1
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Zhang W, Wang X, Zhu G, Zhu B, Peng K, Hsiang T, Zhang L, Liu X. Function Switch of a Fungal Sesterterpene Synthase through Molecular Dynamics Simulation Assisted Alteration of an Aromatic Residue Cluster in the Active Pocket of PfNS. Angew Chem Int Ed Engl 2024; 63:e202406246. [PMID: 38934471 DOI: 10.1002/anie.202406246] [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: 04/02/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024]
Abstract
Terpene synthases (TPSs) play pivotal roles in generating diverse terpenoids through complex cyclization pathways. Protein engineering of TPSs offers a crucial approach to expanding terpene diversity. However, significant potential remains untapped due to limited understanding of the structure-function relationships of TPSs. In this investigation, using a joint approach of molecular dynamics simulations-assisted engineering and site-directed mutagenesis, we manipulated the aromatic residue cluster (ARC) of a bifunctional terpene synthase (BFTPS), Pestalotiopsis fici nigtetraene synthase (PfNS). This led to the discovery of previously unreported catalytic functions yielding different cyclization patterns of sesterterpenes. Specifically, a quadruple variant (F89A/Y113F/W193L/T194W) completely altered PfNS's function, converting it from producing the bicyclic sesterterpene nigtetraene to the tricyclic ophiobolin F. Additionally, analysis of catalytic profiles by double, triple, and quadruple variants demonstrated that the ARC functions as a switch, unprecedently redirecting the production of 5/11 bicyclic (Type B) sesterterpenes to 5/15 bicyclic (Type A) ones. Molecular dynamics simulations and theozyme calculations further elucidated that, in addition to cation-π interactions, C-H⋅⋅⋅π interactions also play a key role in the cyclization patterns. This study offers a feasible strategy in protein engineering of TPSs for various industrial applications.
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Affiliation(s)
- Weiyan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, 200237, Shanghai, China
| | - Xinye Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, 200237, Shanghai, China
- School of Life Sciences, Ludong University, 264025, Yantai, Shandong, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, 200237, Shanghai, China
| | - Bin Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, 200237, Shanghai, China
| | - Kaitong Peng
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, 200237, Shanghai, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, Ontario, Canada
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, 200237, Shanghai, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, 200237, Shanghai, China
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2
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Sato H. Theoretical Study of Natural Product Biosynthesis Using Computational Chemistry. Chem Pharm Bull (Tokyo) 2024; 72:524-528. [PMID: 38825452 DOI: 10.1248/cpb.c24-00082] [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: 06/04/2024]
Abstract
The biosynthetic pathways of natural products are complicated, and it is difficult to fully elucidate their details using experimental chemistry alone. In recent years, efforts have been made to elucidate the biosynthetic reaction mechanisms by combining computational and experimental methods. In this review, we will discuss the biosynthetic studies using computational chemistry for various terpene compounds such as cyclooctatin, sesterfisherol, quiannulatene, trichobrasilenol, asperterpenol, preasperterpenoid, spiroviolene, and mangicol.
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Affiliation(s)
- Hajime Sato
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
- PRESTO, Japan Science and Technology Agency
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3
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Nakano M, Gemma R, Sato H. Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B. Beilstein J Org Chem 2023; 19:1503-1510. [PMID: 37799177 PMCID: PMC10548252 DOI: 10.3762/bjoc.19.107] [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: 06/30/2023] [Accepted: 09/07/2023] [Indexed: 10/07/2023] Open
Abstract
Terpene cyclization reactions involve a number of carbocation intermediates. In some cases, these carbocations are stabilized by through-space interactions with π orbitals. Several terpene/terpenoids, such as sativene, santalene, bergamotene, ophiobolin and mangicol, possess prenyl side chains that do not participate in the cyclization reaction. The role of these prenyl side chains has been partially investigated, but remains elusive in the cyclization cascade. In this study, we focus on variexenol B that is synthesized from iso-GGPP, as recently reported by Dickschat and co-workers, and investigate the possibility of through-space interactions with prenyl side chains using DFT calculations. Our calculations show that (i) the unstable secondary carbocation is stabilized by the cation-π interaction from prenyl side chains, thereby lowering the activation energy, (ii) the four-membered ring formation is completed through bridging from the exomethylene group, and (iii) the annulation from the exomethylene group proceeds in a barrier-free manner.
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Affiliation(s)
- Moe Nakano
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Rintaro Gemma
- 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
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332–0012, Japan
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4
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Spencer TA, Ditchfield R. Tryptophan Stabilization of a Biochemical Carbocation Evaluated by Analysis of π Complexes of 3-Ethylindole with the t-Butyl Cation. ACS OMEGA 2023; 8:26497-26507. [PMID: 37521644 PMCID: PMC10373456 DOI: 10.1021/acsomega.3c03259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
Understanding how the highly unstable carbocation intermediates in terpenoid biosynthesis are stabilized and protected during their transient existence in enzyme active sites is an intriguing challenge which has to be addressed computationally. Our efforts have focused on evaluating the stabilization afforded via carbocation-π complexation between a biochemical carbocation and an aromatic amino acid residue. This has involved making measurements on an X-ray structure of an enzyme active site that shows a π donor proximate to a putative carbocation site and using these to build models which are analyzed computationally to provide an estimated stabilization energy (SE). Previously, we reported estimated SEs for several such carbocation-π complexes involving phenylalanine. Herein, we report the first such estimate involving tryptophan as the π donor. Because there was almost no published information about indole as a π-complexation donor, we first located computationally equilibrium π and σ complexes of 3-ethylindole with the t-butyl cation as relevant background information. Then, measurements on the X-ray structure of the enzyme CotB2 complexed with geranylgeranyl thiodiphosphate (GGSPP), specifically on the geometric relationship of the putative carbocation at C15 of GGSPP to W186, were used to build a model that afforded a computed SE of -15.3 kcal/mol.
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5
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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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6
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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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7
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Jiang L, Lv K, Zhu G, Lin Z, Zhang X, Xing C, Yang H, Zhang W, Wang Z, Liu C, Qu X, Hsiang T, Zhang L, Liu X. Norditerpenoids biosynthesized by variediene synthase-associated P450 machinery along with modifications by the host cell Aspergillus oryzae. Synth Syst Biotechnol 2022; 7:1142-1147. [PMID: 36101897 PMCID: PMC9440366 DOI: 10.1016/j.synbio.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/19/2022] Open
Abstract
The chemical diversity of terpenoids is typically established by terpene synthase-catalyzed cyclization and diversified by post-tailoring modifications. Fungal bifunctional terpene synthase (BFTS) associated P450 enzymes have shown significant catalytic potentials through the development of various new terpenoids with different biological activities. This study discovered the BFTS and its related gene cluster from the plant endophytic fungus Didymosphaeria variabile 17020. Heterologous expression of the BFTS in Saccharomyces cerevisiae resulted in the characterization of a major product diterpene variediene (1), along with two new minor products neovariediene and neoflexibilene. Further heterologous expression of the BFTS and one cytochrome P450 enzyme VndE (CYP6138B1) in Aspergillus oryzae NSAR1 led to the identification of seven norditerpenoids (19 carbons) with a structurally unique 5/5 bicyclic ring system. Interestingly, in vivo experiments suggested that the cyclized terpene variediene (1) was modified by VndE along with the endogenous enzymes from the host cell A. oryzae through serial chemical conversions, followed by multi-site hydroxylation via A. oryzae endogenous enzymes. Our work revealed that the two-enzymes biosynthetic system and host cell machinery could produce structurally unique terpenoids.
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8
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Research Progress on Fungal Sesterterpenoids Biosynthesis. J Fungi (Basel) 2022; 8:jof8101080. [PMID: 36294645 PMCID: PMC9605422 DOI: 10.3390/jof8101080] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Sesterterpenes are 25-carbon terpenoids formed by the cyclization of dimethyl allyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP) as structural units by sesterterpenes synthases. Some (not all) sesterterpenoids are modified by cytochrome P450s (CYP450s), resulting in more intricate structures. These compounds have significant physiological activities and pharmacological effects in anti-inflammatory, antibacterial, antitumour, and hypolipidemic communities. Despite being a rare class of terpenoids, sesterterpenoids derived from fungi show a wide range of structural variations. The discovered fungal sesterterpenoid synthases are composed of C-terminal prenyltransferase (PT) and N-terminal terpene synthase (TS) domains, which were given the name PTTSs. PTTSs have the capacities to catalyze chain lengthening and cyclization concurrently. This review summarizes all 52 fungal PTTSs synthases and their biosynthetic pathways involving 100 sesterterpenoids since the discovery of the first PTTSs synthase from fungi in 2013.
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9
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Jiang L, Yang H, Zhang X, Li X, Lv K, Zhang W, Zhu G, Liu C, Wang Y, Hsiang T, Zhang L, Liu X. Schultriene and nigtetraene: two sesterterpenes characterized from pathogenetic fungi via genome mining approach. Appl Microbiol Biotechnol 2022; 106:6047-6057. [PMID: 36040489 DOI: 10.1007/s00253-022-12125-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/03/2022] [Accepted: 08/06/2022] [Indexed: 01/01/2023]
Abstract
Fungal bifunctional terpene synthases (BFTSs) have been reported to contribute to the biosynthesis of a variety of di/sesterterpenes via different carbocation transportation pathways. Genome mining of new BFTSs from unique fungal resources will, theoretically, allow for the identification of new terpenes. In this study, we surveyed the distribution of BFTSs in our in-house collection of 430 pathogenetic fungi and preferred two BFTSs (CsSS and NnNS), long distance from previously characterized BFTSs and located in relatively independent branches, based on the established phylogenetic tree. The heterologous expression of the two BFTSs in Aspergillus oryzae and Saccharomyces cerevisiae led to the identification of two new sesterterpenes separately, 5/12/5 tricyclic type-A sesterterpene (schultriene, 1) for CsSS and 5/11 bicyclic type-B sesterterpene (nigtetraene, 2) for NnNS. In addition, to the best of our knowledge, 2 is the first 5/11 bicyclic type-B characterized sesterterpene to date. On the basis of this, the plausible cyclization mechanisms of 1 and 2 were proposed based on density functional theory calculations. These new enzymes and their corresponding terpenes suggest that the chemical spaces produced by BFTSs remain large and also provide important evidences for further protein engineering for new terpenes and for understanding of cyclization mechanism catalyzed by BFTSs. KEY POINTS: • Genome mining of two BFTSs yields two new sesterterpenoids correspondingly. • Identification of the first 5/11 ring system type-B product. • Parse out the rational cyclization mechanism of isolated sesterterpenoids.
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Affiliation(s)
- Lan Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai, China
| | - Huanting Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai, China
| | - Xue Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai, China
| | - Xiaoying Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai, China
| | - Kangjie Lv
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai, China
| | - Weiyan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai, China
| | - Chengwei Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Yongheng Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai, China.
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10
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Characterization of two chimeric sesterterpene synthases from a fungal symbiont isolated from a sesterterpenoid-producing Lamiaceae plant Leucosceptrum canum. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.04.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Quan Z, Hou A, Goldfuss B, Dickschat JS. Mechanism of the Bifunctional Multiple Product Sesterterpene Synthase AcAS from Aspergillus calidoustus. Angew Chem Int Ed Engl 2022; 61:e202117273. [PMID: 35072966 PMCID: PMC9303889 DOI: 10.1002/anie.202117273] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Indexed: 01/06/2023]
Abstract
The multiproduct chimeric sesterterpene synthase AcAS from Aspergillus calidoustus yielded spirocyclic calidoustene, which exhibits a novel skeleton, besides five known sesterterpenes. The complex cyclisation mechanism to all six compounds was investigated by isotopic labelling experiments in combination with DFT calculations. Chemically synthesised 8-hydroxyfarnesyl diphosphate was converted with isopentenyl diphosphate and AcAS into four oxygenated sesterterpenoids that structurally resemble cytochrome P450 oxidation products of the sesterterpene hydrocarbons. Protein engineering of AcAS broadened the substrate scope and gave significantly improved enzyme yields.
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Affiliation(s)
- Zhiyang Quan
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Anwei Hou
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Bernd Goldfuss
- Department of ChemistryUniversity of CologneGreinstraße 450939CologneGermany
| | - Jeroen S. Dickschat
- Kekulé-Institute for Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
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12
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Quan Z, Hou A, Goldfuss B, Dickschat JS. Mechanism of the Bifunctional Multiple Product Sesterterpene Synthase AcldAS from Aspergillus calidoustus. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhiyang Quan
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Organic Chemistry GERMANY
| | - Anwei Hou
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Organic Chemistry GERMANY
| | - Bernd Goldfuss
- University of Cologne: Universitat zu Koln Organic Chemistry GERMANY
| | - Jeroen S. Dickschat
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Kekulé Institute for Organic Chemistry and Biochemistry Gerhard-Domagk-Straße 1 53121 Bonn GERMANY
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13
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Qiao Y, Xu Q, Huang Z, Chen X, Ren X, Yuan W, Guan Z, Li P, Li F, Xiong C, Zhu H, Chen C, Gu LH, Zhou Y, Qi C, Hu Z, Liu J, Ye Y, Zhang Y. Genome Mining Reveals a New Cyclopentane-forming Sesterterpene Synthase with Unprecedented Stereo-control. Org Chem Front 2022. [DOI: 10.1039/d2qo00983h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fungal bifunctional terpene synthases (BFTSs) catalyze formation of diverse ring systems in diterpene/sesterterpene structures. Through genome mining of fungal BFTSs, we discovered a novel sesterterpenoids gene cluster pst, consisting of...
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14
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Chen Q, Li J, Ma Y, Yuan W, Zhang P, Wang G. Occurrence and biosynthesis of plant sesterterpenes (C25), a new addition to terpene diversity. PLANT COMMUNICATIONS 2021; 2:100184. [PMID: 34746758 PMCID: PMC8553974 DOI: 10.1016/j.xplc.2021.100184] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/03/2021] [Accepted: 03/28/2021] [Indexed: 05/21/2023]
Abstract
Terpenes, the largest group of plant-specialized metabolites, have received considerable attention for their highly diverse biological activities. Monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), and triterpenes (C30) have been extensively investigated at both the biochemical and molecular levels over the past two decades. Sesterterpenes (C25), an understudied terpenoid group, were recently described by plant scientists at the molecular level. This review summarizes the plant species that produce sesterterpenes and describes recent developments in the field of sesterterpene biosynthesis, placing a special focus on the catalytic mechanism and evolution of geranylfarnesyl diphosphate synthase and sesterterpene synthase. Finally, we propose several questions to be addressed in future studies, which may help to elucidate sesterterpene metabolism in plants.
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Affiliation(s)
- Qingwen Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yihua Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Weiliang Yuan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- Corresponding author
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15
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Sato H, Li BX, Takagi T, Wang C, Miyamoto K, Uchiyama M. DFT Study on the Biosynthesis of Verrucosane Diterpenoids and Mangicol Sesterterpenoids: Involvement of Secondary-Carbocation-Free Reaction Cascades. JACS AU 2021; 1:1231-1239. [PMID: 34467361 PMCID: PMC8397367 DOI: 10.1021/jacsau.1c00178] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Indexed: 05/03/2023]
Abstract
Some experimental observations indicate that a sequential formation of secondary (2°) carbocations might be involved in some biosynthetic pathways, including those of verrucosane-type diterpenoids and mangicol-type sesterterpenoids, but it remains controversial whether or not such 2° cations are viable intermediates. Here, we performed comprehensive density functional theory calculations of these biosynthetic pathways. The results do not support previously proposed pathways/mechanisms: in particular, we find that none of the putative 2° carbocation intermediates is involved in either of the biosynthetic pathways. In verrucosane biosynthesis, the proposed 2° carbocations (II and IV) in the early stage are bypassed by the formation of the adjacent 3° carbocations and by unusual skeletal rearrangement reactions, and in the later stage, the putative 2° carbocation intermediates (VI, VII, and VIII) are not present as the proposed forms but as nonclassical structures between homoallyl and cyclopropylcarbinyl cations. In the mangicol biosynthesis, one of the two proposed 2° carbocations (X) is bypassed by a C-C bond-breaking reaction to generate a 3° carbocation with a C=C bond, while the other (XI) is bypassed by a strong hyperconjugative interaction leading to a nonclassical carbocation. We propose new biosynthetic pathways/mechanisms for the verrucosane-type diterpenoids and mangicol-type sesterterpenoids. These pathways are in good agreement with the findings of previous biosynthetic studies, including isotope-labeling experiments and byproducts analysis, and moreover can account for the biosynthesis of related terpenes.
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Affiliation(s)
- Hajime Sato
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Bi-Xiao Li
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Taisei Takagi
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chao Wang
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunori Miyamoto
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Uchiyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Research
Initiative for Supra-Materials, Shinshu
University, 3-15-1 Tokida,
Ueda, Nagano 386-8567, Japan
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16
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Mu L, Yang Y, Liu J, Du W, Chen J, Shi G, Fang H. Hydrated cation-π interactions of π-electrons with hydrated Li +, Na +, and K + cations. Phys Chem Chem Phys 2021; 23:14662-14670. [PMID: 34213518 DOI: 10.1039/d1cp01609a] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation-π interactions are essential for many chemical, biological, and material processes, and these processes usually involve an aqueous salt solution. However, there is still a lack of a full understanding of the hydrated cation-π interactions between the hydrated cations and the aromatic ring structures on the molecular level. Here, we report a molecular picture of hydrated cation-π interactions, by using the calculations of density functional theory (DFT). Specifically, the graphene sheet can distort the hydration shell of the hydrated K+ to interact with K+ directly, which is hereafter called water-cation-π interactions. In contrast, the hydration shell of the hydrated Li+ is quite stable and the graphene sheet interacts with Li+ indirectly, mediated by water molecules, which we hereafter call the cation-water-π interactions. The behavior of hydrated cations adsorbed on a graphene surface is mainly attributed to the competition between the cation-π interactions and hydration effects. These findings provide valuable details of the structures and the adsorption energy of hydrated cations adsorbed onto the graphene surface.
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Affiliation(s)
- Liuhua Mu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yizhou Yang
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China.
| | - Jian Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wei Du
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jige Chen
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Guosheng Shi
- Shanghai Applied Radiation Institute and State Key Lab. Advanced Special Steel, Shanghai University, Shanghai 200444, China.
| | - Haiping Fang
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China. and Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
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17
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Jiang L, Zhang X, Sato Y, Zhu G, Minami A, Zhang W, Ozaki T, Zhu B, Wang Z, Wang X, Lv K, Zhang J, Wang Y, Gao S, Liu C, Hsiang T, Zhang L, Oikawa H, Liu X. Genome-Based Discovery of Enantiomeric Pentacyclic Sesterterpenes Catalyzed by Fungal Bifunctional Terpene Synthases. Org Lett 2021; 23:4645-4650. [DOI: 10.1021/acs.orglett.1c01361] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Lan Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Xue Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Yuya Sato
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Weiyan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Bin Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
- Engineering Research Centre of Pharmaceutical Process Chemistry, Ministry of Education, and Laboratory of Pharmaceutical Crystal Engineering & Technology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhixin Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Xinye Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Kangjie Lv
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Yongheng Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China
| | - Shushan Gao
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengwei Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
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18
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Hu Z, Ye Y, Zhang Y. Large-scale culture as a complementary and practical method for discovering natural products with novel skeletons. Nat Prod Rep 2021; 38:1775-1793. [PMID: 33650608 DOI: 10.1039/d0np00069h] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: up to July 2020Fungal metabolites with diverse and novel scaffolds can be assembled from well-known biosynthetic precursors through various mechanisms. Recent examples of novel alkaloids (e.g., cytochalasans and diketopiperazine derivatives), terpenes (e.g., sesterterpenes and diterpenes) and polyketides produced by fungi are presented through case studies. We show that large-scale culture is a complementary and practical method for genome mining and OSMAC approaches to discover natural products of unprecedented skeletal classes from fungi. We also summarize the discovery strategies and challenges for characterizing these compounds.
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Affiliation(s)
- Zhengxi Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, People's Republic of China.
| | - Ying Ye
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, People's Republic of China.
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, People's Republic of China.
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19
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Guo J, Cai YS, Cheng F, Yang C, Zhang W, Yu W, Yan J, Deng Z, Hong K. Genome Mining Reveals a Multiproduct Sesterterpenoid Biosynthetic Gene Cluster in Aspergillus ustus. Org Lett 2021; 23:1525-1529. [PMID: 33480256 DOI: 10.1021/acs.orglett.0c03996] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genome mining of Aspergillus ustus 094102 enabled the discovery of a multiproduct bifunctional terpene synthase (BTS), AuAS. Heterologous expression of AuAS led to the discovery of five new sesterterpenes, and coexpression of the upstream CYP450 monooxygenase (AuAP450) generated four new sesterterpene alcohols. Additionally, aspergilol A showed cytotoxic activities against MCF-7, MDA-MB231, and HepG2 cancer cells (IC50 21.20-48.76 μM), and aspergilol B exhibited a cytotoxic effect on MCF-7 cells (IC50 27.41 μM).
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Affiliation(s)
- Jingjing Guo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - You-Sheng Cai
- Institute of TCM and Natural Products, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Fangcai Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Chenjie Yang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Wenqi Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Wulin Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Jingjing Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
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20
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Li K, Gustafson KR. Sesterterpenoids: chemistry, biology, and biosynthesis. Nat Prod Rep 2020; 38:1251-1281. [PMID: 33350420 DOI: 10.1039/d0np00070a] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Covering: July 2012 to December 2019Over the last seven years, expanding research efforts focused on sesterterpenoids has led to the isolation, identification, and characterization of numerous structurally novel and biologically active sesterterpenoids. These newly reported sesterterpenoids provide diverse structures that often incorporate unprecedented ring systems and new carbon skeletons, as well as unusual functional group arrays. Biological activities of potential biomedical importance including suppression of cancer cell growth, inhibition of enzymatic activity, and modulation of receptor signaling, as well as ecologically important functions such as antimicrobial effects and deterrence of herbivorous insects have been associated with a variety of sesterterpenoids. There has also been a rapid growth in our knowledge of the genomics, enzymology, and specific pathways associated with sesterterpene biosynthesis. This has opened up new opportunities for future sesterterpene discovery and diversification through the expression of new cryptic metabolites and the engineered manipulation of associated biosynthetic machinery and processes. In this paper we reviewed 498 new sesterterpenoids, including their structures, source organisms, country of origin, relevant bioactivities, and biosynthesis.
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Affiliation(s)
- Keke Li
- College of Life Science, Dalian Minzu University, Dalian 116600, China.
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21
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Spencer TA, Ditchfield R. A simpler method affords evaluation of π stabilization by phenylalanine of several biochemical carbocations. Org Biomol Chem 2020; 18:7597-7607. [PMID: 32955057 DOI: 10.1039/d0ob01565b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Carbocations are important intermediates in the biosynthesis of terpenes and steroids, and it is challenging to try to understand how these relatively unstable species survive even transiently during biochemical reactions. Carbocation-π interaction with aromatic amino acid residues is an important factor in helping to stabilize these positively charged species. However, the short lifetimes of these active site carbocations makes experimental evaluation of the stabilization afforded by such interaction impossible. Computational studies, however, have provided some insight into this phenomenon. Herein we report a simple, computationally efficient method to estimate such stabilization energies afforded by phenylalanine to biochemical carbocation intermediates. A model is constructed in which the biochemical carbocation is replaced by an appropriate carbocation mimic (t-butyl or dimethylallyl). This substitute carbocation is then aligned with an ethylbenzene serving as a surrogate for each proximate phenylalanine in a geometry that replicates as closely as possible the orientation of that phenylalanine using measurements made on an X-ray structure of an enzyme active site in which a carbocation surrogate is bound. Density functional theory computations on such models were then used to yield estimates of stabilization energies. Application of this method to the tertiary carbocation formed in the reaction catalyzed by geranyl diphosphate C-methyl transferase gave a stabilization energy (-12.3 kcal mol-1) that was essentially identical to that obtained previously by analysis of a much more computationally demanding model of the active site. As a check on the accuracy of the simpler method, it was applied with similar success to the farnesyl cation formed in the reaction catalyzed by aristolochene synthase that is stabilized by cation-π interaction with two phenylalanines. Application of this method is also described to estimate carbocation-π stabilization, by the same two phenylalanines, of the final carbocation intermediate leading to aristolochene through analysis of the X-ray structure of an inhibitor of that carbocation bound in the active site of aristolochene synthase. Finally, the stabilization, by either of two phenylalanines, of six carbocation intermediates in the oxidosqualene cyclase-catalyzed formation of lanosterol is estimated by comparable analysis of an X-ray structure of that reaction product bound in the enzyme active site.
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Affiliation(s)
- Thomas A Spencer
- Department of Chemistry, 6128 Burke Laboratory, Dartmouth College, Hanover, NH 03755, USA.
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22
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Sato H, Yamazaki M, Uchiyama M. DFT Study on the Biosynthesis of Preasperterpenoid A: Role of Secondary Carbocations in the Carbocation Cascade. Chem Pharm Bull (Tokyo) 2020; 68:487-490. [PMID: 32378547 DOI: 10.1248/cpb.c20-00037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Preasperterpenoid A, featuring a 5/7/(3)6/5 pentacyclic structure, is a C25 sesterterpenoid produced by Penicillium verruculosum. The results of density functional calculations on putative biosynthetic carbocation cyclization/rearrangements leading to preasperterpenoid A revealed a highly concerted four-step cyclization mechanism. Interestingly, two secondary carbocation structures were obtained as minima, but appeared almost as shoulders in the energy profile, and may represent essentially transient structures during the highly concerted reaction.
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Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences, Chiba University.,Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Masanobu Uchiyama
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN.,Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Research Initiative for Supra-Materials (RISM), Shinshu University
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23
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McCulley CH, Tantillo DJ. Predicting Rearrangement-Competent Terpenoid Oxidation Levels. J Am Chem Soc 2020; 142:6060-6065. [PMID: 32157874 DOI: 10.1021/jacs.9b12398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Results of density functional theory calculations on rearrangements of potential biosynthetic precursors to the sesquiterpenoid illisimonin A reveal that only some possible precursors, those with certain specific oxidation patterns, are rearrangement-competent.
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Affiliation(s)
- Christina H McCulley
- 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
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24
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Oikawa H. Reconstitution of biosynthetic machinery of fungal natural products in heterologous hosts. Biosci Biotechnol Biochem 2020; 84:433-444. [DOI: 10.1080/09168451.2019.1690976] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
ABSTRACT
Ascomycota and basidiomycota fungi are prolific sources of biologically active natural products. Recent genomic data and bioinformatic analysis indicate that fungi possess a large number of biosynthetic gene clusters for bioactive natural products but more than 90% are silent. Heterologous expression in the filamentous fungi as hosts is one of the powerful tools to expression of the silent gene clusters. This review introduces recent studies on the total biosynthesis of representative family members via common platform intermediates, genome mining of novel di- and sesterterpenoids including detailed cyclization pathway, and development of expression host for basidiomycota genes with efficient genome editing method. In addition, this review will discuss the several strategies, for the generation of structural diversity, which are found through these studies.
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Affiliation(s)
- Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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25
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Abstract
Sesterterpenoids are known as a relatively small group of natural products. However, they represent a variety of simple to more complex structural types. This contribution focuses on the chemical structures of sesterterpenoids and how their structures are constructed in Nature.
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Affiliation(s)
- Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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26
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Zhang Q, Catti L, Syntrivanis LD, Tiefenbacher K. En route to terpene natural products utilizing supramolecular cyclase mimetics. Nat Prod Rep 2019; 36:1619-1627. [PMID: 31021352 DOI: 10.1039/c9np00003h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: literature up to 2018 Terpenes are a class of natural products characterized by remarkable structural diversity. Much of this diversity arises biosynthetically from a handful of linear precursors through the so-called tail-to-head terpene cyclization reaction. This reaction is one of the most complex observed in nature, and historically attempts to replicate it with non-enzymatic means have met with little success. In recent years, however, the development of manmade binding pockets that allow such reactions to take place has been reported. This Highlight provides an overview of this nascent field, and outlines the challenges that need to be overcome moving forward.
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Affiliation(s)
- Qi Zhang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, China
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27
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Yuan W, Lv S, Chen L, Zhao Y, Deng Z, Hong K. Production of sesterterpene ophiobolin by a bifunctional terpene synthase in Escherichia coli. Appl Microbiol Biotechnol 2019; 103:8785-8797. [DOI: 10.1007/s00253-019-10103-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/05/2019] [Accepted: 08/26/2019] [Indexed: 12/01/2022]
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28
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Sato H, Mitsuhashi T, Yamazaki M, Abe I, Uchiyama M. Inherent atomic mobility changes in carbocation intermediates during the sesterterpene cyclization cascade. Beilstein J Org Chem 2019; 15:1890-1897. [PMID: 31467610 PMCID: PMC6693403 DOI: 10.3762/bjoc.15.184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022] Open
Abstract
We previously showed that the regio- and stereoselectivity in terpene-forming reactions are determined by the conformations of the carbocation intermediates, which reflect the initial conformation of the substrate, geranylfarnesyl diphosphate (GFPP). However, it remains unclear how the initial conformation of GFPP is controlled, and which part(s) of the GFPP molecule are important for its fixation inside the substrate-binding pocket. Here, we present the first detailed analysis of the inherent atomic mobility in carbocation intermediates during sesterterpene biosynthesis. We identified two methyl groups as the least mobile of all the carbons of the carbocation intermediates in the first half of the cyclization cascade. Our analysis suggests that these two methyl groups are critical for the preorganization of GFPP in the biosynthetic pathways leading to sesterfisherol and quiannulatene.
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Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan.,Clustering 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, Chuo-ku, 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
- Clustering of Pioneering Research (CPR) Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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29
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Li YL, Gao Y, Liu CY, Sun CJ, Zhao ZT, Lou HX. Asperunguisins A-F, Cytotoxic Asperane Sesterterpenoids from the Endolichenic Fungus Aspergillus unguis. JOURNAL OF NATURAL PRODUCTS 2019; 82:1527-1534. [PMID: 31117521 DOI: 10.1021/acs.jnatprod.8b01066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Six new asperane-type sesterterpenoids, asperunguisins A-F (1-6), were isolated from the endolichenic fungus Aspergillus unguis, together with a known analogue, aspergilloxide (7); these are rare asperane-type sesterterpenoids, characterized by a unique hydroxylated 7/6/6/5 tetracyclic system. The structures of asperunguisins A-F (1-6) were elucidated on the basis of spectroscopic methods (NMR and HRESIMS), X-ray single-crystal diffraction analysis, ECD calculations, and biogenetic considerations. Asperunguisin C (3) showed cytotoxicity against the human cancer cell line A549 with an IC50 value of 6.2 μM. Further investigation revealed that the observed cell death was a result of G0/G1 cell cycle arrest via DNA damage followed by cellular apoptosis.
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Affiliation(s)
- Yue-Lan Li
- Department of Natural Products Chemistry, Key Lab of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences , Shandong University , Jinan 250012 , People's Republic of China
| | - Yun Gao
- Department of Natural Products Chemistry, Key Lab of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences , Shandong University , Jinan 250012 , People's Republic of China
| | - Chun-Yu Liu
- Department of Natural Products Chemistry, Key Lab of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences , Shandong University , Jinan 250012 , People's Republic of China
| | - Chun-Jing Sun
- Department of Natural Products Chemistry, Key Lab of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences , Shandong University , Jinan 250012 , People's Republic of China
| | - Zun-Tian Zhao
- College of Life Sciences , Shandong Normal University , Jinan 250014 , People's Republic of China
| | - Hong-Xiang Lou
- Department of Natural Products Chemistry, Key Lab of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences , Shandong University , Jinan 250012 , People's Republic of China
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30
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Castiñeira Reis M, López CS, Nieto Faza O, Tantillo DJ. Pushing the limits of concertedness. A waltz of wandering carbocations. Chem Sci 2019; 10:2159-2170. [PMID: 30881640 PMCID: PMC6385557 DOI: 10.1039/c8sc03567a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
Among the array of complex terpene-forming carbocation cyclization/rearrangement reactions, the so-called "triple shift" reactions are among the most unexpected. Such reactions involve the asynchronous combination of three 1,n-shifts into a concerted process, e.g., a 1,2-alkyl shift followed by a 1,3-hydride shift followed by a second 1,2-alkyl shift. This type of reaction so far has been proposed to occur during the biosynthesis of diterpenes and the sidechains of sterols. Here we describe efforts to push the limits of concertedness in this type of carbocation reaction by designing, and characterizing with quantum chemical computations, systems that could couple additional 1,n-shift events to a triple shift leading, in principle to quadruple, pentuple, etc. shifts. While our designs did not lead to clear-cut examples of quadruple, etc. shifts, they did lead to reactions with surprisingly flat energy surfaces where more than five chemical events connect reactants and plausible products. Ab initio molecular dynamics simulations demonstrate that the formal minima on these surfaces interchange on short timescales, both with each other and with additional unexpected structures, allowing us a glimpse into a very complex manifold that allows ready access to great structural diversity.
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Affiliation(s)
- Marta Castiñeira Reis
- Departamento de Química Orgánica , Universidade de Vigo , Lagoas-Marcosende , 36310 , Vigo , Spain
| | - Carlos Silva López
- Departamento de Química Orgánica , Universidade de Vigo , Lagoas-Marcosende , 36310 , Vigo , Spain
| | - Olalla Nieto Faza
- Departamento de Química Orgánica , Universidade de Vigo , As Lagoas , 32004 , Ourense , Spain .
| | - Dean J Tantillo
- Department of Chemistry , University of California , One Shields Ave , Davis , CA 95616 , USA .
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31
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Sato H, Saito K, Yamazaki M. Acceleration of Mechanistic Investigation of Plant Secondary Metabolism Based on Computational Chemistry. FRONTIERS IN PLANT SCIENCE 2019; 10:802. [PMID: 31293608 PMCID: PMC6606707 DOI: 10.3389/fpls.2019.00802] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
This review describes the application of computational chemistry to plant secondary metabolism, focusing on the biosynthetic mechanisms of terpene/terpenoid, alkaloid, flavonoid, and lignin as representative examples. Through these biosynthetic studies, we exhibit several computational methods, including density functional theory (DFT) calculations, theozyme calculation, docking simulation, molecular dynamics (MD) simulation, and quantum mechanics/molecular mechanics (QM/MM) calculation. This review demonstrates how modern computational chemistry can be employed as an effective tool for revealing biosynthetic mechanisms and the potential of computational chemistry-for example, elucidating how enzymes regulate regio- and stereoselectivity, finding the key catalytic residue of an enzyme, and assessing the viability of hypothetical pathways. Furthermore, insights for the next research objective involving application of computational chemistry to plant secondary metabolism are provided herein. This review will be helpful for plant scientists who are not well versed with computational chemistry.
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Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
- Center for Sustainable Resource Science, Advanced Elements Chemistry Laboratory, Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
- *Correspondence: Mami Yamazaki,
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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
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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
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Sato H, Uchiyama M, Saito K, Yamazaki M. The Energetic Viability of Δ¹-Piperideine Dimerization in Lysine-derived Alkaloid Biosynthesis. Metabolites 2018; 8:metabo8030048. [PMID: 30200334 PMCID: PMC6161264 DOI: 10.3390/metabo8030048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 11/16/2022] Open
Abstract
Lys-derived alkaloids widely distributed in plant kingdom have received considerable attention and have been intensively studied; however, little is known about their biosynthetic mechanisms. In terms of the skeleton formation, for example, of quinolizidine alkaloid biosynthesis, only the very first two steps have been identified and the later steps remain unknown. In addition, there is no available information on the number of enzymes and reactions required for their skeletal construction. The involvement of the Δ1-piperideine dimerization has been proposed for some of the Lys-derived alkaloid biosyntheses, but no enzymes for this dimerization reaction have been reported to date; moreover, it is not clear whether this dimerization reaction proceeds spontaneously or enzymatically. In this study, the energetic viability of the Δ1-piperideine dimerizations under neutral and acidic conditions was assessed using the density functional theory computations. In addition, a similar type of reaction in the dipiperidine indole alkaloid, nitramidine, biosynthesis was also investigated. Our findings will be useful to narrow down the candidate genes involved in the Lys-derived alkaloid biosynthesis.
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Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan.
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Masanobu Uchiyama
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan.
- RIKEN Center for Sustainable Resource Science (Yokohama campus), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan.
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Mitsuhashi T, Abe I. Chimeric Terpene Synthases Possessing both Terpene Cyclization and Prenyltransfer Activities. Chembiochem 2018; 19:1106-1114. [PMID: 29675947 DOI: 10.1002/cbic.201800120] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Indexed: 12/12/2022]
Abstract
Prenyltransferase (PT) and terpene synthase (TPS) are key enzymes in the formation of the basic carbon skeletons of terpenoids. The PTs determine the prenyl carbon chain length, whereas TPSs generate the structural complexity of the molecular scaffolds, forming various ring structures. Normally, PTs and TPSs are separate, independent enzymes. However, in 2007, a chimeric enzyme, in which the PT was fused with the TPS, was found in a fungus. Recent studies have revealed that such chimeric TPSs are widely distributed in fungi and function in the biosyntheses of various terpene natural products, including sesterterpenes, which are a relatively rare group of terpenoids. This review summarizes the accumulated knowledge of these recently discovered, unique, chimeric TPSs.
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Affiliation(s)
- Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Minami A, Ozaki T, Liu C, Oikawa H. Cyclopentane-forming di/sesterterpene synthases: widely distributed enzymes in bacteria, fungi, and plants. Nat Prod Rep 2018; 35:1330-1346. [DOI: 10.1039/c8np00026c] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cyclization mechanisms and structural diversification strategies of novel cyclopentane-forming terpene synthases from various organisms are reviewed.
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Affiliation(s)
- Atsushi Minami
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
| | - Taro Ozaki
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
| | - Chengwei Liu
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
| | - Hideaki Oikawa
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
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