C-5 Substituted Pyrimidine Nucleotides/Nucleosides: Recent Progress in Synthesis, Functionalization, and Applications

Author(s): Muthian Shanmugasundaram, Annamalai Senthilvelan, Anilkumar R. Kore*.

Journal Name: Current Organic Chemistry

Volume 23 , Issue 13 , 2019

Become EABM
Become Reviewer

Graphical Abstract:


The chemistry of C5 substituted pyrimidine nucleotide serves as a versatile molecular biology probe for the incorporation of DNA/RNA that has been involved in various molecular biology applications such as gene expression, chromosome, and mRNA fluorescence in situ hybridization (FISH) experiment, mutation detection on arrays and microarrays, in situ RT-PCR, and PCR. In addition to C5 substituted pyrimidine nucleotide, C5 substituted pyrimidine nucleoside displays a broad spectrum of biological applications such as antibacterial, antiviral and anticancer activities. This review focusses on the recent development in the synthesis of aminoallyl pyrimidine nucleotide, aminopropargyl pyrimidine nucleotide, fluorescent probes containing C5 substituted pyrimidine nucleotide, 2′-deoxycytidine nucleoside containing vinylsulfonamide and acrylamide modification, C5 alkenyl, C5 alkynyl, and C5 aryl pyrimidine nucleosides through palladium-catalyzed reaction, pyrimidine nucleoside containing triazole moiety through Click reaction, 5-isoxazol-3-yl-pyrimidine nucleoside, C5 azide modified pyrimidine nucleoside, 2′-deoxycytidine nucleotide containing photocleavable moiety, and uridine nucleoside containing germane and their biological applications are outlined.

Keywords: Pyrimidine nucleoside, pyrimidine nucleotide, fluorescent probe, DNA, palladium-catalyst, click chemistry, anticancer, antiviral.

Blackburn, G.M.; Gait, M.J.; Loakes, D.; Williams, D.M. Nucleic acids in chemistry and biology; Royal Society of Chemistry: London, 2006.
Vaghefi, M. Nucleoside Triphosphates and their Analogs, CRC Press, Taylor and Francis Group: Boca Raton. 2005.
Cox, W.G.; Singer, V.L. Fluorescent DNA hybridization probe preparation using amine modification and reactive dye coupling. Biotechniques, 2004, 36(1), 114-122.
[http://dx.doi.org/10.2144/04361RR02] [PMID: 14740493]
Heng, H.H.; Spyropoulos, B.; Moens, P.B. FISH technology in chromosome and genome research. BioEssays, 1997, 19(1), 75-84.
[http://dx.doi.org/10.1002/bies.950190112] [PMID: 9008419]
Brown, P.O.; Botstein, D. Gene expression informatics – it’s all in your mine. Nat. Genet., 1999, 21, 33-37.
[http://dx.doi.org/10.1038/4462] [PMID: 9915498]
Lockhart, D.J.; Winzeler, E.A. Genomics, gene expression and DNA arrays. Nature, 2000, 405(6788), 827-836.
[http://dx.doi.org/10.1038/35015701] [PMID: 10866209]
Giller, G.; Tasara, T.; Angerer, B.; Mühlegger, K.; Amacker, M.; Winter, H. Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. I. Chemical synthesis of various reporter group-labeled 2′-deoxyribonucleoside-5′-triphosphates. Nucleic Acids Res., 2003, 31(10), 2630-2635.
[http://dx.doi.org/10.1093/nar/gkg370] [PMID: 12736313]
Kuwahara, M.; Nagashima, J.; Hasegawa, M.; Tamura, T.; Kitagata, R.; Hanawa, K.; Hososhima, S.; Kasamatsu, T.; Ozaki, H.; Sawai, H. Systematic characterization of 2′-deoxynucleoside- 5′-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA. Nucleic Acids Res., 2006, 34(19), 5383-5394.
[http://dx.doi.org/10.1093/nar/gkl637] [PMID: 17012278]
Hanna, M.M.; Yuriev, E.; Zhang, J.; Riggs, D.L. Probing the environment of nascent RNA in Escherichia coli transcription elongation complexes utilizing a new fluorescent ribonucleotide analog. Nucleic Acids Res., 1999, 27(5), 1369-1376.
[http://dx.doi.org/10.1093/nar/27.5.1369] [PMID: 9973628]
Brazier, J.A.; Shibata, T.; Townsley, J.; Taylor, B.F.; Frary, E.; Williams, N.H.; Williams, D.M. Amino-functionalized DNA: The properties of C5-amino-alkyl substituted 2′-deoxyuridines and their application in DNA triplex formation. Nucleic Acids Res., 2005, 33(4), 1362-1371.
[http://dx.doi.org/10.1093/nar/gki254] [PMID: 15745996]
Burke, M.P.; Borland, K.M.; Litosh, V.A. Base-modified nucleosides as chemotherapeutic agents: Past and future. Curr. Top. Med. Chem., 2016, 16(11), 1231-1241.
[http://dx.doi.org/10.2174/1568026615666150915111933] [PMID: 26369814]
De Clercq, E.; Descamps, J.; De Somer, P.; Barr, P.J.; Jones, A.S.; Walker, R.T. (E)-5-(2-Bromovinyl)-2′-deoxyuridine: A potent and selective anti-herpes agent. Proc. Natl. Acad. Sci. USA, 1979, 76(6), 2947-2951.
[http://dx.doi.org/10.1073/pnas.76.6.2947] [PMID: 223163]
De Clercq, E. Discovery and development of BVDU (brivudin) as a therapeutic for the treatment of herpes zoster. Biochem. Pharmacol., 2004, 68(12), 2301-2315.
[http://dx.doi.org/10.1016/j.bcp.2004.07.039] [PMID: 15548377]
Cristofoli, W.A.; Wiebe, L.I.; De Clercq, E.; Andrei, G.; Snoeck, R.; Balzarini, J.; Knaus, E.E. 5-alkynyl analogs of arabinouridine and 2′-deoxyuridine: Cytostatic activity against herpes simplex virus and varicella-zoster thymidine kinase gene-transfected cells. J. Med. Chem., 2007, 50(12), 2851-2857.
[http://dx.doi.org/10.1021/jm0701472] [PMID: 17518459]
Rai, D.; Johar, M.; Manning, T.; Agrawal, B.; Kunimoto, D.Y.; Kumar, R. Design and studies of novel 5-substituted alkynylpyrimidine nucleosides as potent inhibitors of mycobacteria. J. Med. Chem., 2005, 48(22), 7012-7017.
[http://dx.doi.org/10.1021/jm058167w] [PMID: 16250660]
Meneni, S.; Ott, I.; Sergeant, C.D.; Sniady, A.; Gust, R.; Dembinski, R. 5-Alkynyl-2′-deoxyuridines: Chromatography-free synthesis and cytotoxicity evaluation against human breast cancer cells. Bioorg. Med. Chem., 2007, 15(8), 3082-3088.
[http://dx.doi.org/10.1016/j.bmc.2007.01.048] [PMID: 17336074]
Burness, C.B.; Duggan, S.T. Trifluridine/Tipiracil: A review in metastatic colorectal cancer. Drugs, 2016, 76(14), 1393-1402.
[http://dx.doi.org/10.1007/s40265-016-0633-9] [PMID: 27568360]
Housri, N.; Yarchoan, R.; Kaushal, A. Radiotherapy for patients with the human immunodeficiency virus: Are special precautions necessary? Cancer, 2010, 116(2), 273-283.
[http://dx.doi.org/10.1002/cncr.24878] [PMID: 20014399]
Agrofoglio, L.A.; Gillaizeau, I.; Saito, Y. Palladium-assisted routes to nucleosides. Chem. Rev., 2003, 103(5), 1875-1916.
[http://dx.doi.org/10.1021/cr010374q] [PMID: 12744695]
Shaughnessy, K.H. Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides. Molecules, 2015, 20(5), 9419-9454.
[http://dx.doi.org/10.3390/molecules20059419] [PMID: 26007192]
Liang, Y.; Wnuk, S.F. Modification of purine and pyrimidine nucleosides by direct C-H bond activation. Molecules, 2015, 20(3), 4874-4901.
[http://dx.doi.org/10.3390/molecules20034874] [PMID: 25789821]
Kore, A.; Charles, I. Recent developments in the synthesis and application of C5-substituted pyrimidine nucleosides and nucleotides. Curr. Org. Chem., 2012, 16, 1996-2013.
Jäger, S.; Rasched, G.; Kornreich-Leshem, H.; Engeser, M.; Thum, O.; Famulok, M. A versatile toolbox for variable DNA functionalization at high density. J. Am. Chem. Soc., 2005, 127(43), 15071-15082.
[http://dx.doi.org/10.1021/ja051725b] [PMID: 16248646]
Borsenberger, V.; Kukwikila, M.; Howorka, S. Synthesis and enzymatic incorporation of modified deoxyuridine triphosphates. Org. Biomol. Chem., 2009, 7(18), 3826-3835.
[http://dx.doi.org/10.1039/b906956a] [PMID: 19707689]
Kore, A.R.; Shanmugasundaram, M. Highly stereoselective palladium-catalyzed Heck coupling of 5-iodo-uridine triphosphates with allylamine: A new efficient method for the synthesis of (E)-5-aminoallyl-uridine triphosphates. Tetrahedron Lett., 2012, 53, 2530-2532.
Kore, A.R.; Senthilvelan, A.; Shanmugasundaram, M. Highly regioselective C-5 iodination of pyrimidine nucleotides and subsequent chemoselective Sonogashira coupling with propargylamine. Nucleosides Nucleotides Nucleic Acids, 2015, 34(2), 92-102.
[http://dx.doi.org/10.1080/15257770.2014.964411] [PMID: 25621703]
Kore, A.R.; Senthilvelan, A.; Shanmugasundaram, M. Highly chemoselective palladium-catalyzed Sonogashira coupling of 5-iodouridine-5′-triphosphates with propargylamine: A new efficient method for the synthesis of 5-aminopropargyl-uridine-5′-triphosphates. Tetrahedron Lett., 2012, 53, 3070-3072.
Kore, A.R.; Senthilvelan, A.; Shanmugasundaram, M.; Sandoval, D.; Pardo, A. A new efficient stereoselective method for the synthesis of (E)-5-aminoallyl-pyrimidine-5′-triphosphates using palladium-catalyzed Heck reaction. Nucleosides Nucleotides Nucleic Acids, 2015, 34(3), 221-228.
[http://dx.doi.org/10.1080/15257770.2014.978013] [PMID: 25710357]
Langer, P.R.; Waldrop, A.A.; Ward, D.C. Enzymatic synthesis of biotin-labeled polynucleotides: Novel nucleic acid affinity probes. Proc. Natl. Acad. Sci. USA, 1981, 78(11), 6633-6637.
[http://dx.doi.org/10.1073/pnas.78.11.6633] [PMID: 6273878]
Schoetzau, T.; Langner, J.; Moyroud, E.; Roehl, I.; Vonhoff, S.; Klussmann, S. Aminomodified nucleobases: Functionalized nucleoside triphosphates applicable for SELEX. Bioconjug. Chem., 2003, 14(5), 919-926.
[http://dx.doi.org/10.1021/bc0256547] [PMID: 13129394]
Takeda, S.; Tsukiji, S.; Nagamune, T. A cysteine-appended deoxyuridine for the postsynthetic DNA modification using native chemical ligation. Tetrahedron Lett., 2005, 46, 2235-2238.
Reddington, M.V.; Cunninghan-Bryant, D. Convenient synthesis of (E)-5-aminoallyl-2′-deoxycytidine and some related derivatives. Tetrahedron Lett., 2011, 52, 181-183.
Ren, X.; Gerowska, M.; El-Sagheer, A.H.; Brown, T. Enzymatic incorporation and fluorescent labelling of cyclooctyne-modified deoxyuridine triphosphates in DNA. Bioorg. Med. Chem., 2014, 22(16), 4384-4390.
[http://dx.doi.org/10.1016/j.bmc.2014.05.050] [PMID: 24953951]
Dziuba, D.; Pohl, R.; Hocek, M. Polymerase synthesis of DNA labelled with benzylidene cyanoacetamide-based fluorescent molecular rotors: Fluorescent light-up probes for DNA-binding proteins. Chem. Commun. (Camb.), 2015, 51(23), 4880-4882.
[http://dx.doi.org/10.1039/C5CC00530B] [PMID: 25704490]
Güixens-Gallardo, P.; Zawada, Z.; Matyašovský, J.; Dziuba, D.; Pohl, R.; Kraus, T.; Hocek, M. Brightly fluorescent 2′-deoxyribonucleoside triphosphates bearing methylated bodipy fluorophore for in cellulo incorporation to DNA, imaging, and flow cytometry. Bioconjug. Chem., 2018, 29(11), 3906-3912.
[http://dx.doi.org/10.1021/acs.bioconjchem.8b00721] [PMID: 30365300]
Kuba, M.; Pohl, R.; Hocek, M. Synthesis of 2′-deoxycytidine and its triphosphate bearing tryptophan-based imidazolinone fluorophore for environment sensitive fluorescent labelling of DNA. Tetrahedron, 2018, 74, 6621-6629.
Dadová, J.; Orság, P.; Pohl, R.; Brázdová, M.; Fojta, M.; Hocek, M. Vinylsulfonamide and acrylamide modification of DNA for cross-linking with proteins. Angew. Chem. Int. Ed. Engl., 2013, 52(40), 10515-10518.
[http://dx.doi.org/10.1002/anie.201303577] [PMID: 23939933]
Dadová, J.; Vidláková, P.; Pohl, R.; Havran, L.; Fojta, M.; Hocek, M. Aqueous Heck cross-coupling preparation of acrylate-modified nucleotides and nucleoside triphosphates for polymerase synthesis of acrylate-labeled DNA. J. Org. Chem., 2013, 78(19), 9627-9637.
[http://dx.doi.org/10.1021/jo4011574] [PMID: 23992435]
Liang, Y.; Gloudeman, J.; Wnuk, S.F. Palladium-catalyzed direct arylation of 5-halouracils and 5-halouracil nucleosides with arenes and heteroarenes promoted by TBAF. J. Org. Chem., 2014, 79(9), 4094-4103.
[http://dx.doi.org/10.1021/jo500602p] [PMID: 24724921]
Kapadi, A.; Gayakha, V.; Sanghvi, Y.S.; Garcia, J.; Lozano, P.; Silva, I.D.; Pérez, J.; Serrano, J.L. New water soluble Pd-imidate complexes as highly efficient catalysts for the synthesis of C5-arylated pyrimidine nucleosides. RSC Advances, 2014, 4, 17567-17572.
Ardhapure, A.V.; Sanghvi, Y.S.; Kapdi, A.R.; Garcia, J.; Sanchez, G.; Lozano, P.; Serrano, J.L. Pd-imidate complexes as recyclable catalysts for the synthesis of C5-alkenylated pyrimidine nucleosides via Heck cross- coupling reaction. RCS Adv., 2015, 5, 24558-24563.
Botha, F.; Slavíčková, M.; Pohl, R.; Hocek, M. Copper-mediated arylsulfanylations and arylselanylations of pyrimidine or 7-deazapurine nucleosides and nucleotides. Org. Biomol. Chem., 2016, 14(42), 10018-10022.
[http://dx.doi.org/10.1039/C6OB01917J] [PMID: 27722411]
Kielkowski, P.; Cahová, H.; Pohl, R.; Hocek, M. Flexible double-headed cytosine-linked 2′-deoxycytidine nucleotides. Synthesis, polymerase incorporation to DNA and interaction with DNA methyltransferases. Bioorg. Med. Chem., 2016, 24(6), 1268-1276.
[http://dx.doi.org/10.1016/j.bmc.2016.01.057] [PMID: 26899597]
Simonova, A.; Havran, L.; Pohl, R.; Fojta, M.; Hocek, M. Phenothiazine-linked nucleosides and nucleotides for redox labelling of DNA. Org. Biomol. Chem., 2017, 15(33), 6984-6996.
[http://dx.doi.org/10.1039/C7OB01439B] [PMID: 28792547]
Suzol, S.H.; Howlader, A.H.; Wen, Z.; Ren, Y.; Laverde, E.E.; Garcia, C.; Liu, Y.; Wnuk, S.F. Pyrimidine nucleosides with a reactive (β-Chlorovinyl)sulfone or (β-Keto)sulfone group at the C5 position, their reactions with nucleophiles and electrophiles, and their polymerase-catalyzed incorporation into DNA. ACS Omega, 2018, 3(4), 4276-4288.
[http://dx.doi.org/10.1021/acsomega.8b00584] [PMID: 29732453]
Krömer, M.; Bártová, K.; Raindlová, V.; Hocek, M. Synthesis of dihydroxyalkynyl and dihydroxyalkyl nucleotides as building blocks or precursors for introduction of diol or aldehyde groups to DNA for bioconjugations. Chemistry, 2018, 24(46), 11890-11894.
[http://dx.doi.org/10.1002/chem.201802282] [PMID: 29790604]
Milisavljevič, N.; Perlíková, P.; Pohl, R.; Hocek, M. Enzymatic synthesis of base-modified RNA by T7 RNA polymerase. A systematic study and comparison of 5-substituted pyrimidine and 7-substituted 7-deazapurine nucleoside triphosphates as substrates. Org. Biomol. Chem., 2018, 16(32), 5800-5807.
[http://dx.doi.org/10.1039/C8OB01498A] [PMID: 30063056]
Kumar, P.; Hornum, M.; Nielsen, L.J.; Enderlin, G.; Andersen, N.K.; Len, C.; Hervé, G.; Sartori, G.; Nielsen, P.; High-Affinity, R.N.A. High-affinity RNA targeting by oligonucleotides displaying aromatic stacking and amino groups in the major groove. Comparison of triazoles and phenyl substituents. J. Org. Chem., 2014, 79(7), 2854-2863.
[http://dx.doi.org/10.1021/jo4025896] [PMID: 24611639]
Kumar, P.; Østergaard, M.E.; Baral, B.; Anderson, B.A.; Guenther, D.C.; Kaura, M.; Raible, D.J.; Sharma, P.K.; Hrdlicka, P.J. Synthesis and biophysical properties of C5-functionalized LNA (locked nucleic acid). J. Org. Chem., 2014, 79(11), 5047-5061.
[http://dx.doi.org/10.1021/jo500614a] [PMID: 24825249]
Zayas, J.; Annoual, M.; Das, J.K.; Felty, Q.; Gonzalez, W.G.; Miksovska, J.; Sharifai, N.; Chiba, A.; Wnuk, S.F. annoual, M.; Das, J.K.; Felty, Q.; Gonzalez, W.G.; Miksovska, J.; Sharifai, N.; Chiba, A.; Wnuk, S.F. Strain promoted click chemistry of 2- or 8-azidopurine and 5-azidopyrimidine nucleosides and 8-azidoadenosine triphosphate with cyclooctynes. Application to living Cell fluorescent imaging. Bioconjug. Chem., 2015, 26(8), 1519-1532.
[http://dx.doi.org/10.1021/acs.bioconjchem.5b00300] [PMID: 26086070]
Panattoni, A.; Pohl, R.; Hocek, M. Flexible alkyne-linked thymidine phosphoramidites and triphosphates for chemical or polymerase synthesis and fast postsynthetic DNA functionalization through copper catalyzed alkyne-azide 1,3-dipolar cycloaddition. Org. Lett., 2018, 20(13), 3962-3965.
[http://dx.doi.org/10.1021/acs.orglett.8b01533] [PMID: 29897758]
Guo, S.; Wang, J.; Zhang, X.; Cojean, S.; Loiseau, P.M.; Fan, X. Synthesis of 5-isoxazol-3-yl-pyrimidine nucleosides as potential antileishmanial agents. Bioorg. Med. Chem. Lett., 2015, 25(13), 2617-2620.
[http://dx.doi.org/10.1016/j.bmcl.2015.04.097] [PMID: 25987374]
Bialek-Pietras, M.; Olejniczak, A.B.; Paradowska, E.; Studziṅska, M.; Suski, P.; Jabłoṅska, A.; Lešnikowski, Z.J. Synthesis and in vitro antiviral activity of lipophilic pyrimidine nucleoside/carborane conjugates. J. Organomet. Chem., 2015, 798, 99-105.
Wen, Z.; Suzol, S.H.; Peng, J.; Snoeck, R.; Andrei, G.; Liekens, S.; Wnuk, S.F. Antiviral and cytostatic of 5-(1-halo-2-sulfonylvinyl)- and 5-(2-furyl)uracil nucleosides; 1-9. Arch. Pharm. Chem. Life Sci, 2017, 350(3-4)1700023
Balintová, J.; Simonova, A.; Białek-Pietras, M.; Olejniczak, A.; Lesnikowski, Z.J.; Hocek, M. Carborane-linked 2′-deoxyuridine 5′-O-triphosphate as building block for polymerase synthesis of carborane-modified DNA. Bioorg. Med. Chem. Lett., 2017, 27(21), 4786-4788.
[http://dx.doi.org/10.1016/j.bmcl.2017.09.064] [PMID: 29017785]
Boháčová, S.; Vaníková, Z.; Poštová Slavětínská, L.; Hocek, M. Protected 2′-deoxyribonucleoside triphosphate building blocks for the photocaging of epigenetic 5-(hydroxymethyl)cytosine in DNA. Org. Biomol. Chem., 2018, 16(30), 5427-5432.
[http://dx.doi.org/10.1039/C8OB01106K] [PMID: 29905748]
Wen, Z.; Peng, J.; Tuttle, P.R.; Ren, Y.; Garcia, C.; Debnath, D.; Rishi, S.; Hanson, C.; Ward, S.; Kumar, A.; Liu, Y.; Zhao, W.; Glazer, P.M.; Liu, Y.; Sevilla, M.D.; Adhikary, A.; Wnuk, S.F. Electron-mediated aminyl and iminyl radicals from C5 azido-modified pyrimidine nucleosides augment radiation damage to cancer cells. Org. Lett., 2018, 20(23), 7400-7404.
[http://dx.doi.org/10.1021/acs.orglett.8b03035] [PMID: 30457873]
Liang, Y.; Pitteloud, J.P.; Wnuk, S.F. Hydrogermylation of 5-ethynyluracil nucleosides: Formation of 5-(2-germylvinyl)uracil and 5-(2-germylacetyl)uracil nucleosides. J. Org. Chem., 2013, 78(11), 5761-5767.
[http://dx.doi.org/10.1021/jo400590z] [PMID: 23631719]
Xu, W.; Chan, K.M.; Kool, E.T. Fluorescent nucleobases as tools for studying DNA and RNA. Nat. Chem., 2017, 9(11), 1043-1055.
[http://dx.doi.org/10.1038/nchem.2859] [PMID: 29064490]
Hocek, M. Synthesis of base-modified 2′-deoxyribonucleoside triphosphates and their use in enzymatic synthesis of modified DNA for applications in bioanalysis and chemical biology. J. Org. Chem., 2014, 79(21), 9914-9921.
[http://dx.doi.org/10.1021/jo5020799] [PMID: 25321948]
Cahová, H.; Panattoni, A.; Kielkowski, P.; Fanfrlík, J.; Hocek, M. 5-Substituted pyrimidine and 7-substituted 7-deazapurine dNTPs as substrates for DNA polymerases in competitive primer extension in the presence of natural dNTPs. ACS Chem. Biol., 2016, 11(11), 3165-3171.
[http://dx.doi.org/10.1021/acschembio.6b00714] [PMID: 27668519]
Hottin, A.; Marx, A. Structural insights into the processing of nucleobase-modified nucleotides by DNA polymerases. Acc. Chem. Res., 2016, 49(3), 418-427.
[http://dx.doi.org/10.1021/acs.accounts.5b00544] [PMID: 26947566]

Rights & PermissionsPrintExport Cite as

Article Details

Year: 2019
Page: [1439 - 1468]
Pages: 30
DOI: 10.2174/1385272823666190809124310
Price: $58

Article Metrics

PDF: 13