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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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Tu T, Huan S, Ke G, Zhang X. Functional Xeno Nucleic Acids for Biomedical Application. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-021-2186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Tu T, Huan S, Ke G, Zhang X. Functional Xeno Nucleic Acids for Biomedical Application. Chem Res Chin Univ 2022:1-7. [PMID: 35814030 PMCID: PMC9253239 DOI: 10.1007/s40242-022-2186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/26/2022] [Indexed: 11/26/2022]
Abstract
Functional nucleic acids(FNAs) refer to a type of oligonucleotides with functions over the traditional genetic roles of nucleic acids, which have been widely applied in screening, sensing and imaging fields. However, the potential application of FNAs in biomedical field is still restricted by the unsatisfactory stability, biocompatibility, biodistribution and immunity of natural nucleic acids(DNA/RNA). Xeno nucleic acids(XNAs) are a kind of nucleic acid analogues with chemically modified sugar groups that possess improved biological properties, including improved biological stability, increased binding affinity, reduced immune responses, and enhanced cell penetration or tissue specificity. In the last two decades, scientists have made great progress in the research of functional xeno nucleic acids, which makes it an emerging attractive biomedical application material. In this review, we summarized the design of functional xeno nucleic acids and their applications in the biomedical field.
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Affiliation(s)
- Tingting Tu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Shuangyan Huan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiaobing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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Wang F, Li P, Chu HC, Lo PK. Nucleic Acids and Their Analogues for Biomedical Applications. BIOSENSORS 2022; 12:93. [PMID: 35200353 PMCID: PMC8869748 DOI: 10.3390/bios12020093] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 05/07/2023]
Abstract
Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.
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Affiliation(s)
- Fei Wang
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pan Li
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Hoi Ching Chu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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De Fazio AF, Misatziou D, Baker YR, Muskens OL, Brown T, Kanaras AG. Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly. Chem Soc Rev 2021; 50:13410-13440. [PMID: 34792047 PMCID: PMC8628606 DOI: 10.1039/d1cs00632k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 12/26/2022]
Abstract
The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.
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Affiliation(s)
- Angela F De Fazio
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Doxi Misatziou
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Ysobel R Baker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Otto L Muskens
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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Spriha SE, Rahman FI, Rahman SMA. Synthesis, in vivo and in silico analgesic and anti-inflammatory studies of α-D-ribofuranose derivatives. Saudi Pharm J 2021; 29:981-991. [PMID: 34588844 PMCID: PMC8463446 DOI: 10.1016/j.jsps.2021.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/16/2021] [Indexed: 11/29/2022] Open
Abstract
Five α-D-ribofuranose analogues (2, 3, 4, 5 and 6) were synthesized in good yields from 3-O-benzyl-4-C-(hydroxymethyl)-1, 2-O-isopropylidene-α-D-ribofuranose (1). The synthesized compounds were then subjected to analgesic, anti-inflammatory, antimicrobial and antioxidant assays. Compound 3 demonstrated 79.74% (P < 0.001) writhing inhibition and highest reaction time of 2.55 ± 0.13 min (P < 0.001) after 30 min of oral administration in peripheral and central analgesic assay, respectively, at 50 mg/kg dose. Compound 2 and 6 exhibited significant anti-inflammatory activity at 100 mg/kg dose with paw edema inhibition of 91.15% (P < 0.001) and 95.13% (P < 0.001), respectively, in 4th hour. The synthesized analogues did not show notable antioxidant and antibacterial properties. Molecular docking study revealed higher binding affinity of −8.1 kcal/mol and −8.9 kcal/mol of compound 3 towards cyclooxygenase-1 and phospholipase A2, respectively, compared to −7.7 and −7.6 kcal/mol respectively for corresponding native ligands. Compound 2 demonstrated binding affinity of −9.1 kcal/mol towards interleukin-1 receptor-associated kinase-4 compared to −8.7 kcal/mol of the native ligand. The molecular properties related to drug likeness of compounds were found to be within acceptable range. Synthesized D-ribofuranose analogues demonstrated promising analgesic and anti-inflammatory activities and further development may lead to new potent analgesic and anti-inflammatory agents.
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Affiliation(s)
- Sabiha Enam Spriha
- Department of Clinical Pharmacy & Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - Fahad Imtiaz Rahman
- Department of Clinical Pharmacy & Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - S M Abdur Rahman
- Department of Clinical Pharmacy & Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
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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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Krishna H, Jastrzebska K, Caruthers M. Exploring site-specific activation of bis-N,N'-dialkylaminophosphordiamidites and the synthesis of morpholinophosphoramidate oligonucleotides. FEBS Lett 2019; 593:1459-1467. [PMID: 31206627 DOI: 10.1002/1873-3468.13492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 11/05/2022]
Abstract
Morpholinos are six-membered rings that may provide higher conformational rigidity when incorporated into an oligonucleotide (ODN) backbone. Phosphorodiamidate morpholinos are chemically modified ODNs containing morpholinos in place of 2'-deoxyribose moieties throughout their backbone and have garnered much interest in recent years due to their ability to function as highly effective steric blockers in exon skipping therapy. To further explore the biophysical and biological properties of ODNs derived from morpholino nucleosides, we have replaced the 2'-deoxyribonucleotides of phosphodiester DNA with morpholinonucleotides to generate phosphoramidate ODNs. Here, we evaluate the mechanistic pathways observed during the solution-phase synthesis of morpholinonucleoside phosphoramidites, solid-phase synthesis of morpholinonucleotide phosphoramidates of mA, mG, mC and mT (prefix 'm' represents morpholino) and our first attempts directed at the solid-phase synthesis of chimeric DNA-phosphoramidate ODNs, as well as fully modified 22-mer phosphoramidate ODNs.
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