1
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Guth FM, Lindner F, Rydzek S, Peil A, Friedrich S, Hauer B, Hahn F. Rieske Oxygenase-Catalyzed Oxidative Late-Stage Functionalization during Complex Antifungal Polyketide Biosynthesis. ACS Chem Biol 2023; 18:2450-2456. [PMID: 37948749 DOI: 10.1021/acschembio.3c00498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Rieske oxygenases (ROs) from natural product biosynthetic pathways are a poorly studied group of enzymes with significant potential as oxidative functionalization biocatalysts. A study on the ROs JerL, JerP, and AmbP from the biosynthetic pathways of jerangolid A and ambruticin VS-3 is described. Their activity was successfully reconstituted using whole-cell bioconversion systems coexpressing the ROs and their respective natural flavin-dependent reductase (FDR) partners. Feeding authentic biosynthetic intermediates and synthetic surrogates to these strains confirmed the involvement of the ROs in hydroxymethylpyrone and dihydropyran formation and revealed crucial information about the RO's substrate specificity. The pronounced dependence of JerL and JerP on the presence of a methylenolether allowed the precise temporal assignment of RO catalysis to the ultimate steps of jerangolid biosynthesis. JerP and AmbP stand out among the biosynthetic ROs studied so far for their ability to catalyze clean tetrahydropyran desaturation without further functionalizing the formed electron-rich double bonds. This work highlights the remarkable ability of ROs to highly selectively oxidize complex molecular scaffolds.
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Affiliation(s)
- Florian M Guth
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Frederick Lindner
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Simon Rydzek
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Andreas Peil
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Steffen Friedrich
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
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2
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Wu Y, Wang M, Liu L. Advances on structure, bioactivity, and biosynthesis of amino acid-containing trans-AT polyketides. Eur J Med Chem 2023; 262:115890. [PMID: 37907023 DOI: 10.1016/j.ejmech.2023.115890] [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] [Received: 08/19/2023] [Revised: 10/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023]
Abstract
Trans-AT polyketides represent a class of natural compounds utilizing independent acyltransferase during their biosynthesis. They are well known for their diverse chemical structures and potent bioactivities. Trans-AT polyketides are synthesized through biosynthetic gene clusters predominantly composed of polyketide synthases (PKS), but often found in hybrid with non-ribosomal peptide synthetases (NRPS). This genetic hybridization results in the incorporation of amino acid residues into polyketide structures, significantly enhancing their structural diversity. Numerous amino acid-containing trans-AT polyketides have been identified, drawing significant attention to the mechanisms underlying amino acid incorporation and their impact on the biological activity of polyketides. Here, we discussed their origins, structures, biological activities, and the specific roles of amino acids in modulating both the bioactivity and biosynthesis of 38 trans-AT polyketides containing amino acids for the first time. This comprehensive analysis will serve as a crucial reference for the exploration of novel compounds and the improvement of structures and activities.
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Affiliation(s)
- Yunqiang Wu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Min Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
| | - Liwei Liu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China.
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3
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Du Z, Li Y, Liu Y, Shi T. Molecular Insights into Bifunctional Ambruticin DH3 for Substrate Specificity and Catalytic Mechanism. Chemistry 2023; 29:e202203420. [PMID: 36464909 DOI: 10.1002/chem.202203420] [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: 11/03/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022]
Abstract
Dehydratase (DH), a domain located at polyketide synthase (PKS) modules, commonly catalyzes the dehydration of β-hydroxy to an α,β-unsaturated acyl intermediate. As a unique bifunctional dehydratase, AmbDH3 (the DH domain of module 3 of the ambruticin PKS) is verified to be responsible for both dehydration and the following pyran-forming cyclization. Besides, in vitro studies showed that its catalytic efficiency varies with different chiral substrates. However, the detailed molecular mechanism of AmbDH3 remains unclear. In this work, the structural rationale for the substrate specificity (2R/2S- and 6R/6S-substrates) in AmbDH3 was elucidated and the complete reaction pathways including dehydration and cyclization were presented. Both MD simulations and binding free energy calculations indicated AmbDH3 had a stronger preference for 2R-substrates (2R6R-2, 2R6S-3) than 2S-substrates (2S6R-1), and residue H51 and G61 around the catalytic pocket were emphasized by forming stable hydrogen bonds with 2R-substrates. In addition, AmbDH3's mild tolerance at C6 was explained by comparison of substrate conformation and hydrogen bond network in 6S- and 6R-substrate systems. The QM/MM results supported a consecutive one-base dehydration and cyclization mechanism for 2R6S-3 substrate with the energy barrier of 25.2 kcal mol-1 and 24.5 kcal mol-1 , respectively. Our computational results uncover the substrate recognition and catalytic process of the first bifunctional dehydratase-cyclase AmbDH3, which will shed light on the application of multifunctional DH domains in PKSs for diverse natural product analogs and benefit the chemoenzymatic synthesis of stereoselective pyran-containing products.
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Affiliation(s)
- Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yongzhen Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yihan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Ting Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, P. R. China
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4
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Hobson C, Jenner M, Jian X, Griffiths D, Roberts DM, Rey-Carrizo M, Challis GL. Diene incorporation by a dehydratase domain variant in modular polyketide synthases. Nat Chem Biol 2022; 18:1410-1416. [PMID: 36109649 PMCID: PMC7613849 DOI: 10.1038/s41589-022-01127-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/27/2022] [Indexed: 11/09/2022]
Abstract
Modular polyketide synthases (PKSs) are biosynthetic assembly lines that construct structurally diverse natural products with wide-ranging applications in medicine and agriculture. Various mechanisms contribute to structural diversification during PKS-mediated chain assembly, including dehydratase (DH) domain-mediated elimination of water from R and S-configured 3-hydroxy-thioesters to introduce E- and Z-configured carbon-carbon double bonds, respectively. Here we report the discovery of a DH domain variant that catalyzes the sequential elimination of two molecules of water from a (3R, 5S)-3,5-dihydroxy thioester during polyketide chain assembly, introducing a conjugated E,Z-diene into various modular PKS products. We show that the reaction proceeds via a (2E, 5S)-2-enoyl-5-hydroxy-thioester intermediate and involves an additional universally conserved histidine residue that is absent from the active site of most conventional DH domains. These findings expand the diverse range of chemistries mediated by DH-like domains in modular PKSs, highlighting the catalytic versatility of the double hotdog fold.
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Affiliation(s)
- Christian Hobson
- Department of Chemistry, University of Warwick, Coventry, UK.,Willow Biosciences Inc., Vancouver, British Columbia, Canada
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry, UK.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Xinyun Jian
- Department of Chemistry, University of Warwick, Coventry, UK.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Daniel Griffiths
- Department of Chemistry, University of Warwick, Coventry, UK.,Monash University Accident Research Centre, Clayton, Victoria, Australia
| | | | - Matias Rey-Carrizo
- Department of Chemistry, University of Warwick, Coventry, UK.,BCN Medical Writing, Sabadell, Spain
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, UK. .,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK. .,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, Australia.
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5
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Yin Z, Liebhart E, Stegmann E, Brötz-Oesterhelt H, Dickschat JS. An isotopic probe to follow the stereochemical course of dehydratase reactions in polyketide and fatty acid biosynthesis. Org Chem Front 2022. [DOI: 10.1039/d2qo00272h] [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
Four stereoisomeric and isotopically labelled probes that are suitable to easily follow the stereochemical course of dehydratases have been synthesised.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Elisa Liebhart
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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6
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Avalon NE, Murray AE, Daligault HE, Lo CC, Davenport KW, Dichosa AEK, Chain PSG, Baker BJ. Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian. Front Chem 2021; 9:802574. [PMID: 35004620 PMCID: PMC8739492 DOI: 10.3389/fchem.2021.802574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ∼75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and is found in multiple copies within the metagenome-assembled genome (MAG). Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.
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Affiliation(s)
- Nicole E. Avalon
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Alison E. Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | | | - Chien-Chi Lo
- Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | | | | | - Bill J. Baker
- Department of Chemistry, University of South Florida, Tampa, FL, United States
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7
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Wagner L, Roß T, Hollmann T, Hahn F. Cross-linking of a polyketide synthase domain leads to a recyclable biocatalyst for chiral oxygen heterocycle synthesis. RSC Adv 2021; 11:20248-20251. [PMID: 35479892 PMCID: PMC9033652 DOI: 10.1039/d1ra03692k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/26/2021] [Indexed: 12/17/2022] Open
Abstract
The potential of polyketide synthase (PKS) domains for chemoenzymatic synthesis can often not be tapped due to their low stability and activity in vitro. In this proof-of-principle study, the immobilisation of the heterocycle-forming PKS domain AmbDH3 as a cross-linked enzyme aggregate (CLEA) is described. The AmbDH3-CLEA showed good activity recovery, stability and recyclability. Repetitive reactions on the semi-preparative scale were performed with high conversion and isolated yield. Similar to that observed for the free enzyme, the aggregate retained substrate tolerance and the ability for kinetic resolution. This first example of a successful enzymatic PKS domain immobilisation demonstrates that cross-linking can in principle be applied to this type of enzyme to increase its applicability for chemoenzymatic synthesis. Cross-linking of the polyketide synthase domain AmbDH3 led to an active aggregate with improved properties for the chemoenzymatic synthesis of chiral oxygen heterocycles, such as recyclability and facile purification.![]()
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Affiliation(s)
- Lisa Wagner
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Theresa Roß
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Tim Hollmann
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Frank Hahn
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
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8
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Liu L, Yu Q, Zhang H, Tao W, Wang R, Bai L, Zhao YL, Shi T. Theoretical study on substrate recognition and catalytic mechanisms of gephyronic acid dehydratase DH1. Catal Sci Technol 2021. [DOI: 10.1039/d0cy01776k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bifunctional dehydratase GphF DH1 catalyzes both the dehydration of β-hydroxy and the double bond isomerization with the energy barrier of 27.0 kcal mol−1 and 17.2 kcal mol−1 respectively.
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Affiliation(s)
- Lei Liu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Qian Yu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Haoqing Zhang
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Rufan Wang
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
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9
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Hahn F, Guth FM. The ambruticins and jerangolids - chemistry, biology and chemoenzymatic synthesis of potent antifungal drug candidates. Nat Prod Rep 2020; 37:1300-1315. [PMID: 32420573 DOI: 10.1039/d0np00012d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 1977 to 2020The ambruticins and jerangolids are myxobacterial reduced polyketides, which are produced via highly unusual biosynthetic pathways containing a plethora of non-canonical enzymatic transformations. Since the discovery of the first congeners in the late 1970s, they have been in the focus of drug development due to their good antifungal activity and low toxicity in mammals, which result from interaction with an unusual innercellular target in fungi. Despite significant efforts, which have led to the development of various total syntheses, their structural complexity has yet avoided full exploitation of their pharmacological potential. This article summarises biological, total and semisynthetic as well as biosynthetic studies on both compounds. An outlook on the biosynthesis-based approaches to them and their derivatives is presented. Due to the structural and biosynthetic characteristics of the ambruticins and jerangolids, chemoenzymatic processes that make use of their biosynthetic pathway enzymes are particularly promising to gain efficient access to derivative libraries for structure activity relationship studies.
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Affiliation(s)
- Frank Hahn
- Department of Chemistry, University of Bayreuth, 51427 Bayreuth, Germany.
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10
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Merten C, Golub TP, Kreienborg NM. Absolute Configurations of Synthetic Molecular Scaffolds from Vibrational CD Spectroscopy. J Org Chem 2019; 84:8797-8814. [PMID: 31046276 DOI: 10.1021/acs.joc.9b00466] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is one of the most powerful techniques for the determination of absolute configurations (AC), as it does not require any specific UV/vis chromophores, no chemical derivatization, and no growth of suitable crystals. In the past decade, it has become increasingly recognized by chemists from various fields of synthetic chemistry such as total synthesis and drug discovery as well as from developers of asymmetric catalysts. This perspective article gives an overview about the most important experimental aspects of a VCD-based AC determination and explains the theoretical analysis. The comparison of experimental and computational spectra that leads to the final conclusion about the AC of the target molecules is described. In addition, the review summarizes unique VCD studies carried out in the period 2008-2018 that focus on the determination of unknown ACs of new compounds, which were obtained in its enantiopure form either through direct asymmetric synthesis or chiral chromatography.
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Affiliation(s)
- Christian Merten
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Tino P Golub
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Nora M Kreienborg
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
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11
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Kreienborg NM, Merten C. How to treat C-F stretching vibrations? A vibrational CD study on chiral fluorinated molecules. Phys Chem Chem Phys 2019; 21:3506-3511. [PMID: 29863202 DOI: 10.1039/c8cp02395f] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The analysis of vibrational circular dichroism and infrared spectra typically requires the prediction of spectra on the density functional theory level. In particular for absolute configuration determinations, for which the comparison between experiment and theory is often supported by similarity analysis algorithms, it is important that frequencies, relative band intensities and VCD signs are predicted correctly. Due to the poor prediction of harmonic frequencies, carbon-fluorine stretching vibrations are often strongly misplaced by common hybrid functionals such as B3LYP. Herein we show that the M06-2X functional provides harmonic C-F stretching frequencies with an accuracy sufficient for a reliable spectra analysis. We briefly discuss the origin of this exceptional performance and show that it is likely to be related to a cancellation of errors.
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Affiliation(s)
- Nora M Kreienborg
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie 2, Universitätstraße 150, 44801 Bochum, Germany.
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12
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Hashimoto T, Hashimoto J, Kozone I, Amagai K, Kawahara T, Takahashi S, Ikeda H, Shin-ya K. Biosynthesis of Quinolidomicin, the Largest Known Macrolide of Terrestrial Origin: Identification and Heterologous Expression of a Biosynthetic Gene Cluster over 200 kb. Org Lett 2018; 20:7996-7999. [DOI: 10.1021/acs.orglett.8b03570] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Keita Amagai
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Teppei Kawahara
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Shunji Takahashi
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- The Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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13
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Kreienborg NM, Merten C. How Do Substrates Bind to a Bifunctional Thiourea Catalyst? A Vibrational CD Study on Carboxylic Acid Binding. Chemistry 2018; 24:17948-17954. [PMID: 30230065 DOI: 10.1002/chem.201804230] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Indexed: 01/14/2023]
Abstract
Knowledge about the active conformation of an asymmetric catalyst is highly valuable in order to understand its stereoinductive power, but spectroscopic access to these structures is often limited. For the example of Takemoto's bifunctional thiourea, we demonstrate the capability of VCD spectroscopy to characterize the conformational preferences of the catalyst with and without having a reactant bound to it. In particular we show that the binding orientation of carboxylic acids can easily be derived from a computationally guided analysis of the spectra. Moreover, we identify characteristic marker bands, which are only visible in the VCD spectra of the catalyst/acid mixtures but not in the corresponding IR spectra. Lastly, we also discuss the problem that the popular DFT functional M06-2X, which we found to perform exceptionally well in the calculations of vibrational frequencies for fluorinated molecules, predicts incorrect structures of the molecular clusters. We relate this poor performance in predicting the structure of the binding topologies to an overestimation of dispersive CH-π and π-π interactions, which occur due to a neglect of the solvent molecules in the clusters. VCD spectroscopy is thus shown to be a powerful tool to identify and subsequently correct such mispredictions of solution-phase structures.
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Affiliation(s)
- Nora M Kreienborg
- Ruhr-Universität Bochum, Fakultät für Chemie, Lehrstuhl für Organische Chemie II, Universitätsstraße 150, 44801, Bochum, Germany
| | - Christian Merten
- Ruhr-Universität Bochum, Fakultät für Chemie, Lehrstuhl für Organische Chemie II, Universitätsstraße 150, 44801, Bochum, Germany
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14
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Lindner F, Friedrich S, Hahn F. Total Synthesis of Complex Biosynthetic Late-Stage Intermediates and Bioconversion by a Tailoring Enzyme from Jerangolid Biosynthesis. J Org Chem 2018; 83:14091-14101. [DOI: 10.1021/acs.joc.8b02047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Frederick Lindner
- Professur für Organische Chemie (Lebensmittelchemie), Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Steffen Friedrich
- Professur für Organische Chemie (Lebensmittelchemie), Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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15
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Dodge GJ, Ronnow D, Taylor RE, Smith JL. Molecular Basis for Olefin Rearrangement in the Gephyronic Acid Polyketide Synthase. ACS Chem Biol 2018; 13:2699-2707. [PMID: 30179448 PMCID: PMC6233718 DOI: 10.1021/acschembio.8b00645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyketide synthases (PKS) are a rich source of natural products of varied chemical composition and biological significance. Here, we report the characterization of an atypical dehydratase (DH) domain from the PKS pathway for gephyronic acid, an inhibitor of eukaryotic protein synthesis. Using a library of synthetic substrate mimics, the reaction course, stereospecificity, and tolerance to non-native substrates of GphF DH1 are probed via LC-MS analysis. Taken together, the studies establish GphF DH1 as a dual-function dehydratase/isomerase that installs an odd-to-even double bond and yields a product consistent with the isobutenyl terminus of gephyronic acid. The studies also reveal an unexpected C2 epimerase function in catalytic turnover with the native substrate. A 1.55-Å crystal structure of GphF DH1 guided mutagenesis experiments to elucidate the roles of key amino acids in the multistep DH1 catalysis, identifying critical functions for leucine and tyrosine side chains. The mutagenesis results were applied to add a secondary isomerase functionality to a nonisomerizing DH in the first successful gain-of-function engineering of a PKS DH. Our studies of GphF DH1 catalysis highlight the versatility of the DH active site and adaptation for a specific catalytic outcome with a specific substrate.
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Affiliation(s)
- Greg J. Dodge
- Department of Biological Chemistry and Life Sciences Institute University of Michigan Ann Arbor, Michigan, 48109
| | - Danialle Ronnow
- Department of Chemistry and Biochemistry University of Notre Dame Notre Dame, Indiana 46556
| | - Richard E. Taylor
- Department of Chemistry and Biochemistry University of Notre Dame Notre Dame, Indiana 46556
| | - Janet L. Smith
- Department of Biological Chemistry and Life Sciences Institute University of Michigan Ann Arbor, Michigan, 48109
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16
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Hemmerling F, Lebe KE, Wunderlich J, Hahn F. An Unusual Fatty Acyl:Adenylate Ligase (FAAL)-Acyl Carrier Protein (ACP) Didomain in Ambruticin Biosynthesis. Chembiochem 2018. [DOI: 10.1002/cbic.201800084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Franziska Hemmerling
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Karen E. Lebe
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Johannes Wunderlich
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
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17
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Sung KH, Berkhan G, Hollmann T, Wagner L, Blankenfeldt W, Hahn F. Einblicke in die duale Aktivität einer bifunktionalen Dehydratase-Cyclase-Domäne. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kwang Hoon Sung
- Helmholtz-Zentrum für Infektionsforschung GmbH; Inhoffenstraße 7 38124 Braunschweig Deutschland
- Institut für Biochemie, Biotechnologie und Bioinformatik; Technische Universität Braunschweig; Spielmannstraße 7 38106 Braunschweig Deutschland
| | - Gesche Berkhan
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe, BMWZ; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
| | - Tim Hollmann
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
| | - Lisa Wagner
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
| | - Wulf Blankenfeldt
- Helmholtz-Zentrum für Infektionsforschung GmbH; Inhoffenstraße 7 38124 Braunschweig Deutschland
- Institut für Biochemie, Biotechnologie und Bioinformatik; Technische Universität Braunschweig; Spielmannstraße 7 38106 Braunschweig Deutschland
| | - Frank Hahn
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe, BMWZ; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
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18
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Sung KH, Berkhan G, Hollmann T, Wagner L, Blankenfeldt W, Hahn F. Insights into the Dual Activity of a Bifunctional Dehydratase-Cyclase Domain. Angew Chem Int Ed Engl 2017; 57:343-347. [PMID: 29084363 DOI: 10.1002/anie.201707774] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Indexed: 01/12/2023]
Abstract
Oxygen-containing heterocycles are a common structural motif in polyketide natural products and contribute significantly to their biological activity. Here, we report structural and mechanistic investigations on AmbDH3, a polyketide synthase domain with dual activity as dehydratase (DH) and pyran-forming cyclase in ambruticin biosynthesis. AmbDH3 is similar to monofunctional DH domains, using H51 and D215 for dehydration. V173 was confirmed as a diagnostic residue for cyclization activity by a mutational study and enzymatic in vitro experiments. Similar motifs were observed in the seemingly monofunctional AmbDH2, which also shows an unexpected cyclase activity. Our results pave the way for mining of hidden cyclases in biosynthetic pathways. They also open interesting prospects for the generation of novel biocatalysts for chemoenzymatic synthesis and pyran-polyketides by combinatorial biosynthesis.
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Affiliation(s)
- Kwang Hoon Sung
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - Gesche Berkhan
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany.,Centre for Biomolecular Drug Research, BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Tim Hollmann
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Lisa Wagner
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Wulf Blankenfeldt
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - Frank Hahn
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany.,Centre for Biomolecular Drug Research, BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany
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19
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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20
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Abstract
The enzymology of 135 assembly lines containing primarily cis-acyltransferase modules is comprehensively analyzed, with greater attention paid to less common phenomena. Diverse online transformations, in which the substrate and/or product of the reaction is an acyl chain bound to an acyl carrier protein, are classified so that unusual reactions can be compared and underlying assembly-line logic can emerge. As a complement to the chemistry surrounding the loading, extension, and offloading of assembly lines that construct primarily polyketide products, structural aspects of the assembly-line machinery itself are considered. This review of assembly-line phenomena, covering the literature up to 2017, should thus be informative to the modular polyketide synthase novice and expert alike.
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Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
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21
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Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as hitorin A from Chloranthus japonicus.
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22
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Merten C. Vibrational optical activity as probe for intermolecular interactions. Phys Chem Chem Phys 2017; 19:18803-18812. [DOI: 10.1039/c7cp02544k] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A detailed VCD spectroscopic analysis of well-selected chiral model systems can give valuable and unprecedented insights into intermolecular interactions such as solvation or reactant–substrate binding in catalysis.
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