Natural Product Reports最新文献_第3页

Unlocking the metabolic potential of endophytic fungi through epigenetics: a paradigm shift for natural product discovery and plant-microbe interactions. 通过表观遗传学解锁内生真菌的代谢潜力：天然产物发现和植物-微生物相互作用的范式转变。

IF 10.6 1区化学

Natural Product Reports Pub Date : 2025-07-28 DOI: 10.1039/d5np00028a

Rui Liu, Xiao-Ping Peng, David J Newman, Diane Purchase, Gang Li, Souvik Kusari

{"title":"Unlocking the metabolic potential of endophytic fungi through epigenetics: a paradigm shift for natural product discovery and plant-microbe interactions.","authors":"Rui Liu, Xiao-Ping Peng, David J Newman, Diane Purchase, Gang Li, Souvik Kusari","doi":"10.1039/d5np00028a","DOIUrl":"https://doi.org/10.1039/d5np00028a","url":null,"abstract":"<p><p>Covering: up to December 2024Microbial metabolic pathways, including those of endophytic fungi, offer significant potential for synthesizing secondary metabolites, regardless of their ecological niche. These pathways can be modulated at the molecular level through genome and epigenome manipulation. The metabolic activation of fungal endophytes using epigenetics presents an exciting frontier in science, paving the way for advanced biotechnological applications and enhancing our understanding of these microorganisms' roles in ecosystems. This review examines the significant role of epigenetics in the biosynthesis of secondary metabolites from fungal endophytes, which is vital for drug discovery. Our primary focus centers on studies that explore the epigenetic modulation of endophytic fungi up until December 2024. Acknowledging the rapidly evolving landscape of epigenetic research in this field, which has limited examples for endophytic fungi, we provide crucial foundational insights into fungal epigenetics and relate these insights to the broader context of plant-microbe interactions and endophytic fungal epigenetics, supported by relevant examples. Key mechanisms, such as histone acetylation, histone methylation, and DNA methylation, are discussed alongside recent advances in small-molecule epigenetic modulators that can activate silent biosynthetic gene clusters (BGCs). Further, chromatin-dependent regulation of these BGCs and methods for probing chromatin modifications and secondary metabolism in fungi are discussed. The role of CRISPR-Cas9 genome editing, combined with epigenetic strategies, is highlighted, showcasing its ability to alter the metabolite profiles of fungal endophytes. Finally, we explore how artificial intelligence (AI), machine learning (ML), and deep learning (DL) innovations are transforming research in chemical epigenomics at the plant-microbe interface.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":" ","pages":""},"PeriodicalIF":10.6,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726137","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

The development of Burkholderia bacteria as heterologous hosts. 伯克氏菌作为异源寄主的发展。

IF 10.6 1区化学

Natural Product Reports Pub Date : 2025-07-28 DOI: 10.1039/d5np00024f

Stephanie C Heard, Alessandra S Eustáquio

引用次数: 0

Spiroketal natural products isolated from traditional Chinese medicine: isolation, biological activity, biosynthesis, and synthesis. 从中药中分离的螺酮类天然产物：分离、生物活性、生物合成和合成。

IF 10.2 1区化学

Natural Product Reports Pub Date : 2025-07-21 DOI: 10.1039/d5np00035a

Eilidh G Young, Freda F Li, Margaret A Brimble

引用次数: 0

Green genes from blue greens: challenges and solutions to unlocking the potential of cyanobacteria in drug discovery. 来自蓝色绿色的绿色基因：挑战和解决方案，以解锁药物发现蓝藻的潜力。

IF 10.6 1区化学

Natural Product Reports Pub Date : 2025-07-15 DOI: 10.1039/d5np00016e

Benjamin Philmus, Nicole E Avalon, Yousong Ding, Drew T Doering, Alessandra S Eustáquio, William H Gerwick, Hendrik Luesch, Jimmy Orjala, Shaz Sutherland, Arnaud Taton, Daniel Udwary

引用次数: 0

Exploring microbial natural products through NMR-based metabolomics 通过核磁共振代谢组学探索微生物天然产物。

IF 10.6 1区化学

Natural Product Reports Pub Date : 2025-07-11 DOI: 10.1039/d4np00065j

De-Gao Wang , Jia-Qi Hu , Chao-Yi Wang , Teng Liu , Yue-Zhong Li , Changsheng Wu

{"title":"Exploring microbial natural products through NMR-based metabolomics","authors":"De-Gao Wang , Jia-Qi Hu , Chao-Yi Wang , Teng Liu , Yue-Zhong Li , Changsheng Wu","doi":"10.1039/d4np00065j","DOIUrl":"10.1039/d4np00065j","url":null,"abstract":"<div><div>Covering: 2000. 01 to 2025. 03</div></div><div><div>The soaring demand for novel drugs has led to an increase in the requirement for smart methods to aid in the exploration of microbial natural products (NPs). Cutting-edge metabolomics excels at prompt identification of compounds from complex mixtures and accordingly accelerates the targeted discovery process. Although MS-based metabolomics has become a staple in this field, the utilization of NMR-based metabolomics has severely trailed in comparison. Herein, we summarize the key methodological advancements in 1D and 2D NMR techniques in the past two decades, especially for the invention of computational technologies and/or introduction of artificial intelligence for automated data processing, which significantly strengthen the ability of NMR-based metabolomics to analyze crude microbial extracts. Preliminary fractionation is advocated to deconvolute samples and thus enhance detection sensitivity towards minor components overshadowed by a complex matrix. Particularly, the synergistic application of NMR-based metabolomics and genomics provides an expedient approach to correlate biosynthetic gene clusters with cognate metabolites, greatly improving the efficiency of dereplication and, thus, targeted discovery of novel compounds. A variety of microbial NPs involving distinct chemical skeletons and/or biosynthetic logics are enumerated to prove the genuine prowess of NMR-based metabolomics. Overall, this review aims to encourage the broader adoption of NMR-based metabolomics in the realm of microbial NP research.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 9","pages":"Pages 1459-1488"},"PeriodicalIF":10.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273676","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

Recent advances in discovery and biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPP)-derived lipopeptides 核糖体合成和翻译后修饰肽（RiPP）衍生的脂肽的发现和生物合成的最新进展。

IF 10.6 1区化学

Natural Product Reports Pub Date : 2025-07-11 DOI: 10.1039/d5np00042d

Shumpei Asamizu

{"title":"Recent advances in discovery and biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPP)-derived lipopeptides","authors":"Shumpei Asamizu","doi":"10.1039/d5np00042d","DOIUrl":"10.1039/d5np00042d","url":null,"abstract":"<div><div>Covering: This review summarizes recent advances in the discovery, biosynthesis, and bioactivity of RiPP-derived lipopeptides, covering studies published up to 2024.</div></div><div><div>Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a diverse superfamily of natural products unified by a common biosynthetic logic: The peptide backbone is genetically encoded, and the translated precursor peptide undergoes a series of post-translational modifications catalyzed by maturase enzymes to produce the final bioactive compound. Despite their structural complexity, RiPPs are encoded by relatively small biosynthesis gene clusters. RiPP maturase enzymes are diverse and often promiscuous, offering significant biotechnological potential. However, their lack of conserved features makes genome-based discovery of novel RiPPs challenging. Recent advances in biosynthetic understanding and genome mining techniques have led to the identification of numerous uncharacterized RiPP biosynthetic gene clusters, often flanked by genes encoding non-RiPP moieties, in microbial genomes. Leveraging this information, a new class of natural products, hybrids of RiPPs and non-RiPP elements, has recently been discovered. Among them, RiPPs bearing fatty acyl groups, referred to as RiPP-derived lipopeptides, represent a newly emerging class of lipopeptide natural products with significant antimicrobial activity.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 9","pages":"Pages 1622-1638"},"PeriodicalIF":10.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144641286","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

Natural products targeting the metabolism of amino acids: from discovery to synthetic development† 针对氨基酸代谢的天然产物：从发现到合成发展。

IF 10.6 1区化学

Natural Product Reports Pub Date : 2025-07-11 DOI: 10.1039/d5np00039d

Hyun Su Kim , Ahmed H. E. Hassan , Kyuho Moon , Jaehoon Sim

{"title":"Natural products targeting the metabolism of amino acids: from discovery to synthetic development†","authors":"Hyun Su Kim , Ahmed H. E. Hassan , Kyuho Moon , Jaehoon Sim","doi":"10.1039/d5np00039d","DOIUrl":"10.1039/d5np00039d","url":null,"abstract":"<div><div>Covering: up to 2025</div></div><div><div>Amino acids constitute the essential components of biological systems. Over the recent years, there has been a growing interest in exploring amino acid metabolism as a source of novel druggable targets for intractable diseases such as cancer, metabolic disorders, and degenerative diseases. Culminating research has unveiled novel therapeutic targets associated with amino acid metabolism, including glutamine, cysteine, arginine, and tryptophan metabolism. The pursuit of therapeutic drug targets has resulted in the discovery of potential modulators showing promise for the development of new drug candidates. Many of these modulators have been derived from natural products, employing diverse methods such as traditional medical knowledge, high-throughput screening, and bioinformatics approaches. Based on these discoveries, a variety of synthetic analogues have been developed to improve pharmacological profiles, target selectivity, and drug-like properties. Structural optimization of natural product scaffolds, including derivatization, bioisostere incorporation, and prodrug strategies, has enabled the rational design of potent inhibitors targeting amino acid metabolism. These efforts have expanded the utility of naturally occurring inhibitors, offering enhanced efficacy and therapeutic potential. In this review, we systematically categorize natural products that target enzymes involved in amino acid metabolism, highlighting the recent advances in their development as medicinal agents. This work aims to provide a valuable resource for researchers by outlining the therapeutic potential of natural products and identifying opportunities for future investigation.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 9","pages":"Pages 1575-1621"},"PeriodicalIF":10.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144612051","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

Engineering modular enzyme assembly: synthetic interface strategies for natural products biosynthesis applications 工程模块化酶组装：天然产物生物合成应用的合成界面策略。

IF 10.6 1区化学

Natural Product Reports Pub Date : 2025-07-11 DOI: 10.1039/d5np00027k

Gahyeon Kim , Dukwon Lee , Ji Hun Kim , Seong Do Kim , Hongki Kim , Jae Heon Kim , Sung Sun Yim , Soo-Jin Yeom , Jay D. Keasling , Byung-Kwan Cho

{"title":"Engineering modular enzyme assembly: synthetic interface strategies for natural products biosynthesis applications","authors":"Gahyeon Kim , Dukwon Lee , Ji Hun Kim , Seong Do Kim , Hongki Kim , Jae Heon Kim , Sung Sun Yim , Soo-Jin Yeom , Jay D. Keasling , Byung-Kwan Cho","doi":"10.1039/d5np00027k","DOIUrl":"10.1039/d5np00027k","url":null,"abstract":"<div><div>Covering: 2020 to 2025</div></div><div><div>Natural products remain indispensable sources of therapeutic and bioactive compounds, yet traditional discovery strategies are constrained by compound rediscovery. Modular biosynthetic enzymes, such as type I polyketide synthases (PKSs) and type A non-ribosomal peptide synthetases (NRPSs), offer promising platforms for combinatorial biosynthesis owing to their programmable architectures. However, practical implementation is frequently limited by inter-modular incompatibility and domain-specific interactions. This review highlights recent advances in modular enzyme assembly enabled by synthetic interfaces-including cognate docking domains, synthetic coiled-coils, SpyTag/SpyCatcher, and split inteins-which function as orthogonal, standardized connectors to facilitate post-translational complex formation. These interfaces support rational investigations into substrate specificity, module compatibility, and pathway derivatization as well as general enzyme clustering applications beyond PKS and NRPS systems. Synthetic interfaces can be integrated with computational tools to support a more systematic and scalable framework for modular enzyme engineering by providing predictive insights into domain compatibility and interface design. These approaches within iterative design-build-test-learn workflows can accelerate the programmable assembly of biosynthetic systems and expand the accessible chemical space for natural products.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 9","pages":"Pages 1489-1506"},"PeriodicalIF":10.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504239","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

Trends in metabolite discovery from Actinomycetes† 放线菌代谢物发现趋势。

IF 10.6 1区化学

Natural Product Reports Pub Date : 2025-07-11 DOI: 10.1039/d4np00075g

Paolo Monciardini , Matteo Simone , Marianna Iorio , Sonia I. Maffioli , Margherita Sosio , Stefano Donadio

{"title":"Trends in metabolite discovery from Actinomycetes†","authors":"Paolo Monciardini , Matteo Simone , Marianna Iorio , Sonia I. Maffioli , Margherita Sosio , Stefano Donadio","doi":"10.1039/d4np00075g","DOIUrl":"10.1039/d4np00075g","url":null,"abstract":"<div><div>Covering: 2013 to 2023</div></div><div><div>In this review, we analyzed the scientific literature of the period 2013–2023 that reported novel specialized metabolites from the <em>Actinomycetes</em>, one of the most prolific producers of natural products. The discovered metabolites were categorized on the basis of their chemical originality into two groups: variants of known molecules, or original metabolites. In addition, we subdivided the approaches used to discover these metabolites into four categories: bioassay-based screening, genome mining, metabolome mining, or combinations thereof. We present selected examples of the different approaches used and the resulting original metabolites. Finally, we measure the overall trends of discovery in terms of approaches, of the frequency of original metabolites and of the major biosynthetic classes that have been described. Overall, our analysis indicates that new metabolites continue to be discovered from <em>Actinomycetes</em> at a relatively constant rate and that the frequency of original metabolites seems to be approach-independent and relatively constant within the analyzed time period.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 9","pages":"Pages 1533-1547"},"PeriodicalIF":10.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144245337","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

Technological developments driving industrial natural product discovery 技术发展推动工业天然产物的发现。

IF 10.6 1区化学

Natural Product Reports Pub Date : 2025-07-11 DOI: 10.1039/d4np00072b

Richard Lewis , Richard Hammond , Mark Wilkinson , Nick Allenby

{"title":"Technological developments driving industrial natural product discovery","authors":"Richard Lewis , Richard Hammond , Mark Wilkinson , Nick Allenby","doi":"10.1039/d4np00072b","DOIUrl":"10.1039/d4np00072b","url":null,"abstract":"<div><div>Covering: up to 2025</div></div><div><div>Bacterial natural products have long been the foundation for many therapeutic agents. However, traditional culture-based approaches to discovering these products have been deprioritised by pharmaceutical companies, primarily due to the high rates of rediscovery. To revitalise the pipeline of new drugs, especially antibiotics-an area where natural products have historically played a crucial role-new technologies are essential. Culture-independent, or metagenomic, techniques combined with long-read sequencing technologies are now enabling the identification of novel biosynthetic gene clusters (BGCs). When paired with the heterologous expression of DNA extracted directly from environmental samples (eDNA), these approaches may provide access to untapped microbial biosynthetic diversity. This review explores industrial screening for new compounds and examines how modern technologies such as metagenomics, <em>in situ</em> cultivation, and pico-droplet-based screening are advancing the search for novel natural products. These approaches have the potential to greatly expand the discovery of new bioactive compounds, helping to address the growing need for new therapeutic agents.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"42 9","pages":"Pages 1507-1532"},"PeriodicalIF":10.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214335","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