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Quantitative Modeling of Metabolic NetworksQuantitative Modeling of Metabolic Networks
Sai Jagan Mohan, Ph.D.
Sonali Das, Ph.D.
Anupama Bhat.
© Strand Life Sciences 200604/21/23 2
Overview
Problem definition and approach Modules
The glutathione module The bioenergetics module
Complementary modeling approaches Constraint based modeling Metabolic control analysis (MCA)
Summary
© Strand Life Sciences 200604/21/23 3
Genetic
Physiology / Disease
Drug / Dose
Metabolism
Hepatotoxicity
intricate and dynamic 'system-level' interactions.
Hepatotoxicity prediction is hard
© Strand Life Sciences 200604/21/23 4
Our Approach
A comprehensive model of homeostasis metabolism in a liver cell
Toxicity Drug-induced perturbations
Hepatotoxicity: Mechanisms Cell Death of Functional Liver Cells Impaired Bile Flow Faulty Fat Processing
© Strand Life Sciences 200604/21/23 5
Cytotoxicity Modules
The glutathione metabolism module The bioenergetics module
Characteristics Non-linear ODE’s Two compartments Fluxes: Enzyme Kinetics/Mass Action
© Strand Life Sciences 200604/21/23 6
Enzymes => Non-linearity
VGCS = Vmax{[ATP][Glu][Cys]/KmATPKmGlu(1+[GSH]/KiGSH)KmCys} {1+[Glu]/KmGlu(1+[GSH]/KiGSH) + [Glu] [Cys]/ KmGlu (1+[GSH]/KiGlu)KmCys+[Glu][ATP]/KmATPKmGlu(1+[GSH]/KiGSH) + [Glu][Cys][ATP]/KmATPKmGlu(1+[GSH]/KiGSH) KmCys}
© Strand Life Sciences 200604/21/23 9
The Glutathione Module
d [-GC] /dt = VGCS – VGS
d [GSH] /dt = VGS + VGR – VGPx – Vgsh2ss – Vgsh2ca – VGST – VgshC2M
–VgshM2C
© Strand Life Sciences 200604/21/23 10
Validation
Drug: Ethacrynic Acid (EA)
Simulation
12
3
Experimental
2
1
3
© Strand Life Sciences 200604/21/23 11
Asymptotic Analysis
Simulation: Vgcs= 0 Validation
Toxin: Buthionine Sulfoximine (BSO)
Target: -GlutamylCysteine Synthetase (GCS)
Depletes glutathione with a half –life of ~ 2 hours
© Strand Life Sciences 200604/21/23 13
Metabolic Network for Cellular Energetics
TCAcycle
Glycolysis
Malate-Aspartate shuttle
ADP+Pi
ATP
NADH NAD
NAD NADH
OXPHOS
ADP+Pi
ATP
NADH NAD
EnergyUtilisation
ATP
ADP+Pi
Cytosol
Mitochondria
PFK
ANT
MAL
MAL-mito
21 state variables
17 differential equations
4 conservation laws
© Strand Life Sciences 200604/21/23 14
Total adenine pool in the cytosol = ATPe+ ADP
e+AMP
e= constant
Adenylate kinase (ADK) reaction is rapid (operates near equilibrium)
2ADP ATP + AMPADKKeq
Keq = ATP*AMP ADP*ADP = constant
(Ataullakhanov & Vitvitsky Bioscience Reports. 2002 22:501-511)
Conservation Laws
© Strand Life Sciences 200604/21/23 17
Future Work
MCA for insights into control and regulation Parameter estimation Experimental validation Scaling laws for metabolic networks