1
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Putnam WC, Bashkin JK. Oligonucleotides containing abasic threoninol-terpyridine residues as potential artificial ribonucleases. J Inorg Biochem 2022; 232:111831. [DOI: 10.1016/j.jinorgbio.2022.111831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/24/2022]
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2
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Czescik J, Mancin F, Strömberg R, Scrimin P. The Mechanism of Cleavage of RNA Phosphodiesters by a Gold Nanoparticle Nanozyme. Chemistry 2021; 27:8143-8148. [PMID: 33780067 PMCID: PMC8251847 DOI: 10.1002/chem.202100299] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 01/08/2023]
Abstract
The cleavage of uridine 3'-phosphodiesters bearing alcohols with pKa ranging from 7.14 to 14.5 catalyzed by AuNPs functionalized with 1,4,7-triazacyclononane-Zn(II) complexes has been studied to unravel the source of catalysis by these nanosystems (nanozymes). The results have been compared with those obtained with two Zn(II) dinuclear catalysts for which the mechanism is fairly understood. Binding to the Zn(II) ions by the substrate and the uracil of uridine was observed. The latter leads to inhibition of the process and formation of less productive binding complexes than in the absence of the nucleobase. The nanozyme operates with these substrates mostly via a nucleophilic mechanism with little stabilization of the pentacoordinated phosphorane and moderate assistance in leaving group departure. This is attributed to a decrease of binding strength of the substrate to the catalytic site in reaching the transition state due to an unfavorable binding mode with the uracil. The nanozyme favors substrates with better leaving groups than the less acidic ones.
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Affiliation(s)
- Joanna Czescik
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
- Current address: School of Life and Health SciencesAston UniversityB4 7ETBirminghamUK
| | - Fabrizio Mancin
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
| | | | - Paolo Scrimin
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
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3
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Nath BD, Takaishi K, Ema T. Macrocyclic multinuclear metal complexes acting as catalysts for organic synthesis. Catal Sci Technol 2020. [DOI: 10.1039/c9cy01894h] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent progress in homogeneous catalysis with macrocyclic multinuclear metal complexes (categories A–C) is overviewed.
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Affiliation(s)
- Bikash Dev Nath
- Division of Applied Chemistry
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama 700-8530
- Japan
| | - Kazuto Takaishi
- Division of Applied Chemistry
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama 700-8530
- Japan
| | - Tadashi Ema
- Division of Applied Chemistry
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama 700-8530
- Japan
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4
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Diez-Castellnou M, Salassa G, Mancin F, Scrimin P. The Zn(II)-1,4,7-Trimethyl-1,4,7-Triazacyclononane Complex: A Monometallic Catalyst Active in Two Protonation States. Front Chem 2019; 7:469. [PMID: 31334218 PMCID: PMC6616306 DOI: 10.3389/fchem.2019.00469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 06/19/2019] [Indexed: 11/13/2022] Open
Abstract
In this paper, the unusual reactivity of the complex Zn(II)-1,4,7-trimethyl-1, 4,7-triazacyclononane (2) in the transesterification of the RNA-model substrate, HPNP (3), is reported. The dependence of the reactivity (k2) with pH does not follow the characteristic bell-shape profile typical of complexes with penta-coordinated metal centers. By the contrary, two reactive species, featuring different deprotonation states, are present, with the tri-aqua complex being more reactive than the mono-hydroxy-diaqua one. Apparently, such a difference arises from the total complex charge which plays an important role in the stability of the transition state/s of the reactions. Relevant insight on the reaction mechanism were hence obtained.
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Affiliation(s)
| | - Giovanni Salassa
- Département de Chimie Physique, Université de Genève, Genève, Switzerland
| | - Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, Padova, Italy
| | - Paolo Scrimin
- Dipartimento di Scienze Chimiche, Università di Padova, Padova, Italy
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5
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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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6
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Bencze ES, Zonta C, Mancin F, Prins LJ, Scrimin P. Distance between Metal Centres Affects Catalytic Efficiency of Dinuclear CoIII
Complexes in the Hydrolysis of a Phosphate Diester. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Eva Szusanna Bencze
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
| | - Cristiano Zonta
- 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
| | - Leonard J. Prins
- 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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7
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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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8
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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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9
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Harris ME, York DM, Piccirilli JA, Anderson VE. Kinetic Isotope Effect Analysis of RNA 2′- O -Transphosphorylation. Methods Enzymol 2017; 596:433-457. [DOI: 10.1016/bs.mie.2017.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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10
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Zhang S, Gu H, Chen H, Strong E, Ollie EW, Kellerman D, Liang D, Miyagi M, Anderson VE, Piccirilli JA, York DM, Harris ME. Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2+). Chem Commun (Camb) 2016; 52:4462-5. [PMID: 26859380 DOI: 10.1039/c5cc10212j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Solvent D2O and (18)O kinetic isotope effects on RNA 2'-O-transphosphorylation catalyzed by Zn(2+) demonstrate an altered transition state relative to specific base catalysis. A recent model from DFT calculations involving inner sphere coordination to the non-bridging and leaving group oxygens is consistent with the data.
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Affiliation(s)
- Shuming Zhang
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Hong Gu
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Haoyuan Chen
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University Piscataway, NJ 08854, USA
| | - Emily Strong
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Edward W Ollie
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Daniel Kellerman
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Danni Liang
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vernon E Anderson
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University Piscataway, NJ 08854, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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11
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Laine M, Lönnberg T, Helkearo M, Lönnberg H. Cleavage of short oligoribonucleotides by a Zn2+ binding multi-nucleating azacrown conjugate. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2015.12.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Bím D, Svobodová E, Eigner V, Rulíšek L, Hodačová J. Copper(II) and Zinc(II) Complexes of Conformationally Constrained Polyazamacrocycles as Efficient Catalysts for RNA Model Substrate Cleavage in Aqueous Solution at Physiological pH. Chemistry 2016; 22:10426-37. [DOI: 10.1002/chem.201601175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Daniel Bím
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
- Institute of Organic Chemistry and Biochemistry; v.v.i. and Gilead Sciences Research Center, Academy of Sciences of the Czech Republic; Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Eva Svobodová
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
| | - Václav Eigner
- Department of Solid State Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry; v.v.i. and Gilead Sciences Research Center, Academy of Sciences of the Czech Republic; Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Jana Hodačová
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
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13
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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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14
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Hussain N, Joshi P, Ali SR, Bhardwaj VK. Comparative structure activity relationship for heterogeneous phosphatase-like catalytic activities of one-dimensional Cu(ii) coordination polymers. RSC Adv 2016. [DOI: 10.1039/c6ra11102e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A structure activity relationship for heterogeneous phosphatase-like activities of one-dimensional Cu(ii) coordination polymers, has been studied. Complex 1 exhibits maximum activity due to coordinated water molecules, shorter metal–metal distance and exposed metal centers.
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Affiliation(s)
- Navid Hussain
- Department of Chemistry
- Indian Institute of Technology Ropar
- Rupnagar
- India
| | - Pooja Joshi
- Department of Chemistry
- D.S.B. Campus
- Kumaun University
- Nainital
- India
| | - Shah Raj Ali
- Department of Chemistry
- D.S.B. Campus
- Kumaun University
- Nainital
- India
| | - Vimal K. Bhardwaj
- Department of Chemistry
- Indian Institute of Technology Ropar
- Rupnagar
- India
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15
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Salvio R, Moliterno M, Caramelli D, Pisciottani L, Antenucci A, D'Amico M, Bella M. Kinetic resolution of phosphoric diester by Cinchona alkaloid derivatives provided with a guanidinium unit. Catal Sci Technol 2016. [DOI: 10.1039/c5cy01208b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cinchona alkaloid derivatives featuring a guanidinium group in diverse positions efficiently catalyze the cleavage of the RNA model compound 2-hydroxypropyl p-nitrophenyl phosphate (HPNP).
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Chimica
- Università di Roma – Sapienza
- Italy
- IMC-CNR Sezione Meccanismi di Reazione
- Università di Roma – Sapienza
| | | | | | | | | | | | - Marco Bella
- Dipartimento di Chimica
- Università di Roma – Sapienza
- Italy
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16
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Dano M, Elmeranta M, Hodgson DRW, Jaakkola J, Korhonen H, Mikkola S. Metal ion-promoted cleavage of nucleoside diphosphosugars: a model for reactions of phosphodiester bonds in carbohydrates. J Biol Inorg Chem 2015; 20:1299-306. [DOI: 10.1007/s00775-015-1308-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/23/2015] [Indexed: 11/21/2022]
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17
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Salvio R, Volpi S, Cacciapaglia R, Casnati A, Mandolini L, Sansone F. Ribonuclease Activity of an Artificial Catalyst That Combines a Ligated CuII Ion and a Guanidinium Group at the Upper Rim of a cone-Calix[4]arene Platform. J Org Chem 2015; 80:5887-93. [DOI: 10.1021/acs.joc.5b00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Riccardo Salvio
- Dipartimento
di Chimica and IMC−CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185 Roma, Italy
| | - Stefano Volpi
- Dipartimento
di Chimica, Università degli Studi di Parma, Viale delle
Scienze 17/A, 43124 Parma, Italy
| | - Roberta Cacciapaglia
- Dipartimento
di Chimica and IMC−CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185 Roma, Italy
| | - Alessandro Casnati
- Dipartimento
di Chimica, Università degli Studi di Parma, Viale delle
Scienze 17/A, 43124 Parma, Italy
| | - Luigi Mandolini
- Dipartimento
di Chimica and IMC−CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185 Roma, Italy
| | - Francesco Sansone
- Dipartimento
di Chimica, Università degli Studi di Parma, Viale delle
Scienze 17/A, 43124 Parma, Italy
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18
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Brown RS. Metal Ion-Promoted Leaving Group Assistance in the Light Alcohols. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2015. [DOI: 10.1016/bs.apoc.2015.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Zhang X, Zhu Y, Gao H, Zhao C. Solvolysis Mechanisms of RNA Phosphodiester Analogues Promoted by Mononuclear Zinc(II) Complexes: Mechanisic Determination upon Solvent Medium and Ligand Effects. Inorg Chem 2014; 53:11903-12. [DOI: 10.1021/ic501084a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- 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
| | - Yajie Zhu
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Hui Gao
- Key
Laboratory of Renewable Energy and Gas Hydrate, Guangzhou Institute
of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, P. R. China
| | - 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
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20
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Bhardwaj VK, Singh A. Comparative DNA Binding Abilities and Phosphatase-Like Activities of Mono-, Di-, and Trinuclear Ni(II) Complexes: The Influence of Ligand Denticity, Metal–Metal Distance, and Coordinating Solvent/Anion on Kinetics Studies. Inorg Chem 2014; 53:10731-42. [DOI: 10.1021/ic501961d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Vimal K. Bhardwaj
- Department
of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Ajnesh Singh
- Department of Applied Science and Humanities, Jawaharlal Nehru Government Engineering College, Sundernagar, Mandi, Himachal Pradesh 175010, India
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21
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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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22
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Kellerman DL, York DM, Piccirilli JA, Harris ME. Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation. Curr Opin Chem Biol 2014; 21:96-102. [PMID: 25023967 DOI: 10.1016/j.cbpa.2014.06.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 10/25/2022]
Abstract
Although there have been great strides in defining the mechanisms of RNA strand cleavage by 2'-O-transphosphorylation, long-standing questions remain. How do different catalytic modes such as acid/base and metal ion catalysis influence transition state charge distribution? Does the large rate enhancement characteristic of biological catalysis result in different transition states relative to solution reactions? Answering these questions is important for understanding biological catalysis in general, and revealing principles for designing small molecule inhibitors. Recent application of linear free energy relationships and kinetic isotope effects together with multi-scale computational simulations are providing tentative answers to these questions for this fundamentally important class of phosphoryl transfer reactions.
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Affiliation(s)
- Daniel L Kellerman
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Darrin M York
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, NJ, United States
| | - Joseph A Piccirilli
- Department of Biochemistry & Molecular Biology, and Chemistry, University of Chicago, Chicago, IL, United States
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States.
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