1
|
Site-Selective Artificial Ribonucleases: Renaissance of Oligonucleotide Conjugates for Irreversible Cleavage of RNA Sequences. Molecules 2021; 26:molecules26061732. [PMID: 33808835 PMCID: PMC8003597 DOI: 10.3390/molecules26061732] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
RNA-targeting therapeutics require highly efficient sequence-specific devices capable of RNA irreversible degradation in vivo. The most developed methods of sequence-specific RNA cleavage, such as siRNA or antisense oligonucleotides (ASO), are currently based on recruitment of either intracellular multi-protein complexes or enzymes, leaving alternative approaches (e.g., ribozymes and DNAzymes) far behind. Recently, site-selective artificial ribonucleases combining the oligonucleotide recognition motifs (or their structural analogues) and catalytically active groups in a single molecular scaffold have been proven to be a great competitor to siRNA and ASO. Using the most efficient catalytic groups, utilising both metal ion-dependent (Cu(II)-2,9-dimethylphenanthroline) and metal ion-free (Tris(2-aminobenzimidazole)) on the one hand and PNA as an RNA recognising oligonucleotide on the other, allowed site-selective artificial RNases to be created with half-lives of 0.5-1 h. Artificial RNases based on the catalytic peptide [(ArgLeu)2Gly]2 were able to take progress a step further by demonstrating an ability to cleave miRNA-21 in tumour cells and provide a significant reduction of tumour growth in mice.
Collapse
|
2
|
Mahmoud HK, Gomha SM, Farghaly TA, Awad HM. Synthesis of Thiazole Linked Imidazo[2,1-b]Thiazoles as Anticancer Agents. Polycycl Aromat Compd 2019. [DOI: 10.1080/10406638.2019.1689514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Huda K. Mahmoud
- Faculty of Science, Department of Chemistry, University of Cairo, Giza, Egypt
| | - Sobhi M. Gomha
- Faculty of Science, Department of Chemistry, University of Cairo, Giza, Egypt
- Faculty of Science, Department of Chemistry, Islamic University in Almadinah Almonawara, Almadinah Almonawara, Saudi Arabia
| | - Thoraya A. Farghaly
- Faculty of Science, Department of Chemistry, University of Cairo, Giza, Egypt
- Faculty of Applied Science, Chemistry Department, Umm Al-Qura University, Makkah Almukkarramah, Saudi Arabia
| | - Hanem M. Awad
- Department of Tanning Material and Leather Technology, National Research Center, Dokki, Cairo, Egypt
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Parmar NJ, Pansuriya BR, Labana BM, Kant R, Gupta VK. A convenient 1,3-dipolar cycloaddition–reduction synthetic sequence from 2-allyloxy-5-nitro-salicylaldehyde to aminobenzopyran-annulated heterocycles. RSC Adv 2013. [DOI: 10.1039/c3ra42220h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
5
|
Edwards DR, Neverov AA, Brown RS. Study on the Transesterification of Methyl Aryl Phosphorothioates in Methanol Promoted by Cd(II), Mn(II), and a Synthetic Pd(II) Complex. Inorg Chem 2011; 50:1786-97. [DOI: 10.1021/ic102220m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David R. Edwards
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| |
Collapse
|
6
|
Holmes SC, Gait MJ. Syntheses and Oligonucleotide Incorporation of Nucleoside Analogues Containing Pendant Imidazolyl or Amino Functionalities - The Search for Sequence-Specific Artificial Ribonucleases. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500413] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
7
|
Abstract
Mimicking the action of enzymes by simpler and more robust man-made catalysts has long inspired bioorganic chemists. During the past decade, mimics for RNA-cleaving enzymes, ribonucleases, or, more precisely, mimics of ribozymes that cleave RNA in sequence-selective rather than base-selective manner, have received special attention. These artificial ribonucleases are typically oligonucleotides (or their structural analogs) that bear a catalytically active conjugate group and catalyze sequence-selective hydrolysis of RNA phosphodiester bonds.
Collapse
Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014, Turku, Finland
| | | |
Collapse
|
8
|
Sakamoto S, Tamura T, Furukawa T, Komatsu Y, Ohtsuka E, Kitamura M, Inoue H. Highly efficient catalytic RNA cleavage by the cooperative action of two Cu(II) complexes embodied within an antisense oligonucleotide. Nucleic Acids Res 2003; 31:1416-25. [PMID: 12595549 PMCID: PMC149831 DOI: 10.1093/nar/gkg238] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2002] [Revised: 01/06/2003] [Accepted: 01/06/2003] [Indexed: 11/12/2022] Open
Abstract
Based on our recent studies of RNA cleavage by oligonucleotide-terpyridine.Cu(II) complex 5'- and/or 3'-conjugates, we designed 2'-O-methyloligonucleotides with two terpyridine-attached nucleosides at contiguous internal sites. To connect the 2'-terpyridine-modified uridine residue at the 5'-side to the 5'-O-terpyridyl nucleoside residue at the 3'-side, a dimethoxytrityl derivative of 5-hydroxypropyl-5'-O-terpyridyl-2'-deoxyuridine-3'-phosphoramidite was newly synthesized. Using this unit, we constructed two terpyridine conjugates, with either an unusual phophodiester bond or the bond extended by a propanediol(s)-containing linker. Cleavage reactions of the target RNA oligomer, under the conditions of conjugate excess in the presence of Cu(II), indicated that the conjugates precisely cleaved the RNA at the predetermined site and that one propanediol-containing linker was the most appropriate for inducing high cleavage activity. Furthermore, a comparison of the activity of the propanediol agent with those of the control conjugates with one complex confirmed that the two complexes are required for efficient RNA cleavage. The reaction of the novel cleaver revealed a bell-shaped pH-rate profile with a maximum at pH approximately 7.5, which is a result of the cooperative action of the complexes. In addition, we demonstrated that the agent catalytically cleaves an excess of the RNA, with the kinetic parameter kcat/K(m) = 0.118 nM(-1) x h(-1).
Collapse
Affiliation(s)
- Satoshi Sakamoto
- Department of Applied and Bioapplied Chemistry, Graduate School of Engineering, Osaka City University, Sugimoto 3-3-138, Sumiyoshi-ku, Osaka 558-8585, Japan
| | | | | | | | | | | | | |
Collapse
|
9
|
Lermer L, Hobbs J, Perrin DM. Incorporation of 8-histaminyl-deoxyadenosine [8-(2-(4-imidazolyl)ethylamino)-2'-deoxyriboadenosine] into oligodeoxyribonucleotides by solid phase phosphoramidite coupling. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2002; 21:651-64. [PMID: 12502281 DOI: 10.1081/ncn-120015723] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The 3'phosphoramidite of 8-histaminyl deoxyadenosine has been prepared and successfully incorporated into a short oligodeoxyribonucleotide. The synthetic methodology leading to this preparation is given and the implications for developing new DNAzymes as well as probing unusual nucleic acid structures are discussed.
Collapse
Affiliation(s)
- Leonard Lermer
- Department of Chemistry, 2036 Main Mall, 6174 University Blvd, University of British Columbia, Vancouver, B. C., V6T-1Z1 Canada
| | | | | |
Collapse
|