Biosynthetic Pathway Design

Synthetic Pathway Design for Metabolic Engineering

Using enzymes as biocatalysts would provide a renewable route for the production of specialty and industrial chemicals. The range of desired products often exceeds those for which existing biosynthetic reactions have been reported, therefore, we have created a in silico pipeline for discovering and engineering new (non-natural) biosynthetic routes.

1. Engineered pathways to produce desired compounds TOC


  • Assembly of known & novel biochemical pathways to produce target compounds
  • Combined systems and molecular-level approaches to assess feasibility of designed biosynthetic routes
  • Systems approaches assess feasibility in the context of pathway thermodynamics
  • Molecular-level approaches assess feasibility of the reaction mechanism
    • substrate promiscuity / substrate ambiguity / catalytic promiscuity
  • Computational collaboration with Prof. Vassily Hatzimanikatis and the LCSB (EPFL)
  • Reference Publications:
    • Brunk, Elizabeth, et al.  Biotechnology and bioengineering 109.2 (2012): 572-582.
    • Lechner, A; Brunk, E; Keasling, JD. The Need for Integrated Approaches in Metabolic Engineering Cold Spring Harbor Perspectives (2016)
    • Brunk, E; et. al. Characterizing Strain Variation in Engineered E. coli Using a Multi-omics based workflow. Cell Systems (2016)