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Contini L, Paul A, Mazzei L, Ciurli S, Roncarati D, Braga D, Grepioni F. Is bismuth(III) able to inhibit the activity of urease? Puzzling results in the quest for soluble urease complexes for agrochemical and medicinal applications. Dalton Trans 2024; 53:10553-10562. [PMID: 38847020 DOI: 10.1039/d4dt00778f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Bismuth(III) complexes have been reported to act as inhibitors of the enzyme urease, ubiquitously present in soils and implicated in the pathogenesis of several microorganisms. The general insolubility of Bi(III) complexes in water at neutral pH, however, is an obstacle to their utilization. In our quest to improve the solubility of Bi(III) complexes, we selected a compound reported to inhibit urease, namely [Bi(HEDTA)]·2H2O, and co-crystallized it with (i) racemic DL-histidine to obtain the conglomerate [Bi2(HEDTA)2(μ-D-His)2]·6H2O + [Bi2(HEDTA)2(μ-L-His)2]·6H2O, (ii) enantiopure L-histidine to yield [Bi2(HEDTA)2(μ-L-His)2]·6H2O, and (iii) cytosine to obtain [Bi(HEDTA)]·Cyt·2H2O. All compounds, synthesised by mechanochemical methods and by slurry, were characterized in the solid state by calorimetric (DSC and TGA) and spectroscopic (IR) methods, and their structures were determined using powder X-ray diffraction (PXRD) data. All compounds show an appreciable solubility in water, with values ranging from 6.8 mg mL-1 for the starting compound [Bi(HEDTA)]·2H2O to 36 mg mL-1 for [Bi2(HEDTA)2(μ-L-His)2]·6H2O. The three synthesized compounds as well as [Bi(HEDTA)]·2H2O were then tested for inhibition activity against urease. Surprisingly, no enzymatic inhibition was observed during in vitro assays using Canavalia ensiformis urease and in vivo assays using cultures of Helicobacter pylori, raising questions on the efficacy of Bi(III) compounds to counteract the negative effects of urease activity in the agro-environment and in human health.
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Affiliation(s)
- Laura Contini
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
| | - Arundhati Paul
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy.
| | - Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Viale Giuseppe Fanin 40, Bologna I-40127, Italy.
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Dario Braga
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
| | - Fabrizia Grepioni
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
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Zeng Y, Zhang M, Fu Q, Chen N, Wang Y, Zhou D, Fang G. Formation of reactive intermediates in paddy water from different temperature zones for the promotion of abiotic ammonification. WATER RESEARCH 2024; 255:121523. [PMID: 38554632 DOI: 10.1016/j.watres.2024.121523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/15/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
The paddy field is a hot area of biogeochemical process. The paddy water has a large capacity in photo-generation of reactive intermediates (RIs) due to abundant photosensitive dissolved organic matter (DOM), which is influenced by the spatial heterogeneity of paddy soils but rarely been explored. Our work presents the first investigation of the role of soil properties on photochemistry in paddy water. Soil organic matter (SOM), determined by the temperature, was the dominant factor for the photo-generation of RIs in paddy water of main rice producing areas. The RI concentrations generated with abundant SOM from cool regions are 0.05-8.71 times higher than those for the warm regions in China. The humic-like substance and aromatic-like compounds of DOM plays an essential role in RIs generation, which is abundant in paddy soils rich in SOM from Chinese cool regions. In addition, RIs can efficiently accelerate the photo-ammonification of urea and free amino acids by 15.2 %-164 %, leading to 0.13-0.17 mmol/L/d photo-produced ammonium after fertilization, which is preferentially absorbed by rice. The findings of this study will extend our knowledge of the geochemistry of global paddy field ecosystem. The potential role of RIs in nitrogen cycle should be highlighted in the agroecosystem.
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Affiliation(s)
- Yu Zeng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Mingyang Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Qinglong Fu
- School of Environmental Studies, China University of Geoscience, Wuhan 430074, PR China
| | - Ning Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Yujun Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Dongmei Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Guodong Fang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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Ghanta R, Chowdhury T, Ghosh A, Das AK, Chattopadhyay T. Comparative analysis of Zn(II)-complexes as model metalloenzymes for mimicking Jack bean urease. Dalton Trans 2024; 53:2373-2385. [PMID: 38214577 DOI: 10.1039/d3dt03775d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The inhibitory action of Schiff base complexes of 3d metals against the urease enzyme is well explored in the scientific community. However, the ability of such complexes in mimicking active metallobiosites of urease enzymes, possessing ureolytic behavior, still remains unexplored. With this aim firstly, two Zn(II)-complexes (PPR-HMB-Zn and PZ-HMB-Zn) have been developed from two different Schiff base ligands (HL1 = 2-((E)-(2-(piperidin-1-yl)ethylimino)methyl)-5-methylphenol and HL2 = 2-((E)-(2-(piperizin-1-yl)ethylimino)methyl)-5-methylphenol) and structurally characterized using single crystal XRD. The hydrolytic enzymatic activity of both complexes was demonstrated by the gradual increase in the absorption maxima at 425 nm for the formation of the p-nitrophenolate ion from catalytic hydrolysis mediated by the Zn(II) complexes with a disodium salt of p-nitrophenyl phosphate as a model substrate. Associated kinetic parameters, pH dependency and a relevant hydrolysis mechanism have also been explored. After confirming the hydrolytic ability, the complexes were exploited to mimic the hydrolytic activity of Jack bean urease that catalytically hydrolyses urea into ammonia and CO2. The change in the pH of the solution owing to the formation of ammonia under the complex catalysed hydrolytic action of urea has been monitored spectrophotometrically using the pH dependent structural change of phenol red. The amount of ammonia has been quantified using the Nessler's reagent spectrophotometric method. The ureolytic reaction mechanism has been investigated using density functional theory (DFT) calculations using the B3LYP and TPSSH methods for the systematic calculation of the interaction energy. In contrast to PZ-HMB-Zn, PPR-HMB-Zn functions more effectively as a catalyst due to the existence of a lattice-occluded water molecule in its crystal structure and the protonation of the non-terminal N to attract urea by H-bonding, which was further confirmed by AIM analysis.
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Affiliation(s)
- Rinku Ghanta
- Department of Chemistry, Diamond Harbour Women's University, Diamond Harbour Road, Sarisha, South 24 Pgs, 743368, India.
| | - Tania Chowdhury
- Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Avik Ghosh
- Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Avijit K Das
- Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Tanmay Chattopadhyay
- Department of Chemistry, Diamond Harbour Women's University, Diamond Harbour Road, Sarisha, South 24 Pgs, 743368, India.
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Singh R, Kumar P, Devi M, Sindhu J, Kumar A, Lal S, Singh D, Kumar H, Kumar S. Urease Inhibition and Structure‐Activity Relationship Study of Thiazolidinone‐, Triazole‐, and Benzothiazole‐Based Heterocyclic Derivatives: A Focus Review. ChemistrySelect 2023. [DOI: 10.1002/slct.202300244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Rahul Singh
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Parvin Kumar
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Meena Devi
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Jayant Sindhu
- Department of Chemistry COBS&H, CCS Haryana gricultural University Hisar 125004 India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences GJUS&T Hisar 125001 India
| | - Sohan Lal
- Department of Chemistry Kurukshetra University Kurukshetra 136119 India
| | - Devender Singh
- Department of Chemistry Maharshi Dayanand University Rohtak 124001 India
| | - Harish Kumar
- Department of Chemistry, School of Basic Sciences Central university Haryana Mahendergarh India
| | - Sumit Kumar
- Department of Chemistry DCR University of Science & Technology, Murthal Haryana 131039 India
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Saleem M, Hanif M, Rafiq M, Hassan M, Tahir T. Synthesis, Characterization, Optical Properties, Molecular Modeling and Urease Inhibition Analysis of Organic Ligands and Their Metal Complexes. J Fluoresc 2023; 33:113-124. [PMID: 36282345 DOI: 10.1007/s10895-022-03032-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 02/04/2023]
Abstract
Recently, screening of efficient urease inhibitors by employing organic small molecules metalloderivatives interests the scientific community due to their efficacy for treatment of urease triggered health complications. This study comprises the synthesis, urease inhibition activity, optical analysis and molecular modeling of hydrazinecarbothioamide and hydrazinecarboxamide metalloderivatives. Characterization of synthesized materials was done by UV-visible, fluorescence, NMR and FTIR spectroscopic analysis. Metalloderivatization of ligands induce increment in urease inhibition potential and effect was prominent for copper complexes with 10-fold enhancement, cobalt complex with 3.5 fold's enhancement and palladium with 2-fold increment in the inhibition efficacy toward urease when it was compared with reference urease inhibitor. Zinc and iron complexes cause declined urease inhibition activity of the bare ligand. The overall activity of hydrazinecarbothioamide slightly exceeds than that of hydrazinecarboxamide, possibly due to larger complexation ability of sulfur-based ligand in comparison to oxygenated derivatives i.e., hydrazinecarboxamide. The enzyme inhibition kinetics for the most active complexes represent the mixed type urease inhibition for 3a and competitive urease inhibition for 5a, as determined by Lineweaver-Burk plots. The docked scoring values for both the ligands were calculated to be 61.34, 64.72, 56.68, 62.94, 64.98 and 58.98. Three active hydrogen bonds were observed in docking complex upon computational analysis of most potent metallodrug 3a inside active region of targeted protein.
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Affiliation(s)
- Muhammad Saleem
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan. .,Department of Chemistry, Thal University Bhakkar, 30000, Bhakkar, Pakistan.
| | - Muhammad Hanif
- Department of Chemistry, GC University Faisalabad, Sub campus layyah-31200, Faisalabad, Pakistan
| | - Muhammad Rafiq
- Department of Physiology and Biochemistry, Cholistan University of Veterinary and Animal Sciences, 6300, Bahawalpur, Pakistan
| | - Mubashir Hassan
- Institute of Molecular biology and Biotechnology/(IMBB), The University of Lahore, 1-KM, Defence Road, Bhubtian Chowk, Lahore, Pakistan
| | - Tehreem Tahir
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, 6300, Bahawalpur, Pakistan
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Mazzei L, Cianci M, Ciurli S. Inhibition of Urease by Hydroquinones: A Structural and Kinetic Study. Chemistry 2022; 28:e202201770. [PMID: 35994380 PMCID: PMC9826003 DOI: 10.1002/chem.202201770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 01/11/2023]
Abstract
Hydroquinones are a class of organic compounds abundant in nature that result from the full reduction of the corresponding quinones. Quinones are known to efficiently inhibit urease, a NiII -containing enzyme that catalyzes the hydrolysis of urea to yield ammonia and carbonate and acts as a virulence factor of several human pathogens, in addition to decreasing the efficiency of soil organic nitrogen fertilization. Here, we report the molecular characterization of the inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by 1,4-hydroquinone (HQ) and its methyl and tert-butyl derivatives. The 1.63-Å resolution X-ray crystal structure of the SPU-HQ complex discloses that HQ covalently binds to the thiol group of αCys322, a key residue located on a mobile protein flap directly involved in the catalytic mechanism. Inhibition kinetic data obtained for the three compounds on JBU reveals the occurrence of an irreversible inactivation process that involves a radical-based autocatalytic mechanism.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT)University of BolognaViale Giuseppe Fanin 4040127BolognaItaly
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheVia Brecce Bianche 1060131AnconaItaly
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT)University of BolognaViale Giuseppe Fanin 4040127BolognaItaly
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7
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Peters N, Thiele-Bruhn S. Major metabolites of NBPT degradation pathways contribute to urease inhibition in soil. CHEMOSPHERE 2022; 303:135163. [PMID: 35654230 DOI: 10.1016/j.chemosphere.2022.135163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Urea is the most commonly used nitrogen fertilizer worldwide. However, depending on soil and environmental conditions, high nitrogen losses can occur due to gaseous ammonia emissions. Urease inhibitors like N-(n-butyl)thiophosphoric triamide (NBPT) reduce these losses by blocking the urease enzyme, which catalyzes urea hydrolysis. With the increasing use of NBPT its environmental fate and features of urease inhibition become increasingly important. This study aimed to further elucidate major NBPT degradation pathways and related urease inhibition in soil. This was investigated in a 14-d incubation experiment using practice-relevant application rates of NBPT and four of its metabolites N-(n-butyl)phosphoric triamide (NBPTO), diamido phosphoric acid (DAP), diamido thiophosphoric acid (DATP) and rac-N-(n-butyl)thiophosphoric diamide (NBPD), covering three postulated degradation pathways. Additionally, the urease inhibition by these compounds was determined and further investigated in 2-h tests. The latter provided dose-response curves, showing that all substances inhibited urease, with NBPTO being the most effective. Inhibition of urease in NBPT-spiked soil was also largely, but not completely, attributed to NBPTO formed within the test period. In 14-d incubation tests, all investigated compounds dissipated quickly by >90% within 6 d (NBPTO), 3 d (NBPT) and ≤1 d (DAP, DATP and NBPD). Extensive oxidation of NBPT to NBPTO and subsequent minor formation of DAP was identified as the preferred degradation pathway. Abiotic degradation processes in sterile soil corresponded to 65-90% of total degradation in microbial active soil. Furthermore, pseudo-first order dissipation kinetics were retarded in sterile soil. Urease activity, calculated as a percentage of activity in the urea-fertilized control, was lowest after about 2 d when NBPTO was spiked to soil (17.9%), followed by NBPT (35.7%), DATP (51.3%), NBPD (54.0%), and DAP (54.4%). This shows that urease inhibition depends on the interplay of NBPT and its degradation products.
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Affiliation(s)
- Nils Peters
- EuroChem Agro GmbH, Reichskanzler-Müller-Str. 23, D-68165, Mannheim, Germany
| | - Sören Thiele-Bruhn
- University of Trier, Soil Science, Behringstrasse 21, D-54286, Trier, Germany.
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Bolivar JM, Woodley JM, Fernandez-Lafuente R. Is enzyme immobilization a mature discipline? Some critical considerations to capitalize on the benefits of immobilization. Chem Soc Rev 2022; 51:6251-6290. [PMID: 35838107 DOI: 10.1039/d2cs00083k] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzyme immobilization has been developing since the 1960s and although many industrial biocatalytic processes use the technology to improve enzyme performance, still today we are far from full exploitation of the field. One clear reason is that many evaluate immobilization based on only a few experiments that are not always well-designed. In contrast to many other reviews on the subject, here we highlight the pitfalls of using incorrectly designed immobilization protocols and explain why in many cases sub-optimal results are obtained. We also describe solutions to overcome these challenges and come to the conclusion that recent developments in material science, bioprocess engineering and protein science continue to open new opportunities for the future. In this way, enzyme immobilization, far from being a mature discipline, remains as a subject of high interest and where intense research is still necessary to take full advantage of the possibilities.
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Affiliation(s)
- Juan M Bolivar
- FQPIMA group, Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, 28040, Spain
| | - John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis. ICP-CSIC, C/Marie Curie 2, Campus UAM-CSIC Cantoblanco, Madrid 28049, Spain. .,Center of Excellence in Bionanoscience Research, External Scientific Advisory Academic, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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9
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Parakatawella S, Gogoi D, Deka P, Xu Y, Sandaruwan C, Jayasundera ACA, Arhangelskis M, Thakuria R, Adassooriya NM. Mechanochemical Synthesis of Polymorphic Urea ⋅ Adipic Acid Cocrystal as a Sustained-Release Nitrogen Source. CHEMSUSCHEM 2022; 15:e202102445. [PMID: 34939741 DOI: 10.1002/cssc.202102445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/03/2021] [Indexed: 06/14/2023]
Abstract
A 2 : 1 urea ⋅ adipic acid cocrystal was obtained in two polymorphic forms (Form I reported earlier, and Form II synthesized in this study) using mechanochemistry as well as solution crystallization. Lower solubility and leaching study showed the newly synthesized urea ⋅ adipic acid 2 : 1 cocrystal to be an efficient sustained-release nitrogen fertilizer compared to commercially available urea.
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Affiliation(s)
- Shalika Parakatawella
- Postgraduate Institute of Science, University of Peradeniya, 20400, Peradeniya, Sri Lanka
| | - Diptajyoti Gogoi
- Department of Chemistry, Gauhati University, Guwahati, 781014, Assam, India
| | - Poonam Deka
- Department of Chemistry, Gauhati University, Guwahati, 781014, Assam, India
| | - Yizhi Xu
- Faculty of Chemistry, University of Warsaw, 1 Pasteura Street, 02-093, Warsaw, Poland
| | - Chanaka Sandaruwan
- Sri Lanka Institute of Nanotechnology, Pitipana, 10200 Homagama, Sri Lanka
| | - Anil C A Jayasundera
- Postgraduate Institute of Science, University of Peradeniya, 20400, Peradeniya, Sri Lanka
- Department of Chemistry, University of Peradeniya, 20400, Peradeniya, Sri Lanka
| | - Mihails Arhangelskis
- Faculty of Chemistry, University of Warsaw, 1 Pasteura Street, 02-093, Warsaw, Poland
| | - Ranjit Thakuria
- Department of Chemistry, Gauhati University, Guwahati, 781014, Assam, India
| | - Nadeesh M Adassooriya
- Postgraduate Institute of Science, University of Peradeniya, 20400, Peradeniya, Sri Lanka
- Department of Chemical & Process Engineering, Faculty of Engineering, University of Peradeniya, 20400, Peradeniya, Sri Lanka
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Lee JK, Park HJ, Cha SJ, Kwon SJ, Park JH. Effect of pyroligneous acid on soil urease, amidase, and nitrogen use efficiency by Chinese cabbage (Brassica campestris var. Pekinensis). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118132. [PMID: 34536645 DOI: 10.1016/j.envpol.2021.118132] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/05/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Urea is one of the most commonly used nitrogen fertilizers in agricultural soil and is easily decomposed by soil urease resulting in ammonium release. The produced ammonium can be volatilized or converted to nitrate, which is susceptible to leaching, leading to groundwater contamination unless used by plants. Hence, it is important to control the release of nitrogen from the urea. Pyroligneous acid inhibited the urease activity and decreased ammonium release up to 80% compared to the control. Amidase including asparaginase and glutaminase is an enzyme that catalyzes hydrolysis of amide group, similar to urease. Therefore, the effect of pyroligneous acid on the inhibition of soil amidase was also tested and the results showed that pyroligneous acid competitively inhibited asparaginase while glutaminase was not inhibited. However, inhibitory effect of pyroligneous acid on asparaginase was negligible compared to the urease. The application of pyroligneous acid with a smaller amount of urea for controlled nitrogen release during Chinese cabbage growth showed that dry biomass and nutrient contents of Chinese cabbage were similar to the case of the conventional urea application. The nitrogen utilization efficiency (NUE) was highest for 33% less amount of urea supply with pyroligneous acid (2.21) compared to conventional treatment (1.81). Consequently, the use of pyroligneous acid with urea enhances nitrogen use efficiency while also protecting environments from non-point source contamination.
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Affiliation(s)
- Joo Kyung Lee
- Chungbuk National University, Cheongju, Chungbuk, 28644, South Korea
| | - Hyun Jun Park
- Soil Research Institute, Prumbio Co. Ltd, South Korea
| | - Seung Ju Cha
- Chungbuk National University, Cheongju, Chungbuk, 28644, South Korea
| | - Seon Ju Kwon
- Chungbuk National University, Cheongju, Chungbuk, 28644, South Korea
| | - Jin Hee Park
- Chungbuk National University, Cheongju, Chungbuk, 28644, South Korea.
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11
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Mazzei L, Massai L, Cianci M, Messori L, Ciurli S. Medicinal Au(I) compounds targeting urease as prospective antimicrobial agents: unveiling the structural basis for enzyme inhibition. Dalton Trans 2021; 50:14444-14452. [PMID: 34585201 DOI: 10.1039/d1dt02488d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A few gold compounds were recently found to show antimicrobial properties in vitro, holding great promise for the discovery of new drugs to overcome antibiotic resistance. Here, the inhibition of the bacterial virulence factor urease by four Au(I)-compounds, namely Au(PEt3)Cl, Au(PEt3)Br, Au(PEt3)I and [Au(PEt3)2]Cl, obtained from the antiarthritic Au(I)-drug Auranofin and earlier reported to act as antimicrobials, is investigated. The three monophosphino Au(I) complexes showed IC50 values in the 30-100 nM range, while the diphosphino Au(I) complex, though being less active, still showed a IC50 value of 7 μM. The structural basis for this inhibition was provided by solving the crystal structures of urease co-crystallized with Au(PEt3)I and [Au(PEt3)2]Cl: at least two Au(I) ions bind the enzyme in a flap domain involved in the catalysis, thus obliterating enzyme activity. Peculiar changes observed in the two structures reveal implications for the mechanism of soft metal binding and enzyme inactivation.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna, Italy.
| | - Lara Massai
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, I-60131 Ancona, Italy
| | - Luigi Messori
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna, Italy.
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12
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Franco-Pérez M, Castrejón-Flores JL, González-González S, Landa IB, Zamudio-Medina A. A new tricomponent reaction for the synthesis of symmetric and asymmetric alkyl bisphosphoramidates. PHOSPHORUS SULFUR 2021. [DOI: 10.1080/10426507.2021.1946061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Marco Franco-Pérez
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, CDMX, Mexico
| | | | | | - Israel Bonilla Landa
- Red de Estudios Moleculares Avanzados CAMPUS III, Instituto de Ecología A.C. (INECOL), Xalapa-Enríquez, Mexico
| | - Angel Zamudio-Medina
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, CDMX, Mexico
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13
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Feder D, Mohd-Pahmi SH, Hussein WM, Guddat LW, McGeary RP, Schenk G. Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach. ChemMedChem 2021; 16:3342-3359. [PMID: 34331400 DOI: 10.1002/cmdc.202100486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 11/08/2022]
Abstract
Metallohydrolases form a large group of enzymes that have fundamental importance in a broad range of biological functions. Among them, the purple acid phosphatases (PAPs) have gained attention due to their crucial role in the acquisition and use of phosphate by plants and also as a promising target for novel treatments of bone-related disorders and cancer. To date, no crystal structure of a mammalian PAP with drug-like molecules bound near the active site is available. Herein, we used a fragment-based design approach using structures of a mammalian PAP in complex with the MaybridgeTM fragment CC063346, the amino acid L-glutamine and the buffer molecule HEPES, as well as various solvent molecules to guide the design of highly potent and efficient mammalian PAP inhibitors. These inhibitors have improved aqueous solubility when compared to the clinically most promising PAP inhibitors available to date. Furthermore, drug-like fragments bound in newly discovered binding sites mapped out additional scaffolds for further inhibitor discovery, as well as scaffolds for the design of inhibitors with novel modes of action.
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Affiliation(s)
- Daniel Feder
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Siti H Mohd-Pahmi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
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14
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Zamudio-Medina A, Pérez-Hernández N, Castrejón-Flores JL, Romero-García S, Prado-García H, Bañuelos-Hernández A, Franco-Pérez M. Obtaining symmetric and asymmetric bisphosphoramidates and bisphosphoramidothioates by a single step multicomponent reaction. PHOSPHORUS SULFUR 2021. [DOI: 10.1080/10426507.2021.1878358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Angel Zamudio-Medina
- Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, CDMX, México
| | - Nury Pérez-Hernández
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, CDMX, México
| | | | - Susana Romero-García
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases “Ismael Cosío Villegas”, Mexico City, Mexico
| | - Heriberto Prado-García
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases “Ismael Cosío Villegas”, Mexico City, Mexico
| | | | - Marco Franco-Pérez
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX, México
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15
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Mazzei L, Contaldo U, Musiani F, Cianci M, Bagnolini G, Roberti M, Ciurli S. Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies. Angew Chem Int Ed Engl 2021; 60:6029-6035. [PMID: 33245574 DOI: 10.1002/anie.202014706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Indexed: 12/30/2022]
Abstract
The inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by a class of six aromatic poly-hydroxylated molecules, namely mono- and dimethyl-substituted catechols, was investigated on the basis of the inhibitory efficiency of the catechol scaffold. The aim was to probe the key step of a mechanism proposed for the inhibition of SPU by catechol, namely the sulfanyl radical attack on the aromatic ring, as well as to obtain critical information on the effect of substituents of the catechol aromatic ring on the inhibition efficacy of its derivatives. The crystal structures of all six SPU-inhibitors complexes, determined at high resolution, as well as kinetic data obtained on JBU and theoretical studies of the reaction mechanism using quantum mechanical calculations, revealed the occurrence of an irreversible inactivation of urease by means of a radical-based autocatalytic multistep mechanism, and indicate that, among all tested catechols, the mono-substituted 3-methyl-catechol is the most efficient inhibitor for urease.
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Affiliation(s)
- Luca Mazzei
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, 40127, Bologna, Italy
| | - Umberto Contaldo
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.,Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CEA, CNRS, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, 40127, Bologna, Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Stefano Ciurli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, 40127, Bologna, Italy
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16
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Mazzei L, Contaldo U, Musiani F, Cianci M, Bagnolini G, Roberti M, Ciurli S. Inhibition of Urease, a Ni‐Enzyme: The Reactivity of a Key Thiol With Mono‐ and Di‐Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Luca Mazzei
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
- Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Umberto Contaldo
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
- Laboratory of Chemistry and Biology of Metals Université Grenoble Alpes, CEA CNRS 17 Avenue des Martyrs 38000 Grenoble France
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
- Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences Polytechnic University of Marche Via Brecce Bianche 60131 Ancona Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
| | - Stefano Ciurli
- Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Belmeloro 6 40126 Bologna Italy
- Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) University of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
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17
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Mazzei L, Cirri D, Cianci M, Messori L, Ciurli S. Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes. J Inorg Biochem 2021; 218:111375. [PMID: 33711632 DOI: 10.1016/j.jinorgbio.2021.111375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 01/22/2023]
Abstract
Soft metal ions can inactivate urease, a Ni(II)-dependent enzyme whose hydrolytic activity has significant implications in agro-environmental science and human health. Kinetic and structural studies of the reaction of Canavalia ensiformis urease (JBU) and Sporosarcina pasteurii urease (SPU) with Ag(I) compounds of general formula [Ag(PEt3)X]4 (X = Cl, Br, I), and with the ionic species [Ag(PEt3)2]NO3, revealed the role of the Ag(I) ion and its ligands in modulating the metal-enzyme interaction. The activity of JBU is obliterated by the [Ag(PEt3)X]4 complexes, with IC50 values in the nanomolar range; the efficiency of the inhibition increases in the Cl- < Br- < I- order. The activity of JBU upon [Ag(PEt3)2]NO3 addition decreases to a plateau corresponding to ca. 60% of the original activity and decreases with time at a reduced rate. Synchrotron X-ray crystallography on single crystals obtained after the incubation of SPU with the Ag(I) complexes yielded high-resolution (1.63-1.97 Å) structures. The metal-protein adducts entail a dinuclear Ag(I) cluster bound to the conserved residues αCys322, αHis323, and αMet367, with a bridging cysteine thiolate atom, a weak Ag…Ag bond, and a quasi-linear Ag(I) coordination geometry. These observations suggest a mechanism that involves the initial substitution of the phosphine ligand, followed by a structural rearrangement to yield the dinuclear Ag(I) cluster. These findings indicate that urease, in addition to the active site dinuclear Ni(II) cluster, possesses a secondary metal binding site, located on the mobile flap domain, capable of recognizing pairs of soft metal ions and controlling catalysis.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna, Italy.
| | - Damiano Cirri
- Department of Chemistry and Industrial Chemistry (DCCI), University of Pisa, Via Moruzzi 13, I-56124 Pisa, Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, I-60131 Ancona, Italy
| | - Luigi Messori
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Giuseppe Fanin 40, I-40127 Bologna, Italy.
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18
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A triorganotin(IV) cocrystal with pyridinic phosphoramide: crystal structure and DFT calculations. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-020-01461-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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19
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Pagoni A, Grabowiecka A, Tabor W, Mucha A, Vassiliou S, Berlicki Ł. Covalent Inhibition of Bacterial Urease by Bifunctional Catechol-Based Phosphonates and Phosphinates. J Med Chem 2020; 64:404-416. [PMID: 33369409 DOI: 10.1021/acs.jmedchem.0c01143] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In this study, a new class of bifunctional inhibitors of bacterial ureases, important molecular targets for antimicrobial therapies, was developed. The structures of the inhibitors consist of a combination of a phosphonate or (2-carboxyethyl)phosphinate functionality with a catechol-based fragment, which are designed for complexation of the catalytic nickel ions and covalent bonding with the thiol group of Cys322, respectively. Compounds with three types of frameworks, including β-3,4-dihydroxyphenyl-, α-3,4-dihydroxybenzyl-, and α-3,4-dihydroxybenzylidene-substituted derivatives, exhibited complex and varying structure-dependent kinetics of inhibition. Among irreversible binders, methyl β-(3,4-dihydroxyphenyl)-β-(2-carboxyethyl)phosphorylpropionate was observed to be a remarkably reactive inhibitor of Sporosarcina pasteurii urease (kinact/KI = 10 420 s-1 M-1). The high potential of this group of compounds was also confirmed in Proteus mirabilis whole-cell-based inhibition assays. Some compounds followed slow-binding and reversible kinetics, e.g., methyl β-(3,4-dihydroxyphenyl)-β-phosphonopropionate, with Ki* = 0.13 μM, and an atypical low dissociation rate (residence time τ = 205 min).
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Affiliation(s)
- Aikaterini Pagoni
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 15701 Athens, Greece
| | - Agnieszka Grabowiecka
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Wojciech Tabor
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Artur Mucha
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Stamatia Vassiliou
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 15701 Athens, Greece
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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20
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Castrejón-Flores JL, Reyna-Luna J, Flores-Martinez YM, García-Ventura MI, Zamudio-Medina A, Franco-Pérez M. Characterizing the thermal degradation mechanism of two bisphosphoramidates by TGA, DSC, mass spectrometry and first-principle theoretical protocols. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Righetto RD, Anton L, Adaixo R, Jakob RP, Zivanov J, Mahi MA, Ringler P, Schwede T, Maier T, Stahlberg H. High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica. Nat Commun 2020; 11:5101. [PMID: 33037208 PMCID: PMC7547064 DOI: 10.1038/s41467-020-18870-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/15/2020] [Indexed: 01/09/2023] Open
Abstract
Urease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising the surrounding pH. Here, we report the structure of urease from the pathogen Yersinia enterocolitica at 2 Å resolution from cryo-electron microscopy. Y. enterocolitica urease is a dodecameric assembly of a trimer of three protein chains, ureA, ureB and ureC. The high data quality enables detailed visualization of the urease bimetal active site and of the impact of radiation damage. The obtained structure is of sufficient quality to support drug development efforts. Urease is a nickel enzyme responsible for catalyzing the conversion of urea into ammonia and carbon dioxide. Here the authors report a high resolution cryo-EM structure of urease from the bacterial pathogen Yersinia enterocolitica, providing a detailed visualization of the urease bimetal active site and a basis for drug development.
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Affiliation(s)
- Ricardo D Righetto
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Leonie Anton
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Ricardo Adaixo
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Roman P Jakob
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Jasenko Zivanov
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Mohamed-Ali Mahi
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Philippe Ringler
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Timm Maier
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland.
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland.
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The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate. J Biol Inorg Chem 2020; 25:829-845. [PMID: 32809087 PMCID: PMC7433671 DOI: 10.1007/s00775-020-01808-w] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/29/2020] [Indexed: 01/22/2023]
Abstract
This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry.
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23
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Urease and Nitrification Inhibitors—As Mitigation Tools for Greenhouse Gas Emissions in Sustainable Dairy Systems: A Review. SUSTAINABILITY 2020. [DOI: 10.3390/su12156018] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Currently, nitrogen fertilizers are utilized to meet 48% of the total global food demand. The demand for nitrogen fertilizers is expected to grow as global populations continue to rise. The use of nitrogen fertilizers is associated with many negative environmental impacts and is a key source of greenhouse and harmful gas emissions. In recent years, urease and nitrification inhibitors have emerged as mitigation tools that are presently utilized in agriculture to prevent nitrogen losses and reduce greenhouse and harmful gas emissions that are associated with the use of nitrogen-based fertilizers. Both classes of inhibitor work by different mechanisms and have different physiochemical properties. Consequently, each class must be evaluated on its own merits. Although there are many benefits associated with the use of these inhibitors, little is known about their potential to enter the food chain, an event that may pose challenges to food safety. This phenomenon was highlighted when the nitrification inhibitor dicyandiamide was found as a residual contaminant in milk products in 2013. This comprehensive review aims to discuss the uses of inhibitor technologies in agriculture and their possible impacts on dairy product safety and quality, highlighting areas of concern with regards to the introduction of these inhibitor technologies into the dairy supply chain. Furthermore, this review discusses the benefits and challenges of inhibitor usage with a focus on EU regulations, as well as associated health concerns, chemical behavior, and analytical detection methods for these compounds within milk and environmental matrices.
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Abubaker J, Ibrahim N, Alkanami M, Alaswd A, El-Zeadani H. Response of winter wheat to the application rate of raw and digested sheep manure alone and supplemented with urea in Libyan desert soil. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Targeting the Protein Tunnels of the Urease Accessory Complex: A Theoretical Investigation. Molecules 2020; 25:molecules25122911. [PMID: 32599898 PMCID: PMC7355429 DOI: 10.3390/molecules25122911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Urease is a nickel-containing enzyme that is essential for the survival of several and often deadly pathogenic bacterial strains, including Helicobacter pylori. Notwithstanding several attempts, the development of direct urease inhibitors without side effects for the human host remains, to date, elusive. The recently solved X-ray structure of the HpUreDFG accessory complex involved in the activation of urease opens new perspectives for structure-based drug discovery. In particular, the quaternary assembly and the presence of internal tunnels for nickel translocation offer an intriguing possibility to target the HpUreDFG complex in the search of indirect urease inhibitors. In this work, we adopted a theoretical framework to investigate such a hypothesis. Specifically, we searched for putative binding sites located at the protein–protein interfaces on the HpUreDFG complex, and we challenged their druggability through structure-based virtual screening. We show that, by virtue of the presence of tunnels, some protein–protein interfaces on the HpUreDFG complex are intrinsically well suited for hosting small molecules, and, as such, they possess good potential for future drug design endeavors.
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Inhibition of urease activity by different compounds provides insight into the modulation and association of bacterial nickel import and ureolysis. Sci Rep 2020; 10:8503. [PMID: 32444844 PMCID: PMC7244745 DOI: 10.1038/s41598-020-65107-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/28/2020] [Indexed: 01/29/2023] Open
Abstract
The nickel-dependent urease enzyme is responsible for the hydrolysis of urea to ammonia and carbon dioxide. A number of bacteria produce urease (ureolytic bacteria) and are associated with various infectious diseases and ammonia emissions from agriculture. We report the first comprehensive comparison of the inhibition of urease activity by compounds analysed under the same conditions. Thus, 71 commercially available compounds were screened for their anti-ureolytic properties against both the ureolytic bacterium Klebsiella pneumoniae and purified jack bean urease. Of the tested compounds, 30 showed more than 25% inhibition of the ureolytic activity of Klebsiella pneumoniae or jack bean urease, and among these, carbon disulfide, N-phenylmaleimide, diethylenetriaminepentaacetic acid, sodium pyrrolidinedithiocarbamate, 1,2,4-butanetricarboxylic acid, tannic acid, and gallic acid have not previously been reported to possess anti-ureolytic properties. The diverse effects of metal ion chelators on ureolysis were investigated using a cellular nickel uptake assay. Ethylenediaminetetraacetic acid (EDTA) and dimethylglyoxime (DMG) clearly reduced the nickel import and ureolytic activity of cells, oxalic acid stimulated nickel import but reduced the ureolytic activity of cells, 1,2,4-butanetricarboxylic acid strongly stimulated nickel import and slightly increased the ureolytic activity of cells, while L-cysteine had no effect on nickel import but efficiently reduced the ureolytic activity of cells.
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27
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Zhou S, Huang G, Chen G. Synthesis and biological activities of drugs for the treatment of osteoporosis. Eur J Med Chem 2020; 197:112313. [PMID: 32335412 DOI: 10.1016/j.ejmech.2020.112313] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 12/15/2022]
Abstract
Osteoporosis is an asymptomatic progressive disease. With the improvement of people's living standard and the aging of population, osteoporosis and its fracture have become one of the main diseases threatening the aging society. The serious medical and social burden caused by this has aroused wide public concern. Osteoporosis is listed as one of the three major diseases of the elderly. At present, the drugs for osteoporosis include bone resorption inhibitors and bone formation promoters. The purpose of these anti-osteoporosis drugs is to balance osteoblast bone formation and osteoclast bone resorption. With the development of anti-osteoporosis drugs, new anti osteoporosis drugs have been designed and synthesized. There are many kinds of new compounds with anti osteoporosis activity, but most of them are concentrated on the original drugs with anti osteoporosis activity, or the natural products with anti-osteoporosis activity are extracted from the natural products for structural modification to obtain the corresponding derivatives or analogues. These target compounds showed good ALP activity in vitro and in vivo, promoted osteoblast differentiation and mineralization, or had anti TRAP activity, inhibited osteoclast absorption. This work attempts to systematically review the studies on the synthesis and bioactivity of anti-osteoporosis drugs in the past 10 years. The structure-activity relationship was discussed, which provided a reasonable idea for the design and development of new anti-osteoporosis drugs.
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Affiliation(s)
- Shiyang Zhou
- Key Laboratory of Tropical Medicinal Resource Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, China
| | - Gangliang Huang
- Active Carbohydrate Research Institute, Chongqing Key Laboratory of Green Synthesis and Application, College of Chemistry, Chongqing Normal University, Chongqing, 401331, China.
| | - Guangying Chen
- Key Laboratory of Tropical Medicinal Resource Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, China.
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28
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Zambelli B, Mazzei L, Ciurli S. Intrinsic disorder in the nickel-dependent urease network. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:307-330. [DOI: 10.1016/bs.pmbts.2020.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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29
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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. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 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] [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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Synthesis, evaluation and structural investigations of potent purple acid phosphatase inhibitors as drug leads for osteoporosis. Eur J Med Chem 2019; 182:111611. [DOI: 10.1016/j.ejmech.2019.111611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/31/2019] [Accepted: 08/09/2019] [Indexed: 12/18/2022]
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Mazzei L, Cianci M, Benini S, Ciurli S. The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease, a Nickel Enzyme. Chemistry 2019; 25:12145-12158. [DOI: 10.1002/chem.201902320] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/01/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography LaboratoryFaculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Bologna Italy
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Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme. Angew Chem Int Ed Engl 2019; 58:7415-7419. [DOI: 10.1002/anie.201903565] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl)Faculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
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Gholivand K, Pooyan M, Mohammadpanah F, Pirastefar F, Junk PC, Wang J, Ebrahimi Valmoozi AA, Mani-Varnosfaderani A. Synthesis, crystal structure and biological evaluation of new phosphoramide derivatives as urease inhibitors using docking, QSAR and kinetic studies. Bioorg Chem 2019; 86:482-493. [DOI: 10.1016/j.bioorg.2019.01.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/20/2019] [Accepted: 01/27/2019] [Indexed: 12/24/2022]
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Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl)Faculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
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35
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Mazzei L, Wenzel MN, Cianci M, Palombo M, Casini A, Ciurli S. Inhibition Mechanism of Urease by Au(III) Compounds Unveiled by X-ray Diffraction Analysis. ACS Med Chem Lett 2019; 10:564-570. [PMID: 30996797 DOI: 10.1021/acsmedchemlett.8b00585] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/04/2019] [Indexed: 11/29/2022] Open
Abstract
The nickel-dependent enzyme urease is a virulence factor for a large number of critical human pathogens, making this enzyme a potential target of therapeutics for the treatment of resistant bacterial infections. In the search for novel urease inhibitors, five selected coordination and organometallic Au(III) compounds containing N∧N or C∧N and C∧N∧N ligands were tested for their inhibitory effects against Canavalia ensiformis (jack bean) urease. The results showed potent inhibition effects with IC50 values in the nanomolar range. The 2.14 Å resolution crystal structure of Sporosarcina pasteurii urease inhibited by the most effective Au(III) compound [Au(PbImMe)Cl2]PF6 (PbImMe = 1-methyl-2-(pyridin-2-yl)-benzimidazole) reveals the presence of two Au ions bound to the conserved triad αCys322/αHis323/αMet367. The binding of the Au ions to these residues blocks the movement of a flap, located at the edge of the active site channel and essential for enzyme catalysis, completely obliterating the catalytic activity of urease. Overall, the obtained results constitute the basis for the design of new gold complexes as selective urease inhibitors with future antibacterial applications.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, I-40127 Bologna, Italy
| | - Margot N. Wenzel
- School of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, United Kingdom
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, I-60131 Ancona, Italy
| | - Marta Palombo
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, I-40127 Bologna, Italy
| | - Angela Casini
- School of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, United Kingdom
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, I-40127 Bologna, Italy
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36
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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. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 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] [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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Kafarski P, Talma M. Recent advances in design of new urease inhibitors: A review. J Adv Res 2018; 13:101-112. [PMID: 30094085 PMCID: PMC6077125 DOI: 10.1016/j.jare.2018.01.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/09/2018] [Accepted: 01/16/2018] [Indexed: 12/22/2022] Open
Abstract
Urease is a nickel-dependent metalloenzyme found in plants, some bacteria, and fungi. Bacterial enzyme is of special importance since it has been demonstrated as a potent virulence factor for some species. Especially it is central to Helicobacter pylori metabolism and virulence being necessary for its colonization of the gastric mucosa, and is a potent immunogen that elicits a vigorous immune response. Therefore, it is not surprising that efforts to design, synthesize and evaluate of new inhibitors of urease are and active field of medicinal chemistry. In this paper recent advances on this field are reviewed.
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Affiliation(s)
- Paweł Kafarski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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You Z, Yu H, Li Z, Zhai W, Jiang Y, Li A, Guo S, Li K, Lv C, Zhang C. Inhibition studies of Jack bean urease with hydrazones and their copper(II) complexes. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.05.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Tarsia C, Danielli A, Florini F, Cinelli P, Ciurli S, Zambelli B. Targeting Helicobacter pylori urease activity and maturation: In-cell high-throughput approach for drug discovery. Biochim Biophys Acta Gen Subj 2018; 1862:2245-2253. [PMID: 30048738 DOI: 10.1016/j.bbagen.2018.07.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/12/2018] [Accepted: 07/18/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Helicobacter pylori is a bacterium strongly associated with gastric cancer. It thrives in the acidic environment of the gastric niche of large portions of the human population using a unique adaptive mechanism that involves the catalytic activity of the nickel-dependent enzyme urease. Targeting urease represents a key strategy for drug design and H. pylori eradication. METHOD Here, we describe a novel method to screen, directly in the cellular environment, urease inhibitors. A ureolytic Escherichia coli strain was engineered by cloning the entire urease operon in an expression plasmid and used to test in-cell urease inhibition with a high-throughput colorimetric assay. A two-plasmid system was further developed to evaluate the ability of small peptides to block the protein interactions that lead to urease maturation. RESULTS The developed assay is a robust cellular model to test, directly in the cell environment, urease inhibitors. The efficacy of a co-expressed peptide to affect the interaction between UreF and UreD, two accessory proteins necessary for urease activation, was observed. This event involves a process that occurs through folding upon binding, pointing to the importance of intrinsically disordered hot spots in protein interfaces. CONCLUSIONS The developed system allows the concomitant screening of a large number of drug candidates that interfere with the urease activity both at the level of the enzyme catalysis and maturation. GENERAL SIGNIFICANCE As inhibition of urease has the potential of being a global antibacterial strategy for a large number of infections, this work paves the way for the development of new candidates for antibacterial drugs.
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Affiliation(s)
- Cinzia Tarsia
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Alberto Danielli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Francesca Florini
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Paolo Cinelli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Stefano Ciurli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Barbara Zambelli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy.
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Mazzei L, Cianci M, Gonzalez Vara A, Ciurli S. The structure of urease inactivated by Ag(i): a new paradigm for enzyme inhibition by heavy metals. Dalton Trans 2018; 47:8240-8247. [DOI: 10.1039/c8dt01190g] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular details of the inactivation of urease, a nickel-dependent virulence factor for human pathogens and negatively affecting the efficiency of soil nitrogen fertilization, are elucidated through the crystal structure of the enzyme complex with Ag(i).
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- I-40127 Bologna
- Italy
| | - Michele Cianci
- Department of Agricultural
- Food and Environmental Sciences
- Marche Polytechnic University
- Ancona
- Italy
| | | | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- I-40127 Bologna
- Italy
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Casali L, Mazzei L, Shemchuk O, Honer K, Grepioni F, Ciurli S, Braga D, Baltrusaitis J. Smart urea ionic co-crystals with enhanced urease inhibition activity for improved nitrogen cycle management. Chem Commun (Camb) 2018; 54:7637-7640. [DOI: 10.1039/c8cc03777a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A smart ionic co-crystal of urea with KCl and ZnCl2, obtainedviamechanochemical and solution methods has been proven to be a very efficient urease inhibitor and to provide soil nutrients to complement N supply.
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Affiliation(s)
- Lucia Casali
- Molecular Crystal Engineering Laboratory
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Via F. Selmi 2
- 40126 Bologna
| | - Luca Mazzei
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- Viale Giuseppe Fanin 40
- 40127 Bologna
| | - Oleksii Shemchuk
- Molecular Crystal Engineering Laboratory
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Via F. Selmi 2
- 40126 Bologna
| | - Kenneth Honer
- Department of Chemical and Biomolecular Engineering, Lehigh University
- 111 Research drive
- Bethlehem
- USA
| | - Fabrizia Grepioni
- Molecular Crystal Engineering Laboratory
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Via F. Selmi 2
- 40126 Bologna
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- Viale Giuseppe Fanin 40
- 40127 Bologna
| | - Dario Braga
- Molecular Crystal Engineering Laboratory
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Via F. Selmi 2
- 40126 Bologna
| | - Jonas Baltrusaitis
- Department of Chemical and Biomolecular Engineering, Lehigh University
- 111 Research drive
- Bethlehem
- USA
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Hassan STS, Švajdlenka E. Biological Evaluation and Molecular Docking of Protocatechuic Acid from Hibiscus sabdariffa L. as a Potent Urease Inhibitor by an ESI-MS Based Method. Molecules 2017; 22:E1696. [PMID: 29019930 PMCID: PMC6151788 DOI: 10.3390/molecules22101696] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 10/09/2017] [Indexed: 02/04/2023] Open
Abstract
Studies on enzyme inhibition remain a crucial area in drug discovery since these studies have led to the discoveries of new lead compounds useful in the treatment of several diseases. In this study, protocatechuic acid (PCA), an active compound from Hibiscus sabdariffa L. has been evaluated for its inhibitory properties against jack bean urease (JBU) as well as its possible toxic effect on human gastric epithelial cells (GES-1). Anti-urease activity was evaluated by an Electrospray Ionization-Mass Spectrometry (ESI-MS) based method, while cytotoxicity was assayed by the MTT method. PCA exerted notable anti-JBU activity compared with that of acetohydroxamic acid (AHA), with IC50 values of 1.7 and 3.2 µM, respectively. PCA did not show any significant cytotoxic effect on (GES-1) cells at concentrations ranging from 1.12 to 3.12 µM. Molecular docking study revealed high spontaneous binding ability of PCA to the active site of urease. Additionally, the anti-urease activity was found to be related to the presence of hydroxyl moieties of PCA. This study presents PCA as a natural urease inhibitor, which could be used safely in the treatment of diseases caused by urease-producing bacteria.
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Affiliation(s)
- Sherif T S Hassan
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic.
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21 Praha 6-Suchdol, Czech Republic.
| | - Emil Švajdlenka
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic.
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