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Biochemical Reaction Network Modeling

Biochemical reaction network (BRN) modeling is an outgrowth of biochemistry and reaction network modeling that was historically used in chemical and petroleum engineering and more recently in a limited context for biological applications. It is an in silico approach that can predict the chemical structures of the metabolites of one or a mixture of chemicals, generate the metabolic pathways, and interconnect these pathways through metabolites in common.

We have been working to develop an in silico BRN modeling framework that we call BioTRaNS (Biochemical Tool for Reaction Network Simulation). Once validated with experimental data, this methodology can predict and simulate in a quantitative and time-dependent manner the formation and disappearance of all metabolites, including potentially toxic reactive intermediates, such as epoxides. Thus, it can aid in predicting drug metabolism, toxicity, and understanding the modes of action of individual chemicals as well as chemical mixtures.

Simulation Results
Illustrations of the power and flexibility of the software framework.
Structure and Flow
Details about the structure and flow of information through the software framework.

Representative Group Publications:

  • Mayeno, A., Yang, R.S.H, Reisfeld, B. (2005) Biochemical Reaction Network Modeling: Predicting Metabolism of Organic Chemical Mixtures. Env. Sci. Tech. 39 (14), 5363-71.
  • Yang, R.S.H, El-Masri, H., Thomas, R.S., Dobrev, I.D., Dennison, J.E., Bae, D., Campain, J.A., Liao, K.H., Reisfeld B., Andersen M.E., Mumtaz, M. (2004) Chemical Mixture Toxicology: From Descriptive to Mechanistic, and Going on to In Silico Toxicology. Env. Tox. Pharm. 18 (2), 65-81.
  • Reisfeld, B., Yang, R.S.H. (2004) A Reaction Network Model for CYP2E1-Mediated Metabolism of Toxicant Mixtures. Env. Tox. Pharm. 18 (2), 173-179.
  • Reisfeld, B., Mayeno, A., Yang, R.S.H. (2004) Predictive Metabolomics: The Use Of Biochemical Reaction Network Modeling for the Analysis of Toxicant Metabolism. Drug Met. Rev. 36, Suppl. 1.
  • Reisfeld B, Reardon K, Yang R (2003) A reaction network model for CYP2E1-mediated metabolism of toxicants. Toxicol. Sci. 72 (1): 175 Suppl. S, Mar.