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From reactants to products: computational methods for biosynthetic pathway design

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Title: From reactants to products: computational methods for biosynthetic pathway design
Authors: Shaozhen Ding, Dongliang Liu, Yu Tian, Dachuan Zhang, HuaDong Xing, Junni Chen, Zhiguo Liu, Qian-Nan Hu
Source: Synth Syst Biotechnol
Synthetic and Systems Biotechnology, Vol 10, Iss 3, Pp 1038-1049 (2025)
Publisher Information: Elsevier BV, 2025.
Publication Year: 2025
Subject Terms: QH301-705.5, Review Article, Methods of retrosynthetic analysis, Biology (General), Enzyme engineering, TP248.13-248.65, Biological big-data, Biotechnology
Description: One of the main goals in synthetic biology is to produce value-added compounds from available precursors using enzymatic approaches. The construction of biosynthetic pathways for synthesizing target molecules plays a crucial role in this process. However, it is challenging and time-consuming for researchers to design efficient pathways manually. In recent decades, pathway design has advanced through data- and algorithm-driven approaches. In this article, we review key computational tools involved in biosynthetic pathway design, covering: 1) Biological Big-Data including compounds, reactions/pathways and enzymes. 2) Retrosynthesis methods leveraging multi-dimensional biosynthesis data to predict potential pathways for target compounds synthesis. 3) Enzyme engineering relying on data mining to identify/de novo design enzymes with desired functions. Integrating these three key components can significantly enhance the efficiency and accuracy of biosynthetic pathway design in synthetic biology.
Document Type: Article
Other literature type
Language: English
ISSN: 2405-805X
DOI: 10.1016/j.synbio.2025.05.005
Access URL: https://doaj.org/article/a5076a45cbe74d0e8d8470c3d9dc52e4
Rights: CC BY NC ND
Accession Number: edsair.doi.dedup.....bfb58897151cf90d7a3c30ae03568c48
Database: OpenAIRE
Description
Abstract:One of the main goals in synthetic biology is to produce value-added compounds from available precursors using enzymatic approaches. The construction of biosynthetic pathways for synthesizing target molecules plays a crucial role in this process. However, it is challenging and time-consuming for researchers to design efficient pathways manually. In recent decades, pathway design has advanced through data- and algorithm-driven approaches. In this article, we review key computational tools involved in biosynthetic pathway design, covering: 1) Biological Big-Data including compounds, reactions/pathways and enzymes. 2) Retrosynthesis methods leveraging multi-dimensional biosynthesis data to predict potential pathways for target compounds synthesis. 3) Enzyme engineering relying on data mining to identify/de novo design enzymes with desired functions. Integrating these three key components can significantly enhance the efficiency and accuracy of biosynthetic pathway design in synthetic biology.
ISSN:2405805X
DOI:10.1016/j.synbio.2025.05.005