Quantitative Modeling of Metabolic Networks Sai Jagan Mohan, Ph.D. Sonali Das, Ph.D. Anupama Bhat.
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Transcript of Quantitative Modeling of Metabolic Networks Sai Jagan Mohan, Ph.D. Sonali Das, Ph.D. Anupama Bhat.
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