Application of a simple calorimetric data analysis on the binding study of cyanide ions by Jack bean urease

<正>Cyanide ion was studied as an effector of Jack bean urease(JBU) at 300 K in 30 mmol/LTris buffer,pH 7 by isothermal titration calorimetry(ITC).The simple novel model was used for CN~- + JBU interaction over the whole range of CN~- concentrations.The binding parameters recovered from the simple novel model were attributed to the cyanide ion interaction.It was found that cyanide ion acted as a noncooperative inhibitor of JBU,and there is a set of 12 identical and independent binding sites for CN~- ions.The dissociation equilibrium constant is 750μmol/L.The molar enthalpy of binding is△H= -13.6 kJ mol~(-1).The technique used provided an accurate and quick assessment of the effectiveness of the compounds to inhibit Jack bean urease.     

Inhibition of Urease by Hydroquinones: A Structural and Kinetic Study

Hydroquinones are a class of organic compounds abundant in nature that result from the full reduction of the corresponding quinones. Quinones are known to efficiently inhibit urease, a Ni^II-containing enzyme that catalyzes the hydrolysis of urea to yield ammonia and carbonate and acts as a virulence factor of several human pathogens, in addition to decreasing the efficiency of soil organic nitrogen fertilization. Here, we report the molecular characterization of the inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by 1,4-hydroquinone (HQ) and its methyl and tert-butyl derivatives. The 1.63-Å resolution X-ray crystal structure of the SPU-HQ complex discloses that HQ covalently binds to the thiol group of αCys322, a key residue located on a mobile protein flap directly involved in the catalytic mechanism. Inhibition kinetic data obtained for the three compounds on JBU reveals the occurrence of an irreversible inactivation process that involves a radical-based autocatalytic mechanism.     

A Structural and Calorimetric Study on the Interaction Between Jack Bean Urease and Cyanide Ion

The cyanide ion was studied as an effecter of Jack bean urease at 300 K in 30 mmol⋅L⁻¹ Tris buffer, pH=7. The inhibition was investigated by isothermal titration calorimetry (ITC). The extended solvation model was used for CN⁻+JBU interaction over the whole range of CN⁻ concentrations. The binding parameters recovered from the solvation model were attributed to the interaction with cyanide ion. It was found that cyanide ion acted as a noncooperative inhibitor of urease, and there is a set of 12 identical and independent binding sites for CN⁻ ions. The dissociation equilibrium constant is 749.99 μmol⋅L⁻¹. The molar enthalpy of binding is ΔH=−13.60 kJ⋅mol⁻¹.     

Synthesis,crystal structures,and urease inhibition studies of two new Schiff-base copper complexes derived from n-butylamine

Two Schiff-base copper(II) complexes, bis(N-n-butyl-5-chlorosalicylaldiminato) copper(II) (1) and bis(N-n-butyl-4-methoxysalicylaldiminato) copper(II) (2), were synthesized and their solid-state structures were determined by X-ray crystallography. Complex 1 displays a distorted square-planar geometry, while 2 possesses square-planar geometry. Copper(II) complexes 1 and 2 showed strong inhibitory activity against jack bean urease (IC₅₀?=?2.7, 3.5?µmol?L^?1), compared with acetohydroxamic acid (IC₅₀?=?63.00?µmol?L^?1). A molecular modeling study was carried out via the DOCK program to gain understanding of the potent inhibitory activity of these copper species against jack bean urease.     

Thermodynamic study of CN~- ion inhibition of Jack bean urease using the extended solvation theory

Cyanide ion was studied as an inhibitor of Jack bean urease at 300 K in 30 mmol/L tris buffer,pH 7.The inhibition was investigated by isothermal titration calorimetry(ITC).The extended solvation model was used for CN~- + JBU interaction over the whole range of CN~- concentrations.The binding parameters recovered from the solvation model were attributed to the cyanide ion interaction.It was found that cyanide ion acted as a non-cooperative inhibitor of urease,and there is a set of 12±0.12 identical and in...     

A Calorimetric Study on the Interaction of Zinc and Cadmium Ions with Jack Bean Urease

A thermodynamic study on the interaction of Jack bean urease, JBU, with Zn²⁺ and Cd²⁺ ions was studied by isothermal titration calorimetry (ITC) at 290, 300 and 310 K in 30 mmol/L Tris buffer solution, pH 7.0. The heats of JBU+Zn²⁺ and JBU+ ²⁺ interactions are reported and analyzed in terms of the extended solvation theory. It was indicated that there is a set of 12 identical and non‐interacting binding sites for Zn²⁺ and Cd²⁺ ions. The interactions of Zn²⁺ and Cd²⁺ ions with JBU are exothermic and both enthalpy and entropy driven. The association equilibrium constants for JBU+Zn²⁺ complexes are 4118.20, 3354.70 and 2790.62 L·mol^?1 at 290, 300 and 310 K respectively. The association equilibrium constants for JBU+Cd²⁺ interactions are 2831.6 and 2386.28 L· ^?1 at 300 and 310 K, respectively.     

Synthesis,solid-state structures,and urease inhibition activities of new copper(II) complexes based on O,N,O-tridentate Schiff bases

Six new complexes of copper(II) coordinated with O,N,O-tridentate Schiff base dianions were synthesized and structurally characterized. The solid-state structures of 1–6 contain four-coordinate mononuclear copper(II) units with a slightly distorted square planar geometry. Complexes 1 and 4 derived from d-tyrosine have an infinite 1-D, right-handed helical chain, while 5 derived from l-tyrosine has an infinite 1-D, left-handed helical chain. Inhibitions of jack bean urease by 1–6 have been investigated, and potent inhibitory activities with IC₅₀ range of 2.15 ± 0.11–32.12 ± 0.65 μM have been observed for these copper(II) complexes. A docking analysis using a DOCK program was conducted to position 4 into the jack bean urease active site to determine the probable binding conformation.     

Application of the extended solvation model for thermodynamic study of copper ion binding to Jack bean urease

A Thermodynamic study on the interaction Jack bean urease, JBU, with Cu²⁺ ion was studied by isothermal titration calorimetry (ITC) at 300 and 310 K in 30 mM Tris buffer solution, pH 7.0. The heats of JBU + Cu²⁺ interactions are reported and analyzed in terms of the extended solvation theory. It was indicated that there are a set of 12 identical and non-cooperative sites for Cu²⁺ ion. The binding of Cu²⁺ ion with JBU is exothermic with dissociation equilibrium constants of 284.883 and 345.855 μM at 300 and 310 K, respectively.     

Novel and versatile methodology for synthesis of β-aryl-β-mercapto ketone derivatives as potential urease inhibitors

The objective was to obtain new scaffold of compounds possessing anti-urease activity. For this new and simple method for the synthesis of β-aryl-β-mercapto ketone derivatives based on Michael addition of thiophenol to chalcones in an ionic liquid as a solvent was improved. The products were obtained in good to moderate yields with high purity and characterized by spectral and elemental analyses. The activities of synthesized compounds were investigated as new inhibitors of jack bean urease. Among 22 synthesized compounds, all of them have shown inhibitory effect in micromolar range, and the most potent one has IC₅₀ = 6 μM compared to hydroxyurea IC₅₀ = 100 μM as a reference inhibitor. A docking study was performed using Autodock 4.2 in parallel to in vitro experiments to illustrate the corresponded binding affinities as well as binding site, and involved residues in interaction. These computational results complimented the experimental inhibition activity and enabled us to report a potent urease inhibitors based on β-aryl-β-mercapto ketone scaffold.     

Synthesis and Urease Inhibition Studies of Barbituric and Thiobarbituric Acid Derived Sulphonamides

Various novel barbituric and thiobarbituric acid derived sulphonamides were synthesized in excellent yield via three components single pot reaction; and these were screened for in vitro urease inhibition studies against jack bean urease. The compounds 1‐7 were found to exhibit a low to moderate activity whereas compounds 8‐14 showed a significant activity (88.3‐99.9% inhibition determined at 500 μM concentration). Structures of the synthesized compounds were confirmed by ¹H‐NMR, ¹³C‐NMR, mass spectrometry and elemental analysis data.     

Study of urease inhibitory activity by medicinal plants extract based on new catalyst for Berthelot reaction and Taguchi experimental design

The Berthelot reaction is a well-established colorimetric method for determination of ammonia. In this work, the effects of different bivalent ions (Ba²⁺, Cd²⁺, Co²⁺, Cu²⁺, Fe²⁺, Hg²⁺, Mg²⁺, Mn²⁺, Ni²⁺, and Pb²⁺) were studied as catalyst on the Berthelot reaction efficiency. CuCl₂ was generally found as the best catalyst that provides a rapid and stable blue indophenol color. The Taguchi experimental design methodology has been applied to find optimum conditions. Four factors including temperature, pH, reaction time, and CuCl₂ concentration at five levels were considered to achieve optimum conditions. Blue indophenol color stability for 40 min, and linearity response up to 20 mM of ammonium sulfate were achieved by further validation experiments. Limit of detection and quantification for this approach was 0.15 and 0.5 mM, respectively. Inhibitory activity of three traditional medicinal plants extract (Citrus aurantifolia, Laurus nobilis, and Zingiber officinale) was evaluated against jack bean urease activity by Berthelot reaction in the presence of CuCl₂ as catalyst, and results were compared with traditional Berthelot reaction.     

Synthesis,structure, and urease inhibitory activities of Co(III), Mn(II) and Zn(II) complexes with hydrazone derived from protocatechuic acid

[Co^III(L₁)₂·H₂O]NO₃ (1), [Mn^II(L₁)₂·H₂O] (2), and [Zn^II(L₁)₂·H₂O] (3) with a hydrazone derived from protocatechuic acid (HL₁ = C₁₅H₁₃N₃O₃) were designed, synthesized, and characterized by C, H, N elemental analyses, single-crystal X-ray diffraction, and IR spectra, which revealed that the three complexes are similar structures. Docking study has been done. The urease inhibitory activities of the three complexes were tested. Complexes 1 and 3 showed strong inhibitory activity against jack bean urease with IC₅₀ values of 45.9 and 11.64 μM. Complex 2 had no obvious inhibitory activity to urease; the IC₅₀ was > 50 μM.     

Synthesis,urease inhibitory activities,and molecular docking studies of two Cu(II) complexes

Two mononuclear copper(II) complexes, [Cu(C₄H₃N₂O₂)₂?·?4H₂O] (1) and [Cu(C₁₂H₁₁N₂O₂Cl₂)₂] (2), were synthesized and structurally characterized by single-crystal X-ray analysis. The copper(II) adopts a square-planar environment in 1, while the geometry in 2 can be described as distorted square-pyramidal. Complexes 1 and 2 were evaluated for their inhibitory activities against jack bean urease in vitro and both were found to have strong inhibitory activities comparable to that of acetohydroxamic acid. A docking simulation was performed to position 2 into the jack bean urease active site to determine the probable binding conformation.     

Synthesis,in vitro urease inhibitory activity and molecular docking of 3,5‐disubstituted thiadiazine‐2‐thiones

A series of 3,5‐disubstituted‐tetrahydro‐thiadiazine‐2‐thione ( 1 ‐ 16 ) have been synthesized, characterized by elemental analysis, infrared (IR), UV‐visible, ¹H NMR, ¹³C NMR, and MS spectroscopic techniques, and screened against jack bean urease. Among 16 compounds, compounds ( 1 ), ( 2 ), ( 3 ), ( 4 ), ( 6 ), ( 7 ), and ( 9 ) demonstrated excellent urease inhibitory activity with IC₅₀ values (9.8 ± 0.5, 11.0 ± 0.6, 16.0 ± 1.5, 17.2 ± 0.5, 15.4 ± 0.5, 19.7 ± 0.4, and 15.8 ± 0.2μM), respectively, even better than the standard thiourea (IC₅₀ = 21 ± 0.01μM). However, compound ( 8 ) shows an almost same level of inhibition (IC₅₀ = 22.9 ± 0.3μM), as like standard. In this work, we reported for the first time urease inhibitory activity of thiadiazine thiones and its molecular docking studies.     

Enthalpimetric and Colorimetric Determinations of the Inhibition Constant for the Inhibition of Urease by Boric Acid

Continuous enthalpimetric and fixed-time-point colorimetric analytical studies of jack bean urease-catalyzed hydrolysis of urea uninhibited and inhibited by boric acid were performed. The effect of boric acid on urease activity was studied in 100 mM phosphate buffer of pH 7 (H₃PO₄+NaOH, 2 mM EDTA) at 25°C. The inhibition constant of boric acid was obtained with use of differential and integration methods. It was found that boric acid is a simple competitive inhibitor of urease. The methods produced comparable values of the inhibition constant K_i: the former 0.19 mM and the latter 0.18 mM. This revised version was published online in July 2006 with corrections to the Cover Date.     

Synthesis and dynamics studies of barbituric acid derivatives as urease inhibitors

Background

Discovery of potent inhibitors of urease (jack bean) enzyme is the first step in the development of drugs against diseases caused by ureolytic enzyme.

Results

Thirty-two derivatives of barbituric acid as zwitterionic adducts of diethyl ammonium salts were synthesized. All synthesized compounds (4a–z and 5a–s) were screened for their in vitro inhibition potential against urease enzyme (jack bean urease). The compounds 4i (IC₅₀ = 17.6 ± 0.23 µM) and 5l (IC₅₀ = 17.2 ± 0.44 µM) were found to be the most active members of the series, and showed several fold more urease inhibition activity than the standard compound thiourea (IC₅₀ = 21.2 ± 1.3 µM). Whereas, compounds 4a–b, 4d–e, 4g–h, 4j–4r, 4x, 4z, 5b, 5e, 5k, 5n–5q having IC₅₀ values in the range of 22.7 ± 0.20 µM–43.8 ± 0.33 µM, were also found as potent urease inhibitors. Furthermore, Molecular Dynamics simulation and molecular docking studies were carried out to analyze the binding mode of barbituric acid derivatives using MOE. During MD simulation enol form is found to be more stable over its keto form due to their coordination with catalytic Nickel ion of Urease. Additionally, structural–activity relationship using automated docking method was applied where the compounds with high biological activity are deeply buried within the binding pocket of urease. As multiple hydrophilic crucial interactions with Ala169, KCX219, Asp362 and Ala366 stabilize the compound within the binding site, thus contributing greater activity.

Conclusions

This research study is useful for the discovery of economically, efficient viable new drug against infectious diseases.

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Graphical abstract: STD. Thiourea (IC₅₀ = 21.2 ± 1.3 µM)

     

A thermodynamic study on the binding of mercury and silver ions to urease

In this article, a thermodynamic study on the interaction of Jack bean urease, JBU, with \textHg ²⁺ {\text{Hg}}^{ 2+ } and \textAg ⁺ {\text{Ag}}^{ + } ions were studied by isothermal titration calorimetry (ITC) at 300 and 310 K in 30 mM Tris buffer solution, pH 7.0. The heats of \textJBU + \textHg ²⁺ {\text{JBU}} + {\text{Hg}}^{ 2+ } and \textJBU + \textAg ⁺ {\text{JBU}} + {\text{Ag}}^{ + } interactions are reported and analyzed in terms of the extended solvation model. It was indicated that there are a set of 12 identical and non-cooperative sites for \textHg ²⁺ {\text{Hg}}^{ 2+ } and \textAg ⁺ {\text{Ag}}^{ + } ions. The binding of \textHg ²⁺ {\text{Hg}}^{ 2+ } and \textAg ⁺ {\text{Ag}}^{ + } ions with JBU are exothermic with association equilibrium constants of 5415.65 and 4368.15 for \textAg ⁺ {\text{Ag}}^{ + } and 2389 and 2087 M ^{- 1} M^{ - 1} for \textHg ²⁺ {\text{Hg}}^{ 2+ } at 300 and 310 K, respectively.     

Synthesis,characterization, and biological activities of a Cu(II) complex with the non-steroidal antiinflammatory drug flufenamic acid

[Cu^II(L)₂.C₁₂H₁₀N₂] with flufenamic acid (HL=C₁₄H₁₀F₃NO₂) and phenanthroline (C₁₂H₁₀N₂O) was synthesized and characterized by C, H and N elemental analysis, single-crystal X-ray diffraction and, IR spectra. The urease inhibitory and antibacterial activities of the complex were tested. The complex showed strong inhibitory activity against jack bean urease with an IC₅₀ value of 0.265 μM. Four bacteria, Bacillus subtilis, Escherichia coli, Staphylococcus aureus, and proteusbacillus vulgaris, were used in the antibacterial test. The complex showed strong inhibitory activity against the species with IC₅₀ values of 2.016, 35.037, 10.680, and 3.820 μM. The interactions of the complex with human serum albumin (HSA) were studied through fluorescence spectroscopy. By analyzing the experimental data, we concluded that the fluorescence quenching mechanism of the complex with serum albumin was static quenching. The binding mode of the complex with DNA through UV spectroscopy was electrostatic binding or groove.     

Ethacrynic acid as a lead structure for the development of potent urease inhibitors

Ethacrynic acid and a series of its analogues were synthesized and subsequently evaluated for their inhibitory effect on jack bean urease. Ethacrynic acid showed, even at low concentrations, very potent inhibitory activity against the enzyme. For ethacrynic acid, the inhibition potential increased with increasing preincubation time of ethacrynic acid and enzyme, whereas for some other compounds a higher preincubation time lead to a significant reduction of their activity. We could demonstrate that the α,β-unsaturated carbonyl unit of our compounds is mandatory to inhibit the enzyme, possibly due to its ability to bind to cysteine residues in the active site of the jack bean urease.     

A simple dual-channel sensor for detecting cyanide in water with high selectivity and sensitivity

Taking advantage of the special nucleophilicity of cyanide, a new simple colorimetric chemosensor has been synthesised. This allows a deprotonation reaction to monitoring the cyanide. With the addition of CN^? to the chemosensor aqueous solution, which could induce a change in the solution colour from yellowish to deep yellow, while no colour change could be observed in the presence of other hackneyed anions, by which CN^? can be distinguished from other anions immediate with the naked eye. At the same time, a fluorescence quenching was implemented upon adding cyanide into the chemosensor aqueous solution. The absorption spectra detection limits of the chemosensor for cyanide was 5.35 × 10^?8 M and the fluorescence spectra detection limit was 2.63 × 10^?8 M. The cyanide test strips based on the chemosensor could serve as a convenient cyanide test kits. Furthermore, the chemosensor was successfully applied to detect cyanide in sprouting potatoes.