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Fleuti M, Sanchez-Quirante T, Poštová Slavětínská L, Tloušt'ová E, Tichý M, Gurská S, Džubák P, Hajdúch M, Hocek M. Synthesis and Biological Profiling of Quinolino-Fused 7-Deazapurine Nucleosides. ACS OMEGA 2024; 9:20557-20570. [PMID: 38737052 PMCID: PMC11080019 DOI: 10.1021/acsomega.4c02031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/14/2024]
Abstract
A series of quinolino-fused 7-deazapurine (pyrimido[5',4':4,5]pyrrolo[3,2-f]quinoline) ribonucleosides were designed and synthesized. The synthesis of the key 11-chloro-pyrimido[5',4':4,5]pyrrolo[3,2-f]quinoline was based on the Negishi cross-coupling of iodoquinoline with zincated 4,6-dichloropyrimidine followed by azidation and thermal or photochemical cyclization. Vorbrüggen glycosylation of the tetracyclic heterocycle followed by cross-coupling or substitution reactions at position 11 gave the desired set of final nucleosides that showed moderate to weak cytostatic activity and fluorescent properties. The corresponding fused adenosine derivative was converted to the triphosphate and successfully incorporated to RNA using in vitro transcription with T7 RNA polymerase.
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Affiliation(s)
- Marianne Fleuti
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2 CZ-12843, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
| | - Tania Sanchez-Quirante
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2 CZ-12843, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
| | - Eva Tloušt'ová
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
| | - Michal Tichý
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
| | - Soňa Gurská
- Institute
of Molecular and Translational Medicine, Palacky University and University
Hospital in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská
5, Olomouc CZ-77515, Czech Republic
| | - Petr Džubák
- Institute
of Molecular and Translational Medicine, Palacky University and University
Hospital in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská
5, Olomouc CZ-77515, Czech Republic
| | - Marián Hajdúch
- Institute
of Molecular and Translational Medicine, Palacky University and University
Hospital in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská
5, Olomouc CZ-77515, Czech Republic
| | - Michal Hocek
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2 CZ-12843, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
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2
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Yang C, Slavětínská LP, Fleuti M, Klepetářová B, Tichý M, Gurská S, Pavliš P, Džubák P, Hajdúch M, Hocek M. Synthesis of Polycyclic Hetero-Fused 7-Deazapurine Heterocycles and Nucleosides through C-H Dibenzothiophenation and Negishi Coupling. J Am Chem Soc 2022; 144:19437-19446. [PMID: 36245092 PMCID: PMC9619403 DOI: 10.1021/jacs.2c07517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
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A new approach for synthesizing polycyclic heterofused
7-deazapurine
heterocycles and the corresponding nucleosides was developed based
on C–H functionalization of diverse (hetero)aromatics with
dibenzothiophene-S-oxide followed by the Negishi
cross-cooupling with bis(4,6-dichloropyrimidin-5-yl)zinc. This cross-coupling
afforded a series of (het)aryl-pyrimidines that were converted to
fused deazapurine heterocycles through azidation and thermal cyclization.
The fused heterocycles were glycosylated to the corresponding 2′-deoxy-
and ribonucleosides, and a series of derivatives were prepared by
nucleophilic substitutions at position 4. Four series of new polycyclic
thieno-fused 7-deazapurine nucleosides were synthesized using this
strategy. Most of the deoxyribonucleosides showed good cytotoxic activity,
especially for the CCRF-CEM cell line. Phenyl- and thienyl-substituted
thieno-fused 7-deazapurine nucleosides were fluorescent, and the former
one was converted to 2′-deoxyribonucleoside triphosphate for
enzymatic synthesis of labeled oligonucleotides.
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Affiliation(s)
- Chao Yang
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic,Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Marianne Fleuti
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic,Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Blanka Klepetářová
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Tichý
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Soňa Gurská
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Petr Pavliš
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Petr Džubák
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Marián Hajdúch
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Michal Hocek
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic,Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic,E-mail:
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3
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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4
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Veselovská L, Kudlová N, Gurská S, Lišková B, Medvedíková M, Hodek O, Tloušťová E, Milisavljevic N, Tichý M, Perlíková P, Mertlíková‐Kaiserová H, Trylčová J, Pohl R, Klepetářová B, Džubák P, Hajdúch M, Hocek M. Synthesis and Cytotoxic and Antiviral Activity Profiling of All‐Four Isomeric Series of Pyrido‐Fused 7‐Deazapurine Ribonucleosides. Chemistry 2020; 26:13002-13015. [DOI: 10.1002/chem.202001124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Lucia Veselovská
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Natálie Kudlová
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
- Cancer Research Czech Republic Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Soňa Gurská
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
- Cancer Research Czech Republic Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Barbora Lišková
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Martina Medvedíková
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Ondřej Hodek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Eva Tloušťová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Nemanja Milisavljevic
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Michal Tichý
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Helena Mertlíková‐Kaiserová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Jana Trylčová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Blanka Klepetářová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
- Cancer Research Czech Republic Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
- Cancer Research Czech Republic Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
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5
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Ghosh K, Perlíková P, Havlíček V, Yang C, Pohl R, Tloušťová E, Hodek J, Gurská S, Džubák P, Hajdúch M, Hocek M. Isomeric Naphtho-Fused 7-Deazapurine Nucleosides and Nucleotides: Synthesis, Biological Activity, Photophysical Properties and Enzymatic Incorporation to Nucleic Acids. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ketaki Ghosh
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
| | - Vojtěch Havlíček
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
- Department of Organic Chemistry; Faculty of Science; Charles University in Prague; Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Chao Yang
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
- Department of Organic Chemistry; Faculty of Science; Charles University in Prague; Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
| | - Eva Tloušťová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
| | - Jan Hodek
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
| | - Soňa Gurská
- Institute of Molecular and Translational Medicine; Palacky University and University Hospital in Olomouc; Faculty of Medicine and Dentistry; Hněvotínská 5 CZ-775 15 Olomouc Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine; Palacky University and University Hospital in Olomouc; Faculty of Medicine and Dentistry; Hněvotínská 5 CZ-775 15 Olomouc Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine; Palacky University and University Hospital in Olomouc; Faculty of Medicine and Dentistry; Hněvotínská 5 CZ-775 15 Olomouc Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
- Department of Organic Chemistry; Faculty of Science; Charles University in Prague; Hlavova 8 CZ-12843 Prague 2 Czech Republic
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6
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Ro JJ, Go GH, Wilhelmsson LM, Kim BH. Fluorescence properties of 6-aryl-2'-deoxy-furanouridine and -pyrrolocytidine and their derivatives. Methods Appl Fluoresc 2017; 6:015004. [PMID: 28933349 DOI: 10.1088/2050-6120/aa8e19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
2'-deoxyfuranouridine derivatives presenting various aryl groups have been synthesized through Cu(I)-catalyzed intramolecular cyclizations. Moreover, corresponding pyrrolo-dC derivatives have been synthesized and both families of compounds thoroughly characterized using UV/vis and fluorescence spectroscopy as well as time-dependent density functional theory calculations. The photophysical characterization, show that our newly synthesized derivatives of the important pyrrolo-dC family have high fluorescence quantum yields (QYs) and brightness values. Pyrrolo-dC derivative, 3a, shows an environment sensitive QY of up to >60% and brightness of almost 3000, in low polarity solvents and excitation and emission maxima between 365-381 nm and 479-510 nm, respectively, in solvents of different polarities. Two other derivatives, 3b and 3c, show high QYs and brightness values of up to 3300 that are fairly insensitive to their microenvironment. These promising photophysical features suggest future applicability as fluorescent nucleobase analogs.
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Affiliation(s)
- Jong Jin Ro
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
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7
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Fluorescent nucleobases as tools for studying DNA and RNA. Nat Chem 2017; 9:1043-1055. [PMID: 29064490 DOI: 10.1038/nchem.2859] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023]
Abstract
Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications. In this Review, we will present a brief history of the development of fluorescent nucleobases and explore their utility as tools for addressing questions in biophysics, biochemistry and biology of nucleic acids. We provide chemical insights into the two main classes of these compounds: canonical and non-canonical nucleobases. A point-by-point discussion of the advantages and disadvantages of both types of fluorescent nucleobases is made, along with a perspective into the future challenges and outlook for this burgeoning field.
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Han JH, Yamamoto S, Park S, Sugiyama H. Development of a Vivid FRET System Based on a Highly Emissive dG-dC Analogue Pair. Chemistry 2017; 23:7607-7613. [PMID: 28411372 DOI: 10.1002/chem.201701118] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Indexed: 12/12/2022]
Abstract
A new type of Förster Resonance Energy Transfer (FRET) system using highly emissive isomorphic nucleobase analogues is reported. The FRET pair consists of 2-aminothieno[3,4-d]pyrimidine G-mimic deoxyribonucleoside (th dG) as an energy donor and 1,3-diaza-2-oxophenothiazine (tC) as an energy acceptor. The distance and orientation between donor and acceptor was controlled by systematic incorporation of th dG and tC into DNA sequences to investigate the FRET efficiencies. This is the first Watson-Crick base-pairable FRET pair to produce vivid colors. In addition, this nucleic acid-based FRET pair was used to monitor DNA conformation and achieved visualization of the B-Z transition.
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Affiliation(s)
- Ji Hoon Han
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Seigi Yamamoto
- Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University,Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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