1
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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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2
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McCarty KD, Tateishi Y, Hargrove TY, Lepesheva GI, Guengerich FP. Oxygen-18 Labeling Reveals a Mixed Fe-O Mechanism in the Last Step of Cytochrome P450 51 Sterol 14α-Demethylation. Angew Chem Int Ed Engl 2024; 63:e202317711. [PMID: 38206808 DOI: 10.1002/anie.202317711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 01/13/2024]
Abstract
The 14α-demethylation step is critical in eukaryotic sterol biosynthesis, catalyzed by cytochrome P450 (P450) Family 51 enzymes, for example, with lanosterol in mammals. This conserved three-step reaction terminates in a C-C cleavage step that generates formic acid, the nature of which has been controversial. Proposed mechanisms involve roles of P450 Compound 0 (ferric peroxide anion, FeO2 - ) or Compound I (perferryl oxygen, FeO3+ ) reacting with either the aldehyde or its hydrate, respectively. Analysis of 18 O incorporation into formic acid from 18 O2 provides a means of distinguishing the two mechanisms. Human P450 51A1 incorporated 88 % 18 O (one atom) into formic acid, consistent with a major but not exclusive FeO2 - mechanism. Two P450 51 orthologs from amoeba and yeast showed similar results, while two orthologs from pathogenic trypanosomes showed roughly equal contributions of both mechanisms. An X-ray crystal structure of the human enzyme showed the aldehyde oxygen atom 3.5 Å away from the heme iron atom. Experiments with human P450 51A1 and H2 18 O yielded primarily one 18 O atom but 14 % of the formic acid product with two 18 O atoms, indicative of a minor contribution of a Compound I mechanism. LC-MS evidence for a Compound 0-derived Baeyer-Villiger reaction product (a 14α-formyl ester) was also found.
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Affiliation(s)
- Kevin D McCarty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Yasuhiro Tateishi
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Tatiana Y Hargrove
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Galina I Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
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3
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Tateishi Y, McCarty KD, Martin MV, Guengerich FP. Oxygen-18 Labeling Defines a Ferric Peroxide (Compound 0) Mechanism in the Oxidative Deformylation of Aldehydes by Cytochrome P450 2B4. ACS Catal 2024; 14:2388-2394. [PMID: 38384943 PMCID: PMC10877606 DOI: 10.1021/acscatal.4c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/23/2024]
Abstract
Most cytochrome P450 (P450) oxidations are considered to occur with the active oxidant being a perferryl oxygen (FeO3+, Compound I). However, a ferric peroxide (FeO2®, Compound 0) mechanism has been proposed, as well, particularly for aldehyde substrates. We investigated three of these systems, the oxidative deformylation of the model substrates citronellal, 2-phenylpropionaldehyde, and 2-methyl-2-phenylpropionaldehyde by rabbit P450 2B4, using 18O labeling. The formic acid product contained one 18O derived from 18O2, which is indicative of a dominant Compound 0 mechanism. The formic acid also contained only one 18O derived from H218O, which ruled out a Compound I mechanism. The possibility of a Baeyer-Villiger reaction was examined by using synthesized possible intermediates, but our data do not support its presence. Overall, these findings unambiguously demonstrate the role of the Compound 0 pathway in these aldehyde oxidative deformylation reactions.
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Affiliation(s)
- Yasuhiro Tateishi
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United
States
| | - Kevin D. McCarty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United
States
| | - Martha V. Martin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United
States
| | - F. Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United
States
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4
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Kim K, Oh S, Jeong D, Lee Y, Moon D, Lee S, Cho J. Systematic Electronic Tuning on the Property and Reactivity of Cobalt-(Hydro)peroxo Intermediates. Inorg Chem 2023; 62:7141-7149. [PMID: 37139810 DOI: 10.1021/acs.inorgchem.3c00826] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A series of cobalt(III)-peroxo complexes, [CoIII(R2-TBDAP)(O2)]+ (1R2; R2 = Cl, H, and OMe), and cobalt(III)-hydroperoxo complexes, [CoIII(R2-TBDAP)(O2H)(CH3CN)]2+ (2R2), bearing electronically tuned tetraazamacrocyclic ligands (R2-TBDAP = N,N'-di-tert-butyl-2,11-diaza[3.3](2,6)-p-R2-pyridinophane) were prepared from their cobalt(II) precursors and characterized by various physicochemical methods. The X-ray diffraction and spectroscopic analyses unambiguously showed that all 1R2 compounds have similar octahedral geometry with a side-on peroxocobalt(III) moiety, but the O-O bond lengths of 1Cl [1.398(3) Å] and 1OMe [1.401(4) Å] were shorter than that of 1H [1.456(3) Å] due to the different spin states. For 2R2, the O-O bond vibration energies of 2Cl and 2OMe were identical at 853 cm-1 (856 cm-1 for 2H), but their Co-O bond vibration frequencies were observed at 572 cm-1 for 2Cl and 550 cm-1 for 2OMe, respectively, by resonance Raman spectroscopy (560 cm-1 for 2H). Interestingly, the redox potentials (E1/2) of 2R2 increased in the order of 2OMe (0.19 V) < 2H (0.24 V) < 2Cl (0.34 V) according to the electron richness of the R2-TBDAP ligands, but the oxygen-atom-transfer reactivities of 2R2 showed a reverse trend (k2: 2Cl < 2H < 2OMe) with a 13-fold rate enhancement at 2OMe over 2Cl in a sulfoxidation reaction with thioanisole. Although the reactivity trend contradicts the general consideration that electron-rich metal-oxygen species with low E1/2 values have sluggish electrophilic reactivity, this could be explained by a weak Co-O bond vibration of 2OMe in the unusual reaction pathway. These results provide considerable insight into the electronic nature-reactivity relationship of metal-oxygen species.
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Affiliation(s)
- Kyungmin Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Physics and Chemistry, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Seongmin Oh
- Department of Physics and Chemistry, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Donghyun Jeong
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yuri Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Dohyun Moon
- Beamline Department, Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Sunggi Lee
- Department of Physics and Chemistry, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Jaeheung Cho
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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5
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Podgorski MN, Coleman T, Churchman LR, Bruning JB, De Voss JJ, Bell SG. Investigating the Active Oxidants Involved in Cytochrome P450 Catalyzed Sulfoxidation Reactions. Chemistry 2022; 28:e202202428. [PMID: 36169207 PMCID: PMC10100219 DOI: 10.1002/chem.202202428] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 12/30/2022]
Abstract
Cytochrome P450 (CYP) heme-thiolate monooxygenases catalyze the hydroxylation of the C-H bonds of organic molecules. This reaction is initiated by a ferryl-oxo heme radical cation (Cpd I). These enzymes can also catalyze sulfoxidation reactions and the ferric-hydroperoxy complex (Cpd 0) and the Fe(III)-H2 O2 complex have been proposed as alternative oxidants for this transformation. To investigate this, the oxidation of 4-alkylthiobenzoic acids and 4-methoxybenzoic acid by the CYP199A4 enzyme from Rhodopseudomonas palustris HaA2 was compared using both monooxygenase and peroxygenase pathways. By examining mutants at the mechanistically important, conserved acid alcohol-pair (D251N, T252A and T252E) the relative amounts of the reactive intermediates that would form in these reactions were disturbed. Substrate binding and X-ray crystal structures helped to understand changes in the activity and enabled an attempt to evaluate whether multiple oxidants can participate in these reactions. In peroxygenase reactions the T252E mutant had higher activity towards sulfoxidation than O-demethylation but in the monooxygenase reactions with the WT enzyme the activity of both reactions was similar. The peroxygenase activity of the T252A mutant was greater for sulfoxidation reactions than the WT enzyme, which is the reverse of the activity changes observed for O-demethylation. The monooxygenase activity and coupling efficiency of sulfoxidation and oxidative demethylation were reduced by similar degrees with the T252A mutant. These observations infer that while Cpd I is required for O-dealkylation, another oxidant may contribute to sulfoxidation. Based on the activity of the CYP199A4 mutants it is proposed that this is the Fe(III)-H2 O2 complex which would be more abundant in the peroxide-driven reactions.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Luke R Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
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6
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Wang Q, Jiang X, Gao Y, Yin L, Wei X, Guo K, Gao X, Wang L, Zhang C. Studies on Biosynthesis of Chiral Sulfoxides by Using P450 119 Peroxygenase and Its Mutants. ChemistrySelect 2022. [DOI: 10.1002/slct.202204031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Qin Wang
- Department of Medicinal Chemistry School of Pharmacy Southwest Medical University No. 1, Section 1, XiangLin road, Longmatan District Luzhou 646000 China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province The Affiliated Hospital of Southwest Medical University No. 25 Taiping road, Jiangyang District Luzhou 646000 China
- Dazhou Vocational College of Chinese Medicine Luojiang Town, Tongchuan District Dazhou 635000 China
| | - Xin‐Meng Jiang
- Department of Medicinal Chemistry School of Pharmacy Southwest Medical University No. 1, Section 1, XiangLin road, Longmatan District Luzhou 646000 China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province The Affiliated Hospital of Southwest Medical University No. 25 Taiping road, Jiangyang District Luzhou 646000 China
| | - Yan‐Ping Gao
- Department of Medicinal Chemistry School of Pharmacy Southwest Medical University No. 1, Section 1, XiangLin road, Longmatan District Luzhou 646000 China
| | - Li‐Ping Yin
- Department of Medicinal Chemistry School of Pharmacy Southwest Medical University No. 1, Section 1, XiangLin road, Longmatan District Luzhou 646000 China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province The Affiliated Hospital of Southwest Medical University No. 25 Taiping road, Jiangyang District Luzhou 646000 China
| | - Xiao‐Yao Wei
- Department of Medicinal Chemistry School of Pharmacy Southwest Medical University No. 1, Section 1, XiangLin road, Longmatan District Luzhou 646000 China
| | - Kai Guo
- Department of Medicinal Chemistry School of Pharmacy Southwest Medical University No. 1, Section 1, XiangLin road, Longmatan District Luzhou 646000 China
| | - Xiao‐Wei Gao
- Department of Medicinal Chemistry School of Pharmacy Southwest Medical University No. 1, Section 1, XiangLin road, Longmatan District Luzhou 646000 China
| | - Li Wang
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province The Affiliated Hospital of Southwest Medical University No. 25 Taiping road, Jiangyang District Luzhou 646000 China
- Department of Nuclear Medicine The Affiliated Hospital of Southwest Medical University No. 25 Taiping road, Jiangyang District Luzhou 646000 China
| | - Chun Zhang
- Department of Medicinal Chemistry School of Pharmacy Southwest Medical University No. 1, Section 1, XiangLin road, Longmatan District Luzhou 646000 China
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7
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Meng S, Ji Y, Zhu L, Dhoke GV, Davari MD, Schwaneberg U. The molecular basis and enzyme engineering strategies for improvement of coupling efficiency in cytochrome P450s. Biotechnol Adv 2022; 61:108051. [DOI: 10.1016/j.biotechadv.2022.108051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/26/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022]
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8
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A Promiscuous Bacterial P450: The Unparalleled Diversity of BM3 in Pharmaceutical Metabolism. Int J Mol Sci 2021; 22:ijms222111380. [PMID: 34768811 PMCID: PMC8583553 DOI: 10.3390/ijms222111380] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
CYP102A1 (BM3) is a catalytically self-sufficient flavocytochrome fusion protein isolated from Bacillus megaterium, which displays similar metabolic capabilities to many drug-metabolizing human P450 isoforms. BM3's high catalytic efficiency, ease of production and malleable active site makes the enzyme a desirable tool in the production of small molecule metabolites, especially for compounds that exhibit drug-like chemical properties. The engineering of select key residues within the BM3 active site vastly expands the catalytic repertoire, generating variants which can perform a range of modifications. This provides an attractive alternative route to the production of valuable compounds that are often laborious to synthesize via traditional organic means. Extensive studies have been conducted with the aim of engineering BM3 to expand metabolite production towards a comprehensive range of drug-like compounds, with many key examples found both in the literature and in the wider industrial bioproduction setting of desirable oxy-metabolite production by both wild-type BM3 and related variants. This review covers the past and current research on the engineering of BM3 to produce drug metabolites and highlights its crucial role in the future of biosynthetic pharmaceutical production.
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Shumayrikh NM, Warren JJ, Bennet AJ, Sen D. A heme•DNAzyme activated by hydrogen peroxide catalytically oxidizes thioethers by direct oxygen atom transfer rather than by a Compound I-like intermediate. Nucleic Acids Res 2021; 49:1803-1815. [PMID: 33476369 PMCID: PMC7913675 DOI: 10.1093/nar/gkab007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 12/21/2022] Open
Abstract
Hemin [Fe(III)-protoporphyrin IX] is known to bind tightly to single-stranded DNA and RNA molecules that fold into G-quadruplexes (GQ). Such complexes are strongly activated for oxidative catalysis. These heme•DNAzymes and ribozymes have found broad utility in bioanalytical and medicinal chemistry and have also been shown to occur within living cells. However, how a GQ is able to activate hemin is poorly understood. Herein, we report fast kinetic measurements (using stopped-flow UV-vis spectrophotometry) to identify the H2O2-generated activated heme species within a heme•DNAzyme that is active for the oxidation of a thioether substrate, dibenzothiophene (DBT). Singular value decomposition and global fitting analysis was used to analyze the kinetic data, with the results being consistent with the heme•DNAzyme's DBT oxidation being catalyzed by the initial Fe(III)heme-H2O2 complex. Such a complex has been predicted computationally to be a powerful oxidant for thioether substrates. In the heme•DNAzyme, the DNA GQ enhances both the kinetics of formation of the active intermediate as well as the oxidation step of DBT by the active intermediate. We show, using both stopped flow spectrophotometry and EPR measurements, that a classic Compound I is not observable during the catalytic cycle for thioether sulfoxidation.
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Affiliation(s)
- Nisreen M Shumayrikh
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Jeffrey J Warren
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J Bennet
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dipankar Sen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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10
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Hubbard CD, Chatterjee D, Oszajca M, Polaczek J, Impert O, Chrzanowska M, Katafias A, Puchta R, van Eldik R. Inorganic reaction mechanisms. A personal journey. Dalton Trans 2020; 49:4599-4659. [PMID: 32162632 DOI: 10.1039/c9dt04620h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This review covers highlights of the work performed in the van Eldik group on inorganic reaction mechanisms over the past two decades in the form of a personal journey. Topics that are covered include, from NO to HNO chemistry, peroxide activation in model porphyrin and enzymatic systems, the wonder-world of RuIII(edta) chemistry, redox chemistry of Ru(iii) complexes, Ru(ii) polypyridyl complexes and their application, relevant physicochemical properties and reaction mechanisms in ionic liquids, and mechanistic insight from computational chemistry. In each of these sections, typical examples of mechanistic studies are presented in reference to related work reported in the literature.
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Affiliation(s)
- Colin D Hubbard
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstr. 1, 91058 Erlangen, Germany.
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11
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Wang JB, Huang Q, Peng W, Wu P, Yu D, Chen B, Wang B, Reetz MT. P450-BM3-Catalyzed Sulfoxidation versus Hydroxylation: A Common or Two Different Catalytically Active Species? J Am Chem Soc 2020; 142:2068-2073. [PMID: 31927987 PMCID: PMC7307895 DOI: 10.1021/jacs.9b13061] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
While the mechanism of the P450-catalyzed
oxidative hydroxylation of organic compounds has been studied in detail
for many years, less is known about sulfoxidation. Depending upon
the structure of the respective substrate, heme-Fe=O (Cpd I),
heme–Fe(III)–OOH (Cpd 0), and heme–Fe(III)–H2O2 (protonated Cpd 0) have been proposed as reactive
intermediates. In the present study, we consider the transformation
of isosteric substrates via sulfoxidation and oxidative hydroxylation,
respectively, catalyzed by regio- and enantioselective mutants of
P450-BM3 which were constructed by directed evolution. 1-Thiochromanone
and 1-tetralone were used as the isosteric substrates because, unlike
previous studies involving fully flexible compounds such as thia-fatty
acids and fatty acids, respectively, these compounds are rigid and
cannot occur in a multitude of different conformations and binding
modes in the large P450-BM3 binding pocket. The experimental results
comprising activity and regio- and enantioselectivity, flanked by
molecular dynamics computations within a time scale of 300 ns and
QM/MM calculations of transition-state energies, unequivocally show
that heme-Fe=O (Cpd I) is the common catalytically active intermediate
in both sulfoxidation and oxidative hydroxylation.
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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 , Xiamen University , Xiamen 360015 , P. R. China
| | - Peng Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , 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 , Xiamen University , Xiamen 360015 , P. R. China
| | - Manfred T Reetz
- Chemistry Department , Philipps-University , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany.,Max-Planck Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim , Germany
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12
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Shang Y, Huang S. Engineering Plant Cytochrome P450s for Enhanced Synthesis of Natural Products: Past Achievements and Future Perspectives. PLANT COMMUNICATIONS 2020; 1:100012. [PMID: 33404545 PMCID: PMC7747987 DOI: 10.1016/j.xplc.2019.100012] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cytochrome P450s (P450s) are the most versatile catalysts and are widely used by plants to synthesize a vast array of structurally diverse specialized metabolites that not only play essential ecological roles but also constitute a valuable resource for the development of new drugs. To accelerate the metabolic engineering of these high-value metabolites, it is imperative to identify and characterize pathway P450s, and to further improve their activities through protein engineering. In this review, we focus on P450 engineering and summarize the major strategies for enhancing the stability and activity of P450s and successful cases of P450 engineering. Studies in which the functions of P450s were altered to create de novo metabolic pathways or novel compounds are discussed as well. We also overview emerging tools, specifically DNA synthesis, machine learning, and de novo protein design, as well as the evolutionary patterns of P450s unveiled from a massive number of DNA sequences that could be integrated to accelerate the engineering of these enzymes. These approaches would greatly aid in the exploitation of plant-specialized metabolites or derivatives for various uses including medical applications.
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Affiliation(s)
- Yi Shang
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Sanwen Huang
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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13
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Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
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Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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14
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Wei X, Zhang C, Gao X, Gao Y, Yang Y, Guo K, Du X, Pu L, Wang Q. Enhanced Activity and Substrate Specificity by Site-Directed Mutagenesis for the P450 119 Peroxygenase Catalyzed Sulfoxidation of Thioanisole. ChemistryOpen 2019; 8:1076-1083. [PMID: 31406654 PMCID: PMC6682931 DOI: 10.1002/open.201900157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Indexed: 11/06/2022] Open
Abstract
P450 119 peroxygenase was found to catalyze the sulfoxidation of thioanisole and the sulfonation of sulfoxide in the presence of tert-butyl hydroperoxide (TBHP) for the first time with turnover rates of 1549 min-1 and 196 min-1 respectively. Several mutants were designed to improve the peroxygenation activity and thioanisole specificity by site-directed mutagenesis. The F153G/T213G mutant gave an increase of sulfoxide yield and a decrease of sulfone yield. Moreover the S148P/I161T/K199E/T214V mutant and the K199E mutant with acidic Glu residue contributed to improving the product ratio of sulfoxide to sulfone. Addition of short-alkyl-chain organic acids to the P450 119 peroxygenase-catalyzed sulfur oxidation of thioanisole was investigated. Octanoic acid was found to induce a preferred sulfoxidation of thioanisole catalyzed by the F153G/T213G mutant to give approximately 2.4-fold increase in turnover rate with a k cat value of 3687 min-1 relative to that of the wild-type, and by the F153G mutant to give the R-sulfoxide up to 30 % ee. The experimental control and the proposed mechanism for the P450 119 peroxygenase-catalyzed sulfoxidation of thioanisole in the presence of octanoic acid suggested that octanoic acid could partially occupy the substrate pocket; meanwhile the F153G mutation could enhance the substrate specificity, which could lead to efficiently regulate the spatial orientation of thioanisole and facilitate the formation of Compound I. This is the most effective catalytic system for the P450 119 peroxygenase-catalyzed sulfoxidation of thioanisole.
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Affiliation(s)
- Xiaoyao Wei
- Department of Medicinal Chemistry, School of Pharmacy Southwest Medical University Luzhou Sichuan 646000 P. R. China
| | - Chun Zhang
- Department of Medicinal Chemistry, School of Pharmacy Southwest Medical University Luzhou Sichuan 646000 P. R. China
| | - Xiaowei Gao
- Department of Medicinal Chemistry, School of Pharmacy Southwest Medical University Luzhou Sichuan 646000 P. R. China
| | - Yanping Gao
- Department of Medicinal Chemistry, School of Pharmacy Southwest Medical University Luzhou Sichuan 646000 P. R. China
| | - Ya Yang
- Department of Medicinal Chemistry, School of Pharmacy Southwest Medical University Luzhou Sichuan 646000 P. R. China
| | - Kai Guo
- Department of Medicinal Chemistry, School of Pharmacy Southwest Medical University Luzhou Sichuan 646000 P. R. China
| | - Xi Du
- Department of Medicinal Chemistry, School of Pharmacy Southwest Medical University Luzhou Sichuan 646000 P. R. China
| | - Lin Pu
- Department of Chemistry University of Virginia Charlottesville VA 22904-4319 USA
| | - Qin Wang
- Department of Medicinal Chemistry, School of Pharmacy Southwest Medical University Luzhou Sichuan 646000 P. R. China
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15
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Dezvarei S, Shoji O, Watanabe Y, Bell SG. The effect of decoy molecules on the activity of the P450Bm3 holoenzyme and a heme domain peroxygenase variant. CATAL COMMUN 2019. [DOI: 10.1016/j.catcom.2019.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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16
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Jiang G, Zhang Y, Powell MM, Hylton SM, Hiller NW, Loria R, Ding Y. A Promiscuous Cytochrome P450 Hydroxylates Aliphatic and Aromatic C-H Bonds of Aromatic 2,5-Diketopiperazines. Chembiochem 2019; 20:1068-1077. [PMID: 30604585 PMCID: PMC8162728 DOI: 10.1002/cbic.201800736] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 11/06/2022]
Abstract
Cytochrome P450 enzymes generally functionalize inert C-H bonds, and thus, they are important biocatalysts for chemical synthesis. However, enzymes that catalyze both aliphatic and aromatic hydroxylation in the same biotransformation process have rarely been reported. A recent biochemical study demonstrated the P450 TxtC for the biosynthesis of herbicidal thaxtomins as the first example of this unique type of enzyme. Herein, the detailed characterization of substrate requirements and biocatalytic applications of TxtC are reported. The results reveal the importance of N-methylation of the thaxtomin diketopiperazine (DKP) core on enzyme reactions and demonstrate the tolerance of the enzyme to modifications on the indole and phenyl moieties of its substrates. Furthermore, hydroxylated, methylated, aromatic DKPs are synthesized through a biocatalytic route comprising TxtC and the promiscuous N-methyltransferase Amir_4628; thus providing a basis for the broad application of this unique P450.
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Affiliation(s)
- Guangde Jiang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Magan M Powell
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Sarah M Hylton
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Nicholas W Hiller
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Rosemary Loria
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
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17
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Slessor KE, Stok JE, Chow S, De Voss JJ. Significance of Protein–Substrate Hydrogen Bonding for the Selectivity of P450‐Catalysed Oxidations. Chemistry 2019; 25:4149-4155. [DOI: 10.1002/chem.201805705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Kate E. Slessor
- School of Chemistry and Molecular Biosciences University of Queensland Brisbane 4072 Australia
| | - Jeanette E. Stok
- School of Chemistry and Molecular Biosciences University of Queensland Brisbane 4072 Australia
| | - Sharon Chow
- School of Chemistry and Molecular Biosciences University of Queensland Brisbane 4072 Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences University of Queensland Brisbane 4072 Australia
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18
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Wei WJ, Qian HX, Wang WJ, Liao RZ. Computational Understanding of the Selectivities in Metalloenzymes. Front Chem 2018; 6:638. [PMID: 30622942 PMCID: PMC6308299 DOI: 10.3389/fchem.2018.00638] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/07/2018] [Indexed: 01/26/2023] Open
Abstract
Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.
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Affiliation(s)
| | | | | | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, China
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19
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Coleman T, Wong SH, Podgorski MN, Bruning JB, De Voss JJ, Bell SG. Cytochrome P450 CYP199A4 from Rhodopseudomonas palustris Catalyzes Heteroatom Dealkylations, Sulfoxidation, and Amide and Cyclic Hemiacetal Formation. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00909] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Siew Hoon Wong
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia
| | | | - John B. Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia
| | - Stephen G. Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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20
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Dubey KD, Wang B, Vajpai M, Shaik S. MD simulations and QM/MM calculations show that single-site mutations of cytochrome P450 BM3 alter the active site's complexity and the chemoselectivity of oxidation without changing the active species. Chem Sci 2017; 8:5335-5344. [PMID: 29568477 PMCID: PMC5851339 DOI: 10.1039/c7sc01932g] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/11/2017] [Indexed: 12/28/2022] Open
Abstract
A new water channel appears in the T268A mutant of P450BM3 and plays a role in the enzyme’s chemoselectivity.
It is a long-standing mechanistic consensus that the mutation of the proton-shuttle mediator Threonine (T) in Cytochrome P450 enzymes severs the water channel and thereby quenches the formation of the active species: the high-valent iron(iv)-oxo porphyrin π-cation radical species, compound I (Cpd I). Using MD simulations and hybrid QM/MM calculations of P450BM3 we demonstrate that this is not the case. Thus, while the original water channel is disrupted in the T268A mutant of the enzyme, a new channel is formed that generates Cpd I. With this new understanding, we address the puzzling regiochemical and kinetic-isotope effect (KIE) results (Volz et al., J. Am. Chem. Soc., 2002, 124, 9724–9725) on the sulfoxidation and N-dealkylation of dimethyl-(4-methylsulfanyl-phenyl)-amine by wild type (WT) P450BM3 and its T268A vs. F87A mutants. We show that the observed variable ratio of S/Me oxidation for these enzymes, vis-à-vis the constant KIE, originates from Cpd I being the sole oxidant. Thus, while the conserved KIE probes the conserved nature of the transition state, the variable regiochemical S/Me ratio reflects the active-site reorganization in the mutants: the shifted location of the new water channel in T268A tightens the binding of the S-end by Cpd I and increases the S/Me ratio, whereas the absence of π-interaction with the S-end in F87A creates a looser binding that lowers the S/Me ratio. Our results match the experimental findings. As such, this study sheds light on puzzling experimental results, and may shift a central paradigm in P450 research. The broader implication on enzymatic research is that a single-site mutation is not a localised alteration but one that may lead to a profound change in the active site, sufficiently so as to change the chemoselectivity of catalyzed reactions.
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Affiliation(s)
- Kshatresh Dutta Dubey
- Institute of Chemistry , The Lise Meitner-Minerva Center for Computational Quantum Chemistry , The Hebrew University of Jerusalem , 91904 , Jerusalem , Israel .
| | - Binju Wang
- Institute of Chemistry , The Lise Meitner-Minerva Center for Computational Quantum Chemistry , The Hebrew University of Jerusalem , 91904 , Jerusalem , Israel .
| | - Manu Vajpai
- Department of Biological Sciences and Bioengineering , Indian Institute of Technology-Kanpur , Kanpur-208016 , UP , India
| | - Sason Shaik
- Institute of Chemistry , The Lise Meitner-Minerva Center for Computational Quantum Chemistry , The Hebrew University of Jerusalem , 91904 , Jerusalem , Israel .
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21
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Wang JB, Ilie A, Reetz MT. Chemo- and Stereoselective Cytochrome P450-BM3-Catalyzed Sulfoxidation of 1-Thiochroman-4-ones Enabled by Directed Evolution. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700414] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jian-bo Wang
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim/Ruhr Germany
- Fachbereich Chemie, Philipps-Universität; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Adriana Ilie
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim/Ruhr Germany
- Fachbereich Chemie, Philipps-Universität; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim/Ruhr Germany
- Fachbereich Chemie, Philipps-Universität; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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22
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Faponle AS, de Visser SP. The Role of Nonheme Transition Metal-Oxo, -Peroxo, and -Superoxo Intermediates in Enzyme Catalysis and Reactions of Bioinspired Complexes. ADVANCES IN INORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.adioch.2017.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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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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24
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Stok JE, Chow S, Krenske EH, Farfan Soto C, Matyas C, Poirier RA, Williams CM, De Voss JJ. Direct Observation of an Oxepin from a Bacterial Cytochrome P450‐Catalyzed Oxidation. Chemistry 2016; 22:4408-12. [DOI: 10.1002/chem.201600246] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Jeanette E. Stok
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - Sharon Chow
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - Clementina Farfan Soto
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - Csongor Matyas
- Department of Chemistry Memorial University of Newfoundland St. John's NL A1B 3X7 Canada
| | - Raymond A. Poirier
- Department of Chemistry Memorial University of Newfoundland St. John's NL A1B 3X7 Canada
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
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25
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Wang B, Lee YM, Clémancey M, Seo MS, Sarangi R, Latour JM, Nam W. Mononuclear Nonheme High-Spin Iron(III)-Acylperoxo Complexes in Olefin Epoxidation and Alkane Hydroxylation Reactions. J Am Chem Soc 2016; 138:2426-36. [DOI: 10.1021/jacs.5b13500] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bin Wang
- Department
of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong-Min Lee
- Department
of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Martin Clémancey
- University of Grenoble Alpes, LCBM/PMB and CEA, IRTSV/CBM/PMB and CNRS, LCBM UMR 5249, PMB, 38000 Grenoble, France
| | - Mi Sook Seo
- Department
of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Ritimukta Sarangi
- Stanford
Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025-7015, United States
| | - Jean-Marc Latour
- University of Grenoble Alpes, LCBM/PMB and CEA, IRTSV/CBM/PMB and CNRS, LCBM UMR 5249, PMB, 38000 Grenoble, France
| | - Wonwoo Nam
- Department
of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
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26
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Dubey KD, Wang B, Shaik S. Molecular Dynamics and QM/MM Calculations Predict the Substrate-Induced Gating of Cytochrome P450 BM3 and the Regio- and Stereoselectivity of Fatty Acid Hydroxylation. J Am Chem Soc 2016; 138:837-45. [DOI: 10.1021/jacs.5b08737] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- 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
| | - 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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27
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Oszajca M, Franke A, Brindell M, Stochel G, van Eldik R. Redox cycling in the activation of peroxides by iron porphyrin and manganese complexes. ‘Catching’ catalytic active intermediates. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.01.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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28
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Franke A, van Eldik R. Spectroscopic and Kinetic Evidence for the Crucial Role of Compound 0 in the P450cam -Catalyzed Hydroxylation of Camphor by Hydrogen Peroxide. Chemistry 2015; 21:15201-10. [PMID: 26353996 DOI: 10.1002/chem.201501886] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 11/09/2022]
Abstract
The hydroperoxo iron(III) intermediate P450cam Fe(III) -OOH, being the true Compound 0 (Cpd 0) involved in the natural catalytic cycle of P450cam , could be transiently observed in the peroxo-shunt oxidation of the substrate-free enzyme by hydrogen peroxide under mild basic conditions and low temperature. The prolonged lifetime of Cpd 0 enabled us to kinetically examine the formation and reactivity of P450cam Fe(III) -OOH species as a function of varying reaction conditions, such as pH, and concentration of H2 O2 , camphor, and potassium ions. The mechanism of hydrogen peroxide binding to the substrate-free form of P450cam differs completely from that observed for other heme proteins possessing the distal histidine as a general acid-base catalyst and is mainly governed by the ability of H2 O2 to undergo deprotonation at the hydroxo ligand coordinated to the iron(III) center under conditions of pH≥p${K{{{\rm P450}\hfill \atop {\rm a}\hfill}}}$. Notably, no spectroscopic evidence for the formation of either Cpd I or Cpd II as products of heterolytic or homolytic OO bond cleavage, respectively, in Cpd 0 could be observed under the selected reaction conditions. The kinetic data obtained from the reactivity studies involving (1R)-camphor, provide, for the first time, experimental evidence for the catalytic activity of the P450Fe(III) -OOH intermediate in the oxidation of the natural substrate of P450cam .
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Affiliation(s)
- Alicja Franke
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen (Germany)
| | - Rudi van Eldik
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen (Germany). .,Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow (Poland).
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29
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Wang B, Lee YM, Seo MS, Nam W. Mononuclear Nonheme Iron(III)-Iodosylarene and High-Valent Iron-Oxo Complexes in Olefin Epoxidation Reactions. Angew Chem Int Ed Engl 2015; 54:11740-4. [PMID: 26273792 DOI: 10.1002/anie.201505796] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 11/06/2022]
Abstract
High-spin iron(III)-iodosylarene complexes are highly reactive in the epoxidation of olefins, in which epoxides are formed as the major products with high stereospecificity and enantioselectivity. The reactivity of the iron(III)-iodosylarene intermediates is much greater than that of the corresponding iron(IV)-oxo complex in these reactions. The iron(III)-iodosylarene species-not high-valent iron(IV)-oxo and iron(V)-oxo species-are also shown to be the active oxidants in catalytic olefin epoxidation reactions. The present results are discussed in light of the long-standing controversy on the one oxidant versus multiple oxidants hypothesis in oxidation reactions.
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Affiliation(s)
- Bin Wang
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750 (Korea)
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750 (Korea)
| | - Mi Sook Seo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750 (Korea)
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750 (Korea).
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30
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Wang B, Lee YM, Seo MS, Nam W. Mononuclear Nonheme Iron(III)-Iodosylarene and High-Valent Iron-Oxo Complexes in Olefin Epoxidation Reactions. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505796] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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31
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Wang B, Li C, Dubey KD, Shaik S. Quantum mechanical/molecular mechanical calculated reactivity networks reveal how cytochrome P450cam and Its T252A mutant select their oxidation pathways. J Am Chem Soc 2015; 137:7379-90. [PMID: 26011529 DOI: 10.1021/jacs.5b02800] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum mechanical/molecular mechanical calculations address the longstanding-question of a "second oxidant" in P450 enzymes wherein the proton-shuttle, which leads to formation of the "primary-oxidant" Compound I (Cpd I), was severed by mutating the crucial residue (in P450cam: Threonine-252-to-Alanine, hence T252A). Investigating the oxidant candidates Cpd I, ferric hydroperoxide, and ferric hydrogen peroxide (Fe(III)(O2H2)), and their reactions, generates reactivity networks which enable us to rule out a "second oxidant" and at the same time identify an additional coupling pathway that is responsible for the epoxidation of 5-methylenylcamphor by the T252A mutant. In this "second-coupling pathway", the reaction starts with the Fe(III)(O2H2) intermediate, which transforms to Cpd I via a O-O homolysis/H-abstraction mechanism. The persistence of Fe(III)(O2H2) and its oxidative reactivity are shown to be determined by interplay of substrate and protein. The substrate 5-methylenylcamphor prevents H2O2 release, while the protein controls the Fe(III)(O2H2) conversion to Cpd I by nailing-through hydrogen-bonding interactions-the conformation of the HO(•) radical produced during O-O homolysis. This conformation prevents HO(•) attack on the porphyrin's meso position, as in heme oxygenase, and prefers H-abstraction from Fe(IV)OH thereby generating H2O + Cpd I. Cpd I then performs substrate oxidations. Camphor cannot prevent H2O2 release and hence the T252A mutant does not oxidize camphor. This "second pathway" transpires also during H2O2 shunting of the cycle of wild-type P450cam, where the additional hydrogen-bonding with Thr252 prevents H2O2 release, and contributes to a successful Cpd I formation. The present results lead to a revised catalytic cycle of Cytochrome P450cam.
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Affiliation(s)
- Binju Wang
- †Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Chunsen Li
- ‡State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China.,§Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, China
| | - Kshatresh Dutta Dubey
- †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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Faponle AS, Quesne MG, Sastri CV, Banse F, de Visser SP. Differences and comparisons of the properties and reactivities of iron(III)-hydroperoxo complexes with saturated coordination sphere. Chemistry 2015; 21:1221-36. [PMID: 25399782 PMCID: PMC4316188 DOI: 10.1002/chem.201404918] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Indexed: 11/06/2022]
Abstract
Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high-valent iron(IV)-oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)-hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)-hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)-hydroperoxo reacted directly with substrates or that an initial O-O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)-hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)-hydroperoxo complex with pentadentate ligand system (L5(2)). Direct C-O bond formation by an iron(III)-hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L5(2))Fe(III)(OOH)](2+) should be able to initiate an aromatic hydroxylation process, although a low-energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)-hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O-O bond, whereas a heterolytic O-O bond breaking in heme iron(III)-hydroperoxo is found.
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Affiliation(s)
- Abayomi S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
| | - Matthew G Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati781039, Assam (India)
| | - Frédéric Banse
- Institut de Chimie Moleculaire et des Materiaux d'Orsay, Laboratoire de Chimie Inorganique, Université Paris-Sud11 91405 Orsay Cedex (France) E-mail:
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
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Ray K, Pfaff FF, Wang B, Nam W. Status of Reactive Non-Heme Metal–Oxygen Intermediates in Chemical and Enzymatic Reactions. J Am Chem Soc 2014; 136:13942-58. [DOI: 10.1021/ja507807v] [Citation(s) in RCA: 351] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kallol Ray
- Department
of Chemistry, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Florian Felix Pfaff
- Department
of Chemistry, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Bin Wang
- Department
of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Wonwoo Nam
- Department
of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
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McIntosh JA, Farwell CC, Arnold FH. Expanding P450 catalytic reaction space through evolution and engineering. Curr Opin Chem Biol 2014; 19:126-34. [PMID: 24658056 DOI: 10.1016/j.cbpa.2014.02.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/30/2013] [Accepted: 02/03/2014] [Indexed: 11/27/2022]
Abstract
Advances in protein and metabolic engineering have led to wider use of enzymes to synthesize important molecules. However, many desirable transformations are not catalyzed by any known enzyme, driving interest in understanding how new enzymes can be created. The cytochrome P450 enzyme family, whose members participate in xenobiotic metabolism and natural products biosynthesis, catalyzes an impressive range of difficult chemical reactions that continues to grow as new enzymes are characterized. Recent work has revealed that P450-derived enzymes can also catalyze useful reactions previously accessible only to synthetic chemistry. The evolution and engineering of these enzymes provides an excellent case study for how to genetically encode new chemistry and expand biology's reaction space.
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Affiliation(s)
- John A McIntosh
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Christopher C Farwell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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Oszajca M, Drzewiecka-Matuszek A, Franke A, Rutkowska-Zbik D, Brindell M, Witko M, Stochel G, van Eldik R. Mechanistic insight into peroxo-shunt formation of biomimetic models for compound II, their reactivity toward organic substrates, and the influence of N-methylimidazole axial ligation. Chemistry 2014; 20:2328-43. [PMID: 24443188 DOI: 10.1002/chem.201303694] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Indexed: 11/07/2022]
Abstract
High-valent iron-oxo species have been invoked as reactive intermediates in catalytic cycles of heme and nonheme enzymes. The studies presented herein are devoted to the formation of compound II model complexes, with the application of a water soluble (TMPS)Fe(III)(OH) porphyrin ([meso-tetrakis(2,4,6-trimethyl-3-sulfonatophenyl)porphinato]iron(III) hydroxide) and hydrogen peroxide as oxidant, and their reactivity toward selected organic substrates. The kinetics of the reaction of H2O2 with (TMPS)Fe(III)(OH) was studied as a function of temperature and pressure. The negative values of the activation entropy and activation volume for the formation of (TMPS)Fe(IV)=O(OH) point to the overall associative nature of the process. A pH-dependence study on the formation of (TMPS)Fe(IV)=O(OH) revealed a very high reactivity of OOH(-) toward (TMPS)Fe(III)(OH) in comparison to H2O2. The influence of N-methylimidazole (N-MeIm) ligation on both the formation of iron(IV)-oxo species and their oxidising properties in the reactions with 4-methoxybenzyl alcohol or 4-methoxybenzaldehyde, was investigated in detail. Combined experimental and theoretical studies revealed that among the studied complexes, (TMPS)Fe(III)(H2O)(N-MeIm) is highly reactive toward H2O2 to form the iron(IV)-oxo species, (TMPS)Fe(IV)=O(N-MeIm). The latter species can also be formed in the reaction of (TMPS)Fe(III)(N-MeIm)2 with H2O2 or in the direct reaction of (TMPS)Fe(IV)=O(OH) with N-MeIm. Interestingly, the kinetic studies involving substrate oxidation by (TMPS)Fe(IV)=O(OH) and (TMPS)Fe(IV)=O(N-MeIm) do not display a pronounced effect of the N-MeIm axial ligand on the reactivity of the compound II mimic in comparison to the OH(-) substituted analogue. Similarly, DFT computations revealed that the presence of an axial ligand (OH(-) or N-MeIm) in the trans position to the oxo group in the iron(IV)-oxo species does not significantly affect the activation barriers calculated for C-H dehydrogenation of the selected organic substrates.
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Affiliation(s)
- Maria Oszajca
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow (Poland); Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg, Egerlandstrasse 1, 91058 Erlangen (Germany)
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36
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Kim YM, Cho KB, Cho J, Wang B, Li C, Shaik S, Nam W. A mononuclear non-heme high-spin iron(III)-hydroperoxo complex as an active oxidant in sulfoxidation reactions. J Am Chem Soc 2013; 135:8838-41. [PMID: 23721290 DOI: 10.1021/ja404152q] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the first direct experimental evidence showing that a high-spin iron(III)-hydroperoxo complex bearing an N-methylated cyclam ligand can oxidize thioanisoles. DFT calculations showed that the reaction pathway involves heterolytic O-O bond cleavage and that the choice of the heterolytic pathway versus the homolytic pathway is dependent on the spin state and the number of electrons in the d(xz) orbital of the Fe(III)-OOH species.
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Affiliation(s)
- Yun Mi Kim
- Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Korea
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37
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Wang B, Li C, Cho KB, Nam W, Shaik S. The FeIII(H2O2) Complex as a Highly Efficient Oxidant in Sulfoxidation Reactions: Revival of an Underrated Oxidant in Cytochrome P450. J Chem Theory Comput 2013; 9:2519-25. [DOI: 10.1021/ct400190f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Binju Wang
- Institute of Chemistry and the
Lise Meitner-Minerva Center for Computational Quantum Chemistry, The
Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Chunsen Li
- Institute of Chemistry and the
Lise Meitner-Minerva Center for Computational Quantum Chemistry, The
Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Kyung-Bin Cho
- Department of Bioinspired Science,
Ewha Womans University, Seoul 120-750, Korea
| | - Wonwoo Nam
- Department of Bioinspired Science,
Ewha Womans University, Seoul 120-750, Korea
| | - Sason Shaik
- Institute of Chemistry and the
Lise Meitner-Minerva Center for Computational Quantum Chemistry, The
Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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38
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Glyphosate’s Suppression of Cytochrome P450 Enzymes and Amino Acid Biosynthesis by the Gut Microbiome: Pathways to Modern Diseases. ENTROPY 2013. [DOI: 10.3390/e15041416] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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39
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Zhou X, Chen X, Jin Y, Markó IE. Evidence of Two Key Intermediates Contributing to the Selectivity of P450-Biomimetic Oxidation of Sulfides to Sulfoxides and Sulfones. Chem Asian J 2012; 7:2253-7. [DOI: 10.1002/asia.201200422] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Indexed: 11/09/2022]
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40
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Franke A, Fertinger C, van Eldik R. Axial Ligand and Spin-State Influence on the Formation and Reactivity of Hydroperoxo-Iron(III) Porphyrin Complexes. Chemistry 2012; 18:6935-49. [DOI: 10.1002/chem.201103036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/29/2011] [Indexed: 11/12/2022]
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41
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Warman AJ, Robinson JW, Luciakova D, Lawrence AD, Marshall KR, Warren MJ, Cheesman MR, Rigby SEJ, Munro AW, McLean KJ. Characterization of Cupriavidus metallidurans CYP116B1--a thiocarbamate herbicide oxygenating P450-phthalate dioxygenase reductase fusion protein. FEBS J 2012; 279:1675-93. [PMID: 22356105 DOI: 10.1111/j.1742-4658.2012.08543.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The novel cytochrome P450/redox partner fusion enzyme CYP116B1 from Cupriavidus metallidurans was expressed in and purified from Escherichia coli. Isolated CYP116B1 exhibited a characteristic Fe(II)CO complex with Soret maximum at 449 nm. EPR and resonance Raman analyses indicated low-spin, cysteinate-coordinated ferric haem iron at both 10 K and ambient temperature, respectively, for oxidized CYP116B1. The EPR of reduced CYP116B1 demonstrated stoichiometric binding of a 2Fe-2S cluster in the reductase domain. FMN binding in the reductase domain was confirmed by flavin fluorescence studies. Steady-state reduction of cytochrome c and ferricyanide were supported by both NADPH/NADH, with NADPH used more efficiently (K(m[NADPH]) = 0.9 ± 0.5 μM and K(m[NADH]) = 399.1 ± 52.1 μM). Stopped-flow studies of NAD(P)H-dependent electron transfer to the reductase confirmed the preference for NADPH. The reduction potential of the P450 haem iron was -301 ± 7 mV, with retention of haem thiolate ligation in the ferrous enzyme. Redox potentials for the 2Fe-2S and FMN cofactors were more positive than that of the haem iron. Multi-angle laser light scattering demonstrated CYP116B1 to be monomeric. Type I (substrate-like) binding of selected unsaturated fatty acids (myristoleic, palmitoleic and arachidonic acids) was shown, but these substrates were not oxidized by CYP116B1. However, CYP116B1 catalysed hydroxylation (on propyl chains) of the herbicides S-ethyl dipropylthiocarbamate (EPTC) and S-propyl dipropylthiocarbamate (vernolate), and the subsequent N-dealkylation of vernolate. CYP116B1 thus has similar thiocarbamate-oxidizing catalytic properties to Rhodoccocus erythropolis CYP116A1, a P450 involved in the oxidative degradation of EPTC.
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Affiliation(s)
- Ashley J Warman
- Department of Biochemistry, University of Leicester, Leicester, UK
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42
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Abstract
P450(BM3) (CYP102A1), a fatty acid hydroxylase from Bacillus megaterium, has been extensively studied over a period of almost forty years. The enzyme has been redesigned to catalyse the oxidation of non-natural substrates as diverse as pharmaceuticals, terpenes and gaseous alkanes using a variety of engineering strategies. Crystal structures have provided a basis for several of the catalytic effects brought about by mutagenesis, while changes to reduction potentials, inter-domain electron transfer rates and catalytic parameters have yielded functional insights. Areas of active research interest include drug metabolite production, the development of process-scale techniques, unravelling general mechanistic aspects of P450 chemistry, methane oxidation, and improving selectivity control to allow the synthesis of fine chemicals. This review draws together the disparate research themes and places them in a historical context with the aim of creating a resource that can be used as a gateway to the field.
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Affiliation(s)
- Christopher J C Whitehouse
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
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43
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Mechanistic insight from thermal activation parameters for oxygenation reactions of different substrates with biomimetic iron porphyrin models for compounds I and II. J Biol Inorg Chem 2011; 17:27-36. [DOI: 10.1007/s00775-011-0822-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 07/07/2011] [Indexed: 10/17/2022]
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44
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Lai W, Shaik S. Can Ferric-Superoxide Act as a Potential Oxidant in P450cam? QM/MM Investigation of Hydroxylation, Epoxidation, and Sulfoxidation. J Am Chem Soc 2011; 133:5444-52. [DOI: 10.1021/ja111376n] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Wenzhen Lai
- 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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45
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Cryle MJ, Bell SG, Schlichting I. Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase. Biochemistry 2010; 49:7282-96. [PMID: 20690619 DOI: 10.1021/bi100910y] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cytochrome P450 CypX (CYP134A1), isolated from Bacillus subtilis, has previously been implicated in the three-step oxidative transformation of the diketopiperazine cyclo-l-leucyl-l-leucyl into pulcherriminic acid, a precursor of the extracellular iron chelate pulcherrimin. In this study, we present the first experimental data relating to CYP134A1, where we show that CYP134A1 binds cyclo-l-leucyl-l-leucyl with an affinity of 24.5 +/- 0.5 muM. Structurally related diketopiperazines sharing similar alkyl side chains to cyclo-l-leucyl-l-leucyl also bind to CYP134A1 with comparable affinity. CYP134A1 is capable of catalyzing the in vitro oxidation of diketopiperazine substrates when supported with several alternate electron transfer partner systems. Products containing one additional oxygen atom and which are intermediate products of the expected pulcherriminic acid were identified by GCMS. The oxidation of related diketopiperazines reveals that different oxidative pathways exist for CYP134A1-catalyzed diketopiperazine oxidation. The crystal structure of CYP134A1 has been determined to 2.7 A resolution in the absence of substrate and in the presence of bound phenylimidazole ligands to 3.1 and 3.2 A resolution. The active site is dominated by hydrophobic residues and contains an unusual proline residue in place of the normally conserved alcohol residue that typically plays an important role in oxygen activation. The B-B(2) substrate recognition loop, which forms part of the active site, shows considerable flexibility and was found in both open and closed conformations in different structures. These results represent the first insights into the structural and biochemical basis underlying the multistep oxidation catalyzed by CYP134A1.
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Affiliation(s)
- Max J Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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46
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van Eldik R, Hubbard CD. Application of low-temperature rapid-scan techniques in the elucidation of inorganic reaction mechanisms. Coord Chem Rev 2010. [DOI: 10.1016/j.ccr.2009.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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47
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Fertinger C, Hessenauer-Ilicheva N, Franke A, van Eldik R. Direct Comparison of the Reactivity of Model Complexes for Compounds 0, I, and II in Oxygenation, Hydrogen-Abstraction, and Hydride-Transfer Processes. Chemistry 2009; 15:13435-40. [DOI: 10.1002/chem.200901804] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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48
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Franke A, Wolak M, van Eldik R. Factors That Affect the Nature of the Final Oxidation Products in “Peroxo-Shunt” Reactions of Iron-Porphyrin Complexes. Chemistry 2009; 15:10182-98. [DOI: 10.1002/chem.200900453] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Porro CS, Sutcliffe MJ, de Visser SP. Quantum Mechanics/Molecular Mechanics Studies on the Sulfoxidation of Dimethyl Sulfide by Compound I and Compound 0 of Cytochrome P450: Which Is the Better Oxidant? J Phys Chem A 2009; 113:11635-42. [DOI: 10.1021/jp9023926] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cristina S. Porro
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael J. Sutcliffe
- The Manchester Interdisciplinary Biocenter and the 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 Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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50
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Franke A, Fertinger C, van Eldik R. Welches Oxidationsmittel ist wirklich verantwortlich für Oxygenierungen an P450‐Modellsystemen? – Eine kinetische Betrachtung. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800907] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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