1
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Pal S, Chandra G, Patel S, Singh S. Fluorinated Nucleosides: Synthesis, Modulation in Conformation and Therapeutic Application. CHEM REC 2022; 22:e202100335. [PMID: 35253973 DOI: 10.1002/tcr.202100335] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/22/2022] [Indexed: 12/17/2022]
Abstract
Over the last twenty years, fluorination on nucleoside has established itself as the most promising tool to use to get biologically active compounds that could sustain the clinical trial by affecting the pharmacodynamics and pharmacokinetic properties. Due to fluorine's inherent unique properties and its judicious introduction into the molecule, makes the corresponding nucleoside metabolically very stable, lipophilic, and opens a new site of intermolecular binding. Fluorination on various nucleosides has been extensively studied as a result, a series of fluorinated nucleosides come up for different therapeutic uses which are either approved by the FDA or under the advanced stage of the clinical trial. Here in this review, we are summarizing the latest development in the chemistry of fluorination on nucleoside that led to varieties of new analogs like carbocyclic, acyclic, and conformationally biased nucleoside and their biological properties, the influence of fluorine on conformation, oligonucleotide stability, and their use in therapeutics.
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Affiliation(s)
- Shantanu Pal
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
| | - Girish Chandra
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Samridhi Patel
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Sakshi Singh
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
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2
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Chardet C, Payrastre C, Gerland B, Escudier JM. Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch. Molecules 2021; 26:5925. [PMID: 34641475 PMCID: PMC8512084 DOI: 10.3390/molecules26195925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5'-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson-Crick base-pairing. We show that 5'-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5'-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.
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Affiliation(s)
| | | | - Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d′Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (C.C.); (C.P.)
| | - Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d′Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (C.C.); (C.P.)
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3
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Seneviratne U, Wickramaratne S, Kotandeniya D, Groehler AS, Geraghty RJ, Dreis C, Pujari SS, Tretyakova NY. Synthesis and biological evaluation of pyrrolidine-functionalized nucleoside analogs. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02700-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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4
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Escudier JM, Payrastre C, Gerland B, Tarrat N. Convertible and conformationally constrained nucleic acids (C 2NAs). Org Biomol Chem 2019; 17:6386-6397. [PMID: 31210235 DOI: 10.1039/c9ob01150a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We introduce the concept of Convertible and Constrained Nucleic Acids (C2NAs). By means of the synthesis of a stereocontrolled N-propargyl dioxo-1,3,2-oxaza-phosphorinane as an internucleotidic linkage, the torsional angles α and β can adopt either the canonical (g-, t) set of values able to increase DNA duplex stability or the non-canonical (g+, t) set that stabilized the hairpin structure when installed within the loop moiety. With an appended propargyl function on the nitrogen atom of the six-membered ring, the copper catalysed Huisgen's cycloaddition (CuAAC click chemistry) allows for the introduction of new functionalities at any location on the nucleic acid chain while maintaining the properties brought by the geometrical constraint and the neutral internucleotidic linkage.
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Affiliation(s)
- Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Corinne Payrastre
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29 rue Jeanne Marvig, Toulouse 31055, France
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5
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Popova EA, Ovsepyan GK, Protas AV, Erkhitueva EB, Kukhanova MK, Yesaulkova YL, Zarubaev VV, Starova GL, Suezov RV, Eremin AV, Ostrovskii VA, Trifonov RE. Synthesis and in vitro Biological Evaluation of Novel Thymidine Analogs Containing 1 H-1,2,3-Triazolyl, 1 H-Tetrazolyl, and 2 H-Tetrazolyl Fragments. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:713-731. [PMID: 30991893 DOI: 10.1080/15257770.2018.1541466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
3'-Azidothymidine (AZT) reacts with 1-propargyl-5-R-1H- and 2-propargyl-5-R-2H-tetrazoles (R = H, Me, CH2COOEt, CH2CON(CH3)2, Ph, 2-CH3-C6H4, or 4-NO2-C6H4) via the Cu(I)-catalyzed asymmetric [3 + 2] cycloaddition to give 3'-modified thymidine analogs incorporating 1H-1,2,3-triazolyl, 1H-, and 2H-tetrazolyl fragments in 41-76% yield. The structures of the obtained compounds have been elucidated by means of HRESI+-MS, 1H and 13 C{1H} NMR, and single crystal X-ray diffraction {for 3'-[4-(1H-5-N,N-dimethylaminocarbonylmethyltetrazol-1-yl)-1H-1,2,3-triazol-1-yl]thymidine 10d}. In vitro biological evaluation of the prepared compounds has been performed; they have exhibited low activity against phenotypic HIV-1899A. Moderate anti-influenza activity against influenza virus A/Puerto Rico/8/34 (H1N1) strain has been observed in the cases of 3'-(4-(1H-tetrazol-1-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 10a (IC50 39.6 μg/mL), 3'-(4-(2H-5-ethoxycarbonyltetrazol-2-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 11c (IC50 31.6 μg/mL), and 3'-(4-(2H-5-(4-nitrophenyl)-tetrazol-2-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 11g (IC50 46.4 μg/mL). The tested compounds possess very low cytotoxicity towards MDCK and MT4 cells as well as tumor human cervical carcinoma HeLa and promyelocytic leukemia HL-60 cells.
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Affiliation(s)
- Elena A Popova
- a Saint Petersburg State University , 7/9 Universitetskaya nab., Saint Petersburg , 199034 , Russia
| | - Gayane K Ovsepyan
- a Saint Petersburg State University , 7/9 Universitetskaya nab., Saint Petersburg , 199034 , Russia
| | - Aleksandra V Protas
- a Saint Petersburg State University , 7/9 Universitetskaya nab., Saint Petersburg , 199034 , Russia
| | - Elena B Erkhitueva
- a Saint Petersburg State University , 7/9 Universitetskaya nab., Saint Petersburg , 199034 , Russia
| | - Marina K Kukhanova
- b Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , 32 Vavilova st. , Moscow , 119991 , Russia
| | - Yana L Yesaulkova
- c Saint Petersburg Pasteur Institute , 14 Mira st. , Saint Petersburg , 197101 , Russia
| | - Vladimir V Zarubaev
- c Saint Petersburg Pasteur Institute , 14 Mira st. , Saint Petersburg , 197101 , Russia
| | - Galina L Starova
- a Saint Petersburg State University , 7/9 Universitetskaya nab., Saint Petersburg , 199034 , Russia
| | - Roman V Suezov
- d Institute of Cytology, Russian Academy of Sciences , 4 Tikhoretsky ave. , Saint Petersburg , 194064 , Russia.,e Saint Petersburg State Institute of Technology (Technical University) , 26 Moskovsky pr. , Saint Petersburg , 190013 , Russia
| | - Alexei V Eremin
- e Saint Petersburg State Institute of Technology (Technical University) , 26 Moskovsky pr. , Saint Petersburg , 190013 , Russia.,f Peter the Great St. Petersburg Polytechnic University , 29 Polytechnic st. , Saint Petersburg , 195251 , Russia
| | - Vladimir A Ostrovskii
- e Saint Petersburg State Institute of Technology (Technical University) , 26 Moskovsky pr. , Saint Petersburg , 190013 , Russia
| | - Rostislav E Trifonov
- a Saint Petersburg State University , 7/9 Universitetskaya nab., Saint Petersburg , 199034 , Russia
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6
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Iannazzo L, Fonvielle M, Braud E, Hřebabecký H, Procházková E, Nencka R, Mathé C, Arthur M, Etheve-Quelquejeu M. Synthesis of tRNA analogues containing a terminal ribose locked in the South conformation to study tRNA-dependent enzymes. Org Biomol Chem 2019; 16:1903-1911. [PMID: 29484333 DOI: 10.1039/c8ob00019k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the synthetic route of two constrained dinucleotides and the determination of the sugar puckering by NMR analyses of the starting nucleosides. Enzymatic ligation to microhelix-RNAs provide access to tRNA analogues containing a 3' terminal A76 locked in South conformation. Biological evaluation of our tRNA analogues has been performed using amino-acyl tRNA-dependent transferase FemXWv, which mediates non-ribosomal incorporation of amino acids into the bacterial cell wall. We have shown that our tRNA analogues inhibited the aminoacyl transfer reaction catalyzed by FemXWv with IC50s of 10 and 8 μM. These results indicate that FemXWv displays a moderate preference for tRNAs containing a terminal A76 locked in the South conformation and that a South to North switch in the conformation of the terminal ribose might contribute to the release of the uncharged tRNAAla product of the aminoacyl transfer reaction catalyzed by FemXwv.
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Affiliation(s)
- Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France
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7
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Krishnammagari SK, Jeong YT. An Efficient and Transition Metal-Free Base-Promoted Multi-Component Synthesis of Aza-Fused Polysubstituted Pyrido[2′,3′:3,4]Pyrazolo[1,5-a]Pyrimidine Derivatives. Polycycl Aromat Compd 2018. [DOI: 10.1080/10406638.2018.1526808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - Yeon Tae Jeong
- Department of Image Science and Engineering, Pukyong National University, Busan, Republic of Korea
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8
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Shoji T, Fukutomi H, Okada Y, Chiba K. Artificial bioconjugates with naturally occurring linkages: the use of phosphodiester. Beilstein J Org Chem 2018; 14:1946-1955. [PMID: 30112100 PMCID: PMC6071721 DOI: 10.3762/bjoc.14.169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/06/2018] [Indexed: 12/22/2022] Open
Abstract
Artificial orthogonal bond formations such as the alkyne–azide cycloaddition have enabled selective bioconjugations under mild conditions, yet naturally occurring linkages between native functional groups would be more straightforward to elaborate bioconjugates. Herein, we describe the use of a phosphodiester bond as a versatile option to access various bioconjugates. An opposite activation strategy, involving 5’-phosphitylation of the supported oligonucleotides, has allowed several biomolecules that possess an unactivated alcohol to be directly conjugated. It should be noted that there is no need to pre-install artificial functional groups and undesired and unpredictable perturbations possibly caused by bioconjugation can be minimized.
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Affiliation(s)
- Takao Shoji
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Hiroki Fukutomi
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Yohei Okada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazuhiro Chiba
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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9
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Páv O, Barvík I, Liboska R, Petrová M, Šimák O, Rosenbergová Š, Novák P, Buděšínský M, Rosenberg I. Tuning the hybridization properties of modified oligonucleotides: from flexible to conformationally constrained phosphonate internucleotide linkages. Org Biomol Chem 2018; 15:701-707. [PMID: 27995239 DOI: 10.1039/c6ob02571d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The concept of conformational restriction leading to the preorganization of modified strands has proven to be successful and has afforded nucleic acid analogues with many interesting properties suitable for various biochemical applications. We utilized this concept to prepare a set of constrained oligonucleotides derived from 1,4-dioxane and 1,3-dioxolane-locked nucleoside phosphonates and evaluated their hybridization affinities towards their complementary RNA strands. With an increase of ΔTm per modification up to +5.2 °C, the hybridization experiments revealed the (S)-2',3'-O-phosphonomethylidene internucleotide linkage as one of the most Tm-increasing modifications reported to date. Moreover, we introduced a novel prediction tool for the pre-selection of potentially interesting chemical modifications of oligonucleotides.
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Affiliation(s)
- Ondřej Páv
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Ivan Barvík
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116 Prague, Czech Republic
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Ondřej Šimák
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic. and Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Šárka Rosenbergová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Pavel Novák
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
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10
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Xu F, Song YY, Kang WF, Cui H, Mu QN, Meng YY. An efficient route to highly functionalized benzene derivatives by rhodium-catalyzed dimerization of diynes. CHEMICAL PAPERS 2018. [DOI: 10.1007/s11696-018-0391-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Hřebabecký H, Dračínský M, Procházková E, Šála M, Mackman R, Nencka R. Control of α/β Anomer Formation by a 2',5' Bridge: Toward Nucleoside Derivatives Locked in the South Conformation. J Org Chem 2017; 82:11337-11347. [PMID: 28972760 DOI: 10.1021/acs.joc.7b01000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe a novel stereoselective synthesis of nucleoside derivatives with the ribose ring locked in the South conformation by a bridge between C2' and C5'. Despite the intrinsic constraints of the bicyclic structure, we demonstrate that their synthesis can be achieved by ring closing metathesis of readily accessible precursors. The obtained ribose derivatives are, however, very poor substrates for further installation of the nucleobases, and even simple nucleophiles, such as azido or cyano anions, react with unexpected stereo- or regioselectivity under standard glycosylation conditions. Here we explain this behavior by employing density functional theory (DFT) computations and devise an alternative approach resulting in isomers with the desired orientation of the nucleobase.
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Affiliation(s)
- Hubert Hřebabecký
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Richard Mackman
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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12
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Gerland B, Addamiano C, Renard BL, Payrastre C, Gopaul D, Escudier JM. Thio- and Seleno-Dioxaphosphorinane-Constrained Dinucleotides (D-CNA): Synthesis and Conformational Study. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068; Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Claudia Addamiano
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068; Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Brice-Loïc Renard
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068; Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Corinne Payrastre
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068; Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Deshmukh Gopaul
- Laboratoire de Génomes et Génétique; UMR 3525 Institut Pasteur; 25 rue du Docteur Roux 75015 Paris France
| | - Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068; Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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13
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Castillo JC, Estupiñan D, Nogueras M, Cobo J, Portilla J. 6-(Aryldiazenyl)pyrazolo[1,5-a]pyrimidines as Strategic Intermediates for the Synthesis of Pyrazolo[5,1-b]purines. J Org Chem 2016; 81:12364-12373. [PMID: 27978735 DOI: 10.1021/acs.joc.6b02431] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A microwave-assisted approach for the regioselective synthesis of functionalized 6-(aryldiazenyl)pyrazolo[1,5-a]pyrimidin-7-amines from the cyclization of 3-oxo-2-(2-arylhydrazinylidene)butanenitriles with 5-amino-1H-pyrazoles under solvent-free conditions has been developed. This methodology was distinguished by its broad substrate scope, operational simplicity, high atom economy, and high-yielding without requiring chromatographic purification. In addition, an efficient and versatile palladium-catalyzed reductive azo cleavage is disclosed for the synthesis of diverse heteroaromatic 1,2-diamines, a valuable synthetic building block to develop new fused heteroaromatic systems. As synthetic example, several substituted pyrazolo[5,1-b]purines were synthesized in yields up to 96% by using microwave irradiation in the cyclocondensation of these 1,2-diamines with orthoesters.
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Affiliation(s)
- Juan-Carlos Castillo
- Bioorganic Compounds Research Group, Department of Chemistry, Universidad de los Andes , Carrera 1 No. 18A-10, Bogotá 111711, Colombia
| | - Diego Estupiñan
- Bioorganic Compounds Research Group, Department of Chemistry, Universidad de los Andes , Carrera 1 No. 18A-10, Bogotá 111711, Colombia
| | - Manuel Nogueras
- Departamento de Química Inorgánica y Orgánica, Universidad de Jaén , Jaén 23071, Spain
| | - Justo Cobo
- Departamento de Química Inorgánica y Orgánica, Universidad de Jaén , Jaén 23071, Spain
| | - Jaime Portilla
- Bioorganic Compounds Research Group, Department of Chemistry, Universidad de los Andes , Carrera 1 No. 18A-10, Bogotá 111711, Colombia
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14
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González-Calderón D, Mejía-Dionicio MG, Morales-Reza MA, Aguirre-de Paz JG, Ramírez-Villalva A, Morales-Rodríguez M, Fuentes-Benítes A, González-Romero C. Antifungal activity of 1'-homo-N-1,2,3-triazol-bicyclic carbonucleosides: A novel type of compound afforded by azide-enolate (3+2) cycloaddition. Bioorg Chem 2016; 69:1-6. [PMID: 27656774 DOI: 10.1016/j.bioorg.2016.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/01/2016] [Accepted: 09/14/2016] [Indexed: 01/06/2023]
Abstract
The first report of 1'-homo-N-1,2,3-triazol-bicyclic carbonucleosides (7a and 7b) is described herein. Azide-enolate (3+2) cycloaddition afforded the synthesis of this novel type of compound. Antifungal activity was evaluated in vitro against four filamentous fungi (Aspergillus fumigatus, Trichosporon cutaneum, Rhizopus oryzae and Mucor hiemalis) as well as nine species of Candida spp. as yeast specimens. These pre-clinical studies suggest that compounds 7a and 7b are promising candidates for complementary biological studies due to their good activity against Candida spp.
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Affiliation(s)
- Davir González-Calderón
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico.
| | - María G Mejía-Dionicio
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - Marco A Morales-Reza
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - José G Aguirre-de Paz
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - Alejandra Ramírez-Villalva
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - Macario Morales-Rodríguez
- Departamento de Microbiología, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - Aydeé Fuentes-Benítes
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico
| | - Carlos González-Romero
- Departamento de Química Orgánica, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón/Paseo Tollocan s/n, Toluca, Estado de México 50120, Mexico.
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15
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Abstract
Focusing on the recent literature (since 2000), this review outlines the main synthetic approaches for the preparation of 5'-mono-, 5'-di-, and 5'-triphosphorylated nucleosides, also known as nucleotides, as well as several derivatives, namely, cyclic nucleotides and dinucleotides, dinucleoside 5',5'-polyphosphates, sugar nucleotides, and nucleolipids. Endogenous nucleotides and their analogues can be obtained enzymatically, which is often restricted to natural substrates, or chemically. In chemical synthesis, protected or unprotected nucleosides can be used as the starting material, depending on the nature of the reagents selected from P(III) or P(V) species. Both solution-phase and solid-support syntheses have been developed and are reported here. Although a considerable amount of research has been conducted in this field, further work is required because chemists are still faced with the challenge of developing a universal methodology that is compatible with a large variety of nucleoside analogues.
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Affiliation(s)
- Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Christian Périgaud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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16
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Kumar Kondapi VP, Soueidan OM, Hosseini SN, Jabari N, West FG. Efficient and Easy Access to Optically Pure Tetrasubstituted Tetrahydrofurans via Stereoselective Opening ofC2-Symmetric Epoxide and Aziridine Rings. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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17
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Srivastava S, Singh SK, Sharma VK, Mangla P, Olsen CE, Prasad AK. Design and Synthesis of Triazole-Linked xylo-Nucleoside Dimers. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 34:388-99. [PMID: 25965328 DOI: 10.1080/15257770.2015.1004341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Three triazole-linked nonionic xylo-nucleoside dimers T(L)-t-T(xL), T(L)-t-A(BzxL) and T(L)-t-C(BzxL) have been synthesized for the first time by Cu(I) catalyzed azide-alkyne [3 + 2] cycloaddition reaction (CuAAC) of 1-(3'-azido-3'-deoxy-2'-O,4'-C-methylene-β-D-ribo-furanosyl)thymine with different alkynes, i.e., 1-(5'-deoxy-5'-C-ethynyl-2'-O,4'-C-methylene-β-D-xylofuranosyl)thymine, 9-(5'-deoxy-5'-C-ethynyl-2'-O,4'-C-methylene-β-D-xylo-furanosyl)-N6-benzoyladenine and 1-(5'-deoxy-5'-C-ethynyl-2'-O,4'-C-methylene-β-D-xylofuranosyl)-N4-benzoylcytosine in 90%-92% yields. Among the two Cu(I) reagents, CuSO4.5H2O-sodium ascorbate in THF:(t)BuOH:H2O (1:1:1) and CuBr.SMe2 in THF used for cycloaddition (click) reaction, the former one was found to be better yielding than the latter one.
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Affiliation(s)
- Smriti Srivastava
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
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18
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Zhang DJ, Xie MS, Qu GR, Gao YW, Guo HM. Synthesis of Azacyclic Nucleoside Analogues via Asymmetric [3 + 2] Cycloaddition of 9-(2-Tosylvinyl)-9H-purines. Org Lett 2016; 18:820-3. [DOI: 10.1021/acs.orglett.6b00108] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dan-Jie Zhang
- Key Laboratory of Green Chemical
Media and Reactions, Ministry of Education, Collaborative Innovation
Center of Henan Province for Green Manufacturing of Fine Chemicals,
School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Ming-Sheng Xie
- Key Laboratory of Green Chemical
Media and Reactions, Ministry of Education, Collaborative Innovation
Center of Henan Province for Green Manufacturing of Fine Chemicals,
School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Gui-Rong Qu
- Key Laboratory of Green Chemical
Media and Reactions, Ministry of Education, Collaborative Innovation
Center of Henan Province for Green Manufacturing of Fine Chemicals,
School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Yao-Wei Gao
- Key Laboratory of Green Chemical
Media and Reactions, Ministry of Education, Collaborative Innovation
Center of Henan Province for Green Manufacturing of Fine Chemicals,
School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Hai-Ming Guo
- Key Laboratory of Green Chemical
Media and Reactions, Ministry of Education, Collaborative Innovation
Center of Henan Province for Green Manufacturing of Fine Chemicals,
School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
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19
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Sontakke VA, Lawande PP, Kate AN, Khan A, Joshi R, Kumbhar AA, Shinde VS. Antiproliferative activity of bicyclic benzimidazole nucleosides: synthesis, DNA-binding and cell cycle analysis. Org Biomol Chem 2016; 14:4136-45. [DOI: 10.1039/c6ob00527f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bicyclic benzimidazole nucleosides were synthesized from d-glucose as a starting material. DNA binding, antiproliferative activity and cell cycle analysis were performed.
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Affiliation(s)
- Vyankat A. Sontakke
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
| | - Pravin P. Lawande
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
| | - Anup N. Kate
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
| | - Ayesha Khan
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
| | - Rakesh Joshi
- Institute of Bioinformatics and Biotechnology
- Savitribai Phule Pune University
- Pune-411007
- India
| | - Anupa A. Kumbhar
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
| | - Vaishali S. Shinde
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
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20
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De Coen LM, Heugebaert TSA, García D, Stevens CV. Synthetic Entries to and Biological Activity of Pyrrolopyrimidines. Chem Rev 2015; 116:80-139. [DOI: 10.1021/acs.chemrev.5b00483] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Laurens M. De Coen
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Thomas S. A. Heugebaert
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Daniel García
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Christian V. Stevens
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
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21
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Hervé G, Len C. Heck and Sonogashira couplings in aqueous media – application to unprotected nucleosides and nucleotides. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40508-015-0029-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Abstract
Modified nucleoside analogues are of great biological importance as antiviral and antitumoral agents. There is special interest in the preparation of C-aryl nucleosides with an aromatic ring in different positions of the glycone for their biological activity. Different chemical synthesis strategies for these targets are described in this review.
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Affiliation(s)
- Christophe Len
- Sorbonne Universités, Université de Technologie de Compiègne, Ecole Supérieure de Chimie Organique et Minérale, Transformations Intégrées de la Matière Renouvelable, Centre de Recherche Royallieu, CS 60319, Compiègne cedex F-60203, France.
- Department of Chemistry, University of Hull, Hull HU6 7RX, UK.
| | - Gérald Enderlin
- Sorbonne Universités, Université de Technologie de Compiègne, Ecole Supérieure de Chimie Organique et Minérale, Transformations Intégrées de la Matière Renouvelable, Centre de Recherche Royallieu, CS 60319, Compiègne cedex F-60203, France.
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23
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Zhang D, Johnson S, Cui HL, Tanaka F. Synthesis of Furanose Spirooxindoles via 1,8-Diazabicyclo[5.4.0]undec-7-ene (DBU)-Catalyzed Aldol Reactions of a Pyruvic Aldehyde Derivative. ASIAN J ORG CHEM 2014. [DOI: 10.1002/ajoc.201400016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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24
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25
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Gerland B, Millard P, Dupouy C, Renard BL, Escudier JM. Stabilization of hairpins and bulged secondary structures of nucleic acids by single incorporation of α,β-D-CNA featuring a gauche(+) alpha torsional angle. RSC Adv 2014. [DOI: 10.1039/c4ra09639h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A constrained dinucleotide unit featuring a gauche(+) alpha torsional angle configuration was used to stabilize DNA hairpin or bulged structures.
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Affiliation(s)
- Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Pierre Millard
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Christelle Dupouy
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Brice-Loïc Renard
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
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26
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27
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Hervé G, Sartori G, Enderlin G, Mackenzie G, Len C. Palladium-catalyzed Suzuki reaction in aqueous solvents applied to unprotected nucleosides and nucleotides. RSC Adv 2014. [DOI: 10.1039/c3ra47911k] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nucleoside analogues have attracted much attention due to their potential biological activities.
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Affiliation(s)
- Gwénaëlle Hervé
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
| | - Guillaume Sartori
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
| | - Gérald Enderlin
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
| | | | - Christophe Len
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
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28
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Hanessian S, Schroeder BR, Merner BL, Chen B, Swayze EE, Seth PP. Synthesis of cis- and trans-α-l-[4.3.0]bicyclo-DNA monomers for antisense technology: methods for the diastereoselective formation of bicyclic nucleosides. J Org Chem 2013; 78:9051-63. [PMID: 23937280 DOI: 10.1021/jo401166q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Two α-L-ribo-configured bicyclic nucleic acid modifications, represented by analogues 12 and 13, which are epimeric at C3' and C5' have been synthesized using a carbohydrate-based approach to build the bicyclic core structure. An intramolecular L-proline-mediated aldol reaction was employed to generate the cis-configured ring junction of analogue 12 and represents a rare application of this venerable organocatalytic reaction to a carbohydrate system. In the case of analogue 13, where a trans-ring junction was desired, an intermolecular diastereoselective Grignard reaction followed by ring-closing metathesis was used. In order to set the desired stereochemistry at the C5' positions of both nucleoside targets, a study of diastereoselective Lewis acid mediated allylation reactions on a common bicyclic aldehyde precursor was carried out. Analogue 12 was incorporated in oligonucleotide sequences, and thermal denaturation experiments indicate that it is destabilizing when paired with complementary DNA and RNA. However, this construct shows a significant improvement in nuclease stability relative to a DNA oligonucleotide.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal , Montréal, Québec H3C 3J7, Canada
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29
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Meng B, Huang X, Wu L. Electrophilic Addition of Allylic Carbocations to 2-Cyclopropylidene-2-arylethanols: A Strategy to 3-Oxabicyclo[3.2.0]heptanes. Adv Synth Catal 2013. [DOI: 10.1002/adsc.201201073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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Kiran Y, Wakamatsu H, Natori Y, Takahata H, Yoshimura Y. Design and synthesis of a nucleoside and a phosphonate analogue constructed on a branched-threo-tetrofuranose skeleton. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.05.062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Regioselective and efficient synthesis of N 7-substituted adenines, guanines, and 6-mercaptopurines. MONATSHEFTE FUR CHEMIE 2013. [DOI: 10.1007/s00706-012-0899-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Dioxaphosphorinane-constrained nucleic Acid dinucleotides as tools for structural tuning of nucleic acids. J Nucleic Acids 2012; 2012:215876. [PMID: 23150809 PMCID: PMC3488415 DOI: 10.1155/2012/215876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/02/2012] [Indexed: 01/03/2023] Open
Abstract
We describe a rational approach devoted to modulate the sugar-phosphate backbone geometry of nucleic acids. Constraints were generated by connecting one oxygen of the phosphate group to a carbon of the sugar moiety. The so-called dioxaphosphorinane rings were introduced at key positions along the sugar-phosphate backbone allowing the control of the six-torsion angles α to ζ defining the polymer structure. The syntheses of all the members of the D-CNA family are described, and we emphasize the effect on secondary structure stabilization of a couple of diastereoisomers of α,β-D-CNA exhibiting wether B-type canonical values or not.
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33
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Herndon JW. The chemistry of the carbon–transition metal double and triple bond: Annual survey covering the year 2010. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.02.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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34
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Zhou C, Chattopadhyaya J. Intramolecular free-radical cyclization reactions on pentose sugars for the synthesis of carba-LNA and carba-ENA and the application of their modified oligonucleotides as potential RNA targeted therapeutics. Chem Rev 2012; 112:3808-32. [PMID: 22530946 DOI: 10.1021/cr100306q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chuanzheng Zhou
- Chemical Biology Program, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Sweden
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35
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Figueras A, Miralles-Llumà R, Flores R, Rustullet A, Busqué F, Figueredo M, Font J, Alibés R, Maréchal JD. Synthesis, Anti-HIV Activity Studies, and in silico Rationalization of Cyclobutane-Fused Nucleosides. ChemMedChem 2012; 7:1044-56. [DOI: 10.1002/cmdc.201200059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Indexed: 12/22/2022]
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36
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Haziri AI, Leumann CJ. Synthesis and pairing properties of oligodeoxynucleotides containing bicyclo-RNA and bicyclo-ANA modifications. J Org Chem 2012; 77:5861-9. [PMID: 22486224 DOI: 10.1021/jo300554w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The synthesis of the ribo(bc-rT)- and arabino(bc-araT)-version of bicyclothymidine (bc-dT) has been achieved. A conformational analysis by X-ray and/or (1)H NMR spectroscopy on the corresponding 3',5'-benzyl-protected nucleosides featured a rigid C(2')-endo conformation for the furanose ring, irrespective of the configuration of the OH group at C(2'). The conformation of the carbocyclic ring in these nucleosides was found to be less defined and thus more flexible. Both nucleosides were converted into the corresponding phosphoramidites and incorporated into oligodeoxynucleotides by standard DNA chemistry. T(m)-data of duplexes with cDNA and RNA revealed that a bc-rT unit strongly destabilized duplexes with cDNA and RNA by 6-8 °C/mod, while bc-araT was almost T(m) neutral. A rationale based on a previous structure of a bc-DNA mini duplex suggests that the strong destabilization caused by a bc-rT unit arises from unfavorable steric interactions of the equatorial 2'-OH group with the sugar residue of the 3'-neighboring nucleotide unit.
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Affiliation(s)
- Arben I Haziri
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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37
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Mukherjee S, Mandal SB, Bhattacharjya A. Carbohydrate nitrone and nitrile oxide cycloaddition approach to chiral sulfur heterocycles and nucleosides. RSC Adv 2012. [DOI: 10.1039/c2ra20689g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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38
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Maturano M, Catana DA, Lavedan P, Tarrat N, Saffon N, Payrastre C, Escudier JM. Synthesis and Structural Study of ribo-Dioxaphosphorinane-Constrained Nucleic Acid Dinucleotides (ribo-α,β-D-CNA). European J Org Chem 2011. [DOI: 10.1002/ejoc.201101353] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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39
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Hatton W, Hunault J, Egorov M, Len C, Pipelier M, Blot V, Silvestre V, Fargeas V, Ané A, McBrayer T, Detorio M, Cho JH, Bourgougnon N, Dubreuil D, Schinazi RF, Lebreton J. Synthesis and Biological Evaluation of 4'- C,3'- O-Propylene-Linked Bicyclic Nucleosides. European J Org Chem 2011; 2011:7390-7399. [PMID: 34566488 DOI: 10.1002/ejoc.201100859] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A set of pyrimidine nucleosides fused with a 4'-C,3'-O-propylene bridge was successfully synthesised in 12 steps from 1,2:5,6-di-O-isopropylidene-α-d-glucofuranose, an inexpensive starting material, based on a ring-closing metathesis (RCM) reaction followed by Vorbrüggen-type nucleobase coupling. Antiviral and cytotoxicity activities of the targeted modified nucleosides, as well as their phosphoramidate prodrugs, are described.
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Affiliation(s)
- Wilfried Hatton
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Julie Hunault
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Maxim Egorov
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Christophe Len
- Université de Technologie de Compiègne, Ecole Supérieure de Chimie Organique Minérale, EA 4297, Transformations Intégrées de la Matière Renouvelable, 1 allée du Réseau Jean-Marie Buckmaster, 60200 Compiègne, France
| | - Muriel Pipelier
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Virginie Blot
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Virginie Silvestre
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Valérie Fargeas
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Adjou Ané
- Laboratoire de Chimie Organique, UFR SSMT, Université de Cocody 22, BP 582, Abidjan 22, Cote d'Ivoire
| | - Tami McBrayer
- Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine/Veterans Affair Medical Center, Decatur, Georgia 30033, USA
| | - Mervi Detorio
- Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine/Veterans Affair Medical Center, Decatur, Georgia 30033, USA
| | - Jong-Hyun Cho
- Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine/Veterans Affair Medical Center, Decatur, Georgia 30033, USA
| | - Nathalie Bourgougnon
- Université de Bretagne-Sud Laboratoire de Biotechnologie et Chimie Marines, Campus de Tohannic, 56017 Vannes, France
| | - Didier Dubreuil
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Raymond F Schinazi
- Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine/Veterans Affair Medical Center, Decatur, Georgia 30033, USA
| | - Jacques Lebreton
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
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Catana DA, Maturano M, Payrastre C, Lavedan P, Tarrat N, Escudier JM. Synthesis of Phostone-Constrained Nucleic Acid (P-CNA) Dinucleotides Through Intramolecular Arbuzov's Reaction. European J Org Chem 2011. [DOI: 10.1002/ejoc.201101061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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41
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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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Abstract
Research in nucleic acids has made major advances in the past decade in multiple fields of science and technology. Here we discuss some of the most important findings in DNA and RNA research in the fields of biology, chemistry, biotechnology, synthetic biology, nanostructures and optical materials, with emphasis on how chemistry has impacted, and is impacted by, these developments. Major challenges ahead include the development of new chemical strategies that allow synthetically modified nucleic acids to enter into, and function in, living systems.
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Affiliation(s)
- Omid Khakshoor
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. Fax: +1 650 725 0259; Tel: +1 650 724 4741
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. Fax: +1 650 725 0259; Tel: +1 650 724 4741
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Andersen NK, Døssing H, Jensen F, Vester B, Nielsen P. Duplex and triplex formation of mixed pyrimidine oligonucleotides with stacking of phenyl-triazole moieties in the major groove. J Org Chem 2011; 76:6177-87. [PMID: 21692520 DOI: 10.1021/jo200919y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
5-(1-Phenyl-1,2,3-triazol-4-yl)-2'-deoxycytidine was synthesized from a modified CuAAC protocol and incorporated into mixed pyrimidine oligonucleotide sequences together with the corresponding 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine. With consecutive incorporations of the two modified nucleosides, improved duplex formation with a complementary RNA and improved triplex formation with a complementary DNA duplex were observed. The improvement is due to π-π stacking of the phenyl-triazole moieties in the major groove. The strongest stacking and most pronounced positive influence on thermal stability was found in between the uridine analogues or with the cytidine analogue placed in the 3' direction to the uridine analogue. Modeling indicated a different orientation of the phenyl-triazole moieties in the major groove to account for the difference between the two nucleotides. The modified oligonucleotides were all found to be significantly stabilized toward nucleolytic degration.
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Affiliation(s)
- Nicolai Krog Andersen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
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Flores R, Rustullet A, Alibés R, Álvarez-Larena A, de March P, Figueredo M, Font J. Synthesis of Purine Nucleosides Built on a 3-Oxabicyclo[3.2.0]heptane Scaffold. J Org Chem 2011; 76:5369-83. [DOI: 10.1021/jo200775x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ramon Flores
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Albert Rustullet
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ramon Alibés
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Angel Álvarez-Larena
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Pedro de March
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marta Figueredo
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Josep Font
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Memeo MG, Bovio B, Quadrelli P. RuO4-catalyzed oxidation reactions of isoxazolino-2-azanorbornane derivatives: a short-cut synthesis of tricyclic lactams and peptidomimetic γ-amino acids. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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46
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Liu Y, Xu J, Karimiahmadabadi M, Zhou C, Chattopadhyaya J. Synthesis of 2',4'-propylene-bridged (carba-ENA) thymidine and its analogues: the engineering of electrostatic and steric effects at the bottom of the minor groove for nuclease and thermodynamic stabilities and elicitation of RNase H. J Org Chem 2011; 75:7112-28. [PMID: 20929200 DOI: 10.1021/jo101207d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
2',4'-Propylene-bridged thymidine (carba-ENA-T) and five 8'-Me/NH(2)/OH modified carba-ENA-T analogues have been prepared through intramolecular radical addition to C═N of the tethered oxime-ether. These carba-ENA nucleosides have been subsequently incorporated into 15mer oligodeoxynucleotides (AON), and their affinity toward cDNA and RNA, nuclease resistance, and RNase H recruitment capability have been investigated in comparison with those of the native and ENA counterparts. These carba-ENAs modified AONs are highly RNA-selective since all of them led to slight thermal stabilization effect for the AON:RNA duplex, but quite large destabilization effect for the AON:DNA duplex. It was found that different C8' substituents (at the bottom of the minor groove) on carba-ENA-T only led to rather small variation of thermal stability of the AON:RNA duplexes. We, however, observed that the parent carba-ENA-T modified AONs exhibited higher nucleolytic stability than those of the ENA-T modified counterparts. The nucleolytic stability of carba-ENA-T modified AONs can be further modulated by C8' substituent to variable extents depending on not only the chemical nature but also the stereochemical orientation of the C8' substituents: Thus, (1) 8'S-Me on carba-ENA increases the nucleolytic stability but 8'R-Me leads to a decreased effect; (2) 8'R-OH on carba-ENA had little, if any, effect on nuclease resistance but 8'S-OH resulted in significantly decreased nucleolytic stability; and (3) 8'-NH(2) substituted carba-ENA leads to obvious loss in the nuclease resistance. The RNA strand in all of the carba-ENA derivatives modified AON:RNA hybrid duplexes can be digested by RNase H1 with high efficiency, even at twice the rate of those of the native and ENA modified counterpart.
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Affiliation(s)
- Yi Liu
- Bioorganic Chemistry Program, Department of Cell and Molecular Biology, Box 581, Biomedical Center, Uppsala University, SE-751 23 Uppsala, Sweden
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47
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Boissonnet A, Dupouy C, Millard P, Durrieu MP, Tarrat N, Escudier JM. α,β-D-CNA featuring canonical and noncanonical α/β torsional angles behaviours within oligonucleotides. NEW J CHEM 2011. [DOI: 10.1039/c1nj20086k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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48
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Seth PP, Allerson CR, Berdeja A, Swayze EE. Replacing the 2'-oxygen with an exocyclic methylene group reverses the stabilization effects of α-L-LNA. Bioorg Med Chem Lett 2010; 21:588-91. [PMID: 21075634 DOI: 10.1016/j.bmcl.2010.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 01/22/2023]
Abstract
The synthesis and hybridization properties of an α-L-LNA analog where the 2'-oxygen atom is replaced with an exocyclic methylene group is reported. Contrary to the β-D series where the exocyclic methylene group is extremely well tolerated, this group was very poorly tolerated in the α-L-series and lead to duplex destabilization. Modeling studies showed that the exocyclic methylene group results in a steric clash with the nucleobase 3' to the modified residue. Based on this structural model one can anticipate that replacing the 2'-oxygen atom of α-L-LNA with larger groups is likely to be detrimental to duplex stability. The model also provides insights into what type of 2',4'-bridges are most likely to be tolerated in α-L-LNA modified oligonucleotide duplexes.
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Affiliation(s)
- Punit P Seth
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc, 1891 Rutherford Road, Carlsbad, CA 92008, United States.
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Zhong S, Mondon M, Len C. Synthesis of a novel uridine analogue and its use in attempts to form new cyclonucleosides using ring-closing metathesis. Sci China Chem 2010. [DOI: 10.1007/s11426-010-4063-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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50
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Dupouy C, Millard P, Boissonnet A, Escudier JM. α,β-D-CNA preorganization of unpaired loop moiety stabilizes DNA hairpin. Chem Commun (Camb) 2010; 46:5142-4. [DOI: 10.1039/c0cc00244e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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