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Dias AHS, Cao Y, Skaf MS, de Visser SP. Machine learning-aided engineering of a cytochrome P450 for optimal bioconversion of lignin fragments. Phys Chem Chem Phys 2024; 26:17577-17587. [PMID: 38884162 DOI: 10.1039/d4cp01282h] [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: 06/18/2024]
Abstract
Using machine learning, molecular dynamics simulations, and density functional theory calculations we gain insight into the selectivity patterns of substrate activation by the cytochromes P450. In nature, the reactions catalyzed by the P450s lead to the biodegradation of xenobiotics, but recent work has shown that fungi utilize P450s for the activation of lignin fragments, such as monomer and dimer units. These fragments often are the building blocks of valuable materials, including drug molecules and fragrances, hence a highly selective biocatalyst that can produce these compounds in good yield with high selectivity would be an important step in biotechnology. In this work a detailed computational study is reported on two reaction channels of two P450 isozymes, namely the O-deethylation of guaethol by CYP255A and the O-demethylation versus aromatic hydroxylation of p-anisic acid by CYP199A4. The studies show that the second-coordination sphere plays a major role in substrate binding and positioning, heme access, and in the selectivity patterns. Moreover, the local environment affects the kinetics of the reaction through lowering or raising barrier heights. Furthermore, we predict a site-selective mutation for highly specific reaction channels for CYP199A4.
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Affiliation(s)
- Artur Hermano Sampaio Dias
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
- Institute of Chemistry and Centre for Computing in Engineering & Sciences, University of Campinas, Campinas, SP 13083-861, Brazil
| | - Yuanxin Cao
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Munir S Skaf
- Institute of Chemistry and Centre for Computing in Engineering & Sciences, University of Campinas, Campinas, SP 13083-861, Brazil
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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2
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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3
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Product Distributions of Cytochrome P450 OleT JE with Phenyl-Substituted Fatty Acids: A Computational Study. Int J Mol Sci 2021; 22:ijms22137172. [PMID: 34281222 PMCID: PMC8269385 DOI: 10.3390/ijms22137172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
There are two types of cytochrome P450 enzymes in nature, namely, the monooxygenases and the peroxygenases. Both enzyme classes participate in substrate biodegradation or biosynthesis reactions in nature, but the P450 monooxygenases use dioxygen, while the peroxygenases take H2O2 in their catalytic cycle instead. By contrast to the P450 monooxygenases, the P450 peroxygenases do not require an external redox partner to deliver electrons during the catalytic cycle, and also no external proton source is needed. Therefore, they are fully self-sufficient, which affords them opportunities in biotechnological applications. One specific P450 peroxygenase, namely, P450 OleTJE, reacts with long-chain linear fatty acids through oxidative decarboxylation to form hydrocarbons and, as such, has been implicated as a suitable source for the biosynthesis of biofuels. Unfortunately, the reactions were shown to produce a considerable amount of side products originating from Cα and Cβ hydroxylation and desaturation. These product distributions were found to be strongly dependent on whether the substrate had substituents on the Cα and/or Cβ atoms. To understand the bifurcation pathways of substrate activation by P450 OleTJE leading to decarboxylation, Cα hydroxylation, Cβ hydroxylation and Cα–Cβ desaturation, we performed a computational study using 3-phenylpropionate and 2-phenylbutyrate as substrates. We set up large cluster models containing the heme, the substrate and the key features of the substrate binding pocket and calculated (using density functional theory) the pathways leading to the four possible products. This work predicts that the two substrates will react with different reaction rates due to accessibility differences of the substrates to the active oxidant, and, as a consequence, these two substrates will also generate different products. This work explains how the substrate binding pocket of P450 OleTJE guides a reaction to a chemoselectivity.
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Roach S, Faponle AS, Satpathy JK, Sastri CV, de Visser SP. Substrate sulfoxidation by a biomimetic cytochrome P450 Compound I mimic: How do porphyrin and phthalocyanine equatorial ligands compare? J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01917-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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5
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Density Functional Theory Study into the Reaction Mechanism of Isonitrile Biosynthesis by the Nonheme Iron Enzyme ScoE. Top Catal 2021. [DOI: 10.1007/s11244-021-01460-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AbstractThe nonheme iron enzyme ScoE catalyzes the biosynthesis of an isonitrile substituent in a peptide chain. To understand details of the reaction mechanism we created a large active site cluster model of 212 atoms that contains substrate, the active oxidant and the first- and second-coordination sphere of the protein and solvent. Several possible reaction mechanisms were tested and it is shown that isonitrile can only be formed through two consecutive catalytic cycles that both use one molecule of dioxygen and α-ketoglutarate. In both cycles the active species is an iron(IV)-oxo species that in the first reaction cycle reacts through two consecutive hydrogen atom abstraction steps: first from the N–H group and thereafter from the C–H group to desaturate the NH-CH2 bond. The alternative ordering of hydrogen atom abstraction steps was also tested but found to be higher in energy. Moreover, the electronic configurations along that pathway implicate an initial hydride transfer followed by proton transfer. We highlight an active site Lys residue that is shown to donate charge in the transition states and influences the relative barrier heights and bifurcation pathways. A second catalytic cycle of the reaction of iron(IV)-oxo with desaturated substrate starts with hydrogen atom abstraction followed by decarboxylation to give isonitrile directly. The catalytic cycle is completed with a proton transfer to iron(II)-hydroxo to generate the iron(II)-water resting state. The work is compared with experimental observation and previous computational studies on this system and put in a larger perspective of nonheme iron chemistry.
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6
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Zheng H, Li J, Feng C. An isoform-specific pivot modulates the electron transfer between the flavin mononucleotide and heme centers in inducible nitric oxide synthase. J Biol Inorg Chem 2020; 25:1097-1105. [PMID: 33057871 PMCID: PMC7669679 DOI: 10.1007/s00775-020-01824-w] [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: 06/14/2020] [Accepted: 09/24/2020] [Indexed: 11/25/2022]
Abstract
Intraprotein interdomain electron transfer (IET) between the flavin mononucleotide (FMN) and heme centers is an obligatory step in nitric oxide synthase (NOS) enzymes. An isoform-specific pivotal region near Leu406 in the heme domain of human inducible NOS (iNOS) was proposed to mediate the FMN-heme domain-domain alignment (J Inorg Biochem 153:186-196, 2015). The FMN-heme IET rate is a measure of the interdomain FMN/heme complex formation. In this work, the FMN-heme IET kinetics in the wild type (wt) human iNOS oxygenase/FMN (oxyFMN) construct were directly measured by laser flash photolysis with added synthetic peptide related to the pivotal region, in comparison with the wt construct alone. The IET rates were decreased by the iNOS HKL peptide in a dose-saturable fashion, and the inhibitory effect was abolished by a single L406 → E mutation in the peptide. A similar trend in change of the NO synthesis activity of wt iNOS holoenzyme by the peptides was observed. These data, along with the kinetics and modeling results for the L406T and L406F mutant oxyFMN proteins, indicated that the Leu406 residue modulates the FMN-heme IET through hydrophobic interactions. Moreover, the IET rates were analyzed for the wt iNOS oxyFMN protein in the presence of nNOS or eNOS-derived peptide related to the equivalent pivotal heme domain site. These results together indicate that the isoform-specific pivotal region at the heme domain specifically interacts with the conserved FMN domain surface, to facilitate proper interdomain docking for the FMN-heme IET in NOS.
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Affiliation(s)
- Huayu Zheng
- College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jinghui Li
- College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Changjian Feng
- College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA.
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
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7
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Ali HS, Henchman RH, de Visser SP. Lignin Biodegradation by a Cytochrome P450 Enzyme: A Computational Study into Syringol Activation by GcoA. Chemistry 2020; 26:13093-13102. [PMID: 32613677 PMCID: PMC7590115 DOI: 10.1002/chem.202002203] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 12/12/2022]
Abstract
A recently characterized cytochrome P450 isozyme GcoA activates lignin components through a selective O-demethylation or alternatively an acetal formation reaction. These are important reactions in biotechnology and, because lignin is readily available; it being the main component in plant cell walls. In this work we present a density functional theory study on a large active site model of GcoA to investigate syringol activation by an iron(IV)-oxo heme cation radical oxidant (Compound I) leading to hemiacetal and acetal products. Several substrate-binding positions were tested and full energy landscapes calculated. The study shows that substrate positioning determines the product distributions. Thus, with the phenol group pointing away from the heme, an O-demethylation is predicted, whereas an initial hydrogen-atom abstraction of the weak phenolic O-H group would trigger a pathway leading to ring-closure to form acetal products. Predictions on how to engineer P450 GcoA to get more selective product distributions are given.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterOxford RoadManchesterM13 9PLUnited Kingdom
| | - Richard H. Henchman
- Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUnited Kingdom
- Department of ChemistryThe University of ManchesterOxford RoadManchesterM13 9PLUnited Kingdom
| | - Sam P. de Visser
- Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUnited Kingdom
- Department of Chemical Engineering and Analytical ScienceThe University of ManchesterOxford RoadManchesterM13 9PLUnited Kingdom
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8
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Lee CWZ, Mubarak MQE, Green AP, de Visser SP. How Does Replacement of the Axial Histidine Ligand in Cytochrome c Peroxidase by N δ-Methyl Histidine Affect Its Properties and Functions? A Computational Study. Int J Mol Sci 2020; 21:ijms21197133. [PMID: 32992593 PMCID: PMC7583937 DOI: 10.3390/ijms21197133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/27/2022] Open
Abstract
Heme peroxidases have important functions in nature related to the detoxification of H2O2. They generally undergo a catalytic cycle where, in the first stage, the iron(III)-heme-H2O2 complex is converted into an iron(IV)-oxo-heme cation radical species called Compound I. Cytochrome c peroxidase Compound I has a unique electronic configuration among heme enzymes where a metal-based biradical is coupled to a protein radical on a nearby Trp residue. Recent work using the engineered Nδ-methyl histidine-ligated cytochrome c peroxidase highlighted changes in spectroscopic and catalytic properties upon axial ligand substitution. To understand the axial ligand effect on structure and reactivity of peroxidases and their axially Nδ-methyl histidine engineered forms, we did a computational study. We created active site cluster models of various sizes as mimics of horseradish peroxidase and cytochrome c peroxidase Compound I. Subsequently, we performed density functional theory studies on the structure and reactivity of these complexes with a model substrate (styrene). Thus, the work shows that the Nδ-methyl histidine group has little effect on the electronic configuration and structure of Compound I and little changes in bond lengths and the same orbital occupation is obtained. However, the Nδ-methyl histidine modification impacts electron transfer processes due to a change in the reduction potential and thereby influences reactivity patterns for oxygen atom transfer. As such, the substitution of the axial histidine by Nδ-methyl histidine in peroxidases slows down oxygen atom transfer to substrates and makes Compound I a weaker oxidant. These studies are in line with experimental work on Nδ-methyl histidine-ligated cytochrome c peroxidases and highlight how the hydrogen bonding network in the second coordination sphere has a major impact on the function and properties of the enzyme.
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Affiliation(s)
- Calvin W. Z. Lee
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Anthony P. Green
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (C.W.Z.L.); (M.Q.E.M.); (A.P.G.)
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Correspondence: ; Tel.: +44-161-306-4882
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9
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Bioengineering of Cytochrome P450 OleT JE: How Does Substrate Positioning Affect the Product Distributions? Molecules 2020; 25:molecules25112675. [PMID: 32526971 PMCID: PMC7321372 DOI: 10.3390/molecules25112675] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 02/04/2023] Open
Abstract
The cytochromes P450 are versatile enzymes found in all forms of life. Most P450s use dioxygen on a heme center to activate substrates, but one class of P450s utilizes hydrogen peroxide instead. Within the class of P450 peroxygenases, the P450 OleTJE isozyme binds fatty acid substrates and converts them into a range of products through the α-hydroxylation, β-hydroxylation and decarboxylation of the substrate. The latter produces hydrocarbon products and hence can be used as biofuels. The origin of these product distributions is unclear, and, as such, we decided to investigate substrate positioning in the active site and find out what the effect is on the chemoselectivity of the reaction. In this work we present a detailed computational study on the wild-type and engineered structures of P450 OleTJE using a combination of density functional theory and quantum mechanics/molecular mechanics methods. We initially explore the wild-type structure with a variety of methods and models and show that various substrate activation transition states are close in energy and hence small perturbations as through the protein may affect product distributions. We then engineered the protein by generating an in silico model of the double mutant Asn242Arg/Arg245Asn that moves the position of an active site Arg residue in the substrate-binding pocket that is known to form a salt-bridge with the substrate. The substrate activation by the iron(IV)-oxo heme cation radical species (Compound I) was again studied using quantum mechanics/molecular mechanics (QM/MM) methods. Dramatic differences in reactivity patterns, barrier heights and structure are seen, which shows the importance of correct substrate positioning in the protein and the effect of the second-coordination sphere on the selectivity and activity of enzymes.
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10
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Fu Z, Yang L, Sun D, Qu Z, Zhao Y, Gao J, Wang Y. Coupled electron and proton transfer in the piperidine drug metabolism pathway by the active species of cytochromes P450. Dalton Trans 2020; 49:11099-11107. [DOI: 10.1039/c9dt03056e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
KS-DFT and MSDFT studies reveal a novel CEPT step that triggers ring contraction of piperidines by P450.
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Affiliation(s)
- Zhiqiang Fu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- School of Environmental Science and Technology
- Dalian University of Technology
- Dalian 116024
- China
| | - Lili Yang
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- China
| | - Dongru Sun
- Institute of Drug Discovery Technology
- Ningbo University
- Ningbo 315211
- China
| | - Zexing Qu
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- China
| | - Yufen Zhao
- Institute of Drug Discovery Technology
- Ningbo University
- Ningbo 315211
- China
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
- Institute of Systems and Physical Biology
| | - Yong Wang
- Institute of Drug Discovery Technology
- Ningbo University
- Ningbo 315211
- China
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11
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Mukherjee G, Reinhard FGC, Bagha UK, Sastri CV, de Visser SP. Sluggish reactivity by a nonheme iron(iv)-tosylimido complex as compared to its oxo analogue. Dalton Trans 2020; 49:5921-5931. [DOI: 10.1039/d0dt00018c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A comparative spectroscopic and computational study of reactivity between ferryl-tosylimido and ferryl-oxo complexes of two biomimetic model systems. The Fe(iv)-tosylimido complex was found to be sluggish in comparison to its fellow oxo counterpart.
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Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | - Fabián G. Cantú Reinhard
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
| | | | | | - Sam P. de Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
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12
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Ghafoor S, Mansha A, de Visser SP. Selective Hydrogen Atom Abstraction from Dihydroflavonol by a Nonheme Iron Center Is the Key Step in the Enzymatic Flavonol Synthesis and Avoids Byproducts. J Am Chem Soc 2019; 141:20278-20292. [PMID: 31749356 DOI: 10.1021/jacs.9b10526] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The plant non-heme iron dioxygenase flavonol synthase performs a regioselective desaturation reaction as part of the biosynthesis of the signaling molecule flavonol that triggers the growing of leaves and flowers. These compounds also have health benefits for humans. Desaturation of aliphatic compounds generally proceeds through two consecutive hydrogen atom abstraction steps from two adjacent carbon atoms and in nature often is performed by a high-valent iron(IV)-oxo species. We show that the order of the hydrogen atom abstraction steps, however, is opposite of those expected from the C-H bond strengths in the substrate and determines the product distributions. As such, flavonol synthase follows a negative catalysis mechanism. Using density functional theory methods on large active-site model complexes, we investigated pathways for desaturation and hydroxylation by an iron(IV)-oxo active-site model. Contrary to thermochemical predictions, we find that the oxidant abstracts the hydrogen atom from the strong C2-H bond rather than the weaker C3-H bond of the substrate first. We analyze the origin of this unexpected selective hydrogen atom abstraction pathway and find that the alternative C3-H hydrogen atom abstraction would be followed by a low-energy and competitive substrate hydroxylation mechanism hence, should give considerable amount of byproducts. Our computational modeling studies show that substrate positioning in flavonol synthase is essential, as it guides the reactivity to a chemo- and regioselective substrate desaturation from the C2-H group, leading to desaturation products efficiently.
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Affiliation(s)
- Sidra Ghafoor
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science , The University of Manchester , 131 Princess Street , Manchester M1 7DN , United Kingdom.,Department of Chemistry , Government College University Faisalabad , New Campus, Jhang Road , Faisalabad 38000 , Pakistan
| | - Asim Mansha
- Department of Chemistry , Government College University Faisalabad , New Campus, Jhang Road , Faisalabad 38000 , Pakistan
| | - Sam P de Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science , The University of Manchester , 131 Princess Street , Manchester M1 7DN , United Kingdom
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13
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Mubarak MQE, de Visser SP. Reactivity patterns of vanadium(iv/v)-oxo complexes with olefins in the presence of peroxides: a computational study. Dalton Trans 2019; 48:16899-16910. [PMID: 31670737 DOI: 10.1039/c9dt03048d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vanadium porphyrin complexes are naturally occurring substances found in crude oil and have been shown to have medicinal properties as well. Little is known on their activities with substrates; therefore, we decided to perform a detailed density functional theory study on the properties and reactivities of vanadium(iv)- and vanadium(v)-oxo complexes with a TPPCl8 or 2,3,7,8,12,13,17,18-octachloro-meso-tetraphenylporphyrinato ligand system. In particular, we investigated the reactivity of [VV(O)(TPPCl8)]+ and [VIV(O)(TPPCl8)] with cyclohexene in the presence of H2O2 or HCO4-. The work shows that vanadium(iv)-oxo and vanadium(v)-oxo are sluggish oxidants by themselves and react with olefins slowly. However, in the presence of hydrogen peroxide, these metal-oxo species can be transformed into a side-on vanadium-peroxo complex, which reacts with substrates more efficiently. Particularly with anionic axial ligands, the side-on vanadium-peroxo and vanadium-oxo complexes produced epoxides from cyclohexene via small barrier heights. In addition to olefin epoxidation, we investigated aliphatic hydroxylation mechanisms by the same oxidants and some oxidants show efficient and viable cyclohexene hydroxylation mechanisms. The work implies that vanadium-oxo and vanadium-peroxo complexes can react with double bonds through epoxidation, and under certain conditions also undergo hydroxylation, but the overall reactivity is highly dependent on the equatorial ligand, the local environment and the presence or absence of anionic axial ligands.
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Affiliation(s)
- M Qadri E Mubarak
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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14
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Reyes YIA, Franco FC. DFT study on the effect of proximal residues on the Mycobacterium tuberculosis catalase-peroxidase (katG) heme compound I intermediate and its bonding interaction with isoniazid. Phys Chem Chem Phys 2019; 21:16515-16525. [PMID: 31298238 DOI: 10.1039/c9cp01465a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isoniazid (INH) is converted into isonicotinyl radical through its interaction with the catalase-peroxidase (katG) enzyme present in the cells of Mycobacterium tuberculosis (M. tb.), the bacteria that causes the tuberculosis disease. This process is important because resistance of M. tb. cells to INH treatment has been associated with the failure of completion of this process. However, this process is poorly understood and there are a variety of conflicting theories about the details of the mechanism of this process. One theory suggests that INH binds to katG and transfers a single electron to the heme while the heme is in its two electron oxidized state, compound I [Fe(iv)Por˙+] (CpdI). In this study, DFT calculations at the UB3LYP/6-31g(d)-LANL2DZ level of theory are used to study the M. tb. katG CpdI molecule. Different models of the M. tb. CpdI molecule were prepared and the calculations revealed the impact of Trp321 on the electronic properties of the heme. Without Trp321 the heme assumed a triradical state with single electrons on the πxy and πyz orbitals of Fe and another on the a2u orbital of the porphyrin ring that can either be coupled with the first two, to assume a quartet state, or decoupled to form a doublet state. With Trp321, however, a transfer of an electron from the πTrp orbital to a2u porphyrin orbital leads to loss of radical character of the porphyrin and leaves the Trp321 group with a radical character. INH was observed to have strong interaction with CpdI and the absence of Trp321 significantly decreased the binding energy by 2 kcal mol-1 explaining the importance of Trp321 in the binding of INH. The results in this study show the importance of Trp321 in the binding of INH and its effect on its electronic properties, which is consistent with previous experimental findings that mutation of Trp321 results in an increase in drug resistance.
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Affiliation(s)
- Yves Ira A Reyes
- Chemistry Department, De La Salle University, 2401 Taft Avenue, 0922 Manila, Philippines.
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15
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Bignon E, Rizza S, Filomeni G, Papaleo E. Use of Computational Biochemistry for Elucidating Molecular Mechanisms of Nitric Oxide Synthase. Comput Struct Biotechnol J 2019; 17:415-429. [PMID: 30996821 PMCID: PMC6451115 DOI: 10.1016/j.csbj.2019.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/17/2019] [Accepted: 03/21/2019] [Indexed: 12/25/2022] Open
Abstract
Nitric oxide (NO) is an essential signaling molecule in the regulation of multiple cellular processes. It is endogenously synthesized by NO synthase (NOS) as the product of L-arginine oxidation to L-citrulline, requiring NADPH, molecular oxygen, and a pterin cofactor. Two NOS isoforms are constitutively present in cells, nNOS and eNOS, and a third is inducible (iNOS). Despite their biological relevance, the details of their complex structural features and reactivity mechanisms are still unclear. In this review, we summarized the contribution of computational biochemistry to research on NOS molecular mechanisms. We described in detail its use in studying aspects of structure, dynamics and reactivity. We also focus on the numerous outstanding questions in the field that could benefit from more extensive computational investigations.
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Affiliation(s)
- Emmanuelle Bignon
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Salvatore Rizza
- Redox Signaling and Oxidative Stress Group, Cell Stress and Survival Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Signaling and Oxidative Stress Group, Cell Stress and Survival Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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16
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Zhang P, Hu J, Liu B, Yang J, Hou H. Recent advances in metalloporphyrins for environmental and energy applications. CHEMOSPHERE 2019; 219:617-635. [PMID: 30554049 DOI: 10.1016/j.chemosphere.2018.12.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 06/09/2023]
Abstract
Porphyrin-based chemistry has reached an unprecedented period of rapid development after decades of study. Due to attractive multifunctional properties, porphyrins and their analogues have emerged as multifunctional organometals for environmental and energy purposes. In particular, pioneer works have been conducted to explore their application in pollution abatement, energy conversion and storage and molecule recognition. This review summarizes recent advances of porphyrins chemistry, focusing on elucidating the nature of catalytic process. The Fenton-like redox chemistry and photo-excitability of porphyrins and their analogues are discussed, highlighting the generation of high-valent iron oxo porphyrin species. Finally, challenges in current research are identified and perspectives for future development in this area are presented.
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Affiliation(s)
- Peng Zhang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China
| | - Jingping Hu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China.
| | - Bingchuan Liu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China
| | - Jiakuan Yang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China
| | - Huijie Hou
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China.
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17
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A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases. Catalysts 2018. [DOI: 10.3390/catal8080314] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl−/Br−), they react to form hypohalides (OCl−/OBr−) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl−/Br−) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place.
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18
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Postils V, Saint-André M, Timmins A, Li XX, Wang Y, Luis JM, Solà M, de Visser SP. Quantum Mechanics/Molecular Mechanics Studies on the Relative Reactivities of Compound I and II in Cytochrome P450 Enzymes. Int J Mol Sci 2018; 19:E1974. [PMID: 29986417 PMCID: PMC6073316 DOI: 10.3390/ijms19071974] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 02/03/2023] Open
Abstract
The cytochromes P450 are drug metabolizing enzymes in the body that typically react with substrates through a monoxygenation reaction. During the catalytic cycle two reduction and protonation steps generate a high-valent iron (IV)-oxo heme cation radical species called Compound I. However, with sufficient reduction equivalents present, the catalytic cycle should be able to continue to the reduced species of Compound I, called Compound II, rather than a reaction of Compound I with substrate. In particular, since electron transfer is usually on faster timescales than atom transfer, we considered this process feasible and decided to investigate the reaction computationally. In this work we present a computational study using density functional theory methods on active site model complexes alongside quantum mechanics/molecular mechanics calculations on full enzyme structures of cytochrome P450 enzymes. Specifically, we focus on the relative reactivity of Compound I and II with a model substrate for O⁻H bond activation. We show that generally the barrier heights for hydrogen atom abstraction are higher in energy for Compound II than Compound I for O⁻H bond activation. Nevertheless, for the activation of such bonds, Compound II should still be an active oxidant under enzymatic conditions. As such, our computational modelling predicts that under high-reduction environments the cytochromes P450 can react with substrates via Compound II but the rates will be much slower.
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Affiliation(s)
- Verònica Postils
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany i Farnés, 69, 17003 Girona, Catalonia, Spain.
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Maud Saint-André
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Amy Timmins
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Xiao-Xi Li
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Yong Wang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Josep M Luis
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany i Farnés, 69, 17003 Girona, Catalonia, Spain.
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany i Farnés, 69, 17003 Girona, Catalonia, Spain.
| | - Sam P de Visser
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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Mirzaei S, Taherpour AA, Khalilian H. Importance of Azo-Hydrazo Tautomerization in the Oxidative Degradation of Procarbazine by Cytochrome P450: Computational Insights. ChemistrySelect 2018. [DOI: 10.1002/slct.201800633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Saber Mirzaei
- Department of Chemistry; Marquette University, 1414 W. Clybourn St., Milwaukee; WI 53233 USA
| | - Avat Arman Taherpour
- Department of Organic Chemistry; Faculty of Chemistry; Razi University; 67149-67346, Kermanshah, Iran; Medical Biology Research Centre, Kermanshah University of Medical Sciences, Kermanshah Iran
| | - Hossein Khalilian
- Department of Chemistry; University of British Columbia; Okanagan; 3247 University Way, Kelowna, British Columbia V1 V 1 V7 Canada
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20
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Cantú Reinhard FG, Fornarini S, Crestoni ME, de Visser SP. Hydrogen Atom vs. Hydride Transfer in Cytochrome P450 Oxidations: A Combined Mass Spectrometry and Computational Study. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Fabián G. Cantú Reinhard
- Manchester Institute of Biotechnology; School of Chemical Engineering and Analytical Science; University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco; Università di Roma “La Sapienza”; Piazzale Aldo Moro 5 00185 Roma Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco; Università di Roma “La Sapienza”; Piazzale Aldo Moro 5 00185 Roma Italy
| | - Sam P. de Visser
- Manchester Institute of Biotechnology; School of Chemical Engineering and Analytical Science; University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
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21
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Shamovsky I, Belfield G, Lewis R, Narjes F, Ripa L, Tyrchan C, Öberg L, Sjö P. Theoretical studies of the second step of the nitric oxide synthase reaction: Electron tunneling prevents uncoupling. J Inorg Biochem 2018; 181:28-40. [PMID: 29407906 DOI: 10.1016/j.jinorgbio.2018.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/18/2017] [Accepted: 01/08/2018] [Indexed: 12/27/2022]
Abstract
Nitric oxide (NO·) is a messenger molecule with diverse physiological roles including host defense, neurotransmission and vascular function. The synthesis of NO· from l-arginine is catalyzed by NO-synthases and occurs in two steps through the intermediary Nω-hydroxy-l-arginine (NHA). In both steps the P450-like reaction cycle is coupled with the redox cycle of the cofactor tetrahydrobiopterin (H4B). The mechanism of the second step is studied by Density Functional Theory calculations to ascertain the canonical sequence of proton and electron transfer (PT and ET) events. The proposed mechanism is controlled by the interplay of two electron donors, H4B and NHA. Consistent with experimental data, the catalytic cycle proceeds through the ferric-hydroperoxide complex (Cpd 0) and the following aqua-ferriheme resting state, and involves interim partial oxidation of H4B. The mechanism starts with formation of Cpd 0 from the ferrous-dioxy reactant complex by PT from the C-ring heme propionate coupled with hole transfer to H4B through the highest occupied π-orbital of NHA as a bridge. This enables PT from NHA+· to the proximal oxygen leading to the shallow ferriheme-H2O2 oxidant. Subsequent Fenton-like peroxide bond cleavage triggered by ET from the NHA-derived iminoxy-radical leads to the protonated Cpd II diradicaloid singlet stabilized by spin delocalization in H4B, and the closed-shell coordination complex of HO- with iminoxy-cation. The complex is converted to the transient C-adduct, which releases intended products upon PT to the ferriheme-HO- complex coupled with ET to the H4B+·. Deferred ET from the substrate or undue ET from/to the cofactor leads to side products.
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Affiliation(s)
- Igor Shamovsky
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden.
| | - Graham Belfield
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Richard Lewis
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Frank Narjes
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Lena Ripa
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Christian Tyrchan
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Lisa Öberg
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Peter Sjö
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
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22
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Biodegradation of Cosmetics Products: A Computational Study of Cytochrome P450 Metabolism of Phthalates. INORGANICS 2017. [DOI: 10.3390/inorganics5040077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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23
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Jaladanki CK, Shaikh A, Bharatam PV. Biotransformation of Isoniazid by Cytochromes P450: Analyzing the Molecular Mechanism using Density Functional Theory. Chem Res Toxicol 2017; 30:2060-2073. [DOI: 10.1021/acs.chemrestox.7b00129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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
| | - Akbar Shaikh
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar, Mohali, 160 062 Punjab, India
| | - 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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24
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Faponle AS, Seebeck FP, de Visser SP. Sulfoxide Synthase versus Cysteine Dioxygenase Reactivity in a Nonheme Iron Enzyme. J Am Chem Soc 2017; 139:9259-9270. [PMID: 28602090 DOI: 10.1021/jacs.7b04251] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sulfoxide synthase EgtB represents a unique family of nonheme iron enzymes that catalyze the formation of a C-S bond between N-α-trimethyl histidine and γ-glutamyl cysteine, which is the key step in the biosynthesis of ergothioneine, an important amino acid related to aging. A controversy has arisen regarding its catalytic mechanism related to the function of the active-site Tyr377 residue. The biosynthesis of ergothioneine in EgtB shows structural similarities to cysteine dioxygenase which transfers two oxygen atoms to the thiolate group of cysteine. The question, therefore, is how do EgtB enzymes catalyze the C-S bond-formation reaction, while also preventing a dioxygenation of its cysteinate substrate? In this work we present a quantum mechanics/molecular mechanics study into the mechanism of sulfoxide synthase enzymes as compared to cysteine dioxygenase enzymes and present pathways for both reaction channels in EgtB. We show that EgtB contains a conserved tyrosine residue that reacts via proton-coupled electron transfer with the iron(III)-superoxo species and creates an iron(III)-hydroperoxo intermediate, thereby preventing the possible thiolate dioxygenation side reaction. The nucleophilic C-S bond-formation step happens subsequently concomitant to relay of the proton of the iron(II)-hydroperoxo back to Tyr377. This is the rate-determining step in the reaction cycle and is followed by hydrogen-atom transfer from the CE1-H group of trimethyl histidine substrate to iron(II)-superoxo. In the final step, a quick and almost barrierless sulfoxidation leads to the sulfoxide product complexes. The work highlights a unique machinery and active-site setup of the enzyme that drives the sulfoxide synthase reaction.
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Affiliation(s)
- Abayomi S Faponle
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Florian P Seebeck
- Department for Chemistry, University of Basel , St. Johanns-Ring 19, Basel 4056, Switzerland
| | - Sam P de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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25
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Zhang X, Li XX, Liu Y, Wang Y. Suicide Inhibition of Cytochrome P450 Enzymes by Cyclopropylamines via a Ring-Opening Mechanism: Proton-Coupled Electron Transfer Makes a Difference. Front Chem 2017; 5:3. [PMID: 28197402 PMCID: PMC5281577 DOI: 10.3389/fchem.2017.00003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 01/10/2017] [Indexed: 01/27/2023] Open
Abstract
N-benzyl-N-cyclopropylamine (BCA) has been attracting great interests for decades for its partial suicide inactivation role to cytochrome P450 (P450) via a ring-opening mechanism besides acting as a role of normal substrates. Understanding the mechanism of such partial inactivation is vital to the clinical drug design. Thus, density functional theoretical (DFT) calculations were carried out on such P450-catalyzed reactions, not only on the metabolic pathway, but on the ring-opening inactivation one. Our theoretical results demonstrated that, in the metabolic pathway, besides the normal carbinolamine, an unexpected enamine was formed via the dual hydrogen abstraction (DHA) process, in which the competition between rotation of the H-abstracted substrate radical and the rotation of hydroxyl group of the protonated Cpd II moiety plays a significant role in product branch; In the inactivation pathway, the well-noted single electron transfer (SET) mechanism-involved process was invalidated for its high energy barrier, a proton-coupled electron transfer [PCET(ET)] mechanism plays a role. Our results are consistent with other related theoretical works on heteroatom-hydrogen (X-H, X = O, N) activation and revealed new features. The revealed mechanisms will play a positive role in relative drug design.
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Affiliation(s)
- Xiaoqian Zhang
- College of Physics and Materials Science, Henan Normal University Xinxiang, China
| | - Xiao-Xi Li
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences Lanzhou, China
| | - Yufang Liu
- College of Physics and Materials Science, Henan Normal University Xinxiang, China
| | - Yong Wang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences Lanzhou, China
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26
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Faponle AS, de Visser SP. The Role of Nonheme Transition Metal-Oxo, -Peroxo, and -Superoxo Intermediates in Enzyme Catalysis and Reactions of Bioinspired Complexes. ADVANCES IN INORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.adioch.2017.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Cantú Reinhard FG, Sainna MA, Upadhyay P, Balan GA, Kumar D, Fornarini S, Crestoni ME, de Visser SP. A Systematic Account on Aromatic Hydroxylation by a Cytochrome P450 Model Compound I: A Low-Pressure Mass Spectrometry and Computational Study. Chemistry 2016; 22:18608-18619. [PMID: 27727524 DOI: 10.1002/chem.201604361] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Indexed: 01/20/2023]
Abstract
Cytochrome P450 enzymes are heme-containing mono-oxygenases that mainly react through oxygen-atom transfer. Specific features of substrate and oxidant that determine the reaction rate constant for oxygen atom transfer are still poorly understood and therefore, we did a systematic gas-phase study on reactions by iron(IV)-oxo porphyrin cation radical structures with arenes. We present herein the first results obtained by using Fourier transform-ion cyclotron resonance mass spectrometry and provide rate constants and product distributions for the assayed reactions. Product distributions and kinetic isotope effect studies implicate a rate-determining aromatic hydroxylation reaction that correlates with the ionization energy of the substrate and no evidence of aliphatic hydroxylation products is observed. To further understand the details of the reaction mechanism, a computational study on a model complex was performed. These studies confirm the experimental hypothesis of dominant aromatic over aliphatic hydroxylation and show that the lack of an axial ligand affects the aliphatic pathways. Moreover, a two-parabola valence bond model is used to rationalize the rate constant and identify key properties of the oxidant and substrate that drive the reaction. In particular, the work shows that aromatic hydroxylation rates correlate with the ionization energy of the substrate as well as with the electron affinity of the oxidant.
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Affiliation(s)
- Fabián G Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Mala A Sainna
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Pranav Upadhyay
- Department of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow (UP, 226025, India
| | - G Alex Balan
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Devesh Kumar
- Department of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow (UP, 226025, India
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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28
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Morozov AN, Chatfield DC. How the Proximal Pocket May Influence the Enantiospecificities of Chloroperoxidase-Catalyzed Epoxidations of Olefins. Int J Mol Sci 2016; 17:E1297. [PMID: 27517911 PMCID: PMC5000694 DOI: 10.3390/ijms17081297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/28/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022] Open
Abstract
Chloroperoxidase-catalyzed enantiospecific epoxidations of olefins are of significant biotechnological interest. Typical enantiomeric excesses are in the range of 66%-97% and translate into free energy differences on the order of 1 kcal/mol. These differences are generally attributed to the effect of the distal pocket. In this paper, we show that the influence of the proximal pocket on the electron transfer mechanism in the rate-limiting event may be just as significant for a quantitatively accurate account of the experimentally-measured enantiospecificities.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA.
| | - David C Chatfield
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA.
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29
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de Visser SP, Stillman MJ. Challenging Density Functional Theory Calculations with Hemes and Porphyrins. Int J Mol Sci 2016; 17:519. [PMID: 27070578 PMCID: PMC4848975 DOI: 10.3390/ijms17040519] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 01/09/2023] Open
Abstract
In this paper we review recent advances in computational chemistry and specifically focus on the chemical description of heme proteins and synthetic porphyrins that act as both mimics of natural processes and technological uses. These are challenging biochemical systems involved in electron transfer as well as biocatalysis processes. In recent years computational tools have improved considerably and now can reproduce experimental spectroscopic and reactivity studies within a reasonable error margin (several kcal·mol(-1)). This paper gives recent examples from our groups, where we investigated heme and synthetic metal-porphyrin systems. The four case studies highlight how computational modelling can correctly reproduce experimental product distributions, predicted reactivity trends and guide interpretation of electronic structures of complex systems. The case studies focus on the calculations of a variety of spectroscopic features of porphyrins and show how computational modelling gives important insight that explains the experimental spectra and can lead to the design of porphyrins with tuned properties.
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Affiliation(s)
- Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, the University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Martin J Stillman
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada.
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30
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Quesne MG, Senthilnathan D, Singh D, Kumar D, Maldivi P, Sorokin AB, de Visser SP. Origin of the Enhanced Reactivity of μ-Nitrido-Bridged Diiron(IV)-Oxo Porphyrinoid Complexes over Cytochrome P450 Compound I. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02720] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Matthew G. Quesne
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Dhurairajan Senthilnathan
- Univ. Grenoble Alpes, INAC-SCIB, Reconnaissance
Ionique et Chimie de Coordination, F-38000 Grenoble, France
- Center for
Computational Chemistry, CRD, PRIST University, Vallam, Thanjavur, Tamilnadu 613403, India
| | - Devendra Singh
- Department
of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, Uttar Pradesh 226025, India
| | - Devesh Kumar
- Department
of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, Uttar Pradesh 226025, India
| | - Pascale Maldivi
- Univ. Grenoble Alpes, INAC-SCIB, Reconnaissance
Ionique et Chimie de Coordination, F-38000 Grenoble, France
- CEA, INAC-SCIB, F-38000 Grenoble, France
| | - Alexander B. Sorokin
- Institut
de Recherches sur la Catalyse et l’Environnement de Lyon (IRCELYON),
UMR 5256, CNRS-Université Lyon 1, 2, av. A. Einstein, 69626 Villeurbanne, France
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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31
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Pardillo AD, Morozov AN, Chatfield DC. Proximal Pocket Hydrogen Bonds Significantly Influence the Mechanism of Chloroperoxidase Compound I Formation. J Phys Chem B 2015; 119:12590-602. [DOI: 10.1021/acs.jpcb.5b06324] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Armando D. Pardillo
- Department of Chemistry and
Biochemistry, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, United States
| | - Alexander N. Morozov
- Department of Chemistry and
Biochemistry, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, United States
| | - David C. Chatfield
- Department of Chemistry and
Biochemistry, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, United States
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32
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Postils V, Company A, Solà M, Costas M, Luis JM. Computational Insight into the Mechanism of Alkane Hydroxylation by Non-heme Fe(PyTACN) Iron Complexes. Effects of the Substrate and Solvent. Inorg Chem 2015; 54:8223-36. [DOI: 10.1021/acs.inorgchem.5b00583] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Verònica Postils
- Institut de Química
Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain
| | - Anna Company
- Institut de Química
Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain
| | - Miquel Solà
- Institut de Química
Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain
| | - Miquel Costas
- Institut de Química
Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain
| | - Josep M. Luis
- Institut de Química
Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain
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33
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İşci Ü, Faponle AS, Afanasiev P, Albrieux F, Briois V, Ahsen V, Dumoulin F, Sorokin AB, de Visser SP. Site-selective formation of an iron(iv)-oxo species at the more electron-rich iron atom of heteroleptic μ-nitrido diiron phthalocyanines. Chem Sci 2015; 6:5063-5075. [PMID: 30155008 PMCID: PMC6088558 DOI: 10.1039/c5sc01811k] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/16/2015] [Indexed: 11/21/2022] Open
Abstract
A combination of MS and computation on μ-nitrido bridged diiron complexes reveals H2O2 binding to the complex and generates an oxidant capable of oxidizing methane.
Iron(iv)–oxo species have been identified as the active intermediates in key enzymatic processes, and their catalytic properties are strongly affected by the equatorial and axial ligands bound to the metal, but details of these effects are still unresolved. In our aim to create better and more efficient oxidants of H-atom abstraction reactions, we have investigated a unique heteroleptic diiron phthalocyanine complex. We propose a novel intramolecular approach to determine the structural features that govern the catalytic activity of iron(iv)–oxo sites. Heteroleptic μ-nitrido diiron phthalocyanine complexes having an unsubstituted phthalocyanine (Pc1) and a phthalocyanine ligand substituted with electron-withdrawing alkylsulfonyl groups (PcSO2R) were prepared and characterized. A reaction with terminal oxidants gives two isomeric iron(iv)–oxo and iron(iii)–hydroperoxo species with abundances dependent on the equatorial ligand. Cryospray ionization mass spectrometry (CSI-MS) characterized both hydroperoxo and diiron oxo species in the presence of H2O2. When m-CPBA was used as the oxidant, the formation of diiron oxo species (PcSO2R)FeNFe(Pc1)
Created by potrace 1.16, written by Peter Selinger 2001-2019
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O was also evidenced. Sufficient amounts of these transient species were trapped in the quadrupole region of the mass-spectrometer and underwent a CID-MS/MS fragmentation. Analyses of fragmentation patterns indicated a preferential formation of hydroperoxo and oxo moieties at more electron-rich iron sites of both heteroleptic μ-nitrido complexes. DFT calculations show that both isomers are close in energy. However, the analysis of the iron(iii)–hydroperoxo bond strength reveals major differences for the (Pc1)FeN(PcSO2R)FeIIIOOH system as compared to (PcSO2R)FeN(Pc1)FeIIIOOH system, and, hence binding of a terminal oxidant will be preferentially on more electron-rich sides. Subsequent kinetics studies showed that these oxidants are able to even oxidize methane to formic acid efficiently.
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Affiliation(s)
- Ümit İşci
- Gebze Technical University , Department of Chemistry , P.O. Box 141, Gebze , 41400 Kocaeli , Turkey .
| | - Abayomi S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science , The University of Manchester , 131 Princess Street , Manchester M1 7DN , UK .
| | - Pavel Afanasiev
- Institut de Recherches sur la Catalyse et l'Environnement de Lyon (IRCELYON) , UMR 5256 , CNRS-Université Lyon 1 , 2, av. A. Einstein , 69626 Villeurbanne Cedex , France .
| | - Florian Albrieux
- Centre Commun de Spectrométrie de Masse UMR 5246 , CNRS-Université Claude Bernard Lyon 1 , Université de Lyon , Bâtiment Curien , 43, bd du 11 Novembre , 69622 Villeurbanne Cedex , France
| | - Valérie Briois
- Synchrotron Soleil , L'orme des merisiers, St-Aubin , 91192 Gif-sur-Yvette , France
| | - Vefa Ahsen
- Gebze Technical University , Department of Chemistry , P.O. Box 141, Gebze , 41400 Kocaeli , Turkey .
| | - Fabienne Dumoulin
- Gebze Technical University , Department of Chemistry , P.O. Box 141, Gebze , 41400 Kocaeli , Turkey .
| | - Alexander B Sorokin
- Institut de Recherches sur la Catalyse et l'Environnement de Lyon (IRCELYON) , UMR 5256 , CNRS-Université Lyon 1 , 2, av. A. Einstein , 69626 Villeurbanne Cedex , France .
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science , The University of Manchester , 131 Princess Street , Manchester M1 7DN , UK .
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Karamzadeh B, Singh D, Nam W, Kumar D, de Visser SP. Properties and reactivities of nonheme iron(IV)-oxo versus iron(V)-oxo: long-range electron transfer versus hydrogen atom abstraction. Phys Chem Chem Phys 2015; 16:22611-22. [PMID: 25231726 DOI: 10.1039/c4cp03053b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent work of Nam and co-workers [J. Yoon, S. A. Wilson, Y. K. Jang, M. S. Seo, K. Nehru, B. Hedman, K. O. Hodgson, E. Bill, E. I. Solomon and W. Nam, Angew. Chem., Int. Ed., 2009, 48, 1257] on a biomimetic iron complex implicated a mixture of iron(IV)-oxo and iron(V)-oxo intermediates but the latter could not be spectroscopically characterized, hence its involvement was postulated. To gain insight into the relative activity of these iron(IV)-oxo versus iron(V)-oxo intermediates, we have performed an extensive density functional theory (DFT) study on the chemical properties of the chemical system of Nam et al., namely [Fe(O)(BQEN)(NCCH3)](2+/3+) with BQEN = N,N'-dimethyl-N,N'-bis(8-quinolyl)ethane-1,2-diamine and their reactivity in hydrogen atom abstraction from ethylbenzene. We show that the perceived iron(V)-oxo species actually is an iron(IV)-oxo ligand cation radical, similar to cytochrome P450 compound I. Moreover, this intermediate has an extremely large electron affinity and therefore can abstract electrons from substrates readily. In our particular system, this means that prior to the hydrogen atom abstraction, an electron is abstracted to form an iron(IV)-oxo species, which subsequently abstracts a hydrogen atom from the substrate. Thus, our calculations show for the first time how some nonheme iron complexes react by long-range electron transfer and others directly via hydrogen atom abstraction. We have rationalized our results with detailed thermochemical cycles that explain the observed reactivity patterns.
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Affiliation(s)
- Baharan Karamzadeh
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, the University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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35
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Sainna MA, Singh D, Kumar D, de Visser SP. A Trimetal Carbene with Reactivity Reminiscent of Fischer–Tropsch Catalysis. Organometallics 2015. [DOI: 10.1021/acs.organomet.5b00305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mala A. Sainna
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Devendra Singh
- Department
of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow (U. P.) 226 025, India
| | - Devesh Kumar
- Department
of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow (U. P.) 226 025, India
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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36
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Ji L, Faponle AS, Quesne MG, Sainna MA, Zhang J, Franke A, Kumar D, van Eldik R, Liu W, de Visser SP. Drug metabolism by cytochrome p450 enzymes: what distinguishes the pathways leading to substrate hydroxylation over desaturation? Chemistry 2015; 21:9083-92. [PMID: 25924594 DOI: 10.1002/chem.201500329] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Indexed: 01/05/2023]
Abstract
Cytochrome P450 enzymes are highly versatile biological catalysts in our body that react with a broad range of substrates. Key functions in the liver include the metabolism of drugs and xenobiotics. One particular metabolic pathway that is poorly understood relates to the P450 activation of aliphatic groups leading to either hydroxylation or desaturation pathways. A DFT and QM/MM study has been carried out on the factors that determine the regioselectivity of aliphatic hydroxylation over desaturation of compounds by P450 isozymes. The calculations establish multistate reactivity patterns, whereby the product distributions differ on each of the spin-state surfaces; hence spin-selective product formation was found. The electronic and thermochemical factors that determine the bifurcation pathways were analysed and a model that predicts the regioselectivity of aliphatic hydroxylation over desaturation pathways was established from valence bond and molecular orbital theories. Thus, the difference in energy of the OH versus the OC bond formed and the π-conjugation energy determines the degree of desaturation products. In addition, environmental effects of the substrate binding pocket that affect the regioselectivities were identified. These studies imply that bioengineering P450 isozymes for desaturation reactions will have to include modifications in the substrate binding pocket to restrict the hydroxylation rebound reaction.
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Affiliation(s)
- Li Ji
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China)
| | - Abayomi S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK)
| | - Matthew G Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK)
| | - Mala A Sainna
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK)
| | - Jing Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China)
| | - Alicja Franke
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen (Germany)
| | - Devesh Kumar
- Department of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rai Bareilly Road, Lucknow 226 025 (India)
| | - Rudi van Eldik
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen (Germany).,Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow (Poland)
| | - Weiping Liu
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China).
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK).
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Sahoo D, Quesne MG, de Visser SP, Rath SP. Hydrogen-Bonding Interactions Trigger a Spin-Flip in Iron(III) Porphyrin Complexes. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 127:4878-4882. [PMID: 26109743 PMCID: PMC4470476 DOI: 10.1002/ange.201411399] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Indexed: 11/16/2022]
Abstract
A key step in cytochrome P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure of a five-coordinate iron(III) octaethyltetraarylporphyrin chloride. The spin state of the metal was found to switch reversibly between high (S=5/2) and intermediate spin (S=3/2) with hydrogen bonding. Our study highlights the possible effects and importance of hydrogen-bonding interactions in heme proteins. This is the first example of a synthetic iron(III) complex that can reversibly change its spin state between a high and an intermediate state through weak external perturbations.
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Affiliation(s)
- Dipankar Sahoo
- Department of Chemistry, Indian Institute of Technology KanpurKanpur-208016 (India)
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK)
| | - Matthew G Quesne
- Department of Chemistry, Indian Institute of Technology KanpurKanpur-208016 (India)
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK)
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Chuanprasit P, Goh SH, Hirao H. Benzyne Formation in the Mechanism-Based Inactivation of Cytochrome P450 by 1-Aminobenzotriazole and N-Benzyl-1-Aminobenzotriazole: Computational Insights. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pratanphorn Chuanprasit
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Shu Hui Goh
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Hajime Hirao
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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39
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Samanta S, Das PK, Chatterjee S, Dey A. Effect of axial ligands on electronic structure and O2 reduction by iron porphyrin complexes: Towards a quantitative understanding of the "push effect". J PORPHYR PHTHALOCYA 2015. [DOI: 10.1142/s1088424615300049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Axial ligands play a dominating role in determining the electronic structure and reactivity of iron porphyrin active sites and synthetic models. Several properties unique to the cysteine bound heme enzyme, cytochrome P450, is attributed to the "push effect" of the thiolate axial ligand. In this mini-review the ground state electronic structure of iron porphyrins with imidazole, phenolate and thiolate complexes, derived using a combination of spectroscopy and DFT calculations, are discussed. The differences in kinetics and selectivity of oxygen reduction reaction (ORR), catalyzed by these iron porphyrin complexes with different axial ligands, help elucidate the varying push effects of the different axial ligands on oxygen activation by ferrous porphyrin. The spectroscopic and kinetic data help to develop a quantitative understanding of the "push effect" and, in particular, the electrostatic and covalent contributions to it.
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Affiliation(s)
- Subhra Samanta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Pradip Kumar Das
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sudipta Chatterjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
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40
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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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Sahoo D, Quesne MG, de Visser SP, Rath SP. Hydrogen-bonding interactions trigger a spin-flip in iron(III) porphyrin complexes. Angew Chem Int Ed Engl 2015; 54:4796-800. [PMID: 25645603 PMCID: PMC4687417 DOI: 10.1002/anie.201411399] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Indexed: 12/03/2022]
Abstract
A key step in cytochrome P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure of a five-coordinate iron(III) octaethyltetraarylporphyrin chloride. The spin state of the metal was found to switch reversibly between high (S=5/2) and intermediate spin (S=3/2) with hydrogen bonding. Our study highlights the possible effects and importance of hydrogen-bonding interactions in heme proteins. This is the first example of a synthetic iron(III) complex that can reversibly change its spin state between a high and an intermediate state through weak external perturbations.
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Affiliation(s)
- Dipankar Sahoo
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016 (India)
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42
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An attempt to evaluate the effect of proton-coupled electron transfer on the H-abstraction step of the reaction between 1,1-dimethylhydrazine and cytochrome P450 compound I. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.12.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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43
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Kumar S, Faponle AS, Barman P, Vardhaman AK, Sastri CV, Kumar D, de Visser SP. Long-Range Electron Transfer Triggers Mechanistic Differences between Iron(IV)-Oxo and Iron(IV)-Imido Oxidants. J Am Chem Soc 2014; 136:17102-15. [DOI: 10.1021/ja508403w] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Suresh Kumar
- Department
of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow, 226025 Uttar Pradesh, India
| | - Abayomi S. Faponle
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Prasenjit Barman
- Department
of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Anil Kumar Vardhaman
- Department
of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Chivukula V. Sastri
- Department
of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Devesh Kumar
- Department
of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareilly Road, Lucknow, 226025 Uttar Pradesh, India
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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Ripa L, Mee C, Sjö P, Shamovsky I. Theoretical Studies of the Mechanism of N-Hydroxylation of Primary Aromatic Amines by Cytochrome P450 1A2: Radicaloid or Anionic? Chem Res Toxicol 2014; 27:265-78. [DOI: 10.1021/tx400376u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lena Ripa
- Department of Medicinal Chemistry, RIA iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Christine Mee
- Genetic Toxicology, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Peter Sjö
- Department of Medicinal Chemistry, RIA iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
| | - Igor Shamovsky
- Department of Medicinal Chemistry, RIA iMed, AstraZeneca R&D, Pepparedsleden 1, S-431 83 Mölndal, Sweden
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 436] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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Liu Z, Wang Y, Li J, Zhang R. The effect of γ-Al2O3 surface hydroxylation on the stability and nucleation of Ni in Ni/γ-Al2O3 catalyst: a theoretical study. RSC Adv 2014. [DOI: 10.1039/c3ra46352d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Samanta S, Das PK, Chatterjee S, Sengupta K, Mondal B, Dey A. O2 Reduction Reaction by Biologically Relevant Anionic Ligand Bound Iron Porphyrin Complexes. Inorg Chem 2013; 52:12963-71. [DOI: 10.1021/ic4020652] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Subhra Samanta
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Pradip Kumar Das
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Sudipta Chatterjee
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Kushal Sengupta
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Biswajit Mondal
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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de Visser SP. Differences in chemical properties and reactivity patterns of mono- and dioxomanganese(V) porphyrins as revealed by density functional theory. J PORPHYR PHTHALOCYA 2013. [DOI: 10.1142/s1088424613500661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent experimental studies of Liu and Groves (J. Am. Chem. Soc. 2010; 132: 12847) on dioxomanganese(V) porphyrin complexes implicated substrate halogenation in good yield. Currently, little is known of this unique mechanism, therefore to gain understanding on the halogenation mechanism and the chemical features of this oxidant we decided to do a computational (density functional theory) study. We show that the dioxomanganese(V) complex has considerably different molecular (valence) orbitals as compared to monooxomanganese(V) porphyrin due to mixing of the metal 3d orbitals with 2p orbitals on both oxygen atoms. This results in a set of three pairs of orbitals of which the bonding and nonbonding pairs are doubly occupied and the antibonding orbitals are vacant. As a consequence, the bonding character along the Mn–O bond is less in dioxomanganese(V) as compared to monooxomanganese(V) complexes and therefore this bond can formally be described as a double bond rather than a triple bond. The differences in orbital interactions and orbital energies also affect the intrinsic chemical properties of the oxidants, such as the electron affinity and pKa values, which result in enhanced catalytic potential for dioxomanganese(V) porphyrin. Our calculations predict a halogenation mechanism in line with that proposed by experiment with an initial hydrogen atom abstraction followed by ligand exchange and halogen transfer.
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Affiliation(s)
- Sam P. de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, the University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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Hirao H, Chuanprasit P, Cheong YY, Wang X. How is a metabolic intermediate formed in the mechanism-based inactivation of cytochrome P450 by using 1,1-dimethylhydrazine: hydrogen abstraction or nitrogen oxidation? Chemistry 2013; 19:7361-9. [PMID: 23592585 DOI: 10.1002/chem.201300689] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Indexed: 11/10/2022]
Abstract
A precise understanding of the mechanism-based inactivation of cytochrome P450 enzymes (P450s) at the quantum mechanical level should allow more reliable predictions of drug-drug interactions than those currently available. Hydrazines are among the molecules that act as mechanism-based inactivators to terminate the function of P450s, which are essential heme enzymes responsible for drug metabolism in the human body. Despite its importance, the mechanism explaining how a metabolic intermediate (MI) is formed from hydrazine is not fully understood. We used density functional theory (DFT) calculations to compare four possible mechanisms underlying the reaction between 1,1-dimethylhydrazine (or unsymmetrical dimethylhydrazine, UDMH) and the reactive compound I (Cpd I) intermediate of P450. Our DFT calculations provided a clear view on how an aminonitrene-type MI is formed from UDMH. In the most favorable pathway, hydrogen is spontaneously abstracted from the N2 atom of UDMH by Cpd I, followed by a second hydrogen abstraction from the N2 atom by Cpd II. Nitrogen oxidation of nitrogen atoms and hydrogen abstraction from the C-H bond of the methyl group were found to be less favorable than the hydrogen abstraction from the N-H bond. We also found that the reaction of protonated UDMH with Cpd I is rather sluggish. The aminonitrene-type MI binds to the ferric heme more strongly than a water molecule. This is consistent with the notion that the catalytic cycle of P450 is impeded when such an MI is produced through the P450-catalyzed reaction.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371.
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Taxak N, Desai PV, Patel B, Mohutsky M, Klimkowski VJ, Gombar V, Bharatam PV. Metabolic-intermediate complex formation with cytochrome P450: theoretical studies in elucidating the reaction pathway for the generation of reactive nitroso intermediate. J Comput Chem 2012; 33:1740-7. [PMID: 22610824 DOI: 10.1002/jcc.23008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 04/16/2012] [Accepted: 04/20/2012] [Indexed: 11/10/2022]
Abstract
Mechanism-based inhibition (MBI) of cytochrome P450 (CYP) can lead to drug-drug interactions and often to toxicity. Some aliphatic and aromatic amines can undergo biotransformation reactions to form reactive metabolites such as nitrosoalkanes, leading to MBI of CYPs. It has been proposed that the nitrosoalkanes coordinate with the heme iron, forming metabolic-intermediate complex (MIC), resulting in the quasi-irreversible inhibition of CYPs. Limited mechanistic details regarding the formation of reactive nitroso intermediate and its coordination with heme-iron have been reported. A quantum chemical analysis was performed to elucidate potential reaction pathways for the generation of nitroso intermediate and the formation of MIC. Elucidation of the energy profile along the reaction path, identification of three-dimensional structures of reactive intermediates and transition states, as well as charge and spin density analyses, were performed using the density functional B3LYP method. The study was performed using Cpd I [iron (IV-oxo] heme porphine with SH(-) as the axial ligand) to represent the catalytic domain of CYP, simulating the biotransformation process. Three pathways: (i) N-oxidation followed by proton shuttle, (ii) N-oxidation followed by 1,2-H shift, and (iii) H-abstraction followed by rebound mechanism, were studied. It was observed that the proton shuttle pathway was more favorable over the whole reaction leading to reactive nitroso intermediate. This study revealed that the MIC formation from a primary amine is a favorable exothermic process, involving eight different steps and preferably takes place on the doublet spin surface of Cpd I. The rate-determining step was identified to be the first N-oxidation of primary amine.
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Affiliation(s)
- Nikhil Taxak
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, S. A. S. Nagar, Mohali, Punjab, India
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