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P. O’Donovan F, O’Leary EM, O’Sullivan TP. Synthesis and Biological Evaluation of Novel Thionucleosides. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999200608131955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The search for novel nucleosides has been a major research focus in medicinal
chemistry for several decades, particularly given their proven track record in the treatment
of viral infections and cancer. As bioisosteres of natural nucleosides, thionucleosides are
especially attractive targets as they often display improved biological activity. Furthermore,
the replacement of oxygen with sulfur may sometimes be accompanied by interesting
changes in pharmacological effect. This update covers recent advances in the preparation of
novel thionucleosides, grouped by synthetic strategy. The biological properties of the target
thionucleosides are also summarised, in addition to any reported structure activity relationships.
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Affiliation(s)
| | - Eileen M. O’Leary
- Department of Physical Sciences, Cork Institute of Technology, Cork, Ireland
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2
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Saito-Tarashima N. [Chemical Approaches for RNAi Drug Development]. YAKUGAKU ZASSHI 2020; 140:1259-1268. [PMID: 32999205 DOI: 10.1248/yakushi.20-00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RNA interference (RNAi) is the standard method of suppressing gene expression because of its target specificity, potency, and ability to silence the expression of virtually any gene. Using 21-mer small interfering RNA (siRNA) is the general approach for inducing RNAi, as siRNA can be easily prepared using a DNA/RNA synthesizer. Synthetic siRNA can be chemically modified to increase the potency of RNAi activity and abrogate innate immune stimulation. However, designing chemically modified siRNA requires substantial experimentation. A practical method for understanding the interaction of siRNA and RNAi-related proteins and how modifications affect RNA-protein interactions is therefore needed. Plasmid DNA (pDNA) expressing short hairpin RNA (shRNA) can also be used to induce RNAi. pDNA produces numerous shRNAs that induce RNAi with potent and longterm RNAi activity, even if only one pDNA molecule is delivered to the nucleus. However, this approach has some drawbacks with regard to its therapeutic application, such as a low pDNA transfection efficiency due to its huge molecular size and innate immune responses induced by extra genes, such as CpG motifs. To overcome these issues with RNAi inducers (siRNA and pDNA), our group developed some chemical approaches using chemically modified oligonucleotides. This article focuses on our two original approaches. The first involves the groove modification of siRNA duplexes to understand siRNA-protein interactions using 7-bromo-7-deazaadenosine and 3-bromo-3-deazaadenosine as chemical probes, while the second involves the generation of RNAi medicine using chemically modified DNA, known as an intelligent shRNA expression device (iRed).
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Seley-Radtke KL, Yates MK. The evolution of nucleoside analogue antivirals: A review for chemists and non-chemists. Part 1: Early structural modifications to the nucleoside scaffold. Antiviral Res 2018; 154:66-86. [PMID: 29649496 PMCID: PMC6396324 DOI: 10.1016/j.antiviral.2018.04.004] [Citation(s) in RCA: 301] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/22/2018] [Accepted: 04/04/2018] [Indexed: 02/07/2023]
Abstract
This is the first of two invited articles reviewing the development of nucleoside-analogue antiviral drugs, written for a target audience of virologists and other non-chemists, as well as chemists who may not be familiar with the field. Rather than providing a simple chronological account, we have examined and attempted to explain the thought processes, advances in synthetic chemistry and lessons learned from antiviral testing that led to a few molecules being moved forward to eventual approval for human therapies, while others were discarded. The present paper focuses on early, relatively simplistic changes made to the nucleoside scaffold, beginning with modifications of the nucleoside sugars of Ara-C and other arabinose-derived nucleoside analogues in the 1960's. A future paper will review more recent developments, focusing especially on more complex modifications, particularly those involving multiple changes to the nucleoside scaffold. We hope that these articles will help virologists and others outside the field of medicinal chemistry to understand why certain drugs were successfully developed, while the majority of candidate compounds encountered barriers due to low-yielding synthetic routes, toxicity or other problems that led to their abandonment. This is the first of two invited articles reviewing the development of nucleoside-analogue antiviral drugs. It is written for a target audience of virologists and other non-chemists, and for chemists unfamiliar with the field. Numerous modifications have been made to the nucleoside scaffold in order to impart therapeutic benefits. Nucleoside modifications led to the development of potent antivirals such as acyclovir, entecavir, and tenofovir. We examine thought processes, progress in synthetic chemistry and results of antiviral testing that led to approved drugs.
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Affiliation(s)
- Katherine L Seley-Radtke
- 1000 Hilltop Circle, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA.
| | - Mary K Yates
- 1000 Hilltop Circle, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA
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Saito‐Tarashima N, Ota M, Minakawa N. Synthesis of 4′‐Selenoribonucleosides, the Building Blocks of 4′‐SelenoRNA, Using a Hypervalent Iodine. ACTA ACUST UNITED AC 2018; 70:1.40.1-1.40.21. [DOI: 10.1002/cpnc.34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Noriko Saito‐Tarashima
- Graduate School of Pharmaceutical Science, Tokushima University Shomachi Tokushima Japan
| | - Masashi Ota
- Graduate School of Pharmaceutical Science, Tokushima University Shomachi Tokushima Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University Shomachi Tokushima Japan
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5
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Hirao I, Kimoto M, Lee KH. DNA aptamer generation by ExSELEX using genetic alphabet expansion with a mini-hairpin DNA stabilization method. Biochimie 2017; 145:15-21. [PMID: 28916151 DOI: 10.1016/j.biochi.2017.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/08/2017] [Indexed: 12/21/2022]
Abstract
A novel aptamer generation method to greatly augment the affinity and stability of DNA aptamers was developed by genetic alphabet expansion combined with mini-hairpin DNA technology. The genetic alphabet expansion increases the physicochemical and structural diversities of DNA aptamers by introducing extra components, unnatural bases, as a fifth base, allowing for the enhancement of DNA aptamer affinities. Furthermore, the mini-hairpin DNA technology stabilizes DNA aptamers against nuclease digestion and thermal denaturation, by introducing an extraordinarily stable mini-hairpin DNA containing a GCGAAGC sequence. This novel method provides stabilized high-affinity DNA aptamers for diagnostic and therapeutic applications.
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Affiliation(s)
- Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #09-01, Singapore, 138669, Singapore.
| | - Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #09-01, Singapore, 138669, Singapore
| | - Kyung Hyun Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #09-01, Singapore, 138669, Singapore
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6
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Ishii K, Saito-Tarashima N, Ota M, Yamamoto S, Okamoto Y, Tanaka Y, Minakawa N. Practical synthesis of 4′-selenopurine nucleosides by combining chlorinated purines and ‘armed’ 4-selenosugar. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.08.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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7
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Ram RN, Gupta DK, Soni VK. Copper(I)-Promoted Synthesis of Highly Substituted and Functionalized Tetrahydrothiophenes. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ram N. Ram
- Department of Chemistry; Indian Institute of Technology Delhi; Hauz Khas 110016 New Delhi India
| | - Dharmendra Kumar Gupta
- Department of Chemistry; Indian Institute of Technology Delhi; Hauz Khas 110016 New Delhi India
| | - Vineet Kumar Soni
- Department of Chemistry; Indian Institute of Technology Delhi; Hauz Khas 110016 New Delhi India
- Department of Chemistry; Indian Institute of Technology Jodhpur; Ratanada 342011 Jodhpur India
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8
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Minakawa N, Matsuda A. Practical synthesis of 4'-thioribonucleosides starting from D-ribose. ACTA ACUST UNITED AC 2014; 59:14.12.1-19. [PMID: 25501591 DOI: 10.1002/0471142700.nc1412s59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A practical synthesis of 4'-thioribonucleosides, i.e., 4'-thiouridine, -cytidine, -adenosine, and -guanosine, which are versatile units for nucleic acids-based therapeutics, is described. Large-scale synthesis of 4-thiosugar starting from D-ribose was achieved (33%) in eight steps and with only three chromatographic purifications. After the appropriate chemical conversion of the 4-thiosugar, the resulting sulfoxide was subjected to the Pummerer reaction in the presence of silylated nucleobases. In reactions with silylated pyrimidine bases, the desired 4'-thioribonucleoside derivatives were obtained in good yield and β-selectively. On the other hand, N-7 isomers were obtained mainly in the Pummerer reaction with purine bases under the same conditions. However, the desired N-9 isomers were obtained in moderate yields when the reaction mixtures were subsequently heated under reflux. As a result, effective synthesis of 4'-thioribonucleosides was accomplished.
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Affiliation(s)
- Noriaki Minakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokushima, Tokushima, Japan
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9
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Kojima T, Furukawa K, Maruyama H, Inoue N, Tarashima N, Matsuda A, Minakawa N. PCR amplification of 4'-thioDNA using 2'-deoxy-4'-thionucleoside 5'-triphosphates. ACS Synth Biol 2013; 2:529-36. [PMID: 23957635 DOI: 10.1021/sb400074w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
2'-Deoxy-4'-thioribonucleic acid (4'-thioDNA) having a sulfur atom instead of an oxygen atom in the furanose ring has a nuclease resistance and hybridization ability higher than that of natural DNA. Despite its great potential for various biological applications, a long 4'-thioDNA having all four kinds of 2'-deoxy-4'-thionucleosides has not been reported. In this study, we describe systematic analysis of the incorporation of 2'-deoxy-4'-thionucleoside 5'-triphosphates (dSNTPs) using various DNA polymerases. We found that family B DNA polymerases, which do not have 3'→5' exonuclease activity, could efficiently incorporate dSNTPs via single nucleotide insertion and primer extension. Moreover, 104-mer PCR product was obtained even under the conditions in the presence of all four kinds of dSNTPs when KOD Dash DNA polymerase was used. The resulting PCR product was converted into a natural dsDNA by using PCR with dNTPs, and sequencing of the natural dsDNA revealed that the PCR cycle successfully proceeded without losing the sequence information of the template. To the best of our knowledge, this is the first example of accurate PCR amplification of highly modified DNA in the presence of only unnatural dNTPs.
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Affiliation(s)
- Takamitsu Kojima
- Graduate School of Pharmaceutical
Sciences, The University of Tokushima,
Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Kazuhiro Furukawa
- Graduate School of Pharmaceutical
Sciences, The University of Tokushima,
Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Hideto Maruyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Naonori Inoue
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Noriko Tarashima
- Graduate School of Pharmaceutical
Sciences, The University of Tokushima,
Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical
Sciences, The University of Tokushima,
Shomachi 1-78-1, Tokushima 770-8505, Japan
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Smith G, Sala R, Carroll L, Behan K, Glaser M, Robins E, Nguyen QD, Aboagye EO. Synthesis and evaluation of nucleoside radiotracers for imaging proliferation. Nucl Med Biol 2012; 39:652-65. [PMID: 22321533 DOI: 10.1016/j.nucmedbio.2011.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 11/29/2011] [Accepted: 12/07/2011] [Indexed: 10/14/2022]
Abstract
INTRODUCTION Uncontrolled proliferation is a fundamental characteristic of cancer, and consequently, imaging of tumor proliferative status finds interest clinically both as a diagnostic tool and for evaluation of response to treatment. Positron emission tomography (PET) radiotracers based on a nucleoside core, such as 3'-[18F]fluoro-3'-deoxythymidine ([18F]FLT), have been extensively studied for this purpose. However, [18F]FLT suffers from poor DNA incorporation leading to occasional poor correlation of [18F]FLT tumor uptake with other proliferation indicators such as Ki-67 immunostaining. METHODS N3-((1-(2-[18F]fluoroethyl)-1H-[1,2,3]-triazol-4-yl)methyl)thymidine ([18F]2) and N3-((1-(2-[18F]fluoroethyl)-1H-[1,2,3]-triazol-4-yl)methyl)-4'-thio-β-thymidine ([18F]3) were synthesized by click chemistry from [18F]fluoroethyl azide and by direct nucleophilic substitution of a tosylate precursor. Metabolic stability and phosphorylation potential of the radiotracers were evaluated in vitro and compared to [18F]FLT. Further, metabolic stability and biodistribution analysis of [18F]2 and [18F]3 were evaluated in vivo. RESULTS Stable isotope standards and radiochemistry precursors were synthesized by modification of existing literature procedures. [18F]2 and [18F]3 were synthesized in a radiochemical yield of 8%-12% (end of synthesis, non-decay corrected). Both nucleosides were stable to metabolic degradation by thymidine phosphorylase, and in vivo stability analysis showed only one metabolite for [18F]3. No phosphorylation of [18F]2 could be detected in HCT116 cell homogenates, and in the same assay, only minor (∼8%) phosphorylation of [18F]3 was observed. Biodistribution in Balb/c mice indicated rapid clearance for [18F]2 and [18F]3 to a lesser extent. CONCLUSIONS The favorable biodistribution and metabolic profile of [18F]3 warrant further investigation as a next-generation PET proliferation marker.
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Affiliation(s)
- Graham Smith
- Comprehensive Cancer Imaging Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, W12 0NN London, UK
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11
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Taniike H, Inagaki Y, Matsuda A, Minakawa N. Practical synthesis of 4′-selenopyrimidine nucleosides using hypervalent iodine. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Abstract
Numerous chemically modified oligonucleotides have been developed so far and show their own unique chemical properties and pharmacodynamic/pharmacokinetic characteristics. Among all non-natural nucleotides, to the best of our knowledge, only five chemistries are currently being tested in clinical trials: phosphorothioate, 2´-O-methyl RNA, 2´-O-methoxyethyl RNA, 2´,4´-bridged nucleic acid/locked nucleic acid and the phosphorodiamidate morpholino oligomer. Since phosphorothioate modification can improve the pharmacokinetics of oligonucleotides, this modification is currently used in combination with all other modifications except phosphorodiamidate morpholino oligomer. For the treatment of metabolic, cardiovascular, cancer and other systemic diseases, the phosphorothioate class of drugs is obviously helpful, while superior efficacies can be observed in phosphorodiamidate morpholino oligomer compared to other classes of oligonucleotides for the treatment of Duchenne muscular dystrophy. Which properties of antisense molecules are actually essential for clinical applications? In this article, we provide an overview of the medicinal chemistry of existing non-natural antisense molecules, as well as their clinical applications, to discuss which properties of antisense oligonuculeotides affect therapeutic potency.
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Matsuda A. [Development of highly nuclease-resistant chemically-modified oligonucleotides]. YAKUGAKU ZASSHI 2011; 131:285-98. [PMID: 21297374 DOI: 10.1248/yakushi.131.285] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chemical modification of therapeutic oligodeoxyribonucleotides (ODNs) is necessary to avoid not only degradation by endo- and exo-nucleases but also recognition by sensors such as an innate immune system. We have been developing modified nucleosides having an aminoalky linker at the pyrimidine nucleobase or sugar moiety. ODNs containing 5-N-(6-aminohexyl)carbamoyl-2'-deoxyuridine (7) were thermally stabilized about 3°C per modification and were about 160 times more stable to hydrolysis by snake venom phosphodiesterase (a 3'-exonuclease) than unmodified ODNs, but not by endonucleases. On the other hand, ODNs containing 4'-C-(aminoethyl)thymidine (14b), which was synthesized by a newly developed radical cyclization-ring-enlargement reaction by us, were 87 times more stable to hydrolysis by DNase I (an endonuclease) and 133 times more stable in 50% human serum than unmodified ODNs. The highly stereoselective synthesis of 4'-thioribonuclesides ((S)Ns) was also developed using a Pummerer reaction. Human thrombin RNA aptamer (CII-1-37) containing 4'-thiouridine and 4'-thiocytidine was obtained by SELEX with a K(d) value of 4.7 nM, while a previously known RNA aptamer (RNA-24) has a K(d) value of 85 nM. Studies of the modification pattern-RNAi activity relationships by using (S)Ns have been carried out against luciferase genes. We found that siRNAs, which have 4 residues of (S)Ns on both ends of the sense strand and 4 residues on the 3'-end of the antisense strand, were the most effective. 4'-ThioRNA is about 1100 times more stable in 50% human plasma than unmodified RNA. However, oligoribonucleotides ((SM)ONs) containing 2'-O-methyl-4'-thioribonucleosides were 9800 times more stable in 50% human plasma than unmodified RNA. Since (SM)ON duplexes were thermally more stable than unmodified ON duplexes, therefore they would be quite suitable to use for oligonucleotide therapeutics.
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Affiliation(s)
- Akira Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University.
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14
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Alexander V, Choi WJ, Chun J, Kim HO, Jeon JH, Tosh DK, Lee HW, Chandra G, Choi J, Jeong LS. A new DNA building block, 4'-selenothymidine: synthesis and modification to 4'-seleno-AZT as a potential anti-HIV agent. Org Lett 2010; 12:2242-5. [PMID: 20405850 DOI: 10.1021/ol1005906] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The first synthesis of 4'-selenothymidine (1), a novel DNA building block, and 4'-seleno-AZT (2) was accomplished from 2-deoxy-d-ribose via stereoselective formation of 2-deoxy-4-seleno-d-furanose 17 and a Pummerer-type base condensation as key steps. 4'-Selenothymidine (1) was discovered to adopt the same 2'-endo/3'-exo conformation as thymidine, which is unusual in that 4'-selenouridine has the opposite conformation to that of uridine.
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Affiliation(s)
- Varughese Alexander
- Department of Bioinspired Science and Laboratory of Medicinal Chemistry, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea
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Novel nucleosides as potent influenza viral inhibitors. Bioorg Med Chem 2010; 18:6329-39. [PMID: 20674371 DOI: 10.1016/j.bmc.2010.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 07/07/2010] [Accepted: 07/08/2010] [Indexed: 11/23/2022]
Abstract
Influenza virus infection constitutes a significant health problem in need of more effective therapies. We have recently identified ((2R,3S,4R,5R)-3-acetoxy-5-(4-benzamido-2-oxopyrimidin-1(2H)-yl)-4-fluoro-3,4-dimethyl-tetrahydrofuran-2-yl) methyl benzoate (18c) as a potent influenza virus inhibitor. We now here report the synthesis and evaluation of a series of C-3' modified ribose nucleosides. These novel compounds were prepared, primarily by taking known ((2R,3R,4R)-3-benzoyloxy-4-fluoro-4-methyl-5-oxo-tetrahydrofuran-2-yl)methyl benzoate (1) and converting it in to C-3 keto sugar (7), reacting C-3 keto group with methyl magnesium bromide, followed by coupling these sugars with purine and pyrimidine bases. Anti influenza viral activity was determined by screening against both A and B viral strains.
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Takahashi M, Minakawa N, Matsuda A. Synthesis and characterization of 2'-modified-4'-thioRNA: a comprehensive comparison of nuclease stability. Nucleic Acids Res 2009; 37:1353-62. [PMID: 19151085 PMCID: PMC2651785 DOI: 10.1093/nar/gkn1088] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We report herein the synthesis and physical and physiological characterization of fully modified 2′-modified-4′-thioRNAs, i.e. 2′-fluoro-4′-thioRNA (F-SRNA) and 2′-O-Me-4′-thioRNA (Me-SRNA), which can be considered as a hybrid chemical modification based on 2′-modified oligonucleotides (ONs) and 4′-thioRNA (SRNA). In its hybridization with a complementary RNA, F-SRNA (15mer) showed the highest Tm value (+16°C relative to the natural RNA duplex). In addition, both F-SRNA and Me-SRNA preferred RNA as a complementary partner rather than DNA in duplex formation. The results of a comprehensive comparison of nuclease stability of single-stranded F-SRNA and Me-SRNA along with 2′-fluoroRNA (FRNA), 2′-O-MeRNA (MeRNA), SRNA, and natural RNA and DNA, revealed that Me-SRNA had the highest stability with t1/2 values of > 24 h against S1 nuclease (an endonuclease) and 79.2 min against SVPD (a 3′-exonuclease). Moreover, the stability of Me-SRNA was significantly improved in 50% human plasma (t1/2 = 1631 min) compared with FRNA (t1/2 = 53.2 min) and MeRNA (t1/2 = 187 min), whose modifications are currently used as components of therapeutic aptamers. The results presented in this article will, it is hoped, contribute to the development of 2′-modified-4′-thioRNAs, especially Me-SRNA, as a new RNA molecule for therapeutic applications.
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Affiliation(s)
| | - Noriaki Minakawa
- *To whom correspondence should be addressed. Tel: +81 11 706 3228; Fax: +81 11 706 4980;
| | - Akira Matsuda
- *To whom correspondence should be addressed. Tel: +81 11 706 3228; Fax: +81 11 706 4980;
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17
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Moukha-Chafiq O, Secrist JA, Lazrek HB. Synthesis of Certain 2′-Deoxy-3′,5′-di- O -benzyl-4′-thio-nucleosides Using Natural Phosphate Doped with Trifluoromethanesulfonic Acid as Catalyst. PHOSPHORUS SULFUR 2008. [DOI: 10.1080/10426500802077671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- O. Moukha-Chafiq
- a Drug Discovery Division , Southern Research Institute , Birmingham , Alabama , USA
| | - J. A. Secrist
- a Drug Discovery Division , Southern Research Institute , Birmingham , Alabama , USA
| | - H. B. Lazrek
- b Unité de Chimie des Biomolécules et Médicinale, Faculty of Science Semlalia , Marrakech , Morocco
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18
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Zhichkin PE, Peterson LH, Beer CM, Rennells WM. The Use of Formamidine Protection for the Derivatization of Aminobenzoic Acids. J Org Chem 2008; 73:8954-9. [DOI: 10.1021/jo8017186] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Paul E. Zhichkin
- Medicinal Chemistry Department, AMRI, 26 Corporate Circle P.O. Box 15098, Albany, New York 12212
| | - Lisa H. Peterson
- Medicinal Chemistry Department, AMRI, 26 Corporate Circle P.O. Box 15098, Albany, New York 12212
| | - Catherine M. Beer
- Medicinal Chemistry Department, AMRI, 26 Corporate Circle P.O. Box 15098, Albany, New York 12212
| | - W. Martin Rennells
- Medicinal Chemistry Department, AMRI, 26 Corporate Circle P.O. Box 15098, Albany, New York 12212
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19
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Takahashi M, Daidouji S, Shiro M, Minakawa N, Matsuda A. Synthesis and crystal structure of 2′-deoxy-2′-fluoro-4′-thioribonucleosides: substrates for the synthesis of novel modified RNAs. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.02.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Matsugami A, Ohyama T, Inada M, Inoue N, Minakawa N, Matsuda A, Katahira M. Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance. Nucleic Acids Res 2008; 36:1805-12. [PMID: 18252770 PMCID: PMC2330235 DOI: 10.1093/nar/gkn011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Fully modified 4′-thioDNA, an oligonucleotide only comprising 2′-deoxy-4′-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4′-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4′-thioDNA was found to behave like an RNA molecule, but no details of its structure beyond the results of circular dichroism analysis are available. Here, we have determined the structure of fully modified 4′-thioDNA with the sequence of d(CGCGAATTCGCG) by NMR. Most sugars take on the C3′-endo conformation. The major groove is narrow and deep, while the minor groove is wide and shallow. Thus, fully modified 4′-thioDNA takes on the A-form characteristic of RNA, both locally and globally. The only structure reported for 4′-thioDNA showed that partially modified 4′-thioDNA that contained some 2′-deoxy-4′-thionucleosides took on the B-form in the crystalline form. We have determined the structure of 4′-thioDNA in solution for the first time, and demonstrated unexpected differences between the two structures. The origin of the formation of the A-form is discussed. The remarkable biochemical properties reported for fully modified 4′-thioDNA, including nuclease-resistance, are rationalized in the light of the elucidated structure.
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Affiliation(s)
- Akimasa Matsugami
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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21
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Inoue N, Shionoya A, Minakawa N, Kawakami A, Ogawa N, Matsuda A. Amplification of 4'-thioDNA in the presence of 4'-thio-dTTP and 4'-thio-dCTP, and 4'-thioDNA-directed transcription in vitro and in mammalian cells. J Am Chem Soc 2007; 129:15424-5. [PMID: 18034484 DOI: 10.1021/ja075953c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Naonori Inoue
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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22
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Abstract
The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modifications to the base portion will be discussed followed secondly by modifications to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids (PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.
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Affiliation(s)
- Alexander J A Cobb
- School of Pharmacy, University of Reading, Whiteknights, Reading, Berks RG6 6AD, UK.
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23
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Inoue N, Minakawa N, Matsuda A. Synthesis and properties of 4'-ThioDNA: unexpected RNA-like behavior of 4'-ThioDNA. Nucleic Acids Res 2006; 34:3476-83. [PMID: 16855286 PMCID: PMC1524900 DOI: 10.1093/nar/gkl491] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The synthesis and properties of fully modified 4′-thioDNAs, oligonucleotides consisting of 2′-deoxy-4′-thionucleosides, were examined. In addition to the known literature properties (preferable hybridization with RNA and resistance to endonuclease hydrolysis), we also observed higher resistance of 4′-thioDNA to 3′-exonuclease cleavage. Furthermore, we found that fully modified 4′-thioDNAs behaved like RNA molecules in their hybridization properties and structural aspect, at least in the case of the 4′-thioDNA duplex. This observation was confirmed by experiments using groove binders, in which a 4′-thioDNA duplex interacts with an RNA major groove binder, lividomycin A, but not with DNA groove binders, to give an increase in its thermal stability. Since a 4′-thioDNA duplex competitively inhibited the hydrolysis of an RNA duplex by RNase V1, it was not only the physical properties but also this biological data suggested that a 4′-thioDNA duplex has an RNA-like structure.
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Affiliation(s)
| | - Noriaki Minakawa
- Correspondence may also be addressed to Noriaki Minakawa. Tel: +81 11 706 3230; Fax: +81 11 706 4980;
| | - Akira Matsuda
- To whom correspondence should be addressed: Tel: +81 11 706 3228; Fax: +81 11 706 4980;
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24
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Ichikawa S, Minakawa N, Shuto S, Tanaka M, Sasaki T, Matsuda A. Synthesis of 3′-β-carbamoylmethylcytidine (CAMC) and its derivatives as potential antitumor agents. Org Biomol Chem 2006; 4:1284-96. [PMID: 16557317 DOI: 10.1039/b517602f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
3'-beta-Carbamoylmethylcytidine (CAMC) and its derivatives were synthesized using an intramolecular Reformatsky-type reaction promoted by SmI2 as the key step. In vitro tumor cell growth inhibitory activity was evaluated and CAMC was found to exhibit potent cytotoxicity against various human tumor cell lines. From a structure-activity relationship study it was postulated that the cytotoxic mechanism of action of CAMC did not require phosphorylation at the 5'-hydroxyl group. This study provides a novel strategy for the development of a new type of antitumor nucleoside.
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Affiliation(s)
- Satoshi Ichikawa
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
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