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


Genetic

Physiology / Disease

Drug / Dose

Metabolism

Hepatotoxicity

intricate and dynamic 'system-level' interactions.

Hepatotoxicity prediction is hard


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


Cytotoxicity Modules

The glutathione metabolism module The bioenergetics module

Characteristics Non-linear ODE’s Two compartments Fluxes: Enzyme Kinetics/Mass Action


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}


Perturbations

Venzyme =Vmax * [S]

KM + [S]

Vmax [Enzyme]T


The Oxidative Stress Module


The Glutathione Module

d [-GC] /dt = VGCS – VGS

d [GSH] /dt = VGS + VGR – VGPx – Vgsh2ss – Vgsh2ca – VGST – VgshC2M

–VgshM2C


Validation

Drug: Ethacrynic Acid (EA)

Simulation

12

3

Experimental

2

1

3


Asymptotic Analysis

Simulation: Vgcs= 0 Validation

Toxin: Buthionine Sulfoximine (BSO)

Target: -GlutamylCysteine Synthetase (GCS)

Depletes glutathione with a half –life of ~ 2 hours


Thought simulation


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


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


Constraint Based Modeling


Metabolic Control Analysis (MCA)


Future Work

MCA for insights into control and regulation Parameter estimation Experimental validation Scaling laws for metabolic networks


The Linear Approximation


The Linear Approximation

HomeostasisAsymptotic Simulation VGCS = 0Asymptotic Simulation VGS = 0 SS continuation analysis

Parameter : VmaxGS

quantitative modeling of metabolic networks sai jagan mohan, ph.d. sonali das, ph.d. anupama bhat

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