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Undheim K. Bond Formation at C8 in the Nucleoside and Nucleotide Purine Scaffold: An Informative Selection. Molecules 2024; 29:1815. [PMID: 38675636 PMCID: PMC11054916 DOI: 10.3390/molecules29081815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
This paper presents methods for the introduction and exchange of substituents in a nucleobase and its nucleosides and nucleotides with emphasis on the C8-position in the purine skeleton. The nucleobase is open for electrophilic and nucleophilic chemistry. The nucleophilic chemistry consists mainly of displacement reactions when the C8-substituent is a good leaving group such as a halogen atom. The heteroatom in amines, sulfides, or oxides is a good nucleophile. Halides are good reaction partners. Metal-promoted cross-coupling reactions are important for carbylations. Direct oxidative metalation reactions using sterically hindered metal amides offer chemo- and regio-selectivity besides functional tolerance and simplicity. The carbon site is highly nucleophilic after metalation and adds electrophiles resulting in chemical bond formation. Conditions for metal-assisted reactions are described for nucleobases and their glycosides.
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Affiliation(s)
- Kjell Undheim
- Department of Chemistry, University of Oslo, 0315 Oslo, Norway
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Li L, Hu J, Fu Y, Shi X, Du H, Xu J, Chen N. Direct Regioselective C-H Cyanation of Purines. Molecules 2023; 28:molecules28030914. [PMID: 36770582 PMCID: PMC9920237 DOI: 10.3390/molecules28030914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
A direct regioselective C-H cyanation of purines was developed through a sequential triflic anhydride activation, nucleophilic cyanation with TMSCN, followed by a process of base-mediated elimination of triflous acid (CF3SO2H). In most cases, the direct C-H cyanation occurred on the electron-rich imidazole motif of purines, affording 8-cyanated purine derivatives in moderate to excellent yields. Various functional groups, including allyl, alkynyl, ketone, ester, nitro et al. were tolerated and acted as a C8 directing group. The electron-donating 6-diethylamino, as C2-directing group substituent, can switch the regioselectivity of purine from 8- to 2-position, enabling the synthesis of 8- and 2-cyano 6-dialkylaminopurines from corresponding 6-chloropurine in different reaction order. Further functional manipulations of the cyano group allow the conversions of 8-cyanopurines to corresponding purine amides, imidates, imidothioates, imidamides, oxazolines, and isothiazoles.
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Abstract
3′,5′-O-Bis(tert-butyldimethylsilyl)-8-fluoro-N-2-isobutyryl-2′-deoxyguanosine was synthesized from 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-isobutyryl-2′-deoxyguanosine by the treatment with N-fluorobenzenesulfonimide. A similar fluorination reaction with 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-(N,N-dimethylformamidine)-2′-deoxyguanosine, however, failed to give the corresponding fluorinated product. It was found that 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine is labile under acidic conditions, but sufficiently stable in dichloroacetic acid used in solid phase synthesis. Incorporation of 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis failed to give the desired products. Furthermore, treatment of 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine with aqueous ammonium hydroxide did not give 8-fluoro-2′-deoxyguanosine, but led to the formation of a mixture consisting of 8-amino-N-2-isobutyryl-2′-deoxyguanosine and C8:5′-O-cyclo-2′-deoxyguanosine. Taken together, an alternative N-protecting group and possibly modified solid phase synthetic cycle conditions will be required for the incorporation of 8-fluoro-2′-deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis.
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Yu M, Wang Z, Hu J, Li S, Du H. Copper-Catalyzed Intramolecular Alkoxylation of Purine Nucleosides: One-Step Synthesis of 5′-O,8-Cyclopurine Nucleosides. J Org Chem 2015; 80:9446-53. [DOI: 10.1021/acs.joc.5b01360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mingwu Yu
- Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Zhiqian Wang
- Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Junbin Hu
- Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Shunlai Li
- Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Hongguang Du
- Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
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Ilinova AA, Bregadze VI, Bogomazova AN, Lobanova IA, Mironov AF, Semioshkin AA. New boron-containing 2′-deoxyadenosines. Russ Chem Bull 2014. [DOI: 10.1007/s11172-013-0151-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Zilbershtein-Shklanovsky L, Weitman M, Major DT, Fischer B. Rules for the Design of Highly Fluorescent Nucleoside Probes: 8-(Substituted Cinnamyl)-Adenosine Analogues. J Org Chem 2013; 78:11999-2008. [DOI: 10.1021/jo402050x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lital Zilbershtein-Shklanovsky
- Department of Chemistry, Gonda-Goldschmied Medical Research Center and the Lise-Meitner-Minerva
Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michal Weitman
- Department of Chemistry, Gonda-Goldschmied Medical Research Center and the Lise-Meitner-Minerva
Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry, Gonda-Goldschmied Medical Research Center and the Lise-Meitner-Minerva
Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Bilha Fischer
- Department of Chemistry, Gonda-Goldschmied Medical Research Center and the Lise-Meitner-Minerva
Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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Semioshkin A, Bregadze V, Godovikov I, Ilinova A, Lesnikowski ZJ, Lobanova I. A convenient approach towards boron cluster modifications with adenosine and 2′-deoxyadenosine. J Organomet Chem 2011. [DOI: 10.1016/j.jorganchem.2011.08.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Suchý M, Milne M, Li AX, McVicar N, Dodd DW, Bartha R, Hudson RHE. Mono- and Tetraalkyne Modified Ligands and Their Eu3+ Complexes - Utilizing “Click” Chemistry to Expand the Scope of Conjugation Chemistry. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100945] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Petrelli R, Sham YY, Chen L, Felczak K, Bennett E, Wilson D, Aldrich C, Yu JS, Cappellacci L, Franchetti P, Grifantini M, Mazzola F, Di Stefano M, Magni G, Pankiewicz KW. Selective inhibition of nicotinamide adenine dinucleotide kinases by dinucleoside disulfide mimics of nicotinamide adenine dinucleotide analogues. Bioorg Med Chem 2009; 17:5656-64. [PMID: 19596199 DOI: 10.1016/j.bmc.2009.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/03/2009] [Accepted: 06/06/2009] [Indexed: 11/26/2022]
Abstract
Diadenosine disulfide (5) was reported to inhibit NAD kinase from Listeria monocytogenes and the crystal structure of the enzyme-inhibitor complex has been solved. We have synthesized tiazofurin adenosine disulfide (4) and the disulfide 5, and found that these compounds were moderate inhibitors of human NAD kinase (IC(50)=110 microM and IC(50)=87 microM, respectively) and Mycobacterium tuberculosis NAD kinase (IC(50)=80 microM and IC(50)=45 microM, respectively). We also found that NAD mimics with a short disulfide (-S-S-) moiety were able to bind in the folded (compact) conformation but not in the common extended conformation, which requires the presence of a longer pyrophosphate (-O-P-O-P-O-) linkage. Since majority of NAD-dependent enzymes bind NAD in the extended conformation, selective inhibition of NAD kinases by disulfide analogues has been observed. Introduction of bromine at the C8 of the adenine ring restricted the adenosine moiety of diadenosine disulfides to the syn conformation making it even more compact. The 8-bromoadenosine adenosine disulfide (14) and its di(8-bromoadenosine) analogue (15) were found to be the most potent inhibitors of human (IC(50)=6 microM) and mycobacterium NAD kinase (IC(50)=14-19 microM reported so far. None of the disulfide analogues showed inhibition of lactate-, and inosine monophosphate-dehydrogenase (IMPDH), enzymes that bind NAD in the extended conformation.
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Affiliation(s)
- Riccardo Petrelli
- Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA
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Butler RS, Cohn P, Tenzel P, Abboud KA, Castellano RK. Synthesis, Photophysical Behavior, and Electronic Structure of Push−Pull Purines. J Am Chem Soc 2008; 131:623-33. [DOI: 10.1021/ja806348z] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roslyn S. Butler
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Pamela Cohn
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Phillip Tenzel
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Khalil A. Abboud
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Ronald K. Castellano
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
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Seela F, Xu K. DNA with stable fluorinated dA and dG substitutes: syntheses, base pairing and 19F-NMR spectra of 7-fluoro-7-deaza-2'-deoxyadenosine and 7-fluoro-7-deaza-2'-deoxyguanosine. Org Biomol Chem 2008; 6:3552-60. [PMID: 19082156 DOI: 10.1039/b806145a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorinated DNA containing stable fluorine substituents in the "purine" base were synthesized for the first time. For this, the phosphoramidites of 7-fluoro-7-deaza-2'-deoxyadenosine and 7-fluoro-7-deaza-2'-deoxyguanosine were prepared and oligonucleotides were synthesized. The 7-fluoro substitution leads to increased duplex stability and more selective base pairing compared to the non-functionalized 7-deazapurine oligonucleotides. (19)F NMR spectra of fluorinated nucleosides, single stranded oligonucleotides and DNA duplex show only a single signal for one fluorine modification. The NMR sensitive (19)F spin or the positron emitting (18)F isotope make these compounds applicable for DNA detection or imaging in vitro and in vivo.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
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Ghosh AK, Lagisetty P, Zajc B. Direct Synthesis of 8-Fluoro Purine Nucleosides via Metalation−Fluorination. J Org Chem 2007; 72:8222-6. [PMID: 17902691 DOI: 10.1021/jo071121l] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A straightforward access to protected 8-fluoro nucleosides via metalation-electrophilic fluorination under heterogeneous reaction conditions is reported. This is the first synthesis of 8-fluoro-2'-deoxyribonucleoside derivatives. Phenylsulfonyl substituted nucleosides are accompanying byproducts, possibly indicating a competing radical process. Higher yields of 8-fluoro derivatives were obtained with 2'-deoxyribonucleosides, as compared to ribonucleosides. Deprotection of the hydroxyl groups leading to 8-fluoro-2'-deoxyadenosine using TASF in methylene chloride demonstrates the compatibility of desilylation with 8-fluoro substituted nucleosides. NMR data indicate a syn conformation of the 8-fluoro derivatives.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, USA
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