1
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Lu T, Zhang C, Li Z, Wei Y, Sadewasser A, Yan Y, Sun L, Li J, Wen Y, Lai S, Chen C, Zhong H, Jiménez MR, Klar R, Schell M, Raith S, Michel S, Ke B, Zheng H, Jaschinski F, Zhang N, Xiao H, Bachert C, Wen W. Human angiotensin-converting enzyme 2-specific antisense oligonucleotides reduce infection with SARS-CoV-2 variants. J Allergy Clin Immunol 2024:S0091-6749(24)00631-6. [PMID: 38909634 DOI: 10.1016/j.jaci.2024.06.007] [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: 10/22/2023] [Revised: 05/16/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
BACKGROUND The Spike protein mutation severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to decreased protective effect of various vaccines and mAbs, suggesting that blocking SARS-CoV-2 infection by targeting host factors would make the therapy more resilient against virus mutations. Angiotensin-converting enzyme 2 (ACE2) is the host receptor of SARS-CoV-2 and its variants, as well as many other coronaviruses. Downregulation of ACE2 expression in the respiratory tract may prevent viral infection. Antisense oligonucleotides (ASOs) can be rationally designed on the basis of sequence data, require no delivery system, and can be administered locally. OBJECTIVE We sought to design ASOs that can block SARS-CoV-2 by downregulating ACE2 in human airway. METHODS ACE2-targeting ASOs were designed using a bioinformatic method and screened in cell lines. Human primary nasal epithelial cells cultured at the air-liquid interface and humanized ACE2 mice were used to detect the ACE2 reduction levels and the safety of ASOs. ASO-pretreated nasal epithelial cells and mice were infected and then used to detect the viral infection levels. RESULTS ASOs reduced ACE2 expression on mRNA and protein level in cell lines and in human nasal epithelial cells. Furthermore, they efficiently suppressed virus replication of 3 different SARS-CoV-2 variants in human nasal epithelial cells. In vivo, ASOs also downregulated human ACE2 in humanized ACE2 mice and thereby reduced viral load, histopathologic changes in lungs, and increased survival of mice. CONCLUSIONS ACE2-targeting ASOs can effectively block SARS-CoV-2 infection. Our study provides a new approach for blocking SARS-CoV-2 and other ACE2-targeting virus in high-risk populations.
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Affiliation(s)
- Tong Lu
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Chengcheng Zhang
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Zhengqi Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yi Wei
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | | | - Yan Yan
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Lin Sun
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Jian Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China; Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning, China
| | - Yihui Wen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Shimin Lai
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Changhui Chen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China
| | - Hua Zhong
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | | | - Richard Klar
- Secarna Pharmaceuticals GmbH & Co. KG, Martinsried, Germany
| | - Monika Schell
- Secarna Pharmaceuticals GmbH & Co. KG, Martinsried, Germany
| | - Stefanie Raith
- Secarna Pharmaceuticals GmbH & Co. KG, Martinsried, Germany
| | - Sven Michel
- Secarna Pharmaceuticals GmbH & Co. KG, Martinsried, Germany
| | - Bixia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | | | - Nan Zhang
- Upper Airways Research Laboratory, Department of Oto-Rhino-Laryngology, Ghent University Hospital, Ghent, Belgium
| | - Haipeng Xiao
- Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Claus Bachert
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Department of Otorhinolaryngology - Head and Neck Surgery, University Hospital of Münster, Münster, Germany; Upper Airways Research Laboratory, Department of Oto-Rhino-Laryngology, Ghent University Hospital, Ghent, Belgium
| | - Weiping Wen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou, Guangdong, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, China; Department of Otolaryngology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
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2
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Hanswillemenke A, Hofacker DT, Sorgenfrei M, Fruhner C, Franz-Wachtel M, Schwarzer D, Maček B, Stafforst T. Profiling the interactome of oligonucleotide drugs by proximity biotinylation. Nat Chem Biol 2024; 20:555-565. [PMID: 38233583 PMCID: PMC11062921 DOI: 10.1038/s41589-023-01530-z] [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: 02/06/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024]
Abstract
Drug-ID is a novel method applying proximity biotinylation to identify drug-protein interactions inside living cells. The covalent conjugation of a drug with a biotin ligase enables targeted biotinylation and identification of the drug-bound proteome. We established Drug-ID for two small-molecule drugs, JQ1 and SAHA, and applied it for RNaseH-recruiting antisense oligonucleotides (ASOs). Drug-ID profiles the drug-protein interactome de novo under native conditions, directly inside living cells and at pharmacologically effective drug concentrations. It requires minimal amounts of cell material and might even become applicable in vivo. We studied the dose-dependent aggregation of ASOs and the effect of different wing chemistries (locked nucleic acid, 2'-methoxyethyl and 2'-Fluoro) and ASO lengths on the interactome. Finally, we demonstrate the detection of stress-induced, intracellular interactome changes (actinomycin D treatment) with an in situ variant of the approach, which uses a recombinant biotin ligase and does not require genetic manipulation of the target cell.
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Affiliation(s)
| | | | - Michèle Sorgenfrei
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Carolin Fruhner
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Mirita Franz-Wachtel
- Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Boris Maček
- Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
- Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University of Tübingen, Tübingen, Germany.
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3
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Story S, Bhaduri S, Ganguly S, Dakarapu R, Wicks SL, Bhadra J, Kwange S, Arya DP. Understanding Antisense Oligonucleotide Efficiency in Inhibiting Prokaryotic Gene Expression. ACS Infect Dis 2024; 10:971-987. [PMID: 38385613 DOI: 10.1021/acsinfecdis.3c00645] [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] [Indexed: 02/23/2024]
Abstract
Oligonucleotides offer a unique opportunity for sequence specific regulation of gene expression in bacteria. A fundamental question to address is the choice of oligonucleotide, given the large number of options available. Different modifications varying in RNA binding affinities and cellular uptake are available but no comprehensive comparisons have been performed. Herein, the efficiency of blocking expression of β-galactosidase (β-Gal) in E. coli was evaluated utilizing different antisense oligomers (ASOs). Fluorescein (FAM)-labeled oligomers were used to understand their differences in bacterial uptake. Flow cytometry analysis revealed significant differences in uptake, with high fluorescence seen in cells treated with FAM-labeled peptidic nucleic acid (PNA), phosphorodiamidate morpholino oligonucleotide (PMO) and phosphorothioate (PS) oligomers, and low fluorescence observed in cells treated with phosphodiester (PO) oligomers. Thermal denaturation (Tm) of oligomer:RNA duplexes and isothermal titration calorimetry (ITC) studies reveal that ASO binding to target RNA demonstrates a good correlation between Tm and Kd values. There was no correlation between Kd values and reduction of β-Gal activity in bacterial cells. However, cell-free translation assays demonstrated a direct relationship between Kd values and inhibition of gene expression by antisense oligomers, with tight binding oligomers such as LNA being the most efficient. Membrane active compounds such as polymyxin B and A22 further improved the cellular uptake of FAM-PNA and FAM-PS oligomers in wild-type E. coli cells. PNA and PMO were most effective in cellular uptake and reducing β-Gal activity as compared to oligomers with PS or those with PO linkages. Overall, cell uptake of the oligomers is shown as the key determinant in predicting their differences in bacterial antisense inhibition, and the RNA affinity is the key determinant in inhibition of gene expression in cell free systems.
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Affiliation(s)
- Sandra Story
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | | | - Sudakshina Ganguly
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | | | - Sarah L Wicks
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | - Jhuma Bhadra
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Simeon Kwange
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
- NUBAD, LLC, Greenville, South Carolina 29605, United States
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4
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Sergeeva O, Akhmetova E, Dukova S, Beloglazkina E, Uspenskaya A, Machulkin A, Stetsenko D, Zatsepin T. Structure-activity relationship study of mesyl and busyl phosphoramidate antisense oligonucleotides for unaided and PSMA-mediated uptake into prostate cancer cells. Front Chem 2024; 12:1342178. [PMID: 38501046 PMCID: PMC10944894 DOI: 10.3389/fchem.2024.1342178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/13/2024] [Indexed: 03/20/2024] Open
Abstract
Phosphorothioate (PS) group is a key component of a majority of FDA approved oligonucleotide drugs that increase stability to nucleases whilst maintaining interactions with many proteins, including RNase H in the case of antisense oligonucleotides (ASOs). At the same time, uniform PS modification increases nonspecific protein binding that can trigger toxicity and pro-inflammatory effects, so discovery and characterization of alternative phosphate mimics for RNA therapeutics is an actual task. Here we evaluated the effects of the introduction of several N-alkane sulfonyl phosphoramidate groups such as mesyl (methanesulfonyl) or busyl (1-butanesulfonyl) phosphoramidates into gapmer ASOs on the efficiency and pattern of RNase H cleavage, cellular uptake in vitro, and intracellular localization. Using Malat1 lncRNA as a target, we have identified patterns of mesyl or busyl modifications in the ASOs for optimal knockdown in vitro. Combination of the PSMA ligand-mediated delivery with optimized mesyl and busyl ASOs resulted in the efficient target depletion in the prostate cancer cells. Our study demonstrated that other N-alkanesulfonyl phosphoramidate groups apart from a known mesyl phosphoramidate can serve as an essential component of mixed backbone gapmer ASOs to reduce drawbacks of uniformly PS-modified gapmers, and deserve further investigation in RNA therapeutics.
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Affiliation(s)
- O. Sergeeva
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - E. Akhmetova
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - S. Dukova
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - E. Beloglazkina
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - A. Uspenskaya
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - A. Machulkin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Department for Biochemistry, People’s Friendship University of Russia Named after Patrice Lumumba (RUDN University), Moscow, Russia
| | - D. Stetsenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T. Zatsepin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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5
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Chen S, Heendeniya SN, Le BT, Rahimizadeh K, Rabiee N, Zahra QUA, Veedu RN. Splice-Modulating Antisense Oligonucleotides as Therapeutics for Inherited Metabolic Diseases. BioDrugs 2024; 38:177-203. [PMID: 38252341 PMCID: PMC10912209 DOI: 10.1007/s40259-024-00644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2024] [Indexed: 01/23/2024]
Abstract
The last decade (2013-2023) has seen unprecedented successes in the clinical translation of therapeutic antisense oligonucleotides (ASOs). Eight such molecules have been granted marketing approval by the United States Food and Drug Administration (US FDA) during the decade, after the first ASO drug, fomivirsen, was approved much earlier, in 1998. Splice-modulating ASOs have also been developed for the therapy of inborn errors of metabolism (IEMs), due to their ability to redirect aberrant splicing caused by mutations, thus recovering the expression of normal transcripts, and correcting the deficiency of functional proteins. The feasibility of treating IEM patients with splice-switching ASOs has been supported by FDA permission (2018) of the first "N-of-1" study of milasen, an investigational ASO drug for Batten disease. Although for IEM, owing to the rarity of individual disease and/or pathogenic mutation, only a low number of patients may be treated by ASOs that specifically suppress the aberrant splicing pattern of mutant precursor mRNA (pre-mRNA), splice-switching ASOs represent superior individualized molecular therapeutics for IEM. In this work, we first summarize the ASO technology with respect to its mechanisms of action, chemical modifications of nucleotides, and rational design of modified oligonucleotides; following that, we precisely provide a review of the current understanding of developing splice-modulating ASO-based therapeutics for IEM. In the concluding section, we suggest potential ways to improve and/or optimize the development of ASOs targeting IEM.
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Affiliation(s)
- Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Saumya Nishanga Heendeniya
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Bao T Le
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- ProGenis Pharmaceuticals Pty Ltd, Bentley, WA, 6102, Australia
| | - Kamal Rahimizadeh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Navid Rabiee
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Qurat Ul Ain Zahra
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia.
- ProGenis Pharmaceuticals Pty Ltd, Bentley, WA, 6102, Australia.
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6
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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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7
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Terada C, Oh K, Tsubaki R, Chan B, Aibara N, Ohyama K, Shibata MA, Wada T, Harada-Shiba M, Yamayoshi A, Yamamoto T. Dynamic and static control of the off-target interactions of antisense oligonucleotides using toehold chemistry. Nat Commun 2023; 14:7972. [PMID: 38042877 PMCID: PMC10693639 DOI: 10.1038/s41467-023-43714-0] [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: 09/12/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Off-target interactions between antisense oligonucleotides (ASOs) with state-of-the-art modifications and biological components still pose clinical safety liabilities. To mitigate a broad spectrum of off-target interactions and enhance the safety profile of ASO drugs, we here devise a nanoarchitecture named BRace On a THERapeutic aSo (BROTHERS or BRO), which is composed of a standard gapmer ASO paired with a partially complementary peptide nucleic acid (PNA) strand. We show that these non-canonical ASO/PNA hybrids have reduced non-specific protein-binding capacity. The optimization of the structural and thermodynamic characteristics of this duplex system enables the operation of an in vivo toehold-mediated strand displacement (TMSD) reaction, effectively reducing hybridization with RNA off-targets. The optimized BROs dramatically mitigate hepatotoxicity while maintaining the on-target knockdown activity of their parent ASOs in vivo. This technique not only introduces a BRO class of drugs that could have a transformative impact on the extrahepatic delivery of ASOs, but can also help uncover the toxicity mechanism of ASOs.
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Affiliation(s)
- Chisato Terada
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- JSPS Research Fellow (DC1), Japan Society for the Promotion of Science, Tokyo, Japan
| | - Kaho Oh
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Ryutaro Tsubaki
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Nagasaki, Japan
| | - Nozomi Aibara
- Department of Pharmacy Practice, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kaname Ohyama
- Department of Molecular Pathochemistry, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masa-Aki Shibata
- Department of Anatomy and Cell Biology, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, Sendai, Miyagi, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
- Cardiovascular Center, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Asako Yamayoshi
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Tsuyoshi Yamamoto
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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Ranjbar S, Zhong XB, Manautou J, Lu X. A holistic analysis of the intrinsic and delivery-mediated toxicity of siRNA therapeutics. Adv Drug Deliv Rev 2023; 201:115052. [PMID: 37567502 PMCID: PMC10543595 DOI: 10.1016/j.addr.2023.115052] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 07/15/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Small interfering RNAs (siRNAs) are among the most promising therapeutic platforms in many life-threatening diseases. Owing to the significant advances in siRNA design, many challenges in the stability, specificity and delivery of siRNA have been addressed. However, safety concerns and dose-limiting toxicities still stand among the reasons for the failure of clinical trials of potent siRNA therapies, calling for a need of more comprehensive understanding of their potential mechanisms of toxicity. This review delves into the intrinsic and delivery related toxicity mechanisms of siRNA drugs and takes a holistic look at the safety failure of the clinical trials to identify the underlying causes of toxicity. In the end, the current challenges, and potential solutions for the safety assessment and high throughput screening of investigational siRNA and delivery systems as well as considerations for design strategies of safer siRNA therapeutics are outlined.
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Affiliation(s)
- Sheyda Ranjbar
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
| | - José Manautou
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
| | - Xiuling Lu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA.
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Pandey E, Harris EN. Chloroquine and cytosolic galectins affect endosomal escape of antisense oligonucleotides after Stabilin-mediated endocytosis. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:430-443. [PMID: 37575283 PMCID: PMC10412722 DOI: 10.1016/j.omtn.2023.07.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Abstract
Non-DNA-binding Stabilin-2/HARE receptors expressed on liver sinusoidal endothelial cells specifically bind to and internalize several classes of phosphorothioate antisense oligonucleotides (PS-ASOs). After Stabilin-mediated uptake, PS-ASOs are trafficked within endosomes (>97%-99%), ultimately resulting in destruction in the lysosome. The ASO entrapment in endosomes lowers therapeutic efficacy, thereby increasing the overall dose for patients. Here, we use confocal microscopy to characterize the intracellular route transverse by PS-ASOs after Stabilin receptor-mediated uptake in stable recombinant Stabilin-1 and -2 cell lines. We found that PS-ASOs as well as the Stabilin-2 receptor transverse the classic path: clathrin-coated vesicle-early endosome-late endosome-lysosome. Chloroquine exposure facilitated endosomal escape of PS-ASOs leading to target knockdown by more than 50% as compared to untreated cells, resulting in increased PS-ASO efficacy. We also characterize cytosolic galectins as novel contributor for PS-ASO escape. Galectins knockdown enhances ASO efficacy by more than 60% by modulating EEA1, Rab5C, and Rab7A mRNA expression, leading to a delay in the endosomal vesicle maturation process. Collectively, our results provide additional insight for increasing PS-ASO efficacy by enhancing endosomal escape, which can further be utilized for other nucleic acid-based modalities.
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Affiliation(s)
- Ekta Pandey
- University of Nebraska, Department of Biochemistry, Beadle Center, 1901 Vine St., Lincoln, NE 68588, USA
| | - Edward N. Harris
- University of Nebraska, Department of Biochemistry, Beadle Center, 1901 Vine St., Lincoln, NE 68588, USA
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10
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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11
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Chen L, Wang Y. Interdisciplinary advances reshape the delivery tools for effective NASH treatment. Mol Metab 2023; 73:101730. [PMID: 37142161 DOI: 10.1016/j.molmet.2023.101730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Nonalcoholic steatohepatitis (NASH), a severe systemic and inflammatory subtype of nonalcoholic fatty liver disease, eventually develops into cirrhosis and hepatocellular carcinoma with few options for effective treatment. Currently potent small molecules identified in preclinical studies are confronted with adverse effects and long-term ineffectiveness in clinical trials. Nevertheless, highly specific delivery tools designed from interdisciplinary concepts may address the significant challenges by either effectively increasing the concentrations of drugs in target cell types, or selectively manipulating the gene expression in liver to resolve NASH. SCOPE OF REVIEW We focus on dissecting the detailed principles of the latest interdisciplinary advances and concepts that direct the design of future delivery tools to enhance the efficacy. Recent advances have indicated that cell and organelle-specific vehicles, non-coding RNA research (e.g. saRNA, hybrid miRNA) improve the specificity, while small extracellular vesicles and coacervates increase the cellular uptake of therapeutics. Moreover, strategies based on interdisciplinary advances drastically elevate drug loading capacity and delivery efficiency and ameliorate NASH and other liver diseases. MAJOR CONCLUSIONS The latest concepts and advances in chemistry, biochemistry and machine learning technology provide the framework and strategies for the design of more effective tools to treat NASH, other pivotal liver diseases and metabolic disorders.
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Affiliation(s)
- Linshan Chen
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health.
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12
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Oligonucleotide Enhancing Compound Increases Tricyclo-DNA Mediated Exon-Skipping Efficacy in the Mdx Mouse Model. Cells 2023; 12:cells12050702. [PMID: 36899837 PMCID: PMC10001065 DOI: 10.3390/cells12050702] [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: 01/06/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Nucleic acid-based therapeutics hold great promise for the treatment of numerous diseases, including neuromuscular disorders, such as Duchenne muscular dystrophy (DMD). Some antisense oligonucleotide (ASO) drugs have already been approved by the US FDA for DMD, but the potential of this therapy is still limited by several challenges, including the poor distribution of ASOs to target tissues, but also the entrapment of ASO in the endosomal compartment. Endosomal escape is a well recognized limitation that prevents ASO from reaching their target pre-mRNA in the nucleus. Small molecules named oligonucleotide-enhancing compounds (OEC) have been shown to release ASO from endosomal entrapment, thus increasing ASO nuclear concentration and ultimately correcting more pre-mRNA targets. In this study, we evaluated the impact of a therapy combining ASO and OEC on dystrophin restoration in mdx mice. Analysis of exon-skipping levels at different time points after the co-treatment revealed improved efficacy, particularly at early time points, reaching up to 4.4-fold increase at 72 h post treatment in the heart compared to treatment with ASO alone. Significantly higher levels of dystrophin restoration were detected two weeks after the end of the combined therapy, reaching up to 2.7-fold increase in the heart compared to mice treated with ASO alone. Moreover, we demonstrated a normalization of cardiac function in mdx mice after a 12-week-long treatment with the combined ASO + OEC therapy. Altogether, these findings indicate that compounds facilitating endosomal escape can significantly improve the therapeutic potential of exon-skipping approaches offering promising perspectives for the treatment of DMD.
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13
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Takakusa H, Iwazaki N, Nishikawa M, Yoshida T, Obika S, Inoue T. Drug Metabolism and Pharmacokinetics of Antisense Oligonucleotide Therapeutics: Typical Profiles, Evaluation Approaches, and Points to Consider Compared with Small Molecule Drugs. Nucleic Acid Ther 2023; 33:83-94. [PMID: 36735616 PMCID: PMC10066781 DOI: 10.1089/nat.2022.0054] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Oligonucleotide therapeutics are attracting attention as a new treatment modality for a range of diseases that have been difficult to target using conventional approaches. Technical advances in chemical modification and drug delivery systems have led to the generation of compounds with excellent profiles as pharmaceuticals, and 16 oligonucleotide therapeutics have been marketed to date. There is a growing need to develop optimal and efficient approaches to evaluate drug metabolism and pharmacokinetics (DMPK) and drug-drug interactions (DDIs) of oligonucleotide therapeutics. The DMPK/DDI profiles of small molecule drugs are highly diverse depending on their structural and physicochemical characteristics, whereas oligonucleotide therapeutics share similar DMPK profiles within each chemistry type. Most importantly, the mechanisms and molecules involved in the distribution and metabolism of oligonucleotides differ from those of small molecules. In addition, there are considerations regarding experimental approaches in the evaluation of oligonucleotides, such as bioanalytical challenges, the use of radiolabeled tracers, materials for in vitro metabolism/DDI studies, and methods to study biodistribution. In this review, we attempt to summarize the DMPK characteristics of antisense oligonucleotide (ASO) therapeutics and discuss some of the issues regarding how to optimize the evaluation and prediction of the DMPK and DDI of ASOs.
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Affiliation(s)
- Hideo Takakusa
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Norihiko Iwazaki
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corp., Yokohama, Japan
| | - Makiya Nishikawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Tokuyuki Yoshida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
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14
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Goyenvalle A, Jimenez-Mallebrera C, van Roon W, Sewing S, Krieg AM, Arechavala-Gomeza V, Andersson P. Considerations in the Preclinical Assessment of the Safety of Antisense Oligonucleotides. Nucleic Acid Ther 2023; 33:1-16. [PMID: 36579950 PMCID: PMC9940817 DOI: 10.1089/nat.2022.0061] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nucleic acid therapeutics field has made tremendous progress in the past decades. Continuous advances in chemistry and design have led to many successful clinical applications, eliciting even more interest from researchers including both academic groups and drug development companies. Many preclinical studies in the field focus on improving the delivery of antisense oligonucleotide drugs (ONDs) and/or assessing their efficacy in target tissues, often neglecting the evaluation of toxicity, at least in early phases of development. A series of consensus recommendations regarding regulatory considerations and expectations have been generated by the Oligonucleotide Safety Working Group and the Japanese Research Working Group for the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use S6 and Related Issues (WGS6) in several white papers. However, safety aspects should also be kept in sight in earlier phases while screening and designing OND to avoid subsequent failure in the development phase. Experts and members of the network "DARTER," a COST Action funded by the Cooperation in Science and Technology of the EU, have utilized their collective experience working with OND, as well as their insights into OND-mediated toxicities, to generate a series of consensus recommendations to assess OND toxicity in early stages of preclinical research. In the past few years, several publications have described predictive assays, which can be used to assess OND-mediated toxicity in vitro or ex vivo to filter out potential toxic candidates before moving to in vivo phases of preclinical development, that is, animal toxicity studies. These assays also have the potential to provide translational insight since they allow a safety evaluation in human in vitro systems. Yet, small preliminary in vivo studies should also be considered to complement this early assessment. In this study, we summarize the state of the art and provide guidelines and recommendations on the different tests available for these early stage preclinical assessments.
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Affiliation(s)
- Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, Versailles, France.,Address correspondence to: Aurélie Goyenvalle, PhD, Université Paris-Saclay, UVSQ, Inserm, END-ICAP, Versailles 78000, France
| | - Cecilia Jimenez-Mallebrera
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Departamento de Genética, Microbiología y Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Willeke van Roon
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sabine Sewing
- Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Arthur M. Krieg
- RNA Therapeutics Institute, University of Massachusetts, Worcester, Massachusetts, USA
| | - Virginia Arechavala-Gomeza
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Patrik Andersson
- Safety Innovation, Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden.,Address correspondence to: Patrik Andersson, PhD, Safety Innovation, Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Pepparedsleden 1, Mölndal, Gothenburg 431 83, Sweden
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15
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Roth C, Kilpinen H, Kurian MA, Barral S. Histone lysine methyltransferase-related neurodevelopmental disorders: current knowledge and saRNA future therapies. Front Cell Dev Biol 2023; 11:1090046. [PMID: 36923252 PMCID: PMC10009263 DOI: 10.3389/fcell.2023.1090046] [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: 12/07/2022] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
Neurodevelopmental disorders encompass a group of debilitating diseases presenting with motor and cognitive dysfunction, with variable age of onset and disease severity. Advances in genetic diagnostic tools have facilitated the identification of several monogenic chromatin remodeling diseases that cause Neurodevelopmental disorders. Chromatin remodelers play a key role in the neuro-epigenetic landscape and regulation of brain development; it is therefore not surprising that mutations, leading to loss of protein function, result in aberrant neurodevelopment. Heterozygous, usually de novo mutations in histone lysine methyltransferases have been described in patients leading to haploinsufficiency, dysregulated protein levels and impaired protein function. Studies in animal models and patient-derived cell lines, have highlighted the role of histone lysine methyltransferases in the regulation of cell self-renewal, cell fate specification and apoptosis. To date, in depth studies of histone lysine methyltransferases in oncology have provided strong evidence of histone lysine methyltransferase dysregulation as a determinant of cancer progression and drug resistance. As a result, histone lysine methyltransferases have become an important therapeutic target for the treatment of different cancer forms. Despite recent advances, we still lack knowledge about the role of histone lysine methyltransferases in neuronal development. This has hampered both the study and development of precision therapies for histone lysine methyltransferases-related Neurodevelopmental disorders. In this review, we will discuss the current knowledge of the role of histone lysine methyltransferases in neuronal development and disease progression. We will also discuss how RNA-based technologies using small-activating RNAs could potentially provide a novel therapeutic approach for the future treatment of histone lysine methyltransferase haploinsufficiency in these Neurodevelopmental disorders, and how they could be first tested in state-of-the-art patient-derived neuronal models.
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Affiliation(s)
- Charlotte Roth
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Helena Kilpinen
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Neurology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Serena Barral
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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16
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Sapkota S, Gantier MP. Selecting Therapeutic Antisense Oligonucleotides with Gene Targeting and TLR8 Potentiating Bifunctionality. Methods Mol Biol 2023; 2691:225-234. [PMID: 37355549 DOI: 10.1007/978-1-0716-3331-1_17] [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: 06/26/2023]
Abstract
A growing body of preclinical evidence has led to the hypothesis that human Toll-like receptor 8 (hTLR8) activation in the tumor microenvironment (TME) could have potent anticancer effects through its action on monocytes, myeloid dendritic cells (mDCs), and natural killer (NK) cells. This has motivated the initiation of several clinical trials for chemical hTLR8 agonists in a variety of cancers. Concurrently, a growing number of synthetic antisense oligonucleotides (ASOs) are being developed as cancer therapeutics. We have recently reported that 2'-O-methyl (2'OMe)-modified ASOs can potentiate sensing of hTLR8 chemical agonists in a sequence-dependent manner. This suggests that select gene-targeting ASOs with anticancer activity may synergize with low-dose hTLR8 agonists in the TME. Here, we provide a detailed protocol to rapidly screen and identify such synthetic bifunctional oligonucleotides with synergistic activity on hTLR8 sensing.
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Affiliation(s)
- Sunil Sapkota
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.
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17
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Zhao JC, Saleh A, Crooke ST. SIDT2 Inhibits Phosphorothioate Antisense Oligonucleotide Activity by Regulating Cellular Localization of Lysosomes. Nucleic Acid Ther 2022; 33:108-116. [PMID: 36576400 DOI: 10.1089/nat.2022.0055] [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: 12/29/2022] Open
Abstract
Phosphorothioate (PS)-modified antisense oligonucleotide (ASO) drugs enter cells through endocytic pathways where a majority are entrapped within membrane-bound endosomes and lysosomes, representing a limiting step for antisense activity. While late endosomes have been identified as a major site for productive PS-ASO release, how lysosomes regulate PS-ASO activity beyond macromolecule degradation remains not fully understood. In this study, we reported that SID1 transmembrane family, member 2 (SIDT2), a lysosome transmembrane protein, can robustly regulate PS-ASO activity. We showed that SIDT2 is required for the proper colocalization between PS-ASO and lysosomes, suggesting an important role of SIDT2 in the entrapment of PS-ASOs in lysosomes. Mechanistically, we revealed that SIDT2 regulates lysosome cellular location. Lysosome location is largely determined by its movement along microtubules. Interestingly, we also observed an enrichment of proteins involved in microtubule function among SIDT2-binding proteins, suggesting that SIDT2 regulates lysosome location via its interaction with microtubule-related proteins. Overall, our data suggest that lysosome protein SIDT2 inhibits PS-ASO activity potentially through its interaction with microtubule-related proteins to place lysosomes at perinuclear regions, thus, facilitating PS-ASO's localization to lysosomes for degradation.
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Affiliation(s)
- Jing Crystal Zhao
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Aurian Saleh
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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18
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Nano drug delivery systems for antisense oligonucleotides (ASO) therapeutics. J Control Release 2022; 352:861-878. [PMID: 36397636 DOI: 10.1016/j.jconrel.2022.10.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/02/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022]
Abstract
Cancer, infectious diseases, and metabolic and hereditary genetic disorders are a global health burden affecting millions of people, with contemporary treatments offering limited relief. Antisense technology treats diseases by targeting their causal agents using its ability to alter or inhibit endogenous or malfunctioning genes. Nine antisense oligonucleotide (ASO) drugs that represent four different chemical classes have been approved for the treatment of rare diseases, including nusinersen, the first new oligonucleotide-based drug. Advances in medicinal chemistry, understanding the molecular pathways, and the availability of vast genetic data have resulted in enormous improvements in the therapeutic performance of ASO drugs; however, their susceptibility to degradation in the circulation, rapid renal clearance, and immunostimulatory adverse effects greatly limit their clinical applications. An increasing number of ASO-based therapeutics is being tested in clinical trials. Improvements to the delivery of ASO drugs could potentially change the therapeutic landscape for many conditions in the near future. This review describes the technological advances and developments in drug delivery systems pertaining to ASO therapeutics.
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19
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Terada C, Kawamoto S, Yamayoshi A, Yamamoto T. Chemistry of Therapeutic Oligonucleotides That Drives Interactions with Biomolecules. Pharmaceutics 2022; 14:pharmaceutics14122647. [PMID: 36559141 PMCID: PMC9781680 DOI: 10.3390/pharmaceutics14122647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Oligonucleotide therapeutics that can modulate gene expression have been gradually developed for clinical applications over several decades. However, rapid advances have been made in recent years. Artificial nucleic acid technology has overcome many challenges, such as (1) poor target affinity and selectivity, (2) low in vivo stability, and (3) classical side effects, such as immune responses; thus, its application in a wide range of disorders has been extensively examined. However, even highly optimized oligonucleotides exhibit side effects, which limits the general use of this class of agents. In this review, we discuss the physicochemical characteristics that aid interactions between drugs and molecules that belong to living organisms. By systematically organizing the related data, we hope to explore avenues for symbiotic engineering of oligonucleotide therapeutics that will result in more effective and safer drugs.
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20
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Wang G, Du Y, Ma X, Ye F, Qin Y, Wang Y, Xiang Y, Tao R, Chen T. Thermophilic Nucleic Acid Polymerases and Their Application in Xenobiology. Int J Mol Sci 2022; 23:ijms232314969. [PMID: 36499296 PMCID: PMC9738464 DOI: 10.3390/ijms232314969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
Thermophilic nucleic acid polymerases, isolated from organisms that thrive in extremely hot environments, possess great DNA/RNA synthesis activities under high temperatures. These enzymes play indispensable roles in central life activities involved in DNA replication and repair, as well as RNA transcription, and have already been widely used in bioengineering, biotechnology, and biomedicine. Xeno nucleic acids (XNAs), which are analogs of DNA/RNA with unnatural moieties, have been developed as new carriers of genetic information in the past decades, which contributed to the fast development of a field called xenobiology. The broad application of these XNA molecules in the production of novel drugs, materials, and catalysts greatly relies on the capability of enzymatic synthesis, reverse transcription, and amplification of them, which have been partially achieved with natural or artificially tailored thermophilic nucleic acid polymerases. In this review, we first systematically summarize representative thermophilic and hyperthermophilic polymerases that have been extensively studied and utilized, followed by the introduction of methods and approaches in the engineering of these polymerases for the efficient synthesis, reverse transcription, and amplification of XNAs. The application of XNAs facilitated by these polymerases and their mutants is then discussed. In the end, a perspective for the future direction of further development and application of unnatural nucleic acid polymerases is provided.
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21
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Hyjek-Składanowska M, Anderson BA, Mykhaylyk V, Orr C, Wagner A, Poznański J, Skowronek K, Seth P, Nowotny M. Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding. Nucleic Acids Res 2022; 51:1409-1423. [PMID: 36124719 PMCID: PMC9943651 DOI: 10.1093/nar/gkac774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/09/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
The introduction of phosphorothioate (PS) linkages to the backbone of therapeutic nucleic acids substantially increases their stability and potency. It also affects their interactions with cellular proteins, but the molecular mechanisms that underlie this effect are poorly understood. Here, we report structural and biochemical studies of interactions between annexin A2, a protein that does not possess any known canonical DNA binding domains, and phosphorothioate-modified antisense oligonucleotides. We show that a unique mode of hydrophobic interactions between a sulfur atom of the phosphorothioate group and lysine and arginine residues account for the enhanced affinity of modified nucleic acid for the protein. Our results demonstrate that this mechanism of interaction is observed not only for nucleic acid-binding proteins but can also account for the association of PS oligonucleotides with other proteins. Using the anomalous diffraction of sulfur, we showed that preference for phosphorothioate stereoisomers is determined by the hydrophobic environment around the PS linkage that comes not only from protein but also from additional structural features within the ASO such as 5-Me groups on cytosine nucleobases.
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Affiliation(s)
- Malwina Hyjek-Składanowska
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | | | | | - Christian Orr
- Diamond Light Source, Harwell Campus, Didcot OX11 0DE, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Campus, Didcot OX11 0DE, UK
| | - Jarosław T Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Krzysztof Skowronek
- Biophysics and Structural Biology Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Punit Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Marcin Nowotny
- To whom correspondence should be addressed. Tel: +48 22 597 0717; Fax: +48 22 597 0715;
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22
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Luo M, Lee LKC, Peng B, Choi CHJ, Tong WY, Voelcker NH. Delivering the Promise of Gene Therapy with Nanomedicines in Treating Central Nervous System Diseases. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201740. [PMID: 35851766 PMCID: PMC9475540 DOI: 10.1002/advs.202201740] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/19/2022] [Indexed: 06/01/2023]
Abstract
Central Nervous System (CNS) diseases, such as Alzheimer's diseases (AD), Parkinson's Diseases (PD), brain tumors, Huntington's disease (HD), and stroke, still remain difficult to treat by the conventional molecular drugs. In recent years, various gene therapies have come into the spotlight as versatile therapeutics providing the potential to prevent and treat these diseases. Despite the significant progress that has undoubtedly been achieved in terms of the design and modification of genetic modulators with desired potency and minimized unwanted immune responses, the efficient and safe in vivo delivery of gene therapies still poses major translational challenges. Various non-viral nanomedicines have been recently explored to circumvent this limitation. In this review, an overview of gene therapies for CNS diseases is provided and describes recent advances in the development of nanomedicines, including their unique characteristics, chemical modifications, bioconjugations, and the specific applications that those nanomedicines are harnessed to deliver gene therapies.
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Affiliation(s)
- Meihua Luo
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Australian Institute for Bioengineering and Nanotechnologythe University of QueenslandSt LuciaQLD4072Australia
| | - Leo Kit Cheung Lee
- Department of Biomedical EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong
| | - Bo Peng
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Frontiers Science Center for Flexible ElectronicsXi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical materials & EngineeringNorthwestern Polytechnical UniversityXi'an710072China
| | - Chung Hang Jonathan Choi
- Department of Biomedical EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong
| | - Wing Yin Tong
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
| | - Nicolas H. Voelcker
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO)ClaytonVIC3168Australia
- Melbourne Centre for NanofabricationVictorian Node of the Australian National Fabrication Facility151 Wellington RoadClaytonVIC3168Australia
- Materials Science and EngineeringMonash University14 Alliance LaneClaytonVIC3800Australia
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23
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Zhang L, Liang XH, De Hoyos CL, Migawa M, Nichols JG, Freestone G, Tian J, Seth PP, Crooke ST. The Combination of Mesyl-Phosphoramidate Inter-Nucleotide Linkages and 2'- O-Methyl in Selected Positions in the Antisense Oligonucleotide Enhances the Performance of RNaseH1 Active PS-ASOs. Nucleic Acid Ther 2022; 32:401-411. [PMID: 35861704 PMCID: PMC9595634 DOI: 10.1089/nat.2022.0005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Antisense oligonucleotides (ASOs) that mediate RNA target degradation by RNase H1 are used as drugs to treat various diseases. Previously we found that introduction of a single 2'-O-methyl (2'-OMe) modification in position 2 of the central deoxynucleotide region of a gapmer phosphorothioate (PS) ASO, in which several residues at the termini are 2'-methoxyethyl, 2' constrained ethyl, or locked nucleic acid, dramatically reduced cytotoxicity with only modest effects on potency. More recently, we demonstrated that replacement of the PS linkage at position 2 or 3 in the gap with a mesyl-phosphoramidate (MsPA) linkage also significantly reduced toxicity without meaningful loss of potency and increased the elimination half-life of the ASOs. In this study, we evaluated the effects of the combination of MsPA linkages and 2'-OMe nucleotides on PS ASO performance. We found that two MsPA modifications at the 5' end of the gap or in the 3'-wing of a Gap 2'-OMe PS ASO substantially increased the activity of ASOs with OMe at position 2 of the gap without altering the safety profile. Such effects were observed with multiple sequences in cells and animals. Thus, the MsPA modification improves the RNase H1 cleavage rate of PS ASOs with a 2'-OMe in the gap, significantly reduces binding of proteins involved in cytotoxicity, and prolongs elimination half-lives.
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Affiliation(s)
- Lingdi Zhang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Cheryl Li De Hoyos
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Michael Migawa
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Joshua G Nichols
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Graeme Freestone
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Jun Tian
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Punit P Seth
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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24
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Zhang L, Bernardo KD, Vickers TA, Tian J, Liang XH, Crooke ST. NAT10 and DDX21 Proteins Interact with RNase H1 and Affect the Performance of Phosphorothioate Oligonucleotides. Nucleic Acid Ther 2022; 32:280-299. [PMID: 35852833 PMCID: PMC9416547 DOI: 10.1089/nat.2021.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
RNase H1-dependent phosphorothioate oligonucleotides (PS-ASOs) have been developed to treat various diseases through specific degradation of target RNAs. Although many factors or features of RNA and PS-ASOs have been demonstrated to affect antisense activity of PS-ASOs, little is known regarding the roles of RNase H1-associated proteins in PS-ASO performance. In this study, we report that two nucleolar proteins, NAT10 and DDX21, interact with RNase H1 and affect the potency and safety of PS-ASOs. The interactions of these two proteins with RNase H1 were determined using BioID proximity labeling in cells and confirmed biochemically. Reduction of NAT10 and DDX21 decreased PS-ASO activity in cells, and purified NAT10 and DDX21 proteins enhanced RNase H1 cleavage rates, indicating that these two proteins facilitate RNase H1 endoribonuclease activity. Consistently, reduction of these proteins increased the levels of R-loops, and impaired pre-rRNA processing. In addition, reduction of the two proteins increased the cytotoxicity of toxic PS-ASOs, and treatment of toxic PS-ASOs also altered the localization of these proteins. Together, this study shows for the first time that NAT10 and DDX21 interact with RNase H1 protein and enhance its enzymatic activity, contributing to the potency and safety of PS-ASOs.
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Affiliation(s)
- Lingdi Zhang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Karla D. Bernardo
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Timothy A. Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Jun Tian
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Xue-hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T. Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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25
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Khang M, Bindra RS, Mark Saltzman W. Intrathecal delivery and its applications in leptomeningeal disease. Adv Drug Deliv Rev 2022; 186:114338. [PMID: 35561835 DOI: 10.1016/j.addr.2022.114338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 04/26/2022] [Accepted: 05/06/2022] [Indexed: 12/22/2022]
Abstract
Intrathecal delivery (IT) of opiates into the cerebrospinal fluid (CSF) for anesthesia and pain relief has been used clinically for decades, but this relatively straightforward approach of bypassing the blood-brain barrier has been underutilized for other indications because of its lack of utility in delivering small lipid-soluble drugs. However, emerging evidence suggests that IT drug delivery be an efficacious strategy for the treatment of cancers in which there is leptomeningeal spread of disease. In this review, we discuss CSF flow dynamics and CSF clearance pathways in the context of intrathecal delivery. We discuss human and animal studies of several new classes of therapeutic agents-cellular, protein, nucleic acid, and nanoparticle-based small molecules-that may benefit from IT delivery. The complexity of the CSF compartment presents several key challenges in predicting biodistribution of IT-delivered drugs. New approaches and strategies are needed that can overcome the high rates of turnover in the CSF to reach specific tissues or cellular targets.
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26
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RNA modifications can affect RNase H1-mediated PS-ASO activity. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:814-828. [PMID: 35664704 PMCID: PMC9136273 DOI: 10.1016/j.omtn.2022.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/07/2022] [Indexed: 11/21/2022]
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27
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Flynn LL, Li R, Pitout IL, Aung-Htut MT, Larcher LM, Cooper JAL, Greer KL, Hubbard A, Griffiths L, Bond CS, Wilton SD, Fox AH, Fletcher S. Single Stranded Fully Modified-Phosphorothioate Oligonucleotides can Induce Structured Nuclear Inclusions, Alter Nuclear Protein Localization and Disturb the Transcriptome In Vitro. Front Genet 2022; 13:791416. [PMID: 35464859 PMCID: PMC9019733 DOI: 10.3389/fgene.2022.791416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/02/2022] [Indexed: 01/12/2023] Open
Abstract
Oligonucleotides and nucleic acid analogues that alter gene expression are now showing therapeutic promise in human disease. Whilst the modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, such modifications may also confer unexpected physicochemical and biological properties. Gapmer mixed-modified and DNA oligonucleotides on a phosphorothioate backbone can bind non-specifically to intracellular proteins to form a variety of toxic inclusions, driven by the phosphorothioate linkages, but also influenced by the oligonucleotide sequence. Recently, the non-antisense or other off-target effects of 2′ O- fully modified phosphorothioate linkage oligonucleotides are becoming better understood. Here, we report chemistry-specific effects of oligonucleotides composed of modified or unmodified bases, with phosphorothioate linkages, on subnuclear organelles and show altered distribution of nuclear proteins, the appearance of highly stable and strikingly structured nuclear inclusions, and disturbed RNA processing in primary human fibroblasts and other cultured cells. Phosphodiester, phosphorodiamidate morpholino oligomers, and annealed complimentary phosphorothioate oligomer duplexes elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of transfected fibroblasts exhibiting such disruption. Our data add to the growing body of evidence of off-target effects of some phosphorothioate nucleic acid drugs in primary cells and suggest alternative approaches to mitigate these effects.
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Affiliation(s)
- Loren L Flynn
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,Black Swan Pharmaceuticals, Wake Forest, NC, United States
| | - Ruohan Li
- Cell and Tissue Therapies WA, Royal Perth Hospital, Perth, WA, Australia.,School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Ianthe L Pitout
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,PYC Therapeutics, Nedlands, WA, Australia
| | - May T Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Leon M Larcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Jack A L Cooper
- School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Kane L Greer
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Alysia Hubbard
- Centre for Microscopy, Characterization and Analysis, The University of Western Australia, Nedlands, WA, Australia
| | - Lisa Griffiths
- Anatomical Pathology, Department of Health, Nedlands, WA, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,PYC Therapeutics, Nedlands, WA, Australia
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28
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Andersson P. Preclinical Safety Assessment of Therapeutic Oligonucleotides. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2434:355-370. [PMID: 35213031 DOI: 10.1007/978-1-0716-2010-6_25] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
During the last decade, therapeutic oligonucleotide drugs (OND) have witnessed a tremendous development in chemistry and mechanistic understanding that have translated into successful clinical applications. Depending on the specific OND mechanism, chemistry, and design, the DMPK and toxicity properties can vary significantly between different OND classes and delivery approaches, the latter including lipid formulations or conjugation approaches to enhance productive OND uptake. At the same time, with the only difference between compounds being the nucleobase sequence, ONDs with same mechanism of action, chemistry, and design show relatively consistent behavior, allowing certain extrapolations between compounds within an OND class. This chapter provides a summary of the most common toxicities, the improved mechanistic understanding and the safety assessment activities performed for therapeutic oligonucleotides during the drug discovery and development process. Several of the considerations described for therapeutic applications should also be of value for the scientists mainly using oligonucleotides as research tools to explore various biological processes.
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Affiliation(s)
- Patrik Andersson
- Safety Innovation, Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
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29
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Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
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Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
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30
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Hirano Y, Komatsu Y. Promotion of cytoplasmic localization of oligonucleotides by connecting cross-linked duplexes. RSC Adv 2022; 12:24471-24477. [PMID: 36128385 PMCID: PMC9425837 DOI: 10.1039/d2ra04375k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/22/2022] [Indexed: 11/21/2022] Open
Abstract
An interstrand cross-linked duplex (CD) modification promoted antisense oligonucleotide to be localized in the cytoplasm, resulting in effective knockdown microRNA in cytoplasm. In contrast, single-stranded antisense was confined in the nucleus.
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Affiliation(s)
- Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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31
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Wdowikowska A, Janicka M. Antisense oligonucleotide technology as a research tool in plant biology. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 49:1-12. [PMID: 34794541 DOI: 10.1071/fp21194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
An antisense oligonucleotide (ASO) is a short single-stranded deoxyribonucleotide complementary to the sense strand of a selected nucleic acid. As a result, an ASO can modulate gene expression through several mechanisms. The technology based on ASO has already been applied in studies on gene function in mammalian cells and selective therapeutic strategies for many diseases. The conceptual simplicity and low cost of this method, and the developments in the field of plant genome sequencing observed in the last decades, have paved the way for the ASO method also in plant biology. It is applied in gene function analysis as well as the development of non-invasive plant production technology involving gene modifications without transgenesis. Therefore, the first part of this review provides a comprehensive overview of the structure, mechanism of action and delivery methods of ASOs in plants and shows the most important features essential for the proper design of individual experiments. We also discuss potential issues and difficulties that may arise during practical ASO implementation. The second part of this article contains an analysis of ASO applications in various studies in the field of plant biology. We presented for the first time that ASOs were also successfully applied in cucumber.
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Affiliation(s)
- Anna Wdowikowska
- Department of Plant Molecular Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
| | - Malgorzata Janicka
- Department of Plant Molecular Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
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32
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Epple S, El-Sagheer AH, Brown T. Artificial nucleic acid backbones and their applications in therapeutics, synthetic biology and biotechnology. Emerg Top Life Sci 2021; 5:691-697. [PMID: 34297063 PMCID: PMC8726046 DOI: 10.1042/etls20210169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022]
Abstract
The modification of DNA or RNA backbones is an emerging technology for therapeutic oligonucleotides, synthetic biology and biotechnology. Despite a plethora of reported artificial backbones, their vast potential is not fully utilised. Limited synthetic accessibility remains a major bottleneck for the wider application of backbone-modified oligonucleotides. Thus, a variety of readily accessible artificial backbones and robust methods for their introduction into oligonucleotides are urgently needed to utilise their full potential in therapeutics, synthetic biology and biotechnology.
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Affiliation(s)
- Sven Epple
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Afaf H. El-Sagheer
- Chemistry Research Laboratory, University of Oxford, 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
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
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33
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Intramuscular Evaluation of Chimeric Locked Nucleic Acid/2' OMethyl-Modified Antisense Oligonucleotides for Targeted Exon 23 Skipping in Mdx Mice. Pharmaceuticals (Basel) 2021; 14:ph14111113. [PMID: 34832896 PMCID: PMC8622172 DOI: 10.3390/ph14111113] [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: 10/08/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/02/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal disorder characterised by progressive muscle wasting. It is caused by mutations in the dystrophin gene, which disrupt the open reading frame leading to the loss of functional dystrophin protein in muscle fibres. Antisense oligonucleotide (AON)-mediated skipping of the mutated exon, which allows production of a truncated but partially functional dystrophin protein, has been at the forefront of DMD therapeutic research for over two decades. Nonetheless, novel nucleic acid modifications and AON designs are continuously being developed to improve the clinical benefit profile of current drugs in the DMD pipeline. We herein designed a series of 15mer and 20mer AONs, consisting of 2′O-Methyl (2′OMe)- and locked nucleic acid (LNA)-modified nucleotides in different percentage compositions, and assessed their efficiency in inducing exon 23 skipping and dystrophin restoration in locally injected muscles of mdx mice. We demonstrate that LNA/2′OMe AONs with a 30% LNA composition were significantly more potent in inducing exon skipping and dystrophin restoration in treated mdx muscles, compared to a previously tested 2′OMe AON and LNA/2′OMe chimeras with lower or higher LNA compositions. These results underscore the therapeutic potential of LNA/2′OMe AONs, paving the way for further experimentation to evaluate their benefit-toxicity profile following systemic delivery.
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34
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Anderson BA, Freestone GC, Low A, De-Hoyos CL, Iii WJD, Østergaard ME, Migawa MT, Fazio M, Wan WB, Berdeja A, Scandalis E, Burel SA, Vickers TA, Crooke ST, Swayze EE, Liang X, Seth PP. Towards next generation antisense oligonucleotides: mesylphosphoramidate modification improves therapeutic index and duration of effect of gapmer antisense oligonucleotides. Nucleic Acids Res 2021; 49:9026-9041. [PMID: 34417625 PMCID: PMC8450106 DOI: 10.1093/nar/gkab718] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/30/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022] Open
Abstract
The PS modification enhances the nuclease stability and protein binding properties of gapmer antisense oligonucleotides (ASOs) and is one of very few modifications that support RNaseH1 activity. We evaluated the effect of introducing stereorandom and chiral mesyl-phosphoramidate (MsPA) linkages in the DNA gap and flanks of gapmer PS ASOs and characterized the effect of these linkages on RNA-binding, nuclease stability, protein binding, pro-inflammatory profile, antisense activity and toxicity in cells and in mice. We show that all PS linkages in a gapmer ASO can be replaced with MsPA without compromising chemical stability and RNA binding affinity but these designs reduced activity. However, replacing up to 5 PS in the gap with MsPA was well tolerated and replacing specific PS linkages at appropriate locations was able to greatly reduce both immune stimulation and cytotoxicity. The improved nuclease stability of MsPA over PS translated to significant improvement in the duration of ASO action in mice which was comparable to that of enhanced stabilized siRNA designs. Our work highlights the combination of PS and MsPA linkages as a next generation chemical platform for identifying ASO drugs with improved potency and therapeutic index, reduced pro-inflammatory effects and extended duration of effect.
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Affiliation(s)
| | | | - Audrey Low
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | | | | | - Michael T Migawa
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael Fazio
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - W Brad Wan
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Andres Berdeja
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eli Scandalis
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | | | - Stanley T Crooke
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xuehai Liang
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
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35
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Valenzuela A, Tardiveau C, Ayuso M, Buyssens L, Bars C, Van Ginneken C, Fant P, Leconte I, Braendli-Baiocco A, Parrott N, Schmitt G, Tessier Y, Barrow P, Van Cruchten S. Safety Testing of an Antisense Oligonucleotide Intended for Pediatric Indications in the Juvenile Göttingen Minipig, including an Evaluation of the Ontogeny of Key Nucleases. Pharmaceutics 2021; 13:1442. [PMID: 34575518 PMCID: PMC8470776 DOI: 10.3390/pharmaceutics13091442] [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: 07/27/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
The adult Göttingen Minipig is an acknowledged model for safety assessment of antisense oligonucleotide (ASO) drugs developed for adult indications. To assess whether the juvenile Göttingen Minipig is also a suitable nonclinical model for pediatric safety assessment of ASOs, we performed an 8-week repeat-dose toxicity study in different age groups of minipigs ranging from 1 to 50 days of age. The animals received a weekly dose of a phosphorothioated locked-nucleic-acid-based ASO that was assessed previously for toxicity in adult minipigs. The endpoints included toxicokinetic parameters, in-life monitoring, clinical pathology, and histopathology. Additionally, the ontogeny of key nucleases involved in ASO metabolism and pharmacologic activity was investigated using quantitative polymerase chain reaction and nuclease activity assays. Similar clinical chemistry and toxicity findings were observed; however, differences in plasma and tissue exposures as well as pharmacologic activity were seen in the juvenile minipigs when compared with the adult data. The ontogeny study revealed a differential nuclease expression and activity, which could affect the metabolic pathway and pharmacologic effect of ASOs in different tissues and age groups. These data indicate that the juvenile Göttingen Minipig is a promising nonclinical model for safety assessment of ASOs intended to treat disease in the human pediatric population.
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Affiliation(s)
- Allan Valenzuela
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| | - Claire Tardiveau
- Charles River Laboratories France Safety Assessment SAS, 69210 Saint-Germain-Nuelles, France; (C.T.); (P.F.); (I.L.)
| | - Miriam Ayuso
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| | - Laura Buyssens
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| | - Chloe Bars
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| | - Chris Van Ginneken
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| | - Pierluigi Fant
- Charles River Laboratories France Safety Assessment SAS, 69210 Saint-Germain-Nuelles, France; (C.T.); (P.F.); (I.L.)
| | - Isabelle Leconte
- Charles River Laboratories France Safety Assessment SAS, 69210 Saint-Germain-Nuelles, France; (C.T.); (P.F.); (I.L.)
| | - Annamaria Braendli-Baiocco
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La-Roche, Ltd., 4070 Basel, Switzerland; (A.B.-B.); (N.P.); (G.S.); (Y.T.); (P.B.)
| | - Neil Parrott
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La-Roche, Ltd., 4070 Basel, Switzerland; (A.B.-B.); (N.P.); (G.S.); (Y.T.); (P.B.)
| | - Georg Schmitt
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La-Roche, Ltd., 4070 Basel, Switzerland; (A.B.-B.); (N.P.); (G.S.); (Y.T.); (P.B.)
| | - Yann Tessier
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La-Roche, Ltd., 4070 Basel, Switzerland; (A.B.-B.); (N.P.); (G.S.); (Y.T.); (P.B.)
| | - Paul Barrow
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La-Roche, Ltd., 4070 Basel, Switzerland; (A.B.-B.); (N.P.); (G.S.); (Y.T.); (P.B.)
| | - Steven Van Cruchten
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
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Nanoparticles-Based Oligonucleotides Delivery in Cancer: Role of Zebrafish as Animal Model. Pharmaceutics 2021; 13:pharmaceutics13081106. [PMID: 34452067 PMCID: PMC8400075 DOI: 10.3390/pharmaceutics13081106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 12/29/2022] Open
Abstract
Oligonucleotide (ON) therapeutics are molecular target agents composed of chemically synthesized DNA or RNA molecules capable of inhibiting gene expression or protein function. How ON therapeutics can efficiently reach the inside of target cells remains a problem still to be solved in the majority of potential clinical applications. The chemical structure of ON compounds could affect their capability to pass through the plasma membrane. Other key factors are nuclease degradation in the extracellular space, renal clearance, reticulo-endothelial system, and at the target cell level, the endolysosomal system and the possible export via exocytosis. Several delivery platforms have been proposed to overcome these limits including the use of lipidic, polymeric, and inorganic nanoparticles, or hybrids between them. The possibility of evaluating the efficacy of the proposed therapeutic strategies in useful in vivo models is still a pivotal need, and the employment of zebrafish (ZF) models could expand the range of possibilities. In this review, we briefly describe the main ON therapeutics proposed for anticancer treatment, and the different strategies employed for their delivery to cancer cells. The principal features of ZF models and the pros and cons of their employment in the development of ON-based therapeutic strategies are also discussed.
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Liang XH, Nichols JG, De Hoyos CL, Sun H, Zhang L, Crooke ST. Golgi-58K can re-localize to late endosomes upon cellular uptake of PS-ASOs and facilitates endosomal release of ASOs. Nucleic Acids Res 2021; 49:8277-8293. [PMID: 34244781 PMCID: PMC8373082 DOI: 10.1093/nar/gkab599] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 11/14/2022] Open
Abstract
Phosphorothioate (PS) modified antisense oligonucleotide (ASO) drugs can trigger RNase H1 cleavage of cellular target RNAs to modulate gene expression. Internalized PS-ASOs must be released from membraned endosomal organelles, a rate limiting step that is not well understood. Recently we found that M6PR transport between Golgi and late endosomes facilitates productive release of PS-ASOs, raising the possibility that Golgi-mediated transport may play important roles in PS-ASO activity. Here we further evaluated the involvement of Golgi in PS-ASO activity by examining additional Golgi proteins. Reduction of certain Golgi proteins, including Golgi-58K, GCC1 and TGN46, decreased PS-ASO activity, without substantial effects on Golgi integrity. Upon PS-ASO cellular uptake, Golgi-58K was recruited to late endosomes where it colocalized with PS-ASOs. Reduction of Golgi-58K caused slower PS-ASO release from late endosomes, decreased GCC2 late endosome relocalization, and led to slower retrograde transport of M6PR from late endosomes to trans-Golgi. Late endosome relocalization of Golgi-58K requires Hsc70, and is most likely mediated by PS-ASO-protein interactions. Together, these results suggest a novel function of Golgi-58K in mediating Golgi-endosome transport and indicate that the Golgi apparatus plays an important role in endosomal release of PS-ASO, ensuring antisense activity.
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Affiliation(s)
| | | | | | - Hong Sun
- Antisense Drug Discovery, Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Lingdi Zhang
- Core Antisense Research, Carlsbad, CA 92010, USA
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38
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Barkau CL, O'Reilly D, Eddington SB, Damha MJ, Gagnon KT. Small nucleic acids and the path to the clinic for anti-CRISPR. Biochem Pharmacol 2021; 189:114492. [PMID: 33647260 PMCID: PMC8725204 DOI: 10.1016/j.bcp.2021.114492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
CRISPR-based therapeutics have entered clinical trials but no methods to inhibit Cas enzymes have been demonstrated in a clinical setting. The ability to inhibit CRISPR-based gene editing or gene targeting drugs should be considered a critical step in establishing safety standards for many CRISPR-Cas therapeutics. Inhibitors can act as a failsafe or as an adjuvant to reduce off-target effects in patients. In this review we discuss the need for clinical inhibition of CRISPR-Cas systems and three existing inhibitor technologies: anti-CRISPR (Acr) proteins, small molecule Cas inhibitors, and small nucleic acid-based CRISPR inhibitors, CRISPR SNuBs. Due to their unique properties and the recent successes of other nucleic acid-based therapeutics, CRISPR SNuBs appear poised for clinical application in the near-term.
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Affiliation(s)
- Christopher L Barkau
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Daniel O'Reilly
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Seth B Eddington
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA.
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39
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Zhu Y, Dai H, Wang Y, Liang Y, Feng W, Yuan Y. Targeting FEN1 Suppresses the Proliferation of Chronic Myeloid Leukemia Cells Through Regulating Alternative End-Joining Pathways. DNA Cell Biol 2021; 40:1101-1111. [PMID: 34156283 DOI: 10.1089/dna.2021.0239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Chronic myeloid leukemia (CML) is characterized by the formation of the BCR-ABL fusion gene. The BCR-ABL protein leads to an increased level of reactive oxygen species, which is a major cause of endogenous DNA double-strand breaks (DSBs). CML cells are prone to rely on a highly mutagenic alternative end-joining (Alt-EJ) pathway to cope with enhanced DSBs, which aggravates chromosomal instability. Hence, targeting dysregulated DNA repair proteins provides new insights into cancer treatment. In this study, we discovered the abnormal upregulation of Flap endonuclease 1 (FEN1) in CML, as well as FEN1's participation in the error-prone Alt-EJ repair pathway and its interplay with DNA Ligase1 and proliferating cell nuclear antigen in DSB repair. Knockdown of FEN1 by shRNA not only inhibited the proliferation and induced apoptosis but also enhanced the efficacy of imatinib (IM) in drug-resistant CML cell K562/G01. Moreover, excessive DSB accumulation was detected after FEN1 inhibition. In summary, our results demonstrated that FEN1 is a promising therapeutic target in CML treatment. This work extends the understanding of regulating abnormal DSB repair for cancer treatment.
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Affiliation(s)
- Yalin Zhu
- Department of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hongdan Dai
- Department of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yonghong Wang
- Department of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yang Liang
- Department of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Wenli Feng
- Department of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ying Yuan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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40
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Asada K, Sakaue F, Nagata T, Zhang JC, Yoshida-Tanaka K, Abe A, Nawa M, Nishina K, Yokota T. Short DNA/RNA heteroduplex oligonucleotide interacting proteins are key regulators of target gene silencing. Nucleic Acids Res 2021; 49:4864-4876. [PMID: 33928345 PMCID: PMC8136785 DOI: 10.1093/nar/gkab258] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/25/2021] [Accepted: 04/23/2021] [Indexed: 01/31/2023] Open
Abstract
Antisense oligonucleotide (ASO)-based therapy is one of the next-generation therapy, especially targeting neurological disorders. Many cases of ASO-dependent gene expression suppression have been reported. Recently, we developed a tocopherol conjugated DNA/RNA heteroduplex oligonucleotide (Toc-HDO) as a new type of drug. Toc-HDO is more potent, stable, and efficiently taken up by the target tissues compared to the parental ASO. However, the detailed mechanisms of Toc-HDO, including its binding proteins, are unknown. Here, we developed native gel shift assays with fluorescence-labeled nucleic acids samples extracted from mice livers. These assays revealed two Toc-HDO binding proteins, annexin A5 (ANXA5) and carbonic anhydrase 8 (CA8). Later, we identified two more proteins, apurinic/apyrimidinic endodeoxyribonuclease 1 (APEX1) and flap structure-specific endonuclease 1 (FEN1) by data mining. shRNA knockdown studies demonstrated that all four proteins regulated Toc-HDO activity in Hepa1-6, mouse hepatocellular cells. In vitro binding assays and fluorescence polarization assays with purified recombinant proteins characterized the identified proteins and pull-down assays with cell lysates demonstrated the protein binding to the Toc-HDO and ASO in a biological environment. Taken together, our findings provide a brand new molecular biological insight as well as future directions for HDO-based disease therapy.
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Affiliation(s)
- Ken Asada
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Fumika Sakaue
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Ji-chun Zhang
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Kie Yoshida-Tanaka
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Aya Abe
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Makiko Nawa
- Laboratory of Cytometry and Proteome Research, Nanken-Kyoten and Research Core Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kazutaka Nishina
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
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41
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Overcoming the challenges of tissue delivery for oligonucleotide therapeutics. Trends Pharmacol Sci 2021; 42:588-604. [PMID: 34020790 DOI: 10.1016/j.tips.2021.04.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/07/2021] [Accepted: 04/20/2021] [Indexed: 12/19/2022]
Abstract
Synthetic therapeutic oligonucleotides (STO) represent the third bonafide platform for drug discovery in the pharmaceutical industry after small molecule and protein therapeutics. So far, thirteen STOs have been approved by regulatory agencies and over one hundred of them are in different stages of clinical trials. STOs hybridize to their target RNA or DNA in cells via Watson-Crick base pairing to exert their pharmacological effects. This unique class of therapeutic agents has the potential to target genes and gene products that are considered undruggable by other therapeutic platforms. However, STOs must overcome several extracellular and intracellular obstacles to interact with their biological RNA targets inside cells. These obstacles include degradation by extracellular nucleases, scavenging by the reticuloendothelial system, filtration by the kidney, traversing the capillary endothelium to access the tissue interstitium, cell-surface receptor-mediated endocytic uptake, and escape from endolysosomal compartments to access the nuclear and/or cytoplasmic compartments where their targets reside. In this review, we present the recent advances in this field with a specific focus on antisense oligonucleotides (ASOs) and siRNA therapeutics.
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42
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Hammond SM, Sergeeva OV, Melnikov PA, Goli L, Stoodley J, Zatsepin TS, Stetsenko DA, Wood MJA. Mesyl Phosphoramidate Oligonucleotides as Potential Splice-Switching Agents: Impact of Backbone Structure on Activity and Intracellular Localization. Nucleic Acid Ther 2021; 31:190-200. [PMID: 33989066 DOI: 10.1089/nat.2020.0860] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A series of 2'-deoxy and novel 2'-O-methyl and 2'-O-(2-methoxyethyl) (2'-MOE) oligonucleotides with internucleotide methanesulfonyl (mesyl, μ) or 1-butanesulfonyl (busyl, β) phosphoramidate groups has been synthesized for evaluation as potential splice-switching oligonucleotides. Evaluation of their splice-switching activity in spinal muscular atrophy patient-derived fibroblasts revealed no significant difference in splice-switching efficacy between 2'-MOE mesyl oligonucleotide and the corresponding phosphorothioate (nusinersen). Yet, a survival study with model neonatal mice has shown the antisense 2'-MOE mesyl oligonucleotide to be inferior to nusinersen at the highest dose of 40 mg/kg. A reason for their lower activity in vivo as ascertained by cellular uptake study by fluorescent confocal microscopy in HEK293 cell line could possibly be ascribed to compromised endosomal release and/or nuclear uptake of the 2'-OMe or 2'-MOE μ- and β-oligonucleotides compared to their phosphorothioate analog.
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Affiliation(s)
- Suzan M Hammond
- Department of Paediatrics and Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Olga V Sergeeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Pavel A Melnikov
- Serbsky National Medical Research Center for Psychiatry and Narcology, Moscow, Russia
| | - Larissa Goli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Jessica Stoodley
- Department of Paediatrics and Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A Stetsenko
- Department of Physics, Novosibirsk State University, Novosibirsk, Russia.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Matthew J A Wood
- Department of Paediatrics and Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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43
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Chemical Manipulation of the Endosome Trafficking Machinery: Implications for Oligonucleotide Delivery. Biomedicines 2021; 9:biomedicines9050512. [PMID: 34063104 PMCID: PMC8148136 DOI: 10.3390/biomedicines9050512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/14/2022] Open
Abstract
Antisense oligonucleotides (ASOs), siRNA and splice switching oligonucleotides (SSOs) all have immense potential as therapeutic agents, potential that is now being validated as oligonucleotides enter the clinic. However, progress in oligonucleotide-based therapeutics has been limited by the difficulty in delivering these complex molecules to their sites of action in the cytosol or nucleus of cells within specific tissues. There are two aspects to the delivery problem. The first is that most types of oligonucleotides have poor uptake into non-hepatic tissues. The second is that much of the oligonucleotide that is taken up by cells is entrapped in endosomes where it is pharmacologically inert. It has become increasingly recognized that endosomal trapping is a key constraint on oligonucleotide therapeutics. Thus, many approaches have been devised to address this problem, primarily ones based on various nanoparticle technologies. However, recently an alternative approach has emerged that employs small molecules to manipulate intracellular trafficking processes so as to enhance oligonucleotide actions. This review presents the current status of this chemical biology approach to oligonucleotide delivery and seeks to point out possible paths for future development.
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Gagliardi M, Ashizawa AT. The Challenges and Strategies of Antisense Oligonucleotide Drug Delivery. Biomedicines 2021; 9:biomedicines9040433. [PMID: 33923688 PMCID: PMC8072990 DOI: 10.3390/biomedicines9040433] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/01/2021] [Accepted: 04/15/2021] [Indexed: 12/27/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are used to selectively inhibit the translation of disease-associated genes via Ribonuclease H (RNaseH)-mediated cleavage or steric hindrance. They are being developed as a novel and promising class of drugs targeting a wide range of diseases. Despite the great potential and numerous ASO drugs in preclinical research and clinical trials, there are many limitations to this technology. In this review we will focus on the challenges of ASO delivery and the strategies adopted to improve their stability in the bloodstream, delivery to target sites, and cellular uptake. Focusing on liposomal delivery, we will specifically describe liposome-incorporated growth factor receptor-bound protein-2 (Grb2) antisense oligodeoxynucleotide BP1001. BP1001 is unique because it is uncharged and is essentially non-toxic, as demonstrated in preclinical and clinical studies. Additionally, its enhanced biodistribution makes it an attractive therapeutic modality for hematologic malignancies as well as solid tumors. A detailed understanding of the obstacles that ASOs face prior to reaching their targets and continued advances in methods to overcome them will allow us to harness ASOs’ full potential in precision medicine.
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45
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Kim BS, Naito M, Kamegawa R, Kim HJ, Iizuka R, Funatsu T, Ueno S, Ichiki T, Kishimura A, Miyata K. Photo-reactive oligodeoxynucleotide-embedded nanovesicles (PROsomes) with switchable stability for efficient cellular uptake and gene knockdown. Chem Commun (Camb) 2021; 56:9477-9480. [PMID: 32677638 DOI: 10.1039/d0cc01750g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A photo-responsive nanovesicle is fabricated by polyion complex (PIC) formation between poly(ethylene glycol) (PEG)-block-polypeptides and photo-reactive oligodeoxynucleotides (PROs)/anti-sense oligonucleotides (ASOs). The ultraviolet (UV) light triggers reversible crosslinking between PROs and ASOs in the vesicular membrane, providing the nanovesicle with switchable stability under physiological conditions. The resulting nanovesicle allows efficient cellular internalization, leading to significant UV-triggered gene knockdown in cultured cells.
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Affiliation(s)
- Beob Soo Kim
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Mitsuru Naito
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rimpei Kamegawa
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Hyun Jin Kim
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryo Iizuka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shingo Ueno
- Innovation Center of NanoMedicine, Kawasaki Institute of Inductrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Takanori Ichiki
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. and Innovation Center of NanoMedicine, Kawasaki Institute of Inductrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Akihiro Kishimura
- Center for Molecular Systems, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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46
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Zhang L, Vickers TA, Sun H, Liang XH, Crooke ST. Binding of phosphorothioate oligonucleotides with RNase H1 can cause conformational changes in the protein and alter the interactions of RNase H1 with other proteins. Nucleic Acids Res 2021; 49:2721-2739. [PMID: 33577678 PMCID: PMC7969025 DOI: 10.1093/nar/gkab078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023] Open
Abstract
We recently found that toxic PS-ASOs can cause P54nrb and PSF nucleolar mislocalization in an RNase H1-dependent manner. To better understand the underlying mechanisms of these observations, here we utilize different biochemical approaches to demonstrate that PS-ASO binding can alter the conformations of the bound proteins, as illustrated using recombinant RNase H1, P54nrb, PSF proteins and various isolated domains. While, in general, binding of PS-ASOs or ASO/RNA duplexes stabilizes the conformations of these proteins, PS-ASO binding may also cause the unfolding of RNase H1, including both the hybrid binding domain and the catalytic domain. The extent of conformational change correlates with the binding affinity of PS-ASOs to the proteins. Consequently, PS-ASO binding to RNase H1 induces the interaction of RNase H1 with P54nrb or PSF in a 2′-modification and sequence dependent manner, and toxic PS-ASOs tend to induce more interactions than non-toxic PS-ASOs. PS-ASO binding also enhances the interaction between P54nrb and PSF. However, the interaction between RNase H1 and P32 protein can be disrupted upon binding of PS-ASOs. Together, these results suggest that stronger binding of PS-ASOs can cause greater conformational changes of the bound proteins, subsequently affecting protein–protein interactions. These observations thus provide deeper understanding of the molecular basis of PS-ASO-induced protein mislocalization or degradation observed in cells and advance our understanding of why some PS-ASOs are cytotoxic.
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Affiliation(s)
- Lingdi Zhang
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Timothy A Vickers
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Antisense Drug discovery, Ionis Pharmaceuticals, Inc. Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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47
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Antisense technology: an overview and prospectus. Nat Rev Drug Discov 2021; 20:427-453. [PMID: 33762737 DOI: 10.1038/s41573-021-00162-z] [Citation(s) in RCA: 287] [Impact Index Per Article: 95.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/13/2022]
Abstract
Antisense technology is now beginning to deliver on its promise to treat diseases by targeting RNA. Nine single-stranded antisense oligonucleotide (ASO) drugs representing four chemical classes, two mechanisms of action and four routes of administration have been approved for commercial use, including the first RNA-targeted drug to be a major commercial success, nusinersen. Although all the approved drugs are for use in patients with rare diseases, many of the ASOs in late- and middle-stage clinical development are intended to treat patients with very common diseases. ASOs in development are showing substantial improvements in potency and performance based on advances in medicinal chemistry, understanding of molecular mechanisms and targeted delivery. Moreover, the ASOs in development include additional mechanisms of action and routes of administration such as aerosol and oral formulations. Here, we describe the key technological advances that have enabled this progress and discuss recent clinical trials that illustrate the impact of these advances on the performance of ASOs in a wide range of therapeutic applications. We also consider strategic issues such as target selection and provide perspectives on the future of the field.
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Lacroix A, Sleiman HF. DNA Nanostructures: Current Challenges and Opportunities for Cellular Delivery. ACS NANO 2021; 15:3631-3645. [PMID: 33635620 DOI: 10.1021/acsnano.0c06136] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA nanotechnology has produced a wide range of self-assembled structures, offering unmatched possibilities in terms of structural design. Because of their programmable assembly and precise control of size, shape, and function, DNA particles can be used for numerous biological applications, including imaging, sensing, and drug delivery. While the biocompatibility, programmability, and ease of synthesis of nucleic acids have rapidly made them attractive building blocks, many challenges remain to be addressed before using them in biological conditions. Enzymatic hydrolysis, low cellular uptake, immune cell recognition and degradation, and unclear biodistribution profiles are yet to be solved. Rigorous methodologies are needed to study, understand, and control the fate of self-assembled DNA structures in physiological conditions. In this review, we describe the current challenges faced by the field as well as recent successes, highlighting the potential to solve biology problems or develop smart drug delivery tools. We then propose an outlook to drive the translation of DNA constructs toward preclinical design. We particularly believe that a detailed understanding of the fate of DNA nanostructures within living organisms, achieved through thorough characterization, is the next required step to reach clinical maturity.
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Affiliation(s)
- Aurélie Lacroix
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
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Oligonucleotide-Based Therapies for Renal Diseases. Biomedicines 2021; 9:biomedicines9030303. [PMID: 33809425 PMCID: PMC8001091 DOI: 10.3390/biomedicines9030303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 02/07/2023] Open
Abstract
The global burden of chronic kidney disease (CKD) is increasing every year and represents a great cost for public healthcare systems, as the majority of these diseases are progressive. Therefore, there is an urgent need to develop new therapies. Oligonucleotide-based drugs are emerging as novel and promising alternatives to traditional drugs. Their expansion corresponds with new knowledge regarding the molecular basis underlying CKD, and they are already showing encouraging preclinical results, with two candidates being evaluated in clinical trials. However, despite recent technological advances, efficient kidney delivery remains challenging, and the presence of off-targets and side-effects precludes development and translation to the clinic. In this review, we provide an overview of the various oligotherapeutic strategies used preclinically, emphasizing the most recent findings in the field, together with the different strategies employed to achieve proper kidney delivery. The use of different nanotechnological platforms, including nanocarriers, nanoparticles, viral vectors or aptamers, and their potential for the development of more specific and effective treatments is also outlined.
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Lim KRQ, Yokota T. Genetic Approaches for the Treatment of Facioscapulohumeral Muscular Dystrophy. Front Pharmacol 2021; 12:642858. [PMID: 33776777 PMCID: PMC7996372 DOI: 10.3389/fphar.2021.642858] [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: 12/16/2020] [Accepted: 02/01/2021] [Indexed: 12/26/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant disorder characterized by progressive, asymmetric muscle weakness at the face, shoulders, and upper limbs, which spreads to the lower body with age. It is the third most common inherited muscular disorder worldwide. Around 20% of patients are wheelchair-bound, and some present with extramuscular manifestations. FSHD is caused by aberrant expression of the double homeobox protein 4 (DUX4) gene in muscle. DUX4 codes for a transcription factor which, in skeletal muscle, dysregulates numerous signaling activities that culminate in cytotoxicity. Potential treatments for FSHD therefore aim to reduce the expression of DUX4 or the activity of its toxic protein product. In this article, we review how genetic approaches such as those based on oligonucleotide and genome editing technologies have been developed to achieve these goals. We also outline the challenges these therapies are facing on the road to translation, and discuss possible solutions and future directions.
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Affiliation(s)
- Kenji Rowel Q. Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
- The Friends of Garrett Cumming Research and Muscular Dystrophy Canada, HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada
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