Computational discovery of biochemical routes to specialty chemicals

A computational framework has been developed for the construction and evaluation of metabolic pathways given input substrates and knowledge of enzyme-catalyzed reactions. Application of the framework creates new and existing routes to both chems. known to exist in biol. systems and chems. novel to biol. systems. In the present application, we focus on biosynthetic routes to 7-carboxyindole, a specialty chem. currently produced by org. synthesis, using chorismate as a starting compd. and the enzyme actions native to the biosynthetic route from chorismate to tryptophan. Graph theory and its assocd. algorithms are exploited to represent mols. and perform enzyme-catalyzed reactions. Through repetitive application of the set of operators representing the enzymic reactions of interest to the reactants and their progeny, reaction pathways are generated automatically. The concept of generalized enzyme function is introduced and defined as the third-level enzyme function (EC i.j.k) according to the four-digit transformations of the enzyme classification system (EC i.j.k.l). This concept maps enzyme-catalyzed reactions to transformations of functional groups and enables the generation of novel species and pathways. Thermodn. properties are calcd. using a group contribution method "on-the-fly" in order to provide one assessment of the relative feasibility of the novel pathways. [on SciFinder (R)]


Published in:
Chemical Engineering Science, 59, 22-23, 5051-5060
Year:
2004
Keywords:
Note:
16-6 FIELD Section Title:Fermentation and Bioindustrial Chemistry
10, 48
Department of Chemical and Biological Engineering,Northwestern University,Evanston,IL,USA. FIELD URL:
written in English.
Laboratories:


Note: The status of this file is: EPFL only


 Record created 2007-01-11, last modified 2018-03-17

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