Drug Target Selection for Trypanosoma cruzi Metabolism by Metabolic Control Analysis and Kinetic Modeling

2019 ◽  
Vol 26 (36) ◽  
pp. 6652-6671 ◽  
Author(s):  
Emma Saavedra ◽  
Zabdi González-Chávez ◽  
Rafael Moreno-Sánchez ◽  
Paul A.M. Michels
Keyword(s):  
Trypanosoma Cruzi ◽  
Metabolic Control ◽  
Kinetic Modeling ◽  
Metabolic Pathways ◽  
Drug Target ◽  
Metabolic Modeling ◽  
Metabolic Control Analysis ◽  
Control Analysis ◽  
Control Coefficient ◽  
Flux Control

In the search for therapeutic targets in the intermediary metabolism of trypanosomatids the gene essentiality criterion as determined by using knock-out and knock-down genetic strategies is commonly applied. As most of the evaluated enzymes/transporters have turned out to be essential for parasite survival, additional criteria and approaches are clearly required for suitable drug target prioritization. The fundamentals of Metabolic Control Analysis (MCA; an approach in the study of control and regulation of metabolism) and kinetic modeling of metabolic pathways (a bottom-up systems biology approach) allow quantification of the degree of control that each enzyme exerts on the pathway flux (flux control coefficient) and metabolic intermediate concentrations (concentration control coefficient). MCA studies have demonstrated that metabolic pathways usually have two or three enzymes with the highest control of flux; their inhibition has more negative effects on the pathway function than inhibition of enzymes exerting low flux control. Therefore, the enzymes with the highest pathway control are the most convenient targets for therapeutic intervention. In this review, the fundamentals of MCA as well as experimental strategies to determine the flux control coefficients and metabolic modeling are analyzed. MCA and kinetic modeling have been applied to trypanothione metabolism in Trypanosoma cruzi and the model predictions subsequently validated in vivo. The results showed that three out of ten enzyme reactions analyzed in the T. cruzi anti-oxidant metabolism were the most controlling enzymes. Hence, MCA and metabolic modeling allow a further step in target prioritization for drug development against trypanosomatids and other parasites.

Metabolic control analysis of the Trypanosoma cruzi peroxide detoxification pathway identifies tryparedoxin as a suitable drug target

2015 ◽  
Vol 1850 (2) ◽  
pp. 263-273 ◽  
Author(s):  
Zabdi González-Chávez ◽  
Viridiana Olin-Sandoval ◽  
José Salud Rodíguez-Zavala ◽  
Rafael Moreno-Sánchez ◽  
Emma Saavedra
Keyword(s):  
Trypanosoma Cruzi ◽  
Metabolic Control ◽  
Drug Target ◽  
Metabolic Control Analysis ◽  
Control Analysis ◽  
Detoxification Pathway

scholarly journals Metabolic Control Analysis of Exponential Growth and Product Formation

2018 ◽  
Author(s):  
David Andrew Fell
Keyword(s):  
Steady State ◽  
Metabolic Control ◽  
Product Yield ◽  
Product Formation ◽  
Metabolic Control Analysis ◽  
Control Analysis ◽  
Control Coefficient ◽  
Flux Control ◽  
Flux Control Coefficient ◽  
Metabolic Fluxes

Metabolic Control Analysis defines the relationships between the change in activity of an enzyme and the resulting impacts on metabolic fluxes and metabolite concentrations at steady state. In many biotechnological applications of metabolic engineering, however, the goal is to alter the product yield. In this case, although metabolism may be at a pseudo-steady state, the amount of biomass catalysing the metabolism can be growing exponentially. Here, expressions are derived that relate the change in activity of an enzyme and its flux control coefficient to the change in yield from an exponentially growing system. Conversely, the expressions allow estimation of an enzyme's flux control coefficient over the pathway generating the product from measurements of the changes in enzyme activity and yield.

scholarly journals Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

1997 ◽  
Vol 321 (1) ◽  
pp. 133-138 ◽  
Author(s):  
Jens NIELSEN
Keyword(s):  
Metabolic Control ◽  
Reaction Rate ◽  
Reaction Rates ◽  
Rate Function ◽  
Metabolic Control Analysis ◽  
Control Analysis ◽  
Flux Control ◽  
Biochemical Pathways ◽  
Flux Control Coefficients

Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction affinity. This parameter can often be determined from experiments in vitro. The methodology is applicable only to the analysis of simple two-step pathways, but in many cases larger pathways can be lumped into two overall conversions. In cases where this cannot be done it is necessary to apply an extension of the thermokinetic description of reaction rates to include the influence of effectors. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919–927] can be much more widely applied, although it was originally based on linearized kinetics. The methodology of determining elasticity coefficients directly from pool levels is illustrated with an analysis of the first two steps of the biosynthetic pathway of penicillin. The results compare well with previous findings based on a kinetic analysis.

scholarly journals Thermodynamic constraints on the regulation of metabolic fluxes

2018 ◽  
Author(s):  
Ziwei Dai ◽  
Jason W. Locasale
Keyword(s):  
Metabolic Control ◽  
Metabolic Pathways ◽  
Metabolic Control Analysis ◽  
Control Analysis ◽  
Specific Enzyme ◽  
Metabolic Fluxes ◽  
Activity Of Enzymes ◽  
Far From Equilibrium ◽  
Physical Variables ◽  
The Given

AbstractNutrition and metabolism are fundamental to cellular function in physiological and pathological contexts. Metabolic activity (i.e. rates, flow, or most commonly referred to as flux) is constrained by thermodynamics and regulated by the activity of enzymes. The general principles that relate biological and physical variables to metabolic control are incompletely understood. Using metabolic control analysis in several representative topological structures of metabolic pathways as models, we derive exact results and conduct computer simulations that define relationships between thermodynamics, enzyme activity, and flux control. We confirm that metabolic pathways that are very far from equilibrium are controlled by the activity of upstream enzymes. However, in general, metabolic pathways have a more adaptable pattern of regulation, controlled minimally by thermodynamics and not necessarily by the specific enzyme that generates the given reaction. These findings show how the control of metabolic pathways, which are rarely very far from equilibrium, is largely set by the overall flux through a pathway rather than by the enzyme which generates the flux or by thermodynamics.

Metabolic Control Analysis for Drug Target Prioritization in Trypanosomatids

2020 ◽  
pp. 689-718
Author(s):  
Zabdi González-Chávez ◽  
Citlali Vázquez ◽  
Rafael Moreno-Sánchez ◽  
Emma Saavedra
Keyword(s):  
Metabolic Control ◽  
Drug Target ◽  
Metabolic Control Analysis ◽  
Control Analysis

scholarly journals Metabolic control analysis of anaerobic glycolysis in human hibernating myocardium replaces traditional concepts of flux control

FEBS Letters ◽  
2002 ◽  
Vol 517 (1-3) ◽  
pp. 245-250 ◽  
Author(s):  
Achim M. Vogt ◽  
Holger Nef ◽  
Jutta Schaper ◽  
Mark Poolman ◽  
David A. Fell ◽  
...  
Keyword(s):  
Metabolic Control ◽  
Metabolic Control Analysis ◽  
Hibernating Myocardium ◽  
Control Analysis ◽  
Anaerobic Glycolysis ◽  
Flux Control

scholarly journals Metabolic Control Analysis of glycolysis in tuber tissue of potato (Solanum tuberosum): explanation for the low control coefficient of phosphofructokinase over respiratory flux

1997 ◽  
Vol 322 (1) ◽  
pp. 119-127 ◽  
Author(s):  
Simon THOMAS ◽  
Peter J. F. MOONEY ◽  
Michael M. BURRELL ◽  
David A. FELL
Keyword(s):  
Potato Tuber ◽  
Metabolic Control ◽  
Kinetic Data ◽  
Metabolic Control Analysis ◽  
Glycolytic Flux ◽  
Control Analysis ◽  
Tuber Tissue ◽  
Flux Control ◽  
Calculated Concentration ◽  
Control Coefficients

We have applied Metabolic Control Analysis (MCA) in an attempt to determine the distribution of glycolytic flux control between the steps of glycolysis in aged disks of potato tuber under aerobic conditions, using concentrations of glycolytic metabolites in tuber tissue from a range of transgenic potato plants and published enzyme kinetic data. We modelled the substrate and effector kinetics of potato tuber phosphofructokinase (PFK) by reanalysing published results. Despite the scarcity of reliable kinetic data, our results are in agreement with experimental findings namely that, under the conditions described, PFK has little control over glycolytic flux. Furthermore our analysis predicts that under these conditions far more control lies in the dephosphorylation of phosphoenolpyruvate and/or in the steps beyond. We have validated the results of our analysis in two ways. First, predictions based on calculated concentration control coefficients from the analysis show generally good agreement with observed metabolite deviation indices discussed in the preceding paper [Thomas, Mooney, Burrell, and Fell (1997) Biochem. J.322, 111Ő117]. Second, sensitivity analysis of our results shows that the calculated control coefficients are robust to errors in the elasticities used in the analysis, of which relatively few need to be known accurately. Experimental and control analysis results agree with previous predictions of MCA that strong co-operative feedback inhibition of enzymes serves to move flux control downstream of the inhibiting metabolite. We conclude that MCA can successfully model the outcome of experiments in the genetic manipulation of enzyme amounts.

scholarly journals The flux control coefficient of carnitine palmitoyltransferase I on palmitate β-oxidation in rat hepatocyte cultures

1997 ◽  
Vol 323 (1) ◽  
pp. 119-122 ◽  
Author(s):  
Tracey D. SPURWAY ◽  
H. Stanley A. SHERRATT ◽  
Christopher I. POGSON ◽  
Loranne AGIUS
Keyword(s):  
Metabolic Control Analysis ◽  
Carnitine Palmitoyltransferase ◽  
Control Analysis ◽  
Control Coefficient ◽  
Irreversible Inhibitor ◽  
Rat Hepatocyte ◽  
Flux Control ◽  
Flux Control Coefficient ◽  
Carnitine Palmitoyltransferase I ◽  
Cpt I

Two important factors that determine the flux of hepatic β-oxidation of long-chain fatty acids are the availability of fatty acid and the activity of carnitine palmitoyltransferase I (CPT I). Using Metabolic Control Analysis, the flux control coefficient of CPT I in rat hepatocyte monolayers was determined by titration with 2-[6-(4-chlorophenoxy)hexyl]oxirane-2-carboxylate (Etomoxir), which is converted to Etomoxir-CoA, an irreversible inhibitor of CPT I. We measured CPT I activity and flux through β-oxidation at 0.2 mM and 1.0 mM palmitate to simulate substrate concentrations in fed and fasted states. Rates of β-oxidation were 4.5-fold higher at 1.0 mM palmitate compared with 0.2 mM palmitate. Flux control coefficients of CPT I, estimated by two independent methods, were similar: 0.67 and 0.79 for 0.2 mM palmitate, and 0.68 and 0.77 for 1 mM palmitate. It is concluded that the regulatory potential of CPT I is similar at low and high physiological concentrations of palmitate.

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