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Machine learning-assisted structure annotation of natural products based on MS and NMR data 基于MS和NMR数据的机器学习辅助天然产物结构标注。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2023-11-15 DOI: 10.1039/d3np00025g
Guilin Hu , Minghua Qiu

Covering: up to March 2023

Machine learning (ML) has emerged as a popular tool for analyzing the structures of natural products (NPs). This review presents a summary of the recent advancements in ML-assisted mass spectrometry (MS) and nuclear magnetic resonance (NMR) data analysis to establish the chemical structures of NPs. First, ML-based MS/MS analyses that rely on library matching are discussed, which involves the utilization of ML algorithms to calculate similarity, predict the MS/MS fragments, and form molecular fingerprint. Then, ML assisted MS/MS structural annotation without library matching is reviewed. Furthermore, the cases of ML algorithms in assisting structural studies of NPs based on NMR are discussed from four perspectives: NMR prediction, functional group identification, structural categorization and quantum chemical calculation. Finally, the review concludes with a discussion of the challenges and the trends associated with the structural establishment of NPs based on ML algorithms.

涵盖:截至2023年3月机器学习(ML)已经成为分析天然产物(NPs)结构的流行工具。本文综述了近年来ml辅助质谱(MS)和核磁共振(NMR)数据分析在确定NPs化学结构方面的研究进展。首先,讨论了基于ML的基于文库匹配的MS/MS分析,包括利用ML算法计算相似度,预测MS/MS片段,形成分子指纹。然后对ML辅助MS/MS结构标注进行了综述。从核磁共振预测、官能团识别、结构分类和量子化学计算四个方面讨论了ML算法在核磁共振辅助NPs结构研究中的应用。最后,本文讨论了基于ML算法的np结构建立所面临的挑战和趋势。
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引用次数: 1
Highlights of biosynthetic enzymes and natural products from symbiotic cyanobacteria† 来自共生蓝藻的生物合成酶和天然产物的亮点。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2023-11-15 DOI: 10.1039/d3np00011g
Paul M. D'Agostino

Covering: up to 2023

Cyanobacteria have long been known for their intriguing repertoire of natural product scaffolds, which are often distinct from other phyla. Cyanobacteria are ecologically significant organisms that form a myriad of different symbioses including with sponges and ascidians in the marine environment or with plants and fungi, in the form of lichens, in terrestrial environments. Whilst there have been several high-profile discoveries of symbiotic cyanobacterial natural products, genomic data is scarce and discovery efforts have remained limited. However, the rise of (meta-)genomic sequencing has improved these efforts, emphasized by a steep increase in publications in recent years. This highlight focuses on selected examples of symbiotic cyanobacterial-derived natural products and their biosyntheses to link chemistry with corresponding biosynthetic logic. Further highlighted are remaining gaps in knowledge for the formation of characteristic structural motifs. It is anticipated that the continued rise of (meta-)genomic next-generation sequencing of symbiontic cyanobacterial systems will lead to many exciting discoveries in the future.

覆盖范围:到2023年蓝藻一直以其有趣的天然产物支架而闻名,这通常与其他门不同。蓝藻是生态上重要的生物,形成无数不同的共生关系,包括在海洋环境中与海绵和海鞘,或在陆地环境中与地衣形式的植物和真菌。虽然已经有几个高调的发现共生蓝藻天然产品,基因组数据是稀缺的,发现的努力仍然有限。然而,(元)基因组测序的兴起改善了这些努力,近年来出版物的急剧增加强调了这一点。这个重点集中在共生蓝藻衍生的天然产物及其生物合成的选定例子,以联系化学与相应的生物合成逻辑。进一步强调的是,在形成特征结构基序的知识方面仍然存在空白。可以预见的是,共生蓝藻系统的(元)基因组下一代测序的持续上升将导致许多令人兴奋的发现在未来。
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引用次数: 1
Industrial total synthesis of natural medicines 天然药物的工业全合成。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2023-11-15 DOI: 10.1039/d3np00020f
Xiao-Yu Liu , Yong Qin

Total synthesis offers a key approach to the production of natural medicines if sufficient quantities cannot be obtained due to low natural abundance or lack of efficient fermentation or semi-synthesis methods. This Viewpoint outlines the previous and current states of research as they apply to the total synthesis of natural medicines on an industrial scale and provides a holistic view on the potential for future developments in the field.

如果由于天然丰度低或缺乏有效的发酵或半合成方法而无法获得足够数量的天然药物,则全合成提供了生产天然药物的关键方法。本观点概述了过去和目前的研究状况,因为它们适用于工业规模的天然药物全合成,并提供了该领域未来发展潜力的整体观点。
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引用次数: 0
Natural products as anthelmintics: safeguarding animal health 天然驱虫产品:保障动物健康。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2023-11-15 DOI: 10.1039/d3np00019b
Angela A. Salim , Mark S. Butler , Mark A. T. Blaskovich , Ian R. Henderson , Robert J. Capon

Covering literature to December 2022

This review provides a comprehensive account of all natural products (500 compounds, including 17 semi-synthetic derivatives) described in the primary literature up to December 2022, reported to be capable of inhibiting the egg hatching, motility, larval development and/or the survival of helminths (i.e., nematodes, flukes and tapeworms). These parasitic worms infect and compromise the health and welfare, productivity and lives of commercial livestock (i.e., sheep, cattle, horses, pigs, poultry and fish), companion animals (i.e., dogs and cats) and other high value, endangered and/or exotic animals. Attention is given to chemical structures, as well as source organisms and anthelmintic properties, including the nature of bioassay target species, in vivo animal hosts, and measures of potency.

涵盖截至2022年12月的文献。本综述全面介绍了截至2022年12月的主要文献中描述的所有能够抑制虫卵孵化、运动、幼虫发育和/或蠕虫(即线虫、吸虫和绦虫)存活的天然产物(500种化合物,包括17种半合成衍生物)。这些寄生虫感染并危害商业牲畜(即羊、牛、马、猪、家禽和鱼)、伴侣动物(即狗和猫)和其他高价值、濒危和/或外来动物的健康和福利、生产力和生命。重点是化学结构,以及源生物和驱虫药的性质,包括生物测定目标物种的性质,体内动物宿主,和效力的措施。
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引用次数: 0
Hot off the Press 关掉媒体。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2023-10-04 DOI: 10.1039/D3NP90045B
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 dysambiol from a Dysidea species.

对32篇最近的论文进行了个人选择,涵盖了生物有机化学和新型天然产物的各个方面的最新发展,例如来自一个Dysicidea物种的Dysambil。
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引用次数: 0
Chemistry, biosynthesis and biology of floral volatiles: roles in pollination and other functions 花挥发物的化学、生物合成和生物学:在授粉和其他功能中的作用
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2023-09-04 DOI: 10.1039/D3NP00024A
Stefan Dötterl and Jonathan Gershenzon

Covering: 2010 to 2023

Floral volatiles are a chemically diverse group of plant metabolites that serve multiple functions. Their composition is shaped by environmental, ecological and evolutionary factors. This review will summarize recent advances in floral scent research from chemical, molecular and ecological perspectives. It will focus on the major chemical classes of floral volatiles, on notable new structures, and on recent discoveries regarding the biosynthesis and the regulation of volatile emission. Special attention will be devoted to the various functions of floral volatiles, not only as attractants for different types of pollinators, but also as defenses of flowers against enemies. We will also summarize recent findings on how floral volatiles are affected by abiotic stressors, such as increased temperatures and drought, and by other organisms, such as herbivores and flower-dwelling microbes. Finally, this review will indicate current research gaps, such as the very limited knowledge of the isomeric pattern of chiral compounds and its importance in interspecific interactions.

覆盖时间:2010 年至 2023 年花卉挥发物是一类化学性质多样的植物代谢产物,具有多种功能。它们的组成受环境、生态和进化因素的影响。本综述将从化学、分子和生态学角度总结花香研究的最新进展。它将重点介绍花卉挥发性物质的主要化学类别、显著的新结构以及有关挥发性物质的生物合成和挥发调节的最新发现。我们还将特别关注花卉挥发性物质的各种功能,这些功能不仅可以吸引不同类型的传粉媒介,还可以使花卉抵御敌害。我们还将总结花卉挥发性物质如何受温度升高和干旱等非生物胁迫因素以及食草动物和花居微生物等其他生物影响的最新研究成果。最后,本综述将指出目前的研究空白,例如对手性化合物异构体模式及其在种间相互作用中的重要性的了解非常有限。
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引用次数: 2
Natural products with 1,2-oxazine scaffold: occurrence, chemical diversity, bioactivity, synthesis, and biosynthesis 具有 1,2-恶嗪支架的天然产品:出现、化学多样性、生物活性、合成和生物合成
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2023-08-29 DOI: 10.1039/D3NP00023K
Li-Hong Yan, Xin Li and Bin-Gui Wang

Covering: up to the end of July, 2023

1,2-Oxazine is a heterocyclic scaffold rarely found in natural products and is characterized by a directly connected N–O bond in a six-membered ring. Since the discovery of geneserine, the first 1,2-oxazine-containing natural product (1,2-oxazine NP) being isolated from Calabar bean (Physostigma venenosum) in 1925, a total of 76 naturally occurring 1,2-oxazine NPs have been isolated and identified from various sources, which have attracted the attention of researchers in the field of natural product chemistry, organic synthesis, biosynthesis, and pharmacology. This review summarizes the chemical family of 1,2-oxazine NPs, focusing on their source organisms, structural diversities, chemical synthesis, and biosynthesis.

覆盖范围:截至 2023 年 7 月底1,2-恶嗪是一种在天然产品中很少发现的杂环支架,其特点是在一个六元环中有一个直接连接的 N-O 键。自 1925 年从卡拉巴尔豆(Physostigma venenosum)中分离出第一个含 1,2-恶嗪的天然产物(1,2-恶嗪 NP)--基因丝氨酸(geneserine)以来,已从不同来源分离和鉴定出 76 种天然存在的 1,2- 恶嗪 NP,引起了天然产物化学、有机合成、生物合成和药理学领域研究人员的关注。本综述概述了 1,2-恶嗪 NPs 的化学家族,重点介绍了它们的来源生物、结构多样性、化学合成和生物合成。
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引用次数: 0
The role of Caenorhabditis elegans in the discovery of natural products for healthy aging† 草履虫在发现促进健康老龄化的天然产品中的作用†。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2023-08-16 DOI: 10.1039/D3NP00021D
Benjamin Kirchweger, Julia Zwirchmayr, Ulrike Grienke and Judith M. Rollinger

Covering: 2012 to 2023

The human population is aging. Thus, the greatest risk factor for numerous diseases, such as diabetes, cancer and neurodegenerative disorders, is increasing worldwide. Age-related diseases do not typically occur in isolation, but as a result of multi-factorial causes, which in turn require holistic approaches to identify and decipher the mode of action of potential remedies. With the advent of C. elegans as the primary model organism for aging, researchers now have a powerful in vivo tool for identifying and studying agents that effect lifespan and health span. Natural products have been focal research subjects in this respect. This review article covers key developments of the last decade (2012–2023) that have led to the discovery of natural products with healthy aging properties in C. elegans. We (i) discuss the state of knowledge on the effects of natural products on worm aging including methods, assays and involved pathways; (ii) analyze the literature on natural compounds in terms of their molecular properties and the translatability of effects on mammals; (iii) examine the literature on multi-component mixtures with special attention to the studied organisms, extraction methods and efforts regarding the characterization of their chemical composition and their bioactive components. (iv) We further propose to combine small in vivo model organisms such as C. elegans and sophisticated analytical approaches (“wormomics”) to guide the way to dissect complex natural products with anti-aging properties.

覆盖时间:2012 年至 2023 年人类正在步入老龄化。因此,糖尿病、癌症和神经退行性疾病等众多疾病的最大风险因素正在全球范围内不断增加。与年龄有关的疾病通常不是孤立发生的,而是由多种因素造成的,因此需要采用整体方法来识别和破解潜在疗法的作用模式。随着作为衰老主要模式生物的优雅小尾寒羊的出现,研究人员现在有了一个强大的体内工具来识别和研究影响寿命和健康寿命的物质。天然产品一直是这方面的重点研究对象。这篇综述文章涵盖了过去十年(2012-2023 年)在发现 elegans 具有健康老化特性的天然产品方面取得的主要进展。我们(i)讨论了天然产品对蠕虫衰老影响的知识状况,包括方法、检测和相关途径;(ii)从天然化合物的分子特性和对哺乳动物影响的可转化性方面分析了有关天然化合物的文献;(iii)研究了有关多组分混合物的文献,特别关注所研究的生物、提取方法以及有关其化学成分和生物活性成分特征的工作。(iv) 我们还建议将小型体内模式生物(如秀丽隐杆线虫)与复杂的分析方法("蠕虫组学")结合起来,为剖析具有抗衰老特性的复杂天然产品提供指导。
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引用次数: 1
Structural enzymology of iterative type I polyketide synthases: various routes to catalytic programming 迭代I型聚酮合成酶的结构酶学:催化编程的各种途径
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2023-08-15 DOI: 10.1039/D3NP00015J
Jialiang Wang, Zixin Deng, Jingdan Liang and Zhijun Wang

Time span of literature covered: up to mid-2023

Iterative type I polyketide synthases (iPKSs) are outstanding natural chemists: megaenzymes that repeatedly utilize their catalytic domains to synthesize complex natural products with diverse bioactivities. Perhaps the most fascinating but least understood question about type I iPKSs is how they perform the iterative yet programmed reactions in which the usage of domain combinations varies during the synthetic cycle. The programmed patterns are fulfilled by multiple factors, and strongly influence the complexity of the resulting natural products. This article reviews selected reports on the structural enzymology of iPKSs, focusing on the individual domain structures followed by highlighting the representative programming activities that each domain may contribute.

迭代型I型聚酮合成酶(iPKSs)是杰出的天然化学家,是一种重复利用其催化结构域合成具有多种生物活性的复杂天然产物的巨型酶。也许关于I型ipks最令人着迷但又最不为人所知的问题是,它们是如何在合成周期中执行迭代的程序化反应的,在这种反应中,结构域组合的使用是不同的。编程模式由多种因素实现,并强烈影响最终自然产物的复杂性。本文回顾了iPKSs结构酶学方面的报告,重点介绍了单个结构域结构,然后重点介绍了每个结构域可能贡献的代表性编程活动。
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引用次数: 0
Engineering yeast for the production of plant terpenoids using synthetic biology approaches† 利用合成生物学方法改造酵母生产植物萜类化合物†。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2023-07-31 DOI: 10.1039/D3NP00005B
Jean-Alexandre Bureau, Magdalena Escobar Oliva, Yueming Dong and Codruta Ignea

Covering: 2011–2022

The low amounts of terpenoids produced in plants and the difficulty in synthesizing these complex structures have stimulated the production of terpenoid compounds in microbial hosts by metabolic engineering and synthetic biology approaches. Advances in engineering yeast for terpenoid production will be covered in this review focusing on four directions: (1) manipulation of host metabolism, (2) rewiring and reconstructing metabolic pathways, (3) engineering the catalytic activity, substrate selectivity and product specificity of biosynthetic enzymes, and (4) localizing terpenoid production via enzymatic fusions and scaffolds, or subcellular compartmentalization.

覆盖时间:2011-2022年植物中产生的萜类化合物较少,而合成这些复杂结构的萜类化合物又十分困难,这促使人们通过代谢工程和合成生物学方法在微生物宿主中生产萜类化合物。本综述将介绍酵母工程在生产萜类化合物方面取得的进展,重点关注四个方向:(1) 操纵宿主代谢;(2) 重新布线和重建代谢途径;(3) 生物合成酶的催化活性、底物选择性和产物特异性工程;(4) 通过酶融合和支架或亚细胞区隔实现萜类化合物的本地化生产。
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引用次数: 1
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Natural Product Reports
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