1
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Czescik J, Lyu Y, Neuberg S, Scrimin P, Mancin F. Host-Guest Allosteric Control of an Artificial Phosphatase. J Am Chem Soc 2020; 142:6837-6841. [PMID: 32212681 PMCID: PMC7997383 DOI: 10.1021/jacs.9b12699] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
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The
activity of many enzymes is regulated by associative processes.
To model this mechanism, we report here that the conformation of an
unstructured bimetallic Zn(II) complex can be controlled by its inclusion
in the cavity of a γ-cyclodextrin. This results in the formation
of a catalytic bimetallic site for the hydrolytic cleavage of the
RNA model substrate HPNP, whose reactivity is 30-fold larger with
respect to the unstructured complex. Competitive inhibition with 1-adamantanecarboxylate
displaces the metal complex from the cyclodextrin decreasing the reactivity.
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Affiliation(s)
- Joanna Czescik
- Università di Padova, Dipartimento di Scienze Chimiche, via Marzolo 1, 35131 Padova, Italy
| | - Yanchao Lyu
- Università di Padova, Dipartimento di Scienze Chimiche, via Marzolo 1, 35131 Padova, Italy
| | - Samuele Neuberg
- Università di Padova, Dipartimento di Scienze Chimiche, via Marzolo 1, 35131 Padova, Italy
| | - Paolo Scrimin
- Università di Padova, Dipartimento di Scienze Chimiche, via Marzolo 1, 35131 Padova, Italy
| | - Fabrizio Mancin
- Università di Padova, Dipartimento di Scienze Chimiche, via Marzolo 1, 35131 Padova, Italy
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2
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Guanidine- and purine-functionalized ligands of FeIIIZnII complexes: effects on the hydrolysis of DNA. J Biol Inorg Chem 2019; 24:675-691. [DOI: 10.1007/s00775-019-01680-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/21/2019] [Indexed: 01/01/2023]
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3
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Erxleben A. Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned? Front Chem 2019; 7:82. [PMID: 30847339 PMCID: PMC6393734 DOI: 10.3389/fchem.2019.00082] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.
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Affiliation(s)
- Andrea Erxleben
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
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4
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Mikkola S, Lönnberg T, Lönnberg H. Phosphodiester models for cleavage of nucleic acids. Beilstein J Org Chem 2018; 14:803-837. [PMID: 29719577 PMCID: PMC5905247 DOI: 10.3762/bjoc.14.68] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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5
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Synthesis and Properties of Salicylaldehydes Fine-Tuned by Modular Assembly using “Plug-and-Socket”-Type Extendibility. Chemistry 2017; 23:8286-8294. [DOI: 10.1002/chem.201701141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Indexed: 11/07/2022]
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6
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Barman SK, Mondal T, Koley D, Lloret F, Mukherjee R. A phenoxo-bridged dicopper(ii) complex as a model for phosphatase activity: mechanistic insights from a combined experimental and computational study. Dalton Trans 2017; 46:4038-4054. [PMID: 28271106 DOI: 10.1039/c6dt03514k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A μ-phenoxo-bis(μ2-1,3-acetato)-bridged dicopper(ii) complex [Cu(L1)(μ-O2CMe)2][NO3] (1) has been synthesized from the perspective of modeling phosphodiesterase activity. Structural characterization was done initially with 1·3Et2O (vapour diffusion of Et2O into MeOH solution of 1; poor crystal quality) and finally with its perchlorate salt [Cu(L1)(μ-O2CMe)2][ClO4]·1.375MeCN·0.25H2O, crystallized from vapour diffusion of n-pentane into a MeCN-MeOH mixture (comparatively better crystal quality). An asymmetric unit of such a crystal contains two independent molecules of compositions [Cu(L1)(μ-O2CMe)2][ClO4] and [Cu(L1)(μ-O2CMe)2(MeCN)][ClO4] (coordinated MeCN with 0.75 occupancy), and two molecules of MeCN and H2O (each H2O molecule with 0.25 occupancy) as the solvent of crystallization. These two cations, each having five-coordinate (μ-phenoxo)bis(μ-acetato)-bridged CuII ions, differ by only the coordination environment of only one CuII ion, which has a weakly coordinated acetonitrile molecule in its sixth position. Temperature-dependent magnetic studies on 1 reveal that the copper(ii) centres are antiferromagnetically coupled with the exchange-coupling constant J = -124(1) cm-1. Theoretically calculated J = -126.51 cm-1, employing a broken-symmetry DFT approach, is in excellent agreement with the experimental value. The dicopper(ii) complex has been found to be catalytically efficient in the hydrolysis of 2-hydroxypropyl-p-nitrophenylphosphate (HPNP). Detailed kinetic experiments and solution studies (potentiometry, species distribution and ESI-MS) were performed to elucidate the reaction mechanism. DFT calculations were performed to discriminate between different possible mechanistic pathways. The free-energy barrier for HPNP hydrolysis catalyzed by 1 is comparable to that obtained from the experimentally-determined value. The involvement of non-covalent (hydrogen-bonding) interaction has also been probed by DFT calculations. The activity of 1 is found to be the highest, compared to the structurally-characterized Mn, Co, Ni and Zn complexes of L1(-) reported earlier, under identical experimental conditions, in which each metal centre is six-coordinate.
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Affiliation(s)
- Suman K Barman
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India. and Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246, India
| | - Totan Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246, India
| | - Debasis Koley
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246, India
| | - Francesc Lloret
- Departament de Química Inorgànica/Fundació General de la Universitat de València (FGUV)/Instituto de Ciencia, Molecular (ICMOL), Universitat de València, Polígono de la Coma, s/n, 46980-Paterna, València, Spain
| | - Rabindranath Mukherjee
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India. and Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246, India
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7
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Diez-Castellnou M, Martinez A, Mancin F. Phosphate Ester Hydrolysis: The Path From Mechanistic Investigation to the Realization of Artificial Enzymes. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Wu AZ, Chen L, Wang T. Phosphodiester Cleavage Promoted by an Asymmetric Dinuclear Zinc Complex: Synthesis, Structure, and Catalytic Activity. Z Anorg Allg Chem 2015. [DOI: 10.1002/zaac.201500196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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9
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Sanyal R, Zhang X, Kundu P, Chattopadhyay T, Zhao C, Mautner FA, Das D. Mechanistic Implications in the Phosphatase Activity of Mannich-Based Dinuclear Zinc Complexes with Theoretical Modeling. Inorg Chem 2015; 54:2315-24. [DOI: 10.1021/ic502937a] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ria Sanyal
- Department
of Chemistry, University of Calcutta, 92 A.P.C. Road, Kolkata 700009, India
| | - Xuepeng Zhang
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Priyanka Kundu
- Department
of Chemistry, University of Calcutta, 92 A.P.C. Road, Kolkata 700009, India
| | - Tanmay Chattopadhyay
- Department
of Chemistry, Panchakot Mahavidyalaya, Sarbari, Purulia 723121, India
| | - Cunyuan Zhao
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Franz A. Mautner
- Institut
fuer Physikalische und Theoretische Chemie, Technische Universitaet Graz, A-8010 Graz, Austria
| | - Debasis Das
- Department
of Chemistry, University of Calcutta, 92 A.P.C. Road, Kolkata 700009, India
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10
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The effect of chain size on the modeling of second sphere effects in biomimetic complexes. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcata.2014.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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11
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Zhang X, Zheng X, Phillips DL, Zhao C. Mechanistic investigation of the cleavage of phosphodiester catalyzed by a symmetrical oxyimine-based macrocyclic dinuclear zinc complex: a DFT study. Dalton Trans 2014; 43:16289-99. [DOI: 10.1039/c4dt01491j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Zhang X, Zhu Y, Zheng X, Phillips DL, Zhao C. Mechanismic Investigation on the Cleavage of Phosphate Monoester Catalyzed by Unsymmetrical Macrocyclic Dinuclear Complexes: The Selection of Metal Centers and the Intrinsic Flexibility of the Ligand. Inorg Chem 2014; 53:3354-61. [DOI: 10.1021/ic402717x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xuepeng Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI
of Environment and Energy Chemistry, School of Chemistry and Chemical
Engineering, Sun Yat-Sen University, Guangzhou 510275, People’s Republic of China
| | - Yajie Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI
of Environment and Energy Chemistry, School of Chemistry and Chemical
Engineering, Sun Yat-Sen University, Guangzhou 510275, People’s Republic of China
| | - Xiaowei Zheng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI
of Environment and Energy Chemistry, School of Chemistry and Chemical
Engineering, Sun Yat-Sen University, Guangzhou 510275, People’s Republic of China
| | - David Lee Phillips
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People’s Republic of China
| | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI
of Environment and Energy Chemistry, School of Chemistry and Chemical
Engineering, Sun Yat-Sen University, Guangzhou 510275, People’s Republic of China
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13
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Das B, Daver H, Pyrkosz-Bulska M, Persch E, Barman SK, Mukherjee R, Gumienna-Kontecka E, Jarenmark M, Himo F, Nordlander E. A dinuclear zinc(II) complex of a new unsymmetric ligand with an N(5)O(2) donor set: a structural and functional model for the active site of zinc phosphoesterases. J Inorg Biochem 2014; 132:6-17. [PMID: 24001510 DOI: 10.1016/j.jinorgbio.2013.08.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 08/01/2013] [Accepted: 08/01/2013] [Indexed: 02/03/2023]
Abstract
The dinuclear complex [Zn(2)(DPCPMP)(pivalate)](ClO4), where DPCPMP is the new unsymmetrical ligand [2-(N-(3-((bis((pyridin-2-yl)methyl)amino)methyl)-2-hydroxy-5-methylbenzyl)-N-((pyridin-2-yl)methyl)amino)acetic acid], has been synthesized and characterized. The complex is a functional model for zinc phosphoesterases with dinuclear active sites. The hydrolytic efficacy of the complex has been investigated using bis-(2,4-dinitrophenyl)phosphate (BDNPP), a DNA analog, as substrate. Speciation studies using potentiometric titrations have been performed for both the ligand and the corresponding dizinc complex to elucidate the formation of the active hydrolysis catalyst; they reveals that the dinuclear zinc(II) complexes, [Zn(2)(DPCPMP)](2+) and [Zn(2)(DPCPMP)(OH)](+) predominate the solution above pH4. The relatively high pK(a) of 8.38 for water deprotonation suggests that a terminal hydroxide complex is formed. Kinetic investigations of BDNPP hydrolysis over the pH range 5.5-11.0 and with varying metal to ligand ratio (metal salt:ligand=0.5:1 to 3:1) have been performed. Variable temperature studies gave the activation parameters ΔH(‡)=95.6kJmol(-1), ΔS(‡)=-44.8Jmol(-1)K(-1), and ΔG(‡)=108.0 kJmol(-1). The cumulative results indicate the hydroxido-bridged dinuclear Zn(II) complex [Zn(2)(DPCPMP)(μ-OH)](+) as the effective catalyst. The mechanism of hydrolysis has been probed by computational modeling using density functional theory (DFT). Calculations show that the reaction goes through one concerted step (S(N)2 type) in which the bridging hydroxide in the transition state becomes terminal and performs a nucleophilic attack on the BDNPP phosphorus; the leaving group dissociates simultaneously in an overall inner sphere type activation. The calculated free energy barrier is in good agreement with the experimentally determined activation parameters.
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Affiliation(s)
- Biswanath Das
- Inorganic Chemistry Research Group, Chemical Physics, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Henrik Daver
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Monika Pyrkosz-Bulska
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie Street 14, 50-383 Wroclaw, Poland
| | - Elke Persch
- Inorganic Chemistry Research Group, Chemical Physics, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Suman K Barman
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India
| | | | | | - Martin Jarenmark
- Inorganic Chemistry Research Group, Chemical Physics, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ebbe Nordlander
- Inorganic Chemistry Research Group, Chemical Physics, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100 Lund, Sweden.
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14
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Diez-Castellnou M, Mancin F, Scrimin P. Efficient Phosphodiester Cleaving Nanozymes Resulting from Multivalency and Local Medium Polarity Control. J Am Chem Soc 2014; 136:1158-61. [DOI: 10.1021/ja411969e] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Marta Diez-Castellnou
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Paolo Scrimin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
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15
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Maxwell CI, Mosey NJ, Stan Brown R. DFT Computational Study of the Methanolytic Cleavage of DNA and RNA Phosphodiester Models Promoted by the Dinuclear Zn(II) Complex of 1,3-Bis(1,5,9-triazacyclododec-1-yl)propane. J Am Chem Soc 2013; 135:17209-22. [DOI: 10.1021/ja4088264] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Nicholas J. Mosey
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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16
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Um IH, Song YJ, Kim MY, Lee JI. Metal-Ion Catalysis in Alkaline Ethanolysis of 2-Pyridyl Thionobenzoate: Effects of Modification of Electrophilic Center from C=O to C=S. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.5.1525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Song Y, Zan J, Yan H, Lu ZL, Wang R. Steric effects on the catalytic activities of zinc(II) complexes containing [12]aneN3 ligating units in the cleavage of the RNA and DNA model phosphates. Org Biomol Chem 2013; 10:7714-20. [PMID: 22699360 DOI: 10.1039/c2ob25624j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A series of N-methylated mono- and di-[12]aneN(3) ligands () have been synthesized and characterized. The steric effects on the catalytic activities of their mononuclear and dinuclear zinc(ii) complexes in the cleavage of a RNA model 2-hydroxypropyl 4-nitrophenyl phosphate (HPNPP, ) and a DNA model methyl 4-nitrophenyl phosphates (MPNPP, 4) in methanol have been investigated at 25 °C. In the cleavage of phosphate catalyzed by the mononuclear complexes, derived from the N-methylation in the [12]aneN(3) backbone, the plots of k(obs)versus [Zn(II)] changed from an upward curvature to linearity with increasing level of methylation, indicating that N-methylations led to a reduction of dinuclear association that was responsible for the synergetic effect. Compared to the activities of the complex with non-methylated di-[12]aneN(3) ligand, those of the dinuclear zinc(ii) complex (Zn(2)-8), which has the two N-methyl groups, were reduced by two orders of magnitude as measured by the second-order rate constants and synergetic effect in the cleavage of both model compounds. For reactions catalyzed by the fully N-methylated dinuclear complex (Zn(2)-9), no synergetic effect was observed. Nevertheless, complex Zn(2)-8 still showed the remarkable catalytic efficiency, with rate accelerations of 10(9-10)-fold in the cleavage of each of the two phosphates relative to the background reactions, and the synergetic effects of up to 561 folds. pH jump experiments confirmed that the rate-limiting step in the cleavage of by Zn(2)-8 involved the binding process, while that in the reaction with 4 was the chemical cleavage of the P-O bond. Steric effects in the cleavage reactions were analyzed in detail and were compared with the electronic effect caused by oxy anion bridging group in the di-[12]aneN(3) ligand and also with the hydrophobic effect observed in other systems. The work has further confirmed that the combination of the cooperativity between two metal ions and a medium effect could result in excellent catalytic activities for the cleavage of phosphate diesters.
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Affiliation(s)
- Yang Song
- College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19, Beijing, 100875, China
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18
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Korhonen H, Koivusalo T, Toivola S, Mikkola S. There is no universal mechanism for the cleavage of RNA model compounds in the presence of metal ion catalysts. Org Biomol Chem 2013; 11:8324-39. [DOI: 10.1039/c3ob41554f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Um IH, Kang JS, Shin YH, Buncel E. A kinetic study on nucleophilic displacement reactions of aryl benzenesulfonates with potassium ethoxide: role of K+ ion and reaction mechanism deduced from analyses of LFERs and activation parameters. J Org Chem 2012; 78:490-7. [PMID: 23215678 DOI: 10.1021/jo302373y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudofirst-order rate constants (k(obsd)) have been measured spectrophotometrically for the nucleophilic substitution reactions of 2,4-dinitrophenyl X-substituted benzenesulfonates 4a-f and Y-substituted phenyl benzenesulfonates 5a-k with EtOK in anhydrous ethanol. Dissection of k(obsd) into k(EtO(-)) and k(EtOK) (i.e., the second-order rate constants for the reactions with the dissociated EtO(-) and ion-paired EtOK, respectively) shows that the ion-paired EtOK is more reactive than the dissociated EtO(-), indicating that K(+) ion catalyzes the reaction. The catalytic effect exerted by K(+) ion (e.g., the k(EtOK)/k(EtO(-)) ratio) decreases linearly as the substituent X in the benzenesulfonyl moiety changes from an electron-donating group (EDG) to an electron-withdrawing group (EWG), but it is independent of the electronic nature of the substituent Y in the leaving group. The reactions have been concluded to proceed through a concerted mechanism from analyses of the kinetic data through linear free energy relationships (e.g., the Brønsted-type, Hammett, and Yukawa-Tsuno plots). K(+) ion catalyzes the reactions by increasing the electrophilicity of the reaction center through a cyclic transition state (TS) rather than by increasing the nucleofugality of the leaving group. Activation parameters (e.g., ΔH(‡) and ΔS(‡)) determined from the reactions performed at five different temperatures further support the proposed mechanism and TS structures.
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Affiliation(s)
- Ik-Hwan Um
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea.
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20
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Um IH, Seo JY, Kang JS, An JS. A Kinetic Study on Nucleophilic Displacement Reactions of Phenyl Y-Substituted-Phenyl Carbonates with Alkali Metal Ethoxides: Metal Ion Effect and Reaction Mechanism. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20120104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ik-Hwan Um
- Department of Chemistry and Nano Science, Ewha Womans University
| | - Ji-Yoon Seo
- Department of Chemistry and Nano Science, Ewha Womans University
| | - Ji-Sun Kang
- Department of Chemistry and Nano Science, Ewha Womans University
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21
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Grünwald KR, Volpe M, Mösch-Zanetti NC. Phenolate-bridged zinc(II) complexes relevant to biological phosphoester cleavage. J COORD CHEM 2012. [DOI: 10.1080/00958972.2012.688117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Katrin R. Grünwald
- a Institute of Chemistry, Karl-Franzens-University Graz , Stremayrgasse 16 , A-8010 Graz , Austria
| | - Manuel Volpe
- a Institute of Chemistry, Karl-Franzens-University Graz , Stremayrgasse 16 , A-8010 Graz , Austria
| | - Nadia C. Mösch-Zanetti
- a Institute of Chemistry, Karl-Franzens-University Graz , Stremayrgasse 16 , A-8010 Graz , Austria
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Abstract
The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is still a fascinating challenge. Over the years, many examples have been reported reproducing part of the behaviour of the corresponding natural enzymes. Eventually, even the possibility to apply such systems to the manipulation of DNA of higher organisms has been demonstrated. However, efficiency of enzymes is still unrivalled. This feature article discusses the progress reported toward the realization of synthetic nucleases with particular attention to the comprehension of the reaction mechanisms and to the strategies that need to be addressed to obtain more efficient systems.
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Affiliation(s)
- Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, I -35131 Padova, Italy.
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Arora H, Barman SK, Lloret F, Mukherjee R. Isostructural Dinuclear Phenoxo-/Acetato-Bridged Manganese(II), Cobalt(II), and Zinc(II) Complexes with Labile Sites: Kinetics of Transesterification of 2-Hydroxypropyl-p-nitrophenylphosphate. Inorg Chem 2012; 51:5539-53. [DOI: 10.1021/ic201971t] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Himanshu Arora
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India
| | - Suman K. Barman
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India
| | - Francesc Lloret
- Departament de Quı́mica Inorgànica/Instituto de
Ciencia Molecular (ICMOL), Universitat de València, Polígono de la Coma, s/n, 46980-Paterna
(València), Spain
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24
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Korhonen H, Mikkola S, Williams NH. The mechanism of cleavage and isomerisation of RNA promoted by an efficient dinuclear Zn2+ complex. Chemistry 2011; 18:659-70. [PMID: 22162262 DOI: 10.1002/chem.201100721] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Indexed: 11/11/2022]
Abstract
The cleavage and isomerisation of uridine 3'-alkylphosphates was studied in the presence of a dinuclear Zn(2+) complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 10(6)-fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate-enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500-fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A β(lg) value of -0.92 was determined for the 3-promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of -0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3-promoted cleavage are very similar to those for the cleavage of nucleoside 3'-phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.
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Affiliation(s)
- Heidi Korhonen
- Department of Chemistry, 20014 University of Turku, Turku, Finland
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25
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Mohamed MF, Sánchez-Lombardo I, Neverov AA, Brown RS. Solvent induced cooperativity of Zn(II) complexes cleaving a phosphate diester RNA analog in methanol. Org Biomol Chem 2011; 10:631-9. [PMID: 22116167 DOI: 10.1039/c1ob06482g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The kinetics of cyclization of 2-hydroxypropyl p-nitrophenyl phosphate (1) promoted by two mononuclear Zn(II) catalytic complexes of bis(2-pyridylmethyl)benzylamine (4) and bis(2-methyl 6-pyridylmethyl)benzylamine (5) in methanol were studied under (s)(s)pH-controlled conditions (where (s)(s)pH refers to [H(+)] activity in methanol). Potentiometric titrations of the ligands in the absence and presence of Zn(2+) and a non-reactive model for 1 (2-hydroxylpropyl isopropyl phosphate (HPIPP, 6)) indicate that the phosphate is bound tightly to the 4:Zn(II) and 5:Zn(II) complexes as L:Zn(II):6(-), and that each of these undergoes an additional ionization to produce L:Zn(II):6(-):((-)OCH(3)) or a bound deprotonated form of the phosphate, L:Zn(II):6(2-). Kinetic studies as a function of [L:Zn(II)] indicate that the rate is linear in [L:Zn(II)] at concentrations well above those required for complete binding of the substrate. Plots of the second order rate constants (defined as the gradient of the rate constant vs. [complex] plot) vs. (s)(s)pH in methanol are bell-shaped with rate maxima of 23 dm mol(-1) s(-1) and 146 dm mol(-1) s(-1) for 4:Zn(II) and 5:Zn(II), respectively, at their (s)(s)pH maxima of 10.5 and 10. A mechanism is proposed that involves binding of one molecule of complex to the phosphate to yield a poorly reactive 1 : 1 complex, which associates with a second molecule of complex to produce a transient cooperative 2 : 1 complex within which the cyclization of 1 is rapid. The observations support an effect of the reduced polarity solvent that encourages the cooperative association of phosphate and two independent mononuclear complexes to give a reactive entity.
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Affiliation(s)
- Mark F Mohamed
- Department of Chemistry, Queen's University Kingston, Ontario, Canada K7L 3N6
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26
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27
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An JS, NamKoong G, Kang JS, Um IH. Alkali Metal Ion Catalysis and Inhibition in Nucleophilic Substitution Reactions of 3,4-Dinitrophenyl Diphenylphosphinothioate with Alkali Metal Ethoxides in Anhydrous Ethanol: Effect of Changing Electrophilic Center from P=O to P=S. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.7.2423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Choi SY, Hong YJ, Um IH. Metal Ion Catalysis and Inhibition in Nucleophilic Substitution Reactions of 4-Nitrophenyl Nicotinate and Isonicotinate with Alkali Metal Ethoxides in Anhydrous Ethanol. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.6.1951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Gao H, Ke Z, DeYonker NJ, Wang J, Xu H, Mao ZW, Phillips DL, Zhao C. Dinuclear Zn(II) Complex Catalyzed Phosphodiester Cleavage Proceeds via a Concerted Mechanism: A Density Functional Theory Study. J Am Chem Soc 2011; 133:2904-15. [DOI: 10.1021/ja106456u] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Hui Gao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Zhuofeng Ke
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Nathan J. DeYonker
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152-3550, United States
| | - Juping Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Huiying Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - David Lee Phillips
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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30
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Tang SP, Hu P, Chen HY, Chen S, Mao ZW, Ji LN. Carboxy and diphosphate ester hydrolysis promoted by di- or tri-nuclear zinc(II) complexes based on β-cyclodextrin. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcata.2010.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Lee JI, Kang JS, Im LR, Um IH. Metal Ion Catalysis in Nucleophilic Displacement Reactions of 2-Pyridyl X-Substituted Benzoates with Potassium Ethoxide in Anhydrous Ethanol. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.12.3543] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Mohamed MF, Brown RS. Cleavage of an RNA Model Catalyzed by Dinuclear Zn(II) Complexes Containing Rate-Accelerating Pendants. Comparison of the Catalytic Benefits of H-Bonding and Hydrophobic Substituents. J Org Chem 2010; 75:8471-7. [DOI: 10.1021/jo1017316] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Mark F. Mohamed
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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Lee JI, Kang JS, Kim SI, Um IH. Effect of Alkali Metal Ions on Alkaline Ethanolysis of 2-Pyridyl and 4-Pyridyl Benzoates in Anhydrous Ethanol. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.10.2929] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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34
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Hong YJ, Kim SI, Um IH. Metal Ion Catalysis in Nucleophilic Substitution Reaction of 4-Nitrophenyl Picolinate with Alkali Metal Ethoxides in Anhydrous Ethanol. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.9.2483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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