1
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Wang L, Jiang P, Liu W, Li J, Chen Z, Guo T. Molecularly imprinted self-buffering double network hydrogel containing bi-amidoxime functional groups for the rapid hydrolysis of organophosphates. JOURNAL OF HAZARDOUS MATERIALS 2023; 444:130332. [PMID: 36423451 DOI: 10.1016/j.jhazmat.2022.130332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/06/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
The development of high-performance catalyst materials with high catalytic activity for the hydrolysis of organophosphorus toxicants without additional pH buffer conditions has become an urgent need for practical application. Here, a multifunctional molecularly imprinted polymer double network hydrogel (MIP-DN) material has been prepared by integrating the first polymer network containing the functional group of bi-amidoxime as the catalytic active center and the cationic polymer polyethyleneimine (PEI) with pH buffer function as the main component of the second network. Advantageously, the resultant MIP-DN hydrogel showed excellent catalytic performance without additional pH buffer conditions, exhibiting a half-life of 25 min for the hydrolysis of paraoxon in pure water. Together with multi-functions of high catalytic activity, self-buffering function and excellent processability, the MIP-DN hydrogel prepared in this work provides a new strategy for the preparation of catalytic materials with practical application value toward toxic organophosphates.
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Affiliation(s)
- Lan Wang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Peng Jiang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Weijie Liu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiaqi Li
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhaoming Chen
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Tianying Guo
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
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2
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Anjomshoa M, Amirheidari B. Nuclease-like metalloscissors: Biomimetic candidates for cancer and bacterial and viral infections therapy. Coord Chem Rev 2022; 458:214417. [PMID: 35153301 PMCID: PMC8816526 DOI: 10.1016/j.ccr.2022.214417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/09/2022] [Indexed: 12/25/2022]
Abstract
Despite the extensive and rapid discovery of modern drugs for treatment of cancer, microbial infections, and viral illnesses; these diseases are still among major global health concerns. To take inspiration from natural nucleases and also the therapeutic potential of metallopeptide antibiotics such as the bleomycin family, artificial metallonucleases with the ability of promoting DNA/RNA cleavage and eventually affecting cellular biological processes can be introduced as a new class of therapeutic candidates. Metal complexes can be considered as one of the main categories of artificial metalloscissors, which can prompt nucleic acid strand scission. Accordingly, biologists, inorganic chemists, and medicinal inorganic chemists worldwide have been designing, synthesizing and evaluating the biological properties of metal complexes as artificial metalloscissors. In this review, we try to highlight the recent studies conducted on the nuclease-like metalloscissors and their potential therapeutic applications. Under the light of the concurrent Covid-19 pandemic, the human need for new therapeutics was highlighted much more than ever before. The nuclease-like metalloscissors with the potential of RNA cleavage of invading viral pathogens hence deserve prime attention.
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3
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Zheng S, Pan J, Wang J, Liu S, Zhou T, Wang L, Jia H, Chen Z, Peng Q, Guo T. Ag(I) Pyridine-Amidoxime Complex as the Catalysis Activity Domain for the Rapid Hydrolysis of Organothiophosphate-Based Nerve Agents: Mechanistic Evaluation and Application. ACS APPLIED MATERIALS & INTERFACES 2021; 13:34428-34437. [PMID: 34278774 DOI: 10.1021/acsami.1c09003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Two novel Ag(I) complexes containing synergistic pyridine and amidoxime ligands (Ag-DPAAO and Ag-PAAO) were first designed as complex monomers. Taking advantage of the molecular imprinting technique and solvothermal method, molecular imprinted porous cross-linked polymers (MIPCPs) were developed as a robust platform for the first time to incorporate Ag-PAAO into a polymer material as a recyclable catalyst. Advantageously, the observed pseudo first-order rate constant (kobs) of MIPCP-Ag-PAAO-20% for ethyl-parathion (EP) hydrolysis is about 1.2 × 104-fold higher than that of self-hydrolysis (30 °C, pH = 9). Furthermore, the reaction mechanism of the MIPCP-containing Ag-PAAO-catalyzed organothiophosphate was analyzed in detail using density functional theory and experimental spectra, indicating that the amidoxime can display dual roles for both the key coordination with the silver ion and nucleophilic attack to weaken the P-OAr bond in the catalytic active site.
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Affiliation(s)
- Sujuan Zheng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Jianping Pan
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Junhao Wang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Shuai Liu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Tongtong Zhou
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Lan Wang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Huiting Jia
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Zhaoming Chen
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Qian Peng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Tianying Guo
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
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4
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Saleh LY, Ora M, Lönnberg T. Cleavage of an RNA Model Compound by an Arylmercury Complex. Chembiochem 2021; 22:1761-1764. [PMID: 33448598 PMCID: PMC8247959 DOI: 10.1002/cbic.202000799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/13/2021] [Indexed: 11/22/2022]
Abstract
A water-soluble arylmercury complex has been synthesized, and its ability to catalyze the cleavage of the phosphodiester linkage of the RNA model compound adenylyl-3',5'-(2',3'-O-methyleneadenosine) has been assessed over a pH range of 3-8.5 and a catalyst concentration range of 0-7 mM. In the presence of 1 mM catalyst, the observed pH-rate profile featured a new pH-independent region between pH 6 and 7, the catalyzed reaction being as much as eight times faster than the background reaction. At pH 7, the acceleration increased linearly from three- to 17-fold upon increasing the catalyst concentration from 1 to 7 mM. The linear dependence indicates a relatively low affinity of the catalyst for the substrate and, hence, the potential for considerable improvement on tethering to an appropriate targeting group, such as an oligonucleotide.
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Affiliation(s)
- Lange Yakubu Saleh
- Department of ChemistryUniversity of TurkuVatselankatu 220014TurkuFinland
| | - Mikko Ora
- Department of ChemistryUniversity of TurkuVatselankatu 220014TurkuFinland
| | - Tuomas Lönnberg
- Department of ChemistryUniversity of TurkuVatselankatu 220014TurkuFinland
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5
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Rahman AB, Okamoto H, Miyazawa Y, Aoki S. Design and Synthesis of Supramolecular Phosphatases Formed from a Bis(Zn
2+
‐Cyclen) Complex, Barbital‐Crown‐K
+
Conjugate and Cu
2+
for the Catalytic Hydrolysis of Phosphate Monoester. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202001009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Akib Bin Rahman
- Faculty of Pharmaceutical Science Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
| | - Hirokazu Okamoto
- Faculty of Pharmaceutical Science Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
| | - Yuya Miyazawa
- Faculty of Pharmaceutical Science Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
| | - Shin Aoki
- Faculty of Pharmaceutical Science Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
- Research Institute for Science and Technology Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
- Research Institute for Biomedical Sciences Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
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6
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Development of metallosupramolecular phosphatases based on the combinatorial self-assembly of metal complexes and organic building blocks for the catalytic hydrolysis of phosphate monoesters. RESULTS IN CHEMISTRY 2021. [DOI: 10.1016/j.rechem.2021.100133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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7
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Lugo-González JC, Gómez-Tagle P, Flores-Alamo M, Yatsimirsky AK. Mechanistic study of carboxylic acid and phosphate ester cleavage by oximate metal complexes surpassing the limiting reactivity of highly basic free oximate anions. Dalton Trans 2020; 49:2452-2467. [PMID: 31994558 DOI: 10.1039/c9dt04733f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two tridentate and one tetradentate new ligands containing the terminal oxime group separated from secondary amino and pyridine groups as additional binding sites by two or three methylene groups have been prepared. Their acid-base properties, as well as the composition and stability of their complexes with Zn(ii) and Cd(ii) ions, were determined by potentiometric and spectrophotometric titrations. The X-ray structure of a Cd(ii) complex of a related tridentate oxime ligand previously studied in solution was determined. All oximate complexes show high reactivity in the cleavage of aryl acetates, paraoxon, parathion and 4-nitrophenyl diphenyl phosphate, with rate constants significantly surpassing the limiting rate constants observed for highly basic free oximate anions. The second-order rate constants for individual oximate complexes in solution are assigned to each ligand, metal cation and substrate. The results of the cleavage of 4-substituted phenyl acetates were analyzed in terms of Brønsted correlations with the leaving group pKa, which demonstrated a change in the rate determining step from the nucleophilic attack to the leaving group departure upon an increase in the leaving group basicity. The zero slope of the Brønsted correlation for the nucleophilic attack indicates transition state stabilization through electrophilic assistance by the metal ion. This interpretation is supported by metal selectivity in the relative efficiency of the cleavage of paraoxon and parathion. The existence of the alpha-effect in ester cleavage by coordinated oximates is confirmed by an analysis of the Brønsted correlations with the nucleophile basicity for metal bound oximate and alkoxo or hydroxo nucleophiles. The very high reactivity of the oximate complexes of the new ligands is attributed to transition state stabilization and to the removal of the solvational imbalance of oximate anions that impedes the expected increase in the reactivity of highly basic free anions.
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Affiliation(s)
| | - Paola Gómez-Tagle
- Universidad Nacional Autónoma de México, Facultad de Química, 04510, Mexico City, Mexico.
| | - Marcos Flores-Alamo
- Universidad Nacional Autónoma de México, Facultad de Química, 04510, Mexico City, Mexico.
| | - Anatoly K Yatsimirsky
- Universidad Nacional Autónoma de México, Facultad de Química, 04510, Mexico City, Mexico.
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8
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Pan J, Liu S, Jia H, Yang J, Qin M, Zhou T, Chen Z, Jia X, Guo T. Rapid hydrolysis of nerve agent simulants by molecularly imprinted porous crosslinked polymer incorporating mononuclear zinc(II)-picolinamine-amidoxime module. J Catal 2019. [DOI: 10.1016/j.jcat.2019.10.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Zhou X, Zhang XP, Li W, Jiang J, Xu H, Ke Z, Phillips DL, Zhao C. Unraveling mechanisms of the uncoordinated nucleophiles: theoretical elucidations of the cleavage of bis( p-nitrophenyl) phosphate mediated by zinc-complexes with apical nucleophiles. RSC Adv 2019; 9:37696-37704. [PMID: 35541823 PMCID: PMC9075727 DOI: 10.1039/c9ra06737j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/01/2019] [Indexed: 02/01/2023] Open
Abstract
A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP-) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles. Ligand-based and alternative solvent-based nucleophilic attack reaction models are proposed. The pK a values of the Zn(ii)-bound water molecules or ligands in the [Zn(L n H)(η-H2O)(H2O)]2+ (n = 1, 2 and 3) complexes, as well as the dimerization tendency of the mononuclear Zn(ii)-complexes, were found to significantly influence the reaction mechanisms. The Zn(ii)-L3 complexes were found to be more favorable for the hydrolytic cleavage of the BNPP- via a ligand-based nucleophilic attack pathway. This was due to the lower pK a value for the deprotonation of the oxime ligand, the hard dimerization of the mononuclear Zn(ii)-L3 species, and the presence of an uncoordinated nucleophile. The origins of the uncoordinated reactions were systematically elucidated. The theoretical results reported here are in good agreement with experimental observations and more importantly, help to elucidate the factors that influence intermolecular nucleophilic attack reactions with coordinated/uncoordinated nucleophiles.
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Affiliation(s)
- Xiaoyu Zhou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Xue-Peng Zhang
- School of Chemisty and Chemical Engineering, Shaanxi Normal University Xi'an 710119 P. R. China
| | - Weikang Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Jingxing Jiang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, School of Materials Science and Engineering, Sun Yat-sen University Guangzhou 510275 P. R. China
| | - Huiying Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Zhuofeng Ke
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, School of Materials Science and Engineering, Sun Yat-sen University Guangzhou 510275 P. R. China
| | - David Lee Phillips
- Department of Chemistry, University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
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10
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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: 7] [Impact Index Per Article: 1.4] [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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11
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Rahman AB, Imafuku H, Miyazawa Y, Kafle A, Sakai H, Saga Y, Aoki S. Catalytic Hydrolysis of Phosphate Monoester by Supramolecular Phosphatases Formed from a Monoalkylated Dizinc(II) Complex, Cyclic Diimide Units, and Copper(II) in Two-Phase Solvent System. Inorg Chem 2019; 58:5603-5616. [PMID: 30969761 DOI: 10.1021/acs.inorgchem.8b03586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Design and synthesis of enzyme mimic with programmed molecular interaction among several building blocks including metal complexes and metal chelators is of intellectual and practical significance. The preparation of artificial enzymes that mimic the natural enzymes such as hydrolases, phosphatases, etc. remains a great challenge in the field of supramolecular chemistry. Herein we report on the design and synthesis of asymmetric (nonsymmetric) supermolecules by the 2:2:2 self-assembly of an amphiphilic zinc(II)-cyclen complex containing a 2,2'-bipyridyl linker and one long alkyl chain (Zn2L3), barbital analogues, and Cu2+ as model compounds of an enzyme alkaline phosphatase that catalyzes the hydrolysis of phosphate monoesters such as mono(4-nitrophenyl)phosphate at neutral pH in two-phase solvent system (H2O/CHCl3) in pH 7.4 and 37 °C. Hydrolytic activity of these complexes was found to be catalytic, and their catalytic turnover numbers are 3-4. The mechanistic studies based on the UV/vis and emission spectra of the H2O and CHCl3 phases of the reaction mixtures suggest that the hydrophilicity/hydrophobicity balance of the supramolecular catalysts is an important factor for catalytic activity.
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12
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Wang R, Pan J, Qin M, Guo T. Molecularly imprinted nanocapsule mimicking phosphotriesterase for the catalytic hydrolysis of organophosphorus pesticides. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2018.10.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Krachtus D, Smith JC, Imhof P. Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase. Molecules 2018; 23:E3342. [PMID: 30563005 PMCID: PMC6321591 DOI: 10.3390/molecules23123342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 11/25/2022] Open
Abstract
Phosphoserine phosphatase (PSP), a member of the haloacid dehalogenase (HAD) superfamily that comprises the vast majority of phosphotransferases, is likely a steady-state regulator of the level of d-serine in the brain. The proposed catalytic cycle of PSP consists of a two-step mechanism: formation of a phospho-enzyme intermediate by phosphate transfer to Asp11 and its subsequent hydrolysis. Our combined quantum mechanical/molecular mechanical (QM/MM) calculations of the reaction pathways favour a dissociative mechanism of nucleophilic substitution via a trigonal-planar metaphosphate-like configuration for both steps, associated with proton transfer to the leaving group or from the nucleophile. This proton transfer is facilitated by active site residue Asp13 that acts as both a general base and a general acid. Free energy calculation on the reaction pathways further support the structural role of the enzymatic environment and the active site architecture. The choice of a proper reaction coordinate along which to bias the free energy calculations can be guided by a projection of the canonical reaction coordinate obtained from a chain-of-state optimisation onto important internal coordinates.
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Affiliation(s)
- Dieter Krachtus
- Computational Molecular Biophysics Group, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
| | - Jeremy C Smith
- Computational Molecular Biophysics Group, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831-6255, USA.
| | - Petra Imhof
- Freie Universität Berlin, Institute for Theoretical Physics, Arnimallee 14, 14195 Berlin, Germany.
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14
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Parrot A, Collin S, Bruylants G, Reinaud O. The 3 rd degree of biomimetism: associating the cavity effect, Zn II coordination and internal base assistance for guest binding and activation. Chem Sci 2018; 9:5479-5487. [PMID: 30079177 PMCID: PMC6048688 DOI: 10.1039/c8sc01129j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/29/2018] [Indexed: 12/12/2022] Open
Abstract
The synthesis and characterization of a resorcinarene-based tetra(imidazole) ligand is reported. The properties of the corresponding ZnII complex are studied in depth, notably by NMR spectroscopy. In MeCN, acid-base titration reveals that one out of the four imidazole arms is hemi-labile and can be selectively protonated, thereby opening a coordination site in the exo position. Quite remarkably, the 4th imidazole arm promotes binding of an acidic molecule (a carboxylic acid, a β-diketone or acetamide), by acting as an internal base, which allows guest binding as an anion to the metal center in the endo position. Most importantly, the presence of this labile imidazole arm makes the ZnII complex active for the catalyzed hydration of acetonitrile. It is proposed that it acts as a general base for activating a water molecule in the vicinity of the metal center during its nucleophilic attack to the endo-bound MeCN substrate. This system presents a unique degree of biomimetism when considering zinc enzymes: a pocket for guest binding, a similar first coordination sphere, a coordination site available for water activation in the cis position relative to the substrate and finally an internal imidazole residue that plays the role of a general base.
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Affiliation(s)
- A Parrot
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , CNRS UMR8601 , Université Paris Descartes , Sorbonne Paris Cité , 45 rue des Saints Pères , 75006 Paris , France .
| | - S Collin
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , CNRS UMR8601 , Université Paris Descartes , Sorbonne Paris Cité , 45 rue des Saints Pères , 75006 Paris , France .
| | - G Bruylants
- Engineering of Molecular NanoSystems , Ecole Polytechnique de Bruxelles , Université Libre de Bruxelles (ULB) , Avenue F. D. Roosevelt 50, CP165/64 , B-1050 Brussels , Belgium
| | - O Reinaud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , CNRS UMR8601 , Université Paris Descartes , Sorbonne Paris Cité , 45 rue des Saints Pères , 75006 Paris , France .
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15
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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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16
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Wanderlind EH, Bittencourt CR, Manfredi AM, Gerola AP, Souza BS, Fiedler HD, Nome F. Cu(II)-catalyzed hydrolysis of tris-2-pyridyl phosphate assisted by sodium dodecyl sulfate micelles. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3837] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Eduardo H. Wanderlind
- National Institute of Science and Technology of Catalysis in Molecular and Nanostructured Systems, Department of Chemistry; Federal University of Santa Catarina; Florianópolis SC Brazil
| | - Catiunaiara R. Bittencourt
- National Institute of Science and Technology of Catalysis in Molecular and Nanostructured Systems, Department of Chemistry; Federal University of Santa Catarina; Florianópolis SC Brazil
| | - Alex M. Manfredi
- National Institute of Science and Technology of Catalysis in Molecular and Nanostructured Systems, Department of Chemistry; Federal University of Santa Catarina; Florianópolis SC Brazil
| | - Adriana P. Gerola
- National Institute of Science and Technology of Catalysis in Molecular and Nanostructured Systems, Department of Chemistry; Federal University of Santa Catarina; Florianópolis SC Brazil
| | - Bruno S. Souza
- National Institute of Science and Technology of Catalysis in Molecular and Nanostructured Systems, Department of Chemistry; Federal University of Santa Catarina; Florianópolis SC Brazil
| | - Haidi D. Fiedler
- National Institute of Science and Technology of Catalysis in Molecular and Nanostructured Systems, Department of Chemistry; Federal University of Santa Catarina; Florianópolis SC Brazil
| | - Faruk Nome
- National Institute of Science and Technology of Catalysis in Molecular and Nanostructured Systems, Department of Chemistry; Federal University of Santa Catarina; Florianópolis SC Brazil
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17
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Joshi P, Hussain N, Ali SR, Rishu R, Bhardwaj VK. Enhanced activity of trinuclear Zn(ii) complexes towards phosphate ester bond cleavage by introducing three-metal cooperativity. NEW J CHEM 2018. [DOI: 10.1039/c7nj03759g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The catalytic efficiency (DNA binding followed by phosphate ester bond cleavage) of Zn(ii) complexes has been tuned by variation in the nuclearity, flexibility and coordination environment to explore the structure activity correlation.
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Affiliation(s)
- Pooja Joshi
- Department of Chemistry
- D.S.B. Campus
- Kumaun University
- Nainital
- India
| | - Navid Hussain
- Department of Chemistry
- Indian Institute of Technology Ropar
- Rupnagar
- India
| | - Shah Raj Ali
- Department of Chemistry
- D.S.B. Campus
- Kumaun University
- Nainital
- India
| | - Rishu Rishu
- Department of Chemistry
- MCM DAV College for Women
- Chandigarh-160036
- India
| | - Vimal K. Bhardwaj
- Department of Chemistry
- Indian Institute of Technology Ropar
- Rupnagar
- India
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18
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Lugo-González JC, Gómez-Tagle P, Huang X, M Del Campo J, Yatsimirsky AK. Substrate Specificity and Leaving Group Effect in Ester Cleavage by Metal Complexes of an Oximate Nucleophile. Inorg Chem 2017; 56:2060-2069. [PMID: 28170234 DOI: 10.1021/acs.inorgchem.6b02739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deprotonated zinc(II) and cadmium(II) complexes of a tridentate oxime nucleophile (1, OxH) show a very high reactivity, breaking by 2-3 orders of magnitude the previously established limiting reactivity of oximate nucleophiles in the cleavage of substituted phenyl acetates and phosphate triesters, but are unreactive with p-nitrophenyl phosphate di- and monoesters. With reactive substrates, these complexes operate as true catalysts through an acylation-deacylation mechanism. Detailed speciation and kinetic studies in a wide pH interval allowed us to establish as catalytically active forms [Cd(Ox)]+, [Zn(Ox)(OH)], and [Zn(Ox)(OH)2]- complexes. The formation of an unusual and most reactive zinc(II) oximatodihydroxo complex was confirmed by electrospray ionization mass spectrometry data and supported by density functional theory calculations, which also supported the previously noticed fact that the coordinated water in [Zn(OxH)(H2O)2]2+ deprotonates before the oxime. Analysis of the leaving group effect on the cleavage of phenyl acetates shows that the rate-determining step in the reaction with the free oximate anion is the nucleophilic attack, while with both zinc(II) and cadmium(II) oximate complexes, it changes to the expulsion of the leaving phenolate anion. The major new features of these complexes are (1) a very high esterolytic activity surpassing that of enzyme hydrolysis of aryl acetate esters and (2) an increased reactivity of coordinated oxime compared to free oxime in phosphate triester cleavage, contrary to the previously observed inhibitory effect of oxime coordination with these substrates.
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Affiliation(s)
| | - Paola Gómez-Tagle
- Facultad de Química, Universidad Nacional Autónoma de México , 04510 Mexico City, México
| | - Xiaomin Huang
- Facultad de Química, Universidad Nacional Autónoma de México , 04510 Mexico City, México
| | - Jorge M Del Campo
- Facultad de Química, Universidad Nacional Autónoma de México , 04510 Mexico City, México
| | - Anatoly K Yatsimirsky
- Facultad de Química, Universidad Nacional Autónoma de México , 04510 Mexico City, México
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19
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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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20
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Batebi H, Imhof P. Phosphodiester hydrolysis computed for cluster models of enzymatic active sites. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2020-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Mancin F, Prins LJ, Pengo P, Pasquato L, Tecilla P, Scrimin P. Hydrolytic Metallo-Nanozymes: From Micelles and Vesicles to Gold Nanoparticles. Molecules 2016; 21:molecules21081014. [PMID: 27527134 PMCID: PMC6272841 DOI: 10.3390/molecules21081014] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/01/2016] [Accepted: 08/02/2016] [Indexed: 11/16/2022] Open
Abstract
Although the term nanozymes was coined by us in 2004 to highlight the enzyme-like properties of gold nanoparticles passivated with a monolayer of Zn(II)-complexes in the cleavage of phosphate diesters, systems resembling those metallo-nanoparticles, like micelles and vesicles, have been the subject of investigation since the mid-eighties of the last century. This paper reviews what has been done in the field and compares the different nanosystems highlighting the source of catalysis and frequent misconceptions found in the literature.
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Affiliation(s)
- Fabrizio Mancin
- Department of Chemical Sciences, University of Padova, via Marzolo, 1, Padova 35131, Italy.
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padova, via Marzolo, 1, Padova 35131, Italy.
| | - Paolo Pengo
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via Giorgieri, 1, Trieste 34127, Italy.
| | - Lucia Pasquato
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via Giorgieri, 1, Trieste 34127, Italy.
| | - Paolo Tecilla
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via Giorgieri, 1, Trieste 34127, Italy.
| | - Paolo Scrimin
- Department of Chemical Sciences, University of Padova, via Marzolo, 1, Padova 35131, Italy.
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22
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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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23
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Hisamatsu Y, Miyazawa Y, Yoneda K, Miyauchi M, Zulkefeli M, Aoki S. Supramolecular Complexes Formed by the Self-assembly of Hydrophobic Bis(Zn 2+-cyclen) Complexes, Copper, and Di- or Triimide Units for the Hydrolysis of Phosphate Mono- and Diesters in Two-Phase Solvent Systems (Cyclen=1,4,7,10-Tetraazacyclododecane). Chem Pharm Bull (Tokyo) 2016; 64:451-64. [DOI: 10.1248/cpb.c15-01014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Yuya Miyazawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science
| | - Kakeru Yoneda
- Faculty of Pharmaceutical Sciences, Tokyo University of Science
| | - Miki Miyauchi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science
| | | | - Shin Aoki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science
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24
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Zhang X, Liu X, Phillips DL, Zhao C. Mechanistic Insights Into the Factors That Influence the DNA Nuclease Activity of Mononuclear Facial Copper Complexes Containing Hetero-Substituted Cyclens. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01735] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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
| | - Xueping Liu
- MOE
Key Laboratory of Bioinorganic and Synthetic 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, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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