1
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Memantine derived compounds as potent in vitro inhibitors of urease: Repurposing of memantine, sonication assisted derivatization and in vitro enzyme inhibition, kinetics and molecular docking studies. Med Chem Res 2023. [DOI: 10.1007/s00044-023-03020-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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2
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Urea Decomposition Mechanism by Dinuclear Nickel Complexes. Molecules 2023; 28:molecules28041659. [PMID: 36838646 PMCID: PMC9964345 DOI: 10.3390/molecules28041659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
Urease is an enzyme containing a dinuclear nickel active center responsible for the hydrolysis of urea into carbon dioxide and ammonia. Interestingly, inorganic models of urease are unable to mimic its mechanism despite their similarities to the enzyme active site. The reason behind the discrepancy in urea decomposition mechanisms between inorganic models and urease is still unknown. To evaluate this factor, we synthesized two bis-nickel complexes, [Ni2L(OAc)] (1) and [Ni2L(Cl)(Et3N)2] (2), based on the Trost bis-Pro-Phenol ligand (L) and encompassing different ligand labilities with coordination geometries similar to the active site of jack bean urease. Both mimetic complexes produced ammonia from urea, (1) and (2), were ten- and four-fold slower than urease, respectively. The presence and importance of several reaction intermediates were evaluated both experimentally and theoretically, indicating the aquo intermediate as a key intermediate, coordinating urea in an outer-sphere manner. Both complexes produced isocyanate, revealing an activated water molecule acting as a base. In addition, the reaction with different substrates indicated the biomimetic complexes were able to hydrolyze isocyanate. Thus, our results indicate that the formation of an outer-sphere complex in the urease analogues might be the reason urease performs a different mechanism.
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3
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He B, Dong C, Wang X, Cao Y, Gao Y, Yang M, Zhang J, Jing C, Shi D, You Z. Syntheses, characterization, crystal structures and Jack bean urease inhibitory property of NiII, CdII, CuII and FeIII complexes with bis-Schiff bases. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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Loharch S, Berlicki Ł. Rational Development of Bacterial Ureases Inhibitors. CHEM REC 2022; 22:e202200026. [PMID: 35502852 DOI: 10.1002/tcr.202200026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/28/2022] [Indexed: 12/23/2022]
Abstract
Urease, an enzyme that catalyzes the hydrolysis of urea, is a virulence factor of various pathogenic bacteria. In particular, Helicobacter pylori, that colonizes the digestive tract and Proteus spp., that can infect the urinary tract, are related to urease activity. Therefore, urease inhibitors are considered as potential therapeutics against these infections. This review describes current knowledge of the structures, activity, and biological importance of bacterial ureases. Moreover, the structure-based design of several classes of bacterial urease inhibitors is presented and discussed. Phosphinic and phosphonic acids were applied as transition-state analogues, while Michael acceptors and ebselen derivatives were applied as covalent binders of cysteine residue. This review incorporates bacterial urease inhibitors from literature published between 2008 and 2021.
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Affiliation(s)
- Saurabh Loharch
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
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5
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Wackett LP. Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances. Microb Biotechnol 2021; 15:773-792. [PMID: 34570953 PMCID: PMC8913905 DOI: 10.1111/1751-7915.13928] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Poly‐ and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today’s society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called ‘forever chemicals’ due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.
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Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, 55108, USA
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6
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The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate. J Biol Inorg Chem 2020; 25:829-845. [PMID: 32809087 PMCID: PMC7433671 DOI: 10.1007/s00775-020-01808-w] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/29/2020] [Indexed: 01/22/2023]
Abstract
This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry.
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7
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Dalby FR, Svane S, Sigurdarson JJ, Sørensen MK, Hansen MJ, Karring H, Feilberg A. Synergistic Tannic Acid-Fluoride Inhibition of Ammonia Emissions and Simultaneous Reduction of Methane and Odor Emissions from Livestock Waste. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:7639-7650. [PMID: 32407626 DOI: 10.1021/acs.est.0c01231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gaseous emissions from livestock production are complex mixtures including ammonia, methane, volatile organic compounds (VOC), and H2S. These contribute to eutrophication, reduced air quality, global warming, and odor nuisance. It is imperative that these gases are mitigated in an environmentally sustainable manner. We present the discovery of a microbial inhibitor combo consisting of tannic acid and sodium fluoride (TA-NaF), which exhibits clear synergistic inhibition of ammonia production in pure bacteria culture and in pig manure while simultaneously inhibiting methane and odorant (H2S and VOC) emissions. In laboratory headspace experiments on pig manure, we used proton-transfer-reaction mass spectrometry and cavity ring-down spectroscopy to measure the effect of TA-NaF on gaseous emissions. Ammonia emission was reduced by more than 95%, methane by up to ∼99%, and odor activity value by more than 50%. Microbial community analysis and gas emission data suggest that TA-NaF acts as an efficient generic microbial inhibitor, and we hypothesize that the synergistic inhibitory effect on ammonia production is related to tannic acid causing cell membrane leakage allowing fluoride ions easy access to urease.
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Affiliation(s)
- Frederik R Dalby
- Department of Engineering, Air Quality Engineering, Aarhus University, Finlandsgade 10, 8200 Aarhus N, Denmark
| | - Simon Svane
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jens Jakob Sigurdarson
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Morten K Sørensen
- Department of Engineering, Air Quality Engineering, Aarhus University, Finlandsgade 10, 8200 Aarhus N, Denmark
| | - Michael J Hansen
- Department of Engineering, Air Quality Engineering, Aarhus University, Finlandsgade 10, 8200 Aarhus N, Denmark
| | - Henrik Karring
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Anders Feilberg
- Department of Engineering, Air Quality Engineering, Aarhus University, Finlandsgade 10, 8200 Aarhus N, Denmark
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8
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Inhibition of urease activity by different compounds provides insight into the modulation and association of bacterial nickel import and ureolysis. Sci Rep 2020; 10:8503. [PMID: 32444844 PMCID: PMC7244745 DOI: 10.1038/s41598-020-65107-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/28/2020] [Indexed: 01/29/2023] Open
Abstract
The nickel-dependent urease enzyme is responsible for the hydrolysis of urea to ammonia and carbon dioxide. A number of bacteria produce urease (ureolytic bacteria) and are associated with various infectious diseases and ammonia emissions from agriculture. We report the first comprehensive comparison of the inhibition of urease activity by compounds analysed under the same conditions. Thus, 71 commercially available compounds were screened for their anti-ureolytic properties against both the ureolytic bacterium Klebsiella pneumoniae and purified jack bean urease. Of the tested compounds, 30 showed more than 25% inhibition of the ureolytic activity of Klebsiella pneumoniae or jack bean urease, and among these, carbon disulfide, N-phenylmaleimide, diethylenetriaminepentaacetic acid, sodium pyrrolidinedithiocarbamate, 1,2,4-butanetricarboxylic acid, tannic acid, and gallic acid have not previously been reported to possess anti-ureolytic properties. The diverse effects of metal ion chelators on ureolysis were investigated using a cellular nickel uptake assay. Ethylenediaminetetraacetic acid (EDTA) and dimethylglyoxime (DMG) clearly reduced the nickel import and ureolytic activity of cells, oxalic acid stimulated nickel import but reduced the ureolytic activity of cells, 1,2,4-butanetricarboxylic acid strongly stimulated nickel import and slightly increased the ureolytic activity of cells, while L-cysteine had no effect on nickel import but efficiently reduced the ureolytic activity of cells.
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Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme. Angew Chem Int Ed Engl 2019; 58:7415-7419. [DOI: 10.1002/anie.201903565] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl)Faculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
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10
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Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl)Faculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
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11
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Arora R, Issar U, Kakkar R. Identification of novel urease inhibitors: pharmacophore modeling, virtual screening and molecular docking studies. J Biomol Struct Dyn 2018; 37:4312-4326. [PMID: 30580662 DOI: 10.1080/07391102.2018.1546620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Pharmacophore modeling and atom-based three-dimensional quantitative structure-activity relationship (3D-QSAR) have been developed on N-acylglycino- and hippurohydroxamic acid derivatives, which are known potential inhibitors of urease. This is followed by virtual screening and ADMET (absorption, distribution, metabolism, excretion and toxicity) studies on a large library of known drugs in order to get lead molecules as Helicobacter pylori urease inhibitors. A suitable three-featured pharmacophore model comprising one H-bond acceptor and two H-bond donor features (ADD.10) has been found to be the best QSAR model. An external library of compounds (∼3000 molecules), pre-filtered using Lipinski's rule of five, has been further screened using the pharmacophore model ADD.10. By analyzing the fitness of the hits with respect to the pharmacophore model and their binding interaction inside the urease active site, four molecules have been predicted to be extremely good urease inhibitors. Two of these have significant potential and should be taken up for further drug-designing process.
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Affiliation(s)
- Richa Arora
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi , Delhi , India
| | - Upasana Issar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi , Delhi , India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi , Delhi , India
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12
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Wang H, Zhang X, Zhao Y, Zhang D, Jin F, Fan Y. Three Co(II) complexes with a sexidentate N 2 O 4 -donor bis-Schiff base ligand: Synthesis, crystal structures, DFT studies, urease inhibition and molecular docking studies. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.07.077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Selleck C, Guddat LW, Ollis DL, Schenk G, Pedroso MM. High resolution crystal structure of a fluoride-inhibited organophosphate-degrading metallohydrolase. J Inorg Biochem 2017; 177:287-290. [PMID: 28673485 DOI: 10.1016/j.jinorgbio.2017.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/16/2017] [Accepted: 06/22/2017] [Indexed: 11/17/2022]
Abstract
Metal ion-dependent, organophosphate-degrading enzymes (OP hydrolases) have received increasing attention due to their ability to degrade and thus detoxify commonly used pesticides and nerve agents such as sarin and VX. These enzymes thus garner strong potential as bioremediators. The OP hydrolase from Agrobacterium radiobacter (OpdA) is one of the most efficient members of this group of enzymes. Previous studies have indicated that the choice of the hydrolysis-initiating nucleophile may depend on the pH of the reaction, with a metal ion-bridging hydroxide being preferred at lower pH (i.e. pH≤8.5), and a terminally coordinated hydroxide at higher pH (i.e. pH>9.0). Furthermore, fluoride was shown to be a potent inhibitor of the reaction, but only at low pH. Here, the crystal structure (1.3Å, pH6) of OpdA in presence of fluoride is described. While the first coordination sphere in the active site displays minimal changes in the presence of fluoride, the hydrogen bonding network that connects the dimetallic metal center to the substrate binding pocket is disrupted. Thus, the structure of fluoride-inhibited OpdA demonstrates the significance of this hydrogen bond network in controlling the mechanism and function of this enzyme.
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Affiliation(s)
- Christopher Selleck
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - David L Ollis
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia.
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia.
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14
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Li D, Zhang Y, Song H, Lu L, Liu D, Yuan Y. Aminoalcohol-Induced Activation of Organophosphorus Hydrolase (OPH) towards Diisopropylfluorophosphate (DFP). PLoS One 2017; 12:e0169937. [PMID: 28085964 PMCID: PMC5234802 DOI: 10.1371/journal.pone.0169937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/22/2016] [Indexed: 11/19/2022] Open
Abstract
Aminoalcohols have been addressed as activating buffers for alkaline phosphatase. However, there is no record on the buffer activation regarding organophosphorus hydrolase (OPH). Here we reported the activating effects of aminoalcohols on OPH-catalyzed hydrolysis of diisopropylfluorophosphate (DFP), an analog molecule of G-type warfare agents. The kinetic parametors kcat, Vmax and kcat/Km in the OPH reaction were remarkably increased in the buffers (pH 8.0, 25°C) containing aminoalcohols with C2 between nitrogen (N) and oxygen (O) in their structures, including triethanolamine (TEA), diethanolamine, monoethanolamine, 1-amino-2-propanol, 2-amino-2-methyl-1-propanol, and triisopropanolamine. In contrast, much lower or no rate-enhancing effects were observed in the adding of amines, alcohols, amine/alcohol mixtures, or 3-amino-1-propanol (C3 between N and O). The 300 mM TEA further increased DFP-degrading activities of OPH mutants F132Y and L140Y, the previously reported OPH mutants with desirable activities towards DFP. However, the treatment of ethylenediaminetetraacetate (EDTA) markedly abolished the TEA-induced activation of OPH. The product fluoride effectively inhibited OPH-catalyzed hydrolysis of DFP by a linear mixed inhibition (inhibition constant Ki ~ 3.21 mM), which was partially released by TEA adding at initial or later reaction stage. The obtained results indicate the activation of OPH by aminoalcohol buffers could be attributed to the reduction of fluoride inhibition, which would be beneficial to the hydrolase-based detoxification of organophosphofluoridate.
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Affiliation(s)
- Dandan Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, P. R. China
- Department of Biochemistry, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, P.R. China
| | - Yunze Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Haitao Song
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Liangqiu Lu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Deli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, P. R. China
- * E-mail: (YY); (DL)
| | - Yongze Yuan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, P. R. China
- * E-mail: (YY); (DL)
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15
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Chen ZJ, Chen YN, Xu CN, Zhao SS, Cao QY, Qian SS, Qin J, Zhu HL. Synthesis, crystal structures, molecular docking, and in vitro biological activities evaluation of transition metal complexes with 4-(3,4-dichlorophenyl) piperazine-1-carboxylic acid. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.03.084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Cui Y, Qiao L, Li Y, Jing H, Li Y, Wang Q. Synthesis, solid-state structures, and urease inhibition activities of new copper(II) complexes based on O,N,O-tridentate Schiff bases. J COORD CHEM 2016. [DOI: 10.1080/00958972.2016.1206199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Yongming Cui
- Ministry of Education, Engineering Research Center for Clean Production of Textile Printing and Dyeing, Wuhan Textile University, Wuhan, PR China
| | - Lu Qiao
- Ministry of Education, Engineering Research Center for Clean Production of Textile Printing and Dyeing, Wuhan Textile University, Wuhan, PR China
| | - Yi Li
- Ministry of Education, Engineering Research Center for Clean Production of Textile Printing and Dyeing, Wuhan Textile University, Wuhan, PR China
| | - Hairui Jing
- Ministry of Education, Engineering Research Center for Clean Production of Textile Printing and Dyeing, Wuhan Textile University, Wuhan, PR China
| | - Yuguang Li
- Ministry of Education, Engineering Research Center for Clean Production of Textile Printing and Dyeing, Wuhan Textile University, Wuhan, PR China
| | - Qiang Wang
- Ministry of Education, Engineering Research Center for Clean Production of Textile Printing and Dyeing, Wuhan Textile University, Wuhan, PR China
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17
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Gupta SP. QSAR Studies on Hydroxamic Acids: A Fascinating Family of Chemicals with a Wide Spectrum of Activities. Chem Rev 2015; 115:6427-90. [DOI: 10.1021/cr500483r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Satya P. Gupta
- Department of Applied Sciences, National Institute of Technical Teachers’ Training and Research, Shamla
Hills, Bhopal-462002, India
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18
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Rauf MK, Yaseen S, Badshah A, Zaib S, Arshad R, Tahir MN, Iqbal J. Synthesis, characterization and urease inhibition, in vitro anticancer and antileishmanial studies of Ni(II) complexes with N,N,N'-trisubstituted thioureas. J Biol Inorg Chem 2015; 20:541-54. [PMID: 25604966 DOI: 10.1007/s00775-015-1239-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/07/2015] [Indexed: 12/20/2022]
Abstract
A series of N,N,N'-trisubstituted thioureas (1-12) and their Ni(II) complexes (1a-12a) were synthesized and characterized by multinuclear ((1)H and (13)C) NMR, FT-IR spectroscopy and LC-MS techniques in combination with elemental analysis. The crystal structures of both ligands and Ni(II) chelates of type Ni(L-O, S)2 were determined by single crystal X-ray diffraction analysis. All the complexes were adopted to have square planar geometry, where the N,N,N'-trisubstituted thioureas showed bidentate mode of coordination at nickel centre through oxygen and sulfur atoms. The synthesized complexes were screened for potential inhibitors of Jack bean urease. Compounds 1a and 3a were observed as most potent inhibitors of urease exhibiting IC50 values of 1.17 ± 0.12 and 1.19 ± 0.41 µM, respectively. Cytotoxicity assay on lung carcinoma (H-157) and kidney fibroblast (BHK-21) cell showed that compounds were significant anticancer agents. Additionally, the complexes were tested against Leishmania major and found to be potent antileishmanial agents.
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19
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Benini S, Cianci M, Mazzei L, Ciurli S. Fluoride inhibition of Sporosarcina pasteurii urease: structure and thermodynamics. J Biol Inorg Chem 2014; 19:1243-61. [DOI: 10.1007/s00775-014-1182-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/30/2014] [Indexed: 01/25/2023]
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20
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Comparative investigation of the reaction mechanisms of the organophosphate-degrading phosphotriesterases from Agrobacterium radiobacter (OpdA) and Pseudomonas diminuta (OPH). J Biol Inorg Chem 2014; 19:1263-75. [DOI: 10.1007/s00775-014-1183-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 07/30/2014] [Indexed: 11/26/2022]
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21
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Yao M, Tu W, Chen X, Zhan CG. Reaction pathways and free energy profiles for spontaneous hydrolysis of urea and tetramethylurea: unexpected substituent effects. Org Biomol Chem 2014; 11:7595-605. [PMID: 24097048 DOI: 10.1039/c3ob41055b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It has been difficult to directly measure the spontaneous hydrolysis rate of urea and, thus, 1,1,3,3-tetramethylurea (Me4U) was used as a model to determine the "experimental" rate constant for urea hydrolysis. The use of Me4U was based on an assumption that the rate of urea hydrolysis should be 2.8 times that of Me4U hydrolysis because the rate of acetamide hydrolysis is 2.8 times that of N,N-dimethyl-acetamide hydrolysis. The present first-principles electronic-structure calculations on the competing non-enzymatic hydrolysis pathways have demonstrated that the dominant pathway is the neutral hydrolysis via the CN addition for both urea (when pH < ~11.6) and Me4U (regardless of pH), unlike the non-enzymatic hydrolysis of amides where alkaline hydrolysis is dominant. Based on the computational data, the substituent shift of the free energy barrier calculated for the neutral hydrolysis is remarkably different from that for the alkaline hydrolysis, and the rate constant for the urea hydrolysis should be ~1.3 × 10(9)-fold lower than that (4.2 × 10(-12) s(-1)) measured for the Me4U hydrolysis. As a result, the rate enhancement and catalytic proficiency of urease should be 1.2 × 10(25) and 3 × 10(27) M(-1), respectively, suggesting that urease surpasses proteases and all other enzymes in its power to enhance the rate of reaction. All of the computational results are consistent with available experimental data for Me4U, suggesting that the computational prediction for urea is reliable.
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Affiliation(s)
- Min Yao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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Boer JL, Mulrooney SB, Hausinger RP. Nickel-dependent metalloenzymes. Arch Biochem Biophys 2014; 544:142-52. [PMID: 24036122 PMCID: PMC3946514 DOI: 10.1016/j.abb.2013.09.002] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/31/2013] [Accepted: 09/03/2013] [Indexed: 11/29/2022]
Abstract
This review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase I, acireductone dioxygenase, urease, superoxide dismutase, [NiFe]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme A synthase/decarbonylase, methyl-coenzyme M reductase, and lactate racemase. These enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more complex nickel-containing clusters, and nickel-tetrapyrroles. Selected other enzymes are active with nickel, but the physiological relevance of this metal specificity is unclear. Additional nickel-containing proteins of undefined function have been identified.
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Affiliation(s)
- Jodi L Boer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Scott B Mulrooney
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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23
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Affiliation(s)
- Michael J Maroney
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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24
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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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25
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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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26
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Gou Y, Yu M, Li Y, Peng Y, Chen W. Synthesis, structures and urease inhibition studies of dimeric copper(II) complexes of Schiff bases derived from glycine. Inorganica Chim Acta 2013. [DOI: 10.1016/j.ica.2013.03.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Wang CY, Li JF, Zhang ZS, Liu Y, Yi L, Sheng SJ. Synthesis, Crystal Structures, and Urease Inhibitory Properties of Two Isostructural Dinuclear Zinc(II) Complexes With Schiff Base 5-Methoxy-2-[(2-methylaminoethylimino)methyl]phenol. ACTA ACUST UNITED AC 2012. [DOI: 10.1080/15533174.2012.680151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Chen-Yi Wang
- a Department of Chemistry , Huzhou University , Huzhou , P. R. China
| | - Jing-Fen Li
- a Department of Chemistry , Huzhou University , Huzhou , P. R. China
| | - Zhong-Shan Zhang
- a Department of Chemistry , Huzhou University , Huzhou , P. R. China
| | - Yang Liu
- a Department of Chemistry , Huzhou University , Huzhou , P. R. China
| | - Li Yi
- a Department of Chemistry , Huzhou University , Huzhou , P. R. China
| | - Su-Jun Sheng
- a Department of Chemistry , Huzhou University , Huzhou , P. R. China
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28
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Dong X, Li Y, Li Z, Cui Y, Zhu H. Synthesis, structures and urease inhibition studies of copper(II) and nickel(II) complexes with bidentate N,O-donor Schiff base ligands. J Inorg Biochem 2012; 108:22-9. [DOI: 10.1016/j.jinorgbio.2011.12.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/25/2011] [Accepted: 12/21/2011] [Indexed: 12/23/2022]
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29
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Huang X, Hernick M. Examination of mechanism of N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside deacetylase (MshB) reveals unexpected role for dynamic tyrosine. J Biol Chem 2012; 287:10424-10434. [PMID: 22315231 DOI: 10.1074/jbc.m111.320184] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Actinomycetes are a group of gram-positive bacteria that includes pathogenic mycobacterial species, such as Mycobacterium tuberculosis. These organisms do not have glutathione and instead utilize the small molecule mycothiol (MSH) as their primary reducing agent and for the detoxification of xenobiotics. Due to these important functions, enzymes involved in MSH biosynthesis and MSH-dependent detoxification are targets for drug development. The metal-dependent deacetylase N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside deacetylase (MshB) catalyzes the hydrolysis of N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside to form 1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside and acetate in MSH biosynthesis. Herein we examine the chemical mechanism of MshB. We demonstrate that the side chains of Asp-15, Tyr-142, His-144, and Asp-146 are important for catalytic activity. We show that NaF is an uncompetitive inhibitor of MshB, consistent with a metal-water/hydroxide functioning as the reactive nucleophile in the catalytic mechanism. We have previously shown that MshB activity has a bell-shaped dependence on pH with pK(a) values of ∼7.3 and 10.5 (Huang, X., Kocabas, E. and Hernick, M. (2011) J. Biol. Chem. 286, 20275-20282). Mutagenesis experiments indicate that the observed pK(a) values reflect ionization of Asp-15 and Tyr-142, respectively. Together, findings from our studies suggest that MshB functions through a general acid-base pair mechanism with the side chain of Asp-15 functioning as the general base catalyst and His-144 serving as the general acid catalyst, whereas the side chain of Tyr-142 probably assists in polarizing substrate/stabilizing the oxyanion intermediate. Additionally, our results indicate that Tyr-142 is a dynamic side chain that plays key roles in catalysis, modulating substrate binding, chemistry, and product release.
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Affiliation(s)
- Xinyi Huang
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061
| | - Marcy Hernick
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061.
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Carter EL, Flugga N, Boer JL, Mulrooney SB, Hausinger RP. Interplay of metal ions and urease. Metallomics 2011; 1:207-21. [PMID: 20046957 DOI: 10.1039/b903311d] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Urease, the first enzyme to be crystallized, contains a dinuclear nickel metallocenter that catalyzes the decomposition of urea to produce ammonia, a reaction of great agricultural and medical importance. Several mechanisms of urease catalysis have been proposed on the basis of enzyme crystal structures, model complexes, and computational efforts, but the precise steps in catalysis and the requirement of nickel versus other metals remain unclear. Purified bacterial urease is partially activated via incubation with carbon dioxide plus nickel ions; however, in vitro activation also has been achieved with manganese and cobalt. In vivo activation of most ureases requires accessory proteins that function as nickel metallochaperones and GTP-dependent molecular chaperones or play other roles in the maturation process. In addition, some microorganisms control their levels of urease by metal ion-dependent regulatory mechanisms.
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Affiliation(s)
- Eric L Carter
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
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Misiak K, Casey E, Murphy CD. Factors influencing 4-fluorobenzoate degradation in biofilm cultures of Pseudomonas knackmussii B13. WATER RESEARCH 2011; 45:3512-3520. [PMID: 21536315 DOI: 10.1016/j.watres.2011.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 04/07/2011] [Accepted: 04/13/2011] [Indexed: 05/30/2023]
Abstract
Membrane aerated biofilm reactors (MABRs) have potential in wastewater treatment as they permit simultaneous COD minimisation, nitrification and denitrification. Here we report on the application of the MABR to the removal of fluorinated xenobiotics from wastewater, employing a Pseudomonas knackmussii monoculture to degrade the model compound 4-fluorobenzoate. Growth of biofilm in the MABR using the fluorinated compound as the sole carbon source occurred in two distinct phases, with early rapid growth (up to 0.007 h(-1)) followed by ten-fold slower growth after 200 h operation. Furthermore, the specific 4-fluorobenzoate degradation rate decreased from 1.2 g g(-1) h(-1) to 0.2 g g(-1) h(-1), indicating a diminishing effectiveness of the biofilm as thickness increased. In planktonic cultures stoichiometric conversion of substrate to the fluoride ion was observed, however in the MABR, approximately 85% of the fluorine added was recovered as fluoride, suggesting accumulation of 'fluorine' in the biofilm might account for the decreasing efficiency. This was investigated by culturing the bacterium in a tubular biofilm reactor (TBR), revealing that there was significant fluoride accumulation within the biofilm (0.25 M), which might be responsible for inhibition of 4-fluorobenzoate degradation. This contention was supported by the observation of the inhibition of biofilm accumulation on glass cover slips in the presence of 40 mM fluoride. These experiments highlight the importance of fluoride ion accumulation on biofilm performance when applied to organofluorine remediation.
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Affiliation(s)
- Katarzyna Misiak
- School of Chemical and Bioprocess Engineering, University College Dublin, Ireland
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32
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Wang CY, Ye JY. Synthesis, crystal structures, and urease inhibitory activity of cooper(II) complexes with schiff bases. RUSS J COORD CHEM+ 2011. [DOI: 10.1134/s1070328411020126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Synthesis, crystal structure, and urease inhibition studies of copper(II) and cobalt(III) complexes with bi(2-fluorobenzylaminoethyl)amine. TRANSIT METAL CHEM 2011. [DOI: 10.1007/s11243-011-9472-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Wang CY, Han ZP, Ye JY, Wu X. Syntheses, Crystal Structures, and Urease Inhibitory Activity of Two Zinc Complexes with 2-[(3-Cyclohexylaminopropylimino)methyl]-6-alkoxyphenol. ACTA ACUST UNITED AC 2010. [DOI: 10.1080/15533174.2010.522645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Chen-Yi Wang
- a Department of Chemistry , Huzhou University , Huzhou, P. R. China
| | - Zhi-Ping Han
- a Department of Chemistry , Huzhou University , Huzhou, P. R. China
| | - Jin-Yun Ye
- a Department of Chemistry , Huzhou University , Huzhou, P. R. China
| | - Xiang Wu
- a Department of Chemistry , Huzhou University , Huzhou, P. R. China
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35
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Kumar S, Kayastha AM. Inhibition studies of soybean (Glycine max) urease with heavy metals, sodium salts of mineral acids, boric acid, and boronic acids. J Enzyme Inhib Med Chem 2010; 25:646-52. [PMID: 20014894 DOI: 10.3109/14756360903468155] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Various inhibitors were tested for their inhibitory effects on soybean urease. The K(i) values for boric acid, 4-bromophenylboronic acid, butylboronic acid, and phenylboronic acid were 0.20 +/- 0.05 mM, 0.22 +/- 0.04 mM, 1.50 +/- 0.10 mM, and 2.00 +/- 0.11 mM, respectively. The inhibition was competitive type with boric acid and boronic acids. Heavy metal ions including Ag(+), Hg(2+), and Cu(2+) showed strong inhibition on soybean urease, with the silver ion being a potent inhibitor (IC(50) = 2.3 x 10(-8) mM). Time-dependent inhibition studies exhibited biphasic kinetics with all heavy metal ions. Furthermore, inhibition studies with sodium salts of mineral acids (NaF, NaCl, NaNO(3), and Na(2)SO(4)) showed that only F(-) inhibited soybean urease significantly (IC(50) = 2.9 mM). Competitive type of inhibition was observed for this anion with a K(i) value of 1.30 mM.
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Affiliation(s)
- Sandeep Kumar
- School of Biotechnology, Faculty of science, Banaras Hindu University, Varanasi 221005, India
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36
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Cui YM, Yan WX, Cai YJ, Chen W, Zhu HL. Synthesis, molecular docking, and inhibitory activity of a Ni Schiff-base complex against urease. J COORD CHEM 2010. [DOI: 10.1080/00958972.2010.517268] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yong Ming Cui
- a Engineering Research Center for Clean Production of Textile Printing, Ministry of Education, Wuhan Textile University , Wuhan 430073, P.R. China
- b State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, P.R. China
| | - Wen Xuan Yan
- c Library of Wuhan Textile University , Wuhan 430073, P.R. China
| | - Ying Jie Cai
- a Engineering Research Center for Clean Production of Textile Printing, Ministry of Education, Wuhan Textile University , Wuhan 430073, P.R. China
| | - Wu Chen
- a Engineering Research Center for Clean Production of Textile Printing, Ministry of Education, Wuhan Textile University , Wuhan 430073, P.R. China
| | - Hai Liang Zhu
- a Engineering Research Center for Clean Production of Textile Printing, Ministry of Education, Wuhan Textile University , Wuhan 430073, P.R. China
- b State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, P.R. China
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37
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Lee WZ, Tseng HS, Wang TL, Tsai HL, Kuo TS. Bioinspired Catalytic Conjugate Additions of Thiophenols to α,β-Enones by a Disubstituted Benzoate-Bridged Nickel Mimic for the Active Site of Urease. Organometallics 2010. [DOI: 10.1021/om100103u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Way-Zen Lee
- Department of Chemistry, National Taiwan Normal University, Taipei 11650, Taiwan
| | - Huan-Sheng Tseng
- Department of Chemistry, National Taiwan Normal University, Taipei 11650, Taiwan
| | - Tzu-Li Wang
- Department of Chemistry, National Taiwan Normal University, Taipei 11650, Taiwan
| | - Hui-Lien Tsai
- Department of Chemistry, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ting-Shen Kuo
- Instrumentation Center, Department of Chemistry, National Taiwan Normal University, Taipei 11650, Taiwan
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38
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Wang CY. Synthesis and crystal structures of cobalt(III) and zinc(II) complexes derived from 4-chloro-2-[(2-morpholin-4-ylethylimino)methyl]phenol with urease inhibitory activity. RUSS J COORD CHEM+ 2010. [DOI: 10.1134/s1070328410030036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Eltayeb AZ, Nimir HI, Brown DA, Lan Y, Anson CE, Powell AK. Magnetic and structural studies of novel tetranickel hydroxamates. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2009.12.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Wang CY. Syntheses, crystal structures, and urease inhibitory properties of copper(II) and zinc(II) complexes with 2-bromo-4-chloro-6-[(2-dimethylaminoethylimino)methyl]phenol. J COORD CHEM 2009. [DOI: 10.1080/00958970902946702] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Chen-Yi Wang
- a Department of Chemistry , Huzhou University , Huzhou 313000, P.R. China
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41
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Krajewska B, Piwowarska Z. Free vs chitosan-immobilized urease: Microenvironmental effects on enzyme inhibitions. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500208852] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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43
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Wang CY, Ye JY, Lv CY, Lan WZ, Zhou JB. Syntheses and crystal structures of two Schiff-base copper(II) complexes with urease inhibition. J COORD CHEM 2009. [DOI: 10.1080/00958970902801493] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Chen-Yi Wang
- a Department of Chemistry , Huzhou University , Huzhou 313000, P. R. China
| | - Jin-Yun Ye
- a Department of Chemistry , Huzhou University , Huzhou 313000, P. R. China
| | - Chun-Yan Lv
- a Department of Chemistry , Huzhou University , Huzhou 313000, P. R. China
| | - Wei-Zhen Lan
- a Department of Chemistry , Huzhou University , Huzhou 313000, P. R. China
| | - Jun-Bo Zhou
- a Department of Chemistry , Huzhou University , Huzhou 313000, P. R. China
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44
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Wang CY, Wu X, Tu SJ, Jiang B. Syntheses and Crystal Structures of Two Schiff Base Copper(II) Complexes with Urease Inhibitory Activity. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/15533170902762603] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Chen-Yi Wang
- a Department of Chemistry , Huzhou University , Huzhou, P. R. China
| | - Xiang Wu
- a Department of Chemistry , Huzhou University , Huzhou, P. R. China
| | - Shu-Jiang Tu
- b Department of Chemistry , Xuzhou Normal University , Xuzhou, P. R. China
| | - Bo Jiang
- b Department of Chemistry , Xuzhou Normal University , Xuzhou, P. R. China
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45
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46
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Werner AK, Sparkes IA, Romeis T, Witte CP. Identification, biochemical characterization, and subcellular localization of allantoate amidohydrolases from Arabidopsis and soybean. PLANT PHYSIOLOGY 2008; 146:418-30. [PMID: 18065556 PMCID: PMC2245841 DOI: 10.1104/pp.107.110809] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 11/26/2007] [Indexed: 05/18/2023]
Abstract
Allantoate amidohydrolases (AAHs) hydrolize the ureide allantoate to ureidoglycolate, CO(2), and two molecules of ammonium. Allantoate degradation is required to recycle purine-ring nitrogen in all plants. Tropical legumes additionally transport fixed nitrogen via allantoin and allantoate into the shoot, where it serves as a general nitrogen source. AAHs from Arabidopsis (Arabidopsis thaliana; AtAAH) and from soybean (Glycine max; GmAAH) were cloned, expressed in planta as StrepII-tagged variants, and highly purified from leaf extracts. Both proteins form homodimers and release 2 mol ammonium/mol allantoate. Therefore, they can truly be classified as AAHs. The kinetic constants determined and the half-maximal activation by 2 to 3 microm manganese are consistent with allantoate being the in vivo substrate of manganese-loaded AAHs. The enzymes were strongly inhibited by micromolar concentrations of fluoride as well as by borate, and by millimolar concentrations of L-asparagine and L-aspartate but not D-asparagine. L-Asparagine likely functions as competitive inhibitor. An Ataah T-DNA mutant, unable to grow on allantoin as sole nitrogen source, is rescued by the expression of StrepII-tagged variants of AtAAH and GmAAH, demonstrating that both proteins are functional in vivo. Similarly, an allantoinase (aln) mutant is rescued by a tagged AtAln variant. Fluorescent fusion proteins of allantoinase and both AAHs localize to the endoplasmic reticulum after transient expression and in transgenic plants. These findings demonstrate that after the generation of allantoin in the peroxisome, plant purine degradation continues in the endoplasmic reticulum.
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Affiliation(s)
- Andrea K Werner
- Freie Universität Berlin, Institut für Biologie, Abteilung Biochemie der Pflanzen, 14195 Berlin, Germany
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47
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Krajewska B, Zaborska W. Jack bean urease: The effect of active-site binding inhibitors on the reactivity of enzyme thiol groups. Bioorg Chem 2007; 35:355-65. [PMID: 17418881 DOI: 10.1016/j.bioorg.2007.02.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 02/24/2007] [Accepted: 02/27/2007] [Indexed: 10/23/2022]
Abstract
In view of the complexity of the role of the active site flap cysteine in the urease catalysis, in this work we studied how the presence of typical active-site binding inhibitors of urease, phenylphosphorodiamidate (PPD), acetohydroxamic acid (AHA), boric acid and fluoride, affects the reactivity of enzyme thiol groups, the active site flap thiol in particular. For that the inhibitor-urease complexes were prepared with excess inhibitors and had their thiol groups titrated with DTNB. The effects observed were analyzed in terms of the structures of the inhibitor-urease complexes reported in the literature. We found that the effectiveness in preventing the active site cysteine from the modification by disulfides, varied among the inhibitors studied, even though they all bind to the active site. The variations were accounted for by different extents of geometrical distortion in the active site that the inhibitors introduced upon binding, leaving the flap either open in AHA-, boric acid- and fluoride-inhibited urease, like in the native enzyme or closed in PPD-inhibited urease. Among the inhibitors, only PPD was found to be able to thoroughly protect the flap cysteines from the further reaction with disulfides, this apparently resulting from the closed conformation of the flap. Accordingly, in practical terms PPD may be regarded as the most suitable inhibitor for active-site protection experiments in inhibition studies of urease.
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Affiliation(s)
- Barbara Krajewska
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland.
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48
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Mitić N, Smith SJ, Neves A, Guddat LW, Gahan LR, Schenk G. The catalytic mechanisms of binuclear metallohydrolases. Chem Rev 2007; 106:3338-63. [PMID: 16895331 DOI: 10.1021/cr050318f] [Citation(s) in RCA: 362] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natasa Mitić
- School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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49
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Estiu G, Suárez D, Merz KM. Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. J Comput Chem 2007; 27:1240-62. [PMID: 16773613 DOI: 10.1002/jcc.20411] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Herein we briefly review theoretical contributions that have increased our understanding of the structure and function of metallo-beta-lactamases and ureases. Both are bimetallic metalloenzymes, with the former containing two zinc ions and the latter containing two nickel ions. We describe the use of several different methodologies, including quantum chemical calculations, molecular dynamic simulations, as well as mixed QM/MM approaches and how they have impacted our understanding of the structure and function of metallo-beta-lactamases and ureases.
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Affiliation(s)
- Guillermina Estiu
- Department of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, P.O. Box 118435, Gainesville, Florida 32611-8435, USA
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50
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Estiu G, Merz KM. Competitive Hydrolytic and Elimination Mechanisms in the Urease Catalyzed Decomposition of Urea. J Phys Chem B 2007; 111:10263-74. [PMID: 17676790 DOI: 10.1021/jp072323o] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a high-level quantum chemical study of possible elimination reaction mechanisms associated with the catalytic decomposition of urea at the binuclear nickel active site cluster of urease. Stable intermediates and transition state structures have been identified along several possible reaction pathways. The computed results are compared with those reported by Suarez et al. for the hydrolytic catalyzed decomposition. On the basis of these comparative studies, we propose a monodentate coordination of urea in the active site from which both the elimination and hydrolytic pathways can decompose urea into CO2 and NH3. This observation is counter to what has been experimentally suggested based on the exogenous observation of carbamic acid (the reaction product from the hydrolysis pathway). However, this does not address what has occurred at the active site of urease prior to product release. On the basis of our computed results, the observation that urea prefers the elimination channel in aqueous solution and on the observation of Lippard and co-workers of an elimination reaction channel in a urease biomimetic model, we propose that the elimination channel needs to be re-examined as a viable reaction channel in urease.
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Affiliation(s)
- Guillermina Estiu
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
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