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Desaulniers JP, Tsubaki K, Hammill ML, Kitamura M, Okauchi T. Synthesis of Dinucleotide Non-Symmetrical Triester Phosphate Phosphoramidites and Their Incorporation Within Oligonucleotides. Curr Protoc 2023; 3:e784. [PMID: 37219041 DOI: 10.1002/cpz1.784] [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] [Indexed: 05/24/2023]
Abstract
In this protocol article, the synthesis of dinucleotide non-symmetrical triester phosphate phosphoramidites will be highlighted. Specifically, we use a selective transesterification starting with tris(2,2,2-trifluoroethyl) phosphate to afford a dinucleotide derivative phosphate ester. Substitution of the final trifluoroethyl group with various alcohols affords a dinucleotide triester phosphate with a hydrophobic group, which can then be deprotected and converted to a phosphoramidite for incorporation within oligonucleotides. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of a DMT- and TBS-protected unsymmetrical dinucleotide Basic Protocol 2: Synthesis of a DMT-protected unsymmetrical dinucleotide phosphotriester monoalcohols Basic Protocol 3: Synthesis of DMT-protected phenylethyl phosphotriester dinucleotide phosphoramidites Basic Protocol 4: Synthesis, purification, and characterization of RNAs containing triester phosphate modifications.
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Affiliation(s)
- Jean-Paul Desaulniers
- University of Ontario Institute of Technology, Faculty of Science, Oshawa, Ontario, Canada
| | - Kouta Tsubaki
- University of Ontario Institute of Technology, Faculty of Science, Oshawa, Ontario, Canada
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, Tobata, Kitakyushu, Japan
| | - Matthew L Hammill
- University of Ontario Institute of Technology, Faculty of Science, Oshawa, Ontario, Canada
| | - Mitsuru Kitamura
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, Tobata, Kitakyushu, Japan
| | - Tatsuo Okauchi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, Tobata, Kitakyushu, Japan
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Varley A, Desaulniers JP. Synthesis of 5’-fluorophosphate-modified short-interfering RNAs. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 42:358-370. [PMID: 36408961 DOI: 10.1080/15257770.2022.2148693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have developed an improved scheme for the synthesis of a mono-fluorinated phosphoramidite for the 5'-modification of nucleic acids using standard phosphoramidite chemistry. We describe the first report of a phosphofluoridate modified siRNA strand and have evaluated C18 HPLC for purification of modified strands from unreacted siRNA strands. Lastly, the biological activity of the high purity siRNA strands, when placed on the sense and/or antisense strand, was evaluated to assess the impact of 5' phosphofluoridate modifications on siRNA activity.
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Affiliation(s)
- Andrew Varley
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Canada
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Fan Y, Yang Z. Inhaled siRNA Formulations for Respiratory Diseases: From Basic Research to Clinical Application. Pharmaceutics 2022; 14:1193. [PMID: 35745766 PMCID: PMC9227582 DOI: 10.3390/pharmaceutics14061193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/10/2022] Open
Abstract
The development of siRNA technology has provided new opportunities for gene-specific inhibition and knockdown, as well as new ideas for the treatment of disease. Four siRNA drugs have already been approved for marketing. However, the instability of siRNA in vivo makes systemic delivery ineffective. Inhaled siRNA formulations can deliver drugs directly to the lung, showing great potential for treating respiratory diseases. The clinical applications of inhaled siRNA formulations still face challenges because effective delivery of siRNA to the lung requires overcoming the pulmonary and cellular barriers. This paper reviews the research progress for siRNA inhalation formulations for the treatment of various respiratory diseases and summarizes the chemical structural modifications and the various delivery systems for siRNA. Finally, we conclude the latest clinical application research for inhaled siRNA formulations and discuss the potential difficulty in efficient clinical application.
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Affiliation(s)
| | - Zhijun Yang
- School of Chinese Medicine, Hong Kong Baptist University, 224 Waterloo Rd., Kowloon Tong, Hong Kong, China;
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Hammill ML, Tsubaki K, Salim L, Varley AJ, Giorgees I, Kitamura M, Okauchi T, Desaulniers JP. SiRNAs with Neutral Phosphate Triester Hydrocarbon Tails Exhibit Carrier-Free Gene-Silencing Activity. ACS Med Chem Lett 2022; 13:695-700. [PMID: 35450364 PMCID: PMC9014433 DOI: 10.1021/acsmedchemlett.2c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/08/2022] [Indexed: 12/23/2022] Open
Abstract
Short interfering RNAs (siRNAs) show promise as gene-silencing therapeutics, but their cellular uptake remains a challenge. We have recently shown the synthesis of siRNAs bearing a single neutral phenylethyl phosphotriester linkage within the sense strand. Here, we report the synthesis of siRNAs bearing three different hydrophobic phosphate triester linkages at key positions within the sense strand and assess their gene silencing in the absence of a transfection carrier. The best siRNAs bearing hydrophobic phosphate triester tails were not aromatic and exhibited effective gene silencing (IC50 ≈ 56-141 nM), whereas the aromatic derivative with three hydrophobic tails did not exhibit carrier-free gene silencing.
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Affiliation(s)
- Matthew L. Hammill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
| | - Kouta Tsubaki
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu 804-8550, Japan
| | - Lidya Salim
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
| | - Andrew J. Varley
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
| | - Ifrodet Giorgees
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
| | - Mitsuru Kitamura
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu 804-8550, Japan
| | - Tatsuo Okauchi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu 804-8550, Japan
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario L1G 0C5, Canada
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Shiohama Y, Fujita R, Sonokawa M, Hisano M, Kotake Y, Krstic-Demonacos M, Demonacos C, Kashiwazaki G, Kitayama T, Fujii M. Elimination of Off-Target Effect by Chemical Modification of 5′-End of Small Interfering RNA. Nucleic Acid Ther 2022; 32:438-447. [DOI: 10.1089/nat.2021.0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yasuo Shiohama
- Environmental and Biological Information Group, Tropical Biosphere Research Centre, University of the Ryukyus, Nishihara, Japan
| | - Ryosuke Fujita
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Maika Sonokawa
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Masaaki Hisano
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Yojiro Kotake
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Marija Krstic-Demonacos
- School of Science, Engineering and Environment, University of Salford, Salford, United Kingdom
| | - Constantinos Demonacos
- Division of Pharmacy and Optometry, Faculty of Biology Medicine and Health, School of Health Science, University of Manchester, Manchester, United Kingdom
| | - Gengo Kashiwazaki
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Takashi Kitayama
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Masayuki Fujii
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
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Hammill ML, Salim L, Tsubaki K, Varley AJ, Kitamura M, Okauchi T, Desaulniers JP. Building siRNAs with Cubes: Synthesis and Evaluation of Cubane-Modified siRNAs. Chembiochem 2021; 22:2981-2985. [PMID: 34319643 DOI: 10.1002/cbic.202100334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/27/2021] [Indexed: 11/10/2022]
Abstract
Cubane molecules hold great potential for medicinal chemistry applications due to their inherent stability and low toxicity. In this study, we report the synthesis of a cubane derivative phosphoramidite for the incorporation of cubane into small interfering RNAs (siRNAs). Synthetic siRNAs rely on chemical modifications to improve their pharmacokinetic profiles. However, they are still able to mediate sequence-specific gene silencing via the endogenous RNA interference pathway. We designed a library of siRNAs bearing cubane at different positions within the sense and antisense strands. All siRNAs showed excellent gene-silencing activity, with IC50 values ranging from 45.4 to 305 pM. Incorporating the cubane modification in both the sense and antisense strand led to viable duplexes with good biological activity. To the best of our knowledge, this is the first report of siRNAs bearing a cubane derivative within the backbone.
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Affiliation(s)
- Matthew L Hammill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario, L1G 0C5, Canada
| | - Lidya Salim
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario, L1G 0C5, Canada
| | - Kouta Tsubaki
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario, L1G 0C5, Canada.,Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu, 804-8550, Japan
| | - Andrew J Varley
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario, L1G 0C5, Canada
| | - Mitsuru Kitamura
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu, 804-8550, Japan
| | - Tatsuo Okauchi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu, 804-8550, Japan
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario, L1G 0C5, Canada
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Varley AJ, Desaulniers JP. Chemical strategies for strand selection in short-interfering RNAs. RSC Adv 2021; 11:2415-2426. [PMID: 35424193 PMCID: PMC8693850 DOI: 10.1039/d0ra07747j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Therapeutic small interfering RNAs (siRNAs) are double stranded RNAs capable of potent and specific gene silencing through activation of the RNA interference (RNAi) pathway. The potential of siRNA drugs has recently been highlighted by the approval of multiple siRNA therapeutics. These successes relied heavily on chemically modified nucleic acids and their impact on stability, delivery, potency, and off-target effects. Despite remarkable progress, clinical trials still face failure due to off-target effects such as off-target gene dysregulation. Each siRNA strand can downregulate numerous gene targets while also contributing towards saturation of the RNAi machinery, leading to the upregulation of miRNA-repressed genes. Eliminating sense strand uptake effectively reduces off-target gene silencing and helps limit the disruption to endogenous regulatory mechanisms. Therefore, our understanding of strand selection has a direct impact on the success of future siRNA therapeutics. In this review, the approaches used to improve strand uptake are discussed and effective methods are summarized.
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Affiliation(s)
- Andrew J Varley
- Faculty of Science, University of Ontario Institute of Technology Oshawa Ontario L1G 0C5 Canada +1 905 721 3304 +1 905 721 8668 (ext. 3621)
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology Oshawa Ontario L1G 0C5 Canada +1 905 721 3304 +1 905 721 8668 (ext. 3621)
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