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Zhang L, Ying J. Amino acid analogues provide multiple plausible pathways to prebiotic peptides. J R Soc Interface 2024; 21:20240014. [PMID: 38715323 PMCID: PMC11077012 DOI: 10.1098/rsif.2024.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Prebiotic peptide synthesis has consistently been a prominent topic within the field of the origin of life. While research predominantly centres on the 20 classical amino acids, the synthesis process encounters significant thermodynamic barriers. Consequently, amino acid analogues are being explored as potential building blocks for prebiotic peptide synthesis. This review delves into the pathway of polypeptide formation, identifying specific amino acid analogues that might have existed on early Earth, potentially participating in peptide synthesis and chemical evolution. Moreover, considering the complexity and variability of the environment on early Earth, we propose the plausibility of coevolution between amino acids and their analogues.
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Affiliation(s)
- Li Zhang
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, People's Republic of China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, People's Republic of China
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2
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Dervisevic M, Jara Fornerod MJ, Harberts J, Zangabad PS, Voelcker NH. Wearable Microneedle Patch for Transdermal Electrochemical Monitoring of Urea in Interstitial Fluid. ACS Sens 2024; 9:932-941. [PMID: 38252743 DOI: 10.1021/acssensors.3c02386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Microneedle-based wearable electrochemical biosensors are the new frontier in personalized health monitoring and disease diagnostic devices that provide an alternative tool to traditional blood-based invasive techniques. Advancements in micro- and nanofabrication technologies enabled the fabrication of microneedles using different biomaterials and morphological features with the aim of overcoming existing challenges and enhancing sensing performance. In this work, we report a microneedle array featuring conductive recessed microcavities for monitoring urea levels in the interstitial fluid of the skin. Microcavities are small pockets on the tip of each microneedle that can accommodate the sensing layer, provide protection from delamination during skin insertion or removal, and position the sensing layer in a deep layer of the skin to reach the interstitial fluid. The wearable urea patch has shown to be highly sensitive and selective in monitoring urea, with a sensitivity of 2.5 mV mM-1 and a linear range of 3 to 18 mM making it suitable for monitoring urea levels in healthy individuals and patients. Our ex vivo experiments have shown that recessed microcavities can protect the sensing layer from delamination during skin insertion and monitor changing urea levels in interstitial fluid. This biocompatible platform provides alternative solutions to the critical issue of maintaining the performance of the biosensor upon skin insertion and holds great potential for advancing transdermal sensor technology.
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Affiliation(s)
- Muamer Dervisevic
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria 3168, Australia
| | - Maximiliano Jesus Jara Fornerod
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria 3168, Australia
| | - Jann Harberts
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria 3168, Australia
| | - Parham Sahandi Zangabad
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria 3168, Australia
| | - Nicolas H Voelcker
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria 3168, Australia
- Materials Science and Engineering, Monash University, Clayton, Victoria 3168, Australia
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3
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Huang M, Cui P, Zhou J, Liu C, Wang Y. Theoretical study on the inhibition mechanisms of heavy metal ions on urease activity. CHEMOSPHERE 2023; 345:140416. [PMID: 37827462 DOI: 10.1016/j.chemosphere.2023.140416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
Soil urease is highly sensitive to soil heavy metal pollution, and thus its activity can be used as bio-indicator of soil health. However, little is known about the inhibition mechanisms of heavy metals on urease. The effects of dimetallic substitution (i.e., Cd, Co, Cu, Hg, and Zn) on the binding of urea in the urease and its subsequent decomposition were studied using quantum chemical methodologies with a urease mimic (phthalazine-dinickel complex). The dimetallic substitution altered the structural features of the dimetal complexes and the M-O bond length between the dimetals and the carbonyl-O of coordinated urea molecules, weakening the binding energies of urea in dimetal complexes, which further affected the transformation of urea. In the urea decomposition via intra-molecular proton transfer, all dimetal complexes have a high activation barrier due to the weak binding of urea in complexes and hydrogen bonding within urea molecules, which are therefore difficult to occur spontaneously. In the urea decomposition via water-assisted inter-molecular proton transfer, the addition of water molecules decreased the energy barrier of urea decomposition. Regardless of the urea decomposition pathway, the dimetallic substitution altered the M-O bond length and hydrogen bond pattern of intermediates and transition states, and also affected the leave of the resulting NH3 from the dimetal complexes by regulating the C-N bond length within the decomposed urea molecule. Overall, the theoretical study provided insight into the molecular mechanisms of the inhibitory effects of heavy metals on urease activity.
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Affiliation(s)
- Meiying Huang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peixin Cui
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jing Zhou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cun Liu
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Yujun Wang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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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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Anderlini B, Ughetti A, Cristoni E, Forti L, Rigamonti L, Roncaglia F. Upgrading of Biobased Glycerol to Glycerol Carbonate as a Tool to Reduce the CO 2 Emissions of the Biodiesel Fuel Life Cycle. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120778. [PMID: 36550984 PMCID: PMC9774724 DOI: 10.3390/bioengineering9120778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
With regards to oil-based diesel fuel, the adoption of bio-derived diesel fuel was estimated to reduce CO2 emissions by approximately 75%, considering the whole life cycle. In this paper, we present a novel continuous-flow process able to transfer an equimolar amount of CO2 (through urea) to glycerol, producing glycerol carbonate. This represents a convenient tool, able to both improve the efficiency of the biodiesel production through the conversion of waste streams into added-value chemicals and to beneficially contribute to the whole carbon cycle. By means of a Design of Experiments approach, the influence of key operating variables on the product yield was studied and statistically modeled.
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Affiliation(s)
- Biagio Anderlini
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy
| | - Alberto Ughetti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy
| | - Emma Cristoni
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy
| | - Luca Forti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy
| | - Luca Rigamonti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy
- Interdepartmental Centre H2-MORE, University of Modena and Reggio Emilia, Via Università 4, 41121 Modena, Italy
- INSTM Research Unit of Modena, Via G. Campi 103, 41125 Modena, Italy
| | - Fabrizio Roncaglia
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy
- Interdepartmental Centre H2-MORE, University of Modena and Reggio Emilia, Via Università 4, 41121 Modena, Italy
- INSTM Research Unit of Modena, Via G. Campi 103, 41125 Modena, Italy
- Correspondence:
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6
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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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7
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Abstract
Organic carbonates are considered the chemicals of the future. In particular, propylene carbonate is widely used as a non-reactive solvent, plasticizer, fuel additive, and reagent, especially in the production of environmentally friendly polymers that are not harmful to human health. This paper reviews recent literature findings regarding the development of propylene carbonate synthetic methods starting from propane-1,2-diol and urea. The ammonia formed during the synthesis is recycled to obtain urea from carbon dioxide.
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8
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Kalatuwawege IP, Gunaratna MJ, Udukala DN. Synthesis, In Silico Studies, and Evaluation of Syn and Anti Isomers of N-Substituted Indole-3-carbaldehyde Oxime Derivatives as Urease Inhibitors against Helicobacter pylori. Molecules 2021; 26:molecules26216658. [PMID: 34771067 PMCID: PMC8588131 DOI: 10.3390/molecules26216658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/24/2022] Open
Abstract
Gastrointestinal tract infection caused by Helicobacter pylori is a common virulent disease found worldwide, and the infection rate is much higher in developing countries than in developed ones. In the pathogenesis of H. pylori in the gastrointestinal tract, the secretion of the urease enzyme plays a major role. Therefore, inhibition of urease is a better approach against H. pylori infection. In the present study, a series of syn and anti isomers of N-substituted indole-3-carbaldehyde oxime derivatives was synthesized via Schiff base reaction of appropriate carbaldehyde derivatives with hydroxylamine hydrochloride. The in vitro urease inhibitory activities of those derivatives were evaluated against that of Macrotyloma uniflorum urease using the modified Berthelot reaction. Out of the tested compounds, compound 8 (IC50 = 0.0516 ± 0.0035 mM) and compound 9 (IC50 = 0.0345 ± 0.0008 mM) were identified as the derivatives with potent urease inhibitory activity with compared to thiourea (IC50 = 0.2387 ± 0.0048 mM). Additionally, in silico studies for all oxime compounds were performed to investigate the binding interactions with the active site of the urease enzyme compared to thiourea. Furthermore, the drug-likeness of the synthesized oxime compounds was also predicted.
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Affiliation(s)
- Ishani P. Kalatuwawege
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10100, Sri Lanka; (I.P.K.); (D.N.U.)
| | - Medha J. Gunaratna
- Department of Chemistry, University of Kelaniya, Kelaniya 10300, Sri Lanka
- Correspondence:
| | - Dinusha N. Udukala
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10100, Sri Lanka; (I.P.K.); (D.N.U.)
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9
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10
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Trinuclear nickel(II) amino acid Schiff base complex containing phenolato and acetato bridges: Structural and functional resemblance of urease. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.120109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Liljenberg M, Ripa L, Shamovsky I. Theoretical Studies of the Mechanism of Carbamoylation of Nucleobases by Isocyanates. Chem Res Toxicol 2020; 33:2845-2853. [PMID: 33076655 DOI: 10.1021/acs.chemrestox.0c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isocyanates with the -N═C═O functional group are highly reactive compounds. They are used in various industrial applications and have been found as possible metabolites of hydroxamic acids. Isocyanates interact with biopolymers and are notorious mutagens. Mutagenic effects of isocyanates are caused by the formation of covalent adducts with nucleobases of DNA, primarily cytosines, through carbamoylation of NH2 groups to give the corresponding urea. The mechanism of carbamoylation of nucleobases by aryl isocyanates is studied by high-level density functional theory calculations. Three possible pathways are analyzed. It is demonstrated that the reaction follows the stepwise pathway, which starts with the formation of a π-complex followed by a rate-determining C-N covalent bond formation via the reactive tautomeric imine forms of the nucleobases. The reaction proceeds further through two consecutive proton transfers mediated by water molecules to give the final adduct. The predicted activation free energies of the rate-determining step in water agree with experimental data. In line with experiments, the reactivity of isocyanates toward nucleobases decreases in the order cytosine > adenine > guanine, and we rationalize this order of reactivity by the fall of their basicity and destabilization of the imine forms. Activation barriers of the alternative concerted pathways are higher than that of the preferred stepwise mechanism, and the match to experiment is poor. The kinetic effect of adding electron-withdrawing or electron-donating groups to the aryl group of aryl isocyanate is minute, which suggests that mutagenicity of isocyanates is determined exclusively by the reactivity of the -N═C═O group and as such cannot be removed by structural alterations of the adjacent aryl.
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Affiliation(s)
| | - Lena Ripa
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Igor Shamovsky
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, 431 83 Mölndal, Sweden
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12
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Gratzfeld D, Heitkämper J, Debailleul J, Olzmann M. On the influence of water on urea condensation reactions: a theoretical study. Z PHYS CHEM 2020. [DOI: 10.1515/zpch-2020-1658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The influence of water molecules on the kinetics of urea condensation reactions was studied with high-level quantum chemical methods and statistical rate theory. The study focuses on the production of biuret, triuret, and cyanuric acid from urea because of their relevance as unwanted byproducts in the urea-based selective catalytic reduction (urea-SCR) exhaust after treatment of Diesel engines. In order to characterize the potential energy surfaces and molecular reaction pathways, calculations with explicitly-correlated coupled-cluster methods were performed. It turned out that the reactions proceed via pre-reactive complexes and the inclusion of one or two water molecules into the condensation mechanisms leads to a decrease of the energy barriers. This effect is particularly pronounced in the production of biuret. Due to the pre-reactive equilibria, the rates of the overall reactions can increase or decrease by incorporating water into the mechanism, depending on the temperature and water concentration. Under the conditions of urea-SCR, the studied reactions are too slow to contribute to the observed byproduct formation.
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Affiliation(s)
- Dennis Gratzfeld
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
| | - Juliane Heitkämper
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
| | - Julien Debailleul
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
| | - Matthias Olzmann
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT) , Kaiserstr. 12 , 76131 Karlsruhe , Germany
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13
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Imran M, Waqar S, Ogata K, Ahmed M, Noreen Z, Javed S, Bibi N, Bokhari H, Amjad A, Muddassar M. Identification of novel bacterial urease inhibitors through molecular shape and structure based virtual screening approaches. RSC Adv 2020; 10:16061-16070. [PMID: 35493653 PMCID: PMC9052855 DOI: 10.1039/d0ra02363a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/15/2020] [Indexed: 12/24/2022] Open
Abstract
The enzyme urease is an essential colonizing factor of the notorious carcinogenic pathogen Helicobacter pylori (H. pylori), conferring acid resistance to the bacterium. Recently, antibiotic resistant strains have emerged globally with little to no alternative treatment available. In this study we propose novel urease inhibitors capable of controlling infection by H. pylori and other pathogenic bacteria. We employed hierarchal computational approaches to screen new urease inhibitors from commercial chemical databases followed by in vitro anti-urease assays. Initially ROCS shape-based screening was performed using o-chloro-hippurohydroxamic acid followed by molecular docking studies. Out of 1.83 million compounds, 1700 compounds were retrieved based on having a ROCS Tanimoto combo score in the range of values from 1.216 to 1.679. These compounds were further screened using molecular docking simulations and the 100 top ranked compounds were selected based on their Glide score. After structural classification of the top ranked compounds, eight compounds were selected and purchased for biological assays. The plausible binding modes of the most active compounds were also confirmed using molecular dynamics (MD) simulations. Compounds 1, 2 and 3 demonstrated good urease inhibitory properties (IC50 = 0.32, 0.68 and 0.42 μM) compared to the other compounds. Enzyme kinetic studies revealed that compounds 1 and 3 are competitive inhibitors while 2 is a mixed type inhibitor of the urease enzyme. Cell based urease inhibition and MTT assay showed that these compounds blocked H. pylori urease activity, affecting bacterial growth and acid tolerance. The enzyme urease is an essential colonizing factor of the notorious carcinogenic pathogen Helicobacter pylori (H. pylori), conferring acid resistance to the bacterium.![]()
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Affiliation(s)
- Muhammad Imran
- School of Life Sciences, FC College University Lahore Pakistan
| | - Saba Waqar
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Koji Ogata
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University 1-1-1 Daigaku-Dori, Sanyo-Onoda Yamaguchi 859-0884 Japan
| | | | - Zobia Noreen
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Sundus Javed
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Nazia Bibi
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Habib Bokhari
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Asma Amjad
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
| | - Muhammad Muddassar
- Department of Biosciences, COMSATS University Islamabad Park Road Islamabad Pakistan
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14
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Dynamic multiphase semi-crystalline polymers based on thermally reversible pyrazole-urea bonds. Nat Commun 2019; 10:4753. [PMID: 31628332 PMCID: PMC6802193 DOI: 10.1038/s41467-019-12766-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/27/2019] [Indexed: 12/22/2022] Open
Abstract
Constructing responsive and adaptive materials by dynamic covalent bonds is an attractive strategy in material design. Here, we present a kind of dynamic covalent polyureas which can be prepared from the highly efficient polyaddition reaction of pyrazoles and diisocyanates at ambient temperature in the absence of a catalyst. Owing to multiphase structural design, poly(pyrazole-ureas) (PPzUs) show excellent mechanical properties and unique crystallization behavior. Besides, the crosslinked PPzUs can be successfully recycled upon heating (~130 °C) and the molecular-level blending of polyurea and polyurethane is realized. Theoretical studies prove that the reversibility of pyrazole-urea bonds (PzUBs) arises from the unique aromatic nature of pyrazole and the N-assisting intramolecular hydrogen transfer process. The PzUBs could further broaden the scope of dynamic covalent bonds and are very promising in the fields of dynamic materials. Dynamic polymer materials with reversible covalent bonds can reorganize their macromolecular architectures, and thus produce a macroscopic response to the environment. Here, the authors show dynamic covalent polyureas formed by a polyaddition reaction between pyrazoles and diisocyanates at ambient temperature in the absence of a catalyst.
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15
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Hulla M, Dyson PJ. Pivotal Role of the Basic Character of Organic and Salt Catalysts in C−N Bond Forming Reactions of Amines with CO
2. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906942] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Martin Hulla
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
| | - Paul J. Dyson
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
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16
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Hulla M, Dyson PJ. Pivotal Role of the Basic Character of Organic and Salt Catalysts in C-N Bond Forming Reactions of Amines with CO 2. Angew Chem Int Ed Engl 2019; 59:1002-1017. [PMID: 31364789 DOI: 10.1002/anie.201906942] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/23/2019] [Indexed: 01/12/2023]
Abstract
Organocatalysts promote a range of C-N bond forming reactions of amines with CO2 . Herein, we review these reactions and attempt to identify the unifying features of the catalysts that allows them to promote a multitude of seemingly unrelated reactions. Analysis of the literature shows that these reactions predominantly proceed by carbamate salt formation in the form [BaseH][RR'NCOO]. The anion of the carbamate salt acts as a nucleophile in hydrosilane reductions of CO2 , internal cyclization reactions or after dehydration as an electrophile in the synthesis of urea derivatives. The reactions are enhanced by polar aprotic solvents and can be either promoted or hindered by H-bonding interactions. The predominant role of all types of organic and salt catalysts (including ionic liquids, ILs) is the stabilization of the carbamate salt, mostly by acting as a base. Catalytic enhancement depends on the combination of the amine, the base strength, the solvent, steric factors, ion pairing and H-bonding. A linear relationship between the base strength and the reaction yield has been demonstrated with IL catalysts in the synthesis of formamides and quinazoline-2,4-diones. The role of organocatalysts in the reactions indicates that all bases of sufficient strength should be able to catalyze the reactions. However, a physical limit to the extent of a purely base catalyzed reaction mechanism should exist, which needs to be identified, understood and overcome by synergistic or alternative methods.
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Affiliation(s)
- Martin Hulla
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Paul J Dyson
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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17
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Polino D, Parrinello M. Kinetics of Aqueous Media Reactions via Ab Initio Enhanced Molecular Dynamics: The Case of Urea Decomposition. J Phys Chem B 2019; 123:6851-6856. [PMID: 31286763 DOI: 10.1021/acs.jpcb.9b05271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aqueous solutions provide a medium for many important reactions in chemical synthesis, industrial processes, environmental chemistry, and biological functions. It is an accepted fact that aqueous solvents can be direct participants in the reaction process and not act only as simple passive dielectrics. Assisting water molecules and proton wires are thus essential for the efficiency of many reactions. Here, we study the decomposition of urea into ammonia and isocyanic acid by means of enhanced ab initio molecular dynamics simulations. We highlight the role of the solvent molecules and their interactions with the reactants providing a proper description of the reaction mechanism and how the water hydrogen-bond network affects the reaction dynamics. Reaction free energy and rates have been calculated taking into account this important effect.
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Affiliation(s)
- Daniela Polino
- Department of Chemistry and Applied Biosciences , ETH Zurich , c/o USI Campus, Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland.,Facoltà di Informatica, Istituto di Scienze Computazionali , Università della Svizzera Italiana , Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences , ETH Zurich , c/o USI Campus, Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland.,Facoltà di Informatica, Istituto di Scienze Computazionali , Università della Svizzera Italiana , Via Giuseppe Buffi 13 , CH-6900 Lugano , Switzerland.,Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
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18
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Abstract
The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.
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19
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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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20
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Korschelt K, Schwidetzky R, Pfitzner F, Strugatchi J, Schilling C, von der Au M, Kirchhoff K, Panthöfer M, Lieberwirth I, Tahir MN, Hess C, Meermann B, Tremel W. CeO 2-x nanorods with intrinsic urease-like activity. NANOSCALE 2018; 10:13074-13082. [PMID: 29961799 DOI: 10.1039/c8nr03556c] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The large-scale production and ecotoxicity of urea make its removal from wastewater a health and environmental challenge. Whereas the industrial removal of urea relies on hydrolysis at elevated temperatures and high pressure, nature solves the urea disposal problem with the enzyme urease under ambient conditions. We show that CeO2-x nanorods (NRs) act as the first and efficient green urease mimic that catalyzes the hydrolysis of urea under ambient conditions with an activity (kcat = 9.58 × 101 s-1) about one order of magnitude lower than that of the native jack bean urease. The surface properties of CeO2-x NRs were probed by varying the Ce4+/Ce3+ ratio through La doping. Although La substitution increased the number of surface defects, the reduced number of Ce4+ sites with higher Lewis acidity led to a slight decrease of their catalytic activity. CeO2-x NRs are stable against pH changes and even to the presence of transition metal ions like Cu2+, one of the strongest urease inhibitors. The low costs and environmental compatibility make CeO2-x NRs a green urease substitute that may be applied in polymer membranes for water processing or filters for the waste water reclamation. The biomimicry approach allows the application of CeO2-x NRs as functional enzyme mimics where the use of native or recombinant enzyme is hampered because of its costs or operational stability.
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Affiliation(s)
- K Korschelt
- Institut für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, D-55128 Mainz, Germany.
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21
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Design, synthesis, in vitro Evaluation and docking studies on dihydropyrimidine-based urease inhibitors. Bioorg Chem 2017; 74:53-65. [DOI: 10.1016/j.bioorg.2017.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/11/2017] [Accepted: 07/11/2017] [Indexed: 12/28/2022]
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22
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Ayaz M, Junaid M, Ullah F, Sadiq A, Shahid M, Ahmad W, Ullah I, Ahmad A, Syed NIH. GC-MS Analysis and Gastroprotective Evaluations of Crude Extracts, Isolated Saponins, and Essential Oil from Polygonum hydropiper L. Front Chem 2017; 5:58. [PMID: 28824906 PMCID: PMC5539133 DOI: 10.3389/fchem.2017.00058] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/19/2017] [Indexed: 01/01/2023] Open
Abstract
Peptic ulceration is among the most prevalent gastrointestinal disorders characterized by pepsin and gastric acid mediated mucosal damage, as result of imbalance between defensive and offensive processes. The main objective of the current study was to investigate the antiulcer potentials of Polygonum hydropiper crude methanolic ectract (Ph.Cr) in aspirin induced ulcerogenesis using pylorus ligated rat model. In-vitro urease and Proteus mirabilis inhibitory potentials were evaluated using standard protocols. All fractions were analyzed using GC-MS to identify major components. The aspirin induced ulcerogenesis in pylorus ligated rat model was associated with significant changes in the mean ulcer score [F(5, 30) = 7.141, P = 0.0002], gastric juice volume [F(5, 30) = 8.245, P < 0.0001], gastric juice pH [F(5, 30) = 5.715, P = 0.0008], free acidity [F(5, 30) = 4.544, P = 0.0033], total acidity [F(5, 30) = 2.740, P = 0.0373], and pepsin concentration [F(5, 30) = 2.335, P = 0.0664]. Pre-treatment with Ph.Cr at 100, 200, and 400 mg/kg dose exhibited marked gastroprotective and anti-ulcerogenic effect in the aspirin induced pyloric ligation ulcerogenesis model at 100, 200, and 400 mg/kg as indicated by ulcerative biochemical parameters. In urease inhibition assay, leaves essential oil (Ph.Lo), saponins (Ph.Sp), and chloroform extract (Ph.Chf) exhibited highest activities with IC50 of 90, 98, and 520 μg/ml, respectively. Ph.Sp, Ph.Chf, ethyl acetate (Ph.EtAc), and Ph.Cr showed MICs of 25, 30, 32.25, and 40.50 μg/ml, respectively against P. mirabilis. Several compounds were identified in GC-MS analysis of samples. Significant in-vivo antiulcer, urease inhibitory as well as anti-proteus potentials of P. hydropiper solvent extracts, signify its potential use for the management of peptic ulcers and may provide scientific bases for the traditional uses of the plant.
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Affiliation(s)
- Muhammad Ayaz
- Department of Pharmacy, University of MalakandChakdara dir, Pakistan
| | - Muhammad Junaid
- Department of Pharmacy, University of MalakandChakdara dir, Pakistan
| | - Farhat Ullah
- Department of Pharmacy, University of MalakandChakdara dir, Pakistan
| | - Abdul Sadiq
- Department of Pharmacy, University of MalakandChakdara dir, Pakistan
| | - Muhammad Shahid
- Department of Pharmacy, University of PeshawarPeshawar, Pakistan.,Department of Pharmacy, Sarhad University of Information TechnologyPeshawar, Pakistan
| | - Waqar Ahmad
- Department of Pharmacy, University of MalakandChakdara dir, Pakistan
| | - Ihsan Ullah
- Department of Pharmacy, University of SwabiSwabi, Pakistan
| | - Ashfaq Ahmad
- Department of Pharmacy, University of MalakandChakdara dir, Pakistan.,Department of Pharmacy, Sarhad University of Information TechnologyPeshawar, Pakistan
| | - Nawazish-I-Husain Syed
- Department of Pharmacology, University College of Pharmacy, University of PunjabLahore, Pakistan
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23
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He J, Zhang L, Zhang K, Qin Y, Liu L. Concentrating aqueous urea solution by using continuous-effect membrane distillation. Chem Eng Res Des 2015. [DOI: 10.1016/j.cherd.2015.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Abstract
To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. The free energy barrier of 25.3 kcal/mol predicted for the dominant reaction pathway of urea elimination in aqueous solution is in good agreement with available experimental kinetic data.
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25
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Nguyen HT, Nguyen MT. Decomposition pathways of formamide in the presence of vanadium and titanium monoxides. Phys Chem Chem Phys 2015; 17:16927-36. [DOI: 10.1039/c5cp01456e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermally feasible decomposition pathways of formamide (FM) in the presence of vanadium VO(X4Σ−) and titanium TiO(X3Δ) monoxides are determined using density functional theory (the BP86 functional) and coupled-cluster theory (CCSD(T)) computations with large basis sets.
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Affiliation(s)
| | - Minh Tho Nguyen
- Department of Chemistry
- University of Leuven
- B-3001 Leuven
- Belgium
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26
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Dai X, Karring H. A determination and comparison of urease activity in feces and fresh manure from pig and cattle in relation to ammonia production and pH changes. PLoS One 2014; 9:e110402. [PMID: 25397404 PMCID: PMC4232307 DOI: 10.1371/journal.pone.0110402] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/22/2014] [Indexed: 11/25/2022] Open
Abstract
Ammonia emission from animal production is a major environmental problem and has impacts on the animal health and working environment inside production houses. Ammonia is formed in manure by the enzymatic degradation of urinary urea and catalyzed by urease that is present in feces. We have determined and compared the urease activity in feces and manure (a urine and feces mixture) from pigs and cattle at 25°C by using Michaelis-Menten kinetics. To obtain accurate estimates of kinetic parameters Vmax and K'm, we used a 5 min reaction time to determine the initial reaction velocities based on total ammoniacal nitrogen (TAN) concentrations. The resulting Vmax value (mmol urea hydrolyzed per kg wet feces per min) was 2.06±0.08 mmol urea/kg/min and 0.80±0.04 mmol urea/kg/min for pig feces and cattle feces, respectively. The K'm values were 32.59±5.65 mmol urea/l and 15.43±2.94 mmol urea/l for pig feces and cattle feces, respectively. Thus, our results reveal that both the Vmax and K'm values of the urease activity for pig feces are more than 2-fold higher than those for cattle feces. The difference in urea hydrolysis rates between animal species is even more significant in fresh manure. The initial velocities of TAN formation are 1.53 mM/min and 0.33 mM/min for pig and cattle manure, respectively. Furthermore, our investigation shows that the maximum urease activity for pig feces occurs at approximately pH 7, and in cattle feces it is closer to pH 8, indicating that the predominant fecal ureolytic bacteria species differ between animal species. We believe that our study contributes to a better understanding of the urea hydrolysis process in manure and provides a basis for more accurate and animal-specific prediction models for urea hydrolysis rates and ammonia concentration in manures and thus can be used to predict ammonia volatilization rates from animal production.
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Affiliation(s)
- Xiaorong Dai
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Odense, Denmark
| | - Henrik Karring
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Odense, Denmark
- * E-mail:
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27
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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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28
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Samuilov AY, Valeev AR, Balabanova FB, Samuilov YD, Konovalov AI. Quantum-chemical study on thermal transformations of urea in ethylene glycol. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2013. [DOI: 10.1134/s1070428013010065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Sunoj RB, Anand M. Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms. Phys Chem Chem Phys 2012; 14:12715-36. [PMID: 22893252 DOI: 10.1039/c2cp41719g] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the years, several methods have been developed to effectively represent the chemical behavior of solutes in solvents. The environmental effects arising due to solvation can generally be achieved either through inclusion of discrete solvent molecules or by inscribing into a cavity in a homogeneous and continuum dielectric medium. In both these approaches of computational origin, the perturbations on the solute induced by the surrounding solvent are at the focus of the problem. While the rigor and method of inclusion of solvent effects vary, such solvation models have found widespread applications, as evident from modern chemical literature. A hybrid method, commonly referred to as cluster-continuum model (CCM), brings together the key advantages of discrete and continuum models. In this perspective, we intend to highlight the latent potential of CCM toward obtaining accurate estimates on a number of properties as well as reactions of contemporary significance. The objective has generally been achieved by choosing illustrative examples from the literature, besides expending efforts to bring out the complementary advantages of CCM as compared to continuum or discrete solvation models. The majority of examples emanate from the prevalent applications of CCM to organic reactions, although a handful of interesting organometallic reactions have also been discussed. In addition, increasingly accurate computations of properties like pK(a) and solvation of ions obtained using the CCM protocol are also presented.
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Affiliation(s)
- Raghavan B Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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30
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Shahzada SA, Yar M, Khan ZA, Khan IU, Naqvi SAR, Mahmood N, Khan KM. Microwave-assisted solvent free efficient synthesis of 1,3,4-oxadiazole-2(3H)-thiones and their potent in vitro urease inhibition activity. ACTA ACUST UNITED AC 2012. [DOI: 10.5155/eurjchem.3.2.143-146.551] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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31
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Wolfenden R. Benchmark Reaction Rates, the Stability of Biological Molecules in Water, and the Evolution of Catalytic Power in Enzymes. Annu Rev Biochem 2011; 80:645-67. [DOI: 10.1146/annurev-biochem-060409-093051] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Richard Wolfenden
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599;
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32
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Nabati F, Habibi-Rezaei M, Amanlou M, Moosavi-Movahedi A. Dioxane enhanced immobilization of urease on alkyl modified nano-porous silica using reversible denaturation approach. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2011.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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33
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Kosikowska P, Berlicki Ł. Urease inhibitors as potential drugs for gastric and urinary tract infections: a patent review. Expert Opin Ther Pat 2011; 21:945-57. [PMID: 21457123 DOI: 10.1517/13543776.2011.574615] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Urease is the enzyme that catalyzes the hydrolysis of urea, which is involved in serious infections caused by Helicobacter pylori in the gastric tract, as well as Proteus and related species in the urinary tract. The necessity to treat such infections has stimulated intensive studies on various groups of urease inhibitors. AREAS COVERED Patent literature on urease inhibitors with possible applications in medicine is reviewed in this paper. Hydroxamic acids, phosphoramidates, urea derivatives, quinones and heterocyclic compounds constitute the major classes of structures with such activity. EXPERT OPINION Until now, only one compound, acetohydroxamic acid, has been clinically used for the treatment of urinary tract infections by urease inhibition. Unfortunately, it exhibits severe side effects. Thus, it seems that the full potential of urease inhibition has not yet been fully explored. Several Japanese patents related to the use of herbal extracts as sources of polyphenolic urease inhibitors have been considered as complementary or alternative therapy; however, their accessibility is quite possibly due to reduced restrictions for the introduction of natural products to the market.
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Affiliation(s)
- Paulina Kosikowska
- Wrocław University of Technology, Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław, Poland
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34
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Khan I, Ali S, Hameed S, Rama NH, Hussain MT, Wadood A, Uddin R, Ul-Haq Z, Khan A, Ali S, Choudhary MI. Synthesis, antioxidant activities and urease inhibition of some new 1,2,4-triazole and 1,3,4-thiadiazole derivatives. Eur J Med Chem 2010; 45:5200-7. [DOI: 10.1016/j.ejmech.2010.08.034] [Citation(s) in RCA: 221] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 08/09/2010] [Accepted: 08/12/2010] [Indexed: 11/29/2022]
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35
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Daramola DA, Singh D, Botte GG. Dissociation Rates of Urea in the Presence of NiOOH Catalyst: A DFT Analysis. J Phys Chem A 2010; 114:11513-21. [DOI: 10.1021/jp105159t] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Damilola A. Daramola
- Department of Chemical and Biomolecular Engineering, Center for Electrochemical Engineering Research, Ohio University, Athens, Ohio 45701, United States
| | - Deepika Singh
- Department of Chemical and Biomolecular Engineering, Center for Electrochemical Engineering Research, Ohio University, Athens, Ohio 45701, United States
| | - Gerardine G. Botte
- Department of Chemical and Biomolecular Engineering, Center for Electrochemical Engineering Research, Ohio University, Athens, Ohio 45701, United States
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36
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Scaldaferri MCL, Pimentel AS. Born−Oppenheimer Molecular Dynamics on the H2S + NO3 Reaction in the Presence and Absence of Water: The Kinetic Isotope Effect. J Phys Chem A 2010; 114:8993-8. [DOI: 10.1021/jp103814s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Maria Clara Leite Scaldaferri
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rua Marquês de São Vicente, 225 Gávea, 22453-900 Rio de Janeiro, RJ Brazil
| | - Andre Silva Pimentel
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rua Marquês de São Vicente, 225 Gávea, 22453-900 Rio de Janeiro, RJ Brazil
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37
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Cui G, Ding L, Feng F, Liu Y, Fang W. Insights into mechanistic photochemistry of urea. J Chem Phys 2010; 132:194308. [DOI: 10.1063/1.3397067] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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38
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Sim YL, Khan MN. Kinetics and mechanism of tertiary amine-catalyzed cleavage of N′-morpholino- N-(2′-methoxyphenyl)phthalamide: Kinetic evidence for the presence of a reactive intermediate on the reaction path. INT J CHEM KINET 2010. [DOI: 10.1002/kin.20477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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39
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Yao H, Hu N. pH-Switchable Bioelectrocatalysis of Hydrogen Peroxide on Layer-by-Layer Films Assembled by Concanavalin A and Horseradish Peroxidase with Electroactive Mediator in Solution. J Phys Chem B 2010; 114:3380-6. [DOI: 10.1021/jp912203d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Huiqin Yao
- Department of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China, and Department of Chemistry, Ningxia Medical University, Yinchuan 750004, People’s Republic of China
| | - Naifei Hu
- Department of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China, and Department of Chemistry, Ningxia Medical University, Yinchuan 750004, People’s Republic of China
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41
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Khan MN. Experimental versus theoretical evidence for the rate-limiting steps in uncatalyzed and H+
- and HO−
-catalyzed hydrolysis of the amide bond. INT J CHEM KINET 2009. [DOI: 10.1002/kin.20435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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43
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Kuznetsov AV, Stolyarov AV. Nonempirical studies of the molecular properties and thermodynamic functions of urea in the ideal gas state. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2009. [DOI: 10.1134/s0036024409020216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Urea enzymatic hydrolysis reaction: optimization by response surface methodology based on potentiometric measurements. Bioelectrochemistry 2008; 74:176-82. [PMID: 18835542 DOI: 10.1016/j.bioelechem.2008.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2007] [Revised: 07/22/2008] [Accepted: 07/29/2008] [Indexed: 11/22/2022]
Abstract
The enzymatic hydrolysis reaction of urea by urease is optimized in this work by the chemometric response surface methodology (RSM), based on an initial rate potentiometric measurement using an NH(4)(+) ion-selective electrode (ISE). In this investigation, the ranges of critical variables determined by a preliminary "one at a time" (OVAT) procedure were used as input for the subsequent RSM chemometric analysis. The RSM quadratic response was found to be quite appropriate for modeling and optimization of the hydrolysis reaction as illustrated by the relatively high value of the determination coefficient (R(2)=90.1%), along with the satisfactory results obtained by the analysis of variance (ANOVA). All the evaluated analytical characteristics of the optimized method such as: the linear calibration curve, the upper and lower detection limits, the within-day precisions at low and at high levels, the assay recovery in pool serum media, along with the activation kinetic parameters, were also reported. Further, in order to check the quality of the optimization and the validity of the model, the assay of urea, both in aqueous laboratory and human serum samples, were performed. It has to be noted that the kinetic initial rate measurement method used in this work, permitted to overcome the general problem of NH(4)(+) ISE low selectivity against Na(+) and K(+) interfering ions in real samples.
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Font M, Domínguez MJ, Sanmartín C, Palop JA, San-Francisco S, Urrutia O, Houdusse F, García-Mina JM. Structural characteristics of phosphoramide derivatives as urease inhibitors. Requirements for activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:8451-8460. [PMID: 18729463 DOI: 10.1021/jf801786d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Taking as a reference the structural characteristics of a set of compounds that act as jack bean ( Canavalia ensiformis) urease inhibitors, namely, phenylphosphorodiamidate (PPD), N- n-butylthiophosphorictriamide (NBPT), and N- n-butylphosphorictriamide (NBPTO), we have studied the structure-activity relationships of a series of phosphoramide derivatives for which the activity as urease inhibitors in both in vitro and in vivo assays is known. Molecular modeling studies were carried out, and the results highlighted the relevance of characteristics such as the presence of intramolecular hydrogen bonds, the volume of the fragment involved in the enzyme interaction, and the degree of conformational freedom as well as the HOMO orbital and atomic orbital contributions to the HOMO orbital, electron density, and PEM distributions on the activity of these compounds as urease inhibitors. These data, along with the preliminary docking study carried out, allow us to propose a union mode to the active site of the enzyme for these compounds.
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Affiliation(s)
- María Font
- Molecular Modeling Section, Department of Organic and Pharmaceutical Chemistry, University of Navarra, Irunlarrea 1, E-31008 Pamplona, Spain.
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Liao KT, Chen CM, Huang HJ, Lin CH. Poly(methyl methacrylate) microchip device integrated with gold nanoelectrode ensemble for in-column biochemical reaction and electrochemical detection. J Chromatogr A 2007; 1165:213-8. [PMID: 17692860 DOI: 10.1016/j.chroma.2007.07.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Revised: 07/20/2007] [Accepted: 07/25/2007] [Indexed: 11/22/2022]
Abstract
This paper proposes a poly(methyl methacrylate) (PMMA) based microchip with an integrated gold nanoelectrode ensemble (GNEE) and a quartet-T loading channel for in-column urea/urease reactions and electrochemical detections. The on-chip GNEE electrode is fabricated using an electrodeless deposition process on a thin polycarbonate (PC) film and bonded directly onto a PMMA substrate to carry out high-performance electrochemical detections. The in-column bio-catalytic reaction of urea/urease is successfully demonstrated utilizing a novel approach based on the different electrokinetic mobilities of urea and urease in capillary electrophoresis (CE) channel. The experimental results significantly show that the GNEE electrode provides a better detection response for the reaction product of ammonia (NH(4)(+)) than a conventional planar gold electrode. The detection results demonstrate a satisfactory determination coefficient (R(2) value) and high reproducibility with a detection limit of 14.8 and 62.8 microM while detecting standard ammonia solution and the urea/urease reaction product of NH(4)(+), respectively. These results confirm the capability of the proposed device for the high-resolution CE-electrochemical detection (CE-ED) of bioanalytical reactions.
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Affiliation(s)
- Kuo-Tang Liao
- Department of Chemistry, National Sun Yat-sen University, 804 Kaohsiung, Taiwan
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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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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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Alexandrova AN, Jorgensen WL. Why urea eliminates ammonia rather than hydrolyzes in aqueous solution. J Phys Chem B 2007; 111:720-30. [PMID: 17249815 PMCID: PMC2995377 DOI: 10.1021/jp066478s] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A joint QM/MM and ab initio study on the decomposition of urea in the gas phase and in aqueous solution is reported. Numerous possible mechanisms of intramolecular decomposition and hydrolysis have been explored; intramolecular NH3 elimination assisted by a water molecule is found to have the lowest activation energy. The solvent effects were elucidated using the TIP4P explicit water model with free energy perturbation calculations in conjunction with QM/MM Monte Carlo simulations. The explicit representation of the solvent was found to be essential for detailed resolution of the mechanism, identification of the rate-determining step, and evaluation of the barrier. The assisting water molecule acts as a hydrogen shuttle for the first step of the elimination reaction. The forming zwitterionic intermediate, H3NCONH, participates in 8-9 hydrogen bonds with water molecules. Its decomposition is found to be the rate-limiting step, and the overall free energy of activation for the decomposition of urea in water is computed to be approximately 37 kcal/mol; the barrier for hydrolysis by an addition/elimination mechanism is found to be approximately 40 kcal/mol. The differences in the electronic structure of the transition states of the NH3 elimination and hydrolysis were examined via natural bond order analysis. Destruction of urea's resonance stabilization during hydrolysis via an addition/elimination mechanism and its preservation in the rearrangement to the H3NCONH intermediate were identified as important factors in determining the preferred reaction route.
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Li Q, Zhao N, Wei W, Sun Y. Catalytic performance of metal oxides for the synthesis of propylene carbonate from urea and 1,2-propanediol. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.molcata.2007.01.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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