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Nakayama, Yoichi; Kinoshita, Ayako; Tomita, Masaru

doi:10.1186/1742-4682-2-18

Cited by 51 publications

(14 citation statements)

References 35 publications

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“…For the erythrocyte multiple metabolic networks have been published that comprise the cell's core metabolism, including glycolysis, pentose phosphate pathway, glutathione metabolism and adenine nucleotide metabolism (see [33,34] and contained references). However, these networks lack metabolic pathways providing cofactors such as thiamin diphosphate and pyridoxal phosphate that are required for full cellular function.…”

Section: Resultsmentioning

confidence: 99%

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

et al. 2010

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BackgroundDespite enormous efforts to combat malaria the disease still afflicts up to half a billion people each year of which more than one million die. Currently no approved vaccine is available and resistances to antimalarials are widely spread. Hence, new antimalarial drugs are urgently needed.ResultsHere, we present a computational analysis of the metabolism of Plasmodium falciparum, the deadliest malaria pathogen. We assembled a compartmentalized metabolic model and predicted life cycle stage specific metabolism with the help of a flux balance approach that integrates gene expression data. Predicted metabolite exchanges between parasite and host were found to be in good accordance with experimental findings when the parasite's metabolic network was embedded into that of its host (erythrocyte). Knock-out simulations identified 307 indispensable metabolic reactions within the parasite. 35 out of 57 experimentally demonstrated essential enzymes were recovered and another 16 enzymes, if additionally the assumption was made that nutrient uptake from the host cell is limited and all reactions catalyzed by the inhibited enzyme are blocked. This predicted set of putative drug targets, shown to be enriched with true targets by a factor of at least 2.75, was further analyzed with respect to homology to human enzymes, functional similarity to therapeutic targets in other organisms and their predicted potency for prophylaxis and disease treatment.ConclusionsThe results suggest that the set of essential enzymes predicted by our flux balance approach represents a promising starting point for further drug development.

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Section: Resultsmentioning

confidence: 99%

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

et al. 2010

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“…Yet, as the YMDB, this database is still far from complete. Though all metabolites in our panel of glycolytic and PPP intermediates were entered for body fluids, recordings of intracellular levels were scarce, in fact just collected from one publication describing one specific cell type [67]. The detected differences in the cell lines of our panel indicate that the metabolite levels of one cell type are not necessarily representative of metabolite levels in another cell type.…”

Section: Discussionmentioning

confidence: 98%

Absolute Quantification of the Central Carbon Metabolome in Eight Commonly Applied Prokaryotic and Eukaryotic Model Systems

et al. 2020

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Absolute quantification of intracellular metabolite pools is a prerequisite for modeling and in-depth biological interpretation of metabolomics data. It is the final step of an elaborate metabolomics workflow, with challenges associated with all steps—from sampling to quantifying the physicochemically diverse metabolite pool. Chromatographic separation combined with mass spectrometric (MS) detection is the superior platform for high coverage, selective, and sensitive detection of metabolites. Herein, we apply our quantitative MS-metabolomics workflow to measure and present the central carbon metabolome of a panel of commonly applied biological model systems. The workflow includes three chromatographic methods combined with isotope dilution tandem mass spectrometry to allow for absolute quantification of 68 metabolites of glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and the amino acid and (deoxy) nucleoside pools. The biological model systems; Bacillus subtilis, Saccharomyces cerevisiae, two microalgal species, and four human cell lines were all cultured in commonly applied culture media and sampled in exponential growth phase. Both literature and databases are scarce with comprehensive metabolite datasets, and existing entries range over several orders of magnitude. The workflow and metabolite panel presented herein can be employed to expand the list of reference metabolomes, as encouraged by the metabolomics community, in a continued effort to develop and refine high-quality quantitative metabolomics workflows.

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“…Comprehensive models of erythrocyte glycolysis, the pentose phosphate pathway, 2,3-bisphosphoglycerate metabolism (12,(15)(16)(17), and the regulation of erythrocyte volume, pH, and transmembrane electrolyte distribution (18 -20) have all been developed and used to provide insights into various biophysical and biochemical mechanisms and the regulation of erythrocyte function. Although models used to simulate certain aspects of glutathione function have been developed (21,22), until now there have been no detailed and comprehensive models of glutathione metabolism based on realistic enzyme mechanisms and estimates of steady-state kinetic parameters.An understanding of glutathione metabolism in the erythrocyte has been developed from information gained by investigating the kinetics of isolated enzymes. Such information allows the prediction that increased activity of the ␥-glutamatecysteine ligase (GCL), increased substrate availability, and decreased GSH concentrations in the cell should all increase the rate of glutathione synthesis; but it is not possible to predict the magnitude of the increases or the interactions that produce a particular steady-state concentration without a comprehensive mathematical model (23).…”

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confidence: 99%

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confidence: 99%

Glutathione Synthesis and Turnover in the Human Erythrocyte

Raftos

Whillier

Kuchel

2010

Journal of Biological Chemistry

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The erythrocyte is exposed to reactive oxygen species in the circulation and also to those produced by autoxidation of hemoglobin. Consequently, erythrocytes depend on protection by the antioxidant glutathione. Mathematical models based on realistic kinetic data have provided valuable insights into the regulation of biochemical pathways within the erythrocyte but none have satisfactorily accounted for glutathione metabolism. In the current model, rate equations were derived for the enzyme-catalyzed reactions, and for each equation the nonlinear algebraic relationship between the steady-state kinetic parameters and the unitary rate constants was derived. The model also includes the transport processes that supply the amino acid constituents of glutathione and the export of oxidized glutathione. Values of the kinetic parameters for the individual reactions were measured predominately using isolated enzymes under conditions that differed from the intracellular environment. By comparing the experimental and simulated results, the values of the enzyme-kinetic parameters of the model were refined to yield conformity between model simulations and experimental data. Model output accurately represented the steady-state concentrations of metabolites in erythrocytes suspended in plasma and the changing glutathione concentrations in whole and hemolyzed erythrocytes under specific experimental conditions. Analysis indicated that feedback inhibition of ␥-glutamate-cysteine ligase by glutathione had a limited effect on steady-state glutathione concentrations and was not sufficiently potent to return glutathione concentrations to normal levels in erythrocytes exposed to sustained increases in oxidative load.Erythrocyte glutathione plays a vital role in mitigating the damaging effects of reactive oxygen species (ROS) 4 encountered in the circulation (1) and produced by continuous oxidation of hemoglobin within the cytosol of the erythrocyte (2, 3). Reduced glutathione (GSH) reacts with superoxide reaction products, and via specific enzymes, it degrades hydrogen peroxide and lipid peroxides (glutathione peroxidase, EC 1.11.1.9), and covalently modifies toxic xenobiotics and endogenous electrophiles (glutathione S-transferase, EC 2.5.1.18) to form water-soluble conjugates that are exported from the erythrocyte for excretion (4). In diseases associated with increased production of ROS that results in GSH depletion, restoration of the normal erythrocyte GSH concentration has been shown to have positive therapeutic effects (5, 6).Experimental studies have provided a wealth of information on the individual reactions that together underlie the metabolic processes of the human erythrocyte (7)(8)(9)(10)(11)(12)(13)(14). This information has been used to develop mathematical models to analyze and then predict the way in which the kinetic characteristics and control mechanisms for each reaction combine to regulate particular metabolic processes. Comprehensive models of erythrocyte glycolysis, the pentose phosphate pathway, 2,3-bisphosphogl...

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Abstract: The results of the simulation were consistent with the estimated situation of real G6PD-deficient cells. These results suggest that the de novo glutathione synthesis pathway and the GSSG export system play an important role in alleviating the consequences of G6PD deficiency.

Cited by 51 publications

References 35 publications

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

Absolute Quantification of the Central Carbon Metabolome in Eight Commonly Applied Prokaryotic and Eukaryotic Model Systems

Glutathione Synthesis and Turnover in the Human Erythrocyte

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