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Mallinson SJB, Machovina MM, Silveira RL, Garcia-Borràs M, Gallup N, Johnson CW, Allen MD, Skaf MS, Crowley MF, Neidle EL, Houk KN, Beckham GT, DuBois JL, McGeehan JE. A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion. Nat Commun 2018; 9:2487. [PMID: 29950589 PMCID: PMC6021390 DOI: 10.1038/s41467-018-04878-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/26/2018] [Indexed: 11/18/2022] Open
Abstract
Microbial aromatic catabolism offers a promising approach to convert lignin, a vast source of renewable carbon, into useful products. Aryl-O-demethylation is an essential biochemical reaction to ultimately catabolize coniferyl and sinapyl lignin-derived aromatic compounds, and is often a key bottleneck for both native and engineered bioconversion pathways. Here, we report the comprehensive characterization of a promiscuous P450 aryl-O-demethylase, consisting of a cytochrome P450 protein from the family CYP255A (GcoA) and a three-domain reductase (GcoB) that together represent a new two-component P450 class. Though originally described as converting guaiacol to catechol, we show that this system efficiently demethylates both guaiacol and an unexpectedly wide variety of lignin-relevant monomers. Structural, biochemical, and computational studies of this novel two-component system elucidate the mechanism of its broad substrate specificity, presenting it as a new tool for a critical step in biological lignin conversion.
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Affiliation(s)
- Sam J B Mallinson
- Molecular Biophysics, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Melodie M Machovina
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Rodrigo L Silveira
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- Institute of Chemistry, University of Campinas, Campinas, Sao Paulo, 13083-970, Brazil
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Nathan Gallup
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Christopher W Johnson
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Mark D Allen
- Molecular Biophysics, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas, Campinas, Sao Paulo, 13083-970, Brazil
| | - Michael F Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
| | - John E McGeehan
- Molecular Biophysics, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK.
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52
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Affiliation(s)
- Yujie Liang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Xu Qiu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
- State Key Laboratory of Organometallic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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53
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Petrović D, Bokel A, Allan M, Urlacher VB, Strodel B. Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation. J Chem Inf Model 2018. [PMID: 29522682 DOI: 10.1021/acs.jcim.8b00043] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Engineering high chemo-, regio-, and stereoselectivity is a prerequisite for enzyme usage in organic synthesis. Cytochromes P450 can oxidize a broad range of substrates, including macrocycles, which are becoming popular scaffolds for therapeutic agents. However, a large conformational space explored by macrocycles not only reduces the selectivity of oxidation but also impairs computational enzyme design strategies based on docking and molecular dynamics (MD) simulations. We present a novel design workflow that uses enhanced-sampling Hamiltonian replica exchange (HREX) MD and focuses on quantifying the substrate binding for suggesting the mutations to be made. This computational approach is applied to P450 BM3 with the aim to shift regioselectively toward one of the numerous possible positions during β-cembrenediol oxidation. The predictions are experimentally tested and the resulting product distributions validate our design strategy, as single mutations led up to 5-fold regioselectivity increases. We thus conclude that the HREX-MD-based workflow is a promising tool for the identification of positions for mutagenesis aiming at P450 enzymes with improved regioselectivity.
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Affiliation(s)
- Dušan Petrović
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Ansgar Bokel
- Institute of Biochemistry , Heinrich Heine University Düsseldorf , Universitätsstraße 1 , 40225 Düsseldorf , Germany
| | - Matthew Allan
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany.,Schreyer Honors College , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Vlada B Urlacher
- Institute of Biochemistry , Heinrich Heine University Düsseldorf , Universitätsstraße 1 , 40225 Düsseldorf , Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätsstraße 1 , 40225 Düsseldorf , Germany
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54
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Fan JR, Li H, Zhang HX, Zheng QC. Exploring the structure characteristics and major channels of cytochrome P450 2A6, 2A13, and 2E1 with pilocarpine. Biopolymers 2018; 109:e23108. [PMID: 29484634 DOI: 10.1002/bip.23108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 12/25/2022]
Abstract
The majority of cytochromes P450 play a critical role in metabolism of endogenous and exogenous substrates, some of its products are carcinogens. Therefore, inhibition of P450 enzymes activity can promote the detoxification and elimination of chemical carcinogens. In this study, molecular dynamics (MD) simulations and adaptive steered molecular dynamics (ASMD) simulations were performed to explore the structure features and channel dynamics of three P450 isoforms 2A6, 2A13, and 2E1 bound with the common inhibitor pilocarpine. The binding free energy results combined with the PMF calculations give a reasonable ranking of binding affinity, which are consistent with the experimental data. Our results uncover how a sequence divergence of different CYP2 enzymes causes individual variations in major channel selections. On the basis of channel bottleneck and energy decomposition analysis, we propose a gating mechanism of their respective major channels in three enzymes, which may be attributed to a reversal of Phe209 in CYP2A6/2A13, as well as the rotation of Phe116 and Phe298 in CYP2E1. The hydrophobic residues not only make strong hydrophobic interactions with inhibitor, but also act as gatekeeper to regulate the opening of channel. The present study provides important insights into the structure-function relationships of three cytochrome P450s and the molecular basis for development of potent inhibitors.
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Affiliation(s)
- Jing-Rong Fan
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Heng Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, 130012, People's Republic of China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, 130012, People's Republic of China
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55
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Alberro N, Torrent-Sucarrat M, Arrieta A, Rubiales G, Cossío FP. Density Functional Theory Study on the Demethylation Reaction between Methylamine, Dimethylamine, Trimethylamine, and Tamoxifen Catalyzed by a Fe(IV)-Oxo Porphyrin Complex. J Phys Chem A 2018; 122:1658-1671. [PMID: 29320849 DOI: 10.1021/acs.jpca.7b10654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this work, we studied computationally the N-demethylation reaction of methylamine, dimethylamine, and trimethylamine as archetypal examples of primary, secondary, and tertiary amines catalyzed by high-field low-spin Fe-containing enzymes such as cytochromes P450. Using DFT calculations, we found that the expected C-H hydroxylation process was achieved for trimethylamine. When dimethylamine and methylamine were studied, two different reaction mechanisms (C-H hydroxylation and a double hydrogen atom transfer) were computed to be energetically accessible and both are equally preferred. Both processes led to the formation of formaldehyde and the N-demethylated substrate. Finally, as an illustrative example, the relative contribution of the three primary oxidation routes of tamoxifen was rationalized through energetic barriers obtained from density functional calculations and docking experiments involving CYP3A4 and CYP2D6 isoforms. We found that the N-demethylation process was the intrinsically favored one, whereas other oxidation reactions required most likely preorganization imposed by the residues close to the active sites.
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Affiliation(s)
- Nerea Alberro
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain.,Donostia International Physics Center (DIPC) , Manuel Lardizabal Ibilbidea 4, 20018 San Sebastián/Donostia, Spain.,Ikerbasque, Basque Foundation for Science , María Díaz de Haro 3, 6°, 48013 Bilbao, Spain
| | - Ana Arrieta
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
| | - Gloria Rubiales
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
| | - Fernando P Cossío
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain.,Donostia International Physics Center (DIPC) , Manuel Lardizabal Ibilbidea 4, 20018 San Sebastián/Donostia, Spain
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56
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Li Y, Qin B, Li X, Tang J, Chen Y, Zhou L, You S. Selective Oxidations of Cyperenoic Acid by Slightly Reshaping the Binding Pocket of Cytochrome P450 BM3. ChemCatChem 2018. [DOI: 10.1002/cctc.201701088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yuxin Li
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Bin Qin
- Wuya College of Innovation; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Xiaoqin Li
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Jun Tang
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Yu Chen
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Lina Zhou
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Song You
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
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57
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Dubey KD, Shaik S. Choreography of the Reductase and P450 BM3 Domains Toward Electron Transfer Is Instigated by the Substrate. J Am Chem Soc 2018; 140:683-690. [PMID: 29277994 DOI: 10.1021/jacs.7b10072] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The driving force for the electron transfer (ET) step in the catalytic cycle of cytochrome P450BM3 is investigated using three sets of 1 μs molecular dynamic simulations for the resting state of P450 in complex with the flavin (FMN) in the reductase domain. These sets involve the following: (i) substrate-free (SF), (ii) substrate (N-palmitoyl glycine, i.e., NPG)-bound (SB), and (iii) SB with the semiquinone radical anion (SQ-) of FMN. Starting from the X-ray structure of the SF heme domain, we observe that the α1-helix (of the reductase) and the C-helix (of the heme) undergo reorientation to a parallel orientation, which is the thermochemically stable form. The reorientation of the helices pushes away the FMN to a distance of 18.4 Å from the heme's center. When the substrate binds it causes the I-helix of the heme domain to kink and push the C-helix toward the α1-helix, thereby locking the latter two into a stabilized perpendicular conformation, wherein the FMN-heme distance is 12 Å. The distance drops further in the SQ- form, and upon QM/MM geometry optimization the two moieties approach 8.8 Å, which enhances the ET rate (by 104-106 fold) to the heme's Fe3+ ion. These motions are driven by hydrogen bond strengthening between the C- and the α1-helices. Finally, substrate binding leads to formation of an organized water chain connecting the FMN and heme moieties. The water channel assists the ET and couples it to the proton transfer steps that should activate O2 and create the oxo-iron active species.
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Affiliation(s)
- Kshatresh Dutta Dubey
- Institute of Chemistry, The Hebrew University of Jerusalem , 9190400 Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem , 9190400 Jerusalem, Israel
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58
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Ainsley J, Lodola A, Mulholland AJ, Christov CZ, Karabencheva-Christova TG. Combined Quantum Mechanics and Molecular Mechanics Studies of Enzymatic Reaction Mechanisms. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 113:1-32. [PMID: 30149903 DOI: 10.1016/bs.apcsb.2018.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The combined quantum mechanics/molecular mechanics (QM/MM) methods have become a valuable tool in computational biochemistry and received versatile applications for studying the reaction mechanisms of enzymes. The approach combines the calculations of the electronic structure of the active site by QM, with modeling of the protein environment using MM force field, which allows the long-range electrostatics and steric effects on the enzyme reactivity to be accounted for. In this review, we review some key theoretical and computational aspects of the method and we also present some applications to particular enzymatic reactions such as tryptophan-7-halogenase, cyclooxygenase-1, and the epidermal growth factor receptor.
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Affiliation(s)
- Jon Ainsley
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University, Houghton, MI, United States.
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59
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Han L, Ma X, Liu Y, Yu Z, Liu T. Mechanistic insight into the C7-selective C–H functionalization of N-acyl indole catalyzed by a rhodium complex: a theoretical study. Org Chem Front 2018. [DOI: 10.1039/c7qo00911a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The role of the additive AgNTf2 and the origins of the reaction are clarified through our calculations.
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Affiliation(s)
- Lingli Han
- Department of Chemistry and Chemical Engineering
- Jining University
- Qufu 273155
- China
| | - Xiaoying Ma
- Department of Chemistry and Chemical Engineering
- Jining University
- Qufu 273155
- China
| | - Yuxia Liu
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- China
| | - Zhangyu Yu
- Department of Chemistry and Chemical Engineering
- Jining University
- Qufu 273155
- China
- School of Chemistry and Chemical Engineering
| | - Tao Liu
- Department of Chemistry and Chemical Engineering
- Jining University
- Qufu 273155
- China
- School of Chemistry and Chemical Engineering
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60
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61
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Wang Z, Fu Z, Yu Q, Chen J. Oxidation reactivity of 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE) by Compound I model of cytochrome P450s. J Environ Sci (China) 2017; 62:11-21. [PMID: 29289282 DOI: 10.1016/j.jes.2017.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 06/07/2023]
Abstract
Alternative brominated flame retardants (BFRs) have become prevalent as a consequence of restrictions on the use of polybrominated diphenyl ethers (PBDEs). For risk assessment of these alternatives, knowledge of their metabolism via cytochrome P450 enzymes is needed. We have previously proved that density functional theory (DFT) is able to predict the metabolism of PBDEs by revealing the molecular mechanisms. In the current study, the reactivity of 1,2-bis(2,4,6-tribromophenoxy)ethane and structurally similar chemicals with the Compound I model representing the active site of P450 enzymes was investigated. The DFT calculations delineated reaction pathways which lead to reasonable explanations for products that were detected by wet experiments, meanwhile intermediates which cannot be determined were also proposed. Results showed that alkyl hydrogen abstraction will lead to bis(2,4,6-tribromophenoxy)ethanol, which may undergo hydrolysis yielding 2,4,6-tribromophenol, a neurotoxic compound. In addition, a general pattern of oxidation reactivity regarding the 2,4,6-tribromophenyl moiety was observed among several model compounds. Our study has provided insights for convenient evaluation of the metabolism of other structurally similar BFRs.
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Affiliation(s)
- Zhongyu Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Zhiqiang Fu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qi Yu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
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62
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Li Z, Burnell DJ, Boyd RJ. Computational Study of Engineered Cytochrome P450-Catalyzed C–H Amination: The Origin of the Regio- and Stereoselectivity. J Phys Chem B 2017; 121:10859-10868. [DOI: 10.1021/acs.jpcb.7b10256] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zhe Li
- Department of Chemistry, Dalhousie University,
P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada
| | - D. Jean Burnell
- Department of Chemistry, Dalhousie University,
P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University,
P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada
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63
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Basom EJ, Manifold BA, Thielges MC. Conformational Heterogeneity and the Affinity of Substrate Molecular Recognition by Cytochrome P450cam. Biochemistry 2017; 56:3248-3256. [PMID: 28581729 DOI: 10.1021/acs.biochem.7b00238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The broad and variable substrate specificity of cytochrome P450 enzymes makes them a model system for studying the determinants of protein molecular recognition. The archetypal cytochrome P450cam (P450cam) is a relatively specific P450, a feature once attributed to the high rigidity of its active site. However, increasingly studies have provided evidence of the importance of conformational changes to P450cam activity. Here we used infrared (IR) spectroscopy to investigate the molecular recognition of P450cam. Toward this goal, and to assess the influence of a hydrogen bond (H-bond) between active site residue Y96 and substrates, two variants in which Y96 is replaced by a cyanophenyl (Y96CNF) or phenyl (Y96F) group were characterized in complexes with the substrates camphor, isoborneol, and camphane. These combinations allow for a comparison of complexes in which the moieties on both the protein and substrate can serve as a H-bond donor, acceptor, or neither. The IR spectra of heme-bound CO and the site-specifically incorporated CN of Y96CNF were analyzed to characterize the number and nature of environments in each protein, both in the free and bound states. Although the IR spectra do not support the idea that protein-substrate H-bonding is central to P450cam recognition, the data altogether suggest that the differing conformational heterogeneity in the active site of the P450cam variants and changes in heterogeneity upon binding of different substrates likely contribute to their variable affinities via a conformational selection mechanism. This study further extends our understanding of the molecular recognition of archetypal P450cam and demonstrates the application of IR spectroscopy combined with selective protein modification to delineate protein-ligand interactions.
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Affiliation(s)
- Edward J Basom
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Bryce A Manifold
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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64
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Li A, Wang B, Ilie A, Dubey KD, Bange G, Korendovych IV, Shaik S, Reetz MT. A redox-mediated Kemp eliminase. Nat Commun 2017; 8:14876. [PMID: 28348375 PMCID: PMC5379065 DOI: 10.1038/ncomms14876] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/08/2017] [Indexed: 01/27/2023] Open
Abstract
The acid/base-catalysed Kemp elimination of 5-nitro-benzisoxazole forming 2-cyano-4-nitrophenol has long served as a design platform of enzymes with non-natural reactions, providing new mechanistic insights in protein science. Here we describe an alternative concept based on redox catalysis by P450-BM3, leading to the same Kemp product via a fundamentally different mechanism. QM/MM computations show that it involves coordination of the substrate's N-atom to haem-Fe(II) with electron transfer and concomitant N-O heterolysis liberating an intermediate having a nitrogen radical moiety Fe(III)-N· and a phenoxyl anion. Product formation occurs by bond rotation and H-transfer. Two rationally chosen point mutations cause a notable increase in activity. The results shed light on the prevailing mechanistic uncertainties in human P450-catalysed metabolism of the immunomodulatory drug leflunomide, which likewise undergoes redox-mediated Kemp elimination by P450-BM3. Other isoxazole-based pharmaceuticals are probably also metabolized by a redox mechanism. Our work provides a basis for designing future artificial enzymes.
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Affiliation(s)
- Aitao Li
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany.,Department of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Binju Wang
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Adriana Ilie
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany.,Department of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Kshatresh D Dubey
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244, USA
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Manfred T Reetz
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany.,Department of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
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65
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Molcan T, Swigonska S, Orlowska K, Myszczynski K, Nynca A, Sadowska A, Ruszkowska M, Jastrzebski JP, Ciereszko RE. Structural-functional adaptations of porcine CYP1A1 to metabolize polychlorinated dibenzo-p-dioxins. CHEMOSPHERE 2017; 168:205-216. [PMID: 27783961 DOI: 10.1016/j.chemosphere.2016.10.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 06/06/2023]
Abstract
Polychlorinated dibenzo-p-dioxins (PCDDs) are widespread by-products of human industrial activity. They accumulate in tissues of animals and humans, exerting numerous adverse effects on different systems. In living organisms, dioxins are metabolized by enzymes of the cytochrome P450 family, including CYP1A1. Particular dioxin congeners differ in their toxicity level and ability to undergo biodegradation. Since the molecular mechanisms underlying dioxin susceptibility or resistance to biodegradation are unknown, in the present study the molecular interactions between five selected dioxins and porcine CYP1A1 protein were investigated. It was found that the ability of a dioxin to undergo CYP1A1-mediated degradation is associated mainly with the number and position of chlorine atoms in the dioxin molecule. Among all examined congeners, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) demonstrated the highest affinity to CYP1A1 and, at the same time, the greatest distance to the active site of the enzyme. Interestingly, in contrast to other dioxins, the binding of the TCDD molecule to the porcine CYP1A1 active site resulted in a rapid and continuous closure of substrate channels. All the information may help to explain the extended half-life of TCDD in living organisms as well as its high toxicity.
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Affiliation(s)
- Tomasz Molcan
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Sylwia Swigonska
- Laboratory of Molecular Diagnostics, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland.
| | - Karina Orlowska
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Kamil Myszczynski
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Anna Nynca
- Laboratory of Molecular Diagnostics, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Agnieszka Sadowska
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Monika Ruszkowska
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Jan Pawel Jastrzebski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Renata E Ciereszko
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland; Laboratory of Molecular Diagnostics, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
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66
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Suzuki K, Stanfield JK, Shoji O, Yanagisawa S, Sugimoto H, Shiro Y, Watanabe Y. Control of stereoselectivity of benzylic hydroxylation catalysed by wild-type cytochrome P450BM3 using decoy molecules. Catal Sci Technol 2017. [DOI: 10.1039/c7cy01130j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The benzylic hydroxylation of non-native substrates was catalysed by cytochrome P450BM3, wherein “decoy molecules” controlled the stereoselectivity of the reactions.
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Affiliation(s)
- Kazuto Suzuki
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Osami Shoji
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Sota Yanagisawa
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Hiroshi Sugimoto
- Core Research for Evolutional Science and Technology (CREST)
- Japan Science and Technology Agency
- Tokyo
- Japan
- RIKEN SPring-8 Center
| | | | - Yoshihito Watanabe
- Research Center for Materials Science
- Nagoya University
- Nagoya 464-8602
- Japan
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67
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Zhang S, Wang X, Liu Y. Cleavage mechanism of the aliphatic C–C bond catalyzed by 2,4′-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP: a QM/MM study. Catal Sci Technol 2017. [DOI: 10.1039/c6cy02553f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calculations suggest that the reactant complex may firstly undergo a triplet–quintet crossing to initiate the reaction and then the subsequent chemistry occurs on the multiple-states surfaces. The key C–C bond cleavage is accompanied by an insertion reaction of oxygen radical.
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Affiliation(s)
- Shujun Zhang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Xiya Wang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
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68
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Yang CL, Lin CH, Luo WI, Lee TL, Ramu R, Ng KY, Tsai YF, Wei GT, Yu SSF. Mechanistic Study of the Stereoselective Hydroxylation of [2-2
H1
,3-2
H1
]Butanes Catalyzed by Cytochrome P450 BM3 Variants. Chemistry 2016; 23:2571-2582. [DOI: 10.1002/chem.201603956] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Chung-Ling Yang
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Graduate Institute of Applied Science and Technology; National (Taiwan) University of Science and Technology; Taipei 106 Taiwan
| | - Cheng-Hung Lin
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Department of Chemistry and Biochemistry; National Chung Cheng University; Chiayi 621 Taiwan
| | - Wen-I Luo
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Tsu-Lin Lee
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Graduate Institute of Applied Science and Technology; National (Taiwan) University of Science and Technology; Taipei 106 Taiwan
| | - Ravirala Ramu
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Kok Yaoh Ng
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Yi-Fang Tsai
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Guor-Tzo Wei
- Department of Chemistry and Biochemistry; National Chung Cheng University; Chiayi 621 Taiwan
| | - Steve S.-F. Yu
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Graduate Institute of Applied Science and Technology; National (Taiwan) University of Science and Technology; Taipei 106 Taiwan
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69
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Jang HH, Shin SM, Ma SH, Lee GY, Joung YH, Yun CH. Role of Leu188 in the Fatty Acid Hydroxylase Activity of CYP102A1 from Bacillus megaterium. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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70
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Tyzack JD, Hunt PA, Segall MD. Predicting Regioselectivity and Lability of Cytochrome P450 Metabolism Using Quantum Mechanical Simulations. J Chem Inf Model 2016; 56:2180-2193. [PMID: 27753488 DOI: 10.1021/acs.jcim.6b00233] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe methods for predicting cytochrome P450 (CYP) metabolism incorporating both pathway-specific reactivity and isoform-specific accessibility considerations. Semiempirical quantum mechanical (QM) simulations, parametrized using experimental data and ab initio calculations, estimate the reactivity of each potential site of metabolism (SOM) in the context of the whole molecule. Ligand-based models, trained using high-quality regioselectivity data, correct for orientation and steric effects of the different CYP isoform binding pockets. The resulting models identify a SOM in the top 2 predictions for between 82% and 91% of compounds in independent test sets across seven CYP isoforms. In addition to predicting the relative proportion of metabolite formation at each site, these methods estimate the activation energy at each site, from which additional information can be derived regarding their lability in absolute terms. We illustrate how this can guide the design of compounds to overcome issues with rapid CYP metabolism.
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Affiliation(s)
- Jonathan D Tyzack
- Optibrium Ltd. , 7221 Cambridge Research Park, Beach Drive, Cambridge CB25 9TL, U.K
| | - Peter A Hunt
- Optibrium Ltd. , 7221 Cambridge Research Park, Beach Drive, Cambridge CB25 9TL, U.K
| | - Matthew D Segall
- Optibrium Ltd. , 7221 Cambridge Research Park, Beach Drive, Cambridge CB25 9TL, U.K
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71
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Ramanan R, Dubey KD, Wang B, Mandal D, Shaik S. Emergence of Function in P450-Proteins: A Combined Quantum Mechanical/Molecular Mechanical and Molecular Dynamics Study of the Reactive Species in the H2O2-Dependent Cytochrome P450SPα and Its Regio- and Enantioselective Hydroxylation of Fatty Acids. J Am Chem Soc 2016; 138:6786-97. [DOI: 10.1021/jacs.6b01716] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rajeev Ramanan
- Institute of Chemistry and
the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Kshatresh Dutta Dubey
- Institute of Chemistry and
the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Binju Wang
- Institute of Chemistry and
the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Debasish Mandal
- Institute of Chemistry and
the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry and
the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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72
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Ali Shah MI, Xu ZY, Liu L, Jiang YY, Shi J. Mechanism for the enhanced reactivity of 4-mercaptoprolyl thioesters in native chemical ligation. RSC Adv 2016. [DOI: 10.1039/c6ra13793h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Ring-strain-precluded strategy benefiting from entropy effects and n → π* orbital interaction, enhances the reactivity of C-terminal prolyl thioesters in NCL.
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Affiliation(s)
| | - Zhe-Yuan Xu
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
| | - Lei Liu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Yuan-Ye Jiang
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
| | - Jing Shi
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
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