1
|
Hashimoto Y, Kong WY, Tantillo DJ. Discovery of a Formal Dyotropic Rearrangement during Acid-Mediated Dioxabicyclo[4.2.1]nonanone Formation. Org Lett 2024; 26:5441-5446. [PMID: 38900922 DOI: 10.1021/acs.orglett.4c01616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
A new reaction mechanism for the construction of dioxabicyclo[4.2.1]nonanone skeletons via a cation cascade has been proposed and examined by DFT and ab initio computations. This mechanism features the following steps: (1) intramolecular Friedel-Crafts-type cyclization with a methyl oxocarbenium cation formed by carboxylate disconnection, (2) electron-rich aromatic ring assisted methoxide loss followed by lactone formation, and (3) stepwise dyotropic rearrangement resulting in skeletal isomerization from a dioxabicyclo[3.2.2]nonanone to the dioxabicyclo[4.2.1]nonanone product observed experimentally. The high regioselectivity and driving force for the overall rearrangement were rationalized, and Lewis and Brønsted acid mediated reactivities were compared.
Collapse
Affiliation(s)
- Yoshimitsu Hashimoto
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Wang-Yeuk Kong
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Song Y, Wang W, Yang J, Gao D, Billingsley JM, Wang S, Zhu Y, Wang J, Ju J, Yan Y, Tang Y. β-Terrecyclene synthase constructs the quadrane backbone in terrecyclic acid biosynthesis. Chem Sci 2024; 15:8750-8755. [PMID: 38873062 PMCID: PMC11168084 DOI: 10.1039/d4sc01208a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/18/2024] [Indexed: 06/15/2024] Open
Abstract
Quadrane sesquiterpenes featuring a distinctive tricyclic skeleton exhibit potent antimicrobial and anticancer activities. Although extensive studies have attempted to reveal the multistep carbocation rearrangement involved in the formation of the tricyclic quadrane scaffold, the exact biosynthetic pathway and chemical logic to generate the quadrane structure remains mysterious. Here we identified a novel sesquiterpene synthase that is capable of generating β-terrecyclene possessing the quadrane scaffold and characterized the biosynthetic pathway of a representative fungal quadrane terrecyclic acid. Further mutagenesis coupled with isotopically sensitive branching studies of this β-terrecyclene synthase provided insight into the mechanism involved in the formation of the quadrane scaffold.
Collapse
Affiliation(s)
- Yongxiang Song
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Sanya Institute of Oceanology Eco-Environmental Engineering Yazhou Scientific Bay Sanya 572000 China
- University of Chinese Academy of Science 19 Yuquan Road Beijing 100049 China
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - Wengui Wang
- School of Chemistry and Chemical Engineering, University of Jinan 336 West Road of Nan Xinzhuang Jinan 250022 China
| | - Jiafan Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Sanya Institute of Oceanology Eco-Environmental Engineering Yazhou Scientific Bay Sanya 572000 China
- University of Chinese Academy of Science 19 Yuquan Road Beijing 100049 China
| | - Dewei Gao
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - John M Billingsley
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - Songtao Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Sanya Institute of Oceanology Eco-Environmental Engineering Yazhou Scientific Bay Sanya 572000 China
- University of Chinese Academy of Science 19 Yuquan Road Beijing 100049 China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Sanya Institute of Oceanology Eco-Environmental Engineering Yazhou Scientific Bay Sanya 572000 China
- University of Chinese Academy of Science 19 Yuquan Road Beijing 100049 China
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - Junfeng Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Sanya Institute of Oceanology Eco-Environmental Engineering Yazhou Scientific Bay Sanya 572000 China
- University of Chinese Academy of Science 19 Yuquan Road Beijing 100049 China
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - Jianhua Ju
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- University of Chinese Academy of Science 19 Yuquan Road Beijing 100049 China
| | - Yan Yan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Sanya Institute of Oceanology Eco-Environmental Engineering Yazhou Scientific Bay Sanya 572000 China
- University of Chinese Academy of Science 19 Yuquan Road Beijing 100049 China
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
- Department of Chemistry and Biochemistry, University of California Los Angeles CA 90095 USA
| |
Collapse
|
4
|
Ellenburg WH, Oprian DD. Understanding mechanisms of terpene synthases using substrate analogs. Methods Enzymol 2024; 699:187-205. [PMID: 38942503 DOI: 10.1016/bs.mie.2024.04.003] [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
Terpene synthases (TS) transform achiral prenyl substrates into elaborate hydrocarbon scaffolds with multiple stereocenters through a series of cyclization reactions and carbon skeleton rearrangements. The reactions involve high-energy carbocation intermediates that must be stabilized by the enzyme along the pathway to the desired products. A variety of substrate analogs have been used to investigate TS mechanism. This article will focus on a class of analogs which strategically replace hydrogen atoms with fluorine to inhibit the generation of specific carbocation intermediates. We will explore the synthesis and use of the analogs to study TS mechanism.
Collapse
Affiliation(s)
| | - Daniel D Oprian
- Department of Biochemistry, Brandeis University, Waltham, MA, United States.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Whitehead J, Leferink NGH, Johannissen LO, Hay S, Scrutton NS. Decoding Catalysis by Terpene Synthases. ACS Catal 2023; 13:12774-12802. [PMID: 37822860 PMCID: PMC10563020 DOI: 10.1021/acscatal.3c03047] [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: 07/04/2023] [Revised: 08/31/2023] [Indexed: 10/13/2023]
Abstract
The review by Christianson, published in 2017 on the twentieth anniversary of the emergence of the field, summarizes the foundational discoveries and key advances in terpene synthase/cyclase (TS) biocatalysis (Christianson, D. W. Chem Rev2017, 117 (17), 11570-11648. DOI: 10.1021/acs.chemrev.7b00287). Here, we review the TS literature published since then, bringing the field up to date and looking forward to what could be the near future of TS rational design. Many revealing discoveries have been made in recent years, building on the knowledge and fundamental principles uncovered during those initial two decades of study. We use these to explore TS reaction chemistry and see how a combined experimental and computational approach helps to decipher the complexities of TS catalysis. Revealed are a suite of catalytic motifs which control product outcome in TSs, some obvious, some more subtle. We examine each in detail, using the most recent papers and insights to illustrate how exactly this fascinating class of enzymes takes a single acyclic substrate and turns it into the many thousands of complex terpenoids found in Nature. We then explore some of the recent strategies for TS engineering, including machine learning and other data-driven approaches. From this, rational and predictive engineering of TSs, "designer terpene synthases", will begin to emerge as a realistic goal.
Collapse
Affiliation(s)
- Joshua
N. Whitehead
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole G. H. Leferink
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Liu H, Fang S, Zhao L, Men X, Zhang H. A Single Active-Site Mutagenesis Confers Enhanced Activity and/or Changed Product Distribution to a Pentalenene Synthase from Streptomyces sp. PSKA01. Bioengineering (Basel) 2023; 10:bioengineering10030392. [PMID: 36978783 PMCID: PMC10045451 DOI: 10.3390/bioengineering10030392] [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: 03/01/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Pentalenene is a ternary cyclic sesquiterpene formed via the ionization and cyclization of farnesyl pyrophosphate (FPP), which is catalyzed by pentalenene synthase (PentS). To better understand the cyclization reactions, it is necessary to identify more key sites and elucidate their roles in terms of catalytic activity and product specificity control. Previous studies primarily relied on the crystal structure of PentS to analyze and verify critical active sites in the active cavity, while this study started with the function of PentS and screened a novel key site through random mutagenesis. In this study, we constructed a pentalenene synthetic pathway in E. coli BL21(DE3) and generated PentS variants with random mutations to construct a mutant library. A mutant, PentS-13, with a varied product diversity, was obtained through shake-flask fermentation and product identification. After sequencing and the functional verification of the mutation sites, it was found that T182A, located in the G2 helix, was responsible for the phenotype of PentS-13. The site-saturation mutagenesis of T182 demonstrated that mutations at this site not only affected the solubility and activity of the enzyme but also affected the specificity of the product. The other products were generated through different routes and via different carbocation intermediates, indicating that the 182 active site is crucial for PentS to stabilize and guide the regioselectivity of carbocations. Molecular docking and molecular dynamics simulations suggested that these mutations may induce changes in the shape and volume of the active cavity and disturb hydrophobic/polar interactions that were sufficient to reposition reactive intermediates for alternative reaction pathways. This article provides rational explanations for these findings, which may generally allow for the protein engineering of other terpene synthases to improve their catalytic efficiency or modify their specificities.
Collapse
Affiliation(s)
- Hongshuang Liu
- State Key Laboratory of Bio-Based Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250316, China
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Senbiao Fang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Lin Zhao
- State Key Laboratory of Bio-Based Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250316, China
| | - Xiao Men
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Haibo Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| |
Collapse
|
10
|
Abstract
Herein, we report the enantioselective total synthesis of dysiherbols A, C, and D, a unique group of 6/6/5/6/6 pentacyclic quinone/hydroquinone sesquiterpenes, featuring a photo-induced quinone-alkene [2 + 2] cycloaddition and a tandem [1,2]-anionic rearrangement/cyclopropane fragmentation as key elements. Based on our total synthesis, the originally proposed structures of dysiherbols C and D have been revised. Detailed computational studies were carried out to gain deep insight into the unprecedented [1,2]-anionic rearrangement, which revealed that the transformation, albeit a symmetry-forbidden process, proceeded through a concerted manner owing to the release of high ring-strain energy and the evolution of local aromaticity in the transition state. Taking all, the present work offers a mechanistically interesting and synthetically useful approach to accessing dysiherbols and related congeners.
Collapse
Affiliation(s)
- Shengkun Hu
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yefeng Tang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| |
Collapse
|
11
|
Nguyen QNN, Xia KT, Zhang Y, Chen N, Morimoto M, Pei X, Ha Y, Guo J, Yang W, Wang LP, Bergman RG, Raymond KN, Toste FD, Tantillo DJ. Source of Rate Acceleration for Carbocation Cyclization in Biomimetic Supramolecular Cages. J Am Chem Soc 2022; 144:11413-11424. [PMID: 35699585 DOI: 10.1021/jacs.2c04179] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The results of quantum chemical and molecular dynamics calculations reveal that polyanionic gallium-based cages accelerate cyclization reactions of pentadienyl alcohols as a result of substrate cage interactions, preferential binding of reactive conformations of substrate/H3O+ pairs, and increased substrate basicity. However, the increase in basicity dominates. Experimental structure-activity relationship studies in which the metal vertices and overall charge of the cage are varied confirm the model derived via calculations.
Collapse
Affiliation(s)
- Quynh Nhu N Nguyen
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Kay T Xia
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yue Zhang
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Nanhao Chen
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Mariko Morimoto
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xiaokun Pei
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yang Ha
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jinghua Guo
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Wanli Yang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Robert G Bergman
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kenneth N Raymond
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
12
|
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
Collapse
|
13
|
Harms V, Ravkina V, Kirschning A. Mechanistic Similarities of Sesquiterpene Cyclases PenA, Omp6/7, and BcBOT2 Are Unraveled by an Unnatural "FPP-Ether" Derivative. Org Lett 2021; 23:3162-3166. [PMID: 33826848 DOI: 10.1021/acs.orglett.1c00882] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sesquiterpene cyclases pentalenene synthase (PenA) and two Δ6-protoilludene synthases Omp6 and Omp7 convert a FPP ether into several new tetrahydrofurano terpenoids, one of which is also formed as the main product by the sesquiterpene cyclase BcBOT2. Thus, PenA, Omp6/7, and BcBOT2 follow closely related catalytic pathways and induce similar folding of their diphosphate substrates despite low levels of amino acid sequence similarity. Some of the new terpenoids show pronounced olfactoric properties.
Collapse
Affiliation(s)
- Vanessa Harms
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167 Hannover, Germany
| | - Viktoria Ravkina
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167 Hannover, Germany
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167 Hannover, Germany
| |
Collapse
|
14
|
Xing YY, Chen SS, Chen DZ, Tantillo DJ. Effects of electrostatic drag on the velocity of hydrogen migration - pre- and post-transition state enthalpy/entropy compensation. Phys Chem Chem Phys 2020; 22:26955-26960. [PMID: 33206074 DOI: 10.1039/d0cp05000h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ab initio molecular dynamics calculations were used to explore the underlying factors that modulate the velocity of hydrogen migration for 1,2 hydrogen shifts in carbocations in which different groups interact noncovalently with the migrating hydrogen. Our results indicate that stronger electrostatic interactions between the migrating hydrogen and nearby π-systems lead to slower hydrogen migration, an effect tied to entropic contributions from the hydrogen + neighboring group substructures.
Collapse
Affiliation(s)
- Yang-Yang Xing
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan 250014, P. R. China.
| | | | | | | |
Collapse
|
15
|
Matos JO, Kumar RP, Ma AC, Patterson M, Krauss IJ, Oprian DD. Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase. Biochemistry 2020; 59:3271-3283. [PMID: 32786410 DOI: 10.1021/acs.biochem.0c00518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Most terpene synthase reactions follow Markovnikov rules for formation of high-energy carbenium ion intermediates. However, there are notable exceptions. For example, pentalenene synthase (PS) undergoes an initial anti-Markovnikov cyclization reaction followed by a 1,2-hydride shift to form an intermediate humulyl cation with positive charge on the secondary carbon C9 atom of the farnesyl diphosphate substrate. The mechanism by which these enzymes stabilize and guide the regioselectivity of secondary carbocations has not heretofore been elucidated. In an effort to better understand these reactions, we grew crystals of apo-PS, soaked them with the nonreactive substrate analogue 12,13-difluorofarnesyl diphosphate, and determined the X-ray structure of the resulting complex at 2.2 Å resolution. The most striking feature of the active site structure is that C9 is perfectly positioned to make a C-H···π interaction with the side chain benzene ring of residue F76; this would enhance hyperconjugation to stabilize a developing cation at C10 and thus support the anti-Markovnikov regioselectivity of the cyclization. The benzene ring is also positioned to catalyze the migration of H to C10 and stabilize a C9 carbocation. On the opposite face of C9, further cation stabilization is possible via interactions with the main chain carbonyl of I177 and the neighboring intramolecular C6═C7 bond. Mutagenesis experiments also support a role for residue 76 in these interactions, but most interesting is the F76W mutant, whose crystal structure clearly shows C9 and C10 centered above the fused benzene and pyrrole rings of the indole side chain, respectively, such that a carbocation at either position could be stabilized in this complex, and two anti-Markovnikov products, pentalenene and humulene, are formed. Finally, we show that there is a rough correlation (although not absolute) of an aromatic side chain (F or Y) at position 76 in related terpene synthases from Streptomyces that catalyze similar anti-Markovnikov addition reactions.
Collapse
Affiliation(s)
- Jason O Matos
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Ramasamy P Kumar
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Alison C Ma
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, United States
| | - MacKenzie Patterson
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Isaac J Krauss
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Daniel D Oprian
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, United States
| |
Collapse
|
16
|
Mitschke N, Christoffers J, Wilkes H. A Straightforward Synthesis of Trideuterated α‐Terpinene for Mechanistic Studies. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nico Mitschke
- Institut für Chemie und Biologie des Meeres (ICBM) Carl von Ossietzky Universität Oldenburg 26111 Oldenburg Germany
| | - Jens Christoffers
- Institut für Chemie Carl von Ossietzky Universität Oldenburg 26111 Oldenburg Germany
| | - Heinz Wilkes
- Institut für Chemie und Biologie des Meeres (ICBM) Carl von Ossietzky Universität Oldenburg 26111 Oldenburg Germany
| |
Collapse
|
17
|
Raz K, Levi S, Gupta PK, Major DT. Enzymatic control of product distribution in terpene synthases: insights from multiscale simulations. Curr Opin Biotechnol 2020; 65:248-258. [PMID: 32679412 DOI: 10.1016/j.copbio.2020.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 11/25/2022]
Abstract
In this opinion, we review some recent work on terpene biosynthesis using multiscale simulation approaches, with special focus on contributions from our group. Terpene synthases generate terpenes employing rich carbocation chemistry, including highly specific ring formations, proton, hydride, methyl, and methylene migrations, followed by reaction quenching. In these enzymes, the main catalytic challenge is not rate enhancement, but rather control of intrinsically reactive carbocations and the resulting product distribution. Herein, we review multiscale simulations of selected mono-, sesqui-, and diterpene synthases. We point to the many tools adopted by terpene synthases to achieve correct substrate fold, carbocation formation, carbocation reaction environment, and reaction quenching. A better understanding of the toolbox employed by terpene synthases is expected to aid in the search for new enzymatic and biomimetic synthetic routes to natural and unnatural terpenes.
Collapse
Affiliation(s)
- Keren Raz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Shani Levi
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Prashant Kumar Gupta
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
| |
Collapse
|
18
|
Zech A, Jandl C, Bach T. Concise Access to the Skeleton of Protoilludane Sesquiterpenes through a Photochemical Reaction Cascade: Total Synthesis of Atlanticone C. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908619] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Andreas Zech
- Department Chemie and Catalysis Research Center (CRC) Technische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Christian Jandl
- Department Chemie and Catalysis Research Center (CRC) Technische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Thorsten Bach
- Department Chemie and Catalysis Research Center (CRC) Technische Universität München Lichtenbergstr. 4 85747 Garching Germany
| |
Collapse
|
19
|
Zech A, Jandl C, Bach T. Concise Access to the Skeleton of Protoilludane Sesquiterpenes through a Photochemical Reaction Cascade: Total Synthesis of Atlanticone C. Angew Chem Int Ed Engl 2019; 58:14629-14632. [PMID: 31478314 PMCID: PMC7687024 DOI: 10.1002/anie.201908619] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Indexed: 01/03/2023]
Abstract
In a single photochemical operation (λ≥350 nm) an easily accessible indanone derivative was converted into a structurally complex precursor of the protoilludane sesquiterpenes. The product (60 % yield) contains all 15 carbon atoms of the skeleton in the required connectivity and was transformed into the natural product atlanticone C (9 steps, 6 % overall yield). In addition, it was shown that other protoilludanes, such as Δ6 -protoilludene and paesslerin A, can be prepared in a concise fashion via the photochemical key intermediate. The photochemical reaction cascade comprises an ortho photocycloaddition, a thermal disrotatory ring opening and a regioselective disrotatory [4π] photocyclization.
Collapse
Affiliation(s)
- Andreas Zech
- Department Chemie and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Christian Jandl
- Department Chemie and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Thorsten Bach
- Department Chemie and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| |
Collapse
|
20
|
Martín-Sánchez L, Singh KS, Avalos M, van Wezel GP, Dickschat JS, Garbeva P. Phylogenomic analyses and distribution of terpene synthases among Streptomyces. Beilstein J Org Chem 2019; 15:1181-1193. [PMID: 31293665 PMCID: PMC6604706 DOI: 10.3762/bjoc.15.115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/17/2019] [Indexed: 12/19/2022] Open
Abstract
Terpene synthases are widely distributed among microorganisms and have been mainly studied in members of the genus Streptomyces. However, little is known about the distribution and evolution of the genes for terpene synthases. Here, we performed whole-genome based phylogenetic analysis of Streptomyces species, and compared the distribution of terpene synthase genes among them. Overall, our study revealed that ten major types of terpene synthases are present within the genus Streptomyces, namely those for geosmin, 2-methylisoborneol, epi-isozizaene, 7-epi-α-eudesmol, epi-cubenol, caryolan-1-ol, cyclooctat-9-en-7-ol, isoafricanol, pentalenene and α-amorphene. The Streptomyces species divide in three phylogenetic groups based on their whole genomes for which the distribution of the ten terpene synthases was analysed. Geosmin synthases were the most widely distributed and were found to be evolutionary positively selected. Other terpene synthases were found to be specific for one of the three clades or a subclade within the genus Streptomyces. A phylogenetic analysis of the most widely distributed classes of Streptomyces terpene synthases in comparison to the phylogenomic analysis of this genus is discussed.
Collapse
Affiliation(s)
- Lara Martín-Sánchez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Kumar Saurabh Singh
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, United Kingdom
| | - Mariana Avalos
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden,The Netherlands
| | - Gilles P van Wezel
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden,The Netherlands
| | - Jeroen S Dickschat
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,University of Bonn, Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
21
|
Zeng H, Yin G, Wei Q, Li D, Wang Y, Hu Y, Hu C, Zou Y. Unprecedented [5.5.5.6]Dioxafenestrane Ring Construction in Fungal Insecticidal Sesquiterpene Biosynthesis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Haichun Zeng
- College of Pharmaceutical SciencesSouthwest University Chongqing 400715 China
| | - Guoping Yin
- College of Pharmaceutical SciencesSouthwest University Chongqing 400715 China
| | - Qian Wei
- College of Pharmaceutical SciencesSouthwest University Chongqing 400715 China
| | - Dehai Li
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology Qingdao 266237 China
| | - Yi Wang
- State Key Laboratory of Silkworm Genome BiologySouthwest University Chongqing 400715 China
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences & Peking Union Medical College Beijing 100050 China
| | - Changhua Hu
- College of Pharmaceutical SciencesSouthwest University Chongqing 400715 China
| | - Yi Zou
- College of Pharmaceutical SciencesSouthwest University Chongqing 400715 China
| |
Collapse
|
22
|
Zeng H, Yin G, Wei Q, Li D, Wang Y, Hu Y, Hu C, Zou Y. Unprecedented [5.5.5.6]Dioxafenestrane Ring Construction in Fungal Insecticidal Sesquiterpene Biosynthesis. Angew Chem Int Ed Engl 2019; 58:6569-6573. [PMID: 30908782 DOI: 10.1002/anie.201813722] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 03/11/2019] [Indexed: 11/09/2022]
Abstract
Fenestranes, a specific class of natural products, contain four fused rings that share a central quaternary carbon atom. The fungal natural product penifulvin A (1) is a potent insecticidal sesquiterpene that features the [5.5.5.6]dioxafenestrane ring. Although the chemical synthesis of 1 has been achieved recently, the enzymes catalysing the cyclization and oxidation of FPP to 1 remain unknown. In this work, we identified a concise pathway that uses only three enzymes to produce 1. A new sesquiterpene cyclase (PeniA) generates the angular triquinane scaffold silphinene (6). A cytochrome P450 (PeniB) and a flavin-dependent monooxygenase (PeniC) catalyse a series of oxidation reactions to transform 6 into 1, including oxidation of the C15 methyl group to a carboxylate moiety, oxidative coupling of the C15 carboxylate and the C1-C2 olefin to form a γ-lactone, and Baeyer-Villiger oxidation to form a δ-lactone. Our results demonstrate the highly concise and efficient ways in which fungal biosynthetic pathways can generate complex sesquiterpene scaffolds.
Collapse
Affiliation(s)
- Haichun Zeng
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Guoping Yin
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Qian Wei
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Dehai Li
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yi Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Changhua Hu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| |
Collapse
|
23
|
Rinkel J, Lauterbach L, Dickschat JS. Eine verzweigte Diterpenkaskade: der Mechanismus der Spinodien-Synthase aus Saccharopolyspora spinosa. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812216] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Lukas Lauterbach
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| |
Collapse
|
24
|
Rinkel J, Lauterbach L, Dickschat JS. A Branched Diterpene Cascade: The Mechanism of Spinodiene Synthase from Saccharopolyspora spinosa. Angew Chem Int Ed Engl 2018; 58:452-455. [DOI: 10.1002/anie.201812216] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Lukas Lauterbach
- 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
| |
Collapse
|
25
|
Affiliation(s)
- Shinji Yamada
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| |
Collapse
|
26
|
Sato H, Mitsuhashi T, Yamazaki M, Abe I, Uchiyama M. Computational Studies on Biosynthetic Carbocation Rearrangements Leading to Quiannulatene: Initial Conformation Regulates Biosynthetic Route, Stereochemistry, and Skeleton Type. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences; Chiba University; 1-8-1 Inohana, Chuoku Chiba 260-8675 Japan
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory; RIKEN; 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences; Chiba University; 1-8-1 Inohana, Chuoku Chiba 260-8675 Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory; RIKEN; 2-1 Hirosawa Wako Saitama 351-0198 Japan
| |
Collapse
|
27
|
Blank PN, Pemberton TA, Chow JY, Poulter CD, Christianson DW. Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene. Biochemistry 2018; 57:6326-6335. [PMID: 30346736 DOI: 10.1021/acs.biochem.8b00899] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Linear triquinanes are sesquiterpene natural products with hydrocarbon skeletons consisting of three fused five-membered rings. Importantly, several of these compounds exhibit useful anticancer, anti-inflammatory, and antibiotic properties. However, linear triquinanes pose significant challenges to organic synthesis because of the structural and stereochemical complexity of their hydrocarbon skeletons. To illuminate nature's solution to the generation of linear triquinanes, we now describe the crystal structure of Streptomyces clavuligerus cucumene synthase. This sesquiterpene cyclase catalyzes the stereospecific cyclization of farnesyl diphosphate to form a linear triquinane product, (5 S,7 S,10 R,11 S)-cucumene. Specifically, we report the structure of the wild-type enzyme at 3.05 Å resolution and the structure of the T181N variant at 1.96 Å resolution, both in the open active site conformations without any bound ligands. The high-resolution structure of T181N cucumene synthase enables inspection of the active site contour, which adopts a three-dimensional shape complementary to a linear triquinane. Several aromatic residues outline the active site contour and are believed to facilitate cation-π interactions that would stabilize carbocation intermediates in catalysis. Thus, aromatic residues in the active site not only define the template for catalysis but also play a role in reducing activation barriers in the multistep cyclization cascade.
Collapse
Affiliation(s)
- Patrick N Blank
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Travis A Pemberton
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Jeng-Yeong Chow
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - C Dale Poulter
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| |
Collapse
|
28
|
Sato H, Mitsuhashi T, Yamazaki M, Abe I, Uchiyama M. Computational Studies on Biosynthetic Carbocation Rearrangements Leading to Quiannulatene: Initial Conformation Regulates Biosynthetic Route, Stereochemistry, and Skeleton Type. Angew Chem Int Ed Engl 2018; 57:14752-14757. [DOI: 10.1002/anie.201807139] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences; Chiba University; 1-8-1 Inohana, Chuoku Chiba 260-8675 Japan
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory; RIKEN; 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences; Chiba University; 1-8-1 Inohana, Chuoku Chiba 260-8675 Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory; RIKEN; 2-1 Hirosawa Wako Saitama 351-0198 Japan
| |
Collapse
|
29
|
O’Brien TE, Bertolani SJ, Zhang Y, Siegel JB, Tantillo DJ. Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases-Bornyl Diphosphate Synthase as a Representative Case. ACS Catal 2018; 8:3322-3330. [PMID: 30034923 PMCID: PMC6049084 DOI: 10.1021/acscatal.8b00342] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Terpene synthases comprise a family of enzymes that convert acyclic oligo-isoprenyl diphosphates to terpene natural products with complex, polycyclic carbon backbones via the generation and protection of carbocation intermediates. To accommodate this chemistry, terpene synthase active sites generally are lined with alkyl and aromatic, i.e., nonpolar, sidechains. Predicting the correct, mechanistically relevant binding modes for entire terpene synthase reaction pathways remains an unsolved challenge. Here we describe a method for identifying such modes: TerDockin, a series of protocols to predict the orientation of carbon skeletons of substrates and derived carbocations relative to the bound diphosphate group in terpene synthase active sites. Using this recipe for bornyl diphosphate synthase, we have predicted binding modes that are consistent with all current experimental observations, including the results of isotope labeling experiments and known stereoselectivity. In addition, the predicted binding modes recapitulate key findings of a seminal study involving more computationally demanding QM/MM molecular dynamics methods on part of this pathway. This work illustrates the value of the TerDockin approach as a starting point for more involved calculations and sets the stage for the rational engineering of this family of enzymes.
Collapse
Affiliation(s)
- Terrence E. O’Brien
- Department of Chemistry, University of California Davis, Davis, California, USA
| | - Steven J. Bertolani
- Department of Chemistry, University of California Davis, Davis, California, USA
| | - Yue Zhang
- Department of Chemistry, University of California Davis, Davis, California, USA
| | - Justin B. Siegel
- Department of Chemistry, University of California Davis, Davis, California, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, USA
- Genome Center, University of California Davis, Davis, California, USA
| | - Dean J. Tantillo
- Department of Chemistry, University of California Davis, Davis, California, USA
| |
Collapse
|
30
|
Abstract
![]()
The
year 2017 marks the twentieth anniversary of terpenoid cyclase
structural biology: a trio of terpenoid cyclase structures reported
together in 1997 were the first to set the foundation for understanding
the enzymes largely responsible for the exquisite chemodiversity of
more than 80000 terpenoid natural products. Terpenoid cyclases catalyze
the most complex chemical reactions in biology, in that more than
half of the substrate carbon atoms undergo changes in bonding and
hybridization during a single enzyme-catalyzed cyclization reaction.
The past two decades have witnessed structural, functional, and computational
studies illuminating the modes of substrate activation that initiate
the cyclization cascade, the management and manipulation of high-energy
carbocation intermediates that propagate the cyclization cascade,
and the chemical strategies that terminate the cyclization cascade.
The role of the terpenoid cyclase as a template for catalysis is paramount
to its function, and protein engineering can be used to reprogram
the cyclization cascade to generate alternative and commercially important
products. Here, I review key advances in terpenoid cyclase structural
and chemical biology, focusing mainly on terpenoid cyclases and related
prenyltransferases for which X-ray crystal structures have informed
and advanced our understanding of enzyme structure and function.
Collapse
Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| |
Collapse
|
31
|
Tantillo DJ. Bedeutung der inhärenten Substratreaktivität bei enzymvermittelten Cyclisierungen/Umlagerungen von Carbokationen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702363] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Dean J. Tantillo
- Department of Chemistry University of California—Davis 1 Shields Avenue Davis CA 95616 USA
| |
Collapse
|
32
|
Tantillo DJ. Importance of Inherent Substrate Reactivity in Enzyme-Promoted Carbocation Cyclization/Rearrangements. Angew Chem Int Ed Engl 2017; 56:10040-10045. [PMID: 28349600 DOI: 10.1002/anie.201702363] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Indexed: 11/08/2022]
Abstract
The importance of inherent substrate reactivity for terpene synthase enzymes is discussed, with a focus on recent experimental tests of predictions derived from computations on gas-phase reactivity of carbocations.
Collapse
Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California-Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| |
Collapse
|
33
|
Affiliation(s)
- Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry; Rheinische Friedrich Wilhelms University of Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
| |
Collapse
|
34
|
Hugelshofer CL, Magauer T. Dyotropic rearrangements in natural product total synthesis and biosynthesis. Nat Prod Rep 2017; 34:228-234. [DOI: 10.1039/c7np00005g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Some recent examples of dyotropic rearrangements involved in complex natural product total synthesis and biosynthesis are highlighted.
Collapse
Affiliation(s)
| | - Thomas Magauer
- Department of Chemistry and Pharmacy
- Ludwig-Maximilians-Univeristy Munich
- 81377 Munich
- Germany
| |
Collapse
|
35
|
Hong YJ, Tantillo DJ. The Variediene-Forming Carbocation Cyclization/Rearrangement Cascade. Aust J Chem 2017. [DOI: 10.1071/ch16504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
An energetically viable (on the basis of results from density functional theory computations) pathway to the diterpene variediene is described. Only one of the three secondary carbocations along this pathway is predicted to be a minimum on the potential energy surface.
Collapse
|
36
|
Rabe P, Rinkel J, Nubbemeyer B, Köllner TG, Chen F, Dickschat JS. Terpencyclasen aus sozialen Amöben. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608971] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Britta Nubbemeyer
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Tobias G. Köllner
- Max-Planck-Institut für chemische Ökologie; Hans-Knöll-Straße 8 07745 Jena Deutschland
| | - Feng Chen
- Department of Plant Sciences; University of Tennessee; 2431 Joe Johnson Drive Knoxville TN 37996-4561 USA
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| |
Collapse
|
37
|
Rabe P, Rinkel J, Nubbemeyer B, Köllner TG, Chen F, Dickschat JS. Terpene Cyclases from Social Amoebae. Angew Chem Int Ed Engl 2016; 55:15420-15423. [PMID: 27862766 DOI: 10.1002/anie.201608971] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/26/2016] [Indexed: 11/08/2022]
Abstract
Genome sequences of social amoebae reveal the presence of terpene cyclases (TCs) in these organisms. Two TCs from Dictyostelium discoideum converted farnesyl diphosphate into (2S,3R,6S,9S)-(-)-protoillud-7-ene and (3S)-(+)-asterisca-2(9),6-diene. The enzyme mechanisms and EI-MS fragmentations of the products were studied by labeling experiments.
Collapse
Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Britta Nubbemeyer
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität 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-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| |
Collapse
|
38
|
Tantillo DJ. Does Nature Know Best? Pericyclic Reactions in the Daphniphyllum Alkaloid-Forming Cation Cascade. Org Lett 2016; 18:4482-4. [PMID: 27559932 DOI: 10.1021/acs.orglett.6b01919] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heathcock's classic cyclization/rearrangement cascade for formation of Daphniphyllum alkaloids is subjected to analysis using density functional theory calculations. The results of these calculations are consistent with a two-step pathway involving two pericyclic reactions, a Diels-Alder cycloaddition and an ene reaction.
Collapse
Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California-Davis , Davis, California 95616, United States
| |
Collapse
|
39
|
|
40
|
Zhang F, Chen N, Wu R. Molecular Dynamics Simulations Elucidate Conformational Dynamics Responsible for the Cyclization Reaction in TEAS. J Chem Inf Model 2016; 56:877-85. [PMID: 27082764 DOI: 10.1021/acs.jcim.6b00091] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Mg-dependent 5-epi-aristolochene synthase from Nicotiana tabacum (called TEAS) could catalyze the linear farnesyl pyrophosphate (FPP) substrate to form bicyclic hydrocarbon 5-epi-aristolochene. The cyclization reaction mechanism of TEAS was proposed based on static crystal structures and quantum chemistry calculations in a few previous studies, but substrate FPP binding kinetics and protein conformational dynamics responsible for the enzymatic catalysis are still unclear. Herein, by elaborative and extensive molecular dynamics simulations, the loop conformation change and several crucial residues promoting the cyclization reaction in TEAS are elucidated. It is found that the unusual noncatalytic NH2-terminal domain is essential to stabilize Helix-K and the adjoining J-K loop of the catalytic COOH-terminal domain. It is also illuminated that the induce-fit J-K/A-C loop dynamics is triggered by Y527 and the optimum substrate binding mode in a "U-shape" conformation. The U-shaped ligand binding pose is maintained well with the cooperative interaction of the three Mg(2+)-containing coordination shell and conserved residue W273. Furthermore, the conserved Arg residue pair R264/R266 and aromatic residue pair Y527/W273, whose spatial orientations are also crucial to promote the closure of the active site to a hydrophobic pocket, as well as to form π-stacking interactions with the ligand, would facilitate the carbocation migration and electrophilic attack involving the catalytic reaction. Our investigation more convincingly proves the greater roles of the protein local conformational dynamics than do hints from the static crystal structure observations. Thus, these findings can act as a guide to new protein engineering strategies on diversifying the sesquiterpene products for drug discovery.
Collapse
Affiliation(s)
- Fan Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, Guangdong, P.R. China
| | - Nanhao Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, Guangdong, P.R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, Guangdong, P.R. China
| |
Collapse
|
41
|
Pemberton TA, Christianson DW. General base-general acid catalysis by terpenoid cyclases. J Antibiot (Tokyo) 2016; 69:486-93. [PMID: 27072285 DOI: 10.1038/ja.2016.39] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/22/2016] [Accepted: 03/02/2016] [Indexed: 01/12/2023]
Abstract
Terpenoid cyclases catalyze the most complex reactions in biology, in that more than half of the substrate carbon atoms often undergo changes in bonding during the course of a multistep cyclization cascade that proceeds through multiple carbocation intermediates. Many cyclization mechanisms require stereospecific deprotonation and reprotonation steps, and most cyclization cascades are terminated by deprotonation to yield an olefin product. The first bacterial terpenoid cyclase to yield a crystal structure was pentalenene synthase from Streptomyces exfoliatus UC5319. This cyclase generates the hydrocarbon precursor of the pentalenolactone family of antibiotics. The structures of pentalenene synthase and other terpenoid cyclases reveal predominantly nonpolar active sites typically lacking amino acid side chains capable of serving general base-general acid functions. What chemical species, then, enables the Brønsted acid-base chemistry required in the catalytic mechanisms of these enzymes? The most likely candidate for such general base-general acid chemistry is the co-product inorganic pyrophosphate. Here, we briefly review biological and nonbiological systems in which phosphate and its derivatives serve general base and general acid functions in catalysis. These examples highlight the fact that the Brønsted acid-base activities of phosphate derivatives are comparable to the Brønsted acid-base activities of amino acid side chains.
Collapse
Affiliation(s)
- Travis A Pemberton
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.,Radcliffe Institute for Advanced Study, and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| |
Collapse
|
42
|
O'Brien TE, Bertolani SJ, Tantillo DJ, Siegel JB. Mechanistically informed predictions of binding modes for carbocation intermediates of a sesquiterpene synthase reaction. Chem Sci 2016; 7:4009-4015. [PMID: 30155043 PMCID: PMC6013805 DOI: 10.1039/c6sc00635c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/18/2016] [Indexed: 11/21/2022] Open
Abstract
Sesquiterpenoids comprise a class of terpenoid natural products with thousands of compounds that are highly diverse in structure, generally containing a polycyclic carbon backbone that is constructed by a sesquiterpene synthase. Decades of experimental and computational studies have demonstrated that these enzymes generate a carbocation in the active site, which undergoes a series of structural rearrangements until a product is formed via deprotonation or nucleophile attack. However, for the vast majority of these enzymes the productive binding orientation of the intermediate carbocations has remained unclear. In this work, a method that combines quantum mechanics and computational docking is used to generate an all-atom model of every putative intermediate formed in the context of the enzyme active site for tobacco epi-aristolochene synthase (TEAS). This method identifies a single pathway that links the first intermediate to the last, enabling us to propose the first high-resolution model for the reaction intermediates in the active site of TEAS, and providing testable predictions.
Collapse
Affiliation(s)
- T E O'Brien
- Department of Chemistry , University of California Davis , Davis , California , USA . ;
| | - S J Bertolani
- Department of Chemistry , University of California Davis , Davis , California , USA . ;
| | - D J Tantillo
- Department of Chemistry , University of California Davis , Davis , California , USA . ;
| | - J B Siegel
- Department of Chemistry , University of California Davis , Davis , California , USA . ; .,Department of Biochemistry and Molecular Medicine , University of California Davis , Davis , California , USA.,Genome Center , University of California Davis , Davis , California , USA
| |
Collapse
|
43
|
Potter KC, Jia M, Hong YJ, Tantillo D, Peters RJ. Product Rearrangement from Altering a Single Residue in the Rice syn-Copalyl Diphosphate Synthase. Org Lett 2016; 18:1060-3. [PMID: 26878189 PMCID: PMC4782720 DOI: 10.1021/acs.orglett.6b00181] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Through
site-directed mutagenesis targeted at identification of
the catalytic base in the rice (Oryza sativa) syn-copalyl diphosphate synthase OsCPS4, changes to a single
residue (H501) were found to induce rearrangement rather than immediate
deprotonation of the initially formed bicycle, leading to production
of the novel compound syn-halimadienyl diphosphate.
These mutational results are combined with quantum chemical calculations
to provide insight into the underlying reaction mechanism.
Collapse
Affiliation(s)
- Kevin C Potter
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University , Ames, Iowa 50011, United States
| | - Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University , Ames, Iowa 50011, United States
| | - Young J Hong
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Dean Tantillo
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University , Ames, Iowa 50011, United States
| |
Collapse
|
44
|
Harrison JG, Gutierrez O, Jana N, Driver TG, Tantillo DJ. Mechanism of Rh2(II)-Catalyzed Indole Formation: The Catalyst Does Not Control Product Selectivity. J Am Chem Soc 2016; 138:487-90. [PMID: 26718908 DOI: 10.1021/jacs.5b11427] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jason G. Harrison
- Department
of Chemistry, University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Osvaldo Gutierrez
- Department
of Chemistry, University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Navendu Jana
- Department
of Chemistry, University of Illinois at Chicago, 845 West Taylor
Street, Chicago, Illinois 60607-7061, United States
| | - Tom G. Driver
- Department
of Chemistry, University of Illinois at Chicago, 845 West Taylor
Street, Chicago, Illinois 60607-7061, United States
- Institute
of Next Generation Matter Transformation, College of Chemical Engineering, Huaqiao University, 668 Jimei Blvd., Xiamen, Fujian 361021, P. R. China
| | - Dean J. Tantillo
- Department
of Chemistry, University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
45
|
Abstract
This review summarises the characterised bacterial terpene cyclases and their products and discusses the enzyme mechanisms.
Collapse
Affiliation(s)
- Jeroen S. Dickschat
- University of Bonn
- Kekulé-Institute of Organic Chemistry and Biochemistry
- 53121 Bonn
- Germany
| |
Collapse
|
46
|
Rinkel J, Dickschat JS. Recent highlights in biosynthesis research using stable isotopes. Beilstein J Org Chem 2015; 11:2493-508. [PMID: 26734097 PMCID: PMC4685789 DOI: 10.3762/bjoc.11.271] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/23/2015] [Indexed: 02/03/2023] Open
Abstract
The long and successful history of isotopic labeling experiments within natural products research has both changed and deepened our understanding of biosynthesis. As demonstrated in this article, the usage of isotopes is not at all old-fashioned, but continues to give important insights into biosynthetic pathways of secondary metabolites. This review with 85 cited references is structured by separate discussions of compounds from different classes including polyketides, non-ribosomal peptides, their hybrids, terpenoids, and aromatic compounds formed via the shikimate pathway. The text does not aim at a comprehensive overview, but instead a selection of recent important examples of isotope usage within biosynthetic studies is presented, with a special emphasis on mechanistic surprises.
Collapse
Affiliation(s)
- Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| |
Collapse
|
47
|
Rabe P, Janusko A, Goldfuss B, Dickschat JS. Experimental and Theoretical Studies on Corvol Ether Biosynthesis. Chembiochem 2015; 17:146-9. [DOI: 10.1002/cbic.201500543] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Aron Janusko
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Bernd Goldfuss
- Department für Chemie; Universität zu Köln; Greinstrasse 4 50939 Köln Germany
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| |
Collapse
|
48
|
Potter KC, Zi J, Hong YJ, Schulte S, Malchow B, Tantillo DJ, Peters RJ. Blocking Deprotonation with Retention of Aromaticity in a Plant ent
-Copalyl Diphosphate Synthase Leads to Product Rearrangement. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
49
|
Potter KC, Zi J, Hong YJ, Schulte S, Malchow B, Tantillo DJ, Peters RJ. Blocking Deprotonation with Retention of Aromaticity in a Plant ent-Copalyl Diphosphate Synthase Leads to Product Rearrangement. Angew Chem Int Ed Engl 2015; 55:634-8. [PMID: 26603275 DOI: 10.1002/anie.201509060] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Indexed: 11/06/2022]
Abstract
Substitution of a histidine, comprising part of the catalytic base group in the ent-copalyl diphosphate synthases found in all seed plants for gibberellin phytohormone metabolism, by a larger aromatic residue leads to rearrangements. Through a series of 1,2-hydride and methyl shifts of the initially formed bicycle predominant formation of (-)-kolavenyl diphosphate is observed. Further mutational analysis and quantum chemical calculations provide mechanistic insight into the basis for this profound effect on product outcome.
Collapse
Affiliation(s)
- Kevin C Potter
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Jiachen Zi
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Young J Hong
- Department of Chemistry, University of California, Davis, Davis, CA 95616 (USA)
| | - Samuel Schulte
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Brandi Malchow
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, Davis, CA 95616 (USA)
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA).
| |
Collapse
|
50
|
Hong YJ, Tantillo DJ. Tension between Internal and External Modes of Stabilization in Carbocations Relevant to Terpene Biosynthesis: Modulating Minima Depth via C–H···π Interactions. Org Lett 2015; 17:5388-91. [DOI: 10.1021/acs.orglett.5b02740] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Young J. Hong
- Department
of Chemistry, Univeristy of California—Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department
of Chemistry, Univeristy of California—Davis, Davis, California 95616, United States
| |
Collapse
|