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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Saleh LY, Ora M, Lönnberg T. Organomercury oligonucleotide conjugates as artificial ribonucleases. J Inorg Biochem 2023; 247:112331. [PMID: 37480764 DOI: 10.1016/j.jinorgbio.2023.112331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/03/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Two oligonucleotide conjugates sharing the same sequence but incorporating a different 5'-terminal organometallic moiety were synthesized, by either direct mercuration in solution or oximation with an organomercury aldehyde on solid support. The potential of these conjugates to serve as new type of artificial ribonucleases was tested with a complementary 2´-O-methyl-RNA target sequence featuring a single cleavable RNA phosphodiester linkage. Both organomercury oligonucleotides greatly outperformed their metal-free counterparts as well as the previously reported small molecule organomercury RNA cleaving agent in catalytic activity, providing an important proof-of-concept. Compared to state-of-the-art metal-dependent artificial ribonucleases, however, the observed activity was modest.
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Affiliation(s)
- Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Mikko Ora
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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3
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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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4
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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: 6] [Impact Index Per Article: 2.0] [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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5
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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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6
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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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7
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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: 6] [Impact Index Per Article: 2.0] [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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8
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Salvio R, D'Abramo M. Conformational Mobility and Efficiency in Supramolecular Catalysis. A Computational Approach to Evaluate the Performances of Enzyme Mimics. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Riccardo Salvio
- Dipartimento di Scienze e Tecnologie Chimiche Università degli Studi di Roma “Tor Vergata” Via della Ricerca Scientifica 1 00133 Roma Italy
- ISB CNR Sezione Meccanismi di Reazione Università degli Studi di Roma La Sapienza 00185 Roma Italy
| | - Marco D'Abramo
- Dipartimento di Chimica Università degli Studi di Roma La Sapienza P. le Aldo Moro 5 00185 Roma Italy
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9
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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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10
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Pavlova AS, Ogurtsova PA, Koroleva LS, Serpokrylova IY, Lomzov AA, Pyshnaya IA, Silnikov VN, Pyshnyi DV. Novel Bisimidazole-Containing Peptidomimetic Molecules for Мetal-Independent RNA Cleavage: Synthesis and Solid-Phase Screening Method. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Stasińska AR, Putaj P, Chmielewski MK. Disulfide bridge as a linker in nucleic acids' bioconjugation. Part II: A summary of practical applications. Bioorg Chem 2019; 95:103518. [PMID: 31911308 DOI: 10.1016/j.bioorg.2019.103518] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/15/2022]
Abstract
Disulfide conjugation invariably remains a key tool in research on nucleic acids. This versatile and cost-effective method plays a crucial role in structural studies of DNA and RNA as well as their interactions with other macromolecules in a variety of biological systems. In this article we review applications of disulfide-bridged conjugates of oligonucleotides with other (bio)molecules such as peptides, proteins etc. and present key findings obtained with their help.
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Affiliation(s)
- Anna R Stasińska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Piotr Putaj
- FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland.
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12
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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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13
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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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14
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Wang Y, Liu E, Lam CH, Perrin DM. A densely modified M 2+-independent DNAzyme that cleaves RNA efficiently with multiple catalytic turnover. Chem Sci 2018; 9:1813-1821. [PMID: 29675226 PMCID: PMC5890787 DOI: 10.1039/c7sc04491g] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/04/2018] [Indexed: 12/12/2022] Open
Abstract
Sequence-specific cleavage of RNA targets in the absence of a divalent metal cation (M2+) has been a long-standing goal in bioorganic chemistry. Herein, we report the in vitro selection of novel RNA cleaving DNAzymes that are selected using 8-histaminyl-deoxyadenosine (dAimTP), 5-guanidinoallyl-deoxyuridine (dUgaTP), and 5-aminoallyl-deoxycytidine (dCaaTP) along with dGTP. These modified dNTPs provide key functionalities reminiscent of the active sites of ribonucleases, notably RNase A. Of several such M2+-free DNAymes, DNAzyme 7-38-32 cleaves a 19 nt all-RNA substrate with multiple-turnover, under simulated physiological conditions wherein only 0.5 mM Mg2+ was present, attaining values of kcat of 1.06 min-1 and a KM of 1.37 μM corresponding to a catalytic efficiency of ∼106 M-1 min-1. Therefore, Dz7-38-32 represents a promising candidate towards the development of therapeutically efficient DNAzymes.
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Affiliation(s)
- Yajun Wang
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
| | - Erkai Liu
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
| | - Curtis H Lam
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
| | - David M Perrin
- Chemistry Dept. , UBC , 2036 Main Mall , Vancouver , BC V6T1Z1 , Canada .
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15
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Murtola M, Ghidini A, Virta P, Strömberg R. Zinc Ion-Dependent Peptide Nucleic Acid-Based Artificial Enzyme that Cleaves RNA-Bulge Size and Sequence Dependence. Molecules 2017; 22:molecules22111856. [PMID: 29109368 PMCID: PMC6150328 DOI: 10.3390/molecules22111856] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 11/17/2022] Open
Abstract
In this report, we investigate the efficiency and selectivity of a Zn2+-dependent peptide nucleic acid-based artificial ribonuclease (PNAzyme) that cleaves RNA target sequences. The target RNAs are varied to form different sizes (3 and 4 nucleotides, nt) and sequences in the bulge formed upon binding to the PNAzyme. PNAzyme-promoted cleavage of the target RNAs was observed and variation of the substrate showed a clear dependence on the sequence and size of the bulge. For targets that form 4-nt bulges, we identified systems with an improved efficacy (an estimated half-life of ca 7–8 h as compared to 11–12 h for sequences studied earlier) as well as systems with an improved site selectivity (up to over 70% cleavage at a single site as compared to 50–60% with previous targets sequences). For targets forming 3-nt bulges, the enhancement compared to previous systems was even more pronounced. Compared to a starting point of targets forming 3-nt AAA bulges (half-lives of ca 21–24 h), we could identify target sequences that were cleaved with half-lives three times lower (ca 7–8 h), i.e., at rates similar to those found for the fastest 4-nt bulge system. In addition, with the 3-nt bulge RNA target site selectivity was improved even further to reach well over 80% cleavage at a specific site.
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Affiliation(s)
- Merita Murtola
- Department of Chemistry, University of Turku, 20014 Turku, Finland.
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Stockholm, Sweden.
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Stockholm, Sweden.
| | - Pasi Virta
- Department of Chemistry, University of Turku, 20014 Turku, Finland.
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Stockholm, Sweden.
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16
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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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17
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Yu Z, Cowan JA. Catalytic Metallodrugs: Substrate-Selective Metal Catalysts as Therapeutics. Chemistry 2017; 23:14113-14127. [PMID: 28688119 DOI: 10.1002/chem.201701714] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Zhen Yu
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
| | - James A. Cowan
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
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18
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Patutina OA, Bichenkova EV, Miroshnichenko SK, Mironova NL, Trivoluzzi LT, Burusco KK, Bryce RA, Vlassov VV, Zenkova MA. miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells. Biomaterials 2017; 122:163-178. [PMID: 28126663 DOI: 10.1016/j.biomaterials.2017.01.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/09/2017] [Accepted: 01/12/2017] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are active regulators in malignant growth and constitute potential targets for anticancer therapy. Consequently, considerable effort has focused on identifying effective ways to modulate aberrant miRNA expression. Here we introduce and assess a novel type of chemically engineered biomaterial capable of cleaving specific miRNA sequences, i.e. miRNA-specific artificial ribonucleases (hereafter 'miRNase'). The miRNase template presented here consists of the catalytic peptide Acetyl-[(LeuArg)2Gly]2 covalently attached to a miRNA-targeting oligonucleotide, which can be linear or hairpin. The peptide C-terminus is conjugated to an aminohexyl linker located at either the 3'- or 5'-end of the oligonucleotide. The cleavage efficacy, structural aspects of cleavage and biological relevance of a set of these designed miRNases was assayed with respect to highly oncogenic miR-21. Several miRNases demonstrated effective site-selective cleavage of miR-21 exclusively at G-X bonds. One of the most efficient miRNase was shown to specifically inhibit miR-21 in lymphosarcoma cells and lead to a reduction in their proliferative activity. This report provides the first experimental evidence that metallo-independent peptide-oligonucleotide chemical ribonucleases are able to effectively and selectively down-regulate oncogenic miRNA in tumour cells, thus suggesting their potential in development of novel therapeutics aimed at overcoming overexpression of disease-related miRNAs.
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Affiliation(s)
- Olga A Patutina
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Svetlana K Miroshnichenko
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia
| | - Nadezhda L Mironova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia
| | - Linda T Trivoluzzi
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Kepa K Burusco
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Richard A Bryce
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia
| | - Marina A Zenkova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia.
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19
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Ghidini A, Murtola M, Strömberg R. Influence of conjugation and other structural changes on the activity of Cu²⁺ based PNAzymes. Org Biomol Chem 2016; 14:2768-73. [PMID: 26856621 DOI: 10.1039/c5ob02394g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have previously shown that PNA-neocuproine conjugates can act as artificial RNA restriction enzymes. In the present study we have additionally conjugated the PNA with different entities, such as oligoethers, peptides etc. and also constructed systems where the PNA is designed to clamp the target RNA forming a triplex. Some conjugations are detrimental for the activity while most are silent which means that conjugation can be done to alter physical properties without losing activity. Conjugation with a single oligoether close to the neocuproine does enhance the rate almost twofold compared to the system without the oligoether. The systems designed to clamp the RNA target by forming a triplex retain the activity if the added oligoT sequence is 5 PNA units or shorter and extends the arsenal of artificial RNA restriction enzymes. Changing the direction of a closing base pair, where the target RNA forms a bulge, from a GC to a CG pair enhances the rate of cleavage somewhat without compromising the selectivity, leading to the so far most efficient artificial nuclease reported.
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Affiliation(s)
- A Ghidini
- Karolinska Institutet, Department of Biosciences and Nutrition, Novum, Hälsovägen 7, S-14183 Huddinge, Sweden.
| | - M Murtola
- Karolinska Institutet, Department of Biosciences and Nutrition, Novum, Hälsovägen 7, S-14183 Huddinge, Sweden. and Turku University, Department of Chemistry, Turku 20014, Finland
| | - R Strömberg
- Karolinska Institutet, Department of Biosciences and Nutrition, Novum, Hälsovägen 7, S-14183 Huddinge, Sweden.
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20
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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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21
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Salvio R, Volpi S, Cacciapaglia R, Sansone F, Mandolini L, Casnati A. Upper Rim Bifunctional cone-Calix[4]arenes Based on a Ligated Metal Ion and a Guanidinium Unit as DNAase and RNAase Mimics. J Org Chem 2016; 81:4728-35. [DOI: 10.1021/acs.joc.6b00644] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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, Parco Area
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
| | - Francesco Sansone
- Dipartimento
di Chimica, Università degli Studi di Parma, Parco Area
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
| | - Alessandro Casnati
- Dipartimento
di Chimica, Università degli Studi di Parma, Parco Area
delle Scienze 17/a, 43124 Parma, Italy
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22
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Wang X, Liang X. Azobenzene-modified antisense oligonucleotides for site-specific cleavage of RNA with photocontrollable property. RSC Adv 2016. [DOI: 10.1039/c6ra20954h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Photoresponsive azobenzene-modified antisense oligonucleotides for site-specific RNA cleavage by RNase H.
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Affiliation(s)
- Xingyu Wang
- School of Food Science and Engineering
- Ocean University of China
- Qingdao
- China
- College of Food Engineering and Nutritional Science
| | - Xingguo Liang
- School of Food Science and Engineering
- Ocean University of China
- Qingdao
- China
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23
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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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24
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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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25
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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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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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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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28
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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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29
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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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30
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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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31
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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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32
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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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33
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Prill JM, Šubr V, Pasquarelli N, Engler T, Hoffmeister A, Kochanek S, Ulbrich K, Kreppel F. Traceless bioresponsive shielding of adenovirus hexon with HPMA copolymers maintains transduction capacity in vitro and in vivo. PLoS One 2014; 9:e82716. [PMID: 24475024 PMCID: PMC3903484 DOI: 10.1371/journal.pone.0082716] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 10/27/2013] [Indexed: 11/18/2022] Open
Abstract
Capsid surface shielding of adenovirus vectors with synthetic polymers is an emerging technology to reduce unwanted interactions of the vector particles with cellular and non-cellular host components. While it has been shown that attachment of shielding polymers allows prevention of undesired interactions, it has become evident that a shield which is covalently attached to the vector surface can negatively affect gene transfer efficiency. Reasons are not only a limited receptor-binding ability of the shielded vectors but also a disturbance of intracellular trafficking processes, the latter depending on the interaction of the vector surface with the cellular transport machinery. A solution might be the development of bioresponsive shields that are stably maintained outside the host cell but released upon cell entry to allow for efficient gene delivery to the nucleus. Here we provide a systematic comparison of irreversible versus bioresponsive shields based on synthetic N-(2-hydroxypropyl)methacrylamide (HPMA) copolymers. In addition, the chemical strategy used for generation of the shield allowed for a traceless bioresponsive shielding, i.e., polymers could be released from the vector particles without leaving residual linker residues. Our data demonstrated that only a bioresponsive shield maintained the high gene transfer efficiency of adenovirus vectors both in vitro and in vivo. As an example for bioresponsive HPMA copolymer release, we analyzed the in vivo gene transfer in the liver. We demonstrated that both the copolymer's charge and the mode of shielding (irreversible versus traceless bioresponsive) profoundly affected liver gene transfer and that traceless bioresponsive shielding with positively charged HPMA copolymers mediated FX independent transduction of hepatocytes. In addition, we demonstrated that shielding with HPMA copolymers can mediate a prolonged blood circulation of vector particles in mice. Our results have significant implications for the future design of polymer-shielded Ad and provide a deeper insight into the interaction of shielded adenovirus vector particles with the host after systemic delivery.
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Affiliation(s)
| | - Vladimír Šubr
- Department of Biomedicinal Polymers, Institute of Macromolecular Chemistry, v.v.i., Academy of Sciences, Prague, Czech Republic
| | | | - Tatjana Engler
- Department of Gene Therapy, Ulm University, Ulm, Germany
| | | | | | - Karel Ulbrich
- Department of Biomedicinal Polymers, Institute of Macromolecular Chemistry, v.v.i., Academy of Sciences, Prague, Czech Republic
| | - Florian Kreppel
- Department of Gene Therapy, Ulm University, Ulm, Germany
- * E-mail:
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34
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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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35
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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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36
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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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37
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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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38
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Xu L, Ji C, Bai Y, He J, Liu K. DNA duplex-supported artificial esterase mimicking by cooperative grafting functional groups. Biochem Biophys Res Commun 2013; 434:516-20. [PMID: 23583410 DOI: 10.1016/j.bbrc.2013.03.106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 03/20/2013] [Indexed: 10/26/2022]
Abstract
The molecular structures of enzyme mimics may be modified to optimize their catalytic properties. In this study, to generate artificial enzyme mimics, Watson-Crick base paired DNA duplexes were designed as scaffolds which were assembled by nucleotides modified with specific functional groups. This process allowed various functional groups to be precisely assembled at different sites on the duplexes. By using this strategy, the 5-[2-(1H-imidazolyl-4)-(E)-ethylene]-2'-deoxythymidine (1) analog with the 5-substituted imidazolyl group was incorporated into single strands of DNA. Upon DNA duplex formation, several combinations of the imidazolyl group were formed. Using p-nitrophenyl acetate as the substrate of the catalytic reaction, we evaluated the hydrolysis capabilities of the imidazolyl assemblies. The catalytic ability was closely related to the distribution of imidazolyl groups in the DNA duplex. The most effective catalytic center was that of the duplex O5-O6 construct with three imidazolyl groups. This construct displayed bell-shaped pH-dependent and Mg(2+)-independent kinetic curves, which are typical characteristics of imidazolyl-mediated catalytic reactions.
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Affiliation(s)
- Liang Xu
- Beijing Institute of Pharmacology and Toxicology, 27 Taiping Road, Beijing 100850, China
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39
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Hollenstein M, Hipolito CJ, Lam CH, Perrin DM. Toward the combinatorial selection of chemically modified DNAzyme RNase A mimics active against all-RNA substrates. ACS COMBINATORIAL SCIENCE 2013; 15:174-82. [PMID: 23485334 DOI: 10.1021/co3001378] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The convenient use of SELEX and related combinatorial methods of in vitro selection provides a formidable gateway for the generation of DNA enzymes, especially in the context of improving their potential as gene therapeutic agents. Here, we report on the selection of DNAzyme 12-91, a modified nucleic acid catalyst adorned with imidazole, ammonium, and guanidinium groups that provide for efficient M(2+)-independent cleavage of an all-RNA target sequence (kobs = 0.06 min(-1)). While Dz12-91 was selected for intramolecular cleavage of an all-RNA target, it surprisingly cleaves a target containing a lone ribocytosine unit with even greater efficiency (kobs = 0.27 min(-1)) than Dz9-86 (kobs = 0.13 min(-1)). The sequence composition of Dz12-91 bears a marked resemblance to that of Dz9-86 (kobs = 0.0014 min(-1) with an all-RNA substrate) that was selected from the same library to cleave a target containing a single ribonucleotide. However, small alterations in the sequence composition have a profound impact on the substrate preference and catalytic properties. Indeed, Dz12-91 displays the highest known rate enhancement for the M(2+)-independent cleavage of all-RNA targets. Hence, Dz12-91 represents a step toward the generation of potentially therapeutically active DNAzymes and further underscores the usefulness of modified triphosphates in selection experiments.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - Christopher J. Hipolito
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - Curtis H. Lam
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - David M. Perrin
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
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40
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Synthesis of Aryl-1,2,4,5-tetrazinane-3-thiones, in vitro DNA binding studies, nuclease activity and its antimicrobial activity. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.03.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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41
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Li F, Kang Q, Shan H, Chen L, Xie J. Regioselective N-Alkylation of 2-Aminoimidazoles with Alcohols to 2-(N-Alkylamino)imidazoles Catalyzed by the [Cp*IrCl2]2/K2CO3 System. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200698] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Baldini L, Cacciapaglia R, Casnati A, Mandolini L, Salvio R, Sansone F, Ungaro R. Upper rim guanidinocalix[4]arenes as artificial phosphodiesterases. J Org Chem 2012; 77:3381-9. [PMID: 22364173 DOI: 10.1021/jo300193y] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calix[4]arene derivatives, blocked in the cone conformation and functionalized with two to four guanidinium units at the upper rim were synthesized and investigated as catalysts in the cleavage of the RNA model compound 2-hydroxypropyl p-nitrophenyl phosphate. When compared with the behavior of a monofunctional model compound, the catalytic superiority of the calix[4]arene derivatives points to a high level of cooperation between catalytic groups. Combination of acidity measurements with the pH dependence of catalytic rates unequivocally shows that a necessary requisite for effective catalysis is the simultaneous presence, on the same molecular framework, of a neutral guanidine acting as a general base and a protonated guanidine acting as an electrophilic activator. The additional guanidinium (guanidine) group in the diprotonated (monoprotonated) trifunctional calix[4]arene acts as a more or less innocent spectator. This is not the case with the tetrasubstituted calix[4]arene, whose mono-, di-, and triprotonated forms are slightly less effective than the corresponding di- and triguanidinocalix[4]arene derivatives, most likely on account of a steric interference with HPNP caused by overcrowding.
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Affiliation(s)
- Laura Baldini
- Dipartimento di Chimica Organica e Industriale, Università degli Studi di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
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43
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Li ZF, Chen HL, Zhang LJ, Lu ZL. Synthesis of [12]aneN3-dipeptide conjugates as metal-free DNA nucleases. Bioorg Med Chem Lett 2012; 22:2303-7. [PMID: 22364814 DOI: 10.1016/j.bmcl.2012.01.075] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 01/16/2012] [Accepted: 01/20/2012] [Indexed: 11/28/2022]
Abstract
In this Letter, a series of macrocyclic polyamine [12]aneN(3)-dipeptide conjugates as a new type of metal-free nucleases were synthesized and fully characterized with (1)H NMR, (13)C NMR, IR, and HR-MS. Results indicate that these conjugates can bind to calf thymus DNA mainly through electrostatic interaction and can cleave the plasmid DNA at 200 μM (pH 7.2, 37°C), with an acceleration of 10(6)-fold via hydrolytic pathway.
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Affiliation(s)
- Zhi-Fen Li
- College of Chemistry, Beijing Normal University, Beijing, China
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Patel S, Rana J, Roy J, Huang H. Cleavage of pyrene-stabilized RNA bulge loops by trans-(±)-cyclohexane-1,2-diamine. Chem Cent J 2012; 6:3. [PMID: 22244351 PMCID: PMC3319420 DOI: 10.1186/1752-153x-6-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 01/13/2012] [Indexed: 11/10/2022] Open
Abstract
Chemical agents that cleave HIV genome can be potentially used for anti-HIV therapy. In this report, the cleavage of the upper stem-loop region of HIV-1 TAR RNA was studied in a variety of buffers containing organic catalysts. trans-(±)-Cyclohexane-1,2-diamine was found to cleave the RNA with the highest activity (31%, 37°C, 18 h). Cleavage of the RNA in trans-(±)-cyclohexane-1,2-diamine buffer was also studied when the RNA was hybridized with complementary DNAs. A pyrene-modified C3 spacer was incorporated to the DNA strand to facilitate the formation of a RNA bulge loop in the RNA/DNA duplex. In contrast, unmodified DNAs cannot efficiently generate RNA bulge loops, regardless of the DNA sequences. The results showed that the pyrene-stablized RNA bulge loops were efficiently and site-specifically cleaved by trans-(±)-cyclohexane-1,2-diamine.
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Affiliation(s)
- Sejal Patel
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, 323 Martin L, King Blvd, Newark, NJ, 07102, USA.
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45
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Polypeptide conjugates of D-penicillamine and idarubicin for anticancer therapy. J Control Release 2011; 158:215-23. [PMID: 22063001 DOI: 10.1016/j.jconrel.2011.10.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 10/20/2011] [Accepted: 10/24/2011] [Indexed: 11/22/2022]
Abstract
We investigated anticancer therapy with a novel combination of D-penicillamine (D-pen) and Idarubicin (Ida) in a synthetic dual drug conjugate (DDC). D-pen and Ida were covalently linked to poly(α)-L-glutamic acid (PGA) via reducible disulfide and acid-sensitive hydrazone bonds, respectively. The DDCs showed cell uptake and sustained release of the bound drugs in conditions mimicking the intracellular release media (10mM glutathione and pH 5.2). The in-vitro cytotoxicity of DDCs was comparable to unconjugated Ida in several sensitive and resistant cancer cell lines and correlated with the rate of cell uptake. In a single equivalent-dose pharmacokinetic study, DDCs enhanced the drug exposure by 7-fold and prolonged the plasma circulation half-life (t(1/2)) by 5-fold over unconjugated Ida. The therapeutic index of DDCs was 2-3-fold higher than unconjugated drugs. DDCs caused 89% tumor growth inhibition compared to 60% by unconjugated Ida alone and led to significant enhancement in the median survival (17%) of athymic nu/nu mice bearing NCI-H460 tumor xenografts.
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46
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Saleh AD, Miller PS. Hydrolysis of bulged nucleotides in hybrids formed by RNA and imidazole-derivatized oligo-2'-O-methylribonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:235-55. [PMID: 21491332 DOI: 10.1080/15257770.2011.569810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In order to enhance the efficacy of small antisense molecules, we examined a series of antisense oligonucleotides derivatized with functional groups designed to enable them to hydrolyze their RNA target. Solid phase synthetic methods were used to prepare imidazole-derivatized antisense oligo-2'-O-methylribonucleotides. Upon binding, these oligonucleotides create internal bulged bases in the target RNA that serve as sites for hydrolysis. We observed that an oligonucleotide derivatized with a side chain containing two imidazole groups was capable of hydrolyzing 58% of its RNA target when incubated with the target for 48 hours at 37°C and physiological pH.
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Affiliation(s)
- Anthony D Saleh
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
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Wang MQ, Zhang J, Zhang Y, Zhang DW, Liu Q, Liu JL, Lin HH, Yu XQ. Metal-free cleavage efficiency toward DNA by a novel PNA analog-bridged macrocyclic polyamine. Bioorg Med Chem Lett 2011; 21:5866-9. [PMID: 21855339 DOI: 10.1016/j.bmcl.2011.07.097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/18/2011] [Accepted: 07/26/2011] [Indexed: 10/17/2022]
Abstract
In this report we describe the synthesis of a new class of cyclen-contained compounds with novel peptide nucleic acid (PNA) analog motif. Target bis-cyclen derivative B was prepared and characterized by ESI-MS, NMR and HPLC. Interactions between compound B and calf thymus DNA were studied by thermal denaturation. Results indicate that the DNA binding affinity of B is stronger than that of mono-cyclen compound A, and the binding ability is little affected by the change of ionic strength. Agarose and denaturing polyacrylamide gel electrophoresis were used to assess the DNA cleavage activities. The macrocyclic polyamine-PNA analog conjugate B as a nuclease model can effectively cleave DNA via an oxidative pathway at micromolar concentration (10 μM) without the use of any additional metal ions. Meanwhile, the mono-cyclen compound A shows nearly no DNA cleavage effect under the same conditions.
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Affiliation(s)
- Ming-Qi Wang
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, PR China
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48
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Salvio R, Cacciapaglia R, Mandolini L. General base-guanidinium cooperation in bifunctional artificial phosphodiesterases. J Org Chem 2011; 76:5438-43. [PMID: 21612212 DOI: 10.1021/jo2004007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Artificial phosphodiesterases that combine a guanidinium unit with a general base connected by a m-xylylene linker catalyze the transesterification of the RNA model compound 2-hydroxypropyl p-nitrophenyl phosphate (HPNP). The bifunctional catalysts presented in this work show varying extents of cooperation between catalytic units and a rate enhancement of 4 × 10(4) in the most favorable case.
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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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Chen PY, Liu Y, Gao X, Xu NS, Niu J, Liu SY, Zhao Y. Evaluation Of Single-Stranded Oligonucleotide Cleavage Function Of Seryl-Histidine Dipeptide By Electrospray Ionization Mass Spectrometry. PHOSPHORUS SULFUR 2011. [DOI: 10.1080/10426507.2010.525771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Pei-yan Chen
- a The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , P. R. China
| | - Yan Liu
- a The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , P. R. China
| | - Xiang Gao
- a The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , P. R. China
| | - Niu-sheng Xu
- b Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun Center of Mass Spectrometry , Changchun , P. R. China
| | - Jun Niu
- b Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun Center of Mass Spectrometry , Changchun , P. R. China
| | - Shu-ying Liu
- b Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun Center of Mass Spectrometry , Changchun , P. R. China
| | - Yufen Zhao
- a The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , P. R. China
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50
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Lönnberg H. Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic insight. Org Biomol Chem 2011; 9:1687-703. [PMID: 21258754 DOI: 10.1039/c0ob00486c] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
RNA molecules participate in many fundamental cellular processes either as a carrier of genetic information or as a catalyst, and hence, RNA has received increasing interest both as a chemotherapeutic agent and as a target of chemotherapy. In addition the dual nature of RNA has led to the RNA-world concept, i.e. an assumption that the evolution at an early stage of life was based on RNA-like oligomers that were responsible for the storage and transfer of information and as catalysts maintained primitive metabolism. Accordingly, the kinetics and mechanisms of the cleavage of RNA phosphodiester bonds have received interest and it is hoped they will shed light on the mechanisms of enzyme action and on the development of artificial enzymes. The major mechanistic findings concerning the cleavage by small molecules and ions and their significance for the development of efficient and biologically applicable artificial catalysts for RNA hydrolysis are surveyed in the present perspective.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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