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RetroPath2.0: A retrosynthesis workflow for metabolic engineers.
Baudoin Delépine1, Thomas Duigou2, Pablo Carbonell3
1CNRS-UMR8030/Laboratoire iSSB, Université Paris-Saclay, Évry 91000, France; CEA, DRF, IG, Genoscope, Évry 91000, France; Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
RetroPath2.0 is an automated workflow that simplifies chemical production by enabling rapid and predictable retrosynthesis pathway design. This open-source tool streamlines the discovery of novel biosynthetic routes for industrial biotechnology.
Area of Science:
- Synthetic biology
- Industrial biotechnology
- Metabolic engineering
Background:
- Chemical production via industrial biotechnology is advancing but remains costly.
- Developing novel design tools for chemical diversity is crucial for next-generation compounds.
- Retrosynthesis approaches face challenges due to complex design spaces.
Purpose of the Study:
- To introduce RetroPath2.0, an automated open-source workflow for retrosynthesis.
- To address the complexity hindering retrosynthesis design space exploration.
- To facilitate rapid and predictable protocols for targeting chemical diversity.
Main Methods:
- RetroPath2.0 employs generalized reaction rules for automated retrosynthesis.
- The workflow performs searches from chassis to target in a controlled protocol.
- It is built using existing bioinformatics and cheminformatics tools.
Main Results:
- RetroPath2.0 streamlines retrosynthesis pathway design.
- The workflow aids in identifying alternative biosynthetic routes and developing biosensors.
- It enhances the design-build-test-learn pipeline for bioproduction optimization.
Conclusions:
- RetroPath2.0 is a valuable, user-friendly tool for biological engineers.
- The open-source nature anticipates community contributions to expand features.
- This workflow significantly reshapes bioproduction optimization through efficient pathway design.
