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Gupta R, Salave S, Rana D, Karunakaran B, Butreddy A, Benival D, Kommineni N. Versatility of Liposomes for Antisense Oligonucleotide Delivery: A Special Focus on Various Therapeutic Areas. Pharmaceutics 2023; 15:pharmaceutics15051435. [PMID: 37242677 DOI: 10.3390/pharmaceutics15051435] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Nucleic acid therapeutics, specifically antisense oligonucleotides (ASOs), can effectively modulate gene expression and protein function, leading to long-lasting curative effects. The hydrophilic nature and large size of oligonucleotides present translational challenges, which have led to the exploration of various chemical modifications and delivery systems. The present review provides insights into the potential role of liposomes as a drug delivery system for ASOs. The potential benefits of liposomes as an ASO carrier, along with their method of preparation, characterization, routes of administration, and stability aspects, have been thoroughly discussed. A novel perspective in terms of therapeutic applications of liposomal ASO delivery in several diseases such as cancer, respiratory disease, ophthalmic delivery, infectious diseases, gastrointestinal disease, neuronal disorders, hematological malignancies, myotonic dystrophy, and neuronal disorders remains the major highlights of this review.
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Affiliation(s)
- Raghav Gupta
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, India
| | - Sagar Salave
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, India
| | - Dhwani Rana
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, India
| | - Bharathi Karunakaran
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, India
| | - Arun Butreddy
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, Oxford, MS 38677, USA
| | - Derajram Benival
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, India
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Seth PP, Swayze EE. Unnatural Nucleoside Analogs for Antisense Therapy. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1002/9783527676545.ch12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Seth PP, Jazayeri A, Yu J, Allerson CR, Bhat B, Swayze EE. Structure Activity Relationships of α-L-LNA Modified Phosphorothioate Gapmer Antisense Oligonucleotides in Animals. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e47. [PMID: 23344239 PMCID: PMC3499693 DOI: 10.1038/mtna.2012.34] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the structure activity relationships of short 14-mer phosphorothioate gapmer antisense oligonucleotides (ASOs) modified with α-L-locked nucleic acid (LNA) and related modifications targeting phosphatase and tensin homologue (PTEN) messenger RNA in mice. α-L-LNA represents the α-anomer of enantio-LNA and modified oligonucleotides show LNA like binding affinity for complementary RNA. In contrast to sequence matched LNA gapmer ASOs which showed elevations in plasma alanine aminotransferase (ALT) levels indicative of hepatotoxicity, gapmer ASOs modified with α-L-LNA and related analogs in the flanks showed potent downregulation of PTEN messenger RNA in liver tissue without producing elevations in plasma ALT levels. However, the α-L-LNA ASO showed a moderate dose-dependent increase in liver and spleen weights suggesting a higher propensity for immune stimulation. Interestingly, replacing α-L-LNA nucleotides in the 3′- and 5′-flanks with R-5′-Me-α-L-LNA but not R-6′-Me- or 3′-Me-α-L-LNA nucleotides, reversed the drug induced increase in organ weights. Examination of structural models of dinucleotide units suggested that the 5′-Me group increases steric bulk in close proximity to the phosphorothioate backbone or produces subtle changes in the backbone conformation which could interfere with recognition of the ASO by putative immune receptors. Our data suggests that introducing steric bulk at the 5′-position of the sugar-phosphate backbone could be a general strategy to mitigate the immunostimulatory profile of oligonucleotide drugs. In a clinical setting, proinflammatory effects manifest themselves as injection site reactions and flu-like symptoms. Thus, a mitigation of these effects could increase patient comfort and compliance when treated with ASOs.
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Murray S, Ittig D, Koller E, Berdeja A, Chappell A, Prakash TP, Norrbom M, Swayze EE, Leumann CJ, Seth PP. TricycloDNA-modified oligo-2'-deoxyribonucleotides reduce scavenger receptor B1 mRNA in hepatic and extra-hepatic tissues--a comparative study of oligonucleotide length, design and chemistry. Nucleic Acids Res 2012; 40:6135-43. [PMID: 22467214 PMCID: PMC3401458 DOI: 10.1093/nar/gks273] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We report the evaluation of 20-, 18-, 16- and 14-mer phosphorothioate (PS)-modified tricycloDNA (tcDNA) gapmer antisense oligonucleotides (ASOs) in Tm, cell culture and animal experiments and compare them to their gap-matched 20-mer 2′-O-methoxyethyl (MOE) and 14-mer 2′,4′-constrained ethyl (cEt) counterparts. The sequence-matched 20-mer tcDNA and MOE ASOs showed similar Tm and activity in cell culture under free-uptake and cationic lipid-mediated transfection conditions, while the 18-, 16- and 14-mer tcDNA ASOs were moderate to significantly less active. These observations were recapitulated in the animal experiments where the 20-mer tcDNA ASO formulated in saline showed excellent activity (ED50 3.9 mg/kg) for reducing SR-B1 mRNA in liver. The tcDNA 20-mer ASO also showed better activity than the MOE 20-mer in several extra-hepatic tissues such as kidney, heart, diaphragm, lung, fat, gastrocnemius and quadriceps. Interestingly, the 14-mer cEt ASO showed the best activity in the animal experiments despite significantly lower Tm and 5-fold reduced activity in cell culture relative to the 20-mer tcDNA and MOE-modified ASOs. Our experiments establish tcDNA as a useful modification for antisense therapeutics and highlight the role of chemical modifications in influencing ASO pharmacology and pharmacokinetic properties in animals.
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Affiliation(s)
- Sue Murray
- Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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Efimov VA, Aralov AV, Chakhmakhcheva OG. Synthesis of oligoribonucleotides containing 2'-O-methoxymethyl group by the phosphotriester method. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:565-76. [PMID: 21888547 DOI: 10.1080/15257770.2011.586255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
An effective procedure for the synthesis of ribonucleotide monomers containing a 2 '-О-methoxymethyl-modifying group was developed. These monomers were used for the synthesis of RNA fragments by the solid-phase phosphotriester method under O-nucleophilic intramolecular catalysis. The properties of 2 '-О-methoxymethyl-containing oligoribonucleotides were examined.
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Affiliation(s)
- Vladimir A Efimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Prakash TP, Siwkowski A, Allerson CR, Migawa MT, Lee S, Gaus HJ, Black C, Seth PP, Swayze EE, Bhat B. Antisense oligonucleotides containing conformationally constrained 2',4'-(N-methoxy)aminomethylene and 2',4'-aminooxymethylene and 2'-O,4'-C-aminomethylene bridged nucleoside analogues show improved potency in animal models. J Med Chem 2010; 53:1636-50. [PMID: 20108935 DOI: 10.1021/jm9013295] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To identify chemistries and strategies to improve the potency of MOE second generation ASOs, we have evaluated gapmer antisense oligonucleotides containing BNAs having N-O bonds. These modifications include N-MeO-amino BNA, N-Me-aminooxy BNA, 2',4'-BNA(NC)[NMe], and 2',4'-BNA(NC) bridged nucleoside analogues. These modifications provided increased thermal stability and improved in vitro activity compared to the corresponding ASO containing the MOE modification. Additionally, ASOs containing N-MeO-amino BNA, N-Me-aminooxy BNA, and 2',4'-BNA(NC)[NMe] modifications showed improved in vivo activity (>5-fold) compared to MOE ASO. Importantly, toxicity parameters, such as AST, ALT, liver, kidney, and body weights, were found to be normal for N-MeO-amino BNA, N-Me-aminooxy BNA, and 2',4'-BNA(NC)[NMe] ASO treated animals. The data generated in these experiments suggest that N-MeO-amino BNA, N-Me-aminooxy BNA, and 2',4'-BNA(NC)[NMe] are useful modifications for applications in both antisense and other oligonucleotide based drug discovery efforts.
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Affiliation(s)
- Thazha P Prakash
- Department of Medicinal Chemistry and Antisense Core Research, Isis Pharmaceuticals Inc., 1896 Rutherford Road, Carlsbad, California 92008, USA.
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Cook PD. A brief history, status, and perspective of modified oligonucleotides for chemotherapeutic applications. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.1. [PMID: 18428848 DOI: 10.1002/0471142700.nc0401s00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The advent of rapid and efficient methods of oligonucleotide synthesis has allowed the design of modified oligonucleotides that are complementary to specific nucleotide sequences in mRNA targets. Such modified oligonucleotides can be used to disrupt the flow of genetic information from transcribed mRNAs to proteins. This antisense strategy has been used to develop therapeutic oligonucleotides against cancer and various infectious diseases in humans. This overview reports recent advances in the application of oligonucleotides as drug candidates, describes the relationship between oligonucleotide modifications and their therapeutic profiles, and provides general guidelines for enhancing oligonucleotide drug properties.
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Affiliation(s)
- P D Cook
- Isis Pharmaceuticals, Carlsbad, California, USA
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Swayze EE, Siwkowski AM, Wancewicz EV, Migawa MT, Wyrzykiewicz TK, Hung G, Monia BP, Bennett CF. Antisense oligonucleotides containing locked nucleic acid improve potency but cause significant hepatotoxicity in animals. Nucleic Acids Res 2006; 35:687-700. [PMID: 17182632 PMCID: PMC1802611 DOI: 10.1093/nar/gkl1071] [Citation(s) in RCA: 310] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A series of antisense oligonucleotides (ASOs) containing either 2′-O-methoxyethylribose (MOE) or locked nucleic acid (LNA) modifications were designed to investigate whether LNA antisense oligonucleotides (ASOs) have the potential to improve upon MOE based ASO therapeutics. Some, but not all, LNA containing oligonucleotides increased potency for reducing target mRNA in mouse liver up to 5-fold relative to the corresponding MOE containing ASOs. However, they also showed profound hepatotoxicity as measured by serum transaminases, organ weights and body weights. This toxicity was evident for multiple sequences targeting three different biological targets, as well as in mismatch control sequences having no known mRNA targets. Histopathological evaluation of tissues from LNA treated animals confirmed the hepatocellular involvement. Toxicity was observed as early as 4 days after a single administration. In contrast, the corresponding MOE ASOs showed no evidence for toxicity while maintaining the ability to reduce target mRNA. These studies suggest that while LNA ASOs have the potential to improve potency, they impose a significant risk of hepatotoxicity.
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Affiliation(s)
- Eric E Swayze
- Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad, CA 92008, USA.
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Taj SAS, Gurumurthy P, Suresh R, Narayanan S, Suman Meenakshi S, Sanghvi YS. Process development for the synthesis of 5'-O-(4,4'-dimethoxytrityl)-N2-isobutyryl-2'-O-(2-methoxyethyl)-guanosine--a potential precursor for the second generation antisense oligonucleotides: an improved process for the preparation of 2'-O-alkyl-2,6-diaminopurine riboside. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1327-30. [PMID: 14565410 DOI: 10.1081/ncn-120022957] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An efficient four step process for the preparation of 5'-O-(4,4'-dimethoxytrityl)-N2-isobutyryl-2'-O-(2-methoxyethyl)-guanosine 1 was developed. Direct 2'-O-alkylation of 2,6-diaminopurine riboside 2 was accomplished via inexpensive and commercially available reagents such as KOH, DMSO and alkyl halides at room temperature in 4-6 hrs. Pure 2'-O-(2-methoxyethyl)-DAPR 3 was isolated by crystallization from methanol. Enzymatic deamination of 3 followed by selective N2-isobutyrylation and 5'-O-dimethoxytritylation furnished desired 1 in high yield and purity. Fully optimized four step synthetic process has been scaled up to the pilot plant level.
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Garcı́a J, Fernández S, Ferrero M, Sanghvi YS, Gotor V. Novel enzymatic synthesis of levulinyl protected nucleosides useful for solution phase synthesis of oligonucleotides. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/j.tetasy.2003.07.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Prakash TP, Kawasaki AM, Johnston JF, Graham MJ, Condon TP, Manoharan M. Antisense properties of 2'-O-dimethylaminooxyethyl (2'-O-DMAOE) oligonucleotides. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:829-32. [PMID: 11563125 DOI: 10.1081/ncn-100002439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Antisense oligonucleotides with 2'-O-(2-[N,N-dimethyl)aminooxy]ethyl) or (2'-O-DMAOE) modification were synthesized and evaluated for nuclease resistance and pharmacology both in vitro and in vivo. This modification exhibits very high nuclease resistance and efficacy in various biological (ICAM-1, C-raf and PKC-alpha) targets.
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Affiliation(s)
- T P Prakash
- Isis Pharmaceuticals, 2292 Faraday Ave., Carlsbad, California 92008, USA
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Fennell DA, Cotter FE. A dynamical systems model to simulate the perturbation kinetics of gene expression by antisense oligonucleotides. J Theor Biol 2001; 209:103-12. [PMID: 11237574 DOI: 10.1006/jtbi.2000.2250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Antisense oligonucleotides owe their efficacy to an ability to induce RNase H-dependent suppression of RNA translation, for sufficient time to allow physiological proteolysis. The magnitude and time delay preceding the protein nadir concentration determine the extent and timing of maximum antisense oligonucleotide activity. Antisense oligonucleotide degradation underlies reversal of RNA downregulation. The kinetics of protein downregulation is therefore determined by the complex interaction of both ligand chemistry (nuclease stability, affinity and RNase H activation), and gene expression kinetics. Optimization of antisense oligonucleotide efficacy and experimental design requires understanding of these interactions. The kinetics of protein and RNA downregulation have therefore been simulated by analysing a two-compartment kinetic model incorporating RNase H-dependent transcript degradation. The system of nonlinear differential equations describing this model was solved numerically using Runge-Kutte integration. The timecourse solutions corresponding to the four state variables (RNA, protein, antisense/RNA heteroduplex and antisense oligonucleotide), were determined simultaneously. This allowed systematic in silico examination of the consequences of altering variables such as oligonucleotide concentration, affinity, and stability, or the scheduling of multiple transfections on RNA and protein perturbations. By providing a tool for examining antisense oligonucleotide action theoretically, this heuristic model should facilitate both the rational design and interpretation of antisense experiments.
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Affiliation(s)
- D A Fennell
- Department of Experimental Haematology, St Bartholomew's and The Royal London School of Medicine, Turner Street, London, E1 2AD, UK
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Cook PD. Making drugs out of oligonucleotides: a brief review and perspective. NUCLEOSIDES & NUCLEOTIDES 1999; 18:1141-62. [PMID: 10474215 DOI: 10.1080/07328319908044652] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
I provide a brief review and perspective thoughts concerning the antisense oligonucleotide, drug discovery paradigm.
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Affiliation(s)
- P D Cook
- Isis Pharmaceuticals, Carlsbad, CA 92008, USA
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Legorburu U, Reese CB, Song Q. Conversion of uridine into 2′-O-(2-methoxyethyl)uridine and 2′-O-(2-methoxyethyl)cytidine. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00229-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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