Inhibition of chitosan-immobilized urease by slow-binding inhibitors: Ni2+, F− and acetohydroxamic acid

Chelerythrine Chloride: A Potential Rumen Microbial Urease Inhibitor Screened by Targeting UreG

Inhibition of ruminal microbial urease is of particular interest due to its crucial role in regulating urea-N utilization efficiency and nitrogen pollution in the livestock industry. Acetohydroxamic acid (AHA) is currently the only commercially available urease inhibitor, but it has adverse side effects. The urease accessory protein UreG, which facilitates the functional incorporation of the urease nickel metallocentre, has been proposed in developing urease inhibitor through disrupting urease maturation. The objective of this study was to screen natural compounds as potential urease inhibitors by targeting UreG in a predominant ruminal microbial urease. In silico screening and in vitro tests for potential inhibitors were performed using molecular docking and an assay for the GTPase activity of UreG. Chelerythrine chloride was selected as a potential urease inhibitor of UreG with an inhibition concentration IC₅₀ value of 18.13 μM. It exhibited mixed inhibition, with the K_i value being 26.28 μM. We further explored its inhibition mechanism using isothermal titration calorimetry (ITC) and circular dichroism (CD) spectroscopy, and we found that chelerythrine chloride inhibited the binding of nickel to UreG and induced changes in the secondary structure, especially the α-helix and β-sheet of UreG. Chelerythrine chloride formed a pi-anion interaction with the Asp41 residue of UreG, which is an important residue in initiating the conformational changes of UreG. In conclusion, chelerythrine chloride exhibited a potential inhibitory effect on urease, which provided new evidence for strategies to develop novel urease inhibitors targeting UreG to reduce nitrogen excretion from ruminants.

Kinetics and Computational Evaluation of Eugenol and Vanillic Acid on Inhibition of a Potential Enzyme of a Nosocomial Pathogen that Promotes Struvite Formation

Background:

Struvite/infection stone is one of the major clinical burdens in urinary tract infections that is caused by the ureolytic behavior of pathogenic bacteria.

Objective:

The current strategy for treating infective stones is mostly antibiotic therapy, which ends in promoting resistance to the organisms. Hence in the present study, we investigated two phytocompounds, eugenol (an allyl-substituted guaiacol) and vanillic acid (a phenolic acid) that are found to be effective in inhibiting the urease enzyme of a nosocomial pathogen Proteus mirabilis.

Methods:

The enzyme was purified to apparent homogeneity and the kinetic parameters were studied in the presence and in the absence of eugenol and vanillic acid. Molecular docking and simulation were done to understand the level of protein-ligand interactions and the interacting residues.

Results:

Kinetic parameters obtained from the Michaelis-Menten plot show that both eugenol and vanillic acid exhibit non-competitive inhibition of urease enzyme in a dose-dependent manner. In silico studies showed that eugenol and vanillic acid have almost similar binding affinities to the regulatory pocket of the modeled protein. Dynamics and simulation results indicate that the interaction of ligands with the ARG373 residue of the protein provides a stable bound conformation.

Conclusion:

Overall, our results suggest that both the phytocompounds eugenol and vanillic acid have a potential application as a new therapy for the inhibition of urease enzyme that could possibly replace the complexions related to struvite stone formation.

Urease-aided calcium carbonate mineralization for engineering applications: A review

Inducing calcium carbonate precipitation is another important function of urease in nature. The process takes advantage of the supply of carbonate ions derived from urea hydrolysis and of an increase in pH generated by the reaction, effects that in the presence of Ca²⁺ ions lead to the precipitation of CaCO₃. Further to its importance in nature, if performed in a biomimetic manner, the urease-aided CaCO₃ mineralization offers enormous potential in innovative engineering applications as an eco-friendly technique operative under mild conditions, to be used for remediation and cementation/deposition in field applications in situ. These include among others, the strengthening and consolidation of soil/sand, the protection and restoration of stone and concrete structures, conservation of stone cultural heritage materials, cleaning waste- and groundwater of toxic metals and radionuclides, and plugging geological formations for the enhancement of oil recovery and geologic CO₂ sequestration. In view of the potential of this newly emerging interdisciplinary branch of engineering, this article presents the principles of urease-aided calcium carbonate mineralization apposed to other biomineralization processes, and reviews the advantages and limitations of the technique compared to the conventional techniques presently in use. Further, it presents areas of its existing and potential applications, notably in geotechnical, construction and environmental engineering, and its future perspectives.

Mechanism, kinetics, and antimicrobial activities of 2-hydroxy-1-naphthaldehyde semicarbazone as a new Jack bean urease inhibitor

A new inhibitor of jack bean urease, 2-hydroxy-1-naphthaldehyde semicarbazone, was synthesized and employed to investigate the inhibitory mechanism of HNDSC on jack bean urease by kinetic and fluorescence titration assay, and its antibacterial activities were also investigated.

Andrographolide sodium bisulphite-induced inactivation of urease: inhibitory potency, kinetics and mechanism

BACKGROUND

The inhibitory effect of andrographolide sodium bisulphite (ASB) on jack bean urease (JBU) and Helicobacter pylori urease (HPU) was performed to elucidate the inhibitory potency, kinetics and mechanism of inhibition in 20 mM phosphate buffer, pH 7.0, 2 mM EDTA, 25 °C.

METHODS

The ammonia formations, indicator of urease activity, were examined using modified spectrophotometric Berthelot (phenol-hypochlorite) method. The inhibitory effect of ASB was characterized with IC50 values. Lineweaver-Burk and Dixon plots for JBU inhibition of ASB was constructed from the kinetic data. SH-blocking reagents and competitive active site Ni2+ binding inhibitors were employed for mechanism study. Molecular docking technique was used to provide some information on binding conformations as well as confirm the inhibition mode.

RESULTS

The IC50 of ASB against JBU and HPU was 3.28±0.13 mM and 3.17±0.34 mM, respectively. The inhibition proved to be competitive and concentration- dependent in a slow-binding progress. The rapid formation of initial ASB-JBU complex with an inhibition constant of Ki=2.86×10(-3) mM was followed by a slow isomerization into the final complex with an overall inhibition constant of Ki*=1.33×10(-4) mM. The protective experiment proved that the urease active site is involved in the binding of ASB. Thiol reagents (L-cysteine and dithiothreithol) strongly protect the enzyme from the loss of enzymatic activity, while boric acid and fluoride show weaker protection, indicating that the active-site sulfhydryl group of JBU was potentially involved in the blocking process. Moreover, inhibition of ASB proved to be reversible since ASB-inactivated JBU could be reactivated by dithiothreitol application. Molecular docking assay suggested that ASB made contacts with the important sulfhydryl group Cys-592 residue and restricted the mobility of the active-site flap.

CONCLUSIONS

ASB was a competitive inhibitor targeting thiol groups of urease in a slow-binding manner both reversibly and concentration-dependently, serving as a promising urease inhibitor for the treatment of urease-related diseases.

Kinetics and mechanism study of competitive inhibition of jack-bean urease by baicalin

Baicalin (BA) is the principal component of Radix Scutellariae responsible for its pharmacological activity. In this study, kinetics and mechanism of inhibition by BA against jack-bean urease were investigated for its therapeutic potential. It was revealed that the IC₅₀ of BA against jack-bean urease was 2.74 ± 0.51 mM, which was proved to be a competitive and concentration-dependent inhibition with slow-binding progress curves. The rapid formation of initial BA-urease complex with an inhibition constant of K_i = 3.89 × 10⁻³ mM was followed by a slow isomerization into the final complex with an overall inhibition constant of K_i* = 1.47 × 10⁻⁴ mM. High effectiveness of thiol protectors against BA inhibition indicated that the strategic role of the active-site sulfhydryl group of the urease was involved in the blocking process. Moreover, the inhibition of BA was proved to be reversible due to the fact that urease could be reactivated by dithiothreitol but not reactant dilution. Molecular docking assay suggested that BA made contacts with the important activating sulfhydryl group Cys-592 residues and restricted the mobility of the active-site flap. Taken together, it could be deduced that BA was a competitive inhibitor targeting thiol groups of urease in a slow-binding manner both reversibly and concentration-dependently, serving as a promising urease inhibitor for treatments on urease-related diseases.

Alkaline phosphatase-polyresorcinol complex: characterization and application to seed coating

An alkaline phosphatase (EC 3.1.3.1) from Escherichia coli ATCC27257 was immobilized by copolymerization with resorcinol. The phosphatase-polyresorcinol complex synthesized retained about 74% of the original enzymatic activity. The pH and temperature profile of the immobilized and free enzyme revealed a similar behavior. Kinetic parameters were determined: K(m) and K(i) values were 2.44 and 0.423 mM, respectively, for the phosphatase-polyresorcinol complex and 1.07 and 0.069 mM, respectively, for free phosphatase. The thermal and storage stabilities of the immobilized phosphatase were higher than those of the native one. On addition to soil, free enzyme was completely inactivated in 4 days, whereas the phosphatase-polyresorcinol complex was comparatively stable. Barley seed coated with the immobilized enzyme exhibited higher rhizosphere phosphatase activity. Under pot culture conditions, an increase in the soil inorganic phosphorus was detected when the seed was encapsulated with the phosphatase-polyresorcinol complex, and a positive influence on biomass and inorganic phosphorus concentration of shoot was observed.

Jack bean urease: The effect of active-site binding inhibitors on the reactivity of enzyme thiol groups

In view of the complexity of the role of the active site flap cysteine in the urease catalysis, in this work we studied how the presence of typical active-site binding inhibitors of urease, phenylphosphorodiamidate (PPD), acetohydroxamic acid (AHA), boric acid and fluoride, affects the reactivity of enzyme thiol groups, the active site flap thiol in particular. For that the inhibitor-urease complexes were prepared with excess inhibitors and had their thiol groups titrated with DTNB. The effects observed were analyzed in terms of the structures of the inhibitor-urease complexes reported in the literature. We found that the effectiveness in preventing the active site cysteine from the modification by disulfides, varied among the inhibitors studied, even though they all bind to the active site. The variations were accounted for by different extents of geometrical distortion in the active site that the inhibitors introduced upon binding, leaving the flap either open in AHA-, boric acid- and fluoride-inhibited urease, like in the native enzyme or closed in PPD-inhibited urease. Among the inhibitors, only PPD was found to be able to thoroughly protect the flap cysteines from the further reaction with disulfides, this apparently resulting from the closed conformation of the flap. Accordingly, in practical terms PPD may be regarded as the most suitable inhibitor for active-site protection experiments in inhibition studies of urease.

Kinetic Parameters of Urease Immobilized on Modified Acrylonitrile Copolymer Membranes in the Presence and Absence of Cu(II) Ions

Poly(acrylonitrile-methylmethacrylate-sodium vinylsulfonate) membranes were subjected to seven different chemical modifications and the amount of the newly formed groups was measured for each membrane. Urease was then covalently immobilized onto the modified membranes and the amount of bound protein was determined. The kinetic parameters V(max) and K(m) of the immobilized urease were studied under static and dynamic conditions. Results showed that the rate of the enzyme reaction was higher for the membranes modified with NH(2)OH . H(2)SO(4), NH(2)NH(2) . H(2)SO(4), NaOH + EDA and NaOH + GA + EDA. It was confirmed that the reaction rate, measured under dynamic conditions, was higher than that one determined under static conditions. The influence of Cu(II) ions, as inhibitors, on the enzyme reaction kinetics (V(i) and K(i)) was also investigated. It turned out that the most sensitive membranes towards Cu(II) were those modified with NH(2)NH(2) . H(2)SO(4), NaOH + EDA and H(2)O(2). The results initiated further investigations on the influence of other heavy metal ions (Cd(II), Zn(II), Ni(II) and Pb(II)) over urease bound to a NH(2)OH . H(2)SO(4)-modified membrane. It was found that the inhibition effect of the heavy metal ions over immobilized urease decreases in the order: Cu(II) > Cd(II) > Zn(II) > Ni(II) > Pb(II). [Diagram: see text]

Urease?glutamic dehydrogenase biosensor for screening heavy metals in water and soil samples

A screen-printed three-electrode amperometric biosensor based on urease and the nicotinamide adenine dinucleotide hydrogen (NADH)-glutamic dehydrogenase system was developed and applied to the screening of heavy metals in environmental samples. The development of an amperometric sensor for the monitoring of urease activity was feasible by coupling the urea breakdown reaction catalysed by urease to the reductive ammination of ketoglutarate catalysed by glutamic dehydrogenase (GLDH). The ammonia provided by the urea conversion is required for the conversion of ketoglutarate to glutamate with the concomitant oxidation of the NADH cofactor. NADH oxidation is monitored amperometrically at 0.3 V (vs. Ag/AgCl) after urease immobilization onto the screen-printed three-electrode configuration. Immobilization of urease on the surface of screen-printed electrodes was performed by entrapment in alginate gel and adsorption on the electrode in a nafion film. Low sensitivity to inactivation by metals was recorded after urease entrapment in alginate gel with detection limits of 2.9 and 29.8 mg L(-1) for Hg(II) and Cu(II), respectively. The use of the negatively charged nafion film created a more concentrated environment of cations in proximity to the enzyme, thus enhancing the urease inhibition when compared to gel entrapment. The calculated detection limits were 63.6 and 55.3 microg L(-1) for Hg(II) and Cu(II), respectively, and 4.3 mg L(-1) for Cd(II). A significant urease inactivation was recorded in the presence of trace amounts of metals (microg L(-1)) when the enzyme was used free in solution. Analysis of water and soil samples with the developed nafion-based sensor produced inhibition on urease activity according to their metal contents. The obtained results were in agreement with the standard methods employed for sample analysis. Nevertheless, the use of the amperometric assay (with free urease) proved more feasible for the screening of trace amounts of metals in polluted samples.