1
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Čivić J, McFarlane NR, Masschelein J, Harvey JN. Exploring the selectivity of cytochrome P450 for enhanced novel anticancer agent synthesis. Faraday Discuss 2024. [PMID: 38855920 DOI: 10.1039/d4fd00004h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Cytochrome P450 monooxygenases are an extensive and unique class of enzymes, which can regio- and stereo-selectively functionalise hydrocarbons by way of oxidation reactions. These enzymes are naturally occurring but have also been extensively applied in a synthesis context, where they are used as efficient biocatalysts. Recently, a biosynthetic pathway where a cytochrome P450 monooxygenase catalyses a critical step of the pathway was uncovered, leading to the production of a number of products that display high antitumour potency. In this work, we use computational techniques to gain insight into the factors that determine the relative yields of the different products. We use conformational search algorithms to understand the substrate stereochemistry. On a machine-learned 3D protein structure, we use molecular docking to obtain a library of favourable poses for substrate-protein interaction. With molecular dynamics, we investigate the most favourable poses for reactivity on a molecular level, allowing us to investigate which protein-substrate interactions favour a given product and thus gain insight into the product selectivity.
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Affiliation(s)
- Janko Čivić
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| | - Neil R McFarlane
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| | - Joleen Masschelein
- Department of Biology, Vlaams Instituut voor Biotechnologie VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
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2
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Ueda K, Sato W, Yanagisawa S, Kubo M, Hada M, Fujii H. Resonance Raman study of oxoiron(IV) porphyrin π-cation radical complex: Porphyrin ligand effect on ν(Fe=O) frequency. J Inorg Biochem 2024; 255:112544. [PMID: 38574491 DOI: 10.1016/j.jinorgbio.2024.112544] [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: 01/22/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024]
Abstract
Resonance Raman (rR) spectroscopy has been applied to study the nature of the iron-oxo (Fe=O) moiety of oxoiron(IV) porphyrin π-cation radical complex (CompI). While the axial ligand effect on the nature of the Fe=O moiety has been studied with rR spectroscopy, the porphyrin ligand effect has not been studied well. Here, we investigated the porphyrin ligand effect on the Fe=O moiety with rR spectroscopy. The porphyrin ligand effect was modulated by the electron-withdrawing effect of the porphyrin substituent at the meso-position. This study shows that the frequency of the Fe=O stretching band, ν(Fe=O), hardly change even when the electron-withdrawing effect of the porphyrin substituent changes. This result is further supported by theoretical calculation of CompI. The natural atomic charge analysis reveals that the oxo and axial ligands work to buffer the electron-withdrawing effect of the porphyrin substituent. The electron-withdrawing porphyrin substituent shifts an electron population from the ferryl iron to the porphyrin, but the decreased electron population on the ferryl iron is compensated by the shift of the electron population from the oxo ligand and the axial ligand. The shift of the electron population makes the Fe-axial ligand bond length short, but the Fe=O bond length unchanged, resulting in the invariable ν(Fe=O) frequency.
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Affiliation(s)
- Kaho Ueda
- Department of Chemistry, Biology, and Environmental Science, Graduate School of Humanities and Sciences, Nara Women's University, Nara 630-8506, Japan
| | - Wataru Sato
- Graduate School of Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Sachiko Yanagisawa
- Graduate School of Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Minoru Kubo
- Graduate School of Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Masahiko Hada
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Hiroshi Fujii
- Department of Chemistry, Biology, and Environmental Science, Graduate School of Humanities and Sciences, Nara Women's University, Nara 630-8506, Japan.
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3
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Suzuki K, Stanfield JK, Omura K, Shisaka Y, Ariyasu S, Kasai C, Aiba Y, Sugimoto H, Shoji O. A Compound I Mimic Reveals the Transient Active Species of a Cytochrome P450 Enzyme: Insight into the Stereoselectivity of P450-Catalysed Oxidations. Angew Chem Int Ed Engl 2023; 62:e202215706. [PMID: 36519803 DOI: 10.1002/anie.202215706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Catching the structure of cytochrome P450 enzymes in flagrante is crucial for the development of P450 biocatalysts, as most structures collected are found trapped in a precatalytic conformation. At the heart of P450 catalysis lies Cpd I, a short-lived, highly reactive intermediate, whose recalcitrant nature has thwarted most attempts at capturing catalytically relevant poses of P450s. We report the crystal structure of P450BM3 mimicking the state in the precise moment preceding epoxidation, which is in perfect agreement with the experimentally observed stereoselectivity. This structure was attained by incorporation of the stable Cpd I mimic oxomolybdenum mesoporphyrin IX into P450BM3 in the presence of styrene. The orientation of styrene to the Mo-oxo species in the crystal structures sheds light onto the dynamics involved in the rotation of styrene to present its vinyl group to Cpd I. This method serves as a powerful tool for predicting and modelling the stereoselectivity of P450 reactions.
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Affiliation(s)
- Kazuto Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Keita Omura
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yuma Shisaka
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.,RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinya Ariyasu
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Chie Kasai
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Hiroshi Sugimoto
- RIKEN SPring-8 Centre, 1-1-1, Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 5, Sanbancho, Chiyoda-ku, Tokyo, 102-0075, Japan
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4
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Yan Y, Zheng C, Song W, Wu J, Guo L, Gao C, Liu J, Chen X, Zhu M, Liu L. Efficient Production of Epoxy-Norbornane from Norbornene by an Engineered P450 Peroxygenase. Chembiochem 2023; 24:e202200529. [PMID: 36354378 DOI: 10.1002/cbic.202200529] [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: 09/12/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022]
Abstract
Epoxy-norbornane (EPO-NBE) is a crucial building block for the synthesis of various biologically active heterocyclic systems. To develop an efficient protocol for producing EPO-NBE using norbornene (NBE) as a substrate, cytochrome P450 enzyme from Pseudomonas putida (CYP238A1) was examined and its crystal structure (PDB code: 7X53) was resolved. Molecular mechanism analysis showed a high energy barrier related to iron-alkoxy radical complex formation. Therefore, a protein engineering strategy was developed and an optimal CYP238A1NPV variant containing a local hydrophobic "fence" at the active site was obtained, which increased the H2 O2 -dependent epoxidation activity by 7.5-fold compared with that of CYP238A1WT . Among the "fence", Glu255 participates in an efficient proton transfer system. Whole-cell transformation using CYP238A1NPV achieved an EPO-NBE yield of 77.6 g ⋅ L-1 in a 30-L reactor with 66.3 % conversion. These results demonstrate the potential of this system for industrial production of EPO-NBE and provides a new biocatalytic platform for epoxidation chemistry.
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Affiliation(s)
- Yu Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Chenni Zheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, P. R. China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, P. R. China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Meng Zhu
- Wuxi Acryl Technology Co., Ltd., Wuxi, 214122, P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China
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5
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Zhang C, Gilardi G, Di Nardo G. Depicting the proton relay network in human aromatase: New insights into the role of the alcohol‐acid pair. Protein Sci 2022; 31:e4389. [PMID: 36040260 PMCID: PMC9366932 DOI: 10.1002/pro.4389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022]
Abstract
Human aromatase is the cytochrome P450 catalyzing the conversion of androgens into estrogens in a three steps reaction essential to maintain steroid hormones balance. Here we report the capture and spectroscopic characterization of its compound I (Cpd I), the main reactive species in cytochromes P450. The typical spectroscopic transitions indicating the formation of Cpd I are detected within 0.8 s when mixing aromatase with meta‐chloroperoxybenzoic acid. The estrogen product is obtained from the same reaction mixture, demonstrating the involvement of Cpd I in aromatization reaction. Site‐directed mutagenesis is applied to the acid‐alcohol pair D309 and T310 and to R192, predicted to be part of the proton relay network. Mutants D309N and R192Q do not lead to Cpd I with an associated loss of activity, confirming that these residues are involved in proton delivery for Cpd I generation. Cpd I is captured for T310A mutant and shows 2.9‐ and 4.4‐fold faster rates of formation and decay, respectively, compared to wild‐type (WT). However, its activity is lower than the WT and a larger amount of H2O2 is produced during catalysis, indicating that T310 has an essential role in proton gating for generation of Cpd 0 and Cpd I and for their stabilization. The data provide new evidences on the role of threonine belonging to the conserved “acid‐alcohol” pair and known to be crucial for oxygen activation in cytochromes P450.
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Affiliation(s)
- Chao Zhang
- Department of Life Sciences and Systems Biology University of Turin Turin 10123 Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology University of Turin Turin 10123 Italy
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology University of Turin Turin 10123 Italy
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6
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Nayek A, Ahmed ME, Samanta S, Dinda S, Patra S, Dey SG, Dey A. Bioinorganic Chemistry on Electrodes: Methods to Functional Modeling. J Am Chem Soc 2022; 144:8402-8429. [PMID: 35503922 DOI: 10.1021/jacs.2c01842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One of the major goals of bioinorganic chemistry has been to mimic the function of elegant metalloenzymes. Such functional modeling has been difficult to attain in solution, in particular, for reactions that require multiple protons and multiple electrons (nH+/ne-). Using a combination of heterogeneous electrochemistry, electrode and molecule design one may control both electron transfer (ET) and proton transfer (PT) of these nH+/ne- reactions. Such control can allow functional modeling of hydrogenases (H+ + e- → 1/2 H2), cytochrome c oxidase (O2 + 4 e- + 4 H+ → 2 H2O), monooxygenases (RR'CH2 + O2 + 2 e- + 2 H+ → RR'CHOH + H2O) and dioxygenases (S + O2 → SO2; S = organic substrate) in aqueous medium and at room temperatures. In addition, these heterogeneous constructs allow probing unnatural bioinspired reactions and estimation of the inner- and outer-sphere reorganization energy of small molecules and proteins.
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Affiliation(s)
- Abhijit Nayek
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Md Estak Ahmed
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Soumya Samanta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Souvik Dinda
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Suman Patra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
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7
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Munshi S, Sinha A, Yiga S, Banerjee S, Singh R, Hossain MK, Haukka M, Valiati AF, Huelsmann RD, Martendal E, Peralta R, Xavier F, Wendt OF, Paine TK, Nordlander E. Hydrogen-atom and oxygen-atom transfer reactivities of iron(IV)-oxo complexes of quinoline-substituted pentadentate ligands. Dalton Trans 2022; 51:870-884. [PMID: 34994361 DOI: 10.1039/d1dt03381f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A series of iron(II) complexes with the general formula [FeII(L2-Qn)(L)]n+ (n = 1, L = F-, Cl-; n = 2, L = NCMe, H2O) have been isolated and characterized. The X-ray crystallographic data reveals that metal-ligand bond distances vary with varying ligand field strengths of the sixth ligand. While the complexes with fluoride, chloride and water as axial ligand are high spin, the acetonitrile-coordinated complex is in a mixed spin state. The steric bulk of the quinoline moieties forces the axial ligands to deviate from the Fe-Naxial axis. A higher deviation/tilt is noted for the high spin complexes, while the acetonitrile coordinated complex displays least deviation. This deviation from linearity is slightly less in the analogous low-spin iron(II) complex [FeII(L1-Qn)(NCMe)]2+ of the related asymmetric ligand L1-Qn due to the presence of only one sterically demanding quinoline moiety. The two iron(II)-acetonitrile complexes [FeII(L2-Qn)(NCMe)]2+ and [FeII(L1-Qn)(NCMe)]2+ generate the corresponding iron(IV)-oxo species with higher thermal stability of the species supported by the L1-Qn ligand. The crystallographic and spectroscopic data for [FeIV(O)(L1-Qn)](ClO4)2 bear resemblance to other crystallographically characterized S = 1 iron(IV)-oxo complexes. The hydrogen atom transfer (HAT) and oxygen atom transfer (OAT) reactivities of both the iron(IV)-oxo complexes were investigated, and a Box-Behnken multivariate optimization of the parameters for catalytic oxidation of cyclohexane by [FeII(L2-Qn)(NCMe)]2+ using hydrogen peroxide as the terminal oxidant is presented. An increase in the average Fe-N bond length in [FeII(L1-Qn)(NCMe)]2+ is also manifested in higher HAT and OAT rates relative to the other reported complexes of ligands based on the N4Py framework. The results reported here confirm that the steric influence of the ligand environment is of critical importance for the reactivity of iron(IV)-oxo complexes, but additional electronic factors must influence the reactivity of iron-oxo complexes of N4Py derivatives.
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Affiliation(s)
- Sandip Munshi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, India.
| | - Arup Sinha
- Chemical Physics, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden. .,Department of Chemistry, School of Advanced Science, Vellore Institute of Technology, Vellore, India
| | - Solomon Yiga
- Center for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden. .,Department of Chemistry, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Sridhar Banerjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, India.
| | - Reena Singh
- Chemical Physics, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Md Kamal Hossain
- Chemical Physics, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Matti Haukka
- Department of Chemistry, University of Jyväskylä, Box 35, FI-400 14, Jyväskylä, Finland
| | - Andrei Felipe Valiati
- Department of Chemistry, LABINC, Universidade Federal de Santa Catarina (UFSC), 88040-900 Florianopolis, Santa Catarina, Brazil
| | - Ricardo Dagnoni Huelsmann
- Department of Chemistry, Center for Technological Sciences, Universidade do Estado de Santa Catarina (UDESC), 89219-710 Joinville, Santa Catarina, Brazil
| | - Edmar Martendal
- Department of Chemistry, Center for Technological Sciences, Universidade do Estado de Santa Catarina (UDESC), 89219-710 Joinville, Santa Catarina, Brazil
| | - Rosely Peralta
- Department of Chemistry, LABINC, Universidade Federal de Santa Catarina (UFSC), 88040-900 Florianopolis, Santa Catarina, Brazil
| | - Fernando Xavier
- Department of Chemistry, Center for Technological Sciences, Universidade do Estado de Santa Catarina (UDESC), 89219-710 Joinville, Santa Catarina, Brazil
| | - Ola F Wendt
- Center for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Tapan K Paine
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, India.
| | - Ebbe Nordlander
- Chemical Physics, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden.
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8
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Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
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9
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Shamovsky I, Ripa L, Narjes F, Bonn B, Schiesser S, Terstiege I, Tyrchan C. Mechanism-Based Insights into Removing the Mutagenicity of Aromatic Amines by Small Structural Alterations. J Med Chem 2021; 64:8545-8563. [PMID: 34110134 DOI: 10.1021/acs.jmedchem.1c00514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aromatic and heteroaromatic amines (ArNH2) are activated by cytochrome P450 monooxygenases, primarily CYP1A2, into reactive N-arylhydroxylamines that can lead to covalent adducts with DNA nucleobases. Hereby, we give hands-on mechanism-based guidelines to design mutagenicity-free ArNH2. The mechanism of N-hydroxylation of ArNH2 by CYP1A2 is investigated by density functional theory (DFT) calculations. Two putative pathways are considered, the radicaloid route that goes via the classical ferryl-oxo oxidant and an alternative anionic pathway through Fenton-like oxidation by ferriheme-bound H2O2. Results suggest that bioactivation of ArNH2 follows the anionic pathway. We demonstrate that H-bonding and/or geometric fit of ArNH2 to CYP1A2 as well as feasibility of both proton abstraction by the ferriheme-peroxo base and heterolytic cleavage of arylhydroxylamines render molecules mutagenic. Mutagenicity of ArNH2 can be removed by structural alterations that disrupt geometric and/or electrostatic fit to CYP1A2, decrease the acidity of the NH2 group, destabilize arylnitrenium ions, or disrupt their pre-covalent transition states with guanine.
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10
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Visible light generation of high-valent metal-oxo intermediates and mechanistic insights into catalytic oxidations. J Inorg Biochem 2020; 212:111246. [PMID: 33059321 DOI: 10.1016/j.jinorgbio.2020.111246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/07/2020] [Accepted: 08/22/2020] [Indexed: 11/21/2022]
Abstract
High-valent metal-oxo complexes play central roles as active oxygen atom transfer (OAT) agents in many enzymatic and synthetic oxidation catalysis. This review focuses on our recent advances in application of photochemical approaches to probe the oxidizing metal-oxo species with different metals and macrocyclic ligands. Under visible light irradiation, a variety of important metal-oxo species including iron-oxo porphyrins, manganese-oxo porphyrin/corroles, ruthenium-oxo porphyrins, and chromium-oxo salens have been successfully generated. Kinetical studies in real time have provided mechanistic insights as to the reactivity and reaction pathways of the metal-oxo intermediates in their oxidation reactions. In photo-induced ligand cleavage reactions, metals in n+ oxidation state with the oxygen-containing ligands bromate, chlorate, or nitrites were photolyzed. Homolytic cleavage of the O-X bond in the ligand gives (n + 1)+ oxidation state metal-oxo species, and heterolytic cleavage gives (n + 2)+ oxidation state metal-oxo species. In photo-disproportionation reactions, reactive Mn+1-oxo species can be formed by photolysis of μ-oxo dimeric Mn+ complexes with the concomitant formation of Mn-1 products. Importantly, the oxidation of Mn-1 products by molecular oxygen (O2) to regenerate the μ-oxo dimeric Mn+ complexes in photo-disproportionation reactions represents an attractive and green catalytic cycle for the development of photocatalytic aerobic oxidations.
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11
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Mukherjee S, Nayek A, Bhunia S, Dey SG, Dey A. A Single Iron Porphyrin Shows pH Dependent Switch between "Push" and "Pull" Effects in Electrochemical Oxygen Reduction. Inorg Chem 2020; 59:14564-14576. [PMID: 32970430 DOI: 10.1021/acs.inorgchem.0c02408] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The "push-pull" effects associated with heme enzymes manifest themselves through highly evolved distal amino acid environments and axial ligands to the heme. These conserved residues enhance their reactivities by orders of magnitude relative to small molecules that mimic the primary coordination. An instance of a mononuclear iron porphyrin with covalently attached pendent phenanthroline groups is reported which exhibit reactivity indicating a pH dependent "push" to "pull" transition in the same molecule. The pendant phenanthroline residues provide proton transfer pathways into the iron site, ensuring selective 4e-/4H+ reduction of O2 to water. The protonation of these residues at lower pH mimics the pull effect of peroxidases, and a coordination of an axial hydroxide ligand at high pH emulates the push effect of P450 monooxygenases. Both effects enhance the rate of O2 reduction by orders of magnitude over its value at neutral pH while maintaining exclusive selectivity for 4e-/4H+ oxygen reduction reaction.
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Affiliation(s)
- Sudipta Mukherjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Abhijit Nayek
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Sarmistha Bhunia
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
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12
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Callaghan S, Flanagan KJ, O'Brien JE, Senge MO. Short-Chained Anthracene Strapped Porphyrins and their Endoperoxides. European J Org Chem 2020; 2020:2735-2744. [PMID: 32612450 PMCID: PMC7319435 DOI: 10.1002/ejoc.202000283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Indexed: 01/04/2023]
Abstract
The syntheses of short-chained anthracene-strapped porphyrins and their Zn(II)complexes are reported. The key synthetic step is a [2+2] condensation between a dipyrromethane and an anthracene bisaldehyde, 2,2'-((anthracene-9,10-diylbis(methylene))bis(oxy))dibenzaldehyde. Following exposure to white light, self-sensitized singlet oxygen and the anthracene moieties underwent [4+2] cycloaddition reactions to yield the corresponding endoperoxides. 1H NMR studies demonstrate that the endoperoxide readily formed in [D]chloroform and decayed at 85 °C. X-ray crystallography and absorption spectroscopy were used to confirm macrocyclic distortion in the parent strapped porphyrins and endoperoxides. Additionally, X-ray crystallography indicated that endoperoxide formation occurred exclusively on the outside face of the anthracene moiety.
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Affiliation(s)
- Susan Callaghan
- School of ChemistryTrinity College DublinThe University of DublinTrinity Biomedical Sciences Institute152‐160 Pearse StreetDublin 2Ireland
| | - Keith J. Flanagan
- School of ChemistryTrinity College DublinThe University of DublinTrinity Biomedical Sciences Institute152‐160 Pearse StreetDublin 2Ireland
| | - John E. O'Brien
- School of ChemistryTrinity College DublinThe University of DublinTrinity Biomedical Sciences Institute152‐160 Pearse StreetDublin 2Ireland
| | - Mathias O. Senge
- School of ChemistryTrinity College DublinThe University of DublinTrinity Biomedical Sciences Institute152‐160 Pearse StreetDublin 2Ireland
- Institute for Advanced Study (TUM‐IAS)Technische Universität MünchenLichtenberg‐Str. 2a85748GarchingGermany
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13
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Klaine S, Bratcher F, Winchester CM, Zhang R. Formation and kinetic studies of manganese(IV)-oxo porphyrins: Oxygen atom transfer mechanism of sulfide oxidations. J Inorg Biochem 2019; 204:110986. [PMID: 31924588 DOI: 10.1016/j.jinorgbio.2019.110986] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/27/2019] [Accepted: 12/28/2019] [Indexed: 11/26/2022]
Abstract
Visible light irradiation of photo-labile porphyrin-manganese(III) chlorates or bromates (2) produced manganese(IV)-oxo porphyrins [MnIV(Por)(O)] (Por = porphyrin) (3) in three porphyrin ligands. The same oxo species 3 were also formed by chemical oxidation of the corresponding manganese(III) precursors (1) with iodobenzene diacetate, i.e. PhI(OAc)2. The systems under study include 5,10,15,20-tetra(pentafluorophenyl)porphyrin‑manganese(IV)-oxo (3a), 5,10,15,20-tetra(2,6-difluorophenyl)porphyrin‑manganese(IV)-oxo (3b), and 5,10,15,20-tetramesitylporphyrin‑manganese(IV)-oxo (3c). As expected, complexes 3 reacted with thioanisoles to produce the corresponding sulfoxides and over-oxidized sulfones. The kinetics of oxygen atom transfer (OAT) reactions of these generated 3 with aryl sulfides were studied in CH3CN solutions. Second-order rate constants for sulfide oxidation reactions are comparable to those of alkene epoxidations and activated CH bond oxidations by the same oxo species 3. For a given substrate, the reactivity order for the manganese(IV)-oxo species was 3a > 3b > 3c, consistent with expectations on the basis of the electron-withdrawing capacity of the porphyrin macrocycles. Free-energy Hammett analyses gave near-linear correlations with σ values, indicating no significant positive charge developed at the sulfur during the oxidation process. The mechanistic results strongly suggest [MnIV(Por)(O)] reacts as a direct OAT agent towards sulfide substrates through a manganese(II) intermediate that was detected in this work. However, an alternative pathway that involves a disproportionation of 3 to form a higher oxidized manganese(V)-oxo species may be significant when less reactive substrates are present. The competition product studies with the Hammett correlation plot confirmed that the observed manganese(IV)-oxo species is not the true oxidant for the sulfide oxidations catalyzed by manganese(III) porphyrins with PhI(OAc)2.
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Affiliation(s)
- Seth Klaine
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd #11079, Bowling Green, KY 42101-1079, United States of America
| | - Fox Bratcher
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd #11079, Bowling Green, KY 42101-1079, United States of America
| | - Charles M Winchester
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd #11079, Bowling Green, KY 42101-1079, United States of America
| | - Rui Zhang
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd #11079, Bowling Green, KY 42101-1079, United States of America.
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14
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Su Z, Horner JH, Newcomb M. Cytochrome P450 119 Compounds I Formed by Chemical Oxidation and Photooxidation Are the Same Species. Chemistry 2019; 25:14015-14020. [PMID: 23108625 PMCID: PMC3930626 DOI: 10.1002/chem.201202254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Indexed: 11/07/2022]
Abstract
Compound I from cytochrome P450 119 prepared by the photooxidation method involving peroxynitrite oxidation of the resting enzyme to Compound II followed by photooxidation to Compound I was compared to Compound I generated by m-chloroperoxybenzoic acid (MCPBA) oxidation of the resting enzyme. The two methods gave the same UV/Visible spectra, the same products from oxidations of lauric acid and palmitic acid and their (ω-2,ω-2,ω-3,ω-3)-tetradeuterated analogues, and the same kinetics for oxidations of lauric acid and caprylic acid. The experimental identities between the transients produced by the two methods leave no doubt that the same Compound I species is formed by the two methods.
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Affiliation(s)
- Zhi Su
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL 60617 U.S.A, Fax: (+1) 312-996-0431
| | - John H. Horner
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL 60617 U.S.A, Fax: (+1) 312-996-0431
| | - Martin Newcomb
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL 60617 U.S.A, Fax: (+1) 312-996-0431
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15
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Erdogan H. One small step for cytochrome P450 in its catalytic cycle, one giant leap for enzymology. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619300040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The intermediates operating in the cytochrome P450 catalytic cycle have been investigated for more than half a century, fascinating many enzymologists. Each intermediate has its unique role to carry out diverse oxidations. Natural time course of the catalytic cycle is quite fast, hence, not all of the reactive intermediates could be isolated during physiological catalysis. Different high-valent iron intermediates have been proposed as primary oxidants: the candidates are compound 0 (Cpd 0, [FeOOH][Formula: see text]P450) and compound I (Cpd I, Fe(IV)[Formula: see text]O por[Formula: see text]P450). Among them, the role of Cpd I in hydroxylation is fairly well understood due the discovery of the peroxide shunt. This review endeavors to put the outstanding research efforts conducted to isolate and characterize the intermediates together. In addition to spectral features of each intermediate in the catalytic cycle, the oxidizing powers of Cpd 0 and Cpd I will be discussed along with most recent scientific findings.
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Affiliation(s)
- Huriye Erdogan
- Department of Chemistry, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
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16
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Harmalkar DS, Santosh G, Shetgaonkar SB, Sankaralingam M, Dhuri SN. A putative heme manganese(v)-oxo species in the C–H activation and epoxidation reactions in an aqueous buffer. NEW J CHEM 2019. [DOI: 10.1039/c9nj01381d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Synthesis and reactivity studies of manganese(v)-oxo species in the C–H activation of alkyl hydrocarbons and epoxidation of cyclohexene in aqueous conditions are investigated.
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Affiliation(s)
| | - G. Santosh
- School of Chemical Sciences
- Goa University
- Panaji
- India
- Divison of Chemistry
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17
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Abstract
Enzymes are complex biological catalysts and are critical to life. Most oxidations of chemicals are catalyzed by cytochrome P450 (P450, CYP) enzymes, which generally utilize mixed-function oxidase stoichiometry, utilizing pyridine nucleotides as electron donors: NAD(P)H + O2 + R → NAD(P)+ + RO + H2O (where R is a carbon substrate and RO is an oxidized product). The catalysis of oxidations is largely understood in the context of the heme iron-oxygen complex generally referred to as Compound I, formally FeO3+, whose basis was in peroxidase chemistry. Many X-ray crystal structures of P450s are now available (≥ 822 structures from ≥146 different P450s) and have helped in understanding catalytic specificity. In addition to hydroxylations, P450s catalyze more complex oxidations, including C-C bond formation and cleavage. Enzymes derived from P450s by directed evolution can even catalyze more unusual reactions, e.g. cyclopropanation. Current P450 questions under investigation include the potential role of the intermediate Compound 0 (formally FeIII-O2 -) in catalysis of some reactions, the roles of high- and low-spin forms of Compound I, the mechanism of desaturation, the roles of open and closed structures of P450s in catalysis, the extent of processivity in multi-step oxidations, and the role of the accessory protein cytochrome b 5. More global questions include exactly how structure drives function, prediction of catalysis, and roles of multiple protein conformations.
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Affiliation(s)
- F. Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
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18
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Liu Q, Zhang J, Tang M, Yang Y, Zhang J, Zhou Z. Geometric deconstruction of core and electron activation of a π-system in a series of deformed porphyrins: mimics of heme. Org Biomol Chem 2018; 16:7725-7736. [PMID: 30289139 DOI: 10.1039/c8ob01959b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The predominant distortion of heme is responsible for its electronic activity, catalytic ability and spectral properties. In this work, altogether 12 new X-ray structures of saddled, waved and ruffled porphyrins are reported. Three types of deformed porphyrins as mimics of heme were evaluated and analyzed by geometric deconstruction, spectral comparison, and electrochemical tracking, which shows a unique relationship of deformation fashions and distortion degree to the geometry of the core and electron transfer ability of rings in these enzyme containing porphyrins. These mimics can adjust their core geometry for changing the structures of potential metals; while for rings themselves, they can also regulate the electron activity by switching the HOMO of the large π systems. These deformed porphyrins can be used as ideal mimics for heme. These findings help us to understand the principle and contribution of these deformations to electron transfer in catalytic oxidation and photoreactions. The nonplanar mimics have been synthesized through a modular synthetic approach under Adler-Longo or Lindsey condensation conditions.
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Affiliation(s)
- Qiuhua Liu
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education; and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China.
| | - Jinjin Zhang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education; and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China.
| | - Min Tang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education; and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China.
| | - Yan Yang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education; and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China.
| | - Jian Zhang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, USA.
| | - Zaichun Zhou
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education; and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China.
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19
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Zaitseva SV, Tyulyaeva EY, Simonova OR, Zdanovich SA, Tyurin DV, Koifman OI. Highly reactive μ-carbido diiron tetraphenylporphine oxo-species: chemical generation and the oxidation ability. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1506109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- S. V. Zaitseva
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Science, Ivanovo, Russian Federation
| | - E. Yu. Tyulyaeva
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Science, Ivanovo, Russian Federation
| | - O. R. Simonova
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Science, Ivanovo, Russian Federation
| | - S. A. Zdanovich
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Science, Ivanovo, Russian Federation
| | - D. V. Tyurin
- Ivanovo State University of Chemistry and Technology, Ivanovo, Russian Federation
| | - O. I. Koifman
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Science, Ivanovo, Russian Federation
- Ivanovo State University of Chemistry and Technology, Ivanovo, Russian Federation
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20
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Lee NF, Patel D, Liu H, Zhang R. Insights from kinetic studies of photo-generated compound II models: Reactivity toward aryl sulfides. J Inorg Biochem 2018; 183:58-65. [PMID: 29550659 DOI: 10.1016/j.jinorgbio.2018.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/05/2018] [Accepted: 03/08/2018] [Indexed: 10/17/2022]
Abstract
Iron(IV)-oxo porphyrins [FeIV(Por)O] (Por = poprhyrin), commonly called compound II models, were produced in three electron-deficient ligands by visible light irradiation of highly photo-labile porphyrin-iron(III) bromates or chlorates. The kinetics of oxygen transfer atom (OAT) reactions with aryl sulfides by these photo-generated [FeIV(Por)O] (3) were studied in CH3CN solutions. The iron(IV)-oxo porphyrins under study include 5,10,15,20-tetra(2,6-dichlorophenyl)porphyrin-iron(IV)-oxo (3a), 5,10,15,20-tetra(2,6-difluorophenyl)porphyrin-iron(IV)-oxo (3b), and 5,10,15,20-tetra(pentafluorophenyl)porphyrin-iron(IV)-oxo (3c). As expected, complexes 3 were competent oxidants and reacted rapidly with thioanisoles to give the corresponding sulfoxides with minor over-oxidation sulfones. Apparent second-order rate constants determined under pseudo-first-order conditions for sulfide oxidation reactions are (9.8 ± 0.1) × 102-(3.7 ± 0.3) × 101 M-1 s-1, which are 3 to 4 orders of magnitude greater in comparison to those of alkene epoxidations and activated CH bond oxidations by the same oxo species. Conventional Hammett analyses gave non-linear correlations, indicating no significant charge developed at the sulfur during the oxidation process. For a given substrate, the reactivity order for the iron(IV)-oxo species was 3c < 3b < 3a, which is inverted from expectations on the basis of the electron-withdrawing capacity of the porphyrin macrocycles. The absolute rate constants from kinetic studies provided insights into the transient oxidants in catalytic reactions under turnover conditions where actual reactive intermediates are not observable. Our kinetic and catalytic competition results strongly suggest that 3 may undergo a disproportionation reaction to form a higher oxidized iron(IV)-oxo porphyrin radical cations as the true oxidant.
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Affiliation(s)
- Ngo Fung Lee
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd #11079, Bowling Green, KY 42101-1079, United States
| | - Dharmesh Patel
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd #11079, Bowling Green, KY 42101-1079, United States
| | - Haiyan Liu
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd #11079, Bowling Green, KY 42101-1079, United States
| | - Rui Zhang
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd #11079, Bowling Green, KY 42101-1079, United States.
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21
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Leipzig BK, Rees JA, Kowalska JK, Theisen RM, Kavčič M, Poon PCY, Kaminsky W, DeBeer S, Bill E, Kovacs JA. How Do Ring Size and π-Donating Thiolate Ligands Affect Redox-Active, α-Imino-N-heterocycle Ligand Activation? Inorg Chem 2018; 57:1935-1949. [PMID: 29411979 DOI: 10.1021/acs.inorgchem.7b02748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Considerable effort has been devoted to the development of first-row transition-metal catalysts containing redox-active imino-pyridine ligands that are capable of storing multiple reducing equivalents. This property allows abundant and inexpensive first-row transition metals, which favor sequential one-electron redox processes, to function as competent catalysts in the concerted two-electron reduction of substrates. Herein we report the syntheses and characterization of a series of iron complexes that contain both π-donating thiolate and π-accepting (α-imino)-N-heterocycle redox-active ligands, with progressively larger N-heterocycle rings (imidazole, pyridine, and quinoline). A cooperative interaction between these complementary redox-active ligands is shown to dictate the properties of these complexes. Unusually intense charge-transfer (CT) bands, and intraligand metrical parameters, reminiscent of a reduced (α-imino)-N-heterocycle ligand (L•-), initially suggested that the electron-donating thiolate had reduced the N-heterocycle. Sulfur K-edge X-ray absorption spectroscopic (XAS) data, however, provides evidence for direct communication, via backbonding, between the thiolate sulfur and the formally orthogonal (α-imino)-N-heterocycle ligand π*-orbitals. DFT calculations provide evidence for extensive delocalization of bonds over the sulfur, iron, and (α-imino)-N-heterocycle, and TD-DFT shows that the intense optical CT bands involve transitions between a mixed Fe/S donor, and (α-imino)-N-heterocycle π*-acceptor orbital. The energies and intensities of the optical and S K-edge pre-edge XAS transitions are shown to correlate with N-heterocycle ring size, as do the redox potentials. When the thiolate is replaced with a thioether, or when the low-spin S = 0 Fe(II) is replaced with a high-spin S = 3/2 Co(II), the N-heterocycle ligand metrical parameters and electronic structure do not change relative to the neutral L0 ligand. With respect to the development of future catalysts containing redox-active ligands, the energy cost of storing reducing equivalents is shown to be lowest when a quinoline, as opposed to imidazole or pyridine, is incorporated into the ligand backbone of the corresponding Fe complex.
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Affiliation(s)
- Benjamin K Leipzig
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Julian A Rees
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Joanna K Kowalska
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Roslyn M Theisen
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | | | | | - Werner Kaminsky
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Julie A Kovacs
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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22
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Saghian M, Dehghanpour S, Sharbatdaran M. “Ship in a bottle” Porph@MOMs as highly efficient catalysts for selective controllable oxidation and insights into different mechanisms in heterogeneous and homogeneous environments. NEW J CHEM 2018. [DOI: 10.1039/c8nj00315g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
3D “ship in a bottle” Porph@MOMs with selectivity control capability and interesting catalytic properties were used as biomimetic oxidation catalysts for different reactions.
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Affiliation(s)
- M. Saghian
- Department of Chemistry
- Alzahra University
- Tehran
- Iran
| | | | - M. Sharbatdaran
- Physics and Accelerators School
- Nuclear Science and Technology Research Institute
- Karaj
- Iran
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23
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Lohrey TD, Bergman RG, Arnold J. Olefin‐Supported Rhenium(III) Terminal Oxo Complexes Generated by Nucleophilic Addition to a Cyclopentadienyl Ligand. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Trevor D. Lohrey
- Department of Chemistry University of California, Berkeley 420 Latimer Hall Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Robert G. Bergman
- Department of Chemistry University of California, Berkeley 420 Latimer Hall Berkeley CA 94720 USA
| | - John Arnold
- Department of Chemistry University of California, Berkeley 420 Latimer Hall Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
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24
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Lohrey TD, Bergman RG, Arnold J. Olefin-Supported Rhenium(III) Terminal Oxo Complexes Generated by Nucleophilic Addition to a Cyclopentadienyl Ligand. Angew Chem Int Ed Engl 2017; 56:14241-14245. [PMID: 28929597 DOI: 10.1002/anie.201707957] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/31/2017] [Indexed: 11/10/2022]
Abstract
The reactivity of the oxo ReV β-diketiminate, OReCl2 (BDI), with various cyclopentadienide (Cp) sources has been investigated. As a result, we have developed a route to a new class of terminal oxo complexes of ReIII supported by olefin moieties of substituted cyclopentadienes. The success of this pathway is due to the electrophilic nature of the Cp ligand in the cation, [ORe(η5 -Cp)(BDI)]+ (3+ ), which allows for nucleophilic attack by a variety of reagents under mild conditions. In contrast, t BuNC was found to attack at the oxo moiety to produce isocyanate by oxygen atom transfer.
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Affiliation(s)
- Trevor D Lohrey
- Department of Chemistry, University of California, Berkeley, 420 Latimer Hall, Berkeley, CA, 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Robert G Bergman
- Department of Chemistry, University of California, Berkeley, 420 Latimer Hall, Berkeley, CA, 94720, USA
| | - John Arnold
- Department of Chemistry, University of California, Berkeley, 420 Latimer Hall, Berkeley, CA, 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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25
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Fang X, Duan Y, Liu Y, Adkins G, Zang W, Zhong W, Qiao L, Liu B. Photochemical Bionanoreactor for Efficient Visible-Light-Driven in Vitro Drug Metabolism. Anal Chem 2017; 89:7365-7372. [DOI: 10.1021/acs.analchem.7b00677] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xiaoni Fang
- Department
of Chemistry, Institute of Biomedical Sciences and State Key Lab of
Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Yaokai Duan
- Department
of Chemistry, University of California, Riverside 92501, United States
| | - Yujie Liu
- Department
of Chemistry, Institute of Biomedical Sciences and State Key Lab of
Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Gary Adkins
- Department
of Chemistry, University of California, Riverside 92501, United States
| | - Weijun Zang
- Department
of Chemistry, Institute of Biomedical Sciences and State Key Lab of
Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Wenwan Zhong
- Department
of Chemistry, University of California, Riverside 92501, United States
| | - Liang Qiao
- Department
of Chemistry, Institute of Biomedical Sciences and State Key Lab of
Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Shanghai
Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Baohong Liu
- Department
of Chemistry, Institute of Biomedical Sciences and State Key Lab of
Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
- Shanghai
Stomatological Hospital, Fudan University, Shanghai 200433, China
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26
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Ai CZ, Liu Y, Li W, Chen DM, Zhu XX, Yan YW, Chen DC, Jiang YZ. Computational explanation for bioactivation mechanism of targeted anticancer agents mediated by cytochrome P450s: A case of Erlotinib. PLoS One 2017. [PMID: 28628631 PMCID: PMC5476264 DOI: 10.1371/journal.pone.0179333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
EGFR inhibitors, even with therapeutics superiorities in anticancer, can cause idiosyncratic pulmonary and hepatic toxicities that are associated with the reactive electrophile bioactivated by Cytochrome P450s (P450s). Until now, neither has the electrophilic intermediate been caught experimentally, nor has the subtle mechanism been declared. Herein, the underlying mechanism of bioactivation mediated by P450s was explored by DFT calculations for a case of EGFR inhibitor, Erlotinib. Based on the calculation and analysis, we suggest that with other metabolites, reactive electrophiles of Erlotinib: epoxide and quinine-imine, can be generated by several steps along the oxidative reaction pathway. The generation of epoxide needs two steps: (1) the addition of Erlotinib to Compound I (Cpd I) and (2) the rearrangement of protons. Whereas, quinine-imine needs a further oxidation step (3) via which quinone is generated and ultimately turns into quinine-imine. Although both reactive electrophiles can be produced for either face-on or side-on pose of Erlotinib, the analysis of energy barriers indicates that the side-on path is preferred in solvent environment. In the rate-determining step, e.g. the addition of Erlotinib to the porphyrin, the reaction barrier for side-on conformation is decreased in aqueous and protein environment compared with gas phase, whereas, the barrier for face-on pose is increased in solvent environment. The simulated mechanism is in good agreement with the speculation in previous experiment. The understanding of the subtle mechanism of bioactivation of Erlotinib will provide theoretical support for toxicological mechanism of EGFR inhibitors.
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Affiliation(s)
- Chun-Zhi Ai
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Yong Liu
- School of Life Science and Medicine, Dalian University of Technology, Panjin, Liaoning, China
| | - Wei Li
- College of Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - De-Meng Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- School of Dentistry, University of California, Los Angeles, California, United States of America
| | - Xin-Xing Zhu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Ya-Wei Yan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Du-Chu Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Yi-Zhou Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- * E-mail:
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27
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Lang J, Maréchal A, Couture M, Santolini J. Reaction Intermediates and Molecular Mechanism of Peroxynitrite Activation by NO Synthases. Biophys J 2017; 111:2099-2109. [PMID: 27851935 DOI: 10.1016/j.bpj.2016.05.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022] Open
Abstract
The activation of the peroxynitrite anion (PN) by hemoproteins, which leads to its detoxification or, on the contrary to the enhancement of its cytotoxic activity, is a reaction of physiological importance that is still poorly understood. It has been known for some years that the reaction of hemoproteins, notably cytochrome P450, with PN leads to the buildup of an intermediate species with a Soret band at ∼435 nm (I435). The nature of this intermediate is, however, debated. On the one hand, I435 has been presented as a compound II species that can be photoactivated to compound I. A competing alternative involves the assignment of I435 to a ferric-nitrosyl species. Similar to cytochromes P450, the buildup of I435 occurs in nitric oxide synthases (NOSs) upon their reaction with excess PN. Interestingly, the NOS isoforms vary in their capacity to detoxify/activate PN, although they all show the buildup of I435. To better understand PN activation/detoxification by heme proteins, a definitive assignment of I435 is needed. Here we used a combination of fine kinetic analysis under specific conditions (pH, PN concentrations, and PN/NOSs ratios) to probe the formation of I435. These studies revealed that I435 is not formed upon homolytic cleavage of the O-O bond of PN, but instead arises from side reactions associated with excess PN. Characterization of I435 by resonance Raman spectroscopy allowed its identification as a ferric iron-nitrosyl complex. Our study indicates that the model used so far to depict PN interactions with hemo-thiolate proteins, i.e., leading to the formation and accumulation of compound II, needs to be reconsidered.
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Affiliation(s)
- Jérôme Lang
- Laboratory of Oxidative Stress and Detoxification, iBiTec-S/I2BC, UMR 9198, CEA-Centre National de la Recherche Scientifique Université Paris Sud, CEA Saclay, Gif-sur-Yvette Cedex, France; Department of Biochemistry, Université Laval, Laval, Québec, Canada
| | - Amandine Maréchal
- Laboratory of Oxidative Stress and Detoxification, iBiTec-S/I2BC, UMR 9198, CEA-Centre National de la Recherche Scientifique Université Paris Sud, CEA Saclay, Gif-sur-Yvette Cedex, France
| | - Manon Couture
- Department of Biochemistry, Université Laval, Laval, Québec, Canada
| | - Jérôme Santolini
- Laboratory of Oxidative Stress and Detoxification, iBiTec-S/I2BC, UMR 9198, CEA-Centre National de la Recherche Scientifique Université Paris Sud, CEA Saclay, Gif-sur-Yvette Cedex, France.
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28
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Kwong KW, Patel D, Malone J, Lee NF, Kash B, Zhang R. An investigation of ligand effects on the visible light-induced formation of porphyrin–iron(iv)-oxo intermediates. NEW J CHEM 2017. [DOI: 10.1039/c7nj03296j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Depending on the structure of the porphyrin ligands, the visible light photolysis of porphyrin–iron(iii) bromates produced iron(iv)-oxo radical cations or iron(iv)-oxo porphyrins, permitting direct kinetic studies of their oxidation reactions.
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Affiliation(s)
- Ka Wai Kwong
- Department of Chemistry
- Western Kentucky University
- Bowling Green
- USA
| | - Dharmesh Patel
- Department of Chemistry
- Western Kentucky University
- Bowling Green
- USA
| | - Jonathan Malone
- Department of Chemistry
- Western Kentucky University
- Bowling Green
- USA
| | - Ngo Fung Lee
- Department of Chemistry
- Western Kentucky University
- Bowling Green
- USA
| | - Benjamin Kash
- Department of Chemistry
- Western Kentucky University
- Bowling Green
- USA
| | - Rui Zhang
- Department of Chemistry
- Western Kentucky University
- Bowling Green
- USA
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29
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Liu Q, Tang M, Zeng W, Zhang X, Wang J, Zhou Z. Optimal Size Matching and Minimal Distortion Energy: Implications for Natural Selection by the Macrocycle of the Iron Species in Heme. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Qiuhua Liu
- College of Chemistry and Chemical EngineeringCentral South University410083ChangshaChina
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules of the Ministry of EducationSchool of Chemistry and Chemical EngineeringHunan University of Science and Technology411201XiangtanChina
| | - Min Tang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules of the Ministry of EducationSchool of Chemistry and Chemical EngineeringHunan University of Science and Technology411201XiangtanChina
| | - Wennan Zeng
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules of the Ministry of EducationSchool of Chemistry and Chemical EngineeringHunan University of Science and Technology411201XiangtanChina
| | - Xi Zhang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules of the Ministry of EducationSchool of Chemistry and Chemical EngineeringHunan University of Science and Technology411201XiangtanChina
| | - Jianxiu Wang
- College of Chemistry and Chemical EngineeringCentral South University410083ChangshaChina
| | - Zaichun Zhou
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules of the Ministry of EducationSchool of Chemistry and Chemical EngineeringHunan University of Science and Technology411201XiangtanChina
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30
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Photochemical generation of manganese(IV)-oxo porphyrins by visible light photolysis of dimanganese(III) μ-oxo bis-porphyrins. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.07.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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31
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Liu Q, Zhang X, Zeng W, Wang J, Zhou Z. Origin of d-π Interaction in Cobalt(II) Porphyrins under Synergistic Effects of Core Contraction and Axial Ligation: Implications for a Ligand Effect of Natural Distorted Tetrapyrrole. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201600226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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32
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Spectroscopic and Kinetic Characterization of Peroxidase-Like π-Cation Radical Pinch-Porphyrin-Iron(III) Reaction Intermediate Models of Peroxidase Enzymes. Molecules 2016; 21:molecules21070804. [PMID: 27355940 PMCID: PMC6273987 DOI: 10.3390/molecules21070804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/01/2016] [Accepted: 06/13/2016] [Indexed: 11/17/2022] Open
Abstract
The spectroscopic and kinetic characterization of two intermediates from the H₂O₂ oxidation of three dimethyl ester [(proto), (meso), (deuteroporphyrinato) (picdien)]Fe(III) complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively) pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III) quantum mixed spin (qms) ground states is described herein. The kinetic study by UV/Vis at λmax = 465 nm showed two different types of kinetics during the oxidation process in the guaiacol test for peroxidases (1-3 + guaiacol + H₂O₂ → oxidation guaiacol products). The first intermediate was observed during the first 24 s of the reaction. When the reaction conditions were changed to higher concentration of pinch-porphyrins and hydrogen peroxide only one type of kinetics was observed. Next, the reaction was performed only between pinch-porphyrins-Fe(III) and H₂O₂, resulting in only two types of kinetics that were developed during the first 0-4 s. After this time a self-oxidation process was observed. Our hypotheses state that the formation of the π-cation radicals, reaction intermediates of the pinch-porphyrin-Fe(III) family with the ligand picdien [N,N'-bis-pyridin-2-ylmethyl-propane-1,3-diamine], occurred with unique kinetics that are different from the overall process and was involved in the oxidation pathway. UV-Vis, ¹H-NMR and ESR spectra confirmed the formation of such intermediates. The results in this paper highlight the link between different spectroscopic techniques that positively depict the kinetic traits of artificial compounds with enzyme-like activity.
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33
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Liu Q, Zhou X, Liu H, Zhang X, Zhou Z. Fractional transfer of a free unpaired electron to overcome energy barriers in the formation of Fe(4+) from Fe(3+) during the core contraction of macrocycles: implication for heme distortion. Org Biomol Chem 2016; 13:2939-46. [PMID: 25609455 DOI: 10.1039/c4ob02429j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The free unpaired electron in Fe(3+) ions cannot be directly removed, and needs a transfer pathway with at least four steps to overcome the high energy barriers to form Fe(4+) ions. Fine changes in the electronic structure of Fe(3+) ions on spin conversion were identified through a deeper analysis of the diffraction, spectral and electrochemical data for six non-planar iron porphyrins. Fe(3+) ions can form four d electron tautomers as the compression of the central ion is increased. This indicates that the Fe(3+) ion undergoes a multistep electron transfer where the total energy gap of electron transfer is split into several smaller gaps to form high-valent Fe(4+) ions. We find that the interchange of these four electron tautomers is clearly related to the core size of the macrocycle in the current series. The large energy barrier to produce iron(iv) complexes is overcome through a gradient effect of multiple energy levels. In addition, a possible porphyrin Fe(3+)˙ radical may be formed from its stable isoelectronic form, porphyrin Fe(3+), under strong core contraction. These results indicate the important role of heme distortion in its catalytic oxidation functions.
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Affiliation(s)
- Qiuhua Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of 'Theoretical Organic Chemistry and Function Molecule' of the Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.
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34
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Chen TH, Asiri N, Kwong KW, Malone J, Zhang R. Ligand control in the photochemical generation of high-valent porphyrin-iron-oxo derivatives. Chem Commun (Camb) 2016; 51:9949-52. [PMID: 25999215 DOI: 10.1039/c5cc02852c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Visible-light irradiation of photo-labile bromate porphyrin-iron(III) salts gave iron(IV)-oxo porphyrin radical cations (compound I model) or the neutral iron(IV)-oxo porphyrin (compound II model), depending on the electronic structure of porphyrin ligands.
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Affiliation(s)
- Tse-Hong Chen
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, Kentucky, USA.
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35
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Sengupta K, Chatterjee S, Dey A. Catalytic H2O2 Disproportionation and Electrocatalytic O2 Reduction by a Functional Mimic of Heme Catalase: Direct Observation of Compound 0 and Compound I in Situ. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02668] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kushal Sengupta
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Sudipta Chatterjee
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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36
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Liu Q, Zhang X, Zeng W, Wang J, Zhou Z. Fine-Tuning of Electronic Structure of Cobalt(II) Ion in Nonplanar Porphyrins and Tracking of a Cross-Hybrid Stage: Implications for the Distortion of Natural Tetrapyrrole Macrocycles. J Phys Chem B 2015; 119:14102-10. [DOI: 10.1021/acs.jpcb.5b08431] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qiuhua Liu
- College
of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
- Key
Laboratory of Theoretical Organic Chemistry and Functional Molecule
of the Ministry of Education; School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xi Zhang
- Key
Laboratory of Theoretical Organic Chemistry and Functional Molecule
of the Ministry of Education; School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Wennan Zeng
- Key
Laboratory of Theoretical Organic Chemistry and Functional Molecule
of the Ministry of Education; School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Jianxiu Wang
- College
of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Zaichun Zhou
- Key
Laboratory of Theoretical Organic Chemistry and Functional Molecule
of the Ministry of Education; School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
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37
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Mancini G, Zazza C. F429 Regulation of Tunnels in Cytochrome P450 2B4: A Top Down Study of Multiple Molecular Dynamics Simulations. PLoS One 2015; 10:e0137075. [PMID: 26415031 PMCID: PMC4587367 DOI: 10.1371/journal.pone.0137075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/12/2015] [Indexed: 01/22/2023] Open
Abstract
The root causes of the outcomes of the single-site mutation in enzymes remain by and large not well understood. This is the case of the F429H mutant of the cytochrome P450 (CYP) 2B4 enzyme where the substitution, on the proximal surface of the active site, of a conserved phenylalanine 429 residue with histidine seems to hamper the formation of the active species, Compound I (porphyrin cation radical-Fe(IV) = O, Cpd I) from the ferric hydroperoxo (Fe(III)OOH-, Cpd 0) precursor. Here we report a study based on extensive molecular dynamic (MD) simulations of 4 CYP-2B4 point mutations compared to the WT enzyme, having the goal of better clarifying the importance of the proximal Phe429 residue on CYP 2B4 catalytic properties. To consolidate the huge amount of data coming from five simulations and extract the most distinct structural features of the five species studied we made an extensive use of cluster analysis. The results show that all studied single polymorphisms of F429, with different side chain properties: i) drastically alter the reservoir of conformations accessible by the protein, perturbing global dynamics ii) expose the thiolate group of residue Cys436 to the solvent, altering the electronic properties of Cpd0 and iii) affect the various ingress and egress channels connecting the distal sites with the bulk environment, altering the reversibility of these channels. In particular, it was observed that the wild type enzyme exhibits unique structural features as compared to all mutant species in terms of weak interactions (hydrogen bonds) that generate a completely different dynamical behavior of the complete system. Albeit not conclusive, the current computational investigation sheds some light on the subtle and critical effects that proximal single-site mutations can exert on the functional mechanisms of human microsomal CYPs which should go rather far beyond local structure characterization.
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Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126, Pisa, Italy, and Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127, Pisa, Italy
- * E-mail:
| | - Costantino Zazza
- Università degli Studi di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185, Roma, Italy
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38
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Zhou Z, Zhou X, Liu Q, Zhang X, Liu H. Fixation of Zinc(II) Ion to Dioxygen in a Highly Deformed Porphyrin: Implications for the Oxygen Carrier Mechanism of Distorted Heme. Org Lett 2015; 17:4078-81. [DOI: 10.1021/acs.orglett.5b02010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zaichun Zhou
- Key Laboratory
of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education,
School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xiaochun Zhou
- Key Laboratory
of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education,
School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Qiuhua Liu
- Key Laboratory
of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education,
School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xi Zhang
- Key Laboratory
of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education,
School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Haomin Liu
- Key Laboratory
of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education,
School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
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39
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Borgogno A, Rastrelli F, Bagno A. Characterization of Paramagnetic Reactive Intermediates: Predicting the NMR Spectra of Iron(IV)-Oxo Complexes by DFT. Chemistry 2015; 21:12960-70. [PMID: 26235229 DOI: 10.1002/chem.201500864] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 11/06/2022]
Abstract
The relative energies of spin states of several iron(IV)-oxo complexes and related species have been calculated with DFT methods by employing the B3LYP* functional. We show that such calculations can predict the correct ground spin state of Fe(IV) complexes and can then be used to determine the (1) H NMR spectra of all spin states; the spectral features are remarkably different, hence calculated paramagnetic (1) H NMR spectra can be used to support the structure elucidation of numerous paramagnetic complexes. Applications to a number of stable and reactive iron(IV)-oxo species are described.
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Affiliation(s)
- Andrea Borgogno
- Department of Chemical Sciences, University of Padova via Marzolo 1, 35131 Padova (Italy)
| | - Federico Rastrelli
- Department of Chemical Sciences, University of Padova via Marzolo 1, 35131 Padova (Italy).
| | - Alessandro Bagno
- Department of Chemical Sciences, University of Padova via Marzolo 1, 35131 Padova (Italy)
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40
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Cook SA, Hill EA, Borovik AS. Lessons from Nature: A Bio-Inspired Approach to Molecular Design. Biochemistry 2015; 54:4167-80. [PMID: 26079379 DOI: 10.1021/acs.biochem.5b00249] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metalloproteins contain actives sites with intricate structures that perform specific functions with high selectivity and efficiency. The complexity of these systems complicates the study of their function and the understanding of the properties that give rise to their reactivity. One approach that has contributed to the current level of understanding of their biological function is the study of synthetic constructs that mimic one or more aspects of the native metalloproteins. These systems allow individual contributions to the structure and function to be analyzed and also permit spectroscopic characterization of the metal cofactors without complications from the protein environment. This Current Topic is a review of synthetic constructs as probes for understanding the biological activation of small molecules. These topics are developed from the perspective of seminal molecular design breakthroughs from the past that provide the foundation for the systems used today.
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Affiliation(s)
- Sarah A Cook
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Ethan A Hill
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - A S Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
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41
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Viciano I, Castillo R, Martí S. QM/MM modeling of the hydroxylation of the androstenedione substrate catalyzed by cytochrome P450 aromatase (CYP19A1). J Comput Chem 2015; 36:1736-47. [DOI: 10.1002/jcc.23967] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/07/2015] [Accepted: 05/16/2015] [Indexed: 01/30/2023]
Affiliation(s)
- Ignacio Viciano
- Departament de Química Física i Analítica; Universitat Jaume I; Castelló 12071 Spain
| | - Raquel Castillo
- Departament de Química Física i Analítica; Universitat Jaume I; Castelló 12071 Spain
| | - Sergio Martí
- Departament de Química Física i Analítica; Universitat Jaume I; Castelló 12071 Spain
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42
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Zhang R, Vanover E, Luo W, Newcomb M. Photochemical generation and kinetic studies of a putative porphyrin-ruthenium(V)-oxo species. Dalton Trans 2015; 43:8749-56. [PMID: 24770388 DOI: 10.1039/c4dt00649f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photo-disproportionation of a bis-porphyrin-diruthenium(IV) μ-oxo dimer gave a porphyrin-ruthenium(III) species and a putative porphyrin-ruthenium(V)-oxo species that can be detected and studied in real time via laser flash photolysis methods. As determined by its spectral and kinetic behavior, the same oxo transient was also formed by photolysis of a porphyrin-ruthenium(III) N-oxide adduct. Second-order rate constants for reactions with several substrates at 22 °C were determined; representative values of rate constants were kox = 6.6 × 10(3) M(-1) s(-1) for diphenylmethanol, kox = 2.5 × 10(3) M(-1) s(-1) for styrene, and kox = 1.8 × 10(3) M(-1) s(-1) for cyclohexene. The putative porphyrin-ruthenium(V)-oxo transient reacted 5-6 orders of magnitude faster than the corresponding trans-dioxoruthenium(VI) porphyrins, and the rate constants obtained in this work were similar to those of the corrole-iron(V)-oxo derivative. The high reactivity for the photochemically generated ruthenium-oxo species in comparison to other porphyrin-metal-oxo intermediates suggests that it is a true ruthenium(V)-oxo species.
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Affiliation(s)
- Rui Zhang
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd. # 11079, Bowling Green, KY 42101, USA
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43
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Samanta S, Das PK, Chatterjee S, Dey A. Effect of axial ligands on electronic structure and O2 reduction by iron porphyrin complexes: Towards a quantitative understanding of the "push effect". J PORPHYR PHTHALOCYA 2015. [DOI: 10.1142/s1088424615300049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Axial ligands play a dominating role in determining the electronic structure and reactivity of iron porphyrin active sites and synthetic models. Several properties unique to the cysteine bound heme enzyme, cytochrome P450, is attributed to the "push effect" of the thiolate axial ligand. In this mini-review the ground state electronic structure of iron porphyrins with imidazole, phenolate and thiolate complexes, derived using a combination of spectroscopy and DFT calculations, are discussed. The differences in kinetics and selectivity of oxygen reduction reaction (ORR), catalyzed by these iron porphyrin complexes with different axial ligands, help elucidate the varying push effects of the different axial ligands on oxygen activation by ferrous porphyrin. The spectroscopic and kinetic data help to develop a quantitative understanding of the "push effect" and, in particular, the electrostatic and covalent contributions to it.
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Affiliation(s)
- Subhra Samanta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Pradip Kumar Das
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sudipta Chatterjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
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44
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Das PK, Dey A. Resonance Raman, Electron Paramagnetic Resonance, and Density Functional Theory Calculations of a Phenolate-Bound Iron Porphyrin Complex: Electrostatic versus Covalent Contribution to Bonding. Inorg Chem 2014; 53:7361-70. [DOI: 10.1021/ic500716d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Pradip Kumar Das
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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45
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Zhang C, Li J, Yang B, He F, Yang SY, Yu XQ, Wang Q. Enhanced turnover rate and enantioselectivity in the asymmetric epoxidation of styrene by new T213G mutants of CYP 119. RSC Adv 2014. [DOI: 10.1039/c4ra04626a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
New CYP 119 T213G mutants were constructed and characterized. Introduction of T213G mutation into the wild-type CYP 119 enhances the turnover rate for the styrene epoxidation to 346.2 min−1, and the double T213G/T214V mutant improves the ratio of the S- and R-enantiomers of the epoxide products to 5.8. The molecular docking results support our initial design and experimental data.
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Affiliation(s)
- Chun Zhang
- Department of Medicinal Chemistry
- Luzhou Medical College
- Luzhou 646000, China
| | - Jing Li
- Department of Medicinal Chemistry
- Luzhou Medical College
- Luzhou 646000, China
| | - Bo Yang
- State Key Laboratory of Biotherapy
- West China Hospital
- Sichuan University
- Chengdu 610041, China
| | - Fang He
- Department of Medicinal Chemistry
- Luzhou Medical College
- Luzhou 646000, China
| | - Sheng-Yong Yang
- State Key Laboratory of Biotherapy
- West China Hospital
- Sichuan University
- Chengdu 610041, China
| | - Xiao-Qi Yu
- College of Chemistry
- Sichuan University
- Chengdu 610064, China
| | - Qin Wang
- Department of Medicinal Chemistry
- Luzhou Medical College
- Luzhou 646000, China
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Das PK, Mittra K, Dey A. Spectroscopic characterization of a phenolate bound FeII–O2adduct: gauging the relative “push” effect of a phenolate axial ligand. Chem Commun (Camb) 2014; 50:5218-20. [DOI: 10.1039/c3cc47528j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Samanta S, Das PK, Chatterjee S, Sengupta K, Mondal B, Dey A. O2 Reduction Reaction by Biologically Relevant Anionic Ligand Bound Iron Porphyrin Complexes. Inorg Chem 2013; 52:12963-71. [DOI: 10.1021/ic4020652] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Subhra Samanta
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Pradip Kumar Das
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Sudipta Chatterjee
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Kushal Sengupta
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Biswajit Mondal
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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Elenewski JE, Hackett JC. Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin. J Comput Chem 2013; 34:1647-60. [PMID: 23670855 PMCID: PMC3711018 DOI: 10.1002/jcc.23311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 03/18/2013] [Accepted: 04/07/2013] [Indexed: 11/11/2022]
Abstract
The cytochromes P450 constitute a ubiquitous family of metalloenzymes, catalyzing manifold reactions of biological and synthetic importance via a thiolate-ligated iron-oxo (IV) porphyrin radical species denoted compound I (Cpd I). Experimental investigations have implicated this intermediate in a broad spectrum of biophysically interesting phenomena, further augmenting the importance of a Cpd I model system. Ab initio molecular dynamics, including Car-Parrinello and path integral methods, conjoin electronic structure theory with finite temperature simulation, affording tools most valuable to approach such enzymes. These methods are typically driven by density functional theory (DFT) in a plane-wave pseudopotential framework; however, existing studies of Cpd I have been restricted to localized Gaussian basis sets. The appropriate choice of density functional and pseudopotential for such simulations is accordingly not obvious. To remedy this situation, a systematic benchmarking of thiolate-ligated Cpd I is performed using several generalized-gradient approximation (GGA) functionals in the Martins-Troullier and Vanderbilt ultrasoft pseudopotential schemes. The resultant electronic and structural parameters are compared to localized-basis DFT calculations using GGA and hybrid density functionals. The merits and demerits of each scheme are presented in the context of reproducing existing experimental and theoretical results for Cpd I.
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Affiliation(s)
- Justin E. Elenewski
- Goodwin Research Laboratory, Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540
| | - John C Hackett
- Goodwin Research Laboratory, Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540
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Vidal-Limón A, Águila S, Ayala M, Batista CV, Vazquez-Duhalt R. Peroxidase activity stabilization of cytochrome P450BM3 by rational analysis of intramolecular electron transfer. J Inorg Biochem 2013; 122:18-26. [DOI: 10.1016/j.jinorgbio.2013.01.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/15/2013] [Accepted: 01/16/2013] [Indexed: 11/17/2022]
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Krest CM, Onderko EL, Yosca TH, Calixto JC, Karp RF, Livada J, Rittle J, Green MT. Reactive intermediates in cytochrome p450 catalysis. J Biol Chem 2013; 288:17074-81. [PMID: 23632017 DOI: 10.1074/jbc.r113.473108] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, we reported the spectroscopic and kinetic characterizations of cytochrome P450 compound I in CYP119A1, effectively closing the catalytic cycle of cytochrome P450-mediated hydroxylations. In this minireview, we focus on the developments that made this breakthrough possible. We examine the importance of enzyme purification in the quest for reactive intermediates and report the preparation of compound I in a second P450 (P450ST). In an effort to bring clarity to the field, we also examine the validity of controversial reports claiming the production of P450 compound I through the use of peroxynitrite and laser flash photolysis.
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Affiliation(s)
- Courtney M Krest
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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