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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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2
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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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3
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Matsuyama T, Togashi K, Nakano M, Sato H, Uchiyama M. Revision of the Peniroquesine Biosynthetic Pathway by Retro-Biosynthetic Theoretical Analysis: Ring Strain Controls the Unique Carbocation Rearrangement Cascade. JACS AU 2023; 3:1596-1603. [PMID: 37388688 PMCID: PMC10301677 DOI: 10.1021/jacsau.3c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 07/01/2023]
Abstract
Peniroquesine, a sesterterpenoid featuring a unique 5/6/5/6/5 fused pentacyclic ring system, has been known for a long time, but its biosynthetic pathway/mechanism remains elusive. Based on isotopic labeling experiments, a plausible biosynthetic pathway to peniroquesines A-C and their derivatives was recently proposed, in which the characteristic peniroquesine-type 5/6/5/6/5 pentacyclic skeleton is synthesized from geranyl-farnesyl pyrophosphate (GFPP) via a complex concerted A/B/C-ring formation, repeated reverse-Wagner-Meerwein alkyl shifts, three successive secondary (2°) carbocation intermediates, and a highly distorted trans-fused bicyclo[4.2.1]nonane intermediate. However, our density functional theory calculations do not support this mechanism. By applying a retro-biosynthetic theoretical analysis strategy, we were able to find a preferred pathway for peniroquesine biosynthesis, involving a multistep carbocation cascade including triple skeletal rearrangements, trans-cis isomerization, and 1,3-H shift. This pathway/mechanism is in good agreement with all of the reported isotope-labeling results.
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Affiliation(s)
- Taro Matsuyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ko Togashi
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Moe Nakano
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Hajime Sato
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, 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 (RISM), Shinshu
University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
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4
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Xu H, Goldfuss B, Dickschat JS. Biosynthesis of the Sesquiterpene Kitaviridene through Skeletal Rearrangement with Formation of a Methyl Group Equivalent. Org Lett 2023; 25:3330-3334. [PMID: 37122105 DOI: 10.1021/acs.orglett.3c01211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A sesquiterpene synthase from Kitasatospora viridis was discovered and shown to produce kitaviridene, a sesquiterpene hydrocarbon with an additional methyl group equivalent in comparison to a regular sesquiterpene. Isotopic labeling experiments together with DFT calculations gave detailed insights into the cyclization cascade toward kitaviridene and explained the formation of the additional methyl group equivalent.
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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
| | - 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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Sato H, Nakano M. Concertedness and Activation Energy Control by Distal Methyl Group during Ring Contraction/Expansion in Scalarane-Type Sesterterpenoid Biosynthesis. Chemistry 2023; 29:e202203076. [PMID: 36411271 DOI: 10.1002/chem.202203076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
Salmahyritisol A, similan A, and hippospongide A, which are scalarane-type sesterterpenoids, feature 6/6/5/7/5 pentacyclic skeletons. Although their biosyntheses have been previously proposed to involve a unique skeletal rearrangement reaction, the detailed reaction mechanism remains unclear as none of the corresponding biosynthetic enzymes for this reaction have been reported. Herein, this skeletal rearrangement reaction was investigated using computational techniques, which revealed the following four key features: (i) the distal 24-Me substituent controls both the concertedness and activation energy of this transformation, (ii) enzymes are not responsible for the observed regioselectivity of C12-C20 bond formation, (iii) stereoselectivity is enzyme-regulated, and (iv) protonation is a key step in this skeletal rearrangement process. These new findings provide insight into the C-ring-contraction and D-ring-expansion mechanisms in scalarane-type sesterterpenoid biosyntheses.
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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.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Moe Nakano
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
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Xu H, Dickschat JS. Germacrene B - a central intermediate in sesquiterpene biosynthesis. Beilstein J Org Chem 2023; 19:186-203. [PMID: 36865023 PMCID: PMC9972886 DOI: 10.3762/bjoc.19.18] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
Germacranes are important intermediates in the biosynthesis of eudesmane and guaiane sesquiterpenes. After their initial formation from farnesyl diphosphate, these neutral intermediates can become reprotonated for a second cyclisation to reach the bicyclic eudesmane and guaiane skeletons. This review summarises the accumulated knowledge on eudesmane and guaiane sesquiterpene hydrocarbons and alcohols that potentially arise from the achiral sesquiterpene hydrocarbon germacrene B. Not only compounds isolated from natural sources, but also synthetic compounds are dicussed, with the aim to give a rationale for the structural assignment for each compound. A total number of 64 compounds is presented, with 131 cited references.
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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
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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7
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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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8
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Kourgiantaki M, Demertzidou VP, Zografos AL. Short Scalable Route to Apiaceae Sesquiterpene Scaffolds: Total Synthesis of 4- epi-Epiguaidiol A. Org Lett 2022; 24:8476-8480. [PMID: 36264031 DOI: 10.1021/acs.orglett.2c03215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxy-Cope/ene reaction cascade to form a locked elemane conformer allows the short scalable synthesis of versatile Apiaceae scaffolds. The divergent fate of the obtained macrocyclic germacrane is surveyed under cationic and dioxygen-induced Prins-type reaction conditions to allow the diastereoselective synthesis of oxidized Apiaceae guaiane congeners and the total synthesis of 4-epi-epiguaidiol A. Additionally, the unprecedented reduction of a hydrogen-bond-biased guaiane substrate permits the chemoselective synthesis of desoxo-jungiaguaiane.
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Affiliation(s)
- Maria Kourgiantaki
- Department of Chemistry, Laboratory of Organic Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Vera P Demertzidou
- Department of Chemistry, Laboratory of Organic Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Alexandros L Zografos
- Department of Chemistry, Laboratory of Organic Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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Xu H, Dickschat JS. Hedycaryol – Central Intermediates in Sesquiterpene Biosynthesis, Part II. Chemistry 2022; 28:e202200405. [PMID: 35239190 PMCID: PMC9310801 DOI: 10.1002/chem.202200405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 11/16/2022]
Abstract
The known sesquiterpenes that arise biosynthetically from hedycaryol are summarised. Reasonings for the assignments of their absolute configurations are discussed. The analysis provided here suggests that reprotonations at the C1=C10 double bond of hedycaryol are directed toward C1 and generally lead to 6–6 bicyclic compounds, while reprotonations at the C4=C5 double bond occur at C4 and result in 5–7 bicyclic compounds. Read more in the Review by H. Xu and J. S. Dickschat (DOI: 10.1002/chem.202200405).
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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
| | - Jeroen S. Dickschat
- Kekulé-Institute of 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, 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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11
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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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12
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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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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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Xu H, Goldfuss B, Dickschat JS. 1,2- or 1,3-Hydride Shifts: What Controls Guaiane Biosynthesis? Chemistry 2021; 27:9758-9762. [PMID: 33929065 PMCID: PMC8362104 DOI: 10.1002/chem.202101371] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Indexed: 12/19/2022]
Abstract
A systematic computational study addressing the entire chemical space of guaianes in conjunction with an analysis of all known compounds shows that 1,3‐hydride shifts are rare events in guaiane biosynthesis. As demonstrated here, 1,3‐hydride shifts towards guaianes can only be realized for two stereochemically well defined out of numerous possible stereoisomeric skeletons. One example is given by the mechanism of guaia‐4(15)‐en‐11‐ol synthase from California poplar, an enzyme that yields guaianes with unusual stereochemical properties. The general results from DFT calculations were experimentally verified through isotopic‐labeling experiments with guaia‐4(15)‐en‐11‐ol synthase.
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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
| | - Bernd Goldfuss
- Institute for Organic 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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