1
|
Rani N, Surolia A. Targeted suppression of MEP pathway genes DXS, IspD and IspF to explore the mycobacterial metabolism and survival. Int J Biol Macromol 2024; 272:132727. [PMID: 38823743 DOI: 10.1016/j.ijbiomac.2024.132727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/10/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
Due to the uniqueness and essentiality of MEP pathway for the synthesis of crucial metabolites- isoprenoids, hopanoids, menaquinone etc. in mycobacterium, enzymes of this pathway are considered promising anti-tubercular drug targets. In the present study we seek to understand the consequences of downregulation of three of the essential genes- DXS, IspD, and IspF of MEP pathway using CRISPRi approach combined with transcriptomics in Mycobacterium smegmatis. Conditional knock down of either DXS or IspD or IspF gene showed strong bactericidal effect and a profound change in colony morphology. Impaired MEP pathway due to downregulation of these genes increased the susceptibility to frontline anti-tubercular drugs. Further, reduced EtBr accumulation in all the knock down strains in the presence and absence of efflux inhibitor indicated altered cell wall topology. Subsequently, transcriptional analysis validated by qRT-PCR of +154DXS, +128IspD, +104IspF strains showed that modifying the expression of these MEP pathway enzymes affects the regulation of mycobacterial core components. Among the DEGs, expression of small and large ribosomal binding proteins (rpsL, rpsJ, rplN, rplX, rplM, rplS, etc), essential protein translocases (secE, secY and infA, infC), transcriptional regulator (CarD and SigB) and metabolic enzymes (acpP, hydA, ald and fabD) were significantly depleted causing the bactericidal effect. However, mycobacteria survived under these damaging conditions by upregulating mostly the genes needed for the repair of DNA damage (DNA polymerase IV, dinB), synthesis of essential metabolites (serB, LeuA, atpD) and those strengthening the cell wall integrity (otsA, murA, D-alanyl-D-alanine dipeptidase etc.).
Collapse
Affiliation(s)
- Nidhi Rani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India; Dr.Reddy's Institute of Life Science, Hyderabad 500046, India.
| |
Collapse
|
2
|
Ghebreamlak S, Stoian SA, Lees NS, Cronin B, Smith F, Ross MO, Telser J, Hoffman BM, Duin EC. The Active-Site [4Fe-4S] Cluster in the Isoprenoid Biosynthesis Enzyme IspH Adopts Unexpected Redox States during Ligand Binding and Catalysis. J Am Chem Soc 2024; 146:3926-3942. [PMID: 38291562 DOI: 10.1021/jacs.3c11674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase, or IspH (formerly known as LytB), catalyzes the terminal step of the bacterial methylerythritol phosphate (MEP) pathway for isoprene synthesis. This step converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) into one of two possible isomeric products, either isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). This reaction involves the removal of the C4 hydroxyl group of HMBPP and addition of two electrons. IspH contains a [4Fe-4S] cluster in its active site, and multiple cluster-based paramagnetic species of uncertain redox and ligation states can be detected after incubation with reductant, addition of a ligand, or during catalysis. To characterize the clusters in these species, 57Fe-labeled samples of IspH were prepared and studied by electron paramagnetic resonance (EPR), 57Fe electron-nuclear double resonance (ENDOR), and Mössbauer spectroscopies. Notably, this ENDOR study provides a rarely reported, complete determination of the 57Fe hyperfine tensors for all four Fe ions in a [4Fe-4S] cluster. The resting state of the enzyme (Ox) has a diamagnetic [4Fe-4S]2+ cluster. Reduction generates [4Fe-4S]+ (Red) with both S = 1/2 and S = 3/2 spin ground states. When the reduced enzyme is incubated with substrate, a transient paramagnetic reaction intermediate is detected (Int) which is thought to contain a cluster-bound substrate-derived species. The EPR properties of Int are indicative of a 3+ iron-sulfur cluster oxidation state, and the Mössbauer spectra presented here confirm this. Incubation of reduced enzyme with the product IPP induced yet another paramagnetic [4Fe-4S]+ species (Red+P) with S = 1/2. However, the g-tensor of this state is commonly associated with a 3+ oxidation state, while Mössbauer parameters show features typical for 2+ clusters. Implications of these complicated results are discussed.
Collapse
Affiliation(s)
- Selamawit Ghebreamlak
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Sebastian A Stoian
- Department of Chemistry, University of Idaho, 875 Perimeter Drive, MS 2343 Moscow, Idaho 83844, United States
| | - Nicholas S Lees
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Bryan Cronin
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Forrest Smith
- Department of Drug Discovery & Development, Auburn University, 4306 Walker Building, Auburn, Alabama 36849, United States
| | - Matthew O Ross
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, 430 S. Michigan Avenue, Chicago, Illinois 60605, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| |
Collapse
|
3
|
Soman S, Ram S. Arginine to glutamine mutation in the substrate binding region impaired the isopentenyl activity of Mycobacterium tuberculosis MiaA. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2024; 13:3-9. [PMID: 38164369 PMCID: PMC10644310 DOI: 10.22099/mbrc.2023.47247.1825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
tRNAs act as adaptors during protein synthesis and are chemically modified post-transcriptionally for their structural stability as well as accuracy of the translation. Hypomodifications of tRNAs are known to cause various human diseases, including cancer. Studies in bacteria and yeasts showed that levels of tRNA modifications vary under different stress conditions, enabling the organism to modulate gene expression for survival. Isopentelylation of the base 37 (i6A37) in the anticodon stem-loop by tRNA isopentenyltransferase (MiaA) is well-conserved modification present in prokaryotes and eukaryotes. i6A37 modification increases both the speed and fidelity of translation. A homozygous p.Arg323Gln mutation in the tRNA binding region of tRNA isopentenyltransferase reduced i6A37 levels in humans, affecting mitochondrial translation and thereby causing neurodevelopmental disorder. In this study, we mutated the Arg residue at the conserved position to Gln in Mycobacterium tuberculosis (M. tb) MiaA and analyzed the i6A modification activity of the enzyme on its target tRNAs. We found that p.Arg274Gln mutant MiaA could not modify the target tRNAs, tRNALeuCAA, tRNAPheGAA, and tRNASerCGA from M. tb, confirming the role of Arg residue in tRNA binding.
Collapse
Affiliation(s)
- Smitha Soman
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Greater Noida, Uttar Pradesh, India
| | - Siya Ram
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Greater Noida, Uttar Pradesh, India
- School of Sciences, Indira Gandhi National Open University, Maidan Garhi, New Delhi, India
| |
Collapse
|
4
|
Choi SR, Narayanasamy P. Investigating Novel IspE Inhibitors of the MEP Pathway in Mycobacterium. Microorganisms 2023; 12:18. [PMID: 38276186 PMCID: PMC10819746 DOI: 10.3390/microorganisms12010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
In a recent effort to mitigate harm from human pathogens, many biosynthetic pathways have been extensively evaluated for their ability to inhibit pathogen growth and to determine drug targets. One of the important products/targets of such pathways is isopentenyl diphosphate. Isopentenyl diphosphate is the universal precursor of isoprenoids, which are essential for the normal functioning of microorganisms. In general, two biosynthetic pathways lead to the formation of isopentenyl diphosphate: (1) the mevalonate pathway in animals; and (2) the non-mevalonate or methylerythritol phosphate (MEP) in many bacteria, and some protozoa and plants. Because the MEP pathway is not found in mammalian cells, it is considered an attractive target for the development of antimicrobials against a variety of human pathogens, including Mycobacterium tuberculosis (M.tb). In the MEP pathway, 4-diphosphocytidyl-2-c-methyl-d-erythritol kinase (IspE) phosphorylates 4-diphosphocytidyl-2-C-methyl-D-erythritol (CDPME) to form 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDPME2P). A virtual high-throughput screening against 15 million compounds was carried out by docking IspE protein. We identified an active heterotricyclic compound which showed enzymatic activity; namely, IC50 of 6 µg/mL against M.tb IspE and a MIC of 12 µg/mL against M.tb (H37Rv). Hence, we designed and synthesized similar new heterotricyclic compounds and tested them against mycobacterium, observing a MIC of 5 µg/mL against M. avium. This study will provide the critical insight necessary for developing novel antimicrobials that target the MEP pathways in pathogens.
Collapse
Affiliation(s)
| | - Prabagaran Narayanasamy
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
5
|
Janisch N, Levendosky K, Budell WC, Quadri LEN. Genetic Underpinnings of Carotenogenesis and Light-Induced Transcriptome Remodeling in the Opportunistic Pathogen Mycobacterium kansasii. Pathogens 2023; 12:86. [PMID: 36678434 PMCID: PMC9861118 DOI: 10.3390/pathogens12010086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium kansasii (Mk) causes opportunistic pulmonary infections with tuberculosis-like features. The bacterium is well known for its photochromogenicity, i.e., the production of carotenoid pigments in response to light. The genetics defining the photochromogenic phenotype of Mk has not been investigated and defined pigmentation mutants to facilitate studies on the role of carotenes in the bacterium's biology are not available thus far. In this study, we set out to identify genetic determinants involved in Mk photochromogenicity. We screened a library of ~150,000 transposon mutants for colonies with pigmentation abnormalities. The screen rendered a collection of ~200 mutants. Each of these mutants could be assigned to one of four distinct phenotypic groups. The insertion sites in the mutant collection clustered in three chromosomal regions. A combination of phenotypic analysis, sequence bioinformatics, and gene expression studies linked these regions to carotene biosynthesis, carotene degradation, and monounsaturated fatty acid biosynthesis. Furthermore, introduction of the identified carotenoid biosynthetic gene cluster into non-pigmented Mycobacterium smegmatis endowed the bacterium with photochromogenicity. The studies also led to identification of MarR-type and TetR/AcrR-type regulators controlling photochromogenicity and carotenoid breakdown, respectively. Lastly, the work presented also provides a first insight into the Mk transcriptome changes in response to light.
Collapse
Affiliation(s)
- Niklas Janisch
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Keith Levendosky
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - William C. Budell
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Luis E. N. Quadri
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Biochemistry Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| |
Collapse
|
6
|
Lee YJ, Kim JK, Baek SA, Yu JS, You MK, Ha SH. Differential Regulation of an OsIspH1, the Functional 4-Hydroxy-3-Methylbut-2-Enyl Diphosphate Reductase, for Photosynthetic Pigment Biosynthesis in Rice Leaves and Seeds. FRONTIERS IN PLANT SCIENCE 2022; 13:861036. [PMID: 35498655 PMCID: PMC9044040 DOI: 10.3389/fpls.2022.861036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/10/2022] [Indexed: 06/02/2023]
Abstract
The methylerythritol 4-phosphate (MEP) pathway is responsible for providing common precursors for the biosynthesis of diverse plastidial terpenoids, including chlorophylls, carotenoids, and phytohormones, in plants. In rice (Oryza sativa), the last-step genes encoding 4-hydroxy-3-methylbut-2-enyl diphosphate reductase [HDR/isoprenoid synthesis H (IspH)] have been annotated in two genes (OsIspH1 and OsIspH2) in the rice genome. The spatial transcript levels indicated that OsIspH1 is highly expressed in all tissues at different developmental stages, whereas OsIspH2 is barely expressed due to an early stop in exon 1 caused by splicing error. OsIspH1 localized into plastids and osisph1, a T-DNA inserted knockout mutant, showed an albino phenotype, indicating that OsIspH1 is the only functional gene. To elucidate the role of OsIspH1 in the MEP pathway, we created two single (H145P and K407R) and double (H145P/K407R) mutations and performed complementation tests in two hdr mutants, including Escherichia coli DLYT1 strains and osisph1 rice plants. The results showed that every single mutation retained HDR function, but a double mutation lost it, proposing that the complementary relations of two residues might be important for enzyme activity but not each residue. When overexpressed in rice plants, the double-mutated gene, OsIspH1MUT , reduced chlorophyll and carotenoid biosynthesis in the leaves and seeds. It confirmed the crucial role of OsIspH1 in plastidic terpenoid biosynthesis, revealing organ-specific differential regulation of OsIspH1 in rice plants.
Collapse
Affiliation(s)
- Yeo Jin Lee
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Jae Kwang Kim
- Division of Life Sciences, Bio-Resource and Environmental Center, Incheon National University, Incheon, South Korea
| | - Seung-A Baek
- Division of Life Sciences, Bio-Resource and Environmental Center, Incheon National University, Incheon, South Korea
| | - Ji-Su Yu
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Min Kyoung You
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Sun-Hwa Ha
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
| |
Collapse
|
7
|
Structural and biophysical characterization of the Burkholderia pseudomallei IspF inhibitor L-tryptophan hydroxamate. Bioorg Med Chem Lett 2021; 48:128273. [PMID: 34298132 DOI: 10.1016/j.bmcl.2021.128273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 11/23/2022]
Abstract
The enzyme 2-methylerythritol 2,4-cyclodiphosphate synthase, IspF, is essential for the biosynthesis of isoprenoids in most bacteria, some eukaryotic parasites, and the plastids of plant cells. The development of inhibitors that target IspF may lead to novel classes of anti-infective agents or herbicides. Enantiomers of tryptophan hydroxamate were synthesized and evaluated for binding to Burkholderia pseudomallei (Bp) IspF. The L-isomer possessed the highest potency, binding BpIspF with a KD of 36 µM and inhibited BpIspF activity 55% at 120 µM. The high-resolution crystal structure of the L-tryptophan hydroxamate (3)/BpIspF complex revealed a non-traditional mode of hydroxamate binding where the ligand interacts with the active site zinc ion through the primary amine. In addition, two hydrogen bonds are formed with active site groups, and the indole group is buried within the hydrophobic pocket composed of side chains from the 60 s/70 s loop. Along with the co-crystal structure, STD NMR studies suggest the methylene group and indole ring are potential positions for optimization to enhance binding potency.
Collapse
|
8
|
Eberl M, Oldfield E, Herrmann T. Immuno-antibiotics: targeting microbial metabolic pathways sensed by unconventional T cells. IMMUNOTHERAPY ADVANCES 2021; 1:ltab005. [PMID: 35919736 PMCID: PMC9327107 DOI: 10.1093/immadv/ltab005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/17/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Human Vγ9/Vδ2 T cells, mucosal-associated invariant T (MAIT) cells, and other unconventional T cells are specialised in detecting microbial metabolic pathway intermediates that are absent in humans. The recognition by such semi-invariant innate-like T cells of compounds like (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), the penultimate metabolite in the MEP isoprenoid biosynthesis pathway, and intermediates of the riboflavin biosynthesis pathway and their metabolites allows the immune system to rapidly sense pathogen-associated molecular patterns that are shared by a wide range of micro-organisms. Given the essential nature of these metabolic pathways for microbial viability, they have emerged as promising targets for the development of novel antibiotics. Here, we review recent findings that link enzymatic inhibition of microbial metabolism with alterations in the levels of unconventional T cell ligands produced by treated micro-organisms that have given rise to the concept of 'immuno-antibiotics': combining direct antimicrobial activity with an immunotherapeutic effect via modulation of unconventional T cell responses.
Collapse
Affiliation(s)
- Matthias Eberl
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK,Systems Immunity Research Institute, Cardiff University, Cardiff, UK,Correspondence: Matthias Eberl, Division of Infection and Immunity, Henry Wellcome Building, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, Wales, UK. Tel: +44-29206-87011;
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Thomas Herrmann
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| |
Collapse
|
9
|
Huang H, Han YS, Chen J, Shi LY, Wei LL, Jiang TT, Yi WJ, Yu Y, Li ZB, Li JC. The novel potential biomarkers for multidrug-resistance tuberculosis using UPLC-Q-TOF-MS. Exp Biol Med (Maywood) 2020; 245:501-511. [PMID: 32046521 DOI: 10.1177/1535370220903464] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The lack of rapid and efficient diagnostics impedes largely the epidemic control of multidrug-resistant tuberculosis, and might misguide the therapeutic strategies as well. This study aimed to identify novel multidrug-resistant tuberculosis biomarkers to improve the early intervention, symptomatic treatment and control of the prevalence of multidrug-resistant tuberculosis. The serum small molecule metabolites in healthy controls, patients with drug-susceptible tuberculosis, and patients with multidrug-resistant tuberculosis were screened using ultra-high-performance liquid chromatography combined with quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS). The differentially abundant metabolites were filtered out through multidimensional statistical analysis and bioinformatics analysis. Compared with drug-susceptible tuberculosis patients and healthy controls, the levels of 13 metabolites in multidrug-resistant tuberculosis patients altered. Among them, the most significant changes were found in N1-Methyl-2-pyridone-5-carboxamide (N1M2P5C), 1-Myristoyl-sn-glycerol-3-phosphocholine (MG3P), Caprylic acid (CA), and D-Xylulose (DX). And a multidrug-resistant tuberculosis/drug-susceptible tuberculosis differential diagnostic model was built based on these four metabolites, achieved the accuracy, sensitivity, and specificity of 0.928, 86.7%, and 86.7%, respectively. The enrichment analysis of metabolic pathways showed that the phospholipid remodeling of cell membranes was active in multidrug-resistant tuberculosis patients. In addition, in patients with tuberculosis, the metabolites of dipalmitoyl phosphatidylcholine (DPPC), a major component of pulmonary surfactant, were down-regulated. N1M2P5C, MG3P, CA, and DX may have the potential to serve as novel multidrug-resistant tuberculosis biomarkers. This research provides a preliminary experimental basis to further investigate potential multidrug-resistant tuberculosis biomarkers. Impact statement The MDR-TB incidence remains high, making the effective control of TB epidemic yet challenging. Rapid and accurate diagnosis is vitally important for improving the therapeutic efficacy and controlling the prevalence of drug resistance TB. Metabolomics has dramatic potential to distinguish MDR-TB and DS-TB. N1M2P5C, MG3P, CA, and DX that we identified in this study might have potential as novel MDR-TB biomarkers. The phospholipid remodeling of cell membranes was highly active in MDR-TB. The DPPC metabolites in TB were significantly down-regulated. This work aimed to investigate potential MDR-TB biomarkers to enhance the clinical diagnostic efficacy. The metabolic pathway distinctly altered in MDR-TB might provide novel targets to develop new anti-TB drugs.
Collapse
Affiliation(s)
- Huai Huang
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Yu-Shuai Han
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Jing Chen
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310013, China
| | - Li-Liang Wei
- Department of Pneumology, Shaoxing University Affiliated Hospital, Shaoxing 312099, China
| | - Ting-Ting Jiang
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Wen-Jing Yi
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Yi Yu
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhi-Bin Li
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Ji-Cheng Li
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
10
|
Wang X, Edwards RL, Ball H, Johnson C, Haymond A, Girma M, Manikkam M, Brothers RC, McKay KT, Arnett SD, Osbourn DM, Alvarez S, Boshoff HI, Meyers MJ, Couch RD, Odom John AR, Dowd CS. MEPicides: α,β-Unsaturated Fosmidomycin Analogues as DXR Inhibitors against Malaria. J Med Chem 2018; 61:8847-8858. [PMID: 30192536 DOI: 10.1021/acs.jmedchem.8b01026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Severe malaria due to Plasmodium falciparum remains a significant global health threat. DXR, the second enzyme in the MEP pathway, plays an important role to synthesize building blocks for isoprenoids. This enzyme is a promising drug target for malaria due to its essentiality as well as its absence in humans. In this study, we designed and synthesized a series of α,β-unsaturated analogues of fosmidomycin, a natural product that inhibits DXR in P. falciparum. All compounds were evaluated as inhibitors of P. falciparum. The most promising compound, 18a, displays on-target, potent inhibition against the growth of P. falciparum (IC50 = 13 nM) without significant inhibition of HepG2 cells (IC50 > 50 μM). 18a was also tested in a luciferase-based Plasmodium berghei mouse model of malaria and showed exceptional in vivo efficacy. Together, the data support MEPicide 18a as a novel, potent, and promising drug candidate for the treatment of malaria.
Collapse
Affiliation(s)
- Xu Wang
- Department of Chemistry , George Washington University , Washington D.C. 20052 , United States
| | - Rachel L Edwards
- Department of Pediatrics , Washington University School of Medicine, Washington University , St. Louis , Missouri 63110 , United States
| | - Haley Ball
- Department of Chemistry and Biochemistry , George Mason University , Manassas , Virginia 20110 , United States
| | - Claire Johnson
- Department of Chemistry and Biochemistry , George Mason University , Manassas , Virginia 20110 , United States
| | - Amanda Haymond
- Department of Chemistry and Biochemistry , George Mason University , Manassas , Virginia 20110 , United States
| | - Misgina Girma
- Department of Chemistry and Biochemistry , George Mason University , Manassas , Virginia 20110 , United States
| | - Michelle Manikkam
- Tuberculosis Research Section, LCIM , NIAID/NIH , Bethesda , Maryland 20892 , United States
| | - Robert C Brothers
- Department of Chemistry , George Washington University , Washington D.C. 20052 , United States
| | - Kyle T McKay
- Department of Chemistry , George Washington University , Washington D.C. 20052 , United States
| | - Stacy D Arnett
- Department of Pharmacology and Physiology , Saint Louis University , St. Louis , Missouri 63104 , United States
| | - Damon M Osbourn
- Department of Molecular Microbiology and Immunology , Saint Louis University , St. Louis , Missouri 63104 , United States
| | - Sophie Alvarez
- Proteomics & Metabolomics Facility, Center for Biotechnology, Department of Agronomy and Horticulture , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Helena I Boshoff
- Tuberculosis Research Section, LCIM , NIAID/NIH , Bethesda , Maryland 20892 , United States
| | - Marvin J Meyers
- Department of Pharmacology and Physiology , Saint Louis University , St. Louis , Missouri 63104 , United States.,Department of Chemistry , Saint Louis University , St. Louis , Missouri 63103 , United States
| | - Robin D Couch
- Department of Chemistry and Biochemistry , George Mason University , Manassas , Virginia 20110 , United States
| | - Audrey R Odom John
- Department of Pediatrics , Washington University School of Medicine, Washington University , St. Louis , Missouri 63110 , United States
| | - Cynthia S Dowd
- Department of Chemistry , George Washington University , Washington D.C. 20052 , United States
| |
Collapse
|
11
|
Schwenk S, Moores A, Nobeli I, McHugh TD, Arnvig KB. Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis. Nucleic Acids Res 2018; 46:5837-5849. [PMID: 29618088 PMCID: PMC6009663 DOI: 10.1093/nar/gky226] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/11/2018] [Accepted: 03/15/2018] [Indexed: 01/16/2023] Open
Abstract
The success of Mycobacterium tuberculosis relies on the ability to switch between active growth and non-replicating persistence, associated with latent TB infection. Resuscitation promoting factors (Rpfs) are essential for the transition between these states. Rpf expression is tightly regulated as these enzymes are able to degrade the cell wall, and hence potentially lethal to the bacterium itself. We have identified a regulatory element in the 5' untranslated region (UTR) of rpfB. We demonstrate that this element is a transcriptionally regulated RNA switch/riboswitch candidate, which appears to be restricted to pathogenic mycobacteria, suggesting a role in virulence. We have used translation start site mapping to re-annotate the RpfB start codon and identified and validated a ribosome binding site that is likely to be targeted by an rpfB antisense RNA. Finally, we show that rpfB is co-transcribed with ksgA and ispE downstream. ksgA encodes a universally conserved methyltransferase involved in ribosome maturation and ispE encodes an essential kinase involved in cell wall synthesis. This arrangement implies co-regulation of resuscitation, cell wall synthesis and ribosome maturation via the RNA switch.
Collapse
Affiliation(s)
- Stefan Schwenk
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Alexandra Moores
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Irene Nobeli
- Institute for Structural and Molecular Biology, Birkbeck, London WC1E 7HX, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, Royal Free Campus, University College London, London NW3 2QG, UK
| | - Kristine B Arnvig
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| |
Collapse
|
12
|
Wang X, Dowd CS. The Methylerythritol Phosphate Pathway: Promising Drug Targets in the Fight against Tuberculosis. ACS Infect Dis 2018; 4:278-290. [PMID: 29390176 DOI: 10.1021/acsinfecdis.7b00176] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a severe infectious disease in need of new chemotherapies especially for drug-resistant cases. To meet the urgent requirement of new TB drugs with novel modes of action, the TB research community has been validating numerous targets from several biosynthetic pathways. The methylerythritol phosphate (MEP) pathway is utilized by Mtb for the biosynthesis of isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl pyrophosphate (DMAPP), the universal five-carbon building blocks of isoprenoids. While being a common biosynthetic pathway in pathogens, the MEP pathway is completely absent in humans. Due to its unique presence in pathogens as well as the essentiality of the MEP pathway in Mtb, the enzymes in this pathway are promising targets for the development of new drugs against tuberculosis. In this Review, we discuss three enzymes in the MEP pathway: 1-deoxy-d-xylulose-5-phosphate synthase (DXS), 1-deoxy-d-xylulose-5-phosphate reductoisomerase (IspC/DXR), and 2 C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF), which appear to be the most promising antitubercular drug targets. Structural and mechanistic features of these enzymes are reviewed, as well as selected inhibitors that show promise as antitubercular agents.
Collapse
Affiliation(s)
- Xu Wang
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington, D.C. 20052, United States
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington, D.C. 20052, United States
| |
Collapse
|
13
|
Jin Y, Liu Z, Li Y, Liu W, Tao Y, Wang G. A structural and functional study on the 2-C-methyl-d-erythritol-4-phosphate cytidyltransferase (IspD) from Bacillus subtilis. Sci Rep 2016; 6:36379. [PMID: 27821871 PMCID: PMC5099578 DOI: 10.1038/srep36379] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/13/2016] [Indexed: 12/25/2022] Open
Abstract
2-C-Methyl-D-erythritol-4-phosphate cytidyltransferase (IspD) is an essential enzyme in the mevalonate-independent pathway of isoprenoid biosynthesis. This enzyme catalyzes 2-C-Methyl-d-erythritol 4-phosphate (MEP) and cytosine triphosphate (CTP) to 4-diphosphocytidyl-2-C-methyl-d-erythritol (CDPME) and inorganic pyrophosphate (PPi). Bacillus subtilis was a kind of excellent isoprene producer. However, the studies on the key enzymes of MEP pathway in B. subtilis were still absent. In this work, the crystal structures of IspD and IspD complexed with CTP from B.subtilis were determined. For the first time, the intact P-loop was observed in the apo structure of IspD enzyme. Structural comparisons revealed that the concerted movements of the P-loop and loops close to the active site were essential in the reaction catalyzed by IspD. Meanwhile, kinetic analysis showed that the CTP hydrolytic activity of IspD from B.subtilis was over two times higher than that from Escherichia coli. These results will be useful for future target-based screening of potential inhibitors and the metabolic engineering for isoprenoid biosynthesis.
Collapse
Affiliation(s)
- Yun Jin
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongchuan Liu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, 610041, China
| | - Yanjie Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, 610041, China
| | - Weifeng Liu
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Yong Tao
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Ganggang Wang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, 610041, China
| |
Collapse
|
14
|
Tima HG, Huygen K, Romano M. Innate signaling by mycobacterial cell wall components and relevance for development of adjuvants for subunit vaccines. Expert Rev Vaccines 2016; 15:1409-1420. [PMID: 27206681 DOI: 10.1080/14760584.2016.1187067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Pathogen recognition receptors (PRRs) recognize pathogen-associated molecular patterns, triggering the induction of inflammatory innate responses and contributing to the development of specific adaptive immune responses. Novel adjuvants have been developed based on agonists of PRRs. Areas covered: Lipid pathogen-associated molecular patterns (PAMPs) present in the cell wall of mycobacteria are revised, with emphasis on agonists of C-type lectin receptors, signaling pathways, and preclinical data supporting their use as novel adjuvants inducing cell-mediated immune responses. Their potential use as lipid antigens in novel tuberculosis subunit vaccines is also discussed. Expert commentary: Few adjuvants are licensed for human use and mainly favour antibody-mediated protective immunity. Use of lipid PAMPs that trigger cell-mediated immune responses could lead to the development of adjuvants for vaccines against intracellular pathogens and cancer.
Collapse
Affiliation(s)
- Hermann Giresse Tima
- a Immunology Service, Communicable and Infectious Diseases Department , Scientific Institute of Public Health (WIV-ISP) , Brussels , Belgium
| | - Kris Huygen
- a Immunology Service, Communicable and Infectious Diseases Department , Scientific Institute of Public Health (WIV-ISP) , Brussels , Belgium
| | - Marta Romano
- a Immunology Service, Communicable and Infectious Diseases Department , Scientific Institute of Public Health (WIV-ISP) , Brussels , Belgium
| |
Collapse
|
15
|
Farah SI, Abdelrahman AA, North EJ, Chauhan H. Opportunities and Challenges for Natural Products as Novel Antituberculosis Agents. Assay Drug Dev Technol 2016; 14:29-38. [DOI: 10.1089/adt.2015.673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Shrouq I. Farah
- Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University, Omaha, Nebraska
| | | | - E. Jeffrey North
- Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University, Omaha, Nebraska
| | - Harsh Chauhan
- Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University, Omaha, Nebraska
| |
Collapse
|
16
|
Ajayi RF, Sidwaba U, Feleni U, Douman SF, Tovide O, Botha S, Baker P, Fuku XG, Hamid S, Waryo TT, Vilakazi S, Tshihkudo R, Iwuoha EI. Chemically amplified cytochrome P450-2E1 drug metabolism nanobiosensor for rifampicin anti-tuberculosis drug. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2013.12.147] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
17
|
Hayashi D, Kato N, Kuzuyama T, Sato Y, Ohkanda J. Antimicrobial N-(2-chlorobenzyl)-substituted hydroxamate is an inhibitor of 1-deoxy-D-xylulose 5-phosphate synthase. Chem Commun (Camb) 2013; 49:5535-7. [PMID: 23476925 DOI: 10.1039/c3cc40758f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-(2-Chlorobenzyl)-substituted hydroxamate, readily produced by hydrolysis of ketoclomazone, was identified as an inhibitor of 1-deoxy-D-xylulose 5-phosphate synthase (DXS), with an IC50 value of 1.0 μM. The compound inhibited the growth of Haemophilus influenzae. A convenient spectroscopic method for assaying DXS using NADPH-lactate dehydrogenase (LDH) is also reported.
Collapse
Affiliation(s)
- Daisuke Hayashi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | | | | | | | | |
Collapse
|
18
|
Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum. PLoS Comput Biol 2013; 9:e1003208. [PMID: 24039564 PMCID: PMC3764002 DOI: 10.1371/journal.pcbi.1003208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/19/2013] [Indexed: 11/19/2022] Open
Abstract
Primarily used for metabolic engineering and synthetic biology, genome-scale metabolic modeling shows tremendous potential as a tool for fundamental research and curation of metabolism. Through a novel integration of flux balance analysis and genetic algorithms, a strategy to curate metabolic networks and facilitate identification of metabolic pathways that may not be directly inferable solely from genome annotation was developed. Specifically, metabolites involved in unknown reactions can be determined, and potentially erroneous pathways can be identified. The procedure developed allows for new fundamental insight into metabolism, as well as acting as a semi-automated curation methodology for genome-scale metabolic modeling. To validate the methodology, a genome-scale metabolic model for the bacterium Mycoplasma gallisepticum was created. Several reactions not predicted by the genome annotation were postulated and validated via the literature. The model predicted an average growth rate of 0.358±0.12, closely matching the experimentally determined growth rate of M. gallisepticum of 0.244±0.03. This work presents a powerful algorithm for facilitating the identification and curation of previously known and new metabolic pathways, as well as presenting the first genome-scale reconstruction of M. gallisepticum. Flux balance analysis (FBA) is a powerful approach for genome-scale metabolic modeling. It provides metabolic engineers with a tool for manipulating, predicting, and optimizing metabolism for biotechnological and biomedical purposes. However, we posit that it can also be used as tool for fundamental research in understanding and curating metabolic networks. Specifically, by using a genetic algorithm integrated with FBA, we developed a curation approach to identify missing reactions, incomplete reactions, and erroneous reactions. Additionally, it was possible to take advantage of the ensemble information from the genetic algorithm to identify the most critical reactions for curation. We tested our strategy using Mycoplasma gallisepticum as our model organism. Using the genome annotation as the basis, the preliminary genome-scale metabolic model consisted of 446 metabolites involved in 380 reactions. Carrying out our analysis, we found over 80 incorrect reactions and 16 missing reactions. Based upon the guidance of the algorithm, we were able to curate and resolve all discrepancies. The model predicted an average bacterial growth rate of 0.358±0.12 h−1 compared to the experimentally observed 0.244±0.03 h−1. Thus, our approach facilitated the curation of a genome-scale metabolic network and generated a high quality metabolic model.
Collapse
|
19
|
Nowosielski M, Hoffmann M, Kuron A, Korycka-Machala M, Dziadek J. The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics†. J Comput Chem 2012; 34:750-6. [DOI: 10.1002/jcc.23192] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 11/02/2012] [Accepted: 11/06/2012] [Indexed: 11/10/2022]
|
20
|
Gao P, Yang Y, Xiao C, Liu Y, Gan M, Guan Y, Hao X, Meng J, Zhou S, Chen X, Cui J. Identification and validation of a novel lead compound targeting 4-diphosphocytidyl-2-C-methylerythritol synthetase (IspD) of mycobacteria. Eur J Pharmacol 2012; 694:45-52. [PMID: 22975264 DOI: 10.1016/j.ejphar.2012.08.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 08/21/2012] [Accepted: 08/27/2012] [Indexed: 01/17/2023]
Abstract
Tuberculosis is a serious threat to world-wide public health usually caused in humans by Mycobacterium tuberculosis (M. tuberculosis). It exclusively utilizes the methylerythritol phosphate (MEP) pathway for biosynthesis of isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP), the precursors of all isoprenoid compounds. The 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase (IspD; EC 2.7.7.60) is the key enzyme of the MEP pathway. It is also of interest as a new chemotherapeutic target, as the enzyme is absent in mammals and ispD is an essential gene for growth. A high-throughput screening method was therefore developed to identify compounds that inhibit IspD. This process was applied to identify a lead compound, domiphen bromide (DMB), that may effectively inhibit IspD. The inhibitory action of DMB was confirmed by over-expressing or down-regulating IspD in Mycobacterium smegmatis (M. smegmatis), demonstrating that DMB inhibit M. smegmatis growth additionally through an IspD-independent pathway. This also led to higher levels of growth inhibition when combined with IspD knockdown. This novel IspD inhibitor was also reported to exhibit antimycobacterial activity in vitro, an effect that likely occurs as a result of perturbation of cell wall biosynthesis.
Collapse
Affiliation(s)
- Peng Gao
- Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
A whole-cell phenotypic screening platform for identifying methylerythritol phosphate pathway-selective inhibitors as novel antibacterial agents. Antimicrob Agents Chemother 2012; 56:4906-13. [PMID: 22777049 DOI: 10.1128/aac.00987-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Isoprenoid biosynthesis is essential for survival of all living organisms. More than 50,000 unique isoprenoids occur naturally, with each constructed from two simple five-carbon precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Two pathways for the biosynthesis of IPP and DMAPP are found in nature. Humans exclusively use the mevalonate (MVA) pathway, while most bacteria, including all Gram-negative and many Gram-positive species, use the unrelated methylerythritol phosphate (MEP) pathway. Here we report the development of a novel, whole-cell phenotypic screening platform to identify compounds that selectively inhibit the MEP pathway. Strains of Salmonella enterica serovar Typhimurium were engineered to have separately inducible MEP (native) and MVA (nonnative) pathways. These strains, RMC26 and CT31-7d, were then used to differentiate MVA pathway- and MEP pathway-specific perturbation. Compounds that inhibit MEP pathway-dependent bacterial growth but leave MVA-dependent growth unaffected represent MEP pathway-selective antibacterials. This screening platform offers three significant results. First, the compound is antibacterial and is therefore cell permeant, enabling access to the intracellular target. Second, the compound inhibits one or more MEP pathway enzymes. Third, the MVA pathway is unaffected, suggesting selectivity for targeting the bacterial versus host pathway. The cell lines also display increased sensitivity to two reported MEP pathway-specific inhibitors, further biasing the platform toward inhibitors selective for the MEP pathway. We demonstrate development of a robust, high-throughput screening platform that combines phenotypic and target-based screening that can identify MEP pathway-selective antibacterials simply by monitoring optical density as the readout for cell growth/inhibition.
Collapse
|
22
|
Heuston S, Begley M, Gahan CGM, Hill C. Isoprenoid biosynthesis in bacterial pathogens. Microbiology (Reading) 2012; 158:1389-1401. [DOI: 10.1099/mic.0.051599-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sinéad Heuston
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Máire Begley
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Cormac G. M. Gahan
- School of Pharmacy, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
23
|
Ponaire S, Zinglé C, Tritsch D, Grosdemange-Billiard C, Rohmer M. Growth inhibition of Mycobacterium smegmatis by prodrugs of deoxyxylulose phosphate reducto-isomerase inhibitors, promising anti-mycobacterial agents. Eur J Med Chem 2012; 51:277-85. [DOI: 10.1016/j.ejmech.2012.02.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 02/15/2012] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
|
24
|
Tang M, Odejinmi SI, Vankayalapati H, Wierenga K, Lai K. Innovative therapy for Classic Galactosemia - tale of two HTS. Mol Genet Metab 2012; 105:44-55. [PMID: 22018723 PMCID: PMC3253915 DOI: 10.1016/j.ymgme.2011.09.028] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/21/2011] [Accepted: 09/21/2011] [Indexed: 01/04/2023]
Abstract
Classic Galactosemia is an autosomal recessive disorder caused by the deficiency of galactose-1-phosphate uridylyltransferase (GALT), one of the key enzymes in the Leloir pathway of galactose metabolism. While the neonatal morbidity and mortality of the disease are now mostly prevented by newborn screening and galactose restriction, long-term outcome for older children and adults with this disorder remains unsatisfactory. The pathophysiology of Classic Galactosemia is complex, but there is convincing evidence that galactose-1-phosphate (gal-1P) accumulation is a major, if not the sole pathogenic factor. Galactokinase (GALK) inhibition will eliminate the accumulation of gal-1P from both dietary sources and endogenous production, and efforts toward identification of therapeutic small molecule GALK inhibitors are reviewed in detail. Experimental and computational high-throughput screenings of compound libraries to identify GALK inhibitors have been conducted, and subsequent studies aimed to characterize, prioritize, as well as to optimize the identified positives have been implemented to improve the potency of promising compounds. Although none of the identified GALK inhibitors inhibits glucokinase and hexokinase, some of them cross-inhibit other related enzymes in the GHMP small molecule kinase superfamily. While this finding may render the on-going hit-to-lead process more challenging, there is growing evidence that such cross-inhibition could also lead to advances in antimicrobial and anti-cancer therapies.
Collapse
Affiliation(s)
- M Tang
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, U.S.A
| | - SI Odejinmi
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, U.S.A
| | - H Vankayalapati
- Center for Investigational Therapeutics, Huntsman Cancer Institute, The University of Utah, Salt Lake City, Utah, U.S.A
| | - K Wierenga
- Department of Pediatrics, Section of Genetics, OUHSC, Oklahoma City, Oklahoma, U.S.A
- Corresponding Authors: Kent Lai, Ph.D., Department of Pediatrics, Division of Medical Genetics, University of Utah School of Medicine, 50 N. Mario Capecchi Drive, SOM Room 2C412, Salt Lake City, UT 84132, U.S.A., (); KlaasWierenga, M.D., Department of Pediatrics, Section of Genetics, OUHSC, OUCP Suite 12100, Oklahoma City, OK 73104, U.S.A., ()
| | - K Lai
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, U.S.A
- Corresponding Authors: Kent Lai, Ph.D., Department of Pediatrics, Division of Medical Genetics, University of Utah School of Medicine, 50 N. Mario Capecchi Drive, SOM Room 2C412, Salt Lake City, UT 84132, U.S.A., (); KlaasWierenga, M.D., Department of Pediatrics, Section of Genetics, OUHSC, OUCP Suite 12100, Oklahoma City, OK 73104, U.S.A., ()
| |
Collapse
|
25
|
Abstract
Multidrug-resistant tuberculosis has emerged worldwide, with an increasing incidence due to failure of implementation of apparently effective first-line antituberculous therapy as well as primary infection with drug-resistant strains. Failure of current therapy is attributed to a long duration of treatment leading to nonadherence and irregular therapy, lack of patient education about the disease, poverty, irregular supply by care providers, drug–drug interactions in patients coinfected with human immunodeficiency virus (HIV), inadequate regulations causing market overlap and irresponsible drug usage in the private sector, and lack of research, with no addition of new drugs in the last four decades. Present standards of care for the treatment of drugsusceptible tuberculosis, multidrug-resistant tuberculosis, tuberculosis-HIV coinfection, and latent tuberculosis infection are all unsatisfactory. Since 2000, the World Health Organization (WHO) has focused on drug development for tuberculosis, as well as research in all relevant aspects to discover new regimens by 2015 and to eliminate tuberculosis as a public health concern by 2050. As a result, some 20 promising compounds from 14 groups of drugs have been discovered. Twelve candidates from eight classes are currently being evaluated in clinical trials. Ongoing research should prioritize identification of novel targets and newer application of existing drugs, discovery of multitargeted drugs from natural compounds, strengthening host factors by immunopotentiation with herbal immunomodulators, as well as protective vaccines before and after exposure, consideration of surgical measures when indicated, development of tools for rapid diagnosis, early identification of resistant strains, and markers for adequacy of treatment and an integrative approach to fulfill WHO goals. However, regulatory control over the drug market, as well as public-private partnership to use health program facilities to track patients and ensure completion of adequate therapy will be necessary to exploit fully the potential of the newer regimens to eliminate tuberculosis.
Collapse
Affiliation(s)
- Meghna Adhvaryu
- Department of Biotechnology, SRK Institute of Computer Education and Applied Sciences, Surat, Gujarat, India
| | | |
Collapse
|
26
|
Brammer LA, Smith JM, Wade H, Meyers CF. 1-Deoxy-D-xylulose 5-phosphate synthase catalyzes a novel random sequential mechanism. J Biol Chem 2011; 286:36522-31. [PMID: 21878632 DOI: 10.1074/jbc.m111.259747] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Emerging resistance of human pathogens to anti-infective agents make it necessary to develop new agents to treat infection. The methylerythritol phosphate pathway has been identified as an anti-infective target, as this essential isoprenoid biosynthetic pathway is widespread in human pathogens but absent in humans. The first enzyme of the pathway, 1-deoxy-D-xylulose 5-phosphate (DXP) synthase, catalyzes the formation of DXP via condensation of D-glyceraldehyde 3-phosphate (D-GAP) and pyruvate in a thiamine diphosphate-dependent manner. Structural analysis has revealed a unique domain arrangement suggesting opportunities for the selective targeting of DXP synthase; however, reports on the kinetic mechanism are conflicting. Here, we present the results of tryptophan fluorescence binding and kinetic analyses of DXP synthase and propose a new model for substrate binding and mechanism. Our results are consistent with a random sequential kinetic mechanism, which is unprecedented in this enzyme class.
Collapse
Affiliation(s)
- Leighanne A Brammer
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | | | | |
Collapse
|
27
|
Tang M, Odejinmi SI, Allette YM, Vankayalapati H, Lai K. Identification of novel small molecule inhibitors of 4-diphosphocytidyl-2-C-methyl-D-erythritol (CDP-ME) kinase of Gram-negative bacteria. Bioorg Med Chem 2011; 19:5886-95. [PMID: 21903402 DOI: 10.1016/j.bmc.2011.08.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/02/2011] [Accepted: 08/08/2011] [Indexed: 11/17/2022]
Abstract
The biosyntheses of isoprenoids is essential for the survival in all living organisms, and requires one of the two biochemical pathways: (a) Mevalonate (MVA) Pathway or (b) Methylerythritol Phosphate (MEP) Pathway. The latter pathway, which is used by all Gram-negative bacteria, some Gram-positive bacteria and a few apicomplexan protozoa, provides an attractive target for the development of new antimicrobials because of its absence in humans. In this report, we describe two different approaches that we used to identify novel small molecule inhibitors of Escherichia coli and Yersinia pestis 4-diphosphocytidyl-2-C-methyl D-erythritol (CDP-ME) kinases, key enzymes of the MEP pathway encoded by the E. coli ispE and Y. pestisipk genes, respectively. In the first approach, we explored existing inhibitors of the GHMP kinases while in the second approach; we performed computational high-throughput screening of compound libraries by targeting the CDP-ME binding site of the two bacterial enzymes. From the first approach, we identified two compounds with 6-(benzylthio)-2-(2-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1,3-thiazine-5-carbonitrile and (Z)-3-methyl-4-((5-phenylfuran-2-yl)methylene)isoxazol-5(4H)-one scaffolds which inhibited E. coli CDP-ME kinase in vitro. We then performed substructure search and docking experiments based on these two scaffolds and identified twenty three analogs for structure-activity relationship (SAR) studies. Three new compounds from the isoxazol-5(4H)-one series have shown inhibitory activities against E. coli and Y. pestis CDP-ME kinases with the IC(50) values ranging from 7 to 13 μM. The second approach by computational high-throughput screening (HTS) of two million drug-like compounds yielded two compounds with benzenesulfonamide and acetamide moieties which, at a concentration of 20 μM, inhibited 80% and 65%, respectively, of control CDP-ME kinase activity.
Collapse
Affiliation(s)
- M Tang
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, 50 N. Mario Capecchi Drive, SOM Room 2C412, Salt Lake City, UT 84132, USA
| | | | | | | | | |
Collapse
|
28
|
Shan S, Chen X. Crystallization and preliminary X-ray analysis of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:821-3. [PMID: 21795803 DOI: 10.1107/s1744309111019567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 05/23/2011] [Indexed: 11/10/2022]
Abstract
The 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) from Mycobacterium tuberculosis, an enzyme from the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, is crucial and essential for the survival of this pathogenic bacterium. IspE catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol (CDP-ME) to 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) in an ATP-dependent manner. Solving the crystal structure of M. tuberculosis IspE will shed light on its structural details and mechanism of action and may provide the basis for the future design of drugs for the treatment of multidrug-resistant and extremely drug-resistant M. tuberculosis strains. Recombinant M. tuberculosis IspE was crystallized at 291 K using NaCl or Li2SO4 as a precipitant. A 2.1 Å resolution native data set was collected from a single flash-cooled crystal (100 K) belonging to space group P2(1)2(1)2(1), with unit-cell parameters a=52.5, b=72.3, c=107.3 Å. One molecule was assumed per asymmetric unit, which gives a Matthews coefficient of 3.4 Å3 Da(-1) with 63% solvent content.
Collapse
Affiliation(s)
- Shan Shan
- Structural Biology Laboratory, Tsinghua University, Beijing 100084, People's Republic of China
| | | |
Collapse
|
29
|
Barh D, Jain N, Tiwari S, Parida BP, D'Afonseca V, Li L, Ali A, Santos AR, Guimarães LC, de Castro Soares S, Miyoshi A, Bhattacharjee A, Misra AN, Silva A, Kumar A, Azevedo V. A novel comparative genomics analysis for common drug and vaccine targets in Corynebacterium pseudotuberculosis and other CMN group of human pathogens. Chem Biol Drug Des 2011; 78:73-84. [PMID: 21443692 DOI: 10.1111/j.1747-0285.2011.01118.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Caseous lymphadenitis is a chronic goat and sheep disease caused by Corynebacterium pseudotuberculosis (Cp) that accounts for a huge economic loss worldwide. Proper vaccination or medication is not available because of the lack of understanding of molecular biology of the pathogen. In a recent approach, four Cp (CpFrc41, Cp1002, CpC231, and CpI-19) genomes were sequenced to elucidate the molecular pathology of the bacteria. In this study, using these four genome sequences along with other eight genomes (total 12 genomes) and a novel subtractive genomics approach (first time ever applied to a veterinary pathogen), we identified potential conserved common drug and vaccine targets of these four Cp strains along with other Corybacterium, Mycobacterium and Nocardia (CMN) group of human pathogens (Corynebacterium diphtheriae and Mycobacterium tuberculosis) considering goat, sheep, bovine, horse, and human as the most affected hosts. The minimal genome of Cp1002 was found to consist of 724 genes, and 20 conserved common targets (to all Cp strains as well as CMN group of pathogens) from various metabolic pathways (13 from host-pathogen common and seven from pathogen's unique pathways) are potential targets irrespective of all hosts considered. ubiA from host-pathogen common pathway and an ABC-like transporter from unique pathways may serve dual (drug and vaccine) targets. Two Corynebacterium-specific (mscL and resB) and one broad-spectrum (rpmB) novel targets were also identified. Strain-specific targets are also discussed. Six important targets were subjected to virtual screening, and one compound was found to be potent enough to render two targets (cdc and nrdL). We are currently validating all identified targets and lead compounds.
Collapse
Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Shan S, Chen X, Liu T, Zhao H, Rao Z, Lou Z. Crystal structure of 4‐diphosphocytidyl‐2‐C‐methyl‐D‐erythritol kinase (IspE) from
Mycobacterium tuberculosis. FASEB J 2011; 25:1577-84. [DOI: 10.1096/fj.10-175786] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shan Shan
- Structural Biology LaboratoryTsinghua UniversityBeijingChina
- MOE Laboratory of Protein ScienceTsinghua UniversityBeijingChina
| | - Xuehui Chen
- National Laboratory of MacromoleculesInstitute of BiophysicsChinese Academy of ScienceBeijingChina
| | - Ting Liu
- National Laboratory of MacromoleculesInstitute of BiophysicsChinese Academy of ScienceBeijingChina
| | - Hanchao Zhao
- Structural Biology LaboratoryTsinghua UniversityBeijingChina
- MOE Laboratory of Protein ScienceTsinghua UniversityBeijingChina
| | - Zihe Rao
- Structural Biology LaboratoryTsinghua UniversityBeijingChina
- MOE Laboratory of Protein ScienceTsinghua UniversityBeijingChina
- National Laboratory of MacromoleculesInstitute of BiophysicsChinese Academy of ScienceBeijingChina
- High-Throughput Molecular Drug Discovery CenterTianjin Joint Academy of Biotechnology and MedicineTianjinChina
| | - Zhiyong Lou
- Structural Biology LaboratoryTsinghua UniversityBeijingChina
- MOE Laboratory of Protein ScienceTsinghua UniversityBeijingChina
- High-Throughput Molecular Drug Discovery CenterTianjin Joint Academy of Biotechnology and MedicineTianjinChina
| |
Collapse
|
31
|
Yashodhara BM, Huat CB, Naik LN, Umakanth S, Hande M, Pappachan JM. Multidrug and extensively drug-resistant tuberculosis from a general practice perspective. Infect Drug Resist 2010; 3:115-22. [PMID: 21694900 PMCID: PMC3108735 DOI: 10.2147/idr.s10743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Indexed: 02/05/2023] Open
Abstract
Despite intensive efforts to eradicate the disease, tuberculosis continues to be a major threat to Indian society, with an estimated prevalence of 3.45 million cases in 2006. Emergence of multidrug-resistant tuberculosis has complicated eradication attempts in recent years. Incomplete and/inadequate treatment are the main causes for development of drug resistance. Directly observed therapy, short-course (DOTS) is the World Health Organization (WHO) strategy for worldwide eradication of tuberculosis, and our country achieved 100% coverage for DOTS through the Revised National Tuberculosis Control Program in 2006. For patients with multidrug-resistant tuberculosis, the WHO recommends a DOTS-Plus treatment strategy. Early detection and prompt treatment of multidrug-resistant tuberculosis is crucial to avoid spread of the disease and also because of the chances of development of potentially incurable extensively drug-resistant tuberculosis in these cases. This review discusses the epidemiologic, diagnostic, and therapeutic aspects of multidrug-resistant tuberculosis, and also outlines the role of primary care doctors in the management of this dangerous disease.
Collapse
Affiliation(s)
- BM Yashodhara
- Department of Medicine, Melaka Manipal Medical College, Melaka, India
| | - Choo Beng Huat
- Department of Medicine, Melaka Manipal Medical College, Melaka, India
| | | | | | | | | |
Collapse
|
32
|
Ashforth EJ, Fu C, Liu X, Dai H, Song F, Guo H, Zhang L. Bioprospecting for antituberculosis leads from microbial metabolites. Nat Prod Rep 2010; 27:1709-19. [PMID: 20922218 DOI: 10.1039/c0np00008f] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Elizabeth Jane Ashforth
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
33
|
Pérez-Gil J, Bergua M, Boronat A, Imperial S. Cloning and functional characterization of an enzyme from Helicobacter pylori that catalyzes two steps of the methylerythritol phosphate pathway for isoprenoid biosynthesis. Biochim Biophys Acta Gen Subj 2010; 1800:919-28. [PMID: 20600626 DOI: 10.1016/j.bbagen.2010.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 06/15/2010] [Accepted: 06/16/2010] [Indexed: 11/25/2022]
Abstract
BACKGROUND The methylerythritol phosphate pathway for isoprenoid biosynthesis is an attractive target for the design of new specific antibiotics for the treatment of gastrointestinal diseases associated with the presence of the bacterium Helicobacter pylori since this pathway which is essential to the bacterium is absent in humans. RESULTS This work reports the molecular cloning of one of the genes of the methylerythritol phosphate pathway form H. pylori (ispDF; HP_1440) its expression in Escherichia coli and the functional characterization of the recombinant enzyme. As shown by genetic complementation and in vitro functional assays the product of the ispDF gene form H. pylori is a bifunctional enzyme which can replace both CDP-methylerythritol synthase and methylerythritol cyclodiphosphate synthase from E. coli. GENERAL SIGNIFICANCE Designing inhibitors that affect at the same time both enzyme activities of the H. pylori bifunctional enzyme (i.e. by disrupting protein oligomerization) would result in more effective antibiotics which would be able to continue their action even if the bacterium acquired a resistance to another antibiotic directed against one of the individual activities. CONCLUSION The bifunctional enzyme would be an excellent target for the design of new, selective antibiotics for the treatment of H. pylori associated diseases.
Collapse
Affiliation(s)
- Jordi Pérez-Gil
- Departament de Bioquimica i Biologia Molecular. Universitat de Barcelona, Avda Diagonal 645. 08028-Barcelona, Spain
| | | | | | | |
Collapse
|
34
|
Eoh H, Narayanasamy P, Brown AC, Parish T, Brennan PJ, Crick DC. Expression and characterization of soluble 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase from bacterial pathogens. ACTA ACUST UNITED AC 2010; 16:1230-9. [PMID: 20064433 DOI: 10.1016/j.chembiol.2009.10.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 10/09/2009] [Accepted: 10/21/2009] [Indexed: 11/17/2022]
Abstract
Many bacterial pathogens utilize the 2-C-methyl-D-erythritol 4-phosphate pathway for biosynthesizing isoprenoid precursors, a pathway that is vital for bacterial survival and absent from human cells, providing a potential source of drug targets. However, the characterization of 4-diphosphocytidyl-2-C-methyl-D-erythritol (CDP-ME) kinase (IspE) has been hindered due to a lack of enantiopure CDP-ME and difficulty in obtaining pure IspE. Here, enantiopure CDP-ME was chemically synthesized and recombinant IspE from bacterial pathogens were purified and characterized. Although gene disruption was not possible in Mycobacterium tuberculosis, IspE is essential in Mycobacterium smegmatis. The biochemical and kinetic characteristics of IspE provide the basis for development of a high throughput screen and structural characterization.
Collapse
Affiliation(s)
- Hyungjin Eoh
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | | | | | | | | | | |
Collapse
|
35
|
Narayanasamy P, Eoh H, Brennan PJ, Crick DC. Synthesis of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate and kinetic studies of Mycobacterium tuberculosis IspF. CHEMISTRY & BIOLOGY 2010; 17:117-22. [PMID: 20189102 PMCID: PMC2837070 DOI: 10.1016/j.chembiol.2010.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 01/22/2010] [Accepted: 01/29/2010] [Indexed: 10/19/2022]
Abstract
Many pathogenic bacteria utilize the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for the biosynthesis of isopentenyl diphosphate and dimethylallyl diphosphate, two major building blocks of isoprenoid compounds. The fifth enzyme in the MEP pathway, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) synthase (IspF), catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to ME-CPP with a corresponding release of cytidine 5-monophosphate (CMP). Because there is no ortholog of IspF in human cells, IspF is of interest as a potential drug target. However, study of IspF has been hindered by a lack of enantiopure CDP-ME2P. Herein, we report the first, to our knowledge, synthesis of enantiomerically pure CDP-ME2P from commercially available D-arabinose. Cloned, expressed, and purified M. tuberculosis IspF was able to utilize the synthetic CDP-ME2P as a substrate, a result confirmed by mass spectrometry. A convenient, sensitive, in vitro IspF assay was developed by coupling the CMP released during production of ME-CPP to mononucleotide kinase, which can be used for high throughput screening.
Collapse
Affiliation(s)
| | | | - Patrick J. Brennan
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences. Colorado State University, 1682 Campus Delivery, Fort Collins CO 80523-1682, USA
| | - Dean C. Crick
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences. Colorado State University, 1682 Campus Delivery, Fort Collins CO 80523-1682, USA
| |
Collapse
|
36
|
Seeber F, Soldati-Favre D. Metabolic Pathways in the Apicoplast of Apicomplexa. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 281:161-228. [DOI: 10.1016/s1937-6448(10)81005-6] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
37
|
Brammer LA, Meyers CF. Revealing substrate promiscuity of 1-deoxy-D-xylulose 5-phosphate synthase. Org Lett 2009; 11:4748-51. [PMID: 19778006 DOI: 10.1021/ol901961q] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A study of DXP synthase has revealed flexibility in the acceptor substrate binding pocket for nonpolar substrates and has uncovered new details of the catalytic mechanism to show that pyruvate can act as both donor and acceptor substrate.
Collapse
Affiliation(s)
- Leighanne A Brammer
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | |
Collapse
|
38
|
Obiol-Pardo C, Cordero A, Rubio-Martinez J, Imperial S. Homology modeling of Mycobacterium tuberculosis 2C-methyl-D-erythritol-4-phosphate cytidylyltransferase, the third enzyme in the MEP pathway for isoprenoid biosynthesis. J Mol Model 2009; 16:1061-73. [PMID: 19916033 DOI: 10.1007/s00894-009-0615-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 10/06/2009] [Indexed: 02/02/2023]
Abstract
Tuberculosis is one of the leading infectious diseases in humans. Discovering new treatments for this disease is urgently required, especially in view of the emergence of multiple drug resistant organisms and to reduce the total duration of current treatments. The synthesis of isoprenoids in Mycobacterium tuberculosis has been reported as an interesting pathway to target, and particular attention has been focused on the methylerythritol phosphate (MEP) pathway comprising the early steps of isoprenoid biosynthesis. In this context we have studied the enzyme 2C-methyl-D-erythritol-4-phosphate cytidylyltransferase (CMS), the third enzyme in the MEP pathway, since the lack of a resolved structure of this protein in M. tuberculosis has seriously limited its use as a drug target. We performed homology modeling of M. tuberculosis CMS in order to provide a reliable model for use in structure-based drug design. After evaluating the quality of the model, we performed a thorough study of the catalytic site and the dimerization interface of the model, which suggested the most important sites (conserved and non-conserved) that could be useful for drug discovery and mutagenesis studies. We found that the metal coordination of CDP-methylerythritol in M. tuberculosis CMS differs substantially with respect to the Escherichia coli variant, consistent with the fact that the former is able to utilize several metal ions for catalysis. Moreover, we propose that electrostatic interactions could explain the higher affinity of the MEP substrate compared with the cytosine 5'-triphosphate substrate in the M. tuberculosis enzyme as reported previously.
Collapse
Affiliation(s)
- Cristian Obiol-Pardo
- Dept. de Química Física, Universitat de Barcelona, Intitut de Recerca en Química Teòrica i Computacional (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain
| | | | | | | |
Collapse
|
39
|
Mazikin KV, Ershov YV, Goncharenko AV, Ostrovskii DN. 2-14C-methylerythritol 2,4-cyclodiphosphate incorporation into bacterial and plant isoprenoids. APPL BIOCHEM MICRO+ 2009. [DOI: 10.1134/s0003683809050081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
40
|
Sharma A, Khuller GK, Sharma S. Peptide deformylase--a promising therapeutic target for tuberculosis and antibacterial drug discovery. Expert Opin Ther Targets 2009; 13:753-65. [PMID: 19530983 DOI: 10.1517/14728220903005590] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Tuberculosis (TB) remains the most important infectious disease causing morbidity and death, due to the human pathogen Mycobacterium tuberculosis. The emergence of multi-drug-resistant and extensively-drug-resistant forms of TB have resulted in an increase in the number of TB cases. Thus, there is an urgent need to identify new drugs with novel targets to ensure future therapeutic success. Studies have indicated that peptide deformylase is an interesting potential candidate for discovering antimicrobial agents. OBJECTIVE To explore the role of peptide deformylase, a highly conserved metalloprotease and an essential enzyme in bacterial life cycle, as a target for antibacterial as well as antimycobacterial drug development. METHODS This review is based on recent published literature and online resources related to peptide deformylase inhibitors and their antibacterial potential. RESULTS/CONCLUSION Peptide deformylase is an emerging therapeutic target for the treatment of tuberculosis and peptide deformylase inhibitors can act as potential future antibacterial agents.
Collapse
Affiliation(s)
- Anshika Sharma
- University of Notre Dame, Department of Biological Sciences, Notre Dame, IN-46556, USA
| | | | | |
Collapse
|