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Biosynthesis of invertebrate-derived natural products: an uncharted territory. 无脊椎动物衍生的天然产物的生物合成:一个未知的领域。
IF 10.6 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-22 DOI: 10.1039/d5np00056d
Feng Li, Chengyu Zhou, Yinhao Wang, Mengmeng Yu, Jianhua Ju

Covering: up to 2025Invertebrates, as the majority of macroscopic species on the Earth, are important resources for natural products. Chemical investigations of animals can date back to the early 20th century and have led to the discovery of thousands of compounds with diverse biological functions. These natural products can be structurally classified as terpenoids, polyketides, and alkaloids. Additionally, many compounds have been isolated from symbionts, leading to the widespread belief that animals lack the capability for secondary metabolism. Recent biochemical studies challenge this notion, revealing great potential for animal biosynthesis research. Animals possess larger genomes and more complex metabolic pathways, suggesting untapped biosynthetic potential. In contrast to microorganisms, studies on the biosynthesis of natural products in animals remain limited. Characterized genes represent only a small fraction of their vast genomes. The discovery of biosynthetic gene clusters suggests that the methods used to mine the biosynthetic genes of microorganisms may also be applicable to animals. The characterization of 4-vinylanisole in locusts demonstrates that the pathways lacking clear core biosynthesis enzymes still require multidisciplinary experimental approaches. In summary, further biosynthesis studies will expand methodological approaches and accelerate the characterization of remaining natural product pathways.

覆盖范围:至2025年无脊椎动物作为地球上绝大多数的宏观物种,是重要的天然产物资源。对动物的化学研究可以追溯到20世纪初,并导致发现了数千种具有不同生物功能的化合物。这些天然产物在结构上可分为萜类、聚酮类和生物碱。此外,许多化合物已经从共生体中分离出来,导致人们普遍认为动物缺乏次级代谢的能力。最近的生物化学研究挑战了这一观念,揭示了动物生物合成研究的巨大潜力。动物拥有更大的基因组和更复杂的代谢途径,这表明尚未开发的生物合成潜力。与微生物相比,动物体内天然产物的生物合成研究仍然有限。有特征的基因只代表了它们庞大基因组的一小部分。生物合成基因簇的发现表明,用于挖掘微生物生物合成基因的方法也可能适用于动物。蝗虫4-乙烯基苯醚的表征表明,缺乏明确的核心生物合成酶的途径仍然需要多学科的实验方法。总之,进一步的生物合成研究将扩展方法方法并加速剩余天然产物途径的表征。
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引用次数: 0
From diet to defence: ingestion, sequestration, biotransformation, and therapeutic potential of natural products in nudibranch predator-prey interactions. 从饮食到防御:裸鳃捕食者-猎物相互作用中天然产物的摄取、隔离、生物转化和治疗潜力。
IF 10.6 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-17 DOI: 10.1039/d5np00058k
Lauren Gris, Michèle R Prinsep

Covering: 1975 up to September 2025Nudibranchs have attracted significant interest from natural product researchers due to their intriguing predator-prey interactions and numerous bioactive metabolites. The review below, covering 1975 up to September 2025, focuses on the chemoecological interactions reported between predator and prey within the order Nudibranchia. The emphasis is on the ingestion, sequestration and biotransformation of diet-derived compounds, and when known, the role, localisation and bioactivities of the metabolites are described. The review is arranged by class of compounds sequestered or ingested (alkaloids, terpenoids, macrolides, nucleosides and lipids) for each invertebrate prey (sponges, bryozoans and cnidarians).

裸鳃动物由于其有趣的捕食者-猎物相互作用和大量的生物活性代谢物而引起了天然产物研究人员的极大兴趣。本文回顾了1975年至2025年9月间海颌目捕食者和被捕食者之间的化学生态相互作用。重点是饮食衍生化合物的摄入、隔离和生物转化,当已知时,描述代谢物的作用、定位和生物活性。这篇综述是根据每一种无脊椎猎物(海绵、苔藓虫和刺胞动物)隔离或摄入的化合物(生物碱、萜类、大环内酯类、核苷类和脂类)分类整理的。
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引用次数: 0
Natural product inspired antibiotics approved for human use - 1943 to 2025. 天然产品启发抗生素批准用于人类使用- 1943年至2025年。
IF 10.6 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-11 DOI: 10.1039/d5np00067j
Mark S Butler, Robert J Capon

Covering literature to September 2025This review provides a comprehensive account of the 217 natural product inspired antibiotics that have been approved for human use from 1943 through to September 2025, inclusive of 52 (24%) that are natural products (NPs) and 165 (76%) that are semi-synthetic or synthetic derivatives of natural products (NP-Ds). These are organized into sixteen categories defined by shared structural motifs and, in many cases, common mechanisms of action. Each antibiotic is classified as either a NP or NP-D, annotated by a molecular structure that, where relevant, highlights the relationships between NPs and NP-Ds. Market details are also provided, including the company that brought each antibiotic to market, the year and country of first approval, the spectrum of usage across pathogen classes, routes of administration, current status, and selected commentary on mechanisms of action. The assembled dataset is further analysed through a series of charts that illustrate insightful trends that document the remarkable history and lasting impact of NP inspired antibiotics. The review concludes with observations on the historic impact and future prospects of natural products as a source of inspiration for the development of new generations of antibiotics.

本综述全面分析了1943年至2025年9月批准用于人用的217种天然产物启发抗生素,其中52种(24%)为天然产物(NPs), 165种(76%)为半合成或天然产物的合成衍生物(NP-Ds)。它们被分为16类,由共同的结构主题和许多情况下共同的作用机制来定义。每种抗生素被分类为NP或NP- d,并由分子结构注释,在相关的情况下,突出了NP和NP- d之间的关系。还提供了市场细节,包括将每种抗生素推向市场的公司、首次批准的年份和国家、跨病原体类别的使用范围、给药途径、现状以及对作用机制的精选评论。通过一系列图表进一步分析组装的数据集,这些图表说明了深刻的趋势,记录了NP启发的抗生素的非凡历史和持久影响。本综述总结了天然产物作为新一代抗生素开发灵感来源的历史影响和未来前景。
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引用次数: 0
Cultivar to chemotype: characterizing complex botanicals with mass spectrometry metabolomics. 品种到化学型:用质谱代谢组学表征复杂植物。
IF 10.6 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-03 DOI: 10.1039/d5np00040h
Joshua J Kellogg, R Teal Jordan, Madhusha M Ranaweera, Kelsey Custer, Savannah G Anez, Julia Bendlin, Francisco T Chacon, Xiaoling Chen

Covering up to 2025Plant products, including botanical dietary supplements, nutraceuticals, and herbal medicines, remain central to supporting human health and wellness. Their usage has been steadily increasing over the last few decades, which has also led to raised concerns about proper identification and characterization of plant materials. This information is crucial to evaluate the safety and efficacy of these botanical products and prevent misidentification or adulteration. While there are multiple analytical approaches to characterize botanicals, this review provides insight into how untargeted mass spectrometry metabolomics can profile these commonly complex mixtures and provide detailed datasets that are capable of taxonomically classifying samples, detecting adulteration, and providing insight into variation between plant materials and their nutritional, medicinal, or toxicological effects. We describe data analysis approaches for untargeted metabolomics, case studies on the various applications of this method for characterizing botanicals, and challenges that the growing field of mass spectrometry-based metabolomics is facing. The chosen topics reflect the current state of metabolomics analyses for complex systems with a look to the future of how to conceptualize botanical characterization.

覆盖至2025年的植物产品,包括植物性膳食补充剂、营养保健品和草药,仍然是支持人类健康和保健的核心。在过去的几十年里,它们的使用一直在稳步增加,这也引起了人们对植物材料正确识别和表征的关注。这些信息对于评估这些植物产品的安全性和有效性以及防止误认或掺假至关重要。虽然有多种分析方法来表征植物药物,但本综述提供了非靶向质谱代谢组学如何分析这些常见的复杂混合物的见解,并提供了能够对样品进行分类,检测掺假的详细数据集,并提供了对植物材料及其营养,药物或毒理学作用之间差异的见解。我们描述了非靶向代谢组学的数据分析方法,该方法用于表征植物的各种应用的案例研究,以及基于质谱的代谢组学日益增长的领域所面临的挑战。所选择的主题反映了代谢组学分析复杂系统的现状,并展望了如何概念化植物学表征的未来。
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引用次数: 0
Hot off the Press 刚出版的。
IF 10.6 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-11-27 DOI: 10.1039/D5NP90047F
Robert A. Hill and Andrew Sutherland

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as humulupone A from Humulus lupulus.

个人选择了32篇最近的论文,涵盖了生物有机化学和新的天然产物,如葎草属的葎草酮A的各个方面的最新发展。
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引用次数: 0
AI and mechanistic modeling for characterizing biosynthetic pathways of natural products. 人工智能和机制建模表征天然产物的生物合成途径。
IF 10.6 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-11-07 DOI: 10.1039/d5np00059a
Byung Tae Lee, Byeongsub Lee, Joon Young Kwon, Tilmann Weber, Hyun Uk Kim

Covering: 2020 to 2025Natural products are a major source of bioactive compounds, yet elucidating their biosynthetic pathways remains a major challenge due to complex genotype-phenotype relationships. Recent advances in computational approaches, particularly artificial intelligence (AI) and mechanistic modeling, are transforming this field. This highlight examines key databases that underpin computational studies, AI-driven methods for predicting biosynthetic pathways and enzyme-substrate interactions, and mechanistic simulations that provide energetic and structural insights. We also discuss current challenges and future opportunities for integrating these strategies to accelerate discovery, engineering, and application of natural products in drug discovery, biotechnology, and synthetic biology.

天然产物是生物活性化合物的主要来源,但由于复杂的基因型-表型关系,阐明其生物合成途径仍然是一个重大挑战。计算方法的最新进展,特别是人工智能(AI)和机械建模,正在改变这一领域。本重点介绍了支撑计算研究的关键数据库,用于预测生物合成途径和酶-底物相互作用的人工智能驱动方法,以及提供能量和结构见解的机制模拟。我们还讨论了整合这些策略以加速天然产物在药物发现、生物技术和合成生物学中的发现、工程和应用的当前挑战和未来机遇。
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引用次数: 0
Halogenases and dehalogenases: mechanisms, engineering, and applications. 卤化酶和去卤化酶:机制、工程和应用。
IF 10.6 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-11-03 DOI: 10.1039/d5np00055f
Jing Luo, Na Li, Jia Wang, Yaojie Gao, Hongzhi Tang, Linquan Bai, Sang Yup Lee, Yaojun Tong

Halogenated organic compounds (HOCs) are essential building blocks in pharmaceuticals, agrochemicals, and advanced materials. However, their conventional chemical synthesis often relies on hazardous reagents and generates significant environmental waste. Harnessing nature's solutions, halogenases and dehalogenases offer selective, eco-friendly alternatives for the biosynthesis and degradation of HOCs. Halogenases, including electrophilic (e.g., haloperoxidases, flavin-dependent), radical (α-ketoglutarate-dependent), and nucleophilic (S-adenosylmethionine (SAM)-dependent) types, facilitate precise C-X bond formation under mild conditions. Recent advances in protein engineering, such as the modification of tryptophan halogenases and fluorinases, have greatly expanded the repertoire and efficiency of biocatalytic halogenation, enabling the production of new-to-nature compounds for synthetic biology applications. In parallel, dehalogenases, ranging from reductive to hydrolytic and oxidative enzymes, play crucial roles in removing halogens from persistent pollutants, thereby supporting effective bioremediation and environmental detoxification. This review summarizes recent progress in enzyme discovery, mechanistic elucidation, protein engineering, and applied synthetic biology, with a focus on the integration of halogenases and dehalogenases into scalable platforms for both biosynthetic and remediation. Continued research aimed at improving enzyme stability, substrate scope, and operational robustness will be critical to fully realizing the industrial and environmental potential of these versatile biocatalysts.

卤化有机化合物(hoc)是制药、农用化学品和先进材料的重要组成部分。然而,它们的传统化学合成往往依赖于危险的试剂,并产生大量的环境浪费。利用自然的解决方案,卤化酶和脱卤酶为有机碳的生物合成和降解提供了选择性的、环保的替代品。卤素酶,包括亲电型(例如,黄素依赖的卤素过氧化物酶)、自由基型(α-酮戊二酸依赖)和亲核型(s -腺苷蛋氨酸(SAM)依赖),在温和条件下促进精确的C-X键形成。蛋白质工程方面的最新进展,例如对色氨酸卤化酶和氟酶的修饰,大大扩大了生物催化卤化的范围和效率,使生产用于合成生物学应用的新天然化合物成为可能。与此同时,从还原酶到水解酶和氧化酶等脱卤酶在从持久性污染物中去除卤素方面发挥着至关重要的作用,从而支持有效的生物修复和环境解毒。本文综述了近年来在酶的发现、机制阐明、蛋白质工程和应用合成生物学方面的进展,重点介绍了将卤化酶和脱卤酶整合到可扩展的生物合成和修复平台上的研究进展。持续的研究旨在提高酶的稳定性、底物范围和操作稳健性,对于充分实现这些多功能生物催化剂的工业和环境潜力至关重要。
{"title":"Halogenases and dehalogenases: mechanisms, engineering, and applications.","authors":"Jing Luo, Na Li, Jia Wang, Yaojie Gao, Hongzhi Tang, Linquan Bai, Sang Yup Lee, Yaojun Tong","doi":"10.1039/d5np00055f","DOIUrl":"10.1039/d5np00055f","url":null,"abstract":"<p><p>Halogenated organic compounds (HOCs) are essential building blocks in pharmaceuticals, agrochemicals, and advanced materials. However, their conventional chemical synthesis often relies on hazardous reagents and generates significant environmental waste. Harnessing nature's solutions, halogenases and dehalogenases offer selective, eco-friendly alternatives for the biosynthesis and degradation of HOCs. Halogenases, including electrophilic (<i>e.g.</i>, haloperoxidases, flavin-dependent), radical (α-ketoglutarate-dependent), and nucleophilic (<i>S</i>-adenosylmethionine (SAM)-dependent) types, facilitate precise C-X bond formation under mild conditions. Recent advances in protein engineering, such as the modification of tryptophan halogenases and fluorinases, have greatly expanded the repertoire and efficiency of biocatalytic halogenation, enabling the production of new-to-nature compounds for synthetic biology applications. In parallel, dehalogenases, ranging from reductive to hydrolytic and oxidative enzymes, play crucial roles in removing halogens from persistent pollutants, thereby supporting effective bioremediation and environmental detoxification. This review summarizes recent progress in enzyme discovery, mechanistic elucidation, protein engineering, and applied synthetic biology, with a focus on the integration of halogenases and dehalogenases into scalable platforms for both biosynthetic and remediation. Continued research aimed at improving enzyme stability, substrate scope, and operational robustness will be critical to fully realizing the industrial and environmental potential of these versatile biocatalysts.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":" ","pages":""},"PeriodicalIF":10.6,"publicationDate":"2025-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145429798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Metabolism and bioavailability aspects of natural products of plant origin using mass spectrometry-based and metabolomic approaches. 利用质谱和代谢组学方法研究植物源天然产物的代谢和生物利用度。
IF 10.6 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-28 DOI: 10.1039/d5np00022j
Eleni V Mikropoulou, Aikaterini Basdeki, Maria Halabalaki

Covering: 1982 to 2025The therapeutic value of natural products (NPs) is well established, as evidenced by their rich ethnopharmacological history and the significant proportion of marketed drugs derived from natural sources. Despite their notable advantages such as structural versatility and scaffold diversity, NPs have been increasingly sidelined by the pharmaceutical industry due to the labor-intensive nature of their isolation and structural elucidation as well as issues related to patenting, sustainable sourcing and preclinical evaluation. Moreover, current bioavailability research focuses predominantly on well-known medicinal and edible plants or specific compound classes, leaving many other promising candidates underexplored. The interplay between the gut microbiota and NPs, which is critical for pharmacokinetics and ADME (absorption, distribution, metabolism, and excretion), is also overlooked. Numerous in vitro and in vivo models have been developed to study the ADME properties of xenobiotics, while human clinical trials remain scarce in the field of NPs. Recent technological advancements, including innovations in mass spectrometry (MS), smart library screening, dereplication, molecular networking, and metabolomics, have significantly improved the NP research pipeline, offering faster and more accurate compound identification. High-resolution instruments like Orbitrap, QTOF, FT-ICR, and MRMS, alongside IMS and advanced data acquisition techniques (DDA and DIA), now offer deeper insights into complex mixtures. Despite MS being a cornerstone of pharmacokinetics-pharmacodynamics (PK/PD) studies, the integration of metabolomics and big data analytics remains underutilized, particularly in NP prioritization. This review aims to explore the evolution of MS in NP metabolism studies, from early investigations to current multidisciplinary approaches, proposing a critical reflection on the challenges in NP drug development.

涵盖时间:1982年至2025年天然产物(NPs)的治疗价值已得到很好的确立,其丰富的民族药理学历史和市场上销售的天然来源药物的很大比例证明了这一点。尽管NPs具有结构通用性和支架多样性等显著优势,但由于其分离和结构阐明的劳动密集型性质以及与专利、可持续采购和临床前评估相关的问题,NPs越来越被制药行业边缘化。此外,目前的生物利用度研究主要集中在已知的药用和食用植物或特定的化合物类别,留下许多其他有希望的候选物未被开发。肠道微生物群和NPs之间的相互作用对药代动力学和ADME(吸收、分布、代谢和排泄)至关重要,但也被忽视了。已经建立了许多体外和体内模型来研究外源性抗生素的ADME特性,而在NPs领域的人体临床试验仍然很少。最近的技术进步,包括质谱(MS)、智能文库筛选、去复制、分子网络和代谢组学的创新,显著改善了NP研究管道,提供了更快、更准确的化合物鉴定。高分辨率仪器,如Orbitrap、QTOF、FT-ICR和MRMS,以及IMS和先进的数据采集技术(DDA和DIA),现在可以更深入地了解复杂的混合物。尽管质谱是药代动力学-药效学(PK/PD)研究的基石,但代谢组学和大数据分析的整合仍未得到充分利用,特别是在NP优先级方面。本文旨在探讨多发性硬化在NP代谢研究中的演变,从早期的研究到目前的多学科方法,并对NP药物开发中的挑战提出批判性的反思。
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引用次数: 0
A novel class of oligoarylamide antibiotics defined by albicidins and cystobactamids. 一类新型的低聚芳基酰胺类抗生素,由白杆菌素和囊杆菌素定义。
IF 10.6 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-15 DOI: 10.1039/d5np00053j
Marcel Kulike-Koczula, Dominik Heimann, Tobias Eulberg, Daniel Kohnhäuser, Roderich D Süssmuth, Mark Brönstrup

Covering: 2014/2015 up to 2025.The global rise of antimicrobial resistance imposes a strong demand to develop new antibacterial drugs, and microbes have been a prime source for their discovery. Albicidins and cystobactamids, isolated from xanthomonadaceae and myxococcaceae, respectively, span a novel class of oligoarylamide antibiotics with a unique chemical scaffold featured by para-aminobenzoic acid building blocks. Both compounds exhibit broad spectrum and potent activity against Gram-positive and Gram-negative pathogens through inhibiting DNA gyrase and topoisomerase IV. This article summarizes the insights gained on this class since its initial disclosure in 2014/2015 up to 2025. It discusses natural derivatives, their biosynthesis and chemical synthesis, the unique binding mode to DNA gyrase, and systematic medicinal chemistry programs with >700 analogs that led to resistance-breaking antibiotics with in vivo efficacy. The review illustrates the importance of natural product research to address the global need for new antibiotics.

涵盖:2014/2015至2025年。全球抗菌素耐药性的上升对开发新的抗菌药物提出了强烈的需求,而微生物一直是发现这些药物的主要来源。Albicidins和cystobactamids分别从黄病菌科和粘球菌科中分离出来,它们是一类新型的低聚芳基酰胺类抗生素,具有独特的化学支架,以对氨基苯甲酸为基础。这两种化合物都通过抑制DNA旋切酶和拓扑异构酶IV,对革兰氏阳性和革兰氏阴性病原体表现出广谱和有效的活性。本文总结了自2014/2015年首次披露以来到2025年对该类的见解。它讨论了天然衍生物,它们的生物合成和化学合成,与DNA旋切酶的独特结合模式,以及与bbb700类似物的系统药物化学程序,这些程序导致具有体内疗效的破药抗生素。这篇综述说明了天然产物研究对于解决全球对新抗生素的需求的重要性。
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引用次数: 0
Correction: Unpacking policy developments in marine natural product research: a scientist's guide to DSI and BBNJ 更正:海洋天然产品研究的政策发展:DSI和BBNJ的科学家指南。
IF 10.6 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-10-09 DOI: 10.1039/D5NP90039E
Federica Casolari, Amelia Westmoreland, Thomas Vanagt and Marcel Jaspars

Correction for ‘Unpacking policy developments in marine natural product research: a scientist's guide to DSI and BBNJ’ by Federica Casolari et al., Nat. Prod. Rep., 2025, 42, 1063–1070, https://doi.org/10.1039/D4NP00070F.

更正Federica Casolari等人的“海洋天然产品研究中的政策发展:DSI和BBNJ的科学家指南”,Nat Prod Rep, 2025, 42, 1063-1070, https://doi.org/10.1039/D4NP00070F。
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引用次数: 0
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