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Correction: Biosynthesis, biological activities, and structure-activity relationships of decalin-containing tetramic acid derivatives isolated from fungi. 更正:从真菌中分离出的含蜕皮激素的四元酸衍生物的生物合成、生物活性和结构-活性关系。
IF 10.2 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-10 DOI: 10.1039/d4np90030h
Hyun Woo Kim, Jin Woo Lee, Sang Hee Shim

Correction for 'Biosynthesis, biological activities, and structure-activity relationships of decalin-containing tetramic acid derivatives isolated from fungi' by Hyun Woo Kim et al., Nat. Prod. Rep., 2024, https://doi.org/10.1039/d4np00013g.

Hyun Woo Kim 等人撰写的 "从真菌中分离出的含蜕皮激素的四元酸衍生物的生物合成、生物活性和结构-活性关系 "的更正,Nat.Rep., 2024, .Rep., 2024, https://doi.org/10.1039/d4np00013g.
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引用次数: 0
The dichapetalins and dichapetalin-type compounds: structural diversity, bioactivity, and future research perspectives. 二氢杨梅素和二氢杨梅素类化合物:结构多样性、生物活性和未来研究前景。
IF 10.2 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-04 DOI: 10.1039/d3np00039g
Ivan Addae-Mensah, Godwin Akpeko Dziwornu, Mary Anti Chama, Dorcas Osei-Safo

Covering mainly from 2013 up to 2023 with relevant references to work done before 2013First reported in 1995, the dichapetalins and analogous compounds constitute a novel class of natural dammarane-type merotriterpenoids characterized by their unique 2-phenylpyrano moiety annellated to ring A of the dammarane skeleton. They have been reported from only two genera: Dichapetalum (Dichapetalaceae) and Phyllanthus (Phyllanthaceae). About 100 novel dichapetalins and dichapetalin-type compounds, including the acutissimatriterpenes and their antitumour and other bioactivities have been reported. In the present review, we cover the distribution, ethnobotanical and medicinal importance and the diversity of secondary metabolites reported from the two genera Dichapetalum and Phyllanthus from 2013 to date, with appropriate reference to relevant information prior to 2013. We also propose and discuss possible biosynthetic pathways, antitumour activity against a broad range of human and murine cancer cell lines, structure activity relationships, and other biological activities and mechanisms of action. Finally, the review deals with future perspectives which include expansion of the structural diversity and bioactivity scope, possible simplification of the structural complexity of the compounds to enhance their drug-likeness, in silico studies, and continuation of the search for new dichapetalins and dichapetalin-type compounds from the over 200 Dichapetalum and over 1200 Phyllanthus species yet to be investigated. It is envisaged that the present review will stimulate further multidisciplinary and interdisciplinary studies.

主要涵盖 2013 年至 2023 年的内容,并附有 2013 年之前所做工作的相关参考文献。1995 年首次报道的二廿八烷和类似化合物构成了一类新型的天然达玛烷型三萜类化合物,其特点是在达玛烷骨架的 A 环上具有独特的 2-苯基吡喃分子。目前仅有两个属报道过这种物质:Dichapetalum 属(Dichapetalaceae)和 Phyllanthus 属(Phyllanthusaceae)。目前已报道了约 100 种新型的二柴胡苷和二柴胡苷类化合物,其中包括金合欢苷及其抗肿瘤和其他生物活性。在本综述中,我们介绍了 2013 年至今从 Dichapetalum 和 Phyllanthus 这两个属中报道的次生代谢物的分布、民族植物学和药用重要性以及多样性,并适当参考了 2013 年之前的相关信息。我们还提出并讨论了可能的生物合成途径、对多种人类和鼠类癌症细胞系的抗肿瘤活性、结构活性关系以及其他生物活性和作用机制。最后,本综述探讨了未来的发展前景,包括扩大结构多样性和生物活性的范围,简化化合物结构的复杂性以提高其药物亲和性,进行硅学研究,以及继续从尚未研究的 200 多种 Dichapetalum 和 1200 多种 Phyllanthus 品种中寻找新的 dichapetalins 和 dichapetalin 类化合物。预计本综述将促进进一步的多学科和跨学科研究。
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引用次数: 0
Biosynthesis, biological activities, and structure-activity relationships of decalin-containing tetramic acid derivatives isolated from fungi. 从真菌中分离出的含蜕皮激素的四元酸衍生物的生物合成、生物活性和结构-活性关系。
IF 10.2 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-25 DOI: 10.1039/d4np00013g
Hyun Woo Kim, Jin Woo Lee, Sang Hee Shim

Covering: up to December 2023Decalin-containing tetramic acid derivatives, especially 3-decalinoyltetramic acids (3-DTAs), are commonly found as fungal secondary metabolites. Numerous biological activities of this class of compounds, such as antibiotic, antiviral, antifungal, antiplasmodial, and antiprotozoal properties, have been the subject of ongoing research. For this reason, these molecules have attracted a lot of interest from the scientific community and various efforts including semi-synthesis, co-culturing with bacteria and biosynthetic gene sequencing have been made to obtain more derivatives. In this review, 3-DTAs are classified into four major groups based on the absolute configuration of the bicyclic decalin ring. Their biosynthetic pathways, various biological activities, and structure-activity relationship are then introduced.

报道:截至 2023 年 12 月含癸烷的四元酸衍生物,尤其是 3-癸烷酰基四元酸(3-DTAs),是常见的真菌次级代谢产物。这类化合物具有多种生物活性,如抗生素、抗病毒、抗真菌、抗原生质和抗原虫等特性,一直是研究的主题。因此,这些分子引起了科学界的浓厚兴趣,为了获得更多的衍生物,人们做出了各种努力,包括半合成、与细菌共培养和生物合成基因测序。在本综述中,根据双环癸醛环的绝对构型,3-DTAs 被分为四大类。然后介绍了它们的生物合成途径、各种生物活性以及结构-活性关系。
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引用次数: 0
Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. 天然产品结构活性关系研究方法的进展、机遇和挑战。
IF 10.2 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-24 DOI: 10.1039/d4np00009a
Christine Mae F Ancajas, Abiodun S Oyedele, Caitlin M Butt, Allison S Walker

Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.

文献时间跨度:1985 年至 2024 年初天然产物在药物发现中发挥着关键作用,既是药物的直接来源,也是合成化合物开发的起点。由于活性不足或药代动力学特性不佳,大多数天然产物在未经进一步修饰的情况下不适合用作药物。选择进行何种改造需要了解化合物的结构-活性关系。在药物化学研究中,结构-活性关系的使用非常普遍,而且对人类设计的合成化合物至关重要。结构-活性关系也被用于改善天然产物的特性,但一些挑战仍然限制着这些努力。在此,我们将回顾研究天然产物结构-活性关系的方法及其局限性。具体来说,我们将讨论如何利用合成(包括全合成、后期衍生化、化学酶合成途径以及生物合成途径的工程和基因组挖掘)来生产天然产物类似物,并讨论每种方法所面临的挑战。最后,我们将讨论计算方法,包括用于分析生物合成基因与产品活性之间关系的机器学习方法、计算机辅助药物设计技术和可解释的人工智能方法,以便通过训练有素的模型阐明结构与活性之间的关系,从而根据化学结构预测生物活性。我们的重点将放在后几个主题上,因为它们在天然产品方面的应用尚未得到广泛的研究。我们认为,这些方法都是相辅相成的,只有结合使用这些技术,才能全面了解天然产品的结构-活性关系。
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引用次数: 0
The insect microbiome is a vast source of bioactive small molecules† 昆虫微生物群是生物活性小分子的巨大来源。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2024-06-19 DOI: 10.1039/d3np00054k
Carlismari Oliveira Grundmann , Juan Guzman , Andreas Vilcinskas , Mônica Tallarico Pupo

Covering: September 1964 to June 2023

Bacteria and fungi living in symbiosis with insects have been studied over the last sixty years and found to be important sources of bioactive natural products. Not only classic producers of secondary metabolites such as Streptomyces and other members of the phylum Actinobacteria but also numerous bacteria from the phyla Proteobacteria and Firmicutes and an impressive array of fungi (usually pathogenic) serve as the source of a structurally diverse number of small molecules with important biological activities including antimicrobial, cytotoxic, antiparasitic and specific enzyme inhibitors. The insect niche is often the exclusive provider of microbes producing unique types of biologically active compounds such as gerumycins, pederin, dinactin, and formicamycins. However, numerous insects still have not been described taxonomically, and in most cases, the study of their microbiota is completely unexplored. In this review, we present a comprehensive survey of 553 natural products produced by microorganisms isolated from insects by collating and classifying all the data according to the type of compound (rather than the insect or microbial source). The analysis of the correlations among the metadata related to insects, microbial partners, and their produced compounds provides valuable insights into the intricate dynamics between insects and their symbionts as well as the impact of their metabolites on these relationships. Herein, we focus on the chemical structure, biosynthesis, and biological activities of the most relevant compounds.

覆盖范围:1964 年 9 月至 2023 年 6 月与昆虫共生的细菌和真菌是生物活性天然产品的重要来源。不仅是链霉菌和放线菌门的其他成员等经典的次级代谢产物生产者,还有大量的变形菌门和固醇菌门的细菌以及一系列令人印象深刻的真菌(通常是致病菌),它们都是具有重要生物活性(包括抗菌、细胞毒性、抗寄生虫和特异性酶抑制剂)的结构多样的小分子的来源。昆虫生态位通常是微生物的唯一提供者,这些微生物能产生独特类型的生物活性化合物,如克鲁菌素、 pederin、dinactin 和 formicamycins。然而,许多昆虫仍未在分类学上得到描述,在大多数情况下,对其微生物区系的研究也是完全空白。在这篇综述中,我们根据化合物类型(而不是昆虫或微生物来源)对所有数据进行了整理和分类,从而对从昆虫中分离出的微生物产生的 553 种天然产物进行了全面调查。通过分析与昆虫、微生物伙伴及其产生的化合物相关的元数据,我们可以深入了解昆虫与其共生体之间错综复杂的动态关系,以及昆虫代谢物对这些关系的影响。在此,我们将重点介绍最相关化合物的化学结构、生物合成和生物活性。
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引用次数: 0
Recent advances in discovery and biosynthesis of natural products from myxobacteria: an overview from 2017 to 2023 从霉菌中发现和生物合成天然产物的最新进展:2017 年至 2023 年概览。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2024-06-19 DOI: 10.1039/d3np00062a
Chao-Yi Wang , Jia-Qi Hu , De-Gao Wang , Yue-Zhong Li , Changsheng Wu

Covering: 2017.01 to 2023.11

Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological activities, and intriguing biosynthetic enzymology. This review aims to systematically summarize the advances in the discovery methods, new structures, and bioactivities of myxobacterial NPs reported in the period of 2017–2023. In addition, the peculiar biosynthetic pathways of several structural families are also highlighted.

覆盖时间:2017.01 至 2023.11霉菌生物合成的天然产物因其复杂的化学骨架、显著的生物活性和引人入胜的生物合成酶学而极具吸引力。本综述旨在系统总结 2017-2023 年期间报道的粘菌 NPs 发现方法、新结构和生物活性方面的进展。此外,还重点介绍了几个结构家族的奇特生物合成途径。
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引用次数: 0
Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products 连接代谢组和表型:用于鉴定生物活性天然产物的功能代谢组学工具的最新进展。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2024-06-19 DOI: 10.1039/d3np00050h
Giovanni Andrea Vitale , Christian Geibel , Vidit Minda , Mingxun Wang , Allegra T. Aron , Daniel Petras

Covering: 1995 to 2023

Advances in bioanalytical methods, particularly mass spectrometry, have provided valuable molecular insights into the mechanisms of life. Non-targeted metabolomics aims to detect and (relatively) quantify all observable small molecules present in a biological system. By comparing small molecule abundances between different conditions or timepoints in a biological system, researchers can generate new hypotheses and begin to understand causes of observed phenotypes. Functional metabolomics aims to investigate the functional roles of metabolites at the scale of the metabolome. However, most functional metabolomics studies rely on indirect measurements and correlation analyses, which leads to ambiguity in the precise definition of functional metabolomics. In contrast, the field of natural products has a history of identifying the structures and bioactivities of primary and specialized metabolites. Here, we propose to expand and reframe functional metabolomics by integrating concepts from the fields of natural products and chemical biology. We highlight emerging functional metabolomics approaches that shift the focus from correlation to physical interactions, and we discuss how this allows researchers to uncover causal relationships between molecules and phenotypes.

覆盖范围1995 年至 2023 年生物分析方法的发展,尤其是质谱分析方法的发展,为人们提供了了解生命机理的宝贵分子信息。非靶向代谢组学旨在检测和(相对)量化生物系统中存在的所有可观察到的小分子。通过比较生物系统中不同条件或不同时间点的小分子丰度,研究人员可以提出新的假设,并开始了解观察到的表型的原因。功能代谢组学旨在研究代谢物在代谢组尺度上的功能作用。然而,大多数功能代谢组学研究都依赖于间接测量和相关分析,这导致功能代谢组学的精确定义模糊不清。相比之下,天然产物领域在鉴定初级和特殊代谢物的结构和生物活性方面有着悠久的历史。在此,我们建议通过整合天然产物和化学生物学领域的概念来扩展和重构功能代谢组学。我们将重点介绍新出现的功能代谢组学方法,这些方法将重点从相关性转移到了物理相互作用上,我们还将讨论这种方法如何让研究人员发现分子与表型之间的因果关系。
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引用次数: 0
Purine nucleoside antibiotics: recent synthetic advances harnessing chemistry and biology 嘌呤核苷抗生素:利用化学和生物学的最新合成进展。
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2024-06-19 DOI: 10.1039/d3np00051f
Jonas Motter , Caecilie M. M. Benckendorff , Sarah Westarp , Peter Sunde-Brown , Peter Neubauer , Anke Kurreck , Gavin J. Miller

Covering: 2019 to 2023

Nucleoside analogues represent one of the most important classes of small molecule pharmaceuticals and their therapeutic development is successfully established within oncology and for the treatment of viral infections. However, there are currently no nucleoside analogues in clinical use for the management of bacterial infections. Despite this, a significant number of clinically recognised nucleoside analogues are known to possess some antibiotic activity, thereby establishing a potential source for new therapeutic discovery in this area. Furthermore, given the rise in antibiotic resistance, the discovery of new clinical candidates remains an urgent global priority and natural product-derived nucleoside analogues may also present a rich source of discovery space for new modalities. This Highlight, covering work published from 2019 to 2023, presents a current perspective surrounding the synthesis of natural purine nucleoside antibiotics. By amalgamating recent efforts from synthetic chemistry with advances in biosynthetic understanding and the use of recombinant enzymes, prospects towards different structural classes of purines are detailed.

覆盖时间:2019 年至 2023 年核苷类似物是最重要的小分子药物类别之一,其治疗开发已在肿瘤学和病毒感染治疗领域取得成功。然而,目前还没有核苷类似物用于临床治疗细菌感染。尽管如此,已知大量临床认可的核苷类似物具有一定的抗生素活性,从而为这一领域的新疗法发现提供了潜在的来源。此外,鉴于抗生素耐药性的增加,发现新的临床候选药物仍然是全球的当务之急,而天然产物衍生的核苷类似物也可能为新模式提供丰富的发现空间。本《亮点》涵盖 2019 年至 2023 年发表的研究成果,介绍了当前围绕天然嘌呤核苷类抗生素合成的观点。通过将合成化学的最新研究成果与生物合成认识的进步以及重组酶的使用相结合,详细介绍了不同结构类别嘌呤的前景。
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引用次数: 0
Hot off the Press 新闻热点
IF 11.9 1区 化学 Q1 Chemistry Pub Date : 2024-06-19 DOI: 10.1039/d4np90026j
Robert A. Hill , 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 penihemeroterpenoid A from Penicillium herquei.

该书精选了 32 篇最新论文,涵盖了生物有机化学和新型天然产品(如来自 Herquei 青霉菌的青霉萜 A)当前发展的各个方面。
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引用次数: 0
Unleashing the potential: type I CRISPR-Cas systems in actinomycetes for genome editing. 释放潜能:放线菌中用于基因组编辑的 I 型 CRISPR-Cas 系统。
IF 11.9 1区 化学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-18 DOI: 10.1039/d4np00010b
Shuliu Wang, Xiaoqian Zeng, Yue Jiang, Weishan Wang, Linquan Bai, Yinhua Lu, Lixin Zhang, Gao-Yi Tan

Covering: up to the end of 2023Type I CRISPR-Cas systems are widely distributed, found in over 40% of bacteria and 80% of archaea. Among genome-sequenced actinomycetes (particularly Streptomyces spp.), 45.54% possess type I CRISPR-Cas systems. In comparison to widely used CRISPR systems like Cas9 or Cas12a, these endogenous CRISPR-Cas systems have significant advantages, including better compatibility, wide distribution, and ease of operation (since no exogenous Cas gene delivery is needed). Furthermore, type I CRISPR-Cas systems can simultaneously edit and regulate genes by adjusting the crRNA spacer length. Meanwhile, most actinomycetes are recalcitrant to genetic manipulation, hindering the discovery and engineering of natural products (NPs). The endogenous type I CRISPR-Cas systems in actinomycetes may offer a promising alternative to overcome these barriers. This review summarizes the challenges and recent advances in CRISPR-based genome engineering technologies for actinomycetes. It also presents and discusses how to establish and develop genome editing tools based on type I CRISPR-Cas systems in actinomycetes, with the aim of their future application in gene editing and the discovery of NPs in actinomycetes.

覆盖范围:截至 2023 年底I 型 CRISPR-Cas 系统分布广泛,存在于 40% 以上的细菌和 80% 的古细菌中。在基因组测序的放线菌(尤其是链霉菌属)中,45.54%拥有I型CRISPR-Cas系统。与广泛使用的CRISPR系统(如Cas9或Cas12a)相比,这些内源CRISPR-Cas系统具有显著的优势,包括兼容性更好、分布广泛、操作简便(因为不需要外源Cas基因的传递)。此外,I型CRISPR-Cas系统可以通过调整crRNA间隔长度来同时编辑和调控基因。与此同时,大多数放线菌对基因操作不敏感,阻碍了天然产物(NPs)的发现和工程化。放线菌中的内源性 I 型 CRISPR-Cas 系统可能为克服这些障碍提供了一种有前途的选择。本综述总结了放线菌基于 CRISPR 的基因组工程技术所面临的挑战和最新进展。它还介绍和讨论了如何在放线菌中建立和开发基于 I 型 CRISPR-Cas 系统的基因组编辑工具,目的是将来将其应用于放线菌的基因编辑和 NPs 的发现。
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引用次数: 0
期刊
Natural Product Reports
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