1
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Torrence IS, O'Brien TE, Siegel JB, Tantillo DJ. Docking carbocations into terpene synthase active sites using chemically meaningful constraints-The TerDockin approach. Methods Enzymol 2024; 699:231-263. [PMID: 38942505 DOI: 10.1016/bs.mie.2024.02.006] [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
Terpenes are a diverse class of natural products which have long been sought after for their chemical properties as medicine, perfumes, and for food flavoring. Computational docking studies of terpene mechanisms have been a challenge due to the lack of strong directing groups which many docking programs rely on. In this chapter, we dive into our computational method Terdockin (Terpene-Docking) as a successful methodology in modeling terpene synthase mechanisms. This method could also be used as inspiration for any multi-ligand docking project.
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Affiliation(s)
- Ian S Torrence
- Department of Chemistry, University of California Davis, Davis, CA, United States
| | - Terrence E O'Brien
- Discovery Chemistry, Genentech, Inc., South San Francisco, CA, United States
| | - Justin B Siegel
- Department of Chemistry, University of California Davis, Davis, CA, United States; Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, United States; Genome Center, University of California Davis, Davis, CA, Untied States.
| | - Dean J Tantillo
- Department of Chemistry, University of California Davis, Davis, CA, United States
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2
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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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3
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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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4
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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.
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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
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5
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Sato H, Hashishin T, Kanazawa J, Miyamoto K, Uchiyama M. DFT Study of a Missing Piece in Brasilane-Type Structure Biosynthesis: An Unusual Skeletal Rearrangement. J Am Chem Soc 2020; 142:19830-19834. [PMID: 33124823 DOI: 10.1021/jacs.0c09616] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Brasilane-type sesquiterpenes have been known for a long time, but their biosynthetic pathways and mechanisms remain elusive. Recently, two groups independently characterized a Trichoderma terpene cyclase that produces trichobrasilenol, a brasilane-type sesquiterpene, and a plausible biosynthetic pathway was proposed based on isotopic labeling experiments. In the proposed mechanism, the characteristic brasilane-type 5/6 bicyclic skeleton is synthesized from a 5/7/3 tricyclic intermediate via a complicated concerted reaction, including six chemical events of C-C σ bond metathesis and rearrangements, ring-contraction, π bond formation, and regioselective hydroxylation. However, our density functional theory (DFT) calculations do not support this mechanism. On the basis of DFT calculations, we propose a new pathway for trichobrasilenol biosynthesis, involving a multistep carbocation cascade in which cyclopropylcarbinyl cations in equilibrium with homoallyl cations play a pivotal role. This pathway and mechanism is in good agreement with previous biosynthetic studies on brasilane-type compounds and related terpenoids, including isotope-labeling experiments and byproducts analysis.
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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.,Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Clustering of Pioneering Research (CPR), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takahiro Hashishin
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junichiro Kanazawa
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunori Miyamoto
- 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.,Clustering of Pioneering Research (CPR), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, 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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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.
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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
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7
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Kutateladze DA, Strassfeld DA, Jacobsen EN. Enantioselective Tail-to-Head Cyclizations Catalyzed by Dual-Hydrogen-Bond Donors. J Am Chem Soc 2020; 142:6951-6956. [PMID: 32223127 PMCID: PMC7293861 DOI: 10.1021/jacs.0c02665] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chiral urea derivatives are shown to catalyze enantioselective tail-to-head cyclization reactions of neryl chloride analogues. Experimental data are consistent with a mechanism in which π-participation by the nucleophilic olefin facilitates chloride ionization and thereby circumvents simple elimination pathways. Kinetic and computational studies support a cooperative mode of catalysis wherein two molecules of the urea catalyst engage the substrate and induce enantioselectivity through selective transition state stabilization.
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Affiliation(s)
| | | | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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8
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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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9
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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. [DOI: 10.1039/d0ob01565b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simple models based on measurements taken from X-ray structures of relevant active sites are used to evaluate π stabilization by phenylalanine of several biochemical carbocations.
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Affiliation(s)
- Thomas A. Spencer
- Department of Chemistry
- 6128 Burke Laboratory
- Dartmouth College
- Hanover
- USA
| | - Robert Ditchfield
- Department of Chemistry
- 6128 Burke Laboratory
- Dartmouth College
- Hanover
- USA
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10
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Liang G, Ji Y, Liu H, Pang Y, Zhou B, Cheng M, Liu Y, Lin B, Liu Y. Silver Triflate/
N
‐Fluorobenzenesulfonimide‐Catalyzed Cycloisomerization of Tryptamine‐Ynamide to Spiro[indoline‐3,4′‐piperidine] Induced by Cation‐π‐π Interactions between Substrate and Metal Ligand. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201901175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Guoduan Liang
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University)Ministry of Education Shenyang 110016 People's Republic of China
- Wuya College of InnovationShenyang Pharmaceutical University Shenyang 110016 People's Republic of China
- Institute of Drug Research inMedicine Capital of China Benxi 117000 People's Republic of China
| | - Yanjun Ji
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University)Ministry of Education Shenyang 110016 People's Republic of China
- Institute of Drug Research inMedicine Capital of China Benxi 117000 People's Republic of China
| | - Hairui Liu
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University)Ministry of Education Shenyang 110016 People's Republic of China
- Wuya College of InnovationShenyang Pharmaceutical University Shenyang 110016 People's Republic of China
- Institute of Drug Research inMedicine Capital of China Benxi 117000 People's Republic of China
| | - Yadong Pang
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University)Ministry of Education Shenyang 110016 People's Republic of China
- Wuya College of InnovationShenyang Pharmaceutical University Shenyang 110016 People's Republic of China
- Institute of Drug Research inMedicine Capital of China Benxi 117000 People's Republic of China
| | - Bojun Zhou
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University)Ministry of Education Shenyang 110016 People's Republic of China
- Wuya College of InnovationShenyang Pharmaceutical University Shenyang 110016 People's Republic of China
- Institute of Drug Research inMedicine Capital of China Benxi 117000 People's Republic of China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University)Ministry of Education Shenyang 110016 People's Republic of China
- Institute of Drug Research inMedicine Capital of China Benxi 117000 People's Republic of China
| | - Yang Liu
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University)Ministry of Education Shenyang 110016 People's Republic of China
| | - Bin Lin
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University)Ministry of Education Shenyang 110016 People's Republic of China
- Institute of Drug Research inMedicine Capital of China Benxi 117000 People's Republic of China
| | - Yongxiang Liu
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University)Ministry of Education Shenyang 110016 People's Republic of China
- Wuya College of InnovationShenyang Pharmaceutical University Shenyang 110016 People's Republic of China
- Institute of Drug Research inMedicine Capital of China Benxi 117000 People's Republic of China
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11
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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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12
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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 2018; 10:2159-2170. [PMID: 30881640 PMCID: PMC6385557 DOI: 10.1039/c8sc03567a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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
Coupling multiple 1,n-shifts in reactions of biosynthetically relevant carbocations defies previous limits on the concertedness of multiple chemical events.
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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13
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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.
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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
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14
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Ansbacher T, Freud Y, Major DT. Slow-Starter Enzymes: Role of Active-Site Architecture in the Catalytic Control of the Biosynthesis of Taxadiene by Taxadiene Synthase. Biochemistry 2018; 57:3773-3779. [DOI: 10.1021/acs.biochem.8b00452] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tamar Ansbacher
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
- Hadassah Academic College, 7 Hanevi’im Street, Jerusalem 9101001, Israel
| | - Yehoshua Freud
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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15
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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.
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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
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16
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Yao J, Chen F, Guo H. QM/MM free energy simulations of the reaction catalysed by (4S)-limonene synthase involving linalyl diphosphate (LPP) substrate. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1447106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Jianzhuang Yao
- School of Biological Science and Technology, University of Jinan , Jinan, P.R. China
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee , Knoxville, TN, USA
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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17
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Sato H, Narita K, Minami A, Yamazaki M, Wang C, Suemune H, Nagano S, Tomita T, Oikawa H, Uchiyama M. Theoretical Study of Sesterfisherol Biosynthesis: Computational Prediction of Key Amino Acid Residue in Terpene Synthase. Sci Rep 2018; 8:2473. [PMID: 29410538 PMCID: PMC5802712 DOI: 10.1038/s41598-018-20916-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/17/2018] [Indexed: 01/07/2023] Open
Abstract
The cyclization mechanisms involved in the biosynthesis of sesterterpenes are not fully understood. For example, there are two plausible reaction pathways for sesterfisherol biosynthesis, which differ in the order of ring cyclization: A-D-B/C (Path a) and A-B-C/D (Path b). It is difficult to capture intermediates of terpene cyclization, which is a complex, domino-type reaction, and so here we employed a combination of experimental and computational methods. Density functional theory calculations revealed unexpected intermediates and transition states, and implied that C-H···π interaction between a carbocation intermediate and an aromatic residue of sesterfisherol synthase (NfSS) plays a critical role, serving to accelerate the 1,2-H shift (thereby preventing triquinane carbocation formation) and to protect reactive carbocation intermediates from bases such as pyrophosphate or water in the active site. Site-directed mutagenesis of NfSS guided by docking simulations confirmed that phenylalanine F191 is a critical amino acid residue for sesterfisherol synthase, as the F191A mutant of NfSS produces novel sesterterpenes, but not sesterfisherol. Although both pathways are energetically viable, on the basis of our computational and experimental results, NfSS-mediated sesterfisherol biosynthesis appears to proceed via Path a. These findings may also provide new insight into the cyclization mechanisms in related sesterterpene synthases.
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Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Elements Chemistry Laboratory, RIKEN, and RIKEN Center for Sustainable Resource Science (Wako campus), 2-1 Hirosawa, Wako-shi, Saitama-ken, 351-0198, Japan.
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan.
| | - Koji Narita
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Atsushi Minami
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Chao Wang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Elements Chemistry Laboratory, RIKEN, and RIKEN Center for Sustainable Resource Science (Wako campus), 2-1 Hirosawa, Wako-shi, Saitama-ken, 351-0198, Japan
| | - Hironori Suemune
- Department of Engineering, Graduate School of Sustainability Science, Tottori University, Tottori, 680-8552, Japan
| | - Shingo Nagano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | - Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideaki Oikawa
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Elements Chemistry Laboratory, RIKEN, and RIKEN Center for Sustainable Resource Science (Wako campus), 2-1 Hirosawa, Wako-shi, Saitama-ken, 351-0198, Japan.
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18
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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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19
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Hare SR, Pemberton RP, Tantillo DJ. Navigating Past a Fork in the Road: Carbocation-π Interactions Can Manipulate Dynamic Behavior of Reactions Facing Post-Transition-State Bifurcations. J Am Chem Soc 2017; 139:7485-7493. [PMID: 28504880 DOI: 10.1021/jacs.7b01042] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Dynamics calculations are described for carbocation rearrangements involving product-forming pathways with post-transition-state bifurcations. We show that noncovalent interactions with associated benzene rings (a simple model of aromatic amino acid side chains) can switch inherent dynamical tendencies for competing modes of disrotation, establishing that meaningful changes in dynamically controlled product selectivity can be achieved with few weak noncovalent interactions.
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Affiliation(s)
- Stephanie R Hare
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Ryan P Pemberton
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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20
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Kennedy CR, Lin S, Jacobsen EN. The Cation-π Interaction in Small-Molecule Catalysis. Angew Chem Int Ed Engl 2016; 55:12596-624. [PMID: 27329991 PMCID: PMC5096794 DOI: 10.1002/anie.201600547] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 11/11/2022]
Abstract
Catalysis by small molecules (≤1000 Da, 10(-9) m) that are capable of binding and activating substrates through attractive, noncovalent interactions has emerged as an important approach in organic and organometallic chemistry. While the canonical noncovalent interactions, including hydrogen bonding, ion pairing, and π stacking, have become mainstays of catalyst design, the cation-π interaction has been comparatively underutilized in this context since its discovery in the 1980s. However, like a hydrogen bond, the cation-π interaction exhibits a typical binding affinity of several kcal mol(-1) with substantial directionality. These properties render it attractive as a design element for the development of small-molecule catalysts, and in recent years, the catalysis community has begun to take advantage of these features, drawing inspiration from pioneering research in molecular recognition and structural biology. This Review surveys the burgeoning application of the cation-π interaction in catalysis.
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Affiliation(s)
- C Rose Kennedy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, 02138, USA
| | - Song Lin
- Department of Chemistry, University of California, Berkeley, 535 Latimer Hall, Berkeley, CA, 94720, USA
| | - Eric N Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, 02138, USA.
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21
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Kennedy CR, Lin S, Jacobsen EN. Die Kation-π-Wechselwirkung in der Katalyse mit niedermolekularen Verbindungen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600547] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- C. Rose Kennedy
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge MA 02138 USA
| | - Song Lin
- Department of Chemistry; University of California, Berkeley; 535 Latimer Hall Berkeley CA 94720 USA
| | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge MA 02138 USA
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22
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Purino M, Ardiles AE, Callies O, Jiménez IA, Bazzocchi IL. Montecrinanes A–C: Triterpenes with an Unprecedented Rearranged Tetracyclic Skeleton from
Celastrus vulcanicola
. Insights into Triterpenoid Biosynthesis Based on DFT Calculations. Chemistry 2016; 22:7582-91. [DOI: 10.1002/chem.201600294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Martín Purino
- Instituto Universitario de Bio-Orgánica “Antonio González” and Departamento de Química Universidad de La Laguna C/Astrofísico Francisco Sánchez 2 38206 La Laguna, Tenerife Spain
| | - Alejandro E. Ardiles
- Instituto Universitario de Bio-Orgánica “Antonio González” and Departamento de Química Universidad de La Laguna C/Astrofísico Francisco Sánchez 2 38206 La Laguna, Tenerife Spain
- Departamento de Química Facultad de Ciencias Universidad de Chile Las Palmeras 3425 Ñuñoa, Santiago Chile
| | - Oliver Callies
- Instituto Universitario de Bio-Orgánica “Antonio González” and Departamento de Química Universidad de La Laguna C/Astrofísico Francisco Sánchez 2 38206 La Laguna, Tenerife Spain
| | - Ignacio A. Jiménez
- Instituto Universitario de Bio-Orgánica “Antonio González” and Departamento de Química Universidad de La Laguna C/Astrofísico Francisco Sánchez 2 38206 La Laguna, Tenerife Spain
| | - Isabel L. Bazzocchi
- Instituto Universitario de Bio-Orgánica “Antonio González” and Departamento de Química Universidad de La Laguna C/Astrofísico Francisco Sánchez 2 38206 La Laguna, Tenerife Spain
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