Xueying Xie, Lin Gui, Baixue Qiao, Guohua Wang, Shan Huang, Yuming Zhao, Shanwen Sun
{"title":"Deep learning in template-free de novo biosynthetic pathway design of natural products.","authors":"Xueying Xie, Lin Gui, Baixue Qiao, Guohua Wang, Shan Huang, Yuming Zhao, Shanwen Sun","doi":"10.1093/bib/bbae495","DOIUrl":null,"url":null,"abstract":"<p><p>Natural products (NPs) are indispensable in drug development, particularly in combating infections, cancer, and neurodegenerative diseases. However, their limited availability poses significant challenges. Template-free de novo biosynthetic pathway design provides a strategic solution for NP production, with deep learning standing out as a powerful tool in this domain. This review delves into state-of-the-art deep learning algorithms in NP biosynthesis pathway design. It provides an in-depth discussion of databases like Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and UniProt, which are essential for model training, along with chemical databases such as Reaxys, SciFinder, and PubChem for transfer learning to expand models' understanding of the broader chemical space. It evaluates the potential and challenges of sequence-to-sequence and graph-to-graph translation models for accurate single-step prediction. Additionally, it discusses search algorithms for multistep prediction and deep learning algorithms for predicting enzyme function. The review also highlights the pivotal role of deep learning in improving catalytic efficiency through enzyme engineering, which is essential for enhancing NP production. Moreover, it examines the application of large language models in pathway design, enzyme discovery, and enzyme engineering. Finally, it addresses the challenges and prospects associated with template-free approaches, offering insights into potential advancements in NP biosynthesis pathway design.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":null,"pages":null},"PeriodicalIF":6.8000,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11456888/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Briefings in bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/bib/bbae495","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
Natural products (NPs) are indispensable in drug development, particularly in combating infections, cancer, and neurodegenerative diseases. However, their limited availability poses significant challenges. Template-free de novo biosynthetic pathway design provides a strategic solution for NP production, with deep learning standing out as a powerful tool in this domain. This review delves into state-of-the-art deep learning algorithms in NP biosynthesis pathway design. It provides an in-depth discussion of databases like Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and UniProt, which are essential for model training, along with chemical databases such as Reaxys, SciFinder, and PubChem for transfer learning to expand models' understanding of the broader chemical space. It evaluates the potential and challenges of sequence-to-sequence and graph-to-graph translation models for accurate single-step prediction. Additionally, it discusses search algorithms for multistep prediction and deep learning algorithms for predicting enzyme function. The review also highlights the pivotal role of deep learning in improving catalytic efficiency through enzyme engineering, which is essential for enhancing NP production. Moreover, it examines the application of large language models in pathway design, enzyme discovery, and enzyme engineering. Finally, it addresses the challenges and prospects associated with template-free approaches, offering insights into potential advancements in NP biosynthesis pathway design.
期刊介绍:
Briefings in Bioinformatics is an international journal serving as a platform for researchers and educators in the life sciences. It also appeals to mathematicians, statisticians, and computer scientists applying their expertise to biological challenges. The journal focuses on reviews tailored for users of databases and analytical tools in contemporary genetics, molecular and systems biology. It stands out by offering practical assistance and guidance to non-specialists in computerized methodologies. Covering a wide range from introductory concepts to specific protocols and analyses, the papers address bacterial, plant, fungal, animal, and human data.
The journal's detailed subject areas include genetic studies of phenotypes and genotypes, mapping, DNA sequencing, expression profiling, gene expression studies, microarrays, alignment methods, protein profiles and HMMs, lipids, metabolic and signaling pathways, structure determination and function prediction, phylogenetic studies, and education and training.