1
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Liu M, Li S. Nitrile biosynthesis in nature: how and why? Nat Prod Rep 2024; 41:649-671. [PMID: 38193577 DOI: 10.1039/d3np00028a] [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: 01/10/2024]
Abstract
Covering: up to the end of 2023Natural nitriles comprise a small set of secondary metabolites which however show intriguing chemical and functional diversity. Various patterns of nitrile biosynthesis can be seen in animals, plants, and microorganisms with the characteristics of both evolutionary divergence and convergence. These specialized compounds play important roles in nitrogen metabolism, chemical defense against herbivores, predators and pathogens, and inter- and/or intraspecies communications. Here we review the naturally occurring nitrile-forming pathways from a biochemical perspective and discuss the biological and ecological functions conferred by diversified nitrile biosyntheses in different organisms. Elucidation of the mechanisms and evolutionary trajectories of nitrile biosynthesis underpins better understandings of nitrile-related biology, chemistry, and ecology and will ultimately benefit the development of desirable nitrile-forming biocatalysts for practical applications.
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Affiliation(s)
- Mingyu Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
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2
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Yamaguchi T, Nomura T, Asano Y. Identification and characterization of cytochrome P450 CYP77A59 of loquat (Rhaphiolepis bibas) responsible for biosynthesis of phenylacetonitrile, a floral nitrile compound. PLANTA 2023; 257:114. [PMID: 37166515 DOI: 10.1007/s00425-023-04151-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/02/2023] [Indexed: 05/12/2023]
Abstract
MAIN CONCLUSION Cytochrome P450 CYP77A59 is responsible for the biosynthesis of phenylacetonitrile in loquat flowers. Flowers of some plants emit volatile nitrile compounds, but the biosynthesis of these compounds is unclear. Loquat (Rhaphiolepis bibas) flowers emit characteristic N-containing volatiles, such as phenylacetonitrile (PAN), (E/Z)-phenylacetaldoxime (PAOx), and (2-nitroethyl)benzene (NEB). These volatiles likely play a defense role against pathogens and insects. PAN and NEB are commonly biosynthesized from L-phenylalanine via (E/Z)-PAOx. Two cytochrome P450s-CYP79D80 and "promiscuous fatty acid ω-hydroxylase" CYP94A90, which catalyze the formation of (E/Z)-PAOx from L-phenylalanine and NEB from (E/Z)-PAOx, respectively-are involved in NEB biosynthesis. However, the enzymes catalyzing the formation of PAN from (E/Z)-PAOx in loquat have not been identified. In this study, we aimed to identify candidate cytochrome P450s catalyzing PAN formation in loquat flowers. Yeast whole-cell biocatalyst assays showed that among nine candidate cytochrome P450s, CYP77A58 and CYP77A59 produced PAN from (E/Z)-PAOx. CYP77As catalyzed the dehydration of aldoximes, which is atypical of cytochrome P450; the reaction was NADPH-dependent, with an optimum temperature and pH of 40 °C and 8.0, respectively. CYP77As acted on (E/Z)-PAOx, (E/Z)-4-hydroxyphenylacetaldoxime, and (E/Z)-indole-3-acetaldoxime. Previously characterized CYP77As are known to hydroxylate fatty acids; loquat CYP77As did not act on tested fatty acids. We observed higher expression of CYP77A59 in flowers than in buds; expression of CYP77A58 was remarkably reduced in the flowers. Because the flowers, but not buds, emit PAN, CYP77A59 is likely responsible for the biosynthesis of PAN in loquat flowers. This study will help us understand the biosynthesis of floral nitrile compounds.
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Affiliation(s)
- Takuya Yamaguchi
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
| | - Takuya Nomura
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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3
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Gao H, Chen JY, Peng Z, Feng L, Tung CH, Wang W. Bioinspired Iron-Catalyzed Dehydration of Aldoximes to Nitriles: A General N-O Redox-Cleavage Method. J Org Chem 2022; 87:10848-10857. [PMID: 35914249 DOI: 10.1021/acs.joc.2c01122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inspired by OxdA that operates biocatalytic aldoxime dehydration, we have developed an efficient iron catalyst, Cp*Fe(1,2-Cy2PC6H4O) (1), which rapidly converts various aliphatic and aromatic aldoximes to nitriles with release of H2O at room temperature. The catalysis involves redox activation of the N-O bond by a 1e- transfer from the iron catalyst to the oxime. Such redox-mediated N-O cleavage was demonstrated by the isolation of a ferrous iminato intermediate from the reaction of the ketoxime substrate. This iron-catalyzed acceptorless dehydration approach represents a general method for the preparation of nitriles, and it also delivers salicylonitriles by catalyzing the Kemp elimination reaction.
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Affiliation(s)
- Hongjie Gao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Jia-Yi Chen
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zhiqiang Peng
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lei Feng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Chen-Ho Tung
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Wenguang Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.,College of Chemistry, Beijing Normal University, Beijing 100875, China
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4
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Wang L, Li K, Zhang W. Organoselenium-Catalyzed Conversion of Oximes to Nitriles or Ketones. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202109036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Chen K, Wang Z, Ding K, Chen Y, Asano Y. Recent progress on discovery and research of aldoxime dehydratases. GREEN SYNTHESIS AND CATALYSIS 2021. [DOI: 10.1016/j.gresc.2021.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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6
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Ganesan M, Nagaraaj P. Recent developments in dehydration of primary amides to nitriles. Org Chem Front 2020. [DOI: 10.1039/d0qo00843e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Various dehydration methods available for the direct conversion of amides to the corresponding nitriles have been reviewed.
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Affiliation(s)
- Muthupandian Ganesan
- Toxicology Division
- Regional Forensic Science Laboratory
- Forensic Sciences Department
- Chennai-4
- India
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7
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Li YH, Akula PS, Hong BC, Peng CH, Lee GH. Direct Transformation of Nitroalkanes to Nitriles Enabled by Visible-Light Photoredox Catalysis and a Domino Reaction Process. Org Lett 2019; 21:7750-7754. [PMID: 31513414 DOI: 10.1021/acs.orglett.9b02682] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A mild and convenient process for direct transformation of nitroalkanes to the corresponding nitriles was developed using a visible-light photoredox catalysis strategy with household decorative blue LEDs and the additives of Et3N and DIPIBA (or DIPEA). Application of the process in secondary nitroalkanes bearing a β-alcohol resulted in a domino process of the retro-Henry reaction and the subsequent acetalization, aldol, cyanohydrin, and ring-contraction reactions with stereoselectivities. The photocatalytic reaction was demonstrated by a continuous flow method.
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Affiliation(s)
- Yu-Hsun Li
- Department of Chemistry and Biochemistry , National Chung Cheng University , Chia-Yi 621 , Taiwan, R.O.C
| | - Pavan Sudheer Akula
- Department of Chemistry and Biochemistry , National Chung Cheng University , Chia-Yi 621 , Taiwan, R.O.C
| | - Bor-Cherng Hong
- Department of Chemistry and Biochemistry , National Chung Cheng University , Chia-Yi 621 , Taiwan, R.O.C
| | - Chieh-Hung Peng
- Department of Chemistry and Biochemistry , National Chung Cheng University , Chia-Yi 621 , Taiwan, R.O.C
| | - Gene-Hsiang Lee
- Instrumentation Center , National Taiwan University , Taipei , 106 , Taiwan, R.O.C
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8
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Betke T, Higuchi J, Rommelmann P, Oike K, Nomura T, Kato Y, Asano Y, Gröger H. Biocatalytic Synthesis of Nitriles through Dehydration of Aldoximes: The Substrate Scope of Aldoxime Dehydratases. Chembiochem 2018; 19:768-779. [PMID: 29333684 DOI: 10.1002/cbic.201700571] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Indexed: 11/05/2022]
Abstract
Nitriles, which are mostly needed and produced by the chemical industry, play a major role in various industry segments, ranging from high-volume, low-price sectors, such as polymers, to low-volume, high-price sectors, such as chiral pharma drugs. A common industrial technology for nitrile production is ammoxidation as a gas-phase reaction at high temperature. Further popular approaches are substitution or addition reactions with hydrogen cyanide or derivatives thereof. A major drawback, however, is the very high toxicity of cyanide. Recently, as a synthetic alternative, a novel enzymatic approach towards nitriles has been developed with aldoxime dehydratases, which are capable of converting an aldoxime in one step through dehydration into nitriles. Because the aldoxime substrates are easily accessible, this route is of high interest for synthetic purposes. However, whenever a novel method is developed for organic synthesis, it raises the question of substrate scope as one of the key criteria for application as a "synthetic platform technology". Thus, the scope of this review is to give an overview of the current state of the substrate scope of this enzymatic method for synthesizing nitriles with aldoxime dehydratases. As a recently emerging enzyme class, a range of substrates has already been studied so far, comprising nonchiral and chiral aldoximes. This enzyme class of aldoxime dehydratases shows a broad substrate tolerance and accepts aliphatic and aromatic aldoximes, as well as arylaliphatic aldoximes. Furthermore, aldoximes with a stereogenic center are also recognized and high enantioselectivities are found for 2-arylpropylaldoximes, in particular. It is further noteworthy that the enantiopreference depends on the E and Z isomers. Thus, opposite enantiomers are accessible from the same racemic aldehyde and the same enzyme.
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Affiliation(s)
- Tobias Betke
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany.,Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Jun Higuchi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Philipp Rommelmann
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Keiko Oike
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Taiji Nomura
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuo Kato
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Harald Gröger
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
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9
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Zhang D, Huang Y, Zhang E, Yi R, Chen C, Yu L, Xu Q. Pd/Mn Bimetallic Relay Catalysis for Aerobic Aldoxime Dehydration to Nitriles. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201701154] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dongliang Zhang
- School of Chemistry and Chemical Engineering and Institute of Pesticide of School of Horticulture and Plant Protection; Yangzhou University; Yangzhou, Jiangsu 225002 People's Republic of China
| | - Yaping Huang
- School of Chemistry and Chemical Engineering and Institute of Pesticide of School of Horticulture and Plant Protection; Yangzhou University; Yangzhou, Jiangsu 225002 People's Republic of China
| | - Erlei Zhang
- College of Chemistry and Materials Engineering; Wenzhou University; Wenzhou, Zhejiang 325035 People's Republic of China
| | - Rong Yi
- School of Chemistry and Chemical Engineering and Institute of Pesticide of School of Horticulture and Plant Protection; Yangzhou University; Yangzhou, Jiangsu 225002 People's Republic of China
| | - Chao Chen
- School of Chemistry and Chemical Engineering and Institute of Pesticide of School of Horticulture and Plant Protection; Yangzhou University; Yangzhou, Jiangsu 225002 People's Republic of China
| | - Lei Yu
- School of Chemistry and Chemical Engineering and Institute of Pesticide of School of Horticulture and Plant Protection; Yangzhou University; Yangzhou, Jiangsu 225002 People's Republic of China
| | - Qing Xu
- School of Chemistry and Chemical Engineering and Institute of Pesticide of School of Horticulture and Plant Protection; Yangzhou University; Yangzhou, Jiangsu 225002 People's Republic of China
- College of Chemistry and Materials Engineering; Wenzhou University; Wenzhou, Zhejiang 325035 People's Republic of China
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10
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Hyodo K, Kitagawa S, Yamazaki M, Uchida K. Iron-Catalyzed Dehydration of Aldoximes to Nitriles Requiring Neither Other Reagents Nor Nitrile Media. Chem Asian J 2016; 11:1348-52. [DOI: 10.1002/asia.201600085] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Kengo Hyodo
- Department of Material Chemistry; Faculty of Science and Technology; Ryukoku University; Seta Otsu Shiga 520-2194 Japan
| | - Saki Kitagawa
- Department of Material Chemistry; Faculty of Science and Technology; Ryukoku University; Seta Otsu Shiga 520-2194 Japan
| | - Masayuki Yamazaki
- Department of Material Chemistry; Faculty of Science and Technology; Ryukoku University; Seta Otsu Shiga 520-2194 Japan
| | - Kingo Uchida
- Department of Material Chemistry; Faculty of Science and Technology; Ryukoku University; Seta Otsu Shiga 520-2194 Japan
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11
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Francos J, González-Liste PJ, Menéndez-Rodríguez L, Crochet P, Cadierno V, Borge J, Antiñolo A, Fernández-Galán R, Carrillo-Hermosilla F. Half-Sandwich Guanidinate-Osmium(II) Complexes: Synthesis and Application in the Selective Dehydration of Aldoximes. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201501221] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Clausen M, Kannangara RM, Olsen CE, Blomstedt CK, Gleadow RM, Jørgensen K, Bak S, Motawie MS, Møller BL. The bifurcation of the cyanogenic glucoside and glucosinolate biosynthetic pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:558-73. [PMID: 26361733 DOI: 10.1111/tpj.13023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 08/18/2015] [Accepted: 09/02/2015] [Indexed: 05/08/2023]
Abstract
The biosynthetic pathway for the cyanogenic glucoside dhurrin in sorghum has previously been shown to involve the sequential production of (E)- and (Z)-p-hydroxyphenylacetaldoxime. In this study we used microsomes prepared from wild-type and mutant sorghum or transiently transformed Nicotiana benthamiana to demonstrate that CYP79A1 catalyzes conversion of tyrosine to (E)-p-hydroxyphenylacetaldoxime whereas CYP71E1 catalyzes conversion of (E)-p-hydroxyphenylacetaldoxime into the corresponding geometrical Z-isomer as required for its dehydration into a nitrile, the next intermediate in cyanogenic glucoside synthesis. Glucosinolate biosynthesis is also initiated by the action of a CYP79 family enzyme, but the next enzyme involved belongs to the CYP83 family. We demonstrate that CYP83B1 from Arabidopsis thaliana cannot convert the (E)-p-hydroxyphenylacetaldoxime to the (Z)-isomer, which blocks the route towards cyanogenic glucoside synthesis. Instead CYP83B1 catalyzes the conversion of the (E)-p-hydroxyphenylacetaldoxime into an S-alkyl-thiohydroximate with retention of the configuration of the E-oxime intermediate in the final glucosinolate core structure. Numerous microbial plant pathogens are able to detoxify Z-oximes but not E-oximes. The CYP79-derived E-oximes may play an important role in plant defense.
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Affiliation(s)
- Mette Clausen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for 'Plant Plasticity', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Rubini M Kannangara
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology 'bioSYNergy', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Carl E Olsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for 'Plant Plasticity', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology 'bioSYNergy', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | | | - Roslyn M Gleadow
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Kirsten Jørgensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for 'Plant Plasticity', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology 'bioSYNergy', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Søren Bak
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Mohammed S Motawie
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for 'Plant Plasticity', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology 'bioSYNergy', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for 'Plant Plasticity', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology 'bioSYNergy', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Carlsberg Laboratory, 10 Gamle Carlsberg Vej, DK-1799, Copenhagen V, Denmark
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13
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Rapeyko A, Climent MJ, Corma A, Concepción P, Iborra S. Postsynthesis-Treated Iron-Based Metal-Organic Frameworks as Selective Catalysts for the Sustainable Synthesis of Nitriles. CHEMSUSCHEM 2015; 8:3270-3282. [PMID: 26333197 DOI: 10.1002/cssc.201500695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Indexed: 06/05/2023]
Abstract
The dehydration of aldoximes to the corresponding nitriles can be performed with excellent activity and selectivity by using iron trimesate as a homogeneous catalyst. Iron trimesate has been heterogenized by synthesizing metal-organic frameworks (MOFs) from iron trimesate, that is, Fe(BTC), and MIL-100 (Fe). These materials were active and selective aldoxime dehydration catalysts, and postsynthesis-treated MIL-100 (Fe) produced the desired nitriles with 100 % conversion and selectivities >90 % under mild reaction conditions and in short reaction times. X-ray photoelectron spectroscopy showed the presence of different Fe species in the catalyst, and in situ IR spectroscopy combined with catalytic results indicates that the catalytic activity is associated with Fe framework species. The postsynthesis-treated MIL-100 (Fe)-NH4 F can be recycled several times and has an excellent reaction scope, which gives better catalytic results than other solid acid or base catalysts.
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Affiliation(s)
- Anastasia Rapeyko
- Instituto de Tecnología Química (UPV-CSIC), Universitat Politécnica de València, Avda dels Tarongers s/n, 46022, Valencia, Spain
| | - Maria J Climent
- Instituto de Tecnología Química (UPV-CSIC), Universitat Politécnica de València, Avda dels Tarongers s/n, 46022, Valencia, Spain
| | - Avelino Corma
- Instituto de Tecnología Química (UPV-CSIC), Universitat Politécnica de València, Avda dels Tarongers s/n, 46022, Valencia, Spain.
- King Fahd University of Petroleum and Minerals, P.O. Box 989, Dhahran, 31261, Saudi Arabia.
| | - Patricia Concepción
- Instituto de Tecnología Química (UPV-CSIC), Universitat Politécnica de València, Avda dels Tarongers s/n, 46022, Valencia, Spain
| | - Sara Iborra
- Instituto de Tecnología Química (UPV-CSIC), Universitat Politécnica de València, Avda dels Tarongers s/n, 46022, Valencia, Spain.
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14
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KUMARI PRATIBHA, NAGPAL RITIKA, CHAUHAN PRASHANT, YATINDRANATH VINITH, CHAUHAN SHIVEMS. Efficient iron(III) porphyrins-catalyzed oxidation of guanidoximes to cyanamides in ionic liquids. J CHEM SCI 2015. [DOI: 10.1007/s12039-014-0751-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Irmisch S, Clavijo McCormick A, Günther J, Schmidt A, Boeckler GA, Gershenzon J, Unsicker SB, Köllner TG. Herbivore-induced poplar cytochrome P450 enzymes of the CYP71 family convert aldoximes to nitriles which repel a generalist caterpillar. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:1095-107. [PMID: 25335755 DOI: 10.1111/tpj.12711] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/16/2014] [Accepted: 10/20/2014] [Indexed: 05/05/2023]
Abstract
Numerous plant species emit volatile nitriles upon herbivory, but the biosynthesis as well as the relevance of these nitrogenous compounds in plant-insect interactions remains unknown. Populus trichocarpa has been shown to produce a complex blend of nitrogenous volatiles, including aldoximes and nitriles, after herbivore attack. The aldoximes were previously reported to be derived from amino acids by the action of cytochrome P450 enzymes of the CYP79 family. Here we show that nitriles are derived from aldoximes by another type of P450 enzyme in P. trichocarpa. First, feeding of deuterium-labeled phenylacetaldoxime to poplar leaves resulted in incorporation of the label into benzyl cyanide, demonstrating that poplar volatile nitriles are derived from aldoximes. Then two P450 enzymes, CYP71B40v3 and CYP71B41v2, were characterized that produce aliphatic and aromatic nitriles from their respective aldoxime precursors. Both possess typical P450 sequence motifs but do not require added NADPH or cytochrome P450 reductase for catalysis. Since both enzymes are expressed after feeding by gypsy moth caterpillars, they are likely to be involved in herbivore-induced volatile nitrile emission in P. trichocarpa. Olfactometer experiments showed that these volatile nitriles have a strong repellent activity against gypsy moth caterpillars, suggesting they play a role in induced direct defense against poplar herbivores.
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Affiliation(s)
- Sandra Irmisch
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany
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16
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Yu L, Li H, Zhang X, Ye J, Liu J, Xu Q, Lautens M. Organoselenium-Catalyzed Mild Dehydration of Aldoximes: An Unexpected Practical Method for Organonitrile Synthesis. Org Lett 2014; 16:1346-9. [DOI: 10.1021/ol500075h] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Lei Yu
- Zhejiang
Key Laboratory of Carbon Materials, College of Chemistry and Materials
Engineering, Wenzhou University, Wenzhou, Zhejiang 325035, China
- School
of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, China
- Davenport
Chemistry Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Hongyan Li
- School
of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, China
| | - Xu Zhang
- Zhejiang
Key Laboratory of Carbon Materials, College of Chemistry and Materials
Engineering, Wenzhou University, Wenzhou, Zhejiang 325035, China
- School
of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, China
| | - Jianqing Ye
- School
of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, China
| | - Jianping Liu
- Zhejiang
Key Laboratory of Carbon Materials, College of Chemistry and Materials
Engineering, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Qing Xu
- Zhejiang
Key Laboratory of Carbon Materials, College of Chemistry and Materials
Engineering, Wenzhou University, Wenzhou, Zhejiang 325035, China
- School
of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, China
| | - Mark Lautens
- Davenport
Chemistry Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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Yadav AK, Srivastava VP, Yadav LDS. Visible-light-mediated efficient conversion of aldoximes and primary amides into nitriles. RSC Adv 2014. [DOI: 10.1039/c3ra46553e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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18
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Huang JS, Wong KM, Chan SLF, Tso KCH, Jiang T, Che CM. Ketimido Metallophthalocyanines: An Approach to Phthalocyanine-Supported Mononuclear High-Valent Ruthenium Complexes. Chem Asian J 2013; 9:338-50. [DOI: 10.1002/asia.201301109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 09/16/2013] [Indexed: 11/05/2022]
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19
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Conversion of aldoximes into nitriles catalyzed by simple transition metal salt of the fourth period in acetonitrile. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.01.059] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Rai A, Yadav LDS. Cyclopropenone-Catalyzed Direct Conversion of Aldoximes and Primary Amides into Nitriles. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300059] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Crystal structure of two anti-porphyrin antibodies with peroxidase activity. PLoS One 2012; 7:e51128. [PMID: 23240001 PMCID: PMC3519839 DOI: 10.1371/journal.pone.0051128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/30/2012] [Indexed: 01/07/2023] Open
Abstract
We report the crystal structures at 2.05 and 2.45 Å resolution of two antibodies, 13G10 and 14H7, directed against an iron(III)-αααβ-carboxyphenylporphyrin, which display some peroxidase activity. Although these two antibodies differ by only one amino acid in their variable λ-light chain and display 86% sequence identity in their variable heavy chain, their complementary determining regions (CDR) CDRH1 and CDRH3 adopt very different conformations. The presence of Met or Leu residues at positions preceding residue H101 in CDRH3 in 13G10 and 14H7, respectively, yields to shallow combining sites pockets with different shapes that are mainly hydrophobic. The hapten and other carboxyphenyl-derivatized iron(III)-porphyrins have been modeled in the active sites of both antibodies using protein ligand docking with the program GOLD. The hapten is maintained in the antibody pockets of 13G10 and 14H7 by a strong network of hydrogen bonds with two or three carboxylates of the carboxyphenyl substituents of the porphyrin, respectively, as well as numerous stacking and van der Waals interactions with the very hydrophobic CDRH3. However, no amino acid residue was found to chelate the iron. Modeling also allows us to rationalize the recognition of alternative porphyrinic cofactors by the 13G10 and 14H7 antibodies and the effect of imidazole binding on the peroxidase activity of the 13G10/porphyrin complexes.
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22
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Structures and mechanisms of the dehydration of benzaldoxime over Fe-ZSM-5 zeolites: a DFT study. Struct Chem 2012. [DOI: 10.1007/s11224-012-0161-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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García-Álvarez R, Díaz-Álvarez AE, Borge J, Crochet P, Cadierno V. Ruthenium-Catalyzed Rearrangement of Aldoximes to Primary Amides in Water. Organometallics 2012. [DOI: 10.1021/om3006917] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rocío García-Álvarez
- Laboratorio de Compuestos Organometálicos
y Catálisis (Unidad Asociada al CSIC), Departamento de Química
Orgánica e Inorgánica, Instituto Universitario de Química
Organometálica “Enrique Moles”, Facultad de Química, Universidad de Oviedo, Julián Clavería
8, E-33006 Oviedo, Spain
| | - Alba E. Díaz-Álvarez
- Laboratorio de Compuestos Organometálicos
y Catálisis (Unidad Asociada al CSIC), Departamento de Química
Orgánica e Inorgánica, Instituto Universitario de Química
Organometálica “Enrique Moles”, Facultad de Química, Universidad de Oviedo, Julián Clavería
8, E-33006 Oviedo, Spain
| | - Javier Borge
- Departamento de Química
Física y Analítica, Facultad de Química, Universidad de Oviedo, Julián Clavería
8, E-33006 Oviedo, Spain
| | - Pascale Crochet
- Laboratorio de Compuestos Organometálicos
y Catálisis (Unidad Asociada al CSIC), Departamento de Química
Orgánica e Inorgánica, Instituto Universitario de Química
Organometálica “Enrique Moles”, Facultad de Química, Universidad de Oviedo, Julián Clavería
8, E-33006 Oviedo, Spain
| | - Victorio Cadierno
- Laboratorio de Compuestos Organometálicos
y Catálisis (Unidad Asociada al CSIC), Departamento de Química
Orgánica e Inorgánica, Instituto Universitario de Química
Organometálica “Enrique Moles”, Facultad de Química, Universidad de Oviedo, Julián Clavería
8, E-33006 Oviedo, Spain
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Liao RZ, Thiel W. Why Is the Oxidation State of Iron Crucial for the Activity of Heme-Dependent Aldoxime Dehydratase? A QM/MM Study. J Phys Chem B 2012; 116:9396-408. [DOI: 10.1021/jp305510c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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Pan XL, Cui FC, Liu W, Liu JY. QM/MM Study on the Catalytic Mechanism of Heme-Containing Aliphatic Aldoxime Dehydratase. J Phys Chem B 2012; 116:5689-93. [DOI: 10.1021/jp302114d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiao-Liang Pan
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Feng-Chao Cui
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Wei Liu
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Jing-Yao Liu
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
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26
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Denton RM, An J, Lindovska P, Lewis W. Phosphonium salt-catalysed synthesis of nitriles from in situ activated oximes. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.01.067] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Davoodnia A, Khojastehnezhad A, Bakavoli M, Tavakoli-Hoseini N. SO3H-Functionalized Ionic Liquids:Green, Efficient and Reusable Catalysts for the Facile Dehydration of Aldoximes into Nitriles. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201190199] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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28
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Rad MNS, Khalafi-Nezhad A, Behrouz S, Amini Z, Behrouz M. Simple and Highly Efficient Procedure for Conversion of Aldoximes to Nitriles UsingN-(p-Toluenesulfonyl) Imidazole. SYNTHETIC COMMUN 2010. [DOI: 10.1080/00397910903261395] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Yadav LDS, Srivastava VP, Patel R. Bromodimethylsulfonium bromide (BDMS): a useful reagent for conversion of aldoximes and primary amides to nitriles. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.07.100] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Balcells D, Raynaud C, Crabtree RH, Eisenstein O. A rational basis for the axial ligand effect in C-H oxidation by [MnO(porphyrin)(X)]+ (X = H2O, OH-, O2-) from a DFT study. Inorg Chem 2008; 47:10090-9. [PMID: 18788735 DOI: 10.1021/ic8013706] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Oxyl radical character in the MnO group of the title system is shown from a density functional theory study to be essential for efficient C-H cleavage, which is a key step in C-H oxidation. Since oxyl species have elongated Mn-O bonds relative to the more usual oxo species of type MnO, the normal expectation would be that high trans-influence ligands X should facilitate oxyl character by elongating the Mn-O bond and thus enhance both oxyl character and reactivity. Contrary to this expectation, but in line with the experimental data (Jin, N.; Ibrahim, M.; Spiro, T. G.; Groves, J. T. J. Am. Chem. Soc. 2007, 129, 12416), we find that reactivity increases along the series X = O(2-) < OH(-) < H2O for the following reasons. The ground-state singlet (S) is unreactive for all X, and only the higher-energy triplet (T) and quintet (Q) states have the oxyl character needed for reactivity, but the higher trans-influence X ligands are also shown to increase the S/T and S/Q gaps, thus making attainment of the needed T and Q states harder. The latter effect is dominant, and high trans-influence X ligands thus disfavor reaction. The higher reactivity in the presence of acid noted by Groves and co-workers is thus rationalized by the preference for having X = H2O over OH(-) or O(2-).
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Affiliation(s)
- David Balcells
- Institut Charles Gerhardt Montpellier, UMR 5253 CNRS-UM2-ENSCM-UM1, Universite Montpellier 2, cc-1501 Place Eugene Bataillon, 34095, Montpellier, France
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33
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Marques HM. Insights into porphyrin chemistry provided by the microperoxidases, the haempeptides derived from cytochrome c. Dalton Trans 2007:4371-85. [PMID: 17909648 DOI: 10.1039/b710940g] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The water-soluble haem-containing peptides obtained by proteolytic digestion of cytochrome c, the microperoxidases, have been used to explore aspects of the chemistry of iron porphyrins, and as mimics for some reactions catalysed by the haemoproteins, including the reactions catalysed by the peroxidases and the cytochromes P450. The preparation of the microperoxidases, their physical and chemical properties including their electronic structure, the kinetics and thermodynamics of their reactions with ligands, electrochemical studies and examples of their uses as haemoproteins mimics, is reviewed.
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Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
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34
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Mansuy D. A brief history of the contribution of metalloporphyrin models to cytochrome P450 chemistry and oxidation catalysis. CR CHIM 2007. [DOI: 10.1016/j.crci.2006.11.001] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Furuya Y, Ishihara K, Yamamoto H. Perrhenic Acid-Catalyzed Dehydration from Primary Amides, Aldoximes,N-Monoacylureas, and α-Substituted Ketoximes to Nitrile Compounds. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.400] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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36
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Kobayashi K, Kubo M, Yoshioka S, Kitagawa T, Kato Y, Asano Y, Aono S. Systematic Regulation of the Enzymatic Activity of Phenylacetaldoxime Dehydratase by Exogenous Ligands. Chembiochem 2006; 7:2004-9. [PMID: 17009275 DOI: 10.1002/cbic.200600261] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Phenylacetaldoxime dehydratase from Bacillus sp. OxB-1 (OxdB) contains a heme that acts as the active site for the dehydration reaction of aldoxime. Ferrous heme is the active form, in which the heme is five coordinate with His282 as a proximal ligand. In this work, we evaluated the functional role of the proximal ligand for the catalytic properties of the enzyme by "the cavity mutant technique". The H282G mutant of OxdB lost enzymatic activity, although the heme, which was five coordinate with a water molecule (or OH-) as an axial ligand, existed in the protein matrix. The enzymatic activity was rescued by imidazole or pyridine derivatives that acted as the exogenous proximal ligand. By changing the electron-donation ability of the exogenous ligand with different substituents, the enzymatic activity could be regulated systematically. The stronger the electron-donation ability of the exogenous ligand, the higher was the restored enzymatic activity. Interestingly, H282G OxdB with 2-methyl imidazole showed a higher activity than the wild-type enzyme. Kinetic analyses revealed that the proximal His regulated not only the affinity of substrate binding to the heme but also the elimination of the OH group from the substrate.
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Affiliation(s)
- Katsuaki Kobayashi
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
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Lee K, Han S, Yoo E, Chung S, Oh H, Hong S. Efficient Transformation of Aldoximes to Nitriles Using 2‐Chloro‐1‐methylpyridinium Iodide Under Mild Conditions. SYNTHETIC COMMUN 2006. [DOI: 10.1081/scc-120034158] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kieseung Lee
- a Department of Chemistry , Woosuk University , Chonbuk, 565‐701, South Korea
| | - Sang‐Bae Han
- a Department of Chemistry , Woosuk University , Chonbuk, 565‐701, South Korea
| | - Eun‐Mi Yoo
- a Department of Chemistry , Woosuk University , Chonbuk, 565‐701, South Korea
| | - Soon‐Ryang Chung
- a Department of Chemistry , Woosuk University , Chonbuk, 565‐701, South Korea
| | - Haibum Oh
- a Department of Chemistry , Woosuk University , Chonbuk, 565‐701, South Korea
| | - Sungwan Hong
- a Department of Chemistry , Woosuk University , Chonbuk, 565‐701, South Korea
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38
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New approach to the activation of anti-cancer pro-drugs by metalloporphyrin-based cytochrome P450 mimics in all-aqueous biologically relevant system. J Inorg Biochem 2006; 100:1897-902. [PMID: 16965820 DOI: 10.1016/j.jinorgbio.2006.07.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 07/26/2006] [Accepted: 07/27/2006] [Indexed: 11/23/2022]
Abstract
The low-molecular weight water-soluble Fe(III) and Mn(III) porphyrins--in biologically relevant phosphate-buffered saline medium with ascorbic acid as a source of electrons, under aerobic conditions but without co-oxidant - catalyze the hydroxylation of anti-cancer drug cyclophosphamide to active metabolite 4-hydroxycyclophosphamide in yields similar or higher than those typically obtained by the action of liver enzymes in vivo. The Fe(III) meso tetrakis(2,6-difluoro-3-sulfonatophenyl)porphyrin, highly electron-deficient at the metal site, was the most effective catalyst. If proven viable in vivo, this methodology could be expanded to localized or systemic activation of the entire family of oxazaphosphorine-based (and many other) anti-cancer drugs and become a powerful tool for an aggressive treatment of tumors with less toxic side effects to the patient.
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39
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Lu QZ, Lu Y, Wang JJ. DFT Study of Iron Tetraphenylporphyrin Chloride and Iron Pentafluorophenylporphyrin Chloride. CHINESE J CHEM PHYS 2006. [DOI: 10.1360/cjcp2006.19(3).227.6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Konishi K, Ohta T, Oinuma KI, Hashimoto Y, Kitagawa T, Kobayashi M. Discovery of a reaction intermediate of aliphatic aldoxime dehydratase involving heme as an active center. Proc Natl Acad Sci U S A 2006; 103:564-8. [PMID: 16407114 PMCID: PMC1334632 DOI: 10.1073/pnas.0505412103] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently, we discovered an intriguing hemoprotein [aliphatic aldoxime dehydratase (OxdA)] that catalyzes the dehydration of aliphatic aldoximes [R-CH=N-OH] to the corresponding nitriles [R-C identical withN] in the industrial Pseudomonas chlororaphis B23 strain. Unlike the utilization of H(2)O(2) or O(2) as a mediator of the catalysis by other heme-containing enzymes (e.g., P450), OxdA is notable for the direct binding of a substrate to the heme iron, experimental evidence of which was obtained here by means of resonance Raman (RR) analysis with an isotope technique. We found that the addition of a large amount of butyraldoxime (final concentration, 200 mM) to ferrous OxdA with a low enzyme concentration (final concentration, 5 muM) yields a long-lived OxdA-substrate complex (named OS-II), whose UV-vis spectrum is different from the corresponding spectra of the OxdA-substrate complex I and CO-bound, ferrous, and ferric forms of OxdA. Intriguingly, the RR analysis demonstrated that OS-II includes a highly oxidized heme with strong bonding between a substrate and the heme iron, as judged from the heme oxidation state marker nu(4) band at 1,379 cm(-1) and the (15)N-isotope-substituted butyraldoxime sensitive band at 857 cm(-1) in the RR spectra. It is noteworthy that OS-II has a highly oxidized heme like the ferryl-oxo heme species (e.g., compound II) formed by some general hemoproteins, although the function of OxdA is different from those (transport of electrons, transport of oxygen, sensing of oxygen or carbon monoxide, and catalysis of redox reactions) of general hemoproteins.
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Affiliation(s)
- Kazunobu Konishi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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41
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Bikiel DE, Boechi L, Capece L, Crespo A, De Biase PM, Di Lella S, González Lebrero MC, Martí MA, Nadra AD, Perissinotti LL, Scherlis DA, Estrin DA. Modeling heme proteins using atomistic simulations. Phys Chem Chem Phys 2006; 8:5611-28. [PMID: 17149482 DOI: 10.1039/b611741b] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.
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Affiliation(s)
- Damián E Bikiel
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires, Argentina
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42
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Tu Z, Jang Y, Lin C, Liu JT, Hsu J, Sastry M, Yao CF. The study of reaction mechanism for the transformation of nitronate into nitrile by phosphorus trichloride. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.08.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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43
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Movassagh B, Shokri S. Potassium Fluoride Doped on Alumina: An Efficient Catalyst for Conversion of Aldoximes Into Nitriles. SYNTHETIC COMMUN 2005. [DOI: 10.1081/scc-200051052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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44
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Oinuma KI, Kumita H, Ohta T, Konishi K, Hashimoto Y, Higashibata H, Kitagawa T, Shiro Y, Kobayashi M. Stopped-flow spectrophotometric and resonance Raman analyses of aldoxime dehydratase involved in carbon-nitrogen triple bond synthesis. FEBS Lett 2005; 579:1394-8. [PMID: 15733847 DOI: 10.1016/j.febslet.2005.01.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Revised: 12/28/2004] [Accepted: 01/17/2005] [Indexed: 10/25/2022]
Abstract
On stopped-flow analysis of aliphatic aldoxime dehydratase (OxdA), a novel hemoprotein, a spectrum derived from a reaction intermediate was detected on mixing ferrous OxdA with butyraldoxime; it gradually changed into that of ferrous OxdA with an isosbestic point at 421 nm. The spectral change on the addition of butyraldoxime to the ferrous H320A mutant showed the formation of a substrate-coordinated mutant, the absorption spectrum of which closely resembled that of the above intermediate. These observations and the resonance Raman investigation revealed that the substrate actually binds to the heme in OxdA, forming a hexa-coordinate low-spin heme.
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Affiliation(s)
- Ken-Ichi Oinuma
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Konishi K, Ishida K, Oinuma KI, Ohta T, Hashimoto Y, Higashibata H, Kitagawa T, Kobayashi M. Identification of Crucial Histidines Involved in Carbon-Nitrogen Triple Bond Synthesis by Aldoxime Dehydratase. J Biol Chem 2004; 279:47619-25. [PMID: 15339918 DOI: 10.1074/jbc.m407223200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aldoxime dehydratase (OxdA), which is a novel heme protein, catalyzes the dehydration of an aldoxime to a nitrile even in the presence of water in the reaction mixture. The combination of site-directed mutagenesis of OxdA (mutation of all conserved histidines in the aldoxime dehydratase superfamily), estimation of the heme contents and specific activities of the mutants, and CD and resonance Raman spectroscopic analyses led to the identification of the proximal and distal histidines in this unique enzyme. The heme contents and CD spectra in the far-UV region of all mutants except for the H299A one were almost identical to those of the wild-type OxdA, whereas the H299A mutant lost the ability of binding heme, demonstrating that His(299) is the proximal histidine. On the other hand, substitution of alanine for His(320) did not affect the overall structure of OxdA but caused loss of its ability of carbon-nitrogen triple bond synthesis and a lower shift of the Fe-C stretching band in the resonance Raman spectrum for the CO-bound form. Furthermore, the pH dependence of the wild-type OxdA closely followed the His protonation curves observed for other proteins. These findings suggest that His(320) is located in the distal heme pocket of OxdA and would donate a proton to the substrate in the aldoxime dehydration mechanism.
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Affiliation(s)
- Kazunobu Konishi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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46
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Makarycheva-Mikhailova AV, Bokach NA, Haukka M, Kukushkin VY. The first example of ligand-mediated dehydration of aldoximes. Inorganica Chim Acta 2003. [DOI: 10.1016/s0020-1693(03)00275-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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47
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Verkade JG, Kisanga PB. Proazaphosphatranes: a synthesis methodology trip from their discovery to vitamin A. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)01204-3] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lefèvre-Groboillot D, Frapart Y, Desbois A, Zimmermann JL, Boucher JL, Gorren ACF, Mayer B, Stuehr DJ, Mansuy D. Two modes of binding of N-hydroxyguanidines to NO synthases: first evidence for the formation of iron-N-hydroxyguanidine complexes and key role of tetrahydrobiopterin in determining the binding mode. Biochemistry 2003; 42:3858-67. [PMID: 12667076 DOI: 10.1021/bi0272407] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction of various N-alkyl- and N-aryl-N'-hydroxyguanidines with recombinant NOS containing or not containing tetrahydrobiopterin (BH(4)) was studied by visible, electronic paramagnetic resonance (EPR), and resonance Raman (RR) spectroscopy. N-Hydroxyguanidines interact with the oxygenase domain of BH(4)-free inducible NOS (BH(4)-free iNOS(oxy)), depending on the nature of their substituent, with formation of two types of complexes that are characterized by peaks around 395 (type I) and 438 nm (type II') during difference visible spectroscopy. The complex formed between BH(4)-free iNOS(oxy) and N-benzyl-N'-hydroxyguanidine 1 (type II') exhibited a Soret peak at 430 nm, EPR signals at g = 1.93, 2.24, and 2.38, and RR bands at 1374 and 1502 cm(-)(1) that are characteristic of a low-spin hexacoordinated Fe(III) complex. Analysis of its EPR spectrum according to Taylor's equations indicates that the cysteinate ligand of native BH(4)-free iNOS(oxy) is retained in that complex. Similar iron(III)-ligand complexes were formed upon reaction of 1 and several other N-hydroxyguanidines with BH(4)-free full-length iNOS and BH(4)-free nNOS(oxy). However, none of the tested N-hydroxyguanidines were able to form such iron(III)-ligand complexes with BH(4)-containing iNOS(oxy), indicating that a major factor involved in the mode of binding of N-hydroxyguanidines to NOS is the presence (or absence) of BH(4) in their active site. Another factor that plays a key role in the mode of binding of N-hydroxyguanidines to NOS is the nature of their substituent. The N-hydroxyguanidines bearing an N-alkyl substituent exclusively or mainly led to type II' iron-ligand complexes. Those bearing an N-aryl substituent mainly led to type II' complexes, even though some of them exclusively led to type I complexes. Interestingly, the K(s) values calculated for BH(4)-free iNOS(oxy)-N-hydroxyguanidine complexes were always lower when their substituents bore an aryl group (140-420 microM instead of 1000-3900 microM), suggesting the existence of pi-pi interactions between this group and an aromatic residue of the protein. Comparison of the spectral and physicochemical properties of the N-hydroxyguanidine complexes of BH(4)-free iNOS(oxy) (type II') with those of the previously described corresponding complexes of microperoxidase (MP-8) suggests that, in both cases, N-hydroxyguanidines bind to iron(III) via their oxygen atom after deprotonation or weakening of the O-H bond. The aforementioned results are discussed in relation with recent data about the transient formation of iron-product intermediates during the catalytic cycle of l-arginine oxidation by eNOS. They suggest that N-hydroxyguanidines could constitute a new class of good ligands of heme proteins.
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Affiliation(s)
- David Lefèvre-Groboillot
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris 5, France
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Lefevre-Groboillot D, Dijols S, Boucher JL, Mahy JP, Ricoux R, Desbois A, Zimmermann JL, Mansuy D. N-hydroxyguanidines as new heme ligands: UV-visible, EPR, and resonance Raman studies of the interaction of various compounds bearing a C=NOH function with microperoxidase-8. Biochemistry 2001; 40:9909-17. [PMID: 11502185 DOI: 10.1021/bi010561i] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interaction between microperoxidase-8 (MP8), a water-soluble hemeprotein model, and a wide range of N-aryl and N-alkyl N'-hydroxyguanidines and related compounds has been investigated using UV-visible, EPR, and resonance Raman spectroscopies. All the N-hydroxyguanidines studied bind to the ferric form of MP8 with formation of stable low-spin iron(III) complexes characterized by absorption maxima at 405, 535, and 560 nm. The complex obtained with N-(4-methoxyphenyl) N'-hydroxyguanidine exhibits EPR g-values at 2.55, 2.26, and 1.86. The resonance Raman (RR) spectrum of this complex is also in agreement with an hexacoordinated low-spin iron(III) structure. The dissociation constants (K(s)) of the MP8 complexes with mono- and disubstituted N-hydroxyguanidines vary between 15 and 160 microM at pH 7.4. Amidoximes also form low-spin iron(III) complexes of MP8, although with much larger dissociation constants. Under the same conditions, ketoximes, aldoximes, methoxyguanidines, and guanidines completely fail to form such complexes with MP8. The K(s) values of the MP8-N-hydroxyguanidine complexes decrease as the pH of the solution is increased, and the affinity of the N-hydroxyguanidines toward MP8 increases with the pK(a) of these ligands. Altogether these results show that compounds involving a -C(NHR)=NOH moiety act as good ligands of MP8-Fe(III) with an affinity that depends on the electron-richness of this moiety. The analysis of the EPR spectrum of the MP8-N-hydroxyguanidine complexes according to Taylor's equations shows a strong axial distortion of the iron, typical of those observed for hexacoordinated heme-Fe(III) complexes with at least one pi donor axial ligand (HO(-), RO(-), or RS(-)). These data strongly suggest that N-hydroxyguanidines bind to MP8 iron via their oxygen atom after deprotonation or weakening of their O-H bond. It thus seems that N-hydroxyguanidines could constitute a new class of strong ligands for hemeproteins and iron(III)-porphyrins.
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Affiliation(s)
- D Lefevre-Groboillot
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris V, 45 rue des Saints Pères, 75270 Paris Cedex 06, France
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Guengerich FP. Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity. Chem Res Toxicol 2001; 14:611-50. [PMID: 11409933 DOI: 10.1021/tx0002583] [Citation(s) in RCA: 1120] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome P450 (P450) enzymes catalyze a variety of reactions and convert chemicals to potentially reactive products as well as make compounds less toxic. Most of the P450 reactions are oxidations. The majority of these can be rationalized in the context of an FeO(3+) intermediate and odd electron abstraction/rebound mechanisms; however, other iron-oxygen complexes are possible and alternate chemistries can be considered. Another issue regarding P450-catalyzed reactions is the delineation of rate-limiting steps in the catalytic cycle and the contribution to reaction selectivity. In addition to the rather classical oxidations, P450s also catalyze less generally discussed reactions including reduction, desaturation, ester cleavage, ring expansion, ring formation, aldehyde scission, dehydration, ipso attack, one-electron oxidation, coupling reactions, rearrangement of fatty acid and prostaglandin hydroperoxides, and phospholipase activity. Most of these reactions are rationalized in the context of high-valent iron-oxygen intermediates and Fe(2+) reductions, but others are not and may involve acid-base catalysis. Some of these transformations are involved in the bioactivation and detoxication of xenobiotic chemicals.
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Affiliation(s)
- F P Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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