1
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Zharkov TD, Markov OV, Zhukov SA, Khodyreva SN, Kupryushkin MS. Influence of Combinations of Lipophilic and Phosphate Backbone Modifications on Cellular Uptake of Modified Oligonucleotides. Molecules 2024; 29:452. [PMID: 38257365 PMCID: PMC10818405 DOI: 10.3390/molecules29020452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Numerous types of oligonucleotide modifications have been developed since automated synthesis of DNA/RNA became a common instrument in the creation of synthetic oligonucleotides. Despite the growing number of types of oligonucleotide modifications under development, only a few of them and, moreover, their combinations have been studied widely enough in terms of their influence on the properties of corresponding NA constructions. In the present study, a number of oligonucleotides with combinations of 3'-end lipophilic (a single cholesteryl or a pair of dodecyl residues) and phosphate backbone modifications were synthesized. The influence of the combination of used lipophilic groups with phosphate modifications of various natures and different positions on the efficiency of cell penetration was evaluated. The obtained results indicate that even a couple of phosphate modifications are able to affect a set of oligonucleotide properties in a complex manner and can remarkably change cellular uptake. These data clearly show that the strategy of using different patterns of modification combinations has great potential for the rational design of oligonucleotide structures with desired predefined properties.
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Affiliation(s)
| | | | | | | | - Maxim S. Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (T.D.Z.); (O.V.M.); (S.A.Z.); (S.N.K.)
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2
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Convenient Solid-Phase Attachment of Small-Molecule Ligands to Oligonucleotides via a Biodegradable Acid-Labile P-N-Bond. Molecules 2023; 28:molecules28041904. [PMID: 36838892 PMCID: PMC9961013 DOI: 10.3390/molecules28041904] [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: 01/26/2023] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
One of the key problems in the design of therapeutic and diagnostic oligonucleotides is the attachment of small-molecule ligands for targeted deliveries in such a manner that provides the controlled release of the oligonucleotide at a certain moment. Here, we propose a novel, convenient approach for attaching ligands to the 5'-end of the oligonucleotide via biodegradable, acid-labile phosphoramide linkage. The method includes the activation of the 5'-terminal phosphate of the fully protected, support-bound oligonucleotide, followed by interaction with a ligand bearing the primary amino group. This technique is simple to perform, allows for forcing the reaction to completion by adding excess soluble reactant, eliminates the problem of the limited solubility of reagents, and affords the possibility of using different solvents, including water/organic media. We demonstrated the advantages of this approach by synthesizing and characterizing a wide variety of oligonucleotide 5'-conjugates with different ligands, such as cholesterol, aliphatic oleylamine, and p-anisic acid. The developed method suits different types of oligonucleotides (deoxyribo-, 2'-O-methylribo-, ribo-, and others).
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3
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Nicholson TA, Sagmeister M, Wijesinghe SN, Farah H, Hardy RS, Jones SW. Oligonucleotide Therapeutics for Age-Related Musculoskeletal Disorders: Successes and Challenges. Pharmaceutics 2023; 15:237. [PMID: 36678864 PMCID: PMC9866666 DOI: 10.3390/pharmaceutics15010237] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/04/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
Age-related disorders of the musculoskeletal system including sarcopenia, osteoporosis and arthritis represent some of the most common chronic conditions worldwide, for which there remains a great clinical need to develop safer and more efficacious pharmacological treatments. Collectively, these conditions involve multiple tissues, including skeletal muscle, bone, articular cartilage and the synovium within the joint lining. In this review, we discuss the potential for oligonucleotide therapies to combat the unmet clinical need in musculoskeletal disorders by evaluating the successes of oligonucleotides to modify candidate pathological gene targets and cellular processes in relevant tissues and cells of the musculoskeletal system. Further, we discuss the challenges that remain for the clinical development of oligonucleotides therapies for musculoskeletal disorders and evaluate some of the current approaches to overcome these.
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Affiliation(s)
- Thomas A. Nicholson
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | - Michael Sagmeister
- Institute for Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Susanne N. Wijesinghe
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | - Hussein Farah
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | - Rowan S. Hardy
- Institute for Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Simon W. Jones
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
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4
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Fioretti I, Müller-Späth T, Weldon R, Vogg S, Morbidelli M, Sponchioni M. Continuous countercurrent chromatographic twin-column purification of oligonucleotides: the role of the displacement effect. Biotechnol Bioeng 2022; 119:1861-1872. [PMID: 35338661 PMCID: PMC9322279 DOI: 10.1002/bit.28093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/10/2022]
Abstract
Oligonucleotides (ONs) are breaking through in the biopharmaceutical industry as a promising class of biotherapeutics. The main success of these molecules is due to their peculiar way of acting in the cellular process, regulating the gene expression and hence influencing the protein synthesis at a pre-translational level. Although the Food and Drug Administration (FDA) already approved a few ON-based therapeutics, their production cost strongly limits large scale manufacturing: a situation that can be alleviated through process intensification. In this work, we address this problem by developing an efficient and continuous chromatographic purification process for ONs. In particular, we considered the chromatographic purification of a ON crude prepared by chemical synthesis using anion exchange resins. We demonstrate that in this system the competitive adsorption of the various species on the same sites of the resin leads to the displacement of the more weakly adsorbing species by the more strongly adsorbing ones. This phenomenon affects the behavior of the chromatographic units and it has been investigated in detail. Then, we developed a continuous countercurrent solvent gradient purification (MCSGP) process, which can significantly improve the productivity and buffer consumption compared to a classical single-column, batch chromatographic process. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ismaele Fioretti
- Department of Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Via Mancinelli 7, Milano, 20131, Italy
| | | | - Richard Weldon
- YMC ChromaCon, Technoparkstrasse 1, 8005, Zürich, Switzerland
| | - Sebastian Vogg
- YMC ChromaCon, Technoparkstrasse 1, 8005, Zürich, Switzerland
| | - Massimo Morbidelli
- Department of Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Via Mancinelli 7, Milano, 20131, Italy
| | - Mattia Sponchioni
- Department of Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Via Mancinelli 7, Milano, 20131, Italy
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5
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MacCulloch T, Novacek A, Stephanopoulos N. Proximity-enhanced synthesis of DNA-peptide-DNA triblock molecules. Chem Commun (Camb) 2022; 58:4044-4047. [PMID: 35260875 DOI: 10.1039/d1cc04970d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a proximity-enhanced method to synthesize a peptide flanked by two different oligonucleotide handles. Our method relies on sequential bioorthogonal reactions, and partial hybridization of the second handle to the first. We demonstrate the synthesis of a protease-responsive DNA "latch" and a cyclic bioactive peptide using this method.
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Affiliation(s)
- Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Alexandra Novacek
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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6
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Grijalvo S, Ocampo SM, Perales JC, Eritja R. Preparation of Lipid-Conjugated siRNA Oligonucleotides for Enhanced Gene Inhibition in Mammalian Cells. Methods Mol Biol 2021; 2282:119-136. [PMID: 33928573 DOI: 10.1007/978-1-0716-1298-9_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleic acid conjugates are promising drugs for treating gene-related diseases. Conjugating specific units like lipids, cell-penetrating peptides, polymers, antibodies, and aptamers either at the 3'- or 5'-termini of a siRNA duplex molecule has resulted in a plethora of siRNA bioconjugates with improved stabilities in bloodstream and better pharmacokinetic values than unmodified siRNAs. In this sense, lipid-siRNA conjugates have attracted a remarkable interest for their potential value in facilitating cellular uptake. In this chapter, we describe a series of protocols involving the synthesis of siRNA oligonucleotides carrying either neutral or cationic lipids at the 3'- and 5'-termini. The resulting lipid-siRNA conjugates are aimed to be used as exogenous effectors for inhibiting gene expression by RNA interference. A protocol for the formulation of lipid siRNA using sonication in the presence of serum is described yielding interesting transfection properties for cell culture without the use of transfecting agents.
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Affiliation(s)
- Santiago Grijalvo
- Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER BBN), Barcelona, Spain. .,Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Barcelona, Spain.
| | - Sandra M Ocampo
- Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER BBN), Barcelona, Spain.,Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Barcelona, Spain.,Department of Physiologic Sciences, School of Medicine, University of Barcelona, Barcelona, Spain
| | - José Carlos Perales
- Department of Physiologic Sciences, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Ramon Eritja
- Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER BBN), Barcelona, Spain. .,Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Barcelona, Spain.
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7
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Schlich M, Palomba R, Costabile G, Mizrahy S, Pannuzzo M, Peer D, Decuzzi P. Cytosolic delivery of nucleic acids: The case of ionizable lipid nanoparticles. Bioeng Transl Med 2021; 6:e10213. [PMID: 33786376 PMCID: PMC7995196 DOI: 10.1002/btm2.10213] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/14/2022] Open
Abstract
Ionizable lipid nanoparticles (LNPs) are the most clinically advanced nano-delivery system for therapeutic nucleic acids. The great effort put in the development of ionizable lipids with increased in vivo potency brought LNPs from the laboratory benches to the FDA approval of patisiran in 2018 and the ongoing clinical trials for mRNA-based vaccines against SARS-CoV-2. Despite these success stories, several challenges remain in RNA delivery, including what is known as "endosomal escape." Reaching the cytosol is mandatory for unleashing the therapeutic activity of RNA molecules, as their accumulation in other intracellular compartments would simply result in efficacy loss. In LNPs, the ability of ionizable lipids to form destabilizing non-bilayer structures at acidic pH is recognized as the key for endosomal escape and RNA cytosolic delivery. This is motivating a surge in studies aiming at designing novel ionizable lipids with improved biodegradation and safety profiles. In this work, we describe the journey of RNA-loaded LNPs across multiple intracellular barriers, from the extracellular space to the cytosol. In silico molecular dynamics modeling, in vitro high-resolution microscopy analyses, and in vivo imaging data are systematically reviewed to distill out the regulating mechanisms underlying the endosomal escape of RNA. Finally, a comparison with strategies employed by enveloped viruses to deliver their genetic material into cells is also presented. The combination of a multidisciplinary analytical toolkit for endosomal escape quantification and a nature-inspired design could foster the development of future LNPs with improved cytosolic delivery of nucleic acids.
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Affiliation(s)
- Michele Schlich
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
- Department of Life and Environmental SciencesUniversity of CagliariCagliariItaly
| | - Roberto Palomba
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
| | - Gabriella Costabile
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
| | - Shoshy Mizrahy
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
- Laboratory of Precision NanoMedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of EngineeringTel Aviv UniversityTel AvivIsrael
- Center for Nanoscience and NanotechnologyTel Aviv UniversityTel AvivIsrael
- Cancer Biology Research CenterTel Aviv UniversityTel AvivIsrael
| | - Martina Pannuzzo
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
| | - Dan Peer
- Laboratory of Precision NanoMedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of EngineeringTel Aviv UniversityTel AvivIsrael
- Center for Nanoscience and NanotechnologyTel Aviv UniversityTel AvivIsrael
- Cancer Biology Research CenterTel Aviv UniversityTel AvivIsrael
| | - Paolo Decuzzi
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
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8
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Vinarov Z, Abrahamsson B, Artursson P, Batchelor H, Berben P, Bernkop-Schnürch A, Butler J, Ceulemans J, Davies N, Dupont D, Flaten GE, Fotaki N, Griffin BT, Jannin V, Keemink J, Kesisoglou F, Koziolek M, Kuentz M, Mackie A, Meléndez-Martínez AJ, McAllister M, Müllertz A, O'Driscoll CM, Parrott N, Paszkowska J, Pavek P, Porter CJH, Reppas C, Stillhart C, Sugano K, Toader E, Valentová K, Vertzoni M, De Wildt SN, Wilson CG, Augustijns P. Current challenges and future perspectives in oral absorption research: An opinion of the UNGAP network. Adv Drug Deliv Rev 2021; 171:289-331. [PMID: 33610694 DOI: 10.1016/j.addr.2021.02.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/12/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023]
Abstract
Although oral drug delivery is the preferred administration route and has been used for centuries, modern drug discovery and development pipelines challenge conventional formulation approaches and highlight the insufficient mechanistic understanding of processes critical to oral drug absorption. This review presents the opinion of UNGAP scientists on four key themes across the oral absorption landscape: (1) specific patient populations, (2) regional differences in the gastrointestinal tract, (3) advanced formulations and (4) food-drug interactions. The differences of oral absorption in pediatric and geriatric populations, the specific issues in colonic absorption, the formulation approaches for poorly water-soluble (small molecules) and poorly permeable (peptides, RNA etc.) drugs, as well as the vast realm of food effects, are some of the topics discussed in detail. The identified controversies and gaps in the current understanding of gastrointestinal absorption-related processes are used to create a roadmap for the future of oral drug absorption research.
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Affiliation(s)
- Zahari Vinarov
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium; Department of Chemical and Pharmaceutical Engineering, Sofia University, Sofia, Bulgaria
| | - Bertil Abrahamsson
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Hannah Batchelor
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Philippe Berben
- Pharmaceutical Development, UCB Pharma SA, Braine- l'Alleud, Belgium
| | - Andreas Bernkop-Schnürch
- Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - James Butler
- GlaxoSmithKline Research and Development, Ware, United Kingdom
| | | | - Nigel Davies
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Gøril Eide Flaten
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - Nikoletta Fotaki
- Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom
| | | | | | | | | | | | - Martin Kuentz
- Institute for Pharma Technology, University of Applied Sciences and Arts Northwestern Switzerland, Basel, Switzerland
| | - Alan Mackie
- School of Food Science & Nutrition, University of Leeds, Leeds, United Kingdom
| | | | | | - Anette Müllertz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Petr Pavek
- Faculty of Pharmacy, Charles University, Hradec Králové, Czech Republic
| | | | - Christos Reppas
- Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Kiyohiko Sugano
- College of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
| | - Elena Toader
- Faculty of Medicine, University of Medicine and Pharmacy of Iasi, Romania
| | - Kateřina Valentová
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Maria Vertzoni
- Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Saskia N De Wildt
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Clive G Wilson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Patrick Augustijns
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium.
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9
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Mendonça MCP, Kont A, Aburto MR, Cryan JF, O'Driscoll CM. Advances in the Design of (Nano)Formulations for Delivery of Antisense Oligonucleotides and Small Interfering RNA: Focus on the Central Nervous System. Mol Pharm 2021; 18:1491-1506. [PMID: 33734715 PMCID: PMC8824433 DOI: 10.1021/acs.molpharmaceut.0c01238] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
RNA-based therapeutics have emerged
as one of the most powerful
therapeutic options used for the modulation of gene/protein expression
and gene editing with the potential to treat neurodegenerative diseases.
However, the delivery of nucleic acids to the central nervous system
(CNS), in particular by the systemic route, remains a major hurdle.
This review will focus on the strategies for systemic delivery of
therapeutic nucleic acids designed to overcome these barriers. Pathways
and mechanisms of transport across the blood–brain barrier
which could be exploited for delivery are described, focusing in particular
on smaller nucleic acids including antisense oligonucleotides (ASOs)
and small interfering RNA (siRNA). Approaches used to enhance delivery
including chemical modifications, nanocarrier systems, and target
selection (cell-specific delivery) are critically analyzed. Learnings
achieved from a comparison of the successes and failures reported
for CNS delivery of ASOs versus siRNA will help identify opportunities
for a wider range of nucleic acids and accelerate the clinical translation
of these innovative therapies.
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Affiliation(s)
- Monique C P Mendonça
- Pharmacodelivery Group, School of Pharmacy, University College Cork, T12 YT20 Cork, Ireland
| | - Ayse Kont
- Pharmacodelivery Group, School of Pharmacy, University College Cork, T12 YT20 Cork, Ireland
| | - Maria Rodriguez Aburto
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, T12 XF62 Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, T12 XF62 Cork, Ireland
| | - Caitriona M O'Driscoll
- Pharmacodelivery Group, School of Pharmacy, University College Cork, T12 YT20 Cork, Ireland
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10
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Titze-de-Almeida SS, Brandão PRDP, Faber I, Titze-de-Almeida R. Leading RNA Interference Therapeutics Part 1: Silencing Hereditary Transthyretin Amyloidosis, with a Focus on Patisiran. Mol Diagn Ther 2021; 24:49-59. [PMID: 31701435 DOI: 10.1007/s40291-019-00434-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In 2018, patisiran was the first-ever RNA interference (RNAi)-based drug approved by the US Food and Drug Administration. Now pharmacology textbooks may include a new drug class that results in the effect first described by Fire and Mello 2 decades ago: post-transcriptional gene silencing by a small-interfering RNA (siRNA). Patients with hereditary transthyretin-mediated amyloidosis (hATTR amyloidosis) present with mutations in the transthyretin (TTR) gene that lead to the formation of amyloid deposits in peripheral nerves and heart. The disease may also affect the eye and central nervous system. The formulation of patisiran comprises the RNAi drug encapsulated into a nanoparticle especially developed to deliver the anti-TTR siRNA into the main TTR producer: the liver. Hepatic cells contain apolipoprotein E receptors that recognize ApoE proteins opsonized in the lipid carrier and internalize the drug by endocytosis. Lipid vesicles are disrupted in the cell cytoplasm, and siRNAs are free to trigger the RNAi-based TTR gene silencing. The silencing process involves the binding of siRNA guide strand to 3'-untranslated region sequence of both mutant and wild-type TTR messenger RNA, which culminates in the TTR mRNA cleavage by the RNA-induced silencing complex (RISC) as the first biochemical drug effect. Patisiran 0.3 mg/kg is administered intravenously every 3 weeks. Patients require premedication with anti-inflammatory drugs and antagonists of histamine H1 and H2 receptors to prevent infusion-related reactions and may require vitamin A supplementation. Following patisiran treatment, TTR knockdown remained stable for at least 2 years. Adverse effects were mild to moderate with unchanged hematological, renal, or hepatic parameters. No drug-related severe adverse effects occurred in a 24-month follow-up phase II open-label extension study. At the recommended dosage of patisiran, Cmax and AUC values (mean ± standard deviation) were 7.15 ± 2.14 μg/mL and 184 ± 159 μg·h/mL, respectively. The drug showed stability in circulation with > 95% encapsulated in lipid particles. Metabolization occurred by ribonuclease enzymes, with less than 1% excreted unchanged in the urine. Patisiran ameliorated neuropathy impairment according to the modified Neuropathy Impairment Score + 7 analysis of the phase III study. The Norfolk Quality of Life-Diabetic Neuropathy score and gait speed improved in 51% of the patisiran-treated group in 18 months. Additionally, the modified body mass index showed positive outcomes. Altogether, the data across phase I-III clinical trials points to patisiran as an effective and safe drug for the treatment of hATTR amyloidosis. It is hoped that real-world data from a larger number of patients treated with patisiran will confirm the effectiveness of this first-approved siRNA-based drug.
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Affiliation(s)
- Simoneide S Titze-de-Almeida
- Technology for Gene Therapy Laboratory, Central Institute of Sciences, University of Brasília/FAV, Brasília, DF, Brazil
| | - Pedro Renato de Paula Brandão
- Technology for Gene Therapy Laboratory, Central Institute of Sciences, University of Brasília/FAV, Brasília, DF, Brazil.,Laboratory of Neuroscience and Behavior, University of Brasília, Brasília, DF, Brazil.,Neurology Clinic, Medical Department, Chamber of Deputies, The National Congress, Brasília, DF, Brazil
| | - Ingrid Faber
- Technology for Gene Therapy Laboratory, Central Institute of Sciences, University of Brasília/FAV, Brasília, DF, Brazil.,Laboratory of Neuroscience and Behavior, University of Brasília, Brasília, DF, Brazil
| | - Ricardo Titze-de-Almeida
- Technology for Gene Therapy Laboratory, Central Institute of Sciences, University of Brasília/FAV, Brasília, DF, Brazil.
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11
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Honcharenko D, Druceikaite K, Honcharenko M, Bollmark M, Tedebark U, Strömberg R. New Alkyne and Amine Linkers for Versatile Multiple Conjugation of Oligonucleotides. ACS OMEGA 2021; 6:579-593. [PMID: 33458510 PMCID: PMC7807750 DOI: 10.1021/acsomega.0c05075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/08/2020] [Indexed: 05/08/2023]
Abstract
Oligonucleotide (ON) conjugates are increasingly important tools for various molecular diagnostics, nanotechnological applications, and for the development of nucleic acid-based therapies. Multiple labeling of ONs can further equip ON-conjugates and provide improved or additional tailored properties. Typically, the preparation of ON multiconjugates involves additional synthetic steps and/or manipulations in post-ON assembly. This report describes the simplified methodology allowing for multiple labeling of ONs on a solid support and is compatible with phosphodiester as well as phosphorothioate (PS) ONs. The current approach utilizes two novel alkyne- and amino-functionalized linker phosphoramidites that can be readily synthesized from a common aminodiol intermediate in three steps. The combination of new linkers provides orthogonal functionalities, which allow for multiple attachments of similar or varied moieties. The linkers are incorporated into ONs during automated solid-phase ON synthesis, and the conjugation with functional entities is achieved by either amide bond formation or by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The versatility of the approach is demonstrated by the synthesis of 5'-site ON multiconjugates with small molecules, peptides, and fatty acids as well as in the preparation of an internal peptide-ON conjugate.
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Affiliation(s)
- Dmytro Honcharenko
- Department
of Biosciences and Nutrition, Karolinska
Institutet, 14183 Huddinge, Sweden
| | - Kristina Druceikaite
- Department
of Biosciences and Nutrition, Karolinska
Institutet, 14183 Huddinge, Sweden
- RISE
Chemical Process and Pharmaceutical Development, Forskargatan 20J, 15136 Södertälje, Sweden
| | | | - Martin Bollmark
- RISE
Chemical Process and Pharmaceutical Development, Forskargatan 20J, 15136 Södertälje, Sweden
| | - Ulf Tedebark
- RISE
Chemical Process and Pharmaceutical Development, Forskargatan 20J, 15136 Södertälje, Sweden
| | - Roger Strömberg
- Department
of Biosciences and Nutrition, Karolinska
Institutet, 14183 Huddinge, Sweden
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12
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Noske S, Karimov M, Aigner A, Ewe A. Tyrosine-Modification of Polypropylenimine (PPI) and Polyethylenimine (PEI) Strongly Improves Efficacy of siRNA-Mediated Gene Knockdown. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1809. [PMID: 32927826 PMCID: PMC7557430 DOI: 10.3390/nano10091809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 12/16/2022]
Abstract
The delivery of small interfering RNAs (siRNA) is an efficient method for gene silencing through the induction of RNA interference (RNAi). It critically relies, however, on efficient vehicles for siRNA formulation, for transfection in vitro as well as for their potential use in vivo. While polyethylenimines (PEIs) are among the most studied cationic polymers for nucleic acid delivery including small RNA molecules, polypropylenimines (PPIs) have been explored to a lesser extent. Previous studies have shown the benefit of the modification of small PEIs by tyrosine grafting which are featured in this paper. Additionally, we have now extended this approach towards PPIs, presenting tyrosine-modified PPIs (named PPI-Y) for the first time. In this study, we describe the marked improvement of PPI upon its tyrosine modification, leading to enhanced siRNA complexation, complex stability, siRNA delivery, knockdown efficacy and biocompatibility. Results of PPI-Y/siRNA complexes are also compared with data based on tyrosine-modified linear or branched PEIs (LPxY or PxY). Taken together, this establishes tyrosine-modified PPIs or PEIs as particularly promising polymeric systems for siRNA formulation and delivery.
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Affiliation(s)
| | | | - Achim Aigner
- Rudolf-Boehm-Institute for Pharmacology and Toxicology, Clinical Pharmacology, Leipzig University, Faculty of Medicine, 04107 Leipzig, Germany; (S.N.); (M.K.)
| | - Alexander Ewe
- Rudolf-Boehm-Institute for Pharmacology and Toxicology, Clinical Pharmacology, Leipzig University, Faculty of Medicine, 04107 Leipzig, Germany; (S.N.); (M.K.)
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13
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Nikan M, Tanowitz M, Dwyer CA, Jackson M, Gaus HJ, Swayze EE, Rigo F, Seth PP, Prakash TP. Targeted Delivery of Antisense Oligonucleotides Using Neurotensin Peptides. J Med Chem 2020; 63:8471-8484. [PMID: 32677436 DOI: 10.1021/acs.jmedchem.0c00840] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite recent advances, targeted delivery of therapeutic oligonucleotide to extra-hepatic tissues continues to be a challenging endeavor and efficient ligand-receptor systems need to be identified. To determine the feasibility of using neurotensin to improve the productive uptake of antisense oligonucleotides (ASO), we synthesized neurotensin-ASO conjugates and evaluated their cellular uptake and activity in cells and in mice. We performed a comprehensive structure-activity relationship study of the conjugates and determined the influence of ASO charge, ASO length, peptide charge, linker chemistry and ligand identity on receptor binding and internalization. We identified a modified neurotensin peptide capable of improving the cellular uptake and activity of gapmer ASOs in sortilin expressing cells (sixfold) and in spinal cord in mice (twofold). Neurotensin conjugation also improved the potency of morpholino ASO designed to correct splicing of survival motor neuron pre-mRNA in the cortex and striatum after intracerebroventricular injection. Neurotensin-mediated targeted delivery represents a possible approach for enhancing the potency of ASOs with diverse nucleic acid modifications.
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Affiliation(s)
- Mehran Nikan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael Tanowitz
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Chrissa A Dwyer
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michaela Jackson
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Hans J Gaus
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Frank Rigo
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
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14
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Greenidge PA, Blommers MJJ, Priestle JP, Hunziker J. How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for de Novo siRNA Guide Strand Surrogate Selection. J Chem Inf Model 2019; 59:1897-1908. [PMID: 31021613 DOI: 10.1021/acs.jcim.8b00892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The Argonaute-2 protein is part of the RNA-induced silencing complex (RISC) and anchors the guide strand of the small interfering RNA (siRNA). The 3'-end of the RNA contains two unpaired nucleotides (3'-overhang) that interact with the PAZ (PIWI/Argonaute/Zwille) domain of the protein. Theoretical and experimental evidence points toward a direct connection between the PAZ/3'-overhang binding affinity and siRNA's potency and specificity. Among the challenges to overcome when deploying siRNA molecules as therapeutics are their ready degradation under physiological conditions and off-target effects. It has been demonstrated that nuclease resistance can be improved via replacement of the dinucleotide overhang by small molecules which retain the interactions of the RNA guide strand with the PAZ domain. Most commonly, nucleotide analogues are used to substitute the siRNA overhang. However, in this study we adopt a de novo approach to its modification. The X-ray structure of human Argonaute-2 PAZ domain served to perform virtual screening and molecular interaction energy profiling (i.e., decomposition of the force field calculated protein-ligand interaction energies) of tailored-to-purpose fragment libraries. The binding of fragments to the PAZ domain was validated experimentally by NMR spectroscopy. The in silico guided protocol led to the efficient discovery of a number of PAZ domain ligands with affinities comparable to that of a reference dinucleotide (UpU, Kd = 33 μM). Originally starting from a generic fragment library, hits progress from 930 μM down to 14 μM within three iterations for the fragments selected via in silico molecular interaction energy profiling from a bespoke library. These dinucleotide siRNA guide strand surrogates represent potential new siRNA-based therapeutics (when attached to siRNA to form bioconjugates) featuring improved efficacy, specificity, stability, and cellular uptake. This project yielded a portfolio of seven patent applications, four of which have been granted to date.
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Affiliation(s)
- Paulette A Greenidge
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland.,Sprint Bioscience AB , Hälsovägen 7 , SE-141 57 Huddinge , Sweden
| | - Marcel J J Blommers
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland.,Saverna Therapeutics AG , Pumpmattenweg 3 , CH-4105 Biel-Benken , Switzerland
| | - John P Priestle
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland
| | - Jürg Hunziker
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland
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15
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O'Driscoll CM, Bernkop-Schnürch A, Friedl JD, Préat V, Jannin V. Oral delivery of non-viral nucleic acid-based therapeutics - do we have the guts for this? Eur J Pharm Sci 2019; 133:190-204. [PMID: 30946964 DOI: 10.1016/j.ejps.2019.03.027] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 12/22/2022]
Abstract
Gene therapy with RNA and pDNA-based drugs is limited by poor enzymatic stability and poor cellular permeation. The delivery of nucleic acids, in particular by the oral route, remains a major hurdle. This review will focus on the barriers to the oral delivery of nucleic acids and the strategies, in particular formulation strategies, which have been developed to overcome these barriers. Due to their very low oral bioavailability, the most obvious and most investigated biomedical applications for their oral delivery are related to the local treatment of inflammatory bowel diseases and colorectal cancers. Preclinical data but not yet clinical studies support the potential use of the oral route for the local delivery of formulated nucleic acid-based drugs.
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Affiliation(s)
| | - Andreas Bernkop-Schnürch
- Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
| | - Julian D Friedl
- Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Véronique Préat
- Universite catholique de Louvain, Louvain Drug Research Institute, Advanced Drug Delivery and Biomaterials, Avenue Mounier, 73 bte B1.73.12, 1200 Brussels, Belgium.
| | - Vincent Jannin
- Gattefossé SAS, 36 chemin de Genas, 69804 Saint-Priest cedex, France.
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16
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Hande M, Saher O, Lundin KE, Smith CIE, Zain R, Lönnberg T. Oligonucleotide⁻Palladacycle Conjugates as Splice-Correcting Agents. Molecules 2019; 24:E1180. [PMID: 30917503 PMCID: PMC6470670 DOI: 10.3390/molecules24061180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022] Open
Abstract
2'-O-Methylribo phosphorothioate oligonucleotides incorporating cyclopalladated benzylamine conjugate groups at their 5'-termini have been prepared and their ability to hybridize with a designated target sequence was assessed by conventional UV melting experiments. The oligonucleotides were further examined in splice-switching experiments in human cervical cancer (HeLa Luc/705), human liver (HuH7_705), and human osteosarcoma (U-2 OS_705) reporter cell lines. Melting temperatures of duplexes formed by the modified oligonucleotides were approximately 5 °C lower than melting temperatures of the respective unmodified duplexes. The cyclopalladated oligonucleotides functioned as splice-correcting agents in the HeLa Luc/705 cell line somewhat more efficiently than their unmodified counterparts. Furthermore, the introduction of this chemical modification did not induce toxicity in cells. These results demonstrate the feasibility of using covalently metalated oligonucleotides as therapeutic agents.
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Affiliation(s)
- Madhuri Hande
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - Osama Saher
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
- Department of Pharmaceutics and Industrial Pharmacy, Cairo University, Cairo 11562, Egypt.
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
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17
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MacCulloch T, Buchberger A, Stephanopoulos N. Emerging applications of peptide-oligonucleotide conjugates: bioactive scaffolds, self-assembling systems, and hybrid nanomaterials. Org Biomol Chem 2019; 17:1668-1682. [PMID: 30483688 DOI: 10.1039/c8ob02436g] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Peptide-oligonucleotide conjugates (POCs) are covalent constructs that link a molecule like DNA to a synthetic peptide sequences. These materials merge the programmable self-assembly of oligonucleotides with the bioactivity and chemical diversity of polypeptides. Recent years have seen the widespread use of POCs in a range of fields, driven the by relative advantages of each molecular type. In this review, we will present an overview of the synthesis and application of POCs, with an emphasis on emerging areas where these molecules will have a unique impact. We first discuss two main strategies for synthesizing POCs from synthetic monomers such as phosphoramidites and functionalized amino acids. We then describe four key fields of research in POCs: (1) biomaterials for interfacing with, and controlling the behavior of cells; (2) hybrid self-assembling systems that balance peptide and oligonucleotide intermolecular forces; (3) template-enhanced coupling of POCs into larger molecules; and (4) display of peptides on self-assembled oligonucleotide scaffolds. We also highlight several promising areas for future applications in each of these four directions, and anticipate ever increasing uses of POCs in interdisciplinary research.
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Affiliation(s)
- Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe AZ, USA.
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18
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Benizri S, Gissot A, Martin A, Vialet B, Grinstaff MW, Barthélémy P. Bioconjugated Oligonucleotides: Recent Developments and Therapeutic Applications. Bioconjug Chem 2019; 30:366-383. [PMID: 30608140 PMCID: PMC6766081 DOI: 10.1021/acs.bioconjchem.8b00761] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Oligonucleotide-based agents have the potential to treat or cure almost any disease, and are one of the key therapeutic drug classes of the future. Bioconjugated oligonucleotides, a subset of this class, are emerging from basic research and being successfully translated to the clinic. In this Review, we first briefly describe two approaches for inhibiting specific genes using oligonucleotides-antisense DNA (ASO) and RNA interference (RNAi)-followed by a discussion on delivery to cells. We then summarize and analyze recent developments in bioconjugated oligonucleotides including those possessing GalNAc, cell penetrating peptides, α-tocopherol, aptamers, antibodies, cholesterol, squalene, fatty acids, or nucleolipids. These novel conjugates provide a means to enhance tissue targeting, cell internalization, endosomal escape, target binding specificity, resistance to nucleases, and more. We next describe those bioconjugated oligonucleotides approved for patient use or in clinical trials. Finally, we summarize the state of the field, describe current limitations, and discuss future prospects. Bioconjugation chemistry is at the centerpiece of this therapeutic oligonucleotide revolution, and significant opportunities exist for development of new modification chemistries, for mechanistic studies at the chemical-biology interface, and for translating such agents to the clinic.
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Affiliation(s)
- Sebastien Benizri
- Inserm U1212, F-33076 Bordeaux, France
- CNRS 5320, F-33076 Bordeaux, France
- Universitéde Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux Cedex, France
| | - Arnaud Gissot
- Inserm U1212, F-33076 Bordeaux, France
- CNRS 5320, F-33076 Bordeaux, France
- Universitéde Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux Cedex, France
| | - Andrew Martin
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston, Massachusetts 02215, United States
| | - Brune Vialet
- Inserm U1212, F-33076 Bordeaux, France
- CNRS 5320, F-33076 Bordeaux, France
- Universitéde Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux Cedex, France
| | - Mark W. Grinstaff
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston, Massachusetts 02215, United States
| | - Philippe Barthélémy
- Inserm U1212, F-33076 Bordeaux, France
- CNRS 5320, F-33076 Bordeaux, France
- Universitéde Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux Cedex, France
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19
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Kubo T, Nishimura Y, Hatori Y, Akagi R, Mihara K, Yanagihara K, Seyama T. Antitumor effect of palmitic acid‐conjugated Dsi
RNA
for colon cancer in a mouse subcutaneous tumor model. Chem Biol Drug Des 2019; 93:570-581. [DOI: 10.1111/cbdd.13454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/07/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Takanori Kubo
- Department of Life ScienceFaculty of PharmacyYasuda Women's University Hiroshima Japan
| | - Yoshio Nishimura
- Department of Life ScienceFaculty of PharmacyYasuda Women's University Hiroshima Japan
| | - Yuta Hatori
- Department of Life ScienceFaculty of PharmacyYasuda Women's University Hiroshima Japan
| | - Reiko Akagi
- Department of Life ScienceFaculty of PharmacyYasuda Women's University Hiroshima Japan
| | - Keichiro Mihara
- Department of Hematology and OncologyResearch Institute for Radiation Biology and MedicineHiroshima University Hiroshima Japan
| | - Kazuyoshi Yanagihara
- Exploratory Oncology Research & Clinical Trial CenterNational Cancer Center Kashiwa Chiba Japan
| | - Toshio Seyama
- Department of Life ScienceFaculty of PharmacyYasuda Women's University Hiroshima Japan
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20
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Astakhova K, Ray R, Taskova M, Uhd J, Carstens A, Morris K. "Clicking" Gene Therapeutics: A Successful Union of Chemistry and Biomedicine for New Solutions. Mol Pharm 2018; 15:2892-2899. [PMID: 29300491 PMCID: PMC6078818 DOI: 10.1021/acs.molpharmaceut.7b00765] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The use of nucleic acid, DNA and RNA, based strategies to disrupt gene expression as a therapeutic is quickly emerging. Indeed, synthetic oligonucleotides represent a major component of modern gene therapeutics. However, the efficiency and specificity of intracellular uptake for nonmodified oligonucleotides is rather poor. Utilizing RNA based oligonucleotides as therapeutics is even more challenging to deliver, due to extremely fast enzymatic degradation of the RNAs. RNAs get rapidly degraded in vivo and demonstrate large off-target binding events when they can reach and enter the desired target cells. One approach that holds much promise is the utilization of "click chemistry" to conjugate receptor or cell specific targeting molecules directly to the effector oligonucleotides. We discuss here the applications of the breakthrough technology of CuAAC click chemistry and the immense potential in utilizing "click chemistry" in the development of new age targeted oligonucleotide therapeutics.
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Affiliation(s)
- Kira Astakhova
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Roslyn Ray
- Center for Gene Therapy, City of Hope – Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope. 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Maria Taskova
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Jesper Uhd
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Annika Carstens
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Kevin Morris
- Center for Gene Therapy, City of Hope – Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope. 1500 E. Duarte Rd., Duarte, CA, 91010, USA
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21
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Grijalvo S, Alagia A, Jorge AF, Eritja R. Covalent Strategies for Targeting Messenger and Non-Coding RNAs: An Updated Review on siRNA, miRNA and antimiR Conjugates. Genes (Basel) 2018; 9:E74. [PMID: 29415514 PMCID: PMC5852570 DOI: 10.3390/genes9020074] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 12/11/2022] Open
Abstract
Oligonucleotide-based therapy has become an alternative to classical approaches in the search of novel therapeutics involving gene-related diseases. Several mechanisms have been described in which demonstrate the pivotal role of oligonucleotide for modulating gene expression. Antisense oligonucleotides (ASOs) and more recently siRNAs and miRNAs have made important contributions either in reducing aberrant protein levels by sequence-specific targeting messenger RNAs (mRNAs) or restoring the anomalous levels of non-coding RNAs (ncRNAs) that are involved in a good number of diseases including cancer. In addition to formulation approaches which have contributed to accelerate the presence of ASOs, siRNAs and miRNAs in clinical trials; the covalent linkage between non-viral vectors and nucleic acids has also added value and opened new perspectives to the development of promising nucleic acid-based therapeutics. This review article is mainly focused on the strategies carried out for covalently modifying siRNA and miRNA molecules. Examples involving cell-penetrating peptides (CPPs), carbohydrates, polymers, lipids and aptamers are discussed for the synthesis of siRNA conjugates whereas in the case of miRNA-based drugs, this review article makes special emphasis in using antagomiRs, locked nucleic acids (LNAs), peptide nucleic acids (PNAs) as well as nanoparticles. The biomedical applications of siRNA and miRNA conjugates are also discussed.
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Affiliation(s)
- Santiago Grijalvo
- Institute of Advanced Chemistry of Catalonia (IQAC, CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Adele Alagia
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Andreia F Jorge
- Coimbra Chemistry Centre, (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC, CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
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22
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Chen C, Yang Z, Tang X. Chemical modifications of nucleic acid drugs and their delivery systems for gene-based therapy. Med Res Rev 2018; 38:829-869. [PMID: 29315675 DOI: 10.1002/med.21479] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 12/12/2022]
Abstract
Gene-based therapy is one of essential therapeutic strategies for precision medicine through targeting specific genes in specific cells of target tissues. However, there still exist many problems that need to be solved, such as safety, stability, selectivity, delivery, as well as immunity. Currently, the key challenges of gene-based therapy for clinical potential applications are the safe and effective nucleic acid drugs as well as their safe and efficient gene delivery systems. In this review, we first focus on current nucleic acid drugs and their formulation in clinical trials and on the market, including antisense oligonucleotide, siRNA, aptamer, and plasmid nucleic acid drugs. Subsequently, we summarize different chemical modifications of nucleic acid drugs as well as their delivery systems for gene-based therapeutics in vivo based on nucleic acid chemistry and nanotechnology methods.
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Affiliation(s)
- Changmai Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
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23
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Malhotra M, Gooding M, Evans JC, O'Driscoll D, Darcy R, O'Driscoll CM. Cyclodextrin-siRNA conjugates as versatile gene silencing agents. Eur J Pharm Sci 2017; 114:30-37. [PMID: 29191522 DOI: 10.1016/j.ejps.2017.11.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/26/2017] [Accepted: 11/26/2017] [Indexed: 10/18/2022]
Abstract
Functional siRNAs (luciferase and PLK1) have been conjugated to β-cyclodextrin and the ability of the conjugates to retain gene knockdown activity has been assessed by delivery to cancer cell lines using various formulations. Initially two formulations used complexation with polycations, namely Lipofectamine 2000 and an amphiphilic polycationic cyclodextrin. Gene knockdown results for human glioblastoma cells (U87) and prostate cancer cells (PC3, DU145) showed that conjugation to the cyclodextrin did not reduce gene silencing by the RNA. A third mode of delivery involved formation of targeted nanoparticles in which the conjugate was first complexed with adamantyl-PEG-ligands (targeting ligand RVG peptide or dianisamide) by adamantyl inclusion in the cyclodextrin cavities of the conjugates, followed by charge neutralisation with the cationic polymer chitosan. Enhanced knockdown was achieved by these ligand-targeted formulations. In summary, while this study illustrated the gene silencing efficacy of a simple cyclodextrin-siRNA conjugate it is envisaged that future studies will explore the use of conjugates with a modified cyclodextrin which would be self-delivering. Detailed data such as stability, lysosomal escape etc. will then be reported for each conjugate, since this will be appropriate for conjugates which are intended to exploit, rather than merely demonstrate, the concept. The present paper was intended to demonstrate the viability and generality of this novel concept.
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Affiliation(s)
- Meenakshi Malhotra
- Pharmacodelivery group, School of Pharmacy, University College Cork, Cork, Ireland; Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matt Gooding
- Pharmacodelivery group, School of Pharmacy, University College Cork, Cork, Ireland
| | - James C Evans
- Pharmacodelivery group, School of Pharmacy, University College Cork, Cork, Ireland; Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Daniel O'Driscoll
- Alimentary Pharmabiotic Centre, Microbiome Institute, University College Cork, Ireland
| | - Raphael Darcy
- Pharmacodelivery group, School of Pharmacy, University College Cork, Cork, Ireland
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24
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Lulli M, Cammalleri M, Granucci I, Witort E, Bono S, Di Gesualdo F, Lupia A, Loffredo R, Casini G, Dal Monte M, Capaccioli S. In vitro and in vivo inhibition of proangiogenic retinal phenotype by an antisense oligonucleotide downregulating uPAR expression. Biochem Biophys Res Commun 2017; 490:977-983. [PMID: 28666875 DOI: 10.1016/j.bbrc.2017.06.150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 06/26/2017] [Indexed: 01/10/2023]
Abstract
Neoangiogenesis is the main pathogenic event involved in a variety of retinal diseases. It has been recently demonstrated that inhibiting the urokinase-type plasminogen activator receptor (uPAR) results in reduced angiogenesis in a mouse model of oxygen-induced retinopathy (OIR), establishing uPAR as a therapeutic target in proliferative retinopathies. Here, we evaluated in cultured human retinal endothelial cells (HRECs) and in OIR mice the potential of a specific antisense oligodeoxyribonucleotide (ASO) in blocking the synthesis of uPAR and in providing antiangiogenic effects. uPAR expression in HRECs was inhibited by lipofection with the phosphorotioated 5'-CGGCGGGTGACCCATGTG-3' ASO-uPAR, complementary to the initial translation site of uPAR mRNA. Inhibition of uPAR expression via ASO-uPAR was evaluated in HRECs by analyzing VEGF-induced tube formation and migration. In addition, the well-established and reproducible murine OIR model was used to induce retinal neovascularization in vivo. OIR mice were injected intraperitoneally with ASO-uPAR and retinopathy was evaluated considering the extent of the avascular area in the central retina and neovascular tuft formation. The ASO-uPAR specifically decreased uPAR mRNA and protein levels in HRECs and mitigated VEGF-induced tube formation and cell migration. Noteworthy, in OIR mice ASO-uPAR administration reduced both the avascular area and the formation of neovascular tufts. In conclusion, although the extrapolation of these experimental findings to the clinic is not straightforward, ASO-uPAR may be considered a potential therapeutic tool for treatment of proliferative retinal diseases.
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Affiliation(s)
- Matteo Lulli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, viale GB Morgagni 50, 50134 Florence, Italy.
| | - Maurizio Cammalleri
- Department of Biology, University of Pisa, via San Zeno 31, 56127 Pisa, Italy
| | - Irene Granucci
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, viale GB Morgagni 50, 50134 Florence, Italy
| | - Ewa Witort
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, viale GB Morgagni 50, 50134 Florence, Italy
| | - Silvia Bono
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, viale GB Morgagni 50, 50134 Florence, Italy
| | - Federico Di Gesualdo
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, viale GB Morgagni 50, 50134 Florence, Italy
| | - Antonella Lupia
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, viale GB Morgagni 50, 50134 Florence, Italy
| | - Rosa Loffredo
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, viale GB Morgagni 50, 50134 Florence, Italy
| | - Giovanni Casini
- Department of Biology, University of Pisa, via San Zeno 31, 56127 Pisa, Italy
| | - Massimo Dal Monte
- Department of Biology, University of Pisa, via San Zeno 31, 56127 Pisa, Italy
| | - Sergio Capaccioli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, viale GB Morgagni 50, 50134 Florence, Italy.
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The Race of 10 Synthetic RNAi-Based Drugs to the Pharmaceutical Market. Pharm Res 2017; 34:1339-1363. [PMID: 28389707 DOI: 10.1007/s11095-017-2134-2] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/27/2017] [Indexed: 02/08/2023]
Abstract
Ten years after Fire and Melo's Nobel Prize for discovery of gene silencing by double-stranded RNA, a remarkable progress was achieved in RNA interference (RNAi). Changes in the chemical structure of synthetic oligonucleotides make them more stable and specific, and new delivery strategies became progressively available. The attention of pharmaceutical industry rapidly turned to RNAi, as an opportunity to explore new drug targets. This review addresses nine small-interfering RNAs (siRNAs) and one unique microRNA (miRNA) inhibitor, which entered the phase 2-3 clinical trials. The siRNAs in focus are PF-04523655, TKM-080301, Atu027, SYL040012, SYL1001, siG12D-LODER (phase 2), QPI-1002, QPI-1007, and patisiran (phase 3). Regarding miRNAs, their content can be down- or up-regulated, by using miRNA inhibitors (AntimiRs) or miRNA mimics. Miravirsen is an AntimiR-122 for hepatitis C virus infection. The flexibility of RNAi technology is easily understood taking into account: (i) the different drug targets (i.e. p53, caspase 2, PKN3, β2-adrenergic receptor, mutated KRAS, microRNAs); (ii) therapeutic conditions, including ophthalmic diseases, kidney injury, amyloidosis, pancreatic cancer, viral hepatitis; and (iii) routes of administration (ocular, intravenous, subcutaneous, intratumoral). Although some issues are still matters of concern (delivery, toxicity, cost, and biological barriers), RNAi definitively opens a wide avenue for drug development.
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Heestermans M, van Vlijmen BJ. Oligonucleotides targeting coagulation factor mRNAs: use in thrombosis and hemophilia research and therapy. Thromb J 2017; 15:7. [PMID: 28286423 PMCID: PMC5341404 DOI: 10.1186/s12959-017-0130-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/27/2017] [Indexed: 02/08/2023] Open
Abstract
Small interfering (si) RNAs and antisense oligonucleotides (ASOs; here for simplicity reasons, both referred to as oligonucleotides) are small synthetic RNA or DNA molecules with a sequence complementary to a (pre)mRNA. Although the basic mechanisms of action between siRNAs and ASO are distinct, a sequence-specific interaction of the both oligonucleotides with the target (pre)mRNA alters the target's fate, which includes highly effective sequence-specific blockade of translation and consequently depletion of the corresponding protein. For a number of years, these oligonucleotides have been used as a tool in biological research to study gene function in vitro. More recently, safe and specific delivery of these oligonucleotides to the liver of mammals has been achieved and optimized. This not only allowed their use for in vivo gene studies in physiology and disease, but also opened the opportunity for the development of a new generation of RNA-specific drugs for therapeutic purposes. In 2013, the first oligonucleotide product targeting RNA from the hepatic cholesterol pathway was approved. For blood coagulation, a large portion of key proteins are produced in the liver, and thereby siRNAs and ASOs can also be used as appropriate tools to target these proteins in vivo. In this review, we describe the first use of oligonucleotides for this purpose from zebrafish to primates. As the use of oligonucleotides allows avoidance of early lethality associated with full deficiency of several coagulation factors, it has proved to be of value for studying these proteins in physiology and disease. Currently, oligonucleotides are tested as therapeutics, with the ultimate goal to beneficially modulate the hemostatic balance in thrombosis and hemophilia patients. We discuss both the preclinical and clinical studies of a number of siRNAs and ASOs with the potential to be introduced as drugs for prophylactic and/or treatment of thrombosis or hemophilia. We conclude that for the coagulation field, oligonucleotides are of value for research purposes, and now the moment has come to fulfill their promise as therapeutics.
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Affiliation(s)
- Marco Heestermans
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division of Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, The Netherlands
| | - Bart J.M. van Vlijmen
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division of Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, The Netherlands
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Polk BI, Rosenwasser LJ. Biological Therapies of Immunologic Diseases: Strategies for Immunologic Interventions. Immunol Allergy Clin North Am 2017; 37:247-259. [PMID: 28366475 DOI: 10.1016/j.iac.2017.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The immune system possesses a vast number of potential targets for therapeutic intervention. Although therapies for many pathways have been pursued, only few have yielded significant success. Hindrances in altering biologic pathways include the potential for unwanted downstream effects, ineffectiveness owing to biological redundancy, recognition of a therapeutic molecule as foreign by the body's innate immune system, and the risks of subsequent malignancy and/or autoimmunity. This article covers currently available biotherapeutic agent classes as well as potential direction for future therapy.
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Affiliation(s)
- Brooke I Polk
- Division of Allergy, Asthma and Immunology, Children's Mercy Hospital, 2401 Gillham Road, Kansas City, MO 64108, USA.
| | - Lanny J Rosenwasser
- Department of Medicine, University of Missouri Kansas City School of Medicine, 2411 Holmes Street, Kansas City, MO 64108, USA
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Hwang Y, Park SH, Lee JW. Applications of Functionalized Carbon Nanotubes for the Therapy and Diagnosis of Cancer. Polymers (Basel) 2017; 9:E13. [PMID: 30970690 PMCID: PMC6432390 DOI: 10.3390/polym9010013] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 11/28/2022] Open
Abstract
Carbon nanotubes (CNTs) are attractive nanostructures that serve as multifunctional transporters in biomedical applications, especially in the field of cancer therapy and diagnosis. Owing to their easily tunable nature and remarkable properties, numerous functionalizations and treatments of CNTs have been attempted for their utilization as hybrid nano-carriers in the delivery of various anticancer drugs, genes, proteins, and immunotherapeutic molecules. In this review, we discuss the current advances in the applications of CNT-based novel delivery systems with an emphasis on the various functionalizations of CNTs. We also highlight recent findings that demonstrate their important roles in cancer imaging applications, demonstrating their potential as unique agents with high-level ultrasonic emission, strong Raman scattering resonance, and magnetic properties.
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Affiliation(s)
- Yongsung Hwang
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea.
- Institute of Tissue Regeneration, College of Medicine, Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea.
| | - Sung-Hoon Park
- Department of Mechanical Engineering, Soongsil University, Dongjak-gu, Seoul 06978, Korea.
| | - Jin Woo Lee
- Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 21999, Korea.
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