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Hou Z, Li Y, Zheng M, Liu X, Zhang Q, Wang W. Regioselective oxidation of heterocyclic aromatic hydrocarbons catalyzed by cytochrome P450: A case study of carbazole. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 258:114964. [PMID: 37121081 DOI: 10.1016/j.ecoenv.2023.114964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/11/2023] [Accepted: 04/26/2023] [Indexed: 05/22/2023]
Abstract
Recently there are increasing interests in accurately evaluating the health effects of heterocyclic PAHs. However, the activation mechanism and possible metabolites of heterocyclic PAHs catalyzed by human CYP1A1 is still elusive to a great extent. Here, leveraged to high level QM/MM calculations, the corresponding activation pathways of a representative heterocyclic PAHs, carbazole, were systematically explored. The first stage is electrophilic addition or hydrogen abstraction from N-H group. Electrophilic addition was evidenced to be more feasible and regioselectivity at C3 and C4 sites were identified. Correlations between energy barriers and key structural/electrostatic parameters reveal that O-Cα distance and Fe-O-Cα angle are the main origin for the catalytic regioselectivity. Electrophilic addition was determined as the rate-determining step and the subsequent possible reactions include epoxidation, NIH shift (the hydrogen migration from the site of hydroxylation to the adjacent carbon) and proton shuttle. The corresponding products are epoxides, ketones and hydroxylated carbazoles, respectively. The main metabolites (hydroxylated carbazoles) are estimated to be more toxic than carbazole. The regioselectivity of carbazole activated by CYP1A1 is different from the environmental processes (gas and aqueous phase). Collectively, these results will inform the in-depth understanding the metabolic processes of heterocyclic PAHs and aid the accurate evaluation of their health effects.
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Affiliation(s)
- Zexi Hou
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China; Shenzhen Research Institute, Shandong University, Shenzhen 518057, PR China.
| | - Mingna Zheng
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Xinning Liu
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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Yamaguchi Y, Nishizono N, Kobayashi D, Yoshimura T, Wada K, Kobayashi K, Oda K. Synthesis and biological evaluation of coumarin derivatives as selective CYP2A6 inhibitors. Bioorg Med Chem Lett 2023; 86:129206. [PMID: 36889653 DOI: 10.1016/j.bmcl.2023.129206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023]
Abstract
Cytochrome P450 2A6 (CYP2A6) inhibitors are expected to be suitable as smoking cessation aids and for cancer prevention. Because the typical coumarin-based CYP2A6 inhibitor methoxsalen also inhibits CYP3A4, unintended drug-drug interactions are still a concern. Therefore, the development of selective CYP2A6 inhibitors is desirable. In this study, we synthesized coumarin-based molecules, determined the IC50 values for CYP2A6 inhibition, verified the possibility of mechanism-based inhibition, and compared the selectivity for CYP2A6 versus CYP3A4. The results demonstrated that we developed CYP2A6 inhibitors that were more potent and selective than methoxsalen.
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Affiliation(s)
- Yuki Yamaguchi
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan.
| | - Naozumi Nishizono
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| | - Daisuke Kobayashi
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| | - Teruki Yoshimura
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| | - Keiji Wada
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| | - Kenichi Kobayashi
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
| | - Kazuaki Oda
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan
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Kamel EM, Lamsabhi AM. Water biocatalytic effect attenuates cytochrome P450-mediated carcinogenicity of diethylnitrosamine: A computational insight. Org Biomol Chem 2021; 19:9031-9042. [PMID: 34613323 DOI: 10.1039/d1ob01439k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanism-based mutagenicity and carcinogenicity of diethylnitrosamine (DEN) are believed to act through interactions with cytochrome P450 (P450) enzymes. DFT calculations to explore the conceivable mechanisms underlying the reaction of P450 with DEN with and without water as a biocatalyst were performed. The results shed light on the biocatalytic role of water in lowering the H-abstraction energy barriers because of the electrostatic effect driven by hydrogen bonding. Our DFT analysis revealed how metabolites are formed in the dealkylation (toxification) and denitrosation (detoxification) pathways. Also, our findings uncovered the active position of DEN vulnerable to P450 interactions. Two factors control the toxification and detoxification rates: the stability of denitrosation products and the HS rebound barrier of the α-pathway. Thus, water biocatalytic attenuation of DEN carcinogenicity was attained by stabilizing denitrosation products and slowing the α-HS rebound process. Docking and MD simulations were performed to assess the binding modes of DEN to P450's active site and to inspect the denitrosation and dealkylation processes, respectively.
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Affiliation(s)
- Emadeldin M Kamel
- Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049 Madrid, Spain.
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049 Madrid, Spain.
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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High warfarin sensitivity in carriers of CYP2C9*35 is determined by the impaired interaction with P450 oxidoreductase. THE PHARMACOGENOMICS JOURNAL 2013; 14:343-9. [PMID: 24322786 DOI: 10.1038/tpj.2013.41] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 11/01/2013] [Accepted: 11/06/2013] [Indexed: 12/12/2022]
Abstract
Cytochrome P450 2C9 (CYP2C9) metabolizes many clinically important drugs including warfarin and diclofenac. We have recently reported a new allelic variant, CYP2C9*35, found in a warfarin hypersensitive patient with Arg125Leu and Arg144Cys mutations. Here, we have investigated the molecular basis for the functional consequences of these polymorphic changes. CYP2C9.1 and CYP2C9-Arg144Cys expressed in human embryonic kidney 293 cells effectively metabolized both S-warfarin and diclofenac in NADPH-dependent reactions, whereas CYP2C9-Arg125Leu or CYP2C9.35 were catalytically silent. However, when NADPH was replaced by a direct electron donor to CYPs, cumene hydroperoxide, hereby bypassing the CYP oxidoreductase (POR), all variant enzymes were active, indicating unproductive interactions between CYP2C9.35 and POR. In silico analysis revealed a decrease of the electrostatic potential of CYP2C9-Arg125Leu-POR interacting surface and the loss of stabilizing salt bridges between these proteins. In conclusion, our data strongly suggest that the Arg125Leu mutation in CYP2C9.35 prevents CYP2C9-POR interactions resulting in the absence of NADPH-dependent CYP2C9-catalyzed activity in vivo, thus influencing the warfarin sensitivity in the carriers of this allele.
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Kojima T, Nakayama K, Ikemura K, Ogura T, Fukuzumi S. Formation of a Ruthenium(IV)-Oxo Complex by Electron-Transfer Oxidation of a Coordinatively Saturated Ruthenium(II) Complex and Detection of Oxygen-Rebound Intermediates in C–H Bond Oxygenation. J Am Chem Soc 2011; 133:11692-700. [DOI: 10.1021/ja2037645] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takahiko Kojima
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennoudai, Tsukuba, Ibaraki 305-8571
| | - Kazuya Nakayama
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan
| | - Kenichiro Ikemura
- Graduate School of Life Science, University of Hyogo, Kouto, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Graduate School of Life Science, University of Hyogo, Kouto, Hyogo 678-1297, Japan
| | - Shunichi Fukuzumi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan
- ALCA, Japan Science and Technology Agency (JST), 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
- Department of Bioinspired Science, Ewha Womans University, Seoul, South Korea
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Che CM, Lo VKY, Zhou CY, Huang JS. Selective functionalisation of saturated C–H bonds with metalloporphyrin catalysts. Chem Soc Rev 2011; 40:1950-75. [DOI: 10.1039/c0cs00142b] [Citation(s) in RCA: 495] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Sano E, Li W, Yuki H, Liu X, Furihata T, Kobayashi K, Chiba K, Neya S, Hoshino T. Mechanism of the decrease in catalytic activity of human cytochrome P450 2C9 polymorphic variants investigated by computational analysis. J Comput Chem 2010; 31:2746-58. [DOI: 10.1002/jcc.21568] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Gheidi M, Safari N, Zahedi M. Theoretical investigation of the ring opening process of verdoheme to biliverdin in the presence of dioxygen. J Mol Model 2010; 16:1401-13. [DOI: 10.1007/s00894-010-0644-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 12/10/2009] [Indexed: 10/19/2022]
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9
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Molecular dynamics simulation of a carboxy murine neuroglobin mutated on the proximal side: heme displacement and concomitant rearrangement in loop regions. J Mol Model 2009; 16:759-70. [DOI: 10.1007/s00894-009-0581-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Accepted: 08/17/2009] [Indexed: 11/26/2022]
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Xu J, Li L, Yin G, Li H, Du W. Ligand orientation of human neuroglobin obtained from solution NMR and molecular dynamics simulation as compared with X-ray crystallography. J Inorg Biochem 2009; 103:1693-701. [PMID: 19850349 DOI: 10.1016/j.jinorgbio.2009.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 09/17/2009] [Accepted: 09/21/2009] [Indexed: 10/20/2022]
Abstract
Neuroglobin, a new member of hemoprotein family, can reversibly bind oxygen and take part in many biological processes such as enzymatic reaction, signal transduction and the mitochondria function. Different from myoglobin and hemoglobin, it has a hexacoordinated heme environment, with histidyl imidazole of proximal His(96)(F8) and distal His(64)(E7) directly bound to the metal ion. In the present work, solution (1)H NMR spectroscopy was employed to investigate the electronic structure of heme center of wild-type met-human neuroglobin. The resonances of heme protons and key residues in the heme pocket were assigned. Two heme orientations resulting from a 180 degrees rotation about the alpha-gamma-meso axis with a population ratio about 2:1 were observed. Then the (1)H NMR chemical shifts of the ferriheme methyl groups were used to predict orientations of the axial ligand. The obtained axial ligand plane angle phi is consistent with that from the molecular dynamics simulation but not with those from the crystal data. Compared with mouse neuroglobin, the obtained average ligand orientation of human neuroglobin reflects the changeability of heme environment for the Ngb family.
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Affiliation(s)
- Jia Xu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
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11
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Dey A, Jiang Y, Ortiz de Montellano P, Hodgson KO, Hedman B, Solomon EI. S K-edge XAS and DFT calculations on cytochrome P450: covalent and ionic contributions to the cysteine-Fe bond and their contribution to reactivity. J Am Chem Soc 2009; 131:7869-78. [PMID: 19438234 DOI: 10.1021/ja901868q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Experimental covalencies of the Fe-S bond for the resting low-spin and substrate-bound high-spin active site of cytochrome P450 are reported. DFT calculations on the active site indicate that one H-bonding interaction from the protein backbone is needed to reproduce the experimental values. The H-bonding to the thiolate from the backbone decreases the anisotropic pi covalency of the Fe-S bond lowering the barrier of free rotation of the exchangeable axial ligand, which is important for reactivity. The anionic axial thiolate ligand is calculated to lower the Fe(III/II) reduction potential of the active site by more than 1 V compared to a neutral imidazole ligand. About half of this derives from its covalent bonding and half from its electrostatic interaction with the oxidized Fe. This axial thiolate ligand increases the pK(a) of compound 0 (Fe(III)-hydroperoxo) favoring its protonation which promotes O-O bond heterolysis forming compound I. The reactivity of compound I is calculated to be relatively insensitive to the nature of the axial ligand due to opposing reduction potential and proton affinity contributions to the H-atom abstraction energy.
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Affiliation(s)
- Abhishek Dey
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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12
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Efficient Biomimetic Oxidative Decarboxylation of Some Carboxylic Acids Catalyzed by a Manganese (III) Schiff Base Complex. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.7.1583] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Rapid and efficient aromatization of Hantzsch 1,4-dihydropyridines with Potassium peroxomonosulfate catalyzed by manganese(III) Schiff base complexes. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2008. [DOI: 10.1007/bf03246114] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Hata M, Tanaka Y, Kyoda N, Osakabe T, Yuki H, Ishii I, Kitada M, Neya S, Hoshino T. An epoxidation mechanism of carbamazepine by CYP3A4. Bioorg Med Chem 2008; 16:5134-48. [DOI: 10.1016/j.bmc.2008.03.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 03/05/2008] [Accepted: 03/06/2008] [Indexed: 11/25/2022]
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Torimoto N, Ishii I, Hata M, Kobayashi Y, Nakamura H, Ariyoshi N, Kitada M. Theoretical calculation of triazolam hydroxylation and endogenous steroid inhibition in the active site of CYP3A4. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:223-32. [PMID: 17204458 DOI: 10.1016/j.bbapap.2006.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Revised: 11/13/2006] [Accepted: 11/16/2006] [Indexed: 11/24/2022]
Abstract
CYP3A4 has unusual kinetic characteristics because it has a large active site. CYP3A4 produced more 4-hydroxytriazolam than alpha-hydroxytriazolam at concentrations of more than 60 muM triazolam, and different steroids had different inhibitory effects on the system. To clarify these interesting observations, the interactions between substrate and substrate/steroid were investigated by theoretical calculations. When two triazolam molecules were docked into the active site, the distance between the O-atom and the 4-hydroxylated site was less than the distance to the alpha-hydroxylated site because of interaction between the two triazolam molecules. Estradiol inhibited both alpha- and 4-hydroxytriazolam formation by 50%. Dehydroepiandrosterone (DHEA) inhibited alpha-hydroxylation more than 4-hydroxytriazolam formation, whereas aldosterone had no effect. When one triazolam molecule and one steroid molecule were simultaneously docked, estradiol increased the distance between the O-atom and the two hydroxylated sites, DHEA only increased the distance between the O-atom and alpha-hydroxylated site, and aldosterone did not change the distances. The relevant angles of Fe-O-C in the hydroxylated site of triazolam also widened, together with increased distance. These findings indicate that formation of a substrate and substrate/effector complex in the active site may be a factor for determining the enzyme kinetic parameters of CYP3A4.
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Affiliation(s)
- Nao Torimoto
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
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Torimoto N, Ishii I, Toyama KI, Hata M, Tanaka K, Shimomura H, Nakamura H, Ariyoshi N, Ohmori S, Kitada M. Helices F-G are important for the substrate specificities of CYP3A7. Drug Metab Dispos 2006; 35:484-92. [PMID: 17178770 DOI: 10.1124/dmd.106.011304] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
CYP3A7 is a member of the human CYP3A family and a major form of P450 expressed in human fetal livers. Although CYP3A7 shares nearly 90% base sequence with CYP3A4, CYP3A7 shows striking functional differences in the catalytic preference for several substrates, such as dehydroepiandrosterone (DHEA) or dehydroepiandrosterone 3-sulfate (DHEA-3S). First, to clarify the reason for the differences between CYP3A7 and CYP3A4, a homology model of CYP3A7 was constructed using the CYP3A4 crystal structure. Because these two structures were similar, four kinds of chimeric enzymes were constructed to determine which sequences are important for exhibiting the characteristics of CYP3A7. The results of kinetic analysis of DHEA and DHEA-3S 16alpha-hydroxylations by CYP3A7, CYP3A4, and CYP3A chimeras suggested that the amino acid residues from Leu(210) to Glu(279) were important to express the specificity for substrates as CYP3A7. This region was on the F and G helices of the modeled CYP3A7. Furthermore, to assess which amino acid in this sequence is important for the substrate specificity of CYP3A7, a one-point mutation of CYP3A7 to CYP3A4 was made by site-directed mutagenesis. The mutants of K224T and K244E had lost DHEA and DHEA-3S 16alpha-hydroxylation activities. The mutants also greatly decreased the metabolism of testosterone, erythromycin, nevirapine, and triazolam relative to those activities of CYP3A7 wild-type enzyme. From these results, it is expected that CYP3A7 can recognize specific substrates using the lysines in F-G loops.
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Affiliation(s)
- Nao Torimoto
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
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Gheidi M, Safari N, Bahrami H, Zahedi M. Theoretical investigations of the hydrolysis pathway of verdoheme to biliverdin. J Inorg Biochem 2006; 101:385-95. [PMID: 17197029 DOI: 10.1016/j.jinorgbio.2006.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Revised: 10/19/2006] [Accepted: 10/27/2006] [Indexed: 10/23/2022]
Abstract
Conversion of iron(II) verdoheme to iron biliverdin in the presence of OH(-) was investigated using B3LYP method. Both 3-21G and 6-31G* basis sets were employed for geometry optimization calculation as well as energy stabilization estimation. Calculation at 6-31G* level was found necessary for a correct spin state estimation of the iron complexes. Two possible pathways for the conversion of iron verdoheme to iron biliverdin were considered. In one path the iron was six-coordinate while in the other it was considered to be five-coordinate. In the six-coordinated pathway, the ground state of bis imidazole iron verdoheme is singlet while that for open chain iron biliverdin it is triplet state with 4.86 kcal/mol more stable than the singlet state. The potential energy surface suggests that a spin inversion take place during the course of reaction after TS. The ring opening process in the six-coordinated pathway is in overall -2.26 kcal/mol exothermic with a kinetic barrier of 9.76 kcal/mol. In the five-coordinated pathway the reactant and product are in the ground triplet state. In this path, hydroxyl ion attacks the iron center to produce a complex, which is only 1.59 kcal/mol more stable than when OH(-) directly attacks the macrocycle. The activation barrier for the conversion of iron hydroxy species to the iron biliverdin complex by a rebound mechanism is estimated to be 32.68 kcal/mol. Large barrier for rebound mechanism, small barrier of 4.18 kcal/mol for ring opening process of the hydroxylated macrocycle, and relatively same stabilities for complexes resulted by the attack of nucleophile to the iron and macrocycle indicate that five-coordinated pathway with direct attack of nucleophile to the 5-oxo position of macrocycle might be the path for the conversion of verdoheme to biliverdin.
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Affiliation(s)
- Mahin Gheidi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, Evin 19839-63113, Tehran, Iran
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Nakajima JI, Sato Y, Hoshino T, Yamazaki M, Saito K. Mechanistic Study on the Oxidation of Anthocyanidin Synthase by Quantum Mechanical Calculation. J Biol Chem 2006; 281:21387-21398. [PMID: 16702218 DOI: 10.1074/jbc.m600303200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Anthocyanidin synthase (ANS), a member of the 2-oxoglutarate-dependent dioxygenase family in flavonoid biosynthesis, catalyzes the conversion of leucoanthocyanidins (e.g. 2R,3S,4S-cis-leucocyanidin, LCD) to flav-2-en-3,4-diols, a direct precursor of colored anthocyanidins via flavan-3,3,4-triols. The detailed oxygenation mechanism of 2R,3S,4S-cis-LCD to flav-2-en-3,4-diols was investigated using the density functional theory method. An initial model for the calculation was constructed from a structure obtained by a 100-ps molecular dynamics simulation of Arabidopsis ANS under physiological conditions. This model consisted of an LCD molecule as the substrate together with an iron atom, two histidine residues, an aspartic acid residue, a succinate, and an oxygen atom as ligands of the iron atom. The results of the calculation indicated that both the C-3 and C-4 positions of LCD can be oxidized, although C-4 oxidation is preferable. The C-3 oxidation required several steps to form flavan-3,3,4-triol: 1) formation of Fe(III)-OH and a substrate C-3 radical via hydrogen atom abstraction by Fe(IV)=O, 2) formation of a C-3 ketone and a water molecule, 3) addition of OH(-) into the C-3 position of the ketone, and 4) addition of H(+) to form flavan-3,3,4-triol. On the other hand, C-4 oxidation of 2R,3S,4S-cis-LCD resulted in the direct formation of 2R,3R-trans-dihydroquercetin. These results suggest that the oxidation at C-3 of LCD, a key reaction for coloring in anthocyanin biosynthesis, can be regarded as a "side reaction" from the viewpoint of quantum mechanics of enzymatic reactions. Molecular evolutional implications of ANS and related proteins are discussed in terms of reaction dynamics.
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Affiliation(s)
- Jun-Ichiro Nakajima
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan; Tokiwa Phytochemical Co., Ltd., Chiba 285-0801, Japan
| | - Yoshiharu Sato
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan; Integrated Database Team, Japan Biological Information Research Center (JBIRC), Tokyo 135-0064, Japan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
| | - Mami Yamazaki
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
| | - Kazuki Saito
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan; RIKEN Plant Science Center, Yokohama 230-0045, Japan.
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Mirkhani V, Tangestaninejad S, Moghadam M, Mohammadpoor-Baltork I, Kargar H. Efficient oxidation of sulfides with sodium periodate catalyzed by manganese(III) Schiff base complexes. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.molcata.2005.07.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Choe YK, Nagase S. Effect of the axial cysteine ligand on the electronic structure and reactivity of high-valent iron(IV) oxo-porphyrins (Compound I): A theoretical study. J Comput Chem 2005; 26:1600-11. [PMID: 16155883 DOI: 10.1002/jcc.20302] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The effect of axial ligands on the reactivity of high-valent iron(IV) oxo-porphyrins (Compound I) was investigated using the B3LYP hybrid density functional method. We studied alkane hydroxylation using four models: Compound I with thiolate, imidazole, phenolate, and chloride anions as axial ligands. The first three ligands were employed as models for cysteinate, histidine, and tyrosinate, respectively. Our calculations show that anionic ligands and neutral ligands favor different electronic states for stationary points in the reaction coordinate, and the calculated energy barrier and energy of several reaction intermediates show similar values. A remarkable effect of axial ligands was found in the final product release step. Our calculations show that the thiolate ligand weakens a bond between heme and an alcohol. In contrast, the imidazole ligand significantly increases the interaction between heme and an alcohol, which causes the catalytic cycle to be less efficient.
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Affiliation(s)
- Yoong-Kee Choe
- Research Institute for Computational Sciences, National Institute of Advanced Industrial Science and Technology, Center-2, Umezono 1-1-1, Tsukuba 305-8578, Japan.
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21
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Bathelt CM, Zurek J, Mulholland AJ, Harvey JN. Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling. J Am Chem Soc 2005; 127:12900-8. [PMID: 16159284 DOI: 10.1021/ja0520924] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human cytochromes P450 play a vital role in drug metabolism. The key step in substrate oxidation involves hydrogen atom abstraction or C=C bond addition by the oxygen atom of the Compound I intermediate. The latter has three unpaired electrons, two on the Fe-O center and one shared between the porphyrin ring and the proximal cysteinyl sulfur atom. Changes in its electronic structure have been suggested to affect reactivity. The electronic and geometric structure of Compound I in three important human subfamilies of cytochrome P450 (P450, 2C, 2B, and 3A) that are major contributors to drug metabolism is characterized here using combined quantum mechanical/molecular mechanical (QM/MM) calculations at the B3LYP:CHARMM27 level. Compound I is remarkably similar in all isoforms, with the third unpaired electron located mainly on the porphyrin ring, and this prediction is not very sensitive to details of the QM/MM methodology, such as the DFT functional, the basis set, or the size of the QM region. The presence of substrate also has no effect. The main source of variability in spin density on the cysteinyl sulfur (from 26 to 50%) is the details of the system setup, such as the starting protein geometry used for QM/MM minimization. This conformational effect is larger than the differences between human isoforms, which are therefore not distinguishable on electronic grounds, so it is unlikely that observed large differences in substrate selectivity can be explained to a large extent in these terms.
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Affiliation(s)
- Christine M Bathelt
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS United Kingdom
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22
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Hata M, Tanaka Y, Fujii Y, Neya S, Hoshino T. A Theoretical Study on the Substrate Deacylation Mechanism of Class C β-Lactamase. J Phys Chem B 2005; 109:16153-60. [PMID: 16853052 DOI: 10.1021/jp045403q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The whole reaction of the deacylation of class C beta-lactamase was investigated by performing quantum chemical calculations under physiological conditions. In this study, the X-ray crystallographic structure of the inhibitor moxalactam-bound class C beta-lactamase (Patera et al. J. Am. Chem. Soc. 2000, 122, 10504-10512.) was utilized and moxalactam was changed into the substrate cefaclor. A model for quantum chemical calculations was constructed using an energy-minimized structure of the substrate-bound enzyme obtained by molecular mechanics calculation, in which the enzyme was soaked in thousands of TIP3P water molecules. It was found that the deacylation reaction consisted of two elementary processes. The first process was formation of a tetrahedral intermediate, which was initiated by the activation of catalytic water by Tyr150, and the second process was detachment of the hydroxylated substrate from the enzyme, which associated with proton transfer from the side chain of Lys67 to Ser64O(gamma). The first process is a rate-determining process, and the activation energy was estimated to be 30.47 kcal/mol from density functional theory calculations considering electron correlation (B3LYP/6-31G**). The side chain of Tyr150 was initially in a deprotonated state and was stably present in the active site of the acyl-enzyme complex, being held by Lys67 and Lys315 cooperatively.
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Affiliation(s)
- Masayuki Hata
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan.
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23
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Theoretical study on monooxygenation mechanism by cytochrome P450: an ultimate species in the substrate oxidation process. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2004.11.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Shaik S, Kumar D, de Visser SP, Altun A, Thiel W. Theoretical Perspective on the Structure and Mechanism of Cytochrome P450 Enzymes. Chem Rev 2005; 105:2279-328. [PMID: 15941215 DOI: 10.1021/cr030722j] [Citation(s) in RCA: 958] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sason Shaik
- Department of Organic Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Israel.
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25
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Todoroki Y, Sawada M, Matsumoto M, Tsukada S, Ueno K, Isaka M, Owaki M, Hirai N. Metabolism of 5'alpha,8'-cycloabscisic acid, a highly potent and long-lasting abscisic acid analogue, in radish seedlings. Bioorg Med Chem 2004; 12:363-70. [PMID: 14723955 DOI: 10.1016/j.bmc.2003.10.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We synthesized 5'alpha,8'-cycloabscisic acid (CycloABA), a highly potent and long-lasting abscisic acid (ABA) analogue, by a different method from that reported before. CycloABA fed to radish seedlings had more metabolic tolerance than ABA. The major metabolite of CycloABA was the glucose conjugate, which was the minor metabolite of ABA. The 8'-hydroxylated metabolite and its cyclized isomer, which were major metabolites of ABA, were not found as metabolites of CycloABA. The present results suggest that the highly potent and long-lasting activity of CycloABA is caused by resistance to ABA 8'-hydroxylase, and that CycloABA is partially metabolized to the glucose conjugate by ABA glucosyltransferase.
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Affiliation(s)
- Yasushi Todoroki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan.
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26
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Hata M, Hirano Y, Hoshino T, Nishida R, Tsuda M. Theoretical Study on Compound I Formation in Monooxygenation Mechanism by Cytochrome P450. J Phys Chem B 2004. [DOI: 10.1021/jp0496248] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masayuki Hata
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
| | - Yoshinori Hirano
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
| | - Rie Nishida
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
| | - Minoru Tsuda
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
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27
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Eggink LL, LoBrutto R, Brune DC, Brusslan J, Yamasato A, Tanaka A, Hoober JK. Synthesis of chlorophyll b: localization of chlorophyllide a oxygenase and discovery of a stable radical in the catalytic subunit. BMC PLANT BIOLOGY 2004; 4:5. [PMID: 15086960 PMCID: PMC406501 DOI: 10.1186/1471-2229-4-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2003] [Accepted: 04/15/2004] [Indexed: 05/24/2023]
Abstract
BACKGROUND Assembly of stable light-harvesting complexes (LHCs) in the chloroplast of green algae and plants requires synthesis of chlorophyll (Chl) b, a reaction that involves oxygenation of the 7-methyl group of Chl a to a formyl group. This reaction uses molecular oxygen and is catalyzed by chlorophyllide a oxygenase (CAO). The amino acid sequence of CAO predicts mononuclear iron and Rieske iron-sulfur centers in the protein. The mechanism of synthesis of Chl b and localization of this reaction in the chloroplast are essential steps toward understanding LHC assembly. RESULTS Fluorescence of a CAO-GFP fusion protein, transiently expressed in young pea leaves, was found at the periphery of mature chloroplasts and on thylakoid membranes by confocal fluorescence microscopy. However, when membranes from partially degreened cells of Chlamydomonas reinhardtii cw15 were resolved on sucrose gradients, full-length CAO was detected by immunoblot analysis only on the chloroplast envelope inner membrane. The electron paramagnetic resonance spectrum of CAO included a resonance at g = 4.3, assigned to the predicted mononuclear iron center. Instead of a spectrum of the predicted Rieske iron-sulfur center, a nearly symmetrical, approximately 100 Gauss peak-to-trough signal was observed at g = 2.057, with a sensitivity to temperature characteristic of an iron-sulfur center. A remarkably stable radical in the protein was revealed by an isotropic, 9 Gauss peak-to-trough signal at g = 2.0042. Fragmentation of the protein after incorporation of 125I- identified a conserved tyrosine residue (Tyr-422 in Chlamydomonas and Tyr-518 in Arabidopsis) as the radical species. The radical was quenched by chlorophyll a, an indication that it may be involved in the enzymatic reaction. CONCLUSION CAO was found on the chloroplast envelope and thylakoid membranes in mature chloroplasts but only on the envelope inner membrane in dark-grown C. reinhardtii cells. Such localization provides further support for the envelope membranes as the initial site of Chl b synthesis and assembly of LHCs during chloroplast development. Identification of a tyrosine radical in the protein provides insight into the mechanism of Chl b synthesis.
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Affiliation(s)
- Laura L Eggink
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA
- Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Russell LoBrutto
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA
- Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Daniel C Brune
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA
- Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Judy Brusslan
- Department of Biological Science, California State University, Long Beach, California 90840-3702, USA
| | - Akihiro Yamasato
- The Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Ayumi Tanaka
- The Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - J Kenneth Hoober
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA
- Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287-1604, USA
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28
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Schöneboom JC, Cohen S, Lin H, Shaik S, Thiel W. Quantum Mechanical/Molecular Mechanical Investigation of the Mechanism of C−H Hydroxylation of Camphor by Cytochrome P450cam: Theory Supports a Two-State Rebound Mechanism. J Am Chem Soc 2004; 126:4017-34. [PMID: 15038756 DOI: 10.1021/ja039847w] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stereospecific cytochrome P450-catalyzed hydroxylation of the C(5)-H((5-exo)) bond in camphor has been studied theoretically by a combined quantum mechanical/molecular mechanical (QM/MM) approach. Density functional theory is employed to treat the electronic structure of the active site (40-100 atoms), while the protein and solvent environment (ca. 24,000 atoms) is described by the CHARMM force field. The calculated energy profile of the hydrogen-abstraction oxygen-rebound mechanism indicates that the reaction takes place in two spin states (doublet and quartet), as has been suggested earlier on the basis of calculations on simpler models ("two-state reactivity"). While the reaction on the doublet potential energy surface is nonsynchronous, yet effectively concerted, the quartet pathway is truly stepwise, including formation of a distinct intermediate substrate radical and a hydroxo-iron complex. Comparative calculations in the gas phase demonstrate the effect of the protein environment on the geometry and relative stability of intermediates (in terms of spin states and redox electromers) through steric constraints and electronic polarization.
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Affiliation(s)
- Jan C Schöneboom
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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29
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Urlacher VB, Schmid RD. Protein Engineering of the Cytochrome P450 Monooxygenase from Bacillus megaterium. Methods Enzymol 2004; 388:208-24. [PMID: 15289074 DOI: 10.1016/s0076-6879(04)88019-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Vlada B Urlacher
- Institute of Technical Biochemistry, University of Stuggart, Germany
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30
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Bathelt CM, Ridder L, Mulholland AJ, Harvey JN. Mechanism and structure–reactivity relationships for aromatic hydroxylation by cytochrome P450. Org Biomol Chem 2004; 2:2998-3005. [PMID: 15480465 DOI: 10.1039/b410729b] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytochrome P450 enzymes play a central role in drug metabolism, and models of their mechanism could contribute significantly to pharmaceutical research and development of new drugs. The mechanism of cytochrome P450 mediated hydroxylation of aromatics and the effects of substituents on reactivity have been investigated using B3LYP density functional theory computations in a realistic porphyrin model system. Two different orientations of substrate approach for addition of Compound I to benzene, and also possible subsequent rearrangement pathways have been explored. The rate-limiting Compound I addition to an aromatic carbon atom proceeds on the doublet potential energy surface via a transition state with mixed radical and cationic character. Subsequent formation of epoxide, ketone and phenol products is shown to occur with low barriers, especially starting from a cation-like rather than a radical-like tetrahedral adduct of Compound I with benzene. Effects of ring substituents were explored by calculating the activation barriers for Compound I addition in the meta and para-position for a range of monosubstituted benzenes and for more complex polysubstituted benzenes. Two structure-reactivity relationships including 8 and 10 different substituted benzenes have been determined using (i) experimentally derived Hammett sigma-constants and (ii) a theoretical scale based on bond dissociation energies of hydroxyl adducts of the substrates, respectively. In both cases a dual-parameter approach that employs a combination of radical and cationic electronic descriptors gave good relationships with correlation coefficients R2 of 0.96 and 0.82, respectively. These relationships can be extended to predict the reactivity of other substituted aromatics, and thus can potentially be used in predictive drug metabolism models.
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Affiliation(s)
- Christine M Bathelt
- School of Chemistry and Centre for Computational Chemistry, University of Bristol, UK
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31
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Nakano T, Kawabata S, Sugihara T, Agatsuma N, Kakuda H, Mori Y. On the Mechanism of the Oxidation of Toluenes in Artificial P450 Model Systems: Formation of Benzyl Alcohols, Benzaldehydes, and Phenols. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2003. [DOI: 10.1246/bcsj.76.2353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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32
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Tosha T, Yoshioka S, Takahashi S, Ishimori K, Shimada H, Morishima I. NMR study on the structural changes of cytochrome P450cam upon the complex formation with putidaredoxin. Functional significance of the putidaredoxin-induced structural changes. J Biol Chem 2003; 278:39809-21. [PMID: 12842870 DOI: 10.1074/jbc.m304265200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We investigated putidaredoxin-induced structural changes in carbonmonoxy P450cam by using NMR spectroscopy. The resonance from the beta-proton of the axial cysteine was upfield shifted by 0.12 ppm upon the putidaredoxin binding, indicating that the axial cysteine approaches to the heme-iron by about 0.1 A. The approach of the axial cysteine to the heme-iron would enhance the electronic donation from the axial thiolate to the heme-iron, resulting in the enhanced heterolysis of the dioxygen bond. In addition to the structural perturbation on the axial ligand, the structural changes in the substrate and ligand binding site were observed. The resonances from the 5-exo- and 9-methyl-protons of d-camphor, which were newly identified in this study, were upfield shifted by 1.28 and 0.20 ppm, respectively, implying that d-camphor moves to the heme-iron by 0.15-0.7 A. Based on the radical rebound mechanism, the approach of d-camphor to the heme-iron could promote the oxygen transfer reaction. On the other hand, the downfield shift of the resonance from the gamma-methyl group of Thr-252 reflects the movement of the side chain away from the heme-iron by approximately 0.25 A. Because Thr-252 regulates the heterolysis of the dioxygen bond, the positional rearrangement of Thr-252 might assist the scission of the dioxygen bond. We, therefore, conclude that putidaredoxin induces the specific heme environmental changes of P450cam, which would facilitate the oxygen activation and the oxygen transfer reaction.
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Affiliation(s)
- Takehiko Tosha
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
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33
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Kamachi T, Yoshizawa K. A theoretical study on the mechanism of camphor hydroxylation by compound I of cytochrome p450. J Am Chem Soc 2003; 125:4652-61. [PMID: 12683838 DOI: 10.1021/ja0208862] [Citation(s) in RCA: 188] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mechanistic and energetic aspects for the conversion of camphor to 5-exo-hydroxycamphor by the compound I iron-oxo species of cytochrome P450 are discussed from B3LYP DFT calculations. This reaction occurs in a two-step manner along the lines that the oxygen rebound mechanism suggests. The activation energy for the first transition state of the H atom abstraction at the C5 atom of camphor is computed to be more than 20 kcal/mol. This H atom abstraction is the rate-determining step in this hydroxylation reaction, leading to a reaction intermediate that involves a carbon radical species and the iron-hydroxo species. The second transition state of the rebound step that connects the reaction intermediate and the product alcohol complex lies a few kcal/mol below that for the H atom abstraction on the doublet and quartet potential energy surfaces. This energetic feature allows the virtually barrierless recombination in both spin states, being consistent with experimentally observed high stereoselectivity and brief lifetimes of the reaction intermediate. The overall energetic profile of the catalytic mechanism of camphor hydroxylation particularly with respect to why the high activation energy for the H atom abstraction is accessible under physiological conditions is also considered and calculated. According to a proton source model involving Thr252, Asp251, and two solvent water molecules (Biochemistry 1998, 37, 9211), the energetics for the conversion of the iron-peroxo species to compound I is studied. A significant energy over 50 kcal/mol is released in the course of this dioxygen activation process. The energy released in this chemical process is an important driving force in alkane hydroxylation by cytochrome P450. This energy is used for the access to the high activation energy for the H atom abstraction.
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Affiliation(s)
- Takashi Kamachi
- Institute for Fundamental Research of Organic Chemistry, Kyushu University, Fukuoka 812-8581, Japan
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Kamachi T, Shiota Y, Ohta T, Yoshizawa K. Does the Hydroperoxo Species of Cytochrome P450 Participate in Olefin Epoxidation with the Main Oxidant, Compound I? Criticism from Density Functional Theory Calculations. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2003. [DOI: 10.1246/bcsj.76.721] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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35
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Iwuoha EI, Smyth MR. Reactivities of organic phase biosensors: 6. Square-wave and differential pulse studies of genetically engineered cytochrome P450(cam) (CYP101) bioelectrodes in selected solvents. Biosens Bioelectron 2003; 18:237-44. [PMID: 12485770 DOI: 10.1016/s0956-5663(02)00180-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cytochrome P450(cam) (CYP101) bioelectrodes suitable for application in organic phases were prepared from genetically engineered CYP101 and vesicular dispersions of didodecyldimethylammonium bromide. The amperometric biosensor system was characterised under anaerobic conditions by cyclic and square-wave voltammetric methods. Cyclic- and square-wave-voltammetry studies showed that the biosensors exhibited direct reversible electron transfer between the haem iron atom and the glassy carbon electrode surface. The formal redox potential estimated for the electrode in acetonitrile was -380 mV/Ag-AgCl. The formal potential shifted anodically as the organic phase biosensor responded irreversibly to substrate (camphor) under anaerobic and aerobic conditions in acetonitrile. Differential pulse analysis of the reactivities of the CYP101 enzyme electrode confirmed the square-wave voltammetry result, which showed that the binding of substrate decreased the redox potential necessary for initiating the monooxygenation reaction of cytochrome P450(cam).
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Affiliation(s)
- Emmanuel I Iwuoha
- Department of Chemistry, University of Western Cape, Bellville 7535, South Africa.
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36
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Rohde JU, In JH, Lim MH, Brennessel WW, Bukowski MR, Stubna A, Münck E, Nam W, Que L. Crystallographic and spectroscopic characterization of a nonheme Fe(IV)-O complex. Science 2003; 299:1037-9. [PMID: 12586936 DOI: 10.1126/science.299.5609.1037] [Citation(s) in RCA: 721] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Following the heme paradigm, it is often proposed that dioxygen activation by nonheme monoiron enzymes involves an iron(IV)=oxo intermediate that is responsible for the substrate oxidation step. Such a transient species has now been obtained from a synthetic complex with a nonheme macrocyclic ligand and characterized spectroscopically. Its high-resolution crystal structure reveals an iron-oxygen bond length of 1.646(3) angstroms, demonstrating that a terminal iron(IV)=oxo unit can exist in a nonporphyrin ligand environment and lending credence to proposed mechanisms of nonheme iron catalysis.
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Affiliation(s)
- Jan-Uwe Rohde
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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37
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Fujii Y, Hata M, Hoshino T, Tsuda M. Catalytic Mechanism of Class A β-Lactamase: Role of Lysine 73 and C3-Carboxyl Group of the Substrate Pen G in the Deacylation Step. J Phys Chem B 2002. [DOI: 10.1021/jp021414c] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yasuyuki Fujii
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Masayuki Hata
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Tyuji Hoshino
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Minoru Tsuda
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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38
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Auclair K, Hu Z, Little DM, Ortiz De Montellano PR, Groves JT. Revisiting the mechanism of P450 enzymes with the radical clocks norcarane and spiro[2,5]octane. J Am Chem Soc 2002; 124:6020-7. [PMID: 12022835 DOI: 10.1021/ja025608h] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Norcarane (1) and spiro[2.5]octane (2) yield different product distributions depending on whether they are oxidized via concerted, radical, or cationic mechanisms. For this reason, these two probes were used to investigate the mechanisms of hydrocarbon hydroxylation by two mammalian and two bacterial cytochrome P450 enzymes. Products indicative of a radical intermediate with a lifetime ranging from 16 to 52 ps were detected during the oxidation of norcarane by P450(cam) (CYP101), P450(BM3) (CYP102), CYP2B1, and CYP2E1. Trace amounts of the cation rearrangement product were observed with norcarane for all but CYP2E1, while no cation or radical rearrangement products were observed for spiro[2.5]octane. The results for the oxidation of norcarane with a radical rearrangement rate of 2 x 10(8) s(-1) are consistent with the involvement of a two-state radical rebound mechanism, while for the slower (5 x 10(7) s(-1)) spiro[2,5]oct-4-yl radical rearrangement products were beyond detection. Taken together with earlier data for the hydroxylation of bicyclo[2.1.0]pentane, which also suggested a 50 ps radical lifetime, these three structurally similar and functionally simple substrates show a consistent pattern of rearrangement that supports a radical rebound mechanism for this set of cytochrome P450 enzymes.
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Affiliation(s)
- Karine Auclair
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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39
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Fokin AA, Schreiner PR. Selective alkane transformations via radicals and radical cations: insights into the activation step from experiment and theory. Chem Rev 2002; 102:1551-94. [PMID: 11996544 DOI: 10.1021/cr000453m] [Citation(s) in RCA: 306] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrey A Fokin
- Department of Organic Chemistry, Kiev Polytechnic Institute, 37 Pobedy Avenue, 03056 Kiev, Ukraine.
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Buda C, Burt SK, Cundari TR, Shenkin PS. De novo structural prediction of transition metal complexes: application to technetium. Inorg Chem 2002; 41:2060-9. [PMID: 11952359 DOI: 10.1021/ic0109748] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
De novo structural prediction of transition metal complexes is investigated. Technetium complexes are chosen given their importance in medical imaging and nuclear waste remediation and for the chemical diversity they display. A new conformational searching algorithm (LIGB) for transition metals is described that allows one to search for different conformational and geometric isomers within a single simulation. In the preponderance of cases, both conformational searching techniques (LIGB and high-temperature molecular dynamics/simulated annealing) provide comparable results, while LIGB is superior for macrocyclic complexes. A genetic algorithm-optimized PM3(tm) parametrization for Tc is compared with the standard implementation and found to yield a significant improvement in predictive ability for the most prevalent Tc structural motifs. The utility of a coupled molecular mechanics-semiempirical quantum mechanics protocol is demonstrated for very rapid, efficient, and effective de novo prediction of transition metal complex geometries.
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Affiliation(s)
- Corneliu Buda
- Department of Chemistry, The University of Memphis, Computational Research on Materials Institute (CROMIUM), Memphis, Tennessee 38152, USA
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Lee D, Lippard SJ. Synthetic analogue of the [Fe(2)(mu-OH)(2)(mu-O(2)CR)](3+) core of soluble methane monooxygenase hydroxylase via synthesis and dioxygen reactivity of carboxylate-bridged diiron(II) complexes. Inorg Chem 2002; 41:827-37. [PMID: 11849083 DOI: 10.1021/ic011008s] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the synthesis and dioxygen reactivity of diiron(II) tetracarboxylate complexes [Fe(2)(mu-O(2)CAr(Tol))(2)(O(2)CAr(Tol))(2)(N,N-Me(2)en)(2)] (2) and [Fe(2)(mu-O(2)CAr(Tol))(2)(O(2)CAr(Tol))(2)(N,N-Bn(2)en)(2)] (6), where Ar(Tol)CO(2)(-) = 2,6-di(p-tolyl)benzoate. These complexes were prepared as models for the diiron(II) center in the hydroxylase component of soluble methane monooxygenase (MMOH). Compound 6 reacts with dioxygen to afford PhCHO in approximately 60(5)% yield, following oxidative N-dealkylation of the pendant benzyl group on the diamine ligand. The diiron(III) complex [Fe(2)(mu-OH)(2)(mu-O(2)CAr(Tol))(O(2)CAr(Tol))(3)(N-Bnen)(N,N-Bn(2)en)] (8) was isolated from the reaction mixture. The 4.2 K Mössbauer spectrum of 8 displays a single quadrupole doublet with parameters delta = 0.48(2) mm s(-1) and Delta E(Q) = 0.61(2) mm s(-1). The [Fe(2)(mu-OH)(2)(mu-O(2)CR)](3+) core structure in 8 matches that of the fully oxidized form of MMOH. The conversion of 6 to 8 closely parallels the chemistry of MMOH in which an O(2)-derived oxygen atom is inserted into the C-H bond of methane. Several reaction pathways are considered to account for this novel chemical transformation, and these are compared with mechanistic frameworks previously developed for related cytochrome P450 and copper(I) dioxygen chemistry.
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Affiliation(s)
- Dongwhan Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Hata M, Hirano Y, Hoshino T, Tsuda M. Origin of the Primary Kinetic Hydrogen Isotope Effects on N-dealkylation from N-alkylamine by Hemoproteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.1577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
The concept of Molecular Science of the Living Organism was described, where the living state is explained as the purposive flows of the quantum mechanically controlled chemical reaction systems which support the homeostasis of the living organism. In the 21st century, the post genomic sequence era, the concept may be a self-evident truth. Molecular Science of the Living Organism was presented in the case of G-proteins: i.e., the atomically controlled mechanism of 1. the carcinogenesis which originates from the point mutation of ras p21, 2. the activation of a receptor protein at the cell membrane, especially in the case of bacteriorhodopsin, 3. the activation of an inactive G-protein by the activated receptor protein.
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Affiliation(s)
- M Tsuda
- Laboratory of Physical Chemistry, Faculty of Pharmaceutical Sciences, Chiba University, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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