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Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
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READRetro: natural product biosynthesis predicting with retrieval-augmented dual-view retrosynthesis.
Taein Kim1, Seul Lee2, Yejin Kwak3
1Department of Biological Sciences, KAIST, Daejeon, 34141, Korea.
The New Phytologist
|July 31, 2024
Summary
We developed READRetro, a new tool for predicting plant natural product biosynthesis pathways. This method improves predictions for complex metabolic pathways, aiding in the discovery of plant secondary metabolites.
Area of Science:
- Plant biochemistry and metabolomics
- Bioinformatics and computational biology
- Natural product discovery
Background:
- Plants produce diverse secondary metabolites crucial for ecological interactions and possessing significant biological activity.
- Predicting the complete biosynthetic pathways of these plant natural products from target molecules to metabolic precursors presents a considerable challenge.
- Existing bio-retrosynthesis models often struggle with the complexity of these pathways.
Purpose of the Study:
- To introduce READRetro (retrieval-augmented dual-view retrosynthesis), a novel bio-retrosynthesis tool designed for predicting plant natural product biosynthetic pathways.
- To overcome limitations of conventional models in predicting complex metabolic pathways.
- To provide a practical solution for researchers investigating plant secondary metabolite biosynthesis.
Main Methods:
- READRetro integrates advanced deep learning architectures, an ensemble approach, and dual retrievers for enhanced pathway prediction.
- The model was evaluated on both single- and multi-step retrosynthesis tasks.
- Performance was assessed by its ability to predict known pathways and propose novel ones.
Main Results:
- Each component of READRetro demonstrated a significant improvement in predicting biosynthetic pathways.
- The tool successfully predicted known pathways for secondary metabolites like monoterpene indole alkaloids.
- READRetro also proposed a previously unknown pathway for the natural product menisdaurilide.
Conclusions:
- READRetro offers a practical and effective solution for the bio-retrosynthesis of plant natural products.
- The tool's ability to handle complex pathways and predict novel routes highlights its utility in natural product research.
- A user-friendly website and open-source code are available to facilitate research in plant secondary metabolite biosynthesis and production.
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