MedMeta: An AI-Enabled and Genomics-Based Database for Functional Profiling of Secondary Metabolites in Medicinal Species

IF 11.6 1区 工程技术 Q1 ENGINEERING, MULTIDISCIPLINARY
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
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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.
MedMeta:一个基于人工智能和基因组学的数据库,用于药用物种次生代谢物的功能分析
药用资源中含有大量的次生代谢物,在疾病治疗、健康维护和药物发现中起着至关重要的作用。然而,诸如生物合成复杂性和物种特异性变异性等挑战长期阻碍了它们的系统探索。组学技术和人工智能(AI)驱动的方法的最新进展为解码生物合成途径和使用组学水平数据发现次级代谢物开辟了新的途径。在这项研究中,我们提出了MedMeta,这是一个精心策划的综合数据库,将8个权威的全球药典中记录的1035种药物的次级代谢物与基因组、生化和药理学信息联系起来。MedMeta包括146 101个预测的活性次级代谢物,196 356个生物合成途径和一套广泛的注释分子靶点。为了证明这一原理,我们使用MedMeta研究了三种具有代表性的蜜蜂科物种——普塞丹(pucedanum praeruptorum)、当归(Angelica sinensis)和阿皮(Apium graveolens)——证明了它能够揭示物种特异性代谢物谱,验证酶功能,并识别具有重要治疗潜力的化合物。总体而言,MedMeta可以为天然产品研究提供强大且可扩展的平台,支持基础研究和应用生物医学应用。该数据库为化合物发现、合成生物学、地药学研究和传统医学系统的现代应用提供了宝贵的资源。
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来源期刊
Engineering
Engineering Environmental Science-Environmental Engineering
自引率
1.60%
发文量
335
审稿时长
35 days
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.
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