Peroxynitrite Reactions with Dimethylsulfide and Dimethylselenide: An Experimental Study

Reactive Metabolites from Thiazole-Containing Drugs: Quantum Chemical Insights into Biotransformation and Toxicity

Drugs containing thiazole and aminothiazole groups are known to generate reactive metabolites (RMs) catalyzed by cytochrome P450s (CYPs). These RMs can covalently modify essential cellular macromolecules and lead to toxicity and induce idiosyncratic adverse drug reactions. Molecular docking and quantum chemical hybrid DFT study were carried out to explore the molecular mechanisms involved in the biotransformation of thiazole (TZ) and aminothiazole (ATZ) groups leading to RM epoxide, S-oxide, N-oxide, and oxaziridine. The energy barrier required for the epoxidation is 13.63 kcal/mol, that is lower than that of S-oxidation, N-oxidation, and oxaziridine formation (14.56, 17.90, and 20.20, kcal/mol respectively). The presence of the amino group in ATZ further facilitates all the metabolic pathways, for example, the barrier for the epoxidation reaction is reduced by ∼2.5 kcal/mol. Some of the RMs/their isomers are highly electrophilic and tend to form covalent bonds with nucleophilic amino acids, finally leading to the formation of metabolic intermediate complexes (MICs). The energy profiles of these competitive pathways have also been explored.

Toxicity Originating from Thiophene Containing Drugs: Exploring the Mechanism using Quantum Chemical Methods

Drug metabolism of thiophene containing substrates by cytochrome P450s (CYP450) leads to toxic side effects, for example, nephrotoxicity (suprofen, ticlopidine), hepatotoxicity (tienilic acid), thrombotic thrombocytopenic purpura (clopidogrel), and aplastic anemia (ticlopidine). The origin of toxicity in these cases has been attributed to two different CYP450 mediated metabolic reactions: S-oxidation and epoxidation. In this work, the molecular level details of the bioinorganic chemistry associated with the generation of these competitive reactions are reported. Density functional theory was utilized (i) to explore the molecular mechanism for S-oxidation and epoxidation using the radical cationic center Cpd I [(iron(IV)-oxo-heme porphine system with SH(-) as the axial ligand, to mimic CYP450s] as the model oxidant, (ii) to establish the 3D structures of the reactants, transition states, and products on both the metabolic pathways, and (iii) to examine the potential energy (PE) profile for both the pathways to determine the energetically preferred toxic metabolite formation. The energy barrier required for S-oxidation was observed to be 14.75 kcal/mol as compared to that of the epoxidation reaction (13.23 kcal/mol) on the doublet PE surface of Cpd I. The formation of the epoxide metabolite was found to be highly exothermic (-23.24 kcal/mol), as compared to S-oxidation (-8.08 kcal/mol). Hence, on a relative scale the epoxidation process was observed to be thermodynamically and kinetically more favorable. The energy profiles associated with the reactions of the S-oxide and epoxide toxic metabolites were also explored. This study helps in understanding the CYP450-catalyzed toxic reactions of drugs containing the thiophene ring at the atomic level.

Density functional study on the cytochrome-mediated S-oxidation: identification of crucial reactive intermediate on the metabolic path of thiazolidinediones

S-Oxidation is an important cytochrome P450 (CYP450)-catalyzed reaction, and the structural and energetic details of this process can only be studied by using quantum chemical methods. Thiazolidinedione (TZD) ring metabolism involving initial S-oxidation leads to the generation of reactive metabolites (RMs) and subsequent toxicity forcing the withdrawal of the glitazone class of drugs, thus, the study of the biochemical pathway of TZD ring metabolism is a subject of interest. The S-oxidation of the TZD ring and the formation of the isocyanate intermediate (ISC) was implicated as a possible pathway; however, there are several questions still unanswered in this biochemical pathway. The current study focuses on the CYP450-mediated S-oxidation, fate of the sulfoxide product (TZDSO), ring cleavage to ISC, and formation of nucleophilic adducts. The process of S-oxidation was explored by using Cpd I (iron(IV)-oxo porphyrin, to mimic CYP450) at TZVP/6-311+G(d) basis set. The barriers were calculated after incorporating dispersion and solvent corrections. The metabolic conversion from TZDSO to ISC (studied at B3LYP/6-311++G(2df,3pd)//B3LYP/6-31+G(d)) required a novel protonated intermediate, TZDSOH(+). The effect of higher basis sets (6-311+G(d,p), aug-cc-pvqz) on this conversion was studied. TZDSOH(+) was observed to be more reactive and thermodynamically accessible than ISC, indicating that TZDSOH(+) is the actual reactive intermediate leading to toxicity of the TZD class of compounds.

Visible Photooxidation of Dibenzothiophenes Sensitized by 2-(4-Methoxyphenyl)-4, 6-diphenylpyrylium: An Electron Transfer Mechanism without Involvement of Superoxide

We report here on a new electron-transfer mechanism for visible-light photooxidation of sulfides in which no superoxide ion is involved. Visible-light irradiation of 2-(4-methoxyphenyl)-4, 6-diphenylpyrylium tetrafluoroborate (MOPDPP(+)BF(4)(-)) in an O(2)-saturated acetonitrile solution containing dibenzothiophene (DBT) results in nearly 100% conversion to oxygenated products, DBT sulfoxide and sulfone. The photooxidation of DBT is initiated by a photoinduced electron-transfer process, where the excited MOPDPP(+) traps an electron from the ground-state DBT to form MOPDPP(*) and DBT radical cation. Such a mechanism is consistent with the studies of laser flash photolysis, electron spin resonance, and fluorescence quenching of the irradiated system. The photogenerated DBT radical cation undergoes a coupling reaction with O(2) to produce the intermediate responsible for the formation of the oxygenated products. The presence of O(2) has no effect on the decay kinetics of the transient absorption of MOPDPP(*), indicating that no redox reaction occurs between MOPDPP(*) and O(2), and thus no superoxide ion (O(2)(*-)) is formed. Moreover, the ESR signal of MOPDPP(*) was significantly enhanced in the presence of O(2), consistent with the assumption that the photogenerated DBT radical cation couples with O(2) to form the oxygen-adduct, which is subject to further reactions (Scheme 3) leading to the final oxygenated products. Similar results have been obtained when using 10-methylacridine hexafluorophosphate (AcrH(+)PF(6)(-), which has similar reduction potential in the ground state as MOPDPP(+)) as the sensitizer. This finding provides a possibility for the photooxidation of sulfides with dioxygen utilizing visible light (solar energy) and is also of significance in clarification of the reaction mechanism.

Internal rotation in peroxynitrous acid (ONOOH)

Using higher levels of wave-function-based electronic structure theory than previously applied, as well as density functional theory (B-LYP and B3-LYP functionals), all theoretical models conclude that three ONOOH conformers are stationary point minima, in disagreement with some of the previous studies that we survey. In order of increasing energy, these are the cis-cis, cis-perp, and trans-perp conformers. Basis sets including diffuse functions seem to be needed to obtain a qualitatively correct representation of the internal rotation potential energy surface at higher levels of theory. Internal rotation about the peroxide bond involving the cis-cis, cis-gauche transition structure (TS), cis-perp, and cis-trans TS conformers is studied in detail. To help ascertain the relative stability of the cis-perp conformer, multireference configuration interaction energy calculations are carried out, and rule of thumb estimates of multireference character in the ground-state wave functions of the ONOOH conformers are considered. CCSD(T)/aug-cc-pVTZ physical properties (geometries, rotational constants, electric dipole moments, harmonic vibrational frequencies, and infrared intensities) are compared with the analogous experimental data wherever possible, and also with density functional theory. Where such experimental data are nonexistent, the CCSD(T) and B3-LYP results are useful representations. For example, the electric dipole moment |mu(e)| of the cis-cis conformer is predicted to be 0.97+/-0.03 D. CCSD(T) energies, extrapolated to the aug-cc-pVNZ limit, are employed in isodesmic reaction schemes to derive zero Kelvin heats of formation and bond dissociation energies of the ONOOH stationary point minima. In agreement with recent gas-phase experiments, the peroxide bond dissociation energies of the cis-cis and trans-perp conformers are calculated as 19.3+/-0.4 and 16.0+/-0.4 kcalmol, respectively. The lowest energy cis-cis conformer is less stable than nitric acid by 28.1+/-0.4 kcalmol at 0 K.

Methionine oxidation by reactive oxygen species: reaction mechanisms and relevance to Alzheimer's disease

The oxidation of methionine plays an important role in vivo, during biological conditions of oxidative stress, as well as for protein stability in vitro. Depending on the nature of the oxidizing species, methionine may undergo a two-electron oxidation to methionine sulfoxide or one-electron oxidation to methionine radical cations. Both reaction mechanisms derive catalytic support from neighboring groups, which stabilize electron-deficient reaction centers. In vivo, methionine sulfoxide is subject to reduction by the methionine sulfoxide reductase (Msr) system, suggesting that some methionine sulfoxide residues may only be transiently involved in the deactivation of proteins through reactive oxygen species (ROS). Other methionine sulfoxide residues may accumulate, depending on the accessibility to Msr. Moreover, methionine sulfoxide levels may increase as a result of a lower abundance of active Msr and/or the required cofactors as a consequence of pathologies and biological aging. On the other hand, methionine radical cations will enter predominantly irreversible reaction channels, which ultimately yield carbon-centered and/or peroxyl radicals. These may become starting points for chain reactions of protein oxidation. This review will provide detailed mechanistic schemes for the reactions of various prominent, biologically relevant ROS with methionine and organic model sulfides. Emphasis will be given on the one-electron oxidation pathway, characterizing the physico-chemical parameters, which control this mechanism, and its physiological relevance, specifically for the oxidation and neurotoxicity of the Alzheimer's disease beta-amyloid peptide (betaAP).