1
|
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. THE SCIENCE OF THE TOTAL ENVIRONMENT 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] [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.
Collapse
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
| |
Collapse
|
2
|
Suenaga S, Takano Y, Saito T. Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study. Molecules 2023; 28:molecules28062697. [PMID: 36985670 PMCID: PMC10051795 DOI: 10.3390/molecules28062697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Soil bacteria can produce urease, which catalyzes the hydrolysis of urea to ammonia (NH3) and carbamate. A variety of urease inhibitors have been proposed to reduce NH3 volatilization by interfering with the urease activity. We report a quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) study on the mechanism employed for the inhibition of urease by three representative competitive inhibitors; namely, acetohydroxamic acid (AHA), hydroxyurea (HU), and N-(n-butyl)phosphorictriamide (NBPTO). The possible connections between the structural and thermodynamical properties and the experimentally observed inhibition efficiency were evaluated and characterized. We demonstrate that the binding affinity decreases in the order NBPTO >> AHA > HU in terms of the computed activation and reaction free energies. This trend also indicates that NBPTO shows the highest inhibitory activity and the lowest IC50 value of 2.1 nM, followed by AHA (42 μM) and HU (100 μM). It was also found that the X=O moiety (X = carbon or phosphorous) plays a crucial role in the inhibitor binding process. These findings not only elucidate why the potent urease inhibitors are effective but also have implications for the design of new inhibitors.
Collapse
Affiliation(s)
- Shunya Suenaga
- Faculty of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
| | - Toru Saito
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
- Correspondence: ; Tel.: +81-82-830-1617
| |
Collapse
|
3
|
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: 1] [Impact Index Per Article: 0.5] [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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Loharch S, Berlicki Ł. Rational Development of Bacterial Ureases Inhibitors. CHEM REC 2022; 22:e202200026. [PMID: 35502852 DOI: 10.1002/tcr.202200026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/28/2022] [Indexed: 12/23/2022]
Abstract
Urease, an enzyme that catalyzes the hydrolysis of urea, is a virulence factor of various pathogenic bacteria. In particular, Helicobacter pylori, that colonizes the digestive tract and Proteus spp., that can infect the urinary tract, are related to urease activity. Therefore, urease inhibitors are considered as potential therapeutics against these infections. This review describes current knowledge of the structures, activity, and biological importance of bacterial ureases. Moreover, the structure-based design of several classes of bacterial urease inhibitors is presented and discussed. Phosphinic and phosphonic acids were applied as transition-state analogues, while Michael acceptors and ebselen derivatives were applied as covalent binders of cysteine residue. This review incorporates bacterial urease inhibitors from literature published between 2008 and 2021.
Collapse
Affiliation(s)
- Saurabh Loharch
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| |
Collapse
|
6
|
Degradation of N-(n-butyl) Thiophosphoric Triamide (NBPT) with and without Nitrification Inhibitor in Soils. NITROGEN 2022. [DOI: 10.3390/nitrogen3020012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Recent studies have shown that nitrification inhibitor (NI) impairs the efficacy of urease inhibitor, N-(n-butyl) thiophosphoric triamide (NBPT), in reducing ammonia volatilization and urea hydrolysis rate. A laboratory study was conducted to evaluate the influence of NI (specifically 3,4-dimethyl pyrazole phosphate) on the degradation of NBPT in six soils. Soils were amended with either NBPT (10 mg NBPT kg−1 soil) or NBPT plus NI (DI; 10 mg NBPT + 2.5 mg NI kg−1 soil), incubated at 21 °C, and destructively sampled eight times during a 14-day incubation period. The degradation of NBPT in soil was quantified by measuring NBPT concentration with high-performance liquid chromatography-mass spectrometry, and the degradation rate constant was modeled with an exponential decay function. The study showed that the persistence of NBPT in soil was not influenced by the presence of NI, as the NBPT degradation rate constant across soils was 0.5 d−1 with either NBPT or DI. In contrast, the degradation rate constant was significantly dependent on soils, with values ranging from 0.4 to 1.7 d−1. Soil pH was the most important variable affecting the persistence of NBPT in soils. The half-life of NBPT was 0.4 d in acidic soil and 1.3 to 2.1 d in neutral to alkaline soils. The faster degradation of NBPT in acidic soils may explain its reduced efficacy in such soils.
Collapse
|
7
|
García-Aranda MI, Franco-Pérez M, Bonilla-Landa I, Castrejón-Flores JL, Zamudio-Medina A. Synthesis of new aromatic phosphoramidates under a three-component reaction. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2022.2053854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mónica I. García-Aranda
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Mexico City, Mexico
| | - Marco Franco-Pérez
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F, CP, México
| | - Israel Bonilla-Landa
- Red de Estudios Moleculares Avanzados CAMPUS III, Instituto de Ecología A.C. (INECOL), Xalapa-Enríquez, Veracruz, Mexico
| | - José Luis Castrejón-Flores
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Mexico City, Mexico
| | - Angel Zamudio-Medina
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Mexico City, Mexico
| |
Collapse
|
8
|
Abstract
![]()
Urease
catalyzes the hydrolysis of urea to form ammonia and carbamate,
inducing an overall pH increase that affects both human health and
agriculture. Inhibition, mutagenesis, and kinetic studies have provided
insights into its enzymatic role, but there have been debates on the
substrate binding mode as well as the reaction mechanism. In the present
study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular
mechanics molecular dynamics (QM/MM MD) calculations on urease that
mainly investigate the binding mode of urea and the mechanism of the
urease-catalyzed hydrolysis reaction. Comparison between the experimental
data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that
urea hydrolysis via a complex with bidentate-bound urea is much more
favorable than via that with monodentate-bound urea for both nucleophilic
attack and the subsequent proton transfer steps. We also indicate
that the bidentate coordination of urea fits the active site with
a closed conformation of the mobile flap and can facilitate the stabilization
of transition states and intermediates by forming multiple hydrogen
bonds with certain active site residues.
Collapse
Affiliation(s)
- Toru Saito
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
| |
Collapse
|
9
|
Liu ML, Li WY, Fang HL, Ye YX, Li SY, Song WQ, Xiao ZP, Ouyang H, Zhu HL. Synthesis and Biological Evaluation of Dithiobisacetamides as Novel Urease Inhibitors. ChemMedChem 2021; 17:e202100618. [PMID: 34687265 DOI: 10.1002/cmdc.202100618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Indexed: 12/20/2022]
Abstract
Thirty-eight disulfides containing N-arylacetamide were designed and synthesized in an effort to develop novel urease inhibitors. Biological evaluation revealed that some of the synthetic compounds exhibited strong inhibitory potency against both cell-free urease and urease in intact cell with low cytotoxicity to mammalian cells even at concentration up to 250 μM. Of note, 2,2'-dithiobis(N-(2-fluorophenyl)acetamide) (d7), 2,2'-dithiobis(N-(3,5-difluorophenyl)acetamide) (d24), and 2,2'-dithiobis(N-(3-fluorophenyl)acetamide) (d8) were here identified as the most active inhibitors with IC50 of 0.074, 0.44, and 0.81 μM, showing 32- to 355-fold higher potency than the positive control acetohydroxamic acid. These disulfides were confirmed to bind urease without covalent modification of the cysteine residue and to inhibit urease reversibly with a mixed inhibition mechanism. They also showed very good anti-Helicobacter pylori activities with d8 showing a comparable potency to the clinical used drug amoxicillin. The impressive in vitro biological profile indicated their immense potential as therapeutic agents to tackle H. pylori caused infections.
Collapse
Affiliation(s)
- Mei-Ling Liu
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Wei-Yi Li
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Hai-Lian Fang
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Ya-Xi Ye
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Xianlin Road 163, Nanjing, China
| | - Su-Ya Li
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Wan-Qing Song
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Zhu-Ping Xiao
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Xianlin Road 163, Nanjing, China
| | - Hui Ouyang
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Hai-Liang Zhu
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Xianlin Road 163, Nanjing, China
| |
Collapse
|
10
|
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
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
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
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
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).
Collapse
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
| |
Collapse
|
15
|
The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate. J Biol Inorg Chem 2020; 25:829-845. [PMID: 32809087 PMCID: PMC7433671 DOI: 10.1007/s00775-020-01808-w] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/29/2020] [Indexed: 01/22/2023]
Abstract
This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry.
Collapse
|
16
|
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.
Collapse
|
17
|
Wang H, Xu C, Zhang X, Zhang D, Jin F, Fan Y. Urease inhibition studies of six Ni(II), Co(II) and Cu(II) complexes with two sexidentate N2O4-donor bis-Schiff base ligands: An experimental and DFT computational study. J Inorg Biochem 2020; 204:110959. [DOI: 10.1016/j.jinorgbio.2019.110959] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/03/2019] [Accepted: 12/09/2019] [Indexed: 12/15/2022]
|
18
|
Li WY, Ni WW, Ye YX, Fang HL, Pan XM, He JL, Zhou TL, Yi J, Liu SS, Zhou M, Xiao ZP, Zhu HL. N-monoarylacetothioureas as potent urease inhibitors: synthesis, SAR, and biological evaluation. J Enzyme Inhib Med Chem 2020; 35:404-413. [PMID: 31880473 PMCID: PMC6968641 DOI: 10.1080/14756366.2019.1706503] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A urease inhibitor with good in vivo profile is considered as an alternative agent for treating infections caused by urease-producing bacteria such as Helicobacter pylori. Here, we report a series of N-monosubstituted thioureas, which act as effective urease inhibitors with very low cytotoxicity. One compound (b19) was evaluated in detail and shows promising features for further development as an agent to treat H. pylori caused diseases. Excellent values for the inhibition of b19 against both extracted urease and urease in intact cell were observed, which shows IC50 values of 0.16 ± 0.05 and 3.86 ± 0.10 µM, being 170- and 44-fold more potent than the clinically used drug AHA, respectively. Docking simulations suggested that the monosubstituted thiourea moiety penetrates urea binding site. In addition, b19 is a rapid and reversible urease inhibitor, and displays nM affinity to urease with very slow dissociation (koff=1.60 × 10−3 s−1) from the catalytic domain.
Collapse
Affiliation(s)
- Wei-Yi Li
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China
| | - Wei-Wei Ni
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China
| | - Ya-Xi Ye
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
| | - Hai-Lian Fang
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China
| | - Xing-Ming Pan
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China
| | - Jie-Ling He
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China
| | - Tian-Li Zhou
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China
| | - Juan Yi
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China
| | - Shan-Shan Liu
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China
| | - Mi Zhou
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China
| | - Zhu-Ping Xiao
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
| | - Hai-Liang Zhu
- National Demonstration Center for Experimental Chemistry Education, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Jishou, PR China.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, PR China
| |
Collapse
|
19
|
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]
|
20
|
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
| |
Collapse
|
21
|
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
| |
Collapse
|
22
|
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
| |
Collapse
|