1
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Lakshman MK, Malinchak CT, Shank N, Neary MC, Stahl L. Purinyl N-directed aroylation of 6-arylpurine ribo- and 2'-deoxyribonucleosides, and mechanistic insights. Org Biomol Chem 2024. [PMID: 38916551 DOI: 10.1039/d4ob00689e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The purinyl ring contains four embedded nitrogen atoms of varying basicities. Selective utilization of these ring nitrogen atoms can lead to relatively facile remote functionalization, yielding modified purinyl motifs that are otherwise not easily obtained. Herein, we report previously undescribed N-directed aroylation of 6-arylpurine ribo and the more labile 2'-deoxyribonucleosides. Kinetic isotope analysis as well as reaction with a well-defined dimeric, palladated 9-benzyl 6-arylpurine provided evidence for N-directed cyclometallation as a key step, with a plausible rate-limiting C-H bond cleavage. Radical inhibition experiments indicate the likely intermediacy of aroyl radicals. The chemistry surmounts difficulties often posed in the functionalization of polynitrogenated and polyoxygenated nucleosidic structures that possess complex reactivities and a labile glycosidic bond that is more sensitive in the 2'-deoxy substrates.
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Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
- The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Casina T Malinchak
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
- The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Nathaniel Shank
- Department of Chemistry and Biochemistry, Georgia Southern University, 11935 Abercorn Street, Savannah, GA 31419, USA
| | - Michelle C Neary
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
| | - Lothar Stahl
- Department of Chemistry, University of North Dakota, 151 Cornell Street Stop 9024, Grand Forks, ND 58202, USA
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2
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Shaughnessy KH. Covalent Modification of Nucleobases using Water-Soluble Palladium Catalysts. CHEM REC 2022; 22:e202200190. [PMID: 36074958 DOI: 10.1002/tcr.202200190] [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: 07/29/2022] [Revised: 08/25/2022] [Indexed: 12/15/2022]
Abstract
Nucleosides represent one of the key building blocks of biochemistry. There is significant interest in the synthesis of nucleoside-derived materials for applications as probes, biochemical models, and pharmaceuticals. Palladium-catalyzed cross-coupling reactions are effective methods for making covalent modification of carbon and nitrogen sites on nucleobases under mild conditions. Water-soluble catalysts derived from palladium and hydrophilic ligands, such as tris(3-sulfonatophenyl)phosphine trisodium (TPPTS), are efficient catalysts for a range of coupling reactions of unprotected halonucleosides. Over the past two decades, these methods have been extended to direct functionalization of halonucleotides, as well as RNA and DNA oligonucleotides (ONs) containing halogenated bases. These methods can be run under biocompatible conditions, including examples of Suzuki coupling of modified DNA in whole cells and tissue samples. In this account, development of this methodology by our group and others is highlighted along with the extension of these catalyst systems to modification of nucleotides and ONs.
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Affiliation(s)
- Kevin H Shaughnessy
- Department of Chemistry & Biochemistry, The University of Alabama, Box 870336, Tuscaloosa, AL 35487-0336, USA
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3
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Kanwal I, Rasool N, Zaidi SHM, Zakaria ZA, Bilal M, Hashmi MA, Mubarik A, Ahmad G, Shah SAA. Synthesis of Functionalized Thiophene Based Pyrazole Amides via Various Catalytic Approaches: Structural Features through Computational Applications and Nonlinear Optical Properties. Molecules 2022; 27:molecules27020360. [PMID: 35056676 PMCID: PMC8778362 DOI: 10.3390/molecules27020360] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
In the present study, pyrazole-thiophene-based amide derivatives were synthesized by different methodologies. Here, 5-Bromothiophene carboxylic acid (2) was reacted with substituted, unsubstituted, and protected pyrazole to synthesize the amide. It was observed that unsubstituted amide (5-bromo-N-(5-methyl-1H-pyrazol-3-yl)thiophene-2-carboxamide (7) was obtained at a good yield of about 68 percent. The unsubstituted amide (7) was arylated through Pd (0)-catalyzed Suzuki–Miyaura cross-coupling, in the presence of tripotassium phosphate (K3PO4) as a base, and with 1,4-dioxane as a solvent. Moderate to good yields (66–81%) of newly synthesized derivatives were obtained. The geometry of the synthesized compounds (9a–9h) and other physical properties, like non-linear optical (NLO) properties, nuclear magnetic resonance (NMR), and other chemical reactivity descriptors, including the chemical hardness, electronic chemical potential, ionization potential, electron affinity, and electrophilicity index have also been calculated for the synthesized compounds. In this study, DFT calculations have been used to investigate the electronic structure of the synthesized compounds and to compute their NMR data. It was also observed that the computed NMR data manifested significant agreement with the experimental NMR results. Furthermore, compound (9f) exhibits a better non-linear optical response compared to all other compounds in the series. Based on frontier molecular orbital (FMO) analysis and the reactivity descriptors, compounds (9c) and (9h) were predicted to be the most chemically reactive, while (9d) was estimated to be the most stable among the examined series of compounds.
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Affiliation(s)
- Iram Kanwal
- Department of Chemistry, Government College, University Faisalabad, Faisalabad 38000, Pakistan; (I.K.); (M.B.); (A.M.); (G.A.)
| | - Nasir Rasool
- Department of Chemistry, Government College, University Faisalabad, Faisalabad 38000, Pakistan; (I.K.); (M.B.); (A.M.); (G.A.)
- Correspondence: (N.R.); (Z.A.Z.); Tel.: +92-332-7491790 (N.R.); +60-19-2117090 (Z.A.Z.)
| | - Syeda Huda Mehdi Zaidi
- Department of Chemistry, Division of Science & Technology, University of Education, Lahore 54770, Pakistan; (S.H.M.Z.); (M.A.H.)
| | - Zainul Amiruddin Zakaria
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Malaysia
- Correspondence: (N.R.); (Z.A.Z.); Tel.: +92-332-7491790 (N.R.); +60-19-2117090 (Z.A.Z.)
| | - Muhammad Bilal
- Department of Chemistry, Government College, University Faisalabad, Faisalabad 38000, Pakistan; (I.K.); (M.B.); (A.M.); (G.A.)
| | - Muhammad Ali Hashmi
- Department of Chemistry, Division of Science & Technology, University of Education, Lahore 54770, Pakistan; (S.H.M.Z.); (M.A.H.)
| | - Adeel Mubarik
- Department of Chemistry, Government College, University Faisalabad, Faisalabad 38000, Pakistan; (I.K.); (M.B.); (A.M.); (G.A.)
| | - Gulraiz Ahmad
- Department of Chemistry, Government College, University Faisalabad, Faisalabad 38000, Pakistan; (I.K.); (M.B.); (A.M.); (G.A.)
| | - Syed Adnan Ali Shah
- Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Bandar Puncak Alam, Selangor D.E., Puncak Alam 42300, Malaysia;
- Atta-ur-Rahman Institute for Natural Products Discovery (AuRIns), Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Bandar Puncak Alam, Selangor D.E., Puncak Alam 42300, Malaysia
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4
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Balasubramaniyam T, Oh KI, Jin HS, Ahn HB, Kim BS, Lee JH. Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides. Int J Mol Sci 2021; 22:9552. [PMID: 34502459 PMCID: PMC8430589 DOI: 10.3390/ijms22179552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.
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Affiliation(s)
- Thananjeyan Balasubramaniyam
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Kwnag-Im Oh
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Ho-Seong Jin
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Hye-Bin Ahn
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Byeong-Seon Kim
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
- Department of Chemistry Education, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
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5
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Venkatesham A, Pillalamarri SR, De Wit F, Lescrinier E, Debyser Z, Van Aerschot A. Propargylated Purine Deoxynucleosides: New Tools for Fluorescence Imaging Strategies. Molecules 2019; 24:molecules24030468. [PMID: 30696094 PMCID: PMC6384747 DOI: 10.3390/molecules24030468] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/16/2019] [Accepted: 01/25/2019] [Indexed: 01/01/2023] Open
Abstract
In vivo imaging of biological processes is an important asset of modern cell biology. Selectively reacting fluorophores herein are an important tool and click chemistry reactions take a large share in these events. 5-Ethynyl-2′-deoxyuridine (EdU) is well known for visualizing DNA replication, but does not show any selectivity for incorporation into DNA. Striving for specific visualization of virus replication, in particular HIV replication, a series of propargylated purine deoxynucleosides were prepared aiming for selective incorporation by HIV reverse transcriptase (RT). We here report on the synthesis and preliminary biological effects (cellular toxicity, HIV inhibitory effects, and feasibility of the click reaction) of these nucleoside analogues.
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Affiliation(s)
- Akkaladevi Venkatesham
- Medicinal Chemistry, Rega Institute for Medical Research, Dept. of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Sambasiva Rao Pillalamarri
- Medicinal Chemistry, Rega Institute for Medical Research, Dept. of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Flore De Wit
- Laboratory for Molecular Virology and Gene Therapy, Dept. of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, 3000 Leuven, Belgium.
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, Dept. of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Dept. of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, 3000 Leuven, Belgium.
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, Dept. of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
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6
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García-Iglesias M, Torres T, González-Rodríguez D. Well-defined, persistent, chiral phthalocyanine nanoclusters via G-quadruplex assembly. Chem Commun (Camb) 2018; 52:9446-9. [PMID: 27377372 DOI: 10.1039/c6cc04152c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Octameric near-IR dye nanoclusters are produced by complexation of potassium cations with a phthalocyanine-guanosine conjugate. The combination of hydrogen-bonding, K(+) coordination, π-π stacking and steric interactions between the chiral side groups is responsible for defining a specific helical chromophore arrangement in the clusters, which display high stability and maintain their supramolecular identity onto substrates.
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Affiliation(s)
- Miguel García-Iglesias
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Tomas Torres
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain. and IMDEA Nanociencia, c/Faraday 9, Campus de Cantoblanco, 28049, Spain
| | - David González-Rodríguez
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
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7
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Gayakhe V, Ardhapure A, Kapdi AR, Sanghvi YS, Serrano JL, García L, Pérez J, García J, Sánchez G, Fischer C, Schulzke C. Water-Soluble Pd–Imidate Complexes: Broadly Applicable Catalysts for the Synthesis of Chemically Modified Nucleosides via Pd-Catalyzed Cross-Coupling. J Org Chem 2016; 81:2713-29. [DOI: 10.1021/acs.joc.5b02475] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vijay Gayakhe
- Institute of Chemical Technology, Mumbai Nathalal Road, Matunga, Mumbai 400019, India
| | - Ajaykumar Ardhapure
- Institute of Chemical Technology, Mumbai Nathalal Road, Matunga, Mumbai 400019, India
| | - Anant R. Kapdi
- Institute of Chemical Technology, Mumbai Nathalal Road, Matunga, Mumbai 400019, India
| | - Yogesh S. Sanghvi
- Rasayan, Inc. 2802 Crystal Ridge Road, Encinitas, California 92024-6615, United States
| | - Jose Luis Serrano
- Departamento
de Ingeniería
Minera, Geológica y Cartográfica, Universidad Politécnica
de Cartagena, Área de Química Inorgánica, Regional
Campus of International Excellence “Campus Mare Nostrum”, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Luis García
- Departamento
de Ingeniería
Minera, Geológica y Cartográfica, Universidad Politécnica
de Cartagena, Área de Química Inorgánica, Regional
Campus of International Excellence “Campus Mare Nostrum”, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Jose Pérez
- Departamento
de Ingeniería
Minera, Geológica y Cartográfica, Universidad Politécnica
de Cartagena, Área de Química Inorgánica, Regional
Campus of International Excellence “Campus Mare Nostrum”, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Joaquím García
- Departamento de Química
Inorgánica, Regional Campus of International Excellence “Campus
Mare Nostrum”, Universidad de Murcia, 30071 Murcia, Spain
| | - Gregorio Sánchez
- Departamento de Química
Inorgánica, Regional Campus of International Excellence “Campus
Mare Nostrum”, Universidad de Murcia, 30071 Murcia, Spain
| | - Christian Fischer
- Ernst-Moritz-Arndt-Universität
Greifswald, Institut für Biochemie, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Carola Schulzke
- Ernst-Moritz-Arndt-Universität
Greifswald, Institut für Biochemie, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
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8
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Dadová J, Cahová H, Hocek M. Polymerase Synthesis of Base-Modified DNA. MODIFIED NUCLEIC ACIDS 2016. [DOI: 10.1007/978-3-319-27111-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Bilbao N, Vázquez-González V, Aranda MT, González-Rodríguez D. Synthesis of 5-/8-Halogenated or Ethynylated Lipophilic Nucleobases as Potential Synthetic Intermediates for Supramolecular Chemistry. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Shaughnessy KH. Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides. Molecules 2015; 20:9419-54. [PMID: 26007192 PMCID: PMC6272472 DOI: 10.3390/molecules20059419] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 11/30/2022] Open
Abstract
Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.
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Affiliation(s)
- Kevin H Shaughnessy
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, AL 35487-0336, USA.
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11
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Romero-Pérez S, Camacho-García J, Montoro-García C, López-Pérez AM, Sanz A, Mayoral MJ, González-Rodríguez D. G-Arylated Hydrogen-Bonded Cyclic Tetramer Assemblies with Remarkable Thermodynamic and Kinetic Stability. Org Lett 2015; 17:2664-7. [DOI: 10.1021/acs.orglett.5b01042] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sonia Romero-Pérez
- Nanostructured Molecular
Systems and Materials Group, Departamento de Química Orgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Jorge Camacho-García
- Nanostructured Molecular
Systems and Materials Group, Departamento de Química Orgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Carlos Montoro-García
- Nanostructured Molecular
Systems and Materials Group, Departamento de Química Orgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ana M. López-Pérez
- Nanostructured Molecular
Systems and Materials Group, Departamento de Química Orgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Alfredo Sanz
- Nanostructured Molecular
Systems and Materials Group, Departamento de Química Orgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - María José Mayoral
- Nanostructured Molecular
Systems and Materials Group, Departamento de Química Orgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David González-Rodríguez
- Nanostructured Molecular
Systems and Materials Group, Departamento de Química Orgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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12
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Long J, Lee WS, Chough C, Bae IH, Kim BM. Synthesis toward CRHR1 Antagonists through 2,7-Dimethylpyrazolo[1,5-α][1,3,5]triazin-4(3H)-one C–H Arylation. J Org Chem 2015; 80:4716-21. [DOI: 10.1021/jo502894r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jinghai Long
- Department
of Chemistry,
College of Natural Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Woong-Sup Lee
- Department
of Chemistry,
College of Natural Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Chieyeon Chough
- Department
of Chemistry,
College of Natural Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Il Hak Bae
- Department
of Chemistry,
College of Natural Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - B. Moon Kim
- Department
of Chemistry,
College of Natural Sciences, Seoul National University, Seoul 151-747, Republic of Korea
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13
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Liang Y, Wnuk SF. Modification of purine and pyrimidine nucleosides by direct C-H bond activation. Molecules 2015; 20:4874-901. [PMID: 25789821 PMCID: PMC6272170 DOI: 10.3390/molecules20034874] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/11/2015] [Accepted: 03/13/2015] [Indexed: 12/02/2022] Open
Abstract
Transition metal-catalyzed modifications of the activated heterocyclic bases of nucleosides as well as DNA or RNA fragments employing traditional cross-coupling methods have been well-established in nucleic acid chemistry. This review covers advances in the area of cross-coupling reactions in which nucleosides are functionalized via direct activation of the C8-H bond in purine and the C5-H or C6-H bond in uracil bases. The review focuses on Pd/Cu-catalyzed couplings between unactivated nucleoside bases with aryl halides. It also discusses cross-dehydrogenative arylations and alkenylations as well as other reactions used for modification of nucleoside bases that avoid the use of organometallic precursors and involve direct C-H bond activation in at least one substrate. The scope and efficiency of these coupling reactions along with some mechanistic considerations are discussed.
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Affiliation(s)
- Yong Liang
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Stanislaw F Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
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14
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Bou Zerdan R, Cohn P, Puodziukynaite E, Baker MB, Voisin M, Sarun C, Castellano RK. Synthesis, optical properties, and electronic structures of nucleobase-containing π-conjugated oligomers. J Org Chem 2015; 80:1828-40. [PMID: 25581330 DOI: 10.1021/jo502773g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The molecular recognition properties of the nucleobases instruct the formation of complex three-dimensional architectures in natural and synthetic systems; relatively unexplored is their use as building blocks for π-conjugated materials where they might mutually tune electronic and supramolecular structures. Toward this goal, an introductory set (1a-d and 2a-d) of six purine-terminated and two pyrimidine-terminated π-conjugated oligomers has been synthesized and used to develop experimental electronic and photophysical structure-property trends. Unlike 2,2':5',2″-terthiophene (TTT) derivatives 2a-d, intramolecular charge transfer dominates oligomers 1a-d bearing a 4,7-bisthienylbenzothiadiazole (TBT) spacer due to the strong electron-accepting ability of its benzothiadiazole (BTD) ring. The resulting donor-acceptor-donor systems feature lower HOMO-LUMO gaps than the terthiophene-linked nucleobases (ΔE(g) ∼ 1.8 eV vs 2.4 eV based on electrochemical measurements), and the lowest so far for π-conjugated molecules that include nucleobases within the π-framework. Experiments reveal a dependence of photophysical and electronic structure on the nature of the nucleobase and are in good agreement with theoretical calculations performed at the B3LYP/6-31+G** level. Overall, the results show how nucleobase heterocycles can be installed within π-systems to tune optical and electronic properties. Future work will evaluate the consequences of these information-rich components on supramolecular π-conjugated structure.
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Affiliation(s)
- Raghida Bou Zerdan
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States
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15
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Camacho-García J, Montoro-García C, López-Pérez AM, Bilbao N, Romero-Pérez S, González-Rodríguez D. Synthesis and complementary self-association of novel lipophilic π-conjugated nucleoside oligomers. Org Biomol Chem 2015; 13:4506-13. [DOI: 10.1039/c5ob00098j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of lipophilic nucleosides comprising natural and non-natural bases that are π-conjugated to a short oligophenylene–ethynylene fragment has been synthesized and their respective association constants measured.
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Affiliation(s)
- J. Camacho-García
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Madrid
- Spain
| | - C. Montoro-García
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Madrid
- Spain
| | - A. M. López-Pérez
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Madrid
- Spain
| | - N. Bilbao
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Madrid
- Spain
| | - S. Romero-Pérez
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Madrid
- Spain
| | - D. González-Rodríguez
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Madrid
- Spain
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16
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Hervé G, Sartori G, Enderlin G, Mackenzie G, Len C. Palladium-catalyzed Suzuki reaction in aqueous solvents applied to unprotected nucleosides and nucleotides. RSC Adv 2014. [DOI: 10.1039/c3ra47911k] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nucleoside analogues have attracted much attention due to their potential biological activities.
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Affiliation(s)
- Gwénaëlle Hervé
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
| | - Guillaume Sartori
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
| | - Gérald Enderlin
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
| | | | - Christophe Len
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
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17
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Balintová J, Plucnara M, Vidláková P, Pohl R, Havran L, Fojta M, Hocek M. Benzofurazane as a New Redox Label for Electrochemical Detection of DNA: Towards Multipotential Redox Coding of DNA Bases. Chemistry 2013; 19:12720-31. [DOI: 10.1002/chem.201301868] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/18/2013] [Indexed: 12/24/2022]
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18
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Hikawa H, Suzuki H, Yokoyama Y, Azumaya I. Chemoselective Benzylation of Unprotected Anthranilic Acids with Benzhydryl Alcohols by Water-Soluble Au(III)/TPPMS in Water. J Org Chem 2013; 78:6714-20. [DOI: 10.1021/jo401064f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hidemasa Hikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1, Miyama, Funabashi, Chiba 274-8510,
Japan
| | - Hideharu Suzuki
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1, Miyama, Funabashi, Chiba 274-8510,
Japan
| | - Yuusaku Yokoyama
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1, Miyama, Funabashi, Chiba 274-8510,
Japan
| | - Isao Azumaya
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1, Miyama, Funabashi, Chiba 274-8510,
Japan
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19
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Gurram V, Pottabathini N, Garlapati R, Chaudhary AB, Patro B, Lakshman MK. C-C cross-coupling reactions of O6-alkyl-2-haloinosine derivatives and a one-pot cross-coupling/O6-deprotection procedure. Chem Asian J 2012; 7:1853-61. [PMID: 22570232 PMCID: PMC3518038 DOI: 10.1002/asia.201200093] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Indexed: 11/11/2022]
Abstract
Reaction conditions for the CC cross-coupling of O(6)-alkyl-2-bromo- and 2-chloroinosine derivatives with aryl-, hetaryl-, and alkylboronic acids were studied. Optimization experiments with silyl-protected 2-bromo-O(6)-methylinosine led to the identification of [PdCl(2)(dcpf)]/K(3)PO(4) in 1,4-dioxane as the best conditions for these reactions (dcpf=1,1'-bis(dicyclohexylphosphino)ferrocene). Attempted O(6)-demethylation, as well as the replacement of the C-6 methoxy group by amines, was unsuccessful, which led to the consideration of Pd-cleavable groups such that C-C cross-coupling and O(6)-deprotection could be accomplished in a single step. Thus, inosine 2-chloro-O(6)-allylinosine was chosen as the substrate and, after re-evaluation of the cross-coupling conditions with 2-chloro-O(6)-methylinosine as a model substrate, one-step C-C cross-coupling/deprotection reactions were performed with the O(6)-allyl analogue. These reactions are the first such examples of a one-pot procedure for the modification and deprotection of purine nucleosides under C-C cross-coupling conditions.
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Affiliation(s)
- Venkateshwarlu Gurram
- Medicinal and Analytical Chemistry Divisions, GVK Biosciences Pvt. Ltd., 28A, IDA Nacharam, Hyderabad 500076, Andhra Pradesh, India
- Jawaharlal Nehru Technological University, Kukatpally, Hyderabad 500085, Andhra Pradesh, India
| | - Narender Pottabathini
- Medicinal and Analytical Chemistry Divisions, GVK Biosciences Pvt. Ltd., 28A, IDA Nacharam, Hyderabad 500076, Andhra Pradesh, India
| | - Ramesh Garlapati
- Medicinal and Analytical Chemistry Divisions, GVK Biosciences Pvt. Ltd., 28A, IDA Nacharam, Hyderabad 500076, Andhra Pradesh, India
| | - Avinash B. Chaudhary
- Medicinal and Analytical Chemistry Divisions, GVK Biosciences Pvt. Ltd., 28A, IDA Nacharam, Hyderabad 500076, Andhra Pradesh, India
| | - Balaram Patro
- Medicinal and Analytical Chemistry Divisions, GVK Biosciences Pvt. Ltd., 28A, IDA Nacharam, Hyderabad 500076, Andhra Pradesh, India
| | - Mahesh K. Lakshman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, NY 10031, USA
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20
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Dumas A, Luedtke NW. Site-specific control of N7-metal coordination in DNA by a fluorescent purine derivative. Chemistry 2011; 18:245-54. [PMID: 22143992 DOI: 10.1002/chem.201102349] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Indexed: 12/14/2022]
Abstract
A synthetic strategy that utilizes O6-protected 8-bromoguanosine gives broad access to C8-guanine derivatives with phenyl, pyridine, thiophene, and furan substituents. The resulting 8-substituted 2'-deoxyguanosines are push-pull fluorophores that can exhibit environmentally sensitive quantum yields (Φ=0.001-0.72) due to excited-state proton-transfer reactions with bulk solvent. Changes in nucleoside fluorescence were used to characterize metal-binding affinity and specificity of 8-substituted 2'-deoxyguanosines. One derivative, 8-(2-pyridyl)-2'-deoxyguanosine (2PyG), exhibits selective binding of Cu(II), Ni(II), Cd(II), and Zn(II) through a bidentate effect provided by the N7 position of guanine and the 2-pyridyl nitrogen atom. Upon incorporation into DNA, 2-pyridine-modified guanine residues selectively bind to Cu(II) and Ni(II) with equilibrium dissociation constants (K(d)) that range from 25 to 850 nM; the affinities depend on the folded state of the oligonucleotide (duplex>G-quadruplex) as well as the identity of the metal ion (Cu>Ni≫Cd). These binding affinities are approximately 10 to 1 000 times higher than for unmodified metal binding sites in DNA, thereby providing site-specific control of metal localization in alternatively folded nucleic acids. Temperature-dependent circular-dichroism studies reveal metal-dependent stabilization of duplexes, but destabilization of G-quadruplex structures upon adding Cu(II) to 2PyG-modified oligonucleotides. These results demonstrate how the addition of a single pyridine group to the C8 position of guanine provides a powerful new tool for studying the effects of N7 metalation on the structure, stability, and electronic properties of nucleic acids.
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Affiliation(s)
- Anaëlle Dumas
- Institute of Organic Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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21
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Firth AG, Wilson K, Baumann CG, Fairlamb IJS. Interrogation of a Sonogashira cross-coupling of 8-bromoguanosine with phenylacetylene on amberlite: evidence for Pd/Cu ion binding and propagation of Pd/Cu nanoparticles. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:168-84. [PMID: 21360413 DOI: 10.1080/15257770.2010.548844] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The reactivity of Amberlite (IRA-67) base "heterogeneous" resin in Sonogashira cross-coupling of 8-bromoguanosine 1 with phenylacetylene 3 to give 2 has been examined. Both 1 and 2 coordinate to Pd and Cu ions, which explains why at equivalent catalyst loadings, the homogeneous reaction employing triethylamine base is poor yielding. X-ray photo-electron spectroscopy (XPS) has been used to probe and quantify the active nitrogen base sites of the Amberlite resin, and postreaction Pd and Cu species. The PdCl(2)(PPh(3))(2) precatalyst and CuI cocatalyst degrade to give Amberlite-supported metal nanoparticles (average size ∼2.7 nm). The guanosine product 2 formed using the Amberlite Pd/Cu catalyst system is of higher purity than reactions using a homogeneous Pd precatalyst, a prerequisite for use in biological applications.
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Affiliation(s)
- Andrew G Firth
- Department of Chemistry, University of York, Heslington, York, United Kingdom
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22
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Hocek M, Fojta M. Nucleobase modification as redox DNA labelling for electrochemical detection. Chem Soc Rev 2011; 40:5802-14. [PMID: 21625726 DOI: 10.1039/c1cs15049a] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Basic aspects of DNA electrochemistry with a strong focus on the use of modified nucleobases as redox probes for electrochemical bioanalysis are reviewed. Intrinsic electrochemical properties of nucleobases in combination with artificial redox-active nucleobase modifications are frequently applied in this field. Synthetic approaches (both chemical and enzymatic) to base-modified nucleic acids are briefly summarized and their applications in redox labelling are discussed. Finally, analytical applications including DNA hybridization, primer extension, PCR, SNP typing, DNA damage and DNA-protein interaction analysis are presented (critical review, 91 references).
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Prague, Czech Republic.
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23
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Omumi A, Beach DG, Baker M, Gabryelski W, Manderville RA. Postsynthetic guanine arylation of DNA by Suzuki-Miyaura cross-coupling. J Am Chem Soc 2010; 133:42-50. [PMID: 21067186 DOI: 10.1021/ja106158b] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Direct radical addition reactions at the C(8)-site of 2'-deoxyguanosine (dG) can afford C(8)-Ar-dG adducts that are produced by carcinogenic arylhydrazines, polycyclic aromatic hydrocarbons, and certain phenolic toxins. Such modified nucleobases are also highly fluorescent for sensing applications and possess useful electron transfer properties. The site-specific synthesis of oligonucleotides containing the C(8)-Ar-G adduct can be problematic. These lesions are sensitive to acids and oxidants that are commonly used in solid-phase DNA synthesis and are too bulky to be accepted as substrates for enzymatic synthesis by DNA polymerases. Using the Suzuki-Miyaura cross-coupling reaction, we have synthesized a number of C(8)-Ar-G-modified oligonucleotides (dimers, trimers, decamers, and a 15-mer) using a range of arylboronic acids. Good to excellent yields were obtained, and the reaction is insensitive to the nature of the bases flanking the convertible 8-Br-G nucleobase, as both pyrimidines and purines are tolerated. The impact of the C(8)-Ar-G lesion was also characterized by electrospray ionization tandem mass spectrometry, UV melting temperature analysis, circular dichroism, and fluorescence spectroscopy. The C(8)-Ar-G-modified oligonucleotides are expected to be useful substrates for diagnostic applications and understanding the biological impact of the C(8)-Ar-G lesion.
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Affiliation(s)
- Alireza Omumi
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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24
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Storr TE, Strohmeier JA, Baumann CG, Fairlamb IJS. A sequential direct arylation/Suzuki-Miyaura cross-coupling transformation of unprotected 2'-deoxyadenosine affords a novel class of fluorescent analogues. Chem Commun (Camb) 2010; 46:6470-2. [PMID: 20714566 DOI: 10.1039/c0cc02043e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Novel rigid 8-biaryl-2'-deoxyadenosines with tuneable fluorescent properties can be accessed by an efficient sequential catalytic Pd(0)-coupling approach.
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Affiliation(s)
- Thomas E Storr
- Department of Chemistry, University of York, York, YO10 5DD, UK
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25
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Polshettiwar V, Decottignies A, Len C, Fihri A. Suzuki-Miyaura cross-coupling reactions in aqueous media: green and sustainable syntheses of biaryls. CHEMSUSCHEM 2010; 3:502-22. [PMID: 20191633 DOI: 10.1002/cssc.200900221] [Citation(s) in RCA: 266] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Carbon-carbon cross-coupling reactions are among the most important processes in organic chemistry, and Suzuki-Miyaura reactions are among the most widely used protocols for the formation of carbon-carbon bonds. These reactions are generally catalyzed by soluble palladium complexes with various ligands. However, the use of toxic organic solvents remains a scientific challenge and an aspect of economical and ecological relevance. This Review will summarize various recently developed significant methods by which the Suzuki-Miyaura coupling was conducted in aqueous media, and analyzes if they are "real green" protocols.
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Affiliation(s)
- Vivek Polshettiwar
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia.
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26
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Cho JH, Prickett CD, Shaughnessy KH. Efficient Sonogashira Coupling of Unprotected Halonucleosides in Aqueous Solvents Using Water-Soluble Palladium Catalysts. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000313] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Pratap R, Parrish D, Gunda P, Venkataraman D, Lakshman MK. Influence of Biaryl Phosphine Structure on C−N and C−C Bond Formation. J Am Chem Soc 2009; 131:12240-9. [DOI: 10.1021/ja902679b] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ramendra Pratap
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - Damon Parrish
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - Padmaja Gunda
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - D. Venkataraman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - Mahesh K. Lakshman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
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28
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Pschierer J, Plenio H. Suzuki−Miyaura and Sonogashira Coupling of 6-Chloropurines and -Nucleosides in Water. Org Lett 2009; 11:2551-4. [DOI: 10.1021/ol9007475] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Pschierer
- Anorganische Chemie im Zintl-Institut, TU Darmstadt, Petersenstrasse 18, 64287 Darmstadt, Germany
| | - Herbert Plenio
- Anorganische Chemie im Zintl-Institut, TU Darmstadt, Petersenstrasse 18, 64287 Darmstadt, Germany
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29
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Shaughnessy KH. Hydrophilic ligands and their application in aqueous-phase metal-catalyzed reactions. Chem Rev 2009; 109:643-710. [PMID: 19152291 DOI: 10.1021/cr800403r] [Citation(s) in RCA: 375] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kevin H Shaughnessy
- Department of Chemistry and the Center for Green Manufacturing, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, USA.
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30
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Gibson CL, Huggan JK, Kennedy A, Kiefer L, Lee JH, Suckling CJ, Clements C, Harvey AL, Hunter WN, Tulloch LB. Diversity oriented syntheses of fused pyrimidines designed as potential antifolates. Org Biomol Chem 2009; 7:1829-42. [PMID: 19590778 DOI: 10.1039/b818339b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diversity oriented syntheses of some furo[2,3-d]pyrimidines and pyrrolo[2,3-d]pyrimidines related to folate, guanine, and diaminopyrimidine-containing drugs have been developed for the preparation of potential anti-infective and anticancer compounds. Amide couplings and Suzuki couplings on the basic heterocyclic templates were used, in the latter case yields being especially high using aromatic trifluoroborates as the coupling partner. A new ring synthesis of 6-aryl-substituted deazaguanines bearing 2-alkylthio groups has been developed using Michael addition of substituted nitrostyrenes. Diversity at C-2 has been introduced by oxidation and substitution with a range of amino nucleophiles. The chemical reactivity of these pyrrolopyrimidines with respect to both electrophilic substitution in ring synthesis and nucleophilic substitution for diversity is discussed. Several compounds were found to inhibit pteridine reductases from the protozoan parasites Trypanosoma brucei and Leishmania major at the micromolar level and to inhibit the growth of Trypanosma brucei brucei in cell culture at higher concentrations. From these results, significant structural features required for inhibition of this important drug target enzyme have been identified.
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Affiliation(s)
- Colin L Gibson
- WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, Scotland
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31
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Fleckenstein CA, Plenio H. Highly efficient Suzuki-Miyaura coupling of heterocyclic substrates through rational reaction design. Chemistry 2008; 14:4267-79. [PMID: 18366046 DOI: 10.1002/chem.200701877] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A dicyclohexyl(2-sulfo-9-(3-(4-sulfophenyl)propyl)-9H-fluoren-9-yl)phosphonium salt was synthesized in 64% overall yield in three steps from simple commercially available starting materials. The highly water-soluble catalyst obtained from the corresponding phosphine and [Na(2)PdCl(4)] enabled the Suzuki coupling of a broad variety of N- and S-heterocyclic substrates. Chloropyridines (-quinolines) and aryl chlorides were coupled with aryl-, pyridine- or indoleboronic acids in quantitative yields in water/n-butanol solvent mixtures in the presence of 0.005-0.05 mol % of Pd catalyst at 100 degrees C, chloropurines were quantitatively Suzuki coupled in the presence of 0.5 mol % of catalyst, and S-heterocyclic aryl chlorides and aryl- or 3-pyridylboronic acids required 0.01-0.05 mol % Pd catalyst for full conversion. The key to the high activity of the Pd-phosphine catalyst is the rational design of the reaction parameters (i.e., the presence of water in the reaction mixture, good solubility of reactants and catalyst in n-butanol/water (3:1), and the electron-rich and sterically demanding nature of the phosphine ligand).
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Affiliation(s)
- Christoph A Fleckenstein
- Anorganische Chemie im Zintl-Institut, TU Darmstadt, Petersenstrasse 18, 64287 Darmstadt, Germany
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32
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Hocek M, Fojta M. Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 2008; 6:2233-41. [PMID: 18563253 DOI: 10.1039/b803664k] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.
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Affiliation(s)
- Michal Hocek
- 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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33
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Ferreira M, Bricout H, Sayede A, Ponchel A, Fourmentin S, Tilloy S, Monflier E. Biphasic Aqueous Organometallic Catalysis Promoted by Cyclodextrins: How to Design the Water-Soluble Phenylphosphane to Avoid Interaction with Cyclodextrin. Adv Synth Catal 2008. [DOI: 10.1002/adsc.200700582] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Non-conventional methodologies for transition-metal catalysed carbon–carbon coupling: a critical overview. Part 2: The Suzuki reaction. Tetrahedron 2008. [DOI: 10.1016/j.tet.2007.12.036] [Citation(s) in RCA: 490] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Zhang B, Wagner GK, Weber K, Garnham C, Morgan AJ, Galione A, Guse AH, Potter BVL. 2'-deoxy cyclic adenosine 5'-diphosphate ribose derivatives: importance of the 2'-hydroxyl motif for the antagonistic activity of 8-substituted cADPR derivatives. J Med Chem 2008; 51:1623-36. [PMID: 18303825 DOI: 10.1021/jm7010386] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural features needed for antagonism at the cyclic ADP-ribose (cADPR) receptor are unclear. Chemoenzymatic syntheses of novel 8-substituted 2'-deoxy-cADPR analogues, including 8-bromo-2'-deoxy-cADPR 7, 8-amino-2'-deoxy-cADPR 8, 8- O-methyl-2'-deoxy-cADPR 9, 8-phenyl-2'-deoxy-cADPR 10 and its ribose counterpart 8-phenyl-cADPR 5 are reported, including improved syntheses of established antagonists 8-amino-cADPR 2 and 8-bromo-cADPR 3. Aplysia californica ADP-ribosyl cyclase tolerates even the bulky 8-phenyl-nicotinamide adenine 5'-dinucleotide as a substrate. Structure-activity relationships of 8-substituted cADPR analogues in both Jurkat T-lymphocytes and sea urchin egg homogenate (SUH) were investigated. 2'-OH Deletion decreased antagonistic activity (at least for the 8-amino series), showing it to be an important motif. Some 8-substituted 2'-deoxy analogues showed agonist activity at higher concentrations, among which 8-bromo-2'-deoxy-cADPR 7 was, unexpectedly, a weak but almost full agonist in SUH and was membrane-permeant in whole eggs. Classical antagonists 2 and 3 also showed previously unobserved agonist activity at higher concentrations in both systems. The 2'-OH group, without effect on the Ca (2+)-mobilizing ability of cADPR itself, is an important motif for the antagonistic activities of 8-substituted cADPR analogues.
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Affiliation(s)
- Bo Zhang
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, UK
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36
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37
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Wanninger-Weiß C, Wagenknecht HA. Synthesis of 5-(2-Pyrenyl)-2′-deoxyuridine as a DNA Modification for Electron-Transfer Studies: The Critical Role of the Position of the Chromophore Attachment. European J Org Chem 2008. [DOI: 10.1002/ejoc.200700818] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Cerna I, Pohl R, Hocek M. The first direct C-H arylation of purine nucleosides. Chem Commun (Camb) 2007:4729-30. [PMID: 18004422 DOI: 10.1039/b714253f] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pd-catalyzed direct C-H arylation of unprotected purine nucleosides with aryl iodides at position 8 was developed to allow a straightforward single-step introduction of diverse aryl groups.
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Affiliation(s)
- Igor Cerna
- 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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Capek P, Cahová H, Pohl R, Hocek M, Gloeckner C, Marx A. An efficient method for the construction of functionalized DNA bearing amino acid groups through cross-coupling reactions of nucleoside triphosphates followed by primer extension or PCR. Chemistry 2007; 13:6196-203. [PMID: 17487908 DOI: 10.1002/chem.200700220] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Single-step aqueous cross-coupling reactions of nucleobase-halogenated 2'-deoxynucleosides (8-bromo-2'-deoxyadenosine, 7-iodo-7-deaza-2'-deoxyadenosine, or 5-iodo-2'-deoxy-uridine) or their 5'-triphosphates with 4-boronophenylalanine or 4-ethynylphenylalanine have been developed and used for efficient synthesis of modified 2'-deoxynucleoside triphosphates (dNTPs) bearing amino acid groups. These dNTPs were then tested as substrates for DNA polymerases for construction of functionalized DNA through primer extension and PCR. While 8-substituted adenosine triphosphates were poor substrates for DNA polymerases, the corresponding 7-substituted 7-deazaadenine and 5-substituted uracil nucleotides were efficiently incorporated in place of dATP or dTTP, respectively, by Pwo (Pyrococcus woesei) DNA polymerase. Nucleotides bearing the amino acid connected through the less bulky acetylene linker were incorporated more efficiently than those directly linked through a more bulky phenylene group. In addition, combinations of modified dATPs and dTTPs were incorporated by Pwo polymerase. Novel functionalized DNA duplexes bearing amino acid moieties were prepared by this two-step approach. PCR can be used for amplification of duplexes bearing large number of modifications, while primer extension is suitable for introduction of just one or several modifications in a single DNA strand.
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Affiliation(s)
- Petr Capek
- Gilead Sciences & IOCB Research Center, Institute of Organic Chemistry and Biochemistry, v. v. i. Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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Vrábel M, Pohl R, Klepetárová B, Votruba I, Hocek M. Synthesis of 2'-deoxyadenosine nucleosides bearing bipyridine-type ligands and their Ru-complexes in position 8 through cross-coupling reactions. Org Biomol Chem 2007; 5:2849-57. [PMID: 17700854 DOI: 10.1039/b709245h] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of the title 2'-deoxyadenosine derivatives bearing bipyridine, phenanthroline or terpyridine ligands and their corresponding RuII-complexes in position 8 linked via acetylene or phenylene tethers was accomplished through cross-coupling reactions. The Suzuki-Miyaura reactions of boronic acids or the Sonogashira reactions of terminal acetylene derivatives of oligopyridine ligands were performed either on protected 8-bromoadenosines in organic solvents or, more efficiently, directly on unprotected nucleosides in aqueous acetonitrile or DMF. Direct cross-coupling reactions of unprotected nucleosides with RuII-complexes or the oligopyridine-boronic acids or -acetylenes gave the Ru-labelled nucleosides in one step in fair to good yields. This method was also proven to be applicable for direct Ru-labelling of dATP. Terpyridine-containing 2'-deoxyadenosine exerted significant antiviral and cytostatic effects.
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Affiliation(s)
- Milan Vrábel
- 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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42
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Mizuta M, Seio K, Miyata K, Sekine M. Fluorescent pyrimidopyrimidoindole nucleosides: control of photophysical characterizations by substituent effects. J Org Chem 2007; 72:5046-55. [PMID: 17555352 DOI: 10.1021/jo070206j] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
10-(2-Deoxy-beta-D-ribofuranosyl)pyrimido[4',5':4,5]pyrimido[1,6-a]indole-6,9(7H)-dione (dCPPI) and its derivatives were synthesized via the Suzuki-Miyaura coupling reaction of 5-iododeoxycytidine with 5-substituted N-Boc-indole-2-borates and characterized by UV-vis and fluorescence spectroscopy. The new fluorescent nucleosides showed rather large Stokes shifts (116-139 nm) in an aqueous buffer. The fluorescent intensities were dependent on the nature of the substituents on the indole rings. The electron-withdrawing groups increased the fluorescent intensity while the electron-donating groups having lone pairs decreased it. Among the substituted dCPPI derivatives tested, the trimethylammonium derivative of dCPPI was found to emit the brightest fluorescent light. The solvatochromism of dCPPI and its derivatives was also studied. Some of the dCPPI derivatives showed interesting solvent-dependent fluorescence enhancement and could be useful as new fluorescent structural probes for nucleic acids. The Lippert-Mataga analyses of the Stokes shift were also carried out to obtain estimated values of the dipole moment of the excited states of some of the derivatives.
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Affiliation(s)
- Masahiro Mizuta
- Department of Life Science, Frontier Collaborative Research Center, Tokyo Institute of Technology, and CREST of JST, 4259 Nagatsuta, Midori-ku Yokohama, Japan
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43
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Vrábel M, Hocek M, Havran L, Fojta M, Votruba I, Klepetářová B, Pohl R, Rulíšek L, Zendlová L, Hobza P, Shih IH, Mabery E, Mackman R. Purines Bearing Phenanthroline or Bipyridine Ligands and Their RuII Complexes in Position 8 as Model Compounds for Electrochemical DNA Labeling – Synthesis, Crystal Structure, Electrochemistry, Quantum Chemical Calculations, Cytostatic and Antiviral Activity. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200700030] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Collier A, Wagner G. A facile two-step synthesis of 8-arylated guanosine mono- and triphosphates (8-aryl GXPs). Org Biomol Chem 2006; 4:4526-32. [PMID: 17268649 DOI: 10.1039/b614477b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a simple and high-yielding two-step procedure for the preparation of 8-arylated guanosine mono- and triphosphates (8-aryl GXPs). The key step of our synthesis is the Suzuki-Miyaura coupling of unprotected 8-bromo GMP and 8-bromo GTP with various arylboronic acids in aqueous solution. The 8-bromoguanosine 5'-phosphates required as cross-coupling substrates were prepared from 8-bromoguanosine via an optimised Yoshikawa procedure.
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Affiliation(s)
- Alice Collier
- Centre for Carbohydrate Chemistry, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, UKNR4 7TJ
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Ngassa FN, Dekorver KA, Melistas TS, Yeh EAH, Lakshman MK. Pd−Xantphos-Catalyzed Direct Arylation of Nucleosides. Org Lett 2006; 8:4613-6. [PMID: 16986963 DOI: 10.1021/ol0619516] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Direct arylation of the exocyclic amino groups of nucleosides represents a simple approach to N-aryl nucleoside derivatives. To date, one limitation has been that only electron-deficient aryl bromides and triflates possessed adequate reactivity for efficient, direct N-arylation of nucleosides. We demonstrate herein that Pd-Xantphos catalytic systems lead to successful N-arylation of suitably protected 2'-deoxyadenosine and 2'-deoxyguanosine with a wide range of aryl bromides.
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Affiliation(s)
- Felix N Ngassa
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, USA.
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Capek P, Pohl R, Hocek M. Cross-coupling reactions of unprotected halopurine bases, nucleosides, nucleotides and nucleoside triphosphates with 4-boronophenylalanine in water. Synthesis of (purin-8-yl)- and (purin-6-yl)phenylalanines. Org Biomol Chem 2006; 4:2278-84. [PMID: 16729137 DOI: 10.1039/b604010a] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
An expeditious and highly efficient single-step methodology for the introduction of a phenylalanine moiety into position 8 and 6 of the purine scaffold was developed based on aqueous-phase Pd-catalysed Suzuki-Miyaura cross-coupling reactions of unprotected 4-boronophenylalanine with 8-bromo- or 6-chloropurines. The scope of the methodology was demonstrated by syntheses of unprotected (adenin-8-yl)phenylalanine base, nucleosides, nucleotides and nucleoside triphosphates as well as (purin-6-yl)phenylalanine base and nucleosides. All these products were obtained in high yields and in optically pure form.
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Affiliation(s)
- Petr Capek
- Centre for New Antivirals and Antineoplastics, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, CZ-16610, Prague 6, Czech Republic
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Firth AG, Fairlamb IJ, Darley K, Baumann CG. Sonogashira alkynylation of unprotected 8-brominated adenosines and guanosines: fluorescence properties of compact conjugated acetylenes containing a purine ring. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.03.100] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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McLaughlin CK, Lantero DR, Manderville RA. Conformational Properties of a Phototautomerizable Nucleoside Biomarker for Phenolic Carcinogen Exposure. J Phys Chem A 2006; 110:6224-30. [PMID: 16686455 DOI: 10.1021/jp0617571] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have characterized the conformational properties of the C8-deoxyguanosine (C8-dG) nucleoside adduct, 8-(2"-hydroxyphenyl)-2'-dG (1), which is a potential biomarker for exposure to phenolic carcinogens. Adduct 1 possesses the unique ability to phototautomerize, through an excited-state intramolecular proton transfer (ESIPT) process, to generate its keto form. This tautomerization depends on the presence of an intramolecular hydrogen (H)-bond between the phenolic OH and the imine nitrogen (N7) and has permitted insight into the equilibrium ground states of adduct 1. The results of our studies demonstrate that adduct 1 undergoes an ESIPT despite preferring a nonplanar "twisted" conformation that is imposed by the deoxyribose (dR) sugar moiety. Interestingly, a planar conformation of adduct 1 is also formed in certain aprotic solvents due to the anchoring effect of the intramolecular H-bond. Our results provide a basis for future studies aimed at determining the conformations of adduct 1 within DNA that will aid in our understanding of phenol-mediated carcinogenesis.
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Shaughnessy KH. Beyond TPPTS: New Approaches to the Development of Efficient Palladium‐Catalyzed Aqueous‐Phase Cross‐Coupling Reactions. European J Org Chem 2006. [DOI: 10.1002/ejoc.200500972] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kevin H. Shaughnessy
- Department of Chemistry and the Center for Green Manufacturing, The University of Alabama, Box 870336, Tuscaloosa, AL 35487‐0336, USA, Fax: +1‐205‐348‐4435
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Ren Y, Yu GA, Guan J, Liu SH. New recyclable catalytic system: PdCl2–Dppc+ PF6−–[bmim][PF6] for the Suzuki coupling reaction. Appl Organomet Chem 2006. [DOI: 10.1002/aoc.1156] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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