1
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Tang J, Matsuda Y. Discovery of fungal onoceroid triterpenoids through domainless enzyme-targeted global genome mining. Nat Commun 2024; 15:4312. [PMID: 38773118 PMCID: PMC11109268 DOI: 10.1038/s41467-024-48771-7] [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: 11/10/2023] [Accepted: 05/09/2024] [Indexed: 05/23/2024] Open
Abstract
Genomics-guided methodologies have revolutionized the discovery of natural products. However, a major challenge in the field of genome mining is determining how to selectively extract biosynthetic gene clusters (BGCs) for untapped natural products from numerous available genome sequences. In this study, we developed a fungal genome mining tool that extracts BGCs encoding enzymes that lack a detectable protein domain (i.e., domainless enzymes) and are not recognized as biosynthetic proteins by existing bioinformatic tools. We searched for BGCs encoding a homologue of Pyr4-family terpene cyclases, which are representative examples of apparently domainless enzymes, in approximately 2000 fungal genomes and discovered several BGCs with unique features. The subsequent characterization of selected BGCs led to the discovery of fungal onoceroid triterpenoids and unprecedented onoceroid synthases. Furthermore, in addition to the onoceroids, a previously unreported sesquiterpene hydroquinone, of which the biosynthesis involves a Pyr4-family terpene cyclase, was obtained. Our genome mining tool has broad applicability in fungal genome mining and can serve as a beneficial platform for accessing diverse, unexploited natural products.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
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2
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Ueda D, Matsuda N, Takaba Y, Hirai N, Inoue M, Kameya T, Abe T, Tagaya N, Isogai Y, Kakihara Y, Bartels F, Christmann M, Shinada T, Yasuda K, Sato T. Analysis of vitamin D receptor binding affinities of enzymatically synthesized triterpenes including ambrein and unnatural onoceroids. Sci Rep 2024; 14:1419. [PMID: 38228813 PMCID: PMC10792010 DOI: 10.1038/s41598-024-52013-7] [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] [Received: 10/12/2023] [Accepted: 01/12/2024] [Indexed: 01/18/2024] Open
Abstract
Onoceroids are a rare family of triterpenes. One representative onoceroid is ambrein, which is the main component of ambergris used as a traditional medicine. We have previously identified the onoceroid synthase, BmeTC, in Bacillus megaterium and succeeded in creating ambrein synthase by introducing mutations into BmeTC. Owing to the structural similarity of ambrein to vitamin D, a molecule with diverse biological activities, we hypothesized that some of the activities of ambergris may be induced by the binding of ambrein to the vitamin D receptor (VDR). We demonstrated the VDR binding ability of ambrein. By comparing the structure-activity relationships of triterpenes with both the VDR affinity and osteoclastic differentiation-promoting activity, we observed that the activity of ambrein was not induced via the VDR. Therefore, some of the activities of ambergris, but not all, can be attributed to its VDR interaction. Additionally, six unnatural onoceroids were synthesized using the BmeTC reactions, and these compounds exhibited higher VDR affinity than that of ambrein. Enzymatic syntheses of onoceroid libraries will be valuable in creating a variety of bioactive compounds beyond ambergris.
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Affiliation(s)
- Daijiro Ueda
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Natsu Matsuda
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Yuka Takaba
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Nami Hirai
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Mao Inoue
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Taichi Kameya
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Tohru Abe
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Nao Tagaya
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, Imizu, Japan
| | - Yasuhiro Isogai
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, Imizu, Japan
| | - Yoshito Kakihara
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Florian Bartels
- Institute of Chemistry and Biochemistry, Freie Unversität Berlin, Berlin, Germany
| | - Mathias Christmann
- Institute of Chemistry and Biochemistry, Freie Unversität Berlin, Berlin, Germany
| | - Tetsuro Shinada
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Kaori Yasuda
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, Imizu, Japan.
| | - Tsutomu Sato
- Graduate School of Science and Technology, Niigata University, Niigata, Japan.
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3
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Long X, Li J, Gao F, Wu H, Deng J. Bioinspired Synthesis of Spirochensilide A from Lanosterol. J Am Chem Soc 2022; 144:16292-16297. [PMID: 36054904 DOI: 10.1021/jacs.2c07198] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A bioinspired synthesis of spirochensilide A from commercially available lanosterol is reported. The synthesis features a directed C-H oxidation, a Wagner-Meerwein-type double methyl migration, a Meinwald rearrangement, and a double-bond isomerization/spiroketal formation cascade. The proposed biosynthetic speculation was modified by this synthetic sequence, which also served as a platform for the synthesis of other lanostanes with migrating methyl groups.
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Affiliation(s)
- Xianwen Long
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jun Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Feng Gao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hai Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jun Deng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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4
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Alekseychuk M, Adrian S, Heinze RC, Heretsch P. Biogenesis-Inspired, Divergent Synthesis of Spirochensilide A, Spirochensilide B, and Abifarine B Employing a Radical-Polar Crossover Rearrangement Strategy. J Am Chem Soc 2022; 144:11574-11579. [PMID: 35729679 DOI: 10.1021/jacs.2c05358] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Triterpenoids and related abeo-steroids are of interest to the scientific community for their potent and varied biological activities as well as their unique structures. Within this large and diverse family of natural products, the fir metabolites (-)-spirochensilide A and B are particularly noteworthy for their controversial biogenesis. We herein report the chemical synthesis of the spirochensilides, which involves a concerted sequence of bioinspired rearrangements contributing to its resolution. Points of divergence after each rearrangement step also allow for an approach to the abifarine family of natural products with abifarine B as a synthetic target. Key to this strategy is a radical-polar crossover event to initiate the first rearrangement without the need for a sacrificial functionality to be introduced beforehand.
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Affiliation(s)
- Mykhaylo Alekseychuk
- Institute of Organic Chemistry, Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
| | - Sinan Adrian
- Institute of Organic Chemistry, Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
| | - Robert C Heinze
- Institute of Organic Chemistry, Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
| | - Philipp Heretsch
- Institute of Organic Chemistry, Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
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5
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Millán RE, Rodríguez J, Sarandeses LA, Gómez-Bengoa E, Sestelo JP. Indium(III)-Catalyzed Stereoselective Synthesis of Tricyclic Frameworks by Cascade Cycloisomerization Reactions of Aryl 1,5-Enynes. J Org Chem 2021; 86:9515-9529. [PMID: 34170696 DOI: 10.1021/acs.joc.1c00825] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The indium(III)-catalyzed cascade cycloisomerization reaction of 1,5-enynes with pendant aryl nucleophiles is reported. The reaction proceeds in cascade under mild reaction conditions, using InI3 (5 mol %) as a catalyst with a range of 1,5-enynes furnished with aryl groups (phenyl and phenol) at alkene (E and Z isomers) and with terminal and internal alkynes. Using 1-bromo-1,5-enynes, a one-pot sequential indium-catalyzed cycloisomerization and palladium-catalyzed cross-coupling with triorganoindium reagents were developed. The double cyclization is stereospecific and operates via a biomimetic cascade cation-olefin through 1,5-enyne cyclization (6-endo-dig) and subsequent C-C hydroarylation or C-O phenoxycyclization. Density functional theory (DFT) computational studies on 1,5-enynyl aryl ethers support a two-step mechanism where the first stereoselective 1,5-enyne cyclization produces a nonclassical carbocation intermediate that evolves to the tricyclic reaction product through a SEAr mechanism. Using this approach, a variety of tricyclic heterocycles such as benzo[b]chromenes, phenanthridines, xanthenes, and spiroheterocyclic compounds are efficiently synthesized with high atom economy.
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Affiliation(s)
- Ramón E Millán
- Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química, Universidade da Coruña, E-15071 A Coruña, Spain
| | - Jaime Rodríguez
- Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química, Universidade da Coruña, E-15071 A Coruña, Spain
| | - Luis A Sarandeses
- Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química, Universidade da Coruña, E-15071 A Coruña, Spain
| | - Enrique Gómez-Bengoa
- Departamento de Química Orgánica I, Universidad del País Vasco UPV/EHU, 20009 Donostia-San, Sebastián
| | - José Pérez Sestelo
- Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química, Universidade da Coruña, E-15071 A Coruña, Spain
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6
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Zhu S, Li H, Fu R, Hao W, Wang S, Tu S, Jiang B. Regio‐ and Stereoselective Synthesis of Rotationally Hindered C
12
‐Naphthylated Tribenzo[
a,c,j
]xanthenes through Catalytic Tricyclization of Yne‐Allenones. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Shan‐Shan Zhu
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Heng Li
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Rong Fu
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Wen‐Juan Hao
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Shu‐Liang Wang
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Shu‐Jiang Tu
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Bo Jiang
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
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7
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Bartels F, Weber M, Christmann M. Synthesis of Spongidine A and D and Petrosaspongiolide L Methyl Ester Using Pyridine C-H Functionalization. Org Lett 2020; 22:552-555. [PMID: 31877051 DOI: 10.1021/acs.orglett.9b04315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient strategy for the synthesis of the potent phospholipase A2 inhibitors spongidine A and D is presented. The tetracyclic core of the natural products was assembled via an intramolecular hydrogen atom transfer initiated Minisci reaction. A divergent late-stage functionalization of the tetracyclic ring system was also used to achieve a concise synthesis of petrosaspongiolide L methyl ester.
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Affiliation(s)
- Florian Bartels
- Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Manuela Weber
- Institute of Chemistry and Biochemistry , Freie Universität Berlin , Fabeckstraße 34-36 , 14195 Berlin , Germany
| | - Mathias Christmann
- Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
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8
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Heinze RC, Heretsch P. Translation of a Polar Biogenesis Proposal into a Radical Synthetic Approach: Synthesis of Pleurocin A/Matsutakone and Pleurocin B. J Am Chem Soc 2019; 141:1222-1226. [DOI: 10.1021/jacs.8b13356] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Robert C. Heinze
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Philipp Heretsch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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9
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Driller R, Janke S, Fuchs M, Warner E, Mhashal AR, Major DT, Christmann M, Brück T, Loll B. Towards a comprehensive understanding of the structural dynamics of a bacterial diterpene synthase during catalysis. Nat Commun 2018; 9:3971. [PMID: 30266969 PMCID: PMC6162201 DOI: 10.1038/s41467-018-06325-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/28/2018] [Indexed: 11/24/2022] Open
Abstract
Terpenes constitute the largest and structurally most diverse natural product family. Most terpenoids exhibit a stereochemically complex macrocyclic core, which is generated by C–C bond forming of aliphatic oligo-prenyl precursors. This reaction is catalysed by terpene synthases (TPSs), which are capable of chaperoning highly reactive carbocation intermediates through an enzyme-specific reaction. Due to the instability of carbocation intermediates, the proteins’ structural dynamics and enzyme:substrate interactions during TPS catalysis remain elusive. Here, we present the structure of the diterpene synthase CotB2, in complex with an in crystallo cyclised abrupt reaction product and a substrate-derived diphosphate. We captured additional snapshots of the reaction to gain an overview of CotB2’s catalytic mechanism. To enhance insights into catalysis, structural information is augmented with multiscale molecular dynamic simulations. Our data represent fundamental TPS structure dynamics during catalysis, which ultimately enable rational engineering towards tailored terpene macrocycles that are inaccessible by conventional chemical synthesis. The bacterial diterpene synthase CotB2 catalyses the cyclisation of geranylgeranyl diphosphate to cyclooctat-9-en7-ol. Here the authors present various CotB2 structures including a trapped abrupt reaction product that were used for molecular dynamic simulations and allowed them to model all intermediates along the reaction cascade.
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Affiliation(s)
- Ronja Driller
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195, Berlin, Germany
| | - Sophie Janke
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
| | - Monika Fuchs
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748, Garching, Germany
| | - Evelyn Warner
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
| | - Anil R Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Mathias Christmann
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748, Garching, Germany
| | - Bernhard Loll
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195, Berlin, Germany.
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10
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Menger M, Lentz D, Christmann M. Synthesis of (+)-Vitepyrroloid A and (+)-Vitepyrroloid B by Late-Stage Ni-Catalyzed C(sp2)–C(sp3) Cross-Electrophile Coupling. J Org Chem 2018; 83:6793-6797. [DOI: 10.1021/acs.joc.8b00882] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martina Menger
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195 Berlin, Germany
| | - Dieter Lentz
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195 Berlin, Germany
| | - Mathias Christmann
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustrasse 3, 14195 Berlin, Germany
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