1
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Harmon NM, Gehrke NR, Wiemer DF. Conjugate reduction of vinyl bisphosphonates. Tetrahedron Lett 2022; 106:154078. [PMID: 37521200 PMCID: PMC10373991 DOI: 10.1016/j.tetlet.2022.154078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vinyl bisphosphonates can be readily prepared by condensation of an aromatic aldehyde with the tetraester of a methylenebisphosphonate, and reduction of the resulting olefin is an attractive strategy for the preparation of monoalkyl geminal bisphosphonates. Conjugate reduction through use of variations on the Stryker approach has proven to be an efficient method for that reduction, even in the presence of aromatic substituents that also could be reduced. Furthermore, remote olefins in an isoprenoid chain survive this conjugate reduction unaffected, allowing access to isoprenoid-substituted triazole bisphosphonates of interest as potential inhibitors of terpenoid biosynthesis.
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Affiliation(s)
- Nyema M. Harmon
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242-1294, USA
| | - Nathaniel R. Gehrke
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242-1294, USA
| | - David F. Wiemer
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242-1294, USA
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2
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Fairweather AER, Goetz DB, Schroeder CM, Bhuiyan NH, Varney ML, Wiemer DF, Holstein SA. Impact of α-modifications on the activity of triazole bisphosphonates as geranylgeranyl diphosphate synthase inhibitors. Bioorg Med Chem 2021; 44:116307. [PMID: 34298413 DOI: 10.1016/j.bmc.2021.116307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 10/20/2022]
Abstract
Agents that inhibit the enzyme geranylgeranyl diphosphate synthase (GGDPS) have anti-cancer activity and our prior studies have investigated the structure-function relationship for a family of isoprenoid triazole bisphosphonates as GGDPS inhibitors. To further explore this structure-function relationship, a series of novel α-modified triazole phosphonates was prepared and evaluated for activity as GGDPS inhibitors in enzyme and cell-based assays. These studies revealed flexibility at the α position of the bisphosphonate derivatives with respect to being able to accommodate a variety of substituents without significantly affecting potency compared to the parent unsubstituted inhibitor. However, the monophosphonate derivatives lacked activity. These studies further our understanding of the structure-function relationship of the triazole-based GGDPS inhibitors and lay the foundation for future studies evaluating the impact of α-modifications on in vivo activity.
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Affiliation(s)
| | - Daniel B Goetz
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
| | - Chloe M Schroeder
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
| | - Nazmul H Bhuiyan
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
| | - Michelle L Varney
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David F Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA; Department of Pharmacology, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Sarah A Holstein
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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3
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Haney SL, Varney ML, Chhonker Y, Talmon G, Smith LM, Murry DJ, Holstein SA. In vivo evaluation of combination therapy targeting the isoprenoid biosynthetic pathway. Pharmacol Res 2021; 167:105528. [PMID: 33667685 DOI: 10.1016/j.phrs.2021.105528] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
Geranylgeranyl diphosphate synthase (GGDPS), an enzyme in the isoprenoid biosynthetic pathway (IBP), produces the isoprenoid (geranylgeranyl pyrophosphate, GGPP) used in protein geranylgeranylation reactions. Our prior studies utilizing triazole bisphosphonate-based GGDPS inhibitors (GGSIs) have revealed that these agents represent a novel strategy by which to induce cancer cell death, including multiple myeloma and pancreatic cancer. Statins inhibit the rate-limiting enzyme in the IBP and potentiate the effects of GGSIs in vitro. The in vivo effects of combination therapy with statins and GGSIs have not been determined. Here we evaluated the effects of combining VSW1198, a novel GGSI, with a statin (lovastatin or pravastatin) in CD-1 mice. Twice-weekly dosing with VSW1198 at the previously established maximally tolerated dose in combination with a statin led to hepatotoxicity, while once-weekly VSW1198-based combinations were feasible. No abnormalities in kidney, spleen, brain or skeletal muscle were observed with combination therapy. Combination therapy disrupted protein geranylgeranylation in vivo. Evaluation of hepatic isoprenoid levels revealed decreased GGPP levels in the single drug groups and undetectable GGPP levels in the combination groups. Additional studies with combinations using 50% dose-reductions of either VSW1198 or lovastatin revealed minimal hepatotoxicity with expected on-target effects of diminished GGPP levels and disruption of protein geranylgeranylation. Combination statin/GGSI therapy significantly slowed tumor growth in a myeloma xenograft model. Collectively, these studies are the first to demonstrate that combination IBP inhibitor therapy alters isoprenoid levels and disrupts protein geranylgeranylation in vivo as well as slows tumor growth in a myeloma xenograft model, thus providing the framework for future clinical exploration.
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Affiliation(s)
- Staci L Haney
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Michelle L Varney
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Yashpal Chhonker
- Department of Pharmacy Practice and Science, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Geoffrey Talmon
- Department of Pathology & Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Lynette M Smith
- College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Daryl J Murry
- Department of Pharmacy Practice and Science, University of Nebraska Medical Center, Omaha, NE 68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sarah A Holstein
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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4
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Goetz DB, Varney ML, Wiemer DF, Holstein SA. Amides as bioisosteres of triazole-based geranylgeranyl diphosphate synthase inhibitors. Bioorg Med Chem 2020; 28:115604. [PMID: 32690260 DOI: 10.1016/j.bmc.2020.115604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022]
Abstract
Geranylgeranyl diphosphate synthase (GGDPS) inhibitors are of potential therapeutic interest as a consequence of their activity against the bone marrow cancer multiple myeloma. A series of bisphosphonates linked to an isoprenoid tail through an amide linkage has been prepared and tested for the ability to inhibit GGDPS in enzyme and cell-based assays. The amides were designed as analogues to triazole-based GGDPS inhibitors. Several of the new compounds show GGDPS inhibitory activity in both enzyme and cell assays, with potency dependent on chain length and olefin stereochemistry.
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Affiliation(s)
- Daniel B Goetz
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
| | - Michelle L Varney
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David F Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA; Department of Pharmacology, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Sarah A Holstein
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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Orsi E, Mougiakos I, Post W, Beekwilder J, Dompè M, Eggink G, van der Oost J, Kengen SWM, Weusthuis RA. Growth-uncoupled isoprenoid synthesis in Rhodobacter sphaeroides. Biotechnol Biofuels 2020; 13:123. [PMID: 32684976 PMCID: PMC7359475 DOI: 10.1186/s13068-020-01765-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/07/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Microbial cell factories are usually engineered and employed for cultivations that combine product synthesis with growth. Such a strategy inevitably invests part of the substrate pool towards the generation of biomass and cellular maintenance. Hence, engineering strains for the formation of a specific product under non-growth conditions would allow to reach higher product yields. In this respect, isoprenoid biosynthesis represents an extensively studied example of growth-coupled synthesis with rather unexplored potential for growth-independent production. Rhodobacter sphaeroides is a model bacterium for isoprenoid biosynthesis, either via the native 2-methyl-d-erythritol 4-phosphate (MEP) pathway or the heterologous mevalonate (MVA) pathway, and for poly-β-hydroxybutyrate (PHB) biosynthesis. RESULTS This study investigates the use of this bacterium for growth-independent production of isoprenoids, with amorpha-4,11-diene as reporter molecule. For this purpose, we employed the recently developed Cas9-based genome editing tool for R. sphaeroides to rapidly construct single and double deletion mutant strains of the MEP and PHB pathways, and we subsequently transformed the strains with the amorphadiene producing plasmid. Furthermore, we employed 13C-metabolic flux ratio analysis to monitor the changes in the isoprenoid metabolic fluxes under different cultivation conditions. We demonstrated that active flux via both isoprenoid pathways while inactivating PHB synthesis maximizes growth-coupled isoprenoid synthesis. On the other hand, the strain that showed the highest growth-independent isoprenoid yield and productivity, combined the plasmid-based heterologous expression of the orthogonal MVA pathway with the inactivation of the native MEP and PHB production pathways. CONCLUSIONS Apart from proposing a microbial cell factory for growth-independent isoprenoid synthesis, this work provides novel insights about the interaction of MEP and MVA pathways under different growth conditions.
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Affiliation(s)
- Enrico Orsi
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Present Address: Systems and Synthetic Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ioannis Mougiakos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Present Address: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Wilbert Post
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | | | - Marco Dompè
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Gerrit Eggink
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Food & Biobased Research, 6708WG Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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6
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Bhuiyan NH, Varney ML, Wiemer DF, Holstein SA. Novel benzimidazole phosphonates as potential inhibitors of protein prenylation. Bioorg Med Chem Lett 2019; 29:126757. [PMID: 31699606 DOI: 10.1016/j.bmcl.2019.126757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/11/2019] [Accepted: 10/13/2019] [Indexed: 10/25/2022]
Abstract
Benzimidazole carboxyphosphonates and bisphosphonates have been prepared and evaluated for their activity as inhibitors of protein prenylation or isoprenoid biosynthesis. The nature of the phosphonate head group was found to dictate enzyme specificity. The lead carboxyphosphonate inhibits geranylgeranyl transferase II while its corresponding bisphosphonate analogue potently inhibits farnesyl diphosphate synthase. The most active inhibitors effectively disrupted protein prenylation in human multiple myeloma cells.
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Affiliation(s)
- Nazmul H Bhuiyan
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
| | - Michelle L Varney
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David F Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA; Department of Pharmacology, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Sarah A Holstein
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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7
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Orsi E, Beekwilder J, Peek S, Eggink G, Kengen SWM, Weusthuis RA. Metabolic flux ratio analysis by parallel 13C labeling of isoprenoid biosynthesis in Rhodobacter sphaeroides. Metab Eng 2020; 57:228-38. [PMID: 31843486 DOI: 10.1016/j.ymben.2019.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/02/2019] [Accepted: 12/12/2019] [Indexed: 11/21/2022]
Abstract
Metabolic engineering for increased isoprenoid production often benefits from the simultaneous expression of the two naturally available isoprenoid metabolic routes, namely the 2-methyl-D-erythritol 4-phosphate (MEP) pathway and the mevalonate (MVA) pathway. Quantification of the contribution of these pathways to the overall isoprenoid production can help to obtain a better understanding of the metabolism within a microbial cell factory. Such type of investigation can benefit from 13C metabolic flux ratio studies. Here, we designed a method based on parallel labeling experiments (PLEs), using [1-13C]- and [4-13C]glucose as tracers to quantify the metabolic flux ratios in the glycolytic and isoprenoid pathways. By just analyzing a reporter isoprenoid molecule and employing only four equations, we could describe the metabolism involved from substrate catabolism to product formation. These equations infer 13C atom incorporation into the universal isoprenoid building blocks, isopentenyl-pyrophosphate (IPP) and dimethylallyl-pyrophosphate (DMAPP). Therefore, this renders the method applicable to the study of any of isoprenoid of interest. As proof of principle, we applied it to study amorpha-4,11-diene biosynthesis in the bacterium Rhodobacter sphaeroides. We confirmed that in this species the Entner-Doudoroff pathway is the major pathway for glucose catabolism, while the Embden-Meyerhof-Parnas pathway contributes to a lesser extent. Additionally, we demonstrated that co-expression of the MEP and MVA pathways caused a mutual enhancement of their metabolic flux capacity. Surprisingly, we also observed that the isoprenoid flux ratio remains constant under exponential growth conditions, independently from the expression level of the MVA pathway. Apart from proposing and applying a tool for studying isoprenoid biosynthesis within a microbial cell factory, our work reveals important insights from the co-expression of MEP and MVA pathways, including the existence of a yet unclear interaction between them.
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8
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Bhuiyan NH, Varney ML, Bhattacharya DS, Payne WM, Mohs AM, Holstein SA, Wiemer DF. ω-Hydroxy isoprenoid bisphosphonates as linkable GGDPS inhibitors. Bioorg Med Chem Lett 2019; 29:126633. [PMID: 31474482 DOI: 10.1016/j.bmcl.2019.126633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/20/2019] [Indexed: 02/08/2023]
Abstract
The enzyme geranylgeranyl diphosphate synthase (GGDPS) is a potential therapeutic target for multiple myeloma. Malignant plasma cells produce and secrete large amounts of monoclonal protein, and inhibition of GGDPS results in disruption of protein geranylgeranylation which in turn impairs intracellular protein trafficking. Our previous work has demonstrated that some isoprenoid triazole bisphosphonates are potent and selective inhibitors of GGDPS. To explore the possibility of selective delivery of such compounds to plasma cells, new analogues with an ω-hydroxy group have been synthesized and examined for their enzymatic and cellular activity. These studies demonstrate that incorporation of the ω-hydroxy group minimally impairs GGDPS inhibitory activity. Furthermore conjugation of one of the novel ω-hydroxy GGDPS inhibitors to hyaluronic acid resulted in enhanced cellular activity. These results will allow future studies to focus on the in vivo biodistribution of HA-conjugated GGDPS inhibitors.
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Affiliation(s)
- Nazmul H Bhuiyan
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - Michelle L Varney
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Deep S Bhattacharya
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - William M Payne
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Aaron M Mohs
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, United States; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, United States; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Sarah A Holstein
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, United States; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - David F Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States; Department of Pharmacology, University of Iowa, Iowa City, IA 52242-1109, United States.
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9
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Courtens C, Risseeuw M, Caljon G, Maes L, Cos P, Martin A, Van Calenbergh S. Double prodrugs of a fosmidomycin surrogate as antimalarial and antitubercular agents. Bioorg Med Chem Lett 2019; 29:1232-1235. [PMID: 30879839 DOI: 10.1016/j.bmcl.2019.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/10/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
A series of eleven double prodrug derivatives of a fosmidomycin surrogate were synthesized and investigated for their ability to inhibit in vitro growth of P. falciparum and M. tuberculosis. A pivaloyloxymethyl (POM) phosphonate prodrug modification was combined with various prodrug derivatisations of the hydroxamate moiety. The majority of compounds showed activity comparable with or inferior to fosmidomycin against P. falciparum. N-benzyl substituted carbamate prodrug 6f was the most active antimalarial analog with an IC50 value of 0.64 µM. Contrary to fosmidomycin and parent POM-prodrug 5, 2-nitrofuran and 2-nitrothiophene prodrugs 6i and 6j displayed promising antitubercular activities.
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Affiliation(s)
- Charlotte Courtens
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Martijn Risseeuw
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Guy Caljon
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1 (S7), B-2610 Wilrijk, Belgium
| | - Louis Maes
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1 (S7), B-2610 Wilrijk, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1 (S7), B-2610 Wilrijk, Belgium
| | - Anandi Martin
- Medical Microbiology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Avenue Hippocrate 55, B-1200 Woluwe-Saint-Lambert, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium.
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Uthup TK, Rajamani A, Ravindran M, Saha T. Distinguishing CPT gene family members and vetting the sequence structure of a putative rubber synthesizing variant in Hevea brasiliensis. Gene 2019; 689:183-193. [PMID: 30528269 DOI: 10.1016/j.gene.2018.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/21/2018] [Accepted: 12/01/2018] [Indexed: 11/19/2022]
Abstract
cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. cis-PTs catalyze the cis-1,4-polymerization of isoprene units to generate isoprenoids with carbon skeletons varying from C10 (neryl pyrophosphate) to C > 10,000 (natural rubber). Though the previously reported CPTs in Hevea are designated based on sequence variations, their classification was done mostly by phylogenetic analysis using a mixture of partial as well as full length sequences often excluding the UTRs. In this context an attempt was made to reclassify the CPTs strictly based on their sequence similarity and distinguish the members putatively associated with rubber biosynthesis from the others. Extensive computational analysis was carried out on CPT sequences obtained from public resources and whole genome assemblies of Hevea. Based on the results from BLAST analysis, multiple sequence alignments of protein, nucleotide and untranslated regions, open reading frame analysis, gene prediction analysis and sequence length variations, we conclude that there exists mainly three CPTs namely RubCPT1, RubCPT2 and RubCPT3 putatively associated with rubber biosynthesis in Hevea brasiliensis. The rest were categorised as variants of dehydrodolichyl diphosphate synthase (DHDDS) involved in the synthesis of dolichols having short chain isoprenoids. Analysis of the sequence structure of the most highly expressed RubCPT1 in latex revealed the allele richness and diversity of this important variant prevailing in the popular rubber clones. Haplotypes consisting of SNPs with high degree of heterozygosity were also identified. Segregation and linkage disequilibrium analysis confirmed that recombination is the major contributor towards the generation of allelic diversity rather than point mutations. Alternatively, gene expression analysis indicated the possibility of association between specific haplotypes and RubCPT1 expression in Hevea clones which may have downstream impact up to the level of rubber production. The conclusions from this study may pave way for the identification and better understanding of CPTs directly involved with natural rubber biosynthesis in Hevea and the SNP data generated may aid in the development of molecular markers putatively associated with yield in rubber.
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Affiliation(s)
- Thomas Kadampanattu Uthup
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India.
| | - Anantharamanan Rajamani
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India
| | - Minimol Ravindran
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India
| | - Thakurdas Saha
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India
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11
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Courtens C, Risseeuw M, Caljon G, Cos P, Martin A, Van Calenbergh S. Phosphonodiamidate prodrugs of N-alkoxy analogs of a fosmidomycin surrogate as antimalarial and antitubercular agents. Bioorg Med Chem Lett 2019; 29:1051-3. [PMID: 30857749 DOI: 10.1016/j.bmcl.2019.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 11/23/2022]
Abstract
A series of N-alkoxy analogs of a l-leucine ethyl ester phosphonodiamidate prodrug of a fosmidomycin surrogate were synthesized and investigated for their ability to inhibit in vitro growth of P. falciparum and M. tuberculosis. These compounds originate by merging a previously reported successful phosphonate derivatisation with favorable modifications of the hydroxamate moiety. None of the synthesized compounds showed enhanced activity against either P. falciparum or M. tuberculosis in comparison with the parent free hydroxamate analog.
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12
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Malwal SR, Gao J, Hu X, Yang Y, Liu W, Huang JW, Ko TP, Li L, Chen CC, O’Dowd B, Khade RL, Zhang Y, Zhang Y, Oldfield E, Guo RT. Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes. ACS Catal 2018; 8:4299-4312. [PMID: 30345154 DOI: 10.1021/acscatal.8b00543] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the results of an investigation into the catalytic role of highly conserved amide (asparagine, glutamine) and OH-containing (serine, tyrosine) residues in several prenyltransferases. We first obtained the X-ray structure of cyclolavandulyl diphosphate synthase containing two molecules of the substrate analog dimethylallyl (S)-thiolodiphosphate (DMASPP). The two molecules have similar diphosphate group orientations to those seen in other ζ-fold (cis- head-to-tail and head-to-middle) prenyltransferases with one diphosphate moiety forming a bidentate chelate with Mg2+ in the so-called S1 site (which is typically the allylic binding site in ζ-fold proteins) while the second diphosphate binds to Mg2+ in the so-called S2 site (which is typically the homoallylic binding site in ζ-fold proteins) via a single P1O1 oxygen. The latter interaction can facilitate direct phosphate-mediated proton abstraction via P1O2, or more likely by an indirect mechanism in which P1O2 stabilizes a basic asparagine species that removes H+, which is then eliminated via an Asn-Ser shuttle. The universal occurrence of Asn-Ser pairs in ζ-fold proteins leads to the idea that the highly conserved amide (Asn, Gln) and OH-containing (Tyr) residues seen in many "head-to-head" prenyltransferases such as squalene and dehydrosqualene synthase might play similar roles, in H+ elimination. Structural, bioinformatics and mutagenesis investigations indeed indicate an important role of these residues in catalysis, with the results of density functional theory calculations showing that Asn bound to Mg2+ can act as a general (imine-like) base, while Gln, Tyr and H2O form a proton channel that is adjacent to the conventional (Asp-rich) "active site". Taken together, our results lead to mechanisms of proton-elimination from carbocations in numerous prenyltransferases in which neutral species (Asn, Gln, Ser, Tyr, H2O) act as proton shuttles, complementing the more familiar roles of acidic groups (in Asp and Glu) that bind to Mg2+, and basic groups (primarily Arg) that bind to diphosphates, in isoprenoid biosynthesis.
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Affiliation(s)
- Satish R. Malwal
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Jian Gao
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiangying Hu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yunyun Yang
- School of Pharmaceutical Sciences and MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jian-Wen Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Liping Li
- School of Pharmaceutical Sciences and MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Chun-Chi Chen
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bing O’Dowd
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Rahul L. Khade
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Yonghui Zhang
- School of Pharmaceutical Sciences and MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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13
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Matthiesen RA, Varney ML, Xu PC, Rier AS, Wiemer DF, Holstein SA. α-Methylation enhances the potency of isoprenoid triazole bisphosphonates as geranylgeranyl diphosphate synthase inhibitors. Bioorg Med Chem 2018; 26:376-385. [PMID: 29248353 PMCID: PMC5752576 DOI: 10.1016/j.bmc.2017.10.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/12/2017] [Accepted: 10/18/2017] [Indexed: 12/19/2022]
Abstract
Disruption of protein geranylgeranylation via inhibition of geranylgeranyl diphosphate synthase (GGDPS) represents a novel therapeutic strategy for a variety of malignancies, especially those characterized by excessive protein secretion such as multiple myeloma. Our work has demonstrated that some isoprenoid triazole bisphosphonates are potent and selective inhibitors of GGDPS. Here we present the synthesis and biological evaluation of a new series of isoprenoid triazoles modified by incorporation of a methyl group at the α-carbon. These studies reveal that incorporation of an α-methyl substituent enhances the potency of these compounds as GGDPS inhibitors, and, in the case of the homogeranyl/homoneryl series, abrogates the effects of olefin stereochemistry on inhibitory activity. The incorporation of the methyl group allowed preparation of a POM-prodrug, which displayed a 10-fold increase in cellular activity compared to the corresponding salt. These studies form the basis for future preclinical studies investigating the anti-myeloma activity of these novel α-methyl triazole bisphosphonates.
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Affiliation(s)
- Robert A Matthiesen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - Michelle L Varney
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Pauline C Xu
- College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Alex S Rier
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - David F Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States; Department of Pharmacology, University of Iowa, Iowa City, IA 52242-1109, United States
| | - Sarah A Holstein
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, United States.
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14
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Huang R, Wang Y, Wang P, Li C, Xiao F, Chen N, Li N, Li C, Sun C, Li L, Chen R, Xu Z, Zhu J, Deng X. A single nucleotide mutation of IspF gene involved in the MEP pathway for isoprenoid biosynthesis causes yellow-green leaf phenotype in rice. Plant Mol Biol 2018; 96:5-16. [PMID: 29143298 DOI: 10.1007/s11103-017-0668-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 10/09/2017] [Indexed: 05/20/2023]
Abstract
We identified IspF gene through yellow-green leaf mutant 505ys in rice. OsIspF was expressed in all tissues detected, and its encoded protein was targeted to the chloroplast. On expression levels of genes in this mutant, OsIspF itself and the genes encoding other enzymes of the MEP pathway and chlorophyll synthase were all up-regulated, however, among eight genes associated with photosynthesis, only psaA, psaN and psbA genes for three reaction center subunits of photosystem obviously changed. Isoprenoids are the most abundant natural compounds in all organisms, which originate from the basic five-carbon units isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In plants, IPP and DMAPP are synthesized through two independent pathways, the mevalonic acid pathway in cytoplasm and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway in plastids. The MEP pathway comprises seven enzymatic steps, in which IspF is the fifth enzyme. So far, no IspF gene has been identified in monocotyledonous plants. In this study, we isolated a leaf-color mutant, 505ys, in rice (Oryza sativa). The mutant displayed yellow-green leaf phenotype, reduced level of photosynthetic pigments, and arrested development of chloroplasts. By map-based cloning of this mutant, we identified OsIspF gene (LOC_Os02g45660) showing significant similarity to IspF gene of Arabidopsis, in which a missense mutation occurred in the mutant, resulting in an amino acid change in the encoded protein. OsIspF gene was expressed in all tissues detected, and its encoded protein was targeted to the chloroplast. Further, the mutant phenotype of 505ys was complemented by transformation with the wild-type OsIspF gene. Therefore, we successfully identified an IspF gene in monocotyledonous plants. In addition, real-time quantitative RT-PCR implied that a positive regulation could exist between the OsIspF gene and the genes encoding other enzymes of the MEP pathway and chlorophyll synthase. At the same time, it also implied that the individual genes involved in the MEP pathway might differentially regulated expression levels of the genes associated with photosynthesis.
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Affiliation(s)
- Rui Huang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yang Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Pingrong Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Chunmei Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Fuliang Xiao
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Nenggang Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Na Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Caixia Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Changhui Sun
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lihua Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Rongjun Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhengjun Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jianqing Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaojian Deng
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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15
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Wills VS, Metzger JI, Allen C, Varney ML, Wiemer DF, Holstein SA. Bishomoisoprenoid triazole bisphosphonates as inhibitors of geranylgeranyl diphosphate synthase. Bioorg Med Chem 2017; 25:2437-2444. [PMID: 28302510 PMCID: PMC5450914 DOI: 10.1016/j.bmc.2017.02.066] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 11/23/2022]
Abstract
Protein geranylgeranylation reactions are dependent on the availability of geranylgeranyl diphosphate (GGDP), which serves as the isoprenoid donor. Inhibition of GGDP synthase (GGDPS) is of interest from a drug development perspective as GGDPS inhibition results in impaired protein geranylgeranylation, which in multiple myeloma, disrupts monoclonal protein trafficking and induces apoptosis. We have recently reported a series of isoprenoid triazole bisphosphonates and have demonstrated that a 3:1 mixture of homogeranyl and homoneryl isomers potently, and in a synergistic manner, inhibits GGDPS. We now present the synthesis and biological evaluation of a novel series of bishomoisoprenoid triazoles which furthers our understanding of the structure-function relationship of this class. These studies demonstrate the importance of chain length and olefin stereochemistry on inhibitory activity.
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Affiliation(s)
- Veronica S Wills
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
| | - Joseph I Metzger
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
| | - Cheryl Allen
- Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Michelle L Varney
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David F Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA; Department of Pharmacology, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Sarah A Holstein
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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16
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Foust BJ, Allen C, Holstein SA, Wiemer DF. A new motif for inhibitors of geranylgeranyl diphosphate synthase. Bioorg Med Chem 2016; 24:3734-41. [PMID: 27338660 DOI: 10.1016/j.bmc.2016.06.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 06/07/2016] [Accepted: 06/09/2016] [Indexed: 11/23/2022]
Abstract
The enzyme geranylgeranyl diphosphate synthase (GGDPS) is believed to receive the substrate farnesyl diphosphate through one lipophilic channel and release the product geranylgeranyl diphosphate through another. Bisphosphonates with two isoprenoid chains positioned on the α-carbon have proven to be effective inhibitors of this enzyme. Now a new motif has been prepared with one isoprenoid chain on the α-carbon, a second included as a phosphonate ester, and the potential for a third at the α-carbon. The pivaloyloxymethyl prodrugs of several compounds based on this motif have been prepared and the resulting compounds have been tested for their ability to disrupt protein geranylgeranylation and induce cytotoxicity in myeloma cells. The initial biological studies reveal activity consistent with GGDPS inhibition, and demonstrate a structure-function relationship which is dependent on the nature of the alkyl group at the α-carbon.
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17
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Berthelot K, Estevez Y, Quiliano M, Baldera-Aguayo PA, Zimic M, Pribat A, Bakleh ME, Teyssier E, Gallusci P, Gardrat C, Lecomte S, Peruch F. HbIDI, SlIDI and EcIDI: A comparative study of isopentenyl diphosphate isomerase activity and structure. Biochimie 2016; 127:133-43. [PMID: 27163845 DOI: 10.1016/j.biochi.2016.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
In this study, we cloned, expressed and purified the isopentenyl diphosphate isomerases (IDIs) from two plants, Hevea brasiliensis and Solanum lycopersicum, and compared them to the already well characterized Escherichia coli IDI. Phylogenetic analysis showed high homology between the three enzymes. Their catalytic activity was investigated in vitro with recombinant purified enzymes and in vivo by complementation colorimetric tests. The three enzymes displayed consistent activities both in vitro and in vivo. In term of structure, studied by ATR-FTIR and molecular modeling, it is clear that both plant enzymes are more related to their human homologue than to E. coli IDI. But it is assumed that EcIDI represent the minimalistic part of the catalytic core, as both plant enzymes present a supplementary sequence forming an extra α-helice surrounding the catalytic site that could facilitate the biocatalysis. New potential biotechnological applications may be envisaged.
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Affiliation(s)
- Karine Berthelot
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France; CNRS, CBMN, UMR 5248, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France.
| | - Yannick Estevez
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Miguel Quiliano
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia y Nutrición, Universidad de Navarra, C/. Irunlarrea 1, 31008, Pamplona, Navarra, Spain
| | - Pedro A Baldera-Aguayo
- Department of Systems Biology and Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University in the City of New York, NY, 10032, USA; Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, 31, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, 31, Peru
| | - Anne Pribat
- INRA Bordeaux-Aquitaine, UMR 1332 Biologie du Fruit et Pathologie, F-33882, Villenave d'Ornon, France
| | - Marc-Elias Bakleh
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Emeline Teyssier
- Univ. Bordeaux, Grape Ecophysiology and Functional Biology Laboratory, ISVV, F-33882, Villenave d'Ornon, France
| | - Philippe Gallusci
- Univ. Bordeaux, Grape Ecophysiology and Functional Biology Laboratory, ISVV, F-33882, Villenave d'Ornon, France
| | - Christian Gardrat
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Sophie Lecomte
- CNRS, CBMN, UMR 5248, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France
| | - Frédéric Peruch
- CNRS, LCPO, UMR 5629, Univ. Bordeaux, Bordeaux INP, F-33600, Pessac, France.
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18
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Huchelmann A, Brahim MS, Gerber E, Tritsch D, Bach TJ, Hemmerlin A. Farnesol-mediated shift in the metabolic origin of prenyl groups used for protein prenylation in plants. Biochimie 2016; 127:95-102. [PMID: 27138105 DOI: 10.1016/j.biochi.2016.04.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
Little is known about how plant cells regulate the exchange of prenyl diphosphates between the two compartmentalized isoprenoid biosynthesis pathways. Prenylation of proteins is a suitable model to study such interactions between the plastidial methylerythritol phosphate (MEP) and the cytosolic mevalonate (MVA) pathways because prenyl moieties used to modify proteins rely on both origins. Tobacco cells expressing a prenylatable GFP were treated with specific MEP and/or MVA pathways inhibitors to block the formation of prenyl diphosphates and therefore the possibility to modify the proteins. Chemical complementation assays using prenyl alcohol precursors restore the prenylation. Indeed, geranylgeraniol (C20 prenyl alcohol) and to a lesser but significant level C15-farnesol restored the prenylation of a protein bearing a geranylgeranylation CaaX motif, which under standard conditions is modified by a MEP-derived prenyl group. However, the restoration takes place in different ways. While geranylgeraniol operates directly as a metabolic precursor, the C15-prenyl alcohol functions indirectly as a signal that leads to shift the metabolic origin of prenyl groups in modified proteins, here from the plastidial MEP pathway in favor of the cytosolic MVA pathway. Furthermore, farnesol interferes negatively with the MEP pathway in an engineered Escherichia coli strain synthesizing isoprenoids either starting from MVA or from MEP. Following the cellular uptake of a fluorescent analog of farnesol, we showed its close interaction with tobacco plastids and modification of plastid homeostasis. As a consequence, in tobacco farnesol supposedly inhibits the plastidial MEP pathway and activates the cytosolic MVA pathway, leading to the shift in the metabolic origin and thereby acts as a potential regulator of crosstalk between the two pathways. Together, those results suggest a new role for farnesol (or a metabolite thereof) as a central molecule for the regulation of isoprenoid biosynthesis in plants.
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Affiliation(s)
- Alexandre Huchelmann
- CNRS, Institut de biologie moléculaire des plantes conventionné avec l'Unistra, F-67084 Strasbourg, France
| | - Mathieu Semir Brahim
- CNRS, Institut de biologie moléculaire des plantes conventionné avec l'Unistra, F-67084 Strasbourg, France
| | - Esther Gerber
- CNRS, Institut de biologie moléculaire des plantes conventionné avec l'Unistra, F-67084 Strasbourg, France
| | - Denis Tritsch
- CNRS/Unistra, Institut Le Bel, 4 rue Blaise Pascal, F-67081 Strasbourg, France
| | - Thomas J Bach
- CNRS, Institut de biologie moléculaire des plantes conventionné avec l'Unistra, F-67084 Strasbourg, France
| | - Andréa Hemmerlin
- CNRS, Institut de biologie moléculaire des plantes conventionné avec l'Unistra, F-67084 Strasbourg, France.
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19
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Skaff DA, McWhorter WJ, Geisbrecht BV, Wyckoff GJ, Miziorko HM. Inhibition of bacterial mevalonate diphosphate decarboxylase by eriochrome compounds. Arch Biochem Biophys 2015; 566:1-6. [PMID: 25499551 PMCID: PMC4456016 DOI: 10.1016/j.abb.2014.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 11/20/2022]
Abstract
Mevalonate diphosphate decarboxylase (MDD; EC 4.1.1.33) catalyzes the irreversible decarboxylation of mevalonate diphosphate in the mevalonate pathway to form isopentenyl diphosphate, which is a precursor in the biosynthesis of many essential polyisoprenoid natural products, including sterols. In low G/C Gram-positive bacteria, which utilize the mevalonate pathway, MDD is required for cell viability and thus is a potential target for development of antibiotic drugs. To identify potential inhibitors of the enzyme, the National Cancer Institute's Mechanistic Diversity Set library of compounds was screened for inhibitors of Staphylococcus epidermidis MDD. From this screen, the compound Eriochrome Black A (EBA), an azo dye, was found to inhibit the enzyme with an IC50 value<5μM. Molecular docking of EBA into a crystal structure of S. epidermidis MDD suggested binding at the active site. EBA, along with the related Eriochrome B and T compounds, was evaluated for its ability to not only inhibit enzymatic activity but to inhibit bacterial growth as well. These compounds exhibited competitive inhibition towards the substrate mevalonate diphosphate, with Ki values ranging from 0.6 to 2.7μM. Non-competitive inhibition was observed versus ATP indicating binding of the inhibitor in the mevalonate diphosphate binding site, consistent with molecular docking predictions. Fluorescence quenching analyses also supported active site binding of EBA. These eriochrome compounds are effective at inhibiting S. epidermidis cell growth on both solid media and in liquid culture (MIC50 from 31 to 350μM) raising the possibility that they could be developed into antibiotic leads targeting pathogenic low-G/C Gram-positive cocci.
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Affiliation(s)
- D Andrew Skaff
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, United States
| | - William J McWhorter
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, MO 64110, United States
| | - Brian V Geisbrecht
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, MO 64110, United States
| | - Gerald J Wyckoff
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, United States
| | - Henry M Miziorko
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, United States.
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20
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Abstract
While recent advances in metabolomic measurement technologies have been dramatic, extracting biological insight from complex metabolite profiles remains a challenge. We present an analytical strategy that uses data obtained from high resolution liquid chromatography-mass spectrometry and a bioinformatics toolset for detecting actively changing metabolic pathways upon external perturbation. We begin with untargeted metabolite profiling to nominate altered metabolites and identify pathway candidates, followed by validation of those pathways with transcriptomics. Using the model organisms Rhodospirillum rubrum and Bacillus subtilis, our results reveal metabolic pathways that are interconnected with methionine salvage. The rubrum-type methionine salvage pathway is interconnected with the active methyl cycle in which re-methylation, a key reaction for recycling methionine from homocysteine, is unexpectedly suppressed; instead, homocysteine is catabolized by the transsulfuration pathway. Notably, the non-mevalonate pathway is repressed, whereas the rubrum-type methionine salvage pathway contributes to isoprenoid biosynthesis upon 5'-methylthioadenosine feeding. In this process, glutathione functions as a coenzyme in vivo when 1-methylthio-d-xylulose 5-phosphate (MTXu 5-P) methylsulfurylase catalyzes dethiomethylation of MTXu 5-P. These results clearly show that our analytical approach enables unexpected metabolic pathways to be uncovered.
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Affiliation(s)
- Kyuil Cho
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
| | - Bradley S. Evans
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
| | - B. McKay Wood
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Ritesh Kumar
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Tobias J. Erb
- Institute for Microbiology, Swiss Federal Institute of Technology (ETH) Zurich, CH-8093 Zurich, Switzerland
| | - Benjamin P. Warlick
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - John A. Gerlt
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jonathan V. Sweedler
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
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21
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Zhou X, Ferree SD, Wills VS, Born EJ, Tong H, Wiemer DF, Holstein SA. Geranyl and neryl triazole bisphosphonates as inhibitors of geranylgeranyl diphosphate synthase. Bioorg Med Chem 2014; 22:2791-8. [PMID: 24726306 DOI: 10.1016/j.bmc.2014.03.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 02/26/2014] [Accepted: 03/08/2014] [Indexed: 10/25/2022]
Abstract
When inhibitors of enzymes that utilize isoprenoid pyrophosphates are based on the natural substrates, a significant challenge can be to achieve selective inhibition of a specific enzyme. One element in the design process is the stereochemistry of the isoprenoid olefins. We recently reported preparation of a series of isoprenoid triazoles as potential inhibitors of geranylgeranyl transferase II but these compounds were obtained as a mixture of olefin isomers. We now have accomplished the stereoselective synthesis of these triazoles through the use of epoxy azides for the cycloaddition reaction followed by regeneration of the desired olefin. Both geranyl and neryl derivatives have been prepared as single olefin isomers through parallel reaction sequences. The products were assayed against multiple enzymes as well as in cell culture studies and surprisingly a Z-olefin isomer was found to be a potent and selective inhibitor of geranylgeranyl diphosphate synthase.
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Affiliation(s)
- Xiang Zhou
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Sarah D Ferree
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Veronica S Wills
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Ella J Born
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Huaxiang Tong
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - David F Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA; Department of Pharmacology, University of Iowa, Iowa City, IA 52242, USA.
| | - Sarah A Holstein
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Pharmacology, University of Iowa, Iowa City, IA 52242, USA
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22
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Schwarz BH, Driver J, Peacock RB, Dembinski HE, Corson MH, Gordon SS, Watson JM. Kinetic characterization of an oxidative, cooperative HMG-CoA reductase from Burkholderia cenocepacia. Biochim Biophys Acta 2013; 1844:457-64. [PMID: 24316250 DOI: 10.1016/j.bbapap.2013.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 11/22/2013] [Accepted: 11/25/2013] [Indexed: 01/28/2023]
Abstract
3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is a key enzyme in endogenous cholesterol biosynthesis in mammals and isoprenoid biosynthesis via the mevalonate pathway in other eukaryotes, archaea and some eubacteria. In most organisms that express this enzyme, it catalyzes the NAD(P)H-dependent reduction of HMG-CoA to mevalonate. We have cloned and characterized the 6x-His-tagged HMGR from the opportunistic lung pathogen Burkholderia cenocepacia. Kinetic characterization shows that the enzyme prefers NAD(H) over NADP(H) as a cofactor, suggesting an oxidative physiological role for the enzyme. This hypothesis is supported by the fact that the Burkholderia cenocepacia genome lacks the genes for the downstream enzymes of the mevalonate pathway. The enzyme exhibits positive cooperativity toward the substrates of the reductive reaction, but the oxidative reaction exhibits unusual double-saturation kinetics, distinctive among characterized HMG-CoA reductases. The unusual kinetics may arise from the presence of multiple active oligomeric states, each with different Vmax values.
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Affiliation(s)
- Benjamin H Schwarz
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA, USA, 99258
| | - Joseph Driver
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA, USA, 99258
| | - Riley B Peacock
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA, USA, 99258
| | - Holly E Dembinski
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA, USA, 99258
| | - Melissa H Corson
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA, USA, 99258
| | - Samuel S Gordon
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA, USA, 99258
| | - Jeffrey M Watson
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA, USA, 99258.
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Uthup TK, Saha T, Ravindran M, Bini K. Impact of an intragenic retrotransposon on the structural integrity and evolution of a major isoprenoid biosynthesis pathway gene in Hevea brasiliensis. Plant Physiol Biochem 2013; 73:176-88. [PMID: 24128694 DOI: 10.1016/j.plaphy.2013.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/10/2013] [Indexed: 05/01/2023]
Abstract
Isoprenoids belong to a large family of structurally and functionally different natural compounds found universally from prokaryotes to higher animals and plants. In Hevea brasiliensis, the commercially important cis-polyisoprene (rubber) is synthesised as part of its defence mechanism in addition to other common isoprenoids like phytosterols, growth hormones etc. Farnesyl diphosphate synthase (FDPS) is a key enzyme in this process which catalyses the conversion of isoprene units into polyisoprene. Although prior sequence information is available, the structural variants of the FDPS gene presently existing in Hevea population are largely unknown. Since gene structure has a major role in gene regulation, extensive sequence analysis of this gene from different genotypes was carried out to identify the prevailing structural variants. We identified several SNPs and large indels which were associated with a partial transposable element (TE). Modification of key regulatory motifs and splice sites induced by the retroelement was also identified in the first intron. Screening of popular rubber clones, wild germplasm accessions and Hevea species revealed that the retroelement is responsible for the generation of new alleles with varying degrees of sequence homology. Segregation analysis of a progeny population confirmed that the alleles are not paralogs and are inherited in a Mendelian mode. Our findings suggest that the first intron of the FDPS gene has been subjected to various chromosomal rearrangements due to the interaction of a retrotransposon, resulting in novel alleles which may substantially contribute towards the evolution of this major gene in rubber. Moreover, the results indicate the possible existence of a retrotransposon-mediated epigenetic gene regulatory mechanism in Hevea.
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Affiliation(s)
- Thomas Kadampanattu Uthup
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board, P O, Kottayam, Kerala Pin-686009, India.
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24
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Rekittke I, Olkhova E, Wiesner J, Demmer U, Warkentin E, Jomaa H, Ermler U. Structure of the (E)-4-hydroxy-3-methyl-but-2-enyl-diphosphate reductase from Plasmodium falciparum. FEBS Lett 2013; 587:3968-72. [PMID: 24188825 DOI: 10.1016/j.febslet.2013.10.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/15/2013] [Accepted: 10/20/2013] [Indexed: 11/28/2022]
Abstract
Terpenoid precursor biosynthesis occurs in human and many pathogenic organisms via the mevalonate and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways, respectively. We determined the X-ray structure of the Fe/S containing (E)-4-hydroxy-3-methyl-but-2-enyl-diphosphate reductase (LytB) of the pathogenic protozoa Plasmodium falciparum which catalyzes the terminal step of the MEP pathway. The cloverleaf fold and the active site of P. falciparum LytB corresponds to those of the Aquifex aeolicus and Escherichia coli enzymes. Its distinct electron donor [2Fe-2S] ferredoxin was modeled to its binding site by docking calculations. The presented structural data provide a platform for a rational search of anti-malarian drugs.
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Affiliation(s)
- Ingo Rekittke
- Medizinische Klinik IV (Hämatologie), Justus-Liebig-Universität Giessen, Klinikstrasse 33, D-35392 Giessen, Germany
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25
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Odom AR, Van Voorhis WC. Functional genetic analysis of the Plasmodium falciparum deoxyxylulose 5-phosphate reductoisomerase gene. Mol Biochem Parasitol 2009; 170:108-11. [PMID: 20018214 DOI: 10.1016/j.molbiopara.2009.12.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 11/30/2009] [Accepted: 12/05/2009] [Indexed: 10/20/2022]
Abstract
Novel antimalarial drugs are urgently needed to treat severe malaria caused by Plasmodium falciparum. Isoprenoid biosynthesis is a promising target pathway, since the biosynthetic route in Plasmodia is biochemically distinct from the mevalonate pathway in humans. The small molecule fosmidomycin is an inhibitor of the enzyme responsible for the first dedicated step in isoprenoid biosynthesis, deoxyxylulose 5-phosphate reductoisomerase (DXR). However, the antimalarial effects of fosmidomycin might not be specific to DXR inhibition and further validation of DXR is warranted. We present the first functional genetic validation of P. falciparum DXR (PF14_0641). Using a single cross-over strategy, we show that plasmid integration occurs at the DXR locus but only when DXR gene function is preserved, but not when integration disrupts gene function. These data indicate that DXR is required for intraerythrocytic development of P. falciparum.
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Affiliation(s)
- Audrey R Odom
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8208, St. Louis, MO 63110, USA.
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