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Beghennou A, Rondot O, Corcé V, Botuha C. 1 H-1,2,3-triazolyl-1,6-naphthyridin-7(6 H)-ones as Potential Fluorescent Nucleoside Analogues: Synthesis and Optical Properties. Molecules 2024; 29:687. [PMID: 38338431 PMCID: PMC10856630 DOI: 10.3390/molecules29030687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
In this article, we present the synthesis and the optical properties of three original molecules as potential fluorescent ribonucleoside analogues incorporating a 1,6-naphthyridin-7(6H)-one scaffold as a fluorescent nucleobase and a 1,2,3-triazole as a linkage. The nucleosides were prepared via a Cu alkyne-azide cycloaddition (CuAAC) reaction between a ribofuranosyl azide and a 4-ethynylpyridine partner. Construction of substituted 1,6-naphthyridin-7(6H)-ones was achieved through two additional steps. Optical property studies were investigated on nucleoside analogues. Powerful fluorescence properties have been evidenced with a remarkable change of emissivity depending on the polarity of the solvent, making these molecules suitable as a new class of artificial fluorescent nucleosides for investigating enzyme binding sites as well as probing nucleic acids. In addition, we are convinced that such analogues could be of great interest in the search for new antiviral or antitumoral drugs based on nucleosides.
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Affiliation(s)
| | | | - Vincent Corcé
- Institut Parisien de Chimie Moléculaire, CNRS UMR 9232, Sorbonne Université, F-75252 Paris, France; (A.B.); (O.R.)
| | - Candice Botuha
- Institut Parisien de Chimie Moléculaire, CNRS UMR 9232, Sorbonne Université, F-75252 Paris, France; (A.B.); (O.R.)
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2
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Kumar S, Arora A, Kumar R, Senapati NN, Singh BK. Recent advances in synthesis of sugar and nucleoside coumarin conjugates and their biological impact. Carbohydr Res 2023; 530:108857. [PMID: 37343455 DOI: 10.1016/j.carres.2023.108857] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/23/2023]
Abstract
Naturally occurring coumarin and sugar molecules have a diverse range of applications along with superior biocompatibility. Coumarin, a member of the benzopyrone family, exhibits a wide spectrum of medicinal properties, such as anti-coagulant, anti-bacterial, anti-tumor, anti-oxidant, anti-cancer, anti-inflammatory and anti-viral activities. The sugar moiety functions as the central scaffold for the synthesis of complex molecules, attributing to their excellent biocompatibility, well-defined stereochemistry, benign nature and outstanding aqueous solubility. When the coumarin moiety is conjugated with the sugar or nucleoside molecule, the resulting conjugates exhibit significant biological properties. Due to the remarkable growth of such bioconjugates in the field of science over the last decade, owing to their future prospect as a potential bioactive core, an update to this area is very much needed. The present review focusses on the synthesis, characterization and the various therapeutic applications of coumarin conjugates, i.e., sugar and nucleoside coumarin conjugates along with their perspective for future research.
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Affiliation(s)
- Sumit Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India; Department of Chemistry and Environmental Science, Medgar Evers College, City University of New York, Brooklyn, NY, 11225, USA
| | - Aditi Arora
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Rajesh Kumar
- P.G. Department of Chemistry, R.D.S College, B.R.A. Bihar University, Muzaffarpur, 842002, India.
| | | | - Brajendra K Singh
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India.
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Verma V, Singh A, Tyagi P, Kumar V, Prasad AK. Synthesis of 1,2,3‐Triazole‐Linked Hexopyranosylpyrimidine Nucleosides and Their Application as Hepatitis B Viral DNA, HBsAg and HBeAg Suppressants. ChemistrySelect 2023. [DOI: 10.1002/slct.202204982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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4
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Doe E, Hayth HL, Brumett R, Khisamutdinov EF. Effective, Rapid, and Small-Scale Bioconjugation and Purification of "Clicked" Small-Molecule DNA Oligonucleotide for Nucleic Acid Nanoparticle Functionalization. Int J Mol Sci 2023; 24:4797. [PMID: 36902228 PMCID: PMC10003352 DOI: 10.3390/ijms24054797] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/12/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Nucleic acid-based therapeutics involves the conjugation of small molecule drugs to nucleic acid oligomers to surmount the challenge of solubility, and the inefficient delivery of these drug molecules into cells. "Click" chemistry has become popular conjugation approach due to its simplicity and high conjugation efficiency. However, the major drawback of the conjugation of oligonucleotides is the purification of the products, as traditionally used chromatography techniques are usually time-consuming and laborious, requiring copious quantities of materials. Herein, we introduce a simple and rapid purification methodology to separate the excess of unconjugated small molecules and toxic catalysts using a molecular weight cut-off (MWCO) centrifugation approach. As proof of concept, we deployed "click" chemistry to conjugate a Cy3-alkyne moiety to an azide-functionalized oligodeo-xynucleotide (ODN), as well as a coumarin azide to an alkyne-functionalized ODN. The calculated yields of the conjugated products were found to be 90.3 ± 0.4% and 86.0 ± 1.3% for the ODN-Cy3 and ODN-coumarin, respectively. Analysis of purified products by fluorescence spectroscopy and gel shift assays demonstrated a drastic amplitude of fluorescent intensity by multiple folds of the reporter molecules within DNA nanoparticles. This work is intended to demonstrate a small-scale, cost-effective, and robust approach to purifying ODN conjugates for nucleic acid nanotechnology applications.
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5
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Hu L, Takezawa Y, Shionoya M. Cu II-mediated DNA base pairing of a triazole-4-carboxylate nucleoside prepared by click chemistry. Chem Commun (Camb) 2023; 59:892-895. [PMID: 36594822 DOI: 10.1039/d2cc06205d] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Artificial metal-mediated DNA base pairing is a promising strategy for creating highly functionalized DNA supramolecules. Here we report a novel ligand-type triazole-4-carboxylate (TazC) nucleoside that is readily prepared by the click reaction. TazC nucleosides were found to form a stable TazC-CuII-TazC base pair inside DNA duplexes, resulting in CuII-specific duplex stabilization (ΔTm = +7.7 °C). This study demonstrates that the triazole derivatives are useful in the development of metal-mediated base pairing.
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Affiliation(s)
- Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Regioselective Synthesis and Molecular Docking Studies of 1,5-Disubstituted 1,2,3-Triazole Derivatives of Pyrimidine Nucleobases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238467. [PMID: 36500573 PMCID: PMC9735522 DOI: 10.3390/molecules27238467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
1,2,3-triazoles are versatile building blocks with growing interest in medicinal chemistry. For this reason, organic chemistry focuses on the development of new synthetic pathways to obtain 1,2,3-triazole derivatives, especially with pyridine moieties. In this work, a novel series of 1,5-disubstituted-1,2,3-triazoles functionalized with pyrimidine nucleobases were prepared via 1,3-dipolar cycloaddition reaction in a regioselective manner for the first time. The N1-propargyl nucleobases, used as an alkyne intermediate, were obtained in high yields (87-92%) with a new two-step procedure that selectively led to the monoalkylated compounds. Then, FeCl3 was employed as an efficient Lewis acid catalyst for 1,3-dipolar cycloaddition between different aryl and benzyl azides and the N1-propargyl nucleobases previously synthesized. This new protocol allows the synthesis of a series of new 1,2,3-triazole derivatives with good to excellent yields (82-92%). The ADME (Absorption, Distribution, Metabolism, and Excretion) analysis showed good pharmacokinetic properties and no violations of Lipinsky's rules, suggesting an appropriate drug likeness for these new compounds. Molecular docking simulations, conducted on different targets, revealed that two of these new hybrids could be potential ligands for viral and bacterial protein receptors such as human norovirus capsid protein, SARS-CoV-2 NSP13 helicase, and metallo-β-lactamase.
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Toan VN, Thanh ND, Huyen LT, Hanh NT, Hai DS, Anh HH, Giang NTK, Van HTK. Design, Synthesis, α-Amylase/α-Glucosidase Inhibition Assay, Induced Fit Docking Study of New Hybrid Compounds Containing 4H-Pyrano[2,3-d]pyrimidine, 1H-1,2,3-Triazole and D-Glucose Components. Chem Biodivers 2022; 19:e202200680. [PMID: 36408921 DOI: 10.1002/cbdv.202200680] [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: 07/21/2022] [Accepted: 11/21/2022] [Indexed: 11/22/2022]
Abstract
In this study, the click chemistry between N-propargyl derivatives of substituted 4H-pyrano[2,3-d]pyrimidines and tetra-O-acetyl-α-d-glucopyranosyl azide carried out under catalytic conditions using catalyst CuI@Montmorillonite and additive N,N-diisopropylethylamine (DIPEA). The yields of obtained hybrid compounds having 4H-pyrano[2,3-d]pyrimidine connected to 1H-1,2,3-triazole rings were about 85-94 %. All these synthesized hybrid compounds were examined for in vitro α-amylase (with IC50 values in the range of 103.63±1.13 μM to 295.45±1.11 μM) and α-glucosidase (with IC50 values in the range of 45.63±1.14 μM to 184.52±1.15) inhibitory activity. Amongst this series, ethyl ester 8m showed the best inhibitory activity against α-amylase with IC50 of 103.63±1.13 μM, while ethyl ester 8t exhibited the highest activity against α-glucosidase with IC50 of 45.63±1.14 μM. The kinetics of the inhibition of compound 8t showed the competitive α-glucosidase inhibitor property of this compound. Furthermore, the most potent compounds had any cytotoxicity against human normal cells. Induced fit docking and molecular dynamics simulation calculations indicated that the inhibition potential compounds 8m and 8t had the active interactions with the residues in receptors of corresponding tested enzymes. The calculated binding free energy from MM-GBSA approach showed that the major energy components contributed to the active binding of these studied inhibitors, including Coulomb, lipophilic and van der Waals energy. Further, 300 ns MD simulation showed that studied ligand-protein complexes were stable and indicated the structural observations into mode of binding in these complexes.
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Affiliation(s)
- Vu Ngoc Toan
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam.,Institute of New Technology, Academy of Military Science and Technology, Ministry of Defence, 17 Hoang Sam, Cau Giay, Ha Noi, Viet Nam
| | - Nguyen Dinh Thanh
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam
| | - Le Thi Huyen
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam
| | - Nguyen Thi Hanh
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam
| | - Do Son Hai
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam.,Institute of Science and Technology, Ministry of Public Security of Vietnam, 47 Pham Van Dong, Cau Giay, Ha Noi, Viet Nam
| | - Hoang Huu Anh
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam
| | - Nguyen Thi Kim Giang
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam.,Institute of Science and Technology, Ministry of Public Security of Vietnam, 47 Pham Van Dong, Cau Giay, Ha Noi, Viet Nam
| | - Hoang Thi Kim Van
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam.,Faculty of Chemical Technology, Viet Tri University of Industry, Tien Kien, Lam Thao, Phu Tho, Viet Nam
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Son Hai D, Thi Thu Ha N, Tien Tung D, Thi Kim Giang N, Thi Thu Huong N, Huu Anh H, Thi Kim Van H, Ngoc Toan V, Toan DN, Thanh ND. Synthesis, biological evaluation and induced fit docking simulation study of d-glucose-conjugated 1 H-1,2,3-triazoles having 4 H-pyrano[2,3- d]pyrimidine ring as potential agents against bacteria and fungi. NEW J CHEM 2022. [DOI: 10.1039/d1nj05330b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gluco-conjugated 1H-1,2,3-triazoles having 4H-pyrano[2,3-d]pyrimidines are synthesized via click chemistry of N-propargyl-4H-pyrano[2,3-d]pyrimidines and glucopyaranosyl azide using CuI@Montmorillonite. Their antibacterial, anti-MRSA, and antifungal activity is probed.
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Affiliation(s)
- Do Son Hai
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
- Institute of Science and Technology, Ministry of Public Security of Vietnam, 47 Pham Van Dong, Cau Giay, Ha Noi, Vietnam
| | - Nguyen Thi Thu Ha
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
| | - Do Tien Tung
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
| | - Nguyen Thi Kim Giang
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
- Institute of Science and Technology, Ministry of Public Security of Vietnam, 47 Pham Van Dong, Cau Giay, Ha Noi, Vietnam
| | - Nguyen Thi Thu Huong
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
| | - Hoang Huu Anh
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
| | - Hoang Thi Kim Van
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
- Faculty of Chemical Technology, Viet Tri University of Industry, Tien Kien, Lam Thao, Phu Tho, Vietnam
| | - Vu Ngoc Toan
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
- Institute for Chemistry and Materials, Military Institute of Science and Technology (Ministry of Military), Cau Giay, Ha Noi, Vietnam
| | - Duong Ngoc Toan
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
- Faculty of Chemistry, Thai Nguyen University of Education, 20 Luong Ngoc Quyen, Thai Nguyen, Vietnam
| | - Nguyen Dinh Thanh
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 PMCID: PMC8312718 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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Morais PAB, Francisco CS, de Paula H, Ribeiro R, Eloy MA, Javarini CL, Neto ÁC, Júnior VL. Semisynthetic Triazoles as an Approach in the Discovery of Novel Lead Compounds. CURR ORG CHEM 2021. [DOI: 10.2174/1385272825666210126100227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Historically, medicinal chemistry has been concerned with the approach of organic
chemistry for new drug synthesis. Considering the fruitful collections of new molecular entities,
the dedicated efforts for medicinal chemistry are rewarding. Planning and search for new
and applicable pharmacologic therapies involve the altruistic nature of the scientists. Since
the 19th century, notoriously applying isolated and characterized plant-derived compounds in
modern drug discovery and various stages of clinical development highlight its viability and
significance. Natural products influence a broad range of biological processes, covering transcription,
translation, and post-translational modification, being effective modulators of most
basic cellular processes. The research of new chemical entities through “click chemistry”
continuously opens up a map for the remarkable exploration of chemical space towards leading
natural products optimization by structure-activity relationship. Finally, in this review, we expect to gather a
broad knowledge involving triazolic natural product derivatives, synthetic routes, structures, and their biological activities.
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Affiliation(s)
- Pedro Alves Bezerra Morais
- Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, 29500000, Alegre, ES, Brazil
| | - Carla Santana Francisco
- Programa de Pos-Graduacao em Quimica, Universidade Federal do Espirito Santo, 29075910, Vitória, ES, Brazil
| | - Heberth de Paula
- Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, 29500000, Alegre, ES, Brazil
| | - Rayssa Ribeiro
- Programa de Pos- Graduacao em Agroquimica, Universidade Federal do Espirito Santo, 29500000, Alegre, ES, Brazil
| | - Mariana Alves Eloy
- Programa de Pos- Graduacao em Agroquimica, Universidade Federal do Espirito Santo, 29500000, Alegre, ES, Brazil
| | - Clara Lirian Javarini
- Programa de Pos-Graduacao em Quimica, Universidade Federal do Espirito Santo, 29075910, Vitória, ES, Brazil
| | - Álvaro Cunha Neto
- Programa de Pos-Graduacao em Quimica, Universidade Federal do Espirito Santo, 29075910, Vitória, ES, Brazil
| | - Valdemar Lacerda Júnior
- Programa de Pos-Graduacao em Quimica, Universidade Federal do Espirito Santo, 29075910, Vitória, ES, Brazil
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Baraniak D, Boryski J. Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry. Biomedicines 2021; 9:628. [PMID: 34073038 PMCID: PMC8229351 DOI: 10.3390/biomedicines9060628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.
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Affiliation(s)
- Dagmara Baraniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
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12
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Lin X, Liang C, Zou L, Yin Y, Wang J, Chen D, Lan W. Advance of structural modification of nucleosides scaffold. Eur J Med Chem 2021; 214:113233. [PMID: 33550179 PMCID: PMC7995807 DOI: 10.1016/j.ejmech.2021.113233] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 01/06/2021] [Accepted: 01/23/2021] [Indexed: 12/12/2022]
Abstract
With Remdesivir being approved by FDA as a drug for the treatment of Corona Virus Disease 2019 (COVID-19), nucleoside drugs have once again received widespread attention in the medical community. Herein, we summarized modification of traditional nucleoside framework (sugar + base), traizole nucleosides, nucleoside analogues assembled by other drugs, macromolecule-modified nucleosides, and their bioactivity rules. 2'-"Ara"-substituted by -F or -CN group, and 3'-"ara" substituted by acetylenyl group can greatly influence their anti-tumor activities. Dideoxy dehydrogenation of 2',3'-sites can enhance antiviral efficiencies. Acyclic nucleosides and L-type nucleosides mainly represented antiviral capabilities. 5-F Substituted uracil analogues exihibit anti-tumor effects, and the substrates substituted by -I, -CF3, bromovinyl group usually show antiviral activities. The sugar coupled with 1-N of triazolid usually displays anti-tumor efficiencies, while the sugar coupled with 2-N of triazolid mainly represents antiviral activities. The nucleoside analogues assembled by cholesterol, polyethylene glycol, fatty acid and phospholipid would improve their bioavailabilities and bioactivities, or reduce their toxicities.
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Affiliation(s)
- Xia Lin
- Medical College, Guangxi University, Nanning, 530004, China; College of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Guangxi Medical College, Nanning, 530023, China
| | | | - Lianjia Zou
- Guangxi Medical College, Nanning, 530023, China
| | - Yanchun Yin
- Guangxi Medical College, Nanning, 530023, China
| | - Jianyi Wang
- Medical College, Guangxi University, Nanning, 530004, China; College of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China.
| | - Dandan Chen
- Guangxi Medical College, Nanning, 530023, China
| | - Weisen Lan
- College of Agriculture, Guangxi University, Nanning, 530004, China
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13
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Fantoni NZ, El-Sagheer AH, Brown T. A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids. Chem Rev 2021; 121:7122-7154. [PMID: 33443411 DOI: 10.1021/acs.chemrev.0c00928] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Click chemistry is an immensely powerful technique for the fast and efficient covalent conjugation of molecular entities. Its broad scope has positively impacted on multiple scientific disciplines, and its implementation within the nucleic acid field has enabled researchers to generate a wide variety of tools with application in biology, biochemistry, and biotechnology. Azide-alkyne cycloadditions (AAC) are still the leading technology among click reactions due to the facile modification and incorporation of azide and alkyne groups within biological scaffolds. Application of AAC chemistry to nucleic acids allows labeling, ligation, and cyclization of oligonucleotides efficiently and cost-effectively relative to previously used chemical and enzymatic techniques. In this review, we provide a guide to inexperienced and knowledgeable researchers approaching the field of click chemistry with nucleic acids. We discuss in detail the chemistry, the available modified-nucleosides, and applications of AAC reactions in nucleic acid chemistry and provide a critical view of the advantages, limitations, and open-questions within the field.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
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Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition. Molecules 2020; 25:molecules25092188. [PMID: 32392853 PMCID: PMC7248712 DOI: 10.3390/molecules25092188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/23/2020] [Accepted: 05/03/2020] [Indexed: 11/17/2022] Open
Abstract
We synthesized a new amino acid-fluorescent nucleobase derivative (qAN1-AA) and from it two new fluorescent nucleobase–fluorophore (pyrene) conjugates, whereby only the analogue with the longer and more flexible linker (qAN1-pyr2) self-folded into intramolecularly stacked qAN1/pyrene conformation, yielding characteristic, 100 nm-red-shifted emission (λmax = 500 nm). On the contrary, the shorter and more rigid linker resulted in non-stacked conformation (qAN1-pyr1), characterized by the emission of free pyrene at λmax = 400 nm. Both fluorescent nucleobase–fluorophore (pyrene) conjugates strongly interacted with ds-DNA/RNA grooves with similar affinity but opposite fluorescence response (due to pre-organization), whereas the amino acid-fluorescent base derivative (qAN1-AA) was inactive. However, only intramolecularly self-folded qAN1-pyr2 showed strong fluorescence selectivity toward poly U (Watson–Crick complementary to qAN1 nucleobase) and poly A (reverse Hoogsteen complementary to qAN1 nucleobase), while an opposite emission change was observed for non-complementary poly G and poly C. Non-folded analogue (qAN1-pyr1) showed no ss-RNA selectivity, demonstrating the importance of nucleobase-fluorophore pre-organization.
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Rep V, Piškor M, Šimek H, Mišetić P, Grbčić P, Padovan J, Gabelica Marković V, Jadreško D, Pavelić K, Kraljević Pavelić S, Raić-Malić S. Purine and Purine Isostere Derivatives of Ferrocene: An Evaluation of ADME, Antitumor and Electrochemical Properties. Molecules 2020; 25:molecules25071570. [PMID: 32235404 PMCID: PMC7180452 DOI: 10.3390/molecules25071570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/23/2022] Open
Abstract
Novel purine and purine isosteres containing a ferrocene motif and 4,1-disubstituted (11a-11c, 12a-12c, 13a-13c, 14a-14c, 15a-15c, 16a, 23a-23c, 24a-24c, 25a-25c) and 1,4-disubstituted (34a-34c and 35a-35c) 1,2,3-triazole rings were synthesized. The most potent cytotoxic effect on colorectal adenocarcinoma (SW620) was exerted by the 6-chloro-7-deazapurine 11c (IC50 = 9.07 µM), 6-chloropurine 13a (IC50 = 14.38 µM) and 15b (IC50 = 15.50 µM) ferrocenylalkyl derivatives. The N-9 isomer of 6-chloropurine 13a containing ferrocenylmethylene unit showed a favourable in vitro physicochemical and ADME properties including high solubility, moderate permeability and good metabolic stability in human liver microsomes.
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Affiliation(s)
- Valentina Rep
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb 10000, Croatia; (V.R.); (M.P.); (H.Š.)
| | - Martina Piškor
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb 10000, Croatia; (V.R.); (M.P.); (H.Š.)
| | - Helena Šimek
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb 10000, Croatia; (V.R.); (M.P.); (H.Š.)
| | - Petra Mišetić
- Fidelta d.o.o., Zagreb 10000, Croatia; (P.M.); (J.P.)
| | - Petra Grbčić
- Department of Biotechnology, Center for High-Throughput Technologies, University of Rijeka, Rijeka 51000, Croatia; (P.G.); (S.K.P.)
| | - Jasna Padovan
- Fidelta d.o.o., Zagreb 10000, Croatia; (P.M.); (J.P.)
| | - Vesna Gabelica Marković
- International Relations Office, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb 10000, Croatia;
| | - Dijana Jadreško
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb 10000, Croatia;
| | - Krešimir Pavelić
- Faculty of Medicine, Juraj Dobrila University of Pula, Pula 52100, Croatia;
| | - Sandra Kraljević Pavelić
- Department of Biotechnology, Center for High-Throughput Technologies, University of Rijeka, Rijeka 51000, Croatia; (P.G.); (S.K.P.)
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb 10000, Croatia; (V.R.); (M.P.); (H.Š.)
- Correspondence: ; Tel.: +385-1-4597213
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Morsy HA, Mohammed SM, Abdel Hamid AM, Moustafa AH, El-Sayed HA. Click Synthesis of 1,2,3-Triazole Nucleosides Based on Functionalized Nicotinonitriles. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1070428020010224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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Prasher P, Sharma M. Tailored therapeutics based on 1,2,3-1 H-triazoles: a mini review. MEDCHEMCOMM 2019; 10:1302-1328. [PMID: 31534652 PMCID: PMC6748286 DOI: 10.1039/c9md00218a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
Contemporary drug discovery approaches rely on library synthesis coupled with combinatorial methods and high-throughput screening to identify leads. However, due to the multitude of components involved, a majority of optimization techniques face persistent challenges related to the efficiency of synthetic processes and the purity of compound libraries. These methods have recently found an upgradation as fragment-based approaches for target-guided synthesis of lead molecules with active involvement of their biological target. The click chemistry approach serves as a promising tool for tailoring the therapeutically relevant biomolecules of interest, improving their bioavailability and bioactivity and redirecting them as efficacious drugs. 1,2,3-1H-Triazole nucleus, being a planar and biologically acceptable scaffold, plays a crucial role in the design of biomolecular mimetics and tailor-made molecules with therapeutic relevance. This versatile scaffold also forms an integral part of the current fragment-based approaches for drug design, kinetic target guided synthesis and bioorthogonal methodologies.
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Affiliation(s)
- Parteek Prasher
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India . ;
- Department of Chemistry , University of Petroleum & Energy Studies , Dehradun 248007 , India
| | - Mousmee Sharma
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India . ;
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18
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Synthesis, biological evaluation and molecular docking study of 1,2,3-1H-triazoles having 4H-pyrano[2,3-d]pyrimidine as potential Mycobacterium tuberculosis protein tyrosine phosphatase B inhibitors. Bioorg Med Chem Lett 2019; 29:164-171. [DOI: 10.1016/j.bmcl.2018.12.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/26/2018] [Accepted: 12/04/2018] [Indexed: 11/21/2022]
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19
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Halay E, Ay E, Şalva E, Ay K, Karayıldırım T. Synthesis of triazolylmethyl-linked nucleoside analogs via combination of azidofuranoses with propargylated nucleobases and study on their cytotoxicity. Chem Heterocycl Compd (N Y) 2018. [DOI: 10.1007/s10593-018-2248-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Bakherad M, Rezaeimanesh F, Nasr-Isfahani H. Copper-Catalyzed Click Synthesis of Novel 1,2,3-Triazole-Linked Pyrimidines. ChemistrySelect 2018. [DOI: 10.1002/slct.201703088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mohammad Bakherad
- Faculty of Chemistry; Shahrood University of Technology; Shahrood 3619995161 Iran
| | - Fatemeh Rezaeimanesh
- Faculty of Chemistry; Shahrood University of Technology; Shahrood 3619995161 Iran
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21
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Bistrović A, Grbčić P, Harej A, Sedić M, Kraljević-Pavelić S, Koštrun S, Plavec J, Makuc D, Raić-Malić S. Small molecule purine and pseudopurine derivatives: synthesis, cytostatic evaluations and investigation of growth inhibitory effect in non-small cell lung cancer A549. J Enzyme Inhib Med Chem 2018; 33:271-285. [PMID: 29271659 PMCID: PMC6009932 DOI: 10.1080/14756366.2017.1414807] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Novel halogenated purines and pseudopurines with diverse aryl-substituted 1,2,3-triazoles were prepared. While p-(trifluoromethyl)-substituted 1,2,3-triazole in N-9 alkylated purine and 3-deazapurine was critical for strong albeit unselective activity on pancreatic adenocarcinoma cells CFPAC-1,1-(p-fluorophenyl)-1,2,3-triazole derivative of 7-deazapurine showed selective cytostatic effect on metastatic colon cancer cells SW620. Importantly, 1-(p-chlorophenyl)-1,2,3-triazole-tagged benzimidazole displayed the most pronounced and highly selective inhibitory effect in nM range on non-small cell lung cancer A549. This compound revealed to target molecular processes at the extracellular side and inside the plasma membrane regulated by GPLD1 and growth factor receptors PDGFR and IGF-1R leading to the inhibition of cell proliferation and induction of apoptosis mediated by p38 MAP kinase and NF-κB, respectively. Further optimisation of this compound as to reduce its toxicity in normal cells may lead to the development of novel agent effective against lung cancer.
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Affiliation(s)
- Andrea Bistrović
- a Department of Organic Chemistry, Faculty of Chemical Engineering and Technology , University of Zagreb , Zagreb , Croatia
| | - Petra Grbčić
- b Department of Biotechnology, Center for High-Throughput Technologies , University of Rijeka , Rijeka , Croatia
| | - Anja Harej
- b Department of Biotechnology, Center for High-Throughput Technologies , University of Rijeka , Rijeka , Croatia
| | - Mirela Sedić
- b Department of Biotechnology, Center for High-Throughput Technologies , University of Rijeka , Rijeka , Croatia
| | - Sandra Kraljević-Pavelić
- b Department of Biotechnology, Center for High-Throughput Technologies , University of Rijeka , Rijeka , Croatia
| | - Sanja Koštrun
- c Chemistry Department , Fidelta Ltd. , Zagreb , Croatia
| | - Janez Plavec
- d Slovenian NMR Centre , National Institute of Chemistry , Ljubljana , Slovenia.,e En-FIST Centre of Excellence , Ljubljana , Slovenia.,f Faculty of Chemistry and Chemical Technology , University of Ljubljana , Ljubljana , Slovenia
| | - Damjan Makuc
- d Slovenian NMR Centre , National Institute of Chemistry , Ljubljana , Slovenia.,e En-FIST Centre of Excellence , Ljubljana , Slovenia
| | - Silvana Raić-Malić
- a Department of Organic Chemistry, Faculty of Chemical Engineering and Technology , University of Zagreb , Zagreb , Croatia
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22
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Bistrović A, Harej A, Grbčić P, Sedić M, Kraljević Pavelić S, Cetina M, Raić-Malić S. Synthesis and Anti-Proliferative Effects of Mono- and Bis-Purinomimetics Targeting Kinases. Int J Mol Sci 2017; 18:ijms18112292. [PMID: 29104242 PMCID: PMC5713262 DOI: 10.3390/ijms18112292] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/18/2017] [Accepted: 10/25/2017] [Indexed: 11/16/2022] Open
Abstract
A series of mono-pyrrolo[2,3-d]pyrimidines 4a-4k, unsymmetrical bis-purine isosteres 5a-5e and symmetrical bis-pyrrolo[2,3-d]pyrimidines 6a and 6b connected via di(1,2,3-triazolyl)phenyl linker were synthesized by click chemistry. Whereas mono- 4g and bis-pseudopurine 5e showed selective inhibitory activities on cervical carcinoma (HeLa) cells, bis-pyrrolo[2,3-d]pyrimidine 6b exhibited potent and selective anti-proliferative effect in the nanomolar range on pancreatic carcinoma (CFPAC-1) cells. Among these, compound 6b induced a significant reduction in the expression level of CDK9 (cyclin-dependent kinase 9)/cyclin T1 in CFPAC-1 cells concomitant with attenuation of proliferative signaling mediated by c-Raf (rapidly accelerated fibrosarcoma) and p38 MAP (mitogen-activated protein) kinases. Our findings encourage further development of novel structurally related analog of 6b to obtain more selective anticancer agent for treating pancreatic cancer.
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Affiliation(s)
- Andrea Bistrović
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia.
| | - Anja Harej
- Department of Biotechnology, Center for High-Throughput Technologies, University of Rijeka, Ulica Radmile Matejčić 2, HR-51000 Rijeka, Croatia.
| | - Petra Grbčić
- Department of Biotechnology, Center for High-Throughput Technologies, University of Rijeka, Ulica Radmile Matejčić 2, HR-51000 Rijeka, Croatia.
| | - Mirela Sedić
- Department of Biotechnology, Center for High-Throughput Technologies, University of Rijeka, Ulica Radmile Matejčić 2, HR-51000 Rijeka, Croatia.
| | - Sandra Kraljević Pavelić
- Department of Biotechnology, Center for High-Throughput Technologies, University of Rijeka, Ulica Radmile Matejčić 2, HR-51000 Rijeka, Croatia.
| | - Mario Cetina
- Department of Applied Chemistry, Faculty of Textile Technology, University of Zagreb, Prilaz baruna Filipovića 28a, HR-10000 Zagreb, Croatia.
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia.
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23
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Kapadiya K, Jadeja Y, Khunt R. Synthesis of Purine-based Triazoles by Copper (I)-catalyzed Huisgen Azide-Alkyne Cycloaddition Reaction. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.3025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Khushal Kapadiya
- School of Science, Department of Chemistry; RK University; Rajkot Gujarat India
| | - Yashwantsinh Jadeja
- Center of Excellence, NFDD Center; Saurashtra University; Rajkot Gujarat India
| | - Ranjan Khunt
- Chemical Research Laboratory, Department of Chemistry; Saurashtra University; Rajkot Gujarat India
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Gładysz M, Nowak-Karnowska J, Pasternak A, Milecki J. Synthesis and hybridization properties of oligonucleotide analogues with novel acyclic triazole internucleotide linkages. Bioorg Chem 2017; 72:161-167. [PMID: 28460358 DOI: 10.1016/j.bioorg.2017.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 03/13/2017] [Accepted: 04/08/2017] [Indexed: 12/11/2022]
Abstract
Herein, we describe synthesis of novel acyclic dinucleotide analogues connected via triazole linkage in CuAAC reaction. Synthesis pathway starting from previously obtained building blocks containing alkyne or azide functional group is described. Further functionalization and application of dinucleotide analogues in DNA phosphoramidite solid-phase synthesis is also explained. Additionally, we have examined the influence of novel modifications on DNA duplex thermodynamic stability.
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Affiliation(s)
- Michał Gładysz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
| | - Joanna Nowak-Karnowska
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Umultowska 89 b, 61-614 Poznań, Poland
| | - Anna Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jan Milecki
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Umultowska 89 b, 61-614 Poznań, Poland
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25
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Nucleobase azide-ethynylribose click chemistry contributes to stabilizing oligonucleotide duplexes and stem-loop structures. Bioorg Med Chem Lett 2017; 27:2655-2658. [PMID: 28457755 DOI: 10.1016/j.bmcl.2017.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/25/2017] [Accepted: 04/06/2017] [Indexed: 01/17/2023]
Abstract
The formation of 1,4-disubstituted 1,2,3-triazoles through copper-catalyzed azide-alkyne cycloaddition (CuAAC) in oligonucleotides bearing 1-deoxy-1-ethynyl-β-d-ribofuranose (RE) can have a positive impact on the stability of oligonucleotide duplexes and stem-loop structures.
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26
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Passays J, Rubay C, Marcélis L, Elias B. Synthesis and Photophysical Properties of Triazolyl Ir
III
Nucleosides. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201601227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Johan Passays
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
| | - Christophe Rubay
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
| | - Lionel Marcélis
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
| | - Benjamin Elias
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
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27
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Subhashini NJP, Sravanthi C, Sravanthi K, Shivaraj. Synthesis, characterization, and antimicrobial activity of novel (E)-1-(aryl)-3-{3, 5-dimethoxy-4-[(1-(aryl)-1H-1,2,3-triazol-4-yl)methoxy]phenyl}prop-2-en-1-ones. RUSS J GEN CHEM+ 2016. [DOI: 10.1134/s107036321606027x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Bag SS, Talukdar S, Das SK, Pradhan MK, Mukherjee S. Donor/acceptor chromophores-decorated triazolyl unnatural nucleosides: synthesis, photophysical properties and study of interaction with BSA. Org Biomol Chem 2016; 14:5088-108. [DOI: 10.1039/c6ob00500d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the syntheses and photophysical properties of some triazolyl donor/acceptor unnatural nucleosides and studies on the interaction of one of the fluorescent nucleosides with BSA.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Sangita Talukdar
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Suman Kalyan Das
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Manoj Kumar Pradhan
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Soumen Mukherjee
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
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29
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Bucevicius J, Skardziute L, Dodonova J, Kazlauskas K, Bagdziunas G, Jursenas S, Tumkevicius S. 2,4-Bis(4-aryl-1,2,3-triazol-1-yl)pyrrolo[2,3-d]pyrimidines: synthesis and tuning of optical properties by polar substituents. RSC Adv 2015. [DOI: 10.1039/c5ra05482f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Novel D–π–A–π–D type chromophores – 2,4-bis(4-aryl-1,2,3-triazol-1-yl)pyrrolo[2,3-d]pyrimidines were prepared and their photophysical, electrochemical properties in conjunction with quantum chemical calculations were investigated.
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Affiliation(s)
- Jonas Bucevicius
- Vilnius University
- Department of Organic Chemistry
- LT-03225 Vilnius
- Lithuania
| | - Lina Skardziute
- Institute of Applied Research
- Vilnius University
- LT-10222 Vilnius
- Lithuania
| | - Jelena Dodonova
- Vilnius University
- Department of Organic Chemistry
- LT-03225 Vilnius
- Lithuania
| | - Karolis Kazlauskas
- Institute of Applied Research
- Vilnius University
- LT-10222 Vilnius
- Lithuania
| | - Gintautas Bagdziunas
- Kaunas University of Technology
- Department of Polymer Chemistry and Technology
- LT-50254 Kaunas
- Lithuania
| | - Saulius Jursenas
- Institute of Applied Research
- Vilnius University
- LT-10222 Vilnius
- Lithuania
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Peel BJ, Efthymiou TC, Desaulniers JP. Synthesis of triazole-nucleoside phosphoramidites and their use in solid-phase oligonucleotide synthesis. ACTA ACUST UNITED AC 2014; 55:4.57.1-38. [PMID: 25631534 DOI: 10.1002/0471142700.nc0457s55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Triazole-backbone oligonucleotides are macromolecules that have one or more triazole units that are acting as a backbone mimic. Triazoles within the backbone have been used within oligonucleotides for a variety of applications. This unit describes the preparation and synthesis of two triazole-nucleoside phosphoramidites [uracil-triazole-uracil (UtU) and cytosine-triazole-uracil (CtU)] based on a PNA-like scaffold, and their incorporation within oligonucleotides.
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Affiliation(s)
- Brandon J Peel
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
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Thakur RK, Mishra A, Ramakrishna K, Mahar R, Shukla SK, Srivastava A, Tripathi RP. Synthesis of novel pyrimidine nucleoside analogues owning multiple bases/sugars and their glycosidase inhibitory activity. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.09.078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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32
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Subhashini NJP, Boddu L, Amanaganti J, Shivaraj. Synthesis, characterization, and antimicrobial activity of new bis-1,2,3-triazol-H-yl-substituted 2-arylbenzimidazoles. RUSS J GEN CHEM+ 2014. [DOI: 10.1134/s1070363214070330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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González-Olvera R, Espinoza-Vázquez A, Negrón-Silva GE, Palomar-Pardavé ME, Romero-Romo MA, Santillan R. Multicomponent click synthesis of new 1,2,3-triazole derivatives of pyrimidine nucleobases: promising acidic corrosion inhibitors for steel. Molecules 2013; 18:15064-79. [PMID: 24322491 PMCID: PMC6270236 DOI: 10.3390/molecules181215064] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 11/30/2013] [Accepted: 12/02/2013] [Indexed: 01/13/2023] Open
Abstract
A series of new mono-1,2,3-triazole derivatives of pyrimidine nucleobases were synthesized by one-pot copper(I)-catalyzed 1,3-dipolar cycloaddition reactions between N-1-propargyluracil and thymine, sodium azide and several benzyl halides. The desired heterocyclic compounds were obtained in good yields and characterized by NMR, IR, and high resolution mass spectrometry. These compounds were investigated as corrosion inhibitors for steel in 1 M HCl solution, using electrochemical impedance spectroscopy (EIS) technique. The results indicate that these heterocyclic compounds are promising acidic corrosion inhibitors for steel.
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Affiliation(s)
- Rodrigo González-Olvera
- Departamento de Ciencias Básicas, Universidad Autónoma Metropolitana, Av. San Pablo No. 180, México D.F., C.P. 02200, Mexico; E-Mails: (R.G.-O.); (A.E.-V.)
| | - Araceli Espinoza-Vázquez
- Departamento de Ciencias Básicas, Universidad Autónoma Metropolitana, Av. San Pablo No. 180, México D.F., C.P. 02200, Mexico; E-Mails: (R.G.-O.); (A.E.-V.)
- Departamento de Materiales, Universidad Autónoma Metropolitana, Av. San Pablo No. 180, México D.F., C.P. 02200, Mexico; E-Mails: (M.E.P.-P.); (M.A.R.-R.)
| | - Guillermo E. Negrón-Silva
- Departamento de Ciencias Básicas, Universidad Autónoma Metropolitana, Av. San Pablo No. 180, México D.F., C.P. 02200, Mexico; E-Mails: (R.G.-O.); (A.E.-V.)
| | - Manuel E. Palomar-Pardavé
- Departamento de Materiales, Universidad Autónoma Metropolitana, Av. San Pablo No. 180, México D.F., C.P. 02200, Mexico; E-Mails: (M.E.P.-P.); (M.A.R.-R.)
| | - Mario A. Romero-Romo
- Departamento de Materiales, Universidad Autónoma Metropolitana, Av. San Pablo No. 180, México D.F., C.P. 02200, Mexico; E-Mails: (M.E.P.-P.); (M.A.R.-R.)
| | - Rosa Santillan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, 07000 México D. F., Mexico; E-Mail:
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Głowacka IE, Balzarini J, Wróblewski AE. The synthesis, antiviral, cytostatic and cytotoxic evaluation of a new series of acyclonucleotide analogues with a 1,2,3-triazole linker. Eur J Med Chem 2013; 70:703-22. [PMID: 24219992 PMCID: PMC7115586 DOI: 10.1016/j.ejmech.2013.10.057] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 10/16/2013] [Accepted: 10/23/2013] [Indexed: 11/13/2022]
Abstract
The efficient synthesis of a new series of acyclonucleotide analogues with a 1,2,3-triazole linker is described starting from diethyl azidomethyl-, 2-azidoethyl-, 3-azidopropyl-, 4-azidobutyl-, 2-azido-1-hydroxyethyl-, 3-azido-2-hydroxypropyl- and 3-azido-1-hydroxypropylphosphonates and selected alkynes under microwave irradiation. Several O,O-diethylphosphonate acyclonucleotides were transformed into the respective phosphonic acids. All compounds were evaluated in vitro for activity against a broad variety of DNA and RNA viruses and cytostatic activity against murine leukaemia L1210, human T-lymphocyte CEM and human cervix carcinoma HeLa cells. Acyclonucleotide 22e exhibited activity against both herpes simplex viruses (HSV-1, HSV-2) in HEL cell cultures (EC50 = 17 μM) and feline herpes virus (EC50 = 24 μM) in CRFK cell cultures, while compounds 20k, 21k, 22k and 23k preferentially inhibited proliferation of human T-lymphocyte CEM cells at IC50 in the 2.8–12 μM range. Nucleotide analogues with aliphatic linker between phosphorus and 1,2,3-triazole. Efficient synthesis of 1,2,3-triazole analogues of nucleotides. Antiviral activity and inhibitory effect on the proliferation of CEM cells.
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Affiliation(s)
- Iwona E Głowacka
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Łódź, Muszyńskiego 1, 90-151 Łódź, Poland.
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Segal M, Yavin E, Kafri P, Shav-Tal Y, Fischer B. Detection of mRNA of the cyclin D1 breast cancer marker by a novel duplex-DNA probe. J Med Chem 2013; 56:4860-9. [PMID: 23688195 DOI: 10.1021/jm301838y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Previously, we have described 5-((4-methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6, as a fluorescent uridine analogue exhibiting a 3000-fold higher quantum yield (Φ 0.12) and maximum emission (478 nm) which is 170 nm red-shifted as compared to uridine. Here, we utilized 6 for preparation of labeled oligodeoxynucleotide (ODN) probes based on MS2 and cyclin D1 (a known breast cancer mRNA marker) sequences. Cyclin D1-derived labeled-ssODN showed a 9.5-fold decrease of quantum yield upon duplex formation. On the basis of this finding, we developed the ds-NIF (nucleoside with intrinsic fluorescence)-probe methodology for detection of cyclin D1 mRNA, by which the fluorescent probe is released upon recognition of target mRNA by the relatively dark NIF-duplex-probe. Indeed, we successfully detected, a ss-deoxynucleic acid (DNA) variant of cyclin D1 mRNA using a dark NIF-labeled duplex-probe, and monitoring the recognition process by fluorescence spectroscopy and gel electrophoresis. Furthermore, we successfully detected cyclin D1 mRNA in RNA extracted from cancerous human cells, using ds-NIF methodology.
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Affiliation(s)
- Meirav Segal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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36
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Ménová P, Raindlová V, Hocek M. Scope and limitations of the nicking enzyme amplification reaction for the synthesis of base-modified oligonucleotides and primers for PCR. Bioconjug Chem 2013; 24:1081-93. [PMID: 23682869 DOI: 10.1021/bc400149q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Enzymatic synthesis of short (10-22 nt) base-modified oligonucleotides (ONs) was developed by nicking enzyme amplification reaction (NEAR) using Vent(exo-) polymerase, Nt.BstNBI nicking endonuclease, and a modified deoxyribonucleoside triphosphate (dNTP) derivative. The scope and limitations of the methodology in terms of different nucleobases, length, sequences, and modifications has been thoroughly studied. The methodology including isolation of the modified ONs was scaled up to nanomolar amounts and the modified ONs were successfully used as primers in primer extension and PCR. Two simple and efficient methods for fluorescent labeling of the PCR products were developed, based either on direct fluorescent labeling of primers or on NEAR synthesis of ethynylated primers, PCR, and final click labeling with fluorescent azides.
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Affiliation(s)
- Petra Ménová
- 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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37
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Głowacka IE, Balzarini J, Wróblewski AE. Synthesis and biological evaluation of novel 1,2,3-triazolonucleotides. Arch Pharm (Weinheim) 2013; 346:278-91. [PMID: 23427010 DOI: 10.1002/ardp.201200421] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 12/21/2012] [Indexed: 11/09/2022]
Abstract
A general procedure for the preparation of 1,2,3-triazole analogs of nucleosides from diethyl 2-azidoethoxymethyl- and 2-azidoethoxyethylphosphonates was elaborated. The application of microwave irradiation shortened the reaction time to 10 min in comparison to ca. 48 h when 1,3-dipolar cycloadditions were performed under standard conditions. All compounds were evaluated in vitro for inhibitory activity against a broad variety of DNA and RNA viruses. None of the compounds were antivirally active at subtoxic concentrations. Compound 17k exhibited moderate inhibitory effects on the proliferation of human T-lymphocyte cells (IC50=64 µM for CEM).
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Affiliation(s)
- Iwona E Głowacka
- Faculty of Pharmacy, Bioorganic Chemistry Laboratory, Medical University of Łódź, Łódź, Poland.
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39
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Design, synthesis, antiviral and cytostatic evaluation of novel isoxazolidine nucleotide analogues with a carbamoyl linker. Bioorg Med Chem 2013; 21:1097-108. [PMID: 23380474 PMCID: PMC7127400 DOI: 10.1016/j.bmc.2013.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/27/2012] [Accepted: 01/02/2013] [Indexed: 01/08/2023]
Abstract
5-Arylcarbamoyl-2-methylisoxazolidin-3-yl-3-phosphonates have been synthesised from N-methyl-C-diethoxyphosphorylnitrone and N-arylacrylamides in good yields. cis- and trans-isoxazolidine phosphonates obtained herein were evaluated for activity against a broad range of DNA and RNA viruses. None of the compounds were endowed with antiviral activity at subtoxic concentrations. Isoxazolidines having phenyl substituted with halogen (Ar = 2-F-C6H4; 3-Br-C6H4; and 4-Br-C6H4) have been found to inhibit proliferation of L1210, CEM as well as HeLa cells with IC50 in the 100–170 μM range.
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Bag SS, Talukdar S, Matsumoto K, Kundu R. Triazolyl donor/acceptor chromophore decorated unnatural nucleosides and oligonucleotides with duplex stability comparable to that of a natural adenine/thymine pair. J Org Chem 2012; 78:278-91. [PMID: 23171090 DOI: 10.1021/jo302033f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report the design and synthesis of triazolyl donor/acceptor unnatural nucleosides via click chemistry and studies on the duplex stabilization of DNA containing two such new nucleosides. The observed duplex stabilization among the self-pair/heteropair has been found to be comparable to that of a natural A/T pair. Our observations on the comparable duplex stabilization has been explained on the basis of possible π-π stacking and/or charge transfer interactions between the pairing partners. The evidence of ground-state charge transfer complexation came from the UV-vis spectra and the static quenching of fluorescence in a heteropair. We have also exploited one of our unnatural DNAs in stabilizing abasic DNA.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bio-organic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Guwahati-781039, India.
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41
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Driowya M, Puissant A, Robert G, Auberger P, Benhida R, Bougrin K. Ultrasound-assisted one-pot synthesis of anti-CML nucleosides featuring 1,2,3-triazole nucleobase under iron-copper catalysis. ULTRASONICS SONOCHEMISTRY 2012; 19:1132-1138. [PMID: 22595539 DOI: 10.1016/j.ultsonch.2012.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 03/29/2012] [Accepted: 04/08/2012] [Indexed: 05/31/2023]
Abstract
A simple and efficient synthesis of modified 1,2,3-triazole nucleosides was developed. The strategy involved sequential one-pot acetylation-azidation-cycloaddition procedure and was found to be highly effective under a cooperative effect of ultrasound activation and iron/copper catalysis. The reactions were carried out under both conventional and ultrasonic irradiation conditions. In general, improvement in rates and yields were observed when reactions were carried out under sonication compared with conventional conditions. This one-pot procedure provides several advantages such as operational simplicity, high yield, safety and environment friendly protocol. The resulting substituted nucleosides were evaluated for their anticancer activity against K562 chronic myelogenous leukemia (CML) cell line.
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Affiliation(s)
- Mohsine Driowya
- Institut de Chimie de Nice UMR CNRS 7272, Université de Nice-Sophia Antipolis, Parc Valrose, 06108 Nice Cedex 2, France
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Efthymiou T, Gong W, Desaulniers JP. Chemical architecture and applications of nucleic acid derivatives containing 1,2,3-triazole functionalities synthesized via click chemistry. Molecules 2012; 17:12665-703. [PMID: 23103533 PMCID: PMC6268694 DOI: 10.3390/molecules171112665] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/19/2012] [Accepted: 10/19/2012] [Indexed: 11/16/2022] Open
Abstract
There is considerable attention directed at chemically modifying nucleic acids with robust functional groups in order to alter their properties. Since the breakthrough of copper-assisted azide-alkyne cycloadditions (CuAAC), there have been several reports describing the synthesis and properties of novel triazole-modified nucleic acid derivatives for potential downstream DNA- and RNA-based applications. This review will focus on highlighting representative novel nucleic acid molecular structures that have been synthesized via the “click” azide-alkyne cycloaddition. Many of these derivatives show compatibility for various applications that involve enzymatic transformation, nucleic acid hybridization, molecular tagging and purification, and gene silencing. The details of these applications are discussed. In conclusion, the future of nucleic acid analogues functionalized with triazoles is promising.
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Affiliation(s)
| | | | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, ON L1H 7K4, Canada
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El-Sagheer AH, Brown T. Click Chemistry – a Versatile Method for Nucleic Acid Labelling, Cyclisation and Ligation. DNA CONJUGATES AND SENSORS 2012. [DOI: 10.1039/9781849734936-00119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The copper-catalysed [3+2] alkyne azide cycloaddition reaction (the CuAAC reaction) is the classic example of ‘click’ chemistry, a relatively new concept that has been influential in many areas of science. It is used in the nucleic acid field for DNA cross-linking, oligonucleotide ligation and cyclisation, DNA and RNA labelling, attaching DNA to surfaces, producing modified nucleobases and backbones, synthesising ribozymes and monitoring nucleic acid biosynthesis. More recently a related click reaction, the ring strain-promoted azide–alkyne [3+2] cycloaddition (SPAAC) reaction has been used successfully in DNA strand ligation and labelling. This does not require copper catalysis, and therefore has many potential uses in vivo. In this review we discuss recent developments in nucleic acid click chemistry and their applications in biology, biotechnology and nanotechnology.
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Affiliation(s)
- Afaf H. El-Sagheer
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
- Chemistry Branch Dept. of Science and Mathematics Faculty of Petroleum and Mining Engineering, Suez Canal University, Suez, 43721 Egypt
| | - Tom Brown
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
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Głowacka IE, Balzarini J, Wróblewski AE. Design, synthesis, antiviral, and cytotoxic evaluation of novel phosphonylated 1,2,3-triazoles as acyclic nucleotide analogues. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 31:293-318. [PMID: 22444192 DOI: 10.1080/15257770.2012.662611] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The 1,3-dipolar cycloaddition of diethyl 2-azidoethyl-, 3-azidopropyl-, 2-azido-1-hydroxyethyl-, 3-azido-2-hydroxypropylphosphonates with selected N-propargyl nucleobases gave a series of the phosphonylated 1,2,3-triazole acyclonucleosides in which the phosphonate residue and nucleobases were linked by three- and four-carbon chains. Under standard conditions (TMSBr, ethanol), all synthesized O,O-diethylphosphonates were transformed into the respective phosphonic acids. All compounds were evaluated in vitro for activity against a broad variety of DNA and RNA viruses. Unfortunately, no antiviral activity was observed at 100 μM.
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Affiliation(s)
- Iwona E Głowacka
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Łódź, Łódź, Poland.
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45
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Fedorov AY, Nyuchev AV, Beletskaya IP. Catalytic methods of creation and functionalization of the coumarin skeleton. Chem Heterocycl Compd (N Y) 2012. [DOI: 10.1007/s10593-012-0980-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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46
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Clicked polycyclic aromatic hydrocarbon as a hybridization-responsive fluorescent artificial nucleobase in pyrrolidinyl peptide nucleic acids. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.03.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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47
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Kanishchev OS, Gudz GP, Shermolovich YG, Nesterova NV, Zagorodnya SD, Golovan AV. Synthesis and biological activity of the nucleoside analogs based on polyfluoroalkyl-substituted 1,2,3-triazoles. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 30:768-83. [PMID: 21967288 DOI: 10.1080/15257770.2011.602654] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
This paper offers the results of a synthesis and study of cytotoxicity and the anti-Epstein-Barr virus (EBV) activity of new 2-deoxy-2-chloro-pyranosyl derivatives of 4-tosyl-5-trifluoromethyl-1,2,3-triazole obtained via the addition reaction of the corresponding 2-N-chlorotriazole to the double bond of 3,4,6-tri-O-acetyl-D-glucal. Nucleoside mimetics, derivatives of 4-tosyl-5-polyfluoroalkyl-1,2,3-triazoles containing fragments of 3-chloro-tetrahydrofuran, 3-chloro-tetrahydropyran, tetrahydropyran, dihydrofuran, dihydropyran, or acyclic substituents, were also studied. Evaluation of cytotoxicity (trypan blue and MTT methods) and anti-EBV activity (polymerase chain reaction (PCR) method) showed high selectivity indices for the compounds 4a, 4b, 5b, 6, and 8. A total of 15 novel compounds were examined in this study.
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Sau SP, Hrdlicka PJ. C2'-pyrene-functionalized triazole-linked DNA: universal DNA/RNA hybridization probes. J Org Chem 2012; 77:5-16. [PMID: 22087648 PMCID: PMC3253902 DOI: 10.1021/jo201845z] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Development of universal hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of "universal bases" that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal hybridization without compromising duplex thermostability has proven challenging. Here we have used the "click reaction" to synthesize four C2'-pyrene-functionalized triazole-linked 2'-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal hybridization characteristics (average differences in thermal denaturation temperatures of matched vs mismatched duplexes involving monomer W are <1.7 °C), and (c) exceptional affinity toward DNA targets containing abasic sites opposite of the modification site (ΔT(m) up to +25 °C). The latter observation, along with results from absorption and fluorescence spectroscopy, suggests that the pyrene moiety is intercalating into the duplex whereby the opposing nucleotide is pushed into an extrahelical position. These properties render C2'-pyrene-functionalized triazole-linked DNA as promising universal hybridization probes for applications in nucleic acid chemistry and biotechnology.
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Affiliation(s)
- Sujay P. Sau
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA
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49
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Pospieszny T, Małecka I, Paryzek Z. Synthesis and spectroscopic studies of new bile acid derivatives linked by a 1,2,3-triazole ring. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2011.11.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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50
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Efthymiou TC, Huynh V, Oentoro J, Peel B, Desaulniers JP. Efficient synthesis and cell-based silencing activity of siRNAS that contain triazole backbone linkages. Bioorg Med Chem Lett 2011; 22:1722-6. [PMID: 22260772 DOI: 10.1016/j.bmcl.2011.12.104] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 12/16/2011] [Accepted: 12/20/2011] [Indexed: 10/14/2022]
Abstract
An efficient synthesis of siRNAs modified at the backbone with a triazole functionality is reported. Through the use of 4,4'-dimethoxytrityl (DMT) phosphoramidite chemistry, triazole backbone dimers were site-specifically incorporated throughout various siRNAs targeting both firefly luciferase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene transcripts as representatives of an exogenous and endogenous gene, respectively. Following the successful silencing of the firefly luciferase reporter gene, triazole-modified siRNAs were also found to be capable of silencing GAPDH in a dose-dependent manner. Backbone modifications approaching the 3'-end on the sense strand were tolerated without compromising siRNA potency. This study highlights the compatibility of triazole-modified siRNAs within the RNAi pathway, and the modification's potential to impart favorable properties to siRNAs designed to target other endogenous genes.
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Affiliation(s)
- Tim C Efthymiou
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
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