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1.
Nat Commun ; 15(1): 3919, 2024 May 09.
Article in English | MEDLINE | ID: mdl-38724503

ABSTRACT

Biological macromolecules can condense into liquid domains. In cells, these condensates form membraneless organelles that can organize chemical reactions. However, little is known about the physical consequences of chemical activity in and around condensates. Working with model bovine serum albumin (BSA) condensates, we show that droplets swim along chemical gradients. Active BSA droplets loaded with urease swim toward each other. Passive BSA droplets show diverse responses to externally applied gradients of the enzyme's substrate and products. In all these cases, droplets swim toward solvent conditions that favor their dissolution. We call this behavior "dialytaxis", and expect it to be generic, as conditions which favor dissolution typically reduce interfacial tension, whose gradients are well-known to drive droplet motion through the Marangoni effect. These results could potentially suggest alternative physical mechanisms for active transport in living cells, and may enable the design of fluid micro-robots.


Subject(s)
Serum Albumin, Bovine , Serum Albumin, Bovine/chemistry , Serum Albumin, Bovine/metabolism , Animals , Urease/metabolism , Urease/chemistry , Solubility , Cattle , Solvents/chemistry , Surface Tension
2.
Int J Biol Macromol ; 267(Pt 2): 131286, 2024 May.
Article in English | MEDLINE | ID: mdl-38583851

ABSTRACT

Polymer-based nanomotors are attracting increasing interest in the biomedical field due to their microscopic size and kinematic properties which support overcoming biological barriers, completing cellular uptake and targeted blasting in limited spaces. However, their applications are limited by the complex viscous physiological environment and lack of sufficient biocompatibility. This manuscript firstly reports a natural melanin nano-missile of MNP@HA-EDA@Urease@AIE PS (MHUA) based on photothermally accelerated urease-driven to achieve chemodrug-free phototherapy. Compared to conventional nano-missiles that only provide driving force, this photothermally accelerated urease-driven nanomotor is independent of chemodrug to maximise biocompatibility, and achieve ideal therapeutic effect through targeted PTT/PDT. In particular, the thermal effect can not only boost the catalytic activity of urease but also achieve ideally anti-tumor effect. In addition, guided by and AIE PS, the nanomotor can generate 1O2 to achieve PDT and be traced in real time serving as an effective fluorescent bio-radar for intracellular self-reporting during cancer treatment. Finally, the targeting ability of MUHA is provided by hyaluronan. Taken together, this MHUA platform provides a simple and effective strategy for target/fluorescence radar detective-guided PTT/PDT combination, and achieves good therapeutic results without chemodrug under thermal accelerated strategy, providing a new idea for the construction of chemodrug-free nanomotor-therapy system.


Subject(s)
Hyaluronic Acid , Melanins , Urease , Humans , Cell Line, Tumor , Decapodiformes , Hyaluronic Acid/chemistry , Melanins/chemistry , Nanoparticles/chemistry , Phototherapy/methods , Urease/chemistry , Urease/metabolism , Animals
3.
J Hazard Mater ; 470: 134210, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38581876

ABSTRACT

Modern metallurgical and smelting activities discharge the lead-containing wastewater, causing serious threats to human health. Bacteria and urease applied to microbial-induced carbonate precipitation (MICP) and enzyme-induced carbonate precipitation (EICP) are denatured under high Pb2+ concentration. The nano-hydroxyapatite (nHAP)-assisted biomineralization technology was applied in this study for Pb immobilization. Results showed that the extracellular polymers and cell membranes failed to secure the urease activity when subjected to 60 mM Pb2+. The immobilization efficiency dropped to below 50% under MICP, whereas it due to a lack of extracellular polymers and cell membranes dropped to below 30% under EICP. nHAP prevented the attachment of Pb2+ either through competing with bacteria and urease or promoting Ca2+/Pb2+ ion exchange. Furthermore, CO32- from ureolysis replaced the hydroxyl (-OH) in hydroxylpyromorphite to encourage the formation of carbonate-bearing hydroxylpyromorphite of higher stability (Pb10(PO4)6CO3). Moreover, nHAP application overcame an inability to provide nucleation sites by urease. As a result, the immobilization efficiency, when subjected to 60 mM Pb2+, elevated to above 80% under MICP-nHAP and to some 70% under EICP-nHAP. The findings highlight the potential of applying the nHAP-assisted biomineralization technology to Pb-containing water bodies remediation.


Subject(s)
Biomineralization , Durapatite , Lead , Urease , Water Pollutants, Chemical , Durapatite/chemistry , Lead/chemistry , Urease/metabolism , Urease/chemistry , Water Pollutants, Chemical/chemistry , Water Purification/methods , Carbonates/chemistry , Environmental Restoration and Remediation/methods
4.
Int J Mol Sci ; 25(8)2024 Apr 13.
Article in English | MEDLINE | ID: mdl-38673888

ABSTRACT

Urease, a pivotal enzyme in nitrogen metabolism, plays a crucial role in various microorganisms, including the pathogenic Helicobacter pylori. Inhibiting urease activity offers a promising approach to combating infections and associated ailments, such as chronic kidney diseases and gastric cancer. However, identifying potent urease inhibitors remains challenging due to resistance issues that hinder traditional approaches. Recently, machine learning (ML)-based models have demonstrated the ability to predict the bioactivity of molecules rapidly and effectively. In this study, we present ML models designed to predict urease inhibitors by leveraging essential physicochemical properties. The methodological approach involved constructing a dataset of urease inhibitors through an extensive literature search. Subsequently, these inhibitors were characterized based on physicochemical properties calculations. An exploratory data analysis was then conducted to identify and analyze critical features. Ultimately, 252 classification models were trained, utilizing a combination of seven ML algorithms, three attribute selection methods, and six different strategies for categorizing inhibitory activity. The investigation unveiled discernible trends distinguishing urease inhibitors from non-inhibitors. This differentiation enabled the identification of essential features that are crucial for precise classification. Through a comprehensive comparison of ML algorithms, tree-based methods like random forest, decision tree, and XGBoost exhibited superior performance. Additionally, incorporating the "chemical family type" attribute significantly enhanced model accuracy. Strategies involving a gray-zone categorization demonstrated marked improvements in predictive precision. This research underscores the transformative potential of ML in predicting urease inhibitors. The meticulous methodology outlined herein offers actionable insights for developing robust predictive models within biochemical systems.


Subject(s)
Enzyme Inhibitors , Machine Learning , Urease , Urease/antagonists & inhibitors , Urease/chemistry , Urease/metabolism , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Helicobacter pylori/enzymology , Helicobacter pylori/drug effects , Algorithms , Humans
5.
ACS Sens ; 9(4): 2031-2042, 2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38593209

ABSTRACT

Surface-enhanced Raman scattering (SERS) technology, as an important analytical tool, has been widely applied in the field of chemical and biomedical sensing. Automated testing is often combined with biochemical analysis technologies to shorten the detection time and minimize human error. The present SERS substrates for sample detection are time-consuming and subject to high human error, which are not conducive to the combination of SERS and automated testing. Here, a novel honeycomb-inspired SERS microarray is designed for large-area automated testing of urease in saliva samples to shorten the detection time and minimize human error. The honeycomb-inspired SERS microarray is decorated with hexagonal microwells and a homogeneous distribution of silver nanostars. Compared with the other four common SERS substrates, the optimal honeycomb-inspired SERS microarray exhibits the best SERS performance. The RSD of 100 SERS spectra continuously collected from saliva samples is 6.56%, and the time of one detection is reduced from 5 min to 10 s. There is a noteworthy linear relationship with a R2 of 0.982 between SERS intensity and urease concentration, indicating the quantitative detection capability of the urease activity in saliva samples. The honeycomb-inspired SERS microarray, combined with automated testing, provides a new way in which SERS technology can be widely used in biomedical applications.


Subject(s)
Saliva , Silver , Spectrum Analysis, Raman , Urease , Urease/chemistry , Saliva/chemistry , Saliva/enzymology , Spectrum Analysis, Raman/methods , Humans , Silver/chemistry , Metal Nanoparticles/chemistry , Microarray Analysis
6.
J Am Chem Soc ; 146(18): 12664-12671, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38587543

ABSTRACT

Here, we report DNA-based synthetic nanostructures decorated with enzymes (hereafter referred to as DNA-enzyme swimmers) that self-propel by converting the enzymatic substrate to the product in solution. The DNA-enzyme swimmers are obtained from tubular DNA structures that self-assemble spontaneously by the hybridization of DNA tiles. We functionalize these DNA structures with two different enzymes, urease and catalase, and show that they exhibit concentration-dependent movement and enhanced diffusion upon addition of the enzymatic substrate (i.e., urea and H2O2). To demonstrate the programmability of such DNA-based swimmers, we also engineer DNA strands that displace the enzyme from the DNA scaffold, thus acting as molecular "brakes" on the DNA swimmers. These results serve as a first proof of principle for the development of synthetic DNA-based enzyme-powered swimmers that can self-propel in fluids.


Subject(s)
Catalase , DNA , Urease , DNA/chemistry , DNA/metabolism , Urease/chemistry , Urease/metabolism , Catalase/chemistry , Catalase/metabolism , Nanostructures/chemistry , Biocatalysis , Hydrogen Peroxide/chemistry , Hydrogen Peroxide/metabolism
7.
Spectrochim Acta A Mol Biomol Spectrosc ; 315: 124271, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38613899

ABSTRACT

As an important biomarker for renal related diseases, detection of urea is playing a vital role in human biofluids on clinical diagnosis concern. In this work, a synthetic salicyaldehyde based imine fluorophore was synthesized using sonication method and conjugated with urease which was used as fluorescent biosensor for the detection of urea in serum samples. This enzyme based biosensor has shown a good selectivity and sensitivity towards urea with the linear range from 2 to 80 mM and the detection limit of 73 µM. The sensing response obtain is highly agreeing with existing analytical technique for urea detection which strongly recommends this biosensor for clinical application.


Subject(s)
Biosensing Techniques , Urea , Urease , Humans , Urea/analysis , Urea/blood , Biosensing Techniques/methods , Urease/chemistry , Urease/metabolism , Limit of Detection , Fluorometry/methods , Spectrometry, Fluorescence/methods , Fluorescent Dyes/chemistry , Enzymes, Immobilized/chemistry , Enzymes, Immobilized/metabolism
8.
Int J Biol Macromol ; 265(Pt 2): 131039, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38518938

ABSTRACT

In our present work, an explicit crosslinked thermo-responsive hydrogel platform has been developed, by using polyacrylamide (PAAm), poly(2-hydroxyethyl methacrylate) (PHEMA) and poly(cyclohexyl methacrylate) (PCHMA), and then coupled with urease to yield bioconjugates (BCs). Synergic effect of these polymer units provides thermoresponsive nature, optimum crosslinking with desired swelling behaviour, and stability and improved catalytic to Urease in the resultant BCs. Synthesis of the terpolymer has been achieved by employing HEMA (monomer as well as crosslinker), instead of using the conventional crosslinkers, through free radical solution polymerization technique. Various grades of TRPUBs have been fabricated by varying HEMA and CHMA contents while keeping fixed amounts of AAm. Further, the structural analysis of BCs has been done by fourier transform infra-red spectroscopic study and their thermal stabilities have been studied by thermogravimetric analysis. Urea present in TRPUBs has beenanalysed for its hydrolysis atdifferent temperatures viz., 25 °C, 45 °C and 70 °C. Further, the effect of crosslinking, temperature and reaction time on catalytic activities of TRPUBs has been studied. TRPUBs grades have showna maximum swelling capacity up to 5200 %; excellent catalytic activity even at 70 °C; and 85 % activity retention after 18 days storage in buffer medium.


Subject(s)
Acrylic Resins , Hydrogels , Urease , Hydrogels/chemistry , Urease/chemistry , Methacrylates/chemistry , Polyhydroxyethyl Methacrylate/chemistry , Acrylamides
9.
Environ Sci Pollut Res Int ; 31(16): 24525-24535, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38443533

ABSTRACT

At present, microbial dust suppressants based on microbial communities lack necessary systematic analysis of factors affecting dust suppression performance. Therefore, in this study, the response surface curve method was used to optimize the culture conditions for enrichment of urease-producing microorganisms from activated sludge. The results indicated that when urea = 9.67 g L-1, NH4Cl = 5.21 g L-1, and pH = 9.57, the maximum urease activity of urease-producing microbial community (UPMC) was 8.22 mM min-1. The UPMC under optimized culture conditions reached a mineralization rate of 98.8% on the 1st day of mineralization. Ureolysis is one of the biological mechanisms that trigger microbial mineralization with the consequent effect of dust suppression. The analysis of microbial community structure indicated that the urease-producing bacteria Sporosarcina sp. had the highest abundance at the genus level in the microbial-based dust suppressant compound. Jeotgalicoccus sp. plays an important role in improving and maintaining the stability of urease. In addition, the optimal UPMC had low pathogenicity, which is extremely attractive for the safe application of microbial dust suppressants.


Subject(s)
Calcium Carbonate , Dust , Urease/chemistry , Bacteria , Urea
10.
Anal Chem ; 96(3): 1284-1292, 2024 01 23.
Article in English | MEDLINE | ID: mdl-38194438

ABSTRACT

In this work, a novel nanozyme (Cu@Zr) with all-in-one dual enzyme and fluorescence properties is designed by simple self-assembly. A nanozyme cascade sensor with disodium phenyl phosphate (PPDS) as substrate was first established by exploiting the dual enzymatic activities of phosphatase and laccase. Specifically, phosphatase cleaves the P-O bond of PPDS to produce colorless phenol, which is then oxidized by laccase and complexed with the chromogenic agent 4-aminoantipyrine (4-AP) to produce red quinoneimine (QI). Strikingly, the NH3 produced by the urease hydrolysis of urea can interact with Cu@Zr, accelerating the electron transfer rate and ultimately leading to a significantly improved performance of the cascade reaction. Moreover, the fluorescence at 440 nm of Cu@Zr is further quenched by the inner filter effect (IFE) of QI. Thus, the colorimetric and fluorescence dual-mode strategy for sensitive urease analysis with LODs of 3.56 and 1.83 U/L was established by the proposed cascade sensor. Notably, a portable swab loaded with Cu@Zr was also prepared for in situ urease detection with the aid of a smartphone RGB readout. It also provides a potentially viable analytical avenue for environmental and biological analysis.


Subject(s)
Biosensing Techniques , Urease , Urease/chemistry , Laccase , Hydrolysis , Phosphoric Monoester Hydrolases , Colorimetry
11.
Naunyn Schmiedebergs Arch Pharmacol ; 397(1): 305-315, 2024 01.
Article in English | MEDLINE | ID: mdl-37436497

ABSTRACT

Inhibition of Helicobacter pylori urease is an effective method in the treatment of several gastrointestinal diseases in humans. This bacterium plays an important role in the pathogenesis of gastritis and peptic ulceration. Considering the presence of cysteine and N-arylacetamide derivatives in potent urease inhibitors, here, we designed hybrid derivatives of these pharmacophores. Therefore, cysteine-N-arylacetamide derivatives 5a-l were synthesized through simple nucleophilic reactions with good yield. In vitro urease inhibitory activity assay of these compounds demonstrated that all newly synthesized compounds exhibited high inhibitory activity (IC50 values = 0.35-5.83 µM) when compared with standard drugs (thiourea: IC50 = 21.1 ± 0.11 µM and hydroxyurea: IC50 = 100.0 ± 0.01 µM). Representatively, compound 5e with IC50 = 0.35 µM was 60 times more potent than strong urease inhibitor thiourea. Enzyme kinetic study of this compound revealed that compound 5e is a competitive urease inhibitor. Moreover, a docking study of compound 5e was performed to explore crucial interactions at the urease active site. This study revealed that compound 5e is capable to inhibit urease by interactions with two crucial residues at the active site: Ni and CME592. Furthermore, a molecular dynamics study confirmed the stability of the 5e-urease complex and Ni chelating properties of this compound. It should be considered that, in the following study, the focus was placed on jack bean urease instead of H. pylori urease, and this was acknowledged as a limitation.


Subject(s)
Helicobacter pylori , Urease , Humans , Urease/chemistry , Urease/metabolism , Cysteine/pharmacology , Molecular Docking Simulation , Helicobacter pylori/metabolism , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Thiourea/chemistry , Thiourea/pharmacology , Structure-Activity Relationship
12.
J Inorg Biochem ; 250: 112398, 2024 01.
Article in English | MEDLINE | ID: mdl-37879152

ABSTRACT

This paper reports on the molecular details of the reactivity of urease, a nickel-dependent enzyme that catalyses the last step of organic nitrogen mineralization, with thiuram disulphides, a class of molecules known to inactivate the enzyme with high efficacy but for which the mechanism of action had not been yet established. IC50 values of tetramethylthiuram disulphide (TMTD or Thiram) and tetraethylthiuram disulphide (TETD or Disulfiram) in the low micromolar range were determined for plant and bacterial ureases. The X-ray crystal structure of Sporosarcina pasteurii urease inactivated by Thiram, determined at 1.68 Å resolution, revealed the presence of a covalent modification of the catalytically essential cysteine residue. This is located on the flexible flap that modulates the size of the active site channel and cavity. Formation of a Cys-S-S-C(S)-N(CH3)2 functionality responsible for enzyme inactivation was observed. Quantum-mechanical calculations carried out to rationalise the large reactivity of the active site cysteine support the view that a conserved histidine residue, adjacent to the cysteine in the active site flap, modulates the charge and electron density along the thiol SH bond by shifting electrons towards the sulphur atom and rendering the thiol proton more reactive. We speculate that this proton could be transferred to the nickel-coordinated urea amide group to yield a molecule of ammonia from the generated Curea-NH3+ functionality during catalysis.


Subject(s)
Nickel , Thiram , Nickel/chemistry , Urease/chemistry , Cysteine , Protons , Disulfiram , Urea
13.
Mikrochim Acta ; 191(1): 47, 2023 12 22.
Article in English | MEDLINE | ID: mdl-38133683

ABSTRACT

Amino acid L-arginine (Arg), usually presented in food products and biological liquids, can serve both as a useful indicator of food quality and an important biomarker in medicine. The biosensors based on Arg-selective enzymes are the most promising devices for Arg assay. In this research, three types of amperometric biosensors have been fabricated. They exploit arginine oxidase (ArgO), recombinant arginase I (ARG)/urease, and arginine deiminase (ADI) coupled with the ammonium-chelating redox-active nanoparticles. Cadmium-copper nanoparticles (nCdCu) as the most effective nanochelators were used for the development of ammonium chemosensors and enzyme-coupled Arg biosensors. The fabricated enzyme/nCdCu-containing bioelectrodes show wide linear ranges (up to 200 µM), satisfactory storage stabilities (14 days), and high sensitivities (A⋅M-1⋅m-2) to Arg: 1650, 1700, and 4500 for ADI-, ArgO- and ARG/urease-based sensors, respectively. All biosensors have been exploited to estimate Arg content in commercial juices. The obtained data correlate well with the values obtained by the reference method. A hypothetic scheme for mechanism of action of ammonium nanochelators in electron transfer reaction on the arginine-sensing electrodes has been proposed.


Subject(s)
Ammonium Compounds , Biosensing Techniques , Urease/chemistry , Arginine , Arginase/metabolism
14.
Future Med Chem ; 15(23): 2181-2194, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37997685

ABSTRACT

Background: DNA gyrase and urease enzymes are important targets for the treatment of gastroenteritis, appendicitis, tuberculosis, urinary tract infections and Crohn's disease. Materials & methods: Esterification of norfloxacin was performed to enhance DNA gyrase and urease enzyme inhibition potential. Structure elucidation and chemical characterization were done through spectral (1H NMR, Fourier transform IR, 13C NMR) and carbon, hydrogen, nitrogen and sulfur analysis along with molecular docking. Results & conclusion: The majority of derivatives exhibited significant results but the 3e derivative showed maximum bactericidal, DPPH scavenging (96%), DNA gyrase and urease enzyme inhibitory activity with IC50 of 0.15 ± 0.24 and 1.14 ± 0.11 µM respectively which was further supported by molecular docking studies. So, the active derivatives can serve as a lead compound for the treatment of various pathological conditions.


Subject(s)
DNA Gyrase , Norfloxacin , Molecular Docking Simulation , Norfloxacin/pharmacology , DNA Gyrase/metabolism , Urease/chemistry , Urease/metabolism , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Structure-Activity Relationship , Molecular Structure
15.
Anal Chim Acta ; 1284: 341935, 2023 Dec 15.
Article in English | MEDLINE | ID: mdl-37996167

ABSTRACT

Urea is a common milk adulterant that falsely increases its protein content. Excessive consumption of urea is harmful to the kidney, liver, and gastrointestinal system. The conventional methods for urea detection in milk are time-consuming, costly, and require highly skilled operators. So, there is an increasing demand for the development of rapid, convenient, and cost-efficient methods for the detection of urea adulteration in milk. Herein, we report a novel colorimetric paper-based urea biosensor, consisting of a novel environment-friendly nanocomposite of halloysite nanotubes (HNT), that urease enzyme and an anthocyanin-rich extract, as a natural pH indicator are simultaneously immobilized into its internal and external surfaces. The biosensing mechanism of this biosensor is based on anthocyanin color change, which occurs due to urease-mediated hydrolysis of urea and pH increment of the environment. The colorimetric signal of this biosensor is measured through smartphone-assisted analysis of the mean RGB (Red-Green-Blue) intensity of samples and is capable of detecting urea with a detection limit of 0.2 mM, and a linear range from 0.5 to 100 mM. This biosensor has demonstrated promising results for the detection of urea in milk samples, in the presence of other milk adulterants and interferents.


Subject(s)
Biosensing Techniques , Urea , Animals , Urea/chemistry , Urease/analysis , Urease/chemistry , Urease/metabolism , Milk/chemistry , Colorimetry , Smartphone , Anthocyanins/analysis , Biosensing Techniques/methods , Hydrogen-Ion Concentration
16.
Future Med Chem ; 15(18): 1703-1717, 2023 09.
Article in English | MEDLINE | ID: mdl-37814798

ABSTRACT

Background: Quinoline and acyl thiourea scaffolds have major chemical significance in medicinal chemistry. Quinoline-based acyl thiourea derivatives may potentially target the urease enzyme. Materials & methods: Quinoline-based acyl thiourea derivatives 1-26 were synthesized and tested for urease inhibitory activity. Results: 19 derivatives (1-19) showed enhanced urease enzyme inhibitory potential (IC50 = 1.19-18.92 µM) compared with standard thiourea (IC50 = 19.53 ± 0.032 µM), whereas compounds 20-26 were inactive. Compounds with OCH3, OC2H5, Br and CH3 on the aryl ring showed significantly greater inhibitory potential than compounds with hydrocarbon chains of varying length. Molecular docking studies were conducted to investigate ligand interactions with the enzyme's active site. Conclusion: The identified hits can serve as potential leads against the drug target urease in advanced studies.


Subject(s)
Enzyme Inhibitors , Quinolines , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Urease/chemistry , Urease/metabolism , Kinetics , Molecular Docking Simulation , Thiourea/chemistry , Thiourea/pharmacology , Aminoquinolines , Quinolines/pharmacology , Structure-Activity Relationship , Molecular Structure
17.
Protein Pept Lett ; 30(9): 754-762, 2023.
Article in English | MEDLINE | ID: mdl-37533244

ABSTRACT

BACKGROUND: An increasing prevalence of biofilm forming strains by vancomycinresistance Staphylococcus aureus (VRSA) is one of the most important causes of antimicrobial resistance. VRSA possesses various regulatory factors to form and sustain biofilm in biotic or abiotic conditions. Among them, ureolytic activity is an important factor in the stabilization of biofilms by neutralizing the acidic environment. Various urease accessory proteins are required to activate the urease enzyme inside the biofilm. OBJECTIVE: To optimize the cloning, expression and purification of urease accessory protein E from VRSA for determination of the secondary structure, and functional characterization by using Berthelot's method. METHODS: BAB58453.1 gene (which encodes possible urease accessory protein E), having 38% similarity to Bacillus pasteurii UreE protein, was cloned, expressed, and purified by single-step affinity chromatography for performing secondary structural studies using circular dichroism spectroscopy, and functional analysis using Berthelot's and crystal violet assay. RESULTS: Structure elucidation using NMR and circular dichroism spectroscopy techniques revealed that UreE protein has a partially foldedα-helical structure. Using Berthelot's method, it was identified that the purified UreE protein has enhanced urease enzyme activity, in comparison to the control. From the results of Berthelot's and crystal violet assays, it was deduced that the selected gene (UreE protein) plays a key role in enhancing urease enzyme activity and contributes to biofilm stability. CONCLUSION: Structural studies on VRSA urease accessory proteins could aid in the identification of new drug targets or the development of effective antibiofilm strategies (in combination with other drug targets) against infections caused by biofilm-producing strains.


Subject(s)
Carrier Proteins , Urease , Urease/genetics , Urease/chemistry , Urease/metabolism , Carrier Proteins/chemistry , Vancomycin/pharmacology , Vancomycin/metabolism , Staphylococcus aureus/genetics , Gentian Violet/pharmacology , Bacterial Proteins/chemistry , Nickel/pharmacology
18.
Environ Res ; 234: 116588, 2023 10 01.
Article in English | MEDLINE | ID: mdl-37423368

ABSTRACT

Microbially induced calcite precipitation (MICP) is an efficient and eco-friendly technique that has attracted significant interest for resolving various problems in the soil (erosion, improving structural integrity and water retention, etc.), remediation of heavy metals, production of self-healing concrete or restoration of different concrete structures. The success of most common MICP methods depends on microorganisms degrading urea which leads to the formation of CaCO3 crystals. While Sporosarcina pasteurii is a well-known microorganism for MICP, other soil abundant microorganisms, such as Staphylococcus bacteria have not been thoroughly studied for its efficiency in bioconsolidation though MICP is a very important proccess which can ensure soil quality and health. This study aimed to analyze MICP process at the surface level in Sporosarcina pasteurii and a newly screened Staphylococcus sp. H6 bacterium as well as show the possibility of this new microorganism to perform MICP. It was observed that Staphylococcus sp. H6 culture precipitated 157.35 ± 3.3 mM of Ca2+ ions from 200 mM, compared to 176 ± 4.8 mM precipitated by S. pasteurii. The bioconsolidation of sand particles was confirmed by Raman spectroscopy and XRD analysis, which indicated the formation of CaCO3 crystals for both Staphylococcus sp. H6 and S. pasteurii cells. The water-flow test suggested a significant reduction in water permeability in bioconsolidated sand samples for both Staphylococcus sp. H6 and S. pasteurii. Notably, this study provides the first evidence that CaCO3 precipitation occurs on the surface of Staphylococcus and S. pasteurii cells within the initial 15-30 min after exposure to the biocementation solution. Furthermore, Atomic force microscopy (AFM) indicated rapid changes in cell roughness, with bacterial cells becoming completely coated with CaCO3 crystals after 90 min incubation with a biocementation solution. To our knowledge, this is the first time where atomic force microscopy was used to visualize the dynamic of MICP on cell surface.


Subject(s)
Calcium Carbonate , Urease , Urease/chemistry , Urease/metabolism , Calcium Carbonate/chemistry , Calcium Carbonate/metabolism , Staphylococcus/metabolism , Sand , Bacteria/metabolism , Soil , Water
19.
Sci Total Environ ; 898: 165479, 2023 Nov 10.
Article in English | MEDLINE | ID: mdl-37459989

ABSTRACT

The efficacy of alternative nitrogenous fertilizers for mitigating greenhouse gas and ammonia emissions from a rice-wheat cropping system in northern India was addressed in a laboratory incubation experiment using soil from a 10-year residue management field experiment (crop residue removal, CRR, vs. incorporation, CRI). Neem coated urea (NCU), standard urea (U), urea ammonium sulfate (UAS), and two alternative fertilizers, urea + urease inhibitor NBPT (UUI) and urea + urease inhibitor NBPT + nitrification inhibitor DMPSA (UUINI) were compared to non-fertilized controls for four weeks in incubation under anaerobic condition. Effects of fertilizers on global warming potential (GWP) and ammonia volatilization were dependent on residue treatment. Relative to standard urea, NCU reduced GWP by 11 % in CRI but not significantly in CRR; conversely, UAS reduced GWP by 12 % in CRR but not significantly in CRI. UUI and UUINI reduced GWP in both residue treatments and were more effective in CRI (21 % and 26 %) than CRR (15 % and 14 %). Relative to standard urea, NCU increased ammonia volatilization by 8 % in CRI but not significantly in CRR. Ammonia volatilization was reduced most strongly by UUI (40 % in CRI and 37 % in CRR); it was reduced 28-29 % by UUINI and 12-15 % by UAS. Overall, the urease inhibitor, alone and in combination with the nitrification inhibitor, was more effective in mitigating greenhouse gas and ammonia emissions than NCU. However, these products need to be tested in field settings to validate findings from the controlled laboratory experiment.


Subject(s)
Greenhouse Gases , Oryza , Agriculture , Triticum/metabolism , Oryza/metabolism , Ammonia/metabolism , Urease/chemistry , Greenhouse Gases/metabolism , Global Warming , Urea/chemistry , Nitrification , Volatilization , Fertilizers/analysis , Soil/chemistry
20.
Biophys Chem ; 299: 107042, 2023 08.
Article in English | MEDLINE | ID: mdl-37263179

ABSTRACT

Ureases are enzymes produced by fungi, plants, and bacteria associated with agricultural and clinical problems. The urea hydrolysis in NH3 and CO2 leads to the loss of N-urea fertilizers in soils and changes the human stomach microenvironment, favoring the colonization of H. pylori. In this sense, it is necessary to evaluate potential enzyme inhibitors to mitigate the effects of their activities and respond to scientific and market demands to produce fertilizers with enhanced efficiency. Thus, biophysical and theoretical studies were carried out to evaluate the influence of the N-alkyl chain in benzoyl-thiourea derivatives on urease enzyme inhibition. A screening based on IC50, binding constants, and theoretical studies demonstrated that BTU1 without the N-alkyl chain (R = H) was more active than other compounds, so the magnitude of the interaction was determined as BTU1 > BTU2 > BTU3 > BTU4 > BTU5, corresponding to progressively increased chain length. Thus, BTU1 was selected for interaction and soil application essays. The binding constants (Kb) for the supramolecular urease-BTU1 complex ranged from 7.95 to 5.71 × 103 M-1 at different temperatures (22, 30, and 38 °C), indicating that the preferential forces responsible for the stabilization of the complex are hydrogen bonds and van der Waals forces (ΔH = -15.84 kJ mol-1 and ΔS = -36.61 J mol-1 K-1). Theoretical and experimental results (thermodynamics, synchronous fluorescence, and competition assay) agree and indicate that BTU1 is a mixed inhibitor. Finally, urease inhibition was evaluated in the four soil samples, where BTU1 was as efficient as NBPT (based on ANOVA two-way and Tukey test with 95% confidence), with an average inhibition of 20% of urease activity. Thus, the biophysics and theoretical studies are strategies for evaluating potential inhibitors and showed that increasing the N-alkyl chain in benzoyl-thiourea derivatives did not favor urease inhibition.


Subject(s)
Helicobacter pylori , Soil , Humans , Urease/chemistry , Urease/metabolism , Fertilizers/analysis , Urea/chemistry , Helicobacter pylori/metabolism , Enzyme Inhibitors/pharmacology , Thiourea , Biophysics
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