1
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Zellmann F, Schmauk N, Murmann N, Böhm M, Schwenger A, Göbel MW. Quality Control of mRNA Vaccines by Synthetic Ribonucleases: Analysis of the Poly-A-Tail. Chembiochem 2024; 25:e202400347. [PMID: 38742914 DOI: 10.1002/cbic.202400347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
The effectivity and safety of mRNA vaccines critically depends on the presence of correct 5' caps and poly-A tails. Due to the high molecular mass of full-size mRNAs, however, the direct analysis by mass spectrometry is hardly possible. Here we describe the use of synthetic ribonucleases to cleave off 5' and 3' terminal fragments which can be further analyzed by HPLC or by LC-MS. Compared to existing methods (e. g. RNase H), the new approach uses robust catalysts, is free of sequence limitations, avoids metal ions and combines fast sample preparation with high precision of the cut.
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Affiliation(s)
- Felix Zellmann
- Analytical Development CureVac SE, Friedrich-Miescher-Str. 15, 72076, Tübingen, Germany
| | - Nina Schmauk
- Analytical Development CureVac SE, Friedrich-Miescher-Str. 15, 72076, Tübingen, Germany
| | - Nina Murmann
- Institut für Organische Chemie und Chemische Biologie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Madeleine Böhm
- Analytical Development CureVac SE, Friedrich-Miescher-Str. 15, 72076, Tübingen, Germany
| | - Alexander Schwenger
- Analytical Development CureVac SE, Friedrich-Miescher-Str. 15, 72076, Tübingen, Germany
| | - Michael W Göbel
- Institut für Organische Chemie und Chemische Biologie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
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2
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Lönnberg H. Structural modifications as tools in mechanistic studies of the cleavage of RNA phosphodiester linkages. CHEM REC 2022; 22:e202200141. [PMID: 35832010 DOI: 10.1002/tcr.202200141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/28/2022] [Indexed: 11/06/2022]
Abstract
The cleavage of RNA phosphodiester bonds by RNase A and hammerhead ribozyme at neutral pH fundamentally differs from the spontaneous reactions of these bonds under the same conditions. While the predominant spontaneous reaction is isomerization of the 3',5'-phosphodiester linkages to their 2',5'-counterparts, this reaction has never been reported to compete with the enzymatic cleavage reaction, not even as a minor side reaction. Comparative kinetic measurements with structurally modified di-nucleoside monophosphates and oligomeric phosphodiesters have played an important role in clarification of mechanistic details of the buffer-independent and buffer-catalyzed reactions. More recently, heavy atom isotope effects and theoretical calculations have refined the picture. The primary aim of all these studies has been to form a solid basis for mechanistic analyses of the action of more complicated catalytic machineries. In other words, to contribute to conception of a plausible unified picture of RNA cleavage by biocatalysts, such as RNAse A, hammerhead ribozyme and DNAzymes. In addition, structurally modified trinucleoside monophosphates as transition state models for Group I and II introns have clarified some features of the action of large ribozymes.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FI-20014 University of, Turku
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3
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Perrin D, Paul S, Wong AAWL, Liu LT. Selection of M2+-independent RNA-cleaving DNAzymes with Sidechains Mimicking Arginine and Lysine. Chembiochem 2021; 23:e202100600. [PMID: 34881502 DOI: 10.1002/cbic.202100600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/04/2021] [Indexed: 11/07/2022]
Abstract
Sequence-specific cleavage of RNA by nucleic acid catalysts in the absence of a divalent metal cation (M 2+ ) has remained an important goal in biomimicry with potential therapeutic applications. Given the lack of functional group diversity in canonical nucleotides, modified nucleotides with amino acid-like side chains were used to enhance self-cleavage rates at a single embedded ribonucleoside site. Previous works relied on three functional groups: an amine, a guanidine and an imidazole ensconced on three different nucleosides. However, to date, few studies have systematically addressed the necessity of all three modifications, as the value of any single modified nucleoside is contextualized at the outset of selection. Herein, we report on the use of only two modified dNTPs, excluding an imidazole, i.e. 5-(3-guanidinoallyl)-2'-dUTP (dU ga TP) and 5-aminoallyl-2'-dCTP (dC aa TP), to select in-vitro self-cleaving DNAzymes that cleave in the absence of M 2+ in a pH-independent fashion. Cleavage shows biphasic kinetics with rate constants that are significantly higher than in unmodified DNAzymes and compare favorably to certain DNAzymes involving an imidazole. This work is the first report of a M2+-independent DNAzyme with two cationic modifications; as such it shows appreciable self-cleaving activity in the absence of an imidazole modification.
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Affiliation(s)
- David Perrin
- U. British Columbia, Chemistry, 2036 Main Mall, V6T-1Z1, Vancouver, CANADA
| | - Somdeb Paul
- The University of British Columbia, Chemistry, 2036 Main Mall, Vancouver, V6T1Z1, Vancouver, CANADA
| | - Antonio A W L Wong
- The University of British Columbia, Chemistry, 2036 Main Mall, Vancouver, V6T1Z1, Vancouver, CANADA
| | - Leo T Liu
- The University of British Columbia, Chemistry, 2036 Main Mall, UBC, Vancouver, V6T-1Z1, Vancouver, CANADA
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4
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Danneberg F, Westemeier H, Horx P, Zellmann F, Dörr K, Kalden E, Zeiger M, Akpinar A, Berger R, Göbel MW. RNA Hydrolysis by Heterocyclic Amidines and Guanidines: Parameters Affecting Reactivity. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Friederike Danneberg
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Hauke Westemeier
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Philip Horx
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Felix Zellmann
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Kathrin Dörr
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Elisabeth Kalden
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Mirco Zeiger
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Abdullah Akpinar
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Robert Berger
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Michael W. Göbel
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
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5
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Site-Selective Artificial Ribonucleases: Renaissance of Oligonucleotide Conjugates for Irreversible Cleavage of RNA Sequences. Molecules 2021; 26:molecules26061732. [PMID: 33808835 PMCID: PMC8003597 DOI: 10.3390/molecules26061732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
RNA-targeting therapeutics require highly efficient sequence-specific devices capable of RNA irreversible degradation in vivo. The most developed methods of sequence-specific RNA cleavage, such as siRNA or antisense oligonucleotides (ASO), are currently based on recruitment of either intracellular multi-protein complexes or enzymes, leaving alternative approaches (e.g., ribozymes and DNAzymes) far behind. Recently, site-selective artificial ribonucleases combining the oligonucleotide recognition motifs (or their structural analogues) and catalytically active groups in a single molecular scaffold have been proven to be a great competitor to siRNA and ASO. Using the most efficient catalytic groups, utilising both metal ion-dependent (Cu(II)-2,9-dimethylphenanthroline) and metal ion-free (Tris(2-aminobenzimidazole)) on the one hand and PNA as an RNA recognising oligonucleotide on the other, allowed site-selective artificial RNases to be created with half-lives of 0.5-1 h. Artificial RNases based on the catalytic peptide [(ArgLeu)2Gly]2 were able to take progress a step further by demonstrating an ability to cleave miRNA-21 in tumour cells and provide a significant reduction of tumour growth in mice.
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6
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Zellmann F, Göbel MW. A Trisbenzimidazole Phosphoramidite Building Block Enables High-Yielding Syntheses of RNA-Cleaving Oligonucleotide Conjugates. Molecules 2020; 25:molecules25081842. [PMID: 32316292 PMCID: PMC7221912 DOI: 10.3390/molecules25081842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/03/2022] Open
Abstract
The RNA cleaving catalyst tris(2-aminobenzimidazole) when attached to the 5’ terminus of oligonucleotides cuts complementary RNA strands in a highly site-specific manner. Conjugation was previously achieved by the acylation of an amino linker by an active ester of the catalyst. However, this procedure was low yielding and not reliable. Here, a phosphoramidite building block is described that can be coupled to oligonucleotides by manual solid phase synthesis in total yields around 85%. Based on this chemistry, we have now studied the impact of LNA (locked nucleic acids) nucleotides on the rates and the site-specificities of RNA cleaving conjugates. The highest reaction rates and the most precise cuts can be expected when the catalyst is attached to a strong 5’ closing base pair and when the oligonucleotide contains several LNA units that are equally distributed in the strand. However, when placed in the 5’ position, LNA building blocks tend to diminish the specificity of RNA cleavage.
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7
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Liu J, Morgan S, Hoover JM. Cobalt‐Catalyzed Aerobic Oxidative Cyclization of 2‐Aminoanilines with Isonitriles: Facile Access to 2‐Aminobenzimidazoles. ChemCatChem 2020. [DOI: 10.1002/cctc.201902011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jiaqi Liu
- C. Eugene Bennett Department of Chemistry West Virginia University Morgantown WV 26506 USA
| | - Sarah Morgan
- C. Eugene Bennett Department of Chemistry West Virginia University Morgantown WV 26506 USA
| | - Jessica M. Hoover
- C. Eugene Bennett Department of Chemistry West Virginia University Morgantown WV 26506 USA
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8
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Site-Specific Cleavage of RNAs Derived from the PIM1 3'-UTR by a Metal-Free Artificial Ribonuclease. Molecules 2019; 24:molecules24040807. [PMID: 30813393 PMCID: PMC6412833 DOI: 10.3390/molecules24040807] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 02/19/2019] [Indexed: 11/16/2022] Open
Abstract
Oligonucleotide conjugates of tris(2-aminobenzimidazole) have been reported previously to cleave complementary RNA strands with high levels of sequence and site specificity. The RNA substrates used in these studies were oligonucleotides not longer than 29-mers. Here we show that ~150⁻400-mer model transcripts derived from the 3'-untranslated region of the PIM1 mRNA reacted with rates and specificities comparable to those of short oligonucleotide substrates. The replacement of DNA by DNA/LNA mixmers further increased the cleavage rate. Tris(2-aminobenzimidazoles) were designed to interact with phosphates and phosphate esters. A cell, however, contains large amounts of phosphorylated species that may cause competitive inhibition of RNA cleavage. It is thus important to note that no loss in reaction rates was observed in phosphate buffer. This opens the way to in-cell applications for this type of artificial nuclease. Furthermore, we disclose a new synthetic method giving access to tris(2-aminobenzimidazoles) in multigram amounts.
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9
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Salvio R, Volpi S, Folcarelli T, Casnati A, Cacciapaglia R. A calix[4]arene with acylguanidine units as an efficient catalyst for phosphodiester bond cleavage in RNA and DNA model compounds. Org Biomol Chem 2019; 17:7482-7492. [DOI: 10.1039/c9ob01141b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Conjugated carbonyl units in a calixarene scaffold provide the right amount of flexibility for catalysis with a minimum entropic cost.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Scienze e Tecnologie Chimiche
- Università “Tor Vergata”
- I-00133 Roma
- Italy
- ISB - CNR Sezione Meccanismi di Reazione
| | - Stefano Volpi
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | | | - Alessandro Casnati
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Roberta Cacciapaglia
- ISB - CNR Sezione Meccanismi di Reazione
- Università La Sapienza
- 00185 Roma
- Italy
- Dipartimento di Chimica
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10
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Dar AM, Nabi R, Mir S, Gatoo MA, Lone SH. Synthesis of steroidal imidazolidinthiones as potential apoptotic agents: Investigation by theoretical and experimental studies. Bioorg Chem 2018; 79:190-200. [PMID: 29772469 DOI: 10.1016/j.bioorg.2018.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 11/15/2022]
Abstract
New steroidal imidazolidinthione derivatives (4-6) were synthesized from steroidal thiosemicarbazones and dichloroethane. The synthesized compounds were characterized using spectral data analysis. Theoretical DFT involving B3LYP/6-31G∗∗ level of theory was employed to gain insights into the molecular structure of the target compounds. MEPS and FMO analysis were carried out. HOMO-LUMO energy gap was determined which helped to evaluate various global descriptors like hardness, chemical potential, electronegativity, nucleophilicity and electrophilicity index, etc. The calculated properties established that the synthesized products are more or less similar in their reactivity behaviour. To explore their biological potential, interaction studies of compounds (4-6) with DNA were carried out using various biophysical techniques. The compounds bind DNA preferentially through electrostatic and hydrophobic interactions with Kb of 3.21 × 103 M-1, 2.79 × 103 M-1 and 2.26 × 103 M-1, respectively indicating the higher binding affinity of compound 4 towards DNA. Gel electrophoresis of compound 4 demonstrated strong interaction during the concentration dependent cleavage activity with pBR322 DNA. It was observed that these steroidal imidazolidinthiones are minor groove binders of DNA which was validated using molecular docking studies. An in vitro cytotoxicity screening using MTT assay revealed that the compounds (4-6) exhibit potential toxicity against different human cancer cells. Highest antiproliferative effect was observed on HeLa cells by compound 4. The results suggested that compounds 4-6 cause apoptotic cell death by cleaving apoptotic protein caspase-3 and suppress anti-apoptotic protein Bcl-2 in HeLa cancer cells.
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Affiliation(s)
- Ayaz Mahmood Dar
- Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India; Department of Chemistry, Govt Degree College Kulgam, Kashmir 192231, India.
| | - Rizwan Nabi
- Department of Chemistry, Indian Institute of Technology Powai, Mumbai 400076, India
| | - Shafia Mir
- Department of Chemistry, OPJS University, Churu 331001, Rajasthan, India
| | - Manzoor Ahmad Gatoo
- Department of Biochemistry JNMC, Aligarh Muslim University, Aligarh 202 002, India
| | - Shabir H Lone
- Department of Chemistry, Govt Degree College Anantnag, Kashmir 192101, India.
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11
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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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12
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DNA binding, artificial nuclease activity and cytotoxic studies of newly synthesized steroidal pyrimidines. Int J Biol Macromol 2017; 111:52-61. [PMID: 29292141 DOI: 10.1016/j.ijbiomac.2017.12.128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/09/2017] [Accepted: 12/25/2017] [Indexed: 01/07/2023]
Abstract
The new steroidal pyrimidine derivatives (4-6) were synthesized by the reaction of steroidal thiosemicarbazones with (2-methyl) diethyl malonate in absolute ethanol. After characterization by spectral and analytical data, the DNA interaction studies of compounds (4-6) were carried out by UV-vis, fluorescence spectroscopy, hydrodynamic measurements, molecular docking and gel electrophoresis. The compounds bind to DNA preferentially through electrostatic and hydrophobic interactions with Kb; 2.31×103M-1, 1.93×103M-1 and 2.05×103M-1, respectively indicating the higher binding affinity of compound 4 towards DNA. Gel electrophoresis demonstrated that compound 4 showed a strong interaction during the concentration dependent cleavage activity with pBR322 DNA. The molecular docking study suggested the intercalation of steroidal pyrimidine moiety in the minor groove of DNA. During in vitro cytotoxicity, compounds (4-6) revealed potential toxicity against the different human cancer cells (MTT assay). During DAPI staining, the nuclear fragmentations on cells occurred after treatment with compounds 4 and 5. Western blotting analysis clearly indicates that compound 4 causes apoptosis in MCF-7 cancer cells. The results revealed that compound 4 has better prospectus to act as a cancer chemotherapeutic candidate, which warrants further in vivo anticancer investigations.
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13
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Salvio R, Casnati A. Guanidinium Promoted Cleavage of Phosphoric Diesters: Kinetic Investigations and Calculations Provide Indications on the Operating Mechanism. J Org Chem 2017; 82:10461-10469. [DOI: 10.1021/acs.joc.7b01925] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Riccardo Salvio
- Dipartimento
di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185 Roma, Italy
| | - Alessandro Casnati
- Dipartimento
di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze 17/A, 43124 Parma, Italy
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14
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Qian P, Deng Y, Mei H, Han J, Pan Y. Metal-free nitroxyl radical-mediated β-C(sp3)–H amination of saturated ketones with heteroaryl halides: multiple roles of TEMPO. Chem Commun (Camb) 2017; 53:2958-2961. [DOI: 10.1039/c7cc00145b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first metal-free nitroxyl-radical-mediated β-amination of saturated ketones by using heteroaryl halides as amide precursors has been developed.
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Affiliation(s)
- Ping Qian
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Coordination Chemistry
- Nanjing University
- Nanjing 210093
- P. R. China
| | - Yu Deng
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Coordination Chemistry
- Nanjing University
- Nanjing 210093
- P. R. China
| | - Haibo Mei
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Coordination Chemistry
- Nanjing University
- Nanjing 210093
- P. R. China
| | - Jianlin Han
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Coordination Chemistry
- Nanjing University
- Nanjing 210093
- P. R. China
| | - Yi Pan
- School of Chemistry and Chemical Engineering
- State Key Laboratory of Coordination Chemistry
- Nanjing University
- Nanjing 210093
- P. R. China
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15
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Dar AM, Uzzaman S, Ahmad MS, Khan Y. Steroidal imidazoles: Synthesis, characterization, molecular docking studies with DNA and in vitro cytotoxicity. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1755-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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16
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Salvio R, Volpi S, Cacciapaglia R, Sansone F, Mandolini L, Casnati A. Phosphoryl Transfer Processes Promoted by a Trifunctional Calix[4]arene Inspired by DNA Topoisomerase I. J Org Chem 2016; 81:9012-9019. [DOI: 10.1021/acs.joc.6b01643] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Riccardo Salvio
- Dipartimento
di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Universitá La Sapienza, 00185 Rome, Italy
| | - Stefano Volpi
- Dipartimento
di Chimica, Universitá degli Studi di Parma, Viale delle
Scienze 17/A, 43124 Parma, Italy
| | - Roberta Cacciapaglia
- Dipartimento
di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Universitá La Sapienza, 00185 Rome, Italy
| | - Francesco Sansone
- Dipartimento
di Chimica, Universitá degli Studi di Parma, Viale delle
Scienze 17/A, 43124 Parma, Italy
| | - Luigi Mandolini
- Dipartimento
di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Universitá La Sapienza, 00185 Rome, Italy
| | - Alessandro Casnati
- Dipartimento
di Chimica, Universitá degli Studi di Parma, Viale delle
Scienze 17/A, 43124 Parma, Italy
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17
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Nájera C, Miguel Sansano J, Gómez-Bengoa E. Heterocycle-based bifunctional organocatalysts in asymmetric synthesis. PURE APPL CHEM 2016. [DOI: 10.1515/pac-2016-0403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AbstractDifferent chiral bifunctional organocatalysts derived from trans-cyclohexane-1,2-diamine bearing different types of guanidine units able to form-hydrogen bonding activation have been designed. Conformational rigid 2-aminobenzimidazoles bearing a tertiary amino group have been used in enantioselective Michael type reactions of activated methylene compounds to nitroalkenes. The C2 symmetric bis(2-aminobenzimidazole) derivatives the appropriate organocatalyst for the conjugate addition of 1,3-dicarbonyl compounds to maleimides as well as for the SN1 reaction of benzylic alcohols with carbon nucleophiles. 2-Aminobenzimidazoles bearing a primary amino group have shown excellent catalytic activity in the Michael reaction of aldehydes to maleimides and nitroalkenes. Diastereomeric 2-aminopyrimidines bearing a prolinamide unit have been incorporated in the trans-cyclohexane-1,2-diamine scaffold and have been used for the inter- and intra-molecular direct aldol reaction under solvent-free conditions. For the Michael reaction of aldehydes with maleimides the primary amine 2-aminopyrimidine has shown excellent efficiency as organocatalyst. The bifunctional character of these organocatalysts has been demonstrated by means of DFT calculations.
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Affiliation(s)
- Carmen Nájera
- 1Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universidad de Alicante, Apdo. 99, 03080 Alicante, Spain
| | - José Miguel Sansano
- 1Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universidad de Alicante, Apdo. 99, 03080 Alicante, Spain
| | - Enrique Gómez-Bengoa
- 2Departamento de Química Orgánica I, Facultad de Química, Universidad del País Vasco, Apdo. 1072, E-20018 San Sebastián, Spain
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18
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Tamkovich N, Koroleva L, Kovpak M, Goncharova E, Silnikov V, Vlassov V, Zenkova M. Design, RNA cleavage and antiviral activity of new artificial ribonucleases derived from mono-, di- and tripeptides connected by linkers of different hydrophobicity. Bioorg Med Chem 2016; 24:1346-55. [PMID: 26899594 DOI: 10.1016/j.bmc.2016.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 11/15/2022]
Abstract
A novel series of metal-free artificial ribonucleases (aRNases) was designed, synthesized and assessed in terms of ribonuclease activity and ability to inactivate influenza virus WSN/A33/H1N1 in vitro. The compounds were built of two short peptide fragments, which include Lys, Ser, Arg, Glu and imidazole residues in various combinations, connected by linkers of different hydrophobicity (1,12-diaminododecane or 4,9-dioxa-1,12-diaminododecane). These compounds efficiently cleaved different RNA substrates under physiological conditions at rates three to five times higher than that of artificial ribonucleases described earlier and displayed RNase A-like cleavage specificity. aRNases with the hydrophobic 1,12-diaminododecane linker displayed ribonuclease activity 3-40 times higher than aRNases with the 4,9-dioxa-1,12-diaminododecane linker. The assumed mechanism of RNA cleavage was typical for natural ribonucleases, that is, general acid-base catalysis via the formation of acid/base pairs by functional groups of amino acids present in the aRNases; the pH profile of cleavage confirmed this mechanism. The most active aRNases under study exhibited high antiviral activity and entirely inactivated influenza virus A/WSN/33/(H1N1) after a short incubation period of viral suspension under physiological conditions.
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Affiliation(s)
- Nikolay Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Lyudmila Koroleva
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Mikhail Kovpak
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Elena Goncharova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Vladimir Silnikov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia.
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19
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Mamedov VA. Recent advances in the synthesis of benzimidazol(on)es via rearrangements of quinoxalin(on)es. RSC Adv 2016. [DOI: 10.1039/c6ra03907c] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The review describes all the quinoxaline-benzimidazole rearrangements as a whole and the new quinoxalinone-benzimidazol(on)e rearrangements in particular when exposed to nucleophilic rearrangements which can be used for the synthesis of various biheterocyclic motifs.
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Affiliation(s)
- Vakhid A. Mamedov
- A. E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center of the Russian Academy of Sciences
- Kazan
- Russian Federation
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20
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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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21
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Spectroscopic, Viscositic, DNA Binding and Cytotoxic Studies of Newly Synthesized Steroidal Imidazolidines. J Fluoresc 2015; 26:639-49. [DOI: 10.1007/s10895-015-1750-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
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22
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Dar AM, Gatoo MA. Synthesis of new steroidal imidazo [1,2-a] pyridines: DNA binding studies, cleavage activity and in vitro cytotoxicity. Steroids 2015; 104:163-75. [PMID: 26433147 DOI: 10.1016/j.steroids.2015.09.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 09/21/2015] [Accepted: 09/27/2015] [Indexed: 11/26/2022]
Abstract
A one-pot strategy for the catalytic synthesis of series of new 5α-cholestan-6-spiro-5'-phenylamino-2H-imidazo [1',2'-a] pyridines (4-14) has been investigated. The synthesized products were obtained in good yields (85-90%) and the protocol uses Multi-component Reaction (MCR) involving steroidal ketones, 2-aminopyridines, isocyanides and propylphosphonic anhydride (®T3P) as a catalyst. After characterization by spectral and analytical data, the interaction studies of compounds (4-6) with DNA were studied by UV-vis, fluorescence spectroscopy, gel electrophoresis and molecular docking. The compounds bind to DNA preferentially through electrostatic and hydrophobic interactions with Kb; 2.35×10(4), 3.71×10(4) and 3.24×10(4) M(-1), respectively, indicating the higher binding affinity of compound 5 towards DNA. Gel electrophoresis showed the concentration dependent cleavage activity of compounds 4-6 with DNA. Molecular docking studies suggested that compounds bind through minor groove to DNA. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay depicted promising anti-proliferative activity of compound 4-9 against different given cancer cells. In Western blotting, the expressions of relevant apoptotic markers depicted an apoptosis by steroidal imidazopyridines in A549 cells. Annexin V-FITC/PI staining data indicated that compounds could effectively induce apoptosis in A549 cells in a dose-dependent manner. FACS analysis shows that the compound 6 bring about cell cycle arrest at 2.62 μM concentration.
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Affiliation(s)
- Ayaz Mahmood Dar
- Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India.
| | - Manzoor Ahmad Gatoo
- Department of Biochemistry, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh 202 002, India
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23
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Dogandzhiyski P, Ghidini A, Danneberg F, Strömberg R, Göbel MW. Studies on Tris(2-aminobenzimidazole)-PNA Based Artificial Nucleases: A Comparison of Two Analytical Techniques. Bioconjug Chem 2015; 26:2514-9. [PMID: 26544527 DOI: 10.1021/acs.bioconjchem.5b00534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new peptide nucleic acid (PNA) construct carrying a tris(2-aminobenzimidazole) phosphodiester cleaver is presented. This non-metal-based artificial nuclease hydrolyzes RNA substrates that form a bulge upon binding to the PNA. Reaction rates depend on the bulge sequence. For conjugates of tris(2-aminobenzimidazole), substrate turnover is shown for the first time. Two methods of analysis for the kinetics are compared: IE-HPLC separation of oligonucleotide fragments and analysis of Cy5-labeled oligonucleotide fragments by denaturating PAGE on a DNA sequencer, respectively. The different methods give rates that are in the same range where, in general, the substrates for the sequencer method give slightly lower rates.
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Affiliation(s)
- Plamena Dogandzhiyski
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden
| | - Friederike Danneberg
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden
| | - Michael W Göbel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
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24
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Li Z, Qiao J, Jia Z, Meng S. Synthesis of the Pyridine Hydrazones as Metal-free Artificial Nucleases. CHEM LETT 2015. [DOI: 10.1246/cl.150428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Zhifen Li
- School of Chemical and Environmental Engineering, Datong University
| | - Jun Qiao
- School of Chemical and Environmental Engineering, Datong University
| | - Zhifang Jia
- School of Chemical and Environmental Engineering, Datong University
| | - Shuangming Meng
- School of Chemical and Environmental Engineering, Datong University
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25
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Dar AM, Gatoo MA, Ahmad A, Ahmad MS, Najar MH, Shamsuzzaman. DNA Interaction Studies and In Vitro Cytotoxicity of Newly Synthesized Steroidal Imidazolidinones. J Fluoresc 2015; 25:1377-87. [PMID: 26245453 DOI: 10.1007/s10895-015-1628-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/26/2015] [Indexed: 10/23/2022]
Abstract
New steroidal imidazolidinone derivatives (7-9) were synthesized after reacting steroidal thiosemicarbazones with oxalyl chloride in absolute ethanol. After characterization by spectral and analytical data, the interaction studies of compounds (7-9) with DNA were carried out by UV-vis, fluorescence spectroscopy, circular dichroism, molecular docking and gel electrophoresis. The compounds bind to DNA preferentially through electrostatic and hydrophobic interactions with Kb; 2.31 × 10(4) M(-1), 2.57 × 10(4) M(-1) and 2.16 × 10(4) M(-1), respectively indicating the higher binding affinity of compound 8 towards DNA. Gel electrophoresis demonstrated that the compounds 7-9 show strong interaction during the cleavage activity with pBR322 DNA. The docking study suggested the intercalation of imidazolidinone moiety of steroid derivative in minor groove of DNA. During in vitro cytotoxicity, compounds 7-9 revealed potential toxicity against the different human cancer cells (MTT assay). Apoptotic degradation of DNA in presence of compounds 7-9 was analyzed by agarose gel electrophoresis and visualized by ethidium bromide staining (comet assay). FACS analysis shows that the compound 8 bring about cell cycle arrest at 7 μM concentration.
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Affiliation(s)
- Ayaz Mahmood Dar
- Department of Chemistry, Aligarh Muslim University, Aligarh, 202 002, India. .,Department of Chemistry, Government Degree College, Kulgam Kashmir, 192231, J&K, India.
| | - Manzoor Ahmad Gatoo
- Department of Biochemistry, Jawaharlal Nehru Medical College Aligarh Muslim University, Aligarh, 202 002, India
| | - Ajaz Ahmad
- Department of Biochemistry, Aligarh Muslim University, Aligarh, 202 002, India
| | - Mir Shabeer Ahmad
- Department of Chemistry, Government Degree College, Kulgam Kashmir, 192231, J&K, India
| | | | - Shamsuzzaman
- Department of Chemistry, Aligarh Muslim University, Aligarh, 202 002, India
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26
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2,6-Bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)pyridine and Its Benzene Analog as Nonmetallic Cleaving Agents of RNA Phosphodiester Linkages. Int J Mol Sci 2015; 16:17798-811. [PMID: 26247935 PMCID: PMC4581222 DOI: 10.3390/ijms160817798] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 07/13/2015] [Accepted: 07/28/2015] [Indexed: 01/10/2023] Open
Abstract
2,6-Bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)pyridine (11a) and 1,3-bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)benzene (11b) have been shown to accelerate at 50 mmol·L−1 concentration both the cleavage and mutual isomerization of uridylyl-3′,5′-uridine and uridylyl-2′,5′-uridine by up to two orders of magnitude. The catalytically active ionic forms are the tri- (in the case of 11b) tetra- and pentacations. The pyridine nitrogen is not critical for efficient catalysis, since the activity of 11b is even slightly higher than that of 11a. On the other hand, protonation of the pyridine nitrogen still makes 11a approximately four times more efficient as a catalyst, but only for the cleavage reaction. Interestingly, the respective reactions of adenylyl-3′,5′-adenosine were not accelerated, suggesting that the catalysis is base moiety selective.
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27
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In vitro cytotoxcity and interaction of new steroidal oxadiazinanones with calf thymus DNA using molecular docking, gel electrophoresis and spectroscopic techniques. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 148:340-350. [DOI: 10.1016/j.jphotobiol.2015.04.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/21/2015] [Accepted: 04/27/2015] [Indexed: 11/23/2022]
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28
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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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29
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Salvio R. The guanidinium unit in the catalysis of phosphoryl transfer reactions: from molecular spacers to nanostructured supports. Chemistry 2015; 21:10960-71. [PMID: 25940903 DOI: 10.1002/chem.201500789] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Examples of guanidinium-based artificial phosphodiesterases are illustrated in this review article. A wide set of collected catalytic systems are presented, from the early examples to the most recent developments of the use of this unit in the design of supramolecular catalysts. Special attention is dedicated to illustrate the operating catalytic mechanism and the role of guanidine/ium units in the catalysis. One or more of these units can act by themselves or in conjunction with other active units. The analogy with the mechanism of enzymatic systems is presented and discussed. In the last part of this overview, recent examples of guanidinophosphodiesterases based on nanostructured supports are reported, namely gold-monolayer-protected clusters and polymer brushes grafted to silica nanoparticles. The issue of the dependence of the catalytic performance on the preorganization of the spacer is tackled and discussed in terms of effective molarity, a parameter that can be taken as a quantitative measurement of this preorganization for both conventional molecular linker and nanosized supports.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Chimica and IMC-CNR, Sezione Meccanismi di Reazione, La Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 (Italy).
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30
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31
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Danneberg F, Ghidini A, Dogandzhiyski P, Kalden E, Strömberg R, Göbel MW. Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole). Beilstein J Org Chem 2015; 11:493-8. [PMID: 25977723 PMCID: PMC4419560 DOI: 10.3762/bjoc.11.55] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/02/2015] [Indexed: 12/19/2022] Open
Abstract
Tris(2-aminobenzimidazole) conjugates with antisense oligonucleotides are effective site-specific RNA cleavers. Their mechanism of action is independent of metal ions. Here we investigate conjugates with peptide nucleic acids (PNA). RNA degradation occurs with similar rates and substrate specificities as in experiments with DNA conjugates we performed earlier. Although aggregation phenomena are observed in some cases, proper substrate recognition is not compromised. While our previous synthesis of 2-aminobenzimidazoles required an HgO induced cyclization step, a mercury free variant is described herein.
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Affiliation(s)
- Friederike Danneberg
- Institute for Organic Chemistry and Chemical Biology, Goethe Universität Frankfurt, Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
| | - Alice Ghidini
- Karolinska Institutet, Department of Biosciences and Nutrition, Novum, SE-141 83 Huddinge, Sweden
| | - Plamena Dogandzhiyski
- Institute for Organic Chemistry and Chemical Biology, Goethe Universität Frankfurt, Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
| | - Elisabeth Kalden
- Institute for Organic Chemistry and Chemical Biology, Goethe Universität Frankfurt, Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
| | - Roger Strömberg
- Karolinska Institutet, Department of Biosciences and Nutrition, Novum, SE-141 83 Huddinge, Sweden
| | - Michael W Göbel
- Institute for Organic Chemistry and Chemical Biology, Goethe Universität Frankfurt, Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
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32
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Tahir S, Badshah A, Hussain RA. Guanidines from ‘toxic substances’ to compounds with multiple biological applications – Detailed outlook on synthetic procedures employed for the synthesis of guanidines. Bioorg Chem 2015; 59:39-79. [DOI: 10.1016/j.bioorg.2015.01.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/13/2015] [Accepted: 01/19/2015] [Indexed: 11/25/2022]
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33
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Savelli C, Salvio R. Guanidine-Based Polymer Brushes Grafted onto Silica Nanoparticles as Efficient Artificial Phosphodiesterases. Chemistry 2015; 21:5856-63. [DOI: 10.1002/chem.201406526] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Indexed: 12/20/2022]
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34
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Ma C, Chen H, Li C, Zhang J, Qiao R. An IDB-containing low molecular weight short peptide as an efficient DNA cleavage reagent. Org Biomol Chem 2015; 13:4524-31. [DOI: 10.1039/c4ob02518k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present poly(aspartic acid) grafting bis-amine conjugates as artificial nucleases, which can effectively induce double-strand DNA cleavage.
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Affiliation(s)
- Chunying Ma
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Huan Chen
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Chao Li
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Jin Zhang
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
| | - Renzhong Qiao
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P. R. China
- State Key Laboratory of Medicinal Chemical Biology
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35
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Burakova E, Kovalev N, Zenkova M, Vlassov V, Silnikov V. Structure–activity relationships in new polycationic molecules based on two 1,4-diazabicyclo[2.2.2]octanes as artificial ribonucleases. Bioorg Chem 2014; 57:127-131. [DOI: 10.1016/j.bioorg.2014.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/10/2014] [Accepted: 10/12/2014] [Indexed: 11/30/2022]
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36
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Guo W, Wei J, Liu Y, Li C. Construction of anti-1,2-diols bearing chiral tertiary alcohol moiety using free hydroxyacetone as aldol donor by imidazole-based prolineamide catalyst. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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DNA binding, docking studies, artificial nuclease activity and in vitro cytotoxicity of newly synthesized steroidal 1H–pyrimidines. CR CHIM 2014. [DOI: 10.1016/j.crci.2013.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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38
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Göbel MW, Roussev CD, Scheffer U. RNA Cleavage Catalyzed by Amphoteric Bis(acyl)guanidinium Derivatives. Helv Chim Acta 2014. [DOI: 10.1002/hlca.201300308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Uzzaman S, Dar AM, Sohail A, Bhat S, mustafa MF, Khan Y. Synthesis, molecular docking and biological evaluation of new steroidal 4H-pyrans. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 117:493-501. [PMID: 24021949 DOI: 10.1016/j.saa.2013.08.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 07/27/2013] [Accepted: 08/03/2013] [Indexed: 06/02/2023]
Abstract
A series of new steroidal 4H-pyrans (4-6) have been synthesized from steroidal α, β-unsaturated ketones (1-3). The products (4-6) were characterized by IR, (1)H NMR, (13)C NMR, MS and analytical data. The interaction studies of compounds (4-6) with DNA were carried out by employing gel electrophoresis, UV-vis and fluorescence spectroscopy. The gel electrophoresis pattern revealed that compounds (4-6) bind to DNA and also demonstrated that the compound 6 alone or in presence of Cu (II) causes the nicking of supercoiled pBR322. The compounds 4 and 5 bind to DNA preferentially through electrostatic and hydrophobic interactions with Kb values found to be 5.3×10(3) and 3.7×10(3) M(-1), respectively, indicating the higher binding affinity of compound 4 towards DNA. The docking study suggested the intercalation of compounds in between the nucleotide base pairs. The cytotoxicity and genotoxicity of the newly synthesized compounds were checked by MTT and comet assay, respectively during which compound 6 showed potential behaviour.
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Affiliation(s)
- Shams Uzzaman
- Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India.
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40
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Salvio R, Cincotti A. Guanidine based self-assembled monolayers on Au nanoparticles as artificial phosphodiesterases. RSC Adv 2014. [DOI: 10.1039/c4ra03150d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gold nanoparticles passivated with a catalytic monolayer based on guanidine exhibit high cooperativity and efficiency in the cleavage of phosphodiesters.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Chimica and IMC – CNR Sezione Meccanismi di Reazione
- Università La Sapienza
- 00185 Roma, Italy
| | - Antonio Cincotti
- Dipartimento di Chimica and IMC – CNR Sezione Meccanismi di Reazione
- Università La Sapienza
- 00185 Roma, Italy
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41
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Lee SK, Tan KW, Ng SW. Zinc, copper and nickel derivatives of 2-[2-bromoethyliminomethyl]phenol as topoisomerase inhibitors exhibiting anti-proliferative and anti-metastatic properties. RSC Adv 2014. [DOI: 10.1039/c4ra09256b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Transition metal (Zn, Cu and Ni) derivatives of (2-[2-bromoethyliminomethyl]phenol), were found to inhibit topoisomerase I activity, induce DNA cleavage and bind to calf thymus DNA. The compounds are also cytotoxic and anti-invasive against PC3.
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Affiliation(s)
- Sze Koon Lee
- Department of Chemistry
- University of Malaya
- Kuala Lumpur, Malaysia
| | - Kong Wai Tan
- Department of Chemistry
- University of Malaya
- Kuala Lumpur, Malaysia
| | - Seik Weng Ng
- Department of Chemistry
- University of Malaya
- Kuala Lumpur, Malaysia
- Chemistry Department
- Faculty of Science
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42
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Salvio R, Cacciapaglia R, Mandolini L, Sansone F, Casnati A. Diguanidinocalix[4]arenes as effective and selective catalysts of the cleavage of diribonucleoside monophosphates. RSC Adv 2014. [DOI: 10.1039/c4ra05751a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Upper rim diguanidino-cone-calix[4]arenes catalyze the hydrolytic cleavage of diribonucleoside monophosphates in aqueous DMSO with good substrate selectivity and rate accelerations approaching 105-fold in the most favourable substrate-catalyst combinations.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Chimica and IMC – CNR Sezione Meccanismi di Reazione
- Università La Sapienza
- 00185 Roma, Italy
| | - Roberta Cacciapaglia
- Dipartimento di Chimica and IMC – CNR Sezione Meccanismi di Reazione
- Università La Sapienza
- 00185 Roma, 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
- 43124 Parma, Italy
| | - Alessandro Casnati
- Dipartimento di Chimica
- Università degli Studi di Parma
- 43124 Parma, Italy
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43
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Thiyagarajan D, Goswami S, Kar C, Das G, Ramesh A. A prospective antibacterial for drug-resistant pathogens: a dual warhead amphiphile designed to track interactions and kill pathogenic bacteria by membrane damage and cellular DNA cleavage. Chem Commun (Camb) 2014; 50:7434-6. [DOI: 10.1039/c4cc02354d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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An D, Ye Z. Synthesis and DNA Cleavage Activity of Piperazine Containing Guanidinoethyl and Hydroxyethyl Side Arms. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201300321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Shamsuzzaman, Dar AM, Khan Y, Sohail A. Synthesis and biological studies of steroidal pyran based derivatives. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 129:36-47. [DOI: 10.1016/j.jphotobiol.2013.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 09/17/2013] [Accepted: 09/25/2013] [Indexed: 10/26/2022]
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46
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Feng FM, Cai S, Liu FA, Xie JQ. Studies of DNA-Binding and DNA-Cutting Mechanism of an Azamacrocyclic Cerium Complex with Carboxyl Branch. PROGRESS IN REACTION KINETICS AND MECHANISM 2013. [DOI: 10.3184/146867813x13738207456695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
An azamacrocyclic compound with a carboxyl branch, 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclo-tetradecane- N/-acetic acid (L), and its cerium complex were synthesised and characterised. The mode of combination of the cerium complex with DNA was investigated by fluorescence and UV-Vis absorption spectroscopy. The cutting function of the cerium complex towards supercoiled DNA was studied by the gel electrophoresis method. The results show that metal complex can bind to the phosphate group of DNA double helix and promote the hydrolysis of the phosphodiester bond of supercoiled DNA (Form I); under certain conditions, supercoiled form DNA (Form I) was transformed into the nicked form DNA (Form II) under the strong cutting effect of the macrocyclic cerium complex; the cutting is completed by a hydrolysis mechanism.
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Affiliation(s)
- Fa-mei Feng
- College of Chemistry and Pharmaceutical Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan 643000, P.R. China
| | - Shulan Cai
- College of Chemistry and Pharmaceutical Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan 643000, P.R. China
| | - Fu-an Liu
- College of Chemistry and Pharmaceutical Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan 643000, P.R. China
| | - Jia-qing Xie
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, P.R. China
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47
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Parveen M, Malla AM, Yaseen Z, Ali A, Alam M. Synthesis, characterization, DNA-binding studies and acetylcholinesterase inhibition activity of new 3-formyl chromone derivatives. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 130:179-87. [PMID: 24333766 DOI: 10.1016/j.jphotobiol.2013.11.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/29/2013] [Accepted: 11/18/2013] [Indexed: 01/06/2023]
Abstract
A series of new substituted 3-formyl chromone derivatives (4-6) were synthesized by one step reaction methodology by knoevenagel condensation, structurally similar to known bisintercalators. The new compounds were characterized by IR, (1)H NMR, (13)C NMR, MS and analytical data. The in vitro DNA binding profile of compounds (4-6) was carried out by absorption, fluorescence and viscosity measurements. It was found that synthesized compounds, especially compound 6 (evident from binding constant value) bind strongly with calf thymus DNA, presumably via an intercalation mode. Additionally, molecular docking studies of compounds (4-6) were carried out with B-DNA (PDBID: 1BNA) which revealed that partial intercalative mode of mechanism is operational in synthesized compounds (4-6) with CT-DNA. The binding constants evaluated from fluorescence spectroscopy of compounds with CT-DNA follows the order compound 6>compound 5>compound 4. All the compounds (4-6) were screened for acetylcholinesterase inhibition assay. It can be inferred from data, that compound (6) showed potent AChE inhibition having IC50=0.27μM, almost in vicinity to reference drug Tacrine (IC50=0.19μM).
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Affiliation(s)
- Mehtab Parveen
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India.
| | - Ali Mohammed Malla
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Zahid Yaseen
- Department of Civil Engineering, Islamic University of Science and Technology, Kashmir 192122, India
| | - Akhtar Ali
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Mahboob Alam
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
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48
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Shamsuzzaman, Dar AM, Yaseen Z, Alam K, Hussain A, Gatoo MA. Steroidal pyrimidines: Synthesis, characterization, molecular docking studies with DNA and in vitro cytotoxicity. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.04.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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49
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Salvio R, Mandolini L, Savelli C. Guanidine-guanidinium cooperation in bifunctional artificial phosphodiesterases based on diphenylmethane spacers; gem-dialkyl effect on catalytic efficiency. J Org Chem 2013; 78:7259-63. [PMID: 23772969 DOI: 10.1021/jo401085z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Diphenylmethane derivatives 1-3, decorated with two guanidine units, are effective catalysts of HPNP transesterification. Substitution of the methylene group of the parent diphenylmethane spacer with cyclohexylidene and adamantylidene moieties enhances catalytic efficency, with gem-dialkyl effect accelerations of 4.5 and 9.1, respectively. Activation parameters and DFT calculations of the rotational barriers around the C-Ar bonds indicate that a major contribution to the driving force for enhanced catalysis is entropic in nature.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Chimica and IMC-CNR Sezione Meccanismi di Reazione, Università La Sapienza, P.le Aldo Moro 5, 00185 Roma, Italy.
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50
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Zhu TH, Wang SY, Wang GN, Ji SJ. Cobalt-Catalyzed Oxidative Isocyanide Insertion to Amine-Based Bisnucleophiles: Diverse Synthesis of Substituted 2-Aminobenzimidazoles, 2-Aminobenzothiazoles, and 2-Aminobenzoxazoles. Chemistry 2013; 19:5850-3. [DOI: 10.1002/chem.201300239] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 02/25/2013] [Indexed: 01/14/2023]
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