Urea decomposition facilitated by a urease model complex: a theoretical investigation

Theoretical study on the inhibition mechanisms of heavy metal ions on urease activity

Soil urease is highly sensitive to soil heavy metal pollution, and thus its activity can be used as bio-indicator of soil health. However, little is known about the inhibition mechanisms of heavy metals on urease. The effects of dimetallic substitution (i.e., Cd, Co, Cu, Hg, and Zn) on the binding of urea in the urease and its subsequent decomposition were studied using quantum chemical methodologies with a urease mimic (phthalazine-dinickel complex). The dimetallic substitution altered the structural features of the dimetal complexes and the M-O bond length between the dimetals and the carbonyl-O of coordinated urea molecules, weakening the binding energies of urea in dimetal complexes, which further affected the transformation of urea. In the urea decomposition via intra-molecular proton transfer, all dimetal complexes have a high activation barrier due to the weak binding of urea in complexes and hydrogen bonding within urea molecules, which are therefore difficult to occur spontaneously. In the urea decomposition via water-assisted inter-molecular proton transfer, the addition of water molecules decreased the energy barrier of urea decomposition. Regardless of the urea decomposition pathway, the dimetallic substitution altered the M-O bond length and hydrogen bond pattern of intermediates and transition states, and also affected the leave of the resulting NH3 from the dimetal complexes by regulating the C-N bond length within the decomposed urea molecule. Overall, the theoretical study provided insight into the molecular mechanisms of the inhibitory effects of heavy metals on urease activity.

Urea Decomposition Mechanism by Dinuclear Nickel Complexes

Urease is an enzyme containing a dinuclear nickel active center responsible for the hydrolysis of urea into carbon dioxide and ammonia. Interestingly, inorganic models of urease are unable to mimic its mechanism despite their similarities to the enzyme active site. The reason behind the discrepancy in urea decomposition mechanisms between inorganic models and urease is still unknown. To evaluate this factor, we synthesized two bis-nickel complexes, [Ni₂L(OAc)] (1) and [Ni₂L(Cl)(Et₃N)₂] (2), based on the Trost bis-Pro-Phenol ligand (L) and encompassing different ligand labilities with coordination geometries similar to the active site of jack bean urease. Both mimetic complexes produced ammonia from urea, (1) and (2), were ten- and four-fold slower than urease, respectively. The presence and importance of several reaction intermediates were evaluated both experimentally and theoretically, indicating the aquo intermediate as a key intermediate, coordinating urea in an outer-sphere manner. Both complexes produced isocyanate, revealing an activated water molecule acting as a base. In addition, the reaction with different substrates indicated the biomimetic complexes were able to hydrolyze isocyanate. Thus, our results indicate that the formation of an outer-sphere complex in the urease analogues might be the reason urease performs a different mechanism.

The chemistry of high valent tungsten chlorides with N-substituted ureas, including urea self-protonation reactions triggered by WCl6

N-Substituted ureas are oxidized by WCl₆in dichloromethane, resulting in protonated urea saltsviaactivation of C–H and/or N–H bonds.

A crystallographically characterized salt of self-generated N-protonated tetraethylurea

The first crystallographically characterizedN-protonated urea (1,1,3,3-tetraethylurea, teu) was obtained by a WCl₆-directed electron transfer/C–H activation process.

The effect of lipoic acid on cyanate toxicity in the rat heart

BACKGROUND

Cyanate is a uremic toxin formed principally via spontaneous urea biodegradation. Its active isoform, isocyanate, is capable of reaction with proteins by N and S carbamoylation, which influences their structure and function. Sulfurtransferases implicated in anaerobic cysteine transformation and cyanide detoxification belong to the enzymes possessing SH groups in their active centers. The present studies aimed to demonstrate the effect of cyanate and lipoic acid on the activity of these enzymes as well as on the level of antioxidants and prooxidants in the rat heart.

METHODS

Wistar rats, which received intraperitoneal injections of cyanate and lipoic acid alone and in combination were sacrificed 2.5 h after the first injection. The hearts were isolated and homogenized in phosphate buffer and next biochemical assays were performed comprising determination of the level of glutathione, malondialdehyde and sulfane sulfur and the activity of antioxidant enzymes as well as glutathione S-transferase and gamma glutamyl transferase.

RESULTS

Sulfurtransferases and glutathione S-transferase were deactivated by cyanate treatment. It was accompanied by the decreased level of glutathione and sulfane sulfur and the increased level of reactive oxygen species and malondialdehyde. In parallel, antioxidant enzymes: catalase, glutathione peroxidase and gamma glutamyl transferase were activated under such circumstances. Lipoic acid, administered in combination with cyanate prevented the decrease in the level of glutathione and reduction of a pool of sulfane sulfur-containing compounds, concomitantly preserving the activity of antioxidant enzymes.

CONCLUSIONS

Since uremia, characterized by the elevated cyanate/isocyanate level, is accompanied by frequent cases of cardiovascular diseases, the addition of lipoic acid to the therapy seems promising in prophylaxis of heart diseases in uremic patients.

The effect of lipoic acid on cyanate toxicity in different structures of the rat brain

Cyanate is formed mostly during nonenzymatic urea biodegradation. Its active form isocyanate reacts with protein -NH2 and -SH groups, which changes their structure and function. The present studies aimed to investigate the effect of cyanate on activity of the enzymes, which possess -SH groups in the active centers and are implicated in anaerobic cysteine transformation and cyanide detoxification, as well as on glutathione level and peroxidative processes in different brain structures of the rat: cortex, striatum, hippocampus, and substantia nigra. In addition, we examined whether a concomitant treatment with lipoate, a dithiol that may act as a target of S-carbamoylation, can prevent these changes. Cyanate-inhibited sulfurtransferase activities and lowered sulfide level, which was accompanied by a decrease in glutathione concentration and elevation of reactive oxygen species level in almost all rat brain structures. Lipoate administered in combination with cyanate was able to prevent the above-mentioned negative cyanate-induced changes in a majority of the examined brain structures. These observations can be promising for chronic renal failure patients since lipoate can play a double role in these patients contributing to efficient antioxidant defense and protection against cyanate and cyanide toxicity.

The effect of uremic toxin cyanate (OCN–) on anaerobic sulfur metabolism and prooxidative processes in the rat kidney: a protective role of lipoate

Cyanate and its active form isocyanate are formed mainly in the process of nonenzymatic urea biodegradation. Cyanate is capable of protein S- and N-carbamoylation, which can affect their activity. The present studies aimed to demonstrate the effect of cyanate on activity of the enzymes implicated in anaerobic cysteine metabolism and cyanide detoxification and on glutathione (GSH) level and peroxidative processes in the kidney. In addition, we examined whether a concomitant treatment with lipoate, a dithiol that may act as a target of S-carbamoylation, can prevent these changes. The studies were conducted in Wistar rats. The animals were assigned to four groups, which received injections of physiological saline, cyanate (200 mg/kg), cyanate (200 mg/kg) + lipoate (100 mg/kg) and lipoate alone (100 mg/kg). The animals were killed 2 h after the first injection, the kidneys were isolated and kept at -80°C until biochemical assays were performed. Cyanate inhibited rhodanese (TST) and mercaptopyruvate sulfotransferase (MPST) activity, decreased GSH level and enhanced peroxidative processes in the kidney. All these changes were abolished by cyanate treatment in combination with lipoate.

Synthesis, Reactivity, and DFT Studies of Tantalum Complexes Incorporating Diamido-N-heterocyclic Carbene Ligands. Facile Endocyclic C−H Bond Activation

The syntheses of tantalum derivatives with the potentially tridentate diamido-N-heterocyclic carbene (NHC) ligand are described. Aminolysis and alkane elimination reactions with the diamine-NHC ligands, (Ar)[NCN]H(2) (where (Ar)[NCN]H(2) = (ArNHCH(2)CH(2))(2)(C(3)N(2)); Ar = Mes, p-Tol), provided complexes with a bidentate amide-amine donor configuration. Attempts to promote coordination of the remaining pendent amine donor were unsuccessful. Metathesis reactions with the dilithiated diamido-NHC ligand ((Ar)[NCN]Li(2)) and various Cl(x)Ta(NR'(2))(5-)(x) precursors were successful and generated the desired octahedral (Ar)[NCN]TaCl(x)(NR'(2))(3-)(x) complexes. Attempts to prepare trialkyl tantalum complexes by this methodology resulted in the formation of an unusual metallaaziridine derivative. DFT calculations on model complexes show that the strained metallaaziridine ring forms because it allows the remaining substituents to adopt preferable bonding positions. The calculations predict that the lowest energy pathway involves a tantalum alkylidene intermediate, which undergoes C-H bond activation alpha to the amido to form the metallaaziridine moiety. This mechanism was confirmed by examining the distribution of deuterium atoms in an experiment between (Mes)[NCN]Li(2) and Cl(2)Ta(CD(2)Ph)(3). The single-crystal X-ray structures of (p)(-Tol)[NCNH]Ta(NMe(2))(4) (3), (Mes)[NCNH]Ta=CHPh(CH(2)Ph)(2) (4), (p)(-Tol)[NCN]Ta(NMe(2))(3) (7), (Mes)[NCCN]Ta(CH(2)(t)Bu)(2) (11), and (Mes)[NCCN]TaCl(CH(2)(t)Bu) (14) are included.

Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules?

A set of iron parameters for use in the semiempirical PM3 method have been developed to allow the structure and redox properties of the active sites of iron-containing proteins to be accurately modeled, focussing on iron-sulfur, iron-heme, and iron-only hydrogenases. Data computed at the B3LYP/6-31G* level for a training set of 60 representative complexes have been employed. A gradient-based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted. The derived parameters lead in general to good predictions of the structure and energetics of molecules both within and outside the training set, and overcome the extensive deficiencies of a B3LYP/STO-3G model. Particularly encouraging is the success of the parameters in describing [4Fe-4S] cubanes. The derived parameter set provides a starting point should greater accuracy for a more restricted range of compounds be required.