Evan T. Miller , Oleg V. Tsodikov , Sylvie Garneau-Tsodikova
Covering: 2009 up to August 2023
Prenyltransferases (PTs) are involved in the primary and the secondary metabolism of plants, bacteria, and fungi, and they are key enzymes in the biosynthesis of many clinically relevant natural products (NPs). The continued biochemical and structural characterization of the soluble dimethylallyl tryptophan synthase (DMATS) PTs over the past two decades have revealed the significant promise that these enzymes hold as biocatalysts for the chemoenzymatic synthesis of novel drug leads. This is a comprehensive review of DMATSs describing the structure–function relationships that have shaped the mechanistic underpinnings of these enzymes, as well as the application of this knowledge to the engineering of DMATSs. We summarize the key findings and lessons learned from these studies over the past 14 years (2009–2023). In addition, we identify current gaps in our understanding of these fascinating enzymes.
{"title":"Structural insights into the diverse prenylating capabilities of DMATS prenyltransferases","authors":"Evan T. Miller , Oleg V. Tsodikov , Sylvie Garneau-Tsodikova","doi":"10.1039/d3np00036b","DOIUrl":"10.1039/d3np00036b","url":null,"abstract":"<div><p>Covering: 2009 up to August 2023</p></div><div><p>Prenyltransferases (PTs) are involved in the primary and the secondary metabolism of plants, bacteria, and fungi, and they are key enzymes in the biosynthesis of many clinically relevant natural products (NPs). The continued biochemical and structural characterization of the soluble dimethylallyl tryptophan synthase (DMATS) PTs over the past two decades have revealed the significant promise that these enzymes hold as biocatalysts for the chemoenzymatic synthesis of novel drug leads. This is a comprehensive review of DMATSs describing the structure–function relationships that have shaped the mechanistic underpinnings of these enzymes, as well as the application of this knowledge to the engineering of DMATSs. We summarize the key findings and lessons learned from these studies over the past 14 years (2009–2023). In addition, we identify current gaps in our understanding of these fascinating enzymes.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":null,"pages":null},"PeriodicalIF":11.9,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71475658","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}
Huperzine alkaloids are a group of natural products belonging to the Lycopodium alkaloids family. The representative member huperzine A has a unique structure and exhibits potent inhibitory activity against acetylcholine esterase (AChE). This subfamily of alkaloids provides a great opportunity for developing synthetic methodologies and asymmetric synthesis. The efforts towards the synthesis of huperzine A have cultivated dozens of total syntheses and a rich body of new chemistry. Impressive progress has also been made in the synthesis of other huperzine alkaloids. The total syntheses of huperzines B, U, O, Q and R, structure reassignment and total syntheses of huperzines K, M and N have been reported in the past decade. This review focuses on the synthetic organic chemistry and the biosynthesis and medicinal chemistry of huperzines are also covered briefly.
{"title":"Huperzine alkaloids: forty years of total syntheses","authors":"Bichu Cheng , Lili Song , Fener Chen","doi":"10.1039/d3np00029j","DOIUrl":"10.1039/d3np00029j","url":null,"abstract":"<div><p>Covering: up to 2023</p></div><div><p>Huperzine alkaloids are a group of natural products belonging to the <em>Lycopodium</em> alkaloids family. The representative member huperzine A has a unique structure and exhibits potent inhibitory activity against acetylcholine esterase (AChE). This subfamily of alkaloids provides a great opportunity for developing synthetic methodologies and asymmetric synthesis. The efforts towards the synthesis of huperzine A have cultivated dozens of total syntheses and a rich body of new chemistry. Impressive progress has also been made in the synthesis of other huperzine alkaloids. The total syntheses of huperzines B, U, O, Q and R, structure reassignment and total syntheses of huperzines K, M and N have been reported in the past decade. This review focuses on the synthetic organic chemistry and the biosynthesis and medicinal chemistry of huperzines are also covered briefly.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":null,"pages":null},"PeriodicalIF":11.9,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41186139","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}
Simple phenylpropanoids are a large group of natural products with primary C6–C3 skeletons. They are not only important biomolecules for plant growth but also crucial chemicals for high-value industries, including fragrances, nutraceuticals, biomaterials, and pharmaceuticals. However, with the growing global demand for simple phenylpropanoids, direct plant extraction or chemical synthesis often struggles to meet current needs in terms of yield, titre, cost, and environmental impact. Benefiting from the rapid development of metabolic engineering and synthetic biology, microbial production of natural products from inexpensive and renewable sources provides a feasible solution for sustainable supply. This review outlines the biological activities of simple phenylpropanoids, compares their biosynthetic pathways in different species (plants, bacteria, and fungi), and summarises key research on the microbial production of simple phenylpropanoids over the last decade, with a focus on engineering strategies that seem to hold most potential for further development. Moreover, constructive solutions to the current challenges and future perspectives for industrial production of phenylpropanoids are presented.
{"title":"Simple phenylpropanoids: recent advances in biological activities, biosynthetic pathways, and microbial production†","authors":"Zhanpin Zhu , Ruibing Chen , Lei Zhang","doi":"10.1039/d3np00012e","DOIUrl":"10.1039/d3np00012e","url":null,"abstract":"<div><p>Covering: 2000 to 2023</p></div><div><p>Simple phenylpropanoids are a large group of natural products with primary C6–C3 skeletons. They are not only important biomolecules for plant growth but also crucial chemicals for high-value industries, including fragrances, nutraceuticals, biomaterials, and pharmaceuticals. However, with the growing global demand for simple phenylpropanoids, direct plant extraction or chemical synthesis often struggles to meet current needs in terms of yield, titre, cost, and environmental impact. Benefiting from the rapid development of metabolic engineering and synthetic biology, microbial production of natural products from inexpensive and renewable sources provides a feasible solution for sustainable supply. This review outlines the biological activities of simple phenylpropanoids, compares their biosynthetic pathways in different species (plants, bacteria, and fungi), and summarises key research on the microbial production of simple phenylpropanoids over the last decade, with a focus on engineering strategies that seem to hold most potential for further development. Moreover, constructive solutions to the current challenges and future perspectives for industrial production of phenylpropanoids are presented.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":null,"pages":null},"PeriodicalIF":11.9,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41091109","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}
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.
{"title":"Correction: Biosynthesis, biological activities, and structure–activity relationships of decalin-containing tetramic acid derivatives isolated from fungi","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"<div><p>Correction for ‘Biosynthesis, biological activities, and structure–activity relationships of decalin-containing tetramic acid derivatives isolated from fungi’ by Hyun Woo Kim <em>et al.</em>, <em>Nat. Prod. Rep.</em>, 2024, <span>https://doi.org/10.1039/d4np00013g</span>.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":null,"pages":null},"PeriodicalIF":10.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142040262","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}
{"title":"Correction: Hot off the Press","authors":"Robert A. Hill , Andrew Sutherland","doi":"10.1039/d3np90056h","DOIUrl":"10.1039/d3np90056h","url":null,"abstract":"<div><p>Correction for ‘Hot off the Press’ by Robert A. Hill <em>et al.</em>, <em>Nat. Prod. Rep.</em>, 2023, <strong>40</strong>, 1816–1821, <span>https://doi.org/10.1039/d3np90052e</span>.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":null,"pages":null},"PeriodicalIF":11.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139083531","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}
Correction for ‘The ‘emodin family’ of fungal natural products–amalgamating a century of research with recent genomics-based advances’ by Kate M. J. de Mattos-Shipley et al., Nat. Prod. Rep., 2023, 40, 174–201, https://doi.org/10.1039/D2NP00040G.
对 Kate M. J. de Mattos-Shipley 等人在 Nat.Rep.Rep., 2023, 40, 174-201, https://doi.org/10.1039/D2NP00040G。
{"title":"Correction: The ‘emodin family’ of fungal natural products–amalgamating a century of research with recent genomics-based advances","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"<div><div>Correction for ‘The ‘emodin family’ of fungal natural products–amalgamating a century of research with recent genomics-based advances’ by Kate M. J. de Mattos-Shipley <em>et al.</em>, <em>Nat. Prod. Rep.</em>, 2023, <strong>40</strong>, 174–201, <span>https://doi.org/10.1039/D2NP00040G</span>.</div></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":null,"pages":null},"PeriodicalIF":10.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142356923","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}
Correction for ‘Future antimalarials from Artemisia? A rationale for natural product mining against drug-refractory Plasmodium stages’ by Alexandre Maciuk et al., Nat. Prod. Rep., 2023, 40, 1130–1144, https://doi.org/10.1039/D3NP00001J.
{"title":"Correction: Future antimalarials from Artemisia? A rationale for natural product mining against drug-refractory Plasmodium stages","authors":"Alexandre Maciuk , Dominique Mazier , Romain Duval","doi":"10.1039/d4np90001d","DOIUrl":"10.1039/d4np90001d","url":null,"abstract":"<div><p>Correction for ‘Future antimalarials from <em>Artemisia</em>? A rationale for natural product mining against drug-refractory <em>Plasmodium</em> stages’ by Alexandre Maciuk <em>et al.</em>, <em>Nat. Prod. Rep.</em>, 2023, <strong>40</strong>, 1130–1144, <span>https://doi.org/10.1039/D3NP00001J</span>.</p></div>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":null,"pages":null},"PeriodicalIF":11.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139477800","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 alscholarine A from Alstonia scholaris.
{"title":"Hot off the Press","authors":"Robert A. Hill and Andrew Sutherland","doi":"10.1039/D3NP90052E","DOIUrl":"10.1039/D3NP90052E","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 alscholarine A from <em>Alstonia scholaris</em>.</p>","PeriodicalId":94,"journal":{"name":"Natural Product Reports","volume":null,"pages":null},"PeriodicalIF":11.9,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138476272","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}
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":null,"pages":null},"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":null,"pages":null},"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}