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Breeze CW, Nakano Y, Campbell EC, Frkic RL, Lupton DW, Jackson CJ. Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase. Acta Crystallogr D Struct Biol 2024; 80:289-298. [PMID: 38512071 PMCID: PMC10994177 DOI: 10.1107/s2059798324002316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/10/2024] [Indexed: 03/22/2024] Open
Abstract
Lanthanide ions have ideal chemical properties for catalysis, such as hard Lewis acidity, fast ligand-exchange kinetics, high coordination-number preferences and low geometric requirements for coordination. As a result, many small-molecule lanthanide catalysts have been described in the literature. Yet, despite the ability of enzymes to catalyse highly stereoselective reactions under gentle conditions, very few lanthanoenzymes have been investigated. In this work, the mononuclear binding of europium(III) and gadolinium(III) to the active site of a mutant of the model enzyme phosphotriesterase are described using X-ray crystallography at 1.78 and 1.61 Å resolution, respectively. It is also shown that despite coordinating a single non-natural metal cation, the PTE-R18 mutant is still able to maintain esterase activity.
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Affiliation(s)
- Callum W. Breeze
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Yuji Nakano
- School of Chemistry, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Eleanor C. Campbell
- Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, VIC 3168, Australia
| | - Rebecca L. Frkic
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - David W. Lupton
- School of Chemistry, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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2
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Tomczyk MD, Kuźnik N, Walczak K. Cyclen-based artificial nucleases: Three decades of development (1989–2022). Part a – Hydrolysis of phosphate esters. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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3
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Singh VK, Pillai V, Patel SK, Buch L. Improving Cytotoxicity by Changing a Linker from Diphenylether to Diphenylmethane and now to Phenylene in Binuclear Dithiocarbamate Complexes: Synthesis and Cytotoxicity Study. ChemistrySelect 2019. [DOI: 10.1002/slct.201900938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Vinay K Singh
- Department of ChemistryFaculty of ScienceThe M. S. University of Baroda Vadodara- 390 002 India
| | - Vineeta Pillai
- Department of ChemistryFaculty of ScienceThe M. S. University of Baroda Vadodara- 390 002 India
| | - Shailykumari K. Patel
- Department of ChemistryFaculty of ScienceThe M. S. University of Baroda Vadodara- 390 002 India
| | - Lipi Buch
- Department of ZoologyFaculty of ScienceThe M. S. University of Baroda Vadodara- 390 002 India
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4
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Fanning AM, Plush SE, Gunnlaugsson T. Tri- and tetra-substituted cyclen based lanthanide(III) ion complexes as ribonuclease mimics: a study into the effect of log Ka, hydration and hydrophobicity on phosphodiester hydrolysis of the RNA-model 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP). Org Biomol Chem 2016; 13:5804-16. [PMID: 25909178 DOI: 10.1039/c4ob02384f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A series of tetra-substituted 'pseudo' dipeptide ligands of cyclen (1,4,7,10,-tetraazacyclododecane) and a tri-substituted 3'-pyridine ligand of cyclen, and the corresponding lanthanide(III) complexes were synthesised and characterised as metallo-ribonuclease mimics. All complexes were shown to promote hydrolysis of the phosphodiester bond of 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP, τ1/2 = 5.87 × 10(3) h), a well known RNA mimic. The La(III) and Eu(III) tri-substituted 3'-pyridine lanthanide(III) complexes being the most efficient in promoting such hydrolysis at pH 7.4 and at 37 °C; with τ1/2 = 1.67 h for La(III) and 1.74 h for Eu(III). The series was developed to provide the opportunity to investigate the consequences of altering the lanthanide(III) ion, coordination ability and hydrophobicity of a metallo-cavity on the rate of hydrolysis using the model phosphodiester, HPNP, at 37 °C. To further provide information on the role that the log Ka of the metal bound water plays in phosphodiester hydrolysis the protonation constants and the metal ion stability constants of both a tri and tetra-substituted 3'pyridine complex were determined. Our results highlighted several key features for the design of lanthanide(III) ribonucelase mimics; the presence of two metal bound water molecules are vital for pH dependent rate constants for Eu(III) complexes, optimal pH activity approximating physiological pH (∼7.4) may be achieved if the log Ka values for both MLOH and ML(OH)2 species occur in this region, small changes to hydrophobicity within the metallo cavity influence the rate of hydrolysis greatly and an amide adjacent to the metal ion capable of forming hydrogen bonds with the substrate is required for achieving fast hydrolysis.
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Affiliation(s)
- Ann-Marie Fanning
- School of Chemistry and Trinity Biomedical Sciences Institute, University of Dublin, Trinity College Dublin, Dublin 2, Ireland.
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5
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Designing reactivity-based responsive lanthanide probes for multicolor detection in biological systems. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2013.10.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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6
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Pandey SK, Pandey OP, Sengupta SK. Carboxyester hydrolysis promoted by novel nano-sized macrocyclic Zn(II) complexes. Appl Organomet Chem 2014. [DOI: 10.1002/aoc.3182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sarvesh Kumar Pandey
- Department of Chemistry; DDU Gorakhpur University; Gorakhpur 273009 Uttar Pradesh India
| | - O. P. Pandey
- Department of Chemistry; DDU Gorakhpur University; Gorakhpur 273009 Uttar Pradesh India
| | - S. K. Sengupta
- Department of Chemistry; DDU Gorakhpur University; Gorakhpur 273009 Uttar Pradesh India
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7
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Camargo MA, Neves A, Bortoluzzi AJ, Szpoganicz B, Fischer FL, Terenzi H, Serra OA, Santos VG, Vaz BG, Eberlin MN. Efficient Phosphodiester Hydrolysis by Luminescent Terbium(III) and Europium(III) Complexes. Inorg Chem 2010; 49:6013-25. [DOI: 10.1021/ic100549u] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Maryene A. Camargo
- Laboratório de Bioinorgânica e Crystalografia (LABINC), Departamento de Química
| | - Ademir Neves
- Laboratório de Bioinorgânica e Crystalografia (LABINC), Departamento de Química
| | | | - Bruno Szpoganicz
- Laboratório de Bioinorgânica e Crystalografia (LABINC), Departamento de Química
| | | | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, CCB
| | - Osvaldo A. Serra
- Laboratório de Terras Raras (FFCLRP-USP), Departamento de Química, Universidade de São Paulo, Avenue Bandeirantes 3900, 14040-901, Ribeirão Preto, São Paulo, Brazil
| | - Vanessa G. Santos
- Laboratório ThoMSon de Espectrometria de Massas, Instituto de Química, Universidade Estadual de Campinas, 13083-970, Campinas, São Paulo, Brazil
| | - Boniek G. Vaz
- Laboratório ThoMSon de Espectrometria de Massas, Instituto de Química, Universidade Estadual de Campinas, 13083-970, Campinas, São Paulo, Brazil
| | - Marcos N. Eberlin
- Laboratório ThoMSon de Espectrometria de Massas, Instituto de Química, Universidade Estadual de Campinas, 13083-970, Campinas, São Paulo, Brazil
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8
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Camargo MA, Neves A, Szpoganicz B, Bortoluzzi AJ, Fischer FL, Terenzi H, Castellano EE. Synthesis, Structure, and Phosphatase-Like Activity of a New Trinuclear Gd Complex with the Unsymmetrical Ligand H3L As a Model for Nucleases. Inorg Chem 2010; 49:3057-63. [DOI: 10.1021/ic100276z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Maryene A. Camargo
- Laboratório de Bioinorgânica e Crystalografia (LABINC), Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Ademir Neves
- Laboratório de Bioinorgânica e Crystalografia (LABINC), Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Bruno Szpoganicz
- Laboratório de Bioinorgânica e Crystalografia (LABINC), Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Adailton J. Bortoluzzi
- Laboratório de Bioinorgânica e Crystalografia (LABINC), Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Franciele L. Fischer
- Laboratório de Expressão Gênica, Departamento de Bioquímica, CCB, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Hernán Terenzi
- Laboratório de Expressão Gênica, Departamento de Bioquímica, CCB, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Eduardo E. Castellano
- Instituto de Física, Universidade de São Paulo,13560-970 São Carlos, São Paulo, Brazil
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Liu CT, Neverov AA, Brown RS. A Reductionist Biomimetic Model System That Demonstrates Highly Effective Zn(II)-Catalyzed Cleavage of an RNA Model. Inorg Chem 2007; 46:1778-88. [PMID: 17256929 DOI: 10.1021/ic062065u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cyclization of the RNA model 2-hydroxypropyl p-nitrophenyl phosphate (HPNPP, 1) promoted by Zn2+ alone and the 1,5,9-triazacyclododecane complex of Zn2+ (Zn2+:[12]aneN3) is studied in ethanol in the presence of 0.5 equiv of -OEt/Zn2+ to investigate the effect of a low polarity/dielectric medium on a metal-catalyzed reaction of biological relevance. Ethanol exerts a medium effect that promotes strong binding of HPNPP to Zn2+, followed by a dimerization to form a catalytically active complex (HPNPP:Zn2+)2 in which the phosphate undergoes cyclization with a rate constant of kcat = 2.9 s(-1) at s(s)pH 7.1. In the presence of the triaza ligand:Zn2+ complex, the change from water to methanol and then to ethanol brings about a mechanism where two molecules of the complex, suggested as EtOH:Zn2+:[12]aneN3 and its basic form, EtO-:Zn2+:[12]aneN3, bind to HPNPP and catalyze its decomposition with a rate constant of kcat of 0.13 s(-1) at s(s)pH 7.1. Overall, the acceleration exhibited in these two situations is 4 x 10(14)-fold and 1.7 x 10(12)-fold relative to the background ethoxide-promoted reactions at the respective s(s)pH values. The implications of these findings are discussed within the context of the idea that enzymatic catalysis is enhanced by a reduced effective dielectric constant within the active site.
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Affiliation(s)
- C Tony Liu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada
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Cyclen based lanthanide ion ribonuclease mimics: the effect of pyridine cofactors upon phosphodiester HPNP hydrolysis. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.03.150] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Bifunctional catalysis of ester hydrolysis: novel hydrolytic enzyme models based on xanthene framework. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcata.2004.06.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Gunnlaugsson T, Nieuwenhuyzen M, Nolan C. Synthesis, X-ray crystallographic, spectroscopic investigation and cleavage studies of HPNP by simple bispyridyl iron, copper, cobalt, nickel and zinc complexes as artificial nucleases. Polyhedron 2003. [DOI: 10.1016/s0277-5387(03)00471-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Synthesis, structural and biological evaluation of GlyAla based lanthanide macrocyclic conjugates as supramolecular ribonuclease mimics. Polyhedron 2003. [DOI: 10.1016/s0277-5387(02)01402-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Tsang JSW, Neverov AA, Brown RS. La(3+)-Catalyzed methanolysis of hydroxypropyl-p-nitrophenyl phosphate as a model for the RNA transesterification reaction. J Am Chem Soc 2003; 125:1559-66. [PMID: 12568616 DOI: 10.1021/ja021176z] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The methanolysis of hydroxypropyl-p-nitrophenyl phosphate (HPNPP, 1) promoted by La(OTf)(3) under buffered conditions was studied in methanol as a function of pH at 25 degrees C. (31)P NMR studies at -90 degrees C indicate that there are at least three La/1 complexes formed at pH approximately 5.3 of 1:1, 2:2, and 1:2 stoichiometry. Kinetic studies of the observed pseudo-first-order rate constants for the methanolysis of 1 as a function of [La(3+)] at 4.5 < pH < 10.5 indicate there are two general pH regimes. In the low pH regime between 4.5 and 7.6, the plots of k(obs) versus [La(3+)] exhibit saturation behavior with very strong 1:1 binding, with a plateau rate constant that depends on [OCH(3)(-)]. The catalytically productive species is shown to be a 2:2 complex of La(3+) and 1, where the phosphate is proposed to be doubly activated, thereby promoting the methoxide reaction by some 4.6 x 10(10)-fold. In the high pH regime from 7.9 to 10.5, 1:1, 2:2, and 2:1 La(3+)/1 complexes are formed with the La(3+) coordinated in the form of [La(3+)(OCH(3)(-))](1,2). Throughout this pH regime at high [La(3+)], a saturation complex, (La(3+)OCH(3)(-))(2)/1, is formed that spontaneously decomposes with a rate constant of (5-10) x 10(-)(3) s(-)(1), leading to an acceleration of 10(9)-fold at pH 8.0.
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Affiliation(s)
- Josephine S W Tsang
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada, K7L 3N6
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Gunnlaugsson T, O'Brien JE, Mulready S. Glycine–alanine conjugated macrocyclic lanthanide ion complexes as artificial ribonucleases. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)02071-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Lanthanide ions are remarkably effective catalysts for the hydrolytic cleavage of phosphate ester bonds, including the robust bonds of DNA. This makes Ln(III) and Ce(IV) ions attractive candidates for developing selective and efficient artificial nucleases, which could have many biochemical and clinical applications. Both small-molecule-based and biopolymer-based lanthanide complexes are being pursued.
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Affiliation(s)
- S J Franklin
- Department of Chemistry, University of Iowa, Iowa City 52242, USA.
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Nihan Aka F, Akkaya MS, Akkaya EU. Remarkable cooperative action of two zinc centers in the hydrolysis of plasmid DNA. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1381-1169(00)00369-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Tastan P, Akkaya EU. A novel cyclodextrin homodimer with dual-mode substrate binding and esterase activity. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1169(00)00159-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Baykal U, Akkaya MS, Akkaya EU. Remarkable phosphodiester hydrolysis activity of a novel CeIV complex in neutral aqueous solutions. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1381-1169(99)00160-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Molenveld P, Engbersen JFJ, Reinhoudt DN. Dinuclear Bisimidazolyl-Cu(II) Calix[4]arenes as Metalloenzyme Models. Synthesis and Bifunctional Catalysis in Phosphate Diester Transesterification. J Org Chem 1999. [DOI: 10.1021/jo9905266] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Molenveld
- Laboratory of Supramolecular Chemistry and Technology, MESA+ Research Institute University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Johan F. J. Engbersen
- Laboratory of Supramolecular Chemistry and Technology, MESA+ Research Institute University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - David N. Reinhoudt
- Laboratory of Supramolecular Chemistry and Technology, MESA+ Research Institute University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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Berg T, Simeonov A, Janda KD. A combined parallel synthesis and screening of macrocyclic lanthanide complexes for the cleavage of phospho di- and triesters and double-stranded DNA. JOURNAL OF COMBINATORIAL CHEMISTRY 1999; 1:96-100. [PMID: 10746017 DOI: 10.1021/cc9800125] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A parallel synthesis of macrocyclic lanthanide-ligand complexes 4Ln has been developed in conjunction with a parallel screening of these ligands for catalysis of phosphate ester hydrolysis. Complexes 4Ln were screened on a 96-well plate reader for their ability to catalyze the hydrolysis of a variety of phosphate esters efficiently. The hydrolysis of bis(4-nitrophenyl) phosphate (BNPP) 5 and p-nitrophenylethyl phosphate 6 was accelerated by up to 150-fold in the presence of the complex 4cGd. The cleavage of a double-stranded DNA plasmid with this same complex obeyed saturation kinetics following a Michaelian model (K(m) = 7.4 microM, kcat = 4.5 x 10(-3) min-1). Our findings demonstrate how a combination of parallel synthesis and screening can expedite compound access, accelerate catalyst identification, and thereby dramatically increase the speed of finding good ligand-metal combinations.
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Affiliation(s)
- T Berg
- Scripps Research Institute, Department of Chemistry, La Jolla, California, USA
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