-5-methyl-1H-pyrazol-4-yl]-methanone and 3-(4-iodophenyl)-2-[4-(3,4-dichlorophenyl)-thiazol-2-ylamino]-propionic acid were studied. The former compound, a pyrazole, was an inhibitor of UGM from Mycobacterium tuberculosis and Klebsiella pneumoniae and was effective against Mycobacterium smegmatis, Mycobacterium bovis BCG and M. tuberculosis but ineffective against other bacterial strains tested. This compound showed potency against mycobacteria in infected macrophages but exhibited moderate cellular toxicity and was ineffective against non-replicating persistent mycobacteria. This is the first report of a compound both with UGM inhibitory properties and broad antimycobacterial activities. The latter compound, an aminothiazole, was active against UGM from K. pneumoniae and M. tuberculosis but was ineffective against M. bovis BCG or M. tuberculosis as well as demonstrating higher cellular toxicity. These data validate the choice of UGM as a target for active antimycobacterial therapy and confirm the pyrazole compound as a viable lead candidate.
Bacterial cell wall biosynthesis represents an antibiotic target pathway for therapeutic intervention. An increasing number of natural antibiotic compounds have been demonstrated to inhibit the membrane-associated steps of cell wall biosynthesis by targeting bactoprenol-mediated precursor cycling, particularly at the stage of the completed building block Lipid II. These antibiotic compounds belong to various chemical classes including glycopeptides, lipopeptides and lipodepsipeptides, and lantibiotics and other antimicrobial peptides. The clinical success of vancomycin in the treatment of multiresistant Gram-positive bacteria has stimulated further development of glycopeptide antibiotics and research of other Lipid II-binding compounds. The state-of-the-art in the targeting of cell wall precursors is summarized in this review.