1
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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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2
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Sharma VK, Mangla P, Singh SK, Prasad AK. Triazole-linked Nucleic Acids: Synthesis, Therapeutics and Synthetic Biology Applications. Curr Org Synth 2024; 21:436-455. [PMID: 37138439 DOI: 10.2174/1570179420666230502123950] [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: 09/26/2022] [Revised: 02/27/2023] [Accepted: 03/10/2023] [Indexed: 05/05/2023]
Abstract
This article covers the triazole-linked nucleic acids where the triazole linkage (TL) replaces the natural phosphate backbone. The replacement is done at either a few selected linkages or all the phosphate linkages. Two triazole linkages, the four-atom TL1 and the six-atom TL2, have been discussed in detail. These triazole-modified oligonucleotides have found a wide range of applications, from therapeutics to synthetic biology. For example, the triazole-linked oligonucleotides have been used in the antisense oligonucleotide (ASO), small interfering RNA (siRNA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology as therapeutic agents. Due to the ease of the synthesis and a wide range of biocompatibility, the triazole linkage TL2 has been used to assemble a functional 300-mer DNA from alkyne- and azide-functionalized 100-mer oligonucleotides as well as an epigenetically modified variant of a 335 base-pair gene from ten short oligonucleotides. These outcomes highlight the potential of triazole-linked nucleic acids and open the doors for other TL designs and artificial backbones to fully exploit the vast potential of artificial nucleic acids in therapeutics, synthetic biology and biotechnology.
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Affiliation(s)
- Vivek K Sharma
- Department of Medicine, University of Massachusetts Chan Medical School, Mattapan, MA 02126, USA
- MassBiologics of the University of Massachusetts Chan Medical School, Mattapan, MA 02126, USA
| | - Priyanka Mangla
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sunil K Singh
- Department of Chemistry, Kirori Mal College, University of Delhi, Delhi, 110 007, India
| | - Ashok K Prasad
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi, 110 007, India
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3
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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4
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Fay EM, Newton A, Berney M, El‐Sagheer AH, Brown T, McGouran JF. Two-Step Validation Approach for Tools To Study the DNA Repair Enzyme SNM1A. Chembiochem 2023; 24:e202200756. [PMID: 36917742 PMCID: PMC10962688 DOI: 10.1002/cbic.202200756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023]
Abstract
We report a two-step validation approach to evaluate the suitability of metal-binding groups for targeting DNA damage-repair metalloenzymes using model enzyme SNM1A. A fragment-based screening approach was first used to identify metal-binding fragments suitable for targeting the enzyme. Effective fragments were then incorporated into oligonucleotides using the copper-catalysed azide-alkyne cycloaddition reaction. These modified oligonucleotides were recognised by SNM1A at >1000-fold lower concentrations than their fragment counterparts. The exonuclease SNM1A is a key enzyme involved in the repair of interstrand crosslinks, a highly cytotoxic form of DNA damage. However, SNM1A and other enzymes of this class are poorly understood, as there is a lack of tools available to facilitate their study. Our novel approach of incorporating functional fragments into oligonucleotides is broadly applicable to generating modified oligonucleotide structures with high affinity for DNA damage-repair enzymes.
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Affiliation(s)
- Ellen M. Fay
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Ailish Newton
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Mark Berney
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Afaf H. El‐Sagheer
- Department of ChemistryUniversity of OxfordMansfield RoadOX1 3TAOxfordUK
| | - Tom Brown
- Department of ChemistryUniversity of OxfordMansfield RoadOX1 3TAOxfordUK
| | - Joanna F. McGouran
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
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5
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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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6
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [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: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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7
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Tellurium-Modified Nucleosides, Nucleotides, and Nucleic Acids with Potential Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238379. [PMID: 36500495 PMCID: PMC9737395 DOI: 10.3390/molecules27238379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Tellurium was successfully incorporated into proteins and applied to protein structure determination through X-ray crystallography. However, studies on tellurium modification of DNA and RNA are limited. This review highlights the recent development of Te-modified nucleosides, nucleotides, and nucleic acids, and summarizes the main synthetic approaches for the preparation of 5-PhTe, 2'-MeTe, and 2'-PhTe modifications. Those modifications are compatible with solid-phase synthesis and stable during Te-oligonucleotide purification. Moreover, the ideal electronic and atomic properties of tellurium for generating clear isomorphous signals give Te-modified DNA and RNA great potential applications in 3D crystal structure determination through X-ray diffraction. STM study also shows that Te-modified DNA has strong topographic and current peaks, which immediately suggests potential applications in nucleic acid direct imaging, nanomaterials, molecular electronics, and diagnostics. Theoretical studies indicate the potential application of Te-modified nucleosides in cancer therapy.
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8
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An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides. Nat Commun 2022; 13:4036. [PMID: 35821218 PMCID: PMC9276774 DOI: 10.1038/s41467-022-31636-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotides that target mRNA have great promise as therapeutic agents for life-threatening conditions but suffer from poor bioavailability, hence high cost. As currently untreatable diseases come within the reach of oligonucleotide therapies, new analogues are urgently needed to address this. With this in mind we describe reduced-charge oligonucleotides containing artificial LNA-amide linkages with improved gymnotic cell uptake, RNA affinity, stability and potency. To construct such oligonucleotides, five LNA-amide monomers (A, T, C, 5mC and G), where the 3′-OH is replaced by an ethanoic acid group, are synthesised in good yield and used in solid-phase oligonucleotide synthesis to form amide linkages with high efficiency. The artificial backbone causes minimal structural deviation to the DNA:RNA duplex. These studies indicate that splice-switching oligonucleotides containing LNA-amide linkages and phosphorothioates display improved activity relative to oligonucleotides lacking amides, highlighting the therapeutic potential of this technology. Oligonucleotides targeting mRNA are promising therapeutic agents but suffer from poor bioavailability. Here, the authors develop reduced-charge oligonucleotides with artificial LNA-amide linkages with improved cell uptake and minimal structural deviation to the DNA:RNA duplex.
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9
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Aliouat H, Peng Y, Waseem Z, Wang S, Zhou W. Pure DNA scaffolded drug delivery systems for cancer therapy. Biomaterials 2022; 285:121532. [DOI: 10.1016/j.biomaterials.2022.121532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/04/2022] [Accepted: 04/15/2022] [Indexed: 02/07/2023]
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10
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Müggenburg F, Müller S. Azide-modified Nucleosides as Versatile Tools for Bioorthogonal Labeling and Functionalization. CHEM REC 2022; 22:e202100322. [PMID: 35189013 DOI: 10.1002/tcr.202100322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 02/06/2023]
Abstract
Azide-modified nucleosides are important building blocks for RNA and DNA functionalization by click chemistry based on azide-alkyne cycloaddition. This has put demand on synthetic chemistry to develop approaches for the preparation of azide-modified nucleoside derivatives. We review here the available methods for the synthesis of various nucleosides decorated with azido groups at the sugar residue or nucleobase, their incorporation into oligonucleotides and cellular RNAs, and their application in azide-alkyne cycloadditions for labelling and functionalization.
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Affiliation(s)
- Frederik Müggenburg
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
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11
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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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12
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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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13
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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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14
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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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15
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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16
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Liu EC, Topczewski JJ. Enantioselective Nickel-Catalyzed Alkyne-Azide Cycloaddition by Dynamic Kinetic Resolution. J Am Chem Soc 2021; 143:5308-5313. [PMID: 33798335 PMCID: PMC8130861 DOI: 10.1021/jacs.1c01354] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The triazole heterocycle has been widely adopted as an isostere for the amide bond. Many native amides are α-chiral, being derived from amino acids. This makes α-N-chiral triazoles attractive building blocks. This report describes the first enantioselective triazole synthesis that proceeds via nickel-catalyzed alkyne-azide cycloaddition (NiAAC). This dynamic kinetic resolution is enabled by a spontaneous [3,3]-sigmatropic rearrangement of the allylic azide. The 1,4,5-trisubstituted triazole products, derived from internal alkynes, are complementary to those commonly obtained by the related CuAAC reaction. Initial mechanistic experiments indicate that the NiAAC reaction proceeds through a monometallic Ni complex, which is distinct from the CuAAC manifold.
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Affiliation(s)
- En-Chih Liu
- Department of Chemistry, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Joseph J Topczewski
- Department of Chemistry, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
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17
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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18
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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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19
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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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20
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Gomes CB, Balaguez RA, Larroza A, Smaniotto TA, Domingues M, Casaril AM, Silva MS, Rodrigues OED, Savegnago L, Alves D. Organocatalysis in the Synthesis of 1,2,3‐Triazoyl‐zidovudine Derivatives: Synthesis and Preliminary Antioxidant Activity. ChemistrySelect 2020. [DOI: 10.1002/slct.202003355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Carolina B. Gomes
- LASOL-CCQFA Universidade Federal de Pelotas - UFPel P.O. Box 354 96010-900 Pelotas RS Brazil
| | - Renata A. Balaguez
- LASOL-CCQFA Universidade Federal de Pelotas - UFPel P.O. Box 354 96010-900 Pelotas RS Brazil
| | - Allya Larroza
- LASOL-CCQFA Universidade Federal de Pelotas - UFPel P.O. Box 354 96010-900 Pelotas RS Brazil
| | - Thiago A. Smaniotto
- Programa de Pós-Graduação em Biotecnologia (PPGB) Universidade Federal de Pelotas - UFPel Pelotas RS Brazil
| | - Micaela Domingues
- Programa de Pós-Graduação em Biotecnologia (PPGB) Universidade Federal de Pelotas - UFPel Pelotas RS Brazil
| | - Angela M. Casaril
- Programa de Pós-Graduação em Biotecnologia (PPGB) Universidade Federal de Pelotas - UFPel Pelotas RS Brazil
| | - Márcio S. Silva
- LASOL-CCQFA Universidade Federal de Pelotas - UFPel P.O. Box 354 96010-900 Pelotas RS Brazil
| | - Oscar E. D. Rodrigues
- LabSelen-NanoBio - Departamento de Química Universidade Federal de Santa Maria UFSM 97115-900 Santa Maria RS Brazil
| | - Lucielli Savegnago
- Programa de Pós-Graduação em Biotecnologia (PPGB) Universidade Federal de Pelotas - UFPel Pelotas RS Brazil
| | - Diego Alves
- LASOL-CCQFA Universidade Federal de Pelotas - UFPel P.O. Box 354 96010-900 Pelotas RS Brazil
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21
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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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22
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Maikhuri VK, Bohra K, Srivastava S, Kavita, Prasad AK. Click synthesis of N1-(β-D-ribofuranosyl)-C4-(coumarin-4″-yl)-1,2,3-triazoles. SYNTHETIC COMMUN 2019. [DOI: 10.1080/00397911.2019.1657150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Vipin K. Maikhuri
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Kapil Bohra
- Department of Chemistry, DDU College, University of Delhi, Delhi, India
| | - Smriti Srivastava
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Kavita
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Ashok K. Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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23
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Thorpe C, Epple S, Woods B, El-Sagheer AH, Brown T. Synthesis and biophysical properties of carbamate-locked nucleic acid (LNA) oligonucleotides with potential antisense applications. Org Biomol Chem 2019; 17:5341-5348. [PMID: 31099373 PMCID: PMC6686644 DOI: 10.1039/c9ob00691e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022]
Abstract
Antisense oligonucleotides (ASOs) are becoming important drugs for hard to treat diseases. Modifications to their DNA backbones are essential to inhibit degradation in vivo, but they can reduce binding affinity to RNA targets. To address this problem we have combined the enzymatic resistance of carbamate (CBM) DNA backbone analogues with the thermodynamic stability conferred by locked nucleic acid sugars (LNA). Using a dinucleotide phosphoramidite strategy and automated solid phase synthesis, we have synthesised a set of oligonucleotides modified with multiple LNA-CBM units. The LNA sugars restore binding affinity to RNA targets, and in this respect LNA position with respect to the CBM linkage is important. Oligonucleotides containing carbamate flanked on its 5'and 3'-sides by LNA form stable duplexes with RNA and unstable duplexes with DNA, which is desirable for antisense applications. Carbamate-LNA modified oligonucleotides also show increased stability in the presence of snake venom and foetal bovine serum compared to LNA or CBM backbones alone.
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Affiliation(s)
- Cameron Thorpe
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
| | - Sven Epple
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
| | - Benjamin Woods
- 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
.
- 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
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
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24
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Mangla P, Maity J, Rungta P, Verma V, Sanghvi YS, Prasad AK. Synthesis of 6′‐Methyl‐2′‐
O
,4′‐
C
‐methylene‐
α
‐L‐ ribofuranosyl‐pyrimidine Nucleosides. ChemistrySelect 2019. [DOI: 10.1002/slct.201900809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Priyanka Mangla
- Bioorganic Laboratory, Department of ChemistryUniversity of Delhi Delhi- 110 007 India
| | - Jyotirmoy Maity
- Bioorganic Laboratory, Department of ChemistryUniversity of Delhi Delhi- 110 007 India
| | - Pallavi Rungta
- Bioorganic Laboratory, Department of ChemistryUniversity of Delhi Delhi- 110 007 India
| | - Vineet Verma
- Bioorganic Laboratory, Department of ChemistryUniversity of Delhi Delhi- 110 007 India
| | | | - Ashok K. Prasad
- Bioorganic Laboratory, Department of ChemistryUniversity of Delhi Delhi- 110 007 India
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25
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Bao P, Meng N, Lv Y, Yue H, Li JS, Wei W. Selective assembly of N1- and N2-alkylated 1,2,3-triazoles via copper-catalyzed decarboxylative cycloaddition of alkynyl carboxylic acids with ethers and azidotrimethylsilane. Org Chem Front 2019. [DOI: 10.1039/c9qo01277j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An efficient and regiocontrolled method for the synthesis of various N1- and N2 alkylated 1,2,3-triazoles via copper-catalyzed decarboxylative cycloaddition of alkynyl carboxylic acids with ethers and azidotrimethylsilane.
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Affiliation(s)
- Pengli Bao
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- China
| | - Na Meng
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- China
| | - Yufen Lv
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- China
| | - Huilan Yue
- Qinghai Provincial Key Laboratory of Tibetan Medicine Research and Key Laboratory of Tibetan Medicine Research
- Northwest Institute of Plateau Biology
- Chinese Academy of Sciences
- Qinghai 810008
- China
| | - Jiang-Sheng Li
- School of Chemistry and food Engineering
- Changsha University of Science and Technology
- Changsha
- China
| | - Wei Wei
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- China
- Qinghai Provincial Key Laboratory of Tibetan Medicine Research and Key Laboratory of Tibetan Medicine Research
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26
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Kumar P, Truong L, Baker YR, El-Sagheer AH, Brown T. Synthesis, Affinity for Complementary RNA and DNA, and Enzymatic Stability of Triazole-Linked Locked Nucleic Acids (t-LNAs). ACS OMEGA 2018; 3:6976-6987. [PMID: 29978149 PMCID: PMC6028152 DOI: 10.1021/acsomega.8b01086] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 05/30/2018] [Indexed: 06/08/2023]
Abstract
Dinucleoside phosphoramidites containing a triazole internucleotide linkage flanked by locked nucleic acid (LNA) were synthesized and incorporated into oligonucleotides (ONs). ONs bearing both LNA and triazole at multiple sites were obtained and their biophysical properties including enzymatic stability and binding affinity for RNA and DNA targets were studied. t-LNAs with four incorporations of a dinucleoside monomer having LNA on either side of the triazole linkage bind to their RNA target with significantly higher affinity and greater specificity than unmodified oligonucleotides, and are remarkably stable to nuclease degradation. A similar but reduced effect on enzymatic stability and binding affinity was noted for LNA only on the 3'-side of the triazole linkage. Thus, by combining unnatural triazole linkages and LNA in one unit (t-LNA), we produced a promising class of ONs with reduced anionic charge and potential for antisense applications.
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Affiliation(s)
- Pawan Kumar
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Lynda Truong
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ysobel Ruth Baker
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Afaf Helmy El-Sagheer
- Department
of Chemistry, University of Oxford, 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, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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27
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Cao G, Kong J, Xing Z, Tang Y, Zhang X, Xu X, Kang Z, Fang X, Guan M. Rapid detection of CALR type 1 and type 2 mutations using PNA-LNA clamping loop-mediated isothermal amplification on a CD-like microfluidic chip. Anal Chim Acta 2018; 1024:123-135. [PMID: 29776538 DOI: 10.1016/j.aca.2018.04.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 01/18/2023]
Abstract
Bleeding and thrombosis represent common complications in myeloproliferative neoplasms (MPN) and significantly contribute to morbidity and mortality. Molecular markers, including CALR mutations, were considered not only as diagnostic markers, but also as risk factors for bleeding and thrombosis associated with MPN, especially for patients in remote primary hospitals. We sought to develop an easy-to-use assay for the rapid detection of CALR type 1 (CALR-1) and type 2 (CALR-2) mutations in Philadelphia chromosome-negative MPN patients. Peptide nucleic acid-locked nucleic acid (PNA-LNA) clamping loop-mediated isothermal amplification (LAMP) assays were established, which were integrated into a centrifugal compact disc (CD) microfluidic platform. A total of 158 clinical blood samples were tested simultaneously by this microfluidic platform and an in-house real time PCR assay. The detection performance of the LAMP arrays was validated and conflicting results were identified by Sanger sequencing. The results suggested that the LAMP methods we developed exhibited good sensitivity, specificity, and precision. By real time fluorescence assay the detection limit for CALR-1 and CALR-2 mutations could reach as low as 1% and 0.5% respectively, and 10% and 5% respectively by visual method. There were no nonspecific background amplifications among different detection systems. For the CALR-1 and CALR-2 LAMP detection systems, intra-batch CV values of 1% mutated plasmid were 10.56% and 10.51% respectively, and the inter-batch CV values were 19.55% and 18.39%, respectively. The products were all analyzed by melting curve analysis and electrophoresis followed by Sanger sequencing analysis, which were consistent with the database sequences. The microfluidic platform could complete rapid detection of CALR-1/2 mutations within 60 min. The results of clinical samples detected by our CD-like microfluidic chipLAMP assay and rtPCR assay suggested that 133 samples were CALR wild type, 15 were CALR-1 mutation type, and 9 were CALR-2 mutation type. The correlation coefficient value (Kendall's tau_b) of the two assays was 0.99. Interestingly, by the newly established detection platform, we were surprised to find that one patient of Chinese origin harbored both CALR-1 and CALR-2 mutations. This result was verified by Sanger sequencing analysis. The LAMP detection systems developed herein displayed good sensitivity, specificity, and stability. Additionally, the detection results could be directly judged by color changes of the reaction systems without any auxiliary equipment. Thus, the platform we developed has the potential of being widely used in remote and economically undeveloped areas in the future.
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Affiliation(s)
- Guojun Cao
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China; Shanghai Suxin Co. Ltd., PR China
| | - Zhifang Xing
- Department of Blood Transfusion, Minhang Hospital, Fudan University, Shanghai 201199, PR China
| | - Yigui Tang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China
| | - Xinju Zhang
- Center of Laboratory, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China
| | - Xiao Xu
- Center of Laboratory, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China
| | - Zhihua Kang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China; Shanghai Suxin Co. Ltd., PR China.
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China.
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28
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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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29
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Li L, Shen X, Liu Z, Norrbom M, Prakash TP, O'Reilly D, Sharma VK, Damha MJ, Watts JK, Rigo F, Corey DR. Activation of Frataxin Protein Expression by Antisense Oligonucleotides Targeting the Mutant Expanded Repeat. Nucleic Acid Ther 2018; 28:23-33. [PMID: 29341839 PMCID: PMC5790436 DOI: 10.1089/nat.2017.0703] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/28/2017] [Indexed: 12/31/2022] Open
Abstract
Friedreich's Ataxia (FA) is an inherited neurologic disorder caused by an expanded GAA repeat within intron 1 of the frataxin (FXN) gene that reduces expression of FXN protein. Agents that increase expression of FXN have the potential to alleviate the disease. We previously reported that duplex RNAs (dsRNAs) and antisense oligonucleotides (ASOs) complementary to the GAA repeat could enhance expression of FXN protein. We now explore the potential of a diverse group of chemically modified dsRNAs and ASOs to define the breadth of repeat-targeted synthetic nucleic acids as a platform for therapeutic development for FA. ASOs and dsRNAs can activate FXN protein expression in FA patient-derived cell lines that possess varied numbers of GAA repeats. Increased FXN protein expression was achieved by ASOs incorporating diverse chemical modifications with low nanomolar potencies, suggesting substantial flexibility in choosing compounds for further chemical optimization and animal studies. Our data encourage further development of ASOs as agents to treat FA.
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Affiliation(s)
- Liande Li
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| | - Xiulong Shen
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| | - Zhongtian Liu
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| | | | | | - Daniel O'Reilly
- 4 Department of Chemistry, McGill University , Montreal, Canada
| | - Vivek K Sharma
- 5 RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Masad J Damha
- 4 Department of Chemistry, McGill University , Montreal, Canada
| | - Jonathan K Watts
- 5 RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Frank Rigo
- 3 Ionis Pharmaceuticals , Carlsbad, California
| | - David R Corey
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
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30
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Kumar N, Ansari MY, Kant R, Kumar A. Copper-catalyzed decarboxylative regioselective synthesis of 1,5-disubstituted 1,2,3-triazoles. Chem Commun (Camb) 2018; 54:2627-2630. [DOI: 10.1039/c7cc09934g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A copper-catalyzed decarboxylative regioselective protocol for the synthesis of 1,5-disubstituted 1,2,3-triazoles via direct annulation of cinnamic acids with aryl azides has been developed. This is the first example of 1,5-disubstituted 1,2,3-triazoles using Cu(ii) as the catalyst, which were generally synthesized using a ruthenium(ii) catalyst.
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Affiliation(s)
- Navaneet Kumar
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow 226031
- India
| | - Mohd Yeshab Ansari
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow 226031
- India
| | - Ruchir Kant
- Molecular and Structural Biology
- CSIR-Central Drug Research Institute
- Lucknow 226031
- India
| | - Atul Kumar
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow 226031
- India
- Academy of Scientific and Innovative Research
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