1
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Li H, Goldfuss B, Dickschat JS. Mechanistic characterisation of the diterpene synthase for clitopilene and identification of isopentalenene synthase from the fungus Clitopilus passeckerianus. Chem Commun (Camb) 2024; 60:7041-7044. [PMID: 38904208 DOI: 10.1039/d4cc02286f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Two terpene synthases from the pleuromutilin producing fungus Clitopilus passeckerianus were functionally characterised. The first enzyme CpTS1 produces the new diterpene clitopilene with a novel 6-6-5-5 tetracyclic skeleton, while the second enzyme CpTS2 makes the new sesquiterpene isopentalenene. The CpTS1 reaction mechanism was studied in depth using experimental and theoretical approaches.
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Affiliation(s)
- Heng Li
- 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
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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2
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Xu M, Xu H, Lei Z, Xing B, Dickschat JS, Yang D, Ma M. Structural Insights Into the Terpene Cyclization Domains of Two Fungal Sesterterpene Synthases and Enzymatic Engineering for Sesterterpene Diversification. Angew Chem Int Ed Engl 2024; 63:e202405140. [PMID: 38584136 DOI: 10.1002/anie.202405140] [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: 03/15/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Little is known about the structures and catalytic mechanisms of sesterterpene synthases (StTSs), which greatly hinders the structure-based engineering of StTSs for structural diversity expansion of sesterterpenes. We here report on the crystal structures of the terpene cyclization (TC) domains of two fungal StTSs: sesterfisherol synthase (NfSS) and sesterbrasiliatriene synthase (PbSS). Both TC structures contain benzyltriethylammonium chloride (BTAC), pyrophosphate (PPi), and magnesium ions (Mg2+), clearly defining the catalytic active sites. A combination of theory and experiments including carbocationic intermediates modeling, site-directed mutagenesis, and isotope labeling provided detailed insights into the structural basis for their catalytic mechanisms. Structure-based engineering of NfSS and PbSS resulted in the formation of 20 sesterterpenes including 13 new compounds and four pairs of epimers with different configurations at C18. These results expand the structural diversity of sesterterpenes and provide important insights for future synthetic biology research.
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Affiliation(s)
- Meng Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Houchao Xu
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Zhenyu Lei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Baiying Xing
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Jeroen S Dickschat
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
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3
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Gu B, Goldfuss B, Dickschat JS. Two Sesterterpene Synthases from Lentzea atacamensis Demonstrate the Role of Conformational Variability in Terpene Biosynthesis. Angew Chem Int Ed Engl 2024; 63:e202401539. [PMID: 38372063 DOI: 10.1002/anie.202401539] [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: 01/22/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/20/2024]
Abstract
Mining of two multiproduct sesterterpene synthases from Lentzea atacamensis resulted in the identification of the synthases for lentzeadiene (LaLDS) and atacamatriene (LaATS). The main product of LaLDS (lentzeadiene) is a new compound, while one of the side products (lentzeatetraene) is the enantiomer of brassitetraene B and the other side product (sestermobaraene F) is known from a surprisingly distantly related sesterterpene synthase. LaATS produces six new compounds, one of which is the enantiomer of the known sesterterpene Bm1. Notably, for both enzymes the products cannot all be explained from one and the same starting conformation of geranylfarnesyl diphosphate, demonstrating the requirement of conformational flexibility of the substrate in the enzymes' active sites. For lentzeadiene an intriguing thermal [1,5]-sigmatropic rearrangement was discovered, reminiscent of the biosynthesis of vitamin D3. All enzyme reactions and the [1,5]-sigmatropic rearrangement were investigated through isotopic labeling experiments and DFT calculations. The results also emphasize the importance of conformational changes during terpene cyclizations.
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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
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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4
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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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5
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Xu H, Köllner TG, Chen F, Dickschat JS. Functional and Mechanistic Characterization of the 4,5-diepi-Isoishwarane Synthase from the Liverwort Radula lindenbergiana. Chembiochem 2024; 25:e202400104. [PMID: 38372483 DOI: 10.1002/cbic.202400104] [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: 02/01/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/20/2024]
Abstract
The microbial type sesquiterpene synthase RlMTPSL4 from the liverwort Radula lindenbergiana was investigated for its products, showing the formation of several sesquiterpene hydrocarbons. The main product was structurally characterized as the new compound 4,5-diepi-isoishwarane, while the side products included the known hydrocarbons germacrene A, α-selinene, eremophilene and 4,5-diepi-aristolochene. The cyclization mechanism towards 4,5-diepi-isoishwarane catalyzed by RlMTPSL4 was investigated through isotopic labeling experiments, revealing the stereochemical course for the deprotonation step to the neutral intermediate germacrene A, a reprotonation for its further cyclization, and a 1,2-hydride shift along the cascade. The absolute configuration of 4,5-diepi-isoishwarane was determined using a stereoselective deuteration approach, revealing an absolute configuration typically observed for a microbial type sesquiterpene.
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Affiliation(s)
- Houchao Xu
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN, 37996-4561, USA
| | - Jeroen S Dickschat
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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6
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Scesa PD, Schmidt EW. Brewing coral terpenes-A yeast based approach to soft coral terpene cyclases. Methods Enzymol 2024; 699:373-394. [PMID: 38942511 DOI: 10.1016/bs.mie.2024.03.023] [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
Coral terpenes are important molecules with numerous applications. Here, we describe a robust and simple method to produce coral terpene scaffolds at scale. As an example of the approach, here we discover, express, and characterize further klysimplexin R synthases, expanding the known enzymology of soft coral terpene cyclases. We hope that the underlying method described will enable widespread basic research into the functions of coral terpenes and their biosynthetic genes, as well as the commercial development of biomedically and technologically important molecules.
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Affiliation(s)
- Paul D Scesa
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, United States.
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7
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Nie S, Wang S, Chen R, Ge M, Yan X, Qiao J. Catalytic Mechanism and Heterologous Biosynthesis Application of Sesquiterpene Synthases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6871-6888. [PMID: 38526460 DOI: 10.1021/acs.jafc.4c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Sesquiterpenes comprise a diverse group of natural products with a wide range of applications in cosmetics, food, medicine, agriculture, and biofuels. Heterologous biosynthesis is increasingly employed for sesquiterpene production, aiming to overcome the limitations associated with chemical synthesis and natural extraction. Sesquiterpene synthases (STSs) play a crucial role in the heterologous biosynthesis of sesquiterpene. Under the catalysis of STSs, over 300 skeletons are produced through various cyclization processes (C1-C10 closure, C1-C11 closure, C1-C6 closure, and C1-C7 closure), which are responsible for the diversity of sesquiterpenes. According to the cyclization types, we gave an overview of advances in understanding the mechanism of STSs cyclization from the aspects of protein crystal structures and site-directed mutagenesis. We also summarized the applications of engineering STSs in the heterologous biosynthesis of sesquiterpene. Finally, the bottlenecks and potential research directions related to the STSs cyclization mechanism and application of modified STSs were presented.
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Affiliation(s)
- Shengxin Nie
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University (Shaoxing), Shaoxing 312300, China
| | - Shengli Wang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University (Shaoxing), Shaoxing 312300, China
| | - Ruiqi Chen
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University (Shaoxing), Shaoxing 312300, China
| | - Mingyue Ge
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University (Shaoxing), Shaoxing 312300, China
| | - Xiaoguang Yan
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University (Shaoxing), Shaoxing 312300, China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University (Shaoxing), Shaoxing 312300, China
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8
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Xu H, Köllner TG, Chen F, Dickschat JS. Mechanistic characterisation of a sesquiterpene synthase for asterisca-1,6-diene from the liverwort Radula lindenbergiana and implications for pentalenene biosynthesis. Org Biomol Chem 2024; 22:1360-1364. [PMID: 38240688 DOI: 10.1039/d3ob02088f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
A sesquiterpene synthase from the liverwort Radula lindenbergiana was characterised and shown to produce the new sesquiterpene hydrocarbon (3R,9R)-asterisca-1,6-diene, besides small amounts of pentalenene. The biosynthesis of asterisca-1,6-diene was studied through isotopic labelling experiments, giving additional insights into the long discussed biosynthesis of pentalenene.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN 37996-4561, USA
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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9
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Li H, Dickschat JS. Enzymatic Synthesis of Diterpenoids from iso-GGPP III: A Geranylgeranyl Diphosphate Analog with a Shifted Double Bond. Chemistry 2024; 30:e202303560. [PMID: 37947363 DOI: 10.1002/chem.202303560] [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: 10/27/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/12/2023]
Abstract
The analog of the diterpene precursor geranylgeranyl diphosphate with a double bond shifted from C14=C15 to C15=C16 (named iso-GGPP III) has been synthesized and enzymatically converted with six bacterial diterpene synthases; this allowed the isolation of nine unnatural diterpenes. For some of the enzyme-substrate combinations, the different reactivity implemented in the substrate analog iso-GGPP III opened reaction pathways that are not observed with natural GGPP, resulting in the formation of diterpenes with novel skeletons. A stereoselective deuteration strategy was used to assign the absolute configurations of the isolated diterpenes.
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Affiliation(s)
- Heng Li
- Kekulé-Institute for Organic Chemistry and Biochemistry, 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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10
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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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11
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Taizoumbe KA, Goldfuss B, Dickschat JS. The Diterpenoid Substrate Analogue 19-nor-GGPP Reveals Pronounced Methyl Group Effects in Diterpene Cyclisations. Angew Chem Int Ed Engl 2024; 63:e202318375. [PMID: 38117607 DOI: 10.1002/anie.202318375] [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: 11/30/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 12/22/2023]
Abstract
The substrate analogue 19-nor-geranylgeranyl diphosphate (19-nor-GGPP) was synthesised and incubated with 20 diterpene synthases, resulting in the formation of diterpenoids in all cases. A total of 23 different compounds were isolated from these enzyme reactions and structurally characterised, if possible including the experimental determination of absolute configurations through a stereoselective deuteration approach. In several cases the missing 19-Me group in the substrate analogue resulted in opening of completely new reaction paths towards compounds with novel skeletons. DFT calculations were applied to gain a deeper understanding of these observed methyl group effects in diterpene biosynthesis.
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Affiliation(s)
- Kizerbo A Taizoumbe
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Bernd Goldfuss
- Department of Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Jeroen S Dickschat
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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12
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Klucznik T, Syntrivanis LD, Baś S, Mikulak-Klucznik B, Moskal M, Szymkuć S, Mlynarski J, Gadina L, Beker W, Burke MD, Tiefenbacher K, Grzybowski BA. Computational prediction of complex cationic rearrangement outcomes. Nature 2024; 625:508-515. [PMID: 37967579 PMCID: PMC10864989 DOI: 10.1038/s41586-023-06854-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
Recent years have seen revived interest in computer-assisted organic synthesis1,2. The use of reaction- and neural-network algorithms that can plan multistep synthetic pathways have revolutionized this field1,3-7, including examples leading to advanced natural products6,7. Such methods typically operate on full, literature-derived 'substrate(s)-to-product' reaction rules and cannot be easily extended to the analysis of reaction mechanisms. Here we show that computers equipped with a comprehensive knowledge-base of mechanistic steps augmented by physical-organic chemistry rules, as well as quantum mechanical and kinetic calculations, can use a reaction-network approach to analyse the mechanisms of some of the most complex organic transformations: namely, cationic rearrangements. Such rearrangements are a cornerstone of organic chemistry textbooks and entail notable changes in the molecule's carbon skeleton8-12. The algorithm we describe and deploy at https://HopCat.allchemy.net/ generates, within minutes, networks of possible mechanistic steps, traces plausible step sequences and calculates expected product distributions. We validate this algorithm by three sets of experiments whose analysis would probably prove challenging even to highly trained chemists: (1) predicting the outcomes of tail-to-head terpene (THT) cyclizations in which substantially different outcomes are encoded in modular precursors differing in minute structural details; (2) comparing the outcome of THT cyclizations in solution or in a supramolecular capsule; and (3) analysing complex reaction mixtures. Our results support a vision in which computers no longer just manipulate known reaction types1-7 but will help rationalize and discover new, mechanistically complex transformations.
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Affiliation(s)
- Tomasz Klucznik
- Allchemy, Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Leonidas-Dimitrios Syntrivanis
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Basel, Basel, Switzerland.
| | - Sebastian Baś
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Barbara Mikulak-Klucznik
- Allchemy, Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Jacek Mlynarski
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Louis Gadina
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Wiktor Beker
- Allchemy, Highland, IN, USA.
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Martin D Burke
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Molecule Maker Laboratory Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Molecule Maker Laboratory at the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Konrad Tiefenbacher
- Department of Chemistry, University of Basel, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Bartosz A Grzybowski
- Allchemy, Highland, IN, USA.
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland.
- IBS Center for Algorithmic and Robotized Synthesis, CARS, Eonyang-eup, Ulju-gun, Ulsan, South Korea.
- Department of Chemistry, UNIST, Eonyang-eup, Ulju-gun, Ulsan, South Korea.
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13
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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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14
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Dickschat JS, Quan Z, Schnakenburg G. A Case of Convergent Evolution: The Bacterial Sesquiterpene Synthase for 1-epi-Cubenol from Nonomuraea coxensis. Chembiochem 2023; 24:e202300581. [PMID: 37748088 DOI: 10.1002/cbic.202300581] [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: 08/17/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 09/27/2023]
Abstract
A terpene synthase from Nonomuraea coxensis was identified as (+)-1-epi-cubenol synthase. The enzyme is phylogenetically unrelated to the known enzyme of the same function that is widespread in streptomycetes. Isotopic labelling experiments were performed to unambiguously assign the NMR data and to investigate hydrogen migrations during terpene cyclisations. Epoxidations of (+)-1-epi-cubenol and of the plant derived compounds (-)-cubenol and (-)-1-epi-cubenol confirmed the structure of a natural product isolated from the brown alga Dictyopteris divaricata and allowed to conclude on its absolute configuration. The crystal structures of the epoxides from (+)- and (-)-1-epi-cubenol and the acid catalysed conversion into an isomeric ketone are reported.
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Affiliation(s)
- Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Zhiyang Quan
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Gregor Schnakenburg
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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15
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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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16
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Taizoumbe KA, Steiner ST, Dickschat JS. Mechanistic Characterisation of Collinodiene Synthase, a Diterpene Synthase from Streptomyces collinus. Chemistry 2023; 29:e202302469. [PMID: 37579200 DOI: 10.1002/chem.202302469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/16/2023]
Abstract
Two homologs of the diterpene synthase CotB2 from Streptomyces collinus (ScCotB2) and Streptomyces iakyrus (SiCotB2) were investigated for their products by in vitro incubations of the recombinant enzymes with geranylgeranyl pyrophosphate, followed by compound isolation and structure elucidation by NMR. ScCotB2 produced the new compound collinodiene, besides the canonical CotB2 product cyclooctat-9-en-7-ol, dolabella-3,7,18-triene and dolabella-3,7,12-triene, while SiCotB2 gave mainly cyclooctat-9-en-7-ol and only traces of dolabella-3,7,18-triene. The cyclisation mechanism towards the ScCotB2 products and their absolute configurations were investigated through isotopic labelling experiments.
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Affiliation(s)
- Kizerbo A Taizoumbe
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Simon T Steiner
- Kekulé-Institute for Organic Chemistry and Biochemistry, 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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17
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Yin JJ, Wang YP, Xue J, Zhou FF, Shan XQ, Zhu R, Fang K, Shi L, Zhang SY, Hou SH, Xia W, Tu YQ. Total Syntheses of Polycyclic Diterpenes Phomopsene, Methyl Phomopsenonate, and iso-Phomopsene via Reorganization of C-C Single Bonds. J Am Chem Soc 2023; 145:21170-21175. [PMID: 37605370 DOI: 10.1021/jacs.3c07044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The first total syntheses of polycyclic diterpenes phomopsene (1), methyl phomopsenonate (2), and iso-phomopsene (3) have been accomplished through the unusual cascade reorganization of C-C single bonds. This approach features: (i) a synergistic Nazarov cyclization/double ring expansions in one-step, developed by authors, to rapid and stereospecific construction of the 5/5/5/5 tetraquinane scaffold bearing contiguous quaternary centers and (ii) a one-pot strategic ring expansion through Beckmann fragmentation/recombination to efficiently assemble the requisite 5/5/6/5 tetracyclic skeleton of the target molecules 1-3. This work enables us to determine that the correct structure of iso-phomopsene is, in fact, the C7 epimer of the originally assigned structure. Finally, the absolute configurations of three target molecules were confirmed through enantioselective synthesis.
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Affiliation(s)
- Jun-Jie Yin
- School of Science (Shenzhen), School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Yun-Peng Wang
- School of Chemistry and Chemical Engineering, College of Pharmaceutical Sciences, Frontier Scientific Center of Transformative Molecules, Shanghai key Laboratory of Chiral Drugs and Engineering, Shanghai Jiao Tong University, Shanghai, Minhang 200240, China
| | - Jun Xue
- School of Chemistry and Chemical Engineering, College of Pharmaceutical Sciences, Frontier Scientific Center of Transformative Molecules, Shanghai key Laboratory of Chiral Drugs and Engineering, Shanghai Jiao Tong University, Shanghai, Minhang 200240, China
| | - Feng-Fan Zhou
- School of Chemistry and Chemical Engineering, College of Pharmaceutical Sciences, Frontier Scientific Center of Transformative Molecules, Shanghai key Laboratory of Chiral Drugs and Engineering, Shanghai Jiao Tong University, Shanghai, Minhang 200240, China
| | - Xing-Qian Shan
- School of Chemistry and Chemical Engineering, College of Pharmaceutical Sciences, Frontier Scientific Center of Transformative Molecules, Shanghai key Laboratory of Chiral Drugs and Engineering, Shanghai Jiao Tong University, Shanghai, Minhang 200240, China
| | - Rong Zhu
- School of Chemistry and Chemical Engineering, College of Pharmaceutical Sciences, Frontier Scientific Center of Transformative Molecules, Shanghai key Laboratory of Chiral Drugs and Engineering, Shanghai Jiao Tong University, Shanghai, Minhang 200240, China
| | - Kun Fang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Lei Shi
- School of Science (Shenzhen), School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Shu-Yu Zhang
- School of Chemistry and Chemical Engineering, College of Pharmaceutical Sciences, Frontier Scientific Center of Transformative Molecules, Shanghai key Laboratory of Chiral Drugs and Engineering, Shanghai Jiao Tong University, Shanghai, Minhang 200240, China
| | - Si-Hua Hou
- School of Chemistry and Chemical Engineering, College of Pharmaceutical Sciences, Frontier Scientific Center of Transformative Molecules, Shanghai key Laboratory of Chiral Drugs and Engineering, Shanghai Jiao Tong University, Shanghai, Minhang 200240, China
| | - Wujiong Xia
- School of Science (Shenzhen), School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Yong-Qiang Tu
- School of Chemistry and Chemical Engineering, College of Pharmaceutical Sciences, Frontier Scientific Center of Transformative Molecules, Shanghai key Laboratory of Chiral Drugs and Engineering, Shanghai Jiao Tong University, Shanghai, Minhang 200240, China
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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18
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Chhalodia AK, Xu H, Tabekoueng GB, Gu B, Taizoumbe KA, Lauterbach L, Dickschat JS. Functional characterisation of twelve terpene synthases from actinobacteria. Beilstein J Org Chem 2023; 19:1386-1398. [PMID: 37736393 PMCID: PMC10509563 DOI: 10.3762/bjoc.19.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023] Open
Abstract
Fifteen type I terpene synthase homologs from diverse actinobacteria that were selected based on a phylogenetic analysis of more than 4000 amino acid sequences were investigated for their products. For four enzymes with functions not previously reported from bacterial terpene synthases the products were isolated and their structures were elucidated by NMR spectroscopy, resulting in the discovery of the first terpene synthases for (+)-δ-cadinol and (+)-α-cadinene, besides the first two bacterial (-)-amorpha-4,11-diene synthases. For other terpene synthases with functions reported from bacteria before the products were identified by GC-MS. The characterised enzymes include a new epi-isozizaene synthase with monoterpene synthase side activity, a 7-epi-α-eudesmol synthase that also produces hedycaryol and germacrene A, and four more sesquiterpene synthases that produce mixtures of hedycaryol and germacrene A. Three phylogenetically related enzymes were in one case not expressed and in two cases inactive, suggesting pseudogenisation in the respective branch of the phylogenetic tree. Furthermore, a diterpene synthase for allokutznerene and a sesterterpene synthase for sesterviolene were identified.
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Affiliation(s)
- Anuj K Chhalodia
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Houchao Xu
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Georges B Tabekoueng
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Binbin Gu
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Kizerbo A Taizoumbe
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Lukas Lauterbach
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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19
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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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20
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Liu C, Zhang Z, Fukaya K, Oku N, Harunari E, Urabe D, Igarashi Y. Isolation and structure determination of allopteridic acids A-C and allokutzmicin from an unexplored actinomycete of the genus Allokutzneria. J Antibiot (Tokyo) 2023; 76:305-315. [PMID: 37059821 DOI: 10.1038/s41429-023-00611-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 04/16/2023]
Abstract
Two classes of new polyketides, allopteridic acids A-C (1-3) and allokutzmicin (4), were isolated from the culture extract of an actinomycete of the genus Allokutzneria. The structures of 1-4 were elucidated through the interpretation of NMR and MS analytical data. Compounds 1-3 possess the same carbon skeleton with pteridic acids but their monocyclic core structures are distinct from the spiro-bicyclic acetal structures of pteridic acids. Compound 4 is a linear polyketide of an unprecedented class, featured by a guanidino-terminus and an epoxide modification. Compounds 1-3 promoted the root elongation of germinated lettuce seeds by ca. 10-40% at 1~10 μM whereas 4 retarded the seed growth. Compound 4 exhibited weak antimicrobial activity against Candida albicans with MIC 25 μg mL-1.
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Affiliation(s)
- Chang Liu
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Zhiwei Zhang
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Keisuke Fukaya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Daisuke Urabe
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
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21
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Lin X, Huang Y, Min L, Li CC. Synthesis of Spirotricyclic Core of Bonnadiene. Org Lett 2023; 25:1156-1160. [PMID: 36757147 DOI: 10.1021/acs.orglett.3c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
We herein describe a new approach for the efficient synthesis of the tricyclic core of diterpene bonnadiene. The synthetically challenging and unusual [6-7-5] spirotricyclic skeleton including the all-carbon quaternary stereocenter, was installed diastereoselectively via a type II [5 + 2] cycloaddition, followed by a unique vinylogous semipinacol rearrangement. The described chemistry demonstrates the feasibility of making the [6-7-5] spirotricyclic skeleton of the final product from the strained bridged [7-8-5] ring system.
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Affiliation(s)
- Xiaohong Lin
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yu Huang
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Long Min
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chuang-Chuang Li
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China.,Shenzhen Bay Laboratory, Shenzhen 518132, China
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22
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Gu B, Goldfuss B, Dickschat JS. Mechanistic Characterisation and Engineering of Sesterviolene Synthase from Streptomyces violens. Angew Chem Int Ed Engl 2023; 62:e202215688. [PMID: 36350768 PMCID: PMC10107272 DOI: 10.1002/anie.202215688] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Indexed: 11/10/2022]
Abstract
The sesterviolene synthase from Streptomyces violens was identified and represents the second known sesterterpene synthase from bacteria. Isotopic labelling experiments in conjunction with DFT calculations were performed that provided detailed insight into its complex cyclisation mechanism. Enzyme engineering through site-directed mutagenesis gave access to a high-yielding enzyme variant that provided six additional minor products and the main product in sufficient quantities to study its chemistry.
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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
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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23
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Li H, Dickschat JS. Diterpene Biosynthesis from Geranylgeranyl Diphosphate Analogues with Changed Reactivities Expands Skeletal Diversity. Angew Chem Int Ed Engl 2022; 61:e202211054. [PMID: 36066489 PMCID: PMC9826473 DOI: 10.1002/anie.202211054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Indexed: 01/11/2023]
Abstract
Two analogues of the diterpene precursor geranylgeranyl diphosphate with shifted double bonds, named iso-GGPP I and iso-GGPP II, were enzymatically converted with twelve diterpene synthases from bacteria, fungi and protists. The changed reactivity in the substrate analogues resulted in the formation of 28 new diterpenes, many of which exhibit novel skeletons.
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Affiliation(s)
- Heng Li
- 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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24
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Research Progress on Fungal Sesterterpenoids Biosynthesis. J Fungi (Basel) 2022; 8:jof8101080. [PMID: 36294645 PMCID: PMC9605422 DOI: 10.3390/jof8101080] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Sesterterpenes are 25-carbon terpenoids formed by the cyclization of dimethyl allyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP) as structural units by sesterterpenes synthases. Some (not all) sesterterpenoids are modified by cytochrome P450s (CYP450s), resulting in more intricate structures. These compounds have significant physiological activities and pharmacological effects in anti-inflammatory, antibacterial, antitumour, and hypolipidemic communities. Despite being a rare class of terpenoids, sesterterpenoids derived from fungi show a wide range of structural variations. The discovered fungal sesterterpenoid synthases are composed of C-terminal prenyltransferase (PT) and N-terminal terpene synthase (TS) domains, which were given the name PTTSs. PTTSs have the capacities to catalyze chain lengthening and cyclization concurrently. This review summarizes all 52 fungal PTTSs synthases and their biosynthetic pathways involving 100 sesterterpenoids since the discovery of the first PTTSs synthase from fungi in 2013.
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25
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Li H, Dickschat JS. Diterpene Biosynthesis from Geranylgeranyl Diphosphate Analogues with Changed Reactivities Expands Skeletal Diversity. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Heng Li
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Kekulé-Institute for Organic Chemistry and Biochemistry GERMANY
| | - Jeroen S. Dickschat
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Kekulé Institute for Organic Chemistry and Biochemistry Gerhard-Domagk-Straße 1 53121 Bonn GERMANY
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26
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Xing B, Xu H, Li A, Lou T, Xu M, Wang K, Xu Z, Dickschat JS, Yang D, Ma M. Crystal Structure Based Mutagenesis of Cattleyene Synthase Leads to the Generation of Rearranged Polycyclic Diterpenes. Angew Chem Int Ed Engl 2022; 61:e202209785. [PMID: 35819825 PMCID: PMC9543850 DOI: 10.1002/anie.202209785] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Baiying Xing
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry University of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Annan Li
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Tingting Lou
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Meng Xu
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Kaibiao Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Jeroen S. Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry University of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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27
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Xing B, Xu H, Li A, Lou T, Xu M, Wang K, Xu Z, Dickschat JS, Yang D, Ma M. Crystal Structure Based Mutagenesis of Cattleyene Synthase Leads to the Generation of Rearranged Polycyclic Diterpenes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Baiying Xing
- Peking University School of Pharmaceutical Sciences Department of Natural Medicines CHINA
| | - Houchao Xu
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Organic chemistry and biochemistry GERMANY
| | - Annan Li
- Peking University School of Pharmaceutical Sciences Department of Natural Medicines CHINA
| | - Tingting Lou
- Peking University School of Pharmaceutical Sciences Department of Natural Medicines CHINA
| | - Meng Xu
- Peking University School of Pharmaceutical Sciences Department of Natural Medicines CHINA
| | - Kaibiao Wang
- Peking University School of Pharmaceutical Sciences Department of Natural Medicines CHINA
| | - Zhengren Xu
- Peking University School of Pharmaceutical Sciences Department of Natural Medicines CHINA
| | - Jeroen S. Dickschat
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Organic chemistry and biochemistry GERMANY
| | - Donghui Yang
- Peking University School of Pharmaceutical Sciences Department of Natural Medicines CHINA
| | - Ming Ma
- Peking University School of Pharmaceutical Sciences Department of Natural Medicines 38 Xueyuan Road, Haidian District 100191 Beijing CHINA
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Abstract
All known triterpenes are generated by triterpene synthases (TrTSs) from squalene or oxidosqualene1. This approach is fundamentally different from the biosynthesis of short-chain (C10–C25) terpenes that are formed from polyisoprenyl diphosphates2–4. In this study, two fungal chimeric class I TrTSs, Talaromyces verruculosus talaropentaene synthase (TvTS) and Macrophomina phaseolina macrophomene synthase (MpMS), were characterized. Both enzymes use dimethylallyl diphosphate and isopentenyl diphosphate or hexaprenyl diphosphate as substrates, representing the first examples, to our knowledge, of non-squalene-dependent triterpene biosynthesis. The cyclization mechanisms of TvTS and MpMS and the absolute configurations of their products were investigated in isotopic labelling experiments. Structural analyses of the terpene cyclase domain of TvTS and full-length MpMS provide detailed insights into their catalytic mechanisms. An AlphaFold2-based screening platform was developed to mine a third TrTS, Colletotrichum gloeosporioides colleterpenol synthase (CgCS). Our findings identify a new enzymatic mechanism for the biosynthesis of triterpenes and enhance understanding of terpene biosynthesis in nature. Chimeric triterpene synthases are identified that catalyse non-squalene-dependent triterpene biosynthesis.
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Quan Z, Hou A, Goldfuss B, Dickschat JS. Mechanism of the Bifunctional Multiple Product Sesterterpene Synthase AcAS from Aspergillus calidoustus. Angew Chem Int Ed Engl 2022; 61:e202117273. [PMID: 35072966 PMCID: PMC9303889 DOI: 10.1002/anie.202117273] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Indexed: 01/06/2023]
Abstract
The multiproduct chimeric sesterterpene synthase AcAS from Aspergillus calidoustus yielded spirocyclic calidoustene, which exhibits a novel skeleton, besides five known sesterterpenes. The complex cyclisation mechanism to all six compounds was investigated by isotopic labelling experiments in combination with DFT calculations. Chemically synthesised 8-hydroxyfarnesyl diphosphate was converted with isopentenyl diphosphate and AcAS into four oxygenated sesterterpenoids that structurally resemble cytochrome P450 oxidation products of the sesterterpene hydrocarbons. Protein engineering of AcAS broadened the substrate scope and gave significantly improved enzyme yields.
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Affiliation(s)
- Zhiyang Quan
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Anwei Hou
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Bernd Goldfuss
- Department of ChemistryUniversity of CologneGreinstraße 450939CologneGermany
| | - Jeroen S. Dickschat
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
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30
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Abstract
Five analogs of dimethylallyl diphosphate (DMAPP) with additional or shifted Me groups were converted with isopentenyl diphosphate (IPP) and the fungal variediene synthase from Aspergillus brasiliensis (AbVS). These enzymatic reactions resulted in the formation of several new terpene analogs that were isolated and structurally characterised by NMR spectroscopy. Several DMAPP analogs showed a changed reactivity giving access to compounds with unusual skeletons. Their formation is mechanistically rationalised and the absolute configurations of all obtained compounds were determined through a stereoselective deuteration strategy, revealing absolute configurations that are analogous to that of the natural enzyme product variediene.
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Affiliation(s)
- Lin‐Fu Liang
- Kekulé-Institute for Organic Chemistry and Biochemistry 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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31
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Zhang FL, Feng T. Diterpenes Specially Produced by Fungi: Structures, Biological Activities, and Biosynthesis (2010–2020). J Fungi (Basel) 2022; 8:jof8030244. [PMID: 35330246 PMCID: PMC8951520 DOI: 10.3390/jof8030244] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 12/11/2022] Open
Abstract
Fungi have traditionally been a very rewarding source of biologically active natural products, while diterpenoids from fungi, such as the cyathane-type diterpenoids from Cyathus and Hericium sp., the fusicoccane-type diterpenoids from Fusicoccum and Alternaria sp., the guanacastane-type diterpenoids from Coprinus and Cercospora sp., and the harziene-type diterpenoids from Trichoderma sp., often represent unique carbon skeletons as well as diverse biological functions. The abundances of novel skeletons, biological activities, and biosynthetic pathways present new opportunities for drug discovery, genome mining, and enzymology. In addition, diterpenoids peculiar to fungi also reveal the possibility of differing biological evolution, although they have similar biosynthetic pathways. In this review, we provide an overview about the structures, biological activities, evolution, organic synthesis, and biosynthesis of diterpenoids that have been specially produced by fungi from 2010 to 2020. We hope this review provides timely illumination and beneficial guidance for future research works of scholars who are interested in this area.
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33
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Quan Z, Hou A, Goldfuss B, Dickschat JS. Mechanism of the Bifunctional Multiple Product Sesterterpene Synthase AcldAS from Aspergillus calidoustus. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhiyang Quan
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Organic Chemistry GERMANY
| | - Anwei Hou
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Organic Chemistry GERMANY
| | - Bernd Goldfuss
- University of Cologne: Universitat zu Koln Organic Chemistry GERMANY
| | - Jeroen S. Dickschat
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Kekulé Institute for Organic Chemistry and Biochemistry Gerhard-Domagk-Straße 1 53121 Bonn GERMANY
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34
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Xu H, Lackus ND, Köllner TG, Dickschat JS. Isotopic Labeling Experiments Solve the Hedycaryol Problem. Org Lett 2022; 24:587-591. [PMID: 34985289 DOI: 10.1021/acs.orglett.1c04021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hedycaryol is a widespread sesquiterpene alcohol and important biosynthetic intermediate toward eudesmols and guaiols. A full NMR assignment for this compound has been hampered because of the unique molecular mechanics of its conformers in complex mixtures. This problem was solved through the enzymatic synthesis of isotopically labeled materials using a mutated plant and a bacterial enzyme for access to both enantiomers of hedycaryol, which also allowed us to follow the stereochemical course of its Cope rearrangement.
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Affiliation(s)
- Houchao Xu
- Kekulé Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Nathalie D Lackus
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, 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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35
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Xu H, Goldfuss B, Schnakenburg G, Dickschat JS. The enzyme mechanism of patchoulol synthase. Beilstein J Org Chem 2022; 18:13-24. [PMID: 35047079 PMCID: PMC8744462 DOI: 10.3762/bjoc.18.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022] Open
Abstract
Different mechanisms for the cyclisation of farnesyl pyrophosphate to patchoulol by the patchoulol synthase are discussed in the literature. They are based on isotopic labelling experiments, but the results from these experiments are contradictory. The present work reports on a reinvestigation of patchoulol biosynthesis by isotopic labelling experiments and computational chemistry. The results are in favour of a pathway through the neutral intermediates germacrene A and α-bulnesene that are both reactivated by protonation for further cyclisation steps, while previously discussed intra- and intermolecular hydrogen transfers are not supported. Furthermore, the isolation of the new natural product (2S,3S,7S,10R)-guaia-1,11-dien-10-ol from patchouli oil is reported.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Bernd Goldfuss
- Department of Chemistry, University of Cologne, Greinstraße 4, 50939 Cologne, Germany
| | - Gregor Schnakenburg
- Institute of Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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36
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Li H, Dickschat JS. Isotopic labelling experiments and enzymatic preparation of iso-casbenes with casbene synthase from Ricinus communis. Org Chem Front 2022. [DOI: 10.1039/d1qo01707a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Casbene synthase was used to convert GGPP isomers into iso-casbenes. The enzyme mechanism and absolute configurations were investigated through stereoselective deuteration. 13C-labellings gave insights into the mass spectrometric fragmentation.
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Affiliation(s)
- Heng Li
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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37
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Dickschat JS, Xu H. Mechanistic Investigations on Microbial Type I Terpene Synthases through Site-Directed Mutagenesis. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/a-1675-8208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AbstractDuring the past three decades many terpene synthases have been characterised from all kingdoms of life. Enzymes of type I, from bacteria, fungi and protists, commonly exhibit several highly conserved motifs and single residues, and the available crystal structures show a shared α-helical fold, while the overall sequence identity is generally low. Several enzymes have been studied by site-directed mutagenesis, giving valuable insights into terpene synthase catalysis and the intriguing mechanisms of terpene synthases. Some mutants are also preparatively useful and give higher yields than the wild type or a different product that is otherwise difficult to access. The accumulated knowledge obtained from these studies is presented and discussed in this review.1 Introduction2 Residues for Substrate Binding and Catalysis3 Residues with Structural Function4 Residues Contouring the Active Site Cavity5 Other Residues6 Conclusions
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38
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Hou A, Dickschat JS. Targeting active site residues and structural anchoring positions in terpene synthases. Beilstein J Org Chem 2021; 17:2441-2449. [PMID: 34621406 PMCID: PMC8450962 DOI: 10.3762/bjoc.17.161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/10/2021] [Indexed: 12/22/2022] Open
Abstract
The sesterterpene synthase SmTS1 from Streptomyces mobaraensis contains several unusual residues in positions that are otherwise highly conserved. Site-directed mutagenesis experiments for these residues are reported that showed different effects, resulting in some cases in an improved catalytic activity, but in other cases in a loss of enzyme function. For other enzyme variants a functional switch was observed, turning SmTS1 from a sesterterpene into a diterpene synthase. This article gives rational explanations for these findings that may generally allow for protein engineering of other terpene synthases to improve their catalytic efficiency or to change their functions.
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Affiliation(s)
- Anwei Hou
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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39
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Hou A, Goldfuss B, Dickschat JS. Functional Switch and Ethyl Group Formation in the Bacterial Polytrichastrene Synthase from Chryseobacterium polytrichastri. Angew Chem Int Ed Engl 2021; 60:20781-20785. [PMID: 34318977 PMCID: PMC8518897 DOI: 10.1002/anie.202109465] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/27/2021] [Indexed: 12/19/2022]
Abstract
A reinvestigation of the linalool synthase from Chryseobacterium polytrichastri uncovered its diterpene synthase activity, yielding polytrichastrene A and polytrichastrol A with new skeletons, besides known wanju-2,5-diene and thunbergol. The enzyme mechanism was investigated by isotopic labeling experiments and DFT calculations to explain an unusual ethyl group formation. Rationally designed exchanges of active site residues showed major functional switches, resulting for I66F in the production of five more new compounds, including polytrichastrene B and polytrichastrol B, while A87T, A192V and the double exchange A87T, A192V gave a product shift towards wanju-2,5-diene.
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Affiliation(s)
- Anwei Hou
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Bernd Goldfuss
- Department of ChemistryUniversity of CologneGreinstraße 450939CologneGermany
| | - Jeroen S. Dickschat
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
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40
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Sato H, Li BX, Takagi T, Wang C, Miyamoto K, Uchiyama M. DFT Study on the Biosynthesis of Verrucosane Diterpenoids and Mangicol Sesterterpenoids: Involvement of Secondary-Carbocation-Free Reaction Cascades. JACS AU 2021; 1:1231-1239. [PMID: 34467361 PMCID: PMC8397367 DOI: 10.1021/jacsau.1c00178] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Indexed: 05/03/2023]
Abstract
Some experimental observations indicate that a sequential formation of secondary (2°) carbocations might be involved in some biosynthetic pathways, including those of verrucosane-type diterpenoids and mangicol-type sesterterpenoids, but it remains controversial whether or not such 2° cations are viable intermediates. Here, we performed comprehensive density functional theory calculations of these biosynthetic pathways. The results do not support previously proposed pathways/mechanisms: in particular, we find that none of the putative 2° carbocation intermediates is involved in either of the biosynthetic pathways. In verrucosane biosynthesis, the proposed 2° carbocations (II and IV) in the early stage are bypassed by the formation of the adjacent 3° carbocations and by unusual skeletal rearrangement reactions, and in the later stage, the putative 2° carbocation intermediates (VI, VII, and VIII) are not present as the proposed forms but as nonclassical structures between homoallyl and cyclopropylcarbinyl cations. In the mangicol biosynthesis, one of the two proposed 2° carbocations (X) is bypassed by a C-C bond-breaking reaction to generate a 3° carbocation with a C=C bond, while the other (XI) is bypassed by a strong hyperconjugative interaction leading to a nonclassical carbocation. We propose new biosynthetic pathways/mechanisms for the verrucosane-type diterpenoids and mangicol-type sesterterpenoids. These pathways are in good agreement with the findings of previous biosynthetic studies, including isotope-labeling experiments and byproducts analysis, and moreover can account for the biosynthesis of related terpenes.
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Affiliation(s)
- Hajime Sato
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Bi-Xiao Li
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Taisei Takagi
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chao Wang
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunori Miyamoto
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Uchiyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Research
Initiative for Supra-Materials, Shinshu
University, 3-15-1 Tokida,
Ueda, Nagano 386-8567, Japan
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41
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Hou A, Goldfuss B, Dickschat JS. Funktionaler Schalter und Ethylgruppenbildung der Bakteriellen Polytrichastrensynthase aus
Chryseobacterium polytrichastri. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109465] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anwei Hou
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Bernd Goldfuss
- Department Chemie Universität zu Köln Greinstraße 4 50939 Köln Deutschland
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
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42
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Systematic mining of fungal chimeric terpene synthases using an efficient precursor-providing yeast chassis. Proc Natl Acad Sci U S A 2021; 118:2023247118. [PMID: 34257153 PMCID: PMC8307374 DOI: 10.1073/pnas.2023247118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Chimeric terpene synthases, termed PTTSs, are a unique family of enzymes occurring only in fungi. Characterizing PTTSs is challenging due to the complex reactions they catalyze and the structural complexity of their products. Here, by devising an efficient precursor-providing yeast chassis and incorporating a high-throughput automated platform, we identified 34 active PTTSs, which was considerably more than the number of known functional PTTSs. This effective and rapid pipeline can be employed for the characterization of other PTTSs or related terpenoid biosynthetic enzymes. By systematically analyzing the presence/absence of PTTS genes together with phylogenetic analysis, the ancestral PTTS gene was inferred to have undergone duplication and functional divergence, which led to the development of two distinct cyclization mechanisms. Chimeric terpene synthases, which consist of C-terminal prenyltransferase (PT) and N-terminal class I terpene synthase (TS) domains (termed PTTSs here), is unique to fungi and produces structurally diverse di- and sesterterpenes. Prior to this study, 20 PTTSs had been functionally characterized. Our understanding of the origin and functional evolution of PTTS genes is limited. Our systematic search of sequenced fungal genomes among diverse taxa revealed that PTTS genes were restricted to Dikarya. Phylogenetic findings indicated different potential models of the origin and evolution of PTTS genes. One was that PTTS genes originated in the common Dikarya ancestor and then underwent frequent gene loss among various subsequent lineages. To understand their functional evolution, we selected 74 PTTS genes for biochemical characterization in an efficient precursor-providing yeast system employing chassis-based, robot-assisted, high-throughput automatic assembly. We found 34 PTTS genes that encoded active enzymes and collectively produced 24 di- and sesterterpenes. About half of these di- and sesterterpenes were also the products of the 20 known PTTSs, indicating functional conservation, whereas the PTTS products included the previously unknown sesterterpenes, sesterevisene (1), and sesterorbiculene (2), suggesting that a diversity of PTTS products awaits discovery. Separating functional PTTSs into two monophyletic groups implied that an early gene duplication event occurred during the evolution of the PTTS family followed by functional divergence with the characteristics of distinct cyclization mechanisms.
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43
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Abstract
Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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44
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Lauterbach L, Hou A, Dickschat JS. Rerouting and Improving Dauc-8-en-11-ol Synthase from Streptomyces venezuelae to a High Yielding Biocatalyst. Chemistry 2021; 27:7923-7929. [PMID: 33769623 PMCID: PMC8252471 DOI: 10.1002/chem.202100962] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Indexed: 12/21/2022]
Abstract
The dauc‐8‐en‐11‐ol synthase from Streptomyces venezuelae was investigated for its catalytic activity towards alternative terpene precursors, specifically designed to enable new cyclisation pathways. Exchange of aromatic amino acid residues at the enzyme surface by site‐directed mutagenesis led to a 4‐fold increase of the yield in preparative scale incubations, which likely results from an increased enzyme stability instead of improved enzyme kinetics.
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Affiliation(s)
- Lukas Lauterbach
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms Universität Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Anwei Hou
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms Universität Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms Universität Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
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45
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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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46
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Xu H, Rinkel J, Chen X, Köllner TG, Chen F, Dickschat JS. Mechanistic divergence between (4 S,7 R)-germacra-(1(10) E,5 E)-dien-11-ol synthases from Dictyostelium purpureum and Streptomyces coelicolor. Org Biomol Chem 2021; 19:370-374. [PMID: 33337456 DOI: 10.1039/d0ob02361b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The main product of DpTPS9 from the social amoeba Dictyostelium purpureum was identified as (4S,7R)-germacra-(1(10)E,5E)-dien-11-ol that is also known as an intermediate of bacterial geosmin synthase, but the experimentally verified cyclisation mechanisms differ. Together with the low sequence identity this points to convergent evolution. The functionality of selected residues in DpTPS9 was investigated via site-directed mutagenesis experiments.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
| | - Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN 37996-4561, USA
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN 37996-4561, USA
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Lackus ND, Morawetz J, Xu H, Gershenzon J, Dickschat JS, Köllner TG. The Sesquiterpene Synthase PtTPS5 Produces (1 S,5 S,7 R,10 R)-Guaia-4(15)-en-11-ol and (1 S,7 R,10 R)-Guaia-4-en-11-ol in Oomycete-Infected Poplar Roots. Molecules 2021; 26:555. [PMID: 33494506 PMCID: PMC7866031 DOI: 10.3390/molecules26030555] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 01/15/2023] Open
Abstract
Pathogen infection often leads to the enhanced formation of specialized plant metabolites that act as defensive barriers against microbial attackers. In this study, we investigated the formation of potential defense compounds in roots of the Western balsam poplar (Populus trichocarpa) upon infection with the generalist root pathogen Phytophthora cactorum (Oomycetes). P. cactorum infection led to an induced accumulation of terpenes, aromatic compounds, and fatty acids in poplar roots. Transcriptome analysis of uninfected and P. cactorum-infected roots revealed a terpene synthase gene PtTPS5 that was significantly induced upon pathogen infection. PtTPS5 had been previously reported as a sesquiterpene synthase producing two unidentified sesquiterpene alcohols as major products and hedycaryol as a minor product. Using heterologous expression in Escherichia coli, enzyme assays with deuterium-labeled substrates, and NMR analysis of reaction products, we could identify the major PtTPS5 products as (1S,5S,7R,10R)-guaia-4(15)-en-11-ol and (1S,7R,10R)-guaia-4-en-11-ol, with the former being a novel compound. The transcript accumulation of PtTPS5 in uninfected and P. cactorum-infected poplar roots matched the accumulation of (1S,5S,7R,10R)-guaia-4(15)-en-11-ol, (1S,7R,10R)-guaia-4-en-11-ol, and hedycaryol in this tissue, suggesting that PtTPS5 likely contributes to the pathogen-induced formation of these compounds in planta.
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Affiliation(s)
- Nathalie D. Lackus
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
| | - Jennifer Morawetz
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
| | - Houchao Xu
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; (H.X.); (J.S.D.)
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
| | - Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; (H.X.); (J.S.D.)
| | - Tobias G. Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany; (N.D.L.); (J.M.); (J.G.)
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Abstract
The product of a terpene synthase from Streptomyces lincolnensis has been identified as the new natural product isoishwarane. The enzyme mechanism was studied by isotopic labelling experiments and site-directed mutagenesis.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
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Xu H, Dickschat JS. Germacrene A-A Central Intermediate in Sesquiterpene Biosynthesis. Chemistry 2020; 26:17318-17341. [PMID: 32442350 PMCID: PMC7821278 DOI: 10.1002/chem.202002163] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/20/2020] [Indexed: 01/17/2023]
Abstract
This review summarises known sesquiterpenes whose biosyntheses proceed through the intermediate germacrene A. First, the occurrence and biosynthesis of germacrene A in Nature and its peculiar chemistry will be highlighted, followed by a discussion of 6-6 and 5-7 bicyclic compounds and their more complex derivatives. For each compound the absolute configuration, if it is known, and the reasoning for its assignment is 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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Li G, Guo Y, Dickschat JS. Diterpen‐Biosynthese in
Catenulispora acidiphila
: Über den Mechanismus der Catenul‐14‐en‐6‐ol‐Synthase. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202014180] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Geng Li
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
- 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
- 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
- University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 China
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
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