Unraveling unknowns of plant secondary metabolites through retrosynthesis

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Yönet N., Yilmaz A.

EMBO Workshop: Chemical Biology 2022, Heidelberg, Germany, 5 - 08 September 2022, pp.194

  • Publication Type: Conference Paper / Summary Text
  • City: Heidelberg
  • Country: Germany
  • Page Numbers: pp.194
  • Yıldız Technical University Affiliated: Yes


Plant secondary metabolites constitute a useful array of natural ingredients especially for
therapeutics and additives for the food industry and many other industrial fields. Thereby,
metabolic engineers are looking for alternative strategies that may be more efficient for the
enhancement of valuable secondary metabolite production quality and quantity. However,
the knowledge of production pathways and related enzymes of secondary metabolites is
quite scarce. In this study, we aim to build a database storing paths between source and
target molecules where intermediates are known metabolites of a given organism (plant
and/or Escherichia coli).
The tool that is predominantly used in this study to reveal the unknowns of production
pathways is RetroPath2.0 workflow on KNIME analytics platform. It is a retrosynthesis tool
that can suggest possible production pathways for a given molecule along with precursors
and intermediate molecules and enzymes, by processing reaction rules and available
compounds in the environment. The output of RetroPath2.0 contains possible pathways
ranked according to feasibility.
The RetroPath2.0 tool is being executed for thousands of molecules to discover their
possible production pathways in a common plant metabolites pool, and in E. coli metabolites
pool. The resulting pathway suggestions are integrated to the database. This procedure
serves as a promising method to uncover the unknowns of plant metabolome and propose
new efficient production pathways. Thus, it has the potential to make industrial production
more efficient.
This study is supported by Yildiz Technical University Scientific Research Projects
Coordination Unit with the project number FBA-2021-4698.