Christina Braun , Lukas Martin Wingen , Dirk Menche
Covering: the literature up to 2022
This study discusses various synthetic strategies for the synthesis of lipid II, the pivotal bacterial cell wall precursor. In detail, it examines different solution phase approaches, reviews various solid phase sequences, and evaluates enzymatic ventures. The underlying rationale, scope, limitations, and perspectives of these strategies are discussed. The focus is on the tactics and strategies towards the authentic peptidoglycan compound, as well as analogues thereof with shortened side chains, which are increasingly recognized as more beneficial surrogates with more favorable physicochemical properties.
{"title":"Strategies and tactics for the synthesis of lipid I and II and shortened analogues: functional building blocks of bacterial cell wall biosynthesis","authors":"Christina Braun , Lukas Martin Wingen , Dirk Menche","doi":"10.1039/d3np00018d","DOIUrl":"10.1039/d3np00018d","url":null,"abstract":"<div><p>Covering: the literature up to 2022</p><p>This study discusses various synthetic strategies for the synthesis of lipid II, the pivotal bacterial cell wall precursor. In detail, it examines different solution phase approaches, reviews various solid phase sequences, and evaluates enzymatic ventures. The underlying rationale, scope, limitations, and perspectives of these strategies are discussed. The focus is on the tactics and strategies towards the authentic peptidoglycan compound, as well as analogues thereof with shortened side chains, which are increasingly recognized as more beneficial surrogates with more favorable physicochemical properties.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"40 11","pages":"Pages 1718-1734"},"PeriodicalIF":11.9,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9871351","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}
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.
{"title":"Machine learning-assisted structure annotation of natural products based on MS and NMR data","authors":"Guilin Hu , Minghua Qiu","doi":"10.1039/d3np00025g","DOIUrl":"10.1039/d3np00025g","url":null,"abstract":"<div><p>Covering: up to March 2023</p><p>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.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"40 11","pages":"Pages 1735-1753"},"PeriodicalIF":11.9,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9898277","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}
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.
{"title":"Highlights of biosynthetic enzymes and natural products from symbiotic cyanobacteria†","authors":"Paul M. D'Agostino","doi":"10.1039/d3np00011g","DOIUrl":"10.1039/d3np00011g","url":null,"abstract":"<div><p>Covering: up to 2023</p><p>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.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"40 11","pages":"Pages 1701-1717"},"PeriodicalIF":11.9,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9775012","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}
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.
{"title":"Industrial total synthesis of natural medicines","authors":"Xiao-Yu Liu , Yong Qin","doi":"10.1039/d3np00020f","DOIUrl":"10.1039/d3np00020f","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"40 11","pages":"Pages 1694-1700"},"PeriodicalIF":11.9,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9960685","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}
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.
{"title":"Natural products as anthelmintics: safeguarding animal health","authors":"Angela A. Salim , Mark S. Butler , Mark A. T. Blaskovich , Ian R. Henderson , Robert J. Capon","doi":"10.1039/d3np00019b","DOIUrl":"10.1039/d3np00019b","url":null,"abstract":"<div><p>Covering literature to December 2022</p><p>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 (<em>i.e.</em>, nematodes, flukes and tapeworms). These parasitic worms infect and compromise the health and welfare, productivity and lives of commercial livestock (<em>i.e.</em>, sheep, cattle, horses, pigs, poultry and fish), companion animals (<em>i.e.</em>, 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, <em>in vivo</em> animal hosts, and measures of potency.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":"40 11","pages":"Pages 1754-1808"},"PeriodicalIF":11.9,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9951543","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}
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.
{"title":"Hot off the Press","authors":"Robert A. Hill and Andrew Sutherland","doi":"10.1039/D3NP90045B","DOIUrl":"10.1039/D3NP90045B","url":null,"abstract":"<p >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 <em>Dysidea</em> species.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":" 10","pages":" 1590-1594"},"PeriodicalIF":11.9,"publicationDate":"2023-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41098975","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}
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.
{"title":"Chemistry, biosynthesis and biology of floral volatiles: roles in pollination and other functions","authors":"Stefan Dötterl and Jonathan Gershenzon","doi":"10.1039/D3NP00024A","DOIUrl":"10.1039/D3NP00024A","url":null,"abstract":"<p>Covering: 2010 to 2023</p><p>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.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":" 12","pages":" 1901-1937"},"PeriodicalIF":11.9,"publicationDate":"2023-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2023/np/d3np00024a?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10500272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Natural products with 1,2-oxazine scaffold: occurrence, chemical diversity, bioactivity, synthesis, and biosynthesis","authors":"Li-Hong Yan, Xin Li and Bin-Gui Wang","doi":"10.1039/D3NP00023K","DOIUrl":"10.1039/D3NP00023K","url":null,"abstract":"<p>Covering: up to the end of July, 2023</p><p>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 (<em>Physostigma venenosum</em>) 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.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":" 12","pages":" 1874-1900"},"PeriodicalIF":11.9,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10485356","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}
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.
{"title":"The role of Caenorhabditis elegans in the discovery of natural products for healthy aging†","authors":"Benjamin Kirchweger, Julia Zwirchmayr, Ulrike Grienke and Judith M. Rollinger","doi":"10.1039/D3NP00021D","DOIUrl":"10.1039/D3NP00021D","url":null,"abstract":"<p>Covering: 2012 to 2023</p><p>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 <em>C. elegans</em> as the primary model organism for aging, researchers now have a powerful <em>in vivo</em> 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 <em>C. elegans</em>. 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 <em>in vivo</em> model organisms such as <em>C. elegans</em> and sophisticated analytical approaches (“wormomics”) to guide the way to dissect complex natural products with anti-aging properties.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":" 12","pages":" 1849-1873"},"PeriodicalIF":11.9,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2023/np/d3np00021d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10014017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Structural enzymology of iterative type I polyketide synthases: various routes to catalytic programming","authors":"Jialiang Wang, Zixin Deng, Jingdan Liang and Zhijun Wang","doi":"10.1039/D3NP00015J","DOIUrl":"https://doi.org/10.1039/D3NP00015J","url":null,"abstract":"<p>Time span of literature covered: up to mid-2023</p><p>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.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":" 9","pages":" 1498-1520"},"PeriodicalIF":11.9,"publicationDate":"2023-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2023/np/d3np00015j?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24849496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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