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

Synthesis and anti-ureolitic activity of Biginelli adducts derived from formylphenyl boronic acids

Urease is a metalloenzyme that contains two Ni(II) ions in its active site and catalyzes the hydrolysis of urea into ammonia and carbon dioxide. The development of effective urease inhibitors is crucial not only for mitigating nitrogen losses in agriculture but also for offering an alternative treatment against infections caused by resistant pathogens that utilize urease as a virulence factor. This study focuses on synthesizing and investigating the urease inhibition potential of Biginelli Adducts bearing a boric acid group. An unsubstituted or hydroxy-substituted boronic group in the Biginelli adducts structure enhances the urease inhibitory activity. Biophysical and kinetics studies revealed that the best Biginelli adduct (4e; IC50 = 132 ± 12 µmol/L) is a mixed inhibitor with higher affinity to the urease active site over an allosteric one. Docking studies confirm the interactions of 4e with residues essential for urease activity and demonstrate its potential to coordinate with the nickel atoms through the oxygen atoms of carbonyl or boronic acid groups. Overall, the Biginelli adduct 4e shows great potential as an additive for developing enhanced efficiency fertilizers and/or for medical applications.

Chlorogenic acid, caffeic acid and luteolin from dandelion as urease inhibitors: insights into the molecular interactions and inhibition mechanism

BACKGROUND

Dandelion contains hundreds of active compounds capable of inhibiting urease activity, but the individual compounds have not yet been fully identified, and their effects and underlying mechanisms are not clear. The present study aimed to screen the urease inhibition active compounds of dandelion by urease inhibitory activity evaluation HPLC-tandem mass spectrometry analysis, their mechanism of urease inhibition by polyphenols was explored using enzyme kinetic studies via Lineweaver-Burk plots. Other investigations included isothermal titration calorimetry and surface plasmon resonance sensing, fluorescence quenching experiments, and single ligand molecular docking and two-ligand simultaneous docking techniques.

RESULTS

The results indicated that the ethyl acetate fraction of dandelion flower exhibited the greatest inhibition (lowest IC50 0.184 ± 0.007 mg mL-1). Chlorogenic acid, caffeic acid and luteolin could be effective urease inhibitors that acted in a non-competitive inhibition manner. Individually, chlorogenic acid could not only fast bind to urease, but also dissociate rapidly, whereas luteolin might interact with urease with the weakest affinity. The chlorogenic acid-caffeic acid combination exhibited an additive effect in urease inhibition. However, the chlorogenic acid-luteolin and caffeic acid-luteolin combinations exhibited antagonistic effects, with the caffeic acid-luteolin combination showing greater antagonism.

CONCLUSION

The present study reveals that chlorogenic acid, caffeic acid and luteolin are major bioactive compounds for urease inhibition, indicating the molecular mechanisms. The antagonistic effects were observed between luteolin and chlorogenic acid/caffeic acid, and the interactions of the catalytic site and flap may account for the antagonistic effects. © 2024 Society of Chemical Industry.

Synthesis of 2-aminothiazole sulfonamides as potent biological agents: Synthesis, structural investigations and docking studies

A simplified synthetic approach involving sulfonylation followed by amino group alkylation produced new 2-aminothiazole derivatives. UV/Vis, infrared, and NMR spectroscopies confirmed their structures. Compounds 36, 22, 34, and 35 showed strong inhibition against Jack bean and Bacillus Pasteurii urease, with IC50 values from 14.06 to 20.21 μM/mL. Compounds 20, 26, 21, 29, 30, 31, and 32 exhibited potent inhibitory effects against α-glucosidase and α-amylase, with IC50 values between 20.34 and 37.20 μM/mL. Compounds 33, 26, and 27 demonstrated potent DPPH scavenging, with IC50 values around 34.4-39.2 μM/mL. FMO analysis showed compounds 21, 22, 24, and 25 having parallel aromatic ring systems due to π cloud interactions, while compounds 32 and 38 had distinct electronic density distributions. Compound 22 had HOMO and LUMO energy gaps of 5.805 eV, with bromo and fluoro substitutions in compounds 21 and 24 slightly increasing the gaps to 6.089 eV and 6.078 eV, respectively. Nitro groups in compounds 25 and 32 reduced the gaps to 0.384 eV and 1.187 eV. All compounds demonstrated high gastrointestinal absorption, non-permeability to the blood-brain barrier, and optimal skin permeation (Log Kp between -5.83 and -6.54 cm/s). Compounds 22, 24, and 38 had promising QED scores of 0.719, 0.707, and 0.860, respectively, with synthetic accessibility scores from 2.057 to 2.517. ADMET predictions indicated minimal toxicity, cardiovascular safety, and significant inhibitory potential for CYP enzymes. Strong in silico binding affinities (binding energies -5.75 to -7.63 kcal/mol) and metabolic stability suggest these derivatives are promising candidates for further drug development.

Synergizing structure and function: Cinnamoyl hydroxamic acids as potent urease inhibitors

The current investigation encompasses the structural planning, synthesis, and evaluation of the urease inhibitory activity of a series of molecular hybrids of hydroxamic acids and Michael acceptors, delineated from the structure of cinnamic acids. The synthesized compounds exhibited potent urease inhibitory effects, with IC50 values ranging from 3.8 to 12.8 µM. Kinetic experiments unveiled that the majority of the synthesized hybrids display characteristics of mixed inhibitors. Generally, derivatives containing electron-withdrawing groups on the aromatic ring demonstrate heightened activity, indicating that the increased electrophilicity of the beta carbon in the Michael Acceptor moiety positively influences the antiureolytic properties of this compounds class. Biophysical and theoretical investigations further corroborated the findings obtained from kinetic assays. These studies suggest that the hydroxamic acid core interacts with the urease active site, while the Michael acceptor moiety binds to one or more allosteric sites adjacent to the active site.

Screen-Printed Silver/Silver Chloride Electrodes Inhibit Alcohol Oxidase Activity

Silver/silver chloride (Ag/AgCl) is ubiquitous in the field of electrochemical biosensing due to its suitability as a reference electrode material. However, we recently discovered that screen-printed Ag/AgCl ink has a detrimental effect on Alcohol Oxidase enzyme stability. We performed an optical absorbance assay to isolate the interaction of enzyme and electrode to discover a surprisingly strong inhibition effect. The halftime of enzymatic activity was reduced from nearly 1 week in buffer to 10 h in the presence of the Ag/AgCl electrode. We expect this discovery to have broad implications on enzymatic biosensors that use Ag/AgCl as reference electrode material.

Cephalosporin as Potent Urease and Tyrosinase Inhibitor: Exploration through Enzyme Inhibition, Kinetic Mechanism, and Molecular Docking Studies

In present study, eleven cephalosporin drugs were selected to explore their new medically important enzyme targets with inherited safety advantage. To this end, selected drugs with active ingredient, cefpodoxime proxetil, ceftazidime, cefepime, ceftriaxone sodium, cefaclor, cefotaxime sodium, cefixime trihydrate, cephalexin, cefadroxil, cephradine, and cefuroxime, were evaluated and found to have significant activity against urease (IC50 = 0.06 ± 0.004 to 0.37 ± 0.046 mM) and tyrosinase (IC50 = 0.01 ± 0.0005 to 0.12 ± 0.017 mM) enzymes. Urease activity was lower than standard thiourea; however, tyrosinase activity of all drugs outperforms (ranging 6 to 18 times) the positive control: hydroquinone (IC50 = 0.18 ± 0.02 mM). Moreover, the kinetic analysis of the most active drugs, ceftriaxone sodium and cefotaxime sodium, revealed that they bind irreversibly with both the enzymes; however, their mode of action was competitive for urease and mixed-type, preferentially competitive for tyrosinase enzyme. Like in vitro activity, ceftriaxone sodium and cefotaxime sodium docking analysis showed their considerable binding affinity and significant interactions with both urease and tyrosinase enzymes sufficient for downstream signaling responsible for observed enzyme inhibition in vitro, purposing them as potent candidates to control enzyme-rooted obstructions in future.

Coptisine: A natural plant inhibitor of ruminal bacterial urease screened by molecular docking

Inhibition of ruminal bacterial urease activity could slow down the decomposition of urea to ammonia, which would lead to a decrease in urea synthesis in the liver and urea-N emission in the urine. In order to find a rumen bacterial urease specific inhibitor that is environmentally friendly, we used the homology model of rumen bacterial urease as the target to screen natural compounds from plants by molecular docking. The screening results showed that coptisine had the most potential to inhibit the activity of rumen bacterial urease with an IC₅₀ of 2.45 μM, which was superior to the traditional inhibitor acetohydroxamic acid. The enzyme kinetics results indicated coptisine was mixed type inhibitor of rumen bacterial urease with a K_i value of 0.68 μM. Coptisine significantly decreased the release of NH₃ and decomposition of urea and improved microbial fermentation in a rumen fermentation system in vitro. Thiol-containing compounds or boric acid significantly decreased the inhibitory capacity of coptisine toward rumen bacterial urease, which indicated that coptisine could interact with both the urease active center Ni and amino acid residues possessing sulfhydryl groups in the flap area. The molecular docking results showed that coptisine acted as the metal acceptor for one nickel ion in the active site, and formed hydrogen bonds with the amino acid residues His320 and His362, which were located in the active site and flap region, respectively. These findings emphasized the potential role of coptisine in reducing nitrogen emissions that originate from ruminants by regulating rumen bacterial urease activity.

Inactivation of Jack Bean Urease by Nitidine Chloride from Zanthoxylum nitidum: Elucidation of Inhibitory Efficacy, Kinetics and Mechanism

Urease is a metalloenzyme that catalyzes the hydrolysis of urea into ammonia and carbon dioxide, which has a negative impact on human health and agriculture. In this study, the inactivation of jack bean urease by nitidine chloride (NC) was investigated to elucidate the inhibitory effect, kinetics, and underlying mechanism of action. The results showed that NC acted as a concentration- and time-dependent inhibitor with an IC₅₀ value of 33.2 ± 4.8 μM and exhibited a similar inhibitory effect to acetohydroxamic acid (IC₅₀ = 31.7 ± 5.8 μM). Further kinetic analysis demonstrated that NC was a slow-binding and non-competitive inhibitor for urease. Thiol-blocking reagents (dithiothreitol, glutathione, and l-cysteine) significantly retarded urease inactivation, while Ni²⁺ competitive inhibitors (boric acid and sodium fluoride) synergetically suppressed urease with NC, suggesting that the active site sulfhydryl groups were possibly obligatory for NC blocking urease. Molecular docking simulation further argued its inhibition mechanism. Additionally, NC-induced deactivation of urease was verified to be reversible since the inactivated enzyme could be reactivated by glutathione. Taking together, NC was a non-competitive inhibitor targeting the thiol group at the active site of urease with characteristics of concentration dependence, reversibility, and slow binding, serving as a promising novel urease suppressant.

A review: antimicrobial properties of several medicinal plants widely used in Traditional Chinese Medicine

Due to the dramatic increase in the use of antibiotics and growing health threat of bacterial resistance to many commonly used antibiotics, many studies have been directed at developing new and effective antibacterial compounds, among which many new, natural, and effective antibacterial compounds discovered from medicinal plants have drawn great interest and raised new hope for treating the challenges of antibiotic resistance. This review aimed to summarize the most important and widely used medicinal plants that were reported to have antibacterial activities. A general literature search from 2010 to 2020 was conducted using different databases, including Science Direct, Web of Science, and PubMed. According to the literature, three medicinal plants with outstanding antibacterial activities, Taraxacum officinale, Coptis Rhizome, and Scutellaria baicalensis, were screened and reviewed by prioritization. The extraction methods, antibacterial activities of different parts of plants or the plant-derived compounds, spectra of antibacterial activities, and toxicity were described, respectively. However, the antibacterial activities of the extracts or pure compounds as reported in the reviewed literature were mostly based on in vitro assays, and moreover, the deeper antibacterial mechanisms have not been elucidated clearly. Therefore, further studies are required in the fields of purification and identification of the antibacterial compounds, its mechanisms of action, and synergistic effects in combination with other antibacterial drugs, which may be helpful in the development of new antibacterial drugs.

Paper-based analytical device with colorimetric detection for urease activity determination in soils and evaluation of potential inhibitors

Urease is an enzyme associated with the degradation of urea, an important nitrogen fertilizer in agriculture. Thus, this current report describes the use of a paper-based analytical device (UrePAD) designed to contain a microzone array for colorimetric determination of urease activity in soils in the absence/presence of potential enzyme inhibitors. The UrePAD can be used at the point-of-need (point-of-care), and it offers advantages such as low cost, simplicity in handling, low sample/reagent volumes, and no use of toxic reagents. The acid-base indicator phenol red was used to monitor the urea hydrolysis reaction catalyzed by urease in the evaluated systems. The images were digitalized in a bench scanner, and the analysis was performed using Corel Draw X8 software. The device offered a LOD of 0.10 U mL^-1 with linearity between 0.25 and 4.0 U mL^-1 and a relative standard deviation ≤ 1.38%. UrePAD was tested in four soil samples of different characteristics and with eight urease inhibitors of varied classes. The results obtained through the proposed device did not differ statistically (95% confidence interval) from those employing the classic method based on the Berthelot reaction, thus indicating that UrePAD was effective for determining urease activity and screening inhibitors, besides showing the capacity to simplify fieldwork involving the application of urea in the soil.

Discovery of Novel Dihydropyrimidine and hydroxamic acid hybrids as potent Helicobacter pylori Urease inhibitors

Two novel series of Dihydropyrimidine-hydroxamic acid hybrids (4a-4l and 5a-5l) were designed, synthesized and evaluated for in vitro Helicobacter pylori urease inhibition. In vitro enzyme inhibition screening led to the discovery of three potent urease inhibitors 2-[[4-(4-hydroxy phenyl)-6-oxo-1,6-dihydropyrimidine-2-yl]-amino]-N-hydroxy acetamide (4g), 2-[[4-(4-chloro phenyl)-6-oxo-1,6-dihydropyrimidine-2-yl]-amino]-N-hydroxy acetamide (4b) and 3-[[4-(3-methoxy phenyl)-6-oxo-1,6-dihydropyrimidine-2-yl]-amino]-N-hydroxy propanamide (5l). Compound 4g showed excellent urease inhibition with IC₅₀ value of 14 ± 1 nM, indicated by its strong interactions with both metallic Ni⁺⁺ ions, Gly279, His221, Ala365, Asp362, Asn168, Arg338 and His322 residues of the active site of urease. Further, compounds 4b and 5l displayed very good activity with IC₅₀ value of 0.082 ± 0.004 µM and 0.14 ± 0.013 µM respectively compared to standard Acetohydroxamic acid (IC₅₀ - 27.4 ± 1.2 µM). Kinetic studies revealed that a mixed inhibition with both competitive and non-competitive aspects is involved in the urease inhibition mechanism. The in vitro urease inhibition results were supported by molecular docking studies. Collectively, this study indicates that 4g could be considered as promising lead molecule that can be further developed as a potent drug molecule for the treatment of Helicobacter pylori caused gastritis for further studies.

A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking

Inhibition of the urease activity of ruminal microbiota is not only beneficial for increasing dietary and endogenic urea-N utilization efficiency in ruminants but also might be applicable for the preservation of nitrogen fertilizer in soil and treatment of gastrointestinal and urinary tract infections caused by ureolytic bacteria. To discover urease inhibitors to efficiently target ruminal microbiota, the identified ruminal microbial metagenomic urease gene was used to construct a homology model to virtually screen urease inhibitors from the ChemDiv database by molecular docking. The GMQE and QMEAN values of the homology model were 0.85 and −0.37, respectively, indicating a good model quality. The inhibition effect of the screened urease inhibitor for ruminal urea degradation was assessed by ruminal microbial fermentation in vitro. The toxic effect of the candidate inhibitor was performed using gut Caco-2 cells in vitro. The results showed that compound 3-[1-[(aminocarbonyl)amino]-5-(4-methoxyphenyl)-1H-pyrrol-2-yl] propanoic acid (ChemDiv_ID: 6238-0047, IC₅₀ = 65.86 μM) was found to be the most effective urease inhibitor among the candidate compounds. Compound 6238-0047 significantly lowered the amount of urea degradation and ammonia production in ruminal microbial fermentation. The 24 h degradation rate of compound 6238-0047 in ruminal microbial fermentation was 3.32%–16.00%. In addition, compound 6238-0047 (10–100 μM) had no significant adverse effect on the cell viability of Caco-2 cells. Molecular docking showed that compound 6238-0047 could interact with Asp359 in the active site and Cys318 in the flap region by the hydrogen bond and Pi-Alkyl interaction, respectively. Compound 6238-0047 could be used as a novel inhibitor for decreasing the urease activity of ruminal microbiota.

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.

Synthesis, Biological Evaluation and Molecular Docking of Deferasirox and Substituted 1,2,4-Triazole Derivatives as Novel Potent Urease Inhibitors: Proposing Repositioning Candidate

A series of new deferasirox derivatives were synthesized through the reaction of monosubstituted hydrazides with 2-(2-hydroxyphenyl)-4H-benzo[e][1,3]oxazin-4-one. For the first time, deferasirox and some of its derivatives were evaluated for their in vitro inhibitory activity against Jack bean urease. The potencies of the members of this class of compounds are higher than that of acetohydroxamic acid. Two compounds, bearing tetrazole and hydrazine derivatives (bioisoester of carboxylate group), represented the most potent urease inhibitory activity with IC₅₀ values of 1.268 and 3.254 μm, respectively. In silico docking studies were performed to delineate possible binding modes of the compounds with the enzyme, urease. Docking analysis suggests that the synthesized compounds were anchored well in the catalytic site and extending to the entrance of binding pocket and thus restrict the mobility of the flap by interacting with its crucial amino acid residues, CME592 and His593. The overall results of urease inhibition have shown that these target compounds can be further optimized and developed as a lead skeleton for the discovery of novel urease inhibitors.

Insight into the inhibitory effects of Zanthoxylum nitidum against Helicobacter pylori urease and jack bean urease: Kinetics and mechanism

ETHNOPHARMACOLOGICAL RELEVANCE

Zanthoxylum nitidum (Roxb.) DC. is a traditional Chinese medicine characterised by anti-inflammatory and anti-Helicobacter pylori, which is widely used to treat H. pylori-induced gastric disease in China. However, the underlying mechanism related to its anti-H. pylori activity remains unclear. Urease plays a crucial role in the colonisation and survival of H. pylori.

AIM OF THE STUDY

The root aqueous extract of Z. nitidum against H. pylori urease (HPU) and jack bean urease (JBU) was investigated to illuminate the inhibitory potency, kinetics and potential mechanism.

MATERIALS AND METHODS

Z. nitidum components were determined by UPLC. The enzyme inhibitory effects of Z. nitidum were examined using modified spectrophotometric Berthelot (phenol-hypochlorite) method. Urease inhibition kinetics were determined by Lineweaver-Burk plots. Sulfhydryl group reagents and Ni²⁺-binding inhibitors were used in the mechanism study. Moreover, the molecular docking technique was used to investigate the binding conformations of the main compounds of Z. nitidum on Urease.

RESULTS

According to UPLC results, the major components of Z. nitidum were magnoflorine, sanguinarine, nitidine chloride, chelerythrine, skimmianine and L-Sesamin. Z. nitidum has higher enzyme inhibitory activity on HPU (IC₅₀ = 1.29 ± 0.10 mg/mL) than on JBU (IC₅₀ = 2.04 ± 0.27 mg/mL). Enzyme inhibitory kinetic analysis revealed that the type of Z. nitidum inhibition against HPU was a slow-binding and mixed-type, whereas a slow-binding and non-competitive type inhibited JBU. Further mechanism study indicated that the active site of sulfhydryl group might be the target of inhibition by Z. nitidum. The molecular docking study indicated that the above six main components of Z. nitidum exhibited stronger affinity to HPU than to JBU through interacting with the key amino acid residues located on the mobile flap or interacting with the active site Ni²⁺. Results indicated that these components are potential active ingredients directed against urease.

CONCLUSIONS

Z. nitidum inactivated urease in a concentration-dependent manner through slow-binding inhibition and binding to the urease active site sulfhydryl group. Our investigation might provide experimental evidence for the traditional application of Z. nitidum in the treatment of H. pylori-associated gastric disorders.

Intrinsic enzymatic properties modulate the self-propulsion of micromotors

Bio-catalytic micro- and nanomotors self-propel by the enzymatic conversion of substrates into products. Despite the advances in the field, the fundamental aspects underlying enzyme-powered self-propulsion have rarely been studied. In this work, we select four enzymes (urease, acetylcholinesterase, glucose oxidase, and aldolase) to be attached on silica microcapsules and study how their turnover number and conformational dynamics affect the self-propulsion, combining both an experimental and molecular dynamics simulations approach. Urease and acetylcholinesterase, the enzymes with higher catalytic rates, are the only enzymes capable of producing active motion. Molecular dynamics simulations reveal that urease and acetylcholinesterase display the highest degree of flexibility near the active site, which could play a role on the catalytic process. We experimentally assess this hypothesis for urease micromotors through competitive inhibition (acetohydroxamic acid) and increasing enzyme rigidity (β-mercaptoethanol). We conclude that the conformational changes are a precondition of urease catalysis, which is essential to generate self-propulsion.

Self-propulsion of biocatalytic micro- and nanomotors is facilitated by enzymes converting substrates into products. Here, the authors show that intrinsic enzymatic properties such as conformational changes are crucial for the self-propulsion of silica microcapsules modified with urease.

Interfacing enzymes with silicon nanocrystals through the thiol-ene reaction

This study reports the preparation of functional bioinorganic hybrids, through application of the thiol-ene reaction, that exhibit catalytic activity and photoluminescent properties from enzymes and freestanding silicon nanocrystals. Thermal hydrosilylation of 1,7-octadiene and alkene-terminated poly(ethylene oxide)methyl ether with hydride-terminated silicon nanocrystals afforded nanocrystals functionalized with alkene residues and poly(ethylene oxide) moieties. These silicon nanocrystals were conjugated with representative enzymes through the photochemical thiol-ene reaction to afford bioinorganic hybrids that are dispersible and photostable in buffer, and that exhibit photoluminescence (λ_max = 630 nm) and catalytic activity. They were characterized using Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), dynamic light scattering analysis (DLS), absorption spectroscopy, steady-state and time-resolved photoluminescence spectroscopy, and pertinent enzyme activity assays. The general derivatization approach presented for interfacing enzymes with biocompatible silicon nanocrystals has far reaching implications for many applications ranging from sensors to therapeutic agents. The bioinorganic hybrids presented herein have potential applications in the chemical detection of nitrophenyl esters and urea. They can also be employed in enzyme-based theranostics as they combine long-lived silicon nanocrystal photoluminescence with substrate-specific enzymatic activity.

Coptisine-induced inhibition of Helicobacter pylori: elucidation of specific mechanisms by probing urease active site and its maturation process

In this study, we examined the anti-Helicobactor pylori effects of the main protoberberine-type alkaloids in Rhizoma Coptidis. Coptisine exerted varying antibacterial and bactericidal effects against three standard H. pylori strains and eleven clinical isolates, including four drug-resistant strains, with minimum inhibitory concentrations ranging from 25 to 50 μg/mL and minimal bactericidal concentrations ranging from 37.5 to 125 μg/mL. Coptisine’s anti-H. pylori effects derived from specific inhibition of urease in vivo. In vitro, coptisine inactivated urease in a concentration-dependent manner through slow-binding inhibition and involved binding to the urease active site sulfhydryl group. Coptisine inhibition of H. pylori urease (HPU) was mixed type, while inhibition of jack bean urease was non-competitive. Importantly, coptisine also inhibited HPU by binding to its nickel metallocentre. Besides, coptisine interfered with urease maturation by inhibiting activity of prototypical urease accessory protein UreG and formation of UreG dimers and by promoting dissociation of nickel from UreG dimers. These findings demonstrate that coptisine inhibits urease activity by targeting its active site and inhibiting its maturation, thereby effectively inhibiting H. pylori. Coptisine may thus be an effective anti-H. pylori agent.

In vitroinhibition ofHelicobacter pyloriand interaction studies of lichen natural products with jack bean urease

The interaction between lichen metabolites and jack bean urease was investigated by molecular spectroscopy at pH 7.4 and kinetics assay.

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.

Epiberberine, a natural protoberberine alkaloid, inhibits urease of Helicobacter pylori and jack bean: Susceptibility and mechanism

In our previous study, Rhizoma Coptidis extract was found to exert more potent inhibitory effect than its major component berberine towards urease from Helicobacter pylori (HPU) and jack bean (JBU). In continuation of our work, the present study was designed to further comparatively investigate the urease inhibitory activities of five major protoberberine alkaloids in Rhizoma Coptidis, namely berberine, palmatine, coptisine, epiberberine, jateorhizine to identify the bioactive constituent, and illuminate the potential mechanism of action. Results indicated that the five protoberberine alkaloids acted as concentration-dependent inactivators of urease with IC₅₀ values ranging between 3.0 and 5087μM for HPU and 2.3->10,000μM for JBU, respectively. Notably, epiberberine (EB) was found to be the most potent inhibitor against both ureases with IC₅₀ values of 3.0±0.01μM for HPU and 2.3±0.01μM for JBU, which was more effective than the standard urease inhibitor, acetohydroxamic acid (83±0.01μM for HPU and 22±0.01μM for JBU, respectively). Further kinetic analysis revealed that the type of EB inhibition against HPU was slow-binding and uncompetitive, with K_i of 10.6±0.01μM, while slow-binding and competitive against JBU with K_i of 4.6±0.01μM. Addition of thiol reagents, such as l-cysteine, glutathione and dithiothreitol, significantly abolished the inhibition, while Ni²⁺ competitive inhibitors, boric acid and sodium fluoride, synergetically inhibited urease with EB, indicating the obligatory role of the active site sulfhydryl group for the inhibition. In addition, binding of EB with the urease proved to be reversible, as about 65% and 90% enzymatic activity of HPU and JBU, respectively, could be restored by dithiothreitol application. These findings highlighted the potential role of Rhizoma Coptidis protoberberine alkaloids, especially EB, as a lead urease inhibitor in the treatment of diseases associated with ureolytic bacteria. Thus, EB had good potential for further development into a promising therapeutic approach for the treatment of urease-related diseases.

Inhibition studies of Helicobacter pylori urease with Schiff base copper(ii) complexes

Nine new copper(ii) complexes derived from various Schiff bases were prepared. Five complexes show effective urease inhibitory activities. Complex5has the most effective activity against urease, with a mixed competitive inhibition mechanism.

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.

Synthesis, structures and urease inhibitory activity of cobalt(III) complexes with Schiff bases

A series of new cobalt(III) complexes were prepared. They are [CoL(1)(py)3]·NO3 (1), [CoL(2)(bipy)(N3)]·CH3OH (2), [CoL(3)(HL(3))(N3)]·NO3 (3), and [CoL(4)(MeOH)(N3)] (4), where L(1), L(2), L(3) and L(4) are the deprotonated form of N'-(2-hydroxy-5-methoxybenzylidene)-3-methylbenzohydrazide, N'-(2-hydroxybenzylidene)-3-hydroxylbenzohydrazide, 2-[(2-dimethylaminoethylimino)methyl]-4-methylphenol, and N,N'-bis(5-methylsalicylidene)-o-phenylenediamine, respectively, py is pyridine, and bipy is 2,2'-bipyridine. The complexes were characterized by infrared and UV-Vis spectra, and single crystal X-ray diffraction. The Co atoms in the complexes are in octahedral coordination. Complexes 1 and 4 show effective urease inhibitory activities, with IC50 values of 4.27 and 0.35 μmol L(-1), respectively. Complex 2 has medium activity against urease, with IC50 value of 68.7 μmol L(-1). While complex 3 has no activity against urease. Molecular docking study of the complexes with Helicobacter pylori urease was performed.

Urease immobilized polymer hydrogel: Long-term stability and enhancement of enzymatic activity

A method has been developed in which an enzyme namely urease was immobilized inside hydrogel matrix to study the stability and enzymatic activity in room temperature (∼27-30°C). This urease coupled hydrogel (UCG) was obtained by amine-acid coupling reaction and this procedure is such that it ensured the wider opening of mobile flap of enzyme active site. A systematic comparison of urea-urease assay and the detailed kinetic data clearly revealed that the urease shows activity for more than a month when stored at ∼27-30°C in case of UCG whereas it becomes inactive in case of free urease (enzyme in buffer solution). The aqueous microenvironment inside the hydrogel, unusual morphological features and thermal behaviour were believed to be the reasons for unexpected behaviour. UCG displayed enzyme activity at basic pH and up to 60°C. UCG showed significant enhancement in activity against thermal degradation compared to free urease. In summary, this method is a suitable process to stabilize the biomacromolecules in standard room temperature for many practical uses.

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.

Enzyme Inhibitory Radicinol Derivative from Endophytic fungus Bipolaris sorokiniana LK12, Associated with Rhazya stricta

Endophytes, living inside plant tissues, play an essential role in plant growth and development, whilst producing unique bioactive secondary metabolites. In the current study, the endophytic fungus Bipolaris sorokiniana LK12 was isolated from the leaves of ethno-medicinal and alkaloidal rich Rhazya stricta. The bulk amount of ethyl acetate extract of fungus was subjected to advance column chromatographic techniques, which resulted in the isolation of a new radicinol derivative, bipolarisenol (1). It was found to be a derivative of radicinol. The structure elucidation was carried out by the combined use of 1D and 2D nuclear magnetic resonance, infrared spectroscopy, mass, and UV spectrometric analyses. The bipolarisenol was assessed for its potential role in enzyme inhibition of urease and acetyl cholinesterase (AChE). Results showed that bipolarisenol significantly inhibited the AChE activity with low IC50 (67.23 ± 5.12 µg·mL-1). Bipolarisenol inhibited urease in a dose-dependent manner with high IC50 (81.62 ± 4.61 µg·mL-1). The new compound also showed a moderate anti-lipid peroxidation potential (IC50 = 168.91 ± 4.23 µg·mL-1). In conclusion, endophytes isolated from medicinal plants possess a unique potential to be considered for future drug discovery.

Biological evaluation and molecular docking of baicalin and scutellarin as Helicobacter pylori urease inhibitors

ETHNOPHARMACOLOGICAL RELEVANCE

Baicalin and scutellarin are the principal bioactive components of Scutellaria baicalensis Georgi which has extensively been incorporated into heat-clearing and detoxification formulas for the treatment of Helicobacter pylori-related gastrointestinal disorders in traditional Chinese medicine. However, the mechanism of action remained to be defined.

AIM OF THE STUDY

To explore the inhibitory effect, kinetics and mechanism of Helicobacter pylori urease (the vital pathogenetic factor for Helicobacter pylori infection) inhibition by baicalin and scutellarin, for their therapeutic potential.

MATERIALS AND METHODS

The ammonia formations, indicator of urease activity, were examined using modified spectrophotometric Berthelot (phenol-hypochlorite) method. The inhibitory effect of baicalin and scutellarin was characterized with IC50 values, compared to acetohydroxamic acid (AHA), a well known Helicobacter pylori urease inhibitor. Lineweaver-Burk and Dixon plots for the Helicobacter pylori urease inhibition of baicalin and scutellarin was constructed from the kinetic data. SH-blocking reagents and competitive active site Ni(2+) 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. Moreover, cytotoxicity experiment using Gastric Epithelial Cells (GES-1) was evaluated.

RESULTS

Baicalin and scutellarin effectively suppressed Helicobacter pylori urease in dose-dependent and time-independent manner with IC50 of 0.82±0.07 mM and 0.47±0.04 mM, respectively, compared to AHA (IC50=0.14±0.05 mM). Structure-activity relationship disclosed 4'-hydroxyl gave flavones an advantage to binding with Helicobacter pylori urease. Kinetic analysis revealed that the types of inhibition were non-competitive and reversible with inhibition constant Ki of 0.14±0.01 mM and 0.18±0.02 mM for baicalin and scutellarin, respectively. The mechanism of urease inhibition was considered to be blockage of the SH groups of Helicobacter pylori urease, since thiol reagents (L,D-dithiothreitol, L-cysteine and glutathione) abolished the inhibitory action and competitive active site Ni(2+) binding inhibitors (boric acid and sodium fluoride) carried invalid effect. Molecular docking study further supported the structure-activity analysis and indicated that baicalin and scutellarin interacted with the key residues Cys321 located on the mobile flap through S-H·π interaction, but did not interact with active site Ni(2+). Moreover, Baicalin (at 0.59-1.05 mM concentrations) and scutellarin (at 0.23-0.71 mM concentrations) did not exhibit significant cytotoxicity to GES-1.

CONCLUSIONS

Baicalin and scutellarin were non-competitive inhibitors targeting sulfhydryl groups especially Cys321 around the active site of Helicobacter pylori urease, representing potential to be good candidate for future research as urease inhibitor for treatment of Helicobacter pylori infection. Furthermore, our work gave additional scientific support to the use of Scutellaria baicalensis in traditional Chinese medicine (TCM) to treat gastrointestinal disorders.

Identifying Thermal and pH Stability of Thiols Compound in Garlic Extract

Thiosulfinates are a major compound found in most allium plant. Garlic, an allium species shows its potential to inhibit microbial and enzyme activity. The usage of garlic is widely known especially in the agriculture field. Thiosulfinates are formed by reaction of alliinase enzyme from their respective S-alk(en)yl cysteine sulfoxide after the crushing process of the garlic cloves. The stability of the garlic extract has been tested at variations of temperatures and pH values at different incubation time in terms of concentration (mM). After consecutive 4 hour incubation, thiols show higher concentration at temperature 30-35°C. The minimum concentration shows 22% reduction from the original thiols reading. Meanwhile, pH values of 2 (acidic) at 35°C gives higher thiols concentration compared to other conditions.