1
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Agrawal S. Considerations for Creating the Next Generation of RNA Therapeutics: Oligonucleotide Chemistry and Innate Immune Responses to Nucleic Acids. Nucleic Acid Ther 2024; 34:37-51. [PMID: 38578231 DOI: 10.1089/nat.2024.29009.sud] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
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2
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Batistatou N, Kritzer JA. Investigation of Sequence-Penetration Relationships of Antisense Oligonucleotides. Chembiochem 2023; 24:e202300009. [PMID: 36791388 PMCID: PMC10305730 DOI: 10.1002/cbic.202300009] [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: 01/04/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/17/2023]
Abstract
A major limitation for the development of more effective oligonucleotide therapeutics has been a lack of understanding of their penetration into the cytosol. While prior work has shown how backbone modifications affect cytosolic penetration, it is unclear how cytosolic penetration is affected by other features including base composition, base sequence, length, and degree of secondary structure. We have applied the chloroalkane penetration assay, which exclusively reports on material that reaches the cytosol, to investigate the effects of these characteristics on the cytosolic uptake of druglike oligonucleotides. We found that base composition and base sequence had moderate effects, while length did not correlate directly with the degree of cytosolic penetration. Investigating further, we found that the degree of secondary structure had the largest and most predictable correlations with cytosolic penetration. These methods and observations add a layer of design for maximizing the efficacy of new oligonucleotide therapeutics.
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Affiliation(s)
- Nefeli Batistatou
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Joshua A. Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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3
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Saher O, Zaghloul EM, Umek T, Hagey DW, Mozafari N, Danielsen MB, Gouda AS, Lundin KE, Jørgensen PT, Wengel J, Smith CIE, Zain R. Chemical Modifications and Design Influence the Potency of Huntingtin Anti-Gene Oligonucleotides. Nucleic Acid Ther 2023; 33:117-131. [PMID: 36735581 PMCID: PMC10066784 DOI: 10.1089/nat.2022.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Huntington's disease is a neurodegenerative, trinucleotide repeat (TNR) disorder affecting both males and females. It is caused by an abnormal increase in the length of CAG•CTG TNR in exon 1 of the Huntingtin gene (HTT). The resultant, mutant HTT mRNA and protein cause neuronal toxicity, suggesting that reduction of their levels would constitute a promising therapeutic approach. We previously reported a novel strategy in which chemically modified oligonucleotides (ONs) directly target chromosomal DNA. These anti-gene ONs were able to downregulate both HTT mRNA and protein. In this study, various locked nucleic acid (LNA)/DNA mixmer anti-gene ONs were tested to investigate the effects of varying ON length, LNA content, and fatty acid modification on HTT expression. Altering the length did not significantly influence the ON potency, while LNA content was critical for activity. Utilization of palmitoyl-modified LNA monomers enhanced the ON activity relatively to the corresponding nonmodified LNA under serum starvation conditions. Furthermore, the number of palmitoylated LNA monomers and their positioning greatly affected ON potency. In addition, we performed RNA sequencing analysis, which showed that the anti-gene ONs affect the "immune system process, mRNA processing, and neurogenesis." Furthermore, we observed that for repeat containing genes, there is a higher tendency for antisense off-targeting. Taken together, our findings provide an optimized design of anti-gene ONs that could potentially be developed as DNA-targeting therapeutics for this class of TNR-related diseases.
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Affiliation(s)
- Osama Saher
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Eman M Zaghloul
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Tea Umek
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Mathias B Danielsen
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - Alaa S Gouda
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark.,Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt
| | - Karin E Lundin
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Per T Jørgensen
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, SE-17176 Stockholm, Sweden
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4
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Agrawal S. The Evolution of Antisense Oligonucleotide Chemistry-A Personal Journey. Biomedicines 2021; 9:503. [PMID: 34063675 PMCID: PMC8147625 DOI: 10.3390/biomedicines9050503] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 01/03/2023] Open
Abstract
Over the last four decades, tremendous progress has been made in use of synthetic oligonucleotides as therapeutics. This has been possible largely by introducing chemical modifications to provide drug like properties to oligonucleotides. In this article I have summarized twists and turns on use of chemical modifications and their road to success and highlight areas of future directions.
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Affiliation(s)
- Sudhir Agrawal
- ARNAY Sciences LLC, Shrewsbury, MA 01545, USA; or
- Department of Medicine, University of Massachusetts Medical School, 55 N Lake Ave, Worcester, MA 01655, USA
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5
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Le BT, Agarwal S, Veedu RN. Evaluation of DNA segments in 2′-modified RNA sequences in designing efficient splice switching antisense oligonucleotides. RSC Adv 2021; 11:14029-14035. [PMID: 35423918 PMCID: PMC8697723 DOI: 10.1039/d1ra00878a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/07/2021] [Indexed: 12/25/2022] Open
Abstract
Synthetic antisense oligonucleotides (ASOs) have emerged as one of the most promising therapeutic approaches. So far, nine ASO drugs have received approval for clinical use, and four of them are based on splice-switching principles demonstrating the impact of ASO-mediated splice modulation. Notably, three among them (Exondys 51, Vyondys 53 and Viltepso) are based on phosphorodiamidate morpholino (PMO) chemistry whereas Spinraza is based on 2′-O-methoxyethyl phosphorothioate (2′-MOE PS) chemistry. Although systemic delivery of PMOs has displayed a good safety profile even at high doses, the 2′-O-methyl phosphorothioate modified (2′-OMe PS) ASO drug candidate (drisapersen) failed due to safety issues. The potency of 2′-modified RNA for splice-switching needs to be further improved by novel design strategies for broad applicability. Towards this goal, in this study, we evaluated the potential of incorporating DNA segments at appropriate sites in 2′-OMe PS and 2′-MOE PS ASOs to induce exon skipping. For this purpose, a four-nucleotide DNA segment was systematically incorporated into a 20-mer 2′-OMe PS and 2′-MOE PS ASO designed to skip exon 23 in mdx mouse myotubes in vitro. Our results demonstrated that 2′-modified RNA PS ASOs containing four or less PS DNA nucleotides at the 3′-end yielded improved exon 23 skipping efficacy in line with fully modified ASO controls. Based on these results, we firmly believe that the present study opens new avenues towards designing splice modulating ASOs with limited chemical modifications for enhanced safety and therapeutic efficacy. We evaluated the potential of 2′-modified RNA antisense oligonucleotides (ASOs) incorporated with DNA segments to induce exon skipping. Results demonstrated that ASOs with 4 or less DNA nucleotides at the 3′-end induce more efficient exon skipping compared with the control.![]()
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Affiliation(s)
- Bao T. Le
- Centre for Molecular Medicine and Innovative Therapeutics
- Murdoch University
- Perth
- Australia
- Perron Institute for Neurological and Translational Science
| | | | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics
- Murdoch University
- Perth
- Australia
- Perron Institute for Neurological and Translational Science
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6
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Chen L, Zheng L, Chen P, Liang G. Myeloid Differentiation Primary Response Protein 88 (MyD88): The Central Hub of TLR/IL-1R Signaling. J Med Chem 2020; 63:13316-13329. [DOI: 10.1021/acs.jmedchem.0c00884] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lingfeng Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Lulu Zheng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang 310000, China
| | - Pengqin Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
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7
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A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system. Nat Biotechnol 2019; 37:884-894. [PMID: 31375812 PMCID: PMC6879195 DOI: 10.1038/s41587-019-0205-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 06/27/2019] [Indexed: 12/20/2022]
Abstract
Sustained silencing of gene expression in deep regions of the brain using small interfering RNAs (siRNAs) has not been achieved. Here we describe an siRNA architecture, divalent-siRNA (Di-siRNA), that supports potent, sustained gene silencing in the central nervous system (CNS) of mice and non-human primates following a single injection into cerebrospinal fluid. Di-siRNAs are composed of two fully chemically modified, phosphorothioate-containing siRNAs connected by a linker. In mice, Di-siRNAs induced potent silencing of huntingtin, the causative gene in Huntington’s disease, reducing mRNA and protein throughout the brain. Silencing persisted for at least six months, with the degree of gene silencing correlating to guide strand tissue accumulation levels. In Cynomolgus macaques, a bolus injection of Di-siRNA showed substantial distribution and robust silencing throughout the brain and spinal cord without detectable toxicity and with minimal off-target effects. This siRNA design may enable RNAi-based gene silencing in the CNS for the treatment of neurological disorders.
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8
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Welten SMJ, de Jong RCM, Wezel A, de Vries MR, Boonstra MC, Parma L, Jukema JW, van der Sluis TC, Arens R, Bot I, Agrawal S, Quax PHA, Nossent AY. Inhibition of 14q32 microRNA miR-495 reduces lesion formation, intimal hyperplasia and plasma cholesterol levels in experimental restenosis. Atherosclerosis 2017; 261:26-36. [PMID: 28445809 DOI: 10.1016/j.atherosclerosis.2017.04.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 04/12/2017] [Accepted: 04/12/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS We aimed at investigating the role of 14q32 microRNAs in intimal hyperplasia and accelerated atherosclerosis; two major contributors to restenosis. Restenosis occurs regularly in patients treated for coronary artery disease and peripheral arterial disease. We have previously shown that inhibition of 14q32 microRNAs leads to increased post-ischemic neovascularization, and microRNA miR-494 also decreased atherosclerosis, while increasing plaque stability. We hypothesized that 14q32 microRNA inhibition has beneficial effects on intimal hyperplasia, as well as accelerated atherosclerosis. METHODS Non-constrictive cuffs were placed around both femoral arteries of C57BL/6J mice to induce intimal hyperplasia. Accelerated atherosclerotic plaque formation was induced in hypercholesterolemic ApoE-/- mice by placing semi-constrictive collars around both carotid arteries. 14q32 microRNAs miR-329, miR-494 and miR-495 were inhibited in vivo using Gene Silencing Oligonucleotides (GSOs). RESULTS GSO-495 administration led to a 32% reduction of intimal hyperplasia. Moreover, the number of macrophages in the arterial wall of mice treated with GSO-495 was reduced by 55%. Inhibition of miR-329 and miR-494 had less profound effects on intimal hyperplasia. GSO-495 administration also decreased atherosclerotic plaque formation by 52% and plaques of GSO-495 treated animals showed a more stable phenotype. Finally, cholesterol levels were also decreased in GSO-495 treated animals, via reduction of the VLDL-fraction. CONCLUSIONS GSO-495 administration decreased our primary outcomes, namely intimal hyperplasia, and accelerated atherosclerosis. GSO-495 administration also favourably affected multiple secondary outcomes, including macrophage influx, plaque stability and total plasma cholesterol levels. We conclude that 14q32 microRNA miR-495 is a promising target for prevention of restenosis.
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Affiliation(s)
- Sabine M J Welten
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Rob C M de Jong
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Anouk Wezel
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands; Division of Biopharmaceutics, LACDR, Leiden University, Leiden, The Netherlands
| | - Margreet R de Vries
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Martin C Boonstra
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Laura Parma
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tetje C van der Sluis
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Ilze Bot
- Division of Biopharmaceutics, LACDR, Leiden University, Leiden, The Netherlands
| | | | - Paul H A Quax
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - A Yaël Nossent
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands.
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9
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Welten SMJ, de Vries MR, Peters EAB, Agrawal S, Quax PHA, Nossent AY. Inhibition of Mef2a Enhances Neovascularization via Post-transcriptional Regulation of 14q32 MicroRNAs miR-329 and miR-494. MOLECULAR THERAPY. NUCLEIC ACIDS 2017. [PMID: 28624225 PMCID: PMC5415962 DOI: 10.1016/j.omtn.2017.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Improving the efficacy of neovascularization is a promising strategy to restore perfusion of ischemic tissues in patients with peripheral arterial disease. The 14q32 microRNA cluster is highly involved in neovascularization. The Mef2a transcription factor has been shown to induce transcription of the microRNAs within this cluster. We inhibited expression of Mef2a using gene-silencing oligonucleotides (GSOs) in an in vivo hind limb ischemia model. Treatment with GSO-Mef2a clearly improved blood flow recovery within 3 days (44% recovery versus 25% recovery in control) and persisted until 14 days after ischemia induction (80% recovery versus 60% recovery in control). Animals treated with GSO-Mef2a showed increased arteriogenesis and angiogenesis in the relevant muscle tissues. Inhibition of Mef2a decreased expression of 14q32 microRNAs miR-329 (p = 0.026) and miR-494 (trend, p = 0.06), but not of other 14q32 microRNAs, nor of 14q32 microRNA precursors. Because Mef2a did not influence 14q32 microRNA transcription, we hypothesized it functions as an RNA-binding protein that influences processing of 14q32 microRNA miR-329 and miR-494. Mef2A immunoprecipitation followed by RNA isolation and rt/qPCR confirmed direct binding of MEF2A to pri-miR-494, supporting this hypothesis. Our study demonstrates a novel function for Mef2a in post-ischemic neovascularization via post-transcriptional regulation of 14q32 microRNAs miR-329 and miR-494.
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Affiliation(s)
- Sabine M J Welten
- Department of Surgery, Leiden University Medical Center, 2333 Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Margreet R de Vries
- Department of Surgery, Leiden University Medical Center, 2333 Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Erna A B Peters
- Department of Surgery, Leiden University Medical Center, 2333 Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | | | - Paul H A Quax
- Department of Surgery, Leiden University Medical Center, 2333 Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - A Yaël Nossent
- Department of Surgery, Leiden University Medical Center, 2333 Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 Leiden, the Netherlands.
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10
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Khvorova A, Watts JK. The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol 2017; 35:238-248. [PMID: 28244990 PMCID: PMC5517098 DOI: 10.1038/nbt.3765] [Citation(s) in RCA: 725] [Impact Index Per Article: 103.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
After nearly 40 years of development, oligonucleotide therapeutics are nearing meaningful clinical productivity. One of the key advantages of oligonucleotide drugs is that their delivery and potency are derived primarily from the chemical structure of the oligonucleotide whereas their target is defined by the base sequence. Thus, as oligonucleotides with a particular chemical design show appropriate distribution and safety profiles for clinical gene silencing in a particular tissue, this will open the door to the rapid development of additional drugs targeting other disease-associated genes in the same tissue. To achieve clinical productivity, the chemical architecture of the oligonucleotide needs to be optimized with a combination of sugar, backbone, nucleobase, and 3'- and 5'-terminal modifications. A portfolio of chemistries can be used to confer drug-like properties onto the oligonucleotide as a whole, with minor chemical changes often translating into major improvements in clinical efficacy. One outstanding challenge in oligonucleotide chemical development is the optimization of chemical architectures to ensure long-term safety. There are multiple designs that enable effective targeting of the liver, but a second challenge is to develop architectures that enable robust clinical efficacy in additional tissues.
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Affiliation(s)
- Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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11
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Takata R, Makado G, Kitamura A, Watanabe H, Wada T. A novel dual lock method for down-regulation of genes, in which a target mRNA is captured at 2 independent positions by linked locked nucleic acid antisense oligonucleotides. RNA Biol 2016; 13:279-89. [PMID: 26890856 DOI: 10.1080/15476286.2015.1119364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Nuclear factor κB (NFκB), which is composed of the RelA and p50 subunits, binds to NFκB response elements (NREs) and stimulates the transcription of inflammation-related genes. Here, locked nucleic acid (LNA) antisense oligonucleotides (ASOs) complementary to the termini of the 3'- and 5'-untranslated regions (UTRs) of the RelA mRNA were generated; these molecules were named 3'-LNA and 5'-LNA, respectively. To evaluate their effects on NFκB activity, HeLa cells were co-transfected with the LNA ASOs and a luciferase reporter gene carrying an NRE. Transfection of the cells with 3'-LNA reduced NFκB activity by 30-40%, without affecting RelA mRNA accumulation. Concomitant transfection of HeLa cells with 5'-LNA and 3'-LNA resulted in a 70% reduction in NFκB activity. Furthermore, partial poly(A) tail shortening occurred in LNA ASO-transfected cells. We also employed triethylene glycol as a spacer to link 5'-LNA and 3'-LNA. Reporter gene assays showed that the spacer-linked LNA ASO reduced NFκB activity similarly to a combination of 5'-LNA and 3'-LNA. In addition, an in vitro translation assay revealed that spacer-linked LNA ASOs inhibited the translation of a target mRNA in a specific manner. In summary, this study describes a novel antisense method capturing the target mRNA at independent positions.
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Affiliation(s)
- Ryohei Takata
- a Nucleic Acid Regulation (Yoshindo) Joint Research Laboratory and.,b Bioenvironmental Science , Department of Biotechnology, Osaka University , Suita, Osaka , Japan.,c Research and Development, Yoshindo , Haginoshima, Fuchu-machi, Toyama , Japan
| | - Gouki Makado
- a Nucleic Acid Regulation (Yoshindo) Joint Research Laboratory and.,c Research and Development, Yoshindo , Haginoshima, Fuchu-machi, Toyama , Japan
| | - Ayaka Kitamura
- a Nucleic Acid Regulation (Yoshindo) Joint Research Laboratory and.,b Bioenvironmental Science , Department of Biotechnology, Osaka University , Suita, Osaka , Japan.,c Research and Development, Yoshindo , Haginoshima, Fuchu-machi, Toyama , Japan
| | - Hajime Watanabe
- a Nucleic Acid Regulation (Yoshindo) Joint Research Laboratory and.,b Bioenvironmental Science , Department of Biotechnology, Osaka University , Suita, Osaka , Japan
| | - Tadashi Wada
- a Nucleic Acid Regulation (Yoshindo) Joint Research Laboratory and
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12
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Subramanian RR, Wysk MA, Ogilvie KM, Bhat A, Kuang B, Rockel TD, Weber M, Uhlmann E, Krieg AM. Enhancing antisense efficacy with multimers and multi-targeting oligonucleotides (MTOs) using cleavable linkers. Nucleic Acids Res 2015; 43:9123-32. [PMID: 26446989 PMCID: PMC4627098 DOI: 10.1093/nar/gkv992] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/11/2015] [Indexed: 11/18/2022] Open
Abstract
The in vivo potency of antisense oligonucleotides (ASO) has been significantly increased by reducing their length to 8–15 nucleotides and by the incorporation of high affinity RNA binders such as 2′, 4′-bridged nucleic acids (also known as locked nucleic acid or LNA, and 2′,4′-constrained ethyl [cET]). We now report the development of a novel ASO design in which such short ASO monomers to one or more targets are co-synthesized as homo- or heterodimers or multimers via phosphodiester linkers that are stable in plasma, but cleaved inside cells, releasing the active ASO monomers. Compared to current ASOs, these multimers and multi-targeting oligonucleotides (MTOs) provide increased plasma protein binding and biodistribution to liver, and increased in vivo efficacy against single or multiple targets with a single construct. In vivo, MTOs synthesized in both RNase H-activating and steric-blocking oligonucleotide designs provide ≈4–5-fold increased potency and ≈2-fold increased efficacy, suggesting broad therapeutic applications.
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Affiliation(s)
| | - Mark A Wysk
- RaNA Therapeutics LLC, 790 Memorial Dr., Suite 203, Cambridge, MA 02139, USA
| | - Kathleen M Ogilvie
- Pfizer Worldwide Research and Development, 9381 Judicial Dr., Suite 200, San Diego, CA 92121, USA
| | - Abhijit Bhat
- Pfizer Worldwide Research and Development, 9381 Judicial Dr., Suite 200, San Diego, CA 92121, USA
| | - Bing Kuang
- Pfizer Worldwide Research and Development, 9381 Judicial Dr., Suite 200, San Diego, CA 92121, USA
| | - Thomas D Rockel
- Coley Pharmaceutical GmbH, Merowingerplatz 1a, 40225 Dusseldorf, Germany
| | - Markus Weber
- Coley Pharmaceutical GmbH, Merowingerplatz 1a, 40225 Dusseldorf, Germany
| | - Eugen Uhlmann
- Coley Pharmaceutical GmbH, Merowingerplatz 1a, 40225 Dusseldorf, Germany
| | - Arthur M Krieg
- RaNA Therapeutics LLC, 790 Memorial Dr., Suite 203, Cambridge, MA 02139, USA
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13
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Welten SM, Bastiaansen AJ, de Jong RC, de Vries MR, Peters EA, Boonstra MC, Sheikh SP, La Monica N, Kandimalla ER, Quax PH, Nossent AY. Inhibition of 14q32 MicroRNAs miR-329, miR-487b, miR-494, and miR-495 Increases Neovascularization and Blood Flow Recovery After Ischemia. Circ Res 2014; 115:696-708. [DOI: 10.1161/circresaha.114.304747] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rationale:
Effective neovascularization is crucial for recovery after cardiovascular events.
Objective:
Because microRNAs regulate expression of up to several hundred target genes, we set out to identify microRNAs that target genes in all pathways of the multifactorial neovascularization process. Using
www.targetscan.org
, we performed a reverse target prediction analysis on a set of 197 genes involved in neovascularization. We found enrichment of binding sites for 27 microRNAs in a single microRNA gene cluster. Microarray analyses showed upregulation of 14q32 microRNAs during neovascularization in mice after single femoral artery ligation.
Methods and Results:
Gene silencing oligonucleotides (GSOs) were used to inhibit 4 14q32 microRNAs, miR-329, miR-487b, miR-494, and miR-495, 1 day before double femoral artery ligation. Blood flow recovery was followed by laser Doppler perfusion imaging. All 4 GSOs clearly improved blood flow recovery after ischemia. Mice treated with GSO-495 or GSO-329 showed increased perfusion already after 3 days (30% perfusion versus 15% in control), and those treated with GSO-329 showed a full recovery of perfusion after 7 days (versus 60% in control). Increased collateral artery diameters (arteriogenesis) were observed in adductor muscles of GSO-treated mice, as well as increased capillary densities (angiogenesis) in the ischemic soleus muscle. In vitro, treatment with GSOs led to increased sprout formation and increased arterial endothelial cell proliferation, as well as to increased arterial myofibroblast proliferation.
Conclusions:
The 14q32 microRNA gene cluster is highly involved in neovascularization. Inhibition of 14q32 microRNAs miR-329, miR-487b, miR-494, and miR-495 provides a promising tool for future therapeutic neovascularization.
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Affiliation(s)
- Sabine M.J. Welten
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Antonius J.N.M. Bastiaansen
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Rob C.M. de Jong
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Margreet R. de Vries
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Erna A.B. Peters
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Martin C. Boonstra
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Søren P. Sheikh
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Nicola La Monica
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Ekambar R. Kandimalla
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Paul H.A. Quax
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - A. Yaël Nossent
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
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Zhang J, Lu D, Li A, Yang J, Wang S. Design, synthesis and anti-influenza virus activities of terminal modified antisense oligonucleotides. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2013.10.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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