Metabolic Pathway Alignment Based on Similarity between Chemical Structures

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  • Tohsato Yukako
    Department of Bioscience and Bioinformatics, College of Information Science and Engineering, Ritsumeikan University
  • Nishimura Yu
    Information Science and Systems Engineering, Graduate School of Science and Engineering, Ritsumeikan University

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In many of the chemical reactions in living cells, enzymes act as catalysts in the conversion of certain compounds (substrates) into other compounds (products). Metabolic pathways are formed as the products of these reactions are used as the substrates of other reactions. Comparative analyses of the metabolic pathways among species provide important information on both evolution and potential pharmacological targets. Here, we propose a method to align the metabolic pathways based on similarities between chemical structures. To measure the degree of chemical similarity, we formalized a scoring system using the MACCS keys and the Tanimoto/Jaccard coefficients. To determine the effectiveness of our method, it was applied to analyses of metabolic pathways in Escherichia coli. The results revealed compound similarities between fructose and mannose biosynthesis and galactose biosynthesis pathways.

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