1
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Häcker S, Schrödter M, Kuhlmann A, Wagenknecht HA. Probing of DNA Photochemistry with C-Nucleosides of Xanthones and Triphenylene as Photosensitizers To Study the Formation of Cyclobutane Pyrimidine Dimers. JACS AU 2023; 3:1843-1850. [PMID: 37502149 PMCID: PMC10369418 DOI: 10.1021/jacsau.3c00167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 07/29/2023]
Abstract
The direct and sequence-dependent investigation of photochemical processes in DNA on the way to cyclobutane pyrimidine dimers (CPDs) as DNA damage requires the probing by photochemically different photosensitizers. The C-nucleosides of xanthone, thioxanthone, 3-methoxyxanthone, and triphenylene as photosensitizers were synthesized by Heck couplings and incorporated into ternary photoactive DNA architectures. This structural approach allows the site-selective excitation of the DNA by UV light. Together with a single defined site for T-T dimerization, not only the direct CPD formation but also the distance-dependent CPD formation in DNA as well as the possibility for energy transport processes could be investigated. Direct CPD formation was observed with xanthone, 3-methoxyxanthone, and triphenylene as sensitizers but not with thioxanthone. Only xanthone was able to induce CPDs remotely by a triplet energy transfer over up to six intervening A-T base pairs. Taken together, more precise information on the sequence dependence of the DNA triplet photochemistry was obtained.
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2
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Miyahara R, Taniguchi Y. Selective Unnatural Base Pairing and Recognition of 2-Hydroxy-2'-deoxyadenosine in DNA Using Pseudo-dC Derivatives. J Am Chem Soc 2022; 144:16150-16156. [PMID: 36001794 DOI: 10.1021/jacs.2c07000] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The formation of unnatural base pairs within duplex DNA would facilitate DNA nanotechnology and biotechnology. Iso-2'-deoxyguanosine (iso-dG) forms base pairs with iso-2'-deoxycytidine, and its use as an unnatural base pair was investigated. Iso-dG is one of the tautomers of 2-hydroxy-2'-deoxyadenosine (2-OH-dA), known as an oxidatively damaged nucleobase, and its selective recognition in DNA plays an important role in the diagnosis and pathogenesis of disease. Therefore, we focused on pseudo-dC (ψdC) as a suitable molecule that recognizes 2-OH-dA in DNA. Since 2-OH-dA shows tautomeric structures in DNA, we designed and used ψdC, which also has a tautomeric structure. We successfully synthesized a ψdC phosphoramidite compound for the synthesis of oligonucleotides (ODNs) as well as its triphosphate derivative (ψdCTP). Tm measurements revealed that ODNs including ψdC showed stable base pair formation with ODNs having 2-OH-dA. In contrast, low Tm values were observed for other bases (dG, dA, dC, and T). The results obtained for the single-nucleotide primer extension reaction revealed that ψdCTP was incorporated into the complementary position of 2-OH-dA in template DNA with high selectivity. In addition, the primer elongation reaction was confirmed to proceed in the presence of dNTPs. The present study reports an artificial nucleic acid that selectively and stably forms unnatural base pairs with 2-OH-dA in DNA.
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Affiliation(s)
- Ryo Miyahara
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan
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3
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Benkovics T, Peng F, Phillips EM, An C, Bade RS, Chung CK, Dance ZEX, Fier PS, Forstater JH, Liu Z, Liu Z, Maligres PE, Marshall NM, Salehi Marzijarani N, McIntosh JA, Miller SP, Moore JC, Neel AJ, Obligacion JV, Pan W, Pirnot MT, Poirier M, Reibarkh M, Sherry BD, Song ZJ, Tan L, Turnbull BWH, Verma D, Waldman JH, Wang L, Wang T, Winston MS, Xu F. Diverse Catalytic Reactions for the Stereoselective Synthesis of Cyclic Dinucleotide MK-1454. J Am Chem Soc 2022; 144:5855-5863. [PMID: 35333525 DOI: 10.1021/jacs.1c12106] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
As practitioners of organic chemistry strive to deliver efficient syntheses of the most complex natural products and drug candidates, further innovations in synthetic strategies are required to facilitate their efficient construction. These aspirational breakthroughs often go hand-in-hand with considerable reductions in cost and environmental impact. Enzyme-catalyzed reactions have become an impressive and necessary tool that offers benefits such as increased selectivity and waste limitation. These benefits are amplified when enzymatic processes are conducted in a cascade in combination with novel bond-forming strategies. In this article, we report a highly diastereoselective synthesis of MK-1454, a potent agonist of the stimulator of interferon gene (STING) signaling pathway. The synthesis begins with the asymmetric construction of two fluoride-bearing deoxynucleotides. The routes were designed for maximum convergency and selectivity, relying on the same benign electrophilic fluorinating reagent. From these complex subunits, four enzymes are used to construct the two bridging thiophosphates in a highly selective, high yielding cascade process. Critical to the success of this reaction was a thorough understanding of the role transition metals play in bond formation.
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Affiliation(s)
- Tamas Benkovics
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Feng Peng
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Eric M Phillips
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Chihui An
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Rachel S Bade
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Cheol K Chung
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zachary E X Dance
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Patrick S Fier
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jacob H Forstater
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zhijian Liu
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zhuqing Liu
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Peter E Maligres
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Nicholas M Marshall
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Nastaran Salehi Marzijarani
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - John A McIntosh
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Steven P Miller
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jeffrey C Moore
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Andrew J Neel
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jennifer V Obligacion
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Weilan Pan
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Michael T Pirnot
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Marc Poirier
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Mikhail Reibarkh
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Benjamin D Sherry
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zhiguo Jake Song
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Lushi Tan
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Ben W H Turnbull
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Deeptak Verma
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jacob H Waldman
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Lu Wang
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Tao Wang
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Matthew S Winston
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Feng Xu
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
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4
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Maligres PE, Chung CK, Dance ZEX, Mattern KA, Phillips EM, Poirier M, Sirk KM, Wright TJ. Discovery and Development of an Unusual Organocatalyst for the Conversion of Thymidine to Furanoid Glycal. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00186] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter E. Maligres
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Cheol K. Chung
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zachary E. X. Dance
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Keith A. Mattern
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Eric M. Phillips
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Marc Poirier
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Kevin M. Sirk
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Timothy J. Wright
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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5
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Kishimoto Y, Fujii A, Nakagawa O, Obika S. Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative. Org Biomol Chem 2021; 19:8063-8074. [PMID: 34494641 DOI: 10.1039/d1ob01462e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized an artificial nucleic acid, [3-(1,2-dihydro-2-oxobenzo[b][1,8]naphthyridine)]-2'-deoxy-D-ribofuranose (OBN), with a tricyclic structure in a nucleobase as a thymidine analog. Oligodeoxynucleotides (ODNs) containing consecutive OBN displayed improved duplex-forming ability with complementary single-stranded (ss) RNA and triplex-forming ability with double-stranded DNA in comparison with ODNs composed of natural thymidine. OBN-modified ODNs also displayed enhanced enzymatic resistance compared with ODNs with natural thymidine and phosphorothioate modification, respectively, due to the structural steric hindrance of the nucleobase. The fluorescence spectra of OBN-modified ODNs showed sufficient fluorescence intensity with ssDNA and ssRNA, which is an advantageous feature for fluorescence imaging techniques of nucleic acids with longer emission wavelengths than bicyclic thymine (bT).
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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6
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Lindell SD, Maechling S, Klein R, Freigang J, Laber B, Blanazs L, Leonhardt M, Haupt S, Petry T, Sabina RL. Mechanism and structure based design of inhibitors of AMP and adenosine deaminase. Bioorg Med Chem 2021; 43:116272. [PMID: 34157570 DOI: 10.1016/j.bmc.2021.116272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Inhibitors of the enzyme adenosine monophosphate deaminase (AMPD) show interesting levels of herbicidal activity. An enzyme mechanism-based approach has been used to design new inhibitors of AMPD starting from nebularine (6) and resulting in the synthesis of 2-deoxy isonebularine (16). This compound is a potent inhibitor of the related enzyme adenosine deaminase (ADA; IC50 16 nM), binding over 5000 times more strongly than nebularine. It is proposed that the herbicidal activity of compound 16 is due to 5́-phosphorylation in planta to give an inhibitor of AMPD. Subsequently, an enzyme structure-based approach was used to design new non-ribosyl AMPD inhibitors. The initial lead structure was discovered by in silico screening of a virtual library against plant AMPD. In a second step, binding to AMPD was further optimised via more detailed molecular modeling leading to 2-(benzyloxy)-5-(imidazo[2,1-f][1,2,4]triazin-7-yl)benzoic acid (36) (IC50 300 nM). This compound does not inhibit ADA and shows excellent selectivity for plant over human AMPD.
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Affiliation(s)
- Stephen D Lindell
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany.
| | - Simon Maechling
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Robert Klein
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Jörg Freigang
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Bernd Laber
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Lisa Blanazs
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Merisa Leonhardt
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Susanne Haupt
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Thomas Petry
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Richard L Sabina
- Department of Biomedical Sciences, Oakland University, William Beaumont School of Medicine, Rochester, MI 48309, USA
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7
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Mao E, Chung CK, Ji Y, Lam YH, Maligres PE. Organocatalytic Conversion of Nucleosides to Furanoid Glycals. J Org Chem 2021; 86:7529-7536. [PMID: 34033478 DOI: 10.1021/acs.joc.1c00555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A class of organocatalysts that are highly active for the conversion of 2'-deoxynucleosides to furanoid glycals have been discovered. These phosphorimides, (Ph2PS)2NH and (Ph2PSe)2NH, were shown to effectively mediate persilylation of 2'-deoxynucleosides allowing the elimination of the nucleobase giving the corresponding glycal. These mild conditions were demonstrated in the syntheses of glycals with various substitution patterns while minimizing the formation of undesired byproducts and expanding the scope of this methodology.
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Affiliation(s)
- Edna Mao
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Cheol K Chung
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yining Ji
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yu-Hong Lam
- Department of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Peter E Maligres
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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8
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Hegelein A, Müller D, Größl S, Göbel M, Hengesbach M, Schwalbe H. Genetic Code Expansion Facilitates Position-Selective Labeling of RNA for Biophysical Studies. Chemistry 2020; 26:1800-1810. [PMID: 31692134 PMCID: PMC7027469 DOI: 10.1002/chem.201904623] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/04/2019] [Indexed: 12/13/2022]
Abstract
Nature relies on reading and synthesizing the genetic code with high fidelity. Nucleic acid building blocks that are orthogonal to the canonical A-T and G-C base-pairs are therefore uniquely suitable to facilitate position-specific labeling of nucleic acids. Here, we employ the orthogonal kappa-xanthosine-base-pair for in vitro transcription of labeled RNA. We devised an improved synthetic route to obtain the phosphoramidite of the deoxy-version of the kappa nucleoside in solid phase synthesis. From this DNA template, we demonstrate the reliable incorporation of xanthosine during in vitro transcription. Using NMR spectroscopy, we show that xanthosine introduces only minor structural changes in an RNA helix. We furthermore synthesized a clickable 7-deaza-xanthosine, which allows to site-specifically modify transcribed RNA molecules with fluorophores or other labels.
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Affiliation(s)
- Andreas Hegelein
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Diana Müller
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Sylvester Größl
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Michael Göbel
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
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9
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Abstract
Pseudouridine (1) was synthesized by functional group interconversions of the Heck adduct11from 2,4-dimethoxy-5-iodopyrimidine (8) and ribofuranoid glycal4.
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Affiliation(s)
- Cheng-Ping Yu
- Department of Chemistry
- National Taiwan Normal University
- Taipei 11677
- Taiwan
| | - Hsin-Yun Chang
- Department of Chemistry
- National Taiwan Normal University
- Taipei 11677
- Taiwan
| | - Tun-Cheng Chien
- Department of Chemistry
- National Taiwan Normal University
- Taipei 11677
- Taiwan
- Faculty of Pharmacy
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10
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Kaewsomboon T, Nishizawa S, Kanamori T, Yuasa H, Ohkubo A. pH-Dependent Switching of Base Pairs Using Artificial Nucleobases with Carboxyl Groups. J Org Chem 2018; 83:1320-1327. [PMID: 29322767 DOI: 10.1021/acs.joc.7b02828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we report the synthesis of modified oligonucleotides consisting of benzoic acid or isophthalic acid residues as new nucleobases. As evaluated by UV thermal denaturation analysis at different pH conditions (5.0, 6.0, 7.0, and 8.0), these modified oligonucleotides exhibited pH-dependent recognition of natural nucleobases and one is first found to be capable of base pair switching in response to a pH change. The isophthalic acid residue incorporated into the oligonucleotide on a d-threoninol backbone could preferentially bind with adenine but with guanine in response to a change in the pH conditions from pH 5 to pH 7 (or 8) without significant difference in duplex stability. These findings would be valuable for further developing pH-responsive DNA-based molecular devices.
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Affiliation(s)
- Tanasak Kaewsomboon
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shuhei Nishizawa
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Hideya Yuasa
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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11
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Synthesis and properties of microenvironment-sensitive oligonucleotides containing a small fluorophore, 3-aminobenzonitrile or 3-aminobenzoic acid. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.10.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Novosjolova I, Kennedy SD, Rozners E. 2-Methoxypyridine as a Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies. Chembiochem 2017; 18:2165-2170. [PMID: 28858428 PMCID: PMC5920655 DOI: 10.1002/cbic.201700400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Indexed: 12/21/2022]
Abstract
The development of nucleic acid base-pair analogues that use new modes of molecular recognition is important both for fundamental research and practical applications. The goal of this study was to evaluate 2-methoxypyridine as a cationic thymidine mimic in the A-T base pair. The hypothesis was that including protonation in the Watson-Crick base pairing scheme would enhance the thermal stability of the DNA double helix without compromising the sequence selectivity. DNA and peptide nucleic acid (PNA) sequences containing the new 2-methoxypyridine nucleobase (P) were synthesized and studied by using UV thermal melting and NMR spectroscopy. Introduction of P nucleobase caused a loss of thermal stability of ≈10 °C in DNA-DNA duplexes and ≈20 °C in PNA-DNA duplexes over a range of mildly acidic to neutral pH. Despite the decrease in thermal stability, the NMR structural studies showed that P-A formed the expected protonated base pair at pH 4.3. Our study demonstrates the feasibility of cationic unnatural base pairs; however, future optimization of such analogues will be required.
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Affiliation(s)
- Irina Novosjolova
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
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13
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Serpi M, De Biasi R, Pertusati F, Slusarczyk M, McGuigan C. Synthetic Approaches for the Preparation of Phosphoramidate Prodrugs of 2'-Deoxypseudoisocytidine. ChemistryOpen 2017; 6:424-436. [PMID: 28638776 PMCID: PMC5474688 DOI: 10.1002/open.201700019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 12/17/2022] Open
Abstract
A synthetic procedure for the preparation of phosphoramidate prodrugs of C-nucleosides is reported. Different phosphorochloridates were reacted with 3'-O-protected N-acetyl-2'-deoxypseudoisocytidine or 3'-O-protected 2'-deoxypseudoisocytidine, followed by acidic hydrolysis of the protecting group. In the presence of the N-acetyl moiety, the enolisable keto group of the nucleobase was able to react (like the 5'-OH) with the phosphorochloridates to give bisphosphorylated derivatives. Epimerisation (β to α) occurred if the amino group of the nucleobase was unprotected. These side reactions demonstrate the peculiar behaviour of C-nucleosides compared to their nucleoside analogues. It was demonstrated that the first enzymatic activation step for this new class of prodrugs can be mediated by carboxypeptidase and that it follows the same pathway and rate reported for ProTides of more conventional nucleoside analogues. These new phosphoramidate derivatives deserve further investigation for their therapeutic potential as anti-cancer agents.
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Affiliation(s)
- Michaela Serpi
- School of Pharmacy and Pharmaceutical SciencesCardiff UniversityKing Edward VII AvenueCardiffCF10 3NBUK), Fax: (+44) 02920874537
| | - Roberto De Biasi
- School of Pharmacy and Pharmaceutical SciencesCardiff UniversityKing Edward VII AvenueCardiffCF10 3NBUK), Fax: (+44) 02920874537
- Dipartimento di Scienze FarmaceuticheUniversità degli Studi di PerugiaVia del Liceo 106123PerugiaItaly
| | - Fabrizio Pertusati
- School of Pharmacy and Pharmaceutical SciencesCardiff UniversityKing Edward VII AvenueCardiffCF10 3NBUK), Fax: (+44) 02920874537
| | - Magdalena Slusarczyk
- School of Pharmacy and Pharmaceutical SciencesCardiff UniversityKing Edward VII AvenueCardiffCF10 3NBUK), Fax: (+44) 02920874537
| | - Christopher McGuigan
- School of Pharmacy and Pharmaceutical SciencesCardiff UniversityKing Edward VII AvenueCardiffCF10 3NBUK), Fax: (+44) 02920874537
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14
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Kitamura Y. Synthesis of Nucleic Acid Mimics and Their Application in Nucleic Acid-based Medicine. YAKUGAKU ZASSHI 2017; 136:1491-1499. [PMID: 27803480 DOI: 10.1248/yakushi.16-00180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleic acid-based drugs (NABDs) have recently attracted considerable attention as next-generation medicines, following the development of low molecular-weight and antibody drugs, because it is likely that they will have fewer side effects and greater target specificity than conventional medicines. Short double-stranded RNAs contain a 2-nucleotide overhang at the 3'-end of each strand. Small interfering RNAs (siRNAs) and microRNAs (miRNAs) inhibit gene expression by RNA interference (RNAi) and thus have great potential as NABDs. However, naked RNA strands have many problems that hinder their application as therapeutics, such as their rapid degradation in biological fluids, poor cellular uptake, and off-target effects. Therefore, artificially modified siRNAs and miRNAs have been studied extensively in an effort to overcome these problems. In this review, I summarize my recent studies on the synthesis of nucleic acid mimics and their application in RNAi-based medicine. The following two topics are specifically discussed: 1) the design and synthesis of chemically modified functional RNAs bearing nucleic acid mimics at their 3'-overhang region, which plays a key role in RNAi; and 2) the practical, reliable synthesis of nucleic acid mimics containing ethynyl groups.
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Affiliation(s)
- Yoshiaki Kitamura
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University
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15
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Pal P, Shaw AK. The evolution of comprehensive strategies for furanoid glycal synthesis and their applications. RSC Adv 2017. [DOI: 10.1039/c6ra28598h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cyclic enol ether frameworks, especially stereochemically pure furanoid and pyranoid glycals are well known highly functionalized chiral building blocks.
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Affiliation(s)
- Pinki Pal
- Division of Medicinal & Process Chemistry
- CSIR- Central Drug Research Institut
- Lucknow-226 031
- India
| | - Arun K. Shaw
- Division of Medicinal & Process Chemistry
- CSIR- Central Drug Research Institut
- Lucknow-226 031
- India
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16
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Nagaya Y, Kitamura Y, Nakashima R, Shibata A, Ikeda M, Kitade Y. Practical and Reliable Synthesis of 1,2-Dideoxy-d-ribofuranose and its Application in RNAi Studies. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:64-75. [PMID: 26822569 DOI: 10.1080/15257770.2015.1114128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We developed a practical and reliable method for synthesizing an abasic deoxyribonucleoside, 1,2-dideoxy-d-ribofuranose (dR(H)) via elimination of nucleobase from thymidine. To synthesize oligonucleotides bearing dR(H) by the standard phosphoramidite solid-phase method, dR(H) was converted to the corresponding phosphoramidite derivative and linked to a solid support (controlled pore glass resin). Chemically modified small interfering RNAs (siRNAs) possessing dR(H) at their 3'-overhang regions were synthesized. Introducing dR(H) to the 3'-end of the antisense strand of siRNA reduced its knockdown effect.
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Affiliation(s)
- Yuki Nagaya
- a United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University , 1-1 Yanagido, Gifu , Japan
| | - Yoshiaki Kitamura
- b Department of Biomolecular Science , Graduate School of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan.,c Department of Chemistry and Biomolecular Science , Faculty of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan
| | - Remi Nakashima
- b Department of Biomolecular Science , Graduate School of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan
| | - Aya Shibata
- b Department of Biomolecular Science , Graduate School of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan.,c Department of Chemistry and Biomolecular Science , Faculty of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan
| | - Masato Ikeda
- a United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University , 1-1 Yanagido, Gifu , Japan.,b Department of Biomolecular Science , Graduate School of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan.,c Department of Chemistry and Biomolecular Science , Faculty of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan
| | - Yukio Kitade
- a United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University , 1-1 Yanagido, Gifu , Japan.,b Department of Biomolecular Science , Graduate School of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan.,c Department of Chemistry and Biomolecular Science , Faculty of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan
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17
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Gaß N, Wagenknecht HA. Synthesis of Benzophenone Nucleosides and Their Photocatalytic Evaluation for [2+2] Cycloaddition in Aqueous Media. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500885] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Minuth M, Richert C. A nucleobase analogue that pairs strongly with adenine. Angew Chem Int Ed Engl 2013; 52:10874-7. [PMID: 24038815 DOI: 10.1002/anie.201305555] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Marco Minuth
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
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19
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20
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Ehrenschwender T, Schmucker W, Wellner C, Augenstein T, Carl P, Harmer J, Breher F, Wagenknecht HA. Development of a Metal-Ion-Mediated Base Pair for Electron Transfer in DNA. Chemistry 2013; 19:12547-52. [DOI: 10.1002/chem.201300593] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Indexed: 01/01/2023]
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21
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Kubelka T, Slavětínská L, Eigner V, Hocek M. Synthesis of 2,6-disubstituted pyridin-3-yl C-2'-deoxyribonucleosides through chemoselective transformations of bromo-chloropyridine C-nucleosides. Org Biomol Chem 2013; 11:4702-18. [PMID: 23760109 DOI: 10.1039/c3ob40774h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2-Bromo-6-chloro- and 6-bromo-2-chloropyridin-3-yl deoxyribonucleosides were prepared by the Heck coupling of bromo-chloro-iodopyridines with TBS-protected deoxyribose glycal. Some of their Pd-catalyzed cross-coupling reactions proceeded chemoselectively at the position of the bromine, whereas nucleophilic substitutions were unselective and gave mixtures of products. The mono-substituted intermediates were used for another coupling or nucleophilic substitution giving rise to a small library of title 2,6-disubstituted pyridine C-deoxyribonucleosides. The title nucleosides did not exert antiviral or cytostatic effects.
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Affiliation(s)
- Tomáš Kubelka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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22
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Weinberger M, Berndt F, Mahrwald R, Ernsting NP, Wagenknecht HA. Synthesis of 4-Aminophthalimide and 2,4-Diaminopyrimidine C-Nucleosides as Isosteric Fluorescent DNA Base Substitutes. J Org Chem 2013; 78:2589-99. [DOI: 10.1021/jo302768f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael Weinberger
- Department of Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg
6, Campus Süd, Geb. 30.42, 76131 Karlsruhe, Germany
| | - Falko Berndt
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Rainer Mahrwald
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Nikolaus P. Ernsting
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Hans-Achim Wagenknecht
- Department of Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg
6, Campus Süd, Geb. 30.42, 76131 Karlsruhe, Germany
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23
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Abstract
Acortatarins A and B have been synthesized via stereoselective spirocyclizations of glycals. Mercury-mediated spirocyclization of a pyrrole monoalcohol side chain leads to acortatarin A. Glycal epoxidation and reductive spirocyclization of a pyrrole dialdehyde side chain leads to acortatarin B. Acid equilibration and crystallographic analysis indicate that acortatarin B is a contrathermodynamic spiroketal with distinct ring conformations compared to acortatarin A.
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Affiliation(s)
- Jacqueline M Wurst
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, USA
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24
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Temburnikar K, Zhang Z, Seley-Radtke K. Modified synthesis of 3'-O-TBDPS-protected furanoid glycal. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 31:319-27. [PMID: 22444193 DOI: 10.1080/15257770.2012.656212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Thermolytic cleavage of 3'-OH protected thymidine is the most common method of preparing furanoid glycals. We have observed that glycosidic bond cleavage is more facile when the 5'-OH of thymidine was also protected with a silyl group. Addition of trimethylsilyl chloride facilitated cleavage of the glycosidic bond; thus, both modifications are required for the formation of the furanoid glycal. Investigations into the selective deprotection of 5'-silyl versus 3'-silyl and subsequent glycosidic bond cleavage are reported herein.
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Affiliation(s)
- Kartik Temburnikar
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
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25
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Heo JY, Hwang GT. 2-Aminobenzene Derivatives as Unnatural Nucleobases and Their DNA Duplex Stabilities. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.12.3794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Brawn RA, Panek JS. Stereoselective C-glycosidations with achiral and enantioenriched allenylsilanes. Org Lett 2010; 12:4624-7. [PMID: 20839812 PMCID: PMC3156056 DOI: 10.1021/ol1019629] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Allenylsilanes are used as carbon nucleophiles in highly stereoselective Lewis acid-promoted C-glycosidations, resulting in the introduction of an internal alkyne with an adjacent stereocenter. Both achiral and chiral allenylsilanes form the desired products with high diastereoselectivity, where the nucleophile adds exclusively to the α-face of the intermediate oxonium ion. Reactions with glucal and galactal afford dihydropyran products, while reactions with a ribose derivative yield dihydrofuran products.
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Affiliation(s)
- Ryan A. Brawn
- Department of Chemistry and Center for Chemical Methodology and Library Development, Metcalf Center for Science and Engineering, 590 Commonwealth Avenue, Boston University, Boston, Massachusetts 02215
| | - James S. Panek
- Department of Chemistry and Center for Chemical Methodology and Library Development, Metcalf Center for Science and Engineering, 590 Commonwealth Avenue, Boston University, Boston, Massachusetts 02215
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27
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Wellington KW, Ooi HC, Benner SA. A convenient synthesis of N,N'-dibenzyl-2,4-diaminopyrimidine-2'-deoxyribonucleoside and 1-methyl-2'-deoxypseudoisocytidine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:275-91. [PMID: 20183581 DOI: 10.1080/15257770902946090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The syntheses of N,N'-dibenzyl-2,4-diaminopyrimidine-2'-deoxyribonucleoside and 1-methyl-2'-deoxypseudoisocytidine via Heck coupling are described. A survey of the attempts to use the Heck coupling to synthesize N,N'-dibenzyl-2,4-diaminopyrimidine-2'-deoxyribonucleoside is provided, indicating a remarkable diversity in outcome depending on the specific heterocyclic partner used.
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28
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Pal P, Kumar B, Shaw AK. Synthesis of Enantiomerically Pure Highly Functionalized Furanoid Glycal and 2,5-Dihydrofuran Building Blocks. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801226] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Kobori A, Takaya K, Higuchi M, Yamayoshi A, Murakami A. Synthesis and Photoinduced Cross-linking Reactions of 4,5′,8-Trimethylpsoralen-incorporated Oligodeoxyribonucleotide. CHEM LETT 2009. [DOI: 10.1246/cl.2009.272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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30
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Qiu Z, Lu L, Jian X, He C. A diazirine-based nucleoside analogue for efficient DNA interstrand photocross-linking. J Am Chem Soc 2008; 130:14398-9. [PMID: 18842048 DOI: 10.1021/ja805445j] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A diazirine-based nucleoside analogue (DBN) efficiently forms DNA interstand cross-linking under near-UV irradiation. This new base analogue may find broad applications in biotechnology and phototherapy.
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Affiliation(s)
- Zhihai Qiu
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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31
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Gómez AM, Casillas M, Barrio A, Gawel A, López JC. Synthesis of Pyranoid and Furanoid Glycals from Glycosyl Sulfoxides by Treatment with Organolithium Reagents. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800318] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Oda H, Hanami T, Iwashita T, Kojima M, Itoh M, Hayashizaki Y. Synthesis of 5-acetyl-2-aminopyrrole C-deoxyribonucleoside. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.09.082] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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33
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34
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Robert N, Bonneau AL, Hoarau C, Marsais F. Unusual sterically controlled regioselective lithiation of 3-bromo-5-(4,4'-dimethyl)oxazolinylpyridine. Straightforward access to highly substituted nicotinic acid derivatives. Org Lett 2007; 8:6071-4. [PMID: 17165932 DOI: 10.1021/ol062556i] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[Structure: see text] Lithiation of 5-bromonicotinic acid protected as secondary or tertiary amide as well as (4,4'-dimethyl)oxazoline with lithium amides is reported. The unusual C-2 and C-4 regioselective lithiation of 3-bromo-5-(4,4'-dimethyl)oxazolinylpyridine using LTMP versus LDA was observed, providing a new route to substituted nicotinic acid scaffolds. The methodology was applied to the synthesis of novel C-4 and C-6 arylated 5-bromonicotinic acids.
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Affiliation(s)
- Nicolas Robert
- Laboratoire de Chimie Organique Fine et Hétérocyclique, UMR 6014, INSA et Université de Rouen, IRCOF-INSA Rouen BP08, 76131 Mont Saint Aignan Cedex, France
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35
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Singh I, Seitz O. Diastereoselective synthesis of beta-Aryl-C-nucleosides from 1,2-anhydrosugars. Org Lett 2007; 8:4319-22. [PMID: 16956216 DOI: 10.1021/ol061701p] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cis opening of glycal epoxides with arylaluminum reagents provides strict stereocontrol in C-glycosylation. beta-Aryl-C-2-deoxynucleosides are obtained from known glycals by an epoxidation-glycosylation-deoxygenation sequence.
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Affiliation(s)
- Ishwar Singh
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
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36
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Coleman RS, Berg MA, Murphy CJ. Coumarin base-pair replacement as a fluorescent probe of ultrafast DNA dynamics. Tetrahedron 2007. [DOI: 10.1016/j.tet.2006.12.096] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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37
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Yang Z, Hutter D, Sheng P, Sismour AM, Benner SA. Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern. Nucleic Acids Res 2006; 34:6095-101. [PMID: 17074747 PMCID: PMC1635279 DOI: 10.1093/nar/gkl633] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To support efforts to develop a ‘synthetic biology’ based on an artificially expanded genetic information system (AEGIS), we have developed a route to two components of a non-standard nucleobase pair, the pyrimidine analog 6-amino-5-nitro-3-(1′-β-D-2′-deoxyribofuranosyl)-2(1H)-pyridone (dZ) and its Watson–Crick complement, the purine analog 2-amino-8-(1′-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP). These implement the pyDDA:puAAD hydrogen bonding pattern (where ‘py’ indicates a pyrimidine analog and ‘pu’ indicates a purine analog, while A and D indicate the hydrogen bonding patterns of acceptor and donor groups presented to the complementary nucleobases, from the major to the minor groove). Also described is the synthesis of the triphosphates and protected phosphoramidites of these two nucleosides. We also describe the use of the protected phosphoramidites to synthesize DNA oligonucleotides containing these AEGIS components, verify the absence of epimerization of dZ in those oligonucleotides, and report some hybridization properties of the dZ:dP nucleobase pair, which is rather strong, and the ability of each to effectively discriminate against mismatches in short duplex DNA.
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Affiliation(s)
| | | | | | | | - Steven A. Benner
- To whom correspondence should be addressed at Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville FL 32604-1174, USA. Tel: +1 352 271 7005; Fax: +1 352 271 7076;
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38
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Jean-Baptiste L, Yemets S, Legay R, Lequeux T. Synthesis of 2,3-trans Disubstituted Tetrahydrofurans through Sequential Xanthate Radical Addition−Substitution Reactions. J Org Chem 2006; 71:2352-9. [PMID: 16526784 DOI: 10.1021/jo052528y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A two-step preparation of 2,3-trans disubstituted tetrahydrofuran derivatives is reported from S-alkyl dithiocarbonates. The study of the group transfer reaction from xanthates and alkenes afforded intermediate S-alkyl dithiocarbonates. From 2,3-dihydrofuran derivatives, the displacement of the resulting anomeric xanthates with various nucleophiles in the presence of Lewis acid allowed the formation of new carbon-carbon and carbon-heteroatom bonds. This strategy was illustrated by a two-step synthesis of a precursor of modified 2'-beta-C-branched nucleoside analogues.
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Affiliation(s)
- Laëtitia Jean-Baptiste
- Laboratoire de Chimie Moléculaire et Thioorganique, UMR CNRS 6507; ENSICAEN-Université de Caen, 6 Boulevard du Maréchal Juin, F-14050 Caen Cedex, France
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39
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Kilroy TG, O'Sullivan TP, Guiry PJ. Synthesis of Dihydrofurans Substituted in the 2‐Position. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500489] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Timothy G. Kilroy
- UCD School of Chemistry and Chemical Biology, Centre for Synthesis and Chemical Biology, Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Timothy P. O'Sullivan
- UCD School of Chemistry and Chemical Biology, Centre for Synthesis and Chemical Biology, Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Patrick J. Guiry
- UCD School of Chemistry and Chemical Biology, Centre for Synthesis and Chemical Biology, Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
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40
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Aly YL, Pedersen EB. Synthesis of a New Furanoid Glycal Auxiliary. MONATSHEFTE FUR CHEMIE 2005. [DOI: 10.1007/s00706-005-0342-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Matsuda S, Romesberg FE. Optimization of interstrand hydrophobic packing interactions within unnatural DNA base pairs. J Am Chem Soc 2004; 126:14419-27. [PMID: 15521761 DOI: 10.1021/ja047291m] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As part of an effort to expand the genetic alphabet, we have evaluated a large number of predominantly hydrophobic unnatural base pairs. We now report the synthesis and stability of unnatural base pairs formed between simple phenyl rings modified at different positions with methyl groups. Surprisingly, several of the unnatural base pairs are virtually as stable as a natural base pair in the same sequence context. The results show that neither hydrogen-bonding nor large aromatic surface area are required for base pair stability within duplex DNA and that interstrand interactions between small aromatic rings may be optimized for both stability and selectivity. These smaller nucleobases are not expected to induce the distortions in duplex DNA or at the primer terminus that seem to limit replication of larger unnatural base pairs, and they therefore represent a promising approach to the expansion of the genetic alphabet.
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Affiliation(s)
- Shigeo Matsuda
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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42
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Ivanov SA, Volkov EM, Oretskaya TS, Müller S. Chemical synthesis of an artificially branched hairpin ribozyme variant with RNA cleavage activity. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.07.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Mayer A, Leumann CJ. A short, efficient synthesis of 2'-deoxypseudoisocytidine based on Heck-chemistry. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2004; 22:1919-25. [PMID: 14609231 DOI: 10.1081/ncn-120025239] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A novel synthesis of 2'-deoxypseudoisocytidine as well as of its phosphoramidite building block for oligonucleotide synthesis is presented. The synthesis is based on Heck-coupling between N-protected pseudoisocytosine and a silyl protected furanoid glycal. With this procedure the corresponding phosphoramidite building block is obtained in 5 steps and an overall yield of 28%.
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Affiliation(s)
- Alain Mayer
- Department of Chemistry & Biochemistry, University of Bern, Bern, Switzerland
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44
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Hutter D, Benner SA. Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern. J Org Chem 2004; 68:9839-42. [PMID: 14656120 DOI: 10.1021/jo034900k] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
6-Amino-3-(2'-deoxy-beta-D-ribofuranosyl)-5-nitro-1H-pyridin-2-one (4), a C-glycoside exhibiting the nonstandard pyDDA hydrogen-bonding pattern, was synthesized via Heck coupling. The nitro group greatly enhances the stability of the nucleoside toward acid-catalyzed epimerization without leading to significant deprotonation of the heterocycle at physiological pH. These results make nucleoside 4 a promising candidate for an expanded genetic alphabet.
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Affiliation(s)
- Daniel Hutter
- Department of Chemistry and Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32611-7200
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45
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Abstract
Syntheses of buergerinin F (1) and buergerinin G (2) were carried out to establish the absolute stereochemistry of these natural products. A linear sequence was used to synthesize 1 in 15 steps and 9% overall yield from thymidine. Subsequent oxidation of 1 with ruthenium tetroxide afforded 2 in 77% yield.
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Affiliation(s)
- Jeong-Seok Han
- Department of Chemistry, The Ohio State University, Columbus 43210, USA
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46
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47
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Coleman RS, Mortensen MA. Stereocontrolled synthesis of anthracene β-C-ribosides: fluorescent probes for photophysical studies of DNA. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(02)02791-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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48
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Affiliation(s)
- Robert J Ferrier
- Industrial Research Ltd., P.O. Box 31 310, Lower Hutt, New Zealand
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49
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Raboisson P, Baurand A, Cazenave JP, Gachet C, Schultz D, Spiess B, Bourguignon JJ. A general approach toward the synthesis of C-nucleoside pyrazolo[1,5-a]-1,3,5-triazines and their 3',5'-bisphosphate C-nucleotide analogues as the first reported in vivo stable P2Y(1)-receptor antagonists. J Org Chem 2002; 67:8063-71. [PMID: 12423133 DOI: 10.1021/jo026268l] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In our effort to identify potent purinergic P2Y(1) receptor antagonists as potent platelet aggregation inhibitors with enhanced metabolic stability, we developed an efficient route for the large-scale preparation of 2'-deoxy-C-nucleosides of pyrazolo[1,5-a]-1,3,5-triazine. The key strategic elements of this novel synthetic approach involved the following: (i) the use of a novel activating group, the N-methyl-N-phenylamino group, which was easily generated in high yield by treatment of the pyrazolo[1,5-a]-1,3,5-triazin-4-one (5) with phosphorus oxychloride and dimethylaniline under high pressure, (ii) a regio- and stereospecific palladium-mediated coupling reaction of the readily available unprotected glycal 1,4-anhydro-2-deoxy-D-erythro-pent-1-enitol (4b) and the 8-iodo derivative (16), and (iii) the stereoselective reduction of the ketone group of the furanosyl ring followed by the subsequent displacement of the N-methyl-N-phenylamino group upon treatment with methylamine. The beta configuration at the anomeric C-1' position of the glycal moieties was perfectly retained throughout this conversion. This procedure afforded 8-(2'-deoxy-beta-D-ribofuranosyl)-2-methyl-4-(N-methylamino)pyrazolo[1,5-a]-1,3,5-triazine (21) and 8-(2'-deoxy-beta-D-xylofuranosyl)-2-methyl-4-(N-methylamino)pyrazolo[1,5-a]-1,3,5-triazine (24) with an overall yield of 50% and 39%, respectively. Finally, the conversion of nucleosides 21 and 24 to the pyrazolotriazine C-nucleotides 3',5'-bisphosphate 2 and 3',5'-cyclophosphate 26 is also described herein and represents the first reported nucleotide derivatives within the pyrazolo[1,5-a]-1,3,5-triazine series. Preliminary biological testing has shown that compound 2 strongly inhibits ADP-induced human platelet aggregation and shape change and possesses significant efficacies 30 min after injection in rat, highlighting a strong P2Y(1)-receptor antagonist activity in vitro combined with a prolonged duration of action in vivo.
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Affiliation(s)
- Pierre Raboisson
- Laboratoire de Pharmacochimie de la Communication Cellulaire, UMR 7081 du CNRS, Université Louis Pasteur, Faculté de Pharmacie, 74, route du Rhin, 67401 Illkirch Cedex, France.
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50
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Anderson EA, Davidson JE, Harrison JR, O'Sullivan PT, Burton JW, Collins I, Holmes AB. Synthesis of medium-ring lactones via tandem methylenation/Claisen rearrangement of cyclic carbonates. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00049-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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