1
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Haggett JG, Domaille DW. ortho-Boronic Acid Carbonyl Compounds and Their Applications in Chemical Biology. Chemistry 2024; 30:e202302485. [PMID: 37967030 DOI: 10.1002/chem.202302485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/07/2023] [Accepted: 11/13/2023] [Indexed: 11/17/2023]
Abstract
Iminoboronates and diazaborines are related classes of compounds that feature an imine ortho to an arylboronic acid (iminoboronate) or a hydrazone that cyclizes with an ortho arylboronic acid (diazaborine). Rather than acting as independent chemical motifs, the arylboronic acid impacts the rate of imine/hydrazone formation, hydrolysis, and exchange with competing nucleophiles. Increasing evidence has shown that the imine/hydrazone functionality also impacts arylboronic acid reactivity toward diols and reactive oxygen and nitrogen species (ROS/RNS). Untangling the communication between C=N linked functionalities and arylboronic acids has revealed a powerful and tunable motif for bioconjugation chemistries and other applications in chemical biology. Here, we survey the applications of iminoboronates and diazaborines in these fields with an eye toward understanding their utility as a function of neighboring group effects.
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Affiliation(s)
- Jack G Haggett
- Department of Chemistry, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401, USA
| | - Dylan W Domaille
- Department of Chemistry, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401, USA
- Quantitative Biology and Engineering Program, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401, USA
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2
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Khalifa A, Khalil A, Abdel-Aziz MM, Albohy A, Mohamady S. Isatin-pyrimidine hybrid derivatives as enoyl acyl carrier protein reductase (InhA) inhibitors against Mycobacterium tuberculosis. Bioorg Chem 2023; 138:106591. [PMID: 37201321 DOI: 10.1016/j.bioorg.2023.106591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/20/2023] [Accepted: 05/02/2023] [Indexed: 05/20/2023]
Abstract
Tuberculosis is a worldwide problem that impose a burden on the economy due to continuous development of resistant strains. The development of new antitubercular drugs is a need and can be achieved through inhibition of druggable targets. Mycobacterium tuberculosis enoyl acyl carrier protein (ACP) reductase (InhA) is an important enzyme for Mycobacterium tuberculosis survival. In this study, we report the synthesis of isatin derivatives that could treat TB through inhibition of this enzyme. Compound 4l showed IC50 value (0.6 ± 0.94 µM) similar to isoniazid but is also effective against MDR and XDR Mycobacterium tuberculosis strains (MIC of 0.48 and 3.9 µg/mL, respectively). Molecular docking studies suggest that this compound binds through the use of relatively unexplored hydrophobic pocket in the active site. Molecular dynamics was used to investigate and support the stability of 4l complex with the target enzyme. This study paves the way for the design and synthesis of novel antitubercular drugs.
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Affiliation(s)
- Abdalrahman Khalifa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Amira Khalil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt
| | - Marwa M Abdel-Aziz
- The Regional Center for Mycology & Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Amgad Albohy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt.
| | - Samy Mohamady
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt; The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt.
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3
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Li ZR, Li R, Pasternack L, Chen P, Wong CH. Chemical Synthesis of a Keto Sugar Nucleotide. J Org Chem 2023. [PMID: 37126664 DOI: 10.1021/acs.joc.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Keto sugar nucleotides (KSNs) are common and versatile precursors to various deoxy sugar nucleotides, which are substrates for the corresponding glycosyltransferases involved in the biosynthesis of glycoproteins, glycolipids, and natural products. However, there has been no KSN synthesized chemically due to the inherent instability. Herein, the first chemical synthesis of the archetypal KSN TDP-4-keto-6-deoxy-d-glucose (1) is achieved by an efficient and optimized route, providing feasible access to other KSNs and analogues, thereby opening a new avenue for new applications.
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Affiliation(s)
- Zhong-Rui Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Ruofan Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Laura Pasternack
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Pengxi Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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4
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Rangaswamy AMM, Beh MHR, Soleimani E, Sequeira S, Cormier J, Robertson KN, Jakeman DL. Synthesis of 5'-Thymidine-Conjugated Formylphenylboronic Acids as Potential Lysine Targeting Iminoboronate Reversible Covalent Enzyme Probes. J Org Chem 2022; 87:13542-13555. [PMID: 36265169 DOI: 10.1021/acs.joc.2c01000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The design of reversible-covalent molecules to selectively target the ε-amino functionality of lysine residues in enzymes or proteins is a highly desirable goal. Herein, we describe synthetic methodology used to prepare a series of 5'-thymidine-linked formylphenylboronic acids as probes to interrogate sugar nucleotide processing enzymes that recognize thymidine. The first synthetic strategy mitigated the need for protecting group manipulations of thymidine by capitalizing upon the straightforward preparation, isolation, and reactivity of 5'-azidothymidine. An alkyne cycloaddition partner was installed through either a propargyl or ethynyl phenyl ketone derived boronic acid. The second strategy directly linked formylphenylboronic acids to 5-thymidine through an ether linkage installed using Mitsunobu conditions with 3'-O,3-dibenzoylthymidine. Iminoboronate formation was observed with a selected probe.
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Affiliation(s)
| | | | - Ebrahim Soleimani
- Department of Chemistry, Razi University, Kermanshah, 67149-67346, Iran
| | | | | | - Katherine N Robertson
- Department of Chemistry, Saint Mary's University, 923 Robie Street, Halifax, Nova Scotia B3H 3C3, Canada
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5
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Boni FG, Hamdi I, Moukendza Koundi L, Dai Y, Shrestra K, Abokadoum MA, Ekomi Moure UA, Suleiman IM, Xie J. The Gene and Regulatory Network Involved in Ethambutol Resistance in Mycobacterium tuberculosis. Microb Drug Resist 2022; 29:175-189. [PMID: 35939307 DOI: 10.1089/mdr.2021.0239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ethambutol (EMB) is used in combination with isoniazid and rifampicin for the treatment of tuberculosis caused by Mycobacterium tuberculosis. However, the incidence of EMB resistance is alarming. The EMB targets the cell wall arabinan biosynthesis. It is important to comprehensively understand the molecular basis of EMB to slow down the drug resistance rate of EMB. This study summarized the genes implicated in EMB resistance, regulatory network and the pharmacoproteomic effect of EMB in M. tuberculosis. Many of the genes related to EMB are implicated in membrane components, drug efflux, lipid metabolism, ribosome, and detoxification. The differential response model may help to design a novel anti-tuberculosis antibiotic.
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Affiliation(s)
- Funmilayo Grâce Boni
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Insaf Hamdi
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Liadrine Moukendza Koundi
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Yongdong Dai
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Kanshan Shrestra
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Mohamed Abdellah Abokadoum
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China.,Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assuit, Egypt
| | - Ulrich Aymard Ekomi Moure
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Ismail Mohamed Suleiman
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
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6
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Khan MN, Ahmed I, Ud Din I, Noureldeen A, Darwish H, Khan M. Proteomic insight into soybean response to flooding stress reveals changes in energy metabolism and cell wall modifications. PLoS One 2022; 17:e0264453. [PMID: 35511817 PMCID: PMC9070951 DOI: 10.1371/journal.pone.0264453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/08/2022] [Indexed: 11/19/2022] Open
Abstract
Soybean is a legume crop enriched with proteins and oil. It is frequently exposed to anthropogenic and natural flooding that limits its growth and yield. Current study applied gel-free proteomic techniques to unravel soybean response mechanism to flooding stress. Two-days-old soybeans were flooded for 4 days continuously and root samples were collected at days 2 to 6 for proteomic and enzymatic analyses. Age-matched untreated soybeans were collected as control. After protein extraction, purification and tryptic digestion, the peptides were analyzed on nano-liquid chromatography-mass spectrometry. A total of 539 and 472 proteins with matched peptides 2 or more were identified in control and flooded seedlings, respectively. Among these 364 proteins were commonly identified in both control and flooded soybeans. Fourty-two protein's abundances were changed 4-fold after 2-days of flooding stress as compared to starting point. The cluster analysis showed that highly increased proteins included cupin family proteins, enolase, pectin methylesterase inhibitor, glyoxalase II, alcohol dehydrogenase and aldolase. The enzyme assay of enolase and pectin methylesterase inhibitor confirmed protein abundance changes. These findings suggest that soybean adopts the less energy consuming strategies and brings biochemical and structural changes in the cell wall to effectively respond to flooding stress and for the survival.
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Affiliation(s)
- Mudassar Nawaz Khan
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture Peshawar, Peshawar, Pakistan
- Department of Biotechnology & Genetic Engineering, Hazara University Mansehra, Mansehra, Pakistan
| | - Iftikhar Ahmed
- Bio Resources Conservation Institute, National Agricultural Research Center Islamabad, Islamabad, Pakistan
| | - Israr Ud Din
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Ahmed Noureldeen
- Department of Biology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Hadeer Darwish
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Majid Khan
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture Peshawar, Peshawar, Pakistan
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7
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Vogel U, Beerens K, Desmet T. Nucleotide sugar dehydratases: Structure, mechanism, substrate specificity, and application potential. J Biol Chem 2022; 298:101809. [PMID: 35271853 PMCID: PMC8987622 DOI: 10.1016/j.jbc.2022.101809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 11/14/2022] Open
Abstract
Nucleotide sugar (NS) dehydratases play a central role in the biosynthesis of deoxy and amino sugars, which are involved in a variety of biological functions in all domains of life. Bacteria are true masters of deoxy sugar biosynthesis as they can produce a wide range of highly specialized monosaccharides. Indeed, deoxy and amino sugars play important roles in the virulence of gram-positive and gram-negative pathogenic species and are additionally involved in the biosynthesis of diverse macrolide antibiotics. The biosynthesis of deoxy sugars relies on the activity of NS dehydratases, which can be subdivided into three groups based on their structure and reaction mechanism. The best-characterized NS dehydratases are the 4,6-dehydratases that, together with the 5,6-dehydratases, belong to the NS-short-chain dehydrogenase/reductase superfamily. The other two groups are the less abundant 2,3-dehydratases that belong to the Nudix hydrolase superfamily and 3-dehydratases, which are related to aspartame aminotransferases. 4,6-Dehydratases catalyze the first step in all deoxy sugar biosynthesis pathways, converting nucleoside diphosphate hexoses to nucleoside diphosphate-4-keto-6-deoxy hexoses, which in turn are further deoxygenated by the 2,3- and 3-dehydratases to form dideoxy and trideoxy sugars. In this review, we give an overview of the NS dehydratases focusing on the comparison of their structure and reaction mechanisms, thereby highlighting common features, and investigating differences between closely related members of the same superfamilies.
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Affiliation(s)
- Ulrike Vogel
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.
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8
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The effects of mycobacterial RmlA perturbation on cellular dNTP pool, cell morphology, and replication stress in Mycobacterium smegmatis. PLoS One 2022; 17:e0263975. [PMID: 35202428 PMCID: PMC8870461 DOI: 10.1371/journal.pone.0263975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/01/2022] [Indexed: 11/19/2022] Open
Abstract
The concerted action of DNA replication and cell division has been extensively investigated in eukaryotes. Well demarcated checkpoints have been identified in the cell cycle, which provides the correct DNA stoichiometry and appropriate growth in the progeny. In bacteria, which grow faster and less concerted than eukaryotes, the linkages between cell elongation and DNA synthesis are unclear. dTTP, one of the canonical nucleotide-building blocks of DNA, is also used for cell wall biosynthesis in mycobacteria. We hypothesize that the interconnection between DNA and cell wall biosynthesis through dTTP may require synchronization of these processes by regulating dTTP availability. We investigated growth, morphology, cellular dNTP pool, and possible signs of stress in Mycobacterium smegmatis upon perturbation of rhamnose biosynthesis by the overexpression of RmlA. RmlA is a cell wall synthetic enzyme that uses dTTP as the precursor for cross-linking the peptidoglycan with the arabinogalactan layers by a phosphodiester bond in the mycobacterial cell wall. We found that RmlA overexpression results in changes in cell morphology, causing cell elongation and disruption of the cylindrical cell shape. We also found that the cellular dTTP pool is reduced by half in RmlA overexpressing cells and that this reduced dTTP availability does not restrict cell growth. We observed 2-6-fold increases in the gene expression of replication and cell wall biosynthesis stress factors upon RmlA overexpression. Using super-resolution microscopy, we found that RmlA, acting to crosslink the nascent layers of the cell wall, localizes throughout the whole cell length in a helical pattern in addition to the cellular pole.
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9
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Koller F, Lassak J. Two RmlC homologs catalyze dTDP-4-keto-6-deoxy-D-glucose epimerization in Pseudomonas putida KT2440. Sci Rep 2021; 11:11991. [PMID: 34099824 PMCID: PMC8184846 DOI: 10.1038/s41598-021-91421-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/26/2021] [Indexed: 11/09/2022] Open
Abstract
l-Rhamnose is an important monosaccharide both as nutrient source and as building block in prokaryotic glycoproteins and glycolipids. Generation of those composite molecules requires activated precursors being provided e. g. in form of nucleotide sugars such as dTDP-β-l-rhamnose (dTDP-l-Rha). dTDP-l-Rha is synthesized in a conserved 4-step reaction which is canonically catalyzed by the enzymes RmlABCD. An intact pathway is especially important for the fitness of pseudomonads, as dTDP-l-Rha is essential for the activation of the polyproline specific translation elongation factor EF-P in these bacteria. Within the scope of this study, we investigated the dTDP-l-Rha-biosynthesis route of Pseudomonas putida KT2440 with a focus on the last two steps. Bioinformatic analysis in combination with a screening approach revealed that epimerization of dTDP-4-keto-6-deoxy-d-glucose to dTDP-4-keto-6-deoxy-l-mannose is catalyzed by the two paralogous proteins PP_1782 (RmlC1) and PP_0265 (RmlC2), whereas the reduction to the final product is solely mediated by PP_1784 (RmlD). Thus, we also exclude the distinct RmlD homolog PP_0500 and the genetically linked nucleoside diphosphate-sugar epimerase PP_0501 to be involved in dTDP-l-Rha formation, other than suggested by certain databases. Together our analysis contributes to the molecular understanding how this important nucleotide-sugar is synthesized in pseudomonads.
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Affiliation(s)
- Franziska Koller
- Department Biology I, Microbiology, Ludwig-Maximilians-Universität München, Planegg/Martinsried, Germany
| | - Jürgen Lassak
- Department Biology I, Microbiology, Ludwig-Maximilians-Universität München, Planegg/Martinsried, Germany.
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10
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Qu D, Zhao X, Sun Y, Wu FL, Tao SC. Mycobacterium tuberculosis Thymidylyltransferase RmlA Is Negatively Regulated by Ser/Thr Protein Kinase PknB. Front Microbiol 2021; 12:643951. [PMID: 33868202 PMCID: PMC8044546 DOI: 10.3389/fmicb.2021.643951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/28/2021] [Indexed: 11/13/2022] Open
Abstract
Ser/Thr phosphorylation by serine/threonine protein kinases (STPKs) plays significant roles in molecular regulation, which allows Mycobacteria to adapt their cell wall structure in response to the environment changes. Identifying direct targets of STPKs and determining their activities are therefore critical to revealing their function in Mycobacteria, for example, in cell wall formation and virulence. Herein, we reported that RmlA, a crucial L-rhamnose biosynthesis enzyme, is a substrate of STPK PknB in Mycobacterium tuberculosis (M. tuberculosis). Mass spectrometry analysis revealed that RmlA is phosphorylated at Thr-12, Thr-54, Thr-197, and Thr-12 is located close to the catalytic triad of RmlA. Biochemical and phenotypic analysis of two RmlA mutants, T12A/T12D, showed that their activities were reduced, and cell wall formation was negatively affected. Moreover, virulence of RmlA T12D mutant was attenuated in a macrophage model. Overall, these results provide the first evidence for the role of PknB-dependent RmlA phosphorylation in regulating cell wall formation in Mycobacteria, with significant implications for pathogenicity.
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Affiliation(s)
- Dehui Qu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai, China.,State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaohui Zhao
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai, China
| | - Yao Sun
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai, China
| | - Fan-Lin Wu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai, China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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Ravichandran R, Ridzwan NFW, Mohamad SB. Ensemble-based high-throughput virtual screening of natural ligands using the Super Natural-II database against cell-wall protein dTDP-4-dehydrorhamnose reductase (RmlD) in Mycobacterium tuberculosis. J Biomol Struct Dyn 2020; 40:5069-5078. [PMID: 33382017 DOI: 10.1080/07391102.2020.1867641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The disease Tuberculosis (TB) is caused by a bacterium called Mycobacterium tuberculosis (Mtb). The bacterial cell-wall consists of peptidoglycan layer maintains the cellular integrity and cell viability. The main problem resides in the cell cycle of Mycobacterium tuberculosis in its quiescent form which is not targeted by any drugs hence there is an immediate need for new antibiotics to target the cell wall. The current study deals with the dTDP-4-dehydrorahmnose reductase (RmlD) which is the final enzyme in the series of cell-wall proteins of Mtb. The RmlD is a part of Carbohydrate biosynthesis has been considered as a good drug target for the novel class of antibiotics. Our study begins with the protein structure prediction, Homology studies were conducted using the Phyre2 web server. The structure is then refined and subjected to molecular dynamics simulations for 50 ns using GROMACS. The clustering analysis has been carried out and generated 41 clusters with 2 Å as the cut-off. Blind docking virtual screening was performed against RmlD protein using the Super Natural-II database with AutoDock4.0. its results helped to screen top ligands based on best binding energies. In both dockings, there are some common residues in which the ligands are interacting and forming the Hydrogen bonds such as Asp-105, Val-158, Thr-160, Gly-161, Arg-224, Arg-256. The ligand-567 giving the best results by being in the top-3 of all the clusters in both blind docking as well as the active-site docking. Hence ligand-567 can be a potential inhibitor of RmlD which can further inhibit the cell-wall synthesis of Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahul Ravichandran
- DiSTABiF, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy.,School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | | | - Saharuddin Bin Mohamad
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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12
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Kucerova-Chlupacova M, Halakova D, Majekova M, Treml J, Stefek M, Soltesova Prnova M. (4-Oxo-2-thioxothiazolidin-3-yl)acetic acids as potent and selective aldose reductase inhibitors. Chem Biol Interact 2020; 332:109286. [DOI: 10.1016/j.cbi.2020.109286] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 12/22/2022]
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13
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Pangenome Analysis of Mycobacterium tuberculosis Reveals Core-Drug Targets and Screening of Promising Lead Compounds for Drug Discovery. Antibiotics (Basel) 2020; 9:antibiotics9110819. [PMID: 33213029 PMCID: PMC7698547 DOI: 10.3390/antibiotics9110819] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (M. tuberculosis), is one of the leading causes of human deaths globally according to the WHO TB 2019 report. The continuous rise in multi- and extensive-drug resistance in M. tuberculosis broadens the challenges to control tuberculosis. The availability of a large number of completely sequenced genomes of M. tuberculosis has provided an opportunity to explore the pangenome of the species along with the pan-phylogeny and to identify potential novel drug targets leading to drug discovery. We attempt to calculate the pangenome of M. tuberculosis that comprises a total of 150 complete genomes and performed the phylo-genomic classification and analysis. Further, the conserved core genome (1251 proteins) is subjected to various sequential filters (non-human homology, essentiality, virulence, physicochemical parameters, and pathway analysis) resulted in identification of eight putative broad-spectrum drug targets. Upon molecular docking analyses of these targets with ligands available at the DrugBank database shortlisted a total of five promising ligands with projected inhibitory potential; namely, 2′deoxy-thymidine-5′-diphospho-alpha-d-glucose, uridine diphosphate glucose, 2′-deoxy-thymidine-beta-l-rhamnose, thymidine-5′-triphosphate, and citicoline. We are confident that with further lead optimization and experimental validation, these lead compounds may provide a sound basis to develop safe and effective drugs against tuberculosis disease in humans.
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14
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Ali MA, Farah MA, Lee J, Al-Anazi KM, Al-Hemaid FM. Molecular Insights into the Interaction of Ursolic Acid and Cucurbitacin from Colocynth with Therapeutic Targets of Mycobacterium tuberculosis. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817999200514102750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
Medicinal plants like Citrullus colocynthis are a potential choice to produce helpful
novel antimycobacterial drugs. The existence of a range of natural products in the plants, especially
Ursolic Acid (UA) and cucurbitacin E 2-0-β-d-glucopyranoside (CEG), with promising antibacterial
activity against a variety of bacteria, prompted the need to check its actions against Mycobacterium
tuberculosis (Mtb).
Background:
Mycobacterium tuberculosis (Mtb), an obligate human pathogen causes tuberculosis
and is one of the major causes of death worldwide. A few combinations of drugs are currently accessible
for treating TB patients, but these are inadequate to tackle worldwide TB cases.
Objective:
The molecular interactions between ursolic acid and cucurbitacin E with the eight potential
Mtb target proteins were investigated with the objective of finding drug-like inhibitors.
Methods:
Avogadro v.1.2.0 and Openbabel v.2.4.1 were used for creating file formats required for
docking analysis. Molecular docking was performed with eight different proteins essential for Mtb
metabolism and survival. AutoDock v.4.2 and AutoDock vina v.1.1.2 were used for docking and
Gromacs 5.1.4 was used for simulation studies.
Results and Discussion:
Among the two ligands used in this research, cucurbitacin E showed a better
docking score relative to the drugs presently available for all the target proteins. Rifampicin showed the
best binding affinity (among known inhibitors) i.e. -10.8 kcal/mol with C terminal caspase recruitment
domain. Moreover, ursolic acid and cucurbitacin E showed uniform binding score (above -7.5
kcal/mol) with all the target proteins, acknowledged its availability as a potential multi-target drug.
Conclusion:
Ursolic acid can be useful in the creation of novel, multi-targeted and effective anti-
TB medicines since it showed stable structure with FabH.
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Affiliation(s)
- Mohammad Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Abul Farah
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Khalid M. Al-Anazi
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fahad M.A. Al-Hemaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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15
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Fu TK, Ng SK, Chen YE, Lee YC, Demeter F, Herczeg M, Borbás A, Chiu CH, Lan CY, Chen CL, Chang MDT. Rhamnose Binding Protein as an Anti-Bacterial Agent-Targeting Biofilm of Pseudomonas aeruginosa. Mar Drugs 2019; 17:md17060355. [PMID: 31207891 PMCID: PMC6628293 DOI: 10.3390/md17060355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 01/14/2023] Open
Abstract
More than 80% of infectious bacteria form biofilm, which is a bacterial cell community surrounded by secreted polysaccharides, proteins and glycolipids. Such bacterial superstructure increases resistance to antimicrobials and host defenses. Thus, to control these biofilm-forming pathogenic bacteria requires antimicrobial agents with novel mechanisms or properties. Pseudomonas aeruginosa, a Gram-negative opportunistic nosocomial pathogen, is a model strain to study biofilm development and correlation between biofilm formation and infection. In this study, a recombinant hemolymph plasma lectin (rHPLOE) cloned from Taiwanese Tachypleus tridentatus was expressed in an Escherichia coli system. This rHPLOE was shown to have the following properties: (1) Binding to P. aeruginosa PA14 biofilm through a unique molecular interaction with rhamnose-containing moieties on bacteria, leading to reduction of extracellular di-rhamnolipid (a biofilm regulator); (2) decreasing downstream quorum sensing factors, and inhibiting biofilm formation; (3) dispersing the mature biofilm of P. aeruginosa PA14 to improve the efficacies of antibiotics; (4) reducing P. aeruginosa PA14 cytotoxicity to human lung epithelial cells in vitro and (5) inhibiting P. aeruginosa PA14 infection of zebrafish embryos in vivo. Taken together, rHPLOE serves as an anti-biofilm agent with a novel mechanism of recognizing rhamnose moieties in lipopolysaccharides, di-rhamnolipid and structural polysaccharides (Psl) in biofilms. Thus rHPLOE links glycan-recognition to novel anti-biofilm strategies against pathogenic bacteria.
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Affiliation(s)
- Tse-Kai Fu
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.
- Simpson Biotech Co., Ltd., Taoyuan 333, Taiwan.
| | - Sim-Kun Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Yi-En Chen
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Yuan-Chuan Lee
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.
- Department of Biology, Johns Hopkins University, Baltimore, ML 21218, USA.
| | - Fruzsina Demeter
- Department of Pharmaceutical Chemistry, University of Debrecen, Debrecen 4032, Hungary (F.D.).
| | - Mihály Herczeg
- Department of Pharmaceutical Chemistry, University of Debrecen, Debrecen 4032, Hungary (F.D.).
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Debrecen 4032, Hungary (F.D.).
| | - Cheng-Hsun Chiu
- Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Chung-Yu Lan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.
- Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 333, Taiwan.
| | - Margaret Dah-Tsyr Chang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.
- Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
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16
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Wagstaff BA, Rejzek M, Kuhaudomlarp S, Hill L, Mascia I, Nepogodiev SA, Dorfmueller HC, Field RA. Discovery of an RmlC/D fusion protein in the microalga Prymnesium parvum and its implications for NDP-β-l-rhamnose biosynthesis in microalgae. J Biol Chem 2019; 294:9172-9185. [PMID: 31010825 PMCID: PMC6556577 DOI: 10.1074/jbc.ra118.006440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/19/2019] [Indexed: 11/06/2022] Open
Abstract
The 6-deoxy sugar l-rhamnose (l-Rha) is found widely in plant and microbial polysaccharides and natural products. The importance of this and related compounds in host-pathogen interactions often means that l-Rha plays an essential role in many organisms. l-Rha is most commonly biosynthesized as the activated sugar nucleotide uridine 5'-diphospho-β-l-rhamnose (UDP-β-l-Rha) or thymidine 5'-diphospho-β-l-rhamnose (TDP-β-l-Rha). Enzymes involved in the biosynthesis of these sugar nucleotides have been studied in some detail in bacteria and plants, but the activated form of l-Rha and the corresponding biosynthetic enzymes have yet to be explored in algae. Here, using sugar-nucleotide profiling in two representative algae, Euglena gracilis and the toxin-producing microalga Prymnesium parvum, we show that levels of UDP- and TDP-activated l-Rha differ significantly between these two algal species. Using bioinformatics and biochemical methods, we identified and characterized a fusion of the RmlC and RmlD proteins, two bacteria-like enzymes involved in TDP-β-l-Rha biosynthesis, from P. parvum Using this new sequence and also others, we explored l-Rha biosynthesis among algae, finding that although most algae contain sequences orthologous to plant-like l-Rha biosynthesis machineries, instances of the RmlC-RmlD fusion protein identified here exist across the Haptophyta and Gymnodiniaceae families of microalgae. On the basis of these findings, we propose potential routes for the evolution of nucleoside diphosphate β-l-Rha (NDP-β-l-Rha) pathways among algae.
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Affiliation(s)
- Ben A Wagstaff
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom, and
| | - Martin Rejzek
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sakonwan Kuhaudomlarp
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Lionel Hill
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Ilaria Mascia
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sergey A Nepogodiev
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom, and
| | - Robert A Field
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom,
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17
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van der Beek SL, Zorzoli A, Çanak E, Chapman RN, Lucas K, Meyer BH, Evangelopoulos D, de Carvalho LPS, Boons GJ, Dorfmueller HC, van Sorge NM. Streptococcal dTDP-L-rhamnose biosynthesis enzymes: functional characterization and lead compound identification. Mol Microbiol 2019; 111:951-964. [PMID: 30600561 PMCID: PMC6487966 DOI: 10.1111/mmi.14197] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2018] [Indexed: 12/12/2022]
Abstract
Biosynthesis of the nucleotide sugar precursor dTDP‐L‐rhamnose is critical for the viability and virulence of many human pathogenic bacteria, including Streptococcus pyogenes (Group A Streptococcus; GAS), Streptococcus mutans and Mycobacterium tuberculosis. Streptococcal pathogens require dTDP‐L‐rhamnose for the production of structurally similar rhamnose polysaccharides in their cell wall. Via heterologous expression in S. mutans, we confirmed that GAS RmlB and RmlC are critical for dTDP‐L‐rhamnose biosynthesis through their action as dTDP‐glucose‐4,6‐dehydratase and dTDP‐4‐keto‐6‐deoxyglucose‐3,5‐epimerase enzymes respectively. Complementation with GAS RmlB and RmlC containing specific point mutations corroborated the conservation of previous identified catalytic residues. Bio‐layer interferometry was used to identify and confirm inhibitory lead compounds that bind to GAS dTDP‐rhamnose biosynthesis enzymes RmlB, RmlC and GacA. One of the identified compounds, Ri03, inhibited growth of GAS, other rhamnose‐dependent streptococcal pathogens as well as M. tuberculosis with an IC50 of 120–410 µM. Importantly, we confirmed that Ri03 inhibited dTDP‐L‐rhamnose formation in a concentration‐dependent manner through a biochemical assay with recombinant rhamnose biosynthesis enzymes. We therefore conclude that inhibitors of dTDP‐L‐rhamnose biosynthesis, such as Ri03, affect streptococcal and mycobacterial viability and can serve as lead compounds for the development of a new class of antibiotics that targets dTDP‐rhamnose biosynthesis in pathogenic bacteria.
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Affiliation(s)
- Samantha L van der Beek
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Azul Zorzoli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Ebru Çanak
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Robert N Chapman
- Department of Chemistry, Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, USA
| | - Kieron Lucas
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Benjamin H Meyer
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Dimitrios Evangelopoulos
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
| | - Luiz Pedro S de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
| | - Geert-Jan Boons
- Department of Chemistry, Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, USA.,Department of Medical Chemistry and Chemical Biology, Utrecht Institute Pharmaceutical Science, University Utrecht, Utrecht, 3508 TB, The Netherlands
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Nina M van Sorge
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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18
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Abstract
Actinobacteria is a group of diverse bacteria. Most species in this class of bacteria are filamentous aerobes found in soil, including the genus Streptomyces perhaps best known for their fascinating capabilities of producing antibiotics. These bacteria typically have a Gram-positive cell envelope, comprised of a plasma membrane and a thick peptidoglycan layer. However, there is a notable exception of the Corynebacteriales order, which has evolved a unique type of outer membrane likely as a consequence of convergent evolution. In this chapter, we will focus on the unique cell envelope of this order. This cell envelope features the peptidoglycan layer that is covalently modified by an additional layer of arabinogalactan . Furthermore, the arabinogalactan layer provides the platform for the covalent attachment of mycolic acids , some of the longest natural fatty acids that can contain ~100 carbon atoms per molecule. Mycolic acids are thought to be the main component of the outer membrane, which is composed of many additional lipids including trehalose dimycolate, also known as the cord factor. Importantly, a subset of bacteria in the Corynebacteriales order are pathogens of human and domestic animals, including Mycobacterium tuberculosis. The surface coat of these pathogens are the first point of contact with the host immune system, and we now know a number of host receptors specific to molecular patterns exposed on the pathogen's surface, highlighting the importance of understanding how the cell envelope of Actinobacteria is structured and constructed. This chapter describes the main structural and biosynthetic features of major components found in the actinobacterial cell envelopes and highlights the key differences between them.
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Affiliation(s)
- Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Ian L Sparks
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA.
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19
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Brown HA, Vinogradov E, Gilbert M, Holden HM. The Mycobacterium tuberculosis complex has a pathway for the biosynthesis of 4-formamido-4,6-dideoxy-d-glucose. Protein Sci 2018; 27:1491-1497. [PMID: 29761597 DOI: 10.1002/pro.3443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/10/2018] [Accepted: 05/10/2018] [Indexed: 11/08/2022]
Abstract
Recent studies have demonstrated that the O-antigens of some pathogenic bacteria such as Brucella abortus, Francisella tularensis, and Campylobacter jejuni contain quite unusual N-formylated sugars (3-formamido-3,6-dideoxy-d-glucose or 4-formamido-4,6-dideoxy-d-glucose). Typically, four enzymes are required for the formation of such sugars: a thymidylyltransferase, a 4,6-dehydratase, a pyridoxal 5'-phosphate or PLP-dependent aminotransferase, and an N-formyltransferase. To date, there have been no published reports of N-formylated sugars associated with Mycobacterium tuberculosis. A recent investigation from our laboratories, however, has demonstrated that one gene product from M. tuberculosis, Rv3404c, functions as a sugar N-formyltransferase. Given that M. tuberculosis produces l-rhamnose, both a thymidylyltransferase (Rv0334) and a 4,6-dehydratase (Rv3464) required for its formation have been identified. Thus, there is one remaining enzyme needed for the production of an N-formylated sugar in M. tuberculosis, namely a PLP-dependent aminotransferase. Here we demonstrate that the M. tuberculosis rv3402c gene encodes such an enzyme. Our data prove that M. tuberculosis contains all of the enzymatic activities required for the formation of dTDP-4-formamido-4,6-dideoxy-d-glucose. Indeed, the rv3402c gene product likely contributes to virulence or persistence during infection, though its temporal expression and location remain to be determined.
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Affiliation(s)
- Haley A Brown
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
| | - Evgeny Vinogradov
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A OR6, Canada
| | - Michel Gilbert
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A OR6, Canada
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
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20
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Howlett R, Anttonen K, Read N, Smith MCM. Disruption of the GDP-mannose synthesis pathway in Streptomyces coelicolor results in antibiotic hyper-susceptible phenotypes. MICROBIOLOGY-SGM 2018; 164:614-624. [PMID: 29493491 PMCID: PMC5982138 DOI: 10.1099/mic.0.000636] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Actinomycete bacteria use polyprenol phosphate mannose as a lipid linked sugar donor for extra-cytoplasmic glycosyl transferases that transfer mannose to cell envelope polymers, including glycoproteins and glycolipids. We showed recently that strains of Streptomyces coelicolor with mutations in the gene ppm1 encoding polyprenol phosphate mannose synthase were both resistant to phage φC31 and have greatly increased susceptibility to antibiotics that mostly act on cell wall biogenesis. Here we show that mutations in the genes encoding enzymes that act upstream of Ppm1 in the polyprenol phosphate mannose synthesis pathway can also confer phage resistance and antibiotic hyper-susceptibility. GDP-mannose is a substrate for Ppm1 and is synthesised by GDP-mannose pyrophosphorylase (GMP; ManC) which uses GTP and mannose-1-phosphate as substrates. Phosphomannomutase (PMM; ManB) converts mannose-6-phosphate to mannose-1-phosphate. S. coelicolor strains with knocked down GMP activity or with a mutation in sco3028 encoding PMM acquire phenotypes that resemble those of the ppm1- mutants i.e. φC31 resistant and susceptible to antibiotics. Differences in the phenotypes of the strains were observed, however. While the ppm1- strains have a small colony phenotype, the sco3028 :: Tn5062 mutants had an extremely small colony phenotype indicative of an even greater growth defect. Moreover we were unable to generate a strain in which GMP activity encoded by sco3039 and sco4238 is completely knocked out, indicating that GMP is also an important enzyme for growth. Possibly GDP-mannose is at a metabolic branch point that supplies alternative nucleotide sugar donors.
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Affiliation(s)
| | - Katri Anttonen
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Margaret C M Smith
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK.,Department of Biology, University of York, York, UK
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21
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Brown HA, Thoden JB, Tipton PA, Holden HM. The structure of glucose-1-phosphate thymidylyltransferase from Mycobacterium tuberculosis reveals the location of an essential magnesium ion in the RmlA-type enzymes. Protein Sci 2017; 27:441-450. [PMID: 29076563 DOI: 10.1002/pro.3333] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 11/11/2022]
Abstract
Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, continues to be a major threat to populations worldwide. Whereas the disease is treatable, the drug regimen is arduous at best with the use of four antimicrobials over a six-month period. There is clearly a pressing need for the development of new therapeutics. One potential target for structure-based drug design is the enzyme RmlA, a glucose-1-phosphate thymidylyltransferase. This enzyme catalyzes the first step in the biosynthesis of l-rhamnose, which is a deoxysugar critical for the integrity of the bacterium's cell wall. Here, we report the X-ray structures of M. tuberculosis RmlA in complex with either dTTP or dTDP-glucose to 1.6 Å and 1.85 Å resolution, respectively. In the RmlA/dTTP complex, two magnesium ions were observed binding to the nucleotide, both ligated in octahedral coordination spheres. In the RmlA/dTDP-glucose complex, only a single magnesium ion was observed. Importantly, for RmlA-type enzymes with known three-dimensional structures, not one model shows the position of the magnesium ion bound to the nucleotide-linked sugar. As such, this investigation represents the first direct observation of the manner in which a magnesium ion is coordinated to the RmlA product and thus has important ramifications for structure-based drug design. In the past, molecular modeling procedures have been employed to derive a three-dimensional model of the M. tuberculosis RmlA for drug design. The X-ray structures presented herein provide a superior molecular scaffold for such endeavors in the treatment of one of the world's deadliest diseases.
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Affiliation(s)
- Haley A Brown
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Peter A Tipton
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
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22
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Cyclic di-GMP regulates Mycobacterium tuberculosis resistance to ethionamide. Sci Rep 2017; 7:5860. [PMID: 28725053 PMCID: PMC5517500 DOI: 10.1038/s41598-017-06289-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/12/2017] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis is still on the top of infectious diseases list on both mobility and mortality, especially due to drug-resistance of Mycobacterium tuberculosis (M.tb). Ethionamide (ETH) is one of effective second line anti-TB drugs, a synthetic compound similar to isoniazid (INH) structurally, with existing severe problem of ETH resistance. ETH is a prodrug, which is activated by Etha inside M.tb, and etha is transcriptionally repressed by Ethr. We found that c-di-GMP could bind Ethr, enhanced the binding of Ethr to the promoter of etha, and then repressed the transcription of etha, thus caused resistance of M.tb to ETH. Through docking analysis and in vitro validation, we identified that c-di-GMP binds 3 amino acids of Ethr, i.e., Q125, R181 and E190, while the first 2 were the major binding sites. Homology analysis showed that Ethr was highly conservative among mycobacteria. Further docking analysis showed that c-di-GMP preferentially bound proteins of TetR family at the junction hole of symmetric dimer or tetramer proteins. Our results suggest a possible drug-resistance mechanism of ETH through the regulation of Ethr by c-di-GMP.
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23
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Pardeshi P, Rao KK, Balaji PV. Rv3634c from Mycobacterium tuberculosis H37Rv encodes an enzyme with UDP-Gal/Glc and UDP-GalNAc 4-epimerase activities. PLoS One 2017; 12:e0175193. [PMID: 28403215 PMCID: PMC5389812 DOI: 10.1371/journal.pone.0175193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/22/2017] [Indexed: 01/03/2023] Open
Abstract
A bioinformatics study revealed that Mycobacterium tuberculosis H37Rv (Mtb) contains sequence homologs of Campylobacter jejuni protein glycosylation enzymes. The ORF Rv3634c from Mtb was identified as a sequence homolog of C. jejuni UDP-Gal/GalNAc 4-epimerase. This study reports the cloning of Rv3634c and its expression as an N-terminal His-tagged protein. The recombinant protein was shown to have UDP-Gal/Glc 4-epimerase activity by GOD-POD assay and by reverse phase HPLC. This enzyme was shown to have UDP-GalNAc 4-epimerase activity also. Residues Ser121, Tyr146 and Lys150 were shown by site-directed mutagenesis to be important for enzyme activity. Mutation of Ser121 and Tyr146 to Ala and Phe, respectively, led to complete loss of activity whereas mutation of Lys150 to Arg led to partial loss of activity. There were no gross changes in the secondary structures of any of these three mutants. These results suggest that Ser121 and Tyr146 are essential for epimerase activity of Rv3634c. UDP-Gal/Glc 4-epimerases from other organisms also have a catalytic triad consisting of Ser, Tyr and Lys. The triad carries out proton transfer from nucleotide sugar to NAD+ and back, thus effecting the epimerization of the substrate. Addition of NAD+ to Lys150 significantly abrogates the loss of activity, suggesting that, as in other epimerases, NAD+ is associated with Rv3634c.
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Affiliation(s)
- Peehu Pardeshi
- Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai, Mumbai, India
| | - K. Krishnamurthy Rao
- Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai, Mumbai, India
- * E-mail: (KKR); (PVB)
| | - Petety V. Balaji
- Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai, Mumbai, India
- * E-mail: (KKR); (PVB)
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24
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Anti-tubercular drug discovery: in silico implications and challenges. Eur J Pharm Sci 2017; 104:1-15. [PMID: 28341614 DOI: 10.1016/j.ejps.2017.03.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/08/2017] [Accepted: 03/19/2017] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB) has been reported as a major public health concern, especially in the developing countries. WHO report on tuberculosis 2016 shows a high mortality rate caused by TB leading to 1.8 million deaths worldwide (including deaths due to TB in HIV positive individuals), which is one of the top 10 causes of mortality in 2015. However, the main therapy used for the treatment of TB is still the Direct Observed Therapy Short-course (DOTS) that consists of four main first-line drugs. Due to the prolonged and unorganized use of these drugs, Mycobacterium tuberculosis (Mtb) has developed drug-resistance against them. To overcome this drug-resistance, efforts are continuously being made to develop new therapeutics. New drug-targets of Mtb are pursued by the researchers to develop their inhibitors. For this, new methodologies that comprise of the computational drug designing techniques are vigorously applied. A major limitation that is found with these techniques is the inability of the newly identified target-based inhibitors to inhibit the whole cell bacteria. A foremost factor for this limitation is the inability of these inhibitors to penetrate the bacterial cell wall. In this regard, various strategies to overcome this limitation have been discussed in detail in this review, along with new targets and new methodologies. A bunch of in silico tools available for the prediction of physicochemical properties that need to be explored to deal with the permeability issue of the Mtb inhibitors has also been discussed.
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25
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Strategy for designing selective α-l-rhamnosidase inhibitors: Synthesis and biological evaluation of l-DMDP cyclic isothioureas. Bioorg Med Chem 2017; 25:107-115. [DOI: 10.1016/j.bmc.2016.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 11/17/2022]
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Asención Diez MD, Miah F, Stevenson CEM, Lawson DM, Iglesias AA, Bornemann S. The Production and Utilization of GDP-glucose in the Biosynthesis of Trehalose 6-Phosphate by Streptomyces venezuelae. J Biol Chem 2016; 292:945-954. [PMID: 27903647 PMCID: PMC5247666 DOI: 10.1074/jbc.m116.758664] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/25/2016] [Indexed: 11/25/2022] Open
Abstract
Trehalose-6-phosphate synthase OtsA from streptomycetes is unusual in that it uses GDP-glucose as the donor substrate rather than the more commonly used UDP-glucose. We now confirm that OtsA from Streptomyces venezuelae has such a preference for GDP-glucose and can utilize ADP-glucose to some extent too. A crystal structure of the enzyme shows that it shares twin Rossmann-like domains with the UDP-glucose-specific OtsA from Escherichia coli. However, it is structurally more similar to Streptomyces hygroscopicus VldE, a GDP-valienol-dependent pseudoglycosyltransferase enzyme. Comparison of the donor binding sites reveals that the amino acids associated with the binding of diphosphoribose are almost all identical in these three enzymes. By contrast, the amino acids associated with binding guanine in VldE (Asn, Thr, and Val) are similar in S. venezuelae OtsA (Asp, Ser, and Phe, respectively) but not conserved in E. coli OtsA (His, Leu, and Asp, respectively), providing a rationale for the purine base specificity of S. venezuelae OtsA. To establish which donor is used in vivo, we generated an otsA null mutant in S. venezuelae. The mutant had a cell density-dependent growth phenotype and accumulated galactose 1-phosphate, glucose 1-phosphate, and GDP-glucose when grown on galactose. To determine how the GDP-glucose is generated, we characterized three candidate GDP-glucose pyrophosphorylases. SVEN_3027 is a UDP-glucose pyrophosphorylase, SVEN_3972 is an unusual ITP-mannose pyrophosphorylase, and SVEN_2781 is a pyrophosphorylase that is capable of generating GDP-glucose as well as GDP-mannose. We have therefore established how S. venezuelae can make and utilize GDP-glucose in the biosynthesis of trehalose 6-phosphate.
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Affiliation(s)
- Matías D Asención Diez
- the Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 Km 0, 3000 Santa Fe, Argentina
| | - Farzana Miah
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
| | - Clare E M Stevenson
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
| | - David M Lawson
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
| | - Alberto A Iglesias
- the Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 Km 0, 3000 Santa Fe, Argentina
| | - Stephen Bornemann
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
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Islam MM, Hameed HMA, Mugweru J, Chhotaray C, Wang C, Tan Y, Liu J, Li X, Tan S, Ojima I, Yew WW, Nuermberger E, Lamichhane G, Zhang T. Drug resistance mechanisms and novel drug targets for tuberculosis therapy. J Genet Genomics 2016; 44:21-37. [PMID: 28117224 DOI: 10.1016/j.jgg.2016.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Drug-resistant tuberculosis (TB) poses a significant challenge to the successful treatment and control of TB worldwide. Resistance to anti-TB drugs has existed since the beginning of the chemotherapy era. New insights into the resistant mechanisms of anti-TB drugs have been provided. Better understanding of drug resistance mechanisms helps in the development of new tools for the rapid diagnosis of drug-resistant TB. There is also a pressing need in the development of new drugs with novel targets to improve the current treatment of TB and to prevent the emergence of drug resistance in Mycobacterium tuberculosis. This review summarizes the anti-TB drug resistance mechanisms, furnishes some possible novel drug targets in the development of new agents for TB therapy and discusses the usefulness using known targets to develop new anti-TB drugs. Whole genome sequencing is currently an advanced technology to uncover drug resistance mechanisms in M. tuberculosis. However, further research is required to unravel the significance of some newly discovered gene mutations in their contribution to drug resistance.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Iwao Ojima
- Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Wing Wai Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric Nuermberger
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Mistou MY, Sutcliffe IC, van Sorge NM. Bacterial glycobiology: rhamnose-containing cell wall polysaccharides in Gram-positive bacteria. FEMS Microbiol Rev 2016; 40:464-79. [PMID: 26975195 PMCID: PMC4931226 DOI: 10.1093/femsre/fuw006] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 12/21/2022] Open
Abstract
The composition of the Gram-positive cell wall is typically described as containing peptidoglycan, proteins and essential secondary cell wall structures called teichoic acids, which comprise approximately half of the cell wall mass. The cell walls of many species within the genera Streptococcus, Enterococcus and Lactococcus contain large amounts of the sugar rhamnose, which is incorporated in cell wall-anchored polysaccharides (CWP) that possibly function as homologues of well-studied wall teichoic acids (WTA). The presence and chemical structure of many rhamnose-containing cell wall polysaccharides (RhaCWP) has sometimes been known for decades. In contrast to WTA, insight into the biosynthesis and functional role of RhaCWP has been lacking. Recent studies in human streptococcal and enterococcal pathogens have highlighted critical roles for these complex polysaccharides in bacterial cell wall architecture and pathogenesis. In this review, we provide an overview of the RhaCWP with regards to their biosynthesis, genetics and biological function in species most relevant to human health. We also briefly discuss how increased knowledge in this field can provide interesting leads for new therapeutic compounds and improve biotechnological applications. This review summarizes new insights into the genetics and function of rhamnose-containing cell wall polysaccharides expressed by lactic acid bacteria, which includes medically important pathogens, and discusses perspectives on possible future therapeutic and biotechnological applications.
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Affiliation(s)
- Michel-Yves Mistou
- Laboratory for Food Safety, Université Paris-Est, ANSES, F-94701 Maisons-Alfort, France
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Nina M van Sorge
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
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Abstract
The cell wall of Mycobacterium tuberculosis is unique in that it differs significantly from those of both Gram-negative and Gram-positive bacteria. The thick, carbohydrate- and lipid-rich cell wall with distinct lipoglycans enables mycobacteria to survive under hostile conditions such as shortage of nutrients and antimicrobial exposure. The key features of this highly complex cell wall are the mycolyl-arabinogalactan-peptidoglycan (mAGP)-based and phosphatidyl-myo-inositol-based macromolecular structures, with the latter possessing potent immunomodulatory properties. These structures are crucial for the growth, viability, and virulence of M. tuberculosis and therefore are often the targets of effective chemotherapeutic agents against tuberculosis. Over the past decade, sophisticated genomic and molecular tools have advanced our understanding of the primary structure and biosynthesis of these macromolecules. The availability of the full genome sequences of various mycobacterial species, including M. tuberculosis, Mycobacterium marinum, and Mycobacterium bovis BCG, have greatly facilitated the identification of large numbers of drug targets and antigens specific to tuberculosis. Techniques to manipulate mycobacteria have also improved extensively; the conditional expression-specialized transduction essentiality test (CESTET) is currently used to determine the essentiality of individual genes. Finally, various biosynthetic assays using either purified proteins or synthetic cell wall acceptors have been developed to study enzyme function. This article focuses on the recent advances in determining the structural details and biosynthesis of arabinogalactan, lipoarabinomannan, and related glycoconjugates.
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Abstract
The complex cell envelope is a hallmark of mycobacteria and is anchored by the peptidoglycan layer, which is similar to that of Escherichia coli and a number of other bacteria but with modifications to the monomeric units and other structural complexities that are likely related to a role for the peptidoglycan in stabilizing the mycolyl-arabinogalactan-peptidoglycan complex (MAPc). In this article, we will review the genetics of several aspects of peptidoglycan biosynthesis in mycobacteria, including the production of monomeric precursors in the cytoplasm, assembly of the monomers into the mature wall, cell wall turnover, and cell division. Finally, we will touch upon the resistance of mycobacteria to β-lactam antibiotics, an important class of drugs that, until recently, have not been extensively exploited as potential antimycobacterial agents. We will also note areas of research where there are still unanswered questions.
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Inhibition of Mycobacterium-RmlA by Molecular Modeling, Dynamics Simulation, and Docking. Adv Bioinformatics 2016; 2016:9841250. [PMID: 26981117 PMCID: PMC4769735 DOI: 10.1155/2016/9841250] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/12/2015] [Accepted: 12/24/2015] [Indexed: 11/17/2022] Open
Abstract
The increasing resistance to anti-tb drugs has enforced strategies for finding new drug targets against Mycobacterium tuberculosis (Mtb). In recent years enzymes associated with the rhamnose pathway in Mtb have attracted attention as drug targets. The present work is on α-D-glucose-1-phosphate thymidylyltransferase (RmlA), the first enzyme involved in the biosynthesis of L-rhamnose, of Mtb cell wall. This study aims to derive a 3D structure of RmlA by using a comparative modeling approach. Structural refinement and energy minimization of the built model have been done with molecular dynamics. The reliability assessment of the built model was carried out with various protein checking tools such as Procheck, Whatif, ProsA, Errat, and Verify 3D. The obtained model investigates the relation between the structure and function. Molecular docking interactions of Mtb-RmlA with modified EMB (ethambutol) ligands and natural substrate have revealed specific key residues Arg13, Lys23, Asn109, and Thr223 which play an important role in ligand binding and selection. Compared to all EMB ligands, EMB-1 has shown better interaction with Mtb-RmlA model. The information thus discussed above will be useful for the rational design of safe and effective inhibitors specific to RmlA enzyme pertaining to the treatment of tuberculosis.
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A 96-well microtiter plate assay for high-throughput screening of Mycobacterium tuberculosis dTDP-d-glucose 4,6-dehydratase inhibitors. Anal Biochem 2016; 498:53-8. [PMID: 26778528 DOI: 10.1016/j.ab.2016.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 11/23/2022]
Abstract
Mycobacterium tuberculosis dTDP-d-glucose 4,6-dehydratase (RmlB) is the second enzyme for the biosynthesis of dTDP-l-rhamnose, which is a sugar donor to the synthesis of the cell wall linker, d-N-acetylglucosamine-l-rhamnose. RmlB is essential to mycobacterial growth and is not found in humans; therefore, it is a potential target for developing new anti-tuberculosis drugs. So far, there has been no suitable method for high-throughput screening of RmlB inhibitors. Here, the recombinant M. tuberculosis RmlB was purified and an absorbance-based microtiter plate assay was developed for RmlB activity. It could be used for high-throughput screening of RmlB inhibitors. The kinetic properties of M. tuberculosis RmlB, including optimal pH, optimal temperature, the effect of metal ions, and the kinetic parameters, were determined with this assay. The inhibitory effects of dTTP and dTDP on M. tuberculosis RmlB were also studied with the assay.
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Computational evaluation of phytocompounds for combating drug resistant tuberculosis by multi-targeted therapy. J Mol Model 2015; 21:247. [PMID: 26323856 DOI: 10.1007/s00894-015-2785-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
The cell wall of Mycobacterium tuberculosis interacts with the host counterpart during the pathogenesis of tuberculosis. L-rhamnosyl (L-Rha) residue, a linker connects the arabinogalactan and peptidoglycan moieties in the bacterial cell wall. The biosynthesis of L-rhamnose utilizes four successive enzymes RmlA, RmlB, RmlC and RmlD. Neither rhamnose nor the genes responsible for its synthesis are observed in humans. Thus, drugs inhibiting enzymes of this pathway are unlikely to interfere with metabolic pathways in humans. The adverse drug effects of first and second line drugs along with the development of multi-drug resistance tuberculosis have stimulated the research in search of new therapeutic drugs. Thus, it is attractive to hypothesize that inhibition of the biosynthesis of L-Rha would be lethal to the mycobacteria. Nature provides innumerable secondary metabolites with novel structural architectures with reported activity against M. tuberculosis. Combination of structure based virtual screening with physicochemical and pharmacokinetic studies against rhamnose pathway enzymes identified potential leads. The crucial screening studies recognized four phytocompounds butein, diospyrin, indicanine, and rumexneposide A with good binding affinity towards the rhamnose pathway proteins. Furthermore, the high throughput screening methods recognized butein, a secondary metabolite from Butea monosperma with strong anti-tubercular bioactive spectrum. Butein displayed promising anti-mycobacterial activity which is validated by Microplate alamar blue assay (MABA). The focus on novel agents like these phytocompounds which exhibit preference toward the successive enzymes of a single pathway can prevent the development of bacterial resistance.
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Han X, Qian L, Zhang L, Liu X. Structural and biochemical insights into nucleotide-rhamnose synthase/epimerase-reductase from Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1476-86. [PMID: 26116145 DOI: 10.1016/j.bbapap.2015.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/03/2015] [Accepted: 06/20/2015] [Indexed: 11/26/2022]
Abstract
L-Rhamnose (Rha) is synthesized via a similar enzymatic pathway in bacteria, plants and fungi. In plants, nucleotide-rhamnose synthase/epimerase-reductase (NRS/ER) catalyzes the final step in the conversion of dTDP/UDP-α-D-Glc to dTDP/UDP-β-L-Rha in an NAD(P)H dependent manner. Currently, only biochemical evidence for the function of NRS/ER has been described. In this study, a crystal structure for Arabidopsis thaliana NRS/ER was determined, which is the first report of a eukaryotic rhamnose synthase with both epimerase and reductase activities. NRS/ER functions as a metal ion independent homodimer that forms through hydrophobic interactions via a four-helix bundle. Each monomer exhibits α/β folding that can be divided into two regions, nucleotide cofactor binding domain and sugar substrate binding domain. The affinities of ligands with NRS/ER were measured using isothermal titration calorimetry, which showed that NRS/ER has a preference for dTDP over UDP, while the cofactor binding site has a similar affinity for NADH and NADPH. Structural analysis coupled to site-directed mutagenesis suggested C115 and K183 as the acid/base pair responsible for epimerization, while T113, Y144 and K148 are the conserved residues in reduction. These findings shed light on the molecular mechanism of NRS/ER and were helpful to explore other eukaryotic enzymes involved in L-Rha synthesis.
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Affiliation(s)
- Xiaodong Han
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China; Food and Pharmaceutical Engineering Institute, Shanxi University of Traditional Chinese Medicine, Taiyuan 030024, China.
| | - Lei Qian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China.
| | - Lianwen Zhang
- College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China.
| | - Xinqi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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Alderwick LJ, Harrison J, Lloyd GS, Birch HL. The Mycobacterial Cell Wall--Peptidoglycan and Arabinogalactan. Cold Spring Harb Perspect Med 2015; 5:a021113. [PMID: 25818664 DOI: 10.1101/cshperspect.a021113] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The mycobacterial bacillus is encompassed by a remarkably elaborate cell wall structure. The mycolyl-arabinogalactan-peptidoglycan (mAGP) complex is essential for the viability of Mycobacterium tuberculosis and maintains a robust basal structure supporting the upper "myco-membrane." M. tuberculosis peptidoglycan, although appearing to be unexceptional at first glance, contains a number of unique molecular subtleties that become particularly important as the TB-bacilli enters into nonreplicative growth during dormancy. Arabinogalactan, a highly branched polysaccharide, serves to connect peptidoglycan with the outer mycolic acid layer, and a variety of unique glycolsyltransferases are used for its assembly. In this review, we shall explore the microbial chemistry of this unique heteropolysacchride, examine the molecular genetics that underpins its fabrication, and discuss how the essential biosynthetic process might be exploited for the development of future anti-TB chemotherapies.
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Affiliation(s)
- Luke J Alderwick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - James Harrison
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Georgina S Lloyd
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Helen L Birch
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
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37
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Tonetti MG. Carbohydrates: Translation from sticky to sweet. Nat Chem Biol 2015; 11:243-4. [PMID: 25785425 DOI: 10.1038/nchembio.1773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michela G Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy
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Virtual screening for the identification of novel inhibitors of Mycobacterium tuberculosis cell wall synthesis: inhibitors targeting RmlB and RmlC. Comput Biol Med 2015; 58:110-7. [PMID: 25637777 DOI: 10.1016/j.compbiomed.2014.12.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 11/20/2022]
Abstract
BACKGROUND Tuberculosis remains one of the deadliest infectious diseases in humans. It has caused more than 100 million deaths since its discovery in 1882. Currently, more than 5 million people are infected with TB bacterium each year. The cell wall of Mycobacterium tuberculosis plays an important role in maintaining the ability of mycobacteria to survive in a hostile environment. Therefore, we report a virtual screening (VS) study aiming to identify novel inhibitors that simultaneously target RmlB and RmlC, which are two essential enzymes for the synthesis of the cell wall of M. tuberculosis. METHODS A hybrid VS method that combines drug-likeness prediction, pharmacophore modeling and molecular docking studies was used to indentify inhibitors targeting RmlB and RmlC. RESULTS The pharmacophore models HypoB and HypoC of RmlB inhibitors and RmlC inhibitors, respectively, were developed based on ligands complexing with their corresponding receptors. In total, 20 compounds with good absorption, distribution, metabolism, excretion, and toxicity properties were carefully selected using the hybird VS method. DISCUSSION We have established a hybrid VS method to discover novel inhibitors with new scaffolds. The molecular interactions of the selected potential inhibitors with the active-site residues are discussed in detail. These compounds will be further evaluated using biological activity assays and deserve consideration for further structure-activity relationship studies.
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39
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Ng SK, Huang YT, Lee YC, Low EL, Chiu CH, Chen SL, Mao LC, Chang MDT. A recombinant horseshoe crab plasma lectin recognizes specific pathogen-associated molecular patterns of bacteria through rhamnose. PLoS One 2014; 9:e115296. [PMID: 25541995 PMCID: PMC4277298 DOI: 10.1371/journal.pone.0115296] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 11/21/2014] [Indexed: 11/18/2022] Open
Abstract
Horseshoe crab is an ancient marine arthropod that, in the absence of a vertebrate-like immune system, relies solely on innate immune responses by defense molecules found in hemolymph plasma and granular hemocytes for host defense. A plasma lectin isolated from the hemolymph of Taiwanese Tachypleus tridentatus recognizes bacteria and lipopolysaccharides (LPSs), yet its structure and mechanism of action remain unclear, largely because of limited availability of horseshoe crabs and the lack of a heterogeneous expression system. In this study, we have successfully expressed and purified a soluble and functional recombinant horseshoe crab plasma lectin (rHPL) in an Escherichia coli system. Interestingly, rHPL bound not only to bacteria and LPSs like the native HPL but also to selective medically important pathogens isolated from clinical specimens, such as Gram-negative Pseudomonas aeruginosa and Klebsiella pneumoniae and Gram-positive Streptococcus pneumoniae serotypes. The binding was demonstrated to occur through a specific molecular interaction with rhamnose in pathogen-associated molecular patterns (PAMPs) on the bacterial surface. Additionally, rHPL inhibited the growth of P. aeruginosa PAO1 in a concentration-dependent manner. The results suggest that a specific protein-glycan interaction between rHPL and rhamnosyl residue may further facilitate development of novel diagnostic and therapeutic strategies for microbial pathogens.
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Affiliation(s)
- Sim-Kun Ng
- Institute of Molecular and Cellular Biology & Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Yu-Tsyr Huang
- Institute of Molecular and Cellular Biology & Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Yuan-Chuan Lee
- Institute of Molecular and Cellular Biology & Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Ee-Ling Low
- Institute of Molecular and Cellular Biology & Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Cheng-Hsun Chiu
- Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan Hsien, Taiwan, Republic of China
| | - Shiu-Ling Chen
- Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan Hsien, Taiwan, Republic of China
| | - Liang-Chi Mao
- Simpson Biotech Co., Ltd., Kuei Shan, Taoyuan County, Taiwan, Republic of China
| | - Margaret Dah-Tsyr Chang
- Institute of Molecular and Cellular Biology & Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- * E-mail:
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Angala SK, Belardinelli JM, Huc-Claustre E, Wheat WH, Jackson M. The cell envelope glycoconjugates of Mycobacterium tuberculosis. Crit Rev Biochem Mol Biol 2014; 49:361-99. [PMID: 24915502 PMCID: PMC4436706 DOI: 10.3109/10409238.2014.925420] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Tuberculosis (TB) remains the second most common cause of death due to a single infectious agent. The cell envelope of Mycobacterium tuberculosis (Mtb), the causative agent of the disease in humans, is a source of unique glycoconjugates and the most distinctive feature of the biology of this organism. It is the basis of much of Mtb pathogenesis and one of the major causes of its intrinsic resistance to chemotherapeutic agents. At the same time, the unique structures of Mtb cell envelope glycoconjugates, their antigenicity and essentiality for mycobacterial growth provide opportunities for drug, vaccine, diagnostic and biomarker development, as clearly illustrated by recent advances in all of these translational aspects. This review focuses on our current understanding of the structure and biogenesis of Mtb glycoconjugates with particular emphasis on one of the most intriguing and least understood aspect of the physiology of mycobacteria: the translocation of these complex macromolecules across the different layers of the cell envelope. It further reviews the rather impressive progress made in the last 10 years in the discovery and development of novel inhibitors targeting their biogenesis.
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Affiliation(s)
- Shiva Kumar Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, CO , USA
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41
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Ma G, Dong L, Liu Y. Insights into the catalytic mechanism of dTDP-glucose 4,6-dehydratase from quantum mechanics/molecular mechanics simulations. RSC Adv 2014. [DOI: 10.1039/c4ra04406a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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42
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Chauhan K, Sharma M, Trivedi P, Chaturvedi V, Chauhan PMS. New class of methyl tetrazole based hybrid of (Z)-5-benzylidene-2-(piperazin-1-yl)thiazol-4(%H)-one as potent antitubercular agents. Bioorg Med Chem Lett 2014; 24:4166-70. [PMID: 25127167 DOI: 10.1016/j.bmcl.2014.07.061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 11/30/2022]
Abstract
In search of potential therapeutics for tuberculosis, we describe here the synthesis and in vitro antitubercular activity of a novel series of thiazolone piperazine tetrazole derivatives. Among all the synthesized derivatives, four compounds (10, 14, 20 and 33) exhibited more potent activity (MIC=3.08, 3.01, 2.62 and 2.51 μM) than ethambutol (MIC=9.78 μM) and pyrazinamide (MIC=101.53 μM) against Mycobacterium tuberculosis. Furthermore, they displayed no toxicity against Vero cells (C1008) and mouse bone marrow derived macrophages (MBMDMϕ). These investigated analogues have emerged as possible lead molecule to enlarge the scope of the study.
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Affiliation(s)
- Kuldeep Chauhan
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India
| | - Moni Sharma
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India
| | - Priyanka Trivedi
- Drug Target Discovery and Development Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Vinita Chaturvedi
- Drug Target Discovery and Development Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Prem M S Chauhan
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India.
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Abstract
Prokaryotic glycosylation fulfills an important role in maintaining and protecting the structural integrity and function of the bacterial cell wall, as well as serving as a flexible adaption mechanism to evade environmental and host-induced pressure. The scope of bacterial and archaeal protein glycosylation has considerably expanded over the past decade(s), with numerous examples covering the glycosylation of flagella, pili, glycosylated enzymes, as well as surface-layer proteins. This article addresses structure, analysis, function, genetic basis, biosynthesis, and biomedical and biotechnological applications of cell-envelope glycoconjugates, S-layer glycoprotein glycans, and "nonclassical" secondary-cell wall polysaccharides. The latter group of polymers mediates the important attachment and regular orientation of the S-layer to the cell wall. The structures of these glycopolymers reveal an enormous diversity, resembling the structural variability of bacterial lipopolysaccharides and capsular polysaccharides. While most examples are presented for Gram-positive bacteria, the S-layer glycan of the Gram-negative pathogen Tannerella forsythia is also discussed. In addition, archaeal S-layer glycoproteins are briefly summarized.
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Affiliation(s)
- Paul Messner
- Department of NanoBiotechnology, NanoGlycobiology Unit, University of Natural Resources and Life Sciences, Vienna, Austria
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Tomioka H, Tatano Y, Yasumoto K, Shimizu T. Recent advances in antituberculous drug development and novel drug targets. Expert Rev Respir Med 2014; 2:455-71. [DOI: 10.1586/17476348.2.4.455] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Loranger MW, Forget SM, McCormick NE, Syvitski RT, Jakeman DL. Synthesis and evaluation of l-rhamnose 1C-phosphonates as nucleotidylyltransferase inhibitors. J Org Chem 2013; 78:9822-33. [PMID: 24020932 DOI: 10.1021/jo401542s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report the synthesis of a series of phosphonates and ketosephosphonates possessing an L-rhamnose scaffold with varying degrees of fluorination. These compounds were evaluated as potential inhibitors of α-D-glucose 1-phosphate thymidylyltransferase (Cps2L), the first enzyme in Streptococcus pneumoniae L-rhamnose biosynthesis, and a novel antibiotic target. Enzyme-substrate and enzyme-inhibitor binding experiments were performed using water-ligand observed binding via gradient spectroscopy (WaterLOGSY) NMR for known sugar nucleotide substrates and selected phosphonate analogues. IC50 values were measured and Ki values were calculated for inhibitors. New insights were gained into the binding promiscuity of enzymes within the prokaryotic L-rhamnose biosynthetic pathway (Cps2L, RmlB-D) and into the mechanism of inhibition for the most potent inhibitor in the series, L-rhamnose 1C-phosphonate.
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Affiliation(s)
- Matthew W Loranger
- Department of Chemistry, Dalhousie University , 6274 Coberg Road, P.O. Box 15,000, Halifax, Nova Scotia B3H 4R2, Canada
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Jukič M, Đorđević A, Lazarević J, Gobec M, Šmelcerović A, Anderluh M. Antimicrobial activity and cytotoxicity of some 2-amino-5-alkylidene-thiazol-4-ones. Mol Divers 2013; 17:773-80. [PMID: 24062019 DOI: 10.1007/s11030-013-9474-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 08/12/2013] [Indexed: 01/12/2023]
Abstract
We report a small, focused library of 30 diverse 2-amino-5-alkylidene-thiazol-4-ones that was assayed in a whole-cell antibacterial screen against a panel of several bacterial strains and a yeast. Most of the compounds exhibited modest to significant antibacterial activity against Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus, and no activity against Salmonella typhimurium and Escherichia coli. The antibacterial activity depends markedly upon substituents on the thiazol-4-one core, and the most potent compound assayed ([Formula: see text]-4-((2-(4-methylpiperidin-1-yl)-4-oxothiazol-5(4H)-ylidene)methyl)benzonitrile) reached a minimal inhibitory concentration (MIC) value of [Formula: see text] on P. aeruginosa strain. An important feature of the tested compounds is their low influence on cell viability, as determined in a HEK-293 metabolic activity assay. In light of the encouraging in vitro antimicrobial assay results against several bacterial strains, we have generated a pharmacophore model using the Discovery studio 3.0 package (Accelrys Inc., San Diego, USA), which exposed the spatial arrangement of key molecular properties responsible for our observed MIC results. Considering the absence of a defined target and the limitation of the described approach to pool different scaffolds, the calculated pharmacophore model could be used for library enrichment to identify compounds with a thiazolidinone scaffold with improved antimicrobial potency and physico-chemical properties.
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Affiliation(s)
- Marko Jukič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 , Ljubljana, Slovenia
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Kim MO, Nichols SE, Wang Y, McCammon JA. Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. J Comput Aided Mol Des 2013; 27:235-46. [PMID: 23579613 PMCID: PMC3639364 DOI: 10.1007/s10822-013-9643-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/02/2013] [Indexed: 11/12/2022]
Abstract
While it is well established that protonation and tautomeric states of ligands can significantly affect the results of virtual screening, such effects of ionizable residues of protein receptors are less well understood. In this study, we focus on histidine protonation and rotameric states and their impact on virtual screening of Mycobacterium tuberculosis enzyme RmlC. Depending on the net charge and the location of proton(s), a histidine can adopt three states: HIP (+1 charged, both δ- and ε-nitrogens protonated), HID (neutral, δ-nitrogen protonated), and HIE (neutral, ε-nitrogen protonated). Due to common ambiguities in X-ray crystal structures, a histidine may also be resolved as three additional states with its imidazole ring flipped. Here, we systematically investigate the predictive power of 36 receptor models with different protonation and rotameric states of two histidines in the RmlC active site by using results from a previous high-throughput screening. By measuring enrichment factors and area under the receiver operating characteristic curves, we show that virtual screening results vary depending on hydrogen bonding networks provided by the histidines, even in the cases where the ligand does not obviously interact with the side chain. Our results also suggest that, even with the help of widely used pKa prediction software, assigning histidine protonation and rotameric states for virtual screening can still be challenging and requires further examination and systematic characterization of the receptor-ligand complex.
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Affiliation(s)
- Meekyum Olivia Kim
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
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Ollinger J, Bailey MA, Moraski GC, Casey A, Florio S, Alling T, Miller MJ, Parish T. A dual read-out assay to evaluate the potency of compounds active against Mycobacterium tuberculosis. PLoS One 2013; 8:e60531. [PMID: 23593234 PMCID: PMC3617142 DOI: 10.1371/journal.pone.0060531] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 02/26/2013] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis is a serious global health problem caused by the bacterium Mycobacterium tuberculosis. There is an urgent need for discovery and development of new treatments, but this can only be accomplished through rapid and reproducible M. tuberculosis assays designed to identify potent inhibitors. We developed an automated 96-well assay utilizing a recombinant strain of M. tuberculosis expressing a far-red fluorescent reporter to determine the activity of novel compounds; this allowed us to measure growth by monitoring both optical density and fluorescence. We determined that optical density and fluorescence were correlated with cell number during logarithmic phase growth. Fluorescence was stably maintained without antibiotic selection over 5 days, during which time cells remained actively growing. We optimized parameters for the assay, with the final format being 5 days' growth in 96-well plates in the presence of 2% w/v DMSO. We confirmed reproducibility using rifampicin and other antibiotics. The dual detection method allows for a reproducible calculation of the minimum inhibitory concentration (MIC), at the same time detecting artefacts such as fluorescence quenching or compound precipitation. We used our assay to confirm anti-tubercular activity and establish the structure activity relationship (SAR) around the imidazo[1,2-a]pyridine-3-carboxamides, a promising series of M. tuberculosis inhibitors.
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Affiliation(s)
- Juliane Ollinger
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Mai Ann Bailey
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Garrett C. Moraski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Allen Casey
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Stephanie Florio
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Torey Alling
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Marvin J. Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Tanya Parish
- Infectious Disease Research Institute, Seattle, Washington, United States of America
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Butt AM, Nasrullah I, Tahir S, Tong Y. Comparative genomics analysis of Mycobacterium ulcerans for the identification of putative essential genes and therapeutic candidates. PLoS One 2012; 7:e43080. [PMID: 22912793 PMCID: PMC3418265 DOI: 10.1371/journal.pone.0043080] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 07/16/2012] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium ulcerans, the causative agent of Buruli ulcer, is the third most common mycobacterial disease after tuberculosis and leprosy. The present treatment options are limited and emergence of treatment resistant isolates represents a serious concern and a need for better therapeutics. Conventional drug discovery methods are time consuming and labor-intensive. Unfortunately, the slow growing nature of M. ulcerans in experimental conditions is also a barrier for drug discovery and development. In contrast, recent advancements in complete genome sequencing, in combination with cheminformatics and computational biology, represent an attractive alternative approach for the identification of therapeutic candidates worthy of experimental research. A computational, comparative genomics workflow was defined for the identification of novel therapeutic candidates against M. ulcerans, with the aim that a selected target should be essential to the pathogen, and have no homology in the human host. Initially, a total of 424 genes were predicted as essential from the M. ulcerans genome, via homology searching of essential genome content from 20 different bacteria. Metabolic pathway analysis showed that the most essential genes are associated with carbohydrate and amino acid metabolism. Among these, 236 proteins were identified as non-host and essential, and could serve as potential drug and vaccine candidates. Several drug target prioritization parameters including druggability were also calculated. Enzymes from several pathways are discussed as potential drug targets, including those from cell wall synthesis, thiamine biosynthesis, protein biosynthesis, and histidine biosynthesis. It is expected that our data will facilitate selection of M. ulcerans proteins for successful entry into drug design pipelines.
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Affiliation(s)
- Azeem Mehmood Butt
- National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
- * E-mail: (AMB); (YT)
| | - Izza Nasrullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shifa Tahir
- National Center for Bioinformatics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
- * E-mail: (AMB); (YT)
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50
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Mishra AK, Krumbach K, Rittmann D, Batt SM, Lee OYC, De S, Frunzke J, Besra GS, Eggeling L. Deletion of manC in Corynebacterium glutamicum results in a phospho-myo-inositol mannoside- and lipoglycan-deficient mutant. MICROBIOLOGY-SGM 2012; 158:1908-1917. [PMID: 22539165 DOI: 10.1099/mic.0.057653-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mannose is an important constituent of the immunomodulatory glycoconjugates of the mycobacterial cell wall: lipoarabinomannan (LAM), lipomannan (LM) and the related phospho-myo-inositol mannosides (PIMs). In Mycobacterium tuberculosis and the related bacillus Corynebacterium glutamicum, mannose is either imported from the medium or derived from glycolysis, and is subsequently converted into the nucleotide-based sugar donor guanosine diphosphomannose (GDP-mannose). This can be utilized by the glycosyltranferases of the GT-A/B superfamily or converted to the lipid-based donor polyprenyl monophosphomannose, and used as a substrate by the transmembrane glycosyltransferases of the GT-C superfamily. To investigate GDP-mannose biosynthesis in detail, the gene encoding a putative ManC in C. glutamicum was deleted. Deletion of manC resulted in a slow-growing mutant, with reduced but not totally abrogated guanosine diphosphomannose pyrophosphorylase activity. However, a comprehensive cell wall analysis revealed that C. glutamicumΔmanC is deficient in PIMs and LM/LAM. Closer inspection suggests that promiscuous ManC activity is contributed by additional putative nucleotidyltransferases, PmmB, WbbL1, GalU and GlmU, and a hypothetical protein, NCgl0715. Furthermore, complementation analyses of C. glutamicumΔmanC with Rv3264c suggested that it is a true homologue of ManC in M. tuberculosis, and the essentiality of PIMs in M. tuberculosis makes it an attractive drug target.
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Affiliation(s)
- Arun K Mishra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Karin Krumbach
- Biotechnology (IBG-1), Research Centre Juelich GmbH, D-52425 Juelich, Germany
| | - Doris Rittmann
- Biotechnology (IBG-1), Research Centre Juelich GmbH, D-52425 Juelich, Germany
| | - Sarah M Batt
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Oona Y-C Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sandip De
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Julia Frunzke
- Biotechnology (IBG-1), Research Centre Juelich GmbH, D-52425 Juelich, Germany
| | - Gurdyal S Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Lothar Eggeling
- Biotechnology (IBG-1), Research Centre Juelich GmbH, D-52425 Juelich, Germany
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