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Xie YX, Cheng WC, Xue ZF, Rahman MM, Wang L. Deterioration phenomenon of Pb-contaminated aqueous solution remediation and enhancement mechanism of nano-hydroxyapatite-assisted biomineralization. J Hazard Mater 2024; 470:134210. [PMID: 38581876 DOI: 10.1016/j.jhazmat.2024.134210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024]
Abstract
Modern metallurgical and smelting activities discharge the lead-containing wastewater, causing serious threats to human health. Bacteria and urease applied to microbial-induced carbonate precipitation (MICP) and enzyme-induced carbonate precipitation (EICP) are denatured under high Pb2+ concentration. The nano-hydroxyapatite (nHAP)-assisted biomineralization technology was applied in this study for Pb immobilization. Results showed that the extracellular polymers and cell membranes failed to secure the urease activity when subjected to 60 mM Pb2+. The immobilization efficiency dropped to below 50% under MICP, whereas it due to a lack of extracellular polymers and cell membranes dropped to below 30% under EICP. nHAP prevented the attachment of Pb2+ either through competing with bacteria and urease or promoting Ca2+/Pb2+ ion exchange. Furthermore, CO32- from ureolysis replaced the hydroxyl (-OH) in hydroxylpyromorphite to encourage the formation of carbonate-bearing hydroxylpyromorphite of higher stability (Pb10(PO4)6CO3). Moreover, nHAP application overcame an inability to provide nucleation sites by urease. As a result, the immobilization efficiency, when subjected to 60 mM Pb2+, elevated to above 80% under MICP-nHAP and to some 70% under EICP-nHAP. The findings highlight the potential of applying the nHAP-assisted biomineralization technology to Pb-containing water bodies remediation.
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Affiliation(s)
- Yi-Xin Xie
- School of Civil Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Geotechnical and Underground Space Engineering (XAUAT), Xi'an 710055, China
| | - Wen-Chieh Cheng
- School of Civil Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Geotechnical and Underground Space Engineering (XAUAT), Xi'an 710055, China.
| | - Zhong-Fei Xue
- School of Civil Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Geotechnical and Underground Space Engineering (XAUAT), Xi'an 710055, China
| | - Md Mizanur Rahman
- Geotechnical Engineering, UniSA STEM, ScaRCE, University of South Australia, SA 5000, Australia
| | - Lin Wang
- School of Civil Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Geotechnical and Underground Space Engineering (XAUAT), Xi'an 710055, China
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2
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Hu X, Yang Z, Zhao Y, Dong Y, Wang C, Zhang L, Yu Y, Wu K, Ren L. Medium optimization and dust suppression performance analysis of microbial-based dust suppressant compound by response surface curve method. Environ Sci Pollut Res Int 2024; 31:24525-24535. [PMID: 38443533 DOI: 10.1007/s11356-024-32748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
At present, microbial dust suppressants based on microbial communities lack necessary systematic analysis of factors affecting dust suppression performance. Therefore, in this study, the response surface curve method was used to optimize the culture conditions for enrichment of urease-producing microorganisms from activated sludge. The results indicated that when urea = 9.67 g L-1, NH4Cl = 5.21 g L-1, and pH = 9.57, the maximum urease activity of urease-producing microbial community (UPMC) was 8.22 mM min-1. The UPMC under optimized culture conditions reached a mineralization rate of 98.8% on the 1st day of mineralization. Ureolysis is one of the biological mechanisms that trigger microbial mineralization with the consequent effect of dust suppression. The analysis of microbial community structure indicated that the urease-producing bacteria Sporosarcina sp. had the highest abundance at the genus level in the microbial-based dust suppressant compound. Jeotgalicoccus sp. plays an important role in improving and maintaining the stability of urease. In addition, the optimal UPMC had low pathogenicity, which is extremely attractive for the safe application of microbial dust suppressants.
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Affiliation(s)
- Xiangming Hu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
- State Key Laboratory of Mine Lab Disaster Prevention and Control Co-Found By Shandong Province and the Ministry of Science and Technology, Shandong University of Science and Technology, Qingdao, 266590, Shandong, China
| | - Zhiyuan Yang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Yanyun Zhao
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Yue Dong
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China.
| | - Chengcheng Wang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Linlin Zhang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Yiyun Yu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Kai Wu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Liyan Ren
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
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Chaudhary A, Kumar K, Singh VK, Rai S, Kumar V, Tungala K, Das A, Jana T. Poly(acrylamide)-co-poly(hydroxyethyl)methacrylate-co-poly(cyclohexyl methacrylate) hydrogel platform for stability, storage and biocatalytic applications of urease. Int J Biol Macromol 2024; 265:131039. [PMID: 38518938 DOI: 10.1016/j.ijbiomac.2024.131039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
In our present work, an explicit crosslinked thermo-responsive hydrogel platform has been developed, by using polyacrylamide (PAAm), poly(2-hydroxyethyl methacrylate) (PHEMA) and poly(cyclohexyl methacrylate) (PCHMA), and then coupled with urease to yield bioconjugates (BCs). Synergic effect of these polymer units provides thermoresponsive nature, optimum crosslinking with desired swelling behaviour, and stability and improved catalytic to Urease in the resultant BCs. Synthesis of the terpolymer has been achieved by employing HEMA (monomer as well as crosslinker), instead of using the conventional crosslinkers, through free radical solution polymerization technique. Various grades of TRPUBs have been fabricated by varying HEMA and CHMA contents while keeping fixed amounts of AAm. Further, the structural analysis of BCs has been done by fourier transform infra-red spectroscopic study and their thermal stabilities have been studied by thermogravimetric analysis. Urea present in TRPUBs has beenanalysed for its hydrolysis atdifferent temperatures viz., 25 °C, 45 °C and 70 °C. Further, the effect of crosslinking, temperature and reaction time on catalytic activities of TRPUBs has been studied. TRPUBs grades have showna maximum swelling capacity up to 5200 %; excellent catalytic activity even at 70 °C; and 85 % activity retention after 18 days storage in buffer medium.
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Affiliation(s)
- Aradhana Chaudhary
- Department of Chemistry and Environmental Science, Madan Mohan Malaviya University of Technology, Gorakhpur 273010, Uttar Pradesh, India
| | - Krishna Kumar
- Department of Chemistry and Environmental Science, Madan Mohan Malaviya University of Technology, Gorakhpur 273010, Uttar Pradesh, India; Department of Chemistry, School of Basic & Applied Science, Harcourt Butler Technical University, Kanpur 208002, Uttar Pradesh, India.
| | - Vinai K Singh
- Department of Chemistry and Environmental Science, Madan Mohan Malaviya University of Technology, Gorakhpur 273010, Uttar Pradesh, India
| | - Shailja Rai
- Department of Chemistry and Environmental Science, Madan Mohan Malaviya University of Technology, Gorakhpur 273010, Uttar Pradesh, India
| | - Vinod Kumar
- Department of Chemistry, Babu Shivnath Agrawal College, Mathura 281004, Uttar Pradesh, India
| | - Kranthikumar Tungala
- Department of Chemistry, Ewing Christian College, Allahabad University, Prayagraj 211003, Uttar Pradesh, India
| | - Anupam Das
- School of Chemistry, University of Hyderabad, Gachibowli-500046, Hyderabad, Telangana State, India
| | - Tushar Jana
- School of Chemistry, University of Hyderabad, Gachibowli-500046, Hyderabad, Telangana State, India
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de Athayde Moncorvo Collado A, Socías SB, González-Lizárraga F, Ploper D, Vera Pingitore E, Chehín RN, Chaves S. Magnetic amyloid-based biocatalyst for the hydrolysis of urea. Food Chem 2024; 433:136830. [PMID: 37683486 DOI: 10.1016/j.foodchem.2023.136830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/19/2023] [Accepted: 07/05/2023] [Indexed: 09/10/2023]
Abstract
The presence of urea in wines and other alcoholic beverages represents a critical problem since it can chemically react with ethanol, which leads to the formation of ethyl carbamate, a carcinogenic agent according to the World Health Organization. Here we report the creation of a biocatalyst for the hydrolysis of urea, which could potentially be used before bottling alcoholic drinks. For this, the effective surface area of streptavidin-labeled magnetic microparticles was amplified by functionalization with biotin-labeled hen egg lysozyme amyloid fibers. Subsequently, by using copper and hydrogen peroxide induced cross-linking of unmodified proteins (CHICUP), soybean urease was immobilized to the fibers. This gave rise to a magnetic biocatalyst with remarkable urease activity, which was maintained even after 10 reuses. We propose that this strategy could be used as a platform for immobilizing other molecules to design and develop a myriad of biocatalysts for the food industry.
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Affiliation(s)
- A de Athayde Moncorvo Collado
- Instituto de Medicina Molecular y Celular Aplicada, Universidad Nacional de Tucumán-Consejo Nacional de Investigación Científicas y Técnicas- Sistema Provincial de Salud (UNT-CONICET-SIPROSA), Pasaje Manuel Dorrego, 1080. CP 4000. Tucumán, Argentina; Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT). Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT, Batalla de Chacabuco 461, CP 4000 Tucumán, Argentina.
| | - S B Socías
- Instituto de Medicina Molecular y Celular Aplicada, Universidad Nacional de Tucumán-Consejo Nacional de Investigación Científicas y Técnicas- Sistema Provincial de Salud (UNT-CONICET-SIPROSA), Pasaje Manuel Dorrego, 1080. CP 4000. Tucumán, Argentina.
| | - F González-Lizárraga
- Instituto de Medicina Molecular y Celular Aplicada, Universidad Nacional de Tucumán-Consejo Nacional de Investigación Científicas y Técnicas- Sistema Provincial de Salud (UNT-CONICET-SIPROSA), Pasaje Manuel Dorrego, 1080. CP 4000. Tucumán, Argentina.
| | - D Ploper
- Instituto de Medicina Molecular y Celular Aplicada, Universidad Nacional de Tucumán-Consejo Nacional de Investigación Científicas y Técnicas- Sistema Provincial de Salud (UNT-CONICET-SIPROSA), Pasaje Manuel Dorrego, 1080. CP 4000. Tucumán, Argentina.
| | - E Vera Pingitore
- Instituto de Medicina Molecular y Celular Aplicada, Universidad Nacional de Tucumán-Consejo Nacional de Investigación Científicas y Técnicas- Sistema Provincial de Salud (UNT-CONICET-SIPROSA), Pasaje Manuel Dorrego, 1080. CP 4000. Tucumán, Argentina.
| | - R N Chehín
- Instituto de Medicina Molecular y Celular Aplicada, Universidad Nacional de Tucumán-Consejo Nacional de Investigación Científicas y Técnicas- Sistema Provincial de Salud (UNT-CONICET-SIPROSA), Pasaje Manuel Dorrego, 1080. CP 4000. Tucumán, Argentina; Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT). Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT, Batalla de Chacabuco 461, CP 4000 Tucumán, Argentina.
| | - S Chaves
- Instituto de Medicina Molecular y Celular Aplicada, Universidad Nacional de Tucumán-Consejo Nacional de Investigación Científicas y Técnicas- Sistema Provincial de Salud (UNT-CONICET-SIPROSA), Pasaje Manuel Dorrego, 1080. CP 4000. Tucumán, Argentina.
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5
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Li M, Xie Y, Zhang J, Su X. Self-Assembled Integrated Nanozyme Cascade Biosensor with Dual Catalytic Activity for Portable Urease Analysis. Anal Chem 2024; 96:1284-1292. [PMID: 38194438 DOI: 10.1021/acs.analchem.3c04652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
In this work, a novel nanozyme (Cu@Zr) with all-in-one dual enzyme and fluorescence properties is designed by simple self-assembly. A nanozyme cascade sensor with disodium phenyl phosphate (PPDS) as substrate was first established by exploiting the dual enzymatic activities of phosphatase and laccase. Specifically, phosphatase cleaves the P-O bond of PPDS to produce colorless phenol, which is then oxidized by laccase and complexed with the chromogenic agent 4-aminoantipyrine (4-AP) to produce red quinoneimine (QI). Strikingly, the NH3 produced by the urease hydrolysis of urea can interact with Cu@Zr, accelerating the electron transfer rate and ultimately leading to a significantly improved performance of the cascade reaction. Moreover, the fluorescence at 440 nm of Cu@Zr is further quenched by the inner filter effect (IFE) of QI. Thus, the colorimetric and fluorescence dual-mode strategy for sensitive urease analysis with LODs of 3.56 and 1.83 U/L was established by the proposed cascade sensor. Notably, a portable swab loaded with Cu@Zr was also prepared for in situ urease detection with the aid of a smartphone RGB readout. It also provides a potentially viable analytical avenue for environmental and biological analysis.
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Affiliation(s)
- Meini Li
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Yunfei Xie
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Jiabao Zhang
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xingguang Su
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
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6
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Montazer MN, Asadi M, Moradkhani F, Omrany ZB, Mahdavi M, Amanlou M. Design, synthesis, and biological studies of the new cysteine-N-arylacetamide derivatives as a potent urease inhibitor. Naunyn Schmiedebergs Arch Pharmacol 2024; 397:305-315. [PMID: 37436497 DOI: 10.1007/s00210-023-02596-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/20/2023] [Indexed: 07/13/2023]
Abstract
Inhibition of Helicobacter pylori urease is an effective method in the treatment of several gastrointestinal diseases in humans. This bacterium plays an important role in the pathogenesis of gastritis and peptic ulceration. Considering the presence of cysteine and N-arylacetamide derivatives in potent urease inhibitors, here, we designed hybrid derivatives of these pharmacophores. Therefore, cysteine-N-arylacetamide derivatives 5a-l were synthesized through simple nucleophilic reactions with good yield. In vitro urease inhibitory activity assay of these compounds demonstrated that all newly synthesized compounds exhibited high inhibitory activity (IC50 values = 0.35-5.83 μM) when compared with standard drugs (thiourea: IC50 = 21.1 ± 0.11 μM and hydroxyurea: IC50 = 100.0 ± 0.01 μM). Representatively, compound 5e with IC50 = 0.35 μM was 60 times more potent than strong urease inhibitor thiourea. Enzyme kinetic study of this compound revealed that compound 5e is a competitive urease inhibitor. Moreover, a docking study of compound 5e was performed to explore crucial interactions at the urease active site. This study revealed that compound 5e is capable to inhibit urease by interactions with two crucial residues at the active site: Ni and CME592. Furthermore, a molecular dynamics study confirmed the stability of the 5e-urease complex and Ni chelating properties of this compound. It should be considered that, in the following study, the focus was placed on jack bean urease instead of H. pylori urease, and this was acknowledged as a limitation.
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Affiliation(s)
- Mohammad Nazari Montazer
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Asadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Moradkhani
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Zinat Bahrampour Omrany
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
- Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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Mazzei L, Paul A, Cianci M, Devodier M, Mandelli D, Carloni P, Ciurli S. Kinetic and structural details of urease inactivation by thiuram disulphides. J Inorg Biochem 2024; 250:112398. [PMID: 37879152 DOI: 10.1016/j.jinorgbio.2023.112398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/21/2023] [Accepted: 10/07/2023] [Indexed: 10/27/2023]
Abstract
This paper reports on the molecular details of the reactivity of urease, a nickel-dependent enzyme that catalyses the last step of organic nitrogen mineralization, with thiuram disulphides, a class of molecules known to inactivate the enzyme with high efficacy but for which the mechanism of action had not been yet established. IC50 values of tetramethylthiuram disulphide (TMTD or Thiram) and tetraethylthiuram disulphide (TETD or Disulfiram) in the low micromolar range were determined for plant and bacterial ureases. The X-ray crystal structure of Sporosarcina pasteurii urease inactivated by Thiram, determined at 1.68 Å resolution, revealed the presence of a covalent modification of the catalytically essential cysteine residue. This is located on the flexible flap that modulates the size of the active site channel and cavity. Formation of a Cys-S-S-C(S)-N(CH3)2 functionality responsible for enzyme inactivation was observed. Quantum-mechanical calculations carried out to rationalise the large reactivity of the active site cysteine support the view that a conserved histidine residue, adjacent to the cysteine in the active site flap, modulates the charge and electron density along the thiol SH bond by shifting electrons towards the sulphur atom and rendering the thiol proton more reactive. We speculate that this proton could be transferred to the nickel-coordinated urea amide group to yield a molecule of ammonia from the generated Curea-NH3+ functionality during catalysis.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy.
| | - Arundhati Paul
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche 10, Ancona I-60131, Italy
| | - Marta Devodier
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich D-52428, Germany; Università degli Studi di Parma, Via Università 12, Parma I-43121, Italy
| | - Davide Mandelli
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich D-52428, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich D-52428, Germany; Department of Physics and Universitätsklinikum, RWTH Aachen University, Aachen D-52074, Germany
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy
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Stasyuk N, Gayda G, Nogala W, Holdynski M, Demkiv O, Fayura L, Sibirny A, Gonchar M. Ammonium nanochelators in conjunction with arginine-specific enzymes in amperometric biosensors for arginine assay. Mikrochim Acta 2023; 191:47. [PMID: 38133683 PMCID: PMC10987348 DOI: 10.1007/s00604-023-06114-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Amino acid L-arginine (Arg), usually presented in food products and biological liquids, can serve both as a useful indicator of food quality and an important biomarker in medicine. The biosensors based on Arg-selective enzymes are the most promising devices for Arg assay. In this research, three types of amperometric biosensors have been fabricated. They exploit arginine oxidase (ArgO), recombinant arginase I (ARG)/urease, and arginine deiminase (ADI) coupled with the ammonium-chelating redox-active nanoparticles. Cadmium-copper nanoparticles (nCdCu) as the most effective nanochelators were used for the development of ammonium chemosensors and enzyme-coupled Arg biosensors. The fabricated enzyme/nCdCu-containing bioelectrodes show wide linear ranges (up to 200 µM), satisfactory storage stabilities (14 days), and high sensitivities (A⋅M-1⋅m-2) to Arg: 1650, 1700, and 4500 for ADI-, ArgO- and ARG/urease-based sensors, respectively. All biosensors have been exploited to estimate Arg content in commercial juices. The obtained data correlate well with the values obtained by the reference method. A hypothetic scheme for mechanism of action of ammonium nanochelators in electron transfer reaction on the arginine-sensing electrodes has been proposed.
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Affiliation(s)
- Nataliya Stasyuk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine.
| | - Galina Gayda
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine
| | - Wojciech Nogala
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Marcin Holdynski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Olha Demkiv
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine
| | - Lyubov Fayura
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine
| | - Andriy Sibirny
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine
- Department of Biotechnology and Microbiology, Rzeszow University, 35-601, Rzeszow, Poland
| | - Mykhailo Gonchar
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine.
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Shalileh F, Sabahi H, Golbashy M, Dadmehr M, Hosseini M. A simple smartphone-assisted paper-based colorimetric biosensor for the detection of urea adulteration in milk based on an environment-friendly pH-sensitive nanocomposite. Anal Chim Acta 2023; 1284:341935. [PMID: 37996167 DOI: 10.1016/j.aca.2023.341935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/29/2023] [Accepted: 10/19/2023] [Indexed: 11/25/2023]
Abstract
Urea is a common milk adulterant that falsely increases its protein content. Excessive consumption of urea is harmful to the kidney, liver, and gastrointestinal system. The conventional methods for urea detection in milk are time-consuming, costly, and require highly skilled operators. So, there is an increasing demand for the development of rapid, convenient, and cost-efficient methods for the detection of urea adulteration in milk. Herein, we report a novel colorimetric paper-based urea biosensor, consisting of a novel environment-friendly nanocomposite of halloysite nanotubes (HNT), that urease enzyme and an anthocyanin-rich extract, as a natural pH indicator are simultaneously immobilized into its internal and external surfaces. The biosensing mechanism of this biosensor is based on anthocyanin color change, which occurs due to urease-mediated hydrolysis of urea and pH increment of the environment. The colorimetric signal of this biosensor is measured through smartphone-assisted analysis of the mean RGB (Red-Green-Blue) intensity of samples and is capable of detecting urea with a detection limit of 0.2 mM, and a linear range from 0.5 to 100 mM. This biosensor has demonstrated promising results for the detection of urea in milk samples, in the presence of other milk adulterants and interferents.
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Affiliation(s)
- Farzaneh Shalileh
- Nanobiosensors Lab, Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Hossein Sabahi
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
| | - Mohammad Golbashy
- Department of Plant Production and Genetics, Faculty of Agriculture, Agricultural Sciences and Natural Resources, University of Khuzestan, Ahvaz, Iran
| | - Mehdi Dadmehr
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Morteza Hosseini
- Nanobiosensors Lab, Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran; Medical Biomaterials Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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10
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Moro CF, Nogueira FCS, Almeida CGM, Real-Guerra R, Dalberto PF, Bizarro CV, Ligabue-Braun R, Carlini CR. One enzyme, many faces: urease is also canatoxin. J Biomol Struct Dyn 2023; 41:10750-10761. [PMID: 36546698 DOI: 10.1080/07391102.2022.2158938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Ureases catalyze the hydrolysis of urea into carbamate and ammonia. Well-conserved proteins, most plant ureases are hexamers of a single chain subunit, like the most abundant isoform of the jack bean (Canavalia ensiformis) urease (JBU). Canatoxin (CNTX) was originally isolated from these seeds as a neurotoxic protein, and later characterized as an isoform of JBU with lower molecular mass and enzyme activity. Inactive CNTX oligomers form upon storage and stabilization of CNTX was achieved by treatment with low concentration of formaldehyde, avoiding its oligomerization. Here, nano-LC-MS/MS-based peptide analysis of CNTX revealed 804 amino acids identical to those of JBU's sequence (840 amino acids). De novo sequencing of CNTX revealed 15 different peptides containing substitution of amino acid residues, denoting CNTX as a product of a paralog gene of JBU. The MS/MS analysis of formaldehyde-treated CNTX showed that amino acid residues located at the trimer-trimer interface of JBU's hexamer were modified. The data confirmed that CNTX is an isoform of JBU and elucidated that stabilization by formaldehyde treatment occurs by modification of amino acids at the protein's surface that prevents the formation of the hexamer and of higher molecular mass inactive aggregates. HIGHLIGHTSCanatoxin (CNTX) is an isoform of jack bean urease (JBU, hexamer of 90 kDa chains)MS/MS sequencing of CNTX showed 804 amino acids identical in JBU (840 residues)Formaldehyde treatment of CNTX stabilizes its toxicity and avoids oligomerizationModified amino acid residues in CNTX are at the trimer-trimer interface of JBUCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carlo Frederico Moro
- Graduate Program in Medicine and Health Sciences, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Fábio C S Nogueira
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos Gabriel Moreira Almeida
- Graduate Program in Medicine and Health Sciences, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Rafael Real-Guerra
- Interdisciplinary Department, Universidade Federal do Rio Grande do Sul, Tramandaí, RS, Brazil
| | - Pedro Ferrari Dalberto
- Graduate Program in Cellular and Molecular Biology, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Cristiano V Bizarro
- Graduate Program in Cellular and Molecular Biology, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- National Institute of Science and Technology in Tuberculosis (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Rodrigo Ligabue-Braun
- Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Celia R Carlini
- Brain Institute-Instituto do Cérebro do Rio Grande do Sul (INSCER), Porto Alegre, RS, Brazil
- National Institute of Science and Technology in Brain Diseases, Excitotoxity and Neuroprotection (INCT-EN), Porto Alegre, RS, Brazil
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11
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Awan B, Khan MA, Ahmad I, Masood A, Raza A, Khaliq S, Ullah F, Ahmed J, Khan MR. Norfloxacin derivatives as DNA gyrase and urease inhibitors: synthesis, biological evaluation and molecular docking. Future Med Chem 2023; 15:2181-2194. [PMID: 37997685 DOI: 10.4155/fmc-2023-0225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
Background: DNA gyrase and urease enzymes are important targets for the treatment of gastroenteritis, appendicitis, tuberculosis, urinary tract infections and Crohn's disease. Materials & methods: Esterification of norfloxacin was performed to enhance DNA gyrase and urease enzyme inhibition potential. Structure elucidation and chemical characterization were done through spectral (1H NMR, Fourier transform IR, 13C NMR) and carbon, hydrogen, nitrogen and sulfur analysis along with molecular docking. Results & conclusion: The majority of derivatives exhibited significant results but the 3e derivative showed maximum bactericidal, DPPH scavenging (96%), DNA gyrase and urease enzyme inhibitory activity with IC50 of 0.15 ± 0.24 and 1.14 ± 0.11 μM respectively which was further supported by molecular docking studies. So, the active derivatives can serve as a lead compound for the treatment of various pathological conditions.
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Affiliation(s)
- Breena Awan
- Department of Pharmaceutical chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Mohsin Abbas Khan
- Department of Pharmaceutical chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
- Institute of Pharmaceutical Science, Faculty of Life Science & Medicine, King's College, London, SE1 9NH, UK
| | - Irshad Ahmad
- Department of Pharmaceutical chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Anum Masood
- Department of Pharmaceutical chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Asim Raza
- Department of Pharmaceutical chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Saharish Khaliq
- Department of Pharmaceutical chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Farhat Ullah
- Department of Pharmaceutical chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Javed Ahmed
- Department of Pharmaceutical chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Muhammad Rizwan Khan
- Department of Pharmaceutical chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
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12
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Chakraborty R, Purakayastha TJ, Pendall E, Dey S, Jain N, Kumar S. Nitrification and urease inhibitors mitigate global warming potential and ammonia volatilization from urea in rice-wheat system in India: A field to lab experiment. Sci Total Environ 2023; 898:165479. [PMID: 37459989 DOI: 10.1016/j.scitotenv.2023.165479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/02/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
The efficacy of alternative nitrogenous fertilizers for mitigating greenhouse gas and ammonia emissions from a rice-wheat cropping system in northern India was addressed in a laboratory incubation experiment using soil from a 10-year residue management field experiment (crop residue removal, CRR, vs. incorporation, CRI). Neem coated urea (NCU), standard urea (U), urea ammonium sulfate (UAS), and two alternative fertilizers, urea + urease inhibitor NBPT (UUI) and urea + urease inhibitor NBPT + nitrification inhibitor DMPSA (UUINI) were compared to non-fertilized controls for four weeks in incubation under anaerobic condition. Effects of fertilizers on global warming potential (GWP) and ammonia volatilization were dependent on residue treatment. Relative to standard urea, NCU reduced GWP by 11 % in CRI but not significantly in CRR; conversely, UAS reduced GWP by 12 % in CRR but not significantly in CRI. UUI and UUINI reduced GWP in both residue treatments and were more effective in CRI (21 % and 26 %) than CRR (15 % and 14 %). Relative to standard urea, NCU increased ammonia volatilization by 8 % in CRI but not significantly in CRR. Ammonia volatilization was reduced most strongly by UUI (40 % in CRI and 37 % in CRR); it was reduced 28-29 % by UUINI and 12-15 % by UAS. Overall, the urease inhibitor, alone and in combination with the nitrification inhibitor, was more effective in mitigating greenhouse gas and ammonia emissions than NCU. However, these products need to be tested in field settings to validate findings from the controlled laboratory experiment.
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Affiliation(s)
- Ranabir Chakraborty
- Division of Soil Science and Agricultural Chemistry, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India; Indian Council of Agricultural Research-National Bureau of Soil Survey and Land Use Planning, Regional Centre, Bangalore 560012, India
| | - Tapan Jyoti Purakayastha
- Division of Soil Science and Agricultural Chemistry, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India.
| | - Elise Pendall
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Saptaparnee Dey
- Division of Soil Science and Agricultural Chemistry, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Niveta Jain
- Division of Environment Science, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sarvendra Kumar
- Division of Soil Science and Agricultural Chemistry, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
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13
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Vaskevicius L, Malunavicius V, Jankunec M, Lastauskiene E, Talaikis M, Mikoliunaite L, Maneikis A, Gudiukaite R. Insights in MICP dynamics in urease-positive Staphylococcus sp. H6 and Sporosarcina pasteurii bacterium. Environ Res 2023; 234:116588. [PMID: 37423368 DOI: 10.1016/j.envres.2023.116588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Microbially induced calcite precipitation (MICP) is an efficient and eco-friendly technique that has attracted significant interest for resolving various problems in the soil (erosion, improving structural integrity and water retention, etc.), remediation of heavy metals, production of self-healing concrete or restoration of different concrete structures. The success of most common MICP methods depends on microorganisms degrading urea which leads to the formation of CaCO3 crystals. While Sporosarcina pasteurii is a well-known microorganism for MICP, other soil abundant microorganisms, such as Staphylococcus bacteria have not been thoroughly studied for its efficiency in bioconsolidation though MICP is a very important proccess which can ensure soil quality and health. This study aimed to analyze MICP process at the surface level in Sporosarcina pasteurii and a newly screened Staphylococcus sp. H6 bacterium as well as show the possibility of this new microorganism to perform MICP. It was observed that Staphylococcus sp. H6 culture precipitated 157.35 ± 3.3 mM of Ca2+ ions from 200 mM, compared to 176 ± 4.8 mM precipitated by S. pasteurii. The bioconsolidation of sand particles was confirmed by Raman spectroscopy and XRD analysis, which indicated the formation of CaCO3 crystals for both Staphylococcus sp. H6 and S. pasteurii cells. The water-flow test suggested a significant reduction in water permeability in bioconsolidated sand samples for both Staphylococcus sp. H6 and S. pasteurii. Notably, this study provides the first evidence that CaCO3 precipitation occurs on the surface of Staphylococcus and S. pasteurii cells within the initial 15-30 min after exposure to the biocementation solution. Furthermore, Atomic force microscopy (AFM) indicated rapid changes in cell roughness, with bacterial cells becoming completely coated with CaCO3 crystals after 90 min incubation with a biocementation solution. To our knowledge, this is the first time where atomic force microscopy was used to visualize the dynamic of MICP on cell surface.
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Affiliation(s)
- Laurynas Vaskevicius
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania
| | - Vilius Malunavicius
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania
| | - Marija Jankunec
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania
| | - Egle Lastauskiene
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania
| | - Martynas Talaikis
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania
| | - Lina Mikoliunaite
- Department of Physical Chemistry, Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko St. 24, LT-03225, Vilnius, Lithuania; Laboratory of Spectroelectrochemistry, Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekis Av. 3, LT-10257, Vilnius, Lithuania
| | - Andrius Maneikis
- Vilnius Gediminas Technical University, Sauletekis Av. 11, LT-10223, Vilnius, Lithuania
| | - Renata Gudiukaite
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania.
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14
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Seraj F, Khan KM, Iqbal J, Imran A, Hussain Z, Salar U, Hameed S, Taha M. Evaluation of synthetic aminoquinoline derivatives as urease inhibitors: in vitro, in silico and kinetic studies. Future Med Chem 2023; 15:1703-1717. [PMID: 37814798 DOI: 10.4155/fmc-2023-0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023] Open
Abstract
Background: Quinoline and acyl thiourea scaffolds have major chemical significance in medicinal chemistry. Quinoline-based acyl thiourea derivatives may potentially target the urease enzyme. Materials & methods: Quinoline-based acyl thiourea derivatives 1-26 were synthesized and tested for urease inhibitory activity. Results: 19 derivatives (1-19) showed enhanced urease enzyme inhibitory potential (IC50 = 1.19-18.92 μM) compared with standard thiourea (IC50 = 19.53 ± 0.032 μM), whereas compounds 20-26 were inactive. Compounds with OCH3, OC2H5, Br and CH3 on the aryl ring showed significantly greater inhibitory potential than compounds with hydrocarbon chains of varying length. Molecular docking studies were conducted to investigate ligand interactions with the enzyme's active site. Conclusion: The identified hits can serve as potential leads against the drug target urease in advanced studies.
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Affiliation(s)
- Faiza Seraj
- HEJ Research Institute of Chemistry, International Center for Chemical & Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Khalid Mohammed Khan
- HEJ Research Institute of Chemistry, International Center for Chemical & Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- Department of Clinical Pharmacy, Institute for Research & Medical Consultations, Imam Abdulrahman Bin Faisal University, PO Box 31441, Dammam, Saudi Arabia
| | - Jamshed Iqbal
- Center of Advanced Drug Research, COMSATS University Islamabad, Abbottabad, 22060, Pakistan
| | - Aqeel Imran
- Center of Advanced Drug Research, COMSATS University Islamabad, Abbottabad, 22060, Pakistan
- Department of Pharmacy, COMSATS University Islamabad, Lahore, 54000, Pakistan
| | - Zahid Hussain
- Center of Advanced Drug Research, COMSATS University Islamabad, Abbottabad, 22060, Pakistan
| | - Uzma Salar
- Dr Panjwani Center for Molecular Medicine & Drug Research, International Center for Chemical & Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Shehryar Hameed
- HEJ Research Institute of Chemistry, International Center for Chemical & Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research & Medical Consultations, Imam Abdulrahman Bin Faisal University, PO Box 31441, Dammam, Saudi Arabia
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15
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Adane AM, Park SY. Bilayer Actuator Film for Urea Biosensing with Dual Responsiveness: Bending Actuation and Photonic Color Change. ACS Sens 2023; 8:2290-2297. [PMID: 37213078 DOI: 10.1021/acssensors.3c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A noninvasive sweat-based biosensor was developed for urea detection using a photonic bilayer actuator film (BAF) consisting of an interpenetrating polymer network (IPN) as the active layer and a flexible poly(ethylene terephthalate) (PET) substrate as the passive layer (IPN/PET). The active IPN layer comprises intertwined solid-state cholesteric liquid crystal and poly(acrylic acid) (PAA) networks. Urease was immobilized in the PAA network in the IPN layer of the photonic BAF. The interaction with aqueous urea altered the curvature and photonic color of the photonic urease-immobilized IPN/PET (IPNurease/PET) BAF. The curvature (and wavelength of the photonic color) of the IPNurease/PET BAF increased linearly with urea concentration (Curea) in the range of Curea = 20-65 (and 30-65) mM with a limit of detection value of 1.42 (and 1.34) mM. The developed photonic IPNurease/PET BAF exhibited high selectivity toward urea and excellent spike test results with real human sweat. This novel IPNurease/PET BAF is promising because it enables battery-free, cost-effective, and visual detection-based analysis without the use of sophisticated instruments. Furthermore, the application of this photonic IPN/PET BAF can be easily extended to other biosensors by immobilizing other receptors on the IPN.
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Affiliation(s)
- Amhagiyorgis Mesfin Adane
- School of Applied Chemical Engineering, Polymeric Nano Materials Laboratory, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Soo-Young Park
- School of Applied Chemical Engineering, Polymeric Nano Materials Laboratory, Kyungpook National University, Daegu 41566, Republic of Korea
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16
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Nim YS, Fong IYH, Deme J, Tsang KL, Caesar J, Johnson S, Pang LTH, Yuen NMH, Ng TLC, Choi T, Wong YYH, Lea SM, Wong KB. Delivering a toxic metal to the active site of urease. Sci Adv 2023; 9:eadf7790. [PMID: 37083535 PMCID: PMC10121161 DOI: 10.1126/sciadv.adf7790] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Urease is a nickel (Ni) enzyme that is essential for the colonization of Helicobacter pylori in the human stomach. To solve the problem of delivering the toxic Ni ion to the active site without diffusing into the cytoplasm, cells have evolved metal carrier proteins, or metallochaperones, to deliver the toxic ions to specific protein complexes. Ni delivery requires urease to form an activation complex with the urease accessory proteins UreFD and UreG. Here, we determined the cryo-electron microscopy structures of H. pylori UreFD/urease and Klebsiella pneumoniae UreD/urease complexes at 2.3- and 2.7-angstrom resolutions, respectively. Combining structural, mutagenesis, and biochemical studies, we show that the formation of the activation complex opens a 100-angstrom-long tunnel, where the Ni ion is delivered through UreFD to the active site of urease.
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Affiliation(s)
- Yap Shing Nim
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ivan Yu Hang Fong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Justin Deme
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Ka Lung Tsang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Caesar
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Longson Tsz Hin Pang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Nicholas Man Hon Yuen
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tin Long Chris Ng
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tung Choi
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yakie Yat Hei Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Susan M. Lea
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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17
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Siddiqui H, Atia-Tul-Wahab, Ahmed A, Choudhary MI. Structural and Functional Analysis of Urease Accessory Protein E from Vancomycin-Resistance Staphylococcus aureus MU50 Strain. Protein Pept Lett 2023; 30:754-762. [PMID: 37533244 DOI: 10.2174/0929866530666230801163340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/10/2023] [Accepted: 06/23/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND An increasing prevalence of biofilm forming strains by vancomycinresistance Staphylococcus aureus (VRSA) is one of the most important causes of antimicrobial resistance. VRSA possesses various regulatory factors to form and sustain biofilm in biotic or abiotic conditions. Among them, ureolytic activity is an important factor in the stabilization of biofilms by neutralizing the acidic environment. Various urease accessory proteins are required to activate the urease enzyme inside the biofilm. OBJECTIVE To optimize the cloning, expression and purification of urease accessory protein E from VRSA for determination of the secondary structure, and functional characterization by using Berthelot's method. METHODS BAB58453.1 gene (which encodes possible urease accessory protein E), having 38% similarity to Bacillus pasteurii UreE protein, was cloned, expressed, and purified by single-step affinity chromatography for performing secondary structural studies using circular dichroism spectroscopy, and functional analysis using Berthelot's and crystal violet assay. RESULTS Structure elucidation using NMR and circular dichroism spectroscopy techniques revealed that UreE protein has a partially foldedα-helical structure. Using Berthelot's method, it was identified that the purified UreE protein has enhanced urease enzyme activity, in comparison to the control. From the results of Berthelot's and crystal violet assays, it was deduced that the selected gene (UreE protein) plays a key role in enhancing urease enzyme activity and contributes to biofilm stability. CONCLUSION Structural studies on VRSA urease accessory proteins could aid in the identification of new drug targets or the development of effective antibiofilm strategies (in combination with other drug targets) against infections caused by biofilm-producing strains.
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Affiliation(s)
- Humaira Siddiqui
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Atia-Tul-Wahab
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Aftab Ahmed
- School of Pharmacy, Chapman University, Irvine, CA 92618, USA
| | - M Iqbal Choudhary
- H.E.J. Research-Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah-21412, Saudi Arabia
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
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18
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Yadav N, Kumar K, Singh VK, Rai S, Blahatia K, Das A, Jana T. Newly designed acrylamide derivative-based pH-responsive hydrogel-urease bioconjugates: synthesis and catalytic urea hydrolysis. Soft Matter 2022; 18:8647-8655. [PMID: 36349658 DOI: 10.1039/d2sm00958g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Jack bean urease, the first nickel metalloenzyme, and crystallized enzymes have historical significance due to their several applications in the biomedical and other fields. For the first time, cross-linker free pH-responsive hydrogel-urease bioconjugates have been reported. Without the use of divinyl benzene or divinyl acrylamide derivatives, urease was immobilized inside the hydrogel matrix and various grades of bioconjugates were synthesized. The hydrogel-urease bioconjugate exhibits excellent swelling-deswelling and pH-responsive characteristics without affecting the urease enzyme. The pH-responsive bioconjugates were characterized by FT-IR, powder XRD, SEM, TGA, and UV-vis spectroscopy. Urea hydrolysis and enzyme affinity have been investigated at pH 4, pH 7, and pH 11 using bioconjugates and free urease. At basic pH, BCs showed excellent enzyme activity. In summary, this technique is effective for stabilizing biomacromolecules at different pHs for a variety of real applications.
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Affiliation(s)
- Nisha Yadav
- Department of Chemistry and Environmental Science, Madan Mohan Malaviya University of Technology, Gorakhpur-273010, Uttar Pradesh, India.
| | - Krishna Kumar
- Department of Chemistry and Environmental Science, Madan Mohan Malaviya University of Technology, Gorakhpur-273010, Uttar Pradesh, India.
| | - V K Singh
- Department of Chemistry and Environmental Science, Madan Mohan Malaviya University of Technology, Gorakhpur-273010, Uttar Pradesh, India.
| | - Shailja Rai
- Department of Chemistry and Environmental Science, Madan Mohan Malaviya University of Technology, Gorakhpur-273010, Uttar Pradesh, India.
| | - Kunal Blahatia
- Department of Chemical Engineering, India Institute of Technology Delhi, New Delhi-110016, India
| | - Anupam Das
- School of Chemistry, University of Hyderabad, Gachibowli-500046, Hyderabad, Telangana State, India
| | - Tushar Jana
- School of Chemistry, University of Hyderabad, Gachibowli-500046, Hyderabad, Telangana State, India
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Gao T, McNeill JM, Oliver VA, Xiao L, Mallouk TE. Geometric and Scaling Effects in the Speed of Catalytic Enzyme Micropumps. ACS Appl Mater Interfaces 2022; 14:39515-39523. [PMID: 35984896 DOI: 10.1021/acsami.2c09555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Self-powered, biocompatible pumps in the nanometer to micron length scale have the potential to enable technology in several fields, including chemical analysis and medical diagnostics. Chemically powered, catalytic micropumps have been developed but are not able to function well in biocompatible environments due to their intolerance of salt solutions and the use of toxic fuels. In contrast, enzymatically powered catalytic pumps offer good biocompatibility, selectivity, and scalability, but their performance at length scales below a few millimeters, which is important to many of their possible applications, has not been well tested. Here, urease-based enzyme pumps of millimeter and micrometer dimensions were fabricated and studied. The scaling of the pumping velocity was measured experimentally and simulated by numerical modeling. Pumping speeds were analyzed accurately by eliminating Brownian noise from the data using enzyme patches between 5 mm and 350 μm in size. Pumping speeds of microns per second could be achieved with urease pumps and were fastest when the channel height exceeded the width of the catalytic pump patch. In all cases, pumping was weak when the dimensions of the patch were 100 μm or less. Experimental and simulation results were consistent with a density-driven pumping mechanism at all sizes studied and served as a framework for the in silico study of more complex two-dimensional (2D) and three-dimensional (3D) geometries. Attempts to create directional flow by juxtaposing inward and outward pumps were unsuccessful because of the symmetry of convection rolls produced by millimeter-size pump patches and the slow speeds of smaller pumps. However, simulations of a corrugated ratchet structure showed that directional pumping could be achieved with pump patches in the millimeter size range.
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Affiliation(s)
- Tianyue Gao
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jeffrey M McNeill
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Vincent A Oliver
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Langqiu Xiao
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Thomas E Mallouk
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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20
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Mandal B, Mondal S, Hansda B, Mishra S, Ghosh A, Biswas T, Das B, Mondal TK, Kumari P. Multipoint Immobilization at the Inert Center of Urease on Homofunctional Diazo-Activated Silica Gel: A Way of Restoring Room-Temperature Catalytic Sustainability for Perennial Utilization. Langmuir 2022; 38:6826-6840. [PMID: 35609014 DOI: 10.1021/acs.langmuir.2c00022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
At present, enzyme immobilization is a big issue. It improves enzyme stability, activity, specificity, or selectivity, particularly the enantioselectivity compared to the native enzymes, and by solving the separation problem, it helps in recovering the catalyst with good reusability as desired in vitro. Motivated by these facts, in this work, Jack bean urease (JBU) is immobilized on three-dimensional (3D)-network silica gel (SG) via multipoint covalent bonding employing dimethyldichlorosilane (DMDCS) and p-nitrophenol, respectively, as the second-generation silane-coupling reagent and spacer. The homofunctional diazo group appearing at the functionalized SG unit cell makes a diazo linkage at the inert center, the ortho position of the phenolic-OH of the tyrosine moiety, where all of the amino, thiol, phenol, imidazole, carboxy, etc., groups of the enzyme residues, including those that belong to the active site, remain intact. The coupling process, analyzed using field emission scanning electron microscopy (FESEM), energy-dispersive X-ray analysis (EDX), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FT-IR) spectroscopy, ultraviolet-visible spectroscopy (UV-vis), and fluorescence spectroscopy, occurs without molecular aggregation in borate buffer at pH 8.8 ± 0.4, which is much higher than the iso-electric point (pH 5.1) of the macromolecule where it becomes soluble. Eventually, the immobilization is maximize and also the native-enzyme activities are restored remarkably. The immobilized catalyst converts urea (0.0625-0.15 mmol L-1) to ammonia appreciably (94.50 ± 1.5%) at 27 °C, and the efficiency is well comparable to that of the native enzyme (93.0 ± 0.4%). The efficiency gradually diminishes, coming down to 50% at the 40th cycle, and the enzyme returns to its native conformation within 72 h in tris-EDTA borate buffer at 27 °C for the next 40 cycles of reuse and so on. The efficiency becomes hindered by 8-10% in every 5th subsequent reuse to reach 50% on the 30th reuse, resulting in room-temperature catalytic sustainability of 90 days. The catalytic performances are well restored in rice extract and coconut water.
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Affiliation(s)
- Bhabatosh Mandal
- Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal 731235, India
| | - Sneha Mondal
- Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal 731235, India
| | - Biswajit Hansda
- Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal 731235, India
| | - Shailja Mishra
- Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal 731235, India
| | - Ankit Ghosh
- Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal 731235, India
| | - Tirtha Biswas
- Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal 731235, India
| | - Basudev Das
- Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal 731235, India
| | - Tanay Kumar Mondal
- Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal 731235, India
| | - Pallavi Kumari
- Tilka Manjhi Bhagalpur University, Bhagalpur, Bihar 812007, India
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21
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Xu Y, Zhou C, Wang Q, Zhai H, Yang X, Peng H, Qian X, Shi A, Deng M, Zhu Y, Ren Z, Ma J, Yang B. Technical Note: Comparative Analysis and Evaluation of the Polymerase Chain Reaction and Rapid Urease Test for Diagnosing Helicobacter pylori Infection. Ann Clin Lab Sci 2022; 52:499-503. [PMID: 35777789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study was conducted in order to compare the performance of the rapid urease test (RUT) with that of the polymerase chain reaction (PCR) for H. pylori diagnosis. Of 536 patients, 81% were concordant between RUT and PCR, 16% were concordant between two PCR assays but not between RUT and PCR, and the remaining 3% showed discrepant results between two PCR assays evaluated. Low bacterial load was shown to be a significant factor associated with false-negative diagnosis by RUT, and non-H. pylori urease activity or bacterial alkaline-generating activity was the cause of false-positive diagnosis. Disagreement between the PCR assays was due to single nucleotide polymorphisms in primers or probes causing decreased amplification efficiency and false-negative diagnosis when the bacterial load in the samples was low.
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Affiliation(s)
- Ying Xu
- Taizhou Hospital of Traditional Chinese Medicine, Jiangsu, China
| | | | - Qizhi Wang
- The First Affiliated Hospital of Bengbu Medical College, Anhui, China
| | | | - Xiyin Yang
- Jiangsu Cowin Biotechnology Co., Ltd., Taizhou, Jiangsu, China
| | | | - Xueshen Qian
- Taizhou Hospital of Traditional Chinese Medicine, Jiangsu, China
| | - Anchun Shi
- Taizhou Hospital of Traditional Chinese Medicine, Jiangsu, China
| | - Min Deng
- The First Affiliated Hospital of Bengbu Medical College, Anhui, China
| | - Yu Zhu
- The First Affiliated Hospital of Bengbu Medical College, Anhui, China
| | - Zhi Ren
- The First Affiliated Hospital of Bengbu Medical College, Anhui, China
| | - Jun Ma
- Jiangsu Cowin Biotechnology Co., Ltd., Taizhou, Jiangsu, China
| | - Bin Yang
- Taizhou People's Hospital, Jiangsu, China
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22
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Valles M, Pujals S, Albertazzi L, Sánchez S. Enzyme Purification Improves the Enzyme Loading, Self-Propulsion, and Endurance Performance of Micromotors. ACS Nano 2022; 16:5615-5626. [PMID: 35341250 PMCID: PMC9047656 DOI: 10.1021/acsnano.1c10520] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Enzyme-powered micro- and nanomotors make use of biocatalysis to self-propel in aqueous media and hold immense promise for active and targeted drug delivery. Most (if not all) of these micro- and nanomotors described to date are fabricated using a commercially available enzyme, despite claims that some commercial preparations may not have a sufficiently high degree of purity for downstream applications. In this study, the purity of a commercial urease, an enzyme frequently used to power the motion of micro- and nanomotors, was evaluated and found to be impure. After separating the hexameric urease from the protein impurities by size-exclusion chromatography, the hexameric urease was subsequently characterized and used to functionalize hollow silica microcapsules. Micromotors loaded with purified urease were found to be 2.5 times more motile than the same micromotors loaded with unpurified urease, reaching average speeds of 5.5 μm/s. After comparing a number of parameters, such as enzyme distribution, protein loading, and motor reusability, between micromotors functionalized with purified vs unpurified urease, it was concluded that protein purification was essential for optimal performance of the enzyme-powered micromotor.
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Affiliation(s)
- Morgane Valles
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028 Barcelona, Spain
| | - Sílvia Pujals
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028 Barcelona, Spain
| | - Lorenzo Albertazzi
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Samuel Sánchez
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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23
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Welden M, Poghossian A, Vahidpour F, Wendlandt T, Keusgen M, Wege C, Schöning MJ. Towards Multi-Analyte Detection with Field-Effect Capacitors Modified with Tobacco Mosaic Virus Bioparticles as Enzyme Nanocarriers. Biosensors (Basel) 2022; 12:bios12010043. [PMID: 35049671 PMCID: PMC8773754 DOI: 10.3390/bios12010043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 05/07/2023]
Abstract
Utilizing an appropriate enzyme immobilization strategy is crucial for designing enzyme-based biosensors. Plant virus-like particles represent ideal nanoscaffolds for an extremely dense and precise immobilization of enzymes, due to their regular shape, high surface-to-volume ratio and high density of surface binding sites. In the present work, tobacco mosaic virus (TMV) particles were applied for the co-immobilization of penicillinase and urease onto the gate surface of a field-effect electrolyte-insulator-semiconductor capacitor (EISCAP) with a p-Si-SiO2-Ta2O5 layer structure for the sequential detection of penicillin and urea. The TMV-assisted bi-enzyme EISCAP biosensor exhibited a high urea and penicillin sensitivity of 54 and 85 mV/dec, respectively, in the concentration range of 0.1-3 mM. For comparison, the characteristics of single-enzyme EISCAP biosensors modified with TMV particles immobilized with either penicillinase or urease were also investigated. The surface morphology of the TMV-modified Ta2O5-gate was analyzed by scanning electron microscopy. Additionally, the bi-enzyme EISCAP was applied to mimic an XOR (Exclusive OR) enzyme logic gate.
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Affiliation(s)
- Melanie Welden
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (M.W.); (F.V.)
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, 35032 Marburg, Germany;
| | | | - Farnoosh Vahidpour
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (M.W.); (F.V.)
| | - Tim Wendlandt
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, 70569 Stuttgart, Germany; (T.W.); (C.W.)
| | - Michael Keusgen
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, 35032 Marburg, Germany;
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, 70569 Stuttgart, Germany; (T.W.); (C.W.)
| | - Michael J. Schöning
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (M.W.); (F.V.)
- Institute of Biological Information Processing (IBI-3), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Correspondence:
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24
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Abstract
Hydrogenases and ureases play vital metabolic functions in all three domains of life. However, nickel ions are cytotoxic because they can inactivate enzymes that require less competitive ions (e.g. Mg2+) in the Irving-Williams series to function. Life has evolved elegant mechanisms to solve the problem of delivering the toxic metal to the active site of nickel-containing enzymes inside the cells. Here, we review our current understanding of nickel trafficking along the hydrogenase and urease maturation pathways. Metallochaperones and accessory proteins (SlyD, HypA, HypB, UreD, UreE, UreF, and UreG) form specific protein complexes to allow the transfer of nickel from one protein to another without releasing the toxic metal into the cytoplasm. The role of SlyD is not fully understood, but it can interact with and transfer its nickel to HypB. In the hydrogenase maturation pathway, nickel is transferred from HypB to HypA, which can then deliver its nickel to the hydrogenase large subunit precursor. In Helicobacter pylori, the urease maturation pathway receives its nickel from HypA of the hydrogenase maturation pathway via the formation of a HypA/UreE2 complex. Guanosine triphosphate (GTP) binding promotes the formation of a UreE2G2 complex, where UreG receives a nickel from UreE. In the final step of the urease maturation, nickel/GTP-bound UreG forms an activation complex with UreF, UreD, and apo-urease. Upon GTP hydrolysis, nickel is released from UreG to the urease. Finally, some common themes learned from the hydrogenase-urease maturation pathway are discussed.
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Affiliation(s)
- Ka Lung Tsang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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25
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Ali S, Siddiqui SZ, Abbasi MA, Aziz-Ur-Rehman , Ali Shah SA, Mohammed Khan K, Saleem RSZ, Manzoor S, Ashraf M, Zia-Ur-Rehman . Synthesis and evaluation of novel 1, 2, 4-substituted triazoles for urease and anti-proliferative activity. Pak J Pharm Sci 2022; 35:209-217. [PMID: 35228179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
1,2,4-triazoles are a major group of heterocyclic compounds. In the current work, a concise library of such triazoles synthesized through a multistep protocol. The synthesis involved hydrazinolysis of ethyl-2-(p-Cl-phenoxy) acetate followed by reflux with phenyl isothiocyanate to yield the intermediate 2-[2-(p-Cl-phenoxy)acetyl)-N-phenyl-hydrazinecarbothioamide. This intermediate was then cyclized to form 5-[p-(Cl-phenoxy)-methyl]-4-phenyl-4H-1,2,4-triazole-3-thiol (the parent moiety) at alkaline pH. In parallel, 3-bromopropionyl bromide was reacted with a series of phenylamines to yield N-(substituted-phenyl)bromopropanamides. In the final step, N-substitution of 5-[p-(Cl-phenoxy)-methyl]-4- phenyl-4H-1,2,4-triazole-3-thiol was carried out with N-(substituted-phenyl)bromopropanamides to give desired library of 3-[5-[(p-Cl-phenoxy)-methyl]-4- phenyl-4H-1,2,4-triazole-3-ylthio]-N-(substituted-phenyl) propan-amides (8a-l). The prepared moieties were identified via IR, NMR, & EIMS and evaluated for urease and anti-proliferative activities. 3-[5-[(p-Cl-phenoxy)-methyl]-4- phenyl-4H-1,2,4-triazole-3-ylthio]-N-(3-methyl-phenyl)propanamide 8k, was found to be most prominent hit as urease inhibitor (IC50= 42.57± 0.13 µM) using thiourea as standard (IC50= 21.25±0.15µM). The interaction of 8k with urease were studied using docking studies. Anti-proliferative activity results showed 8k as promising candidates and rest of the synthesized derivatives were found to be moderately anti-proliferative. Molecular docking results also displayed 8k, 8h, and 8c as potential hits for further study.
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Affiliation(s)
- Saima Ali
- Department of Chemistry, Government College University, Lahore, Pakistan
| | | | | | - - Aziz-Ur-Rehman
- Department of Chemistry, Government College University, Lahore, Pakistan
| | - Syed Adnan Ali Shah
- Research Institute of Natural Products for Drug Discovery (RiND), NMR Facility Division, Faculty of Pharmacy, University Teknologi MARA (UiTM), Puncak Alam Campus, Bandar Puncak Alam Selangor D. E. Malaysia
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan/Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam Saudi Arabia
| | - Rahman Shah Zaib Saleem
- Department of Chemistry & Chemical Engineering, SBA School of Sciences and Engineering, Lahore University of Management Sciences, Opposite Sector-U, DHA, Lahore, Pakistan
| | - Safia Manzoor
- Department of Chemistry & Chemical Engineering, SBA School of Sciences and Engineering, Lahore University of Management Sciences, Opposite Sector-U, DHA, Lahore, Pakistan
| | - Muhammad Ashraf
- Department of Chemistry, Baghdad-ul-Jadid Campus, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - - Zia-Ur-Rehman
- Applied Chemistry Research Centre, PCSIR Laboratories Complex, Lahore
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26
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Ahmed A, Saeed A, Ali OM, El-Bahy ZM, Channar PA, Khurshid A, Tehzeeb A, Ashraf Z, Raza H, Ul-Hamid A, Hassan M. Exploring Amantadine Derivatives as Urease Inhibitors: Molecular Docking and Structure-Activity Relationship (SAR) Studies. Molecules 2021; 26:molecules26237150. [PMID: 34885728 PMCID: PMC8658948 DOI: 10.3390/molecules26237150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
This article describes the design and synthesis of a series of novel amantadine-thiourea conjugates (3a–j) as Jack bean urease inhibitors. The synthesized hybrids were assayed for their in vitro urease inhibition. Accordingly, N-(adamantan-1-ylcarbamothioyl)octanamide (3j) possessing a 7-carbon alkyl chain showed excellent activity with IC50 value 0.0085 ± 0.0011 µM indicating that the long alkyl chain plays a vital role in enzyme inhibition. Whilst N-(adamantan-1-ylcarbamothioyl)-2-chlorobenzamide (3g) possessing a 2-chlorophenyl substitution was the next most efficient compound belonging to the aryl series with IC50 value of 0.0087 ± 0.001 µM. The kinetic mechanism analyzed by Lineweaver–Burk plots revealed the non-competitive mode of inhibition for compound 3j. Moreover, in silico molecular docking against target protein (PDBID 4H9M) indicated that most of the synthesized compounds exhibit good binding affinity with protein. The compound 3j forms two hydrogen bonds with amino acid residue VAL391 having a binding distance of 1.858 Å and 2.240 Å. The interaction of 3j with amino acid residue located outside the catalytic site showed its non-competitive mode of inhibition. Based upon these results, it is anticipated that compound 3j may serve as a lead structure for the design of more potent urease inhibitors.
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Affiliation(s)
- Atteeque Ahmed
- Department of Chemistry, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.A.); (P.A.C.); (A.K.)
| | - Aamer Saeed
- Department of Chemistry, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.A.); (P.A.C.); (A.K.)
- Correspondence: or ; Tel.: +92-51-9064-2128
| | - Omar M. Ali
- Department of Chemistry, Turabah University College, Turabah Branch, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Zeinhom M. El-Bahy
- Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt;
| | - Pervaiz Ali Channar
- Department of Chemistry, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.A.); (P.A.C.); (A.K.)
| | - Asma Khurshid
- Department of Chemistry, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.A.); (P.A.C.); (A.K.)
| | - Arfa Tehzeeb
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Zaman Ashraf
- Department of Chemistry, Allama Iqbal Open University, Islamabad 44000, Pakistan;
| | - Hussain Raza
- Department of Biological Sciences, College of Natural Sciences, Kongju National University, 56 Gongjudehak-Ro, Gongju 314-701, Chungnam, Korea;
| | - Anwar Ul-Hamid
- Core Research Facilities, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia;
| | - Mubashir Hassan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan;
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27
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Abstract
The urea-urease clock reaction is a pH switch from acid to basic that can turn into a pH oscillator if it occurs inside a suitable open reactor. We numerically study the confinement of the reaction to lipid vesicles, which permit the exchange with an external reservoir by differential transport, enabling the recovery of the pH level and yielding a constant supply of urea molecules. For microscopically small vesicles, the discreteness of the number of molecules requires a stochastic treatment of the reaction dynamics. Our analysis shows that intrinsic noise induces a significant statistical variation of the oscillation period, which increases as the vesicles become smaller. The mean period, however, is found to be remarkably robust for vesicle sizes down to approximately 200 nm, but the periodicity of the rhythm is gradually destroyed for smaller vesicles. The observed oscillations are explained as a canard-like limit cycle that differs from the wide class of conventional feedback oscillators.
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Affiliation(s)
| | | | - Christof Schütte
- Zuse Institute Berlin, Takustraße 7, 14195 Berlin, Germany
- Freie Universität Berlin, Department of Mathematics and Computer Science, Arnimallee 6, 14195 Berlin, Germany
| | - Felix Höfling
- Zuse Institute Berlin, Takustraße 7, 14195 Berlin, Germany
- Freie Universität Berlin, Department of Mathematics and Computer Science, Arnimallee 6, 14195 Berlin, Germany
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28
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Wells PK, Smutok O, Melman A, Katz E. Switchable Biocatalytic Reactions Controlled by Interfacial pH Changes Produced by Orthogonal Biocatalytic Processes. ACS Appl Mater Interfaces 2021; 13:33830-33839. [PMID: 34264645 DOI: 10.1021/acsami.1c07393] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Enzymes immobilized on a nano-structured surface were used to switch the activity of one enzyme by a local pH change produced by another enzyme. Immobilized amyloglucosidase (AMG) and trypsin were studied as examples of the pH-dependent switchable "target enzymes." The reactions catalyzed by co-immobilized urease or esterase were increasing or decreasing the local pH, respectively, thus operating as "actuator enzymes." Both kinds of the enzymes, producing local pH changes and changing biocatalytic activity with the pH variation, were orthogonal in terms of the biocatalytic reactions; however, their operation was coupled with the local pH produced near the surface with the immobilized enzymes. The "target enzymes" (AMG and trypsin) were changed reversibly between the active and inactive states by applying input signals (urea or ester, substrates for the urease or esterase operating as the "actuator enzymes") and washing them out with a new portion of the background solution. The developed approach can potentially lead to switchable operation of several enzymes, while some of them are inhibited when the others are activated upon receiving external signals processed by the "actuator enzymes." More complex systems with branched biocatalytic cascades can be controlled by orthogonal biocatalytic reactions activating selected pathways and changing the final output.
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Affiliation(s)
- Paulina K Wells
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States
| | - Oleh Smutok
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States
| | - Artem Melman
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States
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29
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Grahl MVC, Uberti AF, Broll V, Bacaicoa-Caruso P, Meirelles EF, Carlini CR. Proteus mirabilis Urease: Unsuspected Non-Enzymatic Properties Relevant to Pathogenicity. Int J Mol Sci 2021; 22:ijms22137205. [PMID: 34281258 PMCID: PMC8268090 DOI: 10.3390/ijms22137205] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/22/2022] Open
Abstract
Infection by Proteus mirabilis causes urinary stones and catheter incrustation due to ammonia formed by urease (PMU), one of its virulence factors. Non-enzymatic properties, such as pro-inflammatory and neurotoxic activities, were previously reported for distinct ureases, including that of the gastric pathogen Helicobacter pylori. Here, PMU was assayed on isolated cells to evaluate its non-enzymatic properties. Purified PMU (nanomolar range) was tested in human (platelets, HEK293 and SH-SY5Y) cells, and in murine microglia (BV-2). PMU promoted platelet aggregation. It did not affect cellular viability and no ammonia was detected in the cultures’ supernatants. PMU-treated HEK293 cells acquired a pro-inflammatory phenotype, producing reactive oxygen species (ROS) and cytokines IL-1β and TNF-α. SH-SY5Y cells stimulated with PMU showed high levels of intracellular Ca2+ and ROS production, but unlike BV-2 cells, SH-SY5Y did not synthesize TNF-α and IL-1β. Texas Red-labeled PMU was found in the cytoplasm and in the nucleus of all cell types. Bioinformatic analysis revealed two bipartite nuclear localization sequences in PMU. We have shown that PMU, besides urinary stone formation, can potentially contribute in other ways to pathogenesis. Our data suggest that PMU triggers pro-inflammatory effects and may affect cells beyond the renal system, indicating a possible role in extra-urinary diseases.
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Affiliation(s)
- Matheus V. C. Grahl
- Laboratory of Neurotoxins, Brain Institute of Rio Grande do Sul (BRAINS) and Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil; (M.V.C.G.); (A.F.U.)
| | - Augusto F. Uberti
- Laboratory of Neurotoxins, Brain Institute of Rio Grande do Sul (BRAINS) and Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil; (M.V.C.G.); (A.F.U.)
| | - Valquiria Broll
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil;
| | - Paula Bacaicoa-Caruso
- Laboratory of Neurotoxins, Brain Institute of Rio Grande do Sul (BRAINS) and Graduate Program in Cellular and Molecular Biology, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil;
| | - Evelin F. Meirelles
- Laboratory of Neurotoxins, Brain Institute of Rio Grande do Sul (BRAINS), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil;
| | - Celia R. Carlini
- Laboratory of Neurotoxins, Brain Institute of Rio Grande do Sul (BRAINS) and School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil
- Correspondence: ; Tel.: +55-51-33205986
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Rashid M, Rafique H, Roshan S, Shamas S, Iqbal Z, Ashraf Z, Abbas Q, Hassan M, Qureshi ZUR, Asad MHHB. Enzyme Inhibitory Kinetics and Molecular Docking Studies of Halo-Substituted Mixed Ester/Amide-Based Derivatives as Jack Bean Urease Inhibitors. Biomed Res Int 2020; 2020:8867407. [PMID: 33426080 PMCID: PMC7775144 DOI: 10.1155/2020/8867407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/28/2020] [Accepted: 12/15/2020] [Indexed: 12/22/2022]
Abstract
A series of halo-substituted mixed ester/amide-based analogues 4a-l have been prepared as jack bean urease inhibitor, which showed good to excellent inhibition of enzyme activity. The role of halo-substituted benzoyl moieties and alkyl substituted anilines in urease inhibitory kinetics was also investigated. The alkyl-substituted anilines 1a-b reacted with chloroacetyl chloride to afford intermediates 2a-b, which were then reacted with different halo-substituted benzoic acids 3a-f to prepare the title compounds 4a-l. The chemical structures of final products 4a-l were ascertained by FTIR, 1H NMR, 13C NMR, and mass spectra. The compound 4b showed remarkable activity with IC501.6 ± 0.2 nM, better than the standard thiourea having IC50472.1 ± 135.1 nM. The 2-chloro-substituted phenyl ring on one side of compound 4b and 4-isopropyl-substituted benzene on the other side play an essential role in inhibition of urease activity. Lineweaver-Burk plots (kinetics study) indicated about 4b derivative as a mixed type of inhibitor. The virtual screening performed against urease enzyme (PDBID 4H9M) showed that compounds 4b and 4e have binding energies of -7.8 and -7.9 Kcal/mol, respectively. Based upon our results, it was found that derivative 4b is a highly potent urease inhibitor, better than the standard thiourea.
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Affiliation(s)
- Muhammad Rashid
- Department of Chemistry, Allama Iqbal Open University, Islamabad 44000, Pakistan
| | - Hummera Rafique
- Department of Chemistry, University of Gujrat, Gujrat 50700, Pakistan
| | - Sadia Roshan
- Department of Zoology, University of Gujrat, Gujrat 50700, Pakistan
| | - Shazia Shamas
- Department of Zoology, University of Gujrat, Gujrat 50700, Pakistan
| | - Zafar Iqbal
- Department of Chemistry, Allama Iqbal Open University, Islamabad 44000, Pakistan
| | - Zaman Ashraf
- Department of Chemistry, Allama Iqbal Open University, Islamabad 44000, Pakistan
| | - Qamar Abbas
- Department of Physiology, University of Sindh, Jamshoro, Pakistan
| | - Mubashir Hassan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | | | - Muhammad Hassham Hassan Bin Asad
- Department of Pharmacy, COMSATS University Islamabad, Abbottabad Campus, Pakistan
- Institute of Fundamental Medicine, Department of Genetics, Kazan Federal University, Russia
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31
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Grahl MVC, Lopes FC, Martinelli AHS, Carlini CR, Fruttero LL. Structure-Function Insights of Jaburetox and Soyuretox: Novel Intrinsically Disordered Polypeptides Derived from Plant Ureases. Molecules 2020; 25:molecules25225338. [PMID: 33207637 PMCID: PMC7696265 DOI: 10.3390/molecules25225338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 12/24/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) do not have a stable 3D structure but still have important biological activities. Jaburetox is a recombinant peptide derived from the jack bean (Canavalia ensiformis) urease and presents entomotoxic and antimicrobial actions. The structure of Jaburetox was elucidated using nuclear magnetic resonance which reveals it is an IDP with small amounts of secondary structure. Different approaches have demonstrated that Jaburetox acquires certain folding upon interaction with lipid membranes, a characteristic commonly found in other IDPs and usually important for their biological functions. Soyuretox, a recombinant peptide derived from the soybean (Glycine max) ubiquitous urease and homologous to Jaburetox, was also characterized for its biological activities and structural properties. Soyuretox is also an IDP, presenting more secondary structure in comparison with Jaburetox and similar entomotoxic and fungitoxic effects. Moreover, Soyuretox was found to be nontoxic to zebra fish, while Jaburetox was innocuous to mice and rats. This profile of toxicity affecting detrimental species without damaging mammals or the environment qualified them to be used in biotechnological applications. Both peptides were employed to develop transgenic crops and these plants were active against insects and nematodes, unveiling their immense potentiality for field applications.
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Affiliation(s)
- Matheus V. Coste Grahl
- Graduate Program in Medicine and Health Sciences, Brain Institute of Rio Grande do Sul (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, Brazil;
| | - Fernanda Cortez Lopes
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Building 43431, Porto Alegre CEP 91501-970, RS, Brazil;
| | - Anne H. Souza Martinelli
- Department of Biophysics & Deparment of Molecular Biology and Biotechnology-Biosciences Institute (IB), Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre 91501-970, RS, Brazil;
| | - Celia R. Carlini
- Graduate Program in Medicine and Health Sciences, Brain Institute of Rio Grande do Sul (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, Brazil;
- Brain Institute and School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
- Correspondence: (C.R.C.); (L.L.F.); Tel.: +55-51-3320-3485 (C.R.C.); +54-351-535-3850 (L.L.F.)
| | - Leonardo L. Fruttero
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba CP 5000, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba CP 5000, Argentina
- Correspondence: (C.R.C.); (L.L.F.); Tel.: +55-51-3320-3485 (C.R.C.); +54-351-535-3850 (L.L.F.)
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Zhang X, Zhao S, He Y, Zheng N, Yan X, Wang J. Substitution of residues in UreG to investigate UreE interactions and nickel binding in a predominant urease gene cluster from the ruminal metagenome. Int J Biol Macromol 2020; 161:1591-1601. [PMID: 32755703 DOI: 10.1016/j.ijbiomac.2020.07.260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 11/17/2022]
Abstract
Microbial ureases catalyze the hydrolysis of urea to ammonia, and inhibition of these enzymes in rumen has the potential to improve urea utilization efficiency and reduce urinary nitrogen excretion. Urease activity is catalyzed by a protein complex encoded by a gene cluster, and its accessory proteins (especially UreE and UreG) play important roles in transferring nickel to the active site for urease maturation. In this study, a predominant urease gene cluster (5290 bp) from the ruminal microbial metagenome was identified. Isothermal titration calorimetry (ITC) and analytical ultracentrifugation (AUC) analyses showed that the reaction of identified UreE with UreG was endothermic, and was dominated by a hydrophobic interaction, in which each UreE dimer bound 2 M equivalents of UreG monomer to form a UreE2-2UreG complex. Mutagenesis analyses showed that the UreG residues Glu-23, Asp-41, Glu-46, Glu-66, Cys-70, His-72, Asp-78, and Asp-118 were involved in the GTPase activity of UreG. Furthermore, variants of Cys-70 and His-72 involved in CPH motif of UreG, as well as the nearby Glu-66 and Asp-78, not only prevented interactions with UreE, but also prevented nickel binding. These data provide additional information regarding UreG residues that may be targeted for the design of new urease inhibitors.
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Affiliation(s)
- Xiaoyin Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue He
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianghua Yan
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Luo J, Cao M, Zhang C, Wu J, Gu XWS. The influence of light combination on the physicochemical characteristics and enzymatic activity of soil with multi-metal pollution in phytoremediation. J Hazard Mater 2020; 393:122406. [PMID: 32172059 DOI: 10.1016/j.jhazmat.2020.122406] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
Light irradiation with suitable quality and intensity could influence the success of phytoremediation by improving the biomass yield of plants. However, mechanisms involved in this influence on the contaminant accumulation and translocation ability of plants have rarely been studied. Five light combinations with different red (R) and blue (B) ratios (0, 10, 50, 75 and 100 % blue) at the same intensity (220 μmol m-2 s-1) were used to assist phytoremediation using Noccaea caerulescens, and the change in physicochemical characteristics and enzymatic activities of soils after phytoremediation were evaluated. Compared with the control, the light combinations and monochromic blue light significantly increased the activities of soil ureases, invertases, and phosphatases, whereas monochromic red light strongly inhibited the activities of these enzymes, because different light irradiations altered the formation and excretion of carbohydrates from plants for soil microorganism consumption. Plants under B50R50 treatment accumulated the highest concentrations of metals, but their chlorophyll concentrations and lipid peroxidation were similar to those other species with lower metal concentrations. Hence, light with a proper blue/red ratio can simultaneously improve the physicochemical characteristics and enzymatic activities of soils, increase the metal uptake capacity and oxidation resistance of plants, and reduce the leaching risk during phytoremediation processes.
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Affiliation(s)
- Jie Luo
- KLETOR Ministry of Education, Yangtze University, Wuhan, China.
| | - Min Cao
- University of Leicester, University Road, Leicester, LE1 7RH, United Kingdom
| | - Chunming Zhang
- KLETOR Ministry of Education, Yangtze University, Wuhan, China
| | - Jian Wu
- China University of Geosciences, Wuhan, 430074, China
| | - X W Sophie Gu
- The University of Melbourne, VIC 3010, Victoria, Australia
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Montes de Oca-Vásquez G, Solano-Campos F, Vega-Baudrit JR, López-Mondéjar R, Odriozola I, Vera A, Moreno JL, Bastida F. Environmentally relevant concentrations of silver nanoparticles diminish soil microbial biomass but do not alter enzyme activities or microbial diversity. J Hazard Mater 2020; 391:122224. [PMID: 32058228 DOI: 10.1016/j.jhazmat.2020.122224] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/03/2020] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
The increasing use of silver nanoparticles (AgNPs) due to their well-known antimicrobial activity, has led to their accumulation in soil ecosystems. However, the impact of environmental realistic concentrations of AgNPs on the soil microbial community has been scarcely studied. In this work, we have assessed the impact of AgNPs, that mimic real concentrations in nature, on tropical soils cultivated with Coffea arabica under conventional and organic management systems. We evaluated the biomass, extracellular enzyme activities, and diversity of the soil microbial community, in a microcosm experiment as a function of time. After seven days of incubation, we found an increase in microbial biomass in an AgNPs-concentration-independent manner. In contrast, after 60-day-incubation, there was a decrease in Gram+ and actinobacterial biomass, in both soils and all AgNPs concentrations. Soil physico-chemical properties and enzyme activities were not affected overall by AgNPs. Regarding the microbial community composition, only some differences in the relative abundance at phylum and genus level in the fungal community were observed. Our results suggest that environmental concentrations of AgNPs affected microbial biomass but had little impact on microbial diversity and may have little effects on the soil biogeochemical cycles mediated by extracellular enzyme activities.
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Affiliation(s)
- Gabriela Montes de Oca-Vásquez
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica; Doctorado en Ciencias Naturales para el Desarrollo (DOCINADE), Instituto Tecnológico de Costa Rica, Universidad Nacional, Universidad Estatal a Distancia, Costa Rica.
| | - Frank Solano-Campos
- School of Biological Sciences, Universidad Nacional, Campus Omar Dengo, 86-3000 Heredia, Costa Rica
| | - José R Vega-Baudrit
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica; Laboratory of Polymer Science and Technology, School of Chemistry, Universidad Nacional, Campus Omar Dengo, 86-3000 Heredia, Costa Rica
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, Praha 4 14220, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, Praha 4 14220, Czech Republic
| | - Alfonso Vera
- CEBAS-CSIC. Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - José L Moreno
- CEBAS-CSIC. Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Felipe Bastida
- CEBAS-CSIC. Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100, Murcia, Spain
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Zhao H, Tan XP, Peng QA, Shi CZ, Zhao YF, Cui YM. N’-(2-Hydroxybenzylidene)-3-Methylbenzohydrazide and its Copper(II) Complex: Syntheses, Characterization, Crystal Structures and Biological Activity. Acta Chim Slov 2020; 67:638-643. [PMID: 33855579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023] Open
Abstract
The hydrazone compound N'-(2-hydroxybenzylidene)-3-methylbenzohydrazide (H2L) was prepared. With H2L and copper acetate a new copper complex [Cu(HL)(NCS)]·CH3OH was synthesized. Both the hydrazone and the copper complex were characterized by physico-chemical methods and single crystal X-ray diffraction techniques. The complex is a thiocyanato-coordinated copper(II) species. The Cu atom in the complex is in square planar geometry. The complex is a promising urease inhibitor.
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Akçay HT, Menteşe E, Sökmen BB. Synthesis and spectroscopic characterization of novel methoxy bridged benzimidazolyl-substituted phthalocyanines as potent inhibitors of urease. Spectrochim Acta A Mol Biomol Spectrosc 2020; 228:117804. [PMID: 31806475 DOI: 10.1016/j.saa.2019.117804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In this study, novel peripherally 4-[(1H-benzimidazol-1-yl)methoxy] substituted Zn(II) (3) Cu(II) (4) and Co(II) (5) phthalocyanines were prepared and their structures were characterized spectroscopically. The light absorption behaviors of the synthesized compounds (3-5) were studied by UV-Vis spectroscopy at different concentrations in different solvents. The urease inhibition activities of the synthesized compounds were also investigated. Among the synthesized molecules, compound 4 showed the best inhibitory effect against jack bean urease with IC50 values of 0.0036 ± 0.0010 μM.
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Affiliation(s)
- Hakkı Türker Akçay
- Department of Chemistry, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, Rize, Turkey.
| | - Emre Menteşe
- Department of Chemistry, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, Rize, Turkey
| | - Bahar Bilgin Sökmen
- Department of Chemistry, Faculty of Arts and Sciences, Giresun University, 28049 Giresun, Turkey
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Lu Q, Li C, Wu G. Insight into the inhibitory effects of Zanthoxylum nitidum against Helicobacter pylori urease and jack bean urease: Kinetics and mechanism. J Ethnopharmacol 2020; 249:112419. [PMID: 31759110 DOI: 10.1016/j.jep.2019.112419] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Zanthoxylum nitidum (Roxb.) DC. is a traditional Chinese medicine characterised by anti-inflammatory and anti-Helicobacter pylori, which is widely used to treat H. pylori-induced gastric disease in China. However, the underlying mechanism related to its anti-H. pylori activity remains unclear. Urease plays a crucial role in the colonisation and survival of H. pylori. AIM OF THE STUDY The root aqueous extract of Z. nitidum against H. pylori urease (HPU) and jack bean urease (JBU) was investigated to illuminate the inhibitory potency, kinetics and potential mechanism. MATERIALS AND METHODS Z. nitidum components were determined by UPLC. The enzyme inhibitory effects of Z. nitidum were examined using modified spectrophotometric Berthelot (phenol-hypochlorite) method. Urease inhibition kinetics were determined by Lineweaver-Burk plots. Sulfhydryl group reagents and Ni2+-binding inhibitors were used in the mechanism study. Moreover, the molecular docking technique was used to investigate the binding conformations of the main compounds of Z. nitidum on Urease. RESULTS According to UPLC results, the major components of Z. nitidum were magnoflorine, sanguinarine, nitidine chloride, chelerythrine, skimmianine and L-Sesamin. Z. nitidum has higher enzyme inhibitory activity on HPU (IC50 = 1.29 ± 0.10 mg/mL) than on JBU (IC50 = 2.04 ± 0.27 mg/mL). Enzyme inhibitory kinetic analysis revealed that the type of Z. nitidum inhibition against HPU was a slow-binding and mixed-type, whereas a slow-binding and non-competitive type inhibited JBU. Further mechanism study indicated that the active site of sulfhydryl group might be the target of inhibition by Z. nitidum. The molecular docking study indicated that the above six main components of Z. nitidum exhibited stronger affinity to HPU than to JBU through interacting with the key amino acid residues located on the mobile flap or interacting with the active site Ni2+. Results indicated that these components are potential active ingredients directed against urease. CONCLUSIONS Z. nitidum inactivated urease in a concentration-dependent manner through slow-binding inhibition and binding to the urease active site sulfhydryl group. Our investigation might provide experimental evidence for the traditional application of Z. nitidum in the treatment of H. pylori-associated gastric disorders.
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Affiliation(s)
- Qiang Lu
- Department of Pharmaceutical Sciences, Zunyi Medical University, Zhuhai Campus, Zhuhai, 519041, PR China.
| | - Cailan Li
- Department of Pharmacology, Zunyi Medical University, Zhuhai Campus, Zhuhai, 519041, PR China.
| | - Guosong Wu
- Pharmacy Department, Guangzhou the People's Hospital of Baiyun District, Guangzhou, 510500, PR China.
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Abstract
Highly ordered superstructures composed of inorganic nanoparticles appear in natural and synthetic systems, however the mechanisms of non-equilibrium self-organization that may be involved are still poorly understood. Herein, we performed a kinetic investigation of the precipitation of calcium phosphate using a process widely found in microorganisms: the hydrolysis of urea by enzyme urease. With high initial ratio of calcium ion to phosphate, periodic precipitation was obtained accompanied by pH oscillations in a well-stirred, closed reactor. We propose that an internal pH-regulated change in the concentration of phosphate ion is the driving force for periodicity. A simple model involving the biocatalytic reaction network coupled with burst nucleation of nanoparticles above a critical supersaturation reproduced key features of the experiments. These findings may provide insight to the self-organization of nanoparticles in biomineralization and improve design strategies of biomaterials for medical applications.
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Affiliation(s)
- Bíborka Bohner
- Department of Physical Chemistry and Materials ScienceUniversity of SzegedRerrich Béla tér 1.6720SzegedHungary
| | - Tamás Bánsági
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Ágota Tóth
- Department of Physical Chemistry and Materials ScienceUniversity of SzegedRerrich Béla tér 1.6720SzegedHungary
| | - Dezső Horváth
- Department of Applied and Environmental ChemistryUniversity of SzegedRerrich Béla tér 1.6720SzegedHungary
| | - Annette F. Taylor
- Department of Chemical and Biological EngineeringUniversity of SheffieldMappin StreetSheffieldS1 3JDUK
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Choi YJ, Kim MH, Yu KY, Kim J. Suppression of urease, which affects nitrogen metabolism and biological efficacy, by Ca 2+/calmodulin in Cordyceps militaris. Biochim Biophys Acta Mol Cell Res 2019; 1867:118568. [PMID: 31676355 DOI: 10.1016/j.bbamcr.2019.118568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022]
Affiliation(s)
- Young-Ji Choi
- Jeonju AgroBio-Materials Institute, Jeonju-si, Jeonbuk 54810, Republic of Korea; National Marine Biodiversity Institute of Korea, Seocheon-gun, Chungnam 33662, Republic of Korea
| | - Mi-Hee Kim
- Jeonju AgroBio-Materials Institute, Jeonju-si, Jeonbuk 54810, Republic of Korea
| | - Kang-Yeol Yu
- Jeonju AgroBio-Materials Institute, Jeonju-si, Jeonbuk 54810, Republic of Korea
| | - Jiyoung Kim
- Jeonju AgroBio-Materials Institute, Jeonju-si, Jeonbuk 54810, Republic of Korea.
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Kappaun K, Martinelli AHS, Broll V, Zambelli B, Lopes FC, Ligabue-Braun R, Fruttero LL, Moyetta NR, Bonan CD, Carlini CR, Ciurli S. Soyuretox, an Intrinsically Disordered Polypeptide Derived from Soybean (Glycine Max) Ubiquitous Urease with Potential Use as a Biopesticide. Int J Mol Sci 2019; 20:E5401. [PMID: 31671552 PMCID: PMC6862595 DOI: 10.3390/ijms20215401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/27/2019] [Accepted: 10/28/2019] [Indexed: 02/07/2023] Open
Abstract
Ureases from different biological sources display non-ureolytic properties that contribute to plant defense, in addition to their classical enzymatic urea hydrolysis. Antifungal and entomotoxic effects were demonstrated for Jaburetox, an intrinsically disordered polypeptide derived from jack bean (Canavalia ensiformis) urease. Here we describe the properties of Soyuretox, a polypeptide derived from soybean (Glycine max) ubiquitous urease. Soyuretox was fungitoxic to Candida albicans, leading to the production of reactive oxygen species. Soyuretox further induced aggregation of Rhodnius prolixus hemocytes, indicating an interference on the insect immune response. No relevant toxicity of Soyuretox to zebrafish larvae was observed. These data suggest the presence of antifungal and entomotoxic portions of the amino acid sequences encompassing both Soyuretox and Jaburetox, despite their small sequence identity. Nuclear Magnetic Resonance (NMR) and circular dichroism (CD) spectroscopic data revealed that Soyuretox, in analogy with Jaburetox, possesses an intrinsic and largely disordered nature. Some folding is observed upon interaction of Soyuretox with sodium dodecyl sulfate (SDS) micelles, taken here as models for membranes. This observation suggests the possibility for this protein to modify its secondary structure upon interaction with the cells of the affected organisms, leading to alterations of membrane integrity. Altogether, Soyuretox can be considered a promising biopesticide for use in plant protection.
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Affiliation(s)
- Karine Kappaun
- Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil.
| | - Anne H S Martinelli
- Department of Biophysics and Center of Biotechnology, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre 91501-970, RS, Brazil.
| | - Valquiria Broll
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre 91501-970, RS, Brazil.
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy.
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy.
| | - Fernanda C Lopes
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre 91501-970, RS, Brazil.
| | - Rodrigo Ligabue-Braun
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre 91501-970, RS, Brazil.
| | - Leonardo L Fruttero
- Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil.
- Department of Clinical Biochemistry, CIBICI-CONICET, Facultad de Ciencias Quimicas, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.
| | - Natalia R Moyetta
- Department of Clinical Biochemistry, CIBICI-CONICET, Facultad de Ciencias Quimicas, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.
| | - Carla D Bonan
- Department of Cellular and Molecular Biology, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 91501-970, RS, Brazil.
| | - Celia R Carlini
- Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil.
- Brain Institute-InsCer, Laboratory of Neurotoxins, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy.
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41
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Xu M, Ross JL, Valdez L, Sen A. Direct Single Molecule Imaging of Enhanced Enzyme Diffusion. Phys Rev Lett 2019; 123:128101. [PMID: 31633990 DOI: 10.1103/physrevlett.123.128101] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/15/2019] [Indexed: 06/10/2023]
Abstract
Recent experimental results have shown that enzymes can diffuse faster when they are in the presence of their reactants (substrate). This faster diffusion has been termed enhanced diffusion. Fluorescence correlation spectroscopy (FCS), which has been employed as the only method to make these measurements, relies on analyzing the fluctuations in fluorescence intensity to measure the diffusion coefficient of particles. Recently, artifacts in FCS measurements due to its sensitivity to environmental conditions have been evaluated, calling prior enhanced diffusion results into question. It behooves us to adopt complementary and direct methods to measure the mobility of enzymes. Herein, we use a technique of direct single molecule imaging to observe the diffusion of individual enzymes in solution. This technique is less sensitive to intensity fluctuations and deduces the diffusion coefficient directly based on the trajectory of the enzyme. Our measurements recapitulate that enzyme diffusion is enhanced in the presence of its substrate and find that the relative increase in diffusion of a single enzyme is even higher than those previously reported using FCS. We also use this complementary method to test if the total enzyme concentration affects the relative increase in diffusion and if the enzyme oligomerization state changes during its catalytic turnover. We find that the diffusion increase is independent of the total concentration of enzymes and the presence of substrate does not change the oligomerization state of enzymes.
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Affiliation(s)
- Mengqi Xu
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Jennifer L Ross
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Lyanne Valdez
- Department of Chemistry, Pennsylvania State University, State College, Pennsylvania 18602, USA
| | - Aysuman Sen
- Department of Chemistry, Pennsylvania State University, State College, Pennsylvania 18602, USA
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42
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Abstract
Food fraud includes the addition of inferior components or the substitution of substances. Besides being of economic concern, this might furthermore pose a health risk for consumers. Therefore, the detection of replacements is of high importance. For the identification of species, in recent years proteomic methods gained more and more importance. In this work, an easy and efficient approach of targeted peptide analytics for revealing food fraud is presented. One of the most common workflows for protein analytics was improved by the application of urease to hydrolyze the urea in the extraction buffer; therefore, no further cleanup is required. By considering only selected compounds and the use of open-source databases for the selection of the target peptides for the adoption of the analytical methods, no time-consuming basic research is required. For the detection of the substitutes, it is not necessary to know the absolute concentration of the component. In these cases, the calculation of the proportion of a species in relation to the total content of all analyzed compounds is sufficient.
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Affiliation(s)
- Monika Ruhland
- Bavarian Health and Food Safety Authority, Veterinärstraße 2, D-85764 Oberschleißheim, Germany
| | - Richard Klinger
- Bavarian Health and Food Safety Authority, Veterinärstraße 2, D-85764 Oberschleißheim, Germany
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43
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Erfkamp J, Guenther M, Gerlach G. Enzyme-Functionalized Piezoresistive Hydrogel Biosensors for the Detection of Urea. Sensors (Basel) 2019; 19:s19132858. [PMID: 31252618 PMCID: PMC6651757 DOI: 10.3390/s19132858] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 06/21/2019] [Accepted: 06/26/2019] [Indexed: 02/05/2023]
Abstract
Urea is used in a wide variety of industrial applications such as the production of fertilizers. Furthermore, urea as a metabolic product is an important indicator in biomedical diagnostics. For these applications, reliable urea sensors are essential. In this work, we present a novel hydrogel-based biosensor for the detection of urea. The hydrolysis of urea by the enzyme urease leads to an alkaline pH change, which is detected with a pH-sensitive poly(acrylic acid-co-dimethylaminoethyl methacrylate) hydrogel. For this purpose, the enzyme is physically entrapped during polymerization. This enzyme-hydrogel system shows a large sensitivity in the range from 1 mmol/L up to 20 mmol/L urea with a high long-term stability over at least eight weeks. Furthermore, this urea-sensitive hydrogel is highly selective to urea in comparison to similar species like thiourea or N-methylurea. For sensory applications, the swelling pressure of this hydrogel system is transformed via a piezoresistive pressure sensor into a measurable output voltage. In this way, the basic principle of hydrogel-based piezoresistive urea biosensors was demonstrated.
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Affiliation(s)
- Jan Erfkamp
- Solid-State Electronics Laboratory, Technische Universität Dresden, 01069 Dresden, Germany.
| | - Margarita Guenther
- Solid-State Electronics Laboratory, Technische Universität Dresden, 01069 Dresden, Germany
| | - Gerald Gerlach
- Solid-State Electronics Laboratory, Technische Universität Dresden, 01069 Dresden, Germany
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44
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Patino T, Porchetta A, Jannasch A, Lladó A, Stumpp T, Schäffer E, Ricci F, Sánchez S. Self-Sensing Enzyme-Powered Micromotors Equipped with pH-Responsive DNA Nanoswitches. Nano Lett 2019; 19:3440-3447. [PMID: 30704240 DOI: 10.1021/acs.nanolett.8b04794] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Biocatalytic micro- and nanomotors have emerged as a new class of active matter self-propelled through enzymatic reactions. The incorporation of functional nanotools could enable the rational design of multifunctional micromotors for simultaneous real-time monitoring of their environment and activity. Herein, we report the combination of DNA nanotechnology and urease-powered micromotors as multifunctional tools able to swim, simultaneously sense the pH of their surrounding environment, and monitor their intrinsic activity. With this purpose, a FRET-labeled triplex DNA nanoswitch for pH sensing was immobilized onto the surface of mesoporous silica-based micromotors. During self-propulsion, urea decomposition and the subsequent release of ammonia led to a fast pH increase, which was detected by real-time monitoring of the FRET efficiency through confocal laser scanning microscopy at different time points (i.e., 30 s, 2 and 10 min). Furthermore, the analysis of speed, enzymatic activity, and propulsive force displayed a similar exponential decay, matching the trend observed for the FRET efficiency. These results illustrate the potential of using specific DNA nanoswitches not only for sensing the micromotors' surrounding microenvironment but also as an indicator of the micromotor activity status, which may aid to the understanding of their performance in different media and in different applications.
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Affiliation(s)
- Tania Patino
- Institute for Bioengineering of Catalonia (IBEC) , The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12 , Barcelona 08028 , Spain
| | - Alessandro Porchetta
- Department of Chemistry , University of Rome , Tor Vergata, Via della Ricerca Scientifica 1 , Rome 00133 , Italy
| | - Anita Jannasch
- Center for Plant Molecular Biology (ZMBP) , University of Tübingen , Auf der Morgenstelle 32 , Tübingen 72076 , Germany
| | - Anna Lladó
- Advanced Digital Microscopy , Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Barcelona 08010 , Spain
| | - Tom Stumpp
- Center for Plant Molecular Biology (ZMBP) , University of Tübingen , Auf der Morgenstelle 32 , Tübingen 72076 , Germany
| | - Erik Schäffer
- Center for Plant Molecular Biology (ZMBP) , University of Tübingen , Auf der Morgenstelle 32 , Tübingen 72076 , Germany
| | - Francesco Ricci
- Department of Chemistry , University of Rome , Tor Vergata, Via della Ricerca Scientifica 1 , Rome 00133 , Italy
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC) , The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12 , Barcelona 08028 , Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) , Pg. Lluís Companys 23 , Barcelona 08010 , Spain
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45
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Rizvi F, Khan M, Jabeen A, Siddiqui H, Choudhary MI. Studies on Isoniazid Derivatives through a Medicinal Chemistry Approach for the Identification of New Inhibitors of Urease and Inflammatory Markers. Sci Rep 2019; 9:6738. [PMID: 31043636 PMCID: PMC6494997 DOI: 10.1038/s41598-019-43082-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/16/2019] [Indexed: 01/09/2023] Open
Abstract
A library of thiosemicarbazide derivatives of isoniazid 3-27, was synthesized and evaluated for their anti-inflammatory and urease inhibition activities, by using in vitro bioassays. Among these compounds 9, 10, 12, 21, and 26 were identified as new derivatives. Prolonged use of non-steroidal anti-inflammatory drugs (NSAIDs) and infections caused by Helicobacter pylori (ureolytic bacteria), are the two most significant causes of gastric and peptic ulcers. We focused on the identification of the dual inhibitors of inflammation and urease enzyme. Compound 23 was identified as the best dual inhibitor of inflammation (ROS; IC50 = 12.3 µg/mL), and urease enzyme inhibition activity (IC50 = 22.4 µM). Many of these compounds showed comparable activities to the standard anti-inflammatory drug (ibuprofen, IC50 = 11.2 µg/mL) and urease inhibitor (thiourea/acetohydraoxamic acid, IC50 = 21.1/20.3 µM). Compound 12 was found to be the most potent urease inhibitor (IC50 = 12.3 µM) and good inhibitor of inflammation (IC50 = 27.7 µg/mL). Compounds 19, 11, 13, 9, 17, 10, and 16, were also found to be potent inhibitors of urease. Cytotoxicity was also evaluated and all the compounds were found to be non-cytotoxic, except compound 18 and the parent drug isoniazid (IC50 = 29.5 and 28.5 µM, respectively).
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Affiliation(s)
- Fazila Rizvi
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Majid Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Almas Jabeen
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Hina Siddiqui
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21452, Saudi Arabia.
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46
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Qamar N, Sultan H, Raheel A, Ashfaq M, Azmat R, Naz R, Lateef M, Khan KM, Arshad T. Heterochelates of metals as an effective anti - Urease agents couple with their docking studies. Pak J Pharm Sci 2019; 32:1179-1183. [PMID: 31303588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The current article discusses the activities of several synthesized metal heterochelates in in-vitro as anti-ulcer agents followed by their docking study. For this purpose, two important ligands like 8-hydroxyquinoline and DL-methionine were used in synthesis of heterochelates of metal including Cr (III), Mn (II), Fe (III), Co (II), Ni (II), Cu (II), Zn (II), Cd (II) and Pb (II). It was observed that these complexes showed excellent urease inhibition activities in which thiourea was the standard having IC50 value 21.6 ± 0.12μM. The Cu (II) complex showed potent inhibitory activity (22.6 ± 0.72 μM) when compared with the standard thiourea (21.6±0.12μM) among the nine synthesized complexes while Mn (II), Fe (III), Cd (II) and Pb (II) also showed better inhibitory activities. The urease inhibitory activities of hetercochelates also tested and validated by docking analysis.
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Affiliation(s)
- Noshab Qamar
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Hira Sultan
- Department of Chemistry, NED University of Engineering and Technology, Karachi, Pakistan
| | - Ahmad Raheel
- Department of Chemistry, Quaid-e-Azam University, Islamabad, Pakistan
| | - Maria Ashfaq
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Rafia Azmat
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Raheela Naz
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Mehreen Lateef
- MDRL, Baharia University of Medical & Dental College, Karachi, Pakistan
| | - Khalid Mohammed Khan
- HEJ Research Institute of Chemistry, International Center of Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan / Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Tanzila Arshad
- Department of Applied Chemistry and Chemical Technology, University of Karachi, Karachi, Pakistan
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47
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Røyne A, Phua YJ, Balzer Le S, Eikjeland IG, Josefsen KD, Markussen S, Myhr A, Throne-Holst H, Sikorski P, Wentzel A. Towards a low CO2 emission building material employing bacterial metabolism (1/2): The bacterial system and prototype production. PLoS One 2019; 14:e0212990. [PMID: 30990806 PMCID: PMC6467371 DOI: 10.1371/journal.pone.0212990] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 02/10/2019] [Indexed: 11/18/2022] Open
Abstract
The production of concrete for construction purposes is a major source of anthropogenic CO2 emissions. One promising avenue towards a more sustainable construction industry is to make use of naturally occurring mineral-microbe interactions, such as microbial-induced carbonate precipitation (MICP), to produce solid materials. In this paper, we present a new process where calcium carbonate in the form of powdered limestone is transformed to a binder material (termed BioZEment) through microbial dissolution and recrystallization. For the dissolution step, a suitable bacterial strain, closely related to Bacillus pumilus, was isolated from soil near a limestone quarry. We show that this strain produces organic acids from glucose, inducing the dissolution of calcium carbonate in an aqueous slurry of powdered limestone. In the second step, the dissolved limestone solution is used as the calcium source for MICP in sand packed syringe moulds. The amounts of acid produced and calcium carbonate dissolved are shown to depend on the amount of available oxygen as well as the degree of mixing. Precipitation is induced through the pH increase caused by the hydrolysis of urea, mediated by the enzyme urease, which is produced in situ by the bacterium Sporosarcina pasteurii DSM33. The degree of successful consolidation of sand by BioZEment was found to depend on both the amount of urea and the amount of glucose available in the dissolution reaction.
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Affiliation(s)
- Anja Røyne
- Department of Physics, University of Oslo, Oslo, Norway
- * E-mail:
| | - Yi Jing Phua
- Department of Physics, University of Oslo, Oslo, Norway
| | - Simone Balzer Le
- SINTEF Industry, Department of Biotechnology and Nanomedicine, Trondheim, Norway
| | | | | | - Sidsel Markussen
- SINTEF Industry, Department of Biotechnology and Nanomedicine, Trondheim, Norway
| | | | - Harald Throne-Holst
- Consumption Research Norway (SIFO), OsloMet–Oslo Metropolitan University, Oslo, Norway
| | - Pawel Sikorski
- Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Alexander Wentzel
- SINTEF Industry, Department of Biotechnology and Nanomedicine, Trondheim, Norway
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48
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Chen X, Achal V. Biostimulation of carbonate precipitation process in soil for copper immobilization. J Hazard Mater 2019; 368:705-713. [PMID: 30739023 DOI: 10.1016/j.jhazmat.2019.01.108] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/23/2019] [Accepted: 01/30/2019] [Indexed: 05/27/2023]
Abstract
The urease-based microbially induced carbonate precipitation (MICP) is known as effective remediation strategy in soil metals remediation; however, all related studies confined to bioaugmentation. In the present study, biostimulation process was adopted for the first time in accelerating MICP in copper (Cu) immobilization in soil. The abundance, composition, and diversity of the bacterial community after biostimulation were assessed with MiSeq Illumina sequencing analysis that confirmed number and types of ureolytic and calcifying bacteria grown significantly leading to MICP process, compared to untreated soil. The results demonstrated that biostimulation induced calcite precipitation in soil that immobilized Cu mainly in carbonated fraction of soil, while soluble-exchangeable fraction decreased from 45.54 mg kg-1 to 1.55 mg kg-1 Cu in soil. Scanning electron microscopy (SEM) cum energy-dispersive X-ray spectroscopy (EDX) evaluated structure and elemental composition in Cu immobilization after biostimulation. Fourier Transform-Infra Red (FTIR) spectroscopy depicted functional chemical groups involved in copper immobilization, while X-Ray Diffraction (XRD) identified main crystalline phases or biominerals formed during biostimulation in order to carryout Cu remediation from soil.
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Affiliation(s)
- Xueyan Chen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Varenyam Achal
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China; Environmental Engineering Program, Guangdong Technion-Israel Institute of Technology, Shantou, 515063, China.
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49
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Mazzei L, Cianci M, Contaldo U, Ciurli S. Insights into Urease Inhibition by N-( n-Butyl) Phosphoric Triamide through an Integrated Structural and Kinetic Approach. J Agric Food Chem 2019; 67:2127-2138. [PMID: 30735374 DOI: 10.1021/acs.jafc.8b04791] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The nickel-dependent enzyme urease represents a negative element for the efficiency of soil nitrogen fertilization as well as a virulence factor for a large number of pathogenic and antibiotic-resistant bacteria. The development of ever more efficient urease inhibitors demands knowledge of their modes of action at the molecular level. N-( n-Butyl)-phosphoric triamide (NBPTO) is the oxo-derivative of N-( n-butyl)-thiophosphoric triamide (NBPT), which is extensively employed in agriculture to increase the efficiency of urea-based fertilizers. The 1.45 Å resolution structure of the enzyme-inhibitor complex obtained upon incubation of Sporosarcina pasteurii urease (SPU) with NBPTO shows the presence of diamido phosphoric acid (DAP), generated upon enzymatic hydrolysis of NBPTO with the release of n-butyl amine. DAP is bound in a tridentate binding mode to the two Ni(II) ions in the active site of urease via two O atoms and an amide NH2 group, whereas the second amide group of DAP points away from the metal center into the active-site channel. The mobile flap modulating the size of the active-site cavity is found in a disordered closed-open conformation. A kinetic characterization of the NBPTO-based inhibition of both bacterial (SPU) and plant ( Canavalia ensiformis or jack bean, JBU) ureases, carried out by calorimetric measurements, indicates the occurrence of a reversible slow-inhibition mode of action. The latter is characterized by a very small value of the equilibrium dissociation constant of the urease-DAP complex caused, in turn, by the large rate constant for the formation of the enzyme-inhibitor complex. The much greater capability of NBPTO to inhibit urease, as compared with that of NBPT, is thus not caused by the presence of a P═O moiety versus a P═S moiety, as previously suggested, but rather by the readiness of NBPTO to react with urease without the need to convert one of the P-NH2 amide moieties to its P-OH acid derivative, as in the case of NBPT. The latter process is indeed characterized by a very small equilibrium constant that reduces drastically the concentration of the active form of the inhibitor in the case of NBPT. This indicates that high-efficiency phosphoramide-based urease inhibitors must have at least one O atom bound to the central P atom in order for the molecule to efficiently and rapidly bind to the dinickel center of the enzyme.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology , University of Bologna , 40126 Bologna , Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences , Polytechnic University of Marche , 60121 Ancona , Italy
| | - Umberto Contaldo
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology , University of Bologna , 40126 Bologna , Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology , University of Bologna , 40126 Bologna , Italy
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50
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Bhattacharya A, Naik SN, Khare SK. Efficacy of ureolytic Enterobacter cloacae EMB19 mediated calcite precipitation in remediation of Zn (II). J Environ Sci Health A Tox Hazard Subst Environ Eng 2019; 54:526-532. [PMID: 30729861 DOI: 10.1080/10934529.2019.1567184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/29/2018] [Accepted: 01/05/2019] [Indexed: 05/27/2023]
Abstract
In this study, urease mediated calcite precipitation technique was used for remediation of Zn (II). A urease positive Enterobacter cloacae EMB19 was used to produce calcite impregnated with Zn ions. In co-presence of Ca (II), Zn (II) concentrations of 10 and 20 mg L-1 were completely remediated by the bacterium from the media at 72 and 96 h of incubation, respectively. Co-precipitation of Ca (II) and Zn (II) to form calcite-Zn precipitate is one of the major mechanisms of Zn remediation in the present study. Role of urease in calcite-Zn precipitation was substantiated by using urease/carbonate and ammonium enriched cell free culture supernatant (CFS) obtained after sufficient microbial growth. Using CFS, 68% removal of initial 50 mg L-1 Zn (II) was detected. Energy dispersive X-ray spectroscopy (EDX) and X-ray diffraction pattern (XRD) of the precipitate supports calcite mediated remediation of Zn. Remediation of multiple metals viz. Cd, Zn, Cu was also analyzed using CFS laden with urease. The preparation showed 40% Cd, 23% Zn, and 8% Cu reduction from the solution containing initial 25 mg L-1 of each metal. Overall, it can be concluded that, the E. cloacae mediated calcite precipitation technique could effectively be used for alleviation of Zn (II) and other heavy metals from the contaminated environment.
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Affiliation(s)
- Amrik Bhattacharya
- a Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry , Indian Institute of Technology, Delhi , New Delhi , India
- b Center for Rural Development and Technology, Indian Institute of Technology, Delhi , New Delhi , India
| | - S N Naik
- b Center for Rural Development and Technology, Indian Institute of Technology, Delhi , New Delhi , India
| | - S K Khare
- a Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry , Indian Institute of Technology, Delhi , New Delhi , India
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