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Hassan SS, Shams R, Camps I, Basharat Z, Sohail S, Khan Y, Ullah A, Irfan M, Ali J, Bilal M, Morel CM. Subtractive sequence analysis aided druggable targets mining in Burkholderia cepacia complex and finding inhibitors through bioinformatics approach. Mol Divers 2023; 27:2823-2847. [PMID: 36567421 PMCID: PMC9790820 DOI: 10.1007/s11030-022-10584-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/05/2022] [Indexed: 12/27/2022]
Abstract
Burkholderia cepacia complex (BCC) is a group of gram-negative bacteria composed of at least 20 different species that cause diseases in plants, animals as well as humans (cystic fibrosis and airway infection). Here, we analyzed the proteomic data of 47 BCC strains by classifying them in three groups. Phylogenetic analyses were performed followed by individual core region identification for each group. Comparative analysis of the three individual core protein fractions resulted in 1766 ortholog/proteins. Non-human homologous proteins from the core region gave 1680 proteins. Essential protein analyses reduced the target list to 37 proteins, which were further compared to a closely related out-group, Burkholderia gladioli ATCC 10,248 strain, resulting in 21 proteins. 3D structure modeling, validation, and druggability step gave six targets that were subjected to further target prioritization parameters which ultimately resulted in two BCC targets. A library of 12,000 ZINC drug-like compounds was screened, where only the top hits were selected for docking orientations. These included ZINC01405842 (against Chorismate synthase aroC) and ZINC06055530 (against Bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/Glucosamine-1-phosphate acetyltransferase glmU). Finally, dynamics simulation (200 ns) was performed for each ligand-receptor complex, followed by ADMET profiling. Of these targets, details of their applicability as drug targets have not yet been elucidated experimentally, hence making our predictions novel and it is suggested that further wet-lab experimentations should be conducted to test the identified BCC targets and ZINC scaffolds to inhibit them.
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Affiliation(s)
- Syed Shah Hassan
- Jamil–ur–Rehman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building “Expansão”, 8th Floor Room 814, Av. Brasil 4036, Manguinhos, Rio de Janeiro, RJ 21040-361 Brazil
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000 KP Pakistan
| | - Rida Shams
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000 KP Pakistan
| | - Ihosvany Camps
- Laboratório de Modelagem Computacional—LaModel, Instituto de Ciências Exatas—ICEx. Universidade Federal de Alfenas—UNIFAL-MG, Alfenas, Minas Gerais Brazil
- High Performance & Quantum Computing Labs, Waterloo, Canada
| | - Zarrin Basharat
- Jamil–ur–Rehman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Saman Sohail
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000 KP Pakistan
| | - Yasmin Khan
- Jamil–ur–Rehman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Asad Ullah
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000 KP Pakistan
| | - Muhammad Irfan
- Jamil–ur–Rehman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Javed Ali
- Department of Chemistry, Kohat University of Science & Technology–KUST, Kohat, KP Pakistan
| | - Muhammad Bilal
- Department of Chemistry, Kohat University of Science & Technology–KUST, Kohat, KP Pakistan
| | - Carlos M. Morel
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building “Expansão”, 8th Floor Room 814, Av. Brasil 4036, Manguinhos, Rio de Janeiro, RJ 21040-361 Brazil
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Hegde P, Orimoloye MO, Sharma S, Engelhart CA, Schnappinger D, Aldrich CC. Polyfluorinated salicylic acid analogs do not interfere with siderophore biosynthesis. Tuberculosis (Edinb) 2023; 140:102346. [PMID: 37119793 PMCID: PMC10247463 DOI: 10.1016/j.tube.2023.102346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/01/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) is a leading cause of infectious disease mortality. The salicylic acid derived small molecule siderophores known as mycobactins are essential in vivo for iron acquisition of Mtb where iron is restricted in the host. Herein, we synthesize and explore the mechanism of action of polyfluorinated salicylic acid derivates, which were previously reported to possess potent antimycobacterial activity. We hypothesized fluorinated salicylic acid derivates may inhibit mycobactin biosynthesis through initial bioactivation and conversion to downstream metabolites that block late steps in assembly of the mycobactins. Enzymatic studies demonstrated that some of the fluorinated salicylic acid derivatives compounds were readily activated by the bifunctional adenylating enzyme MbtA, responsible for incorporation of salicylic acid into the mycobactin biosynthetic pathway; however, they did not inhibit mycobactin biosynthesis as confirmed by LS-MS/MS using an authentic synthetic mycobactin standard. Further mechanistic analysis of the most active derivative (Sal-4) using an MbtA-overexpressing Mtb strain as well as complementation studies with iron and salicylic acid revealed Sal-4 cannot be antagonized by overexpression of MbtA or through supplementation with iron or salicylic acid. Taken together, our results indicate the observed antimycobacterial activity of polyfluorinated salicylic acid derivative is independent of mycobactin biosynthesis.
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Affiliation(s)
- Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Moyosore O Orimoloye
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA.
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3
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Møller TSB, Liu G, Hartman HB, Rau MH, Mortensen S, Thamsborg K, Johansen AE, Sommer MOA, Guardabassi L, Poolman MG, Olsen JE. Global responses to oxytetracycline treatment in tetracycline-resistant Escherichia coli. Sci Rep 2020; 10:8438. [PMID: 32439837 PMCID: PMC7242477 DOI: 10.1038/s41598-020-64995-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/22/2020] [Indexed: 11/09/2022] Open
Abstract
We characterized the global transcriptome of Escherichia coli MG1655:: tetA grown in the presence of ½ MIC (14 mg/L) of OTC, and for comparison WT MG1655 strain grown with 1//2 MIC of OTC (0.25 mg/L OTC). 1646 genes changed expression significantly (FDR > 0.05) in the resistant strain, the majority of which (1246) were also regulated in WT strain. Genes involved in purine synthesis and ribosome structure and function were top-enriched among up-regulated genes, and anaerobic respiration, nitrate metabolism and aromatic amino acid biosynthesis genes among down-regulated genes. Blocking of the purine-synthesis- did not affect resistance phenotypes (MIC and growth rate with OTC), while blocking of protein synthesis using low concentrations of chloramphenicol or gentamicin, lowered MIC towards OTC. Metabolic-modeling, using a novel model for MG1655 and continuous weighing factor that reflected the degree of up or down regulation of genes encoding a reaction, identified 102 metabolic reactions with significant change in flux in MG1655:: tetA when grown in the presence of OTC compared to growth without OTC. These pathways could not have been predicted by simply analyzing functions of the up and down regulated genes, and thus this work has provided a novel method for identification of reactions which are essential in the adaptation to growth in the presence of antimicrobials.
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Affiliation(s)
- Thea S B Møller
- University of Copenhagen, Department of Veterinary and Animal Sciences, 1870, Frederiksberg C, Denmark
| | - Gang Liu
- University of Copenhagen, Department of Veterinary and Animal Sciences, 1870, Frederiksberg C, Denmark
| | - Hassan B Hartman
- Oxford Brookes University, Department of Medical and Biological Sciences, Gipsy Lane, Headington, Oxford, OX3 OBP, United Kingdom
| | - Martin H Rau
- Technical University of Denmark, Department of Systems Biology, 2800, Lyngby, Denmark
| | - Sisse Mortensen
- University of Copenhagen, Department of Veterinary and Animal Sciences, 1870, Frederiksberg C, Denmark
| | - Kristian Thamsborg
- University of Copenhagen, Department of Veterinary and Animal Sciences, 1870, Frederiksberg C, Denmark
| | - Andreas E Johansen
- University of Copenhagen, Department of Veterinary and Animal Sciences, 1870, Frederiksberg C, Denmark
| | - Morten O A Sommer
- Technical University of Denmark, Department of Systems Biology, 2800, Lyngby, Denmark.,Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, 2970, Hørsholm, Denmark
| | - Luca Guardabassi
- University of Copenhagen, Department of Veterinary and Animal Sciences, 1870, Frederiksberg C, Denmark
| | - Mark G Poolman
- Oxford Brookes University, Department of Medical and Biological Sciences, Gipsy Lane, Headington, Oxford, OX3 OBP, United Kingdom
| | - John E Olsen
- University of Copenhagen, Department of Veterinary and Animal Sciences, 1870, Frederiksberg C, Denmark.
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González-Bello C. Recently developed synthetic compounds with anti-infective activity. Curr Opin Pharmacol 2019; 48:17-23. [DOI: 10.1016/j.coph.2019.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
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Parthasarathy A, Cross PJ, Dobson RCJ, Adams LE, Savka MA, Hudson AO. A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals. Front Mol Biosci 2018; 5:29. [PMID: 29682508 PMCID: PMC5897657 DOI: 10.3389/fmolb.2018.00029] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed.
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Affiliation(s)
- Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Penelope J. Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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6
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Wang PM, Choera T, Wiemann P, Pisithkul T, Amador-Noguez D, Keller NP. TrpE feedback mutants reveal roadblocks and conduits toward increasing secondary metabolism in Aspergillus fumigatus. Fungal Genet Biol 2015; 89:102-113. [PMID: 26701311 DOI: 10.1016/j.fgb.2015.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 11/23/2015] [Accepted: 12/05/2015] [Indexed: 12/11/2022]
Abstract
Small peptides formed from non-ribosomal peptide synthetases (NRPS) are bioactive molecules produced by many fungi including the genus Aspergillus. A subset of NRPS utilizes tryptophan and its precursor, the non-proteinogenic amino acid anthranilate, in synthesis of various metabolites such as Aspergillus fumigatus fumiquinazolines (Fqs) produced by the fmq gene cluster. The A. fumigatus genome contains two putative anthranilate synthases - a key enzyme in conversion of anthranilic acid to tryptophan - one beside the fmq cluster and one in a region of co-linearity with other Aspergillus spp. Only the gene found in the co-linear region, trpE, was involved in tryptophan biosynthesis. We found that site-specific mutations of the TrpE feedback domain resulted in significantly increased production of anthranilate, tryptophan, p-aminobenzoate and fumiquinazolines FqF and FqC. Supplementation with tryptophan restored metabolism to near wild type levels in the feedback mutants and suggested that synthesis of the tryptophan degradation product kynurenine could negatively impact Fq synthesis. The second putative anthranilate synthase gene next to the fmq cluster was termed icsA for its considerable identity to isochorismate synthases in bacteria. Although icsA had no impact on A. fumigatus Fq production, deletion and over-expression of icsA increased and decreased respectively aromatic amino acid levels suggesting that IcsA can draw from the cellular chorismate pool.
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Affiliation(s)
- Pin-Mei Wang
- Ocean College, Zhejiang University, Hangzhou 310058, Zhejiang Province, PR China
| | - Tsokyi Choera
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, USA
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, USA
| | | | | | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, USA; Department of Bacteriology, University of Wisconsin, Madison, USA.
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7
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Camara D, Bisanz C, Barette C, Van Daele J, Human E, Barnard B, Van der Straeten D, Stove CP, Lambert WE, Douce R, Maréchal E, Birkholtz LM, Cesbron-Delauw MF, Dumas R, Rébeillé F. Inhibition of p-aminobenzoate and folate syntheses in plants and apicomplexan parasites by natural product rubreserine. J Biol Chem 2012; 287:22367-76. [PMID: 22577137 DOI: 10.1074/jbc.m112.365833] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Glutamine amidotransferase/aminodeoxychorismate synthase (GAT-ADCS) is a bifunctional enzyme involved in the synthesis of p-aminobenzoate, a central component part of folate cofactors. GAT-ADCS is found in eukaryotic organisms autonomous for folate biosynthesis, such as plants or parasites of the phylum Apicomplexa. Based on an automated screening to search for new inhibitors of folate biosynthesis, we found that rubreserine was able to inhibit the glutamine amidotransferase activity of the plant GAT-ADCS with an apparent IC(50) of about 8 μM. The growth rates of Arabidopsis thaliana, Toxoplasma gondii, and Plasmodium falciparum were inhibited by rubreserine with respective IC(50) values of 65, 20, and 1 μM. The correlation between folate biosynthesis and growth inhibition was studied with Arabidopsis and Toxoplasma. In both organisms, the folate content was decreased by 40-50% in the presence of rubreserine. In both organisms, the addition of p-aminobenzoate or 5-formyltetrahydrofolate in the external medium restored the growth for inhibitor concentrations up to the IC(50) value, indicating that, within this range of concentrations, rubreserine was specific for folate biosynthesis. Rubreserine appeared to be more efficient than sulfonamides, antifolate drugs known to inhibit the invasion and proliferation of T. gondii in human fibroblasts. Altogether, these results validate the use of the bifunctional GAT-ADCS as an efficient drug target in eukaryotic cells and indicate that the chemical structure of rubreserine presents interesting anti-parasitic (toxoplasmosis, malaria) potential.
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Affiliation(s)
- Djeneb Camara
- Laboratoire de Physiologie Cellulaire Végétale, Commissariat à l'Energie Atomique/CNRS UMR5168/INRA USC1200/Université Joseph Fourier Grenoble I, Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France
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Vasan M, Neres J, Williams J, Wilson DJ, Teitelbaum AM, Remmel RP, Aldrich CC. Inhibitors of the salicylate synthase (MbtI) from Mycobacterium tuberculosis discovered by high-throughput screening. ChemMedChem 2011; 5:2079-87. [PMID: 21053346 DOI: 10.1002/cmdc.201000275] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A simple steady-state kinetic high-throughput assay was developed for the salicylate synthase MbtI from Mycobacterium tuberculosis, which catalyzes the first committed step of mycobactin biosynthesis. The mycobactins are small-molecule iron chelators produced by M. tuberculosis, and their biosynthesis has been identified as a promising target for the development of new antitubercular agents. The assay was miniaturized to a 384-well plate format and high-throughput screening was performed at the National Screening Laboratory for the Regional Centers of Excellence in Biodefense and Emerging Infectious Diseases (NSRB). Three classes of compounds were identified comprising the benzisothiazolones (class I), diarylsulfones (class II), and benzimidazole-2-thiones (class III). Each of these compound series was further pursued to investigate their biochemical mechanism and structure-activity relationships. Benzimidazole-2-thione 4 emerged as the most promising inhibitor owing to its potent reversible inhibition.
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Affiliation(s)
- Mahalakshmi Vasan
- Center for Drug Design, University of Minnesota, Minneapolis, 55455, USA
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9
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Camara D, Richefeu-Contesto C, Gambonnet B, Dumas R, Rébeillé F. The synthesis of pABA: Coupling between the glutamine amidotransferase and aminodeoxychorismate synthase domains of the bifunctional aminodeoxychorismate synthase from Arabidopsis thaliana. Arch Biochem Biophys 2011; 505:83-90. [DOI: 10.1016/j.abb.2010.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 09/09/2010] [Accepted: 09/09/2010] [Indexed: 10/19/2022]
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10
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Manos-Turvey A, Bulloch EMM, Rutledge PJ, Baker EN, Lott JS, Payne RJ. Inhibition studies of Mycobacterium tuberculosis salicylate synthase (MbtI). ChemMedChem 2010; 5:1067-79. [PMID: 20512795 DOI: 10.1002/cmdc.201000137] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis salicylate synthase (MbtI), a member of the chorismate-utilizing enzyme family, catalyses the first committed step in the biosynthesis of the siderophore mycobactin T. This complex secondary metabolite is essential for both virulence and survival of M. tuberculosis, the etiological agent of tuberculosis (TB). It is therefore anticipated that inhibitors of this enzyme may serve as TB therapies with a novel mode of action. Herein we describe the first inhibition study of M. tuberculosis MbtI using a library of functionalized benzoate-based inhibitors designed to mimic the substrate (chorismate) and intermediate (isochorismate) of the MbtI-catalyzed reaction. The most potent inhibitors prepared were those designed to mimic the enzyme intermediate, isochorismate. These compounds, based on a 2,3-dihydroxybenzoate scaffold, proved to be low-micromolar inhibitors of MbtI. The most potent inhibitors in this series possessed hydrophobic enol ether side chains at C3 in place of the enol-pyruvyl side chain found in chorismate and isochorismate.
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Payne RJ, Bulloch EMM, Kerbarh O, Abell C. Inhibition of chorismate-utilising enzymes by 2-amino-4-carboxypyridine and 4-carboxypyridone and 5-carboxypyridone analogues. Org Biomol Chem 2010; 8:3534-42. [PMID: 20532401 DOI: 10.1039/c004062b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several 2-amino-4-carboxypyridine, 4- and 5-carboxypyridone-based compounds were prepared and tested against three members of the chorismate-utilising enzyme family, anthranilate synthase, isochorismate synthase and salicylate synthase. Most compounds exhibited low micromolar inhibition of these three enzymes. The most potent inhibitor was a 4-carboxypyridone analogue bearing a lactate side chain on the pyridyl nitrogen which exhibited inhibition constants of 5, 91 and 54 muM against anthranilate synthase, isochorismate synthase and salicylate synthase respectively.
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Affiliation(s)
- Richard J Payne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UKCB2 1EW.
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12
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Thoden JB, Holden HM, Paritala H, Firestine SM. Structural and functional studies of Aspergillus clavatus N(5)-carboxyaminoimidazole ribonucleotide synthetase . Biochemistry 2010; 49:752-60. [PMID: 20050602 DOI: 10.1021/bi901599u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N(5)-Carboxyaminoimidazole ribonucleotide synthetase (N(5)-CAIR synthetase), a key enzyme in microbial de novo purine biosynthesis, catalyzes the conversion of aminoimidazole ribonucleotide (AIR) to N(5)-CAIR. To date, this enzyme has been observed only in microorganisms, and thus, it represents an ideal target for antimicrobial drug development. Here we report the cloning, crystallization, and three-dimensional structural analysis of Aspergillus clavatus N(5)-CAIR synthetase solved in the presence of either Mg(2)ATP or MgADP and AIR. These structures, determined to 2.1 and 2.0 A, respectively, revealed that AIR binds in a pocket analogous to that observed for other ATP-grasp enzymes involved in purine metabolism. On the basis of these models, a site-directed mutagenesis study was subsequently conducted that focused on five amino acid residues located in the active site region of the enzyme. These investigations demonstrated that Asp 153 and Lys 353 play critical roles in catalysis without affecting substrate binding. All other mutations affected substrate binding and, in some instances, catalysis as well. Taken together, the structural and kinetic data presented here suggest a catalytic mechanism whereby Mg(2)ATP and bicarbonate first react to form the unstable intermediate carboxyphosphate. This intermediate subsequently decarboxylates to CO(2) and inorganic phosphate, and the amino group of AIR, through general base assistance by Asp 153, attacks CO(2) to form N(5)-CAIR.
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Affiliation(s)
- James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Walker SR, Cumming H, Parker EJ. Substrate and reaction intermediate mimics as inhibitors of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase. Org Biomol Chem 2009. [DOI: 10.1039/b909241b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Payne RJ, Bulloch EMM, Toscano MM, Jones MA, Kerbarh O, Abell C. Synthesis and evaluation of 2,5-dihydrochorismate analogues as inhibitors of the chorismate-utilising enzymes. Org Biomol Chem 2009; 7:2421-9. [DOI: 10.1039/b901694e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Pacheco MC, Purser S, Gouverneur V. The chemistry of propargylic and allylic fluorides. Chem Rev 2008; 108:1943-81. [PMID: 18543877 DOI: 10.1021/cr068410e] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M Carmen Pacheco
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, UK
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16
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Keller S, Schadt HS, Ortel I, Süssmuth RD. Action of atrop-Abyssomicin C as an Inhibitor of 4-Amino-4-deoxychorismate Synthase PabB. Angew Chem Int Ed Engl 2007; 46:8284-6. [PMID: 17886307 DOI: 10.1002/anie.200701836] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Simone Keller
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623 Berlin, Germany
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Keller S, Schadt H, Ortel I, Süssmuth R. atrop-Abyssomicin C als Inhibitor der 4-Amino-4-desoxychorismat-Synthase PabB. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701836] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kolappan S, Zwahlen J, Zhou R, Truglio JJ, Tonge PJ, Kisker C. Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: implications for an enzyme family. Biochemistry 2007; 46:946-53. [PMID: 17240978 DOI: 10.1021/bi0608515] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Menaquinone biosynthesis is initiated by the conversion of chorismate to isochorismate, a reaction that is catalyzed by the menaquinone-specific isochorismate synthase, MenF. The catalytic mechanism of MenF has been probed using a combination of structural and biochemical studies, including the 2.5 A structure of the enzyme, and Lys190 has been identified as the base that activates water for nucleophilic attack at the chorismate C2 carbon. MenF is a member of a larger family of Mg2+ dependent chorismate binding enzymes catalyzing distinct chorismate transformations. The studies reported here extend the mechanism recently proposed for this enzyme family by He et al.: He, Z., Stigers Lavoie, K. D., Bartlett, P. A., and Toney, M. D. (2004) J. Am. Chem. Soc. 126, 2378-85.
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Affiliation(s)
- Subramaniapillai Kolappan
- Department of Pharmacological Sciences and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5115, USA
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19
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Scott DE, Ciulli A, Abell C. Coenzyme biosynthesis: enzyme mechanism, structure and inhibition. Nat Prod Rep 2007; 24:1009-26. [PMID: 17898895 DOI: 10.1039/b703108b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review highlights five key reactions in vitamin biosynthesis and in particular focuses on their mechanisms and inhibition and insights from structural studies. Each of the enzymes has the potential to be a target for novel antimicrobial agents.
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Affiliation(s)
- Duncan E Scott
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
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20
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González-Bello C, Castedo L. Progress in type II dehydroquinase inhibitors: From concept to practice. Med Res Rev 2007; 27:177-208. [PMID: 17004270 DOI: 10.1002/med.20076] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Scientists are concerned by an ever-increasing rise in bacterial resistance to antibiotics, particularly in diseases such as malaria, toxoplasmosis, tuberculosis, and pneumonia, where the currently used therapies become progressively less efficient. It is therefore necessary to develop new, safe, and more efficient antibiotics. Recently, the existence of the shikimic acid pathway has been demonstrated in certain parasites such as the malaria parasite. These types of parasites cause more than a million casualties per year, and their effects are particularly strong in people with a compromised immune system such as HIV patients. In such cases it is possible that inhibitors of this pathway could be active against a large variety of microorganisms responsible for the more opportunistic infections in HIV patients. Interest in this pathway has resulted in the development of a wide variety of inhibitors for the enzymes involved. This review covers recent progress made in the development of inhibitors of the third enzyme of this pathway, i.e., the type II dehydroquinase. The X-ray crystal structures of several dehydroquinases (Streptomyces coelicolor, Mycobacterium tuberculosis, etc.) with an inhibitor bound in the active site have recently been solved. These complexes identified a number of key interactions involved in inhibitor binding and have shed light on several aspects of the catalytic mechanism. These crystal structures have also proven to be a useful tool for the design of potent and selective enzyme inhibitors, a feature that will also be discussed.
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Affiliation(s)
- Concepción González-Bello
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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21
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Harrison AJ, Yu M, Gårdenborg T, Middleditch M, Ramsay RJ, Baker EN, Lott JS. The structure of MbtI from Mycobacterium tuberculosis, the first enzyme in the biosynthesis of the siderophore mycobactin, reveals it to be a salicylate synthase. J Bacteriol 2006; 188:6081-91. [PMID: 16923875 PMCID: PMC1595383 DOI: 10.1128/jb.00338-06] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Accepted: 06/21/2006] [Indexed: 11/20/2022] Open
Abstract
The ability to acquire iron from the extracellular environment is a key determinant of pathogenicity in mycobacteria. Mycobacterium tuberculosis acquires iron exclusively via the siderophore mycobactin T, the biosynthesis of which depends on the production of salicylate from chorismate. Salicylate production in other bacteria is either a two-step process involving an isochorismate synthase (chorismate isomerase) and a pyruvate lyase, as observed for Pseudomonas aeruginosa, or a single-step conversion catalyzed by a salicylate synthase, as with Yersinia enterocolitica. Here we present the structure of the enzyme MbtI (Rv2386c) from M. tuberculosis, solved by multiwavelength anomalous diffraction at a resolution of 1.8 A, and biochemical evidence that it is the salicylate synthase necessary for mycobactin biosynthesis. The enzyme is critically dependent on Mg2+ for activity and produces salicylate via an isochorismate intermediate. MbtI is structurally similar to salicylate synthase (Irp9) from Y. enterocolitica and the large subunit of anthranilate synthase (TrpE) and shares the overall architecture of other chorismate-utilizing enzymes, such as the related aminodeoxychorismate synthase PabB. Like Irp9, but unlike TrpE or PabB, MbtI is neither regulated by nor structurally stabilized by bound tryptophan. The structure of MbtI is the starting point for the design of inhibitors of siderophore biosynthesis, which may make useful lead compounds for the production of new antituberculosis drugs, given the strong dependence of pathogenesis on iron acquisition in M. tuberculosis.
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Affiliation(s)
- Anthony J Harrison
- Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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22
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Walker SR, Parker EJ. Synthesis and evaluation of a mechanism-based inhibitor of a 3-deoxy-d-arabino heptulosonate 7-phosphate synthase. Bioorg Med Chem Lett 2006; 16:2951-4. [PMID: 16563755 DOI: 10.1016/j.bmcl.2006.02.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 02/27/2006] [Indexed: 12/01/2022]
Abstract
The first mechanism-based inhibitor of a 3-deoxy-D-arabino heptulosonate 7-phosphate (DAH7P) synthase has been synthesised in 12 steps from D-arabinose, and has been found to be a very slow binding inhibitor of Escherichia coli DAH7P synthase.
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Affiliation(s)
- Scott R Walker
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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23
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Sahr T, Ravanel S, Basset G, Nichols B, Hanson A, Rébeillé F. Folate synthesis in plants: purification, kinetic properties, and inhibition of aminodeoxychorismate synthase. Biochem J 2006; 396:157-62. [PMID: 16466344 PMCID: PMC1449997 DOI: 10.1042/bj20051851] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
pABA (p-aminobenzoate) is a precursor of folates and, besides esterification to glucose, has no other known metabolic fate in plants. It is synthesized in two steps from chorismate and glutamine, the first step being their conversion into glutamate and ADC (4-aminodeoxychorismate). In Escherichia coli, two proteins forming a heterodimeric complex are required for this reaction, but, in plants and lower eukaryotes, a single protein is involved. The Arabidopsis enzyme was expressed in E. coli and was purified to homogeneity. The monomeric enzyme (95 kDa) catalyses two reactions: release of NH3 from glutamine (glutaminase activity) and substitution of NH3 for the hydroxy group at position 4 of chorismate (ADC synthase activity). The kinetic parameters of the plant enzyme are broadly similar to those of the bacterial complex, with K(m) values for glutamine and chorismate of 600 and 1.5 microM respectively. As with the bacterial enzyme, externally added NH3 was a very poor substrate for the plant enzyme, suggesting that NH3 released from glutamine is preferentially channelled to chorismate. The glutaminase activity could operate alone, but the presence of chorismate increased the efficiency of the reaction 10-fold, showing the interdependency of the two domains. The plant enzyme was inhibited by dihydrofolate and its analogue methotrexate, a feature never reported for the prokaryotic system. These molecules were inhibitors of the glutaminase reaction, competitive with respect to glutamine (K(i) values of 10 and 1 microM for dihydrofolate and methotrexate respectively). These findings support the view that the monomeric ADC synthase is a potential target for antifolate drugs.
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Affiliation(s)
- Tobias Sahr
- *Laboratoire de Physiologie Cellulaire Végétale, UMR5168 CNRS-CEA-INRA-Université Joseph Fourier Grenoble I, Département Réponse et Dynamique Cellulaires, CEA-Grenoble, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Stéphane Ravanel
- *Laboratoire de Physiologie Cellulaire Végétale, UMR5168 CNRS-CEA-INRA-Université Joseph Fourier Grenoble I, Département Réponse et Dynamique Cellulaires, CEA-Grenoble, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Gilles Basset
- †Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, U.S.A
| | - Brian P. Nichols
- ‡Department of Biological Sciences, University of Illinois, Chicago, IL 60607, U.S.A
| | - Andrew D. Hanson
- †Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, U.S.A
| | - Fabrice Rébeillé
- *Laboratoire de Physiologie Cellulaire Végétale, UMR5168 CNRS-CEA-INRA-Université Joseph Fourier Grenoble I, Département Réponse et Dynamique Cellulaires, CEA-Grenoble, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
- To whom correspondence should be addressed (email )
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24
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He Z, Toney MD. Direct detection and kinetic analysis of covalent intermediate formation in the 4-amino-4-deoxychorismate synthase catalyzed reaction. Biochemistry 2006; 45:5019-28. [PMID: 16605270 DOI: 10.1021/bi052216p] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chorismate-utilizing enzymes catalyze diverse reactions, providing critical physiological functions unique to plants, bacteria, fungi, and some parasites. Their absence in animals makes them excellent targets for antimicrobials and herbicides. 4-Amino-4-deoxychorismate synthase (ADCS) catalyzes the first step in folate biosynthsis and shares a common core mechanism with isochorismate synthase (IS) and anthranilate synthase (AS), in which nucleophile addition at C2 initiates these reactions. Evidence was presented previously [He, Z., Stigers Lavoie, K. D., Bartlett, P. A., and Toney, M. D. (2004) J. Am. Chem. Soc. 126, 2378-2385] that K274 is the nucleophile in ADCS, implying formation of a covalent intermediate. Herein, we report the direct detection of this covalent intermediate formed in ADCS-catalyzed reactions by ESI-MS. Difference spectra show the covalent intermediate has an absorption maximum at 310 nm. This was used to study the pre-steady-state kinetics of covalent intermediate formation under various conditions. Additionally, E258 in ADCS was shown to be critical to formation of the covalent intermediate by acting as a general acid catalyst for loss of the C4 hydroxyl group. The E258A/D mutants both exhibit very low activity. Acetate is a poor chemical rescue agent for E258D but an excellent one for E258A, with a 20000-fold and 3000-fold rate increase for Gln-dependent and NH(4)(+)-dependent activities, respectively. Lastly, A213 in IS (structurally homologous to K274 in ADCS) was changed to lysine in an attempt to convert IS to an ADCS-like enzyme. HPLC studies support the formation of a covalent intermediate with this mutant.
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Affiliation(s)
- Ze He
- Department of Chemistry, Central Connecticut State University, 1615 Stanley Street, New Britain, Connecticut 06050, USA
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25
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Humphreys JL, Lowes DJ, Wesson KA, Whitehead RC. Arene cis-dihydrodiols—useful precursors for the preparation of antimetabolites of the shikimic acid pathway: application to the synthesis of 6,6-difluoroshikimic acid and (6S)-6-fluoroshikimic acid. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.03.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Kerbarh O, Chirgadze DY, Blundell TL, Abell C. Crystal structures of Yersinia enterocolitica salicylate synthase and its complex with the reaction products salicylate and pyruvate. J Mol Biol 2006; 357:524-34. [PMID: 16434053 DOI: 10.1016/j.jmb.2005.12.078] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Revised: 12/20/2005] [Accepted: 12/20/2005] [Indexed: 11/25/2022]
Abstract
The salicylate synthase, Irp9, from Yersinia enterocolitica is involved in the biosynthesis of the siderophore yersiniabactin. It is a bifunctional enzyme that forms salicylate and pyruvate from chorismate and water via the intermediate isochorismate. Here we report the first crystal structure of Irp9 and also of its complex with the reaction products salicylate and pyruvate at 1.85 A and 2.1 A resolution, respectively. Like other members of the chorismate-utilizing enzyme family, e.g. the TrpE subunit of anthranilate synthase and the PabB subunit of 4-amino-4-deoxychorismate synthase, Irp9 has a complex alpha/beta fold. The crystal structure of Irp9 contains one molecule each of phosphate and acetate derived from the crystallization buffer. The Irp9-products complex structure was obtained by soaking chorismate into Irp9, demonstrating that the enzyme is still catalytically active in the crystal. Both structures contain Mg(2+) in the active site. There is no evidence of the allosteric tryptophan binding site found in TrpE and PabB. Mutagenesis of Glu240, His321 and Tyr372 provided some insight into the mechanism of the two transformations catalyzed by Irp9. Knowledge of the structure of Irp9 will guide the search for potent inhibitors of salicylate formation, and hence of bacterial iron uptake, which is directly related to the virulence of Yersinia.
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Affiliation(s)
- Olivier Kerbarh
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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27
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Bulloch EMM, Abell C. Detection of covalent intermediates formed in the reaction of 4-amino-4-deoxychorismate synthase. Chembiochem 2006; 6:832-4. [PMID: 15770625 DOI: 10.1002/cbic.200400385] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Esther M M Bulloch
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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28
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Williamson RM, Pietersma AL, Jameson GB, Parker EJ. Stereospecific deuteration of 2-deoxyerythrose 4-phosphate using 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase. Bioorg Med Chem Lett 2005; 15:2339-42. [PMID: 15837321 DOI: 10.1016/j.bmcl.2005.02.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2005] [Revised: 02/24/2005] [Accepted: 02/28/2005] [Indexed: 11/29/2022]
Abstract
Racemic 2-deoxyerythrose 4-phosphate was synthesized and one enantiomer of this compound was found to be a substrate for Escherichia coli 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, the first enzyme of the shikimate pathway. When the reaction was carried out in deuterium oxide, an enzyme-catalyzed regio- and stereoselective incorporation of deuterium into the product was observed.
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Affiliation(s)
- Rachel M Williamson
- Institute of Fundamental Sciences, Massey University, Palmerston North 5301, New Zealand
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29
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Kerbarh O, Bulloch EMM, Payne RJ, Sahr T, Rébeillé F, Abell C. Mechanistic and inhibition studies of chorismate-utilizing enzymes. Biochem Soc Trans 2005; 33:763-6. [PMID: 16042594 DOI: 10.1042/bst0330763] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The shikimate biosynthetic pathway is utilized in algae, higher plants, bacteria, fungi and apicomplexan parasites; it involves seven enzymatic steps in which phosphoenolpyruvate and erythrose 4-phosphate are converted into chorismate. In Escherichia coli, five chorismate-utilizing enzymes catalyse the synthesis of aromatic compounds such as L-phenylalanine, L-tyrosine, L-tryptophan, folate, ubiquinone and siderophores such as yersiniabactin and enterobactin. As mammals do not possess such a biosynthetic system, the enzymes involved in the pathway have aroused considerable interest as potential targets for the development of antimicrobial drugs and herbicides. As an initiative to investigate the mechanism of some of these enzymes, we showed that the antimicrobial effect of (6S)-6-fluoroshikimate is the result of irreversible inhibition of 4-amino-4-deoxychorismate synthase by 2-fluorochorismate. Based on this study, a catalytic mechanism for this enzyme was proposed, in which the residue Lys-274 is involved in the formation of a covalent intermediate. In another study, Yersinia enterocolitica Irp9, which is involved in the biosynthesis of the siderophore yersiniabactin, was for the first time biochemically characterized and shown to catalyse the formation of salicylate from chorismate via isochorismate as a reaction intermediate. A three-dimensional model for this enzyme was constructed that will guide the search for potent inhibitors of salicylate formation, and hence of bacterial iron uptake.
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Affiliation(s)
- O Kerbarh
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
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30
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Payne RJ, Toscano MD, Bulloch EMM, Abell AD, Abell C. Design and synthesis of aromatic inhibitors of anthranilate synthase. Org Biomol Chem 2005; 3:2271-81. [PMID: 16010361 DOI: 10.1039/b503802b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aromatic analogues of chorismate were synthesised as potential inhibitors of anthranilate synthase. Molecular modelling using GOLD2.1 showed that these analogues docked into the active site of Serratia marcescens anthranilate synthase in the same conformation as chorismate. Most compounds were found to be micromolar inhibitors of S. marcescens anthranilate synthase. The most potent analogue, 3-(1-carboxy-ethoxy)-4-hydroxybenzoate (K(I) 3 microM), included a lactyl ether side chain. This appears to be a good replacement for the enol-pyruvyl side chain of chorismate.
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Affiliation(s)
- Richard J Payne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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31
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Abstract
The development of new antibiotics is crucial to controlling current and future infectious diseases caused by antibiotic-resistant bacteria. Increased development costs, the difficulty in identifying new drug classes, unanticipated drug toxicities, the ease by which bacteria develop resistance to new antibiotics and the failure of many agents to address antibiotic resistance specifically, however, have all led to an overall decline in the number of antibiotics that are being introduced into clinical practice. Although there are few, if any, advances likely in the immediate future, there are agents in both clinical and preclinical development that can address some of the concerns of the infectious disease community. Many of these antibiotics will be tailored to specific infections caused by a relatively modest number of susceptible and resistant organisms.
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Affiliation(s)
- Michael N Alekshun
- Paratek Pharmaceuticals, Inc., 75 Kneeland Street, Boston, MA 02111, USA.
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32
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Becker SA, Palsson BØ. Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol 2005; 5:8. [PMID: 15752426 PMCID: PMC1079855 DOI: 10.1186/1471-2180-5-8] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Accepted: 03/07/2005] [Indexed: 11/30/2022] Open
Abstract
Background Several strains of bacteria have sequenced and annotated genomes, which have been used in conjunction with biochemical and physiological data to reconstruct genome-scale metabolic networks. Such reconstruction amounts to a two-dimensional annotation of the genome. These networks have been analyzed with a constraint-based formalism and a variety of biologically meaningful results have emerged. Staphylococcus aureus is a pathogenic bacterium that has evolved resistance to many antibiotics, representing a significant health care concern. We present the first manually curated elementally and charge balanced genome-scale reconstruction and model of S. aureus' metabolic networks and compute some of its properties. Results We reconstructed a genome-scale metabolic network of S. aureus strain N315. This reconstruction, termed iSB619, consists of 619 genes that catalyze 640 metabolic reactions. For 91% of the reactions, open reading frames are explicitly linked to proteins and to the reaction. All but three of the metabolic reactions are both charge and elementally balanced. The reaction list is the most complete to date for this pathogen. When the capabilities of the reconstructed network were analyzed in the context of maximal growth, we formed hypotheses regarding growth requirements, the efficiency of growth on different carbon sources, and potential drug targets. These hypotheses can be tested experimentally and the data gathered can be used to improve subsequent versions of the reconstruction. Conclusion iSB619 represents comprehensive biochemically and genetically structured information about the metabolism of S. aureus to date. The reconstructed metabolic network can be used to predict cellular phenotypes and thus advance our understanding of a troublesome pathogen.
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Affiliation(s)
- Scott A Becker
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Bernhard Ø Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
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33
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Payne RJ, Bulloch EMM, Abell AD, Abell C. Design and synthesis of aromatic inhibitors of anthranilate synthase. Org Biomol Chem 2005; 3:3629-35. [PMID: 16211099 DOI: 10.1039/b510633h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anthranilate synthase catalyses the conversion of chorismate to anthranilate, a key step in tryptophan biosynthesis. A series of 3-(1-carboxy-ethoxy) benzoic acids were synthesised as chorismate analogues, with varying functionality at C-4, the position of the departing hydroxyl group in chorismate. Most of the compounds were moderate inhibitors of anthranilate synthase, with inhibition constants between 20-30 microM. The exception was 3-(1-carboxy-ethoxy) benzoic acid, (C-4 = H), for which K(I)= 2.4 microM. These results suggest that a hydrogen bonding interaction with the active site general acid (Glu309) is less important than previously assumed for inhibition of the enzyme by these aromatic chorismate analogues.
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Affiliation(s)
- Richard J Payne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UKCB2 1EW
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