51
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Kazaryan A, Baerends EJ. Ligand Field Effects and the High Spin–High Reactivity Correlation in the H Abstraction by Non-Heme Iron(IV)–Oxo Complexes: A DFT Frontier Orbital Perspective. ACS Catal 2015. [DOI: 10.1021/cs501721y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Andranik Kazaryan
- VU University Amsterdam, Theoretical Chemistry,
FEW, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Evert Jan Baerends
- VU University Amsterdam, Theoretical Chemistry,
FEW, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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52
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Krámos B, Oláh J. The mechanism of human aromatase (CYP 19A1) revisited: DFT and QM/MM calculations support a compound I-mediated pathway for the aromatization process. Struct Chem 2014. [DOI: 10.1007/s11224-014-0545-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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53
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Arfeen M, Patel DS, Abbat S, Taxak N, Bharatam PV. Importance of cytochromes in cyclization reactions: Quantum chemical study on a model reaction of proguanil to cycloguanil. J Comput Chem 2014; 35:2047-55. [DOI: 10.1002/jcc.23719] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Minhajul Arfeen
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Dhilon S. Patel
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Sheenu Abbat
- Department of Pharmacoinformatics; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Nikhil Taxak
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
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54
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Altun A, Breidung J, Neese F, Thiel W. Correlated Ab Initio and Density Functional Studies on H2 Activation by FeO+. J Chem Theory Comput 2014; 10:3807-20. [DOI: 10.1021/ct500522d] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ahmet Altun
- Department
of Physics, Fatih University, 34500 B.Çekmece, Istanbul, Turkey
| | - Jürgen Breidung
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz
1, D-45470 Mülheim
an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz
1, D-45470 Mülheim
an der Ruhr, Germany
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55
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Xiao Y, Ji WX, Wei-Xu, Chen XY, Wang SG. Investigation on spin-flip reaction of Re + CH3CN by relativistic density functional theory. Dalton Trans 2014; 43:9508-17. [PMID: 24825539 DOI: 10.1039/c4dt00193a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To explore the integrated reaction mechanisms for Re atom with acetonitrile theoretically, density functional theory with zero-order regular approximation (ZORA) relativistic corrections has been employed at the BP86/TZ2P level. There have been three adiabatic potential energy surfaces in the study along sextet, quartet and doublet spin states. However, the detailed minimum energy reaction pathway altogether contains six stationary states () to (), five transition states (), and two intersystem crossings with spin inversion (marked by ⇒): (6)Re + CH3CN → η(1)-ReNCCH3 () → ⇒ η(2)-Re(NC)CH3 () → → η(3)-HRe(NCCH2) () → → CH3-ReNC () → → CH2[double bond, length as m-dash]Re(H)NC () ⇒ → CH[triple bond, length as m-dash]Re(H)2NC (). Thereinto, the lowest energy crossing points (LECP) have been determined by the DFT fractional-occupation-number (FON) approach. The first spin inversion has transferred the potential energy surfaces from high-spin sextet to the quartet intermediate () with the subsequent C-C bond breakage. The second one from the quartet to the low-spin doublet state accompanies the C-H activation, decreasing the transition barrier by 157 kJ mol(-1). The overall reaction could be exothermic by about 210 kJ mol(-1). Harmonic vibration frequencies and NBO, WBO analysis are also applied to verified the experimental observed information.
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Affiliation(s)
- Yi Xiao
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 200240 Shanghai, China.
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56
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Reetz MT. One Hundred Years of the Max-Planck-Institut für Kohlenforschung. Angew Chem Int Ed Engl 2014; 53:8562-86. [DOI: 10.1002/anie.201403217] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Indexed: 12/27/2022]
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57
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58
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Hirao H, Thellamurege N, Zhang X. Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem 2014; 2:14. [PMID: 24809043 PMCID: PMC4010748 DOI: 10.3389/fchem.2014.00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022] Open
Abstract
The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological UniversitySingapore, Singapore
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59
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Park J, Morimoto Y, Lee YM, Nam W, Fukuzumi S. Unified view of oxidative C-H bond cleavage and sulfoxidation by a nonheme iron(IV)-oxo complex via Lewis acid-promoted electron transfer. Inorg Chem 2014; 53:3618-28. [PMID: 24605985 DOI: 10.1021/ic403124u] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Oxidative C-H bond cleavage of toluene derivatives and sulfoxidation of thioanisole derivatives by a nonheme iron(IV)-oxo complex, [(N4Py)Fe(IV)(O)](2+) (N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine), were remarkably enhanced by the presence of triflic acid (HOTf) and Sc(OTf)3 in acetonitrile at 298 K. All the logarithms of the observed second-order rate constants of both the oxidative C-H bond cleavage and sulfoxidation reactions exhibit remarkably unified correlations with the driving forces of proton-coupled electron transfer (PCET) and metal ion-coupled electron transfer (MCET) in light of the Marcus theory of electron transfer when the differences in the formation constants of precursor complexes between PCET and MCET were taken into account, respectively. Thus, the mechanisms of both the oxidative C-H bond cleavage of toluene derivatives and sulfoxidation of thioanisole derivatives by [(N4Py)Fe(IV)(O)](2+) in the presence of HOTf and Sc(OTf)3 have been unified as the rate-determining electron transfer, which is coupled with binding of [(N4Py)Fe(IV)(O)](2+) by proton (PCET) and Sc(OTf)3 (MCET). There was no deuterium kinetic isotope effect (KIE) on the oxidative C-H bond cleavage of toluene via the PCET pathway, whereas a large KIE value was observed with Sc(OTf)3, which exhibited no acceleration of the oxidative C-H bond cleavage of toluene. When HOTf was replaced by DOTf, an inverse KIE (0.4) was observed for PCET from both toluene and [Ru(II)(bpy)3](2+) (bpy =2,2'-bipyridine) to [(N4Py)Fe(IV)(O)](2+). The PCET and MCET reactivities of [(N4Py)Fe(IV)(O)](2+) with Brønsted acids and various metal triflates have also been unified as a single correlation with a quantitative measure of the Lewis acidity.
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Affiliation(s)
- Jiyun Park
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, ALCA , Japan Science and Technology Agency (JST) , Suita, Osaka 565-0871, Japan
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60
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Thellamurege NM, Hirao H. Effect of protein environment within cytochrome P450cam evaluated using a polarizable-embedding QM/MM method. J Phys Chem B 2014; 118:2084-92. [PMID: 24484442 DOI: 10.1021/jp412538n] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metalloenzymes accommodate cofactors and substrates in their active sites, thereby exerting powerful catalytic effects. Understanding the key elements of the mechanism via which such binding is accomplished using a number of atoms in a protein is a fundamental challenge. To address this issue computationally, here we used mechanical-embedding (ME), electronic-embedding (EE), and polarizable-embedding (PE) hybrid quantum mechanics and molecular mechanics (QM/MM) methods and performed an energy decomposition analysis (EDA) of the nonbonding protein environmental effect in the "compound I" intermediate state of cytochrome P450cam. The B3LYP and AMBER99/QP302 methods were used to deal with the QM and MM subsystems, respectively, and the nonbonding interaction energy between these subsystems was decomposed into electrostatic, van der Waals, and polarization contributions. The PE-QM/MM calculation was performed using polarizable force fields that were capable of describing induced dipoles within the MM subsystem, which arose in response to the electric field generated by QM electron density, QM nuclei, and MM point charges. The present QM/MM EDA revealed that the electrostatic term constituted the largest stabilizing interaction between the QM and MM subsystems. When proper adjustment was made for the point charges of the MM atoms located at the QM-MM boundary, EE-QM/MM and PE-QM/MM calculations yielded similar QM electron density distributions, indicating that the MM polarization effect does not have a significant influence on the extent of QM polarization in this particular enzyme system.
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Affiliation(s)
- Nandun M Thellamurege
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University , 21 Nanyang Link, Singapore 637371
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61
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Ji L, Zhang J, Liu W, de Visser SP. Metabolism of Halogenated Alkanes by Cytochrome P450 enzymes. Aerobic Oxidation versus Anaerobic Reduction. Chem Asian J 2014; 9:1175-82. [DOI: 10.1002/asia.201301608] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/02/2014] [Indexed: 11/11/2022]
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62
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Krámos B, Oláh J. Enolization as an Alternative Proton Delivery Pathway in Human Aromatase (P450 19A1). J Phys Chem B 2014; 118:390-405. [DOI: 10.1021/jp407365x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Balázs Krámos
- Department of Inorganic and
Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and
Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary
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63
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Dumas VG, Defelipe LA, Petruk AA, Turjanski AG, Marti MA. QM/MM study of the C-C coupling reaction mechanism of CYP121, an essential cytochrome p450 of Mycobacterium tuberculosis. Proteins 2013; 82:1004-21. [PMID: 24356896 DOI: 10.1002/prot.24474] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/15/2013] [Accepted: 11/04/2013] [Indexed: 11/06/2022]
Abstract
Among 20 p450s of Mycobacterium tuberculosis (Mt), CYP121 has received an outstanding interest, not only due to its essentiality for bacterial viability but also because it catalyzes an unusual carbon-carbon coupling reaction. Based on the structure of the substrate bound enzyme, several reaction mechanisms were proposed involving first Tyr radical formation, second Tyr radical formation, and C-C coupling. Key and unknown features, being the nature of the species that generate the first and second radicals, and the role played by the protein scaffold each step. In the present work we have used classical and quantum based computer simulation methods to study in detail its reaction mechanism. Our results show that substrate binding promotes formation of the initial oxy complex, Compound I is the responsible for first Tyr radical formation, and that the second Tyr radical is formed subsequently, through a PCET reaction, promoted by the presence of key residue Arg386. The final C-C coupling reaction possibly occurs in bulk solution, thus yielding the product in one oxygen reduction cycle. Our results thus contribute to a better comprehension of MtCYP121 reaction mechanism, with direct implications for inhibitor design, and also contribute to our general understanding of these type of enzymes.
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Affiliation(s)
- Victoria G Dumas
- Departamento de Quimica Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Química Física de los Materiales Medio Ambiente y Energia (INQUIMAE), UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes, 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
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64
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Cho KB, Kang H, Woo J, Park YJ, Seo MS, Cho J, Nam W. Mechanistic Insights into the C–H Bond Activation of Hydrocarbons by Chromium(IV) Oxo and Chromium(III) Superoxo Complexes. Inorg Chem 2013; 53:645-52. [DOI: 10.1021/ic402831f] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kyung-Bin Cho
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Hyeona Kang
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Jaeyoung Woo
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Young Jun Park
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Mi Sook Seo
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Jaeheung Cho
- Department
of Emerging Materials Science, DGIST, Daegu 711-873, Korea
| | - Wonwoo Nam
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
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65
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Rydberg P, Jørgensen FS, Olsen L. Use of density functional theory in drug metabolism studies. Expert Opin Drug Metab Toxicol 2013; 10:215-27. [PMID: 24295134 DOI: 10.1517/17425255.2014.864278] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The cytochrome P450 enzymes (CYPs) metabolize many drug compounds. They catalyze a wide variety of reactions, and potentially, a large number of different metabolites can be generated. Density functional theory (DFT) has, over the past decade, been shown to be a powerful tool to rationalize and predict the possible metabolites generated by the CYPs as well as other drug-metabolizing enzymes. AREAS COVERED We review applications of DFT on reactions performed by the CYPs and other drug-metabolizing enzymes able to perform oxidation reactions, with an emphasis on predicting which metabolites are produced. We also cover calculations of binding energies for complexes in which the ligands interact directly with the heme iron atom. EXPERT OPINION DFT is a useful tool for prediction of the site of metabolism. The use of small models of the enzymes work surprisingly well for most CYP isoforms. This is probably due to the fact that the binding of the substrates is not the major determinant. When binding of the substrate plays a significant role, the well-known issue of determining the free energy of binding is the challenge. How approaches taking the protein environment into account, like docking, MD and QM/MM, can be used are discussed.
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Affiliation(s)
- Patrik Rydberg
- University of Copenhagen, Department of Drug Design and Pharmacology , Denmark
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66
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Xiao Y, Chen XY, Qiu YX, Wang SG. Spin-flip reactions of Zr + C2H6 researched by relativistic density functional theory. J Mol Model 2013; 19:4003-12. [PMID: 23851999 DOI: 10.1007/s00894-013-1932-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 06/19/2013] [Indexed: 11/25/2022]
Abstract
Density functional theory (DFT) with relativistic corrections of zero-order regular approximation (ZORA) has been applied to explore the reaction mechanisms of ethane dehydrogenation by Zr atom with triplet and singlet spin-states. Among the complicated minimum energy reaction path, the available states involves three transition states (TS), and four stationary states (1) to (4) and one intersystem crossing with spin-flip (marked by -->): (3) Zr + C 2 H 6 → (3) Zr-CH 3 -CH 3 ((3)1) → (3)TS 1/2 → (3) ZrH-CH 2 -CH 3 ((3)2) → (3) TS 2/3 --> (1) ZrH2-CH2 = CH2 ((1) 3) → (1) TS 3/4 → (1) ZrH 3 -CH = CH 2 ((1)4). The minimum energy crossing point is determined with the help of the DFT fractional-occupation-number (FON) approach. The spin inversion leads the reaction pathway transferring from the triplet potential energy surface (PES) to the singlet's accompanying with the activation of the second C-H bond. The overall reaction is calculated to be exothermic by about 231 kJ mol(-1). Frequency and NBO analysis are also applied to confirm with the experimental observed data.
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Affiliation(s)
- Yi Xiao
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China
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67
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Water complexes of cytochrome P450: insights from energy decomposition analysis. Molecules 2013; 18:6782-91. [PMID: 23752465 PMCID: PMC6270449 DOI: 10.3390/molecules18066782] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 06/04/2013] [Accepted: 06/05/2013] [Indexed: 11/16/2022] Open
Abstract
Water is a small molecule that nevertheless perturbs, sometimes significantly, the electronic properties of an enzyme’s active site. In this study, interactions of a water molecule with the ferric heme and the compound I (Cpd I) intermediate of cytochrome P450 are studied. Energy decomposition analysis (EDA) schemes are used to investigate the physical origins of these interactions. Localized molecular orbital EDA (LMOEDA) implemented in the quantum chemistry software GAMESS and the EDA method implemented in the ADF quantum chemistry program are used. EDA reveals that the electrostatic and polarization effects act as the major driving force in both of these interactions. The hydrogen bonding in the Cpd I•••H2O complex is similar to that in the water dimer; however, the relative importance of the electrostatic effect is somewhat larger in the water dimer.
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68
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Lonsdale R, Houghton KT, Żurek J, Bathelt CM, Foloppe N, de Groot MJ, Harvey JN, Mulholland AJ. Quantum mechanics/molecular mechanics modeling of regioselectivity of drug metabolism in cytochrome P450 2C9. J Am Chem Soc 2013; 135:8001-15. [PMID: 23641937 PMCID: PMC3670427 DOI: 10.1021/ja402016p] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Cytochrome P450 enzymes (P450s) are
important in drug metabolism
and have been linked to adverse drug reactions. P450s display broad
substrate reactivity, and prediction of metabolites is complex. QM/MM
studies of P450 reactivity have provided insight into important details
of the reaction mechanisms and have the potential to make predictions
of metabolite formation. Here we present a comprehensive study of
the oxidation of three widely used pharmaceutical compounds (S-ibuprofen, diclofenac, and S-warfarin)
by one of the major drug-metabolizing P450 isoforms, CYP2C9. The reaction
barriers to substrate oxidation by the iron-oxo species (Compound
I) have been calculated at the B3LYP-D/CHARMM27 level for different
possible metabolism sites for each drug, on multiple pathways. In
the cases of ibuprofen and warfarin, the process with the lowest activation
energy is consistent with the experimentally preferred metabolite.
For diclofenac, the pathway leading to the experimentally observed
metabolite is not the one with the lowest activation energy. This
apparent inconsistency with experiment might be explained by the two
very different binding modes involved in oxidation at the two competing
positions. The carboxylate of diclofenac interacts strongly with the
CYP2C9 Arg108 side chain in the transition state for formation of
the observed metabolite—but not in that for the competing pathway.
We compare reaction barriers calculated both in the presence and in
the absence of the protein and observe a marked improvement in selectivity
prediction ability upon inclusion of the protein for all of the substrates
studied. The barriers calculated with the protein are generally higher
than those calculated in the gas phase. This suggests that active-site
residues surrounding the substrate play an important role in controlling
selectivity in CYP2C9. The results show that inclusion of sampling
(particularly) and dispersion effects is important in making accurate
predictions of drug metabolism selectivity of P450s using QM/MM methods.
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Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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69
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van der Kamp MW, Mulholland AJ. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 2013; 52:2708-28. [PMID: 23557014 DOI: 10.1021/bi400215w] [Citation(s) in RCA: 407] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.
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Affiliation(s)
- Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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70
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Park J, Lee YM, Nam W, Fukuzumi S. Brønsted Acid-Promoted C–H Bond Cleavage via Electron Transfer from Toluene Derivatives to a Protonated Nonheme Iron(IV)-Oxo Complex with No Kinetic Isotope Effect. J Am Chem Soc 2013; 135:5052-61. [DOI: 10.1021/ja311662w] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jiyun Park
- Department
of Material and Life
Science, Graduate School of Engineering, ALCA, Japan Science and Technology
Agency, Osaka University, Suita, Osaka
565-0871, Japan
| | - Yong-Min Lee
- Department
of Bioinspired Science, Ewha Womans University, Seoul 120-750, Korea
| | - Wonwoo Nam
- Department
of Bioinspired Science, Ewha Womans University, Seoul 120-750, Korea
| | - Shunichi Fukuzumi
- Department
of Material and Life
Science, Graduate School of Engineering, ALCA, Japan Science and Technology
Agency, Osaka University, Suita, Osaka
565-0871, Japan
- Department
of Bioinspired Science, Ewha Womans University, Seoul 120-750, Korea
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71
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Ansari A, Kaushik A, Rajaraman G. Mechanistic Insights on the ortho-Hydroxylation of Aromatic Compounds by Non-heme Iron Complex: A Computational Case Study on the Comparative Oxidative Ability of Ferric-Hydroperoxo and High-Valent FeIV═O and FeV═O Intermediates. J Am Chem Soc 2013; 135:4235-49. [DOI: 10.1021/ja307077f] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Azaj Ansari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Abhishek Kaushik
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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72
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Tang H, Guan J, Liu H, Huang X. Comparative Insight into Electronic Properties and Reactivities toward C–H Bond Activation by Iron(IV)–Nitrido, Iron(IV)–Oxo, and Iron(IV)–Sulfido Complexes: A Theoretical Investigation. Inorg Chem 2013; 52:2684-96. [DOI: 10.1021/ic302766f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hao Tang
- Institute of Theoretical
Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Jia Guan
- Institute of Theoretical
Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Huiling Liu
- Institute of Theoretical
Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Xuri Huang
- Institute of Theoretical
Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
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73
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Li C, Shaik S. How Do Perfluorinated Alkanoic Acids Elicit Cytochrome P450 to Catalyze Methane Hydroxylation? An MD and QM/MM Study. RSC Adv 2013; 3:2995-3005. [PMID: 23682310 DOI: 10.1039/c2ra22294a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recent experimental studies show that usage of perfluoro decanoic acid (PFDA), as a dummy substrate, can elicit P450BM3 to perform hydroxylation of small alkanes, such as methane (ref. 17) and propane (ref. 17 and ref. 18). To comprehend the mechanism whereby PFDA operates to potentiate P450BM3 to catalyze the hydroxylation of small alkanes, we used molecular dynamics (MD) and hybrid quantum mechanical / molecular mechanical (QM/MM) calculations. The MD results show that without the PFDA, methane escapes the active site, while the presence of PFDA can potentially induce a productive Cpd I-Methane juxtaposition for rapid oxidation. Nevertheless, when only a single methane molecule is present near the PFDA, it still escapes the pocket within less than a nanosecond. However, when three methane molecules are present in the pocket, they alternate quasi-periodically such that at all times (within 10 ns), a molecule of methane is always present in the proximity of Cpd I in a reactive conformation. Our results further demonstrate that the PFDA does not exert any electrostatic catalysis, whether the PFDA is in the protonated or deprotonated forms. Taken together, we conclude that methane hydroxylation requires, in addition to PFDA, a high partial pressure of methane that will cause a high methane concentration in the active site. Further study of ethane and propane hydroxylations demonstrates that higher alkane concentration is helpful for all the three small alkanes. Thus for the smallest alkane, methane, at least three molecules are necessary whereas for the larger ethane, two molecules are needed to force one ethane to be closer to Cpd I. Finally, for propane a second molecule is helpful but not absolutely necessary; for this molecule the PFDA may well be sufficient to keep propane close to Cpd I for efficient oxidation. We therefore propose that high alkane pressure should assist small alkane hydroxylation by P450 in a manner inversely proportional to the size of the alkanes.
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Affiliation(s)
- Chunsen Li
- 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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74
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Tang H, Guan J, Liu H, Huang X. Analysis of an alternative to the H-atom abstraction mechanism in methane C–H bond activation by nonheme iron(iv)-oxo oxidants. Dalton Trans 2013; 42:10260-70. [DOI: 10.1039/c3dt50866h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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75
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Ye S, Geng CY, Shaik S, Neese F. Electronic structure analysis of multistate reactivity in transition metal catalyzed reactions: the case of C–H bond activation by non-heme iron(iv)–oxo cores. Phys Chem Chem Phys 2013; 15:8017-30. [DOI: 10.1039/c3cp00080j] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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76
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Intrinsic properties and reactivities of mononuclear nonheme iron–oxygen complexes bearing the tetramethylcyclam ligand. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.06.002] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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77
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Lonsdale R, Harvey JN, Mulholland AJ. Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions. J Chem Theory Comput 2012; 8:4637-45. [PMID: 26605619 DOI: 10.1021/ct300329h] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory (DFT) based quantum mechanical/molecular mechanical (QM/MM) calculations have provided valuable insight into the reactivity of the cytochrome P450 family of enzymes (P450s). A failure of commonly used DFT methods, such as B3LYP, is the neglect of dispersion interactions. An empirical dispersion correction has been shown to improve the accuracy of gas phase DFT calculations of P450s. The current work examines the effect of the dispersion correction in QM/MM calculations on P450s. The hydrogen abstraction from camphor, and hydrogen abstraction and C-O addition of cyclohexene and propene by P450cam have been modeled, along with the addition of benzene to Compound I in CYP2C9, at the B3LYP-D2/CHARMM27 level of theory. Single point energy calculations were also performed at the B3LYP-D3//B3LYP-D2/CHARMM27 level. The dispersion corrections lower activation energy barriers significantly (by ∼5 kcal/mol), as seen for gas phase calculations, but has a small effect on optimized geometries.These effects are likely to be important in modeling reactions catalyzed by other enzymes also. Given the low computational cost of including such dispersion corrections, we recommend doing so in all B3LYP based QM/MM calculations.
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Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Jeremy N Harvey
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
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78
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Hu B, Sun C, Deng Q, Liu Z. Synthesis and catalytic properties of a series of cobalt porphyrins as cytochrome P450 model: the effect of substituents on the catalytic activity. J INCL PHENOM MACRO 2012; 76:345-352. [PMID: 23853521 PMCID: PMC3701136 DOI: 10.1007/s10847-012-0205-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 06/14/2012] [Indexed: 11/27/2022]
Abstract
A series of cobalt porphyrins derived from hemin was prepared as cytochrome P450 models. Effects of substituents at the cobalt deuteroporphyrin-propionate side chains are investigated in oxidation of toluene with air to benzaldehyde and benzyl alcohol without the use of solvent and sacrificial co-reductant. The catalytic activity of cobalt porphyrins depends on the type of substituents. When the electron-withdrawing groups like -Cl, -Br, were introduced into the double propionate side chains, they can increase the catalyst stability and selectivity to benzaldehyde. In comparison with these electron-withdrawing groups, the electron-donor groups, such as -CH3, -S-S- and -NH2 groups, can improve their catalytic activities. Moreover, the electron-donor group containing an unpaired electron (such as -S-S-, -NH2) is benefit for improving its catalytic efficiency and promoting the electron delivery. It can be concluded that the double propionate side chains in the deuteroporphyrin complex may participate in oxidation process and effect electron transfer from the high-valent metalloporphyrin species to the substrate.
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Affiliation(s)
- Bingcheng Hu
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094 Jiangsu China
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79
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Li D, Wang Y, Han K. Recent density functional theory model calculations of drug metabolism by cytochrome P450. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.01.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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80
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Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC. Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model 2012; 52:617-48. [PMID: 22339582 PMCID: PMC3317594 DOI: 10.1021/ci200542m] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Metabolism of xenobiotics remains a central challenge
for the discovery
and development of drugs, cosmetics, nutritional supplements, and
agrochemicals. Metabolic transformations are frequently related to
the incidence of toxic effects that may result from the emergence
of reactive species, the systemic accumulation of metabolites, or
by induction of metabolic pathways. Experimental investigation of
the metabolism of small organic molecules is particularly resource
demanding; hence, computational methods are of considerable interest
to complement experimental approaches. This review provides a broad
overview of structure- and ligand-based computational methods for
the prediction of xenobiotic metabolism. Current computational approaches
to address xenobiotic metabolism are discussed from three major perspectives:
(i) prediction of sites of metabolism (SOMs), (ii) elucidation of
potential metabolites and their chemical structures, and (iii) prediction
of direct and indirect effects of xenobiotics on metabolizing enzymes,
where the focus is on the cytochrome P450 (CYP) superfamily of enzymes,
the cardinal xenobiotics metabolizing enzymes. For each of these domains,
a variety of approaches and their applications are systematically
reviewed, including expert systems, data mining approaches, quantitative
structure–activity relationships (QSARs), and machine learning-based
methods, pharmacophore-based algorithms, shape-focused techniques,
molecular interaction fields (MIFs), reactivity-focused techniques,
protein–ligand docking, molecular dynamics (MD) simulations,
and combinations of methods. Predictive metabolism is a developing
area, and there is still enormous potential for improvement. However,
it is clear that the combination of rapidly increasing amounts of
available ligand- and structure-related experimental data (in particular,
quantitative data) with novel and diverse simulation and modeling
approaches is accelerating the development of effective tools for
prediction of in vivo metabolism, which is reflected by the diverse
and comprehensive data sources and methods for metabolism prediction
reviewed here. This review attempts to survey the range and scope
of computational methods applied to metabolism prediction and also
to compare and contrast their applicability and performance.
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Affiliation(s)
- Johannes Kirchmair
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
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81
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Sun XL, Huang XR, Li JL, Huo RP, Sun CC. Mechanism Insights of Ethane C–H Bond Activations by Bare [FeIII═O]+: Explicit Electronic Structure Analysis. J Phys Chem A 2012; 116:1475-85. [DOI: 10.1021/jp2120302] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Xiao-Li Sun
- State Key
Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Xu-Ri Huang
- State Key
Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Ji-Lai Li
- State Key
Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
- Department of Theoretical
Chemistry, Lund University,
Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Rui-Ping Huo
- State Key
Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
| | - Chia-Chung Sun
- State Key
Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s
Republic of China
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82
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Substitution of the Catalytic Metal and Protein PEGylation Enhances Activity and Stability of Bacterial Phosphotriesterase. Appl Biochem Biotechnol 2012; 166:1236-47. [DOI: 10.1007/s12010-011-9510-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 12/14/2011] [Indexed: 10/14/2022]
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83
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Zhou M, Balcells D, Parent AR, Crabtree RH, Eisenstein O. Cp* Iridium Precatalysts for Selective C–H Oxidation via Direct Oxygen Insertion: A Joint Experimental/Computational Study. ACS Catal 2012. [DOI: 10.1021/cs2005899] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Meng Zhou
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520, United States
| | - David Balcells
- Department
of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra,
Barcelona, Catalonia, Spain
| | - Alexander R. Parent
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520, United States
| | - Robert H. Crabtree
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520, United States
| | - Odile Eisenstein
- Institut Charles Gerhardt, Université Montpellier 2, CNRS 5253, cc 15001,
Place Eugène Bataillon 34095, Montpellier, France
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84
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Tang H, Guan J, Zhang L, Liu H, Huang X. The effect of the axial ligand on distinct reaction tunneling for methane hydroxylation by nonheme iron(iv)–oxo complexes. Phys Chem Chem Phys 2012; 14:12863-74. [DOI: 10.1039/c2cp42423a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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85
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Li JL, Zhang X, Huang XR. Mechanism of benzenehydroxylation by high-valent bare FeivO2+: explicit electronic structure analysis. Phys Chem Chem Phys 2012; 14:246-56. [DOI: 10.1039/c1cp22187f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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86
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Gopakumar G, Belanzoni P, Baerends EJ. Hydroxylation catalysis by mononuclear and dinuclear iron oxo catalysts: a methane monooxygenase model system versus the Fenton reagent Fe(IV)O(H2O)5(2+). Inorg Chem 2011; 51:63-75. [PMID: 22221279 DOI: 10.1021/ic200754w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylation of aliphatic C-H bonds is a chemically and biologically important reaction, which is catalyzed by the oxidoiron group FeO(2+) in both mononuclear (heme and nonheme) and dinuclear complexes. We investigate the similarities and dissimilarities of the action of the FeO(2+) group in these two configurations, using the Fenton-type reagent [FeO(2+) in a water solution, FeO(H(2)O)(5)(2+)] and a model system for the methane monooxygenase (MMO) enzyme as representatives. The high-valent iron oxo intermediate MMOH(Q) (compound Q) is regarded as the active species in methane oxidation. We show that the electronic structure of compound Q can be understood as a dimer of two Fe(IV)O(2+) units. This implies that the insights from the past years in the oxidative action of this ubiquitous moiety in oxidation catalysis can be applied immediately to MMOH(Q). Electronically the dinuclear system is not fundamentally different from the mononuclear system. However, there is an important difference of MMOH(Q) from FeO(H(2)O)(5)(2+): the largest contribution to the transition state (TS) barrier in the case of MMOH(Q) is not the activation strain (which is in this case the energy for the C-H bond lengthening to the TS value), but it is the steric hindrance of the incoming CH(4) with the ligands representing glutamate residues. The importance of the steric factor in the dinuclear system suggests that it may be exploited, through variation in the ligand framework, to build a synthetic oxidation catalyst with the desired selectivity for the methane substrate.
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Affiliation(s)
- G Gopakumar
- Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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87
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Wu X, Seo MS, Davis KM, Lee YM, Chen J, Cho KB, Pushkar YN, Nam W. A highly reactive mononuclear non-heme manganese(IV)-oxo complex that can activate the strong C-H bonds of alkanes. J Am Chem Soc 2011; 133:20088-91. [PMID: 22091637 DOI: 10.1021/ja208523u] [Citation(s) in RCA: 182] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A mononuclear non-heme manganese(IV)-oxo complex has been synthesized and characterized using various spectroscopic methods. The Mn(IV)-oxo complex shows high reactivity in oxidation reactions, such as C-H bond activation, oxidations of olefins, alcohols, sulfides, and aromatic compounds, and N-dealkylation. In C-H bond activation, the Mn(IV)-oxo complex can activate C-H bonds as strong as those in cyclohexane. It is proposed that C-H bond activation by the non-heme Mn(IV)-oxo complex does not occur via an oxygen-rebound mechanism. The electrophilic character of the non-heme Mn(IV)-oxo complex is demonstrated by a large negative ρ value of -4.4 in the oxidation of para-substituted thioanisoles.
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Affiliation(s)
- Xiujuan Wu
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
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88
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Shahrokh K, Orendt A, Yost GS, Cheatham TE. Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle. J Comput Chem 2011; 33:119-33. [PMID: 21997754 DOI: 10.1002/jcc.21922] [Citation(s) in RCA: 203] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 07/28/2011] [Accepted: 07/30/2011] [Indexed: 01/31/2023]
Abstract
Molecular mechanics (MM) methods are computationally affordable tools for screening chemical libraries of novel compounds for sites of P450 metabolism. One challenge for MM methods has been the absence of a consistent and transferable set of parameters for the heme within the P450 active site. Experimental data indicate that mammalian P450 enzymes vary greatly in the size, architecture, and plasticity of their active sites. Thus, obtaining X-ray-based geometries for the development of accurate MM parameters for the major classes of hepatic P450 remains a daunting task. Our previous work with preliminary gas-phase quantum mechanics (QM)-derived atomic partial charges greatly improved the accuracy of docking studies of raloxifene to CYP3A4. We have therefore developed and tested a consistent set of transferable MM parameters based on gas-phase QM calculations of two model systems of the heme-a truncated (T-HM) and a full (F-HM) for four states of the P450 catalytic cycle. Our results indicate that the use of the atomic partial charges from the F-HM further improves the accuracy of docked predictions for raloxifene to CYP3A4. Different patterns for substrate docking are also observed depending on the choice of heme model and state. Newly parameterized heme models are tested in implicit and explicitly solvated MD simulations in the absence and presence of enzyme structures, for CYP3A4, and appear to be stable on the nanosecond simulation timescale. The new force field for the various heme states may aid the community for simulations of P450 enzymes and other heme-containing enzymes.
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Affiliation(s)
- Kiumars Shahrokh
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah 84112, USA
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89
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Hirao H. Energy Decomposition Analysis of the Protein Environmental Effect: The Case of Cytochrome P450cam Compound I. CHEM LETT 2011. [DOI: 10.1246/cl.2011.1179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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90
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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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91
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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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92
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93
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Cho KB, Lai W, Hamberg M, Raman C, Shaik S. The reaction mechanism of allene oxide synthase: Interplay of theoretical QM/MM calculations and experimental investigations. Arch Biochem Biophys 2011; 507:14-25. [DOI: 10.1016/j.abb.2010.07.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/28/2010] [Accepted: 07/16/2010] [Indexed: 11/28/2022]
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94
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Kumar D, Thiel W, de Visser SP. Theoretical Study on the Mechanism of the Oxygen Activation Process in Cysteine Dioxygenase Enzymes. J Am Chem Soc 2011; 133:3869-82. [DOI: 10.1021/ja107514f] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Devesh Kumar
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
D-45470 Mülheim an der Ruhr, Germany
- Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad
500 607, India
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
D-45470 Mülheim an der Ruhr, Germany
| | - Sam P. de Visser
- The Manchester Interdisciplinary
Biocenter and School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester
M1 7DN, United Kingdom
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95
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Wallrapp FH, Guallar V. Mixed quantum mechanics and molecular mechanics methods: Looking inside proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.27] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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96
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Kumar D, Altun A, Shaik S, Thiel W. Water as biocatalyst in cytochrome P450. Faraday Discuss 2011; 148:373-83; discussion 421-41. [DOI: 10.1039/c004950f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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97
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Abu-Omar MM. High-valent iron and manganese complexes of corrole and porphyrin in atom transfer and dioxygen evolving catalysis. Dalton Trans 2011; 40:3435-44. [DOI: 10.1039/c0dt01341b] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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98
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Robles VM, Ortega-Carrasco E, Fuentes EG, Lledós A, Maréchal JD. What can molecular modelling bring to the design of artificial inorganic cofactors? Faraday Discuss 2011; 148:137-59; discussion 207-28. [DOI: 10.1039/c004578k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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99
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Bach RD. The rate-limiting step in P450 hydroxylation of hydrocarbons a direct comparison of the "somersault" versus the "consensus" mechanism involving compound I. J Phys Chem A 2010; 114:9319-32. [PMID: 20690650 DOI: 10.1021/jp1045518] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Model theoretical quantum mechanical (QM) calculations are described for the P-450 hydroxylation of methane, isobutane, and camphor that compare the concerted somersault H-abstraction mechanism with the oxidation step involving Cpd I. Special emphasis has been placed on maintaining a balanced basis set in the oxidation step. QM calculations, employing the 6-311+G(d,p) basis set on the Fe atom and all of the key surrounding atoms involved in the C-H abstraction step, reaffirm a mechanism involving rearrangement of the iron hydroperoxide group (FeO-OH --> FeO...HO(*)) in concert with hydrogen abstraction from the C-H bond of the substrate by the incipient bound hydroxyl radical HO(*). The barrier for the somersault rearrangement of model Cpd 0 (FeO-OH) is calculated to be 21.4 kcal/mol in the absence of substrate. The overall activation energy for the oxidation of camphor involving the somersault motion of the FeO-OH group of P450 model porphyrin iron(III) hydroperoxide [Por(SH)Fe(III)-OOH(-)] --> [Por(SH)Fe(III)-O....HO(-)] in concert with hydrogen abstraction is DeltaE(++) = 12.4 kcal/mol. The corresponding abstraction of the hydrogen atom from the C-H bond of camphor by Cpd I has an activation barrier of 17.6 kcal/mol. Arguments are presented that the somersault rearrangement is induced by steric compression at the active site. Kinetic isotope effect data are discussed that provides compelling evidence for a rate-limiting step involving C-H bond cleavage.
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Affiliation(s)
- Robert D Bach
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
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Kumar D, Karamzadeh B, Sastry GN, de Visser SP. What factors influence the rate constant of substrate epoxidation by compound I of cytochrome P450 and analogous iron(IV)-oxo oxidants? J Am Chem Soc 2010; 132:7656-67. [PMID: 20481499 DOI: 10.1021/ja9106176] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cytochromes P450 are a versatile range of mono-oxygenase enzymes that catalyze a variety of different chemical reactions, of which the key reactions include aliphatic hydroxylation and C=C double bond epoxidation. To establish the fundamental factors that govern substrate epoxidation by these enzymes we have done a systematic density functional theory study on substrate epoxidation by the active species of P450 enzymes, namely the iron(IV)-oxo porphyrin cation radical oxidant or Compound I. We show here, for the first time, that the rate constant of substrate epoxidation, and hence the activation energy, correlates with the ionization potential of the substrate as well as with intrinsic electronic properties of the active oxidant such as the polarizability volume. To explain these findings we present an electron-transfer model for the reaction mechanism that explains the factors that determine the barrier heights and developed a valence bond (VB) curve crossing mechanism to rationalize the observed trends. In addition, we have found a correlation for substrate epoxidation reactions catalyzed by a range of heme and nonheme iron(IV)-oxo oxidants with the strength of the O-H bond in the iron-hydroxo complex, i.e. BDE(OH), which is supported by the VB model. Finally, the fundamental factors that determine the regioselectivity change between substrate hydroxylation and epoxidation are discussed. It is shown that the regioselectivity of aliphatic hydroxylation versus double bond epoxidation is not influenced by the choice of the oxidant but is purely substrate dependent.
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Affiliation(s)
- Devesh Kumar
- Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India.
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