1
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Zhou TP, Feng J, Wang Y, Li S, Wang B. Substrate Conformational Switch Enables the Stereoselective Dimerization in P450 NascB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. JACS AU 2024; 4:1591-1604. [PMID: 38665654 PMCID: PMC11040706 DOI: 10.1021/jacsau.4c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024]
Abstract
P450 NascB catalyzes the coupling of cyclo-(l-tryptophan-l-proline) (1) to generate (-)-naseseazine C (2) through intramolecular C-N bond formation and intermolecular C-C coupling. A thorough understanding of its catalytic mechanism is crucial for the engineering or design of P450-catalyzed C-N dimerization reactions. By employing MD simulations, QM/MM calculations, and enhanced sampling, we assessed various mechanisms from recent works. Our study demonstrates that the most favorable pathway entails the transfer of a hydrogen atom from N7-H to Cpd I. Subsequently, there is a conformational change in the substrate radical, shifting it from the Re-face to the Si-face of N7 in Substrate 1. The Si-face conformation of Substrate 1 is stabilized by the protein environment and the π-π stacking interaction between the indole ring and heme porphyrin. The subsequent intermolecular C3-C6' bond formation between Substrate 1 radical and Substrate 2 occurs via a radical attack mechanism. The conformational switch of the Substrate 1 radical not only lowers the barrier of the intermolecular C3-C6' bond formation but also yields the correct stereoselectivity observed in experiments. In addition, we evaluated the reactivity of the ferric-superoxide species, showing it is not reactive enough to initiate the hydrogen atom abstraction from the indole NH group of the substrate. Our simulation provides a comprehensive mechanistic insight into how the P450 enzyme precisely controls both the intramolecular C-N cyclization and intermolecular C-C coupling. The current findings align with the available experimental data, emphasizing the pivotal role of substrate dynamics in governing P450 catalysis.
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Affiliation(s)
- Tai-Ping Zhou
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianqiang Feng
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yongchao Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shengying Li
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Binju Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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2
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Kamel EM, Alwaili MA, Rudayni HA, Allam AA, Lamsabhi AM. Deciphering the Molecular Mechanisms of Reactive Metabolite Formation in the Mechanism-Based Inactivation of Cytochrome p450 1B1 by 8-Methoxypsoralen and Assessing the Driving Effect of phe268. Molecules 2024; 29:1433. [PMID: 38611713 PMCID: PMC11012842 DOI: 10.3390/molecules29071433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
This study provides a comprehensive computational exploration of the inhibitory activity and metabolic pathways of 8-methoxypsoralen (8-MP), a furocoumarin derivative used for treating various skin disorders, on cytochrome P450 (P450). Employing quantum chemical DFT calculations, molecular docking, and molecular dynamics (MD) simulations analyses, the biotransformation mechanisms and the active site binding profile of 8-MP in CYP1B1 were investigated. Three plausible inactivation mechanisms were minutely scrutinized. Further analysis explored the formation of reactive metabolites in subsequent P450 metabolic processes, including covalent adduct formation through nucleophilic addition to the epoxide, 8-MP epoxide hydrolysis, and non-CYP-catalyzed epoxide ring opening. Special attention was paid to the catalytic effect of residue Phe268 on the mechanism-based inactivation (MBI) of P450 by 8-MP. Energetic profiles and facilitating conditions revealed a slight preference for the C4'=C5' epoxidation pathway, while recognizing a potential kinetic competition with the 8-OMe demethylation pathway due to comparable energy demands. The formation of covalent adducts via nucleophilic addition, particularly by phenylalanine, and the generation of potentially harmful reactive metabolites through autocatalyzed ring cleavage are likely to contribute significantly to P450 metabolism of 8-MP. Our findings highlight the key role of Phe268 in retaining 8-MP within the active site of CYP1B1, thereby facilitating initial oxygen addition transition states. This research offers crucial molecular-level insights that may guide the early stages of drug discovery and risk assessment related to the use of 8-MP.
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Affiliation(s)
- Emadeldin M. Kamel
- Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt;
| | - Maha A. Alwaili
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Hassan A. Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia; (H.A.R.); (A.A.A.)
| | - Ahmed A. Allam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia; (H.A.R.); (A.A.A.)
- Department of Zoology, Faculty of Science, Beni-Suef University, Beni-Suef 65211, Egypt
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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3
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Costa GJ, Egbemhenghe A, Liang R. Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases. J Phys Chem B 2023; 127:10987-10999. [PMID: 38096487 DOI: 10.1021/acs.jpcb.3c06311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Unspecific peroxygenases (UPOs) are emerging as promising biocatalysts for selective oxyfunctionalization of unactivated C-H bonds. However, their potential in large-scale synthesis is currently constrained by suboptimal chemical selectivity. Improving the selectivity of UPOs requires a deep understanding of the molecular basis of their catalysis. Recent molecular simulations have sought to unravel UPO's selectivity and inform their design principles. However, most of these studies focused on substrate-binding poses. Few researchers have investigated how the reactivity of CpdI, the principal oxidizing intermediate in the catalytic cycle, influences selectivity in a realistic protein environment. Moreover, the influence of protein electrostatics on the reaction kinetics of CpdI has also been largely overlooked. To bridge this gap, we used multiscale simulations to interpret the regio- and enantioselective hydroxylation of the n-heptane substrate catalyzed by Agrocybe aegerita UPO (AaeUPO). We comprehensively characterized the energetics and kinetics of the hydrogen atom-transfer (HAT) step, initiated by CpdI, and the subsequent oxygen rebound step forming the product. Notably, our approach involved both free energy and potential energy evaluations in a quantum mechanics/molecular mechanics (QM/MM) setting, mitigating the dependence of results on the choice of initial conditions. These calculations illuminate the thermodynamics and kinetics of the HAT and oxygen rebound steps. Our findings highlight that both the conformational selection and the distinct chemical reactivity of different substrate hydrogen atoms together dictate the regio- and enantio-selectivity. Building on our previous study of CpdI's formation in AaeUPO, our results indicate that the HAT step is the rate-limiting step in the overall catalytic cycle. The subsequent oxygen rebound step is swift and retains the selectivity determined by the HAT step. We also pinpointed several polar and charged amino acid residues whose electrostatic potentials considerably influence the reaction barrier of the HAT step. Notably, the Glu196 residue is pivotal for both the CpdI's formation and participation in the HAT step. Our research offers in-depth insights into the catalytic cycle of AaeUPO, which will be instrumental in the rational design of UPOs with enhanced properties.
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Affiliation(s)
- Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Abel Egbemhenghe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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4
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Panda S, Phan H, Karlin KD. Heme-copper and Heme O 2-derived synthetic (bioinorganic) chemistry toward an understanding of cytochrome c oxidase dioxygen chemistry. J Inorg Biochem 2023; 249:112367. [PMID: 37742491 PMCID: PMC10615892 DOI: 10.1016/j.jinorgbio.2023.112367] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/22/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
Cytochrome c oxidase (CcO), also widely known as mitochondrial electron-transport-chain complex IV, is a multi-subunit transmembrane protein responsible for catalyzing the last step of the electron transport chain, dioxygen reduction to water, which is essential to the establishment and maintenance of the membrane proton gradient that drives ATP synthesis. Although many intermediates in the CcO catalytic cycle have been spectroscopically and/or computationally authenticated, the specifics regarding the IP intermediate, hypothesized to be a heme-Cu (hydro)peroxo species whose O-O bond homolysis is supported by a hydrogen-bonding network of water molecules, are largely obscured by the fast kinetics of the A (FeIII-O2•-/CuI/Tyr) → PM (FeIV=O/CuII-OH/Tyr•) step. In this review, we have focused on the recent advancements in the design, development, and characterization of synthetic heme-peroxo‑copper model complexes, which can circumvent the abovementioned limitation, for the investigation of the formation of IP and its O-O cleavage chemistry. Novel findings regarding (a) proton and electron transfer (PT/ET) processes, together with their contributions to exogenous phenol induced O-O cleavage, (b) the stereo-electronic tunability of the secondary coordination sphere (especially hydrogen-bonding) on the geometric and spin state alteration of the heme-peroxo‑copper unit, and (c) a plausible mechanism for the Tyr-His cofactor biogenesis, are discussed in great detail. Additionally, since the ferric-superoxide and the ferryl-oxo (Compound II) species are critically involved in the CcO catalytic cycle, this review also highlights a few fundamental aspects of these heme-only (i.e., without copper) species, including the structural and reactivity influences of electron-donating trans-axial ligands and Lewis acid-promoted H-bonding.
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Affiliation(s)
- Sanjib Panda
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hai Phan
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
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5
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Gering HE, Li X, Tang H, Swartz PD, Chang WC, Makris TM. A Ferric-Superoxide Intermediate Initiates P450-Catalyzed Cyclic Dipeptide Dimerization. J Am Chem Soc 2023; 145:19256-19264. [PMID: 37611404 DOI: 10.1021/jacs.3c04542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The cytochrome P450 (CYP) AspB is involved in the biosynthesis of the diketopiperazine (DKP) aspergilazine A. Tryptophan-linked dimeric DKP alkaloids are a large family of natural products that are found in numerous species and exhibit broad and often potent bioactivity. The proposed mechanisms for C-N bond formation by AspB, and similar C-C bond formations by related CYPs, have invoked the use of a ferryl-intermediate as an oxidant to promote substrate dimerization. Here, the parallel application of steady-state and transient kinetic approaches reveals a very different mechanism that involves a ferric-superoxide species as a primary oxidant to initiate DKP-assembly. Single turnover kinetic isotope effects and a substrate analog suggest the probable nature and site for abstraction. The direct observation of CYP-superoxide reactivity rationalizes the atypical outcome of AspB and reveals a new reaction manifold in heme enzymes.
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Affiliation(s)
- Hannah E Gering
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Haoyu Tang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Paul D Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas M Makris
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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6
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Mondal P, Ishigami I, Yeh SR, Wijeratne GB. The Role of Heme Peroxo Oxidants in the Rational Mechanistic Modeling of Nitric Oxide Synthase: Characterization of Key Intermediates and Elucidation of the Mechanism. Angew Chem Int Ed Engl 2022; 61:e202211521. [PMID: 36169890 PMCID: PMC9675724 DOI: 10.1002/anie.202211521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/08/2022]
Abstract
Mammalian nitric oxide synthase (NOS) mediates the two-step O2 -dependent oxidative degradation of arginine, and has been linked to a medley of disease situations in humans. Nonetheless, its exact mechanism of action still remains unclear. This work presents the first NOS model system where biologically proposed heme superoxo and peroxo intermediates are assessed as active oxidants against oxime substrates. Markedly, heme peroxo intermediates engaged in a bioinspired oxime oxidation reaction pathway, converting oximes to ketones and nitroxyl anions (NO- ). Detailed thermodynamic, kinetic, and mechanistic interrogations all evince a rate-limiting step primarily driven by the nucleophilicity of the heme peroxo moiety. Coherent with other findings, 18 O and 15 N isotope substitution experiments herein suffice compelling evidence toward a detailed mechanism, which draw close parallels to one of the enzymatic proposals. Intriguingly, recent enzymatic studies also lend credence to these findings, and several relevant reaction intermediates have been observed during NOS turnover.
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Affiliation(s)
- Pritam Mondal
- Department of Chemistry and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Izumi Ishigami
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | - Gayan B Wijeratne
- Department of Chemistry and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35205, USA
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7
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Peng W, Yan S, Zhang X, Liao L, Zhang J, Shaik S, Wang B. How Do Preorganized Electric Fields Function in Catalytic Cycles? The Case of the Enzyme Tyrosine Hydroxylase. J Am Chem Soc 2022; 144:20484-20494. [DOI: 10.1021/jacs.2c09263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
| | - Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
| | - Xuan Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
| | - Langxing Liao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
| | - Jinyan Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407 Jerusalem, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, People Republic of China
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8
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Zhang H, Wang C, Guo F, Jin L, Song R, Yang F, Ji L, Yu H. In Silico simulation of Cytochrome P450-Mediated metabolism of aromatic amines: A case study of N-Hydroxylation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 237:113544. [PMID: 35483145 DOI: 10.1016/j.ecoenv.2022.113544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 06/14/2023]
Abstract
Aromatic amines, the widely used raw materials in industry, cause long-term exposure to human bodies. They can be metabolized by cytochrome P450 enzymes to form active electrophilic compounds, which will potentially react with nucleophilic DNA to exert carcinogenesis. The short lifetime and versatility of the oxidant (a high-valent iron (IV)-oxo species, compound I) of P450 enzymes prompts us to use theoretical methods to investigate the metabolism of aromatic amines. In this work, the density functional theory (DFT) has been employed to simulate the hydroxylation metabolism through H-abstraction and to calculate the activation energy of this reaction for 28 aromatic amines. The results indicate that the steric effects, inductive effects and conjugative effects greatly contribute to the metabolism activity of the chemicals. The further correlation reveals that the dissociation energy of -NH2 (BDEN-H) can successfully predict the time-consuming calculated activation energy (R2 for aromatic and heteroaromatic amines are 0.93 and 0.86, respectively), so BDEN-H can be taken as a key parameter to characterize the relative stability of aromatic amines in P450 enzymes and further to quickly assess their potential toxicity. The validation results prove such relationship has good statistical performance (qcv2 for aromatic and heteroaromatic amines are 0.95 and 0.90, respectively) and can be used to other aromatic amines in the application domain, greatly reducing computational cost and providing useful support for experimental research.
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Affiliation(s)
- Huanni Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Chenchen Wang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Fangjie Guo
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; Quality and Safety Engineering Institute of Food and Drug, School of Management Engineering and Electronic Commerce, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, China
| | - Lingmin Jin
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, Jinhua 321004, China
| | - Runqian Song
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Fangxing Yang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Li Ji
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, Jinhua 321004, China.
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Medvedev AG, Grishanov DA, Mikhaylov AA, Churakov AV, Tripol'skaya TA, Ottenbacher RV, Bryliakov KP, Shames AI, Lev O, Prikhodchenko PV. Triphenyllead Hydroperoxide: A 1D Coordination Peroxo Polymer, Single-Crystal-to-Single-Crystal Disproportionation to a Superoxo/Hydroxo Complex, and Application in Catalysis. Inorg Chem 2022; 61:8193-8205. [PMID: 35578736 DOI: 10.1021/acs.inorgchem.2c00487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis, transformation, and application in catalysis of triphenyllead hydroperoxide, the first dioxygen lead complex, are described. Triphenyllead hydroperoxide is characterized by 207Pb nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, and single-crystal X-ray diffraction, revealing the first one-dimensional (1D) coordination peroxo polymer. Photolytic isomorphous transformation of Ph3PbOOH yields a mixed hydroxo/superoxo crystalline structure, the first nonalkali superoxo crystalline metal salt, which is stable up to 100 °C. Upon further photolysis, another isomorphous transformation of the superoxide to hydroxide is observed. These are the first single-crystal-to-single-crystal hydroperoxide-to-superoxide and then to hydroxide transformations reported to date. Photolysis of triphenyllead hydroperoxide yields two forms of superoxide-doped crystalline structures that are distinguished by widely different characteristic relaxation times. The use of Ph3PbOOH as an easy-to-handle solid two-electron oxidant for the highly enantioselective epoxidation of olefins is described.
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Affiliation(s)
- Alexander G Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Dmitry A Grishanov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.,Casali Center of Applied Chemistry, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Alexey A Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Andrei V Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Tatiana A Tripol'skaya
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Roman V Ottenbacher
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
| | - Konstantin P Bryliakov
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
| | - Alexander I Shames
- Department of Physics, Ben-Gurion University of Negev, Be'er-Sheva 8410501, Israel
| | - Ovadia Lev
- Casali Center of Applied Chemistry, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Petr V Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
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10
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Gu D, Liang N, Li Q, Li G, Yu D, Liu Y. Selective Photocatalyst for styrene epoxidation with atmospheric O 2 using covalent organic frameworks. Catal Sci Technol 2022. [DOI: 10.1039/d1cy02299g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fe@POG-OH was synthetized and used to photo-catalyze styrene epoxidation with high selectivity and high conversion at room temperature. O2˙− plays crucial roles in the effective and selective oxidation of styrene to styrene oxide.
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Affiliation(s)
- Defa Gu
- School of Chemistry, Beihang University, 37 Xueyuan Rd, Beijing, 100191, China
| | - Nianjie Liang
- School of Chemistry, Beihang University, 37 Xueyuan Rd, Beijing, 100191, China
| | - Qiaosheng Li
- School of Chemistry, Beihang University, 37 Xueyuan Rd, Beijing, 100191, China
| | - Guangwen Li
- Research Institute of Petroleum Processing, SINOPEC, Beijing 100083, China
| | - Dongdong Yu
- School of Chemistry, Beihang University, 37 Xueyuan Rd, Beijing, 100191, China
| | - Yuzhou Liu
- School of Chemistry, Beihang University, 37 Xueyuan Rd, Beijing, 100191, China
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, 37 Xueyuan Rd, Beijing, 100191, China
- Beijing Shenyun Zhihe Technology Co., Ltd., 2 Yongcheng North Rd, Beijing, 100094, China
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11
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Zhang S, Li X, Wang Y, Yan L, Wei J, Liu Y. Computational Study of the C5-Hydroxylation Mechanism Catalyzed by the Diiron Monooxygenase PtmU3 as Part of the Platensimycin Biosynthesis. Inorg Chem 2021; 60:17783-17796. [PMID: 34762413 DOI: 10.1021/acs.inorgchem.1c02407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PtmU3 is a newly identified nonheme diiron monooxygenase, which installs a C-5 β-hydroxyl group into the C-19 CoA-ester intermediate involved in the biosynthesis of unique diterpene-derived scaffolds of platensimycin and platencin. PtmU3 possesses a noncanonical diiron active site architecture of a saturated six-coordinate iron center and lacks the μ-oxo bridge. Although the hydroxylation process is a simple reaction for nonheme mononuclear iron-dependent enzymes, how PtmU3 employs the diiron center to catalyze the H-abstraction and OH-rebound is still unknown. In particular, the electronic characteristic of diiron is also unclear. To understand the catalytic mechanism of PtmU3, we constructed two reactant models in which both the Fe1II-Fe2III-superoxo and Fe1II-Fe2IV═O are considered to trigger the H-abstraction and performed a series of quantum mechanics/molecular mechanics calculations. Our calculation results reveal that PtmU3 is a special monooxygenase, that is, both atoms of the dioxygen molecule can be incorporated into two molecules of the substrate by the successive reactions. In the first-round reaction, PtmU3 uses the Fe1II-Fe2III-superoxo to install a hydroxyl group into the substrate, generating the high-reactive Fe1II-Fe2IV═O complex. In the second-round reaction, the Fe1II-Fe2IV═O species is responsible for the hydroxylation of another molecule of the substrate. In the diiron center, Fe2 adopts the high spin state (S = 5/2) during the catalysis, whereas for Fe1, in addition to its structural role, it may also play an assistant role for Fe1 catalysis. In the two successive OH-installing steps, the H-abstraction is always the rate-liming step. E241 and D308 not only act as bridging ligands to connect two Fe ions but also take part in the electron reorganization. Owing to the high reactivity of Fe1II-Fe2IV═O compared to Fe1II-Fe2III-superoxo, besides the C5-hydroxylation, the C3- or C18-hydroxylation was also calculated to be feasible.
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Affiliation(s)
- Shiqing Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Lijuan Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
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12
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Mondal P, Ishigami I, Gérard EF, Lim C, Yeh SR, de Visser SP, Wijeratne GB. Proton-coupled electron transfer reactivities of electronically divergent heme superoxide intermediates: a kinetic, thermodynamic, and theoretical study. Chem Sci 2021; 12:8872-8883. [PMID: 34257888 PMCID: PMC8246096 DOI: 10.1039/d1sc01952j] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/26/2021] [Indexed: 01/11/2023] Open
Abstract
Heme superoxides are one of the most versatile metallo-intermediates in biology, and they mediate a vast variety of oxidation and oxygenation reactions involving O2(g). Overall proton-coupled electron transfer (PCET) processes they facilitate may proceed via several different mechanistic pathways, attributes of which are not yet fully understood. Herein we present a detailed investigation into concerted PCET events of a series of geometrically similar, but electronically disparate synthetic heme superoxide mimics, where unprecedented, PCET feasibility-determining electronic effects of the heme center have been identified. These electronic factors firmly modulate both thermodynamic and kinetic parameters that are central to PCET, as supported by our experimental and theoretical observations. Consistently, the most electron-deficient superoxide adduct shows the strongest driving force for PCET, whereas the most electron-rich system remains unreactive. The pivotal role of these findings in understanding significant heme systems in biology, as well as in alternative energy applications is also discussed.
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Affiliation(s)
- Pritam Mondal
- Department of Chemistry, University of Alabama at Birmingham Birmingham AL 35205 USA
| | - Izumi Ishigami
- Department of Physiology and Biophysics, Albert Einstein College of Medicine The Bronx New York 10461 USA
| | - Emilie F Gérard
- Manchester Institute of Biotechnology, Department of Chemical Engineering and Analytical Science, The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Chaeeun Lim
- Department of Chemistry, University of Alabama at Birmingham Birmingham AL 35205 USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine The Bronx New York 10461 USA
| | - Sam P de Visser
- Manchester Institute of Biotechnology, Department of Chemical Engineering and Analytical Science, The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Gayan B Wijeratne
- Department of Chemistry, University of Alabama at Birmingham Birmingham AL 35205 USA
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13
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Yan L, Wang Y, Zhang S, Li X, Wei J, Wang Z, Liu Y. Inactivation Mechanism of Neuronal Nitric Oxide Synthase by ( S)-2-Amino-5-(2-(methylthio)acetimidamido)pentanoic Acid: Chemical Conversion of the Inactivator in the Active Site. Inorg Chem 2021; 60:9345-9358. [PMID: 34137256 DOI: 10.1021/acs.inorgchem.1c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neuronal nitric oxide synthase (nNOS) is one of the three isoforms of nitric oxide synthase (NOS). The other two isoforms include inducible NOS (iNOS) and endothelial NOS (eNOS). These three isoforms of NOS are widely present in both human and other mammals and are responsible for the biosynthesis of NO. As an essential biological molecule, NO plays an essential role in neurotransmission, immune response, and vasodilation; however, the overproduction of NO can cause a series of diseases. Thus, the selective inhibition of three isoforms of NOS has been considered to be important in treating related diseases. The active sites of the three enzymes are highly conserved, causing the selective inhibition of the three enzymes to be a great challenge. (S)-2-Amino-5-(2-(methylthio)acetimidamido)pentanoic acid (1) has been experimentally proved to be a selective and time-dependent irreversible inhibitor of nNOS, and three pathways, including sulfide oxidation, oxidative dethiolation, and oxidative demethylation, have been suggested. In this work, we performed quantum mechanics/molecular mechanics calculations to verify the chemical conversion of inactivator 1. Although we agree with the previously suggested chemical transformation process, our calculations demonstrated that there are lower energy pathways to accomplish both oxidative dethiolation and oxidative demethylation. These three branching reactions are competitive, but only dethiolation and demethylation reactions can generate inhibitory intermediates. As a powerful time-dependent irreversible inhibitor of nNOS, the key sulfur atom and middle imine are all necessary. Our calculation results not only verified the chemical reaction of inhibitor 1 occurring in the enzymatic active site but also explained the inactivation mechanism of inhibitor 1. This is also the first verified example of the heme-enzyme-catalyzed S-demethylation mechanism.
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Affiliation(s)
- Lijuan Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Shiqing Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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14
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Liu J, Wu P, Yan S, Li Y, Cao Z, Wang B. Spin-Regulated Inner-Sphere Electron Transfer Enables Efficient O—O Bond Activation in Nonheme Diiron Monooxygenase MIOX. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jia Liu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Peng Wu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Shengheng Yan
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuanyuan Li
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Zexing Cao
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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15
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Jaladanki CK, Khatun S, Gohlke H, Bharatam PV. Reactive Metabolites from Thiazole-Containing Drugs: Quantum Chemical Insights into Biotransformation and Toxicity. Chem Res Toxicol 2021; 34:1503-1517. [PMID: 33900062 DOI: 10.1021/acs.chemrestox.0c00450] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Drugs containing thiazole and aminothiazole groups are known to generate reactive metabolites (RMs) catalyzed by cytochrome P450s (CYPs). These RMs can covalently modify essential cellular macromolecules and lead to toxicity and induce idiosyncratic adverse drug reactions. Molecular docking and quantum chemical hybrid DFT study were carried out to explore the molecular mechanisms involved in the biotransformation of thiazole (TZ) and aminothiazole (ATZ) groups leading to RM epoxide, S-oxide, N-oxide, and oxaziridine. The energy barrier required for the epoxidation is 13.63 kcal/mol, that is lower than that of S-oxidation, N-oxidation, and oxaziridine formation (14.56, 17.90, and 20.20, kcal/mol respectively). The presence of the amino group in ATZ further facilitates all the metabolic pathways, for example, the barrier for the epoxidation reaction is reduced by ∼2.5 kcal/mol. Some of the RMs/their isomers are highly electrophilic and tend to form covalent bonds with nucleophilic amino acids, finally leading to the formation of metabolic intermediate complexes (MICs). The energy profiles of these competitive pathways have also been explored.
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Affiliation(s)
- Chaitanya K Jaladanki
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Samima Khatun
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.,Forschungszentrum Jülich GmbH, John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
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16
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Coleman T, Kirk AM, Chao RR, Podgorski MN, Harbort JS, Churchman LR, Bruning JB, Bernhardt PV, Harmer JR, Krenske EH, De Voss JJ, Bell SG. Understanding the Mechanistic Requirements for Efficient and Stereoselective Alkene Epoxidation by a Cytochrome P450 Enzyme. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04872] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tom Coleman
- Department of Chemistry, University Adelaide, Adelaide, South Australia 5005, Australia
| | - Alicia M. Kirk
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Rebecca R. Chao
- Department of Chemistry, University Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew N. Podgorski
- Department of Chemistry, University Adelaide, Adelaide, South Australia 5005, Australia
| | - Joshua S. Harbort
- Center for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Luke R. Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - John B. Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jeffrey R. Harmer
- Center for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephen G. Bell
- Department of Chemistry, University Adelaide, Adelaide, South Australia 5005, Australia
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17
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Kim H, Rogler PJ, Sharma SK, Schaefer AW, Solomon EI, Karlin KD. Heme-Fe III Superoxide, Peroxide and Hydroperoxide Thermodynamic Relationships: Fe III-O 2•- Complex H-Atom Abstraction Reactivity. J Am Chem Soc 2020; 142:3104-3116. [PMID: 31913628 DOI: 10.1021/jacs.9b12571] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Establishing redox and thermodynamic relationships between metal-ion-bound O2 and its reduced (and protonated) derivatives is critically important for a full understanding of (bio)chemical processes involving dioxygen processing. Here, a ferric heme peroxide complex, [(F8)FeIII-(O22-)]- (P) (F8 = tetrakis(2,6-difluorophenyl)porphyrinate), and a superoxide complex, [(F8)FeIII-(O2•-)] (S), are shown to be redox interconvertible. Using Cr(η-C6H6)2, an equilibrium state where S and P are present is established in tetrahydrofuran (THF) at -80 °C, allowing determination of the reduction potential of S as -1.17 V vs Fc+/0. P could be protonated with 2,6-lutidinium triflate, yielding the low-spin ferric hydroperoxide species, [(F8)FeIII-(OOH)] (HP). Partial conversion of HP back to P using a derivatized phosphazene base gave a P/HP equilibrium mixture, leading to the determination of pKa = 28.8 for HP (THF, -80 °C). With the measured reduction potential and pKa, the O-H bond dissociation free energy (BDFE) of hydroperoxide species HP was calculated to be 73.5 kcal/mol, employing the thermodynamic square scheme and Bordwell relationship. This calculated O-H BDFE of HP, in fact, lines up with an experimental demonstration of the oxidizing ability of S via hydrogen atom transfer (HAT) from TEMPO-H (2,2,6,6-tetramethylpiperdine-N-hydroxide, BDFE = 66.5 kcal/mol in THF), forming the hydroperoxide species HP and TEMPO radical. Kinetic studies carried out with TEMPO-H(D) reveal second-order behavior, kH = 0.5, kD = 0.08 M-1 s-1 (THF, -80 °C); thus, the hydrogen/deuterium kinetic isotope effect (KIE) = 6, consistent with H-atom abstraction by S being the rate-determining step. This appears to be the first case where experimentally derived thermodynamics lead to a ferric heme hydroperoxide OO-H BDFE determination, that FeIII-OOH species being formed via HAT reactivity of the partner ferric heme superoxide complex.
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Affiliation(s)
- Hyun Kim
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Patrick J Rogler
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Savita K Sharma
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Andrew W Schaefer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Kenneth D Karlin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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18
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Mondal P, Wijeratne GB. Modeling Tryptophan/Indoleamine 2,3-Dioxygenase with Heme Superoxide Mimics: Is Ferryl the Key Intermediate? J Am Chem Soc 2020; 142:1846-1856. [PMID: 31870154 DOI: 10.1021/jacs.9b10498] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Tryptophan oxidation in biology has been recently implicated in a vast array of paramount pathogenic conditions in humans, including multiple sclerosis, rheumatoid arthritis, type-I diabetes, and cancer. This 2,3-dioxygenative cleavage of the indole ring of tryptophan with dioxygen is mediated by two heme enzymes, tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO), during its conversion to N-formylkynurenine in the first and rate-limiting step of kynurenine pathway. Despite the pivotal significance of this enzymatic transformation, a vivid viewpoint of the precise mechanistic events is far from complete. A heme superoxide adduct is thought to be the active oxidant in both TDO and IDO, which, following O-O bond cleavage, presumably generates a key ferryl (FeIV=O) reaction intermediate. This study, for the first time in model chemistry, demonstrates the potential of synthetic heme superoxide adducts to mimic the bioinorganic chemistry of indole dioxygenation by TDO and IDO, challenging the widely accepted categorization of these metal adducts as weak oxidants. Herein, an electronically divergent series of ferric heme superoxo oxidants mediates the facile conversion of an array of indole substrates into their corresponding 2,3-dioxygenated products, while shedding light on an unequivocally occurring, putative ferryl intermediate. The oxygenated indole products have been isolated in ∼31% yield, and characterized by LC-MS, 1H and 13C NMR, and FT-IR methodologies, as well as by 18O2(g) labeling experiments. Distinctly, the most electron-deficient superoxo adduct is observed to react the fastest, specifically with the most electron-rich indole substrate, underscoring the cruciality of electrophilicity of the heme superoxide moiety in facilitating the initial indole activation step. Comprehensive understanding of such mechanistic subtleties will benefit future attempts in the rational design of salient therapeutic agents, including next generation anticancer drug targets with amplified effectivity.
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Affiliation(s)
- Pritam Mondal
- Department of Chemistry , University of Alabama at Birmingham , Birmingham , Alabama 35205 , United States
| | - Gayan B Wijeratne
- Department of Chemistry , University of Alabama at Birmingham , Birmingham , Alabama 35205 , United States
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19
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Cherrier MV, Amara P, Talbi B, Salmain M, Fontecilla-Camps JC. Crystallographic evidence for unexpected selective tyrosine hydroxylations in an aerated achiral Ru-papain conjugate. Metallomics 2018; 10:1452-1459. [PMID: 30175357 DOI: 10.1039/c8mt00160j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The X-ray structure of an aerated achiral Ru-papain conjugate has revealed the hydroxylation of two tyrosine residues found near the ruthenium ion. The most likely mechanism involves a ruthenium-bound superoxide as the reactive species responsible for the first hydroxylation and the resulting high valent Ru(iv)[double bond, length as m-dash]O species for the second one.
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Affiliation(s)
- Mickaël V Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins, F-38000 Grenoble, France.
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins, F-38000 Grenoble, France.
| | - Barisa Talbi
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), 4 place Jussieu, 75005, Paris, France
| | - Michèle Salmain
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), 4 place Jussieu, 75005, Paris, France
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20
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Ahmad S, Gautam R, Singhal A, Chauhan S. Significant effect of 5,10,15,20-meso-tetraarylporphyrinatoiron(III) chloride/triflate and acidic/neutral/basic imidazolium ionic liquids in catalytic oxidation of phenols. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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21
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Tian G, Su H, Liu Y. Mechanism of Sulfoxidation and C–S Bond Formation Involved in the Biosynthesis of Ergothioneine Catalyzed by Ergothioneine Synthase (EgtB). ACS Catal 2018. [DOI: 10.1021/acscatal.8b01473] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ge Tian
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
| | - Hao Su
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
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22
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Jana K, Bandyopadhyay T, Ganguly B. Stereoselective Metabolism of Omeprazole by Cytochrome P450 2C19 and 3A4: Mechanistic Insights from DFT Study. J Phys Chem B 2018; 122:5765-5775. [PMID: 29741901 DOI: 10.1021/acs.jpcb.8b01179] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The efficacy of S-omeprazole as a proton pump inhibitor compared with that of its enantiomer R-omeprazole is studied using density functional theoretical calculations. The pharmacokinetic studies suggest that the efficacy of S-omeprazole presumably depends on metabolic pathway and excretion from the human body. The density functional theory calculations at SMDwater-B3LYP-D3/6-311+G(d,p)/LANL2DZ//B3LYP/6-31G(d)/LANL2DZ with triradicaloid model active species, [Por•+FeIV(SH)O], of CYP2C19 enzyme with high-spin quartet and low-spin doublet states demonstrate C-H bond activation mechanism through a two-state rebound process for the hydroxylation of R-omeprazole and S-omeprazole. The calculated activation free energy barriers for the hydrogen abstraction are 15.7 and 17.5 kcal/mol for R-omeprazole and S-omeprazole, respectively. The hydroxylation of R-omeprazole and S-omeprazole is thermodynamically favored; however, the hydroxylated intermediate of S-omeprazole further disintegrates to metabolite 5- O-desmethylomeprazole with a higher kinetic barrier. We have examined the sulfoxidation of S-omeprazole to omeprazole sulfone metabolite by CYP3A4, and the observed activation free energy barrier is 9.9 kcal/mol. The computational results reveal that CYP2C19 exclusively metabolizes R-omeprazole to hydroxyomeprazole, which is hydrophilic and can easily excrete, whereas CYP3A4 metabolizes S-omeprazole to lipophilic sulfone; hence, the excretion of this metabolite would be relatively slower from the body. The spin density analysis and molecular orbital analysis performed using biorthogonalization calculations indicate that R-omeprazole favors high-spin pathway for metabolism process whereas S-omeprazole prefers the low-spin pathway.
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Affiliation(s)
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Chemistry Group MOD LAB , Bhabha Atomic Research Centre , Trombay , Mumbai 400085 , India
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23
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Coleman T, Wong SH, Podgorski MN, Bruning JB, De Voss JJ, Bell SG. Cytochrome P450 CYP199A4 from Rhodopseudomonas palustris Catalyzes Heteroatom Dealkylations, Sulfoxidation, and Amide and Cyclic Hemiacetal Formation. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00909] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Siew Hoon Wong
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia
| | | | - John B. Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia
| | - Stephen G. Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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24
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Zhang LL, Wang XY, Jiang KY, Zhao BY, Yan HM, Zhang XY, Zhang ZX, Guo Z, Che CM. A theoretical study on the oxidation of alkenes to aldehydes catalyzed by ruthenium porphyrins using O 2 as the sole oxidant. Dalton Trans 2018; 47:5286-5297. [PMID: 29569676 DOI: 10.1039/c8dt00614h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Density functional theory (DFT) calculations were used to study the ruthenium porphyrin-catalyzed oxidation of styrene to generate an aldehyde. The results indicate that two reactive oxidants, dioxoruthenium and monooxoruthenium-superoxo porphyrins, participate in the catalytic oxidation. In the mechanism, the resultant monooxoruthenium porphyrin acts in the tandem epoxide isomerization (E-I) to selectively yield an aldehyde and generate a dioxoruthenium porphyrin, thereby triggering new oxidation reaction cycles. In this calculation, several key elements responsible for the observed oxidative ability have been established by using Frontier molecular orbital (FMO) theory, natural bond orbital (NBO) analysis, etc., which include the reaction energy, the spin exchange effect, the spin-state conversion process, and the energy level of the lowest unoccupied molecular orbitals (LUMOs) of the reactive oxidants. The comparative oxidative abilities of the ruthenium-oxo/superoxo compounds with different axial ligands are also investigated. The results suggest that the ruthenium-oxo/superoxo species featuring a chlorine axial ligand is more reactive than that substituted with oxygen. This tuneable reactivity can be understood when considering the different electronic characters of the two ligands and the effective atomic number rule (EAN).
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Affiliation(s)
- Lin-Lin Zhang
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Xiang-Yun Wang
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Kun-Yao Jiang
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Bing-Yuan Zhao
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Hui-Min Yan
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Xiao-Yun Zhang
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Zhu-Xia Zhang
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Zhen Guo
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Chi-Ming Che
- Department of Chemistry, the University of Hong Kong, Hong Kong, P. R. China.
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25
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Fang M, Wilson SR, Suslick KS. A siloxyl bis-pocket thiolate-tailed Fe(III) porphyrin complex. J PORPHYR PHTHALOCYA 2018. [DOI: 10.1142/s1088424617500912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We report the synthesis and characterization of a bis-pocket iron(III) porphyrin complex that has a covalently attached siloxy thiolate group as the axial ligand. As a new cytochrome P450 model compound, this siloxyl bis-pocket thiolate-tailed iron(III) porphyrin is easily synthesized and is surprisingly stable under air due to the extreme steric protection of the siloxy pockets on both faces of the porphyrin. A single-crystal XRD structure has been determined; the Fe–S bond distance is 2.237 (7) Å with Fe–N bond distances of 2.100 (8) and the Fe is 0.5 Å out of the mean porphyrin plane. The Fe–S bond distance in the siloxy thiolate-tailed iron(III) porphyrin is very similar to that in cytochrome P450 and this structure represents a very rare crystallographically-characterized five-coordinate high spin alkylthiolate-tailed ferric porphyrin. EPR spectrum of this compound showed g values and an E/D ratio very similar to those of cytochrome P450 (CYP450) enzyme, demonstrating the importance of using a very basic thiolate group as the axial ligand in P450 model studies. UV-vis studies of its reduced form with carbon monoxide shows a hyper spectrum, which is characteristic of carbonyl complexes of Fe(II)porphyrin thiolates.
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Affiliation(s)
- Ming Fang
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Scott R. Wilson
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kenneth S. Suslick
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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26
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Lai R, Li H. Hydrogen Abstraction of Camphor Catalyzed by Cytochrome P450 cam: A QM/MM Study. J Phys Chem B 2016; 120:12312-12320. [PMID: 27934231 DOI: 10.1021/acs.jpcb.6b09923] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A combined quantum mechanics and molecular mechanics (QM/MM, QM = UB3LYP-D3, MM = AMBER) method is used to study the hydrogen abstraction reaction in P450cam catalyzed hydroxylation of camphor in the quartet state. Compared to QM/MM calculations in the literature, this study uses larger basis sets for the most important atoms at the active site and QM/MM Hessian harmonic frequency calculations to determine the standard Gibbs free energy of activation and kinetic isotope effect. The QM/MM covalent boundary is treated with a capping hydrogen atom method, which is simple and robust. An energy barrier of 21.3 kcal/mol and a standard free energy of activation of 16.8 kcal/mol are obtained for this hydrogen abstraction reaction. These values are similar to those reported in the literature, suggesting that when a general protocol is followed, QM/MM results are reproducible. It is found that using a sufficiently large basis set is important to minimize basis set errors.
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Affiliation(s)
- Rui Lai
- Department of Chemistry and Nebraska Center for Materials and Nanoscience, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States
| | - Hui Li
- Department of Chemistry and Nebraska Center for Materials and Nanoscience, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States
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27
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Al-hunaiti A, Räisänen M, Repo T. From DNA to catalysis: a thymine-acetate ligated non-heme iron(III) catalyst for oxidative activation of aliphatic C-H bonds. Chem Commun (Camb) 2016; 52:2043-6. [PMID: 26685988 DOI: 10.1039/c5cc07597a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A non-heme, iron(III)/THA(thymine-1-acetate) catalyst together with H2O2 as an oxidant is efficient in oxidative C-H activation of alkanes. Although having a higher preference for tertiary C-H bonds, the catalyst also oxidizes aliphatic secondary C-H bonds into carbonyl compounds with good to excellent conversions. Based on the site selectivity of the catalyst and our mechanistic studies the reaction proceeds via an Fe-oxo species without long lived carbon centered radicals.
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Affiliation(s)
- Afnan Al-hunaiti
- Department of Chemistry, University of Helsinki, A. I. Virtasen Aukio 1, P.O. Box 55, 00014 University of Helsinki, Finland.
| | - Minnä Räisänen
- Department of Chemistry, University of Helsinki, A. I. Virtasen Aukio 1, P.O. Box 55, 00014 University of Helsinki, Finland.
| | - Timo Repo
- Department of Chemistry, University of Helsinki, A. I. Virtasen Aukio 1, P.O. Box 55, 00014 University of Helsinki, Finland.
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28
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Dong G, Lu J, Lai W. Insights into the Mechanism of Aromatic Ring Cleavage of Noncatecholic Compound 2-Aminophenol by Aminophenol Dioxygenase: A Quantum Mechanics/Molecular Mechanics Study. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00372] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Geng Dong
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Jiarui Lu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Wenzhen Lai
- Department of Chemistry, Renmin University of China, Beijing 100872, China
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29
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Korobkova EA. Effect of Natural Polyphenols on CYP Metabolism: Implications for Diseases. Chem Res Toxicol 2015; 28:1359-90. [PMID: 26042469 DOI: 10.1021/acs.chemrestox.5b00121] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cytochromes P450 (CYPs) are a large group of hemeproteins located on mitochondrial membranes or the endoplasmic reticulum. They play a crucial role in the metabolism of endogenous and exogenous molecules. The activity of CYP is associated with a number of factors including redox potential, protein conformation, the accessibility of the active site by substrates, and others. This activity may be potentially modulated by a variety of small molecules. Extensive experimental data collected over the past decade point at the active role of natural polyphenols in modulating the catalytic activity of CYP. Polyphenols are widespread micronutrients present in human diets of plant origin and in medicinal herbs. These compounds may alter the activity of CYP either via direct interactions with the enzymes or by affecting CYP gene expression. The polyphenol-CYP interactions may significantly alter the pharmacokinetics of drugs and thus influence the effectiveness of chemical therapies used in the treatment of different types of cancers, diabetes, obesity, and cardiovascular diseases (CVD). CYPs are involved in the oxidation and activation of external carcinogenic agents, in which case the inhibition of the CYP activity is beneficial for health. CYPs also support detoxification processes. In this case, it is the upregulation of CYP genes that would be favorable for the organism. A CYP enzyme aromatase catalyzes the formation of estrone and estradiol from their precursors. CYPs also catalyze multiple reactions leading to the oxidation of estrogen. Estrogen signaling and oxidative metabolism of estrogen are associated with the development of cancer. Thus, polyphenol-mediated modulation of the CYP's activity also plays a vital role in estrogen carcinogenesis. The aim of the present review is to summarize the data collected over the last five to six years on the following topics: (1) the mechanisms of the interactions of CYP with food constituents that occur via the direct binding of polyphenols to the enzymes and (2) the mechanisms of the regulation of CYP gene expression mediated by polyphenols. The structure-activity relationship relevant to the ability of polyphenols to affect the activity of CYP is analyzed. The application of polyphenol-CYP interactions to diseases is discussed.
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Affiliation(s)
- Ekaterina A Korobkova
- John Jay College of Criminal Justice, The Department of Sciences, City University of New York, 524 W 59th Street, New York, New York 10019, United States
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Makino R, Obayashi E, Hori H, Iizuka T, Mashima K, Shiro Y, Ishimura Y. Initial O2 Insertion Step of the Tryptophan Dioxygenase Reaction Proposed by a Heme-Modification Study. Biochemistry 2015; 54:3604-16. [DOI: 10.1021/acs.biochem.5b00048] [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)
- Ryu Makino
- Department
of Life Science, College of Science, Rikkyo University, Nishi-ikebukuro
3-34-1, Toshima-ku, Tokyo 171-8501, Japan
| | - Eiji Obayashi
- Department
of Biochemistry, Shimane University School of Medicine, Izumo, Shimane 693-8501, Japan
| | - Hiroshi Hori
- Center
for Quantum Science and Technology under Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tetsutaro Iizuka
- RIKEN Harima Institute/Spring 8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Keisuke Mashima
- Department
of Life Science, College of Science, Rikkyo University, Nishi-ikebukuro
3-34-1, Toshima-ku, Tokyo 171-8501, Japan
| | - Yoshitsugu Shiro
- RIKEN Harima Institute/Spring 8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yuzuru Ishimura
- Department
of Biochemistry, School of Medicine, Keio University, 35 Shinanomachi,
Shinjuku-ku, Tokyo 160-8582, Japan
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31
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Ji L, Schüürmann G. Computational biotransformation profile of paracetamol catalyzed by cytochrome P450. Chem Res Toxicol 2015; 28:585-96. [PMID: 25548954 DOI: 10.1021/tx5003645] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The P450-catalyzed biotransformation of the analgesic drug paracetamol (PAR) is a long-debated topic, involving different mechanistic hypotheses as well as experimental evidence for the metabolites N-acetyl-p-benzoquinone imine (NAPQI), p-benzoquinone, acetamide, and 3-hydroxy-PAR. During the catalytic cycle of P450, a high-valent iron(IV)-oxo species known as Compound I (Cpd I) is formed as the ultimate oxidant, featuring two energetically close-lying ground states in the doublet (low-spin) and quartet (high-spin) spin states, respectively. In order to clarify the catalytic mechanism, a computational chemistry analysis has been undertaken for both the high- and low-spin routes, employing density functional theory (DFT) including PCM (polarized continuum-solvation model) that yields an approximate simulation of the bulk polarization exerted through the protein. The results demonstrate that hydrogen abstraction transfer (HAT) by the P450 oxidant Cpd I (FeO) is kinetically strongly preferred over the alternative pathways of an oxygen addition reaction (OAR) or two consecutive single-electron transfers (SET). Moreover, only the respective high-spin route yields N-acetyl-p-semiquinone imine (NAPSQI) as an intermediate that is converted to the electrophile N-acetyl-p-benzoquinone imine (NAPQI). By contrast, 3-hydroxy-PAR, acetamide, and p-benzoquinone as electrophilic and redox-active agent are formed predominantly in the low-spin state through reactions that do not involve NAPSQI. Thus, all experimentally observed PAR metabolites are in accord with an initial HAT from the phenolic oxygen, and NAPSQI should indeed be the precursor of NAPQI, both of which are generated only via the high-spin pathway.
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Affiliation(s)
- Li Ji
- †MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.,‡UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318 Leipzig, Germany.,§Institute for Organic Chemistry, Technical University Bergakademie Freiberg, Leipziger Strasse 29, 09596 Freiberg, Germany
| | - Gerrit Schüürmann
- ‡UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318 Leipzig, Germany.,§Institute for Organic Chemistry, Technical University Bergakademie Freiberg, Leipziger Strasse 29, 09596 Freiberg, Germany
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Hirao H, Thellamurege N, Zhang X. Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem 2014; 2:14. [PMID: 24809043 PMCID: PMC4010748 DOI: 10.3389/fchem.2014.00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022] Open
Abstract
The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological UniversitySingapore, Singapore
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33
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Ji L, Zhang J, Liu W, de Visser SP. Metabolism of Halogenated Alkanes by Cytochrome P450 enzymes. Aerobic Oxidation versus Anaerobic Reduction. Chem Asian J 2014; 9:1175-82. [DOI: 10.1002/asia.201301608] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/02/2014] [Indexed: 11/11/2022]
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Dumas VG, Defelipe LA, Petruk AA, Turjanski AG, Marti MA. QM/MM study of the C-C coupling reaction mechanism of CYP121, an essential cytochrome p450 of Mycobacterium tuberculosis. Proteins 2013; 82:1004-21. [PMID: 24356896 DOI: 10.1002/prot.24474] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/15/2013] [Accepted: 11/04/2013] [Indexed: 11/06/2022]
Abstract
Among 20 p450s of Mycobacterium tuberculosis (Mt), CYP121 has received an outstanding interest, not only due to its essentiality for bacterial viability but also because it catalyzes an unusual carbon-carbon coupling reaction. Based on the structure of the substrate bound enzyme, several reaction mechanisms were proposed involving first Tyr radical formation, second Tyr radical formation, and C-C coupling. Key and unknown features, being the nature of the species that generate the first and second radicals, and the role played by the protein scaffold each step. In the present work we have used classical and quantum based computer simulation methods to study in detail its reaction mechanism. Our results show that substrate binding promotes formation of the initial oxy complex, Compound I is the responsible for first Tyr radical formation, and that the second Tyr radical is formed subsequently, through a PCET reaction, promoted by the presence of key residue Arg386. The final C-C coupling reaction possibly occurs in bulk solution, thus yielding the product in one oxygen reduction cycle. Our results thus contribute to a better comprehension of MtCYP121 reaction mechanism, with direct implications for inhibitor design, and also contribute to our general understanding of these type of enzymes.
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Affiliation(s)
- Victoria G Dumas
- Departamento de Quimica Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Química Física de los Materiales Medio Ambiente y Energia (INQUIMAE), UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes, 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
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35
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Cho KB, Kang H, Woo J, Park YJ, Seo MS, Cho J, Nam W. Mechanistic Insights into the C–H Bond Activation of Hydrocarbons by Chromium(IV) Oxo and Chromium(III) Superoxo Complexes. Inorg Chem 2013; 53:645-52. [DOI: 10.1021/ic402831f] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kyung-Bin Cho
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Hyeona Kang
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Jaeyoung Woo
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Young Jun Park
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Mi Sook Seo
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Jaeheung Cho
- Department
of Emerging Materials Science, DGIST, Daegu 711-873, Korea
| | - Wonwoo Nam
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
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36
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Geng J, Liu A. Heme-dependent dioxygenases in tryptophan oxidation. Arch Biochem Biophys 2013; 544:18-26. [PMID: 24295960 DOI: 10.1016/j.abb.2013.11.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 12/29/2022]
Abstract
L-Tryptophan is an essential amino acid for mammals. It is utilized not only for protein synthesis but also for the biosynthesis of serotonin and melatonin by the serotonin pathway as well as nicotinamide adenine dinucleotide by the kynurenine pathway. Although the kynurenine pathway is responsible for the catabolism of over 90% of l-tryptophan in the mammalian intracellular and extracellular pools, the scientific field was dominated in the last century by studies of the serotonin pathway, due to the physiological significance of the latter's catabolic intermediates and products. However, in the past decade, the focus gradually reversed as the link between the kynurenine pathway and various neurodegenerative disorders and immune diseases is increasingly highlighted. Notably, the first step of this pathway, which is catalyzed by heme-dependent dioxygenases, has been proven to be a potential target for immune regulation and cancer treatment. A thorough understanding of the intriguing chemistry of the heme-dependent dioxygenases may yield insight for the drug discovery of these prevalent illnesses. In this review, we survey enzymatic and mechanistic studies, initially started by Kotake and Masayama over 70 years ago, at the molecular level on the heme-dependent tryptophan dioxygenation reactions.
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Affiliation(s)
- Jiafeng Geng
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA 30303, United States
| | - Aimin Liu
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA 30303, United States.
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37
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Sun S, Li ZS, Chen SL. A dominant homolytic O-Cl bond cleavage with low-spin triplet-state Fe(IV)=O formed is revealed in the mechanism of heme-dependent chlorite dismutase. Dalton Trans 2013; 43:973-81. [PMID: 24162174 DOI: 10.1039/c3dt52171k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chlorite dismutase (Cld) is a heme-dependent enzyme that catalyzes the decomposition of toxic chlorite (ClO2(-)) into innocuous chloride and O2. In this paper, using the hybrid B3LYP density functional theory (DFT) method including dispersion interactions, the Cld reaction mechanism has been studied with a chemical model constructed on the X-ray crystal structure. The calculations indicate that the reaction proceeds along a stepwise pathway in the doublet state, i.e. a homolytic O-Cl bond cleavage of the substrate leading to an O-Fe(heme) species and a ClO˙ radical, followed by a rebinding O-O bond formation between them. The O-Fe(heme) species is demonstrated to be a low-spin triplet-state Fe(IV)=O diradicaloid. A low-spin singlet-state Fe(IV)=O is much less stable than the former, with an energy difference of 9.2 kcal mol(-1). The O-Cl bond cleavage is rate-limiting with a barrier of 10.6 kcal mol(-1), in good agreement with the experimental reaction rate of 2.0 × 10(5) s(-1). Furthermore, a heterolytic O-Cl bond dissociation in the initial step is shown to be unreachable, which ensures the high efficiency of the Cld enzyme by avoiding the generation of chlorate byproduct observed in the reactions of synthetic Fe porphyrins. Also, the pathways in the quartet and sextet states are unfavorable for the Cld reaction. The present results reveal a detailed mechanism III (defined in the text) including an interesting di-radical intermediate composed of a low-spin triplet-state Fe(IV)=O and a ClO˙ radical. Compared to a competitive heterolytic Cl-O cleavage in synthetic Fe porphyrins, the revelation of the domination of homolysis in Cld indicates not only the high efficiency of enzyme, but also the sensitivity of a heme and the significance of the enzymatic active-site surroundings (the His170 and Arg183 residues in the present case), which gives more insights into heme chemistry.
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Affiliation(s)
- Shuo Sun
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China.
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Drzewiecka-Matuszek A, Rutkowska-Zbik D, Witko M. Hydrogen peroxide as oxidant in bio-mimetic catalysis by manganese porphyrin: Theoretical DFT studies. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The aim of this study is to elucidate the geometry and electronic structure of various adducts that may be formed between manganese(III) (Mn(III)) porphyrin and hydrogen peroxide. Hydrogen peroxide may interact with Mn(III) porphyrin either as H2O2 or, after dissociation, as OOH–. In the former, it may decompose into two hydroxo groups, which acquire OH– character or an oxo group (=O) and a water molecule. Therefore, the following systems are considered: MnP(H2O2)+, MnP(H2O2)(OH), MnP(OH)3, [Formula: see text], MnPO+, MnPO(OH), MnP(OOH), MnP(OOH)(OH)–, and the possible transformations between them are taken into account. The reported studies are performed within the Density Functional Theory (DFT) method with the GGA-BP functional. The geometry and electronic structures of the structures found along the studied reaction pathways are discussed in terms of interatomic distances, valence angles, Mulliken charges, and spin densities. It was found that different active oxygen species may be formed in the reaction between Mn(III) porphyrin and hydrogen peroxide. As manganese is a transition metal, numerous possible spin states for each of the studied structures are found, where the relative energies of different multiplicities depend strongly on the ligands present in the complex. In view of the catalytic properties, all oxygen-containing ligands are negatively charged, which results in their behaviour as nucleophiles towards hydrocarbons. Finally, the analysis of charge and spin populations on different parts of the studied systems indicate the porphyrin ligand as active in charge transfer processes.
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Affiliation(s)
- Agnieszka Drzewiecka-Matuszek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Krakow, Poland
| | - Dorota Rutkowska-Zbik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Krakow, Poland
| | - Malgorzata Witko
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Krakow, Poland
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39
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van der Kamp MW, Mulholland AJ. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 2013; 52:2708-28. [PMID: 23557014 DOI: 10.1021/bi400215w] [Citation(s) in RCA: 399] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.
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Affiliation(s)
- Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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Davydov R, Dawson JH, Perera R, Hoffman BM. The use of deuterated camphor as a substrate in (1)H ENDOR studies of hydroxylation by cryoreduced oxy P450cam provides new evidence of the involvement of compound I. Biochemistry 2013; 52:667-71. [PMID: 23215047 DOI: 10.1021/bi301527c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Electron paramagnetic resonance and (1)H electron nuclear double resonance (ENDOR) spectroscopies have been used to analyze intermediate states formed during the hydroxylation of (1R)-camphor (H(2)-camphor) and (1R)-5,5-dideuterocamphor (D(2)-camphor) as induced by cryoreduction (77 K) and annealing of the ternary ferrous cytochrome P450cam-O(2)-substrate complex. Hydroxylation of H(2)-camphor produced a primary product state in which 5-exo-hydroxycamphor is coordinated with Fe(III). ENDOR spectra contained signals derived from two protons [Fe(III)-bound C5-OH(exo) and C5-H(endo)] from camphor. When D(2)-camphor was hydroxylated under the same condition in H(2)O or D(2)O buffer, both ENDOR H(exo) and H(endo) signals are absent. For D(2)-camphor in H(2)O buffer, H/D exchange causes the C5-OH(exo) signal to reappear during relaxation upon annealing to 230 K; for H(2)-camphor in D(2)O, the magnitude of the C5-OH(exo) signal decreases via H/D exchange. These observations clearly show that Compound I is the reactive species in the hydroxylation of camphor in P450cam.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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41
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Bushnell EAC, Fortowsky GB, Gauld JW. Model iron-oxo species and the oxidation of imidazole: insights into the mechanism of OvoA and EgtB? Inorg Chem 2012; 51:13351-6. [PMID: 23215044 DOI: 10.1021/ic3021172] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A density functional theory cluster and first-principles quantum and statistical mechanics approach have been used to investigate the ability of iron-oxygen intermediates to oxidize a histidine cosubstrate, which may then allow for the possible formation of 2- and 5-histidylcysteine sulfoxide, respectively. Namely, the ability of ferric superoxo (Fe(III)O(2)(•-)), Fe(IV)═O, and ferrous peroxysulfur (Fe(III)OOS) complexes to oxidize the imidazole of histidine via an electron transfer (ET) or a proton-coupled electron transfer (PCET) was considered. While the high-valent mononuclear Fe(IV)═O species is generally considered the ultimate biooxidant, the free energies for its reduction (via ET or PCET) suggest that it is unable to directly oxidize histidine's imidazole. Instead, only the ferrous peroxysulfur complexes are sufficiently powerful enough oxidants to generate a histidyl-derived radical via a PCET process. Furthermore, while this process preferably forms a HisN(δ)(-H)(•) radical, several such oxidants are also suggested to be capable of generating the higher-energy HisC(δ)(-H)(•) and HisC(ε)(-H)(•) radicals. Importantly, the present results suggest that formation of the sulfoxide-containing products (seen in both OvoA and EgtB) is a consequence of the reduction of a powerful Fe(III)OOS oxidant via a PCET.
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Affiliation(s)
- Eric A C Bushnell
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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Liao RZ, Thiel W. Why Is the Oxidation State of Iron Crucial for the Activity of Heme-Dependent Aldoxime Dehydratase? A QM/MM Study. J Phys Chem B 2012; 116:9396-408. [DOI: 10.1021/jp305510c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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Gonzalez-Ovalle LE, Quesne MG, Kumar D, Goldberg DP, de Visser SP. Axial and equatorial ligand effects on biomimetic cysteine dioxygenase model complexes. Org Biomol Chem 2012; 10:5401-9. [PMID: 22714822 PMCID: PMC3454459 DOI: 10.1039/c2ob25406a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Density functional theory (DFT) calculations are presented on biomimetic model complexes of cysteine dioxygenase and focus on the effect of axial and equatorial ligand placement. Recent studies by one of us [Y. M. Badiei, M. A. Siegler and D. P. Goldberg, J. Am. Chem. Soc. 2011, 133, 1274] gave evidence of a nonheme iron biomimetic model of cysteine dioxygenase using an i-propyl-bis(imino)pyridine, equatorial tridentate ligand. Addition of thiophenol, an anion - either chloride or triflate - and molecular oxygen, led to several possible stereoisomers of this cysteine dioxygenase biomimetic complex. Moreover, large differences in reactivity using chloride as compared to triflate as the binding anion were observed. Here we present a series of DFT calculations on the origin of these reactivity differences and show that it is caused by the preference of coordination site of anion versus thiophenol binding to the chemical system. Thus, stereochemical interactions of triflate and the bulky iso-propyl substituents of the ligand prevent binding of thiophenol in the trans position using triflate. By contrast, smaller anions, such as chloride, can bind in either cis or trans ligand positions and give isomers with similar stability. Our calculations help to explain the observance of thiophenol dioxygenation by this biomimetic system and gives details of the reactivity differences of ligated chloride versus triflate.
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Affiliation(s)
- Luis E. Gonzalez-Ovalle
- Manchester Interdisciplinary Biocenter and School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. Fax: +44 161306 5201
| | - Matthew G. Quesne
- Manchester Interdisciplinary Biocenter and School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. Fax: +44 161306 5201
| | - Devesh Kumar
- Department of Applied Physics, School of Physical Sciences, Babasaheb, Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow 226-025, India
| | - David P. Goldberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
| | - Sam P. de Visser
- Manchester Interdisciplinary Biocenter and School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. Fax: +44 161306 5201
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44
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1,2,3-triazole: unique ligand in promoting iron-catalyzed propargyl alcohol dehydration. Org Lett 2012; 14:2358-61. [PMID: 22524511 DOI: 10.1021/ol300778e] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A 1,2,3-traizole-promoted iron(III)-catalyzed propargyl alcohol dehydration was developed for the synthesis of conjugated enynes. The desired conjugated enynes were prepared in good to excellent yields (up to 95%) with a large substrate scope and excellent stereoselectivity (only Z-isomers).
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45
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Chen H, Cho KB, Lai W, Nam W, Shaik S. Dioxygen Activation by a Non-Heme Iron(II) Complex: Theoretical Study toward Understanding Ferric–Superoxo Complexes. J Chem Theory Comput 2012; 8:915-26. [DOI: 10.1021/ct300015y] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hui Chen
- Beijing National Laboratory for Molecular
Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Kyung-Bin Cho
- Department of Bioinspired Science, Department of Chemistry
and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
| | - Wenzhen Lai
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
- Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Wonwoo Nam
- Department of Bioinspired Science, Department of Chemistry
and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
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46
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Sun XL, Huang XR, Li JL, Huo RP, Sun CC. Mechanism Insights of Ethane C–H Bond Activations by Bare [FeIII═O]+: Explicit Electronic Structure Analysis. J Phys Chem A 2012; 116:1475-85. [DOI: 10.1021/jp2120302] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Xiao-Li Sun
- State Key
Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Xu-Ri Huang
- State Key
Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Ji-Lai Li
- State Key
Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
- Department of Theoretical
Chemistry, Lund University,
Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Rui-Ping Huo
- State Key
Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Chia-Chung Sun
- State Key
Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
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47
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Cho KB, Chen H, Janardanan D, de Visser SP, Shaik S, Nam W. Nonheme iron-oxo and -superoxo reactivities: O2 binding and spin inversion probability matter. Chem Commun (Camb) 2012; 48:2189-91. [DOI: 10.1039/c2cc17610f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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48
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Latifi R, Tahsini L, Nam W, de Visser SP. Regioselectivity of aliphatic versus aromatic hydroxylation by a nonheme iron(ii)-superoxo complex. Phys Chem Chem Phys 2012; 14:2518-24. [DOI: 10.1039/c2cp23352e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Kumar D, Sastry GN, Goldberg DP, de Visser SP. Mechanism of S-oxygenation by a cysteine dioxygenase model complex. J Phys Chem A 2011; 116:582-91. [PMID: 22091701 DOI: 10.1021/jp208230g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, we present the first computational study on a biomimetic cysteine dioxygenase model complex, [Fe(II)(LN(3)S)](+), in which LN(3)S is a tetradentate ligand with a bis(imino)pyridyl scaffold and a pendant arylthiolate group. The reaction mechanism of sulfur dioxygenation with O(2) was examined by density functional theory (DFT) methods and compared with results obtained for cysteine dioxygenase. The reaction proceeds via multistate reactivity patterns on competing singlet, triplet, and quintet spin state surfaces. The reaction mechanism is analogous to that found for cysteine dioxygenase enzymes (Kumar, D.; Thiel, W.; de Visser, S. P. J. Am. Chem. Soc. 2011, 133, 3869-3882); hence, the computations indicate that this complex can closely mimic the enzymatic process. The catalytic mechanism starts from an iron(III)-superoxo complex and the attack of the terminal oxygen atom of the superoxo group on the sulfur atom of the ligand. Subsequently, the dioxygen bond breaks to form an iron(IV)-oxo complex with a bound sulfenato group. After reorganization, the second oxygen atom is transferred to the substrate to give a sulfinic acid product. An alternative mechanism involving the direct attack of dioxygen on the sulfur, without involving any iron-oxygen intermediates, was also examined. Importantly, a significant energetic preference for dioxygen coordinating to the iron center prior to attack at sulfur was discovered and serves to elucidate the function of the metal ion in the reaction process. The computational results are in good agreement with experimental observations, and the differences and similarities of the biomimetic complex and the enzymatic cysteine dioxygenase center are highlighted.
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Affiliation(s)
- Devesh Kumar
- Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India.
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50
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Chung LW, Li X, Hirao H, Morokuma K. Comparative reactivity of ferric-superoxo and ferryl-oxo species in heme and non-heme complexes. J Am Chem Soc 2011; 133:20076-9. [PMID: 22047171 DOI: 10.1021/ja2084898] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ferryl-oxo species have been recognized as a key oxidant in many heme and non-heme enzymes. Recently, less-characterized ferric-superoxo species have been found or suggested to be another electrophilic oxidant. Reactivity of several vital ferryl-oxo and ferric-superoxo model complexes was examined by DFT calculations. Reactivity is found to correlate well with thermodynamic driving force and can increase with higher electrophilicity of the oxidant. Reactivity of the ferric-superoxo oxidants generally is not "superior" to the ferryl-oxo ones. Compared to the high-spin non-heme ferric-superoxo, the lower reactivity of low-spin heme ferric-superoxo, seldom utilized in nature, can be attributed to lower electrophilicity and more pronounced quenching of anti-ferromagnetic coupling between the ferric and superoxo parts. The present comparison should shed some light on mechanistic strategies in heme and non-heme enzymes and provide clues to rational design of ferric-superoxo oxidants.
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Affiliation(s)
- Lung Wa Chung
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan.
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