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Kong Y, Liu Y, Wang K, Wang T, Wang C, Ai B, Jia H, Pan G, Yin M, Xu Z. Confirmation of the stereochemistry of spiroviolene. Beilstein J Org Chem 2024; 20:852-858. [PMID: 38655555 PMCID: PMC11035986 DOI: 10.3762/bjoc.20.77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
We confirm the previously revised stereochemistry of spiroviolene by X-ray crystallographically characterizing a hydrazone derivative of 9-oxospiroviolane, which is synthesized by hydroboration/oxidation of spiroviolene followed by oxidation of the resultant hydroxy group. An unexpected thermal boron migration occurred during the hydroboration process of spiroviolene that resulted in the production of a mixture of 1α-hydroxyspiroviolane, 9α- and 9β-hydroxyspiroviolane after oxidation. The assertion of the cis-orientation of the 19- and 20-methyl groups provided further support for the revised cyclization mechanism of spiroviolene.
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Affiliation(s)
- Yao Kong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Yuanning Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Kaibiao Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Tao Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Chen Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Ben Ai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Hongli Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Yin
- School of Medicine, Yunnan University, 2 North Cui Hu Road, Kunming 650091, China
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
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2
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Xu H, Dickschat JS. Isotopic labelings for mechanistic studies. Methods Enzymol 2024; 699:163-186. [PMID: 38942502 DOI: 10.1016/bs.mie.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
The intricate mechanisms in the biosynthesis of terpenes belong to the most challenging problems in natural product chemistry. Methods to address these problems include the structure-based site-directed mutagenesis of terpene synthases, computational approaches, and isotopic labeling experiments. The latter approach has a long tradition in biosynthesis studies and has recently experienced a revival, after genome sequencing enabled rapid access to biosynthetic genes and enzymes. Today, this allows for a combined approach in which isotopically labeled substrates can be incubated with recombinant terpene synthases. These clearly defined reaction setups can give detailed mechanistic insights into the reactions catalyzed by terpene synthases, and recent developments have substantially deepened our understanding of terpene biosynthesis. This chapter will discuss the state of the art and introduce some of the most important methods that make use of isotopic labelings in mechanistic studies on terpene synthases.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany.
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3
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Huang ZY, Taizoumbe KA, Liang C, Goldfuss B, Xu JH, Dickschat JS. Spiroluchuene A Synthase: A Cyclase from Aspergillus luchuensis Forming a Spirotetracyclic Diterpene. Angew Chem Int Ed Engl 2023; 62:e202315659. [PMID: 37962519 DOI: 10.1002/anie.202315659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/15/2023]
Abstract
The diterpene synthase AlTS was identified from Aspergillus luchuensis. AlTS catalyses the formation of the diterpene hydrocarbon spiroluchuene A, which exhibits a novel skeleton characterised by a spirocyclic ring system. The cyclisation mechanism towards this compound was elucidated through isotopic labelling experiments in conjunction with DFT calculations and metadynamic simulations. The biosynthetic intermediate luchudiene, besides the derivative spiroluchuene B, was captured from an enzyme variant obtained through site-directed mutagenesis. With its 10-membered ring luchudiene is structurally related to germacrenes and can undergo a Cope rearrangement to luchuelemene.
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Affiliation(s)
- Zheng-Yu Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Kizerbo A Taizoumbe
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Chengqin Liang
- College of Pharmacy, Guilin Medical University, Guilin, 541004, China
| | - Bernd Goldfuss
- Department of Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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4
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Gu B, Goldfuss B, Schnakenburg G, Dickschat JS. Subrutilane-A Hexacyclic Sesterterpene from Streptomyces subrutilus. Angew Chem Int Ed Engl 2023; 62:e202313789. [PMID: 37846897 DOI: 10.1002/anie.202313789] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/18/2023]
Abstract
Mining of a terpene synthase from Streptomyces subrutilus resulted in the identification of the hexacyclic sesterterpene subrutilane, besides eight pentacyclic side products. Subrutilane represents the first case of a saturated sesterterpene hydrocarbon. Its structure, including the absolute configuration, was unambiguously determined through X-ray crystallographic analysis and stereoselective deuteration. The cyclisation mechanism to subrutilane and its side products was investigated in all detail by isotopic labelling experiments and DFT calculations. The subrutilane synthase (SrS) also converted (2Z)-GFPP into one major product. Additional compounds were obtained from the substrate analogues (7R)-6,7-dihydro-GFPP and (2Z,7R)-6,7-dihydro-GFPP with blocked reactivity at the C6-C7 bond. Interestingly, the early steps of the cyclisation cascade with (2Z)-GFPP and the saturated substrate analogues were analogous to those of GFPP, but then deviations from the natural cyclisation mode occur.
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Affiliation(s)
- Binbin Gu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Bernd Goldfuss
- Department for Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Gregor Schnakenburg
- Institute for Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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5
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Tarasova EV, Luchnikova NA, Grishko VV, Ivshina IB. Actinomycetes as Producers of Biologically Active Terpenoids: Current Trends and Patents. Pharmaceuticals (Basel) 2023; 16:872. [PMID: 37375819 DOI: 10.3390/ph16060872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Terpenes and their derivatives (terpenoids and meroterpenoids, in particular) constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.
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Affiliation(s)
- Ekaterina V Tarasova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Natalia A Luchnikova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Victoria V Grishko
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Irina B Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
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6
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Gong K, Yong D, Fu J, Li A, Zhang Y, Li R. Diterpenoids from Streptomyces: Structures, Biosyntheses and Bioactivities. Chembiochem 2022; 23:e202200231. [PMID: 35585772 DOI: 10.1002/cbic.202200231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/16/2022] [Indexed: 11/09/2022]
Abstract
Bacteria, especially Streptomyces spp., have been emerging as rich sources of natural diterpenoids with diverse structures and broad bioactivities. Here, we review diterpenoids biosynthesized by Streptomyces , with an emphasis on their structures, biosyntheses, and bioactivities. Although diterpenoids from Streptomyces are relatively rare compared to those from plants and fungi, their novel skeletons, biosyntheses and bioactivities present opportunities for discovering new drugs, enzyme mechanisms, and applications in bio-catalysis and metabolic pathway engineering.
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Affiliation(s)
- Kai Gong
- Shandong University, State Key Laboratory of Microbial Technology, CHINA
| | - Daojing Yong
- Shandong University, State Key Laboratory of Microbial Technology, CHINA
| | - Jun Fu
- Shandong University, State Key Laboratory of Microbial Technology, CHINA
| | - Aiying Li
- Shandong University, State Key Laboratory of Microbial Technology, CHINA
| | - Youming Zhang
- Shandong University, State Key Laboratory of Microbial Technology, CHINA
| | - Ruijuan Li
- Shandong University, State Key Laboratory of Microbial Technology, Binhai Road 72, 266237, Qingdao, CHINA
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7
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Sato H, Takagi T, Miyamoto K, Uchiyama M. Theoretical Study on the Mechanism of Spirocyclization in Spiroviolene Biosynthesis. Chem Pharm Bull (Tokyo) 2021; 69:1034-1038. [PMID: 34602572 DOI: 10.1248/cpb.c21-00536] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Spiroviolene is a spirocyclic triquinane diterpene produced by Streptomyces violens. Recently, a biosynthetic pathway that includes secondary carbocation intermediates and a complicated concerted skeletal rearrangement was proposed for spiroviolene, based upon careful labeling experiments. On the basis of density functional theory (DFT) calculations, we propose a revised pathway for spiroviolene biosynthesis, involving a multistep carbocation cascade that bypasses the formation of unstable secondary carbocations by breaking the adjacent C-C bond to form a more stable tertiary carbocation (IM3) and by Wagner-Meerwein 1,2-methyl rearrangement (IM7).
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Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
| | - Taisei Takagi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | | | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Research Initiative for Supra-Materials (RISM), Shinshu University
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8
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Li G, Guo YW, Dickschat JS. The mass spectrometric fragmentation mechanisms of catenulane and isocatenulane diterpenes. Org Biomol Chem 2021; 19:2224-2232. [PMID: 33624667 DOI: 10.1039/d1ob00160d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Two new diterpene derivatives were obtained by semisynthesis from enzymatically generated catenul-14-en-6-ol. The EI-MS fragmentation mechanisms of three enzyme products and the two semisynthetic derivatives were investigated by extensive 13C-labelling experiments.
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Affiliation(s)
- Geng Li
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany. and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, 201203, Shanghai, China. and University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, 201203, Shanghai, China. and University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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9
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Schriever K, Saenz-Mendez P, Rudraraju RS, Hendrikse NM, Hudson EP, Biundo A, Schnell R, Syrén PO. Engineering of Ancestors as a Tool to Elucidate Structure, Mechanism, and Specificity of Extant Terpene Cyclase. J Am Chem Soc 2021; 143:3794-3807. [PMID: 33496585 PMCID: PMC8023661 DOI: 10.1021/jacs.0c10214] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Indexed: 12/21/2022]
Abstract
Structural information is crucial for understanding catalytic mechanisms and to guide enzyme engineering efforts of biocatalysts, such as terpene cyclases. However, low sequence similarity can impede homology modeling, and inherent protein instability presents challenges for structural studies. We hypothesized that X-ray crystallography of engineered thermostable ancestral enzymes can enable access to reliable homology models of extant biocatalysts. We have applied this concept in concert with molecular modeling and enzymatic assays to understand the structure activity relationship of spiroviolene synthase, a class I terpene cyclase, aiming to engineer its specificity. Engineering a surface patch in the reconstructed ancestor afforded a template structure for generation of a high-confidence homology model of the extant enzyme. On the basis of structural considerations, we designed and crystallized ancestral variants with single residue exchanges that exhibited tailored substrate specificity and preserved thermostability. We show how the two single amino acid alterations identified in the ancestral scaffold can be transferred to the extant enzyme, conferring a specificity switch that impacts the extant enzyme's specificity for formation of the diterpene spiroviolene over formation of sesquiterpenes hedycaryol and farnesol by up to 25-fold. This study emphasizes the value of ancestral sequence reconstruction combined with enzyme engineering as a versatile tool in chemical biology.
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Affiliation(s)
- Karen Schriever
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, KTH Royal
Institute of Technology, 114 28 Stockholm, Sweden
| | - Patricia Saenz-Mendez
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, KTH Royal
Institute of Technology, 114 28 Stockholm, Sweden
| | | | - Natalie M. Hendrikse
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, KTH Royal
Institute of Technology, 114 28 Stockholm, Sweden
- Swedish
Orphan Biovitrum AB, 112
76 Stockholm, Sweden
| | - Elton P. Hudson
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Protein Science, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
| | - Antonino Biundo
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, KTH Royal
Institute of Technology, 114 28 Stockholm, Sweden
| | - Robert Schnell
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 165 Stockholm, Sweden
| | - Per-Olof Syrén
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, 114 28 Stockholm, Sweden
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Fibre and Polymer Technology, KTH Royal
Institute of Technology, 114 28 Stockholm, Sweden
- Wallenberg
Wood Science Center, Teknikringen 56−58, 100 44 Stockholm, Sweden
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10
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Xu H, Dickschat JS. Revision of the Cyclisation Mechanism for the Diterpene Spiroviolene and Investigations of Its Mass Spectrometric Fragmentation. Chembiochem 2021; 22:850-854. [PMID: 33084237 PMCID: PMC7983979 DOI: 10.1002/cbic.202000682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/21/2020] [Indexed: 01/15/2023]
Abstract
The diterpene spiroviolene, its diterpene synthase from Streptomyces violens and the experimentally determined terpene cyclisation mechanism were reported in 2017. Recently, the structure of spiroviolene was revised based on a total synthesis, with consequences for the cyclisation mechanism. Herein, a reinvestigation of the terpene cyclisation to spiroviolene and the mass spectrometric fragmentation mechanism investigated by 13 C-labelling experiments are presented.
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Affiliation(s)
- Houchao Xu
- Kekulé Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Jeroen S. Dickschat
- Kekulé Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
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