1
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Zengin Kurt B, Dhara D, El-Sagheer AH, Brown T. Synthesis and Properties of Oligonucleotides Containing LNA-Sulfamate and Sulfamide Backbone Linkages. Org Lett 2024; 26:4137-4141. [PMID: 38717429 PMCID: PMC11110047 DOI: 10.1021/acs.orglett.4c01232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Oligonucleotides hold great promise as therapeutic agents but poor bioavailability limits their utility. Hence, new analogues with improved cell uptake are urgently needed. Here, we report the synthesis and physical study of reduced-charge oligonucleotides containing artificial LNA-sulfamate and sulfamide linkages combined with 2'-O-methyl sugars and phosphorothioate backbones. These oligonucleotides have high affinity for RNA and excellent nuclease resistance.
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Affiliation(s)
- Belma Zengin Kurt
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Bezmialem Vakif University, 34093 Istanbul, Turkey
| | - Debashis Dhara
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
| | - Afaf H. El-Sagheer
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.
| | - Tom Brown
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
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2
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Banerjee A, Das A, Ghosh A, Gupta A, Sinha S. Synthesis and Biophysical Properties of Triazole-Incorporated PMOs (TzPMOs): A Convergent, Click Ligation Approach. J Org Chem 2024; 89:2895-2903. [PMID: 38344977 DOI: 10.1021/acs.joc.3c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The synthesis of phosphorodiamidate morpholino oligonucleotides (PMOs) incorporating single or double triazole rings in the backbone has been achieved via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The synthetic approach implemented is fundamentally convergent, involving the ligation of a 5'-azide PMO fragment to a 3'-alkyne fragment both in solution and on solid support. To access the 3'-alkyne PMO fragment, we synthesized 3'-N-propargyl chlorophosphoramidate morpholino monomers for all four nucleobases. The resulting triazole-incorporated PMOs (TzPMOs) have exhibited comparable or improved binding affinity toward complementary deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) strands compared to its regular analogues. Finally, a full-length TzPMO was designed to target the Nanog gene, demonstrating almost identical hybridization properties when compared to its regular version. Circular dichroism studies revealed a B-type helical conformation for the duplexes formed by TzPMOs.
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Affiliation(s)
- Arpan Banerjee
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Abhishek Gupta
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
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3
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Das U, Kundu J, Shaw P, Bose C, Ghosh A, Gupta S, Sarkar S, Bhadra J, Sinha S. Self-transfecting GMO-PMO chimera targeting Nanog enable gene silencing in vitro and suppresses tumor growth in 4T1 allografts in mouse. MOLECULAR THERAPY - NUCLEIC ACIDS 2023; 32:203-228. [PMID: 37078062 PMCID: PMC10106836 DOI: 10.1016/j.omtn.2023.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 03/16/2023] [Indexed: 04/05/2023]
Abstract
Phosphorodiamidate morpholino oligonucleotide (PMO)-based antisense reagents cannot enter cells without the help of a delivery technique, which limits their clinical applications. To overcome this problem, self-transfecting guanidinium-linked morpholino (GMO)-PMO or PMO-GMO chimeras have been explored as antisense agents. GMO facilitates cellular internalization and participates in Watson-Crick base pairing. Targeting NANOG in MCF7 cells resulted in decline of the whole epithelial to mesenchymal transition (EMT) and stemness pathway, evident through its phenotypic manifestations, all of which were promulgated in combination with Taxol due to downregulation of MDR1 and ABCG2. GMO-PMO-mediated knockdown of no tail gene resulted in desired phenotypes in zebrafish even upon delivery after 16-cell stages. In BALB/c mice, 4T1 allografts were found to regress via intra-tumoral administration of NANOG GMO-PMO antisense oligonucleotides (ASOs), which was associated with occurrence of necrotic regions. GMO-PMO-mediated tumor regression restored histopathological damage in liver, kidney, and spleen caused by 4T1 mammary carcinoma. Serum parameters of systemic toxicity indicated that GMO-PMO chimeras are safe. To the best of our knowledge, self-transfecting antisense reagent is the first report since the discovery of guanidinium-linked DNA (DNG), which could be useful as a combination cancer therapy and, in principle, can render inhibition of any target gene without using any delivery vehicle.
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4
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Ghosh A, Akabane-Nakata M, Kundu J, Harp JM, Madaoui M, Egli M, Manoharan M, Sinha S. Synthesis and Biophysical Properties of Phosphorodiamidate Piperidino Oligomers. Org Lett 2023; 25:901-906. [PMID: 36734846 DOI: 10.1021/acs.orglett.2c04067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We report the synthesis of piperidino nucleoside phosphoramidates functionalized with uracil, cytosine, guanine, and adenine and their incorporation into oligomers. High-performance liquid chromatography analyses demonstrated that a phosphorodiamidate piperidino oligomer (PPO) is more lipophilic than a phosphorodiamidate morpholino oligomer (PMO) of the same tetrameric sequence. A PMO containing piperidino residues formed duplexes with both DNA and RNA, and the PPO had higher stability at endosomolytic pH and higher hydrophobicity than the PMO.
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Affiliation(s)
- Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | | | - Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Mimouna Madaoui
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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5
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Albaneze-Walker J, Urbanietz G, Horvath A, Lancianesi S, Gimenez Molina A, De Vijlder T, Baeten M, Canters M. Synthesis of Phosphorodiamidate Oligonucleotide Dimers. J Org Chem 2022; 87:13363-13366. [PMID: 36161801 DOI: 10.1021/acs.joc.2c01582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Azido nucleosides couple with phosphoramidites via an initial iminophosphorane, which eliminates acrylonitrile to generate the coupled dimer P(V) product. The vulnerable phosphite triester intermediate is bypassed entirely, making the methodology very suitable to solution-phase synthesis. This new coupling protocol requires no protection of the 5'-OH function and provides a new method of installing internucleosidic phosphorodiamidate bonds with near quantitative yields.
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Affiliation(s)
- Jennifer Albaneze-Walker
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Gregor Urbanietz
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Andras Horvath
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Stefano Lancianesi
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Alejandro Gimenez Molina
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Thomas De Vijlder
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Mattijs Baeten
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Martine Canters
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
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6
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Santos GC, Rocha IO, Stefanello FS, Copetti JPP, Tisoco I, Martins MAP, Zanatta N, Frizzo CP, Iglesias BA, Bonacorso HG. Investigating ESIPT and donor-acceptor substituent effects on the photophysical and electrochemical properties of fluorescent 3,5-diaryl-substituted 1-phenyl-2-pyrazolines. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 269:120768. [PMID: 34952444 DOI: 10.1016/j.saa.2021.120768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/01/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
This paper describes the synthesis, structural study, and evaluation of electrochemical and photophysical properties by UV-Vis absorption and fluorescence emission analysis (solution and solid-state) of a series of eight 3,5-aryl-substituted 1-phenyl-2-pyrazolines (5), where 3-aryl = 2-OH-C6H4 (5a-g) or Ph (5h), and 5-aryl = Ph (a, h), 1-naphthyl (b), 4-Br-C6H4 (c), 4-F-C6H4 (d), 4-OCH3-C6H4(e), 4-NO2-C6H4 (f), 4-(N(CH3)2)-C6H4(g). The UV-Vis absorption properties of 2-pyrazolines were evaluated in DCM, MeCN, AcOEt, EtOH, and DMSO as the solvent and showed a fluorescence shift for the polar aprotic solvents. The steady-state fluorescence emission exhibited a band in the blue region when excited at the least energetic transition of each compound, although the excited-state intramolecular proton (ESIPT) effect was not detected. In the solid state, compounds presented similar behavior regarding absorption and emission properties compared to the solution assays. With the electrochemical analyses performed for the synthesized 2-pyrazolines, it was possible to conclude that the redox potentials were influenced by the electronic and steric effects of the substituents on the aryl rings and, according to the electronic nature of the substituents, which electron-donating groups were favored. Finally, the TD-DFT analyses revealed that all compounds had delocalized electron density throughout the 2-pyrazolines unit and were not influenced by the substituent bonded at C-5. Nonetheless, LUMO orbital analysis showed that only derivatives 5b and 5f have this localized density over the substituents.
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Affiliation(s)
- Gabriel C Santos
- Núcleo de Química de Heterociclos (NUQUIMHE), Departamento de Química, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Inaiá O Rocha
- Núcleo de Química de Heterociclos (NUQUIMHE), Departamento de Química, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Felipe S Stefanello
- Núcleo de Química de Heterociclos (NUQUIMHE), Departamento de Química, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - João P P Copetti
- Núcleo de Química de Heterociclos (NUQUIMHE), Departamento de Química, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Isadora Tisoco
- Laboratório de Bioinorgânica e Materiais Porfirínicos, Departamento de Química, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Marcos A P Martins
- Núcleo de Química de Heterociclos (NUQUIMHE), Departamento de Química, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Nilo Zanatta
- Núcleo de Química de Heterociclos (NUQUIMHE), Departamento de Química, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Clarissa P Frizzo
- Núcleo de Química de Heterociclos (NUQUIMHE), Departamento de Química, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Bernardo A Iglesias
- Laboratório de Bioinorgânica e Materiais Porfirínicos, Departamento de Química, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Helio G Bonacorso
- Núcleo de Química de Heterociclos (NUQUIMHE), Departamento de Química, Universidade Federal de Santa Maria, 97105-900 Santa Maria, RS, Brazil.
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7
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Papis M, Loro C, Penso M, Broggini G, Foschi F. Synthesis of Morpholino Nucleosides Starting From Enantiopure Glycidol. Org Chem Front 2022. [DOI: 10.1039/d2qo00400c] [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
A protocol for the synthesis of modified morpholino monomers was performed in few steps through the condensation between 6-hydroxymethyl-morpholine acetal and nucleobases under Lewis acid conditions. The key common precursor...
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8
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Dysko A, Baker YR, McClorey G, Wood MJA, Fenner S, Williams G, El-Sagheer A, Brown T. Covalently attached intercalators restore duplex stability and splice-switching activity to triazole-modified oligonucleotides. RSC Chem Biol 2022; 3:765-772. [PMID: 35755188 PMCID: PMC9175110 DOI: 10.1039/d2cb00100d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/15/2022] [Indexed: 11/29/2022] Open
Abstract
Oligonucleotides are rapidly emerging as powerful therapeutics for hard to treat diseases. Short single-stranded oligonucleotides can base pair with target RNA and alter gene expression, providing an attractive therapeutic approach at the genetic level. Whilst conceptually appealing, oligonucleotides require chemical modification for clinical use. One emerging approach is to substitute the phosphodiester backbone with other chemical linkages such as triazole. The triazole linkage is inherently resistant to enzymatic degradation, providing stability in vivo, and is uncharged, potentially improving cell-penetration and in vivo distribution. Triazole linkages, however, are known to reduce RNA target binding affinity. Here we show that by attaching pyrene or anthraquinone to the ribose sugar on the 5′-side of the triazole, it is possible to recover duplex stability and restore the splice switching ability of triazole-containing oligonucleotides. Oligonucleotides can bind to mRNA and alter gene expression, but require backbone modifications for clinical use. We show that attaching pyrene or anthraquinone to the ribose sugar next to an artificial triazole backbone restores duplex stability and splice switching ability in cells.![]()
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Affiliation(s)
- Anna Dysko
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford 12 Mansfield Road Oxford, OX1 3TA UK
| | - Ysobel R Baker
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford 12 Mansfield Road Oxford, OX1 3TA UK
| | - Graham McClorey
- Department of Physiology, Anatomy and Genetics, University of Oxford Oxford UK
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford Oxford UK
| | - Sabine Fenner
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage Hertfordshire SG1 2NY UK
| | - Glynn Williams
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage Hertfordshire SG1 2NY UK
| | - Afaf El-Sagheer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford 12 Mansfield Road Oxford, OX1 3TA UK
- Chemistry Branch Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University Suez 43721 Egypt
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford 12 Mansfield Road Oxford, OX1 3TA UK
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9
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Epple S, Modi A, Baker YR, Wȩgrzyn E, Traoré D, Wanat P, Tyburn AES, Shivalingam A, Taemaitree L, El-Sagheer AH, Brown T. A New 1,5-Disubstituted Triazole DNA Backbone Mimic with Enhanced Polymerase Compatibility. J Am Chem Soc 2021; 143:16293-16301. [PMID: 34546729 PMCID: PMC8499026 DOI: 10.1021/jacs.1c08057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Triazole linkages
(TLs) are mimics of the phosphodiester bond in
oligonucleotides with applications in synthetic biology and biotechnology.
Here we report the RuAAC-catalyzed synthesis of a novel 1,5-disubstituted
triazole (TL2) dinucleoside phosphoramidite as well as
its incorporation into oligonucleotides and compare its DNA polymerase
replication competency with other TL analogues. We demonstrate that
TL2 has superior replication kinetics to these analogues
and is accurately replicated by polymerases. Derived structure–biocompatibility
relationships show that linker length and the orientation of a hydrogen
bond acceptor are critical and provide further guidance for the rational
design of artificial biocompatible nucleic acid backbones.
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Affiliation(s)
- Sven Epple
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, U.K
| | - Aman Modi
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, U.K
| | - Ysobel R Baker
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, U.K
| | - Ewa Wȩgrzyn
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, U.K
| | - Diallo Traoré
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, U.K
| | - Przemyslaw Wanat
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, U.K
| | - Agnes E S Tyburn
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, U.K
| | - Arun Shivalingam
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, U.K
| | | | - Afaf H El-Sagheer
- Chemistry Research Laboratory, University of Oxford, 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
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, U.K
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10
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Perrone D, Marchesi E, Preti L, Navacchia ML. Modified Nucleosides, Nucleotides and Nucleic Acids via Click Azide-Alkyne Cycloaddition for Pharmacological Applications. Molecules 2021; 26:3100. [PMID: 34067312 PMCID: PMC8196910 DOI: 10.3390/molecules26113100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 11/17/2022] Open
Abstract
The click azide = alkyne 1,3-dipolar cycloaddition (click chemistry) has become the approach of choice for bioconjugations in medicinal chemistry, providing facile reaction conditions amenable to both small and biological molecules. Many nucleoside analogs are known for their marked impact in cancer therapy and for the treatment of virus diseases and new targeted oligonucleotides have been developed for different purposes. The click chemistry allowing the tolerated union between units with a wide diversity of functional groups represents a robust means of designing new hybrid compounds with an extraordinary diversity of applications. This review provides an overview of the most recent works related to the use of click chemistry methodology in the field of nucleosides, nucleotides and nucleic acids for pharmacological applications.
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Affiliation(s)
- Daniela Perrone
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy; (E.M.); (L.P.)
| | - Elena Marchesi
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy; (E.M.); (L.P.)
| | - Lorenzo Preti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy; (E.M.); (L.P.)
| | - Maria Luisa Navacchia
- Institute of Organic Synthesis and Photoreactivity National Research Council, 40129 Bologna, Italy
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11
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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: 131] [Impact Index Per Article: 43.7] [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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12
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Wang L, Huang S, Wang M, Liu ZY, Chen XM, Yang H. Synthesis and Self-Assembly of Alternating Heterodinucleoside Polytriazoles. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c02276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li Wang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Shuai Huang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Meng Wang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Zhi-Yang Liu
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Xu-Man Chen
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
| | - Hong Yang
- School of Chemistry and Chemical Engineering, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Institute of Advanced Materials, Southeast University, Nanjing, Jiangsu Province 211189, China
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13
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Langner HK, Jastrzebska K, Caruthers MH. Synthesis and Characterization of Thiophosphoramidate Morpholino Oligonucleotides and Chimeras. J Am Chem Soc 2020; 142:16240-16253. [PMID: 32866014 DOI: 10.1021/jacs.0c04335] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This Article outlines the optimized chemical synthesis and preliminary biochemical characterization of a new oligonucleotide analogue called thiophosphoramidate morpholinos (TMOs). Their rational design hinges upon integrating two well-studied pharmacophores, namely, phosphorothioates (pS) and morpholinos, to create morpholino-pS hybrid oligonucleotides. Our simple synthesis strategy enables the easy incorporation of morpholino-pS moieties and therapeutically relevant sugar modifications in tandem to create novel oligonucleotide (ON) analogues that are hitherto unexplored in the oligotherapeutics arena. Exclusively TMO-modified ONs demonstrate high stability toward 3'-exonuclease. Hybridization studies show that TMO chimeras consisting of alternating TMO and DNA-pS subunits exhibit higher binding affinity toward complementary RNA relative to the canonical DNA/RNA duplex (∼10 °C). Oligonucleotides that consist entirely of TMO linkages also show higher RNA binding affinity but do not recruit ribonuclease H1 (RNase H1). Chimeric TMO analogues demonstrate high gene silencing efficacy, comparable to that of a chimeric 2'-OMe-pS/pO control, during in vitro bioassay screens designed to evaluate their potential as microRNA inhibitors of hsa-miR-15b-5p in HeLa cells.
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Affiliation(s)
- Heera K Langner
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Katarzyna Jastrzebska
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Marvin H Caruthers
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
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14
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Searching for the ideal triazole: Investigating the 1,5-triazole as a charge neutral DNA backbone mimic. Tetrahedron 2020. [DOI: 10.1016/j.tet.2019.130914] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Tan Y, Li Y, Tang F. Nucleic Acid Aptamer: A Novel Potential Diagnostic and Therapeutic Tool for Leukemia. Onco Targets Ther 2019; 12:10597-10613. [PMID: 31824168 PMCID: PMC6900352 DOI: 10.2147/ott.s223946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/14/2019] [Indexed: 12/23/2022] Open
Abstract
Leukemia immunotherapy has been dominant via using synthetic antibodies to target cluster of differentiation (CD) molecules, nevertheless inevitable cytotoxicity and immunogenicity would limit its development. Recently, increasing reports have focused on nucleic acid aptamers, a class of high-affinity nucleic acid ligands. Aptamers purportedly serve as “chemical antibodies”, have negligible cytotoxicity and low immunogenicity, and would be widely applied for the therapy and diagnosis of various diseases, especially leukemia. In the preclinical applications, nucleic acid aptamers have displayed the augmented specificity and selectivity via recognizing targets on leukemia cells based on unique three-dimensional conformations. As small molecules with nucleic acid characteristics, aptamers need to be chemically modified to resist nuclease degradation, renal clearance and improve binding affinities. Moreover, aptamers can be linked with neoteric detection techniques to enhance sensitivity and selectivity of diagnosis and therapy. In this review, we summarized aptamers’ preparation, chemical modification and conjugation, and discussed the application of aptamers in diagnosis and treatment of leukemia through highly specifically recognizing target molecules. Significantly, the application prospect of aptamers in fusion genes would be introduced.
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Affiliation(s)
- Yuan Tan
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Yuejin Li
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Faqing Tang
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
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Korotkovs V, Reichenbach LF, Pescheteau C, Burley GA, Liskamp RMJ. Molecular Construction of Sulfonamide Antisense Oligonucleotides. J Org Chem 2019; 84:10635-10648. [PMID: 31379169 DOI: 10.1021/acs.joc.9b00941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
An efficient and scalable synthesis of new oligonucleotide monomers was developed for replacement of the phosphodiester backbone of RNA by a sulfonamide-containing backbone to enable construction of sulfonamide antisense oligonucleotides (SaASOs). It was shown that by employing these sulfonamide RNA (SaRNA) monomers, it was possible to synthesize oligomers in solution. The properties of a sulfonamide moiety replacement were evaluated by incorporation of a SaRNA-monomer into a DNA strand and performing thermal stability tests of the resulting DNA and RNA-double-strand hybrids. Although sulfonamide modification caused a decrease in melting temperature (Tm) of both hybrids, it was lower for the sulfonamide-containing DNA-RNA hybrid than that for the sulfonamide-containing DNA-DNA hybrid.
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Affiliation(s)
- Valerijs Korotkovs
- School of Chemistry , University of Glasgow , Joseph Black Building, University Avenue , Glasgow G12 8QQ , U.K
| | - Linus F Reichenbach
- Department of Pure and Applied Chemistry , University of Strathclyde , 295 Cathedral Street , Glasgow G1 1XL , U.K
| | - Clémentine Pescheteau
- School of Chemistry , University of Glasgow , Joseph Black Building, University Avenue , Glasgow G12 8QQ , U.K
| | - Glenn A Burley
- Department of Pure and Applied Chemistry , University of Strathclyde , 295 Cathedral Street , Glasgow G1 1XL , U.K
| | - Rob M J Liskamp
- School of Chemistry , University of Glasgow , Joseph Black Building, University Avenue , Glasgow G12 8QQ , U.K.,Department of Pharmaceutical Sciences, Faculty of Science , Utrecht University , P.O. Box 80082, NL-3508 TB Utrecht , The Netherlands
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17
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Bonacorso HG, Ketzer A, Rosa WC, Calheiro TP, Rodrigues MB, Zanatta N, Martins MA, Frizzo CP. Useful approach for O-functionalization of trifluoromethyl-substituted spirotetracyclic isoxazolines, and their application in the synthesis of 1,2,3-triazole derivatives. J Fluor Chem 2018. [DOI: 10.1016/j.jfluchem.2018.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Kumar P, El-Sagheer AH, Truong L, Brown T. Locked nucleic acid (LNA) enhances binding affinity of triazole-linked DNA towards RNA. Chem Commun (Camb) 2018; 53:8910-8913. [PMID: 28748236 PMCID: PMC5708354 DOI: 10.1039/c7cc05159j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
LNA improves the RNA-binding affinity and enzymatic stability of triazole-linked DNA.
Oligonucleotides containing internal triazole–3′-LNA linkages bind to complementary RNA with similar affinity and specificity to unmodified oligonucleotides, and significantly better than oligonucleotides containing triazole alone. In contrast LNA on the 5′-side of the triazole does not stabilise duplexes. Triazole–LNA confers great resistance towards enzymatic degradation relative to LNA alone.
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Affiliation(s)
- Pawan Kumar
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Lynda Truong
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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Goel R, Luxami V, Paul K. Synthesis of energy transfer cassettes via click and Suzuki–Miyaura cross coupling reactions. RSC Adv 2016. [DOI: 10.1039/c6ra07861c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Novel cassettes capable of energy transfer involving simple synthetic methodsviz., click reaction at C-8 position and palladium catalyzed Suzuki–Miyaura cross coupling at C-6 position of imidazo[1,2-a]pyrazine, have been represented.
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Affiliation(s)
- Richa Goel
- School of Chemistry and Biochemistry
- Thapar University
- Patiala-147004
- India
| | - Vijay Luxami
- School of Chemistry and Biochemistry
- Thapar University
- Patiala-147004
- India
| | - Kamaldeep Paul
- School of Chemistry and Biochemistry
- Thapar University
- Patiala-147004
- India
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