The Elusive Oxidant Species of Cytochrome P450 Enzymes:  Characterization by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Calculations

Schöneboom, Jan; Lin, Hai; Reuter, Nathalie; Thiel, Walter; Cohen, Shimrit; Ogliaro, François; Shaik, Sason

doi:10.1021/ja026279w

Cited by 293 publications

(464 citation statements)

References 52 publications

Supporting

Mentioning

404

Contrasting

Unclassified

Order By: Relevance

“…However, the hydrogen bond between the sulfur and the Q360 backbone hydrogen elongates after MD followed by QM(B3LYP)/MM optimization. 25 The large flexibility of M445, in CYP3A4, manifested in all MDs is not associated with sulfur spin density variations. Coupled with the fact that in the initial structure the NH---S bond has an angle of 82°, which is not favored for a hydrogen bond we conclude that in contrast to CYP cam , the M445 residue in the CYP3A4 does not influence to a large extent the electronic structure of the thiolate ligand of Cpd I.…”

Section: Sulfur H-bonding Network and Ligand Influencementioning

confidence: 91%

QM/MM Study of the Active Species of the Human Cytochrome P450 3A4, and the Influence Thereof of the Multiple Substrate Binding

et al. 2007

Self Cite

View full text Add to dashboard Cite

Cytochrome P450 3A4 is involved in the metabolism of 50% of all swallowed drugs. The enzyme functions by means of a high-valent iron-oxo species, called Compound I (Cpd I), which is formed after entrance of the substrate to the active site. We explored the features of Cpd I using hybrid quantum mechanical/molecular mechanical calculations on various models that are either substratefree or containing one and two molecules of diazepam as a substrate. Mössbauer parameters of Cpd I were computed. Our major finding shows that without the substrate, Cpd I tends to elongate its Fe-S bond, localize the radical on the sulfur, and form hydrogen bonds with A305 and T309, which may hypothetically lead to Cpd I consumption by H-abstraction. However, the positioning of diazepam close to Cpd I, as enforced by the effector molecule, was found to strengthen the NH---S interactions of the conserved I443 and G444 residues with the proximal cysteinate ligand. These interactions are known to stabilize the Fe-S bond, and as such, the presence of the substrate leads to a shorter Fe-S bond and it prevents the localization of the radical on the sulfur. This diazepam-Cpd I stabilization was manifested in the 1W0E conformer. The effector substrate did not influence Cpd I directly but rather by positioning the active substrate close to Cpd I, thus displacing the hydrogen bonds with A305 and T309, and thereby giving preference to substrate oxidation. It is hypothesized that these effects on Cpd I, promoted by the restrained substrate, may be behind the special metabolic behavior observed in cases of multiple substrate binding (called also cooperative binding). This restraint constitutes a mechanism whereby substrates stabilize Cpd I sufficiently long to affect monooxygenation by P450s at the expense of Cpd I destruction by the protein residues.

show abstract

Section: Sulfur H-bonding Network and Ligand Influencementioning

confidence: 91%

QM/MM Study of the Active Species of the Human Cytochrome P450 3A4, and the Influence Thereof of the Multiple Substrate Binding

et al. 2007

Self Cite

View full text Add to dashboard Cite

show abstract

“…The resulting system (protein in a water droplet, overall hydration shell thickness 12 Å) consisting of 81,587 atoms (24,622 water molecules, 7,721 atoms in the protein) was energyminimized in CHARMM (adopted basis Newton-Raphson method). In this and the subsequent steps, the following constraints were applied: the outer 6 Å of water hydration shell, the oxoferryl heme (porphyrine ring, iron, and oxygen atoms) were fixed, soft restrains were applied to the distances from thiolate to the NH-backbone groups of the three residues after the coordinating cysteine [values according to Shaik et al (21)]. …”

Section: Chemicals and Reagents Ellipticine Nadpmentioning

confidence: 99%

The Anticancer Drug Ellipticine Forms Covalent DNA Adducts, Mediated by Human Cytochromes P450, through Metabolism to 13-Hydroxyellipticine and EllipticineN2-Oxide

et al. 2004

View full text Add to dashboard Cite

Ellipticine is an antineoplastic agent, the mode of action of which is considered to be based on DNA intercalation and inhibition of topoisomerase II. We found that ellipticine also forms the cytochrome P450 (CYP)-mediated covalent DNA adducts. We now identified the ellipticine metabolites formed by human CYPs and elucidated the metabolites responsible for DNA binding. The 7-hydroxyellipticine, 9-hydroxyellipticine, 12-hydroxyellipticine, 13-hydroxyellipticine, and ellipticine N 2 -oxide are generated by hepatic microsomes from eight human donors. The role of specific CYPs in the oxidation of ellipticine and the role of the ellipticine metabolites in the formation of DNA adducts were investigated by correlating the levels of metabolites formed in each microsomal sample with CYP activities and with the levels of the ellipticine-derived deoxyguanosine adducts in DNA. On the basis of this analysis, formation of 9-hydroxyellipticine and 7-hydroxyellipticine was attributable to CYP1A1/2, whereas production of 13-hydroxyellipticine and ellipticine N 2 -oxide, the metabolites responsible for formation of two major DNA adducts, was attributable to CYP3A4. Using recombinant human enzymes, oxidation of ellipticine to 9-hydroxyellipticine and 7-hydroxyellipticine by CYP1A1/2 and to 13-hydroxyellipticine and N 2 -oxide by CYP3A4 was corroborated. Homologue modeling and docking of ellipticine to the CYP3A4 active center was used to explain the predominance of ellipticine oxidation by CYP3A4 to 13-hydroxyellipticine and N 2 -oxide.

show abstract

“…Shaik et al reported from QM/MM calculations that the inclusion of hydrogen bonds to the axial ligand transforms the electronic structure of compound I from a sulfur-centered radical to a porphyrin centered radical cation. 21) They have shown that the FeO unit remains with a spin density of about 2.0 even if its electronic structure is changed in a fashion similar to the compound I treated here (see Table 1). …”

Section: Reactant Complexmentioning

confidence: 59%

A DFT Study of the Heme Role in the N-Demethylation of Theophylline Mediated by Compound I of Cytochrome P450

et al. 2007

View full text Add to dashboard Cite

Using accurate DFT calculations we have examined the role that Compound I of cytochrome P450 plays as a catalyst in the conversion of theophylline to 1-methylxanthine. This reaction proceeds in two steps according to the characteristics of the oxygen rebound mechanism. In this study we found that the activation energy for the transition state corresponding to the abstraction of the H atom at the C13 in theophylline is 9.3 kcal/mol. This H atom abstraction is the rate-determining step in this reaction which takes place via a single electron transfer (SET) mechanism and leads to an intermediate containing theophylline cationic and iron-hydroxo species. The rebounding step between the reaction intermediate and the product alcohol complex is a barrierless step. The alcohol complex is then separated from the heme moiety and yields 1-methylxanthine by intramolecular rearrangement.

show abstract

The Elusive Oxidant Species of Cytochrome P450 Enzymes: Characterization by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Calculations

Cited by 293 publications

References 52 publications

QM/MM Study of the Active Species of the Human Cytochrome P450 3A4, and the Influence Thereof of the Multiple Substrate Binding

QM/MM Study of the Active Species of the Human Cytochrome P450 3A4, and the Influence Thereof of the Multiple Substrate Binding

The Anticancer Drug Ellipticine Forms Covalent DNA Adducts, Mediated by Human Cytochromes P450, through Metabolism to 13-Hydroxyellipticine and EllipticineN2-Oxide

A DFT Study of the Heme Role in the N-Demethylation of Theophylline Mediated by Compound I of Cytochrome P450

Contact Info

Product

Resources

About