1
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Orner KD, Deleu E, Rabaey K, Nelson KL. Accelerating urea hydrolysis in fresh urine by modifying operating conditions of a sequencing batch reactor. ENVIRONMENTAL TECHNOLOGY 2024; 45:845-853. [PMID: 36161873 DOI: 10.1080/09593330.2022.2129456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
A number of existing and emerging technologies can recover nitrogen from urine. A preliminary step in many nitrogen recovery processes is hydrolyzing urea to ammonium, a biologically-mediated process that can take days to weeks without intervention. The ability to achieve urea hydrolysis quickly and reliably would increase the feasibility of decentralized nitrogen recovery, especially where space and treatment time are constrained. The goal of this research was to determine whether urea hydrolysis could be accelerated by providing an inoculum containing microorganisms likely to have urease activity (feces or soil), providing a carrier to support attached growth (plastic carriers, granular activated carbon, or no carrier), and modifying the hydraulic retention time (HRT; 1.3, 2, and 4 days) and feeding frequency (Δt = 4, 24 h). Inoculated reactors achieved significantly more urea hydrolysis, and reactors inoculated with soil were able to sustain higher urea hydrolysis rates over time than those inoculated with feces. The mean zero-order rate constants (mM/hr) for reactors with a soil inoculum (15.1) were about three times higher than that of reactors with an inoculum of feces (4.9). A reactor with GAC and an inoculum of soil fed daily with fresh urine achieved greater than 90% hydrolysis with an HRT of 2 days; results suggest the HRT could be reduced to 16 h without reducing performance. No significant benefit was provided by increasing the frequency of feedings for the same HRT, likely because urease enzymes were saturated and operating at maximum hydrolysis rates during most of the reaction period.
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Affiliation(s)
- Kevin D Orner
- Department of Civil & Environmental Engineering, University of California, Berkeley, CA, USA
| | - Emma Deleu
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Center for Advanced Process Technology for Urban REsource recovery (CAPTURE), Ghent, Belgium
| | - Kara L Nelson
- Department of Civil & Environmental Engineering, University of California, Berkeley, CA, USA
- National Science Foundation Engineering Research Center for Re-inventing the Nation's Urban Water Infrastructure, Berkeley, CA, USA
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2
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Yang W, Peng Z, Wang G. An overview: metal-based inhibitors of urease. J Enzyme Inhib Med Chem 2023; 38:361-375. [PMID: 36446640 PMCID: PMC11003495 DOI: 10.1080/14756366.2022.2150182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Urease is a kind of nickel-dependent metalloenzyme, which exists in the biological world widely, and can catalyse the hydrolysis of urea into ammonia and carbon dioxide to provide a nitrogen source for organisms. Urease has important uses in agriculture and medicine because it can catalyse the production of ammonia. Therefore, in this review, metal-based inhibitors of urease will be summarised according to different transition metal ions. Including the urease inhibition, structure-activity relationship, and molecular docking. Importantly, among these reviewed effective urease inhibitors, most of copper metal complexes exhibited stronger urease inhibition with IC50 values ranging from 0.46 μM to 41.1 μM. Significantly, the collected comprehensive information looks forward to providing rational guidance and effective strategies for the development of novel, potent, and safe metal-based urease inhibitors, which are better for practical applications in the future.
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Affiliation(s)
- Wei Yang
- Clinical Trails Center, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China
| | - Zhiyun Peng
- Clinical Trails Center, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Guangcheng Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China
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3
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Stanojević SP, Kostić AŽ, Milinčić DD, Pešić MB. Assessment of soy genotype and processing method on trypsin inhibitors, urease and lectins content of tofu. Nat Prod Res 2023:1-8. [PMID: 37976506 DOI: 10.1080/14786419.2023.2280858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Tofu has a high nutritional value, but it may also contain components that may have an antinutritional effect, such as trypsin inhibitors (TI), lectins and ureases. The aim of this study was to investigate the influence of the hydrothermal-cooking process of soybean in combination with commercial chymosin-pepsin rennet on the content and activity of TI, urease and lectins in tofu. High total TI content was found in tofu (5.00-16.87%). In addition, Kunitz (KTI = 3.52-4.32%) and Bowman-Birk (BBI = 5.00-12.53%) TI were registered, and BBI was detected in polymeric (1.38-2.71%) and monomeric (3.42-9.82%) forms. TI activity of tofu was very low (5.86-9.34%), corresponding to the very low activity of urease (0.51-3.07%). The percentage of lectin (2.62-4.63%) and urease (0.03-0.12%) in tofu was low. The results showed that the applied tofu production process is very effective in reducing the content and activity of TI, urease and lectin and provides the values without nutritional harmful effect.
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Affiliation(s)
- Sladjana P Stanojević
- Department of Chemistry and Biochemistry, University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Aleksandar Ž Kostić
- Department of Chemistry and Biochemistry, University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Danijel D Milinčić
- Department of Chemistry and Biochemistry, University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Mirjana B Pešić
- Department of Chemistry and Biochemistry, University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
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4
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Murtaza G, Khan M, Farooq S, Choudhary MI, Yousuf S. New cocrystals of heterocyclic drugs: structural, antileishmanial, larvicidal and urease inhibition studies. Acta Crystallogr C Struct Chem 2023; 79:237-248. [PMID: 37140892 DOI: 10.1107/s2053229623003753] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023] Open
Abstract
Many heterocycles have been developed as drugs due to their capacity to interact productively with biological systems. The present study aimed to synthesize cocrystals of the heterocyclic antitubercular agent pyrazinamide (PYZ, 1, BCS III) and the commercially available anticonvulsant drug carbamazepine (CBZ, 2, BCS class II) to study the effect of cocrystallization on the stability and biological activities of these drugs. Two new cocrystals, namely, pyrazinamide-homophthalic acid (1/1) (PYZ:HMA, 3) and carbamazepine-5-chlorosalicylic acid (1/1) (CBZ:5-SA, 4), were synthesized. The single-crystal X-ray diffraction-based structure of carbamazepine-trans-cinnamic acid (1/1) (CBZ:TCA, 5) was also studied for the first time, along with the known cocrystal carbamazepine-nicotinamide (1/1) (CBZ:NA, 6). From a combination drug perspective, these are interesting pharmaceutical cocrystals to overcome the known side effects of PYZ (1) therapy, and the poor biopharmaceutical properties of CBZ (2). The purity and homogeneity of all the synthesized cocrystals were confirmed by single-crystal X-ray diffraction, powder X-ray diffraction and FT-IR analysis, followed by thermal stability studies based on differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Detailed intermolecular interactions and the role of hydrogen bonding towards crystal stability were evaluated quantitatively via Hirshfeld surface analysis. The solubility of CBZ at pH 6.8 and 7.4 in 0.1 N HCl and H2O were compared with the values of cocrystal CBZ:5-SA (4). The solubility of CBZ:5-SA was found to be significantly improved at pH 6.8 and 7.4 in H2O. All the synthesized cocrystals 3-6 exhibited a potent urease inhibition (IC50 values range from 17.32 ± 0.89 to 12.3 ± 0.8 µM), several times more potent than standard acetohydroxamic acid (IC50 = 20.34 ± 0.43 µM). PYZ:HMA (3) also exhibited potent larvicidal activity against Aedes aegypti. Among the synthesized cocrystals, PYZ:HMA (3) and CBZ:TCA (5) were found to possess antileishmanial activity against the miltefosine-induced resistant strain of Leishmania major, with IC50 values of 111.98 ± 0.99 and 111.90 ± 1.44 µM, respectively, in comparison with miltefosine (IC50 = 169.55 ± 0.20 µM).
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Affiliation(s)
- Ghulam Murtaza
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Majid Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Saba Farooq
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sammer Yousuf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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5
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Yang W, Feng Q, Peng Z, Wang G. An overview on the synthetic urease inhibitors with structure-activity relationship and molecular docking. Eur J Med Chem 2022; 234:114273. [PMID: 35305460 DOI: 10.1016/j.ejmech.2022.114273] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 01/06/2023]
Abstract
Urease is a kind of enzyme which could be found in various bacteria, fungi, plants, and algae, which can quickly catalyze the hydrolysis of urea into ammonia and carbon dioxide. With the ammonia concentration increasing, the activity of Helicobacter pylori has got an obvious enhancement and leads to mucosal damage in the stomach, gastroduodenal infection, peptic ulcers, and gastric cancer. The infectious diseases caused by Helicobacter pylori can be controlled to a certain extent by inhibiting urease activity with urease inhibitors. Hence, studies of urease inhibitors have attracted great attention all over the world and a variety of effective urease inhibitors have been synthesized in recent years. In this review, we will draw summaries for these inhibitors including urease inhibitory activity, inhibition kinetics, structure-activity relationship, and molecular docking. The collected information is expected to provide rational guidance and effective strategy to develop novel, potent, and safe urease inhibitors for better practical applications in the future.
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Affiliation(s)
- Wei Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China; Teaching and Research Section of Natural Medicinal Chemistry, School of Pharmacy, Guizhou Medical University, Guiyang, China
| | - Qianqian Feng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China; Teaching and Research Section of Natural Medicinal Chemistry, School of Pharmacy, Guizhou Medical University, Guiyang, China
| | - Zhiyun Peng
- Office of Drug Clinical Trial Institutions, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.
| | - Guangcheng Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, China; Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang, China.
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6
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Abstract
![]()
Urease
catalyzes the hydrolysis of urea to form ammonia and carbamate,
inducing an overall pH increase that affects both human health and
agriculture. Inhibition, mutagenesis, and kinetic studies have provided
insights into its enzymatic role, but there have been debates on the
substrate binding mode as well as the reaction mechanism. In the present
study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular
mechanics molecular dynamics (QM/MM MD) calculations on urease that
mainly investigate the binding mode of urea and the mechanism of the
urease-catalyzed hydrolysis reaction. Comparison between the experimental
data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that
urea hydrolysis via a complex with bidentate-bound urea is much more
favorable than via that with monodentate-bound urea for both nucleophilic
attack and the subsequent proton transfer steps. We also indicate
that the bidentate coordination of urea fits the active site with
a closed conformation of the mobile flap and can facilitate the stabilization
of transition states and intermediates by forming multiple hydrogen
bonds with certain active site residues.
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Affiliation(s)
- Toru Saito
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
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Rajasekar A, Wilkinson S, Moy CK. MICP as a potential sustainable technique to treat or entrap contaminants in the natural environment: A review. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2021; 6:100096. [PMID: 36159179 PMCID: PMC9488051 DOI: 10.1016/j.ese.2021.100096] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 05/25/2023]
Abstract
In the last two decades, developments in the area of biomineralization has yielded promising results making it a potentially environmentally friendly technique for a wide range of applications in engineering and wastewater/heavy metal remediation. Microbially Induced Carbonate Precipitation (MICP) has led to numerous patented applications ranging from novel strains and nutrient sources for the precipitation of biominerals. Studies are being constantly published to optimize the process to become a promising, cost effective, ecofriendly approach when compared with the existing traditional remediation technologies which are implemented to solve multiple contamination/pollution issues. Heavy metal pollution still poses a major threat towards compromising the ecosystem. The removal of heavy metals is of high importance due to their recalcitrance and persistence in the environment. In that perspective, this paper reviews the current and most significant discoveries and applications of MICP towards the conversion of heavy metals into heavy metal carbonates and removal of calcium from contaminated media such as polluted water. It is evident from the literature survey that although heavy metal carbonate research is very effective in removal, is still in its early stages but could serve as a solution if the microorganisms are stimulated directly in the heavy metal environment.
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Affiliation(s)
- Adharsh Rajasekar
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), Nanjing University of Information Science &Technology, Nanjing, 210044, China
| | - Stephen Wilkinson
- Department of Civil Engineering, University of Wollongong in Dubai, Dubai, United Arab Emirates
| | - Charles K.S. Moy
- Department of Civil Engineering, Xi'an Jiaotong Liverpool University, Suzhou, Jiangsu, China
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8
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Rashid M, Rafique H, Roshan S, Shamas S, Iqbal Z, Ashraf Z, Abbas Q, Hassan M, Qureshi ZUR, Asad MHHB. Enzyme Inhibitory Kinetics and Molecular Docking Studies of Halo-Substituted Mixed Ester/Amide-Based Derivatives as Jack Bean Urease Inhibitors. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8867407. [PMID: 33426080 PMCID: PMC7775144 DOI: 10.1155/2020/8867407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/28/2020] [Accepted: 12/15/2020] [Indexed: 12/22/2022]
Abstract
A series of halo-substituted mixed ester/amide-based analogues 4a-l have been prepared as jack bean urease inhibitor, which showed good to excellent inhibition of enzyme activity. The role of halo-substituted benzoyl moieties and alkyl substituted anilines in urease inhibitory kinetics was also investigated. The alkyl-substituted anilines 1a-b reacted with chloroacetyl chloride to afford intermediates 2a-b, which were then reacted with different halo-substituted benzoic acids 3a-f to prepare the title compounds 4a-l. The chemical structures of final products 4a-l were ascertained by FTIR, 1H NMR, 13C NMR, and mass spectra. The compound 4b showed remarkable activity with IC501.6 ± 0.2 nM, better than the standard thiourea having IC50472.1 ± 135.1 nM. The 2-chloro-substituted phenyl ring on one side of compound 4b and 4-isopropyl-substituted benzene on the other side play an essential role in inhibition of urease activity. Lineweaver-Burk plots (kinetics study) indicated about 4b derivative as a mixed type of inhibitor. The virtual screening performed against urease enzyme (PDBID 4H9M) showed that compounds 4b and 4e have binding energies of -7.8 and -7.9 Kcal/mol, respectively. Based upon our results, it was found that derivative 4b is a highly potent urease inhibitor, better than the standard thiourea.
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Affiliation(s)
- Muhammad Rashid
- Department of Chemistry, Allama Iqbal Open University, Islamabad 44000, Pakistan
| | - Hummera Rafique
- Department of Chemistry, University of Gujrat, Gujrat 50700, Pakistan
| | - Sadia Roshan
- Department of Zoology, University of Gujrat, Gujrat 50700, Pakistan
| | - Shazia Shamas
- Department of Zoology, University of Gujrat, Gujrat 50700, Pakistan
| | - Zafar Iqbal
- Department of Chemistry, Allama Iqbal Open University, Islamabad 44000, Pakistan
| | - Zaman Ashraf
- Department of Chemistry, Allama Iqbal Open University, Islamabad 44000, Pakistan
| | - Qamar Abbas
- Department of Physiology, University of Sindh, Jamshoro, Pakistan
| | - Mubashir Hassan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | | | - Muhammad Hassham Hassan Bin Asad
- Department of Pharmacy, COMSATS University Islamabad, Abbottabad Campus, Pakistan
- Institute of Fundamental Medicine, Department of Genetics, Kazan Federal University, Russia
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9
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Jagannathan V, Venkatesan A, Viswanathan P. Kinetics and Computational Evaluation of Eugenol and Vanillic Acid on Inhibition of a Potential Enzyme of a Nosocomial Pathogen that Promotes Struvite Formation. CURRENT ENZYME INHIBITION 2020. [DOI: 10.2174/1573408016999200415115754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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.
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Affiliation(s)
- Venkataseshan Jagannathan
- Renal Research Laboratory, Department of Biosciences, Centre for Biomedical Research, Vellore - 632 014, Tamil Nadu, India
| | - Arthi Venkatesan
- Department of Integrative Biology, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore - 632 014, Tamil Nadu, India
| | - Pragasam Viswanathan
- Renal Research Laboratory, Department of Biosciences, Centre for Biomedical Research, Vellore - 632 014, Tamil Nadu, India
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10
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Swain KK, Balasubramaniam R, Bhand S. A portable microfluidic device-based Fe 3O 4-urease nanoprobe-enhanced colorimetric sensor for the detection of heavy metals in fish tissue. Prep Biochem Biotechnol 2020; 50:1000-1013. [PMID: 32564658 DOI: 10.1080/10826068.2020.1780611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A portable microfluidic device with highly sensitive enzyme nanoprobe (Fe3O4 MNPs-urease, average size 34.6 nm) was demonstrated for the analysis of heavy metals ions (Hg2+, Cd2+ and Pb2+) in fish gill and muscle tissue. The immobilized urease nanoprobe (Km = 0.05 mM) exhibited twofold sensitivity over the free enzyme assay (apparent Km = 0.1 mM). The nanoprobe was characterized using SEM, EDAX, PSA and FT-IR. The inhibition measurements were carried out for individual as well as the mixture of metal ions (CRM standards of 9 elements (CRMmix-9)). The lower limit of quantification (LOQ) (0.5, 0.1, and 0.1 ng L-1 for Hg2+, Cd2+, and Pb2+) and lower limit of detection (LOD) was achieved at 0.1 ng L-1 with sensitivity 8-14% per decade for Hg2+, Cd2+, and Pb2+ ions. A visual result can be observed by the naked eye through the microfluidic device as well as with 96 transparent microwell plates. The order of relative inhibition was found to be CRMmix-9 > (Hg2+ + Cd2+ + Pb2+) > (Cd2+ + Pb2+) > (Pb2+ + Hg2+) > (Hg2+ + Cd2+) > Pb2+ > Cd2+ > Hg2+, respectively. The recovery % in fish tissues were found to be 88-98% for Hg2+, Cd2+ and Pb2+ ions.
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Affiliation(s)
- Krishna Kumari Swain
- Biosensor Lab, Department of Chemistry, BITS Pilani KK Birla Goa Campus, South Goa, India
| | - R Balasubramaniam
- Precision Machining Section, Precision Engineering Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sunil Bhand
- Biosensor Lab, Department of Chemistry, BITS Pilani KK Birla Goa Campus, South Goa, India
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11
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GÜMRÜKÇÜOĞLU N, BİLGİN SÖKMEN B. Synthesis of New Ligands Containing Azomethine Group and Investigation of Antioxidant, Antiurease Activities. GAZI UNIVERSITY JOURNAL OF SCIENCE 2020. [DOI: 10.35378/gujs.615818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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12
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Chinnaraja E, Arunachalam R, Samanta K, Natarajan R, Subramanian PS. Enantioselective Michael Addition Reaction Catalysed by Enantiopure Binuclear Nickel(II) Close‐Ended Helicates. Adv Synth Catal 2020. [DOI: 10.1002/adsc.201901350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Eswaran Chinnaraja
- Inorganic Materials and Catalysis DivisionCSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI) Bhavnagar 364 002, Gujarat India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Rajendran Arunachalam
- Inorganic Materials and Catalysis DivisionCSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI) Bhavnagar 364 002, Gujarat India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Krishanu Samanta
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Organic & Medicinal Chemistry DivisionCSIR-Indian Institute of Chemical Biology Kolkata India
| | - Ramalingam Natarajan
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Organic & Medicinal Chemistry DivisionCSIR-Indian Institute of Chemical Biology Kolkata India
| | - Palani S. Subramanian
- Inorganic Materials and Catalysis DivisionCSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI) Bhavnagar 364 002, Gujarat India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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13
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Zaman K, Rahim F, Taha M, Ullah H, Wadood A, Nawaz M, Khan F, Wahab Z, Shah SAA, Rehman AU, Kawde AN, Gollapalli M. Synthesis, in vitro urease inhibitory potential and molecular docking study of Benzimidazole analogues. Bioorg Chem 2019; 89:103024. [DOI: 10.1016/j.bioorg.2019.103024] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/21/2019] [Accepted: 05/30/2019] [Indexed: 02/04/2023]
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14
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Fernandes HS, Teixeira CSS, Sousa SF, Cerqueira NMFSA. Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:E2462. [PMID: 31277490 PMCID: PMC6651669 DOI: 10.3390/molecules24132462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.
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Affiliation(s)
- Henrique S Fernandes
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Carla S Silva Teixeira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
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16
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Uprety B, Arderne C, Bernal I. Catalytic Cleavage of the Amide Bond in Urea Using a Cobalt(III) Amino-Based Complex. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Bhawna Uprety
- Department of Chemistry; University of Johannesburg; PO Box 524, Auckland Park 2006 Johannesburg South Africa
| | - Charmaine Arderne
- Department of Chemistry; University of Johannesburg; PO Box 524, Auckland Park 2006 Johannesburg South Africa
| | - Ivan Bernal
- Molecular Sciences Institute; School of Chemistry; University of the Witwatersrand; 2050 Johannesburg South Africa
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17
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Abstract
Catalysis and mobility of reactants in fluid are normally thought to be decoupled. Violating this classical paradigm, this paper presents the catalyst laws of motion. Comparing experimental data to the theory presented here, we conclude that part of the free energy released by chemical reaction is channeled into driving catalysts to execute wormlike trajectories by piconewton forces performing work of a few kBT against fluid viscosity, where the rotational diffusion rate dictates the trajectory persistence length. This active motion agitates the fluid medium and produces antichemotaxis, the migration of catalyst down the gradient of the reactant concentration. Alternative explanations of enhanced catalyst mobility are examined critically. Using a microscopic theory to analyze experiments, we demonstrate that enzymes are active matter. Superresolution fluorescence measurements—performed across four orders of magnitude of substrate concentration, with emphasis on the biologically relevant regime around or below the Michaelis–Menten constant—show that catalysis boosts the motion of enzymes to be superdiffusive for a few microseconds, enhancing their effective diffusivity over longer timescales. Occurring at the catalytic turnover rate, these fast ballistic leaps maintain direction over a duration limited by rotational diffusion, driving enzymes to execute wormlike trajectories by piconewton forces performing work of a few kBT against viscosity. The boosts are more frequent at high substrate concentrations, biasing the trajectories toward substrate-poor regions, thus exhibiting antichemotaxis, demonstrated here experimentally over a wide range of aqueous concentrations. Alternative noncatalytic, passive mechanisms that predict chemotaxis, cross-diffusion, and phoresis, are critically analyzed. We examine the physical interpretation of our findings, speculate on the underlying mechanism, and discuss the avenues they open with biological and technological implications. These findings violate the classical paradigm that chemical reaction and motility are distinct processes, and suggest reaction–motion coupling as a general principle of catalysis.
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18
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Kappaun K, Piovesan AR, Carlini CR, Ligabue-Braun R. Ureases: Historical aspects, catalytic, and non-catalytic properties - A review. J Adv Res 2018; 13:3-17. [PMID: 30094078 PMCID: PMC6077230 DOI: 10.1016/j.jare.2018.05.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 12/11/2022] Open
Abstract
Urease (urea amidohydrolase, EC 3.5.1.5) is a nickel-containing enzyme produced by plants, fungi, and bacteria that catalyzes the hydrolysis of urea into ammonia and carbamate. Urease is of historical importance in Biochemistry as it was the first enzyme ever to be crystallized (1926). Finding nickel in urease's active site (1975) was the first indication of a biological role for this metal. In this review, historical and structural features, kinetics aspects, activation of the metallocenter and inhibitors of the urea hydrolyzing activity of ureases are discussed. The review also deals with the non-enzymatic biological properties, whose discovery 40 years ago started a new chapter in the study of ureases. Well recognized as virulence factors due to the production of ammonia and alkalinization in diseases by urease-positive microorganisms, ureases have pro-inflammatory, endocytosis-inducing and neurotoxic activities that do not require ureolysis. Particularly relevant in plants, ureases exert insecticidal and fungitoxic effects. Data on the jack bean urease and on jaburetox, a recombinant urease-derived peptide, have indicated that interactions with cell membrane lipids may be the basis of the non-enzymatic biological properties of ureases. Altogether, with this review we wanted to invite the readers to take a second look at ureases, very versatile proteins that happen also to catalyze the breakdown of urea into ammonia and carbamate.
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Affiliation(s)
- Karine Kappaun
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Medicine and Health Sciences, School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Angela Regina Piovesan
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Celia Regina Carlini
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Medicine and Health Sciences, School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Rodrigo Ligabue-Braun
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Yang YS, Su MM, Zhang XP, Liu QX, He ZX, Xu C, Zhu HL. Developing potential Helicobacter pylori urease inhibitors from novel oxoindoline derivatives: Synthesis, biological evaluation and in silico study. Bioorg Med Chem Lett 2018; 28:3182-3186. [PMID: 30170940 DOI: 10.1016/j.bmcl.2018.08.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/13/2018] [Accepted: 08/24/2018] [Indexed: 11/26/2022]
Abstract
By recruiting the important moiety from Shikonin, a series of novel oxoindoline derivatives S1-S20 have been synthesized for inhibiting H. pylori urease. The most potent compound S18 displayed better activity (IC50 = 0.71 μM; MIC = 0.48 μM) than the positive controls AHA (IC50 = 17.2 μM) and Metronidazole (MIC = 31.3 μM). With low cytotoxicity, it showed considerable potential for further development. Docking simulation revealed the possible binding pattern of this series. 3D QSAR model was built to discuss SAR and give useful hints for future modification.
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Affiliation(s)
- Yu-Shun Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Mi-Mi Su
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Xu-Ping Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Qi-Xing Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Zhen-Xiang He
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China.
| | - Chen Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China.
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China.
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20
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Jaworek MW, Schuabb V, Winter R. The effects of glycine, TMAO and osmolyte mixtures on the pressure dependent enzymatic activity of α-chymotrypsin. Phys Chem Chem Phys 2018; 20:1347-1354. [DOI: 10.1039/c7cp06042d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different natural osmolytes modulate the pressure dependent enzyme kinetics in different ways.
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Affiliation(s)
- Michel W. Jaworek
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
| | - Vitor Schuabb
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
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21
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Krajewska B. Urease-aided calcium carbonate mineralization for engineering applications: A review. J Adv Res 2017; 13:59-67. [PMID: 30094083 PMCID: PMC6077181 DOI: 10.1016/j.jare.2017.10.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/23/2017] [Accepted: 10/26/2017] [Indexed: 12/21/2022] Open
Abstract
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.
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22
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Yousaf M. A Comparative Kinetic Study of Free and Immobilized Urease on Commercial and Glutaraldehyde Activated Cotton. ACTA ACUST UNITED AC 2017. [DOI: 10.6000/1927-5129.2017.13.53] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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23
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Detection of DNA Amplicons of Polymerase Chain Reaction Using Litmus Test. Sci Rep 2017; 7:3110. [PMID: 28596600 PMCID: PMC5465217 DOI: 10.1038/s41598-017-03009-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/20/2017] [Indexed: 12/18/2022] Open
Abstract
We report on a new colorimetric DNA detection method that takes advantage of the power of polymerase chain reaction (PCR) and the simplicity of the classic litmus test. The strategy makes use of a modified set of primers for PCR to facilitate ensuing manipulations of resultant DNA amplicons: their tagging with urease and immobilization onto magnetic beads. The amplicon/urease-laden beads are then used to hydrolyze urea, resulting in the increase of pH that can be conveniently reported by a pH-sensitive dye. We have successfully applied this strategy for the detection of two hypervirulent strains of the bacterium Clostridium difficile that are responsible for the recent increase in the global incidence and severity of C. difficile infections. Furthermore, the viability of this test for diagnostic applications is demonstrated using clinically validated stool samples from C. difficile infected patients.
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Maithani S, Pal M, Maity A, Pradhan M. Isotope selective activation: a new insight into the catalytic activity of urease. RSC Adv 2017. [DOI: 10.1039/c7ra05489k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Isotope selective enzymatic activity of urease.
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Affiliation(s)
- Sanchi Maithani
- Department of Chemical, Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata-700098
- India
| | - Mithun Pal
- Department of Chemical, Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata-700098
- India
| | - Abhijit Maity
- Department of Chemical, Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata-700098
- India
| | - Manik Pradhan
- Department of Chemical, Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata-700098
- India
- Technical Research Centre (TRC)
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Inhibition of Urease by Disulfiram, an FDA-Approved Thiol Reagent Used in Humans. Molecules 2016; 21:molecules21121628. [PMID: 27898047 PMCID: PMC6274061 DOI: 10.3390/molecules21121628] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022] Open
Abstract
Urease is a nickel-dependent amidohydrolase that catalyses the decomposition of urea into carbamate and ammonia, a reaction that constitutes an important source of nitrogen for bacteria, fungi and plants. It is recognized as a potential antimicrobial target with an impact on medicine, agriculture, and the environment. The list of possible urease inhibitors is continuously increasing, with a special interest in those that interact with and block the flexible active site flap. We show that disulfiram inhibits urease in Citrullus vulgaris (CVU), following a non-competitive mechanism, and may be one of this kind of inhibitors. Disulfiram is a well-known thiol reagent that has been approved by the FDA for treatment of chronic alcoholism. We also found that other thiol reactive compounds (l-captopril and Bithionol) and quercetin inhibits CVU. These inhibitors protect the enzyme against its full inactivation by the thiol-specific reagent Aldrithiol (2,2'-dipyridyl disulphide, DPS), suggesting that the three drugs bind to the same subsite. Enzyme kinetics, competing inhibition experiments, auto-fluorescence binding experiments, and docking suggest that the disulfiram reactive site is Cys592, which has been proposed as a "hinge" located in the flexible active site flap. This study presents the basis for the use of disulfiram as one potential inhibitor to control urease activity.
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26
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Decaneto E, Suladze S, Rosin C, Havenith M, Lubitz W, Winter R. Pressure and Temperature Effects on the Activity and Structure of the Catalytic Domain of Human MT1-MMP. Biophys J 2016; 109:2371-81. [PMID: 26636948 DOI: 10.1016/j.bpj.2015.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/12/2015] [Accepted: 10/19/2015] [Indexed: 11/19/2022] Open
Abstract
Membrane type 1-matrix metalloproteinase (MT1-MMP or MMP-14) is a zinc-transmembrane metalloprotease involved in the degradation of extracellular matrix and tumor invasion. While changes in solvation of MT1-MMP have been recently studied, little is known about the structural and energetic changes associated with MT1-MMP while interacting with substrates. Steady-state kinetic and thermodynamic data (including activation energies and activation volumes) were measured over a wide range of temperatures and pressures by means of a stopped-flow fluorescence technique. Complementary temperature- and pressure-dependent Fourier-transform infrared measurements provided corresponding structural information of the protein. MT1-MMP is stable and active over a wide range of temperatures (10-55 °C). A small conformational change was detected at 37 °C, which is responsible for the change in activity observed at the same temperature. Pressure decreases the enzymatic activity until complete inactivation occurs at 2 kbar. The inactivation is associated with changes in the rate-limiting step of the reaction caused by additional hydration of the active site upon compression and/or minor conformational changes in the active site region. Based on these data, an energy and volume diagram could be established for the various steps of the enzymatic reaction.
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Affiliation(s)
- Elena Decaneto
- Max Planck Institute for Chemical Energy Conversion, Mülheim a. d. Ruhr, Germany; Department of Physical Chemistry II, Ruhr-University Bochum, Bochum, Germany
| | - Saba Suladze
- Department of Chemistry and Chemical Biology, Physical Chemistry, Technische Universität Dortmund, Dortmund, Germany
| | - Christopher Rosin
- Department of Chemistry and Chemical Biology, Physical Chemistry, Technische Universität Dortmund, Dortmund, Germany
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr-University Bochum, Bochum, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Mülheim a. d. Ruhr, Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Physical Chemistry, Technische Universität Dortmund, Dortmund, Germany.
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27
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Wang CF, Chen ZJ, Zhao KD, Chen XF, Zhang CY, Sheng GH, Zhu HL. Synthesis, structure, and urease inhibitory activities of Co(III), Mn(II) and Zn(II) complexes with hydrazone derived from protocatechuic acid. J COORD CHEM 2016. [DOI: 10.1080/00958972.2016.1213819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Cun-Fang Wang
- School of Life Sciences, Shandong University of Technology, ZiBo, PR China
| | - Zhi-Jian Chen
- School of Life Sciences, Shandong University of Technology, ZiBo, PR China
| | - Ke-Dong Zhao
- School of Life Sciences, Shandong University of Technology, ZiBo, PR China
| | - Xiang-Fei Chen
- School of Life Sciences, Shandong University of Technology, ZiBo, PR China
| | - Chun-Yang Zhang
- School of Life Sciences, Shandong University of Technology, ZiBo, PR China
| | - Gui-Hua Sheng
- School of Life Sciences, Shandong University of Technology, ZiBo, PR China
| | - Hai-Liang Zhu
- School of Life Sciences, Shandong University of Technology, ZiBo, PR China
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28
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A combined temperature-pH study of urease kinetics. Assigning pKa values to ionizable groups of the active site involved in the catalytic reaction. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.11.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Mazzei L, Ciurli S, Zambelli B. Isothermal Titration Calorimetry to Characterize Enzymatic Reactions. Methods Enzymol 2016; 567:215-36. [DOI: 10.1016/bs.mie.2015.07.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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30
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Jiang XY, Sheng LQ, Song CF, Du NN, Xu HJ, Liu ZD, Chen SS. Mechanism, kinetics, and antimicrobial activities of 2-hydroxy-1-naphthaldehyde semicarbazone as a new Jack bean urease inhibitor. NEW J CHEM 2016. [DOI: 10.1039/c5nj01601k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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.
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Affiliation(s)
- Xue-Yue Jiang
- School of Chemistry and Material Engineering
- Fuyang Normal College
- Fuyang
- China
| | - Liang-Quan Sheng
- School of Chemistry and Material Engineering
- Fuyang Normal College
- Fuyang
- China
- College of Chemistry and Chemical Engineering
| | - Chong-Fu Song
- School of Chemistry and Material Engineering
- Fuyang Normal College
- Fuyang
- China
| | - Na-Na Du
- School of Chemistry and Material Engineering
- Fuyang Normal College
- Fuyang
- China
| | - Hua-Jie Xu
- School of Chemistry and Material Engineering
- Fuyang Normal College
- Fuyang
- China
| | - Zhao-Di Liu
- School of Chemistry and Material Engineering
- Fuyang Normal College
- Fuyang
- China
| | - Shui-Sheng Chen
- School of Chemistry and Material Engineering
- Fuyang Normal College
- Fuyang
- China
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31
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Suladze S, Cinar S, Sperlich B, Winter R. Pressure Modulation of the Enzymatic Activity of Phospholipase A2, A Putative Membrane-Associated Pressure Sensor. J Am Chem Soc 2015; 137:12588-96. [DOI: 10.1021/jacs.5b07009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Saba Suladze
- Department of Chemistry and
Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, D-44221 Dortmund, Germany
| | - Suleyman Cinar
- Department of Chemistry and
Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, D-44221 Dortmund, Germany
| | - Benjamin Sperlich
- Department of Chemistry and
Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, D-44221 Dortmund, Germany
| | - Roland Winter
- Department of Chemistry and
Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, D-44221 Dortmund, Germany
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32
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Lauchnor EG, Topp DM, Parker AE, Gerlach R. Whole cell kinetics of ureolysis by Sporosarcina pasteurii. J Appl Microbiol 2015; 118:1321-32. [PMID: 25809221 DOI: 10.1111/jam.12804] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/10/2015] [Accepted: 02/26/2015] [Indexed: 12/21/2022]
Abstract
AIMS Ureolysis drives microbially induced calcium carbonate precipitation (MICP). MICP models typically employ simplified urea hydrolysis kinetics that do not account for cell density, pH effect or product inhibition. Here, ureolysis rate studies with whole cells of Sporosarcina pasteurii aimed to determine the relationship between ureolysis rate and concentrations of (i) urea, (ii) cells, (iii) NH4+ and (iv) pH (H(+) activity). METHODS AND RESULTS Batch ureolysis rate experiments were performed with suspended cells of S. pasteurii and one parameter was varied in each set of experiments. A Michaelis-Menten model for urea dependence was fitted to the rate data (R(2) = 0·95) using a nonlinear mixed effects statistical model. The resulting half-saturation coefficient, Km , was 305 mmol l(-1) and maximum rate constant, Vmax , was 200 mmol l(-1) h(-1) . However, a first-order model with k1 = 0·35 h(-1) fit the data better (R(2) = 0·99) for urea concentrations up to 330 mmol l(-1) . Cell concentrations in the range tested (1 × 10(7) -2 × 10(8) CFU ml(-1) ) were linearly correlated with ureolysis rate (cell dependent Vmax' = 6·4 × 10(-9) mmol CFU(-1) h(-1) ). CONCLUSIONS Neither pH (6-9) nor ammonium concentrations up to 0·19 mol l(-1) had significant effects on the ureolysis rate and are not necessary in kinetic modelling of ureolysis. Thus, we conclude that first-order kinetics with respect to urea and cell concentrations are likely sufficient to describe urea hydrolysis rates at most relevant concentrations. SIGNIFICANCE AND IMPACT OF THE STUDY These results can be used in simulations of ureolysis driven processes such as microbially induced mineral precipitation and they verify that under the stated conditions, a simplified first-order rate for ureolysis can be employed. The study shows that the kinetic models developed for enzyme kinetics of urease do not apply to whole cells of S. pasteurii.
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Affiliation(s)
- E G Lauchnor
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Civil Engineering, Montana State University, Bozeman, MT, USA
| | - D M Topp
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - A E Parker
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - R Gerlach
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
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Mulec J, Krištůfek V, Chroňáková A, Oarga A, Scharfen J, Šestauberová M. Microbiology of healing mud (fango) from Roman thermae aquae iasae archaeological site (Varaždinske Toplice, Croatia). MICROBIAL ECOLOGY 2015; 69:293-306. [PMID: 25241172 DOI: 10.1007/s00248-014-0491-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/01/2014] [Indexed: 06/03/2023]
Abstract
We found well-preserved, rocky artefacts that had been buried in the healing mud (fango) for more than 1,500 years at the Roman archaeological site at Varaždinske Toplice. This Roman pool with fango sediments and artefacts is fed from hot sulphidic springs. The fango exhibited nearly neutral pH, a high level of organic C, an elevated concentration of heavy metals and a high total microbial biomass, greater than 10(8) cells per gram of dry weight. The dominant microbes, assessed by molecular profiling (denaturing gradient gel electrophoresis), were affiliated with Thiobacillus, Sulfuricurvum, Polaromonas, and Bdellovibrio. Polymerase chain reaction screening for microbial functional guilds revealed the presence of sulphur oxidizers and methanogens but no sulphate reducers. The dominance of four Proteobacterial classes (α-, β-, δ- and ε-Proteobacteria) was confirmed by fluorescence in situ hybridisation; Actinobacteria were less abundant. Cultivable bacteria represented up to 23.4 % of the total bacterial counts when cultivation media was enriched with fango. These bacteria represented the genera Acinetobacter, Aeromonas, Arthrobacter, Comamonas, Ewingella, Flavobacterium, Pseudomonas, Rahnella and Staphylococcus. This study showed that the heterogeneous nature of fango at neutral pH created various microniches, which largely supported microbial life based on sulphur-driven, autotrophic denitrification.
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Affiliation(s)
- Janez Mulec
- Research Centre of the Slovenian Academy of Sciences and Arts, Karst Research Institute, Titov trg 2, 6230, Postojna, Slovenia,
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Luong TQ, Winter R. Combined pressure and cosolvent effects on enzyme activity – a high-pressure stopped-flow kinetic study on α-chymotrypsin. Phys Chem Chem Phys 2015; 17:23273-8. [DOI: 10.1039/c5cp03529e] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pressure enhances the hydrolysis of peptides catalysed by α-CT, which is efficiently and differently modulated by chaotropic and kosmotropic cosolvents.
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Affiliation(s)
- Trung Quan Luong
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44221 Dortmund
- Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44221 Dortmund
- Germany
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35
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Sokmen BB, Gumrukcuoglu N, Ugras S, Sahin H, Sagkal Y, Ugras HI. Synthesis, Antibacterial, Antiurease, and Antioxidant Activities of Some New 1,2,4-Triazole Schiff Base and Amine Derivatives. Appl Biochem Biotechnol 2014; 175:705-14. [DOI: 10.1007/s12010-014-1307-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
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36
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Khan R, Quradha MM, Saif AQ, Ali J, Rauf A, Khan A. Comparative urease enzyme inhibition profile of leaves and stems ofRumex nervosusvahl. Nat Prod Res 2014; 28:2355-7. [DOI: 10.1080/14786419.2014.940346] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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37
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Qin J, Lei N, Zhu HL. Synthesis, structural characterization, molecular docking, and urease inhibition studies of dinuclear cobalt(II) complexes derived from 3,5-bis(pyridin-2-yl)-4-amino-1,2,4-triazole. J COORD CHEM 2014. [DOI: 10.1080/00958972.2014.909591] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jie Qin
- School of Life Sciences, Shandong University of Technology, Zibo, PR China
| | - Na Lei
- School of Life Sciences, Shandong University of Technology, Zibo, PR China
| | - Hai-Liang Zhu
- School of Life Sciences, Shandong University of Technology, Zibo, PR China
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39
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Mazzei L, Ciurli S, Zambelli B. Hot biological catalysis: isothermal titration calorimetry to characterize enzymatic reactions. J Vis Exp 2014. [PMID: 24747990 DOI: 10.3791/51487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Isothermal titration calorimetry (ITC) is a well-described technique that measures the heat released or absorbed during a chemical reaction, using it as an intrinsic probe to characterize virtually every chemical process. Nowadays, this technique is extensively applied to determine thermodynamic parameters of biomolecular binding equilibria. In addition, ITC has been demonstrated to be able of directly measuring kinetics and thermodynamic parameters (kcat, KM, ΔH) of enzymatic reactions, even though this application is still underexploited. As heat changes spontaneously occur during enzymatic catalysis, ITC does not require any modification or labeling of the system under analysis and can be performed in solution. Moreover, the method needs little amount of material. These properties make ITC an invaluable, powerful and unique tool to study enzyme kinetics in several applications, such as, for example, drug discovery. In this work an experimental ITC-based method to quantify kinetics and thermodynamics of enzymatic reactions is thoroughly described. This method is applied to determine kcat and KM of the enzymatic hydrolysis of urea by Canavalia ensiformis (jack bean) urease. Calculation of intrinsic molar enthalpy (ΔHint) of the reaction is performed. The values thus obtained are consistent with previous data reported in literature, demonstrating the reliability of the methodology.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna;
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Li X, Yang X, Li Y, Gou Y, Wang Q. Synthesis, structure and urease inhibition studies of dimeric copper(II) complexes with a tridentate Schiff base ligand derived from tetrahydrofurfurylamine. Inorganica Chim Acta 2013. [DOI: 10.1016/j.ica.2013.08.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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41
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Synthesis, molecular docking and kinetic properties of β-hydroxy-β-phenylpropionyl-hydroxamic acids as Helicobacter pylori urease inhibitors. Eur J Med Chem 2013; 68:212-21. [DOI: 10.1016/j.ejmech.2013.07.047] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 07/03/2013] [Accepted: 07/05/2013] [Indexed: 11/23/2022]
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42
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Dong X, Guo T, Li Y, Cui Y, Wang Q. Synthesis, structure and urease inhibition studies of Schiff base copper(II) complexes with planar four-coordinate copper(II) centers. J Inorg Biochem 2013; 127:82-9. [DOI: 10.1016/j.jinorgbio.2013.07.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 07/27/2013] [Accepted: 07/27/2013] [Indexed: 12/21/2022]
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43
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Xiao ZP, Peng ZY, Dong JJ, He J, Ouyang H, Feng YT, Lu CL, Lin WQ, Wang JX, Xiang YP, Zhu HL. Synthesis, structure-activity relationship analysis and kinetics study of reductive derivatives of flavonoids as Helicobacter pylori urease inhibitors. Eur J Med Chem 2013; 63:685-95. [PMID: 23567958 DOI: 10.1016/j.ejmech.2013.03.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/04/2013] [Accepted: 03/08/2013] [Indexed: 11/29/2022]
Abstract
In a continuing study for discovering urease inhibitors based on flavonoids, nineteen reductive derivatives of flavonoids were synthesized and evaluated against Helicobacter pylori urease. Analysis of structure-activity relationship disclosed that 4-deoxy analogues are more potent than other reductive products. Out of them, 4',7,8-trihydroxyl-2-isoflavene (13) was found to be the most active with IC50 of 0.85 μM, being over 20-fold more potent than the commercial available urease inhibitor, acetohydroxamic acid (AHA). Kinetics study revealed that 13 is a competitive inhibitor of H. pylori urease with a Ki value of 0.641 μM, which is well matched with the results of molecular docking. Biological evaluation and mechanism study of 13 suggest that it is a good candidate for discovering novel anti-gastritis and anti-gastric ulcer agent.
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Affiliation(s)
- Zhu-Ping Xiao
- College of Chemistry and Chemical Engineering, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, Jishou University, Jishou 416000, PR China.
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Du N, Chen M, Liu Z, Sheng L, Xu H, Chen S. Kinetics and mechanism of jack bean urease inhibition by Hg2+. Chem Cent J 2012; 6:154. [PMID: 23228101 PMCID: PMC3537586 DOI: 10.1186/1752-153x-6-154] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 11/30/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND Jack bean urease (EC 3.5.1.5) is a metalloenzyme, which catalyzes the hydrolysis of urea to produce ammonia and carbon dioxide. The heavy metal ions are common inhibitors to control the rate of the enzymatic urea hydrolysis, which take the Hg2+ as the representative. Hg2+ affects the enzyme activity causing loss of the biological function of the enzyme, which threatens the survival of many microorganism and plants. However, inhibitory kinetics of urease by the low concentration Hg2+ has not been explored fully. In this study, the inhibitory effect of the low concentration Hg2+ on jack bean urease was investigated in order to elucidate the mechanism of Hg2+ inhibition. RESULTS According to the kinetic parameters for the enzyme obtained from Lineweaver-Burk plot, it is shown that the Km is equal to 4.6±0.3 mM and Vm is equal to 29.8±1.7 μmol NH3/min mg. The results show that the inhibition of jack bean urease by Hg2+ at low concentration is a reversible reaction. Equilibrium constants have been determined for Hg2+ binding with the enzyme or the enzyme-substrate complexes (Ki =0.012 μM). The results show that the Hg2+ is a noncompetitive inhibitor. In addition, the kinetics of enzyme inhibition by the low concentration Hg2+ has been studied using the kinetic method of the substrate reaction. The results suggest that the enzyme first reversibly and quickly binds Hg2+ and then undergoes a slow reversible course to inactivation. Furthermore, the rate constant of the forward reactions (k+0) is much larger than the rate constant of the reverse reactions (k-0). By combining with the fact that the enzyme activity is almost completely lost at high concentration, the enzyme is completely inactivated when the Hg2+ concentration is high enough. CONCLUSIONS These results suggest that Hg2+ has great impacts on the urease activity and the established inhibition kinetics model is suitable.
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Affiliation(s)
- Nana Du
- Fuyang Normal College, College of Chemistry and Chemical Engineering, Fuyang, 236037, People’s Republic of China
| | - Mingming Chen
- Fuyang Normal College, College of Chemistry and Chemical Engineering, Fuyang, 236037, People’s Republic of China
- Anhui University, College of Chemistry and Chemical Engineering, Hefei, 230039, People’s Republic of China
| | - Zhaodi Liu
- Fuyang Normal College, College of Chemistry and Chemical Engineering, Fuyang, 236037, People’s Republic of China
| | - Liangquan Sheng
- Fuyang Normal College, College of Chemistry and Chemical Engineering, Fuyang, 236037, People’s Republic of China
- Anhui University, College of Chemistry and Chemical Engineering, Hefei, 230039, People’s Republic of China
| | - Huajie Xu
- Fuyang Normal College, College of Chemistry and Chemical Engineering, Fuyang, 236037, People’s Republic of China
| | - Shuisheng Chen
- Fuyang Normal College, College of Chemistry and Chemical Engineering, Fuyang, 236037, People’s Republic of China
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