1
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Chan AHY, Ho TCS, Fathoni I, Hamid R, Hirsch AKH, Saliba KJ, Leeper FJ. Evaluation of ketoclomazone and its analogues as inhibitors of 1-deoxy-d-xylulose 5-phosphate synthases and other thiamine diphosphate (ThDP)-dependent enzymes. RSC Med Chem 2024; 15:1773-1781. [PMID: 38784473 PMCID: PMC11110791 DOI: 10.1039/d4md00083h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/27/2024] [Indexed: 05/25/2024] Open
Abstract
Most pathogenic bacteria, apicomplexan parasites and plants rely on the methylerythritol phosphate (MEP) pathway to obtain precursors of isoprenoids. 1-Deoxy-d-xylulose 5-phosphate synthase (DXPS), a thiamine diphosphate (ThDP)-dependent enzyme, catalyses the first and rate-limiting step of the MEP pathway. Due to its absence in humans, DXPS is considered as an attractive target for the development of anti-infectious agents and herbicides. Ketoclomazone is one of the earliest reported inhibitors of DXPS and antibacterial and herbicidal activities have been documented. This study investigated the activity of ketoclomazone on DXPS from various species, as well as the broader ThDP-dependent enzyme family. To gain further insights into the inhibition, we have prepared analogues of ketoclomazone and evaluated their activity in biochemical and computational studies. Our findings support the potential of ketoclomazone as a selective antibacterial agent.
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Affiliation(s)
- Alex H Y Chan
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Terence C S Ho
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Imam Fathoni
- Research School of Biology, The Australian National University Canberra ACT 2601 Australia
| | - Rawia Hamid
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Kevin J Saliba
- Research School of Biology, The Australian National University Canberra ACT 2601 Australia
| | - Finian J Leeper
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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2
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Coco L, Toci EM, Chen PYT, Drennan CL, Freel Meyers CL. Potent Inhibition of E. coli DXP Synthase by a gem-Diaryl Bisubstrate Analog. ACS Infect Dis 2024; 10:1312-1326. [PMID: 38513073 PMCID: PMC11019550 DOI: 10.1021/acsinfecdis.3c00734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
New antimicrobial strategies are needed to address pathogen resistance to currently used antibiotics. Bacterial central metabolism is a promising target space for the development of agents that selectively target bacterial pathogens. 1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) converts pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) to DXP, which is required for synthesis of essential vitamins and isoprenoids in bacterial pathogens. Thus, DXPS is a promising antimicrobial target. Toward this goal, our lab has demonstrated selective inhibition of Escherichia coli DXPS by alkyl acetylphosphonate (alkylAP)-based bisubstrate analogs that exploit the requirement for ternary complex formation in the DXPS mechanism. Here, we present the first DXPS structure with a bisubstrate analog bound in the active site. Insights gained from this cocrystal structure guided structure-activity relationship studies of the bisubstrate scaffold. A low nanomolar inhibitor (compound 8) bearing a gem-dibenzyl glycine moiety conjugated to the acetylphosphonate pyruvate mimic via a triazole-based linker emerged from this study. Compound 8 was found to exhibit slow, tight-binding inhibition, with contacts to E. coli DXPS residues R99 and R478 demonstrated to be important for this behavior. This work has discovered the most potent DXPS inhibitor to date and highlights a new role of R99 that can be exploited in future inhibitor designs toward the development of a novel class of antimicrobial agents.
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Affiliation(s)
- Lauren
B. Coco
- Department
of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Eucolona M. Toci
- Department
of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Percival Yang-Ting Chen
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- Howard
Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Caren L. Freel Meyers
- Department
of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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3
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Toci EM, Austin SL, Majumdar A, Woodcock HL, Freel Meyers CL. Disruption of an Active Site Network Leads to Activation of C2α-Lactylthiamin Diphosphate on the Antibacterial Target 1-Deoxy-d-xylulose-5-phosphate Synthase. Biochemistry 2024; 63:671-687. [PMID: 38393327 PMCID: PMC11015862 DOI: 10.1021/acs.biochem.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The bacterial metabolic enzyme 1-deoxy-d-xylulose-5-phosphate synthase (DXPS) catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde-3-phosphate (d-GAP). DXP is an essential bacteria-specific metabolite that feeds into the biosynthesis of isoprenoids, pyridoxal phosphate (PLP), and ThDP. DXPS catalyzes the activation of pyruvate to give the C2α-lactylThDP (LThDP) adduct that is long-lived on DXPS in a closed state in the absence of the cosubstrate. Binding of d-GAP shifts the DXPS-LThDP complex to an open state which coincides with LThDP decarboxylation. This gated mechanism distinguishes DXPS in ThDP enzymology. How LThDP persists on DXPS in the absence of cosubstrate, while other pyruvate decarboxylases readily activate LThDP for decarboxylation, is a long-standing question in the field. We propose that an active site network functions to prevent LThDP activation on DXPS until the cosubstrate binds. Binding of d-GAP coincides with a conformational shift and disrupts the network causing changes in the active site that promote LThDP activation. Here, we show that the substitution of putative network residues, as well as nearby residues believed to contribute to network charge distribution, predictably affects LThDP reactivity. Substitutions predicted to disrupt the network have the effect to activate LThDP for decarboxylation, resulting in CO2 and acetate production. In contrast, a substitution predicted to strengthen the network fails to activate LThDP and has the effect to shift DXPS toward the closed state. Network-disrupting substitutions near the carboxylate of LThDP also have a pronounced effect to shift DXPS to an open state. These results offer initial insights to explain the long-lived LThDP intermediate and its activation through disruption of an active site network, which is unique to DXPS. These findings have important implications for DXPS function in bacteria and its development as an antibacterial target.
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Affiliation(s)
- Eucolona M Toci
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Steven L Austin
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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4
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Johnston ML, Bonett EM, DeColli AA, Freel Meyers CL. Antibacterial Target DXP Synthase Catalyzes the Cleavage of d-Xylulose 5-Phosphate: a Study of Ketose Phosphate Binding and Ketol Transfer Reaction. Biochemistry 2022; 61:1810-1823. [PMID: 35998648 PMCID: PMC9531112 DOI: 10.1021/acs.biochem.2c00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) in a thiamin diphosphate (ThDP)-dependent manner. In addition to its role in isoprenoid biosynthesis, DXP is required for ThDP and pyridoxal phosphate biosynthesis. Due to its function as a branch-point enzyme and its demonstrated substrate and catalytic promiscuity, we hypothesize that DXPS could be key for bacterial adaptation in the dynamic metabolic landscape during infection. Prior work in the Freel Meyers laboratory has illustrated that DXPS displays relaxed specificity toward donor and acceptor substrates and varies acceptor specificity according to the donor used. We have reported that DXPS forms dihydroxyethyl (DHE)ThDP from ketoacid or aldehyde donor substrates via decarboxylation and deprotonation, respectively. Here, we tested other DHE donors and found that DXPS cleaves d-xylulose 5-phosphate (X5P) at C2-C3, producing DHEThDP through a third mechanism involving d-GAP elimination. We interrogated DXPS-catalyzed reactions using X5P as a donor substrate and illustrated (1) production of a semi-stable enzyme-bound intermediate and (2) O2, H+, and d-erythrose 4-phosphate act as acceptor substrates, highlighting a new transketolase-like activity of DXPS. Furthermore, we examined X5P binding to DXPS and suggest that the d-GAP binding pocket plays a crucial role in X5P binding and turnover. Overall, this study reveals a ketose-cleavage reaction catalyzed by DXPS, highlighting the remarkable flexibility for donor substrate usage by DXPS compared to other C-C bond-forming enzymes.
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Affiliation(s)
- Melanie L. Johnston
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eucolona M. Bonett
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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5
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Gierse RM, Oerlemans R, Reddem ER, Gawriljuk VO, Alhayek A, Baitinger D, Jakobi H, Laber B, Lange G, Hirsch AKH, Groves MR. First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization. Sci Rep 2022; 12:7221. [PMID: 35508530 PMCID: PMC9068908 DOI: 10.1038/s41598-022-11205-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/15/2022] [Indexed: 11/18/2022] Open
Abstract
The development of drug resistance by Mycobacterium tuberculosis and other pathogenic bacteria emphasizes the need for new antibiotics. Unlike animals, most bacteria synthesize isoprenoid precursors through the MEP pathway. 1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the first reaction of the MEP pathway and is an attractive target for the development of new antibiotics. We report here the successful use of a loop truncation to crystallize and solve the first DXPS structures of a pathogen, namely M. tuberculosis (MtDXPS). The main difference found to other DXPS structures is in the active site where a highly coordinated water was found, showing a new mechanism for the enamine-intermediate stabilization. Unlike other DXPS structures, a “fork-like” motif could be identified in the enamine structure, using a different residue for the interaction with the cofactor, potentially leading to a decrease in the stability of the intermediate. In addition, electron density suggesting a phosphate group could be found close to the active site, provides new evidence for the D-GAP binding site. These results provide the opportunity to improve or develop new inhibitors specific for MtDXPS through structure-based drug design.
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Affiliation(s)
- Robin M Gierse
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Rick Oerlemans
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands
| | - Eswar R Reddem
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands
| | - Victor O Gawriljuk
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands.,São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100-Santa Angelina, São Carlos, SP, 13563-120, Brazil
| | - Alaa Alhayek
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Dominik Baitinger
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany
| | - Harald Jakobi
- Research & Development Crop Science, Bayer AG, Industriepark Höchst, 65926, Frankfurt, Germany
| | - Bernd Laber
- Research & Development Crop Science, Bayer AG, Industriepark Höchst, 65926, Frankfurt, Germany
| | - Gudrun Lange
- Research & Development Crop Science, Bayer AG, Industriepark Höchst, 65926, Frankfurt, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany. .,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany. .,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Matthew R Groves
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands.
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6
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Johnston ML, Freel Meyers CL. Revealing Donor Substrate-Dependent Mechanistic Control on DXPS, an Enzyme in Bacterial Central Metabolism. Biochemistry 2021; 60:929-939. [PMID: 33660509 PMCID: PMC8015787 DOI: 10.1021/acs.biochem.1c00019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/23/2021] [Indexed: 11/28/2022]
Abstract
The thiamin diphosphate-dependent enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the formation of DXP from pyruvate (donor) and d-glyceraldehyde 3-phosphate (d-GAP, acceptor). DXPS is essential in bacteria but absent in human metabolism, highlighting it as a potential antibacterial drug target. The enzyme possesses unique structural and mechanistic features that enable development of selective inhibition strategies and raise interesting questions about DXPS function in bacterial pathogens. DXPS distinguishes itself within the ThDP enzyme class by its exceptionally large active site and random sequential mechanism in DXP formation. In addition, DXPS displays catalytic promiscuity and relaxed acceptor substrate specificity, yet previous studies have suggested a preference for pyruvate as the donor substrate when d-GAP is the acceptor substrate. However, such donor specificity studies are potentially hindered by a lack of knowledge about specific, alternative donor-acceptor pairs. In this study, we exploited the promiscuous oxygenase activity of DXPS to uncover alternative donor substrates for DXPS. Characterization of glycolaldehyde, hydroxypyruvate, and ketobutyrate as donor substrates revealed differences in stabilization of enzyme-bound intermediates and acceptor substrate usage, illustrating the influence of the donor substrate on reaction mechanism and acceptor specificity. In addition, we found that DXPS prevents abortive acetyl-ThDP formation from a DHEThDP carbanion/enamine intermediate, similar to transketolase, supporting the potential physiological relevance of this intermediate on DXPS. Taken together, these results offer clues toward alternative roles for DXPS in bacterial pathogen metabolism.
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Affiliation(s)
- Melanie L. Johnston
- Department of Pharmacology and Molecular Sciences,
Johns Hopkins University School of Medicine, Baltimore,
Maryland 21205, United States
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences,
Johns Hopkins University School of Medicine, Baltimore,
Maryland 21205, United States
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7
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Runthala A, Sai TH, Kamjula V, Phulara SC, Rajput VS, Sangapillai K. Excavating the functionally crucial active-site residues of the DXS protein of Bacillus subtilis by exploring its closest homologues. J Genet Eng Biotechnol 2020; 18:76. [PMID: 33242110 PMCID: PMC7691408 DOI: 10.1186/s43141-020-00087-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/21/2020] [Indexed: 11/10/2022]
Abstract
Abstract
Background
To achieve a high yield of terpenoid-based therapeutics, 1-deoxy-d-xylulose-5-phosphate (DXP) pathway has been significantly exploited for the production of downstream enzymes. The DXP synthase (DXS) enzyme, the initiator of this pathway, is pivotal for the convergence of carbon flux, and is computationally studied well for the industrially utilized generally regarded as safe (GRAS) bacterium Bacillus subtilis to decode its vital regions for aiding the construction of a functionally improved mutant library.
Results
For the 546 sequence dataset of DXS sequences, a representative set of 108 sequences is created, and it shows a significant evolutionary divergence across different species clubbed into 37 clades, whereas three clades are observed for the 76 sequence dataset of Bacillus subtilis. The DXS enzyme, sharing a statistically significant homology to transketolase, is shown to be evolutionarily too distant. By the mutual information-based co-evolutionary network and hotspot analysis, the most crucial loci within the active site are deciphered. The 650-residue representative structure displays a complete conservation of 114 loci, and only two co-evolving residues ASP154 and ILE371 are found to be the conserved ones. Lastly, P318D is predicted to be the top-ranked mutation causing the increase in the thermodynamic stability of 6OUW.
Conclusion
The study excavates the vital functional, phylogenetic, and conserved residues across the active site of the DXS protein, the key rate-limiting controller of the entire pathway. It would aid to computationally understand the evolutionary landscape of this industrially useful enzyme and would allow us to widen its substrate repertoire to increase the enzymatic yield of unnatural molecules for in vivo and in vitro applications.
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8
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Liang YF, Liu H, Li H, Gao WY. Determination of the Activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase by Pre-column Derivatization-HPLC Using 1,2-Diamino-4,5-Methylenedioxybenzene as a Derivatizing Reagent. Protein J 2019; 38:160-166. [PMID: 30707333 DOI: 10.1007/s10930-019-09816-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
α-Ketoacids can be determined by HPLC through pre-column derivatization with 1,2-diamino-4,5-methylenedioxybenzene (DMB) as a derivatizing reagent. Using this method, the specific activity and the steady-state kinetic of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) were measured. Firstly, DXS substrate pyruvate was derivatized with DMB in acidic solution; then the corresponding quinoxalinone was elucidated by LC-ESI-MS and quantified by HPLC-UV. The optimum derivatization conditions were as follows: aqueous medium at pH 1.0, reaction temperature 80 °C, reaction time 60 min, molar ratio of DMB to pyruvate 10:1. The HPLC was run with isocratic elution using the mixture of methanol and water (60:40, v/v) as a mobile phase. The detective limit and the linear correlation range of the method were 0.05 µM and 0.002-1.0 mM (R = 0.994), respectively. The relative standard deviation (RSD) of six determinations was 2.48%. The steady-state kinetic parameters of DXS for pyruvate determined with the method were identical to the reported data. The established method is a practical route for evaluation of DXS activity, especially in the research and development of DXS inhibitors.
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Affiliation(s)
- Yan-Fei Liang
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, China
| | - Hui Liu
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, China
| | - Heng Li
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, China
| | - Wen-Yun Gao
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, China.
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9
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Investigation of the methylerythritol 4-phosphate pathway for microbial terpenoid production through metabolic control analysis. Microb Cell Fact 2019; 18:192. [PMID: 31690314 PMCID: PMC6833178 DOI: 10.1186/s12934-019-1235-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Terpenoids are of high interest as chemical building blocks and pharmaceuticals. In microbes, terpenoids can be synthesized via the methylerythritol phosphate (MEP) or mevalonate (MVA) pathways. Although the MEP pathway has a higher theoretical yield, metabolic engineering has met with little success because the regulation of the pathway is poorly understood. RESULTS We applied metabolic control analysis to the MEP pathway in Escherichia coli expressing a heterologous isoprene synthase gene (ispS). The expression of ispS led to the accumulation of isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP) and severely impaired bacterial growth, but the coexpression of ispS and isopentenyl diphosphate isomerase (idi) restored normal growth and wild-type IPP/DMAPP levels. Targeted proteomics and metabolomics analysis provided a quantitative description of the pathway, which was perturbed by randomizing the ribosome binding site in the gene encoding 1-deoxyxylulose 5-phosphate synthase (Dxs). Dxs has a flux control coefficient of 0.35 (i.e., a 1% increase in Dxs activity resulted in a 0.35% increase in pathway flux) in the isoprene-producing strain and therefore exerted significant control over the flux though the MEP pathway. At higher dxs expression levels, the intracellular concentration of 2-C-methyl-D-erythritol-2,4-cyclopyrophosphate (MEcPP) increased substantially in contrast to the other MEP pathway intermediates, which were linearly dependent on the abundance of Dxs. This indicates that 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (IspG), which consumes MEcPP, became saturated and therefore limited the flux towards isoprene. The higher intracellular concentrations of MEcPP led to the efflux of this intermediate into the growth medium. DISCUSSION These findings show the importance of Dxs, Idi and IspG and metabolite export for metabolic engineering of the MEP pathway and will facilitate further approaches for the microbial production of valuable isoprenoids.
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10
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Chen PYT, DeColli AA, Freel Meyers CL, Drennan CL. X-ray crystallography-based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate. J Biol Chem 2019; 294:12405-12414. [PMID: 31239351 PMCID: PMC6699841 DOI: 10.1074/jbc.ra119.009321] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/16/2019] [Indexed: 01/07/2023] Open
Abstract
1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) uses thiamine diphosphate (ThDP) to convert pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) into 1-deoxy-d-xylulose 5-phosphate (DXP), an essential bacterial metabolite. DXP is not utilized by humans; hence, DXPS has been an attractive antibacterial target. Here, we investigate DXPS from Deinococcus radiodurans (DrDXPS), showing that it has similar kinetic parameters Kmd-GAP and Kmpyruvate (54 ± 3 and 11 ± 1 μm, respectively) and comparable catalytic activity (kcat = 45 ± 2 min-1) with previously studied bacterial DXPS enzymes and employing it to obtain missing structural data on this enzyme family. In particular, we have determined crystallographic snapshots of DrDXPS in two states along the reaction coordinate: a structure of DrDXPS bound to C2α-phosphonolactylThDP (PLThDP), mimicking the native pre-decarboxylation intermediate C2α-lactylThDP (LThDP), and a native post-decarboxylation state with a bound enamine intermediate. The 1.94-Å-resolution structure of PLThDP-bound DrDXPS delineates how two active-site histidine residues stabilize the LThDP intermediate. Meanwhile, the 2.40-Å-resolution structure of an enamine intermediate-bound DrDXPS reveals how a previously unknown 17-Å conformational change removes one of the two histidine residues from the active site, likely triggering LThDP decarboxylation to form the enamine intermediate. These results provide insight into how the bi-substrate enzyme DXPS limits side reactions by arresting the reaction on the less reactive LThDP intermediate when its cosubstrate is absent. They also offer a molecular basis for previous low-resolution experimental observations that correlate decarboxylation of LThDP with protein conformational changes.
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Affiliation(s)
- Percival Yang-Ting Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Alicia A. DeColli
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, To whom correspondence may be addressed:
Dept. of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205. Tel.:
410-502-4807; Fax:
410-955-3023; E-mail:
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, A Howard Hughes Medical Institute investigator and a senior fellow of the Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR). To whom correspondence may be addressed:
Depts. of Biology and Chemistry, Massachusetts Institute of Technology, 31 Ames St., Bldg. 68-680, Cambridge, MA 02139. Tel.:
617-253-5622; Fax:
617-258-7847; E-mail:
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11
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Bartee D, Sanders S, Phillips PD, Harrison MJ, Koppisch AT, Freel Meyers CL. Enamide Prodrugs of Acetyl Phosphonate Deoxy-d-xylulose-5-phosphate Synthase Inhibitors as Potent Antibacterial Agents. ACS Infect Dis 2019; 5:406-417. [PMID: 30614674 DOI: 10.1021/acsinfecdis.8b00307] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To fight the growing threat of antibiotic resistance, new antibiotics are required that target essential bacterial processes other than protein, DNA/RNA, and cell wall synthesis, which constitute the majority of currently used antibiotics. 1-Deoxy-d-xylulose-5-phosphate (DXP) synthase is a vital enzyme in bacterial central metabolism, feeding into the de novo synthesis of thiamine diphosphate, pyridoxal phosphate, and essential isoprenoid precursors isopentenyl diphosphate and dimethylallyl diphosphate. While potent and selective inhibitors of DXP synthase in vitro activity have been discovered, their antibacterial activity is modest. To improve the antibacterial activity of selective alkyl acetylphosphonate (alkylAP) inhibitors of DXP synthase, we synthesized peptidic enamide prodrugs of alkylAPs inspired by the natural product dehydrophos, a prodrug of methyl acetylphosphonate. This prodrug strategy achieves dramatic increases in activity against Gram-negative pathogens for two alkylAPs, butyl acetylphosphonate and homopropargyl acetylphosphonate, decreasing minimum inhibitory concentrations against Escherichia coli by 33- and nearly 2000-fold, respectively. Antimicrobial studies and LC-MS/MS analysis of alkylAP-treated E. coli establish that the increased potency of prodrugs is due to increased accumulation of alkylAP inhibitors of DXP synthase via transport of the prodrug through the OppA peptide permease and subsequent amide hydrolysis. This work demonstrates the promise of targeting DXP synthase for the development of novel antibacterial agents.
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Affiliation(s)
- David Bartee
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21205, United States
| | - Sara Sanders
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21205, United States
| | - Paul D. Phillips
- Department of Chemistry, Northern Arizona University, 700 South Osborne Drive, Flagstaff, Arizona 86011, United States
| | - Mackenzie J. Harrison
- Department of Chemistry, Northern Arizona University, 700 South Osborne Drive, Flagstaff, Arizona 86011, United States
| | - Andrew T. Koppisch
- Department of Chemistry, Northern Arizona University, 700 South Osborne Drive, Flagstaff, Arizona 86011, United States
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21205, United States
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12
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Bartee D, Freel Meyers CL. Toward Understanding the Chemistry and Biology of 1-Deoxy-d-xylulose 5-Phosphate (DXP) Synthase: A Unique Antimicrobial Target at the Heart of Bacterial Metabolism. Acc Chem Res 2018; 51:2546-2555. [PMID: 30203647 DOI: 10.1021/acs.accounts.8b00321] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antibiotics are the cornerstone of modern healthcare. The 20th century discovery of sulfonamides and β-lactam antibiotics altered human society immensely. Simple bacterial infections were no longer a leading cause of morbidity and mortality, and antibiotic prophylaxis greatly reduced the risk of infection from surgery. The current healthcare system requires effective antibiotics to function. However, antibiotic-resistant infections are becoming increasingly prevalent, threatening the emergence of a postantibiotic era. To prevent this public health crisis, antibiotics with novel modes of action are needed. Currently available antibiotics target just a few cellular processes to exert their activity: DNA, RNA, protein, and cell wall biosynthesis. Bacterial central metabolism is underexploited, offering a wealth of potential new targets that can be pursued toward expanding the armamentarium against microbial infections. Discovered in 1997 as the first enzyme in the methylerythritol phosphate (MEP) pathway, 1-deoxy-d-xylulose 5-phosphate (DXP) synthase is a thiamine diphosphate (ThDP)-dependent enzyme that catalyzes the decarboxylative condensation of pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) to form DXP. This five-carbon metabolite feeds into three separate essential pathways for bacterial central metabolism: ThDP synthesis, pyridoxal phosphate (PLP) synthesis, and the MEP pathway for isoprenoid synthesis. While it has long been identified as a target for the development of antimicrobial agents, limited progress has been made toward developing selective inhibitors of the enzyme. This Account highlights advances from our lab over the past decade to understand this important and unique enzyme. Unlike all other known ThDP-dependent enzymes, DXP synthase uses a random-sequential mechanism that requires the formation of a ternary complex prior to decarboxylation of the lactyl-ThDP intermediate. Its large active site accommodates a variety of acceptor substrates, lending itself to a number of alternative activities, such as the production of α-hydroxy ketones, hydroxamates, amides, acetolactate, and peracetate. Knowledge gained from mechanistic and substrate-specificity studies has guided the development of selective inhibitors with antibacterial activity and provides a biochemical foundation toward understanding DXP synthase function in bacterial cells. Although it is a promising drug target, the centrality of DXP synthase in bacterial metabolism imparts specific challenges to assessing antibacterial activity of DXP synthase inhibitors, and the susceptibility of most bacteria to current DXP synthase inhibitors is remarkably culture-medium-dependent. Despite these challenges, the study of DXP synthase is poised to reveal the role of DXP synthase in bacterial metabolic adaptability during infection, ultimately providing a more complete picture of how inhibiting this crucial enzyme can be used to develop novel antibiotics.
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Affiliation(s)
- David Bartee
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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13
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Bartee D, Freel Meyers CL. Targeting the Unique Mechanism of Bacterial 1-Deoxy-d-xylulose-5-phosphate Synthase. Biochemistry 2018; 57:4349-4356. [PMID: 29944345 DOI: 10.1021/acs.biochem.8b00548] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial metabolite 1-deoxy-d-xyulose 5-phosphate (DXP) is essential in bacterial central metabolism feeding into isoprenoid, thiamin diphosphate (ThDP), and pyridoxal phosphate de novo biosynthesis. Halting its production through the inhibition of DXP synthase is an attractive strategy for the development of novel antibiotics. Recent work has revealed that DXP synthase utilizes a unique random sequential mechanism that requires formation of a ternary complex among pyruvate-derived C2α-lactylthiamin diphosphate (LThDP), d-glyceraldehyde 3-phosphate (d-GAP), and enzyme, setting it apart from all other known ThDP-dependent enzymes. Herein, we describe the development of bisubstrate inhibitors bearing an acetylphosphonate (AP) pyruvate mimic and a distal negative charge mimicking the phosphoryl group of d-GAP, designed to target the unique form of DXP synthase that binds LThDP and d-GAP in a ternary complex. A d-phenylalanine-derived triazole acetylphosphonate (d-PheTrAP) emerged as the most potent inhibitor in this series, displaying slow, tight-binding inhibition with a Ki* of 90 ± 10 nM, forward ( k1) and reverse ( k2) isomerization rates of 1.1 and 0.14 min-1, respectively, and exquisite selectivity (>15000-fold) for DXP synthase over mammalian pyruvate dehydrogenase. d-PheTrAP is the most potent, selective DXP synthase inhibitor described to date and represents the first inhibitor class designed specifically to exploit the unique E-LThDP-GAP ternary complex in ThDP enzymology.
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Affiliation(s)
- David Bartee
- Department of Pharmacology and Molecular Sciences , The Johns Hopkins University School of Medicine , Baltimore , Maryland 21205 , United States
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences , The Johns Hopkins University School of Medicine , Baltimore , Maryland 21205 , United States
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14
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DeColli AA, Nemeria NS, Majumdar A, Gerfen GJ, Jordan F, Freel Meyers CL. Oxidative decarboxylation of pyruvate by 1-deoxy-d-xyulose 5-phosphate synthase, a central metabolic enzyme in bacteria. J Biol Chem 2018; 293:10857-10869. [PMID: 29784878 DOI: 10.1074/jbc.ra118.001980] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/17/2018] [Indexed: 01/06/2023] Open
Abstract
The underexploited antibacterial target 1-deoxy-d-xyluose 5-phosphate (DXP) synthase catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate (d-GAP). DXP is an essential intermediate in the biosynthesis of ThDP, pyridoxal phosphate, and isoprenoids in many pathogenic bacteria. DXP synthase catalyzes a distinct mechanism in ThDP decarboxylative enzymology in which the first enzyme-bound pre-decarboxylation intermediate, C2α-lactyl-ThDP (LThDP), is stabilized by DXP synthase in the absence of d-GAP, and d-GAP then induces efficient LThDP decarboxylation. Despite the observed LThDP accumulation and lack of evidence for C2α-carbanion formation in the absence of d-GAP, CO2 is released at appreciable levels under these conditions. Here, seeking to resolve these conflicting observations, we show that DXP synthase catalyzes the oxidative decarboxylation of pyruvate under conditions in which LThDP accumulates. O2-dependent LThDP decarboxylation led to one-electron transfer from the C2α-carbanion/enamine to O2, with intermediate ThDP-enamine radical formation, followed by peracetic acid formation en route to acetate. Thus, LThDP formation and decarboxylation and DXP formation were studied under anaerobic conditions. Our results support a model in which O2-dependent LThDP decarboxylation and peracetic acid formation occur in the absence of d-GAP, decreasing the levels of pyruvate and O2 in solution. The relative pyruvate and O2 concentrations then dictate the extent of LThDP accumulation, and its buildup can be observed when [pyruvate] > [O2]. The finding that O2 acts as a structurally distinct trigger of LThDP decarboxylation supports the hypothesis that a mechanism involving small molecule-dependent LThDP decarboxylation equips DXP synthase for diverse, yet uncharacterized cellular functions.
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Affiliation(s)
| | - Natalia S Nemeria
- the Department of Chemistry, Rutgers University, Newark, New Jersey 07102, and
| | - Ananya Majumdar
- Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Gary J Gerfen
- the Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Frank Jordan
- the Department of Chemistry, Rutgers University, Newark, New Jersey 07102, and
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15
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Handa S, Dempsey DR, Ramamoorthy D, Cook N, Guida WC, Spradling TJ, White JK, Woodcock HL, Merkler DJ. Mechanistic Studies of 1-Deoxy-D-Xylulose-5-Phosphate Synthase from Deinococcus radiodurans. ACTA ACUST UNITED AC 2018; 4. [PMID: 29552677 PMCID: PMC5851014 DOI: 10.21767/2471-8084.100051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The non-mevalonate dependent (NMVA) pathway for the biosynthesis of isopentenyl pyrophosphate and dimethylallyl pyrophosphate is the sole source of these terpenoids for the production of isoprenoids in the apicomplexan parasites, in many eubacteria, and in plants. The absence of this pathway in higher organisms has opened a new platform for the development of novel antibiotics and anti-malarials. The enzyme catalyzing the first step of the NMVA pathway is 1-deoxy-D-xylulose-5-phosphate synthase (DXPS). DXPS catalyzes the thiamine pyrophosphate- and Mg (II)-dependent conjugation of pyruvate and D-glyceraldehyde-3-phosphate to form 1-deoxy-D-xylulose-5-phosphate and CO2. The kinetic mechanism of DXPS from Deinococcus radiodurans most consistent with our data is random sequential as shown using a combination of kinetic analysis and product and dead-end inhibition studies. The role of active site amino acids, identified by sequence alignment to other DXPS proteins, was probed by constructing and analyzing the catalytic efficacy of a set of targeted site-directed mutants.
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Affiliation(s)
- Sumit Handa
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel R Dempsey
- Departments of Medicine, Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, UK
| | | | - Nanci Cook
- Department of Chemistry, University of South Florida, USA
| | - Wayne C Guida
- Department of Chemistry, University of South Florida, USA
| | | | - Justin K White
- Department of Chemistry, University of South Florida, USA
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, USA
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16
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Sanders S, Vierling RJ, Bartee D, DeColli AA, Harrison MJ, Aklinski JL, Koppisch AT, Freel Meyers CL. Challenges and Hallmarks of Establishing Alkylacetylphosphonates as Probes of Bacterial 1-Deoxy-d-xylulose 5-Phosphate Synthase. ACS Infect Dis 2017. [PMID: 28636325 DOI: 10.1021/acsinfecdis.6b00168] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
1-Deoxy-d-xylulose 5-phosphate (DXP) synthase catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate. DXP is at a metabolic branch point in bacteria, feeding into the methylerythritol phosphate pathway to indispensable isoprenoids and acting as a precursor for biosynthesis of essential cofactors in central metabolism, pyridoxal phosphate and ThDP, the latter of which is also required for DXP synthase catalysis. DXP synthase follows a unique random sequential mechanism and possesses an unusually large active site. These features have guided the design of sterically demanding alkylacetylphosphonates (alkylAPs) toward the development of selective DXP synthase inhibitors. alkylAPs studied here display selective, low μM inhibitory activity against DXP synthase. They are weak inhibitors of bacterial growth in standard nutrient rich conditions. However, bacteria are significantly sensitized to most alkylAPs in defined minimal growth medium, with minimal inhibitory concentrations (MICs) ranging from low μM to low mM and influenced by alkyl-chain length. The longest analog (C8) displays the weakest antimicrobial activity and is a substrate for efflux via AcrAB-TolC. The dependence of inhibitor potency on growth environment emphasizes the need for antimicrobial screening conditions that are relevant to the in vivo microbial microenvironment during infection. DXP synthase expression and thiamin supplementation studies offer support for DXP synthase as an intracellular target for some alkylAPs and reveal both the challenges and intriguing aspects of these approaches to study target engagement.
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Affiliation(s)
- Sara Sanders
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Ryan J. Vierling
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - David Bartee
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Alicia A. DeColli
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Mackenzie J. Harrison
- Department
of Chemistry, Northern Arizona University, Flagstaff, Arizona 86011, United States
| | - Joseph L. Aklinski
- Department
of Chemistry, Northern Arizona University, Flagstaff, Arizona 86011, United States
| | - Andrew T. Koppisch
- Department
of Chemistry, Northern Arizona University, Flagstaff, Arizona 86011, United States
| | - Caren L. Freel Meyers
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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17
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White JK, Handa S, Vankayala SL, Merkler DJ, Woodcock HL. Thiamin Diphosphate Activation in 1-Deoxy-d-xylulose 5-Phosphate Synthase: Insights into the Mechanism and Underlying Intermolecular Interactions. J Phys Chem B 2016; 120:9922-34. [PMID: 27537621 PMCID: PMC5379999 DOI: 10.1021/acs.jpcb.6b07248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
1-Deoxy-d-xylulose 5-phosphate synthase (DXS) is a thiamin diphosphate (TDP) dependent enzyme that marks the beginning of the methylerythritol 4-phosphate isoprenoid biosynthesis pathway. The mechanism of action for DXS is still poorly understood and begins with the formation of a thiazolium ylide. This TDP activation step is thought to proceed through an intramolecular deprotonation by the 4'-aminopyrimidine ring of TDP; however, this step would occur only after an initial deprotonation of its own 4'-amino group. The mechanism of the initial deprotonation has been hypothesized, by analogy to transketolases, to occur via a histidine or an active site water molecule. Results from hybrid quantum mechanical/molecular mechanical (QM/MM) reaction path calculations reveal an ∼10 kcal/mol difference in transition state energies, favoring a water mediated mechanism over direct deprotonation by histidine. This difference was determined to be largely governed by electrostatic changes induced by conformational variations in the active site. Additionally, mutagenesis studies reveal DXS to be an evolutionarily resilient enzyme. Particularly, we hypothesize that residues H82 and H304 may act in a compensatory fashion if the other is lost due to mutation. Further, nucleus-independent chemical shifts (NICSs) and aromatic stabilization energy (ASE) calculations suggest that reduction in TDP aromaticity also serves as a factor for regulating ylide formation and controlling reactivity.
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Affiliation(s)
- Justin K. White
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - Sumit Handa
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0332, United States
| | - Sai Lakshmana Vankayala
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - David J. Merkler
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
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18
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Nemeria NS, Shome B, DeColli AA, Heflin K, Begley TP, Meyers CF, Jordan F. Competence of Thiamin Diphosphate-Dependent Enzymes with 2'-Methoxythiamin Diphosphate Derived from Bacimethrin, a Naturally Occurring Thiamin Anti-vitamin. Biochemistry 2016; 55:1135-48. [PMID: 26813608 PMCID: PMC4852132 DOI: 10.1021/acs.biochem.5b01300] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacimethrin (4-amino-5-hydroxymethyl-2-methoxypyrimidine), a natural product isolated from some bacteria, has been implicated as an inhibitor of bacterial and yeast growth, as well as in inhibition of thiamin biosynthesis. Given that thiamin biosynthetic enzymes could convert bacimethrin to 2'-methoxythiamin diphosphate (MeOThDP), it is important to evaluate the effect of this coenzyme analogue on thiamin diphosphate (ThDP)-dependent enzymes. The potential functions of MeOThDP were explored on five ThDP-dependent enzymes: the human and Escherichia coli pyruvate dehydrogenase complexes (PDHc-h and PDHc-ec, respectively), the E. coli 1-deoxy-D-xylulose 5-phosphate synthase (DXPS), and the human and E. coli 2-oxoglutarate dehydrogenase complexes (OGDHc-h and OGDHc-ec, respectively). Using several mechanistic tools (fluorescence, circular dichroism, kinetics, and mass spectrometry), it was demonstrated that MeOThDP binds in the active centers of ThDP-dependent enzymes, however, with a binding mode different from that of ThDP. While modest activities resulted from addition of MeOThDP to E. coli PDHc (6-11%) and DXPS (9-14%), suggesting that MeOThDP-derived covalent intermediates are converted to the corresponding products (albeit with rates slower than that with ThDP), remarkably strong activity (up to 75%) resulted upon addition of the coenzyme analogue to PDHc-h. With PDHc-ec and PDHc-h, the coenzyme analogue could support all reactions, including communication between components in the complex. No functional substitution of MeOThDP for ThDP was in evidence with either OGDH-h or OGDH-ec, shown to be due to tight binding of ThDP.
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Affiliation(s)
- Natalia S. Nemeria
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Brateen Shome
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Alicia A. DeColli
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Kathryn Heflin
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Caren Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Frank Jordan
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
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19
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Battistini MR, Shoji C, Handa S, Breydo L, Merkler DJ. Mechanistic binding insights for 1-deoxy-D-Xylulose-5-Phosphate synthase, the enzyme catalyzing the first reaction of isoprenoid biosynthesis in the malaria-causing protists, Plasmodium falciparum and Plasmodium vivax. Protein Expr Purif 2015; 120:16-27. [PMID: 26699947 DOI: 10.1016/j.pep.2015.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/04/2015] [Accepted: 12/09/2015] [Indexed: 11/30/2022]
Abstract
We have successfully truncated and recombinantly-expressed 1-deoxy-D-xylulose-5-phosphate synthase (DXS) from both Plasmodium vivax and Plasmodium falciparum. We elucidated the order of substrate binding for both of these ThDP-dependent enzymes using steady-state kinetic analyses, dead-end inhibition, and intrinsic tryptophan fluorescence titrations. Both enzymes adhere to a random sequential mechanism with respect to binding of both substrates: pyruvate and D-glyceraldehyde-3-phosphate. These findings are in contrast to other ThDP-dependent enzymes, which exhibit classical ordered and/or ping-pong kinetic mechanisms. A better understanding of the kinetic mechanism for these two Plasmodial enzymes could aid in the development of novel DXS-specific inhibitors that might prove useful in treatment of malaria.
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Affiliation(s)
- Matthew R Battistini
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
| | - Christopher Shoji
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
| | - Sumit Handa
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Leonid Breydo
- College of Medicine and Molecular Medicine, University of South Florida Health, 12901 Bruce B. Downs Blvd., MDC 3529, Tampa, FL 33612, USA
| | - David J Merkler
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA.
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20
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Bartee D, Morris F, Al-Khouja A, Freel Meyers CL. Hydroxybenzaldoximes Are D-GAP-Competitive Inhibitors of E. coli 1-Deoxy-D-Xylulose-5-Phosphate Synthase. Chembiochem 2015; 16:1771-81. [PMID: 26174207 PMCID: PMC4609000 DOI: 10.1002/cbic.201500119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 11/05/2022]
Abstract
1-Deoxy-D-xylulose 5-phosphate (DXP) synthase is the first enzyme in the methylerythritol phosphate pathway to essential isoprenoids in pathogenic bacteria and apicomplexan parasites. In bacterial pathogens, DXP lies at a metabolic branch point, serving also as a precursor in the biosynthesis of vitamins B1 and B6, which are critical for central metabolism. In an effort to identify new bisubstrate analogue inhibitors that exploit the large active site and distinct mechanism of DXP synthase, a library of aryl mixed oximes was prepared and evaluated. Trihydroxybenzaldoximes emerged as reversible, low-micromolar inhibitors, competitive against D-glyceraldehyde 3-phosphate (D-GAP) and either uncompetitive or noncompetitive against pyruvate. Hydroxybenzaldoximes are the first class of D-GAP-competitive DXP synthase inhibitors, offering new tools for mechanistic studies of DXP synthase and a new direction for the development of antimicrobial agents targeting isoprenoid biosynthesis.
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Affiliation(s)
- David Bartee
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA)
| | - Francine Morris
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA)
- Present address: Albert Einstein College of Medicine, Department of Biochemistry, 1301 Morris Park Avenue, Bronx, NY 10461 (USA)
| | - Amer Al-Khouja
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA)
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 (USA).
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21
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Yin S, Zhou H, Xiao X, Lang T, Liang J, Wang C. Improving 2-Phenylethanol Production via Ehrlich Pathway Using Genetic Engineered Saccharomyces cerevisiae Strains. Curr Microbiol 2015; 70:762-7. [DOI: 10.1007/s00284-015-0785-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/05/2015] [Indexed: 11/24/2022]
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22
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Yin S, Lang T, Xiao X, Liu L, Sun B, Wang C. Significant enhancement of methionol production by co-expression of the aminotransferase gene ARO8 and the decarboxylase gene ARO10 in Saccharomyces cerevisiae. FEMS Microbiol Lett 2014; 362:fnu043. [PMID: 25743068 DOI: 10.1093/femsle/fnu043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Methionol is an important volatile sulfur flavor compound, which can be produced via the Ehrlich pathway in Saccharomyces cerevisiae. Aminotransferase and decarboxylase are essential enzymes catalyzing methionol biosynthesis. In this work, two aminotransferase genes ARO8 and ARO9 and one decarboxylase gene ARO10 were introduced into S. cerevisiae S288c, respectively, via an expression vector. Over-expression of ARO8 resulted in higher aminotransferase activity than that of ARO9. And the cellular decarboxylase activity was remarkably increased by over-expression of ARO10. A co-expression vector carrying both ARO8 and ARO10 was further constructed to generate the recombinant strain S810. Shaking flask experiments showed that the methionol yield from S810 reached 1.27 g L(-1), which was increased by 51.8 and 68.8% compared to that from the wild-type strain and the control strain harboring the empty vector. The fed-batch fermentation by strain S810 produced 3.24 g L(-1) of methionol after 72 h of cultivation in a bioreactor. These results demonstrated that co-expression of ARO8 and ARO10 significantly boosted the methionol production. It is the first time that more than 3.0 g L(-1) of methionol produced by genetically engineered yeast strain was reported by co-expression of the aminotransferase and decarboxylase via the Ehrlich pathway.
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Affiliation(s)
- Sheng Yin
- School of Food and Chemical Engineering, Beijing Technology & Business University, Beijing 100048, China Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China Beijing Key Laboratory of Flavor Chemistry, Beijing Technology & Business University, Beijing 100048, China
| | - Tiandan Lang
- School of Food and Chemical Engineering, Beijing Technology & Business University, Beijing 100048, China Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China
| | - Xiao Xiao
- School of Food and Chemical Engineering, Beijing Technology & Business University, Beijing 100048, China Beijing Key Laboratory of Flavor Chemistry, Beijing Technology & Business University, Beijing 100048, China
| | - Li Liu
- School of Food and Chemical Engineering, Beijing Technology & Business University, Beijing 100048, China Beijing Key Laboratory of Flavor Chemistry, Beijing Technology & Business University, Beijing 100048, China
| | - Baoguo Sun
- School of Food and Chemical Engineering, Beijing Technology & Business University, Beijing 100048, China Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China Beijing Key Laboratory of Flavor Chemistry, Beijing Technology & Business University, Beijing 100048, China
| | - Chengtao Wang
- School of Food and Chemical Engineering, Beijing Technology & Business University, Beijing 100048, China Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China Beijing Key Laboratory of Flavor Chemistry, Beijing Technology & Business University, Beijing 100048, China
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23
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A chemical rescue screen identifies a Plasmodium falciparum apicoplast inhibitor targeting MEP isoprenoid precursor biosynthesis. Antimicrob Agents Chemother 2014; 59:356-64. [PMID: 25367906 DOI: 10.1128/aac.03342-14] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The apicoplast is an essential plastid organelle found in Plasmodium parasites which contains several clinically validated antimalarial-drug targets. A chemical rescue screen identified MMV-08138 from the "Malaria Box" library of growth-inhibitory antimalarial compounds as having specific activity against the apicoplast. MMV-08138 inhibition of blood-stage Plasmodium falciparum growth is stereospecific and potent, with the most active diastereomer demonstrating a 50% effective concentration (EC50) of 110 nM. Whole-genome sequencing of 3 drug-resistant parasite populations from two independent selections revealed E688Q and L244I mutations in P. falciparum IspD, an enzyme in the MEP (methyl-d-erythritol-4-phosphate) isoprenoid precursor biosynthesis pathway in the apicoplast. The active diastereomer of MMV-08138 directly inhibited PfIspD activity in vitro with a 50% inhibitory concentration (IC50) of 7.0 nM. MMV-08138 is the first PfIspD inhibitor to be identified and, together with heterologously expressed PfIspD, provides the foundation for further development of this promising antimalarial drug candidate lead. Furthermore, this report validates the use of the apicoplast chemical rescue screen coupled with target elucidation as a discovery tool to identify specific apicoplast-targeting compounds with new mechanisms of action.
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24
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Masini T, Hirsch AKH. Development of Inhibitors of the 2C-Methyl-d-erythritol 4-Phosphate (MEP) Pathway Enzymes as Potential Anti-Infective Agents. J Med Chem 2014; 57:9740-63. [DOI: 10.1021/jm5010978] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tiziana Masini
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
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25
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Basta LAB, Patel H, Kakalis L, Jordan F, Meyers CLF. Defining critical residues for substrate binding to 1-deoxy-D-xylulose 5-phosphate synthase--active site substitutions stabilize the predecarboxylation intermediate C2α-lactylthiamin diphosphate. FEBS J 2014; 281:2820-2837. [PMID: 24767541 PMCID: PMC4065394 DOI: 10.1111/febs.12823] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/06/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
Abstract
1-Deoxy-D-xylulose 5-phosphate (DXP) synthase catalyzes the formation of DXP from pyruvate and D-glyceraldehyde 3-phosphate (GraP) in a thiamin diphosphate-dependent manner, and is the first step in the essential pathway to isoprenoids in human pathogens. Understanding the mechanism of this unique enzyme is critical for developing new anti-infective agents that selectively target isoprenoid biosynthesis. The present study used mutagenesis and a combination of protein fluorescence, CD and kinetics experiments to investigate the roles of Arg420, Arg478 and Tyr392 in substrate binding and catalysis. The results support a random sequential, preferred order mechanism, and predict that Arg420 and Arg478 are involved in binding of the acceptor substrate, GraP. D-Glyceraldehyde, an alternative acceptor substrate lacking the phosphoryl group predicted to interact with Arg420 and Arg478, also accelerates decarboxylation of the predecarboxylation intermediate C2α-lactylthiamin diphosphate (LThDP) on DXP synthase, indicating that this binding interaction is not absolutely required, and that the hydroxyaldehyde sufficiently triggers decarboxylation. Unexpectedly, Tyr392 contributes to GraP affinity, and is not required for LThDP formation or its GraP-promoted decarboxylation. Time-resolved CD spectroscopy and NMR experiments indicate that LThDP is significantly stabilized on R420A and Y392F variants as compared with wild-type DXP synthase in the absence of acceptor substrate, but these substitutions do not appear to affect the rate of GraP-promoted LThDP decarboxylation in the presence of high levels of GraP, and LThDP formation remains the rate-limiting step. These results suggest a role of these residues in promoting GraP binding, which in turn facilitates decarboxylation, and also highlight interesting differences between DXP synthase and other thiamin diphosphate-dependent enzymes.
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Affiliation(s)
- Leighanne A. Brammer Basta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hetalben Patel
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Lazaros Kakalis
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Frank Jordan
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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26
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Smith JM, Warrington NV, Vierling RJ, Kuhn ML, Anderson WF, Koppisch AT, Freel Meyers CL. Targeting DXP synthase in human pathogens: enzyme inhibition and antimicrobial activity of butylacetylphosphonate. J Antibiot (Tokyo) 2014; 67:77-83. [PMID: 24169798 PMCID: PMC3946878 DOI: 10.1038/ja.2013.105] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 09/20/2013] [Accepted: 09/30/2013] [Indexed: 11/24/2022]
Abstract
The unique methylerythritol phosphate pathway for isoprenoid biosynthesis is essential in most bacterial pathogens. The first enzyme in this pathway, 1-deoxy-D-xylulose 5-phosphate (DXP) synthase, catalyzes a distinct thiamin diphosphate (ThDP)-dependent reaction to form DXP from D-glyceraldehyde 3-phosphate (D-GAP) and pyruvate and represents a potential anti-infective drug target. We have previously demonstrated that the unnatural bisubstrate analog, butylacetylphosphonate (BAP), exhibits selective inhibition of Escherichia coli DXP synthase over mammalian ThDP-dependent enzymes. Here, we report the selective inhibition by BAP against recombinant DXP synthase homologs from Mycobacterium tuberculosis, Yersinia pestis and Salmonella enterica. We also demonstrate antimicrobial activity of BAP against both Gram-negative and Gram-positive strains (including E. coli, S. enterica and Bacillus anthracis), and several clinically isolated pathogens. Our results suggest a mechanism of action involving inhibition of DXP synthase and show that BAP acts synergistically with established antimicrobial agents, highlighting a potential strategy to combat emerging resistance in bacterial pathogens.
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Affiliation(s)
- Jessica M Smith
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nicole V Warrington
- Deptartment of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, USA
| | - Ryan J Vierling
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Misty L Kuhn
- Center for Structural Genomics of Infectious Diseases, Northwestern Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Chicago, IL, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Northwestern Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Chicago, IL, USA
| | - Andrew T Koppisch
- Deptartment of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, USA
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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27
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Patel H, Shim DJ, Farinas ET, Jordan F. Investigation of the donor and acceptor range for chiral carboligation catalyzed by the E1 component of the 2-oxoglutarate dehydrogenase complex. ACTA ACUST UNITED AC 2013; 98. [PMID: 24277992 DOI: 10.1016/j.molcatb.2013.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The potential of thiamin diphosphate (ThDP)-dependent enzymes to catalyze C-C bond forming (carboligase) reactions with high enantiomeric excess has been recognized for many years. Here we report the application of the E1 component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex in the synthesis of chiral compounds with multiple functional groups in good yield and high enantiomeric excess, by varying both the donor substrate (different 2-oxo acids) and the acceptor substrate (glyoxylate, ethyl glyoxylate and methyl glyoxal). Major findings include the demonstration that the enzyme can accept 2-oxovalerate and 2-oxoisovalerate in addition to its natural substrate 2-oxoglutarate, and that the tested acceptors are also acceptable in the carboligation reaction, thereby very much expanding the repertory of the enzyme in chiral synthesis.
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Affiliation(s)
- Hetalben Patel
- Department of Chemistry, Rutgers University, Newark, NJ 07102
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28
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Morris F, Vierling R, Boucher L, Bosch J, Freel Meyers CL. DXP synthase-catalyzed C-N bond formation: nitroso substrate specificity studies guide selective inhibitor design. Chembiochem 2013; 14:1309-15. [PMID: 23824585 DOI: 10.1002/cbic.201300187] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Indexed: 11/12/2022]
Abstract
1-Deoxy-D-xylulose 5-phosphate (DXP) synthase catalyzes the first step in the nonmammalian isoprenoid biosynthetic pathway to form DXP from pyruvate and D-glyceraldehyde 3-phosphate (D-GAP) in a thiamin diphosphate-dependent manner. Its unique structure and mechanism distinguish DXP synthase from its homologues and suggest that it should be pursued as an anti-infective drug target. However, few reports describe any development of selective inhibitors of this enzyme. Here, we reveal that DXP synthase catalyzes C-N bond formation and exploit aromatic nitroso substrates as active site probes. Substrate specificity studies reveal a high affinity of DXP synthase for aromatic nitroso substrates compared to the related ThDP-dependent enzyme pyruvate dehydrogenase (PDH). Results from inhibition and mutagenesis studies indicate that nitroso substrates bind to E. coli DXP synthase in a manner distinct from that of D-GAP. Our results suggest that the incorporation of aryl acceptor substrate mimics into unnatural bisubstrate analogues will impart selectivity to DXP synthase inhibitors. As a proof of concept, we show selective inhibition of DXP synthase by benzylacetylphosphonate (BnAP).
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Affiliation(s)
- Francine Morris
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe St, Baltimore, MD 21205, USA
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29
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Müller M, Sprenger GA, Pohl M. CC bond formation using ThDP-dependent lyases. Curr Opin Chem Biol 2013; 17:261-70. [PMID: 23523314 DOI: 10.1016/j.cbpa.2013.02.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/02/2013] [Accepted: 02/14/2013] [Indexed: 01/17/2023]
Abstract
The present review summarizes recent achievements in enzymatic thiamine catalysis during the past three years. With well-established enzymes such as BAL, PDC and TK new reactions have been identified and respective variants were prepared, which enable access to stereoisomeric products. Further we highlight recent progress with 'new' ThDP-dependent enzymes like MenD and PigD, which catalyze the Stetter-like 1,4 addition of aldehydes and YerE, which is the first known ThDP-dependent enzyme accepting ketones as acceptors.
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Affiliation(s)
- Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104 Freiburg, Germany.
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30
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HU Y, WANG XJ, LI H, GAO WY. Determination of Steady-State Kinetic Parameters of 1-Deoxy-D-xylulose-5-phosphate Synthase by Pre-column Derivatization High Performance Liquid Chromatography Using 2,4-Dinitrophenylhydrazine as Derivative Reagent. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2012. [DOI: 10.1016/s1872-2040(11)60595-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Patel H, Nemeria NS, Brammer LA, Freel Meyers CL, Jordan F. Observation of thiamin-bound intermediates and microscopic rate constants for their interconversion on 1-deoxy-D-xylulose 5-phosphate synthase: 600-fold rate acceleration of pyruvate decarboxylation by D-glyceraldehyde-3-phosphate. J Am Chem Soc 2012; 134:18374-9. [PMID: 23072514 DOI: 10.1021/ja307315u] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The thiamin diphosphate (ThDP)-dependent enzyme 1-deoxy-D-xylulose 5-phosphate (DXP) synthase carries out the condensation of pyruvate as a 2-hydroxyethyl donor with d-glyceraldehyde-3-phosphate (d-GAP) as acceptor forming DXP. Toward understanding catalysis of this potential anti-infective drug target, we examined the pathway of the enzyme using steady state and presteady state kinetic methods. It was found that DXP synthase stabilizes the ThDP-bound predecarboxylation intermediate formed between ThDP and pyruvate (C2α-lactylThDP or LThDP) in the absence of D-GAP, while addition of D-GAP enhanced the rate of decarboxylation by at least 600-fold. We postulate that decarboxylation requires formation of a ternary complex with both LThDP and D-GAP bound, and the central enzyme-bound enamine reacts with D-GAP to form DXP. This appears to be the first study of a ThDP enzyme where the individual rate constants could be evaluated by time-resolved circular dichroism spectroscopy, and the results could have relevance to other ThDP enzymes in which decarboxylation is coupled to a ligation reaction. The acceleration of the rate of decarboxylation of enzyme-bound LThDP in the presence of D-GAP suggests a new approach to inhibitor design.
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Affiliation(s)
- Hetalben Patel
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
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32
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Li H, Dai SB, Gao WY. Preparation of Isotope Labeled/Unlabeled Key Intermediates in 2-Methyl-D-erythritol 4-Phosphate Terpenoid Biosynthetic Pathway. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201100396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Smith JM, Vierling RJ, Meyers CF. Selective inhibition of E. coli 1-deoxy-D-xylulose-5-phosphate synthase by acetylphosphonates(). MEDCHEMCOMM 2011; 3:65-67. [PMID: 23326631 DOI: 10.1039/c1md00233c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DXP synthase catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate, an essential precursor in pathogen isoprenoid biosynthesis. The selective inhibition of this ThDP-dependent transformation is a challenging goal in the development of isoprenoid biosynthesis inhibitors. Potent, selective inhibitors could lead to new anti-infective agents. Here, we demonstrate selective inhibition of E. coli DXP synthase by butylacetylphosphonate.
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Affiliation(s)
- Jessica M Smith
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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34
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Brammer LA, Smith JM, Wade H, Meyers CF. 1-Deoxy-D-xylulose 5-phosphate synthase catalyzes a novel random sequential mechanism. J Biol Chem 2011; 286:36522-31. [PMID: 21878632 DOI: 10.1074/jbc.m111.259747] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Emerging resistance of human pathogens to anti-infective agents make it necessary to develop new agents to treat infection. The methylerythritol phosphate pathway has been identified as an anti-infective target, as this essential isoprenoid biosynthetic pathway is widespread in human pathogens but absent in humans. The first enzyme of the pathway, 1-deoxy-D-xylulose 5-phosphate (DXP) synthase, catalyzes the formation of DXP via condensation of D-glyceraldehyde 3-phosphate (D-GAP) and pyruvate in a thiamine diphosphate-dependent manner. Structural analysis has revealed a unique domain arrangement suggesting opportunities for the selective targeting of DXP synthase; however, reports on the kinetic mechanism are conflicting. Here, we present the results of tryptophan fluorescence binding and kinetic analyses of DXP synthase and propose a new model for substrate binding and mechanism. Our results are consistent with a random sequential kinetic mechanism, which is unprecedented in this enzyme class.
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Affiliation(s)
- Leighanne A Brammer
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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35
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Green KD, Porter VR, Zhang Y, Garneau-Tsodikova S. Redesign of Cosubstrate Specificity and Identification of Important Residues for Substrate Binding to hChAT. Biochemistry 2010; 49:6219-27. [DOI: 10.1021/bi1007996] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | - Vanessa R. Porter
- Department of Medicinal Chemistry
- Life Sciences Institute, 210 Washtenaw Avenue
| | - Yaru Zhang
- Life Sciences Institute, 210 Washtenaw Avenue
- Chemical Biology Doctoral Program
| | - Sylvie Garneau-Tsodikova
- Department of Medicinal Chemistry
- Life Sciences Institute, 210 Washtenaw Avenue
- Chemical Biology Doctoral Program
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