Theoretical studies on cytochrome P-450 mediated hydroxylation: a predictive model for hydrogen atom abstractions

Korzekwa, Kenneth R.; Jones, Jeffery P.; Gillette, James R.

doi:10.1021/ja00175a040

Cited by 139 publications

(167 citation statements)

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“…The employed energy cutoff for susceptible sites is in agreement with other approaches relying on AM1 functionals [40,61]. O-and N-dealkylations suitable for VOC generation are found to yield reaction intermediates of relative high stability [41].…”

Section: Som Predictionsupporting

confidence: 75%

Precursors for cytochrome P450 profiling breath tests from an in silico screening approach

et al. 2014

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The family of cytochrome P450 enzymes (CYPs) is a major player in the metabolism of drugs and xenobiotics. Genetic polymorphisms and transcriptional regulation give a complex patientindividual CYP activity profile for each human being. Therefore, personalized medicine demands easy and non-invasive measurement of the CYP phenotype. Breath tests detect volatile organic compounds (VOCs) in the patients' exhaled air after administration of a precursor molecule. CYP breath tests established for individual CYP isoforms are based on the detection of 13 CO 2 or 14 CO 2 originating from CYP-catalyzed oxidative degradation reactions of isotopically labeled precursors.We present an in silico work-flow aiming at the identification of novel precursor molecules, likely to result in VOCs other than CO 2 upon oxidative degradation as we aim at label-free precursor molecules. The ligand-based work-flow comprises five parts: (1) CYP profiling was encoded as a decision tree based on 2D molecular descriptors derived from established models in the literature and validated against publicly available data extracted from the DrugBank. (2) Likely sites of metabolism were identified by reactivity and accessibility estimation for abstractable hydrogen radical. (3) Oxidative degradation reactions (O-and N-dealkylations) were found to be most promising in the release of VOCs. Thus, the CYP-catalyzed oxidative degradation reaction was encoded as SMIRKS (a programming language style to implement reactions based on the SMARTS description) to enumerate possible reaction products. (4) A quantitative structure property relation (QSPR) model aiming to predict the Henry constant H was derived from data for 488 organic compounds and identifies potentially VOCs amongst CYP reaction products.(5) A blacklist of naturally occurring breath components was implemented to identify marker molecules allowing straightforward detection within the exhaled air.

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Section: Som Predictionsupporting

confidence: 75%

Precursors for cytochrome P450 profiling breath tests from an in silico screening approach

et al. 2014

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“…As indicated earlier, hydrogen abstraction is generally disfavored for primary C-H bonds due to their higher bond strengths relative to adjacent secondary or tertiary C-H bonds or sites where functionalization reduces the bond strength, e.g. benzyl groups or allylic carbons (15)(16)(17). As a consequence, P450 4B1 must restrict access of the adjacent secondary C-H bonds to reactive intermediate to display a preference for hydroxylation of the primary C-H bond in P450 4B1 (46) as well as in other -hydroxylases (18).…”

Section: Resultsmentioning

confidence: 95%

“…Oxygenation of aliphatic C-H bonds is thought to proceed by abstraction of a hydrogen by the iron oxo intermediate followed by recombination of the resulting substrate radical with the transiently iron-bound hydroxyl radical (14). As the strength of primary C-H bonds is greater than that of secondary C-H bonds, oxygen addition at the -1 or -2 positions of fatty acids is typically seen for less specialized enzymes (15)(16)(17). These considerations suggest that the -hydroxylases have structural features that favor the approach to the reactive iron oxo species of the -carbon relative to the -1 carbon (18).…”

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confidence: 99%

The Crystal Structure of Cytochrome P450 4B1 (CYP4B1) Monooxygenase Complexed with Octane Discloses Several Structural Adaptations for ω-Hydroxylation

Hsu

Baer

Rettie

et al. 2017

Journal of Biological Chemistry

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Edited by Ruma BanerjeeP450 family 4 fatty acid -hydroxylases preferentially oxygenate primary C-H bonds over adjacent, energetically favored secondary C-H bonds, but the mechanism explaining this intriguing preference is unclear. To this end, the structure of rabbit P450 4B1 complexed with its substrate octane was determined by X-ray crystallography to define features of the active site that contribute to a preference for -hydroxylation. The structure indicated that octane is bound in a narrow active-site cavity that limits access of the secondary C-H bond to the reactive intermediate. A highly conserved sequence motif on helix I contributes to positioning the terminal carbon of octane for -hydroxylation. Glu-310 of this motif auto-catalytically forms an ester bond with the heme 5-methyl, and the immobilized Glu-310 contributes to substrate positioning. The preference for -hydroxylation was decreased in an E310A mutant having a shorter side chain, but the overall rates of metabolism were retained. E310D and E310Q substitutions having longer side chains exhibit lower overall rates, likely due to higher conformational entropy for these residues, but they retained high preferences for octane -hydroxylation. Sequence comparisons indicated that active-site residues constraining octane for -hydroxylation are conserved in family 4 P450s. Moreover, the heme 7-propionate is positioned in the active site and provides additional restraints on substrate binding. In conclusion, P450 4B1 exhibits structural adaptations for -hydroxylation that include changes in the conformation of the heme and changes in a highly conserved helix I motif that is associated with selective oxygenation of unactivated primary C-H bonds.Cytochrome P450 family 4 fatty acid -hydroxylases are heme-containing monooxygenases that provide pathways for the reduction of potentially toxic non-esterified fatty acids and for the elimination of excess nutritive and non-nutritive lipids by catalyzing the addition of oxygen to a C-H bond of the terminal -carbon of fatty acids (1, 2). The resulting -alcohols are generally oxidized further to produce dicarboxylic acids, but they also may be transformed to glucuronides or esterified to glycerolipids. Urinary dicarboxylic fatty acids are elevated in humans by fasting or in uncontrolled diabetes, which are conditions where adipocyte lipolysis increases the availability of non-esterified fatty acids to fuel metabolism (3). It is estimated that roughly 15% of fatty acids undergo -hydroxylation during peak periods of fatty acid catabolism (4), whereas this fraction is much smaller under conditions where concentrations of nonesterified fatty acids are low (5). Collectively, these enzymes provide pathways for the metabolic clearance of branched chain fatty acids, eicosanoids, and xenobiotic substrates such as dietary phytanic acid, drugs, toxins, and vitamins E and K (1, 2, 6).Similar to other P450 2 gene families encoding multipurpose enzymes for the elimination of xenobiotic compounds, family 4 exhibits genetic diversi...

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“…The PNR model can be used to calculate activation energies from ground-state energies with the established free-energy relationship shown in Eq. 1 (8): AHact = 2.60 + 0.22(AHreac) + 2.38(I.P. ), [1] where AHact is the activation energy, AHreac iS the heat of reaction, and I.P.…”

mentioning

confidence: 99%

Designing safer chemicals: predicting the rates of metabolism of halogenated alkanes.

Yin

Anders

Korzekwa

et al. 1995

Proc. Natl. Acad. Sci. U.S.A.

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A computational model is presented that can be used as a tool in the design of safer chemicals. This model predicts the rate of hydrogen-atom abstraction by cytochrome P450 enzymes. Excellent correlations between biotransformation rates and the calculated activation energies (AHact) of the cytochrome P450-mediated hydrogen-atom abstractions were obtained for the in vitro biotransformation of six halogenated alkanes (1-fluoro-1,1,2,2-tetrachloroethane, 1,1-difluoro-1,2,2-trichloroethane, 1,1,1-trifluoro-2,2-dichloroethane, 1,1,1,2-tetrafluoro-2-chloroethane, 1,1,1,2,2-pentafluoroethane, and 2-bromo-2-chloro-1,1,1-trifluoroethane) with both rat and human enzyme preparations: ln(rate, rat liver microsomes) = The design of chemicals with lowest possible toxicity would decrease the damage to the environment; decrease the costs of production, health care, and site remediation; and increase the safety in the workplace (1). Although many factors are involved in the design of safer chemicals, one significant aspect is the prediction of rates of bioactivation of protoxins and procarcinogens to toxic metabolites (2). Bioactivation plays a major role in the toxicity of many chemicals, and the most important enzymes involved are the cytochromes P450 (CYPs) (2). The CYP enzymes catalyze the activation of molecular oxygen to a reactive monooxygen species (3), which can oxidize a variety of compounds (4). The transition state for the hydrogen-atom abstraction reaction is not, however, stabilized by the enzyme (3). Furthermore, the energetics of the active oxygen species is conserved among the several CYP enzymes studied (5). These factors make the CYP enzymes ideal candidates for predictive computational methods.We describe herein the application of a computational method for predicting the CYP-mediated oxidation rates of halogenated alkanes. Developing strategies for the design of safer halogenated alkanes is a particularly relevant objective, since hydro (chloro) Chemicals. 1-Fluoro-1,1,2,2-tetrachloroethane (HCFC-121), 1,1-difluoro-1,2,2-trichloroethane (HCFC-122), 1,1,1-trifluoro-2,2-dichloroethane (HCFC-123), 1,1,1,2-tetrafluoro-2-chloroethane (HCFC-124), pentafluoroethane (HFC-125), dichlorofluoroacetic acid, and chlorodifluoroacetic acid were obtained from PCR Research Chemicals (Gainesville, FL) and were used as received. 2-Bromo-2-chloro-1,1,1-trifluoroeth-

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Theoretical studies on cytochrome P-450 mediated hydroxylation: a predictive model for hydrogen atom abstractions

Cited by 139 publications

References 3 publications

Precursors for cytochrome P450 profiling breath tests from an in silico screening approach

Precursors for cytochrome P450 profiling breath tests from an in silico screening approach

The Crystal Structure of Cytochrome P450 4B1 (CYP4B1) Monooxygenase Complexed with Octane Discloses Several Structural Adaptations for ω-Hydroxylation

Designing safer chemicals: predicting the rates of metabolism of halogenated alkanes.

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