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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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2
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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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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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Fujino T, Suzuki T, Ooi T, Ikemoto K, Isobe H. Duplex-forming Oligonucleotide of Triazole-linked RNA. Chem Asian J 2019; 14:3380-3385. [PMID: 31478313 DOI: 10.1002/asia.201901112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 08/29/2019] [Indexed: 02/02/2023]
Abstract
An oligonucleotide of triazole-linked RNA (TL RNA) was synthesized by performing consecutive copper-catalyzed azide-alkyne cycloaddition reactions for elongation. The reaction conditions that had been optimized for the synthesis of 3-mer TL RNA were found to be inappropriate for longer oligonucleotides, and the conditions were reoptimized for the solid-phase synthesis of an 11-mer TL RNA oligonucleotide. Duplex formation of the 11-mer TL RNA oligonucleotide was examined with the complementary oligonucleotide of natural RNA to reveal the effects of the 2'-OH groups on the duplex stability.
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Affiliation(s)
- Tomoko Fujino
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
- Present address: Institute for Solid State Physics, The University of Tokyo, Kashiwanoha 5-1-5, Chiba, 277-8581, Japan
| | - Takeru Suzuki
- Department of Chemistry, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Tsugumi Ooi
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koki Ikemoto
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
- JST, ERATO Isobe Degenerate π-Integration Project, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroyuki Isobe
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
- JST, ERATO Isobe Degenerate π-Integration Project, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
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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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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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Sharma VK, Singh SK, Krishnamurthy PM, Alterman JF, Haraszti RA, Khvorova A, Prasad AK, Watts JK. Synthesis and biological properties of triazole-linked locked nucleic acid. Chem Commun (Camb) 2018; 53:8906-8909. [PMID: 28736781 DOI: 10.1039/c7cc04092j] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We have synthesized and studied the biological and biophysical properties of triazole-linked ribo and xylo locked nucleic acid (LNA). The combination of LNA with the Isobe triazole linkage gave high binding affinity when incorporated at the 3' or 5' termini of oligonucleotides, but low binding affinity at internal positions. Antisense oligonucleotides (ASOs) and siRNAs containing triazole dimers were highly active and nuclease resistant. Surprisingly, the xyloLNA-modified siRNA was the most active of the series.
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Affiliation(s)
- Vivek K Sharma
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Fujino T, Suzuki T, Okada K, Kogashi K, Yasumoto KI, Sogawa K, Isobe H. Chimeric RNA Oligonucleotides Incorporating Triazole-Linked Trinucleotides: Synthesis and Function as mRNA in Cell-Free Translation Reactions. J Org Chem 2016; 81:8967-8976. [PMID: 27579606 DOI: 10.1021/acs.joc.6b01618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A method for the synthesis of chimeric oligonucleotides was developed to incorporate purine nucleobases and multiple triazole linkers in natural, phosphate-linked structures of RNA. A solution-phase synthesis method for triazole-linked RNA oligomers via copper-catalyzed azide-alkyne cycloaddition reaction was optimized and tolerated purine nucleobases and protecting groups for further transformations. Three TLRNA trinucleotides with 5'-protected hydroxy and 3'-phosphoramidite groups were prepared, and one congener with a representative sequence was subjected to automated, solid-phase phosphoramidite synthesis. The synthesis allowed the efficient preparation of 13-mer chimeric RNA oligonucleotides with two triazole linkers, ten phosphate linkers and purine/pyrimidine nucleobases. The chimeric oligonucleotide was found applicable to a cell-free translation system as mRNA and provided the genetic code for dipeptide production.
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Affiliation(s)
- Tomoko Fujino
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Takeru Suzuki
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Koudai Okada
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Kanako Kogashi
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Ken-Ichi Yasumoto
- Department of Biomolecular Sciences, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Kazuhiro Sogawa
- Department of Biomolecular Sciences, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Hiroyuki Isobe
- JST ERATO, Isobe Degenerate π-Integration Project and Advanced Institute for Materials Research, Tohoku University , Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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