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Ota M, Takahashi H, Nogi Y, Kagotani Y, Saito-Tarashima N, Kondo J, Minakawa N. Synthesis and properties of fully-modified 4'-selenoRNA, an endonuclease-resistant RNA analog. Bioorg Med Chem 2022; 76:117093. [PMID: 36434923 DOI: 10.1016/j.bmc.2022.117093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/21/2022]
Abstract
A large number of chemically modified oligonucleotides (ONs) have been developed for RNA-based technologies. In most modified RNAs, the characteristic 2'-hydroxyl (2'-OH) groups are removed to enhance both nuclease resistance and hybridization ability. However, the importance of the 2'-OH group in RNA structure and function is well known. Here, we report the synthesis and properties of 4'-selenoRNA in which all four nucleoside units retain the 2'-OH groups but contain a selenium atom instead of an oxygen atom at the 4'-position of the furanose ring. 4'-SelenoRNA has enhanced ability to form duplexes with RNA, and high endonuclease resistance despite the presence of the 2'-OH groups. X-ray crystallography analysis showed that the 4'-selenoRNA duplex adopts an A-conformation, similar to natural RNA, although one 4'-selenocytidine residue has unusual South-type sugar puckering. Furthermore, preliminary studies using 4'-seleno-modified siRNAs suggest that 4'-selenoRNA may be applicable to RNA interference technology. Collectively, our results raise the possibility of a new class of modified RNA in which 2'-OH groups do not need to be masked.
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Affiliation(s)
- Masashi Ota
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Hiromi Takahashi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan
| | - Yuhei Nogi
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Yuma Kagotani
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Noriko Saito-Tarashima
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan.
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2
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Iwaoka M, Hiyoshi Y, Arai S, Ito T. Synthesis of 4-Selenothreofuranose Derivatives via Pummerer-Type Reactions of trans-3,4-Dioxygenated Tetrahydroselenophenes Mediated by a Selenonium Intermediate. ACS OMEGA 2021; 6:17621-17634. [PMID: 34278147 PMCID: PMC8280693 DOI: 10.1021/acsomega.1c02160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/15/2021] [Indexed: 05/14/2023]
Abstract
Selenosugars are interesting targets of organic synthesis as they would possess potential biological activities. However, 4-selenotherofuranose derivatives, which have trans configuration for the two dihydroxy substituents at the 2,3-positions and a glycoside bond at the anomeric position, are not available in the current selenosugar library. In this study, racemic 4-selenothreofuranose derivatives were synthesized from trans-3,4-dioxygenated tetrahydroselenophenes in 77-99% yields with the α/β selectivity about 7:3 via oxidation and subsequent seleno-Pummerer rearrangement. The acetoxy group introduced at the anomeric position was then substituted with various nucleophiles, including activated 6-chloropurine, which afforded 4'-selenothreonucleoside derivatives, in the presence of BF3·OEt2 or TMSOTf. The stereochemistry of the selenosugar products was established by 1H NMR spectroscopy as well as X-ray analysis. The similar α/β selectivity observed in the latter glycosylation reaction to that in the former seleno-Pummerer rearrangement suggested the mediation of a common selenonium intermediate (-Se+=C<). It was also suggested that an unexpected interaction between the ester protecting group at the 3-position of the selenofuranose ring and the anomeric carbon atom decreases the α/β selectivity.
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Ota M, Saito-Tarashima N, Minakawa N. Chemistry for Nucleic Acid Analogs Having Sulfur and Selenium Atoms in Place of Furanose Ring Oxygen. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Conlon PF, Eguaogie O, Wilson JJ, Sweet JST, Steinhoegl J, Englert K, Hancox OGA, Law CJ, Allman SA, Tucker JHR, Hall JP, Vyle JS. Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: a backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography. Chem Sci 2019; 10:10948-10957. [PMID: 32190252 PMCID: PMC7066676 DOI: 10.1039/c9sc04098f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/11/2019] [Indexed: 01/20/2023] Open
Abstract
Oligodeoxynucleotides incorporating internucleotide phosphoroselenolate linkages have been prepared under solid-phase synthesis conditions using dimer phosphoramidites. These dimers were constructed following the high yielding Michaelis-Arbuzov (M-A) reaction of nucleoside H-phosphonate derivatives with 5'-deoxythymidine-5'-selenocyanate and subsequent phosphitylation. Efficient coupling of the dimer phosphoramidites to solid-supported substrates was observed under both manual and automated conditions and required only minor modifications to the standard DNA synthesis cycle. In a further demonstration of the utility of M-A chemistry, the support-bound selenonucleoside was reacted with an H-phosphonate and then chain extended using phosphoramidite chemistry. Following initial unmasking of methyl-protected phosphoroselenolate diesters, pure oligodeoxynucleotides were isolated using standard deprotection and purification procedures and subsequently characterised by mass spectrometry and circular dichroism. The CD spectra of both modified and native duplexes derived from self-complementary sequences with A-form, B-form or mixed conformational preferences were essentially superimposable. These sequences were also used to study the effect of the modification upon duplex stability which showed context-dependent destabilisation (-0.4 to -3.1 °C per phosphoroselenolate) when introduced at the 5'-termini of A-form or mixed duplexes or at juxtaposed central loci within a B-form duplex (-1.0 °C per modification). As found with other nucleic acids incorporating selenium, expeditious crystallisation of a modified decanucleotide A-form duplex was observed and the structure solved to a resolution of 1.45 Å. The DNA structure adjacent to the modification was not significantly perturbed. The phosphoroselenolate linkage was found to impart resistance to nuclease activity.
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Affiliation(s)
- Patrick F Conlon
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Olga Eguaogie
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Jordan J Wilson
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Jamie S T Sweet
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Julian Steinhoegl
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - Klaudia Englert
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK
| | - Oliver G A Hancox
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - Christopher J Law
- School of Biological Sciences , Queen's University Belfast , 15 Chlorine Gardens , Belfast BT9 5AH , UK
| | - Sarah A Allman
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - James H R Tucker
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK
| | - James P Hall
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
- Diamond Light Source , Chilton , Didcot , Oxfordshire OX11 0DE , UK
| | - Joseph S Vyle
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
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Di Leo I, Messina F, Nascimento V, Nacca FG, Pietrella D, Lenardão EJ, Perin G, Sancineto L. Synthetic Approaches to Organoselenium Derivatives with Antimicrobial and Anti-Biofilm Activity. MINI-REV ORG CHEM 2019. [DOI: 10.2174/1570193x16666181227111038] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the recent years, an increasing attention has been given to the biological activities exerted
by organoselenium compounds. In 1984, Sies reported for the first time the ability of ebselen to
mimic the activity of glutathione peroxidase. From this milestone, several studies reported the pharmacological
properties of selenium-containing compounds including their exploitation as antimicrobials.
In this context, this minireview presents the most recent examples of seleno derivatives endowed
with antimicrobial activities while discussing the most interesting and recent synthetic procedures
used to obtain these compounds.
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Affiliation(s)
- Iris Di Leo
- Universidade Federal Fluminense, Departamento de Quimica Organica, Programa de Pos-Graduacao em Quimica, Outeiro de Sao Joao Batista, 24020-141 Niteroi, RJ, Brazil
| | | | - Vanessa Nascimento
- Universidade Federal Fluminense, Departamento de Quimica Organica, Programa de Pos-Graduacao em Quimica, Outeiro de Sao Joao Batista, 24020-141 Niteroi, RJ, Brazil
| | - Francesca G. Nacca
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Donatella Pietrella
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Eder J. Lenardão
- Laboratorio de Síntese Organica Limpa - LASOL, CCQFA, Universidade Federal de Pelotas, P.O. Box 354, 96010-900, Pelotas, RS, Brazil
| | - Gelson Perin
- Laboratorio de Síntese Organica Limpa - LASOL, CCQFA, Universidade Federal de Pelotas, P.O. Box 354, 96010-900, Pelotas, RS, Brazil
| | - Luca Sancineto
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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Yoshimura Y, Wakamatsu H, Natori Y, Saito Y, Minakawa N. Glycosylation reactions mediated by hypervalent iodine: application to the synthesis of nucleosides and carbohydrates. Beilstein J Org Chem 2018; 14:1595-1618. [PMID: 30013687 PMCID: PMC6037013 DOI: 10.3762/bjoc.14.137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/15/2018] [Indexed: 12/23/2022] Open
Abstract
To synthesize nucleoside and oligosaccharide derivatives, we often use a glycosylation reaction to form a glycoside bond. Coupling reactions between a nucleobase and a sugar donor in the former case, and the reaction between an acceptor and a sugar donor of in the latter are carried out in the presence of an appropriate activator. As an activator of the glycosylation, a combination of a Lewis acid catalyst and a hypervalent iodine was developed for synthesizing 4'-thionucleosides, which could be applied for the synthesis of 4'-selenonucleosides as well. The extension of hypervalent iodine-mediated glycosylation allowed us to couple a nucleobase with cyclic allylsilanes and glycal derivatives to yield carbocyclic nucleosides and 2',3'-unsaturated nucleosides, respectively. In addition, the combination of hypervalent iodine and Lewis acid could be used for the glycosylation of glycals and thioglycosides to produce disaccharides. In this paper, we review the use of hypervalent iodine-mediated glycosylation reactions for the synthesis of nucleosides and oligosaccharide derivatives.
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Affiliation(s)
- Yuichi Yoshimura
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai, 981-8558, Japan
| | - Hideaki Wakamatsu
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai, 981-8558, Japan
| | - Yoshihiro Natori
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai, 981-8558, Japan
| | - Yukako Saito
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai, 981-8558, Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima, 770-8505, Japan
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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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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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Kim G, Choi Y, Sahu PK, Yu J, Qu S, Lee D, Jeong LS. Stereoselective Synthesis of D-5-Homo-4-selenoribose as a Versatile Intermediate for 4'-Selenonucleosides. Org Lett 2015; 17:4636-9. [PMID: 26348005 DOI: 10.1021/acs.orglett.5b02393] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stereoselective synthesis of D-5-homo-4-selenoribose, serving as a versatile intermediate for the synthesis of 4'-selenonucleosides 12a-c, was accomplished using Sharpless asymmetric epoxidation, regioselective cleavage of the α,β-epoxide, and stereoselective reduction of the ketone as the key steps.
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Affiliation(s)
- Gyudong Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul 151-742, Korea
| | - Yoojin Choi
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul 151-742, Korea
| | - Pramod K Sahu
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul 151-742, Korea
| | - Jinha Yu
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul 151-742, Korea
| | - Shuhao Qu
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul 151-742, Korea
| | - Dongjoo Lee
- College of Pharmacy, Ajou University , Suwon 443-749, Korea
| | - Lak Shin Jeong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul 151-742, Korea
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10
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Sahu PK, Naik SD, Yu J, Jeong LS. 4′-Selenonucleosides as Next-Generation Nucleosides. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500429] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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11
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Tarashima N, Sumitomo T, Ando H, Furukawa K, Ishida T, Minakawa N. Synthesis of DNA fragments containing 2′-deoxy-4′-selenonucleoside units using DNA polymerases: comparison of dNTPs with O, S and Se at the 4′-position in replication. Org Biomol Chem 2015; 13:6949-52. [DOI: 10.1039/c5ob00941c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The first synthesis of 4′-selenoDNA was achieved using 4′-selenothymidine triphosphate by taking advantage of its bioequivalence against DNA polymerases.
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Affiliation(s)
- N. Tarashima
- Graduate School of Pharmaceutical Sciences
- Tokushima University
- Tokushima 770-8505
- Japan
| | - T. Sumitomo
- Graduate School of Pharmaceutical Sciences
- Tokushima University
- Tokushima 770-8505
- Japan
| | - H. Ando
- Graduate School of Pharmaceutical Sciences
- Tokushima University
- Tokushima 770-8505
- Japan
| | - K. Furukawa
- Graduate School of Pharmaceutical Sciences
- Tokushima University
- Tokushima 770-8505
- Japan
| | - T. Ishida
- Graduate School of Pharmaceutical Sciences
- Tokushima University
- Tokushima 770-8505
- Japan
| | - N. Minakawa
- Graduate School of Pharmaceutical Sciences
- Tokushima University
- Tokushima 770-8505
- Japan
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Tarashima N, Hayashi K, Terasaki M, Taniike H, Inagaki Y, Hirose K, Furukawa K, Matsuda A, Minakawa N. First synthesis of fully modified 4'-selenoRNA and 2'-OMe-4'-selenoRNA based on the mechanistic considerations of an unexpected strand break. Org Lett 2014; 16:4710-3. [PMID: 25181546 DOI: 10.1021/ol502077h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This study investigated oligonucleotide (ON) synthesis containing 4'-selenoribonucleoside(s) under standard phosphoramidite conditions. Careful operation using a manual ON synthetic system revealed that an unexpected strand break occurred to afford a C2-symmetric homodimer as a byproduct. In addition, this side reaction occurred during I2 oxidation. On the basis of these findings, the first synthesis of fully modified 4'-selenoRNA and 2'-OMe-4'-selenoRNA was achieved using tert-butyl hydroperoxide (TBHP) as the alternative oxidant.
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Affiliation(s)
- Noriko Tarashima
- Graduate School of Pharmaceutical Sciences, The University of Tokushima , Shomachi 1-78-1, Tokushima 770-8505, Japan
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