1
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Qureshi M, Mokkawes T, Cao Y, de Visser SP. Mechanism of the Oxidative Ring-Closure Reaction during Gliotoxin Biosynthesis by Cytochrome P450 GliF. Int J Mol Sci 2024; 25:8567. [PMID: 39201254 PMCID: PMC11354885 DOI: 10.3390/ijms25168567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
During gliotoxin biosynthesis in fungi, the cytochrome P450 GliF enzyme catalyzes an unusual C-N ring-closure step while also an aromatic ring is hydroxylated in the same reaction cycle, which may have relevance to drug synthesis reactions in biotechnology. However, as the details of the reaction mechanism are still controversial, no applications have been developed yet. To resolve the mechanism of gliotoxin biosynthesis and gain insight into the steps leading to ring-closure, we ran a combination of molecular dynamics and density functional theory calculations on the structure and reactivity of P450 GliF and tested a range of possible reaction mechanisms, pathways and models. The calculations show that, rather than hydrogen atom transfer from the substrate to Compound I, an initial proton transfer transition state is followed by a fast electron transfer en route to the radical intermediate, and hence a non-synchronous hydrogen atom abstraction takes place. The radical intermediate then reacts by OH rebound to the aromatic ring to form a biradical in the substrate that, through ring-closure between the radical centers, gives gliotoxin products. Interestingly, the structure and energetics of the reaction mechanisms appear little affected by the addition of polar groups to the model and hence we predict that the reaction can be catalyzed by other P450 isozymes that also bind the same substrate. Alternative pathways, such as a pathway starting with an electrophilic attack on the arene to form an epoxide, are high in energy and are ruled out.
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Affiliation(s)
| | | | | | - Sam P. de Visser
- Manchester Institute of Biotechnology, Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK (Y.C.)
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2
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Peng W, Wang Z, Zhang Q, Yan S, Wang B. Unraveling the Valence State and Reactivity of Copper Centers in Membrane-Bound Particulate Methane Monooxygenase. J Am Chem Soc 2023; 145:25304-25317. [PMID: 37955571 DOI: 10.1021/jacs.3c08834] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Particulate methane monooxygenase (pMMO) plays a critical role in catalyzing the conversion of methane to methanol, constituting the initial step in the C1 metabolic pathway within methanotrophic bacteria. However, the membrane-bound pMMO's structure and catalytic mechanism, notably the copper's valence state and genuine active site for methane oxidation, have remained elusive. Based on the recently characterized structure of membrane-bound pMMO, extensive computational studies were conducted to address these long-standing issues. A comprehensive analysis comparing the quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulated structures with cryo-EM data indicates that both the CuC and CuD sites tend to stay in the Cu(I) valence state within the membrane environment. Additionally, the concurrent presence of Cu(I) at both CuC and CuD sites leads to the significant reduction of the ligand-binding cavity situated between them, making it less likely to accommodate a reductant molecule such as durohydroquinone (DQH2). Subsequent QM/MM calculations reveal that the CuD(I) site is more reactive than the CuC(I) site in oxygen activation, en route to H2O2 formation and the generation of Cu(II)-O•- species. Finally, our simulations demonstrate that the natural reductant ubiquinol (CoQH2) assumes a productive binding conformation at the CuD(I) site but not at the CuC(I) site. This provides evidence that the true active site of membrane-bound pMMOs may be CuD rather than CuC. These findings clarify pMMO's catalytic mechanism and emphasize the membrane environment's pivotal role in modulating the coordination structure and the activity of copper centers within pMMO.
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Affiliation(s)
- Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
- Key Laboratory of Aerosol Chemistry and Physics, State Key Laboratory of Loess and Quaternary Geology (SKLLQG), Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Qiaoyu Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
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3
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Mokkawes T, De Visser T, Cao Y, De Visser SP. Melatonin Activation by Human Cytochrome P450 Enzymes: A Comparison between Different Isozymes. Molecules 2023; 28:6961. [PMID: 37836804 PMCID: PMC10574541 DOI: 10.3390/molecules28196961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Cytochrome P450 enzymes in the human body play a pivotal role in both the biosynthesis and the degradation of the hormone melatonin. Melatonin plays a key role in circadian rhythms in the body, but its concentration is also linked to mood fluctuations as well as emotional well-being. In the present study, we present a computational analysis of the binding and activation of melatonin by various P450 isozymes that are known to yield different products and product distributions. In particular, the P450 isozymes 1A1, 1A2, and 1B1 generally react with melatonin to provide dominant aromatic hydroxylation at the C6-position, whereas the P450 2C19 isozyme mostly provides O-demethylation products. To gain insight into the origin of these product distributions of the P450 isozymes, we performed a comprehensive computational study of P450 2C19 isozymes and compared our work with previous studies on alternative isozymes. The work covers molecular mechanics, molecular dynamics and quantum mechanics approaches. Our work highlights major differences in the size and shape of the substrate binding pocket amongst the different P450 isozymes. Consequently, substrate binding and positioning in the active site varies substantially within the P450 isozymes. Thus, in P450 2C19, the substrate is oriented with its methoxy group pointing towards the heme, and therefore reacts favorably through hydrogen atom abstraction, leading to the production of O-demethylation products. On the other hand, the substrate-binding pockets in P450 1A1, 1A2, and 1B1 are tighter, direct the methoxy group away from the heme, and consequently activate an alternative site and lead to aromatic hydroxylation instead.
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Affiliation(s)
| | | | | | - Sam P. De Visser
- Department of Chemical Engineering, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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4
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Zhang Y, Chu JM. Computational Mechanistic Investigations of Biocatalytic Nitrenoid C-H Functionalizations via Engineered Heme Proteins. Chembiochem 2023; 24:e202300260. [PMID: 37134298 DOI: 10.1002/cbic.202300260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/05/2023]
Abstract
Engineered heme proteins were developed to possess numerous excellent biocatalytic nitrenoid C-H functionalizations. Computational approaches such as density functional theory (DFT), hybrid quantum mechanics/molecular mechanics (QM/MM), and molecular dynamics (MD) calculations were employed to help understand some important mechanistic aspects of these heme nitrene transfer reactions. This review summarizes advances of computational reaction pathway results of these biocatalytic intramolecular and intermolecular C-H aminations/amidations, focusing on mechanistic origins of reactivity, regioselectivity, enantioselectivity, diastereoselectivity as well as effects of substrate substituent, axial ligand, metal center, and protein environment. Some important common and distinctive mechanistic features of these reactions were also described with brief outlook of future development.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
| | - Jia-Min Chu
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
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5
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Mokkawes T, de Visser SP. Melatonin Activation by Cytochrome P450 Isozymes: How Does CYP1A2 Compare to CYP1A1? Int J Mol Sci 2023; 24:3651. [PMID: 36835057 PMCID: PMC9959256 DOI: 10.3390/ijms24043651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Cytochrome P450 enzymes are versatile enzymes found in most biosystems that catalyze mono-oxygenation reactions as a means of biosynthesis and biodegradation steps. In the liver, they metabolize xenobiotics, but there are a range of isozymes with differences in three-dimensional structure and protein chain. Consequently, the various P450 isozymes react with substrates differently and give varying product distributions. To understand how melatonin is activated by the P450s in the liver, we did a thorough molecular dynamics and quantum mechanics study on cytochrome P450 1A2 activation of melatonin forming 6-hydroxymelatonin and N-acetylserotonin products through aromatic hydroxylation and O-demethylation pathways, respectively. We started from crystal structure coordinates and docked substrate into the model, and obtained ten strong binding conformations with the substrate in the active site. Subsequently, for each of the ten substrate orientations, long (up to 1 μs) molecular dynamics simulations were run. We then analyzed the orientations of the substrate with respect to the heme for all snapshots. Interestingly, the shortest distance does not correspond to the group that is expected to be activated. However, the substrate positioning gives insight into the protein residues it interacts with. Thereafter, quantum chemical cluster models were created and the substrate hydroxylation pathways calculated with density functional theory. These relative barrier heights confirm the experimental product distributions and highlight why certain products are obtained. We make a detailed comparison with previous results on CYP1A1 and identify their reactivity differences with melatonin.
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Affiliation(s)
- Thirakorn Mokkawes
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Department of Chemical Engineering, 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
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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6
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Spotlight on CYP4B1. Int J Mol Sci 2023; 24:ijms24032038. [PMID: 36768362 PMCID: PMC9916508 DOI: 10.3390/ijms24032038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The mammalian cytochrome P450 monooxygenase CYP4B1 can bioactivate a wide range of xenobiotics, such as its defining/hallmark substrate 4-ipomeanol leading to tissue-specific toxicities. Similar to other members of the CYP4 family, CYP4B1 has the ability to hydroxylate fatty acids and fatty alcohols. Structural insights into the enigmatic role of CYP4B1 with functions in both, xenobiotic and endobiotic metabolism, as well as its unusual heme-binding characteristics are now possible by the recently solved crystal structures of native rabbit CYP4B1 and the p.E310A variant. Importantly, CYP4B1 does not play a major role in hepatic P450-catalyzed phase I drug metabolism due to its predominant extra-hepatic expression, mainly in the lung. In addition, no catalytic activity of human CYP4B1 has been observed owing to a unique substitution of an evolutionary strongly conserved proline 427 to serine. Nevertheless, association of CYP4B1 expression patterns with various cancers and potential roles in cancer development have been reported for the human enzyme. This review will summarize the current status of CYP4B1 research with a spotlight on its roles in the metabolism of endogenous and exogenous compounds, structural properties, and cancer association, as well as its potential application in suicide gene approaches for targeted cancer therapy.
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7
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Hermano Sampaio Dias A, Yadav R, Mokkawes T, Kumar A, Skaf MS, Sastri CV, Kumar D, de Visser SP. Biotransformation of Bisphenol by Human Cytochrome P450 2C9 Enzymes: A Density Functional Theory Study. Inorg Chem 2023; 62:2244-2256. [PMID: 36651185 PMCID: PMC9923688 DOI: 10.1021/acs.inorgchem.2c03984] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Bisphenol A (BPA, 2,2-bis-(4-hydroxyphenyl)propane) is used as a precursor in the synthesis of polycarbonate and epoxy plastics; however, its availability in the environment is causing toxicity as an endocrine-disrupting chemical. Metabolism of BPA and their analogues (substitutes) is generally performed by liver cytochrome P450 enzymes and often leads to a mixture of products, and some of those are toxic. To understand the product distributions of P450 activation of BPA, we have performed a computational study into the mechanisms and reactivities using large model structures of a human P450 isozyme (P450 2C9) with BPA bound. Density functional theory (DFT) calculations on mechanisms of BPA activation by a P450 compound I model were investigated, leading to a number of possible products. The substrate-binding pocket is tight, and as a consequence, aliphatic hydroxylation is not feasible as the methyl substituents of BPA cannot reach compound I well due to constraints of the substrate-binding pocket. Instead, we find low-energy pathways that are initiated with phenol hydrogen atom abstraction followed by OH rebound to the phenolic ortho- or para-position. The barriers of para-rebound are well lower in energy than those for ortho-rebound, and consequently, our P450 2C9 model predicts dominant hydroxycumyl alcohol products. The reactions proceed through two-state reactivity on competing doublet and quartet spin state surfaces. The calculations show fast and efficient substrate activation on a doublet spin state surface with a rate-determining electrophilic addition step, while the quartet spin state surface has multiple high-energy barriers that can also lead to various side products including C4-aromatic hydroxylation. This work shows that product formation is more feasible on the low spin state, while the physicochemical properties of the substrate govern barrier heights of the rate-determining step of the reaction. Finally, the importance of the second-coordination sphere is highlighted that determines the product distributions and guides the bifurcation pathways.
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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, ManchesterM1 7DN, United Kingdom,Center
for Computing in Engineering & Sciences, University of Campinas, Rua Josué de Castro, s/n, Campinas13083-861, Brazil
| | - Rolly Yadav
- Department
of Chemistry, Indian Institute of Technology
Guwahati, Guwahati, Assam781039, India
| | - Thirakorn Mokkawes
- Manchester
Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, ManchesterM1 7DN, United Kingdom
| | - Asheesh Kumar
- Department
of Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh (U.P.)226025, India
| | - Munir S. Skaf
- Center
for Computing in Engineering & Sciences, University of Campinas, Rua Josué de Castro, s/n, Campinas13083-861, Brazil
| | - Chivukula V. Sastri
- Department
of Chemistry, Indian Institute of Technology
Guwahati, Guwahati, Assam781039, India,
| | - Devesh Kumar
- Department
of Physics, Siddharth University, Kapilvastu, Siddharthnagar272202, India,
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, ManchesterM1 7DN, United Kingdom,
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8
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Ansari M, Rajaraman G. Comparative oxidative ability of mononuclear and dinuclear high-valent iron-oxo species towards the activation of methane: does the axial/bridge atom modulate the reactivity? Dalton Trans 2023; 52:308-325. [PMID: 36504243 DOI: 10.1039/d2dt02559k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Over the years, mononuclear FeIVO species have been extensively studied, but the presence of dinuclear FeIVO species in soluble methane monooxygenase (sMMO) has inspired the development of biomimic models that could activate inert substrates such as methane. There are some successful attempts; particularly the [(Por)(m-CBA) FeIV(μ-N)FeIV(O)(Por˙+)]- species has been reported to activate methane and yield decent catalytic turnover numbers and therefore regarded as the closest to the sMMO enzyme functional model, as no mononuclear FeIVO analogues could achieve this feat. In this work, we have studied a series of mono and dinuclear models using DFT and ab initio DLPNO-CCSD(T) calculations to probe the importance of nuclearity in enhancing the reactivity. We have probed the catalytic activities of four complexes: [(HO)FeIV(O)(Por)]- (1), [(HO)FeIV(O)(Por˙+)] (2), μ-oxo dinuclear iron species [(Por)(m-CBA)FeIV(μ-O)FeIV(O) (Por˙+)]- (3) and N-bridged dinuclear iron species [(Por)(m-CBA)FeIV(μ-N)FeIV(O)(Por˙+)]- (4) towards the activation of methane. Additionally, calculations were performed on the mononuclear models [(X)FeIV(O)(Por˙+)]n {X = N 4a (n = -2), NH 4b (n = -1) and NH24c (n = 0)} to understand the role of nuclearity in the reactivity. DFT calculations performed on species 1-4 suggest an interesting variation among them, with species 1-3 possessing an intermediate spin (S = 1) as a ground state and species 4 possessing a high-spin (S = 2) as a ground state. Furthermore, the two FeIV centres in species 3 and 4 are antiferromagnetically coupled, yielding a singlet state with a distinct difference in their electronic structure. On the other hand, species 2 exhibits a ferromagnetic coupling between the FeIV and the Por˙+ moiety. Our calculations suggest that the higher barriers for the C-H bond activation of methane and the rebound step for species 1 and 3 are very high in energy, rendering them unreactive towards methane, while species 2 and 4 have lower barriers, suggesting their reactivity towards methane. Studies on the system reveal that model 4a has multiple FeN bonds facilitating greater reactivity, whereas the other two models have longer Fe-N bonds and less radical character with steeper barriers. Strong electronic cooperativity is found to be facilitated by the bridging nitride atom, and this cooperativity is suppressed by substituents such as oxygen, rendering them inactive. Thus, our study unravels that apart from enhancing the nuclearity, bridging atoms that facilitate strong cooperation between the metals are required to activate very inert substrates such as methane, and our results are broadly in agreement with earlier experimental findings.
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Affiliation(s)
- Mursaleem Ansari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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9
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Coleman T, Doherty DZ, Zhang T, Podgorski MN, Qiao R, Lee JHZ, Bruning JB, De Voss JJ, Zhou W, Bell SG. Exploring the Factors which Result in Cytochrome P450 Catalyzed Desaturation Versus Hydroxylation. Chem Asian J 2022; 17:e202200986. [PMID: 36268769 PMCID: PMC10100021 DOI: 10.1002/asia.202200986] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/18/2022] [Indexed: 11/07/2022]
Abstract
The cytochrome P450 family of monooxygenase enzymes have essential biological roles involving the selective oxidation of carbon-hydrogen bonds. They can also catalyze other important metabolic reactions including desaturation to form alkenes. Currently the factors that control the partition between P450 hydroxylation and desaturation pathways are poorly defined. The CYP199A4 enzyme from the bacterium Rhodopseudomonas palustris HaA2 catalyzes the oxidation of 4-ethyl- and 4-isopropyl- benzoic acids with hydroxylation and desaturation occurring in significant quantities. Here we demonstrate that 4-cyclopropylbenzoic acid is regioselectively hydroxylated by CYP199A4 at the benzylic carbon. In contrast, the oxidation of 4-n-propylbenzoic acid by CYP199A4 results in three major metabolites: an alkene from desaturation and two hydroxylation products at the benzylic (Cα) and Cβ carbons in similar quantities. Extending the length of the alkyl substituent resulted in 4-n-butylbenzoic acid being oxidized at the benzylic position (45%) and desaturated (55%). In contrast, 4-isobutylbenzoic generated very little alkene (5%) but was hydroxylated at the benzylic position (54%) and at the tertiary Cβ position (41%). The oxidation of 4-n-propylbenzoic acid by the F298 V mutant of CYP199A4 occurred with no hydroxylation at Cβ and a significant increase in metabolites arising from desaturation (73%). The X-ray crystal structures of CYP199A4 with each substrate revealed that they bind in the active site with the alkyl substituent positioned over the heme. However, the longer alkylbenzoic acids were bound in a different conformation as was 4-n-propylbenzoic acid in the F298 V mutant. Overall, the changes in metabolite distribution could be ascribed to bond strength differences and the position of the alkyl group relative to the heme.
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Affiliation(s)
- Tom Coleman
- Department of ChemistryUniversity of AdelaideAdelaideSA, 5005Australia
| | - Daniel Z. Doherty
- Department of ChemistryUniversity of AdelaideAdelaideSA, 5005Australia
| | - Ting Zhang
- College of Life Sciences and The State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjin300071P. R. China
| | | | - Ruihong Qiao
- College of Life Sciences and The State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjin300071P. R. China
| | - Joel H. Z. Lee
- Department of ChemistryUniversity of AdelaideAdelaideSA, 5005Australia
| | - John B. Bruning
- School of Biological SciencesUniversity of AdelaideAdelaideSA, 5005Australia
| | - James J. De Voss
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQLD, 4072Australia
| | - Weihong Zhou
- College of Life Sciences and The State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjin300071P. R. China
| | - Stephen G. Bell
- Department of ChemistryUniversity of AdelaideAdelaideSA, 5005Australia
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10
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Mokkawes T, Lim ZQ, de Visser SP. Mechanism of Melatonin Metabolism by CYP1A1: What Determines the Bifurcation Pathways of Hydroxylation versus Deformylation? J Phys Chem B 2022; 126:9591-9606. [PMID: 36380557 PMCID: PMC9706573 DOI: 10.1021/acs.jpcb.2c07200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Melatonin, a widely applied cosmetic active ingredient, has a variety of uses as a skin protector through antioxidant and anti-inflammatory functions as well as giving the body UV-induced defenses and immune system support. In the body, melatonin is synthesized from a tryptophan amino acid in a cascade of reactions, but as melatonin is toxic at high concentrations, it is metabolized in the human skin by the cytochrome P450 enzymes. The P450s are diverse heme-based mono-oxygenases that catalyze oxygen atom-transfer processes that trigger metabolism and detoxification reactions in the body. In the catalytic cycle of the P450s, a short-lived high-valent iron(IV)-oxo heme cation radical is formed that has been proposed to be the active oxidant. How and why it activates melatonin in the human body and what the origin of the product distributions is, are unknown. This encouraged us to do a detailed computational study on a typical human P450 isozyme, namely CYP1A1. We initially did a series of molecular dynamics simulations with substrate docked into several orientations. These simulations reveal a number of stable substrate-bound positions in the active site, which may lead to differences in substrate activation channels. Using tunneling analysis on the full protein structures, we show that two of the four binding conformations lead to open substrate-binding pockets. As a result, in these open pockets, the substrate is not tightly bound and can escape back into the solution. In the closed conformations, in contrast, the substrate is mainly oriented with the methoxy group pointing toward the heme, although under a different angle. We then created large quantum cluster models of the enzyme and focused on the chemical reaction mechanisms for melatonin activation, leading to competitive O-demethylation and C6-aromatic hydroxylation pathways. The calculations show that active site positioning determines the product distributions, but the bond that is activated is not necessarily closest to the heme in the enzyme-substrate complex. As such, the docking and molecular dynamics positioning of the substrate versus oxidant can give misleading predictions on product distributions. In particular, in quantum mechanics cluster model I, we observe that through a tight hydrogen bonding network, a preferential 6-hydroxylation of melatonin is obtained. However, O-demethylation becomes possible in alternative substrate-binding orientations that have the C6-aromatic ring position shielded. Finally, we investigated enzymatic and non-enzymatic O-demethylation processes and show that the hydrogen bonding network in the substrate-binding pocket can assist and perform this step prior to product release from the enzyme.
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Affiliation(s)
- Thirakorn Mokkawes
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Ze Qing Lim
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.,
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11
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Ma S, Wang S, Cao J, Liu F. Rapid and Accurate Estimation of Activation Free Energy in Hydrogen Atom Transfer-Based C-H Activation Reactions: From Empirical Model to Artificial Neural Networks. ACS OMEGA 2022; 7:34858-34867. [PMID: 36211072 PMCID: PMC9535641 DOI: 10.1021/acsomega.2c03252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
A well-performing machine learning (ML) model is obtained by using proper descriptors and artificial neural network (ANN) algorithms, which can quickly and accurately predict activation free energy in hydrogen atom transfer (HAT)-based sp3 C-H activation. Density functional theory calculations (UωB97X-D) are used to establish the reaction system data sets of methoxyl (CH3O·), trifluoroethoxyl (CF3CH2O·), tert-butoxyl (tBuO·), and cumyloxyl (CumO·) radicals. The simplified Roberts' equation proposed in our recent study works here [R 2 = 0.84, mean absolute error (MAE) = 0.85 kcal/mol]. Its performance is comparable with univariate Mulliken-type electronegativity (χ) with the ANN model. The ANN model with bond dissociation free energy, χ, α-unsaturation, and Nolan buried volume (%V buried) successively improves R 2 and MAE to 0.93 and 0.54 kcal/mol, respectively. It reproduces the test sets of trichloroethoxyl (CCl3CH2O·) with R 2 = 0.87 and MAE = 0.89 kcal/mol and accurately predicts the relative experimental barrier of the HAT reactions with CumO· and the site selectivity of CH3O·.
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Affiliation(s)
- Siqi Ma
- School
of Chemistry and Chemical Engineering, Shanghai
University of Engineering Science, Shanghai 201620, China
| | - Shipeng Wang
- School
of Chemistry and Chemical Engineering, Shanghai
University of Engineering Science, Shanghai 201620, China
| | - Jiawei Cao
- School
of Chemistry and Chemical Engineering, Shanghai
University of Engineering Science, Shanghai 201620, China
| | - Fengjiao Liu
- School
of Chemistry and Chemical Engineering, Shanghai
University of Engineering Science, Shanghai 201620, China
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
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12
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Mai BK, Neris NM, Yang Y, Liu P. C-N Bond Forming Radical Rebound Is the Enantioselectivity-Determining Step in P411-Catalyzed Enantioselective C(sp 3)-H Amination: A Combined Computational and Experimental Investigation. J Am Chem Soc 2022; 144:11215-11225. [PMID: 35583461 DOI: 10.1021/jacs.2c02283] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Engineered metalloenzymes represent promising catalysts for stereoselective C-H functionalization reactions. Recently, P450 enzymes have been evolved to allow for new-to-nature intramolecular C(sp3)-H amination reactions via a nitrene transfer mechanism, giving rise to diamine derivatives with excellent enantiocontrol. To shed light on the origin of enantioselectivity, a combined computational and experimental study was carried out. Hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the activation energies and enantioselectivities of both the hydrogen atom transfer (HAT) and the subsequent C-N bond forming radical rebound steps. Contrary to previously hypothesized enantioinduction mechanisms, our calculations show that the radical rebound step is enantioselectivity-determining, whereas the preceding HAT step is only moderately stereoselective. Furthermore, the selectivity in the initial HAT is ablated by rapid conformational change of the radical intermediate prior to C-N bond formation. This finding is corroborated by our experimental study using a set of enantiomerically pure, monodeuterated substrates. Furthermore, classical and ab initio molecular dynamics simulations were carried out to investigate the conformational flexibility of the carbon-centered radical intermediate. This key radical species undergoes a facile conformational change in the enzyme active site from the pro-(R) to the pro-(S) configuration, whereas the radical rebound is slower due to the spin-state change and ring strain of the cyclization process, thereby allowing stereoablative C-N bond formation. Together, these studies revealed an underappreciated enantioinduction mechanism in biocatalytic C(sp3)-H functionalizations involving radical intermediates, opening up new avenues for the development of other challenging asymmetric C(sp3)-H functionalizations.
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Affiliation(s)
- Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Natalia M Neris
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, California 93106, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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13
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Zhang H, Wang C, Guo F, Jin L, Song R, Yang F, Ji L, Yu H. In Silico simulation of Cytochrome P450-Mediated metabolism of aromatic amines: A case study of N-Hydroxylation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 237:113544. [PMID: 35483145 DOI: 10.1016/j.ecoenv.2022.113544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 06/14/2023]
Abstract
Aromatic amines, the widely used raw materials in industry, cause long-term exposure to human bodies. They can be metabolized by cytochrome P450 enzymes to form active electrophilic compounds, which will potentially react with nucleophilic DNA to exert carcinogenesis. The short lifetime and versatility of the oxidant (a high-valent iron (IV)-oxo species, compound I) of P450 enzymes prompts us to use theoretical methods to investigate the metabolism of aromatic amines. In this work, the density functional theory (DFT) has been employed to simulate the hydroxylation metabolism through H-abstraction and to calculate the activation energy of this reaction for 28 aromatic amines. The results indicate that the steric effects, inductive effects and conjugative effects greatly contribute to the metabolism activity of the chemicals. The further correlation reveals that the dissociation energy of -NH2 (BDEN-H) can successfully predict the time-consuming calculated activation energy (R2 for aromatic and heteroaromatic amines are 0.93 and 0.86, respectively), so BDEN-H can be taken as a key parameter to characterize the relative stability of aromatic amines in P450 enzymes and further to quickly assess their potential toxicity. The validation results prove such relationship has good statistical performance (qcv2 for aromatic and heteroaromatic amines are 0.95 and 0.90, respectively) and can be used to other aromatic amines in the application domain, greatly reducing computational cost and providing useful support for experimental research.
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Affiliation(s)
- Huanni Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Chenchen Wang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Fangjie Guo
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; Quality and Safety Engineering Institute of Food and Drug, School of Management Engineering and Electronic Commerce, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, China
| | - Lingmin Jin
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, Jinhua 321004, China
| | - Runqian Song
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Fangxing Yang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Li Ji
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, Jinhua 321004, China.
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14
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Zhang H, Song R, Guo F, Chai L, Wang W, Zeng J, Yu H, Ji L. Using Physical Organic Chemistry Knowledge to Predict Unusual Metabolites of Synthetic Phenolic Antioxidants by Cytochrome P450. Chem Res Toxicol 2022; 35:840-848. [PMID: 35416036 DOI: 10.1021/acs.chemrestox.2c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biotransformation, especially by human CYP450 enzymes, plays a crucial role in regulating the toxicity of organic compounds in organisms, but is poorly understood for most emerging pollutants, as their numerous "unusual" biotransformation reactions cannot retrieve examples from the textbooks. Therefore, in order to predict the unknown metabolites with altering toxicological profiles, there is a realistic need to develop efficient methods to reveal the "unusual" metabolic mechanism of emerging pollutants. Combining experimental work with computational predictions has been widely accepted as an effective approach in studying complex metabolic reactions; however, the full quantum chemical computations may not be easily accessible for most environmentalists. Alternatively, this work practiced using the concepts from physical organic chemistry for studying the interrelationships between structure and reactivity of organic molecules, to reveal the "unusual" metabolic mechanism of synthetic phenolic antioxidants catalyzed by CYP450, for which the simple pencil-and-paper and property-computation methods based on physical organic chemistry were performed. The phenol-coupling product of butylated hydroxyanisole (BHA) (based on spin aromatic delocalization) and ipso-addition quinol metabolite of butylated hydroxytoluene (BHT) (based on hyperconjugative effect) were predicted as two "unusual" metabolites, which were further confirmed by our in vitro analysis. We hope this easily handled approach will promote environmentalists to attach importance to physical organic chemistry, with an eye to being able to use the knowledge gained to efficiently predict the fates of substantial unknown synthesized organic compounds in the future.
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Affiliation(s)
- Huanni Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China.,School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Runqian Song
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China.,School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Fangjie Guo
- School of Management Engineering and Electronic Commerce, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Lihong Chai
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 81377 Munich, Germany
| | - Wuwei Wang
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Jingyi Zeng
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Li Ji
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
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15
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Liu F, Ma S, Lu Z, Nangia A, Duan M, Yu Y, Xu G, Mei Y, Bietti M, Houk KN. Hydrogen Abstraction by Alkoxyl Radicals: Computational Studies of Thermodynamic and Polarity Effects on Reactivities and Selectivities. J Am Chem Soc 2022; 144:6802-6812. [PMID: 35378978 DOI: 10.1021/jacs.2c00389] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Density functional theory calculations (ωB97X-D) are reported for the reactions of methoxy, tert-butoxy, trichloroethoxy, and trifluoroethoxy radicals with a series of 26 C-H bonds in different environments characteristic of a variety of hydrocarbons and substituted derivatives. The variations in activation barriers are analyzed with modified Evans-Polanyi treatments to account for polarity and unsaturation effects. The treatments by Roberts and Steel and by Mayer have inspired the development of a simple treatment involving the thermodynamics of reactions, the difference between the reactant radical and product radical electronegativities, and the absence or presence of α-unsaturation. The three-parameter equation (ΔH⧧ = 0.52ΔHrxn(1 - d) - 0.35ΔχAB2 + 10.0, where d = 0.44 when there is α-unsaturation to the reacting C-H bond), correlates well with quantum mechanically computed barriers and shows the quantitative importance of the thermodynamics of reactions (dictated by the reactant and the product bond dissociation energies) and polar effects.
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Affiliation(s)
- Fengjiao Liu
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.,Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Siqi Ma
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Zeying Lu
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Anjanay Nangia
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Meng Duan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yanmin Yu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States.,Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing 100124, China
| | - Guochao Xu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Massimo Bietti
- Dipartimento di Scienze e Tecnologie Chimiche, Università ″Tor Vergata″, Via della Ricerca Scientifica, 1 Rome I-00133, Italy
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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16
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Tao Y, Li Z, Zhang Y, Sun K, Liu Z. Determining the inherent selectivity for carbon radical hydroxylation versus halogenation with high-spin oxoiron(iv)-halide complexes: a concerted rebound step. RSC Adv 2022; 12:9891-9897. [PMID: 35424943 PMCID: PMC8963258 DOI: 10.1039/d2ra01384c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/22/2022] [Indexed: 11/23/2022] Open
Abstract
A synthetic iron model can process both halogenation and hydroxylation with vague selectivity, which is different from halogenase even though these structures are used for the simulation of halogenase. The key factor of the synthetic oxo-iron model mediated hydroxylation or the halogenation is still under debate. Herein density functional theory calculation is used to investigate the hydroxylation versus halogenation of propylene by the complex [FeIV(O)(TQA)(X)]+ (X = F, Cl, Br). Our results suggest that a concerted rebound mechanism (between the -X and the hydroxyl ligands after the hydrogen abstraction) leads to the formation of two different kinds of products. DFT calculation for the hydroxylation versus halogenation of propylene by [FeIV(O)(TQA)X]+ (X = F, Cl and Br) reveals that after hydrogen abstraction, halogen and oxygen rebound reactions are a synergistic process.![]()
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Affiliation(s)
- Yaping Tao
- College of Physics and Electronic Information & Henan Key Laboratory of Electromagnetic Transformation and Detection, Luoyang Normal University Luoyang 471934 China
| | - Zixian Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology Beijing 100029 China
| | - Yiman Zhang
- College of Physics and Electronic Information & Henan Key Laboratory of Electromagnetic Transformation and Detection, Luoyang Normal University Luoyang 471934 China
| | - Kexi Sun
- College of Physics and Electronic Information & Henan Key Laboratory of Electromagnetic Transformation and Detection, Luoyang Normal University Luoyang 471934 China
| | - Zhaojun Liu
- College of Physics and Electronic Information & Henan Key Laboratory of Electromagnetic Transformation and Detection, Luoyang Normal University Luoyang 471934 China
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17
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Wang H, Liu Y, Su C, Schulz CE, Fan Y, Bian Y, Li J. Perspectives on Ligand Properties of N-Heterocyclic Carbenes in Iron Porphyrin Complexes. Inorg Chem 2021; 61:847-856. [PMID: 34962794 DOI: 10.1021/acs.inorgchem.1c02444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There has been considerable research interest in the ligand nature of N-heterocyclic carbenes (NHCs). In this work, two six-coordinate NHC iron porphyrin complexes [FeII(TTP)(1,3-Me2Imd)2] (TTP = tetratolylporphyrin, 1,3-Me2Imd = 1,3-dimethylimidazol-2-ylidene) and [FeIII(TDCPP)(1,3-Me2Imd)2]ClO4 (TDCPP = 5,10,15,20-tetrakis(2,6-dichlorophenyl)porphyrin) are reported. Single-crystal X-ray characterizations demonstrate that both complexes have strongly ruffled conformations and relatively perpendicular ligand orientations which are forced by the sterically bulky 1,3-Me2Imd NHC ligands. Multitemperature (4.2-300 K) and high magnetic field (0-9 T) Mössbauer and low-temperature (4.0 K) EPR spectroscopies definitely confirmed the low-spin states of [FeII(TTP)(1,3-Me2Imd)2] (S = 0) and [FeIII(TDCPP)(1,3-Me2Imd)2]ClO4 (S = 1/2). The similarity of 1,3-Me2Imd and imidazole, as well as the well-established correlations between the ligand nature and spectroscopic characteristics of [FeII,III(Porph)(L)2]0,+ (Porph: porphyrin; L: planar base ligand) species, allowed direct comparisons between the pair of ligands which revealed for the first time that NHC has a stronger π-acceptor ability than imidazoles, in addition to its very strong σ-donation.
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Affiliation(s)
- Haimang Wang
- College of Materials Science and Optoelectronic Technology & CAS Center for Excellence in Topological Quantum Computation, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
| | - Yulong Liu
- College of Materials Science and Optoelectronic Technology & CAS Center for Excellence in Topological Quantum Computation, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
| | - Chaorui Su
- Department of Chemistry, School of Chemistry and Biological Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, and Daxing Research Institute, University of Science and Technology Beijing, Beijing 100083, China
| | - Charles E Schulz
- Department of Physics, Knox College, Galesburg, Illinois 61401, United States
| | - Yingying Fan
- College of Materials Science and Optoelectronic Technology & CAS Center for Excellence in Topological Quantum Computation, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
| | - Yongzhong Bian
- Department of Chemistry, School of Chemistry and Biological Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, and Daxing Research Institute, University of Science and Technology Beijing, Beijing 100083, China
| | - Jianfeng Li
- Department of Chemistry, School of Chemistry and Biological Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, and Daxing Research Institute, University of Science and Technology Beijing, Beijing 100083, China
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18
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Kamel EM, Lamsabhi AM. Water biocatalytic effect attenuates cytochrome P450-mediated carcinogenicity of diethylnitrosamine: A computational insight. Org Biomol Chem 2021; 19:9031-9042. [PMID: 34613323 DOI: 10.1039/d1ob01439k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanism-based mutagenicity and carcinogenicity of diethylnitrosamine (DEN) are believed to act through interactions with cytochrome P450 (P450) enzymes. DFT calculations to explore the conceivable mechanisms underlying the reaction of P450 with DEN with and without water as a biocatalyst were performed. The results shed light on the biocatalytic role of water in lowering the H-abstraction energy barriers because of the electrostatic effect driven by hydrogen bonding. Our DFT analysis revealed how metabolites are formed in the dealkylation (toxification) and denitrosation (detoxification) pathways. Also, our findings uncovered the active position of DEN vulnerable to P450 interactions. Two factors control the toxification and detoxification rates: the stability of denitrosation products and the HS rebound barrier of the α-pathway. Thus, water biocatalytic attenuation of DEN carcinogenicity was attained by stabilizing denitrosation products and slowing the α-HS rebound process. Docking and MD simulations were performed to assess the binding modes of DEN to P450's active site and to inspect the denitrosation and dealkylation processes, respectively.
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Affiliation(s)
- Emadeldin M Kamel
- Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049 Madrid, Spain.
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049 Madrid, Spain.
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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19
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Salamone M, Galeotti M, Romero-Montalvo E, van Santen JA, Groff BD, Mayer JM, DiLabio GA, Bietti M. Bimodal Evans-Polanyi Relationships in Hydrogen Atom Transfer from C(sp 3)-H Bonds to the Cumyloxyl Radical. A Combined Time-Resolved Kinetic and Computational Study. J Am Chem Soc 2021; 143:11759-11776. [PMID: 34309387 PMCID: PMC8343544 DOI: 10.1021/jacs.1c05566] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Indexed: 12/11/2022]
Abstract
The applicability of the Evans-Polanyi (EP) relationship to HAT reactions from C(sp3)-H bonds to the cumyloxyl radical (CumO•) has been investigated. A consistent set of rate constants, kH, for HAT from the C-H bonds of 56 substrates to CumO•, spanning a range of more than 4 orders of magnitude, has been measured under identical experimental conditions. A corresponding set of consistent gas-phase C-H bond dissociation enthalpies (BDEs) spanning 27 kcal mol-1 has been calculated using the (RO)CBS-QB3 method. The log kH' vs C-H BDE plot shows two distinct EP relationships, one for substrates bearing benzylic and allylic C-H bonds (unsaturated group) and the other one, with a steeper slope, for saturated hydrocarbons, alcohols, ethers, diols, amines, and carbamates (saturated group), in line with the bimodal behavior observed previously in theoretical studies of reactions promoted by other HAT reagents. The parallel use of BDFEs instead of BDEs allows the transformation of this correlation into a linear free energy relationship, analyzed within the framework of the Marcus theory. The ΔG⧧HAT vs ΔG°HAT plot shows again distinct behaviors for the two groups. A good fit to the Marcus equation is observed only for the saturated group, with λ = 58 kcal mol-1, indicating that with the unsaturated group λ must increase with increasing driving force. Taken together these results provide a qualitative connection between Bernasconi's principle of nonperfect synchronization and Marcus theory and suggest that the observed bimodal behavior is a general feature in the reactions of oxygen-based HAT reagents with C(sp3)-H donors.
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Affiliation(s)
- Michela Salamone
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Marco Galeotti
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Eduardo Romero-Montalvo
- Department
of Chemistry, The University of British
Columbia, 3247 University Way, Kelowna, British Columbia, Canada, V1V 1V7
| | - Jeffrey A. van Santen
- Department
of Chemistry, The University of British
Columbia, 3247 University Way, Kelowna, British Columbia, Canada, V1V 1V7
| | - Benjamin D. Groff
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - James M. Mayer
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Gino A. DiLabio
- Department
of Chemistry, The University of British
Columbia, 3247 University Way, Kelowna, British Columbia, Canada, V1V 1V7
| | - Massimo Bietti
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
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20
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Lin YT, de Visser SP. Product Distributions of Cytochrome P450 OleT JE with Phenyl-Substituted Fatty Acids: A Computational Study. Int J Mol Sci 2021; 22:7172. [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] [MESH Headings] [Track Full Text] [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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Affiliation(s)
- Yen-Ting Lin
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK;
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M13 9PL, UK
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK;
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M13 9PL, UK
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21
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Negative catalysis / non-Bell-Evans-Polanyi reactivity by metalloenzymes: Examples from mononuclear heme and non-heme iron oxygenases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213914] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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22
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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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23
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Yadav R, Awasthi N, Shukla A, Kumar D. Modeling the hydroxylation of estragole via human liver cytochrome P450. J Mol Model 2021; 27:199. [PMID: 34117581 DOI: 10.1007/s00894-021-04815-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
Natural compounds derived from plants are generally regarded safe and devoid of adverse effects. However, there are individual ingredients that possess toxic, genotoxic, and carcinogenic activities. These compounds when exposed at specific level become hazardous to health. Estragole (1-allyl-4-methoxybenzene) is a common component of spice plants. Its toxicity gets activated with the hydroxylation at benzylic carbon (C1') position by P450 enzymes present in the human liver. The present study grounds to explore the reaction mechanism of conversion of estragole to hydroxylated metabolite using computational methodology. Density functional theory (DFT)-based calculations were employed to explore the cytochrome P450-catalyzed mechanism at C1 position aliphatic hydroxylation of estragole. Overall reaction energy profile, electronic configuration, and 3D structure of all intermediates, transition states, and product complexes formed during the reaction along with their free energies were tried to be investigated.
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Affiliation(s)
- Rolly Yadav
- Molecular Modeling Lab, Department of Physics, School of Physical and Decision Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, UP, 226025, India
| | - Nidhi Awasthi
- Molecular Modeling Lab, Department of Physics, School of Physical and Decision Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, UP, 226025, India
| | - Anamika Shukla
- Molecular Modeling Lab, Department of Physics, School of Physical and Decision Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, UP, 226025, India
| | - Devesh Kumar
- Molecular Modeling Lab, Department of Physics, School of Physical and Decision Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, UP, 226025, India.
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24
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Ali HS, Henchman RH, Visser SP. Mechanism of Oxidative Ring‐Closure as Part of the Hygromycin Biosynthesis Step by a Nonheme Iron Dioxygenase. ChemCatChem 2021. [DOI: 10.1002/cctc.202100393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
- Department of Chemistry The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Richard H. Henchman
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
- Department of Chemistry The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Sam P. Visser
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
- Department of Chemical Engineering and Analytical Science The University of Manchester Oxford Road Manchester M13 9PL UK
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Yuan C, Ouyang Q, Wang X, Li X, Tan H, Chen G. Interactive Regulation between Aliphatic Hydroxylation and Aromatic Hydroxylation of Thaxtomin D in TxtC: A Theoretical Investigation. Inorg Chem 2021; 60:6433-6445. [PMID: 33861573 DOI: 10.1021/acs.inorgchem.1c00154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
TxtC is an unusual bifunctional cytochrome P450 that is able to perform sequential aliphatic and aromatic hydroxylation of the diketopiperazine substrate thaxtomin D in two distinct sites to produce thaxtomin A. Though the X-ray structure of TxtC complexed with thaxtomin D revealed a binding mode for its aromatic hydroxylation, the preferential hydroxylation site is aliphatic C14. It is thus intriguing to unravel how TxtC accomplishes such two-step catalytic hydroxylation on distinct aliphatic and aromatic carbons and why the aliphatic site is preferred in the hydroxylation step. In this work, by employing molecular docking and molecular dynamics (MD) simulation, we revealed that thaxtomin D could adopt two different conformations in the TxtC active site, which were equal in energy with either the aromatic C20-H or aliphatic C14-H pointing toward the active Cpd I oxyferryl moiety. Further ONIOM calculations indicated that the energy barrier for the rate-limiting hydroxylation step on the aliphatic C14 site was 9.6 kcal/mol more favorable than that on the aromatic C20 site. The hydroxyl group on the monohydroxylated intermediate thaxtomin B C14 site formed hydrogen bonds with Ser280 and Thr385, which induced the l-Phe moiety to rotate around the Cβ-Cγ bond of the 4-nitrotryptophan moiety. Thus, it adopted an energetically favorable conformation with aromatic C20 adjacent to the oxyferryl moiety. In addition, the hydroxyl group induced solvent water molecules to enter the active site, which propelled thaxtomin B toward the heme plane and resulted in heme distortion. Based on this geometrical layout, the rate-limiting aromatic hydroxylation energy barrier decreased to 15.4 kcal/mol, which was comparable to that of the thaxtomin D aliphatic hydroxylation process. Our calculations indicated that heme distortion lowered the energy level of the lowest Cpd I α-vacant orbital, which promoted electron transfer in the rate-limiting thaxtomin B aromatic hydroxylation step in TxtC.
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Affiliation(s)
- Chang Yuan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Qingwen Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Xixi Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
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Mirzaei MS, Ivanov MV, Taherpour AA, Mirzaei S. Mechanism-Based Inactivation of Cytochrome P450 Enzymes: Computational Insights. Chem Res Toxicol 2021; 34:959-987. [PMID: 33769041 DOI: 10.1021/acs.chemrestox.0c00483] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mechanism-based inactivation (MBI) refers to the metabolic bioactivation of a xenobiotic by cytochrome P450s to a highly reactive intermediate which subsequently binds to the enzyme and leads to the quasi-irreversible or irreversible inhibition. Xenobiotics, mainly drugs with specific functional units, are the major sources of MBI. Two possible consequences of MBI by medicinal compounds are drug-drug interaction and severe toxicity that are observed and highlighted by clinical experiments. Today almost all of these latent functional groups (e.g., thiophene, furan, alkylamines, etc.) are known, and their features and mechanisms of action, owing to the vast experimental and theoretical studies, are determined. In the past decade, molecular modeling techniques, mostly density functional theory, have revealed the most feasible mechanism that a drug undergoes by P450 enzymes to generate a highly reactive intermediate. In this review, we provide a comprehensive and detailed picture of computational advances toward the elucidation of the activation mechanisms of various known groups with MBI activity. To this aim, we briefly describe the computational concepts to carry out and analyze the mechanistic investigations, and then, we summarize the studies on compounds with known inhibition activity including thiophene, furan, alkylamines, terminal acetylene, etc. This study can be reference literature for both theoretical and experimental (bio)chemists in several different fields including rational drug design, the process of toxicity prevention, and the discovery of novel inhibitors and catalysts.
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Affiliation(s)
- M Saeed Mirzaei
- Department of Organic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran 67149-67346
| | - Maxim V Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Avat Arman Taherpour
- Department of Organic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran 67149-67346.,Medical Biology Research Centre, University of Medical Sciences, Kermanshah, Iran 67149-67346
| | - Saber Mirzaei
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Han SB, Ali HS, de Visser SP. Glutarate Hydroxylation by the Carbon Starvation-Induced Protein D: A Computational Study into the Stereo- and Regioselectivities of the Reaction. Inorg Chem 2021; 60:4800-4815. [DOI: 10.1021/acs.inorgchem.0c03749] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Sungho Bosco Han
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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28
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Ali HS, Henchman RH, Warwicker J, de Visser SP. How Do Electrostatic Perturbations of the Protein Affect the Bifurcation Pathways of Substrate Hydroxylation versus Desaturation in the Nonheme Iron-Dependent Viomycin Biosynthesis Enzyme? J Phys Chem A 2021; 125:1720-1737. [DOI: 10.1021/acs.jpca.1c00141] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Richard H. Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jim Warwicker
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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Bai FY, Chen MY, Liu XH, Ni S, Tang YZ, Pan XM, Zhao Z. Kinetics and mechanism of OH-mediated degradation of three pentanols in the atmosphere. NEW J CHEM 2021. [DOI: 10.1039/d1nj01955d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pentanols as potential biofuels have attracted considerable interest, and thus it is of great importance to gain insights into their combustion and atmospheric chemistry.
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Affiliation(s)
- Feng-Yang Bai
- Institute of Catalysis for Energy and Environment, College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang, 110034, People's Republic of China
| | - Mei-Yan Chen
- Institute of Catalysis for Energy and Environment, College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang, 110034, People's Republic of China
| | - Xiang-Huan Liu
- Institute of Catalysis for Energy and Environment, College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang, 110034, People's Republic of China
| | - Shuang Ni
- Institute of Catalysis for Energy and Environment, College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang, 110034, People's Republic of China
- National & Local United Engineering Lab for Power Battery, Faculty of Chemistry, Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Yi-Zhen Tang
- School of Environmental and Municipal Engineering, Qingdao Technological University, Qingdao, 266033, People's Republic of China
| | - Xiu-Mei Pan
- National & Local United Engineering Lab for Power Battery, Faculty of Chemistry, Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Zhen Zhao
- Institute of Catalysis for Energy and Environment, College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang, 110034, People's Republic of China
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Chang Ping, Beijing 102249, People's Republic of China
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30
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Miyagawa K, Isobe H, Shoji M, Kawakami T, Yamanaka S, Yamaguchi K. A three states model for hydrogen abstraction reactions with the cytochrome P450 compound I is revisited. Isolobal and isospin analogy among Fe(IV)=O, O = O and O. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Yamaguchi K, Miyagawa K, Isobe H, Shoji M, Kawakami T, Yamanaka S. Isolobal and isospin analogy between organic and inorganic open-shell molecules—Application to oxygenation reactions by active oxygen and oxy-radicals and water oxidation in the native and artificial photosynthesis. ADVANCES IN QUANTUM CHEMISTRY 2021. [DOI: 10.1016/bs.aiq.2021.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Don CG, Smieško M. Deciphering Reaction Determinants of Altered-Activity CYP2D6 Variants by Well-Tempered Metadynamics Simulation and QM/MM Calculations. J Chem Inf Model 2020; 60:6642-6653. [PMID: 33269921 DOI: 10.1021/acs.jcim.0c01091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The xenobiotic metabolizing enzyme CYP2D6 is the P450 cytochrome family member with the highest rate of polymorphism. This causes changes in the enzyme activity and specificity, which can ultimately lead to adverse reactions during drug treatment. To avoid or lower CYP-related toxicity risks, prediction of the most likely positions within a molecule where a metabolic reaction might occur is paramount. In order to obtain accurate predictions, it is crucial to understand all phenomena within the active site of the enzyme that contribute to an efficient substrate recognition and the subsequent catalytic reaction together with their relative weight within the overall thermodynamic context. This study aims to define the weight of the driving forces upon the C-H bond activation within CYP2D6 wild-type and a clinically relevant allelic variant with increased activity (CYP2D6*53) featuring two amino acid mutations in close vicinity of the heme. First, we investigated the steric and electrostatic complementarity of the substrate bufuralol using well-tempered metadynamics simulations with the aim to obtain the free energy profiles for each site of metabolism (SoM) within the different active sites. Second, the stereoelectronic complementarity was determined for each SoM within the two different active-site environments. Relying on the well-tempered metadynamics simulation energy profiles of each SoM, we identified the binding mode that was closest to the preferred transition-state geometry for efficient C-H bond activation. The binding modes were then used as starting structures for the quantum mechanics/molecular mechanics calculations performed to quantify the corresponding activation barriers. Our results show the relevance of the steric component in orienting the SoM in an energetically accessible position toward the heme. However, the corresponding intrinsic reactivity and electronic complementarity within the active site must be accurately evaluated in order to obtain a meaningful reaction prediction, from which the predominant SoM can be determined. The F120I mutation lowered the activation barrier for the major site and one of the minor SoMs. However, it had an impact neither on the CYP2D6 enantioselectivity preference of the oxidation reaction nor on the stereoselectivity from the substrate point of view.
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Affiliation(s)
- Charleen G Don
- Computational Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Martin Smieško
- Computational Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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Ansari M, Senthilnathan D, Rajaraman G. Deciphering the origin of million-fold reactivity observed for the open core diiron [HO-Fe III-O-Fe IV[double bond, length as m-dash]O] 2+ species towards C-H bond activation: role of spin-states, spin-coupling, and spin-cooperation. Chem Sci 2020; 11:10669-10687. [PMID: 33209248 PMCID: PMC7654192 DOI: 10.1039/d0sc02624g] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/16/2020] [Indexed: 01/26/2023] Open
Abstract
High-valent metal-oxo species have been characterised as key intermediates in both heme and non-heme enzymes that are found to perform efficient aliphatic hydroxylation, epoxidation, halogenation, and dehydrogenation reactions. Several biomimetic model complexes have been synthesised over the years to mimic both the structure and function of metalloenzymes. The diamond-core [Fe2(μ-O)2] is one of the celebrated models in this context as this has been proposed as the catalytically active species in soluble methane monooxygenase enzymes (sMMO), which perform the challenging chemical conversion of methane to methanol at ease. In this context, a report of open core [HO(L)FeIII-O-FeIV(O)(L)]2+ (1) gains attention as this activates C-H bonds a million-fold faster compared to the diamond-core structure and has the dual catalytic ability to perform hydroxylation as well as desaturation with organic substrates. In this study, we have employed density functional methods to probe the origin of the very high reactivity observed for this complex and also to shed light on how this complex performs efficient hydroxylation and desaturation of alkanes. By modelling fifteen possible spin-states for 1 that could potentially participate in the reaction mechanism, our calculations reveal a doublet ground state for 1 arising from antiferromagnetic coupling between the quartet FeIV centre and the sextet FeIII centre, which regulates the reactivity of this species. The unusual stabilisation of the high-spin ground state for FeIV[double bond, length as m-dash]O is due to the strong overlap of with the orbital, reducing the antibonding interactions via spin-cooperation. The electronic structure features computed for 1 are consistent with experiments offering confidence in the methodology chosen. Further, we have probed various mechanistic pathways for the C-H bond activation as well as -OH rebound/desaturation of alkanes. An extremely small barrier height computed for the first hydrogen atom abstraction by the terminal FeIV[double bond, length as m-dash]O unit was found to be responsible for the million-fold activation observed in the experiments. The barrier height computed for -OH rebound by the FeIII-OH unit is also smaller suggesting a facile hydroxylation of organic substrates by 1. A strong spin-cooperation between the two iron centres also reduces the barrier for second hydrogen atom abstraction, thus making the desaturation pathway competitive. Both the spin-state as well as spin-coupling between the two metal centres play a crucial role in dictating the reactivity for species 1. By exploring various mechanistic pathways, our study unveils the fact that the bridged μ-oxo group is a poor electrophile for both C-H activation as well for -OH rebound. As more and more evidence is gathered in recent years for the open core geometry of sMMO enzymes, the idea of enhancing the reactivity via an open-core motif has far-reaching consequences.
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Affiliation(s)
- Mursaleem Ansari
- Department of Chemistry , Indian Institute of Technology Bombay , Mumbai 400076 , India .
| | - Dhurairajan Senthilnathan
- Center for Computational Chemistry , CRD , PRIST University , Vallam , Thanjavur , Tamilnadu 613403 , India
| | - Gopalan Rajaraman
- Department of Chemistry , Indian Institute of Technology Bombay , Mumbai 400076 , India .
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Kumar R, Pandey B, Sen A, Ansari M, Sharma S, Rajaraman G. Role of oxidation state, ferryl-oxygen, and ligand architecture on the reactivity of popular high-valent FeIV=O species: A theoretical perspective. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213397] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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35
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Zhang C, Crawford JJ, Landry ML, Chen H, Kenny JR, Khojasteh SC, Lee W, Ma S, Young WB. Strategies to Mitigate the Bioactivation of Aryl Amines. Chem Res Toxicol 2020; 33:1950-1959. [PMID: 32508087 DOI: 10.1021/acs.chemrestox.0c00138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bioactivation of xenobiotics to yield reactive metabolites can lead to tolerability and toxicity concerns within a drug discovery program. Development of strategies for mitigating the metabolic liability of commonly encountered toxicophores, such as anilines, relies on an understanding of the relative tendency of these functionalities to undergo bioactivation. In this report, we present the first systematic study of the structure-activity relationships of the bioactivation of aryl amine fragments (molecular weight < 250 Da) using a glutathione (GSH) trapping assay in the presence of human liver microsomes and the reduced form of nicotinamide adenine dinucleotide phosphate. This study demonstrates that conversion of anilines to nitrogen-containing heteroarylamines results in a lower abundance of GSH conjugates in the order phenyl > pyrimidine ≈ pyridine > pyridazine. Introduction of electron-withdrawing functionality on the aromatic ring had a less pronounced effect on the extent of GSH conjugation. Examination of more drug-like compounds sourced from in-house drug discovery programs revealed similar trends in bioactivation between matched pairs containing (hetero)aryl amines. This study provides medicinal chemists with insights and qualitative guidance for the minimization of risks related to aryl amine metabolism.
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Affiliation(s)
- Chenghong Zhang
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - James J Crawford
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Matthew L Landry
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Huifen Chen
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jane R Kenny
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - S Cyrus Khojasteh
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wendy Lee
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Shuguang Ma
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wendy B Young
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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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: 18] [Impact Index Per Article: 4.5] [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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Chai L, Ji S, Zhang S, Yu H, Zhao M, Ji L. Biotransformation Mechanism of Pesticides by Cytochrome P450: A DFT Study on Dieldrin. Chem Res Toxicol 2020; 33:1442-1448. [DOI: 10.1021/acs.chemrestox.0c00013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lihong Chai
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Shujing Ji
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Shubin Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, Jinhua 321004, China
| | - Meirong Zhao
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Li Ji
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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Ali HS, Henchman RH, de Visser SP. Cross-linking of aromatic phenolate groups by cytochrome P450 enzymes: a model for the biosynthesis of vancomycin by OxyB. Org Biomol Chem 2020; 18:4610-4618. [DOI: 10.1039/d0ob01023e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Aromatic cross-linking by cytochrome P450 enzymes was studied computationally. P450 Compound I rapidly abstracts two weak phenolic H-atoms that link up via a rate-determining C–O bond formation.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester M1 7DN
- UK
- Department of Chemistry
| | - Richard H. Henchman
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester M1 7DN
- UK
- Department of Chemistry
| | - Sam P. de Visser
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester M1 7DN
- UK
- Department of Chemical Engineering and Analytical Science
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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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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: 64] [Impact Index Per Article: 12.8] [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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41
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Saito T, Kambara H, Takano Y. Quantitative assessment of reparameterized PM6 (rPM6) for hydrogen abstraction reactions. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1700313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Toru Saito
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima Japan
| | - Hiroki Kambara
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima Japan
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42
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Properties and reactivity of μ-nitrido-bridged dimetal porphyrinoid complexes: how does ruthenium compare to iron? J Biol Inorg Chem 2019; 24:1127-1134. [PMID: 31560098 DOI: 10.1007/s00775-019-01725-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/19/2019] [Indexed: 12/23/2022]
Abstract
Methane hydroxylation by metal-oxo oxidants is one of the Holy Grails in biomimetic and biotechnological chemistry. The only enzymes known to perform this reaction in Nature are iron-containing soluble methane monooxygenase and copper-containing particulate methane monooxygenase. Furthermore, few biomimetic iron-containing oxidants have been designed that can hydroxylate methane efficiently. Recent studies reported that μ-nitrido-bridged diiron(IV)-oxo porphyrin and phthalocyanine complexes hydroxylate methane to methanol efficiently. To find out whether the reaction rates are enhanced by replacing iron by ruthenium, we performed a detailed computational study. Our work shows that the μ-nitrido-bridged diruthenium(IV)-oxo reacts with methane via hydrogen atom abstraction barriers that are considerably lower in energy (by about 5 kcal mol‒1) as compared to the analogous diiron(IV)-oxo complex. An analysis of the electronic structure implicates similar spin and charge distributions for the diiron(IV)-oxo and diruthenium(IV)-oxo complexes, but the strength of the O‒H bond formed during the reaction is much stronger for the latter. As such a larger hydrogen atom abstraction driving force for the Ru complex than for the Fe complex is found, which should result in higher reactivity in the oxidation of methane.
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43
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Conformational turn triggers regio-selectivity in the bioactivation of thiophene-contained compounds mediated by cytochrome P450. J Biol Inorg Chem 2019; 24:1023-1033. [PMID: 31506822 DOI: 10.1007/s00775-019-01699-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/24/2019] [Indexed: 10/26/2022]
Abstract
In the present work, we performed Density Functional Theory calculations to explore the bioactivation mechanism of thiophene-containing molecules mediated by P450s. For this purpose, relatively large size compounds, 2,5-diaminothiophene derivatives were selected particularly for this investigation. Here we found the successive regio-selectivity triggered by conformational turn played a significant role in the occurrence of bioactivation. 2,5-Diaminothiophene was oxidized to a 2,5-diimine thiophene-reactive intermediate by Compound I (Cpd I) through successive activations of two N-H bonds (H3-N11 and H1-N6). This reaction exhibited three special characteristics: (1) self-controlled regio-selectivity during the oxidation process. There was a large scale of conformational turn in the abstraction of the first H atom which triggers the selection of the second H for abstraction. (2) Proton-shuttle mechanism. In high spin (HS) state, proton-shuttle mechanism was observed for the abstraction of the second H atom. (3) Spin-selective manner. In protein environment, the energy barrier in HS state was much lower than that in low spin state. The novel proposed bioactivation mechanism of 2,5-diaminothiophene compounds can help us in rational design of thiophene-contained drugs avoiding the occurrence of bioactivation.
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44
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Zhang Y. Computational Investigations of Heme Carbenes and Heme Carbene Transfer Reactions. Chemistry 2019; 25:13231-13247. [DOI: 10.1002/chem.201901984] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/19/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Yong Zhang
- Department of Chemistry and Chemical Biology Stevens Institute of Technology 1 Castle Point on Hudson Hoboken NJ 07030 USA
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45
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Davethu PA, de Visser SP. CO2 Reduction on an Iron-Porphyrin Center: A Computational Study. J Phys Chem A 2019; 123:6527-6535. [DOI: 10.1021/acs.jpca.9b05102] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Paul A. Davethu
- 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
| | - 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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46
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Zeb N, Rashid MH, Mubarak MQE, Ghafoor S, de Visser SP. Flavonol biosynthesis by nonheme iron dioxygenases: A computational study into the structure and mechanism. J Inorg Biochem 2019; 198:110728. [PMID: 31203088 DOI: 10.1016/j.jinorgbio.2019.110728] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
Plants produce flavonol compounds for vital functions regarding plant growth, fruit and flower colouring as well as fruit ripening processes. Several of these biosynthesis steps are stereo- and regioselective and are being carried out by nonheme iron enzymes. Using density functional theory calculations on a large active site model complex of flavanone-3β-hydroxylase (FHT), we established the mechanism for conversion of naringenin to its dihydroflavonol, which is a key step in the mechanism of flavonol biosynthesis. The reaction starts with dioxygen binding to the iron(II) centre and a reaction with α-ketoglutarate co-substrate gives succinate, an iron(IV)-oxo species and CO2 with large exothermicity and small reaction barriers. The rate-determining reaction step in the mechanism; however, is hydrogen atom abstraction of an aliphatic CH bond by the iron(IV)-oxo species. We identify a large kinetic isotope effect for the replacement of the transferring hydrogen atom by deuterium. In a final step the OH and substrate radicals combine to form the alcohol product with a barrier of several kcal mol-1. We show that the latter is the result of geometric constraints in the active site pocket. Furthermore, the calculations show that a weak tertiary CH bond is shielded from the iron(IV)-oxo species in the substrate binding position and therefore the enzyme is able to activate a stronger CH bond. As such, the flavanone-3β-hydroxylase enzyme reacts regioselectively with one specific CH bond of naringenin by avoiding activation of weaker bonds through tight substrate and oxidant positioning.
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Affiliation(s)
- Neelam Zeb
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom; National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad H Rashid
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - M Qadri E Mubarak
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sidra Ghafoor
- Manchester Institute of Biotechnology and School 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, Jhang Road, 3800 Faisalabad, Pakistan
| | - 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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47
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Pattanayak S, Cantú Reinhard FG, Rana A, Gupta SS, de Visser SP. The Equatorial Ligand Effect on the Properties and Reactivity of Iron(V) Oxo Intermediates. Chemistry 2019; 25:8092-8104. [DOI: 10.1002/chem.201900708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Santanu Pattanayak
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246 India
| | - Fabián G. Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Atanu Rana
- Indian Association for the Cultivation of Sciences 2A Raja S. C. Mullick Road Kolkata 700032 India
| | - Sayam Sen Gupta
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246 India
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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48
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Quesne MG, Silveri F, de Leeuw NH, Catlow CRA. Advances in Sustainable Catalysis: A Computational Perspective. Front Chem 2019; 7:182. [PMID: 31032245 PMCID: PMC6473102 DOI: 10.3389/fchem.2019.00182] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/07/2019] [Indexed: 11/13/2022] Open
Abstract
The enormous challenge of moving our societies to a more sustainable future offers several exciting opportunities for computational chemists. The first principles approach to "catalysis by design" will enable new and much greener chemical routes to produce vital fuels and fine chemicals. This prospective outlines a wide variety of case studies to underscore how the use of theoretical techniques, from QM/MM to unrestricted DFT and periodic boundary conditions, can be applied to biocatalysis and to both homogeneous and heterogenous catalysts of all sizes and morphologies to provide invaluable insights into the reaction mechanisms they catalyze.
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49
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Wang J, Zhao YY, Lee PH, Wu K. Computational analysis of non-heme iron-oxo formation by direct NO release in nitrite reduction. Phys Chem Chem Phys 2019; 21:6643-6650. [PMID: 30855607 DOI: 10.1039/c9cp00370c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A direct NO-releasing reaction of nitrite catalyzed by [N(afaCy)3Fe(OTf)]+ (afa (azafulvene-amine); OTf (trifluoromethanesulfonate); Cy (cyclohexyl)) was investigated using density functional theory (DFT) with D3 dispersion correction. The complex featured a secondary coordination sphere that facilitated the formation of the iron-oxo product [N(afaCy)3FeO]+ with three (Fe)OH-N hydrogen bonds. As a high-spin iron(ii), the O-binding initial intermediate Fe(O)-nitrito was thermodynamically favorable in the S = 2 state. The cleavage of the (Fe)O-NO bond was performed by a β-electron shift to produce Fe(iii)-O by electron rearrangement in the S = 5/2 state. The different electron configurations are responsible for the structural properties, the valence of iron in the complexes, and the pathways of the reactions. Moreover, the two different H-bonds, (Fe)OH-N and (Fe)O-HN (by O-protonation), in the product complexes played a role in determining the reaction channels by impacting the N-H bond rotation. Thus, an exothermic sequence of conversions Fe(ii) → Fe(iii)-O → Fe(iii)-OH → Fe(iii)-O was established for the targeted product formation. This process provided a clue to build two key intermediates, iron-oxo and iron-hydroxo, in a variety of biological and synthetic systems. The results of this study are in agreement with experimental observations and describe the roles of H-bonding in nitrite reduction catalyzed by the non-heme iron complex.
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Affiliation(s)
- Jian Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China. and Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, People's Republic of China
| | - Yuan-Yuan Zhao
- Frankfurt Institute for Advanced Studies (FIAS), Goethe-University, Ruth-Moufang-Str. 1, D-60438 Frankfurt am Main, Germany
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, People's Republic of China
| | - Kechen Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China. and Center for Advanced Marine Materials and Smart Sensors, Minjiang University, Fuzhou 350116, China
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50
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Mukherjee G, Alili A, Barman P, Kumar D, Sastri CV, de Visser SP. Interplay Between Steric and Electronic Effects: A Joint Spectroscopy and Computational Study of Nonheme Iron(IV)-Oxo Complexes. Chemistry 2019; 25:5086-5098. [PMID: 30720909 DOI: 10.1002/chem.201806430] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Indexed: 01/05/2023]
Abstract
Iron is an essential element in nonheme enzymes that plays a crucial role in many vital oxidative transformations and metabolic reactions in the human body. Many of those reactions are regio- and stereospecific and it is believed that the selectivity is guided by second-coordination sphere effects in the protein. Here, results are shown of a few engineered biomimetic ligand frameworks based on the N4Py (N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) scaffold and the second-coordination sphere effects are studied. For the first time, selective substitutions in the ligand framework have been shown to tune the catalytic properties of the iron(IV)-oxo complexes by regulating the steric and electronic factors. In particular, a better positioning of the oxidant and substrate in the rate-determining transition state lowers the reaction barriers. Therefore, an optimum balance between steric and electronic factors mediates the ideal positioning of oxidant and substrate in the rate-determining transition state that affects the reactivity of high-valent reaction intermediates.
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Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Aligulu Alili
- The Manchester Institute of Biotechnology and School of Chemical, Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Prasenjit Barman
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Devesh Kumar
- Department of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, 226025, UP, India
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - 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, UK
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