Extreme Pathway Analysis of Human Red Blood Cell Metabolism

Wiback, Sharon J.; Palsson, Bernhard Ø.

doi:10.1016/s0006-3495(02)75210-7

Cited by 149 publications

(132 citation statements)

References 18 publications

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“…The resulting distributions were compared with one another to ensure that no difference was observed. In addition, we sampled the steady-state flux space of the red blood cell model (41) with the ACHR algorithm and evaluated our results with the previously published results from an elimination algorithm to confirm that both algorithms (15) led to the same distributions.…”

Section: Verification Of the Sampling Proceduresmentioning

confidence: 89%

Candidate Metabolic Network States in Human Mitochondria

Thiele

Price

et al. 2005

Journal of Biological Chemistry

136

123

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The human mitochondrial metabolic network was recently reconstructed based on proteomic and biochemical data. Linear programming and uniform random sampling were applied herein to identify candidate steady states of the metabolic network that were consistent with the imposed physico-chemical constraints and available experimental data. The activity of the mitochondrion was studied under four metabolic conditions: normal physiologic, diabetic, ischemic, and dietetic. Pairwise correlations between steady-state reaction fluxes were calculated in each condition to evaluate the dependence among the reactions in the network. Applying constraints on exchange fluxes resulted in predictions for intracellular fluxes that agreed with experimental data. Analyses of the steady-state flux distributions showed that the experimentally observed reduced activity of pyruvate dehydrogenase in vivo could be a result of stoichiometric constraints and therefore would not necessarily require enzymatic inhibition. The observed changes in the energy metabolism of the mitochondrion under diabetic conditions were used to evaluate the impact of previously suggested treatments. The results showed that neither normalized glucose uptake nor decreased ketone body uptake have a positive effect on the mitochondrial energy metabolism or network flexibility. Taken together, this study showed that sampling of the steady-state flux space is a powerful method to investigate network properties under different conditions and provides a basis for in silico evaluations of effects of potential disease treatments.The emergence of genomic, metabolic, and proteomic data has facilitated the reconstruction of genome-scale metabolic networks. Various network reconstructions have been carried out in recent years for microorganisms such as Escherichia coli (1), Saccharomyces cerevisiae (2), Helicobacter pylori (3), Haemophilus influenzae (4), and Geobacter sulferreducans.1 Most recently, proteomics data (6, 7) were utilized to reconstruct the metabolic network of the human cardiac mitochondrion (8).Constraint-based analyses have proven to be valuable for studying genome-scale metabolic networks. The constraintbased approach is based on the fact that cellular networks are constrained to operate within boundaries set by physico-chemical constraints (mass conservation, directional flow, enzymatic capacity, etc). In this study, uniform random sampling was used to calculate candidate steady-state flux distributions in the human cardiac mitochondrion under different sets of constraints representing various physiological conditions. Experimental data from many literature sources were integrated as physico-chemical constraints of the mitochondrial metabolic network. Constraints based on these experimental data were applied to segment the steady-state flux space defined by mass-balance constraints. This segmentation resulted in a characterization of all feasible steadystate flux distributions, termed candidate steady-state flux distributions, that occurred under each speci...

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Section: Verification Of the Sampling Proceduresmentioning

confidence: 89%

Candidate Metabolic Network States in Human Mitochondria

Thiele

Price

et al. 2005

Journal of Biological Chemistry

136

123

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“…Experiments demonstrate that this works well under controlled conditions [12,13], and it can be supported by examining population dynamics for continuous culture growth in a chemostat [19]. Other choices could and perhaps should be made in different circumstances [20,21,22]. In terms of the thermodynamic LP problem, this biologically-motivated component is translated into the existence of a growth reaction with a minimal free energy drain B * .…”

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confidence: 99%

Duality, Thermodynamics, and the Linear Programming Problem in Constraint-Based Models of Metabolism

Warren

Jones

2007

Phys. Rev. Lett.

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It is shown that the dual to the linear programming problem that arises in constraint-based models of metabolism can be given a thermodynamic interpretation in which the shadow prices are chemical potential analogues, and the objective is to minimise free energy consumption given a free energy drain corresponding to growth. The interpretation is distinct from conventional non-equilibrium thermodynamics, although it does satisfy a minimum entropy production principle. It can be used to motivate extensions of constraint-based modelling, for example to microbial ecosystems.PACS numbers: 05.70. Ln, In biology, the metabolism of an organism provides energy and raw materials for maintenance and growth. As such, an interesting and important question concerns the application of thermodynamics to metabolic reaction networks [1,2,3,4]. For example, Prigogine and Wiame suggested a long time ago that an organism's metabolism might be governed by a minimum entropy production (MEP) principle [5]. From the physical point of view, a metabolic reaction network is an excellent example of a system in a non-equilibrium steady state, since one can usually assume that the metabolite concentrations are unchanging after a short transient relaxation period. The appropriate generalisation of thermodynamics and statistical mechanics to non-equilibrium steady-states is a large field [6], which continues to attract attention to this present day [7]. In this Letter, we show that a novel thermodynamic interpretation can be given to the dual linear programming problem which arises in constraintbased models of metabolism. The resulting interpretation is rigorously defined, and uniquely determined by the mathematics. It is closely analogous to, but distinctly different from, conventional non-equilibrium thermodynamics. We also show that it satisfies an MEP principle similar to that proposed by Prigogine and Wiame.Constraint-based modelling (CBM) of metabolic networks has been pioneered by Palsson and co-workers [8]. In a typical application, described in more detail below, the steady-state assumption is combined with a target function to make a linear optimisation or linear programming (LP) problem. The LP variables are the fluxes through the various reactions that comprise the network, and the LP constraints arise from basic considerations of stoichiometry and from the reversibility or otherwise of the reactions. The LP objective function is biologically motivated, for example a 'growth' reaction is commonly inserted, and the target is to maximise flux through this reaction to correspond to maximal growth rate. CBM has been applied to microorganisms from all three domains of life [9,10,11], and has been remarkably successful in predicting phenotypic behaviour [12,13,14].Mathematically, every LP problem has a unique dual [15]. It was in determining the dual to the CBM LP problem that we noticed a striking analogy to non-equilibrium thermodynamics. Let us start therefore with a general discussion of LP duality, before specialising to the case of ...

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“…The primary physiological objective of red blood cells (RBCs) is gas transport and exchange. Beyond this, they perform metabolic functions to produce the necessary cofactors (ATP, NADPH, and NADH) enzymatically for their own persistence (Bossi and Giardina, 1996;Wiback and Palsson, 2002). Though various enzymes in RBCs can metabolize drugs (Carruthers and Melchior, 1988;Hooks, 1994), systematic investigation of whole blood metabolism of therapeutic drugs has been, according to some researchers, traditionally neglected in drug discovery and development (Cossum, 1988;Hinderling, 1997).…”

mentioning

confidence: 99%

Identification of the in Vitro Metabolites of 3,4-Dihydro-2,2-dimethyl-2H-naphthol[1,2-b]pyran-5,6-dione (ARQ 501; β-Lapachone) in Whole Blood

Miao¹,

Song²,

Savage³

et al. 2008

Drug Metab Dispos

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ABSTRACT:3,4-Dihydro-2,2-dimethyl-2H-naphthol[1,2-b]pyran-5,6-dione (ARQ 501; ␤-lapachone) showed promising anticancer activity in phase I clinical trials as monotherapy and in combination with cytotoxic drugs. ARQ 501 is currently in multiple phase II clinical trials. In vitro incubation in fresh whole blood at 37°C revealed that ARQ 501 is stable in plasma but disappears rapidly in whole blood. Our data showed that extensive metabolism in red blood cells (RBCs) was mainly responsible for the rapid disappearance of ARQ 501 in whole blood. By comparison, covalent binding of ARQ 501 and/or its metabolites to whole blood components was a minor contributor to the disappearance of this compound. Sequestration of intact ARQ 501 in RBCs was not observed. Cross-species metabolite profiles from incubating [ 14 C]ARQ 501 in freshly drawn blood were characterized using a liquid chromatography-mass spectrometry-accurate radioactivity counter. The results show that ARQ 501 was metabolized more rapidly in mouse and rat blood than in dog, monkey, and human blood, with qualitatively similar metabolite profiles. Six metabolites were identified in human blood using ultra-high performance liquid chromatography/time-of-flight mass spectrometry, and the postulated structure of five metabolites was confirmed using synthetic standards. We conclude that the primary metabolic pathway of ARQ 501 in human blood involved oxidation of the two adjacent carbonyl groups to produce dicarboxylic and monocarboxylic metabolites, elimination of a carbonyl group to form a ring-contracted metabolite, and lactonization to produce two metabolites with a pyrone ring to form a ring-contracted metabolite. Metabolism by RBCs may play a role in clearance of ARQ 501 from the blood compartment in cancer patients.

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Extreme Pathway Analysis of Human Red Blood Cell Metabolism

Cited by 149 publications

References 18 publications

Candidate Metabolic Network States in Human Mitochondria

Candidate Metabolic Network States in Human Mitochondria

Duality, Thermodynamics, and the Linear Programming Problem in Constraint-Based Models of Metabolism

Identification of the in Vitro Metabolites of 3,4-Dihydro-2,2-dimethyl-2H-naphthol[1,2-b]pyran-5,6-dione (ARQ 501; β-Lapachone) in Whole Blood

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