1
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Cantara S, Simoncelli G, Ricci C. Antisense Oligonucleotides (ASOs) in Motor Neuron Diseases: A Road to Cure in Light and Shade. Int J Mol Sci 2024; 25:4809. [PMID: 38732027 PMCID: PMC11083842 DOI: 10.3390/ijms25094809] [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: 02/28/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Antisense oligonucleotides (ASOs) are short oligodeoxynucleotides designed to bind to specific regions of target mRNA. ASOs can modulate pre-mRNA splicing, increase levels of functional proteins, and decrease levels of toxic proteins. ASOs are being developed for the treatment of motor neuron diseases (MNDs), including spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and spinal and bulbar muscular atrophy (SBMA). The biggest success has been the ASO known as nusinersen, the first effective therapy for SMA, able to improve symptoms and slow disease progression. Another success is tofersen, an ASO designed to treat ALS patients with SOD1 gene mutations. Both ASOs have been approved by the FDA and EMA. On the other hand, ASO treatment in ALS patients with the C9orf72 gene mutation did not show any improvement in disease progression. The aim of this review is to provide an up-to-date overview of ASO research in MNDs, from preclinical studies to clinical trials and, where available, regulatory approval. We highlight the successes and failures, underline the strengths and limitations of the current ASO research, and suggest possible approaches that could lead to more effective treatments.
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Affiliation(s)
- Silvia Cantara
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy;
| | - Giorgia Simoncelli
- Unit of Neurology and Clinical Neurophysiology, Department of Neurological and Motor Sciences, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy;
| | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy;
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2
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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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3
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Winter J, Meyer M, Berger I, Royer M, Bianchi M, Kuffner K, Peters S, Stang S, Langgartner D, Hartmann F, Schmidtner AK, Reber SO, Bosch OJ, Bludau A, Slattery DA, van den Burg EH, Jurek B, Neumann ID. Chronic oxytocin-driven alternative splicing of Crfr2α induces anxiety. Mol Psychiatry 2023; 28:4742-4755. [PMID: 34035479 PMCID: PMC10914602 DOI: 10.1038/s41380-021-01141-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/25/2021] [Accepted: 04/20/2021] [Indexed: 12/26/2022]
Abstract
The neuropeptide oxytocin (OXT) has generated considerable interest as potential treatment for psychiatric disorders, including anxiety and autism spectrum disorders. However, the behavioral and molecular consequences associated with chronic OXT treatment and chronic receptor (OXTR) activation have scarcely been studied, despite the potential therapeutic long-term use of intranasal OXT. Here, we reveal that chronic OXT treatment over two weeks increased anxiety-like behavior in rats, with higher sensitivity in females, contrasting the well-known anxiolytic effect of acute OXT. The increase in anxiety was transient and waned 5 days after the infusion has ended. The behavioral effects of chronic OXT were paralleled by activation of an intracellular signaling pathway, which ultimately led to alternative splicing of hypothalamic corticotropin-releasing factor receptor 2α (Crfr2α), an important modulator of anxiety. In detail, chronic OXT shifted the splicing ratio from the anxiolytic membrane-bound (mCRFR2α) form of CRFR2α towards the soluble CRFR2α (sCRFR2α) form. Experimental induction of alternative splicing mimicked the anxiogenic effects of chronic OXT, while sCRFR2α-knock down reduced anxiety-related behavior of male rats. Furthermore, chronic OXT treatment triggered the release of sCRFR2α into the cerebrospinal fluid with sCRFR2α levels positively correlating with anxiety-like behavior. In summary, we revealed that the shifted splicing ratio towards expression of the anxiogenic sCRFR2α underlies the adverse effects of chronic OXT treatment on anxiety.
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Affiliation(s)
- Julia Winter
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - Magdalena Meyer
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - Ilona Berger
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - Melanie Royer
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - Marta Bianchi
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - Kerstin Kuffner
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - Sebastian Peters
- Department of Neurology, University Hospital Regensburg, Regensburg, Germany
| | - Simone Stang
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - Dominik Langgartner
- Laboratory for Molecular Psychosomatics, Department of Psychosomatic Medicine and Psychotherapy, University of Ulm, Ulm, Germany
| | - Finn Hartmann
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - Anna K Schmidtner
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - Stefan O Reber
- Laboratory for Molecular Psychosomatics, Department of Psychosomatic Medicine and Psychotherapy, University of Ulm, Ulm, Germany
| | - Oliver J Bosch
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - Anna Bludau
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
| | - David A Slattery
- Laboratory of Translational Psychiatry, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University of Frankfurt, Frankfurt am Main, Germany
| | - Erwin H van den Burg
- Center for Psychiatric Neurosciences, University Hospital Lausanne, Lausanne, Switzerland
| | - Benjamin Jurek
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany
| | - Inga D Neumann
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, Germany.
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4
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Kaushal A. Innate immune regulations and various siRNA modalities. Drug Deliv Transl Res 2023; 13:2704-2718. [PMID: 37219704 PMCID: PMC10204684 DOI: 10.1007/s13346-023-01361-4] [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] [Accepted: 04/29/2023] [Indexed: 05/24/2023]
Abstract
RNAi therapeutics are designed to produce the precise silencing effects against the gene-linked diseases which were known to be untreatable in the past. The highly immunostimulatory nature of siRNA enhances the off-target effects and easily get attacked by nucleases; hence, their modulation is essentially required for accurate alterations to be made in the structures to intensify the pharmacological attributes. The phosphonate modifications act as shield against undue phosphorylation effects, and the molecular changes in ribose sugar lowers the level of immunogenicity and increases the binding efficacy. When bases are substituted with virtual/or pseudo bases, they eventually reduce the off-target effects. These changes modulate the nucleic acid sensors and control the hyper-activation of innate immune response. Various modification designs based on STC (universal pattern), ESC, ESC + (advanced patterns) and disubstrate have been explored to silence the gene expression of various diseases e.g., hepatitis, HIV, influenza, RSV, CNV and acute kidney injury. This review describes the various innovative siRNA therapeutics and their implications on the developed immune regulations to silence the disease effects. siRNA causes the silencing effects through RISC processing. The innate immune signalling is induced by both TLR-dependent and TLR-independent pathways. Modification chemistries are utilized to modulate the immune response.
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Affiliation(s)
- Anju Kaushal
- New Zealand Organization for Quality-Member, Auckland, New Zealand.
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5
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Ota K, Nagao K, Hata D, Sugiyama H, Segawa Y, Tokunoh R, Seki T, Miyamoto N, Sasaki Y, Ohmiya H. Synthesis of tertiary alkylphosphonate oligonucleotides through light-driven radical-polar crossover reactions. Nat Commun 2023; 14:6856. [PMID: 37907473 PMCID: PMC10618202 DOI: 10.1038/s41467-023-42639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023] Open
Abstract
Chemical modification of nucleotides can improve the metabolic stability and target specificity of oligonucleotide therapeutics, and alkylphosphonates have been employed as charge-neutral replacements for naturally-occurring phosphodiester backbones in these compounds. However, at present, the alkyl moieties that can be attached to phosphorus atoms in these compounds are limited to methyl groups or primary/secondary alkyls, and such alkylphosphonate moieties can degrade during oligonucleotide synthesis. The present work demonstrates the tertiary alkylation of the phosphorus atoms of phosphites bearing two 2'-deoxynuclosides. This process utilizes a carbocation generated via a light-driven radical-polar crossover mechanism. This protocol provides tertiary alkylphosphonate structures that are difficult to synthesize using existing methods. The conversion of these species to oligonucleotides having charge-neutral alkylphosphonate linkages through a phosphoramidite-based approach was also confirmed in this study.
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Affiliation(s)
- Kenji Ota
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Kazunori Nagao
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
| | - Dai Hata
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan.
| | - Haruki Sugiyama
- Institute for Molecular Science Myodaiji, Okazaki, Japan
- Comprehensive Research Organization for Science and Society Neutron Industrial Application Promotion Center, Tokai, Ibaraki, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Myodaiji, Okazaki, Japan
| | - Yasutomo Segawa
- Institute for Molecular Science Myodaiji, Okazaki, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Myodaiji, Okazaki, Japan
| | - Ryosuke Tokunoh
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Tomohiro Seki
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Naoya Miyamoto
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Yusuke Sasaki
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Hirohisa Ohmiya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, Japan.
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6
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Ali Zaidi SS, Fatima F, Ali Zaidi SA, Zhou D, Deng W, Liu S. Engineering siRNA therapeutics: challenges and strategies. J Nanobiotechnology 2023; 21:381. [PMID: 37848888 PMCID: PMC10583313 DOI: 10.1186/s12951-023-02147-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023] Open
Abstract
Small interfering RNA (siRNA) is a potential method of gene silencing to target specific genes. Although the U.S. Food and Drug Administration (FDA) has approved multiple siRNA-based therapeutics, many biological barriers limit their use for treating diseases. Such limitations include challenges concerning systemic or local administration, short half-life, rapid clearance rates, nonspecific binding, cell membrane penetration inability, ineffective endosomal escape, pH sensitivity, endonuclease degradation, immunological responses, and intracellular trafficking. To overcome these barriers, various strategies have been developed to stabilize siRNA, ensuring their delivery to the target site. Chemical modifications implemented with nucleotides or the phosphate backbone can reduce off-target binding and immune stimulation. Encapsulation or formulation can protect siRNA from endonuclease degradation and enhance cellular uptake while promoting endosomal escape. Additionally, various techniques such as viral vectors, aptamers, cell-penetrating peptides, liposomes, and polymers have been developed for delivering siRNA, greatly improving their bioavailability and therapeutic potential.
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Affiliation(s)
- Syed Saqib Ali Zaidi
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Faria Fatima
- College of Medical Technology, Ziauddin University, Karachi, 74700, Pakistan
| | - Syed Aqib Ali Zaidi
- Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Dezhong Zhou
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Wuquan Deng
- Department of Endocrinology and Metabolism, Chongqing Diabetic Foot Medical Research Center, Chongqing University Central Hospital, Chongqing Emergency Medical Center, Chongqing, 400014, China.
| | - Shuai Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
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7
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Pontarelli A, Wilds CJ. C5-Propynyl modified 2'-fluoroarabinonucleic acids form stable duplexes with RNA that are RNase H competent. Org Biomol Chem 2023; 21:7437-7446. [PMID: 37667655 DOI: 10.1039/d3ob01297b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The clinical success of the antisense approach for the treatment of genetic disorders is indisputably the result of chemical modifications along the oligonucleotide (ON) scaffold, which impart desirable properties including high RNA affinity, nuclease stability and improved drug delivery. While effective, many modifications are not capable of eliciting an RNase H response limiting their application in antisense systems. To contribute to the structural design and inventory of nucleoside analogues with favorable antisense properties, herein we describe the synthesis of C5-propynyl-2'-fluoroarabinonucleic acids (FANAP). Incorporation of individual and multiple uridine (FaraUP) and cytidine (FaraCP) inserts into ONs revealed, both stabilized duplexes formed with RNA. In contrast, these modifications demonstrated a negligible (FaraUP) or reduced (FaraCP) effect on DNA binding. Moreover, modified ONs containing these analogues supported E. coli RNase H cleavage of RNA with an altered cleavage pattern observed relative to controls. Moreover, a 2'-O-methoxyethyl (2'-O-MOE) gapmer with a FANAP core was able to elicit RNA cleavage at an increased rate compared to C5-propynyl-arabinonucleic acids (ANAP). Enzymatic hydrolysis of these gapmers was assessed with nuclease S1 digestion and revealed greater stability of ANAP compared to FANAP. These results suggest C5-propynyl ANA/FANA modifications demonstrate promising potential for the design of therapeutic ONs.
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Affiliation(s)
- Alexander Pontarelli
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec H4B 1R6, Canada.
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec H4B 1R6, Canada.
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8
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Mangla P, Vicentini Q, Biscans A. Therapeutic Oligonucleotides: An Outlook on Chemical Strategies to Improve Endosomal Trafficking. Cells 2023; 12:2253. [PMID: 37759475 PMCID: PMC10527716 DOI: 10.3390/cells12182253] [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: 06/21/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The potential of oligonucleotide therapeutics is undeniable as more than 15 drugs have been approved to treat various diseases in the liver, central nervous system (CNS), and muscles. However, achieving effective delivery of oligonucleotide therapeutics to specific tissues still remains a major challenge, limiting their widespread use. Chemical modifications play a crucial role to overcome biological barriers to enable efficient oligonucleotide delivery to the tissues/cells of interest. They provide oligonucleotide metabolic stability and confer favourable pharmacokinetic/pharmacodynamic properties. This review focuses on the various chemical approaches implicated in mitigating the delivery problem of oligonucleotides and their limitations. It highlights the importance of linkers in designing oligonucleotide conjugates and discusses their potential role in escaping the endosomal barrier, a bottleneck in the development of oligonucleotide therapeutics.
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Affiliation(s)
- Priyanka Mangla
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
| | - Quentin Vicentini
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
- Department of Laboratory Medicine, Clinical Research Centre, Karolinska Institute, 141 57 Stockholm, Sweden
| | - Annabelle Biscans
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
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9
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Takahashi Y, Kakuta K, Namioka Y, Igarashi A, Sakamoto T, Iwata Hara R, Sato K, Wada T. Synthesis of P-Modified DNA from Boranophosphate DNA as a Precursor via Acyl Phosphite Intermediates. J Org Chem 2023; 88:10617-10631. [PMID: 37462534 PMCID: PMC10407935 DOI: 10.1021/acs.joc.3c00659] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 08/05/2023]
Abstract
In this study, we successfully synthesized several kinds of P-modified nucleic acids from boranophosphate DNAs via an acyl phosphite intermediate in solution and on a solid support. In the solution-phase synthesis, phosphorothioate diester, phosphotriester, and phosphoramidate diester were synthesized in a one-pot reaction from boranophosphodiester via the conversion of an acyl phosphite as a key intermediate. In addition, doubly P-modified nucleic acid derivatives which were difficult to synthesize by the phosphoramidite and H-phosphonate methods were also obtained by the conversion reaction. In the solid-phase synthesis, a boranophosphate derivative was synthesized on a solid support using the H-boranophosphonate method. Then, an acyl phosphite intermediate was formed by treatment with pivaloyl chloride in pyridine, followed by appropriate transformations to obtain the P-modified derivatives such as phosphotriester and phosphorothioate diester. Notably, it was suggested that the conversion reaction of a boranophosphate to a phosphorothioate diester proceeded with retention of the stereochemistry of the phosphorous center. In addition, a phosphorothioate/phosphate chimeric dodecamer was successfully synthesized from a boranophosphate/phosphate chimeric dodecamer using the same strategy. Therefore, boranophosphate derivatives are versatile precursors for the synthesis of P-modified DNA, including chimeric derivatives.
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Affiliation(s)
- Yuhei Takahashi
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kiyoshi Kakuta
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yukichi Namioka
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ayumi Igarashi
- Department
of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Taiichi Sakamoto
- Department
of Life Science, Chiba Institute of Technology, Graduate School of Advanced Engineering, Chiba 275-0016, Japan
| | - Rintaro Iwata Hara
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department
of Neurology and Neurological Science, Graduate School of Medicinal
and Dental Sciences, Tokyo Medical and Dental
University, Tokyo 113-8519, Japan
| | - Kazuki Sato
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takeshi Wada
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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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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Khorkova O, Stahl J, Joji A, Volmar CH, Zeier Z, Wahlestedt C. Long non-coding RNA-targeting therapeutics: discovery and development update. Expert Opin Drug Discov 2023; 18:1011-1029. [PMID: 37466388 DOI: 10.1080/17460441.2023.2236552] [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: 03/14/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023]
Abstract
INTRODUCTION lncRNAs are major players in regulatory networks orchestrating multiple cellular functions, such as 3D chromosomal interactions, epigenetic modifications, gene expression and others. Due to progress in the development of nucleic acid-based therapeutics, lncRNAs potentially represent easily accessible therapeutic targets. AREAS COVERED Currently, significant efforts are directed at studies that can tap the enormous therapeutic potential of lncRNAs. This review describes recent developments in this field, particularly focusing on clinical applications. EXPERT OPINION Extensive druggable target range of lncRNA combined with high specificity and accelerated development process of nucleic acid-based therapeutics open new prospects for treatment in areas of extreme unmet medical need, such as genetic diseases, aggressive cancers, protein deficiencies, and subsets of common diseases caused by known mutations. Although currently wide acceptance of lncRNA-targeting nucleic acid-based therapeutics is impeded by the need for parenteral or direct-to-CNS administration, development of less invasive techniques and orally available/BBB-penetrant nucleic acid-based therapeutics is showing early successes. Recently, mRNA-based COVID-19 vaccines have demonstrated clinical safety of all aspects of nucleic acid-based therapeutic technology, including multiple chemical modifications of nucleic acids and nanoparticle delivery. These trends position lncRNA-targeting drugs as significant players in the future of drug development, especially in the area of personalized medicine.
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Affiliation(s)
- Olga Khorkova
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Zane Zeier
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
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12
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Khorkova O, Stahl J, Joji A, Volmar CH, Wahlestedt C. Amplifying gene expression with RNA-targeted therapeutics. Nat Rev Drug Discov 2023; 22:539-561. [PMID: 37253858 PMCID: PMC10227815 DOI: 10.1038/s41573-023-00704-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2023] [Indexed: 06/01/2023]
Abstract
Many diseases are caused by insufficient expression of mutated genes and would benefit from increased expression of the corresponding protein. However, in drug development, it has been historically easier to develop drugs with inhibitory or antagonistic effects. Protein replacement and gene therapy can achieve the goal of increased protein expression but have limitations. Recent discoveries of the extensive regulatory networks formed by non-coding RNAs offer alternative targets and strategies to amplify the production of a specific protein. In addition to RNA-targeting small molecules, new nucleic acid-based therapeutic modalities that allow highly specific modulation of RNA-based regulatory networks are being developed. Such approaches can directly target the stability of mRNAs or modulate non-coding RNA-mediated regulation of transcription and translation. This Review highlights emerging RNA-targeted therapeutics for gene activation, focusing on opportunities and challenges for translation to the clinic.
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Affiliation(s)
- Olga Khorkova
- OPKO Health, Miami, FL, USA
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Chemistry, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA.
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA.
- Department of Chemistry, University of Miami, Miami, FL, USA.
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13
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Larcher LM, Pitout IL, Keegan NP, Veedu RN, Fletcher S. DNAzymes: Expanding the Potential of Nucleic Acid Therapeutics. Nucleic Acid Ther 2023. [PMID: 37093127 DOI: 10.1089/nat.2022.0066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Nucleic acids drugs have been proven in the clinic as a powerful modality to treat inherited and acquired diseases. However, key challenges including drug stability, renal clearance, cellular uptake, and movement across biological barriers (foremost the blood-brain barrier) limit the translation and clinical efficacy of nucleic acid-based therapies, both systemically and in the central nervous system. In this study we provide an overview of an emerging class of nucleic acid therapeutic, called DNAzymes. In particular, we review the use of chemical modifications and carrier molecules for the stabilization and/or delivery of DNAzymes in cell and animal models. Although this review focuses on DNAzymes, the strategies described are broadly applicable to most nucleic acid technologies. This review should serve as a general guide for selecting chemical modifications to improve the therapeutic performance of DNAzymes.
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Affiliation(s)
- Leon M Larcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia
| | - Ianthe L Pitout
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia
| | - Niall P Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia
- Discovery, PYC Therapeutics, Nedlands, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Perth, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia
- Discovery, PYC Therapeutics, Nedlands, Australia
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14
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Hall J. Future directions for medicinal chemistry in the field of oligonucleotide therapeutics. RNA (NEW YORK, N.Y.) 2023; 29:423-433. [PMID: 36693762 PMCID: PMC10019366 DOI: 10.1261/rna.079511.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 05/13/2023]
Abstract
In the last decade, the field of oligonucleotide therapeutics has matured, with the regulatory approval of several single-stranded and double-stranded RNA drugs. In this Perspective, I discuss enabling developments and likely future directions in the field from the perspective of oligonucleotide chemistry.
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Affiliation(s)
- Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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15
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Sakurai Y, Yamaguchi T, Yoshida T, Horiba M, Inoue T, Obika S. Synthesis and Properties of Nucleobase-Sugar Dual Modified Nucleic Acids: 2 '-OMe-RNA and scpBNA Bearing a 5-Hydroxycytosine Nucleobase. J Org Chem 2023; 88:154-162. [PMID: 36520114 DOI: 10.1021/acs.joc.2c02038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Naturally occurring 5-hydroxycytosine (5-OHCyt), which is associated with DNA damage, was recently found to reduce the hepatotoxicity of antisense oligonucleotides (ASOs) without compromising its antisense activity when used as a replacement for cytosine (Cyt). Additionally, sugar-modified nucleic acids, such as 2'-O-methylribonucleic acid (2'-OMe-RNA) and 2'-O,4'-C-spirocyclopropylene-bridged nucleic acid (scpBNA), have emerged as useful antisense materials. Herein, we aimed to combine these two advantages by designing dual modified nucleic acids 2'-OMe-RNA-5-OHCyt and scpBNA-5-OHCyt bearing the 5-OHCyt nucleobase to develop efficient and safe ASOs. We describe the synthesis of 2'-OMe-RNA-5-OHCyt and scpBNA-5-OHCyt phosphoramidites and their incorporation into oligonucleotides (ONs). The duplex-forming ability and base discrimination properties of 2'-OMe-RNA-5-OHCyt- and scpBNA-5-OHCyt-modified ONs were similar to those of 2'-OMe-RNA-Cyt- and scpBNA-mCyt-modified ONs, respectively. We also synthesized two 2'-OMe-RNA-5-OHCyt-modified ASOs, and one of the two was found to exhibit reduced hepatotoxicity while retaining target mRNA knockdown activity in in vivo experiments.
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Affiliation(s)
- Yota Sakurai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tokuyuki Yoshida
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Masahiko Horiba
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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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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Wu H, Wahane A, Alhamadani F, Zhang K, Parikh R, Lee S, McCabe EM, Rasmussen TP, Bahal R, Zhong XB, Manautou JE. Nephrotoxicity of marketed antisense oligonucleotide drugs. CURRENT OPINION IN TOXICOLOGY 2022; 32:100373. [PMID: 37193356 PMCID: PMC10174585 DOI: 10.1016/j.cotox.2022.100373] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The field of antisense oligonucleotide (ASO)-based therapies have been making strides in precision medicine due to their potent therapeutic application. Early successes in treating some genetic diseases are now attributed to an emerging class of antisense drugs. After two decades, the US Food and Drug Administration (FDA) has approved a considerable number of ASO drugs, primarily to treat rare diseases with optimal therapeutic outcomes. However, safety is one of the biggest challenges to the therapeutic utility of ASO drugs. Due to patients' and health care practitioners' urgent demands for medicines for untreatable conditions, many ASO drugs have been approved. However, a complete understanding of the mechanisms of adverse drug reactions (ADRs) and toxicities of ASOs still need to be resolved. The range of ADRs is unique to a specific drug, while few ADRs are common to a section of drugs as a whole. Nephrotoxicity is an important concern that needs to be addressed considering the clinical translation of any drug candidates ranging from small molecules to ASO-based drugs. This article encompasses what is known about the nephrotoxicity of ASO drugs, the potential mechanisms of action(s), and recommendations for future investigations on the safety of ASO drugs.
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Affiliation(s)
- Hangyu Wu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Aniket Wahane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Feryal Alhamadani
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Kristy Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Rajvi Parikh
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - SooWan Lee
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Evan M McCabe
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Theodore P Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, USA
| | - José E Manautou
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, USA
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18
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Abstract
The highly specific induction of RNA interference-mediated gene knockdown, based on the direct application of small interfering RNAs (siRNAs), opens novel avenues towards innovative therapies. Two decades after the discovery of the RNA interference mechanism, the first siRNA drugs received approval for clinical use by the US Food and Drug Administration and the European Medicines Agency between 2018 and 2022. These are mainly based on an siRNA conjugation with a targeting moiety for liver hepatocytes, N-acetylgalactosamine, and cover the treatment of acute hepatic porphyria, transthyretin-mediated amyloidosis, hypercholesterolemia, and primary hyperoxaluria type 1. Still, the development of siRNA therapeutics faces several challenges and issues, including the definition of optimal siRNAs in terms of target, sequence, and chemical modifications, siRNA delivery to its intended site of action, and the absence of unspecific off-target effects. Further siRNA drugs are in clinical studies, based on different delivery systems and covering a wide range of different pathologies including metabolic diseases, hematology, infectious diseases, oncology, ocular diseases, and others. This article reviews the knowledge on siRNA design and chemical modification, as well as issues related to siRNA delivery that may be addressed using different delivery systems. Details on the mode of action and clinical status of the various siRNA therapeutics are provided, before giving an outlook on issues regarding the future of siRNA drugs and on their potential as one emerging standard modality in pharmacotherapy. Notably, this may also cover otherwise un-druggable diseases, the definition of non-coding RNAs as targets, and novel concepts of personalized and combination treatment regimens.
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Affiliation(s)
- Maik Friedrich
- Faculty of Leipzig, Institute of Clinical Immunology, Max-Bürger-Forschungszentrum (MBFZ), University of Leipzig, Leipzig, Germany.,Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Achim Aigner
- Rudolf-Boehm Institute for Pharmacology and Toxicology, Clinical Pharmacology, University of Leipzig, Haertelstrasse 16-18, 04107, Leipzig, Germany.
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19
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Helm J, Schöls L, Hauser S. Towards Personalized Allele-Specific Antisense Oligonucleotide Therapies for Toxic Gain-of-Function Neurodegenerative Diseases. Pharmaceutics 2022; 14:pharmaceutics14081708. [PMID: 36015334 PMCID: PMC9416334 DOI: 10.3390/pharmaceutics14081708] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are single-stranded nucleic acid strings that can be used to selectively modify protein synthesis by binding complementary (pre-)mRNA sequences. By specific arrangements of DNA and RNA into a chain of nucleic acids and additional modifications of the backbone, sugar, and base, the specificity and functionality of the designed ASOs can be adjusted. Thereby cellular uptake, toxicity, and nuclease resistance, as well as binding affinity and specificity to its target (pre-)mRNA, can be modified. Several neurodegenerative diseases are caused by autosomal dominant toxic gain-of-function mutations, which lead to toxic protein products driving disease progression. ASOs targeting such mutations—or even more comprehensively, associated variants, such as single nucleotide polymorphisms (SNPs)—promise a selective degradation of the mutant (pre-)mRNA while sparing the wild type allele. By this approach, protein expression from the wild type strand is preserved, and side effects from an unselective knockdown of both alleles can be prevented. This makes allele-specific targeting strategies a focus for future personalized therapies. Here, we provide an overview of current strategies to develop personalized, allele-specific ASO therapies for the treatment of neurodegenerative diseases, such Huntington’s disease (HD) and spinocerebellar ataxia type 3 (SCA3/MJD).
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Affiliation(s)
- Jacob Helm
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Hertie Institute for Clinical Brain Research and Department of Neurology, University of Tübingen, 72076 Tübingen, Germany
- Graduate School of Cellular and Molecular Neuroscience, University of Tübingen, 72076 Tübingen, Germany
| | - Ludger Schöls
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Hertie Institute for Clinical Brain Research and Department of Neurology, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Hauser
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Hertie Institute for Clinical Brain Research and Department of Neurology, University of Tübingen, 72076 Tübingen, Germany
- Correspondence:
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20
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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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21
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Yoshida T, Morihiro K, Naito Y, Mikami A, Kasahara Y, Inoue T, Obika S. Identification of nucleobase chemical modifications that reduce the hepatotoxicity of gapmer antisense oligonucleotides. Nucleic Acids Res 2022; 50:7224-7234. [PMID: 35801870 PMCID: PMC9303313 DOI: 10.1093/nar/gkac562] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 12/26/2022] Open
Abstract
Currently, gapmer antisense oligonucleotide (ASO) therapeutics are under clinical development for the treatment of various diseases, including previously intractable human disorders; however, they have the potential to induce hepatotoxicity. Although several groups have reported the reduced hepatotoxicity of gapmer ASOs following chemical modifications of sugar residues or internucleotide linkages, only few studies have described nucleobase modifications to reduce hepatotoxicity. In this study, we introduced single or multiple combinations of 17 nucleobase derivatives, including four novel derivatives, into hepatotoxic locked nucleic acid gapmer ASOs and examined their effects on hepatotoxicity. The results demonstrated successful identification of chemical modifications that strongly reduced the hepatotoxicity of gapmer ASOs. This approach expands the ability to design gapmer ASOs with optimal therapeutic profiles.
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Affiliation(s)
- Tokuyuki Yoshida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Yuki Naito
- Database Center for Life Science (DBCLS), 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi Mikami
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
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22
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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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23
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Synthesis of 4'-C-(aminoethyl)thymidine and 4'-C-[(N-methyl)aminoethyl]thymidine by a new synthetic route and evaluation of the properties of the DNAs containing the nucleoside analogs. Bioorg Med Chem 2022; 60:116690. [PMID: 35259549 DOI: 10.1016/j.bmc.2022.116690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 11/21/2022]
Abstract
A gapmer-type antisense oligonucleotide is an oligonucleotide therapeutic that targets pathogenic mRNA directly, and it is expected to be a next-generation therapeutic drug. In this study, we designed and synthesized 4'-C-[(N-methyl)aminoethyl]-thymidine (4'-MAE-T) as a novel nucleoside analog and compared its properties with those of 4'-C-aminoethyl-thymidine (4'-AE-T). Furthermore, we designed a new synthetic route for 4'-C-aminoethyl-modified nucleosides and accomplished the synthesis of 4'-AE-T via a novel pathway with high total yield. DNA containing 4'-MAE-T analogs decreased RNA affinity slightly more than unmodified DNA and DNA containing 4'-AE-T, but significantly improved nuclease resistance compared to unmodified DNA in a solution containing bovine serum. In addition, the impact of 4'-MAE-T on DNA stability was higher than that of 4'-AE-T. Also, DNA containing these analogs can activate Escherichia coli-derived RNase H. Thus, 4'-MAE-T has the potential to be used in gapmer-type antisense nucleic acids as a suitable candidate for the development of therapeutic antisense oligonucleotides.
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24
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Honcharenko D, Rocha CSJ, Lundin KE, Maity J, Milton S, Tedebark U, Murtola M, Honcharenko M, Slaitas A, Smith CIE, Zain R, Strömberg R. 2'- O-( N-(Aminoethyl)carbamoyl)methyl Modification Allows for Lower Phosphorothioate Content in Splice-Switching Oligonucleotides with Retained Activity. Nucleic Acid Ther 2022; 32:221-233. [PMID: 35238623 PMCID: PMC9221157 DOI: 10.1089/nat.2021.0086] [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] [Indexed: 11/23/2022] Open
Abstract
2′-O-(N-(Aminoethyl)carbamoyl)methyl (2′-O-AECM)-modified oligonucleotides (ONs) and their mixmers with 2′-O-methyl oligonucleotides (2′-OMe ONs) with phosphodiester linkers as well as with partial and full phosphorothioate (PS) inclusion were synthesized and functionally evaluated as splice-switching oligonucleotides in several different reporter cell lines originating from different tissues. This was enabled by first preparing the AECM-modified A, C, G and U, which required a different strategy for each building block. The AECM modification has previously been shown to provide high resistance to enzymatic degradation, even without PS linkages. It is therefore particularly interesting and unprecedented that the 2′-O-AECM ONs are shown to have efficient splice-switching activity even without inclusion of PS linkages and found to be as effective as 2′-OMe PS ONs. Importantly, the PS linkages can be partially included, without any significant reduction in splice-switching efficacy. This suggests that AECM modification has the potential to be used in balancing the PS content of ONs. Furthermore, conjugation of 2′-O-AECM ONs to an endosomal escape peptide significantly increased splice-switching suggesting that this effect could possibly be due to an increase in uptake of ON to the site of action.
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Affiliation(s)
- Dmytro Honcharenko
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Cristina S J Rocha
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Jyotirmoy Maity
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Stefan Milton
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ulf Tedebark
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | | | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden.,Department of Clinical Genetics, Center for Rare Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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25
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Pierce JB, Zhou H, Simion V, Feinberg MW. Long Noncoding RNAs as Therapeutic Targets. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:161-175. [PMID: 35220570 DOI: 10.1007/978-3-030-92034-0_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as critical regulators of cellular functions including maintenance of cellular homeostasis as well as the onset and progression of disease. LncRNAs often exhibit cell-, tissue-, and disease-specific expression patterns, making them desirable therapeutic targets. LncRNAs are commonly targeted using oligonucleotide therapeutics, and advances in oligonucleotide chemistry including C2 ribose sugar modifications such as 2'-fluoro, 2'-O-methyl, and 2-O-methoxyethyl modifications; 2'4'-constrained nucleotides such as locked nucleic acids and constrained 2'-O-ethyl (cEt) nucleotides; and phosphorothioate bonds have dramatically improved efficacy of oligonucleotide therapies. Novel delivery platforms such as viral vectors and nanoparticles have also improved pharmacokinetic properties of oligonucleotides targeting lncRNAs. Accumulating pre-clinical studies have utilized these strategies to therapeutically target lncRNAs and alter progression of many different disease states including Snhg12 and Chast in cardiovascular disease, Mirt2 and HOTTIP in sepsis and autoimmune disease, and Malat1 and HOXB-AS3 in cancer. Emerging oligonucleotide conjugation methods including the use of peptide nucleic acids hold promise to facilitate targeting to specific tissue types. Here, we review recent advances in lncRNA therapeutics and provide examples of how lncRNAs have been successfully targeted in pre-clinical models of disease. Finally, we detail remaining challenges facing the lncRNA field and how advances in delivery platforms and oligonucleotide chemistry might help overcome these barriers to catalyze the translation of pre-clinical studies to successful pharmaceutical development.
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Affiliation(s)
- Jacob B Pierce
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Haoyang Zhou
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Cardiology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Viorel Simion
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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26
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Jana SK, Harikrishna S, Sudhakar S, El-Khoury R, Pradeepkumar PI, Damha MJ. Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA-RNA Hybrids. J Org Chem 2022; 87:2367-2379. [PMID: 35133166 DOI: 10.1021/acs.joc.1c02254] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we describe results on the pairing properties of synthetic DNA and RNA oligonucleotides that contain nucleotide analogues with a 7-membered sugar ring (oxepane nucleotides). Specifically, we describe the stereoselective synthesis of a set of three oxepane thymine nucleosides (OxT), their conversion to phosphoramidite derivatives, and their use in solid-phase synthesis to yield chimeric OxT-DNA and OxT-RNA strands. The different regioisomeric OxT phosphoramidites allowed for positional variations of the phosphate bridge and assessment of duplex stability when the oxepane nucleotides were incorporated in dsDNA, dsRNA, and DNA-RNA hybrids. Little to no destabilization was observed when two of the three regioisomeric OxT units were incorporated in the DNA strand of DNA-RNA hybrids, a remarkable result considering the dramatically different structure of oxepanes in comparison to 2'-deoxynucleosides. Extensive molecular modeling and dynamics studies further revealed the various structural features responsible for the tolerance of both OxT modifications in DNA-RNA duplexes, such as base-base stacking and sugar-phosphate H-bond interactions. These studies suggest that oxepane nucleotide analogues may find applications in synthetic biology, where synthetic oligonucleotides can be used to create new tools for biotechnology and medicine.
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Affiliation(s)
- Sunit Kumar Jana
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - S Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Roberto El-Khoury
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
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27
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Rajasekaran T, Freestone GC, Galindo-Murillo R, Lugato B, Rico L, Salinas JC, Gaus H, Migawa MT, Swayze EE, Cheatham TE, Hanessian S, Seth PP. Backbone Hydrocarbon-Constrained Nucleic Acids Modulate Hybridization Kinetics for RNA. J Am Chem Soc 2022; 144:1941-1950. [PMID: 35041415 DOI: 10.1021/jacs.1c12323] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The binding affinity of therapeutic oligonucleotides (ONs) for their cognate RNA is determined by the rates of association (ka) and dissociation (kd). Single-stranded ONs are highly flexible and can adopt multiple conformations in solution, some of which may not be conducive for hybridization. We investigated if restricting rotation around the sugar-phosphate backbone, by tethering two adjacent backbone phosphonate esters using hydrocarbon bridges, can modulate hybridization kinetics of the modified ONs for complementary RNA. Given the large number of possible analogues with different tether lengths and configurations at the phosphorus atoms, we employed molecular dynamic simulations to optimize the size of the hydrocarbon bridge to guide the synthetic efforts. The backbone-constrained nucleotide trimers with stereodefined configurations at the contiguous backbone phosphorus atoms were assembled using a ring-closing metathesis reaction, then incorporated into oligonucleotides by an in situ synthesis of the phosphoramidites followed by coupling to solid supports. Evaluation of the modified oligonucleotides revealed that 15-membered macrocyclic-constrained analogues displayed similar or slightly improved on-rates but significantly increased off-rates compared to unmodified DNA ONs, resulting in reduced duplex stability. In contrast, LNA ONs with conformationally preorganized furanose rings showed similar on-rates to DNA ONs but very slow off-rates, resulting in net improvement in duplex stability. Furthermore, the experimental data generally supported the molecular dynamics simulation results, suggesting that this strategy can be used as a predictive tool for designing the next generation of constrained backbone ON analogues with improved hybridization properties.
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Affiliation(s)
| | - Graeme C Freestone
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 201, Salt Lake City, Utah 84112, United States
| | - Barbara Lugato
- Department of Chemistry, Université de Montréal, Quebec H3C 3J7, Canada
| | - Lorena Rico
- Department of Chemistry, Université de Montréal, Quebec H3C 3J7, Canada
| | - Juan C Salinas
- Department of Chemistry, Université de Montréal, Quebec H3C 3J7, Canada
| | - Hans Gaus
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael T Migawa
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Eric E Swayze
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 201, Salt Lake City, Utah 84112, United States
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Quebec H3C 3J7, Canada
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
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28
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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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29
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Masaki Y, Tabira A, Hattori S, Wakatsuki S, Seio K. Insertion of a methylene group into the backbone of an antisense oligonucleotide reveals the importance of deoxyribose recognition by RNase H. Org Biomol Chem 2022; 20:8917-8924. [DOI: 10.1039/d2ob01667b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Methylene-inserted oligonucleotides showed an inserted-position-dependent inhibitory effect on cleavage reaction which suggested the importance of deoxyribose recognition.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8501, Japan
- PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Ayano Tabira
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8501, Japan
| | - Shihori Hattori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8501, Japan
| | - Shunsuke Wakatsuki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8501, Japan
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30
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Takahashi Y, Sato K, Wada T. Solid-Phase Synthesis of Boranophosphate/Phosphorothioate/Phosphate Chimeric Oligonucleotides and Their Potential as Antisense Oligonucleotides. J Org Chem 2021; 87:3895-3909. [PMID: 34908418 PMCID: PMC8938928 DOI: 10.1021/acs.joc.1c01812] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
In this study, we
successfully synthesized boranophosphate (PB),
phosphorothioate (PS), and phosphate (PO) chimeric oligonucleotides
(ODNs) as a candidate for the antisense oligonucleotides (ASOs). The
PB/PS/PO-ODNs were synthesized utilizing H-boranophosphonate, H-phosphonothioate, and H-phosphonate monomers.
Each monomer was condensed with a hydroxy group to create H-boranophosphonate, H-phosphonothioate,
and H-phosphonate diester linkages, which were oxidized
into PB, PS, and PO linkages in the final stage of the synthesis,
respectively. As for condensation of an H-phosphonothioate
monomer, regulating chemoselectivity was necessary since the monomer
has two nucleophilic centers: S and O atoms. To deal with this problem,
we used phosphonium-type condensing reagents, which could control
the chemoselectivity. In this strategy, we could synthesize PB/PS/PO
oligomers, including a 2′-OMe gapmer-type dodecamer. The physiological
and biological properties of the synthesized chimeric ODNs were also
evaluated. Insights from the evaluation of physiological and biological
properties suggested that the introduction of suitable P-modification and sugar modification at proper sites of ODNs would
control the duplex stability, nuclease resistance, RNase H-inducing
ability, and one base mismatch discrimination ability, which are critical
properties as potent ASOs.
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Affiliation(s)
- Yuhei Takahashi
- Department of Medicinal and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kazuki Sato
- Department of Medicinal and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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31
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Relizani K, Echevarría L, Zarrouki F, Gastaldi C, Dambrune C, Aupy P, Haeberli A, Komisarski M, Tensorer T, Larcher T, Svinartchouk F, Vaillend C, Garcia L, Goyenvalle A. Palmitic acid conjugation enhances potency of tricyclo-DNA splice switching oligonucleotides. Nucleic Acids Res 2021; 50:17-34. [PMID: 34893881 PMCID: PMC8754652 DOI: 10.1093/nar/gkab1199] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 01/16/2023] Open
Abstract
Tricyclo-DNA (tcDNA) is a conformationally constrained oligonucleotide analog that has demonstrated great therapeutic potential as antisense oligonucleotide (ASO) for several diseases. Like most ASOs in clinical development, tcDNA were modified with phosphorothioate (PS) backbone for therapeutic purposes in order to improve their biodistribution by enhancing association with plasma and cell protein. Despite the advantageous protein binding properties, systemic delivery of PS-ASO remains limited and PS modifications can result in dose limiting toxicities in the clinic. Improving extra-hepatic delivery of ASO is highly desirable for the treatment of a variety of diseases including neuromuscular disorders such as Duchenne muscular dystrophy. We hypothesized that conjugation of palmitic acid to tcDNA could facilitate the delivery of the ASO from the bloodstream to the interstitium of the muscle tissues. We demonstrate here that palmitic acid conjugation enhances the potency of tcDNA-ASO in skeletal and cardiac muscles, leading to functional improvement in dystrophic mice with significantly reduced dose of administered ASO. Interestingly, palmitic acid-conjugated tcDNA with a full phosphodiester backbone proved effective with a particularly encouraging safety profile, offering new perspectives for the clinical development of PS-free tcDNA-ASO for neuromuscular diseases.
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Affiliation(s)
- Karima Relizani
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.,SQY Therapeutics, UVSQ, 78180 Montigny le Bretonneux, France
| | - Lucía Echevarría
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.,SQY Therapeutics, UVSQ, 78180 Montigny le Bretonneux, France
| | - Faouzi Zarrouki
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.,Université Paris-Saclay, CNRS, Institut des Neurosciences Paris Saclay, 91190, Gif-sur-Yvette, France
| | | | - Chloe Dambrune
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | - Philippine Aupy
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | | | | | - Thomas Tensorer
- SQY Therapeutics, UVSQ, 78180 Montigny le Bretonneux, France.,SYNTHENA AG, Bern, Switzerland
| | | | | | - Cyrille Vaillend
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris Saclay, 91190, Gif-sur-Yvette, France
| | - Luis Garcia
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.,LIA BAHN, centre scientifique de Monaco, 98000, Monaco
| | - Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.,LIA BAHN, centre scientifique de Monaco, 98000, Monaco
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32
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Wada F, Yamamoto T, Kobayashi T, Tachibana K, Ito KR, Hamasaki M, Kayaba Y, Terada C, Yamayoshi A, Obika S, Harada-Shiba M. Drug discovery and development scheme for liver-targeting bridged nucleic acid antisense oligonucleotides. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:957-969. [PMID: 34760338 PMCID: PMC8560717 DOI: 10.1016/j.omtn.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/15/2021] [Accepted: 10/06/2021] [Indexed: 11/21/2022]
Abstract
Antisense oligonucleotides (ASOs) containing bridged nucleic acids (BNAs) have been proven to be very powerful. However, ensuring a reliable discovery and translational development scheme for this class of ASOs with wider therapeutic windows remains a fundamental challenge. We here demonstrate the robustness of our scheme in the context of the selection of ASOs having two different BNA chemistries (2,′4′-BNA/locked nucleic acid [LNA] and amido-bridged nucleic acid [AmNA]) targeting human proprotein convertase subtilisin/kexin type 9 (PCSK9). The scheme features a two-step process, including (1) a unique and sensitive in vitro screening approach, called Ca2+ enrichment of medium (CEM) transfection, and (2) a ligand-targeted drug delivery approach to better reach target tissues, averting unintended accumulation of ASOs. Using CEM screening, we identified a candidate ASO that shows >70% cholesterol-lowering action in monkeys. An N-acetylgalactosamine (GalNAc) ligand then was appended to the candidate ASO to further broaden the therapeutic margin by altering the molecule’s pharmacokinetics. The GalNAc conjugate, HsPCSK9-1811-LNA, was found to be at least ten times more potent in non-human primates (compared with the unconjugated counterpart), with reduced nephrotoxicity in rats. Overall, we successfully showed that our drug development scheme is better suited for selecting clinically relevant BNA-based ASOs, especially for the treatment of liver-associated diseases.
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Affiliation(s)
- Fumito Wada
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Tadayuki Kobayashi
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keisuke Tachibana
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kosuke Ramon Ito
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mayumi Hamasaki
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Yukina Kayaba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Chisato Terada
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
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33
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Matsuda H, Ito H, Nukaga Y, Uehara S, Sato K, Hara RI, Wada T. Solid-phase synthesis of oligouridine boranophosphates using the H-boranophosphonate method with 2′-O-(2-cyanoethoxymethyl) protection. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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34
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Kajino R, Ueno Y. Synthesis and Properties of Artificial Oligonucleotides Containing Novel Nucleoside Analogs with Cationic Alkyl Sidechains. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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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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36
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Vasquez G, Migawa MT, Wan WB, Low A, Tanowitz M, Swayze EE, Seth PP. Evaluation of Phosphorus and Non-Phosphorus Neutral Oligonucleotide Backbones for Enhancing Therapeutic Index of Gapmer Antisense Oligonucleotides. Nucleic Acid Ther 2021; 32:40-50. [PMID: 34698585 DOI: 10.1089/nat.2021.0064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The phosphorothioate (PS) linkage in an essential component of therapeutic oligonucleotides. PS in the DNA region of gapmer antisense oligonucleotides (ASOs) supports RNaseH1 activity and enhances nuclease stability. PS also promotes binding to plasma, cell surface, and intracellular proteins, which facilitates tissue distribution, cellular uptake, and endosomal escape of PS ASOs. We recently showed that site-specific replacement of PS in the DNA gap with methoxylpropyl phosphonate (MOP) linkages can enhance the therapeutic index of gapmer ASOs. In this article, we explored 18 phosphorus- and non-phosphorus-based neutral backbone modifications to determine the structure-activity relationship of neutral linkages for enhancing therapeutic index. Replacing MOP with other alkyl phosphonate and phosphotriester linkages enhanced therapeutic index, but these linkages were susceptible to chemical degradation during oligonucleotide deprotection from solid supports following synthesis. Replacing MOP with non-phosphorus linkages resulted in improved chemical stability, but these linkages were introduced into ASOs as nucleotide dimers, which limits their versatility. Overall, linkages such as isopropyl and isobutyl phosphonates and O-isopropyl and O-tetrahydrofuranosyl phosphotriesters, formacetal, and C3-amide showed improved activity in mice relative to MOP. Our data suggest that site-specific incorporation of any neutral backbone linkage can improve therapeutic index, but the size, hydrophobicity, and RNA-binding affinity of the linkage influence ASO activity.
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Affiliation(s)
- Guillermo Vasquez
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Michael T Migawa
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - W Brad Wan
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Audrey Low
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Michael Tanowitz
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Eric E Swayze
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Carlsbad, California, USA
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37
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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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38
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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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39
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Hara RI, Wada T. Inhibition of off-target cleavage by RNase H using an artificial cationic oligosaccharide. Org Biomol Chem 2021; 19:6865-6870. [PMID: 34323246 DOI: 10.1039/d1ob00983d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequence-dependent off-target effects are a serious problem of antisense oligonucleotide-based drugs. Some of these side effects are induced by ribonuclease H (RNase H)-mediated cleavage of non-target RNAs with base sequences similar to that of the target RNA. We found that an artificial cationic oligosaccharide, ODAGal4, improved single-base discrimination for RNase H cleavage.
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Affiliation(s)
- Rintaro Iwata Hara
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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40
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Danielsen MB, Wengel J. Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides. Beilstein J Org Chem 2021; 17:1828-1848. [PMID: 34386102 PMCID: PMC8329367 DOI: 10.3762/bjoc.17.125] [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: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 12/20/2022] Open
Abstract
Antisense oligonucleotides (ASOs) have the ability of binding to endogenous nucleic acid targets, thereby inhibiting the gene expression. Although ASOs have great potential in the treatment of many diseases, the search for favorable toxicity profiles and distribution has been challenging and consequently impeded the widespread use of ASOs as conventional medicine. One strategy that has been employed to optimize the delivery profile of ASOs, is the functionalization of ASOs with cationic amine groups, either by direct conjugation onto the sugar, nucleobase or internucleotide linkage. The introduction of these positively charged groups has improved properties like nuclease resistance, increased binding to the nucleic acid target and improved cell uptake for oligonucleotides (ONs) and ASOs. The modifications highlighted in this review are some of the most prevalent cationic amine groups which have been attached as single modifications onto ONs/ASOs. The review has been separated into three sections, nucleobase, sugar and backbone modifications, highlighting what impact the cationic amine groups have on the ONs/ASOs physiochemical and biological properties. Finally, a concluding section has been added, summarizing the important knowledge from the three chapters, and examining the future design for ASOs.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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41
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Sun X, Feinberg MW. Vascular Endothelial Senescence: Pathobiological Insights, Emerging Long Noncoding RNA Targets, Challenges and Therapeutic Opportunities. Front Physiol 2021; 12:693067. [PMID: 34220553 PMCID: PMC8242592 DOI: 10.3389/fphys.2021.693067] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a stable form of cell cycle arrest in response to various stressors. While it serves as an endogenous pro-resolving mechanism, detrimental effects ensue when it is dysregulated. In this review, we introduce recent advances for cellular senescence and inflammaging, the underlying mechanisms for the reduction of nicotinamide adenine dinucleotide in tissues during aging, new knowledge learned from p16 reporter mice, and the development of machine learning algorithms in cellular senescence. We focus on pathobiological insights underlying cellular senescence of the vascular endothelium, a critical interface between blood and all tissues. Common causes and hallmarks of endothelial senescence are highlighted as well as recent advances in endothelial senescence. The regulation of cellular senescence involves multiple mechanistic layers involving chromatin, DNA, RNA, and protein levels. New targets are discussed including the roles of long noncoding RNAs in regulating endothelial cellular senescence. Emerging small molecules are highlighted that have anti-aging or anti-senescence effects in age-related diseases and impact homeostatic control of the vascular endothelium. Lastly, challenges and future directions are discussed including heterogeneity of endothelial cells and endothelial senescence, senescent markers and detection of senescent endothelial cells, evolutionary differences for immune surveillance in mice and humans, and long noncoding RNAs as therapeutic targets in attenuating cellular senescence. Accumulating studies indicate that cellular senescence is reversible. A better understanding of endothelial cellular senescence through lifestyle and pharmacological interventions holds promise to foster a new frontier in the management of cardiovascular disease risk.
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Affiliation(s)
- Xinghui Sun
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.,Nebraska Center for the Prevention of Obesity Diseases Through Dietary Molecules, University of Nebraska-Lincoln, Lincoln, NE, United States.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Mark W Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
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42
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Prakash TP, Yu J, Shen W, De Hoyos CL, Berdeja A, Gaus H, Liang XH, Crooke ST, Seth PP. Site-specific Incorporation of 2',5'-Linked Nucleic Acids Enhances Therapeutic Profile of Antisense Oligonucleotides. ACS Med Chem Lett 2021; 12:922-927. [PMID: 34141070 DOI: 10.1021/acsmedchemlett.1c00072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/01/2021] [Indexed: 12/30/2022] Open
Abstract
Site-specific incorporation of 2'-modifications and neutral linkages in the deoxynucleotide gap region of toxic phosphorothioate (PS) gapmer ASOs can enhance therapeutic index and safety. In this manuscript, we determined the effect of introducing 2',5'-linked RNA in the deoxynucleotide gap region on toxicity and potency of PS ASOs. Our results demonstrate that incorporation of 2',5'-linked RNA in the gap region dramatically improved hepatotoxicity profile of PS-ASOs without compromising potency and provide a novel alternate chemical approach for improving therapeutic index of ASO drugs.
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Affiliation(s)
- Thazha P. Prakash
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Jinghua Yu
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Wen Shen
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Cheryl Li De Hoyos
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Andres Berdeja
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Hans Gaus
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Xue-hai Liang
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Stanley T. Crooke
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P. Seth
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
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43
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Alkhouri N, Reddy GK, Lawitz E. Oligonucleotide-Based Therapeutics: An Emerging Strategy for the Treatment of Chronic Liver Diseases. Hepatology 2021; 73:1581-1593. [PMID: 32978989 DOI: 10.1002/hep.31569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Naim Alkhouri
- Texas Liver Institute, University of Texas Health San Antonio, San Antonio, TX
| | - G Kesava Reddy
- Texas Liver Institute, University of Texas Health San Antonio, San Antonio, TX
| | - Eric Lawitz
- Texas Liver Institute, University of Texas Health San Antonio, San Antonio, TX
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44
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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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45
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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: 274] [Impact Index Per Article: 91.3] [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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46
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Development of LNA Gapmer Oligonucleotide-Based Therapy for ALS/FTD Caused by the C9orf72 Repeat Expansion. Methods Mol Biol 2021; 2176:185-208. [PMID: 32865792 DOI: 10.1007/978-1-0716-0771-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), have a complex genetic background, in addition to cases where the disease appears to manifest sporadically. The recent discovery of the hexanucleotide repeat expansion in the C9orf72 gene as the causative agent of ALS (C9ALS) gives rise to the opportunity to develop new therapies directed at this mutation , which is responsible for a large proportion of ALS and/or frontotemporal dementia cases. Mammalian models conscientiously replicating the late-onset motor defects and cellular pathologies seen in human patients do not exist. In this context, patient-derived cells give us a platform to test potential antisense oligonucleotide therapies, which could be the key to treat this subtype of motor neuron disease. Recently, we described that locked nucleic acid gapmer oligonucleotide-based treatment targeting C9orf72 repeat expanded transcripts resulted in recovery from the disease-related phenotypes in patient-derived fibroblasts. Our findings highlight the therapeutic potential of C9ALS using this gapmer oligonucleotide-based approach.
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47
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Vasquez G, Freestone GC, Wan WB, Low A, De Hoyos CL, Yu J, Prakash TP, Ǿstergaard ME, Liang XH, Crooke ST, Swayze EE, Migawa MT, Seth PP. Site-specific incorporation of 5'-methyl DNA enhances the therapeutic profile of gapmer ASOs. Nucleic Acids Res 2021; 49:1828-1839. [PMID: 33544849 PMCID: PMC7913697 DOI: 10.1093/nar/gkab047] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/07/2021] [Accepted: 02/02/2021] [Indexed: 01/01/2023] Open
Abstract
We recently showed that site-specific incorporation of 2′-modifications or neutral linkages in the oligo-deoxynucleotide gap region of toxic phosphorothioate (PS) gapmer ASOs can enhance therapeutic index and safety. In this manuscript, we determined if introducing substitution at the 5′-position of deoxynucleotide monomers in the gap can also enhance therapeutic index. Introducing R- or S-configured 5′-Me DNA at positions 3 and 4 in the oligodeoxynucleotide gap enhanced the therapeutic profile of the modified ASOs suggesting a different positional preference as compared to the 2′-OMe gap modification strategy. The generality of these observations was demonstrated by evaluating R-5′-Me and R-5′-Ethyl DNA modifications in multiple ASOs targeting HDAC2, FXI and Dynamin2 mRNA in the liver. The current work adds to a growing body of evidence that small structural changes can modulate the therapeutic properties of PS ASOs and ushers a new era of chemical optimization with a focus on enhancing the therapeutic profile as opposed to nuclease stability, RNA-affinity and pharmacokinetic properties. The 5′-methyl DNA modified ASOs exhibited excellent safety and antisense activity in mice highlighting the therapeutic potential of this class of nucleic acid analogs for next generation ASO designs.
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Affiliation(s)
- Guillermo Vasquez
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - W Brad Wan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Audrey Low
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Jinghua Yu
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Xue-Hai Liang
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael T Migawa
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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48
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Liang XH, De Hoyos CL, Shen W, Zhang L, Fazio M, Crooke ST. Solid-Phase Separation of Toxic Phosphorothioate Antisense Oligonucleotide-Protein Nucleolar Aggregates Is Cytoprotective. Nucleic Acid Ther 2021; 31:126-144. [PMID: 33534636 DOI: 10.1089/nat.2020.0923] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phosphorothioate antisense oligonucleotides (PS-ASOs) interact with proteins and can localize to or induce the formation of a variety of subcellular PS-ASO-protein or PS-ASO-ribonucleoprotein aggregates. In this study, we show that these different aggregates that form with varying compositions at various concentrations in the cytosol, nucleus, and nucleolus may undergo phase separations in cells. Some aggregates can form with both nontoxic and toxic PS-ASOs, such as PS bodies, paraspeckles, and nuclear filaments. However, toxic PS-ASOs have been shown to form unique nucleolar aggregates that result in nucleolar dysfunction and apoptosis. These include liquid-like aggregates that we labeled "cloudy nucleoli" and solid-like perinucleolar filaments. Toxic nucleolar aggregates may undergo solid-phase separation and in the solid phase, protein mobility in and out of the aggregates is limited. Other aggregates appear to undergo liquid-phase separation, including paraspeckles and perinucleolar caps, in which protein mobility is negatively correlated with the binding affinity of the proteins to PS-ASOs. However, PS bodies and nuclear filaments are solid-like aggregates. Importantly, in cells that survived treatment with toxic PS-ASOs, solid-like PS-ASO aggregates accumulated, especially Hsc70-containing nucleolus-like structures, in which modest pre-rRNA transcriptional activity was retained and appeared to mitigate the nucleolar toxicity. This is the first demonstration that exogenous drugs, PS-ASOs, can form aggregates that undergo phase separations and that solid-phase separation of toxic PS-ASO-induced nucleolar aggregates is cytoprotective.
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Affiliation(s)
- Xue-Hai Liang
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Cheryl Li De Hoyos
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Wen Shen
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Lingdi Zhang
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Michael Fazio
- Medicinal Chemistry, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T Crooke
- Core Antisense Research and Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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49
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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50
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Epple S, Thorpe C, Baker YR, El-Sagheer AH, Brown T. Consecutive 5'- and 3'-amide linkages stabilise antisense oligonucleotides and elicit an efficient RNase H response. Chem Commun (Camb) 2021; 56:5496-5499. [PMID: 32292963 DOI: 10.1039/d0cc00444h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Antisense oligonucleotides are now entering the clinic for hard-to-treat diseases. New chemical modifications are urgently required to enhance their drug-like properties. We combine amide coupling with standard oligonucleotide synthesis to assemble backbone chimera gapmers that trigger an efficient RNase H response while improving serum life time and cellular uptake.
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Affiliation(s)
- Sven Epple
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
| | - Cameron Thorpe
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
| | - Ysobel R Baker
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK. and 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, UK.
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