151
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Wang B, Shaik S. The Nickel-Pincer Complex in Lactate Racemase Is an Electron Relay and Sink that acts through Proton-Coupled Electron Transfer. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Binju Wang
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
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153
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Singha Mahapatra T, Roy A, Chaudhury S, Dasgupta S, Lal Shrivastava S, Bertolasi V, Ray D. Trapping of a Methanoato Bridge in µ‐1,1,3,3 Mode for [Cu
4
] Aggregate Formation: Synthesis, Steric Control on Nuclearity, Antimicrobial Activity, and DNA‐Interaction Properties. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201601092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | - Anupam Roy
- Agricultural and Food Engineering Department Indian Institute of Technology Kharagpur West Bengal India
| | | | - Swagata Dasgupta
- Department of Chemistry Indian Institute of Technology 721302 Kharagpur India
| | - Shankar Lal Shrivastava
- Agricultural and Food Engineering Department Indian Institute of Technology Kharagpur West Bengal India
| | - Valerio Bertolasi
- Dipartimento di Scienze Chimiche e Farmaceutiche and Centro di Strutturistica Diffrattometrica Università di Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Debashis Ray
- Department of Chemistry Indian Institute of Technology 721302 Kharagpur India
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154
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Zambelli B, Uversky VN, Ciurli S. Nickel impact on human health: An intrinsic disorder perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1714-1731. [DOI: 10.1016/j.bbapap.2016.09.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/31/2016] [Accepted: 09/14/2016] [Indexed: 01/26/2023]
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155
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Inhibition of Urease by Disulfiram, an FDA-Approved Thiol Reagent Used in Humans. Molecules 2016; 21:molecules21121628. [PMID: 27898047 PMCID: PMC6274061 DOI: 10.3390/molecules21121628] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022] Open
Abstract
Urease is a nickel-dependent amidohydrolase that catalyses the decomposition of urea into carbamate and ammonia, a reaction that constitutes an important source of nitrogen for bacteria, fungi and plants. It is recognized as a potential antimicrobial target with an impact on medicine, agriculture, and the environment. The list of possible urease inhibitors is continuously increasing, with a special interest in those that interact with and block the flexible active site flap. We show that disulfiram inhibits urease in Citrullus vulgaris (CVU), following a non-competitive mechanism, and may be one of this kind of inhibitors. Disulfiram is a well-known thiol reagent that has been approved by the FDA for treatment of chronic alcoholism. We also found that other thiol reactive compounds (l-captopril and Bithionol) and quercetin inhibits CVU. These inhibitors protect the enzyme against its full inactivation by the thiol-specific reagent Aldrithiol (2,2'-dipyridyl disulphide, DPS), suggesting that the three drugs bind to the same subsite. Enzyme kinetics, competing inhibition experiments, auto-fluorescence binding experiments, and docking suggest that the disulfiram reactive site is Cys592, which has been proposed as a "hinge" located in the flexible active site flap. This study presents the basis for the use of disulfiram as one potential inhibitor to control urease activity.
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156
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Oxygen activation by mononuclear Mn, Co, and Ni centers in biology and synthetic complexes. J Biol Inorg Chem 2016; 22:407-424. [PMID: 27853875 DOI: 10.1007/s00775-016-1402-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
Abstract
The active sites of metalloenzymes that catalyze O2-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O2 at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O2 reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or oxo-ligands. Collectively, the biochemical and synthetic studies discussed herein reveal the possibilities and limitations of O2 activation at these three "overlooked" metals.
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157
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Mazzei L, Cianci M, Musiani F, Lente G, Palombo M, Ciurli S. Inactivation of urease by catechol: Kinetics and structure. J Inorg Biochem 2016; 166:182-189. [PMID: 27888701 DOI: 10.1016/j.jinorgbio.2016.11.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/14/2016] [Accepted: 11/08/2016] [Indexed: 10/20/2022]
Abstract
Urease is a Ni(II)-containing enzyme that catalyzes the hydrolysis of urea to yield ammonia and carbamate at a rate 1015 times higher than the uncatalyzed reaction. Urease is a virulence factor of several human pathogens, in addition to decreasing the efficiency of soil organic nitrogen fertilization. Therefore, efficient urease inhibitors are actively sought. In this study, we describe a molecular characterization of the interaction between urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) with catechol, a model polyphenol. In particular, catechol irreversibly inactivates both SPU and JBU with a complex radical-based autocatalytic multistep mechanism. The crystal structure of the SPU-catechol complex, determined at 1.50Å resolution, reveals the structural details of the enzyme inhibition.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Michele Cianci
- European Molecular Biology Laboratory, DESY, Hamburg, Germany
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Gábor Lente
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Hungary
| | - Marta Palombo
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy.
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158
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You B, Liu X, Jiang N, Sun Y. A General Strategy for Decoupled Hydrogen Production from Water Splitting by Integrating Oxidative Biomass Valorization. J Am Chem Soc 2016; 138:13639-13646. [DOI: 10.1021/jacs.6b07127] [Citation(s) in RCA: 465] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Bo You
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Xuan Liu
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Nan Jiang
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Yujie Sun
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322, United States
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159
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3-Arylpropionylhydroxamic acid derivatives as Helicobacter pylori urease inhibitors: Synthesis, molecular docking and biological evaluation. Bioorg Med Chem 2016; 24:4519-4527. [DOI: 10.1016/j.bmc.2016.07.052] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 07/22/2016] [Accepted: 07/23/2016] [Indexed: 12/14/2022]
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160
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Fabini E, Zambelli B, Mazzei L, Ciurli S, Bertucci C. Surface plasmon resonance and isothermal titration calorimetry to monitor the Ni(II)-dependent binding of Helicobacter pylori NikR to DNA. Anal Bioanal Chem 2016; 408:7971-7980. [DOI: 10.1007/s00216-016-9894-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/28/2016] [Accepted: 08/17/2016] [Indexed: 02/03/2023]
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161
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Corona T, Company A. Spectroscopically Characterized Synthetic Mononuclear Nickel-Oxygen Species. Chemistry 2016; 22:13422-9. [PMID: 27484613 DOI: 10.1002/chem.201602414] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 11/07/2022]
Abstract
Iron, copper, and manganese are the predominant metals found in oxygenases that perform efficient and selective hydrocarbon oxidations and for this reason, a large number of the corresponding metal-oxygen species has been described. However, in recent years nickel has been found in the active site of enzymes involved in oxidation processes, in which nickel-dioxygen species are proposed to play a key role. Owing to this biological relevance and to the existence of different catalytic protocols that involve the use of nickel catalysts in oxidation reactions, there is a growing interest in the detection and characterization of nickel-oxygen species relevant to these processes. In this Minireview the spectroscopically/structurally characterized synthetic superoxo, peroxo, and oxonickel species that have been reported to date are described. From these studies it becomes clear that nickel is a very promising metal in the field of oxidation chemistry with still unexplored possibilities.
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Affiliation(s)
- Teresa Corona
- Grup de Química Bioinspirada, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17003, Girona, Catalonia, Spain
| | - Anna Company
- Grup de Química Bioinspirada, Supramolecular i Catàlisi (QBIS-CAT), Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17003, Girona, Catalonia, Spain.
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162
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The synthesis and characterization of new nickel complexes with unusual coordination modes. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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163
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Ul-Haq Z, Ashraf S, Al-Majid AM, Barakat A. 3D-QSAR Studies on Barbituric Acid Derivatives as Urease Inhibitors and the Effect of Charges on the Quality of a Model. Int J Mol Sci 2016; 17:ijms17050657. [PMID: 27144563 PMCID: PMC4881483 DOI: 10.3390/ijms17050657] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/05/2016] [Accepted: 04/26/2016] [Indexed: 01/02/2023] Open
Abstract
Urease enzyme (EC 3.5.1.5) has been determined as a virulence factor in pathogenic microorganisms that are accountable for the development of different diseases in humans and animals. In continuance of our earlier study on the helicobacter pylori urease inhibition by barbituric acid derivatives, 3D-QSAR (three dimensional quantitative structural activity relationship) advance studies were performed by Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) methods. Different partial charges were calculated to examine their consequences on the predictive ability of the developed models. The finest developed model for CoMFA and CoMSIA were achieved by using MMFF94 charges. The developed CoMFA model gives significant results with cross-validation (q²) value of 0.597 and correlation coefficients (r²) of 0.897. Moreover, five different fields i.e., steric, electrostatic, and hydrophobic, H-bond acceptor and H-bond donors were used to produce a CoMSIA model, with q² and r² of 0.602 and 0.98, respectively. The generated models were further validated by using an external test set. Both models display good predictive power with r²pred ≥ 0.8. The analysis of obtained CoMFA and CoMSIA contour maps provided detailed insight for the promising modification of the barbituric acid derivatives with an enhanced biological activity.
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Affiliation(s)
- Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical & Biological Sciences, University of Karachi, Karachi 75210, Pakistan.
| | - Sajda Ashraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical & Biological Sciences, University of Karachi, Karachi 75210, Pakistan.
| | - Abdullah Mohammed Al-Majid
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
- Department of Chemistry, Faculty of Science, Alexandria University, P.O. Box 426-Ibrahimia, Alexandria 21321, Egypt.
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164
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Catalytic strategies of the non-heme iron dependent oxygenases and their roles in plant biology. Curr Opin Chem Biol 2016; 31:126-35. [PMID: 27015291 PMCID: PMC4879150 DOI: 10.1016/j.cbpa.2016.02.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 12/18/2022]
Abstract
Current evidence for iron-oxo reactive intermediates is reviewed. In crystallo intermediates detected in a native extradiol dioxygenase reaction. Carotenoid cleavage dioxygenases catalyse strigolactone biosynthesis. Identification of plant cysteine oxidases involved in the plant hypoxic response. Applications of enzyme manipulation to plant biology and agriculture are discussed.
Non-heme iron-dependent oxygenases catalyse the incorporation of O2 into a wide range of biological molecules and use diverse strategies to activate their substrates. Recent kinetic studies, including in crystallo, have provided experimental support for some of the intermediates used by different subclasses of this enzyme family. Plant non-heme iron-dependent oxygenases have diverse and important biological roles, including in growth signalling, stress responses and secondary metabolism. Recently identified roles include in strigolactone biosynthesis, O-demethylation in morphine biosynthesis and regulating the stability of hypoxia-responsive transcription factors. We discuss current structural and mechanistic understanding of plant non-heme iron oxygenases, and how their chemical/genetic manipulation could have agricultural benefit, for example, for improved yield, stress tolerance or herbicide development.
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165
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Sun Y, Tang H, Chen K, Hu L, Yao J, Shaik S, Chen H. Two-State Reactivity in Low-Valent Iron-Mediated C–H Activation and the Implications for Other First-Row Transition Metals. J Am Chem Soc 2016; 138:3715-30. [DOI: 10.1021/jacs.5b12150] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yihua Sun
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hao Tang
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Kejuan Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Lianrui Hu
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Jiannian Yao
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Sason Shaik
- Institute
of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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166
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Deshpande AR, Wagenpfeil K, Pochapsky TC, Petsko GA, Ringe D. Metal-Dependent Function of a Mammalian Acireductone Dioxygenase. Biochemistry 2016; 55:1398-407. [PMID: 26858196 PMCID: PMC5319410 DOI: 10.1021/acs.biochem.5b01319] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella oxytoca are the only known pair of naturally occurring metalloenzymes with distinct chemical and physical properties determined solely by the identity of the divalent transition metal ion (Fe(2+) or Ni(2+)) in the active site. We now show that this dual chemistry can also occur in mammals. ARD from Mus musculus (MmARD) was studied to relate the metal ion identity and three-dimensional structure to enzyme function. The iron-containing isozyme catalyzes the cleavage of 1,2-dihydroxy-3-keto-5-(thiomethyl)pent-1-ene (acireductone) by O2 to formate and the ketoacid precursor of methionine, which is the penultimate step in methionine salvage. The nickel-bound form of ARD catalyzes an off-pathway reaction resulting in formate, carbon monoxide (CO), and 3-(thiomethyl) propionate. Recombinant MmARD was expressed and purified to obtain a homogeneous enzyme with a single transition metal ion bound. The Fe(2+)-bound protein, which shows about 10-fold higher activity than that of others, catalyzes on-pathway chemistry, whereas the Ni(2+), Co(2+), or Mn(2+) forms exhibit off-pathway chemistry, as has been seen with ARD from Klebsiella. Thermal stability of the isozymes is strongly affected by the metal ion identity, with Ni(2+)-bound MmARD being the most stable, followed by Co(2+) and Fe(2+), and Mn(2+)-bound ARD being the least stable. Ni(2+)- and Co(2+)-bound MmARD were crystallized, and the structures of the two proteins found to be similar. Enzyme-ligand complexes provide insight into substrate binding, metal coordination, and the catalytic mechanism.
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Affiliation(s)
| | | | - Thomas C. Pochapsky
- Department of Biochemistry, Brandeis University, Waltham, MA 02454,Department of Chemistry, Brandeis University, Waltham, MA 02454,Rosenstiel Institute for Basic Biomedical Research, Brandeis University, Waltham, MA 02454
| | - Gregory A. Petsko
- Department of Biochemistry, Brandeis University, Waltham, MA 02454,Department of Chemistry, Brandeis University, Waltham, MA 02454,Helen and Robert Appel Alzheimer’s Disease Research Institute, Weill Cornell Medical College, New York, NY 10065
| | - Dagmar Ringe
- Department of Biochemistry, Brandeis University, Waltham, MA 02454,Department of Chemistry, Brandeis University, Waltham, MA 02454,Rosenstiel Institute for Basic Biomedical Research, Brandeis University, Waltham, MA 02454,Corresponding Author. To whom correspondence should be addressed. . Phone: 781-736-4902
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167
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A combined temperature-pH study of urease kinetics. Assigning pKa values to ionizable groups of the active site involved in the catalytic reaction. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.11.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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168
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Kinetic and structural studies reveal a unique binding mode of sulfite to the nickel center in urease. J Inorg Biochem 2016; 154:42-9. [DOI: 10.1016/j.jinorgbio.2015.11.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/22/2015] [Accepted: 11/01/2015] [Indexed: 11/21/2022]
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169
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Mazzei L, Ciurli S, Zambelli B. Isothermal Titration Calorimetry to Characterize Enzymatic Reactions. Methods Enzymol 2016; 567:215-36. [DOI: 10.1016/bs.mie.2015.07.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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170
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Mazzei L, Cianci M, Musiani F, Ciurli S. Inactivation of urease by 1,4-benzoquinone: chemistry at the protein surface. Dalton Trans 2016; 45:5455-9. [DOI: 10.1039/c6dt00652c] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The high activity of urease, a Ni(ii) enzyme, has several adverse effects on human health and agriculture, and its modulation needs the use of inhibitors.
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Affiliation(s)
- L. Mazzei
- Laboratory of bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- Bologna
- Italy
| | - M. Cianci
- European Molecular Biology Laboratory
- 22607 Hamburg
- Germany
| | - F. Musiani
- Laboratory of bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- Bologna
- Italy
| | - S. Ciurli
- Laboratory of bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- Bologna
- Italy
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171
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Ghosh AC, Weisz K, Schulzke C. Selective Capture of Ni2+Ions by Naphthalene- and Coumarin-Substituted Dithiolenes. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500847] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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172
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Barakat A, Al-Majid AM, Lotfy G, Arshad F, Yousuf S, Choudhary MI, Ashraf S, Ul-Haq Z. Synthesis and dynamics studies of barbituric acid derivatives as urease inhibitors. Chem Cent J 2015; 9:63. [PMID: 26583043 PMCID: PMC4648982 DOI: 10.1186/s13065-015-0140-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/01/2015] [Indexed: 12/31/2022] Open
Abstract
Background Discovery of potent inhibitors of urease (jack bean) enzyme is the first step in the development of drugs against diseases caused by ureolytic enzyme. Results Thirty-two derivatives of barbituric acid as zwitterionic adducts of diethyl ammonium salts were synthesized. All synthesized compounds (4a–z and 5a–s) were screened for their in vitro inhibition potential against urease enzyme (jack bean urease). The compounds 4i (IC50 = 17.6 ± 0.23 µM) and 5l (IC50 = 17.2 ± 0.44 µM) were found to be the most active members of the series, and showed several fold more urease inhibition activity than the standard compound thiourea (IC50 = 21.2 ± 1.3 µM). Whereas, compounds 4a–b, 4d–e, 4g–h, 4j–4r, 4x, 4z, 5b, 5e, 5k, 5n–5q having IC50 values in the range of 22.7 ± 0.20 µM–43.8 ± 0.33 µM, were also found as potent urease inhibitors. Furthermore, Molecular Dynamics simulation and molecular docking studies were carried out to analyze the binding mode of barbituric acid derivatives using MOE. During MD simulation enol form is found to be more stable over its keto form due to their coordination with catalytic Nickel ion of Urease. Additionally, structural–activity relationship using automated docking method was applied where the compounds with high biological activity are deeply buried within the binding pocket of urease. As multiple hydrophilic crucial interactions with Ala169, KCX219, Asp362 and Ala366 stabilize the compound within the binding site, thus contributing greater activity. Conclusions This research study is useful for the discovery of economically, efficient viable new drug against infectious diseases.STD. Thiourea (IC50 = 21.2 ± 1.3 µM) ![]() Electronic supplementary material The online version of this article (doi:10.1186/s13065-015-0140-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Assem Barakat
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451 Saudi Arabia.,Department of Chemistry, Faculty of Science, Alexandria University, P.O. Box 426, Ibrahimia, Alexandria, 21321 Egypt
| | - Abdullah Mohammed Al-Majid
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451 Saudi Arabia
| | - Gehad Lotfy
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Fiza Arshad
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Sammer Yousuf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - M Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Sajda Ashraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
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173
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Naureen S, Chaudhry F, Asif N, Munawar MA, Ashraf M, Nasim FH, Arshad H, Khan MA. Discovery of indole-based tetraarylimidazoles as potent inhibitors of urease with low antilipoxygenase activity. Eur J Med Chem 2015; 102:464-70. [DOI: 10.1016/j.ejmech.2015.08.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 07/20/2015] [Accepted: 08/05/2015] [Indexed: 01/18/2023]
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174
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Schmidt AD, Sun Y, Thiel WR. Coordination of Nickel(II) by 3-(2-(Diphenylphosphanyl)phenyl)-1H-pyrazole. Z Anorg Allg Chem 2015. [DOI: 10.1002/zaac.201500579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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175
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Musiani F, Ciurli S. Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria. Molecules 2015; 20:14265-92. [PMID: 26251891 PMCID: PMC6332059 DOI: 10.3390/molecules200814265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 11/24/2022] Open
Abstract
The interaction between macromolecules is a fundamental aspect of most biological processes. The computational techniques used to study protein-protein and protein-nucleic acid interactions have evolved in the last few years because of the development of new algorithms that allow the a priori incorporation, in the docking process, of experimentally derived information, together with the possibility of accounting for the flexibility of the interacting molecules. Here we review the results and the evolution of the techniques used to study the interaction between metallo-proteins and DNA operators, all involved in the nickel and iron metabolism of pathogenic bacteria, focusing in particular on Helicobacter pylori (Hp). In the first part of the article we discuss the methods used to calculate the structure of complexes of proteins involved in the activation of the nickel-dependent enzyme urease. In the second part of the article, we concentrate on two applications of protein-DNA docking conducted on the transcription factors HpFur (ferric uptake regulator) and HpNikR (nickel regulator). In both cases we discuss the technical expedients used to take into account the conformational variability of the multi-domain proteins involved in the calculations.
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Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna I-40127, Italy.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna I-40127, Italy.
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176
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Mazzei L, Dobrovolska O, Musiani F, Zambelli B, Ciurli S. On the interaction of Helicobacter pylori NikR, a Ni(II)-responsive transcription factor, with the urease operator: in solution and in silico studies. J Biol Inorg Chem 2015. [PMID: 26204982 DOI: 10.1007/s00775-015-1284-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Helicobacter pylori (Hp) is a carcinogen that relies on Ni(II) to survive in the extreme pH conditions of the human guts. The regulation of genes coding for Ni(II) enzymes and proteins is effected by the nickel-responsive transcription factor NikR, composed of a DNA-binding domain (DBD) and a metal-binding domain (MBD). The scope of this study is to obtain the molecular details of the HpNikR interaction with the urease operator OP ureA , in solution. The size of the full-length protein prevents the characterization of the HpNikR-OP ureA interaction using NMR. We thus investigated the two separate domains of HpNikR. The conservation of their oligomeric state was established by multiple-angle light scattering. Isothermal calorimetric titrations indicated that the thermodynamics of Ni(II) binding to the isolated MBD is independent of the presence of the adjacent DBDs. The NMR spectra of the isolated DBD support considerable conservation of its structural properties. The spectral perturbations induced on the DBD by OP ureA provided information useful to calculate a structural model of the HpNikR-OP ureA complex using a docking computational protocol. The NMR assignment of the residues involved in the protein-DNA interaction represents a starting point for the development of drugs potentially able to eradicate H. pylori infections. All evidences so far collected, in this and previous studies, consistently indicate that binding of Ni(II) to the MBD increases the HpNikR-DNA affinity by modulating the dynamic, and not the structural, properties of the protein, suggesting that the formation of a stable complex relies upon an induced fit mechanism.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40127, Italy
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177
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178
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Miraula M, Ciurli S, Zambelli B. Intrinsic disorder and metal binding in UreG proteins from Archae hyperthermophiles: GTPase enzymes involved in the activation of Ni(II) dependent urease. J Biol Inorg Chem 2015; 20:739-55. [PMID: 25846143 DOI: 10.1007/s00775-015-1261-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/20/2015] [Indexed: 02/03/2023]
Abstract
Urease is a Ni(II) enzyme present in every domain of life, in charge for nitrogen recycling through urea hydrolysis. Its activity requires the presence of two Ni(II) ions in the active site. These are delivered by the concerted action of four accessory proteins, named UreD, UreF, UreG and UreE. This process requires protein flexibility at different levels and some disorder-to-order transition events that coordinate the mechanism of protein-protein interaction. In particular, UreG, the GTPase in charge of nucleotide hydrolysis required for urease activation, presents a significant degree of intrinsic disorder, existing as a conformational ensemble featuring characteristics that recall a molten globule. Here, the folding properties of UreG were explored in Archaea hyperthermophiles, known to generally feature significantly low level of structural disorder in their proteome. UreG proteins from Methanocaldococcus jannaschii (Mj) and Metallosphaera sedula (Ms) were structurally and functionally analyzed by integrating circular dichroism, NMR, light scattering and enzymatic assays. Metal-binding properties were studied using isothermal titration calorimetry. The results indicate that, as the mesophilic counterparts, both proteins contain a significant amount of secondary structure but maintain a flexible fold and a low GTPase activity. As opposed to other UreGs, secondary structure is lost at high temperatures (68 and 75 °C, respectively) with an apparent two-state mechanism. Both proteins bind Zn(II) and Ni(II), with affinities two orders of magnitude higher for Zn(II) than for Ni(II). No major modifications of the average conformational ensemble are observed, but binding of Zn(II) yields a more compact dimeric form in MsUreG.
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Affiliation(s)
- Manfredi Miraula
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127, Bologna, Italy
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179
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Lopes FC, Dobrovolska O, Real-Guerra R, Broll V, Zambelli B, Musiani F, Uversky VN, Carlini CR, Ciurli S. Pliable natural biocide: Jaburetox is an intrinsically disordered insecticidal and fungicidal polypeptide derived from jack bean urease. FEBS J 2015; 282:1043-64. [DOI: 10.1111/febs.13201] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Fernanda C. Lopes
- Graduate Program in Cellular and Molecular Biology - Center of Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre Brazil
| | - Olena Dobrovolska
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Italy
| | - Rafael Real-Guerra
- Department of Biophysics and Center of Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre Brazil
| | - Valquiria Broll
- Graduate Program in Cellular and Molecular Biology - Center of Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre Brazil
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Italy
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa USA
- Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino Moscow Region Russia
- Department of Biological Science; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Célia R. Carlini
- Graduate Program in Cellular and Molecular Biology - Center of Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre Brazil
- Department of Biophysics and Center of Biotechnology; Federal University of Rio Grande do Sul; Porto Alegre Brazil
- Instituto do Cérebro; Pontifícia Universidade Católica do Rio Grande do Sul; Porto Alegre Brazil
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Italy
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180
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Musiani F, Zambelli B, Bazzani M, Mazzei L, Ciurli S. Nickel-responsive transcriptional regulators. Metallomics 2015; 7:1305-18. [DOI: 10.1039/c5mt00072f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The structural features, metal coordination modes and metal binding thermodynamics of known Ni(ii)-dependent transcriptional regulators are highlighted and discussed.
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Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- 40127 Bologna, Italy
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- 40127 Bologna, Italy
| | - Micaela Bazzani
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- 40127 Bologna, Italy
| | - Luca Mazzei
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- 40127 Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- 40127 Bologna, Italy
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181
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Pereira Araujo D, Santos Morais VS, de Fátima Â, Modolo LV. Efficient sodium bisulfite-catalyzed synthesis of benzothiazoles and their potential as ureases inhibitors. RSC Adv 2015. [DOI: 10.1039/c5ra01081k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In this work we report the successful use of sodium bisulfite as catalyst for the synthesis of 19 benzothiazoles (BZTs) under microwave irradiation with yields from 80% to 100%.
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Affiliation(s)
- Débora Pereira Araujo
- Grupo de Estudos em Química Orgânica e Biológica (GEQOB)
- Departamento de Química
- Instituto de Ciências Exatas
- Universidade Federal de Minas Gerais
- Belo Horizonte
| | - Vinicius Stefano Santos Morais
- Grupo de Estudos em Bioquímica de Plantas (GEBioPlan)
- Departamento de Botânica
- Instituto de Ciências Biológicas
- Universidade Federal de Minas Gerais
- Belo Horizonte
| | - Ângelo de Fátima
- Grupo de Estudos em Química Orgânica e Biológica (GEQOB)
- Departamento de Química
- Instituto de Ciências Exatas
- Universidade Federal de Minas Gerais
- Belo Horizonte
| | - Luzia Valentina Modolo
- Grupo de Estudos em Bioquímica de Plantas (GEBioPlan)
- Departamento de Botânica
- Instituto de Ciências Biológicas
- Universidade Federal de Minas Gerais
- Belo Horizonte
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182
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Hou YL, Li SX, Sun RWY, Liu XY, Weng Ng S, Li D. Facile preparation and dual catalytic activity of copper(i)–metallosalen coordination polymers. Dalton Trans 2015; 44:17360-5. [DOI: 10.1039/c5dt00741k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three copper(i)–metallosalen coordination polymers (CPs), {[NiII(SalImCy)]2(CuICN)9}n (1), {[CuII(SalImCy)]2(CuICN)9}n (2) and {[NiII(SalImCy)](CuII)2·DMF}n (3) were prepared by direct combination of NiII/CuII(salen) motifs with [CuICN]n chains and Cu2I2 clusters via the metalloligand strategy.
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Affiliation(s)
- Yun-Long Hou
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province
- Shantou University
- Guangdong 515063
- P. R. China
| | - Sheng-Xia Li
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province
- Shantou University
- Guangdong 515063
- P. R. China
| | - Raymond Wai-Yin Sun
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province
- Shantou University
- Guangdong 515063
- P. R. China
| | - Xin-Yuan Liu
- Department of Chemistry
- South University of Science and Technology of China
- Shenzhen 518055
- P. R. China
| | - Seik Weng Ng
- Department of Chemistry
- University of Malaya
- 50603 Kuala Lumpur
- Malaysia
- Chemistry Department
| | - Dan Li
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province
- Shantou University
- Guangdong 515063
- P. R. China
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183
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Valdez CE, Smith QA, Nechay MR, Alexandrova AN. Mysteries of metals in metalloenzymes. Acc Chem Res 2014; 47:3110-7. [PMID: 25207938 DOI: 10.1021/ar500227u] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Natural metalloenzymes are often the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions. However, metalloenzymes are occasionally surprising in their selection of catalytic metals, and in their responses to metal substitution. Indeed, from the isolated standpoint of producing the best catalyst, a chemist designing from first-principles would likely choose a different metal. For example, some enzymes employ a redox active metal where a simple Lewis acid is needed. Such are several hydrolases. In other cases, substitution of a non-native metal leads to radical improvements in reactivity. For example, histone deacetylase 8 naturally operates with Zn(2+) in the active site but becomes much more active with Fe(2+). For β-lactamases, the replacement of the native Zn(2+) with Ni(2+) was suggested to lead to higher activity as predicted computationally. There are also intriguing cases, such as Fe(2+)- and Mn(2+)-dependent ribonucleotide reductases and W(4+)- and Mo(4+)-dependent DMSO reductases, where organisms manage to circumvent the scarcity of one metal (e.g., Fe(2+)) by creating protein structures that utilize another metal (e.g., Mn(2+)) for the catalysis of the same reaction. Naturally, even though both metal forms are active, one of the metals is preferred in every-day life, and the other metal variant remains dormant until an emergency strikes in the cell. These examples lead to certain questions. When are catalytic metals selected purely for electronic or structural reasons, implying that enzymatic catalysis is optimized to its maximum? When are metal selections a manifestation of competing evolutionary pressures, where choices are dictated not just by catalytic efficiency but also by other factors in the cell? In other words, how can enzymes be improved as catalysts merely through the use of common biological building blocks available to cells? Addressing these questions is highly relevant to the enzyme design community, where the goal is to prepare maximally efficient quasi-natural enzymes for the catalysis of reactions that interest humankind. Due to competing evolutionary pressures, many natural enzymes may not have evolved to be ideal catalysts and can be improved for the isolated purpose of catalysis in vitro when the competing factors are removed. The goal of this Account is not to cover all the possible stories but rather to highlight how variable enzymatic catalysis can be. We want to bring up possible factors affecting the evolution of enzyme structure, and the large- and intermediate-scale structural and electronic effects that metals can induce in the protein, and most importantly, the opportunities for optimization of these enzymes for catalysis in vitro.
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Affiliation(s)
- Crystal E. Valdez
- Department
of Chemistry and Biochemistry, and ‡California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Quentin A. Smith
- Department
of Chemistry and Biochemistry, and ‡California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Michael R. Nechay
- Department
of Chemistry and Biochemistry, and ‡California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry, and ‡California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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184
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Modolo LV, de Souza AX, Horta LP, Araujo DP, de Fátima Â. An overview on the potential of natural products as ureases inhibitors: A review. J Adv Res 2014; 6:35-44. [PMID: 25685542 PMCID: PMC4293669 DOI: 10.1016/j.jare.2014.09.001] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/21/2014] [Accepted: 09/22/2014] [Indexed: 01/18/2023] Open
Abstract
Ureases, enzymes that catalyze urea hydrolysis, have received considerable attention for their impact on living organisms’ health and life quality. On the one hand, the persistence of urease activity in human and animal cells can be the cause of some diseases and pathogen infections. On the other hand, food production can be negatively affected by ureases of soil microbiota that, in turn, lead to losses of nitrogenous nutrients in fields supplemented with urea as fertilizer. In this context, nature has proven to be a rich resource of natural products bearing a variety of scaffolds that decrease the ureolytic activity of ureases from different organisms. Therefore, this work compiles the state-of-the-art researches focused on the potential of plant natural products (present in extracts or as pure compounds) as urease inhibitors of clinical and/or agricultural interests. Emphasis is given to ureases of Helicobacter pylori, Canavalia ensiformis and soil microbiota although the active site of this class of hydrolases is conserved among living organisms.
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Affiliation(s)
- Luzia V. Modolo
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil
- Corresponding authors. Tel./fax: +55 31 3409 3008 (L.V. Modolo). Tel.: +55 31 3409 6373; fax: +55 31 3409 5700 (A. de Fátima).
| | - Aline X. de Souza
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Lívia P. Horta
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Débora P. Araujo
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Ângelo de Fátima
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil
- Corresponding authors. Tel./fax: +55 31 3409 3008 (L.V. Modolo). Tel.: +55 31 3409 6373; fax: +55 31 3409 5700 (A. de Fátima).
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185
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The conformational response to Zn(II) and Ni(II) binding of Sporosarcina pasteurii UreG, an intrinsically disordered GTPase. J Biol Inorg Chem 2014; 19:1341-54. [PMID: 25200810 DOI: 10.1007/s00775-014-1191-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
Abstract
Urease is an essential Ni(II) enzyme involved in the nitrogen metabolism of bacteria, plants and fungi. Ni(II) delivery into the enzyme active site requires the presence of four accessory proteins, named UreD, UreF, UreG and UreE, acting through a complex protein network regulated by metal binding and GTP hydrolysis. The GTPase activity is catalyzed by UreG, which couples this function to a non-enzymatic role as a molecular chaperone. This moonlighting activity is reflected in a flexible fold that makes UreG the first discovered intrinsically disordered enzyme. UreG binds Ni(II) and Zn(II),which in turn modulate the interactions with other urease chaperones. The aim of this study is to understand the structural implications of metal binding to Sporosarcina pasteurii UreG (SpUreG). A combination of light scattering, calorimetry, mass spectrometry, and NMR spectroscopy revealed that SpUreG exists in monomer-dimer equilibrium (K(d)= 45 µM), sampling three distinct folding populations with different degrees of compactness. Binding of Zn(II) ions, occurring in two distinct sites (K(d1) = 3 nM, K(d2) = 0.53 µM), shifts the protein conformational landscape toward the more compact population, while maintaining the overall protein structural plasticity. Differently, binding of Ni(II) ions occurs in three binding sites (K(d1(= 14 µM; K(d2) = 270 µM; K(d3)= 160 µM), with much weaker influence on the protein conformational equilibrium. These distinct conformational responses of SpUreG to Ni(II) and Zn(II) binding suggest that selective metal binding modulates protein plasticity, possibly having an impact on the protein-protein interactions and the enzymatic activity of UreG.
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186
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Lebrette H, Brochier-Armanet C, Zambelli B, de Reuse H, Borezée-Durant E, Ciurli S, Cavazza C. Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins. Structure 2014; 22:1421-32. [PMID: 25199691 DOI: 10.1016/j.str.2014.07.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/16/2014] [Accepted: 07/13/2014] [Indexed: 10/24/2022]
Abstract
In human pathogenic bacteria, nickel is required for the activation of two enzymes, urease and [NiFe]-hydrogenase, necessary for host infection. Acquisition of Ni(II) is mediated by either permeases or ABC-importers, the latter including a subclass that involves an extracytoplasmic nickel-binding protein, Ni-BP. This study reports on the structure of three Ni-BPs from a diversity of human pathogens and on the existence of three new nickel-binding motifs. These are different from that previously described for Escherichia coli Ni-BP NikA, known to bind nickel via a nickelophore, and indicate a variegated ligand selectivity for Ni-BPs. The structures are consistent with ligand affinities measured in solution by calorimetry and challenge the hypothesis of a general requirement of nickelophores for nickel uptake by canonical ABC importers. Phylogenetic analyses showed that Ni-BPs have different evolutionary origins and emerged independently from peptide-binding proteins, possibly explaining the promiscuous behavior of this class of Ni(II) carriers.
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Affiliation(s)
- Hugo Lebrette
- University Grenoble Alpes, Institut de Biologie Structurale (IBS), 38044 Grenoble, France; CNRS, IBS, 38044 Grenoble, France; CEA, IBS, 38044 Grenoble, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin, 40, 40127 Bologna, Italy
| | - Hilde de Reuse
- Département de Microbiologie, Unité Pathogenèse de Helicobacter, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Elise Borezée-Durant
- INRA, UMR 1319 Micalis, 78350 Jouy en Josas, France; Agro ParisTech, UMR Micalis, 78350 Jouy en Josas, France
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin, 40, 40127 Bologna, Italy.
| | - Christine Cavazza
- University Grenoble Alpes, LCBM, 17, Avenue des Martyrs, 38054 Grenoble Cedex 09, France.
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187
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Allpress CJ, Berreau LM. A Nickel‐Containing Model System of Acireductone Dioxygenases that Utilizes a C(1)‐H Acireductone Substrate. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Caleb J. Allpress
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322‐0300, USA, http://lisaberreau.org/
| | - Lisa M. Berreau
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322‐0300, USA, http://lisaberreau.org/
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188
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Benini S, Cianci M, Mazzei L, Ciurli S. Fluoride inhibition of Sporosarcina pasteurii urease: structure and thermodynamics. J Biol Inorg Chem 2014; 19:1243-61. [DOI: 10.1007/s00775-014-1182-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/30/2014] [Indexed: 01/25/2023]
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189
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Merloni A, Dobrovolska O, Zambelli B, Agostini F, Bazzani M, Musiani F, Ciurli S. Molecular landscape of the interaction between the urease accessory proteins UreE and UreG. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1662-74. [PMID: 24982029 DOI: 10.1016/j.bbapap.2014.06.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/12/2014] [Accepted: 06/19/2014] [Indexed: 01/07/2023]
Abstract
Urease, the most efficient enzyme so far discovered, depends on the presence of nickel ions in the catalytic site for its activity. The transformation of inactive apo-urease into active holo-urease requires the insertion of two Ni(II) ions in the substrate binding site, a process that involves the interaction of four accessory proteins named UreD, UreF, UreG and UreE. This study, carried out using calorimetric and NMR-based structural analysis, is focused on the interaction between UreE and UreG from Sporosarcina pasteurii, a highly ureolytic bacterium. Isothermal calorimetric protein-protein titrations revealed the occurrence of a binding event between SpUreE and SpUreG, entailing two independent steps with positive cooperativity (Kd1=42±9μM; Kd2=1.7±0.3μM). This was interpreted as indicating the formation of the (UreE)2(UreG)2 hetero-oligomer upon binding of two UreG monomers onto the pre-formed UreE dimer. The molecular details of this interaction were elucidated using high-resolution NMR spectroscopy. The occurrence of SpUreE chemical shift perturbations upon addition of SpUreG was investigated and analyzed to establish the protein-protein interaction site. The latter appears to involve the Ni(II) binding site as well as mobile portions on the C-terminal and the N-terminal domains. Docking calculations based on the information obtained from NMR provided a structural basis for the protein-protein contact site. The high sequence and structural similarity within these protein classes suggests a generality of the interaction mode among homologous proteins. The implications of these results on the molecular details of the urease activation process are considered and analyzed.
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Affiliation(s)
- Anna Merloni
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Olena Dobrovolska
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Federico Agostini
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Micaela Bazzani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Italy.
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