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Scardovi AL, Bartolucci D, Montemurro L, Bortolotti S, Angelucci S, Amadesi C, Nieddu G, Oosterholt S, Cerisoli L, Della Pasqua O, Hrelia P, Tonelli R. Preclinical Pharmacokinetics in Tumors and Normal Tissues of the Antigene PNA Oligonucleotide MYCN-Inhibitor BGA002. Nucleic Acid Ther 2024. [PMID: 38957973 DOI: 10.1089/nat.2024.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024] Open
Abstract
Although MYCN has been considered an undruggable target, MYCN alterations confer poor prognosis in many pediatric and adult cancers. The novel MYCN-specific inhibitor BGA002 is an antigene peptide nucleic acid oligonucleotide covalently bound to a nuclear localization signal peptide. In the present study, we characterized the pharmacokinetics (PK) of BGA002 after single and repeated administration to mice using a novel specific enzyme-linked immunosorbent assay. BGA002 concentrations in plasma showed linear PK, with dose proportional increase across the tested dose levels and similar exposure between male and female and between intravenous and subcutaneous route of administration. Repeated dosing resulted in no accumulation in plasma. Biodistribution up to 7 days after single subcutaneous administration of [14C]-radiolabeled BGA002 showed broad tissues and organ distribution (suggesting a potential capability to reach primary tumor and metastasis in several body sites), with high concentrations in kidney, liver, spleen, lymph nodes, adrenals, and bone marrow. Remarkably, we demonstrated that BGA002 concentrates in tumors after repeated systemic administrations in three mouse models with MYCN amplification (neuroblastoma, rhabdomyosarcoma, and small-cell lung cancer), leading to a significant reduction in tumor weight. Taking into account the available safety profile of BGA002, these data support further evaluation of BGA002 in patients with MYCN-positive tumors.
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Affiliation(s)
| | | | - Luca Montemurro
- AGEOP Ricerca OdV, IRCCS S. Orsola Hospital, Pediatric Oncology and Hematology Unit, Bologna, Italy
| | | | | | | | | | - Sean Oosterholt
- Clinical Pharmacology & Therapeutics Group, University College London, London, United Kingdom
| | | | - Oscar Della Pasqua
- Clinical Pharmacology & Therapeutics Group, University College London, London, United Kingdom
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Roberto Tonelli
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
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2
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Ivanov GS, Tribulovich VG, Pestov NB, David TI, Amoah AS, Korneenko TV, Barlev NA. Artificial genetic polymers against human pathologies. Biol Direct 2022; 17:39. [PMID: 36474260 PMCID: PMC9727881 DOI: 10.1186/s13062-022-00353-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Originally discovered by Nielsen in 1991, peptide nucleic acids and other artificial genetic polymers have gained a lot of interest from the scientific community. Due to their unique biophysical features these artificial hybrid polymers are now being employed in various areas of theranostics (therapy and diagnostics). The current review provides an overview of their structure, principles of rational design, and biophysical features as well as highlights the areas of their successful implementation in biology and biomedicine. Finally, the review discusses the areas of improvement that would allow their use as a new class of therapeutics in the future.
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Affiliation(s)
- Gleb S Ivanov
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Vyacheslav G Tribulovich
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Nikolay B Pestov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia, 108819
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б
| | - Temitope I David
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Abdul-Saleem Amoah
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Tatyana V Korneenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
| | - Nikolai A Barlev
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064.
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б.
- School of Medicine, Nazarbayev University, 010000, Astana, Kazakhstan.
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3
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Clausse V, Zheng H, Amarasekara H, Kruhlak M, Appella DH. Thyclotides, tetrahydrofuran-modified peptide nucleic acids that efficiently penetrate cells and inhibit microRNA-21. Nucleic Acids Res 2022; 50:10839-10856. [PMID: 36215040 DOI: 10.1093/nar/gkac864] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/14/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Peptide nucleic acids (PNAs) are promising therapeutic molecules for gene modulation; however, they suffer from poor cell uptake. Delivery of PNAs into cells requires conjugation of the PNA to another large molecule, typically a cell-penetrating peptide or nanoparticle. In this study, we describe a new PNA-based molecule with cyclic tetrahydrofuran (THF) backbone modifications that in some cases considerably improve cell uptake. We refer to these THF-PNA oligomers as thyclotides. With THF groups at every position of the oligomer, the cell uptake of thyclotides targeted to miR-21 is enhanced compared with the corresponding unmodified PNA based on an aminoethylglycine backbone. An optimized thyclotide can efficiently enter cells without the use of cell-penetrating peptides, bind miR-21, its designated microRNA target, decrease expression of miR-21 and increase expression of three downstream targets (PTEN, Cdc25a and KRIT1). Using a plasmid with the PTEN-3'UTR coupled with luciferase, we further confirmed that a miR-21-targeted thyclotide prevents miR-21 from binding to its target RNA. Additionally, the thyclotide shows no cytotoxicity when administered at 200 times its active concentration. We propose that thyclotides be further explored as therapeutic candidates to modulate miRNA levels.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongchao Zheng
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harsha Amarasekara
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Kruhlak
- Microscopy Core Facility, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
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4
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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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5
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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6
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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7
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Hnedzko D, McGee DW, Karamitas YA, Rozners E. Sequence-selective recognition of double-stranded RNA and enhanced cellular uptake of cationic nucleobase and backbone-modified peptide nucleic acids. RNA (NEW YORK, N.Y.) 2017; 23:58-69. [PMID: 27742909 PMCID: PMC5159649 DOI: 10.1261/rna.058362.116] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/08/2016] [Indexed: 05/07/2023]
Abstract
Sequence-selective recognition of complex RNAs in live cells could find broad applications in biology, biomedical research, and biotechnology. However, specific recognition of structured RNA is challenging, and generally applicable and effective methods are lacking. Recently, we found that peptide nucleic acids (PNAs) were unusually well-suited ligands for recognition of double-stranded RNAs. Herein, we report that 2-aminopyridine (M) modified PNAs and their conjugates with lysine and arginine tripeptides form strong (Ka = 9.4 to 17 × 107 M-1) and sequence-selective triple helices with RNA hairpins at physiological pH and salt concentration. The affinity of PNA-peptide conjugates for the matched RNA hairpins was unusually high compared to the much lower affinity for DNA hairpins of the same sequence (Ka = 0.05 to 1.1 × 107 M-1). The binding of double-stranded RNA by M-modified PNA-peptide conjugates was a relatively fast process (kon = 2.9 × 104 M-1 sec-1) compared to the notoriously slow triple helix formation by oligodeoxynucleotides (kon ∼ 103 M-1 sec-1). M-modified PNA-peptide conjugates were not cytotoxic and were efficiently delivered in the cytosol of HEK293 cells at 10 µM. Surprisingly, M-modified PNAs without peptide conjugation were also taken up by HEK293 cells, which, to the best of our knowledge, is the first example of heterocyclic base modification that enhances the cellular uptake of PNA. Our results suggest that M-modified PNA-peptide conjugates are promising probes for sequence-selective recognition of double-stranded RNA in live cells and other biological systems.
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Affiliation(s)
- Dziyana Hnedzko
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Dennis W McGee
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Yannis A Karamitas
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
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8
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Gustincich S, Zucchelli S, Mallamaci A. The Yin and Yang of nucleic acid-based therapy in the brain. Prog Neurobiol 2016; 155:194-211. [PMID: 27887908 DOI: 10.1016/j.pneurobio.2016.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 11/16/2016] [Accepted: 11/20/2016] [Indexed: 02/06/2023]
Abstract
The post-genomic era has unveiled the existence of a large repertory of non-coding RNAs and repetitive elements that play a fundamental role in cellular homeostasis and dysfunction. These may represent unprecedented opportunities to modify gene expression at the right time in the correct space in vivo, providing an almost unlimited reservoir of new potential pharmacological agents. Hijacking their mode of actions, the druggable genome can be extended to regulatory RNAs and DNA elements in a scalable fashion. Here, we discuss the state-of-the-art of nucleic acid-based drugs to treat neurodegenerative diseases. Beneficial effects can be obtained by inhibiting (Yin) and increasing (Yang) gene expression, depending on the disease and the drug target. Together with the description of the current use of inhibitory RNAs (small inhibitory RNAs and antisense oligonucleotides) in animal models and clinical trials, we discuss the molecular basis and applications of new classes of activatory RNAs at transcriptional (RNAa) and translational (SINEUP) levels.
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Affiliation(s)
- Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy; Area of Neuroscience, SISSA, Trieste, Italy.
| | - Silvia Zucchelli
- Area of Neuroscience, SISSA, Trieste, Italy; Department of Health Sciences, Universita' del Piemonte Orientale, Novara, Italy
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9
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Gooding M, Malhotra M, Evans JC, Darcy R, O'Driscoll CM. Oligonucleotide conjugates - Candidates for gene silencing therapeutics. Eur J Pharm Biopharm 2016; 107:321-40. [PMID: 27521696 DOI: 10.1016/j.ejpb.2016.07.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/24/2016] [Accepted: 07/25/2016] [Indexed: 11/18/2022]
Abstract
The potential therapeutic and diagnostic applications of oligonucleotides (ONs) have attracted great attention in recent years. The capability of ONs to selectively inhibit target genes through antisense and RNA interference mechanisms, without causing un-intended sideeffects has led them to be investigated for various biomedical applications, especially for the treatment of viral diseases and cancer. In recent years, many researchers have focused on enhancing the stability and target specificity of ONs by encapsulating/complexing them with polymers or lipid chains to formulate nanoparticles/nanocomplexes/micelles. Also, chemical modification of nucleic acids has emerged as an alternative to impart stability to ONs against nucleases and other degrading enzymes and proteins found in blood. In addition to chemically modifying the nucleic acids directly, another strategy that has emerged, involves conjugating polymers/peptide/aptamers/antibodies/proteins, preferably to the sense strand (3'end) of siRNAs. Conjugation to the siRNA not only enhances the stability and targeting specificity of the siRNA, but also allows for the development of self-administering siRNA formulations, with a much smaller size than what is usually observed for nanoparticle (∼200nm). This review concentrates mainly on approaches and studies involving ON-conjugates for biomedical applications.
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Affiliation(s)
- Matt Gooding
- Pharmacodelivery Group, School of Pharmacy, University College Cork, Cork, Ireland
| | - Meenakshi Malhotra
- Pharmacodelivery Group, School of Pharmacy, University College Cork, Cork, Ireland
| | - James C Evans
- Pharmacodelivery Group, School of Pharmacy, University College Cork, Cork, Ireland
| | - Raphael Darcy
- Pharmacodelivery Group, School of Pharmacy, University College Cork, Cork, Ireland
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10
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Abstract
Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.
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Affiliation(s)
- W Brad Wan
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
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11
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Silencing CCR2 in Macrophages Alleviates Adipose Tissue Inflammation and the Associated Metabolic Syndrome in Dietary Obese Mice. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e280. [PMID: 26812653 PMCID: PMC5012549 DOI: 10.1038/mtna.2015.51] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/23/2015] [Indexed: 12/17/2022]
Abstract
Adipose tissue macrophage (ATM)-mediated inflammation is a key feature contributing to the adverse metabolic outcomes of dietary obesity. Recruitment of macrophages to obese adipose tissues (AT) can occur through the engagement of CCR2, the receptor for MCP-1 (monocyte chemoattractant protein-1), which is expressed on peripheral monocytes/macrophages. Here, we show that i.p. administration of a rabies virus glycoprotein-derived acetylcholine receptor-binding peptide effectively delivers complexed siRNA into peritoneal macrophages and ATMs in a mouse model of high-fat diet-induced obesity. Treatment with siRNA against CCR2 inhibited macrophage infiltration and accumulation in AT and, therefore, proinflammatory cytokines produced by macrophages. Consequently, the treatment significantly improved glucose tolerance and insulin sensitivity profiles, and also alleviated the associated symptoms of hepatic steatosis and reduced hepatic triglyceride production. These results demonstrate that disruption of macrophage chemotaxis to the AT through cell-targeted gene knockdown strategies can provide a therapeutic intervention for obesity-related metabolic diseases. The study also highlights a siRNA delivery approach for targeting specific monocyte subsets that contribute to obesity-associated inflammation without affecting the function of other tissue-resident macrophages that are essential for host homeostasis and survival.
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12
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Brolin C, Shiraishi T, Hojman P, Krag TO, Nielsen PE, Gehl J. Electroporation Enhanced Effect of Dystrophin Splice Switching PNA Oligomers in Normal and Dystrophic Muscle. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e267. [PMID: 26623939 PMCID: PMC5014535 DOI: 10.1038/mtna.2015.41] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/09/2015] [Indexed: 01/16/2023]
Abstract
Peptide nucleic acid (PNA) is a synthetic DNA mimic that has shown potential for discovery of novel splice switching antisense drugs. However, in vivo cellular delivery has been a limiting factor for development, and only few successful studies have been reported. As a possible modality for improvement of in vivo cellular availability, we have investigated the effect of electrotransfer upon intramuscular (i.m.) PNA administration in vivo. Antisense PNA targeting exon 23 of the murine dystrophin gene was administered by i.m. injection to the tibialis anterior (TA) muscle of normal NMRI and dystrophic mdx mice with or without electroporation. At low, single PNA doses (1.5, 3, or 10 µg/TA), electroporation augmented the antisense exon skipping induced by an unmodified PNA by twofold to fourfold in healthy mouse muscle with optimized electric parameters, measured after 7 days. The PNA splice switching was detected at the RNA level up to 4 weeks after a single-dose treatment. In dystrophic muscles of the MDX mouse, electroporation increased the number of dystrophin-positive fibers about 2.5-fold at 2 weeks after a single PNA administration compared to injection only. In conclusion, we find that electroporation can enhance PNA antisense effects in muscle tissue.
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Affiliation(s)
- Camilla Brolin
- Center for Experimental Drug and Gene Electrotransfer (CEDGE), Department of Oncology, Copenhagen University Hospital Herlev, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen, Denmark
| | - Takehiko Shiraishi
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen, Denmark
| | - Pernille Hojman
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Thomas O Krag
- Neuromuscular Research Unit, Department of Neurology Rigshospitalet, University of Copenhagen, Denmark
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen, Denmark.,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen, Denmark
| | - Julie Gehl
- Center for Experimental Drug and Gene Electrotransfer (CEDGE), Department of Oncology, Copenhagen University Hospital Herlev, Denmark
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13
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Boisguérin P, Deshayes S, Gait MJ, O'Donovan L, Godfrey C, Betts CA, Wood MJA, Lebleu B. Delivery of therapeutic oligonucleotides with cell penetrating peptides. Adv Drug Deliv Rev 2015; 87:52-67. [PMID: 25747758 PMCID: PMC7102600 DOI: 10.1016/j.addr.2015.02.008] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 12/15/2022]
Abstract
Oligonucleotide-based drugs have received considerable attention for their capacity to modulate gene expression very specifically and as a consequence they have found applications in the treatment of many human acquired or genetic diseases. Clinical translation has been often hampered by poor biodistribution, however. Cell-penetrating peptides (CPPs) appear as a possibility to increase the cellular delivery of non-permeant biomolecules such as nucleic acids. This review focuses on CPP-delivery of several classes of oligonucleotides (ONs), namely antisense oligonucleotides, splice switching oligonucleotides (SSOs) and siRNAs. Two main strategies have been used to transport ONs with CPPs: covalent conjugation (which is more appropriate for charge-neutral ON analogues) and non-covalent complexation (which has been used for siRNA delivery essentially). Chemical synthesis, mechanisms of cellular internalization and various applications will be reviewed. A comprehensive coverage of the enormous amount of published data was not possible. Instead, emphasis has been put on strategies that have proven to be effective in animal models of important human diseases and on examples taken from the authors' own expertise.
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Affiliation(s)
- Prisca Boisguérin
- Centre de Recherche de Biochimie Macromoléculaire, UMR 5237 CNRS, 1919 Route de Mende, 34293 Montpellier, France.
| | - Sébastien Deshayes
- Centre de Recherche de Biochimie Macromoléculaire, UMR 5237 CNRS, 1919 Route de Mende, 34293 Montpellier, France
| | - Michael J Gait
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Liz O'Donovan
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Caroline Godfrey
- University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
| | - Corinne A Betts
- University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
| | - Matthew J A Wood
- University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
| | - Bernard Lebleu
- UMR 5235 CNRS, Université Montpellier 2, Place Eugene Bataillon, Montpellier 34095, France
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14
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Rigo F, Seth PP, Bennett CF. Antisense oligonucleotide-based therapies for diseases caused by pre-mRNA processing defects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:303-52. [PMID: 25201110 DOI: 10.1007/978-1-4939-1221-6_9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Before a messenger RNA (mRNA) is translated into a protein in the cytoplasm, its pre-mRNA precursor is extensively processed through capping, splicing and polyadenylation in the nucleus. Defects in the processing of pre-mRNAs due to mutations in RNA sequences often cause disease. Traditional small molecules or protein-based therapeutics are not well suited for correcting processing defects by targeting RNA. However, antisense oligonucleotides (ASOs) designed to bind RNA by Watson-Crick base pairing can target most RNA transcripts and have emerged as the ideal therapeutic agents for diseases that are caused by pre-mRNA processing defects. Here we review the diverse ASO-based mechanisms that can be exploited to modulate the expression of RNA. We also discuss how advancements in medicinal chemistry and a deeper understanding of the pharmacokinetic and toxicological properties of ASOs have enabled their use as therapeutic agents. We end by describing how ASOs have been used successfully to treat various pre-mRNA processing diseases in animal models.
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Affiliation(s)
- Frank Rigo
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA, USA,
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15
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Abstract
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RNA
interference (RNAi) is an endogenous process in which small
noncoding RNAs, including small interfering RNAs (siRNAs) and microRNAs
(miRNAs), post-transcriptionally regulate gene expressions. In general,
siRNA and miRNA/miRNA mimics are similar in nature and activity except
their origin and specificity. Although both siRNAs and miRNAs have
been extensively studied as novel therapeutics for a wide range of
diseases, the large molecular weight, anionic surface charges, instability
in blood circulation, and intracellular trafficking to the RISC after
cellular uptake have hindered the translation of these RNAs from bench
to clinic. As a result, a great variety of delivery systems have been
investigated for safe and effective delivery of small noncoding RNAs.
Among these systems, peptides, especially cationic peptides, have
emerged as a promising type of carrier due to their inherent ability
to condense negatively charged RNAs, ease of synthesis, controllable
size, and tunable structure. In this review, we will focus on three
major types of cationic peptides, including poly(l-lysine)
(PLL), protamine, and cell penetrating peptides (CPP), as well as
peptide targeting ligands that have been extensively used in RNA delivery.
The delivery strategies, applications, and limitations of these cationic
peptides in siRNA/miRNA delivery will be discussed.
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Affiliation(s)
- Ravi S Shukla
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City , Kansas City, Missouri 64108, United States
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16
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Järver P, O'Donovan L, Gait MJ. A chemical view of oligonucleotides for exon skipping and related drug applications. Nucleic Acid Ther 2013; 24:37-47. [PMID: 24171481 DOI: 10.1089/nat.2013.0454] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Peter Järver
- Medical Research Council , Laboratory of Molecular Biology, Cambridge, United Kingdom
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17
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Is there a future for cell-penetrating peptides in oligonucleotide delivery? Eur J Pharm Biopharm 2013; 85:5-11. [DOI: 10.1016/j.ejpb.2013.03.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/18/2013] [Accepted: 03/19/2013] [Indexed: 11/23/2022]
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18
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Browne EC, Langford SJ, Abbott BM. Synthesis and effects of conjugated tocopherol analogues on peptide nucleic acid hybridisation. Org Biomol Chem 2013; 11:6744-50. [PMID: 23995261 DOI: 10.1039/c3ob41613e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To the N-terminus of a nonamer peptide nucleic acid sequence, H-GCACGACTT-NH2, was attached a number of lipophilic conjugate molecules including three synthetic tocopherol (vitamin E) analogues. Studies were then undertaken with complementary PNA and DNA sequences to explore the effects of the conjugates using the techniques of UV monitored melting curves and isothermal calorimetry. Duplex formation was observed when the benzopyran group of vitamin E was conjugated. However, in the presence of the phytyl chain of vitamin E, binding was found to be temperature dependent.
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Affiliation(s)
- Elisse C Browne
- Department of Chemistry, La Trobe University, Bundoora, Australia.
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19
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Muse O, Zengeya T, Mwaura J, Hnedzko D, McGee DW, Grewer CT, Rozners E. Sequence selective recognition of double-stranded RNA at physiologically relevant conditions using PNA-peptide conjugates. ACS Chem Biol 2013; 8:1683-6. [PMID: 23721369 DOI: 10.1021/cb400144x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conjugation of short peptide nucleic acids (PNA) with tetralysine peptides strongly enhanced triple helical binding to RNA at physiologically relevant conditions. The PNA hexamers and heptamers carrying cationic nucleobase and tetralysine modifications displayed high binding affinity for complementary double-stranded RNA without compromising sequence selectivity. The PNA-peptide conjugates had unique preference for binding double-stranded RNA, while having little, if any, affinity for double-stranded DNA. The cationic PNAs were efficiently taken up by HEK293 cells, whereas little uptake was observed for unmodified PNA.
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Affiliation(s)
- Oluwatoyosi Muse
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Thomas Zengeya
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Juddy Mwaura
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Dziyana Hnedzko
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Dennis W. McGee
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Christof T. Grewer
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Eriks Rozners
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
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Recent advances in chemical modification of Peptide nucleic acids. J Nucleic Acids 2012; 2012:518162. [PMID: 22991652 PMCID: PMC3443988 DOI: 10.1155/2012/518162] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 07/12/2012] [Accepted: 07/20/2012] [Indexed: 12/14/2022] Open
Abstract
Peptide nucleic acid (PNA) has become an extremely powerful tool in chemistry and biology. Although PNA recognizes single-stranded nucleic acids with exceptionally high affinity and sequence selectivity, there is considerable ongoing effort to further improve properties of PNA for both fundamental science and practical applications. The present paper discusses selected recent studies that improve on cellular uptake and binding of PNA to double-stranded DNA and RNA. The focus is on chemical modifications of PNA's backbone and heterocyclic nucleobases. The paper selects representative recent studies and does not attempt to provide comprehensive coverage of the broad and vibrant field of PNA modification.
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Järver P, Coursindel T, Andaloussi SEL, Godfrey C, Wood MJA, Gait MJ. Peptide-mediated Cell and In Vivo Delivery of Antisense Oligonucleotides and siRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e27. [PMID: 23344079 PMCID: PMC3390225 DOI: 10.1038/mtna.2012.18] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/26/2012] [Accepted: 04/26/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Peter Järver
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Samir EL Andaloussi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
- Department of Laboratory Medicine, Karolinska Institute, Hudidnge, Sweden
| | - Caroline Godfrey
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Matthew JA Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Michael J Gait
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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22
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Coursindel T, Järver P, Gait MJ. Peptide-based in vivo delivery agents for oligonucleotides and siRNA. Nucleic Acid Ther 2012; 22:71-6. [PMID: 22409235 DOI: 10.1089/nat.2012.0341] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Abstract
The chemistry of the oligonucleotide backbone is crucial to obtaining high activity in vivo in exon skipping applications. Apart from the ability to bind strongly and sequence-specifically to pre-mRNA targets, the type of backbone also influences cell delivery, in vivo pharmacology, bio-distribution, toxicology, and ultimately the therapeutic use in humans. Reviewed here are classes of oligonucleotide commonly used for exon skipping applications, namely negatively charged backbones typified by RNA analogues having 2'-O-substitution and a phosphorothioate linkage and charge-neutral backbones such as PNA and PMO. Also discussed are peptide conjugates of PNA and PMO that enhance cellular and in vivo delivery and their potential for drug development. Finally, the prospects for development of other analogue types in exon skipping applications are outlined.
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