1
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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- 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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2
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Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
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Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
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3
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Luige O, Karalė K, Bose PP, Bollmark M, Tedebark U, Murtola M, Strömberg R. Influence of sequence variation on the RNA cleavage activity of Zn 2+-dimethyl-dppz-PNA-based artificial enzymes. RSC Adv 2022; 12:5398-5406. [PMID: 35425588 PMCID: PMC8981518 DOI: 10.1039/d1ra08319h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/30/2022] [Indexed: 11/21/2022] Open
Abstract
The development of Zn2+-dependent dimethyl-dppz-PNA conjugates (PNAzymes) as efficient site-specific artificial ribonucleases enables rapid sequence-specific degradation of clinically relevant RNA target sequences, but the significance of the RNA/PNAzyme sequence and structural demands for the identification of novel RNA targets are not fully understood. In the present study, we investigated the influence of sequence variation in the recognition arms of the RNA/PNAzyme complex on the RNA cleavage activity of the artificial enzymes. The base pairs closing the 3-nucleotide bulge region on both sides of the bulge as well as the neighbouring nucleobases were shown to significantly influence the RNA cleavage activity. Elongation of the RNA/PNAzyme complex was shown to be tolerated, although potentially prohibitive for catalytic turnover. The specificity of PNAzyme action was clearly demonstrated by the significantly reduced or absent cleavage activity in complexes containing mismatches. Further investigation into 2- and 4-nucleotide RNA bulges indicated that formation of 3-nucleotide bulges in the target RNA gives the optimal cleavage rates, while some potential off-target cleavage of formed 4-nucleotide bulges of select sequences should be considered.
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Affiliation(s)
- Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet Neo, 141 83 Huddinge Sweden
| | - Kristina Karalė
- Department of Biosciences and Nutrition, Karolinska Institutet Neo, 141 83 Huddinge Sweden
- RISE, Department of Chemical Process and Pharmaceutical Development Forskargatan 18 15136 Södertälje Sweden
| | - Partha Pratim Bose
- Department of Biosciences and Nutrition, Karolinska Institutet Neo, 141 83 Huddinge Sweden
| | - Martin Bollmark
- RISE, Department of Chemical Process and Pharmaceutical Development Forskargatan 18 15136 Södertälje Sweden
| | - Ulf Tedebark
- RISE, Department of Chemical Process and Pharmaceutical Development Forskargatan 18 15136 Södertälje Sweden
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet Neo, 141 83 Huddinge Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet Neo, 141 83 Huddinge Sweden
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4
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Synthetic strategies and structures of zinc(II) complexes with di-azine ligands based on salicylaldehyde or its derivatives. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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5
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Amirloo B, Staroseletz Y, Yousaf S, Clarke DJ, Brown T, Aojula H, Zenkova MA, Bichenkova EV. "Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge-loop inducing supramolecular conjugates. Nucleic Acids Res 2021; 50:651-673. [PMID: 34967410 PMCID: PMC8789077 DOI: 10.1093/nar/gkab1273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
Antisense sequence-specific knockdown of pathogenic RNA offers opportunities to find new solutions for therapeutic treatments. However, to gain a desired therapeutic effect, the multiple turnover catalysis is critical to inactivate many copies of emerging RNA sequences, which is difficult to achieve without sacrificing the sequence-specificity of cleavage. Here, engineering two or three catalytic peptides into the bulge-loop inducing molecular framework of antisense oligonucleotides achieved catalytic turnover of targeted RNA. Different supramolecular configurations revealed that cleavage of the RNA backbone upon sequence-specific hybridization with the catalyst accelerated with increase in the number of catalytic guanidinium groups, with almost complete demolition of target RNA in 24 h. Multiple sequence-specific cuts at different locations within and around the bulge-loop facilitated release of the catalyst for subsequent attacks of at least 10 further RNA substrate copies, such that delivery of only a few catalytic molecules could be sufficient to maintain knockdown of typical RNA copy numbers. We have developed fluorescent assay and kinetic simulation tools to characterise how the limited availability of different targets and catalysts had restrained catalytic reaction progress considerably, and to inform how to accelerate the catalytic destruction of shorter linear and larger RNAs even further.
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Affiliation(s)
- Bahareh Amirloo
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Sameen Yousaf
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Harmesh Aojula
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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6
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Luige O, Bose PP, Stulz R, Steunenberg P, Brun O, Andersson S, Murtola M, Strömberg R. Zn 2+-Dependent peptide nucleic acid-based artificial ribonucleases with unprecedented efficiency and specificity. Chem Commun (Camb) 2021; 57:10911-10914. [PMID: 34590632 DOI: 10.1039/d1cc04383h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present Zn2+-dependent dimethyl-dipyridophenazine PNA conjugates as efficient RNA cleaving artificial enzymes. These PNAzymes display site-specific RNA cleavage with 10 minute half-lives and cleave clinically relevant RNA models.
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Affiliation(s)
- Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Partha Pratim Bose
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Rouven Stulz
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden. .,Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Peter Steunenberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Omar Brun
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
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7
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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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8
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Thang Pham C, Thuy Pham T, Ha Nguyen V, Nguyet Trieu T, Huy Nguyen H. Syntheses, Structures, and Bioactivity Evaluation of some Transition Metal Complexes with Aroylbis(
N
,
N
‐diethylthioureas) Derived from Natural Compounds. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202100063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chien Thang Pham
- Department of Inorganic Chemistry VNU University of Science Vietnam National University, Hanoi 19 Le Thanh Tong, Hoan Kiem 10021 Hanoi Vietnam
| | - Thu Thuy Pham
- Department of Inorganic Chemistry VNU University of Science Vietnam National University, Hanoi 19 Le Thanh Tong, Hoan Kiem 10021 Hanoi Vietnam
| | - Viet Ha Nguyen
- Faculty of Education Hanoi Metropolitan University 98 Duong Quang Ham, Cau Giay 11306 Hanoi Vietnam
| | - Thi Nguyet Trieu
- Department of Inorganic Chemistry VNU University of Science Vietnam National University, Hanoi 19 Le Thanh Tong, Hoan Kiem 10021 Hanoi Vietnam
| | - Hung Huy Nguyen
- Department of Inorganic Chemistry VNU University of Science Vietnam National University, Hanoi 19 Le Thanh Tong, Hoan Kiem 10021 Hanoi Vietnam
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9
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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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10
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Staroseletz Y, Amirloo B, Williams A, Lomzov A, Burusco KK, Clarke DJ, Brown T, Zenkova MA, Bichenkova EV. Strict conformational demands of RNA cleavage in bulge-loops created by peptidyl-oligonucleotide conjugates. Nucleic Acids Res 2020; 48:10662-10679. [PMID: 33010175 PMCID: PMC7641753 DOI: 10.1093/nar/gkaa780] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/04/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Potent knockdown of pathogenic RNA in vivo is an urgent health need unmet by both small-molecule and biologic drugs. ‘Smart’ supramolecular assembly of catalysts offers precise recognition and potent destruction of targeted RNA, hitherto not found in nature. Peptidyl-oligonucleotide ribonucleases are here chemically engineered to create and attack bulge-loop regions upon hybridization to target RNA. Catalytic peptide was incorporated either via a centrally modified nucleotide (Type 1) or through an abasic sugar residue (Type 2) within the RNA-recognition motif to reveal striking differences in biological performance and strict structural demands of ribonuclease activity. None of the Type 1 conjugates were catalytically active, whereas all Type 2 conjugates cleaved RNA target in a sequence-specific manner, with up to 90% cleavage from 5-nt bulge-loops (BC5-α and BC5L-β anomers) through multiple cuts, including in folds nearby. Molecular dynamics simulations provided structural explanation of accessibility of the RNA cleavage sites to the peptide with adoption of an ‘in-line’ attack conformation for catalysis. Hybridization assays and enzymatic probing with RNases illuminated how RNA binding specificity and dissociation after cleavage can be balanced to permit turnover of the catalytic reaction. This is an essential requirement for inactivation of multiple copies of disease-associated RNA and therapeutic efficacy.
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Affiliation(s)
- Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russia
| | - Bahareh Amirloo
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Aled Williams
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Alexander Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russia
| | - Kepa K Burusco
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russia
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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11
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Zhu YF, Guan WQ, Lin F, Chen WH. A New Luminescent Zn(II) Complex: Selective Sensing of Cr 2O 72- and Prevention Activity Against Orthodontic Root Absorption by Suppressing Inflammatory Response. J Fluoresc 2020; 30:1233-1240. [PMID: 32757089 DOI: 10.1007/s10895-020-02597-w] [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: 05/13/2020] [Accepted: 07/28/2020] [Indexed: 11/26/2022]
Abstract
A novel luminescent coordination polymer (CP) based on Zn(II) ions as nodes [Zn(OPY)1.5(Hbtc)]n (1), [H3btc = trimesic acid and OPY = 4,4'-(oxybis(4,1-phenylene))dipyridine] has been prepared via the solvothermal assembly of a tripodal multicarboxylic acid ligand, a bis-pyridyl ligand with V-shape containing two diverse coordination patterns as well as Zn2 + ion. The experiments of photoluminescence also reflect that the coordination polymer 1 has high sensitivity to potassium dichromate, and its quenching efficiency is Ksv of 2.12 × 104 L·mol- 1. Furthermore, its treatment activity on orthodontic root absorption was evaluated in vivo. Firstly, the CCK-8 assay was performed in this research to evaluate the biotoxicity of the synthetic compound. Next, the TNF-α and Cbfα1 released by the periodontal ligament fibroblast was determined via the ELISA test kit. In addition to this, the signaling pathway of NF-κB activation after treated with compound was measured by the RT-PCR.
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Affiliation(s)
- Yan-Feng Zhu
- Department of Stomatology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Wei-Qun Guan
- Department of Stomatology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Fei Lin
- Department of Stomatology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Wei-Hui Chen
- Department of Stomatology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China.
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12
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Pham CT, Pham TT, Nguyen HH, Trieu TN. Syntheses, Structures, and Bioactivities Evaluation of some Transition Metal Complexes with 4,4'-Diacetylcurcumin. Z Anorg Allg Chem 2020. [DOI: 10.1002/zaac.202000088] [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]
Affiliation(s)
- Chien Thang Pham
- Department of Inorganic Chemistry; VNU University of Science; Vietnam National University Hanoi; 19 Le Thanh Tong Hoan Kiem Hanoi Vietnam
| | - Thu Thuy Pham
- Department of Inorganic Chemistry; VNU University of Science; Vietnam National University Hanoi; 19 Le Thanh Tong Hoan Kiem Hanoi Vietnam
| | - Hung Huy Nguyen
- Department of Inorganic Chemistry; VNU University of Science; Vietnam National University Hanoi; 19 Le Thanh Tong Hoan Kiem Hanoi Vietnam
| | - Thi Nguyet Trieu
- Department of Inorganic Chemistry; VNU University of Science; Vietnam National University Hanoi; 19 Le Thanh Tong Hoan Kiem Hanoi Vietnam
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13
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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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14
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Gebrezgiabher M, Zalloum WA, Clarke DJ, Miles SM, Fedorova AA, Zenkova MA, Bichenkova EV. RNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions. J Biomol Struct Dyn 2020; 39:2555-2574. [PMID: 32248755 DOI: 10.1080/07391102.2020.1751711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Sequence-specific protein-based ribonucleases are not found in nature. Absolute sequence selectivity in RNA cleavage in vivo normally requires multi-component complexes that recruit a guide RNA or DNA for target recognition and a protein-RNA assembly for catalytic functioning (e.g. RNAi molecular machinery, RNase H). Recently discovered peptidyl-oligonucleotide synthetic ribonucleases selectively knock down pathogenic RNAs by irreversible cleavage to offer unprecedented opportunities for control of disease-relevant RNA. Understanding how to increase their potency, selectivity and catalytic turnover will open the translational pathway to successful therapeutics. Yet, very little is known about how these chemical ribonucleases bind, cleave and leave their target. Rational design awaits this understanding in order to control therapy, particularly how to overcome the trade-off between sequence specificity and potency through catalytic turnover. We illuminate this here by characterizing the interactions of these chemical RNases with both complementary and non-complementary RNAs using Tm profiles, fluorescence, UV-visible and NMR spectroscopies. Crucially, the level of counter cations, which are tightly-controlled within cellular compartments, also controlled these interactions. The oligonucleotide component dominated interaction between conjugates and complementary targets in the presence of physiological levels of counter cations (K+), sufficient to prevent repulsion between the complementary nucleic acid strands to allow Watson-Crick hydrogen bonding. In contrast, the positively-charged catalytic peptide interacted poorly with target RNA, when counter cations similarly screened the negatively-charged sugar-phosphate RNA backbones. The peptide only became the key player, when counter cations were insufficient for charge screening; moreover, only under such non-physiological conditions did conjugates form strong complexes with non-complementary RNAs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mengisteab Gebrezgiabher
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Waleed A Zalloum
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David J Clarke
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Steven M Miles
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Antonina A Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena V Bichenkova
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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15
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Hu Q, Jayasinghe‐Arachchige VM, Sharma G, Serafim LF, Paul TJ, Prabhakar R. Mechanisms of peptide and phosphoester hydrolysis catalyzed by two promiscuous metalloenzymes (insulin degrading enzyme and glycerophosphodiesterase) and their synthetic analogues. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Qiaoyu Hu
- Department of Chemistry, University of Miami Coral Gables Florida
| | | | - Gaurav Sharma
- Department of Chemistry, University of Miami Coral Gables Florida
| | | | - Thomas J. Paul
- Department of Chemistry, University of Miami Coral Gables Florida
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami Coral Gables Florida
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16
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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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17
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Guney Eskiler G, Kani I. In vitro apoptotic effect of Zinc(II) complex with N-donor heterocyclic ligand on breast cancer cells. ACTA ACUST UNITED AC 2019. [DOI: 10.1515/tjb-2019-0013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
Background
The synthesis of new ligand and transition metal complexes have drawn great attention in cancer treatment due to excellent DNA cleavage activities and high antitumor activity.
Objective
The purpose of this study was to synthesize a new Zn(II) complex with 2,2′-bipyridine (bpy) ligand, [Zn(bpy)2(H2O)]2(ClO4), and to investigate the potential therapeutic activity against breast cancer.
Materials and methods
Zn(II) complex was obtained and structurally characterized using crystallography and other spectroscopic methods. The cytotoxic and apoptotic effects of Zn(II) complex on MCF7 breast cancer and HUVEC control cells were evaluated by WST-1, Annexin V and cell cycle analysis.
Results
The spectroscopic data demonstrated that Zn(II) complex was successfully synthesized. Furthermore, Zn(II) complex exhibited significant cytotoxic effect on MCF7 breast cancer and HUVEC cells (p < 0.01). MCF7 and HUVEC cells proliferation was reduced to 11.0% and 52.6%, respectively at 10 μM for 48 h. Additionally, Zn(II) complex significantly induced apoptotic cell death (84.87%) and caused S phase arrest (36.4%) in MCF7 cells at 10 μM (p < 0.01).
Conclusions
Zn(II) complex has great therapeutic potential for the treatment of breast cancer. However, further studies are warranted to identify the underlying mechanisms of apoptotic cell death and to reduce the toxicity of Zn(II) complex on control cells.
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18
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Zhou X, Zhang XP, Li W, Jiang J, Xu H, Ke Z, Phillips DL, Zhao C. Unraveling mechanisms of the uncoordinated nucleophiles: theoretical elucidations of the cleavage of bis( p-nitrophenyl) phosphate mediated by zinc-complexes with apical nucleophiles. RSC Adv 2019; 9:37696-37704. [PMID: 35541823 PMCID: PMC9075727 DOI: 10.1039/c9ra06737j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/01/2019] [Indexed: 02/01/2023] Open
Abstract
A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP−) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles. Ligand-based and alternative solvent-based nucleophilic attack reaction models are proposed. The pKa values of the Zn(ii)-bound water molecules or ligands in the [Zn(LnH)(η-H2O)(H2O)]2+ (n = 1, 2 and 3) complexes, as well as the dimerization tendency of the mononuclear Zn(ii)-complexes, were found to significantly influence the reaction mechanisms. The Zn(ii)-L3 complexes were found to be more favorable for the hydrolytic cleavage of the BNPP−via a ligand-based nucleophilic attack pathway. This was due to the lower pKa value for the deprotonation of the oxime ligand, the hard dimerization of the mononuclear Zn(ii)-L3 species, and the presence of an uncoordinated nucleophile. The origins of the uncoordinated reactions were systematically elucidated. The theoretical results reported here are in good agreement with experimental observations and more importantly, help to elucidate the factors that influence intermolecular nucleophilic attack reactions with coordinated/uncoordinated nucleophiles. A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP−) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles.![]()
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Affiliation(s)
- Xiaoyu Zhou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Xue-Peng Zhang
- School of Chemisty and Chemical Engineering, Shaanxi Normal University Xi'an 710119 P. R. China
| | - Weikang Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Jingxing Jiang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, School of Materials Science and Engineering, Sun Yat-sen University Guangzhou 510275 P. R. China
| | - Huiying Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Zhuofeng Ke
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, School of Materials Science and Engineering, Sun Yat-sen University Guangzhou 510275 P. R. China
| | - David Lee Phillips
- Department of Chemistry, University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 P. R. China
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19
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Le CD, Pham CT, Nguyen HH. Zinc(II) {2}-metallacoronates and {2}-metallacryptates based on dipicolinoylbis(N,N-diethylthiourea): Structures and biological activities. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.114143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Patutina OA, Miroshnichenko SK, Mironova NL, Sen'kova AV, Bichenkova EV, Clarke DJ, Vlassov VV, Zenkova MA. Catalytic Knockdown of miR-21 by Artificial Ribonuclease: Biological Performance in Tumor Model. Front Pharmacol 2019; 10:879. [PMID: 31456683 PMCID: PMC6698794 DOI: 10.3389/fphar.2019.00879] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/10/2019] [Indexed: 12/25/2022] Open
Abstract
Control of the expression of oncogenic small non-coding RNAs, notably microRNAs (miRNAs), is an attractive therapeutic approach. We report a design platform for catalytic knockdown of miRNA targets with artificial, sequence-specific ribonucleases. miRNases comprise a peptide [(LeuArg)2Gly]2 capable of RNA cleavage conjugated to the miRNA-targeted oligodeoxyribonucleotide, which becomes nuclease-resistant within the conjugate design, without resort to chemically modified nucleotides. Our data presented here showed for the first time a truly catalytic character of our miR-21-miRNase and its ability to cleave miR-21 in a multiple catalytic turnover mode. We demonstrate that miRNase targeted to miR-21 (miR-21-miRNase) knocked down malignant behavior of tumor cells, including induction of apoptosis, inhibition of cell invasiveness, and retardation of tumor growth, which persisted on transplantation into mice of tumor cells treated once with miR-21-miRNase. Crucially, we discover that the high biological activity of miR-21-miRNase can be directly related not only to its truly catalytic sequence-specific cleavage of miRNA but also to its ability to recruit the non-sequence specific RNase H found in most cells to elevate catalytic turnover further. miR-21-miRNase worked synergistically even with low levels of RNase H. Estimated degradation in the presence of RNase H exceeded 103 miRNA target molecules per hour for each miR-21-miRNase molecule, which provides the potency to minimize delivery requirements to a few molecules per cell. In contrast to the comparatively high doses required for the simple steric block of antisense oligonucleotides, truly catalytic inactivation of miRNA offers more effective, irreversible, and persistent suppression of many copy target sequences. miRNase design can be readily adapted to target other pathogenic microRNAs overexpressed in many disease states.
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Affiliation(s)
- Olga A Patutina
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Svetlana K Miroshnichenko
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Nadezhda L Mironova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Aleksandra V Sen'kova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Marina A Zenkova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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21
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Hu Q, Jayasinghe-Arachchige VM, Zuchniarz J, Prabhakar R. Effects of the Metal Ion on the Mechanism of Phosphodiester Hydrolysis Catalyzed by Metal-Cyclen Complexes. Front Chem 2019; 7:195. [PMID: 31024887 PMCID: PMC6460053 DOI: 10.3389/fchem.2019.00195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/14/2019] [Indexed: 12/01/2022] Open
Abstract
In this study, mechanisms of phosphodiester hydrolysis catalyzed by six di- and tetravalent metal-cyclen (M-C) complexes (Zn-C, Cu-C, Co-C, Ce-C, Zr-C and Ti-C) have been investigated using DFT calculations. The activities of these complexes were studied using three distinct mechanisms: (1) direct attack ( DA ), (2) catalyst-assisted ( CA ), and (3) water-assisted ( WA ). All divalent metal complexes (Zn-C, Cu-C and Co-C) coordinated to the BNPP substrate in a monodentate fashion and activated its scissile phosphoester bond. However, all tetravalent metal complexes (Ce-C, Zr-C, and Ti-C) interacted with BNPP in a bidentate manner and strengthened this bond. The DA mechanism was energetically the most feasible for all divalent M-C complexes, while the WA mechanism was favored by the tetravalent complexes, except Ce-C. The divalent complexes were found to be more reactive than their tetravalent counterparts. Zn-C catalyzed the hydrolysis with the lowest barrier among all M-C complexes, while Ti-C was the most reactive tetravalent complex. The activities of Ce-C and Zr-C, except Ti-C, were improved with an increase in the coordination number of the metal ion. The structural and mechanistic information provided in this study will be very helpful in the development of more efficient metal complexes for this critical reaction.
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Affiliation(s)
| | | | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL, United States
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22
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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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23
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Luige O, Murtola M, Ghidini A, Strömberg R. Further Probing of Cu 2+-Dependent PNAzymes Acting as Artificial RNA Restriction Enzymes. Molecules 2019; 24:molecules24040672. [PMID: 30769777 PMCID: PMC6412939 DOI: 10.3390/molecules24040672] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 11/16/2022] Open
Abstract
Peptide nucleic acid (PNA)-neocuproine conjugates have been shown to efficiently catalyse the cleavage of RNA target sequences in the presence of Cu2+ ions in a site-specific manner. These artificial enzymes are designed to force the formation of a bulge in the RNA target, the sequence of which has been shown to be key to the catalytic activity. Here, we present a further investigation into the action of Cu2+-dependent PNAzymes with respect to the dependence on bulge composition in 3- and 4-nucleotide bulge systems. Cu2+-dependent PNAzymes were shown to have a clear preference for 4-nucleotide bulges, as the cleavage of 3-nucleotide bulge-forming RNA sequences was significantly slower, which is illustrated by a shift in the half-lives from approximately 30 min to 24 h. Nonetheless, the nucleotide preferences at different positions in the bulge displayed similar trends in both systems. Moreover, the cleavage site was probed by introducing critical chemical modifications to one of the cleavage site nucleotides of the fastest cleaved 4-nucleotide RNA bulge. Namely, the exclusion of the exocyclic amine of the central adenine and the replacement of the 2′-hydroxyl nucleophile with 2′-H or 2′-OMe substituents in the RNA severely diminished the rate of RNA cleavage by the Cu2+-dependent PNAzyme, giving insight into the mechanism of cleavage. Moreover, the shorter recognition arm of the RNA/PNAzyme complex was modified by extending the PNAzyme by two additional nucleobases. The new PNAzyme was able to efficiently promote the cleavage of RNA when fully hybridised to a longer RNA target and even outperform the previous fastest PNAzyme. The improvement was demonstrated in cleavage studies with stoichiometric amounts of either PNAzyme present, and the extended PNAzyme was also shown to give turnover with a 10-fold excess of the RNA target.
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Affiliation(s)
- Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland.
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
- Institut für Pharmazeutische Wissenschaften (IPW), Eidgenössische Technische Hochschule Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
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24
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Smolkin B, Khononov A, Pieńko T, Shavit M, Belakhov V, Trylska J, Baasov T. Towards Catalytic Antibiotics: Redesign of Aminoglycosides To Catalytically Disable Bacterial Ribosomes. Chembiochem 2018; 20:247-259. [DOI: 10.1002/cbic.201800549] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/20/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Boris Smolkin
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Alina Khononov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Tomasz Pieńko
- Centre of New Technologies; University of Warsaw; Banacha 2c 02-097 Warsaw Poland
- Department of Drug Chemistry; Faculty of Pharmacy with the Laboratory Medicine Division; Medical University of Warsaw; Banacha 1a 02-097 Warsaw Poland
| | - Michal Shavit
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Valery Belakhov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Joanna Trylska
- Centre of New Technologies; University of Warsaw; Banacha 2c 02-097 Warsaw Poland
| | - Timor Baasov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
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25
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Majumdar D, Biswas JK, Mondal M, Surendra Babu M, Metre RK, Das S, Bankura K, Mishra D. Coordination of N,O-donor appended Schiff base ligand (H 2 L 1 ) towards Zinc(II) in presence of pseudohalides: Syntheses, crystal structures, photoluminescence, antimicrobial activities and Hirshfeld surfaces. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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26
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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: 52] [Impact Index Per Article: 8.7] [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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27
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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: 12] [Impact Index Per Article: 1.7] [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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28
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Kuzuya A, Machida K, Shi Y, Tanaka K, Komiyama M. Site-Selective RNA Activation by Acridine-Modified Oligodeoxynucleotides in Metal-Ion Catalyzed Hydrolysis: A Comprehensive Study. ACS OMEGA 2017; 2:5370-5377. [PMID: 31457805 PMCID: PMC6644747 DOI: 10.1021/acsomega.7b00966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/21/2017] [Indexed: 06/10/2023]
Abstract
Various types of acridine were conjugated to DNA and used for site-selective RNA scission together with another unmodified DNA and a Lu(III) ion. The target phosphodiester linkage in the substrate RNA was selectively and efficiently activated, and was hydrolyzed by the free Lu(III) ion. Among the investigated 14 conjugates, the conjugate bearing 9-amino-2-isopropoxy-6-nitroacridine was the best RNA-activator. Systematic evaluation of the RNA-activating ability of the acridines showed that (1) the acridines act as an acid catalyst within the RNA activation, (2) the amino-group at the 9-position of acridine is essential to modulate the acidity of acridine, (3) the electron-withdrawing group at the 3-position further enhances the acid catalysis, and (4) the substituent at the 2-position sterically modulates the orientation of acridine-intercalation favorably for the catalysis. Moreover, it is revealed that the opposite base of acridine does not inhibit direct interaction of acridine with the target phosphodiester linkage.
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Affiliation(s)
- Akinori Kuzuya
- Department
of Chemistry and Materials Engineering, Kansai University, 3-3-35
Yamate, Suita, Osaka 564-8680, Japan
| | - Kenzo Machida
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Yun Shi
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Keita Tanaka
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Makoto Komiyama
- International
Center for Materials Nanoarchitechtonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
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29
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Zhu D, Zhu W, Wang W, Liu X. Gold functionalised attapulgite for discrimination of hydrogen peroxide and oxidising ions. IET Nanobiotechnol 2017; 11:200-204. [DOI: 10.1049/iet-nbt.2016.0006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Dan Zhu
- Key Laboratory for Soft Chemistry and Functional Materials of Ministry of EducationNanjing University of Science and Technology200 Xiaolingwei StreetNanjing 210094People's Republic of China
| | - Wenfeng Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyInstitute of High Energy Physics, Chinese Academy of SciencesBeijing 100049People's Republic of China
| | - Weiwei Wang
- Key Laboratory for Soft Chemistry and Functional Materials of Ministry of EducationNanjing University of Science and Technology200 Xiaolingwei StreetNanjing 210094People's Republic of China
| | - Xiaoheng Liu
- Key Laboratory for Soft Chemistry and Functional Materials of Ministry of EducationNanjing University of Science and Technology200 Xiaolingwei StreetNanjing 210094People's Republic of China
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30
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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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32
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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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33
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Staroseletz Y, Williams A, Burusco KK, Alibay I, Vlassov VV, Zenkova MA, Bichenkova EV. 'Dual' peptidyl-oligonucleotide conjugates: Role of conformational flexibility in catalytic cleavage of RNA. Biomaterials 2016; 112:44-61. [PMID: 27744220 DOI: 10.1016/j.biomaterials.2016.09.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/23/2016] [Accepted: 09/26/2016] [Indexed: 02/06/2023]
Abstract
Traditional therapeutic interventions against abnormal gene expression in disease states at the level of expressed proteins are becoming increasingly difficult due to poor selectivity, off-target effects and associated toxicity. Upstream catalytic targeting of specific RNA sequences offers an alternative platform for drug discovery to achieve more potent and selective treatment through antisense interference with disease-relevant RNAs. We report a novel class of catalytic biomaterials, comprising amphipathic RNA-cleaving peptides placed between two RNA recognition motifs, here demonstrated to target the TΨC loop and 3'- acceptor stem of tRNAPhe. These unique peptidyl-oligonucleotide 'dual' conjugates (DCs) were created by phosphoramidate or thiol-maleimide conjugation chemistry of a TΨC-targeting oligonucleotide to the N-terminus of the amphipathic peptide sequence, followed by amide coupling of a 3'-acceptor stem-targeting oligonucleotide to the free C-terminal carboxylic acid functionality of the same peptide. Hybridization of the DCs bearing two spatially-separated recognition motifs with the target tRNAPhe placed the peptide adjacent to a single-stranded RNA region and promoted cleavage within the 'action radius' of the catalytic peptide. Up to 100% cleavage of the target tRNAPhe was achieved by the best candidate (i.e. DC6) within 4 h, when conformational flexibility was introduced into the linker regions between the peptide and oligonucleotide components. This study provides the strong position for future development of highly selective RNA-targeting agents that can potentially be used for disease-selective treatment at the level of messenger, micro, and genomic viral RNA.
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Affiliation(s)
- Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Aled Williams
- 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
| | - Irfan Alibay
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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34
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Laine M, Lönnberg T, Helkearo M, Lönnberg H. Cleavage of short oligoribonucleotides by a Zn2+ binding multi-nucleating azacrown conjugate. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2015.12.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Fedorova AA, Goncharova EP, Koroleva LS, Burakova EA, Ryabchikova EI, Bichenkova EV, Silnikov VN, Vlassov VV, Zenkova MA. Artificial ribonucleases inactivate a wide range of viruses using their ribonuclease, membranolytic, and chaotropic-like activities. Antiviral Res 2016; 133:73-84. [PMID: 27476043 DOI: 10.1016/j.antiviral.2016.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 07/12/2016] [Accepted: 07/21/2016] [Indexed: 10/21/2022]
Abstract
Artificial ribonucleases (aRNases) are small compounds catalysing RNA cleavage. Recently we demonstrated that aRNases readily inactivate various viruses in vitro. Here, for three series of aRNases (1,4-diazabicyclo [2.2.2]octane-based and peptide-like compounds) we show that apart from ribonuclease activity the aRNases display chaotropic-like and membranolytic activities. The levels of membranolytic and chaotropic-like activities correlate well with the efficiency of various viruses inactivation (enveloped, non-enveloped, RNA-, DNA-containing). We evaluated the impact of these activities on the efficiency of virus inactivation and found: i) the synergism between membranolytic and chaotropic-like activities is sufficient for the inactivation of enveloped viruses (influenza A, encephalitis, vaccinia viruses) for 1,4-diazabicyclo [2.2.2]octane based aRNases, ii) the inactivation of non-enveloped viruses (encephalomyocarditis, acute bee paralysis viruses) is totally dependent on the synergism of chaotropic-like and ribonuclease activities, iii) ribonuclease activity plays a leading role in the inactivation of RNA viruses by aRNases Dp12F6, Dtr12 and K-D-1, iv) peptide-like aRNases (L2-3, K-2) being effective virus killers have a more specific mode of action. Obtained results clearly demonstrate that aRNases represent a new class of broad-spectrum virus-inactivating agents.
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Affiliation(s)
- Antonina A Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Elena P Goncharova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Lyudmila S Koroleva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Ekatherina A Burakova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Elena I Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Elena V Bichenkova
- School of Pharmacy, University of Manchester, Oxford Road, M13 9PT, Manchester, United Kingdom
| | - Vladimir N Silnikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation.
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36
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Bím D, Svobodová E, Eigner V, Rulíšek L, Hodačová J. Copper(II) and Zinc(II) Complexes of Conformationally Constrained Polyazamacrocycles as Efficient Catalysts for RNA Model Substrate Cleavage in Aqueous Solution at Physiological pH. Chemistry 2016; 22:10426-37. [DOI: 10.1002/chem.201601175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Daniel Bím
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
- Institute of Organic Chemistry and Biochemistry; v.v.i. and Gilead Sciences Research Center, Academy of Sciences of the Czech Republic; Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Eva Svobodová
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
| | - Václav Eigner
- Department of Solid State Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry; v.v.i. and Gilead Sciences Research Center, Academy of Sciences of the Czech Republic; Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Jana Hodačová
- Department of Organic Chemistry, Faculty of Chemical Technology; University of Chemistry and Technology; Technická 5 166 28 Prague 6 Czech Republic), Fax: (+420) 220-444-288
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37
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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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38
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Chen JLY, Pezzato C, Scrimin P, Prins LJ. Chiral Nanozymes-Gold Nanoparticle-Based Transphosphorylation Catalysts Capable of Enantiomeric Discrimination. Chemistry 2016; 22:7028-32. [PMID: 26919202 DOI: 10.1002/chem.201600853] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/08/2022]
Abstract
Enantioselectivity in RNA cleavage by a synthetic metalloenzyme has been demonstrated for the first time. Thiols containing chiral Zn(II) -binding head groups have been self-assembled on the surface of gold nanoparticles. This results in the spontaneous formation of chiral bimetallic catalytic sites that display different activities (kcat ) towards the enantiomers of an RNA model substrate. Substrate selectivity is observed when the nanozyme is applied to the cleavage of the dinucleotides UpU, GpG, ApA, and CpC, and remarkable differences in reactivity are observed for the cleavage of the enantiomerically pure dinucleotide UpU.
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Affiliation(s)
- Jack L-Y Chen
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Cristian Pezzato
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Paolo Scrimin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy.
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39
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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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40
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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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41
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Zhang X, Liu X, Phillips DL, Zhao C. Hydrolysis mechanisms of BNPP mediated by facial copper(ii) complexes bearing single alkyl guanidine pendants: cooperation between the metal centers and the guanidine pendants. Dalton Trans 2016; 45:1593-603. [DOI: 10.1039/c5dt03949e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The inter-complex and intra-complex nucleophilic attacks by metal-bound hydroxide were investigated by considering the second coordination spheres.
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Affiliation(s)
- Xuepeng Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- P. R. China
| | - Xueping Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- P. R. China
| | | | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- P. R. China
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42
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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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43
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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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44
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Sequence-specific RNA Photocleavage by Single-stranded DNA in Presence of Riboflavin. Sci Rep 2015; 5:15039. [PMID: 26461456 PMCID: PMC4602204 DOI: 10.1038/srep15039] [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: 08/11/2015] [Accepted: 08/24/2015] [Indexed: 02/07/2023] Open
Abstract
Constant efforts have been made to develop new method to realize sequence-specific RNA degradation, which could cause inhibition of the expression of targeted gene. Herein, by using an unmodified short DNA oligonucleotide for sequence recognition and endogenic small molecue, vitamin B2 (riboflavin) as photosensitizer, we report a simple strategy to realize the sequence-specific photocleavage of targeted RNA. The DNA strand is complimentary to the target sequence to form DNA/RNA duplex containing a G•U wobble in the middle. The cleavage reaction goes through oxidative elimination mechanism at the nucleoside downstream of U of the G•U wobble in duplex to obtain unnatural RNA terminal, and the whole process is under tight control by using light as switch, which means the cleavage could be carried out according to specific spatial and temporal requirements. The biocompatibility of this method makes the DNA strand in combination with riboflavin a promising molecular tool for RNA manipulation.
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45
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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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46
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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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47
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Williams A, Staroseletz Y, Zenkova MA, Jeannin L, Aojula H, Bichenkova EV. Peptidyl-oligonucleotide conjugates demonstrate efficient cleavage of RNA in a sequence-specific manner. Bioconjug Chem 2015; 26:1129-43. [PMID: 25955796 DOI: 10.1021/acs.bioconjchem.5b00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Described here is a new class of peptidyl-oligonucleotide conjugates (POCs) which show efficient cleavage of a target RNA in a sequence-specific manner. Through phosphoramidate attachment of a 17-mer TΨC-targeting oligonucleotide to amphiphilic peptide sequences containing leucine, arginine, and glycine, zero-linker conjugates are created which exhibit targeted phosphodiester cleavage under physiological conditions. tRNA(Phe) from brewer's yeast was used as a model target sequence in order to probe different structural variants of POCs in terms of selective TΨC-arm directed cleavage. Almost quantitative (97-100%) sequence-specific tRNA cleavage is observed for several POCs over a 24 h period with a reaction half-life of less than 1 h. Nontargeted cleavage of tRNA(Phe) or HIV-1 RNA is absent. Structure-activity relationships reveal that removal of the peptide's central glycine residue significantly decreases tRNA cleavage activity; however, this can be entirely restored through replacement of the peptide's C-terminal carboxylic acid group with the carboxamide functionality. Truncation of the catalytic peptide also has a detrimental effect on POC activity. Based on the encouraging results presented, POCs could be further developed with the aim of creating useful tools for molecular biology or novel therapeutics targeting specific messenger, miRNA, and genomic viral RNA sequences.
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Affiliation(s)
- Aled Williams
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
| | - Yaroslav Staroseletz
- ‡Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Marina A Zenkova
- ‡Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Laurent Jeannin
- §Peptisyntha S.A., 310 Rue de Ransbeek, 1120 Brussels, Belgium
| | - Harmesh Aojula
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
| | - Elena V Bichenkova
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
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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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49
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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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50
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Bhattacharyya A, Sen S, Harms K, Chattopadhyay S. Formation of three photoluminescent zinc(II) complexes with Zn2O2 cores: Examples of bi-dentate bonding modes of potentially tri- and tetra-dentate Schiff bases. Polyhedron 2015. [DOI: 10.1016/j.poly.2014.12.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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