Oxidative cleavage of alpha-keto, alpha-hydroxy, and alpha-halo ketones, esters, and carboxylic acids by superoxide

Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations

Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the mechanism of dioxygen activation, oxygen atom exchange and substrate epoxidation processes by AsqJ, an Fe^II/α-ketoglutarate-dependent dioxygenase (α-KGD) using a 2-His-1-Asp facial triad. Our results demonstrated that the whole reaction proceeds through a quintet surface. The dioxygen activation by AsqJ leads to a quintet penta-coordinated Fe^IV-oxo species, which has a square pyramidal geometry with the oxo group trans to His134. This penta-coordinated Fe^IV-oxo species is not the reactive one in the substrate epoxidation reaction since its oxo group is pointing away from the target C[double bond, length as m-dash]C bond. Instead, it can undergo the oxo group isomerization followed by water binding or the water binding followed by oxygen atom exchange to form the reactive hexa-coordinated Fe^IV-oxo species with the oxo group trans to His211. The calculated parameters of Mössbauer spectra for this hexa-coordinated Fe^IV-oxo intermediate are in excellent agreement with the experimental values, suggesting that it is most likely the experimentally trapped species. The calculated energetics indicated that the rate-limiting step is the substrate C[double bond, length as m-dash]C bond activation. This work improves our understanding of the dioxygen activation by α-KGD and provides important structural information about the reactive Fe^IV-oxo species.

Superoxide chemistry revisited: synthesis of tetrachloro-substituted methylenenortricyclenes

An unexpected reactivity of the superoxide ion leading to the synthesis of tetrachloroaryl/vinyl-substituted nortricyclenes through its dual mode of action has been reported. KO2 was found to be superior and the only reagent to perform this kind of reaction over other conventional bases. Addition of the antioxidant BHT (2,6-di-tert-butyl-4-methylphenol) improved the yields of methylenenortricyclenes. A complete deuterium incorporation was observed in the superoxide-mediated reaction in DMSO-d 6. Friedel-Crafts acylation reactions of 3-methylenenorticyclenes yielded 2-propanone-substituted pentachloronorbornenes.

Applications of Potential Energy Surfaces in the Study of Enzymatic Reactions

From a generated PES, one can determine the relative energies of species involved, the sequence in which they occur, and the activation barrier(s) associated with individual steps or the overall mechanism. Furthermore, they can provide more insights than a simple indication of a path of sequential mechanistic structures and their energetic relationships. The investigation into the activation of O2 by alpha-ketoglutarate-dependent dioxygenase (AlkB) clearly shows the opportunity for spin inversion, where one can see that the lowest energy product may be formed via several possible routes. In the investigation of uroporphyrinogen decarboxylase III (UROD), the use of QM/MM methods allowed for the inclusion of the anisotropic protein environment providing greater insight into the rate-limiting barrier. Lastly, the mechanism of 6-phospho-α-glucosidase (GlvA) was discussed using different active site models. In particular, a continuum model PES was compared to the gas-phase PES.

A DFT study of nucleobase dealkylation by the DNA repair enzyme AlkB

Oxidative dealkylation is a unique mechanistic pathway found in the alpha-ketoglutarate-Fe(II)-dependent AlkB family of enzymes to remove the alkylation damage to DNA bases and regenerate nucleobases to their native state. The B3LYP density functional combined with a self-consistent reaction field was used to explore the triplet, quintet, and septet spin-state potential energy surfaces of the multistep catalytic mechanism of AlkB. The mechanism was found to consist of four stages. First, binding of dioxygen to iron in the active-site complex occurs concerted with electron transfer, thereby yielding a ferric-superoxido species. Second, competing initiation for the activation of oxygen to generate the high-valent iron-oxygen intermediates (ferryl-oxo Fe(IV)O and ferric-oxyl Fe(III)O(*) species) was found to occur on the quintet and septet surfaces. Then, conformational reorientation of the activated iron-oxygen ligand was found to be nearly thermoneutral with a barrier of ca. 50 kJ mol(-1). The final stage is the oxidative dealkylation of the damaged nucleobase with the rate-controlling step being the abstraction of a hydrogen atom from the damaging methyl group by the ferryl-oxo ligand. For this step, the calculated barrier of 87.4 kJ mol(-1) is in good agreement with the experimental activation energy of ca. 83 kJ mol(-1) for the enzyme-catalyzed reaction.

Levels of pros-methylimidazoleacetic acid: correlation with severity of Parkinson's disease in CSF of patients and with the depletion of striatal dopamine and its metabolites in MPTP-treated mice

The cerebrospinal fluid (CSF) levels of pros-methylimidazoleacetic acid (p-MIAA) in thirteen medication-free patients with mild to moderate Parkinson's disease were highly correlated (Spearman's rho = 0.749, p less than 0.005) with the severity of signs of the disease as scored on the Columbia University Rating Scale. Levels of p-MIAA in males (n = 8) and females (n = 5) were each significantly correlated with scores of severity (rho = 0.78, p less than 0.05 and rho = 1.0, p less than 0.05, respectively). In C57BL/6 mice treated with 1-methyl-4-phenyl-1,2,3,6-tetra-hydropyridine (MPTP), levels of p-MIAA were significantly correlated with the depleted levels of dopamine (r = 0.85, p less than 0.01), homovanillic acid (r = 0.79, p less than 0.02), 3,4-dihydroxyphenylacetic acid (r = 0.84, p less than 0.01) and norepinephrine (r = 0.91, p less than 0.002) in striatum, but not in cortex of the same mice. No such correlations were observed in either striatum or cortex of saline-treated control mice. Mean levels of p-MIAA in CSF did not differ significantly between patients and age-matched controls; and mean levels of p-MIAA in striatum did not differ between MPTP-treated mice and controls. The simplest hypothesis to account for these strong correlations in the absence of differences in mean levels of p-MIAA is that accumulation of p-MIAA [or process(es) that govern its accumulation] influences a failing nigrostriatal system. It is also possible (in analogy with findings in other diseases and with other drugs) that measurements of the putative metabolite(s) of p-MIAA may distinguish the patients and the MPTP-treated mice from their respective controls. Elucidation of the processes that regulate formation and disposition of p-MIAA in brain and information on the neural effects of p-MIAA, its precursors and its putative metabolites may yield insight into factors that regulate the progression of Parkinson's disease, and may shed additional light on the cause(s) of this disease.

Histamine metabolites and pros-methylimidazoleacetic acid in human cerebrospinal fluid

In cerebrospinal fluid, levels of the histamine metabolites, tele-methylhistamine and tele-methylimidazole-acetic acid, were higher in elderly than in young people, and women had higher levels than men. Therefore, age and gender should be considered in studies of histamine metabolites as exemplified by their measurements in cerebrospinal fluid of patients with Huntington's disease. Levels of pros-methylimidazoleacetic acid, an isomer of tele-methylimidazoleacetic acid and not a metabolite of histamine, were higher in cerebrospinal fluid of men than of women. Levels of pros-methylimidazoleacetic acid in cerebrospinal fluid were highly positively correlated with the severity of Parkinson's disease in a group of non-medicated, mildly to moderately affected patients.

Formation of hydrogen peroxide during precipitation of red cells with perchloric acid. A cautionary note for precise determination of pyruvate, GSH, and NAD(P)H

The instability of pyruvate in neutralized perchloric acid extracts of erythrocytes is well-known from the literature. As shown in this study, the main reason for this phenomenon is a reaction of pyruvate with hydrogen peroxide, which is formed from oxyhemoglobin during acid precipitation. Thereby, pyruvate is oxidized to carbon dioxide and acetate. This decomposition is easily prevented by addition of catalase to the neutralized extracts, whereby authentic pyruvate can be determined precisely. Similarly, GSH and NAD(P)H oxidation in the extracts is prevented by addition of catalase.