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Adelbert Bacher - One of the best experts on this subject based on the ideXlab platform.
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8‐Substituted, syn‐Configured Adenosine Derivatives as Potential Inhibitors of the Enzyme IspE from the Non‐Mevalonate Pathway of Isoprenoid Biosynthesis
European Journal of Organic Chemistry, 2015Co-Authors: Michael Harder, Adelbert Bacher, Elisabeth Schäfer, Tobias Kümin, Boris Illarionov, Markus Fischer, François Diederich, Bruno BernetAbstract:The enzymes of the Non-Mevalonate Pathway for isoprenoid biosynthesis are attractive targets for drugs against various diseases, including malaria. We describe herein the structure-based design, synthesis, conformational analysis, and biological evaluation of several 8-brominated or 8-aminated adenosine derivatives with different substituents at C(5′), targeting the ATP-adenine binding site of the IspE protein from the Non-Mevalonate Pathway. An exhaustive conformational analysis of the adenosine derivatives both in solution and in the solid state confirmed the desired syn orientation of the adenine moiety. Despite this favorable pre-organization for binding to the cofactor pocket, biological evaluation of the inhibitors showed only a very modest inhibitory activity.
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atomic resolution structures of discrete stages on the reaction coordinate of the fe4s4 enzyme ispg gcpe
Journal of Molecular Biology, 2015Co-Authors: Felix Quitterer, Adelbert Bacher, Jörg Eppinger, A Frank, Ke Wang, Guodong Rao, Bing Odowd, Francisco Guerra, Safwat Abdelazeim, Eric OldfieldAbstract:IspG is the penultimate enzyme in Non-Mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. Its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. Using a moderate reducing agent and an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the IspG-catalyzed conversion of 2-C-methyl-d-erythritol-2,4-cyclo-diphosphate into (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate. In addition, the enzyme's structure was determined in complex with several inhibitors. These results, combined with recent electron paramagnetic resonance data, allowed us to deduce a detailed and complete IspG catalytic mechanism, which describes all stages from initial ring opening to formation of (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate via discrete radical and carbanion intermediates. The data presented in this article provide a guide for the design of selective drugs against many prokaryotic and eukaryotic pathogens to which the Non-Mevalonate Pathway is essential for survival and virulence.
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5‐Substituted (1‐Thiolan‐2‐yl)cytosines as Inhibitors of A. aeolicus and E. coli IspE Kinases: Very Different Affinities to Similar Substrate‐Binding Sites
European Journal of Organic Chemistry, 2013Co-Authors: Andri Schütz, Adelbert Bacher, Boris Illarionov, Markus Fischer, Bruno Bernet, Sebastian Locher, François DiederichAbstract:The enzymes of the Non-Mevalonate Pathway for isoprenoid biosynthesis are potential new targets for the development of selective drugs for the treatment of important infectious diseases. This Pathway is used by major human pathogens, such as Plasmodium falciparum and Mycobacterium tuberculosis, but not by humans. The fourth enzyme in the Pathway is the kinase IspE, and we report here the development and biological evaluation of new ligands for this enzyme from Escherichia coli and Aquifex aeolicus species as model systems for the pathogenic enzymes. The study focuses on analysis of the methylerythritol pocket of the 4-diphosphocytidyl-2-C-methyl-D-erythritol binding site. A series of 5-substituted 1-(thiolan-2-yl)cytosines with increasingly polar substituents were synthesized, opting for possible water-replacements in that sub-pocket as well as a high water-solubility of the ligands. In vitro studies showed IC50 values in the micromolar range against E. coli IspE, but, unexpectedly, no inhibition against A. aeolicus IspE within the measurement range of the biological tests.
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α-Substituted β-Oxa Isosteres of Fosmidomycin: Synthesis and Biological Evaluation
Journal of medicinal chemistry, 2012Co-Authors: Karin Brücher, Adelbert Bacher, Boris Illarionov, Andrea Kunfermann, Miriam Pein, Tobias Gräwert, Jana Held, Serena Tschan, Louis Maes, Benjamin MordmüllerAbstract:Specific inhibition of enzymes of the Non-Mevalonate Pathway is a promising strategy for the development of novel antiplasmodial drugs. α-Aryl-substituted β-oxa isosteres of fosmidomycin with a reverse orientation of the hydroxamic acid group were synthesized and evaluated for their inhibitory activity against recombinant 1-deoxy-d-xylulose 5-phosphate reductoisomerase (IspC) of Plasmodium falciparum and for their in vitro antiplasmodial activity against chloroquine-sensitive and resistant strains of P. falciparum. The most active derivative inhibits IspC protein of P. falciparum (PfIspC) with an IC50 value of 12 nM and shows potent in vitro antiplasmodial activity. In addition, lipophilic ester prodrugs demonstrated improved P. falciparum growth inhibition in vitro.
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Exploring the Ribose Sub-Pocket of the Substrate-Binding Site in Escherichia coli IspE: Structure-Based Design, Synthesis, and Biological Evaluation of Cytosines and Cytosine Analogues
European Journal of Organic Chemistry, 2012Co-Authors: Andri Schütz, Anna K. H. Hirsch, Adelbert Bacher, Boris Illarionov, Markus Fischer, Bruno Bernet, Sho Osawa, Jennifer Mathis, François DiederichAbstract:The enzymes of the Non-Mevalonate Pathway for the isoprenoid biosynthesis are promising targets for the development of selective drugs for the treatment of important infectious diseases. This Pathway is used by plants, many eubacteria, and apicomplexan protozoa, including major human pathogens such as Plasmodium falciparum and Mycobacterium tuberculosis, but not by humans who use the mevalonate Pathway. In this work, we report on the design, synthesis, and biological evaluation of new ligands for the E. coli enzyme IspE. The focus of the study lies in the analysis of the ribose sub-pocket of the CDP-ME binding site. Therefore, we synthesized cytosine- and 2-aminopyridine-based inhibitors with various substituents targeting this sub-pocket at the enzyme active site. As cytosines display unexpectedly low solubilities in aqueous solution, special efforts were made to increase the water solubility of some compounds while maintaining the good binding affinities measured in earlier studies. In vitro studies showed IC50 values in the low micromolar to submicromolar range against E. coli IspE.
Wolfgang Eisenreich - One of the best experts on this subject based on the ideXlab platform.
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Pseudilins: Halogenated, Allosteric Inhibitors of the Non‐Mevalonate Pathway Enzyme IspD
Angewandte Chemie (International ed. in English), 2014Co-Authors: Andrea Kunfermann, Wolfgang Eisenreich, Matthias Witschel, Boris Illarionov, René Martin, Matthias Rottmann, H. Wolfgang Höffken, Michael Seet, Hans-joachim Knölker, Markus FischerAbstract:The enzymes of the Non-Mevalonate Pathway for isoprenoid biosynthesis have been identified as attractive targets with novel modes of action for the development of herbicides for crop protection and agents against infectious diseases. This Pathway is present in many pathogenic organisms and plants, but absent in mammals. By using high-throughput screening, we identified highly halogenated marine natural products, the pseudilins, to be inhibitors of the third enzyme, IspD, in the Pathway. Their activity against the IspD enzymes from Arabidopsis thaliana and Plasmodium vivax was determined in photometric and NMR-based assays. Cocrystal structures revealed that pseudilins bind to an allosteric pocket by using both divalent metal ion coordination and halogen bonding. The allosteric mode of action for preventing cosubstrate (CTP) binding at the active site was elucidated. Pseudilins show herbicidal activity in plant assays and antiplasmodial activity in cell-based assays.
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NMR-based isotopologue profiling of microbial carotenoids.
Methods in molecular biology (Clifton N.J.), 2012Co-Authors: Eva Eylert, Adelbert Bacher, Wolfgang EisenreichAbstract:C-Isotopologue profiling is a powerful tool to determine on a quantitative basis the biosynthetic origin of carotenoids in microorganisms. To this aim, the carotenoid-producing microorganism is grown in medium containing (13)C-labeled glucose. After growth, the (13)C-isotopologue distribution in a given biosynthetic carotenoid is determined by quantitative NMR spectroscopy. The labeling pattern provides a fingerprint of processes involved in the metabolism of glucose and the formation of the carotenoid. For example, the (13)C-profile shows whether the isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate, are formed by the mevalonate or the Non-Mevalonate Pathway. The labeling data also specify the Pathways of glucose utilization, e.g., via the Entner-Doudoroff Pathway or glycolysis. The method is exemplified with the analysis of zeaxanthin biosynthesis in the Alphaproteobacterium, Paracoccus zeaxanthinifaciens.
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Biochemistry of the Non-Mevalonate isoprenoid Pathway
Cellular and Molecular Life Sciences, 2011Co-Authors: Tobias Gräwert, Felix Rohdich, Adelbert Bacher, Michael Groll, Wolfgang EisenreichAbstract:The Non-Mevalonate Pathway of isoprenoid (terpenoid) biosynthesis is essential in many eubacteria including the major human pathogen, Mycobacterium tuberculosis , in apicomplexan protozoa including the Plasmodium spp . causing malaria, and in the plastids of plants. The metabolic route is absent in humans and is therefore qualified as a promising target for new anti-infective drugs and herbicides. Biochemical and structural knowledge about all enzymes involved in the Pathway established the basis for discovery and development of inhibitors by high-throughput screening of compound libraries and/or structure-based rational design.
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Reverse fosmidomycin derivatives against the antimalarial drug target IspC (Dxr).
Journal of medicinal chemistry, 2011Co-Authors: Christoph T. Behrendt, Adelbert Bacher, Wolfgang Eisenreich, Andrea Kunfermann, Victoria Illarionova, Johannes Kaiser, An Matheeussen, Miriam Pein, Tobias Gräwert, Boris IllarionovAbstract:Reverse hydroxamate-based inhibitors of IspC, a key enzyme of the Non-Mevalonate Pathway of isoprenoid biosynthesis and a validated antimalarial target, were synthesized and biologically evaluated. The binding mode of one derivative in complex with EcIspC and a divalent metal ion was clarified by X-ray analysis. Pilot experiments have demonstrated in vivo potential.
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Biosynthesis of Isoprenoids: Crystal Structure of the [4Fe–4S] Cluster Protein IspG
Journal of molecular biology, 2010Co-Authors: Matthias Lee, Felix Rohdich, Adelbert Bacher, Wolfgang Eisenreich, Tobias Gräwert, Jörg Eppinger, Felix Quitterer, Michael GrollAbstract:Abstract IspG protein serves as the penultimate enzyme of the recently discovered Non-Mevalonate Pathway for the biosynthesis of the universal isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. The enzyme catalyzes the reductive ring opening of 2 C -methyl- d- erythritol 2,4-cyclodiphosphate, which affords 1-hydroxy-2-methyl-2-( E )-butenyl 4-diphosphate. The protein was crystallized under anaerobic conditions, and its three-dimensional structure was determined to a resolution of 2.7 A. Each subunit of the c 2 symmetric homodimer folds into two domains connected by a short linker sequence. The N-terminal domain (N domain) is an eight-stranded β barrel that belongs to the large TIM-barrel superfamily. The C-terminal domain (C domain) consists of a β sheet that is flanked on both sides by helices. One glutamate and three cysteine residues of the C domain coordinate a [4Fe–4S] cluster. Homodimer formation involves an extended contact area (about 1100 A 2 ) between helices 8 and 9 of each respective β barrel. Moreover, each C domain contacts the N domain of the partner subunit, but the interface regions are small (about 430 A 2 ). We propose that the enzyme substrate binds to the positively charged surface area at the C-terminal pole of the β barrel. The C domain carrying the iron–sulfur cluster could then move over to form a closed conformation where the substrate is sandwiched between the N domain and the C domain. This article completes the set of three-dimensional structures of the Non-Mevalonate Pathway enzymes, which are of specific interest as potential targets for tuberculostatic and antimalarial drugs.
Philip Proteau - One of the best experts on this subject based on the ideXlab platform.
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the crystal structure of e coli 1 deoxy d xylulose 5 phosphate reductoisomerase in a ternary complex with the antimalarial compound fosmidomycin and nadph reveals a tight binding closed enzyme conformation
Journal of Molecular Biology, 2005Co-Authors: Aengus Mac Sweeney, Philip Proteau, Roland Lange, Roberta P M Fernandes, Henk Schulz, Glenn E Dale, Alice Douangamath, Christian OefnerAbstract:The key enzyme in the Non-Mevalonate Pathway of isoprenoid biosynthesis, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) has been shown to be the target enzyme of fosmidomycin, an antimalarial, antibacterial and herbicidal compound. Here we report the crystal structure of selenomethionine-labelled Escherichia coli DXR in a ternary complex with NADPH and fosmidomycin at 2.2 A resolution. The structure reveals a considerable conformational rearrangement upon fosmidomycin binding and provides insights into the slow, tight binding inhibition mode of the inhibitor. Although the inhibitor displays an unusual non-metal mediated mode of inhibition, which is an artefact most likely due to the low metal affinity of DXR at the pH used for crystallization, the structural data add valuable information for the rational design of novel DXR inhibitors. Using this structure together with the published structural data and the 1.9 A crystal structure of DXR in a ternary complex with NADPH and the substrate 1-deoxy-D-xylulose 5-phosphate, a model for the physiologically relevant tight-binding mode of inhibition is proposed. The structure of the substrate complex must be interpreted with caution due to the presence of a second diastereomer in the active site.
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probing the non mevalonate Pathway to phytol in the cyanobacterium synechocystis sp utex 2470 using deuterium labeled glucose
Tetrahedron Letters, 1998Co-Authors: Philip ProteauAbstract:Abstract The biosynthesis of phytol in the cyanobacterium Synechocystis sp. UTEX 2470 was examined using 1- 2 H-D-glucose, 2- 2 H-D-glucose, 2,3,4,6,6- 2 H 5 -D-glucose, and 1,2,3,4,5,6,6- 2 H 7 -D-glucose. Analysis of deuterium NMR spectra indicated that deuterium from the glucose precursors labels C1, C4, and C5 of the IPP units of phytol, while no labeling is observed at C2 of the IPP derived units.
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biosynthesis of phytol in the cyanobacterium synechocystis sp utex 2470 utilization of the non mevalonate Pathway
Journal of Natural Products, 1998Co-Authors: Philip ProteauAbstract:The biosynthesis of phytol in the cyanobacterium Synechocystis sp. UTEX 2470 has been examined using 6,6-2H2-d-glucose, 2-13C−d-glucose, and U-13C6-d-glucose as precursors. Analysis of the isolated...
Serge Van Calenbergh - One of the best experts on this subject based on the ideXlab platform.
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Resistance of the complex to fosmidomycin and fosmidomycin derivatives
International Journal of Antimicrobial Agents, 2011Co-Authors: Anne-sophie Messiaen, Serge Van Calenbergh, Thomas Verbrugghen, Charlotte Declerck, Regina Ortmann, Martin Schlitzer, Hans Nelis, Tom CoenyeAbstract:The complex (BCC) is a group of 17 closely related opportunistic pathogens that are able to infect the respiratory tract of cystic fibrosis patients. BCC bacteria are intrinsically resistant to many antibiotics and are therefore difficult to eradicate. Fosmidomycin could be a new therapeutic agent to treat BCC infections as it inhibits 1-deoxy--xylulose-5-phosphate reductoisomerase (Dxr), a key enzyme in the Non-Mevalonate Pathway essential in BCC bacteria for isoprenoid synthesis. In this study, the antimicrobial activity of fosmidomycin and eight fosmidomycin derivatives towards 40 BCC strains was investigated. All BCC strains were resistant to fosmidomycin, although addition of glucose-6-phosphate reduced the minimum inhibitory concentrations values of FR900098, the fosmidomycin acetyl derivative, from 512mg/L to 64mg/L for and . This enhanced activity was linked to increased expression of the genes involved in glycerol-3-phosphate transport, which appears to be the only route for fosmidomycin import in BCC bacteria. Furthermore, upregulation of a fosmidomycin resistance gene () encoding an efflux pump was observed during fosmidomycin and FR900098 treatment. These results strongly suggest that the observed resistance in BCC bacteria is due to insufficient uptake accompanied by fosmidomycin and FR900098 efflux.
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Synthesis of Analogues of (E)-1-Hydroxy-2-methylbut-2-enyl 4-Diphosphate, an Isoprenoid Precursor and Human γδ T Cell Activator
The Journal of organic chemistry, 2008Co-Authors: Steven Van Hoof, Carl Jeffrey Lacey, René C. Röhrich, Jochen Wiesner, Hassan Jomaa, Serge Van CalenberghAbstract:(E)-1-Hydroxy-2-methyl-but-2-enyl 4-diphosphate (HMBPP) is an intermediate in the Non-Mevalonate Pathway for the biosynthesis of isoprenoids and also serves as a very strong activator of human gamma delta T cells expressing Vgamma9Vdelta2 receptors. This paper describes the synthesis of analogues of HMBPP, in which the diphosphate group is replaced by potential isosteric moieties, i.e., carbamate, N-acyl-N'-oxy sulfamate, or aminosulfonyl carbamate functionalities. The potential of the synthesized analogues to stimulate Vgamma9/Vdelta2 T cell response or to inhibit GcpE and LytB, the last enzymes in the Non-Mevalonate Pathway, was assessed.
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Synthesis and evaluation of α,β-unsaturated α-aryl-substituted fosmidomycin analogues as DXR inhibitors
Bioorganic & medicinal chemistry letters, 2007Co-Authors: Vincent Devreux, Jochen Wiesner, Hassan Jomaa, Johan Van Der Eycken, Serge Van CalenberghAbstract:Abstract Fosmidomycin, which acts through inhibition of 1-deoxy- d -xylulose phosphate reductoisomerase (DXR) in the Non-Mevalonate Pathway, represents a valuable recent addition to the armamentarium against uncomplicated malaria. In this paper, we describe the synthesis and biological evaluation of E- and Z-α,β-unsaturated α-aryl-substituted analogues of FR900098, a fosmidomycin congener, utilizing a Stille or a Suzuki coupling to introduce the aryl group. In contrast with our expectations based on the promising activity earlier observed for several α-substituted fosmidomycin analogues, all synthesized analogues exhibited much lower binding affinity for DXR than fosmidomycin.
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Divergent strategy for the synthesis of α-aryl-substituted fosmidomycin analogues
The Journal of organic chemistry, 2007Co-Authors: Vincent Devreux, Jochen Wiesner, Hassan Jomaa, Jef Rozenski, Johan Van Der Eycken, Serge Van CalenberghAbstract:Fosmidomycin is the first representative of a new class of antimalarial drugs acting through inhibition of 1-deoxy-D-xylulose 5-phosphate ( DOXP) reductoisomerase (DXR), an essential enzyme in the Non-Mevalonate Pathway for the synthesis of isoprenoids. This work describes a divergent strategy for the synthesis of a series of alpha-aryl-substituted fosmidomycin analogues, featuring a palladium-catalyzed Stille coupling as the key step. An alpha-(4-cyanophenyl)fosmidomycin analogue emerged as the most potent analogue in the present series. Its antimalarial activity clearly surpasses that of the reference compound fosmidomycin.
Felix Rohdich - One of the best experts on this subject based on the ideXlab platform.
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Biochemistry of the Non-Mevalonate isoprenoid Pathway
Cellular and Molecular Life Sciences, 2011Co-Authors: Tobias Gräwert, Felix Rohdich, Adelbert Bacher, Michael Groll, Wolfgang EisenreichAbstract:The Non-Mevalonate Pathway of isoprenoid (terpenoid) biosynthesis is essential in many eubacteria including the major human pathogen, Mycobacterium tuberculosis , in apicomplexan protozoa including the Plasmodium spp . causing malaria, and in the plastids of plants. The metabolic route is absent in humans and is therefore qualified as a promising target for new anti-infective drugs and herbicides. Biochemical and structural knowledge about all enzymes involved in the Pathway established the basis for discovery and development of inhibitors by high-throughput screening of compound libraries and/or structure-based rational design.
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Biosynthesis of Isoprenoids: Crystal Structure of the [4Fe–4S] Cluster Protein IspG
Journal of molecular biology, 2010Co-Authors: Matthias Lee, Felix Rohdich, Adelbert Bacher, Wolfgang Eisenreich, Tobias Gräwert, Jörg Eppinger, Felix Quitterer, Michael GrollAbstract:Abstract IspG protein serves as the penultimate enzyme of the recently discovered Non-Mevalonate Pathway for the biosynthesis of the universal isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. The enzyme catalyzes the reductive ring opening of 2 C -methyl- d- erythritol 2,4-cyclodiphosphate, which affords 1-hydroxy-2-methyl-2-( E )-butenyl 4-diphosphate. The protein was crystallized under anaerobic conditions, and its three-dimensional structure was determined to a resolution of 2.7 A. Each subunit of the c 2 symmetric homodimer folds into two domains connected by a short linker sequence. The N-terminal domain (N domain) is an eight-stranded β barrel that belongs to the large TIM-barrel superfamily. The C-terminal domain (C domain) consists of a β sheet that is flanked on both sides by helices. One glutamate and three cysteine residues of the C domain coordinate a [4Fe–4S] cluster. Homodimer formation involves an extended contact area (about 1100 A 2 ) between helices 8 and 9 of each respective β barrel. Moreover, each C domain contacts the N domain of the partner subunit, but the interface regions are small (about 430 A 2 ). We propose that the enzyme substrate binds to the positively charged surface area at the C-terminal pole of the β barrel. The C domain carrying the iron–sulfur cluster could then move over to form a closed conformation where the substrate is sandwiched between the N domain and the C domain. This article completes the set of three-dimensional structures of the Non-Mevalonate Pathway enzymes, which are of specific interest as potential targets for tuberculostatic and antimalarial drugs.
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Artemisinin biosynthesis in growing plants of Artemisia annua. A 13CO2 study.
Phytochemistry, 2009Co-Authors: Nicholas Schramek, Felix Rohdich, Adelbert Bacher, Huahong Wang, Werner Römisch-margl, Birgit Keil, Tanja Radykewicz, Bernhard Winzenhörlein, Ludger Beerhues, Jonathan GershenzonAbstract:Artemisinin from Artemisia annua has become one of the most important drugs for malaria therapy. Its biosynthesis proceeds via amorpha-4,11-diene, but it is still unknown whether the isoprenoid precursors units are obtained by the mevalonate Pathway or the more recently discovered Non-Mevalonate Pathway. In order to address that question, a plant of A. annua was grown in an atmosphere containing 700 ppm of 13CO2 for 100 min. Following a chase period of 10 days, artemisinin was isolated and analyzed by 13C NMR spectroscopy. The isotopologue pattern shows that artemisinin was predominantly biosynthesized from (E,E)-farnesyl diphosphate (FPP) whose central isoprenoid unit had been obtained via the Non-Mevalonate Pathway. The isotopologue data confirm the previously proposed mechanisms for the cyclization of (E,E)-FPP to amorphadiene and its oxidative conversion to artemisinin. They also support deprotonation of a terminal allyl cation intermediate as the final step in the enzymatic conversion of FPP to amorphadiene and show that either of the two methyl groups can undergo deprotonation.
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Structure of Active IspH Enzyme from Escherichia coli Provides Mechanistic Insights into Substrate Reduction
Angewandte Chemie (International ed. in English), 2009Co-Authors: Tobias Gräwert, Felix Rohdich, Adelbert Bacher, Wolfgang Eisenreich, Ingrid Span, Jörg Eppinger, Michael GrollAbstract:The terminal step of the Non-Mevalonate Pathway of terpene biosynthesis is catalyzed by IspH (see scheme). In the crystal structure of IspH from E. coli, a bound inorganic diphosphate ligand occupies the position of the diphosphate residue of the substrate. Together with mutation studies and theoretical calculations, these data support a mechanism which is analogous to the Birch reduction of allylic alcohols. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA
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Synthesis and Characterization of Cytidine Derivatives that Inhibit the Kinase Ispe of the Non-Mevalonate Pathway for Isoprenoid Biosynthesis.
ChemMedChem, 2008Co-Authors: Christine M. Crane, Magnus S Alphey, Felix Rohdich, Anna K. H. Hirsch, William N Hunter, Wolfgang Eisenreich, Susan Lauw, Tanja Sgraja, Victoria Illarionova, Adelbert BacherAbstract:The enzymes of the Non-Mevalonate Pathway for isoprenoid biosynthesis are attractive targets for the development of novel drugs against malaria and tuberculosis. This Pathway is used exclusively by the corresponding pathogens, but not by humans. A series of water-soluble, cytidine-based inhibitors that were originally designed for the fourth enzyme in the Pathway, IspD, were shown to inhibit the subsequent enzyme, the kinase IspE (from Escherichia coli). The binding mode of the inhibitors was verified by co-crystal structure analysis, using Aquifex aeolicus IspE. The crystal structures represent the first reported example of a co-crystal structure of IspE with a synthetic ligand and confirmed that ligand binding affinity originates mainly from the interactions of the nucleobase moiety in the cytidine binding pocket of the enzyme. In contrast, the appended benzimidazole moieties of the ligands adopt various orientations in the active site and establish only poor intermolecular contacts with the protein. Defined binding sites for sulfate ions and glycerol molecules, components in the crystallization buffer, near the well-conserved ATP-binding Gly-rich loop of IspE were observed. The crystal structures of A. aeolicus IspE nicely complement the one from E. coli IspE for use in structure-based design, namely by providing invaluable structural information for the design of inhibitors targeting IspE from Mycobacterium tuberculosis and Plasmodium falciparum. Similar to the enzymes from these pathogens, A. aeolicus IspE directs the OH group of a tyrosine residue into a pocket in the active site. In the E. coli enzyme, on the other hand, this pocket is lined by phenylalanine and has a more pronounced hydrophobic character.