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Mukhin EM, Savateev KV, Rusinov VL. Approaches to the synthesis of heterocyclic C-nucleosides. Russ Chem Bull 2023; 72:425-481. [PMID: 37073401 PMCID: PMC10092924 DOI: 10.1007/s11172-023-3810-1] [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: 05/24/2023] [Revised: 07/29/2023] [Accepted: 09/02/2023] [Indexed: 04/20/2023]
Abstract
This review is focused on the synthetic strategies to heterocyclic C-nucleosides and covers the literature from 2011 to 2021. The main attention is paid to the following three approaches: the direct C-C coupling of a carbohydrate moiety with a preformed aglycon unit, the construction of a (pseudo)sugar residue on a pre-formed aglycon, and the construction of an aglycon on a pre-formed (pseudo)sugar. In each Section, the literature data are categorized in terms of the size of aglycon from simple to complex, the advantages and drawbacks of the reviewed approaches are discussed.
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Affiliation(s)
- E. M. Mukhin
- Ural Federal University named after the First President of Russia B. N. Yeltsin, 19 ul. Mira, 620002 Ekaterinburg, Russian Federation
| | - K. V. Savateev
- Ural Federal University named after the First President of Russia B. N. Yeltsin, 19 ul. Mira, 620002 Ekaterinburg, Russian Federation
| | - V. L. Rusinov
- Ural Federal University named after the First President of Russia B. N. Yeltsin, 19 ul. Mira, 620002 Ekaterinburg, Russian Federation
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2
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Kuznetsova VE, Shershov VE, Guseinov TO, Miftakhov RA, Solyev PN, Novikov RA, Levashova AI, Zasedatelev AS, Lapa SA, Chudinov AV. Synthesis of Cy5-Labelled C5-Alkynyl-modified cytidine triphosphates via Sonogashira coupling for DNA labelling. Bioorg Chem 2023; 131:106315. [PMID: 36528924 DOI: 10.1016/j.bioorg.2022.106315] [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: 10/04/2022] [Revised: 11/15/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
New applications of palladium-catalyzed Sonogashira-type cross-coupling reaction between C5-halogenated 2'-deoxycytidine-5'-monophosphate and novel cyanine dyes with a terminal alkyne group have been developed. The present methodology allows to synthesize of fluorescently labeled C5-nucleoside triphosphates with different acetylene linkers between the fluorophore and pyrimidine base in good to excellent yields under mild reaction conditions. Modified 2'-deoxycytidine-5'-triphosphates were shown to be good substrates for DNA polymerases and were incorporated into the DNA by polymerase chain reaction.
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Affiliation(s)
- Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Teimur O Guseinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Rinat A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Roman A Novikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna I Levashova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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3
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Liu BK, Teng KX, Niu LY, Yang QZ. Progress in the Synthesis of Boron Dipyrromethene (BODIPY) Fluorescent Dyes. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202111001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Ramsingh Girase T, Bhilare S, Sankar Murthy Bandaru S, Chrysochos N, Schulzke C, Sanghvi YS, Kapdi AR. Carbazole‐Based N‐Heterocyclic Carbenes for the Promotion of Copper‐Catalyzed Palladium‐Free Homo‐/Hetero‐Coupling of Alkynes and Sonogashira Reactions. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Shatrughn Bhilare
- Department of ChemistryInstitute of Chemical Technology Nathalal Parekh road, Matunga Mumbai 400019 India
| | | | - Nicolas Chrysochos
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Straße 4 D-17487 Greifswald Germany
| | - Carola Schulzke
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Straße 4 D-17487 Greifswald Germany
| | - Yogesh S. Sanghvi
- Rasayan Inc. 2802, Crystal Ridge Road Encinitas, California 92024-6615 USA
| | - Anant R. Kapdi
- Department of ChemistryInstitute of Chemical Technology Nathalal Parekh road, Matunga Mumbai 400019 India
- Institute of Chemical Technology-Indian Oil Odisha CampusIIT Kharagpur extension Centre Mouza Samantpuri Bhubaneswar 751013, Odisha India
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Taskova M, Astakhova K. Fluorescent Oligonucleotides with Bis(prop-2-yn-1-yloxy)butane-1,3-diol Scaffold Rapidly Detect Disease-Associated Nucleic Acids. Bioconjug Chem 2019; 30:3007-3012. [DOI: 10.1021/acs.bioconjchem.9b00746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Taskova
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs. Lyngby, Denmark
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs. Lyngby, Denmark
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6
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Triazolyl C-nucleosides via the intermediacy of β-1′-ethynyl-2′-deoxyribose derived from a Nicholas reaction: Synthesis, photophysical properties and interaction with BSA. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.04.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Zhang W, Ma H, Li CC, Dai WM. Synthesis of the C6–C18 bis-tetrahydrofuran fragment of the proposed structure of iriomoteolide-2a via stepwise double SN2 cyclization reactions. Tetrahedron 2019. [DOI: 10.1016/j.tet.2018.12.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Su YX, Dai WM. Synthesis of the C18–C26 tetrahydrofuran-containing fragment of amphidinolide C congeners via tandem asymmetric dihydroxylation and S N 2 cyclization. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.02.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
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Aparin IO, Proskurin GV, Golovin AV, Ustinov AV, Formanovsky AA, Zatsepin TS, Korshun VA. Fine Tuning of Pyrene Excimer Fluorescence in Molecular Beacons by Alteration of the Monomer Structure. J Org Chem 2017; 82:10015-10024. [PMID: 28856889 DOI: 10.1021/acs.joc.7b01451] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Oligonucleotide probes labeled with pyrene pairs that form excimers have a number of applications in hybridization analysis of nucleic acids. A long excited state lifetime, large Stokes shift, and chemical stability make pyrene excimer an attractive fluorescent label. Here we report synthesis of chiral phosphoramidite building blocks based on (R)-4-amino-2,2-dimethylbutane-1,3-diol, easily available from an inexpensive d-(-)-pantolactone. 1-Pyreneacetamide, 1-pyrenecarboxamide, and DABCYL derivatives have been used in preparation of molecular beacon (MB) probes labeled with one or two pyrenes/quenchers. We observed significant difference in the excimer emission maxima (475-510 nm; Stokes shifts 125-160 nm or 7520-8960 cm-1) and excimer/monomer ratio (from 0.5 to 5.9) in fluorescence spectra depending on the structure and position of monomers in the pyrene pair. The pyrene excimer formed by two rigid 1-pyrenecarboxamide residues showed the brightest emission. This is consistent with molecular dynamics data on excimer stability. Increase of the excimer fluorescence for MBs after hybridization with DNA was up to 24-fold.
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Affiliation(s)
- Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Gleb V Proskurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Andrey V Golovin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Leninskie gory 1-73, Moscow 119992, Russia
| | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Andrey A Formanovsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology , 143026 Skolkovo, Russia
- Central Research Institute of Epidemiology , 111123 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 1-73, 119992 Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics , 119021 Moscow, Russia
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Bhilare S, Gayakhe V, Ardhapure AV, Sanghvi YS, Schulzke C, Borozdina Y, Kapdi AR. Novel water-soluble phosphatriazenes: versatile ligands for Suzuki–Miyaura, Sonogashira and Heck reactions of nucleosides. RSC Adv 2016. [DOI: 10.1039/c6ra19039a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Two new water-soluble phosphatriazene as versatile ligands for catalyzing Suzuki–Miyaura reactions of purines and pyrimidines in neat water with the possibility of recycling. Copper-free Sonogashira and Heck reaction were also made possible.
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Affiliation(s)
- Shatrughn Bhilare
- Department of Chemistry
- Institute of Chemical Technology
- Mumbai-400019
- India
| | - Vijay Gayakhe
- Department of Chemistry
- Institute of Chemical Technology
- Mumbai-400019
- India
| | | | | | - Carola Schulzke
- Institute for Biochemie
- Ernst-Moritz-Arndt-Universität Greifswald
- 17489 Greifswald
- Germany
| | - Yulia Borozdina
- Institute for Biochemie
- Ernst-Moritz-Arndt-Universität Greifswald
- 17489 Greifswald
- Germany
| | - Anant R. Kapdi
- Department of Chemistry
- Institute of Chemical Technology
- Mumbai-400019
- India
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