{"title":"MedMeta: An AI-Enabled and Genomics-Based Database for Functional Profiling of Secondary Metabolites in Medicinal Species","authors":"Fanbo Meng, Guiyang Zhang, Wenke Xiao, Yufei Mao, Yun Shu, Xiuping Yang, Guoqing Xu, Xinyu Tang, Mengqing Zhang, Zhiyu Liu, Xunzhi Zhang, Shengjie You, Bin Wang, Zhiyin Yu, Shilin Chen, Wei Chen","doi":"10.1016/j.eng.2025.09.007","DOIUrl":null,"url":null,"abstract":"Medicinal resources contain a vast array of secondary metabolites that play critical roles in disease treatment, health maintenance, and drug discovery. Nevertheless, challenges such as biosynthetic complexity and species-specific variability have long hindered their systematic exploration. Recent advances in omics technologies and artificial intelligence (AI)-driven approaches have opened new avenues via which to decode biosynthetic pathways and discover secondary metabolites using omics-level data. In this study, we present MedMeta, a curated and integrative database that connects secondary metabolites with genomic, biochemical, and pharmacological information across 1035 medicinal species documented in eight authoritative global pharmacopoeias. MedMeta comprises 146 101 predicted active secondary metabolites, 196 356 biosynthetic pathways, and an extensive set of annotated molecular targets. As a proof of principle, we employed MedMeta to investigate three representative Apiaceae species—<em>Pucedanum praeruptorum</em>, <em>Angelica sinensis</em>, and <em>Apium graveolens</em>—demonstrating its ability to uncover species-specific metabolite profiles, validate enzymatic functions, and identify compounds with important therapeutic potential. Overall, MedMeta can provide a powerful and scalable platform for natural product research, supporting both fundamental studies and applied biomedical applications. This database offers an invaluable resource for compound discovery, synthetic biology, geoherbalism studies, and the modern application of traditional medicinal systems.","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"125 1","pages":""},"PeriodicalIF":11.6000,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Engineering","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1016/j.eng.2025.09.007","RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"ENGINEERING, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
Abstract
Medicinal resources contain a vast array of secondary metabolites that play critical roles in disease treatment, health maintenance, and drug discovery. Nevertheless, challenges such as biosynthetic complexity and species-specific variability have long hindered their systematic exploration. Recent advances in omics technologies and artificial intelligence (AI)-driven approaches have opened new avenues via which to decode biosynthetic pathways and discover secondary metabolites using omics-level data. In this study, we present MedMeta, a curated and integrative database that connects secondary metabolites with genomic, biochemical, and pharmacological information across 1035 medicinal species documented in eight authoritative global pharmacopoeias. MedMeta comprises 146 101 predicted active secondary metabolites, 196 356 biosynthetic pathways, and an extensive set of annotated molecular targets. As a proof of principle, we employed MedMeta to investigate three representative Apiaceae species—Pucedanum praeruptorum, Angelica sinensis, and Apium graveolens—demonstrating its ability to uncover species-specific metabolite profiles, validate enzymatic functions, and identify compounds with important therapeutic potential. Overall, MedMeta can provide a powerful and scalable platform for natural product research, supporting both fundamental studies and applied biomedical applications. This database offers an invaluable resource for compound discovery, synthetic biology, geoherbalism studies, and the modern application of traditional medicinal systems.
期刊介绍:
Engineering, an international open-access journal initiated by the Chinese Academy of Engineering (CAE) in 2015, serves as a distinguished platform for disseminating cutting-edge advancements in engineering R&D, sharing major research outputs, and highlighting key achievements worldwide. The journal's objectives encompass reporting progress in engineering science, fostering discussions on hot topics, addressing areas of interest, challenges, and prospects in engineering development, while considering human and environmental well-being and ethics in engineering. It aims to inspire breakthroughs and innovations with profound economic and social significance, propelling them to advanced international standards and transforming them into a new productive force. Ultimately, this endeavor seeks to bring about positive changes globally, benefit humanity, and shape a new future.