1
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Dume B, Licarete E, Banciu M. Advancing cancer treatments: The role of oligonucleotide-based therapies in driving progress. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102256. [PMID: 39045515 PMCID: PMC11264197 DOI: 10.1016/j.omtn.2024.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Although recent advancements in cancer immunology have resulted in the approval of numerous immunotherapies, minimal progress has been observed in addressing hard-to-treat cancers. In this context, therapeutic oligonucleotides, including interfering RNAs, antisense oligonucleotides, aptamers, and DNAzymes, have gained a central role in cancer therapeutic approaches due to their capacity to regulate gene expression and protein function with reduced toxicity compared with conventional chemotherapeutics. Nevertheless, systemic administration of naked oligonucleotides faces many extra- and intracellular challenges that can be overcome by using effective delivery systems. Thus, viral and non-viral carriers can improve oligonucleotide stability and intracellular uptake, enhance tumor accumulation, and increase the probability of endosomal escape while minimizing other adverse effects. Therefore, gaining more insight into fundamental mechanisms of actions of various oligonucleotides and the challenges posed by naked oligonucleotide administration, this article provides a comprehensive review of the recent progress on oligonucleotide delivery systems and an overview of completed and ongoing cancer clinical trials that can shape future oncological treatments.
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Affiliation(s)
- Bogdan Dume
- Doctoral School in Integrative Biology, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Emilia Licarete
- Department of Molecular Biology and Biotechnology, Centre of Systems Biology, Biodiversity and Bioresources, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Manuela Banciu
- Department of Molecular Biology and Biotechnology, Centre of Systems Biology, Biodiversity and Bioresources, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
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2
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Iannacci F, Medeiros Garcia Alcântara J, Marani M, Camesasca P, Chen M, Sousa F, Morbidelli M, Sponchioni M. High-density perfusion cultures of the marine bacterium Rhodovulum sulfidophilum for the biomanufacturing of oligonucleotides. J Biotechnol 2024; 392:152-160. [PMID: 39025367 DOI: 10.1016/j.jbiotec.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/14/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
Therapeutic oligonucleotides (ONs) are typically manufactured via solid-phase synthesis, characterized by limited scalability and huge environmental footprint, limiting their availability. Biomanufactured ONs have the potential to reduce the immunogenic side-effects, and to improve the sustainability of their chemical counterparts. Rhodovulum sulfidophilum was demonstrated a valuable host for the extracellular production of recombinant ONs. However, low viable cell densities and product titer were reported so far. In this work, perfusion cell cultures were established for the intensification of ON biomanufacturing. First, the perfusion conditions were simulated in 50 mL spin tubes, selected as a scale-down model of the process, with the aim of optimizing the medium composition and process parameters. This optimization stage led to an increase in the cell density by 44 % compared to the reference medium formulation. In addition, tests at increasing perfusion rates were conducted until achieving the maximum viable cell density (VCDmax), allowing the determination of the minimum cell-specific perfusion rate (CSPRmin) required to sustain the cell culture. Intriguingly, we discovered in this system also a maximum CSPR, above which growth inhibition starts. By leveraging this process optimization, we show for the first time the conduction of perfusion cultures of R. sulfidophilum in bench-scale bioreactors. This process development pipeline allowed stable cultures for more than 20 days and the continuous biomanufacturing of ONs, testifying the great potential of perfusion processes.
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Affiliation(s)
- Francesco Iannacci
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - João Medeiros Garcia Alcântara
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Martina Marani
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Paolo Camesasca
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Michele Chen
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Fani Sousa
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, Covilhã 6200-506, Portugal
| | - Massimo Morbidelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Mattia Sponchioni
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy.
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3
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024; 25:578-595. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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4
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Kage M, Hayashi R, Matsuo A, Tamiya M, Kuramoto S, Ohara K, Irie M, Chiyoda A, Takano K, Ito T, Kotake T, Takeyama R, Ishikawa S, Nomura K, Furuichi N, Morita Y, Hashimoto S, Kawada H, Nishimura Y, Nii K, Sase H, Ohta A, Kojima T, Iikura H, Tanada M, Shiraishi T. Structure-activity relationships of middle-size cyclic peptides, KRAS inhibitors derived from an mRNA display. Bioorg Med Chem 2024; 110:117830. [PMID: 38981216 DOI: 10.1016/j.bmc.2024.117830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/11/2024]
Abstract
Cyclic peptides are attracting attention as therapeutic agents due to their potential for oral absorption and easy access to tough intracellular targets. LUNA18, a clinical KRAS inhibitor, was transformed-without scaffold hopping-from the initial hit by using an mRNA display library that met our criteria for drug-likeness. In drug discovery using mRNA display libraries, hit compounds always possess a site linked to an mRNA tag. Here, we describe our examination of the Structure-Activity Relationship (SAR) using X-ray structures for chemical optimization near the site linked to the mRNA tag, equivalent to the C-terminus. Structural modifications near the C-terminus demonstrated a relatively wide range of tolerance for side chains. Furthermore, we show that a single atom modification is enough to change the pharmacokinetic (PK) profile. Since there are four positions where side chain modification is permissible in terms of activity, it is possible to flexibly adjust the pharmacokinetic profile by structurally optimizing the side chain. The side chain transformation findings demonstrated here may be generally applicable to hits obtained from mRNA display libraries.
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Affiliation(s)
- Mirai Kage
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuji Hayashi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan.
| | - Atsushi Matsuo
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Minoru Tamiya
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shino Kuramoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kazuhiro Ohara
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Aya Chiyoda
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Koji Takano
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Toshiya Ito
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Tomoya Kotake
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Ryuuichi Takeyama
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Shiho Ishikawa
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Kenichi Nomura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Noriyuki Furuichi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yuya Morita
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Satoshi Hashimoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hatsuo Kawada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Yoshikazu Nishimura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Keiji Nii
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Sase
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Atsushi Ohta
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Tetsuo Kojima
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Hitoshi Iikura
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan
| | - Mikimasa Tanada
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan.
| | - Takuya Shiraishi
- Research Division, Chugai Pharmaceutical Co. Ltd., 216, Totsuka-cho, Totsuka-ku, Yokohama, Kanagawa 244-8602, Japan.
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5
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Palepšienė R, Muralidharan A, Maciulevičius M, Ruzgys P, Chopra S, Boukany PE, Šatkauskas S. New insights into the mechanism of electrotransfer of small nucleic acids. Bioelectrochemistry 2024; 158:108696. [PMID: 38583283 DOI: 10.1016/j.bioelechem.2024.108696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
RNA interference (RNAi) is a powerful and rapidly developing technology that enables precise silencing of genes of interest. However, the clinical development of RNAi is hampered by the limited cellular uptake and stability of the transferred molecules. Electroporation (EP) is an efficient and versatile technique for the transfer of both RNA and DNA. Although the mechanism of electrotransfer of small nucleic acids has been studied previously, too little is known about the potential effects of significantly larger pDNA on this process. Here we present a fundamental study of the mechanism of electrotransfer of oligonucleotides and siRNA that occur independently and simultaneously with pDNA by employing confocal fluorescence microscopy. In contrast to the conditional understanding of the mechanism, we have shown that the electrotransfer of oligonucleotides and siRNA is driven by both electrophoretic forces and diffusion after EP, followed by subsequent entry into the nucleus within 5 min after treatment. The study also revealed that the efficiency of siRNA electrotransfer decreases in response to an increase in pDNA concentration. Overall, the study provides new insights into the mechanism of electrotransfer of small nucleic acids which may have broader implications for the future application of RNAi-based strategies.
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Affiliation(s)
- Rūta Palepšienė
- Research Institute of Natural Sciences and Technology, Vytautas Magnus University, Universiteto str. 10, Akademija, Kaunas district LT-53361, Lithuania.
| | - Aswin Muralidharan
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ Delft, Netherlands; Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ Delft, Netherlands.
| | - Martynas Maciulevičius
- Research Institute of Natural Sciences and Technology, Vytautas Magnus University, Universiteto str. 10, Akademija, Kaunas district LT-53361, Lithuania.
| | - Paulius Ruzgys
- Research Institute of Natural Sciences and Technology, Vytautas Magnus University, Universiteto str. 10, Akademija, Kaunas district LT-53361, Lithuania.
| | - Sonam Chopra
- Research Institute of Natural Sciences and Technology, Vytautas Magnus University, Universiteto str. 10, Akademija, Kaunas district LT-53361, Lithuania.
| | - Pouyan E Boukany
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9 2629 HZ Delft, Netherlands.
| | - Saulius Šatkauskas
- Research Institute of Natural Sciences and Technology, Vytautas Magnus University, Universiteto str. 10, Akademija, Kaunas district LT-53361, Lithuania.
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6
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Chasov V, Ganeeva I, Zmievskaya E, Davletshin D, Gilyazova E, Valiullina A, Bulatov E. Cell-Based Therapy and Genome Editing as Emerging Therapeutic Approaches to Treat Rheumatoid Arthritis. Cells 2024; 13:1282. [PMID: 39120313 PMCID: PMC11312096 DOI: 10.3390/cells13151282] [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: 06/17/2024] [Revised: 07/19/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammation of the joints. Although much remains unknown about the pathogenesis of RA, there is evidence that impaired immune tolerance and the development of RA are related. And it is precisely the restoration of immune tolerance at the site of the inflammation that is the ultimate goal of the treatment of RA. Over the past few decades, significant progress has been made in the treatment of RA, with higher rates of disease remission and improved long-term outcomes. Unfortunately, despite these successes, the proportion of patients with persistent, difficult-to-treat disease remains high, and the task of improving our understanding of the basic mechanisms of disease development and developing new ways to treat RA remains relevant. This review focuses on describing new treatments for RA, including cell therapies and gene editing technologies that have shown potential in preclinical and early clinical trials. In addition, we discuss the opportunities and limitations associated with the use of these new approaches in the treatment of RA.
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Affiliation(s)
- Vitaly Chasov
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Irina Ganeeva
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Ekaterina Zmievskaya
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Damir Davletshin
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Elvina Gilyazova
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Aygul Valiullina
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Emil Bulatov
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119048, Russia
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7
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Jiang D, Li P, Yuan L. Bioanalysis of free antisense oligonucleotide payload from antibody-oligonucleotide conjugate by hybridization LC-MS/MS. Bioanalysis 2024:1-10. [PMID: 39041663 DOI: 10.1080/17576180.2024.2368339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 06/06/2024] [Indexed: 07/24/2024] Open
Abstract
Background: Antisense oligonucleotides (ASOs) have been conjugated to various moieties, such as peptides, antibodies or Fab regions of antibodies, to enhance their delivery to target tissues. The quantitation of free ASO (ASO payload) is critical to characterize its pharmacokinetics/pharmacodynamics (PK/PD) properties and biodistribution after delivery of the peptide/antibody/Fab ASO conjugates. Results: We developed a hybridization-based LC-MS/MS methodology for quantification of free ASO in tissues in the presence of Fab-ASO and ASO with linker (ASO-linker). Conclusion: The developed method was applied to measure accurately the free ASO concentrations in liver and gastrocnemius in mice that were dosed with Fab-ASO. This methodology has also been applied to free ASO bioanalysis for other antibody-ASO and Fab-ASO conjugates in various tissues and plasma/serum samples.
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Affiliation(s)
- Di Jiang
- Drug Metabolism & Pharmacokinetics, Biogen, 225 Binney St, Cambridge, MA 02142, USA
- Current address: Denali Therapeutics, 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Pei Li
- Drug Metabolism & Pharmacokinetics, Biogen, 225 Binney St, Cambridge, MA 02142, USA
- Current address: Vertex Pharmaceuticals, 50 Northern Avenue, Boston, MA 02210, USA
| | - Long Yuan
- Drug Metabolism & Pharmacokinetics, Biogen, 225 Binney St, Cambridge, MA 02142, USA
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8
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Lippens JL, Florenzi B, Da Silva KM, Liu Y, Neefs T, Sauwen N, De Vijlder T. SynONIM: A Comprehensive Database of Synthetic Oligonucleotide Modifications and Impurities to Aid in Their Characterization by Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39009439 DOI: 10.1021/jasms.4c00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Given the resurgence of oligonucleotides in the biotherapeutic space, there is a profound focus on their characterization by mass spectrometry. These therapeutic moieties commonly employ synthetic modifications to aid in increasing efficacy and stability; however, these modifications can also increase the complexity of mass spectrometry data analysis. Additionally, various stress conditions can affect both the observed level and type of impurities stemming from the variety of utilized modifications. Within the oligonucleotide analytical development community, a clear desire exists for a unified database of synthetic oligonucleotide modifications and impurities where information regarding structure, mass, and shorthand nomenclature can be contained. To address this, the authors have prepared an online database and webtool of synthetic oligonucleotide impurities and modifications, SynONIM, to centrally locate information key to the mass spectrometry community. SynONIM can be queried by elemental composition lost or gained, mass shift, shorthand notation, nucleotide location, and species origin.
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Affiliation(s)
| | | | | | - Youzhong Liu
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Thomas Neefs
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Nicolas Sauwen
- Open Analytics NV, Jupiterstraat 20, 2600 Antwerpen, Belgium
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9
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Ren Q, Osawa T, Tatsuno M, Obika S. THF peroxide as a factor in generating desulphurised products from the solid-phase synthesis of phosphorothioate-modified oligonucleotides. RSC Adv 2024; 14:21590-21596. [PMID: 38979452 PMCID: PMC11229082 DOI: 10.1039/d4ra03592e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
Antisense oligonucleotides (ASOs) are generally obtained via chemical synthesis on a solid support and phosphorothioate (PS) modification with a phosphate backbone to increase their in vivo stability and activity. However, desulphurised products, in which PS is partially replaced by phosphodiesters, are generally formed during the chemical synthesis of ASO and are difficult to separate from the desired PS-modified ASO by chromatography. Therefore, revealing the unknown factors that cause the formation of desulphurised products and proposing methods to inhibit their formation are highly desirable. In this study, it was found that peroxides in THF, which is used as a solvent for the acetyl capping agent, oxidise phosphite triesters to produce desulphurisation products. The use of THF with antioxidants effectively suppresses the oxidation caused by THF peroxides. Moreover, THF peroxide was found to oxidise phosphoramidites, which are the building blocks of oligonucleotide chemical syntheses, indicating that caution should be taken with the organic solvents used during the synthesis and purification of phosphoramidites.
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Affiliation(s)
- Qin Ren
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
| | - Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
| | - Michiaki Tatsuno
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University 1-3 Yamadaoka Suita Osaka 565-0871 Japan
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10
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Qu Y, Henderson KA, Harper TA, Vargas HM. Scientific Review of the Proarrhythmic Risks of Oligonucleotide Therapeutics: Are Dedicated ICH S7B/E14 Studies Needed for Low-Risk Modalities? Clin Pharmacol Ther 2024; 116:96-105. [PMID: 38362953 DOI: 10.1002/cpt.3204] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024]
Abstract
Oligonucleotide therapeutics (ONTs) represent a new modality with unique pharmacological and chemical properties that modulate gene expression with a high degree of target specificity mediated by complementary Watson-Crick base pair hybridization. To date, the proarrhythmic assessment of ONTs has been influenced by International Conference on Harmonization (ICH) E14 and S7B guidance. To document current hERG/QTc evaluation practices, we reviewed US Food and Drug Administration (FDA) and the European Medicines Agency (EMA) Approval Packages (source: PharmaPendium.com) and collated preclinical and clinical studies for 17 marketed ONTs. In addition, clinical QTc data from 12 investigational ONTs were obtained from the literature. Of the marketed ONTs, eight were tested in the hERG assay with no inhibitory effect identified at the top concentration (range: 34-3,000 μM) tested. Fourteen of the ONTs were evaluated in nonhuman primate cardiovascular studies with 11 of them in dedicated telemetry studies. No effect on QTc intervals were observed (at high exposure multiples) in all studies. Clinically, four ONTs were evaluated in TQT studies; an additional six ONTs were assessed by concentration-QTc interval analysis, and six by routine safety electrocardiogram monitoring. None of the clinical studies identified a QTc prolongation risk; the same was true for the 12 investigational ONTs. A search of the FDA Adverse Event Database indicated no association between approved ONTs and proarrhythmias. Overall, the collective weight of evidence from 29 ONTs demonstrate no clinical proarrhythmic risk based on data obtained from ICH S7B/E14 studies. Thus, new ONTs may benefit from reduced testing strategies because they have no proarrhythmic risk, a similar cardiac safety profile as monoclonal antibodies, proteins, and peptides.
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Affiliation(s)
- Yusheng Qu
- Amgen Research, Translational Safety & Bioanalytical Sciences, Amgen Inc., Thousand Oaks, California, USA
| | - Kim A Henderson
- Amgen Research, Translational Safety & Bioanalytical Sciences, Amgen Inc., Thousand Oaks, California, USA
| | - Tod A Harper
- Amgen Research, Translational Safety & Bioanalytical Sciences, Amgen Inc., Thousand Oaks, California, USA
| | - Hugo M Vargas
- Amgen Research, Translational Safety & Bioanalytical Sciences, Amgen Inc., Thousand Oaks, California, USA
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11
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Wilton-Clark H, Yan E, Yokota T. Preparing for Patient-Customized N-of-1 Antisense Oligonucleotide Therapy to Treat Rare Diseases. Genes (Basel) 2024; 15:821. [PMID: 39062600 PMCID: PMC11275492 DOI: 10.3390/genes15070821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/15/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
The process of developing therapies to treat rare diseases is fraught with financial, regulatory, and logistical challenges that have limited our ability to build effective treatments. Recently, a novel type of therapy called antisense therapy has shown immense potential for the treatment of rare diseases, particularly through single-patient N-of-1 trials. Several N-of-1 antisense therapies have been developed recently for rare diseases, including the landmark study of milasen. In response to the success of N-of-1 antisense therapy, the Food and Drug Administration (FDA) has developed unique guidelines specifically for the development of antisense therapy to treat N-of-1 rare diseases. This policy change establishes a strong foundation for future therapy development and addresses some of the major limitations that previously hindered the development of therapies for rare diseases.
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Affiliation(s)
- Harry Wilton-Clark
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - Eric Yan
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada;
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12
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Li S, Xiong F, Zhang S, Liu J, Gao G, Xie J, Wang Y. Oligonucleotide therapies for nonalcoholic steatohepatitis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102184. [PMID: 38665220 PMCID: PMC11044058 DOI: 10.1016/j.omtn.2024.102184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Nonalcoholic steatohepatitis (NASH) represents a severe disease subtype of nonalcoholic fatty liver disease (NAFLD) that is thought to be highly associated with systemic metabolic abnormalities. It is characterized by a series of substantial liver damage, including hepatocellular steatosis, inflammation, and fibrosis. The end stage of NASH, in some cases, may result in cirrhosis and hepatocellular carcinoma (HCC). Nowadays a large number of investigations are actively under way to test various therapeutic strategies, including emerging oligonucleotide drugs (e.g., antisense oligonucleotide, small interfering RNA, microRNA, mimic/inhibitor RNA, and small activating RNA) that have shown high potential in treating this fatal liver disease. This article systematically reviews the pathogenesis of NASH/NAFLD, the promising druggable targets proven by current studies in chemical compounds or biological drug development, and the feasibility and limitations of oligonucleotide-based therapeutic approaches under clinical or pre-clinical studies.
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Affiliation(s)
- Sixu Li
- Department of Pathophysiology, West China College of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610066, China
| | - Feng Xiong
- Department of Cardiology, The Third People’s Hospital of Chengdu, Chengdu 610031, China
| | - Songbo Zhang
- Department of Breast Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Jinghua Liu
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
| | - Yi Wang
- Department of Pathophysiology, West China College of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610066, China
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13
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Lei L, Harp JM, Chaput JC, Wassarman K, Schlegel MK, Manoharan M, Egli M. Structure and Stability of Ago2 MID-Nucleotide Complexes: All-in-One (Drop) His 6-SUMO Tag Removal, Nucleotide Binding, and Crystal Growth. Curr Protoc 2024; 4:e1088. [PMID: 38923271 DOI: 10.1002/cpz1.1088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
The middle (MID) domain of eukaryotic Argonaute (Ago) proteins and archaeal and bacterial homologues mediates the interaction with the 5'-terminal nucleotide of miRNA and siRNA guide strands. The MID domain of human Ago2 (hAgo2) is comprised of 139 amino acids with a molecular weight of 15.56 kDa. MID adopts a Rossman-like beta1-alpha1-beta2-alpha2-beta3-alpha3-beta4-alpha4 fold with a nucleotide specificity loop between beta3 and alpha3. Multiple crystal structures of nucleotides bound to hAgo2 MID have been reported, whereby complexes were obtained by soaking ligands into crystals of MID domain alone. This protocol describes a simplified one-step approach to grow well-diffracting crystals of hAgo2 MID-nucleotide complexes by mixing purified His6-SUMO-MID fusion protein, Ulp1 protease, and excess nucleotide in the presence of buffer and precipitant. The crystal structures of MID complexes with UMP, UTP and 2'-3' linked α-L-threofuranosyl thymidine-3'-triphosphate (tTTP) are presented. This article also describes fluorescence-based assays to measure dissociation constants (Kd) of MID-nucleotide interactions for nucleoside 5'-monophosphates and nucleoside 3',5'-bisphosphates. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Crystallization of Ago2 MID-nucleotide complexes Basic Protocol 2: Measurement of dissociation constant Kd between Ago2 MID and nucleotides.
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Affiliation(s)
- Li Lei
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, California
| | | | | | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
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14
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Giorgees I, Affe V, Williams I, Desaulniers JP. Direct Conjugation of Gallium-(III)-Corroles to Short Interfering RNA(siRNA) Providing Real-Time siRNA Imaging and Gene Silencing. Chempluschem 2024; 89:e202400084. [PMID: 38457624 DOI: 10.1002/cplu.202400084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
Discovering new modifications for oligonucleotide therapeutics is essential for expanding its application to new targets and diseases. In this project, we focus on conjugating metaled ligands to short interfering RNAs (siRNAs) to investigate robust and simple conjugation methods for adding new properties such as real-time imaging to the siRNA. Here we report the chemical synthesis of novel Ga-(III)-corroles for their direct conjugation to siRNAs. Ga-(III)-corrole-siRNAs showed promising results when evaluated for gene silencing and live cell imaging. The knockdown activity of the firefly luciferase reporter gene was measured to evaluate gene silencing activity. Gene silencing studies from two 5'-Ga-(III)-labeled-siRNAs exhibited dose-dependent knockdown with IC50s of 812.7 and 451.4 pM, which is comparable to wild-type (IC50=439.7 pM) in the absence of red light, and IC50s of 562.9 and 354.5 pM, which is also comparable to wild-type (IC50=337.4 pM), in the presence of red light. In addition, imaging studies with Ga-(III)-corrole-modified siRNAs showed intense fluorescence in HeLa cells, highlighting that the Ga-(III)-corrole modification is an effective fluorophore for siRNA tracing and imaging. Moreover, the photodynamic activity of free base corrole vs the Ga-(III)-corrole was evaluated. Results show an increase of light cytotoxicity of the corrole ligand upon the addition of Ga-(III); however, no phototoxicity was observed when Ga-(III) ligands were linked to siRNA. In conclusion, Ga-(III)-corrole-siRNAs show promising results for applications in simultaneous real-time imaging and gene silencing.
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Affiliation(s)
- Ifrodet Giorgees
- Faculty of Science, Ontario Tech University, 2000 Simcoe Street North, Oshawa, Ontario, Canada, L1G 0C5
| | - Vanessa Affe
- Faculty of Science, Ontario Tech University, 2000 Simcoe Street North, Oshawa, Ontario, Canada, L1G 0C5
| | - Islah Williams
- Faculty of Science, Ontario Tech University, 2000 Simcoe Street North, Oshawa, Ontario, Canada, L1G 0C5
| | - Jean-Paul Desaulniers
- Faculty of Science, Ontario Tech University, 2000 Simcoe Street North, Oshawa, Ontario, Canada, L1G 0C5
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15
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Yang R, Liu Y, Yang N, Zhang T, Hou J, He Z, Wang Y, Sun X, Shen J, Jiang H, Xie Y, Lang T. Combination of miR159 Mimics and Irinotecan Utilizing Lipid Nanoparticles for Enhanced Treatment of Colorectal Cancer. Pharmaceutics 2024; 16:570. [PMID: 38675231 PMCID: PMC11054162 DOI: 10.3390/pharmaceutics16040570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/27/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Colorectal cancer (CRC) ranks as the third most prevalent global malignancy, marked by significant metastasis and post-surgical recurrence, posing formidable challenges to treatment efficacy. The integration of oligonucleotides with chemotherapeutic drugs emerges as a promising strategy for synergistic CRC therapy. The nanoformulation, lipid nanoparticle (LNP), presents the capability to achieve co-delivery of oligonucleotides and chemotherapeutic drugs for cancer therapy. In this study, we constructed lipid nanoparticles, termed as LNP-I-V by microfluidics to co-deliver oligonucleotides miR159 mimics (VDX05001SI) and irinotecan (IRT), demonstrating effective treatment of CRC both in vitro and in vivo. The LNP-I-V exhibited a particle size of 118.67 ± 1.27 nm, ensuring excellent stability and targeting delivery to tumor tissues, where it was internalized and escaped from the endosome with a pH-sensitive profile. Ultimately, LNP-I-V significantly inhibited CRC growth, extended the survival of tumor-bearing mice, and displayed favorable safety profiles. Thus, LNP-I-V held promise as an innovative platform to combine gene therapy and chemotherapy for improving CRC treatment.
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Affiliation(s)
- Rulei Yang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; (R.Y.); (J.S.); (H.J.)
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;
- Vigonvita Life Sciences Co., Ltd., Suzhou 215125, China
| | - Yiran Liu
- Lingang Laboratory, Shanghai 200031, China; (Y.L.); (N.Y.); (T.Z.); (J.H.); (Z.H.); (Y.W.)
| | - Ning Yang
- Lingang Laboratory, Shanghai 200031, China; (Y.L.); (N.Y.); (T.Z.); (J.H.); (Z.H.); (Y.W.)
| | - Tian Zhang
- Lingang Laboratory, Shanghai 200031, China; (Y.L.); (N.Y.); (T.Z.); (J.H.); (Z.H.); (Y.W.)
| | - Jiazhen Hou
- Lingang Laboratory, Shanghai 200031, China; (Y.L.); (N.Y.); (T.Z.); (J.H.); (Z.H.); (Y.W.)
| | - Zongyan He
- Lingang Laboratory, Shanghai 200031, China; (Y.L.); (N.Y.); (T.Z.); (J.H.); (Z.H.); (Y.W.)
| | - Yutong Wang
- Lingang Laboratory, Shanghai 200031, China; (Y.L.); (N.Y.); (T.Z.); (J.H.); (Z.H.); (Y.W.)
| | - Xujie Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;
- Lingang Laboratory, Shanghai 200031, China; (Y.L.); (N.Y.); (T.Z.); (J.H.); (Z.H.); (Y.W.)
| | - Jingshan Shen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; (R.Y.); (J.S.); (H.J.)
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;
| | - Hualiang Jiang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; (R.Y.); (J.S.); (H.J.)
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;
- Lingang Laboratory, Shanghai 200031, China; (Y.L.); (N.Y.); (T.Z.); (J.H.); (Z.H.); (Y.W.)
| | - Yuanchao Xie
- Lingang Laboratory, Shanghai 200031, China; (Y.L.); (N.Y.); (T.Z.); (J.H.); (Z.H.); (Y.W.)
| | - Tianqun Lang
- Lingang Laboratory, Shanghai 200031, China; (Y.L.); (N.Y.); (T.Z.); (J.H.); (Z.H.); (Y.W.)
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16
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Wohlrábová L, Sahlbach M, Heckel A, Slanina T. BODIPY phototether enables oligonucleotide cyclization and subsequent deprotection by tissue-transparent red light. Chem Commun (Camb) 2024; 60:4366-4369. [PMID: 38563214 DOI: 10.1039/d4cc00272e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
meso-methyl-BODIPY photocages release a leaving group upon visible light irradiation but often lack thermal stability. In turn, our thermally-stable, red-shifted BODIPY phototether allows oligonucleotide cyclization, preventing complementary strand hybridization. Hybridization resumes upon red-NIR irradiation, disconnecting the phototether by oxidative cleavage, which is easily monitored by a blue shift in fluorescence.
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Affiliation(s)
- Lucie Wohlrábová
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 542, Prague 160 00, Czech Republic.
- Department of Organic Chemistry, University of Chemistry and Technology Prague, 166 28, Prague 6, Czech Republic
| | - Marlen Sahlbach
- Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, Frankfurt am Main 60438, Germany
| | - Alexander Heckel
- Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, Frankfurt am Main 60438, Germany
| | - Tomáš Slanina
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 542, Prague 160 00, Czech Republic.
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17
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Agu PC, Obulose CN. Piquing artificial intelligence towards drug discovery: Tools, techniques, and applications. Drug Dev Res 2024; 85:e22159. [PMID: 38375772 DOI: 10.1002/ddr.22159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
The purpose of this study was to discuss how artificial intelligence (AI) methods have affected the field of drug development. It looks at how AI models and data resources are reshaping the drug development process by offering more affordable and expedient options to conventional approaches. The paper opens with an overview of well-known information sources for drug development. The discussion then moves on to molecular representation techniques that make it possible to convert data into representations that computers can understand. The paper also gives a general overview of the algorithms used in the creation of drug discovery models based on AI. In particular, the paper looks at how AI algorithms might be used to forecast drug toxicity, drug bioactivity, and drug physicochemical properties. De novo drug design, binding affinity prediction, and other AI-based models for drug-target interaction were covered in deeper detail. Modern applications of AI in nanomedicine design and pharmacological synergism/antagonism prediction were also covered. The potential advantages of AI in drug development are highlighted as the evaluation comes to a close. It underlines how AI may greatly speed up and improve the efficiency of drug discovery, resulting in the creation of new and better medicines. To fully realize the promise of AI in drug discovery, the review acknowledges the difficulties that come with its uses in this field and advocates for more study and development.
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Affiliation(s)
- Peter Chinedu Agu
- Department of Biochemistry, College of Science, Evangel University, Akaeze, Ebonyi State, Nigeria
| | - Chidiebere Nwiboko Obulose
- Department of Computer Sciences, Our Savior Institute of Science, Agriculture, and Technology (OSISATECH Polytechnic), Enugu, Nigeria
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18
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Chakraborty C, Bhattacharya M, Sharma AR, Chatterjee S, Agoramoorthy G, Lee SS. Structural Landscape of nsp Coding Genomic Regions of SARS-CoV-2-ssRNA Genome: A Structural Genomics Approach Toward Identification of Druggable Genome, Ligand-Binding Pockets, and Structure-Based Druggability. Mol Biotechnol 2024; 66:641-662. [PMID: 36463562 PMCID: PMC9735222 DOI: 10.1007/s12033-022-00605-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022]
Abstract
SARS-CoV-2 has a single-stranded RNA genome (+ssRNA), and synthesizes structural and non-structural proteins (nsps). All 16 nsp are synthesized from the ORF1a, and ORF1b regions associated with different life cycle preprocesses, including replication. The regions of ORF1a synthesizes nsp1 to 11, and ORF1b synthesizes nsp12 to 16. In this paper, we have predicted the secondary structure conformations, entropy & mountain plots, RNA secondary structure in a linear fashion, and 3D structure of nsp coding genes of the SARS-CoV-2 genome. We have also analyzed the A, T, G, C, A+T, and G+C contents, GC-profiling of these genes, showing the range of the GC content from 34.23 to 48.52%. We have observed that the GC-profile value of the nsp coding genomic regions was less (about 0.375) compared to the whole genome (about 0.38). Additionally, druggable pockets were identified from the secondary structure-guided 3D structural conformations. For secondary structure generation of all the nsp coding genes (nsp 1-16), we used a recent algorithm-based tool (deep learning-based) along with the conventional algorithms (centroid and MFE-based) to develop secondary structural conformations, and we found stem-loop, multi-branch loop, pseudoknot, and the bulge structural components, etc. The 3D model shows bound and unbound forms, branched structures, duplex structures, three-way junctions, four-way junctions, etc. Finally, we identified binding pockets of nsp coding genes which will help as a fundamental resource for future researchers to develop RNA-targeted therapeutics using the druggable genome.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, Odisha, 756020, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, Gangwon-do, 24252, Republic of Korea
| | - Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, Gangwon-do, 24252, Republic of Korea
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19
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Chen S, Heendeniya SN, Le BT, Rahimizadeh K, Rabiee N, Zahra QUA, Veedu RN. Splice-Modulating Antisense Oligonucleotides as Therapeutics for Inherited Metabolic Diseases. BioDrugs 2024; 38:177-203. [PMID: 38252341 PMCID: PMC10912209 DOI: 10.1007/s40259-024-00644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2024] [Indexed: 01/23/2024]
Abstract
The last decade (2013-2023) has seen unprecedented successes in the clinical translation of therapeutic antisense oligonucleotides (ASOs). Eight such molecules have been granted marketing approval by the United States Food and Drug Administration (US FDA) during the decade, after the first ASO drug, fomivirsen, was approved much earlier, in 1998. Splice-modulating ASOs have also been developed for the therapy of inborn errors of metabolism (IEMs), due to their ability to redirect aberrant splicing caused by mutations, thus recovering the expression of normal transcripts, and correcting the deficiency of functional proteins. The feasibility of treating IEM patients with splice-switching ASOs has been supported by FDA permission (2018) of the first "N-of-1" study of milasen, an investigational ASO drug for Batten disease. Although for IEM, owing to the rarity of individual disease and/or pathogenic mutation, only a low number of patients may be treated by ASOs that specifically suppress the aberrant splicing pattern of mutant precursor mRNA (pre-mRNA), splice-switching ASOs represent superior individualized molecular therapeutics for IEM. In this work, we first summarize the ASO technology with respect to its mechanisms of action, chemical modifications of nucleotides, and rational design of modified oligonucleotides; following that, we precisely provide a review of the current understanding of developing splice-modulating ASO-based therapeutics for IEM. In the concluding section, we suggest potential ways to improve and/or optimize the development of ASOs targeting IEM.
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Affiliation(s)
- Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Saumya Nishanga Heendeniya
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Bao T Le
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- ProGenis Pharmaceuticals Pty Ltd, Bentley, WA, 6102, Australia
| | - Kamal Rahimizadeh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Navid Rabiee
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Qurat Ul Ain Zahra
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia.
- ProGenis Pharmaceuticals Pty Ltd, Bentley, WA, 6102, Australia.
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20
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Bouvarel T, Camperi J, Guillarme D. Multi-dimensional technology - Recent advances and applications for biotherapeutic characterization. J Sep Sci 2024; 47:e2300928. [PMID: 38471977 DOI: 10.1002/jssc.202300928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 03/14/2024]
Abstract
This review provides an overview of the latest advancements and applications in multi-dimensional liquid chromatography coupled with mass spectrometry (mD-LC-MS), covering aspects such as inter-laboratory studies, digestion strategy, trapping column, and multi-level analysis. The shift from an offline to an online workflow reduces sample processing artifacts, analytical variability, analysis time, and the labor required for data acquisition. Over the past few years, this technique has demonstrated sufficient maturity for application across a diverse range of complex products. Moreover, there is potential for this strategy to evolve into an integrated process analytical technology tool for the real-time monitoring of monoclonal antibody quality. This review also identifies emerging trends, including its application to new modalities, the possibility of evaluating biological activity within the mD-LC set-up, and the consideration of multi-dimensional capillary electrophoresis as an alternative to mD-LC. As mD-LC-MS continues to evolve and integrate emerging trends, it holds the potential to shape the next generation of analytical tools, offering exciting possibilities for enhanced characterization and monitoring of complex biopharmaceutical products.
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Affiliation(s)
- Thomas Bouvarel
- Protein Analytical Chemistry, Genentech, South San Francisco, California, USA
| | - Julien Camperi
- Cell Therapy Engineering and Development, Genentech, South San Francisco, California, USA
| | - Davy Guillarme
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
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21
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Moazzam M, Zhang M, Hussain A, Yu X, Huang J, Huang Y. The landscape of nanoparticle-based siRNA delivery and therapeutic development. Mol Ther 2024; 32:284-312. [PMID: 38204162 PMCID: PMC10861989 DOI: 10.1016/j.ymthe.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/01/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024] Open
Abstract
Five small interfering RNA (siRNA)-based therapeutics have been approved by the Food and Drug Administration (FDA), namely patisiran, givosiran, lumasiran, inclisiran, and vutrisiran. Besides, siRNA delivery to the target site without toxicity is a big challenge for researchers, and naked-siRNA delivery possesses several challenges, including membrane impermeability, enzymatic degradation, mononuclear phagocyte system (MPS) entrapment, fast renal excretion, endosomal escape, and off-target effects. The siRNA therapeutics can silence any disease-specific gene, but their intracellular and extracellular barriers limit their clinical applications. For this purpose, several modifications have been employed to siRNA for better transfection efficiency. Still, there is a quest for better delivery systems for siRNA delivery to the target site. In recent years, nanoparticles have shown promising results in siRNA delivery with minimum toxicity and off-target effects. Patisiran is a lipid nanoparticle (LNP)-based siRNA formulation for treating hereditary transthyretin-mediated amyloidosis that ultimately warrants the use of nanoparticles from different classes, especially lipid-based nanoparticles. These nanoparticles may belong to different categories, including lipid-based, polymer-based, and inorganic nanoparticles. This review briefly discusses the lipid, polymer, and inorganic nanoparticles and their sub-types for siRNA delivery. Finally, several clinical trials related to siRNA therapeutics are addressed, followed by the future prospects and conclusions.
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Affiliation(s)
- Muhammad Moazzam
- Faculty of Engineering and Science, University of Greenwich, Medway Campus, Chatham Maritime, Kent ME4 4TB, UK
| | - Mengjie Zhang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, School of Medical Technology, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Abid Hussain
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, School of Medical Technology, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaotong Yu
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Health, Peking University, Beijing 100191, China.
| | - Jia Huang
- Department of Hepatobiliary Surgery, China-Japan Friendship Hospital, Beijing 100029, China.
| | - Yuanyu Huang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, School of Medical Technology, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China; Rigerna Therapeutics Co. Ltd., Suzhou 215127, China.
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22
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Klabenkova KV, Zhdanova PV, Burakova EA, Bizyaev SN, Fokina AA, Stetsenko DA. A Convenient Oligonucleotide Conjugation via Tandem Staudinger Reaction and Amide Bond Formation at the Internucleotidic Phosphate Position. Int J Mol Sci 2024; 25:2007. [PMID: 38396686 PMCID: PMC10889076 DOI: 10.3390/ijms25042007] [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: 12/11/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Staudinger reaction on the solid phase between an electronodeficit organic azide, such as sulfonyl azide, and the phosphite triester formed upon phosphoramidite coupling is a convenient method for the chemical modification of oligonucleotides at the internucleotidic phosphate position. In this work, 4-carboxybenzenesulfonyl azide, either with a free carboxy group or in the form of an activated ester such as pentafluorophenyl, 4-nitrophenyl, or pentafluorobenzyl, was used to introduce a carboxylic acid function to the terminal or internal internucleotidic phosphate of an oligonucleotide via the Staudinger reaction. A subsequent treatment with excess primary alkyl amine followed by the usual work-up, after prior activation with a suitable peptide coupling agent such as a uronium salt/1-hydroxybenzotriazole in the case of a free carboxyl, afforded amide-linked oligonucleotide conjugates in good yields including multiple conjugations of up to the exhaustive modification at each phosphate position for a weakly activated pentafluorobenzyl ester, whereas more strongly activated and, thus, more reactive aryl esters provided only single conjugations at the 5'-end. The conjugates synthesized include those with di- and polyamines that introduce a positively charged side chain to potentially assist the intracellular delivery of the oligonucleotide.
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Affiliation(s)
- Kristina V. Klabenkova
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Polina V. Zhdanova
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia;
| | - Ekaterina A. Burakova
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Sergei N. Bizyaev
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Alesya A. Fokina
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Dmitry A. Stetsenko
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
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23
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Gaál Z. Role of microRNAs in Immune Regulation with Translational and Clinical Applications. Int J Mol Sci 2024; 25:1942. [PMID: 38339220 PMCID: PMC10856342 DOI: 10.3390/ijms25031942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
MicroRNAs (miRNAs) are 19-23 nucleotide long, evolutionarily conserved noncoding RNA molecules that regulate gene expression at the post-transcriptional level. In this review, involvement of miRNAs is summarized in the differentiation and function of immune cells, in anti-infective immune responses, immunodeficiencies and autoimmune diseases. Roles of miRNAs in anticancer immunity and in the transplantation of solid organs and hematopoietic stem cells are also discussed. Major focus is put on the translational clinical applications of miRNAs, including the establishment of noninvasive biomarkers for differential diagnosis and prediction of prognosis. Patient selection and response prediction to biological therapy is one of the most promising fields of application. Replacement or inhibition of miRNAs has enormous therapeutic potential, with constantly expanding possibilities. Although important challenges still await solutions, evaluation of miRNA fingerprints may contribute to an increasingly personalized management of immune dysregulation with a remarkable reduction in toxicity and treatment side effects. More detailed knowledge of the molecular effects of physical exercise and nutrition on the immune system may facilitate self-tailored lifestyle recommendations and advances in prevention.
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Affiliation(s)
- Zsuzsanna Gaál
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt, 4032 Debrecen, Hungary
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24
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Tanaka Y, Kitamura H, Fuse S. Microflow Synthesis of Unsymmetrical H-Phosphonates via Sequential and Direct Substitution of Chlorine Atoms in Phosphorus Trichloride with Alkoxy Groups. J Org Chem 2024; 89:1777-1783. [PMID: 38163754 DOI: 10.1021/acs.joc.3c02467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Unsymmetrical H-phosphonates were synthesized by a rapid (<15 s) and mild (20 °C) process in a microflow reactor as the first example of the sequential direct substitution of the chlorine atoms in PCl3 with alkoxyl/aryloxy groups using equivalent amounts of PCl3 and alcohols. The optimal base concentration differed in each step, presumably attributed to differences in the Brønsted basicity of the electrophilic intermediates. Phosphite hydrolysis was observed, and the structure-hydrolysis relationship was quantitatively evaluated.
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Affiliation(s)
- Yuma Tanaka
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hiroshi Kitamura
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Shinichiro Fuse
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
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25
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Chen P, Wei Y, Sun T, Lin J, Zhang K. Enabling safer, more potent oligonucleotide therapeutics with bottlebrush polymer conjugates. J Control Release 2024; 366:44-51. [PMID: 38145661 PMCID: PMC10922259 DOI: 10.1016/j.jconrel.2023.12.035] [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: 07/04/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/27/2023]
Abstract
Oligonucleotide therapeutics have the unique ability to address traditionally undruggable targets through various target engagement pathways. However, despite advances in chemically modified oligonucleotides and carrier-assisted delivery systems such as lipid nanoparticles and protein/peptide conjugates, the development of oligonucleotide drugs is still plagued with lackluster potency, narrow therapeutic window, poor delivery to non-liver target sites, and/or high potential for toxicity and unwanted immune system activation. In this perspective, we discuss an unconventional delivery solution based upon bottlebrush polymers, which overcomes many key challenges in oligonucleotide drug development. We address the molecular basis of the polymer's ability to enhance tissue bioavailability and drug potency, reduce side effects, and suppress anti-carrier immunity. Furthermore, we discuss the potential of the technology in advancing oligonucleotide-based therapies for non-liver targets.
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Affiliation(s)
- Peiru Chen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Yun Wei
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Tingyu Sun
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jiachen Lin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Chemical Engineering and Bioengineering, Northeastern University, Boston, MA 02115, USA.
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26
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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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27
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Jones CH, Androsavich JR, So N, Jenkins MP, MacCormack D, Prigodich A, Welch V, True JM, Dolsten M. Breaking the mold with RNA-a "RNAissance" of life science. NPJ Genom Med 2024; 9:2. [PMID: 38195675 PMCID: PMC10776758 DOI: 10.1038/s41525-023-00387-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
In the past decade, RNA therapeutics have gone from being a promising concept to one of the most exciting frontiers in healthcare and pharmaceuticals. The field is now entering what many call a renaissance or "RNAissance" which is being fueled by advances in genetic engineering and delivery systems to take on more ambitious development efforts. However, this renaissance is occurring at an unprecedented pace, which will require a different way of thinking if the field is to live up to its full potential. Recognizing this need, this article will provide a forward-looking perspective on the field of RNA medical products and the potential long-term innovations and policy shifts enabled by this revolutionary and game-changing technological platform.
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Affiliation(s)
| | | | - Nina So
- Pfizer, 66 Hudson Boulevard, New York, NY, 10018, USA
| | | | | | | | - Verna Welch
- Pfizer, 66 Hudson Boulevard, New York, NY, 10018, USA
| | - Jane M True
- Pfizer, 66 Hudson Boulevard, New York, NY, 10018, USA.
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28
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Wang L, Ling Y, Tian Y, Wang X, Sasaki S, Taniguchi Y. The Development of Non-natural Type Nucleoside to Stabilize Triplex DNA Formation against CG and TA Inversion Site. Curr Med Chem 2024; 31:2663-2686. [PMID: 37183460 DOI: 10.2174/0929867330666230512114130] [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: 12/17/2022] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 05/16/2023]
Abstract
Based on the sequence-specific recognition of target duplex DNA by triplexforming oligonucleotides (TFOs) at the major groove side, the antigene strategy has been exploited as a gene-targeting tool with considerable attention. Triplex DNA is formed via the specific base triplets by the Hoogsteen or reverse Hoogsteen hydrogen bond interaction between TFOs and the homo-purine strand from the target duplex DNA, leading to the established sequence-specificity. However, the presence of inversion sites, which are known as non-natural nucleosides that can form satisfactory interactions with 2'- deoxythymidine (dT) and 2'-deoxycytidine (dC) in TA and CG base pairs in the target homo-purine DNA sequences, drastically restricts the formation of classically stable base triplets and even the triplex DNA. Therefore, the design of non-natural type nucleosides, which can effectively recognize CG or/and TA inversion sites with satisfactory selectivity, should be of great significance to expanding the triplex-forming sequence. Here, this review mainly provides a comprehensive review of the current development of novel nonnatural nucleosides to recognize CG or/and TA inversion sites in triplex DNA formation against double-strand DNA (dsDNA).
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Affiliation(s)
- Lei Wang
- School of Pharmacy, Nantong University, Nantong, China
| | - Yong Ling
- School of Pharmacy, Nantong University, Nantong, China
| | - Yan Tian
- School of Pharmacy, Nantong University, Nantong, China
| | - Xiao Wang
- School of Pharmacy, Nantong University, Nantong, China
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, Nagasaki City, Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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29
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Chen X, Xie L, Zhang C, Tian S, Tang Z, Xiang M, Tian W, Lu P, Yang X. Synthesis of Nucleotides Bearing the 2'-O-Trifluoromethyl Group and Their Application in RNA Analogs Preparation. Curr Protoc 2024; 4:e956. [PMID: 38230581 DOI: 10.1002/cpz1.956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The integration of fluorine atoms into biologically active organic compounds has proved to be a vital technique in small molecule drugs. This technique can substantially enhance crucial properties, including metabolic stability, lipophilicity, and bioavailability, often with a mere addition of a single fluorine atom or a trifluoromethyl group. Over the past few decades, this concept has also been applied in nucleic acid chemistry. A commonly employed 2'-OH substitution is the introduction of a 2'-deoxy-2'-fluoro (2'-F) group. The strong electronegativity of fluorine prompts the modified siRNA to readily adopt a C3'-endo conformation, resulting in significant advantages in terms of binding affinity. To enrich the toolbox of chemical modification of oligonucleotides, the replacement of the 2'-OH with the 2'-O-trifluoromethyl group has been developed in RNA analog synthesis. Oligodeoxynucleotides containing the 2'-O-trifluoromethyl group can greatly increase the thermal stability of DNA/RNA duplexes depending on the position and amount of the modification. Moreover, 2'-O-trifluoromethylated oligodeoxynucleotide also exhibited a slightly higher resistance to snake venom phosphodiesterase than the unmodified oligodeoxynucleotide. The 2'-O-trifluoromethylated oligonucleotides can emerge as a label to study RNA structure and function as well, or to develop DNA/RNA-based diagnostics. Hence, it is necessary to report an effective method for the synthesis, deprotection, purification, and characterization of oligonucleotides bearing a 2'-O-trifluoromethyl group. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 6-N-benzoyl-5'-O-dimethoxytrityl-2'-O-trifluoromethyl adenosine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 2: Preparation of 4-N-acetyl-5'-O-dimethoxytrityl-2'-O-trifluoromethyl cytidine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 3: Preparation of 2-N-isobutyryl-5'-O-dimethoxytrityl-2'-O-trifluoromethyl guanine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 4: Preparation of 5'-O-dimethoxytrityl-2'-O-2-trifluoromethyl uridine 3'-(2-cyanoethyl N,N-diisopropyl) phosphoramidite Basic Protocol 5: Solid-phase synthesis of 2'-O-trifluoromethylated RNA analogs Basic Protocol 6: Deprotection and purification of 2'-O-trifluoromethyl-RNAs.
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30
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van der Zon AAM, Verduin J, van den Hurk RS, Gargano AFG, Pirok BWJ. Sample transformation in online separations: how chemical conversion advances analytical technology. Chem Commun (Camb) 2023; 60:36-50. [PMID: 38053451 PMCID: PMC10729587 DOI: 10.1039/d3cc03599a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023]
Abstract
While the advent of modern analytical technology has allowed scientists to determine the complexity of mixtures, it also spurred the demand to understand these sophisticated mixtures better. Chemical transformation can be used to provide insights into properties of complex samples such as degradation pathways or molecular heterogeneity that are otherwise unaccessible. In this article, we explore how sample transformation is exploited across different application fields to empower analytical methods. Transformation mechanisms include molecular-weight reduction, controlled degradation, and derivatization. Both offline and online transformation methods have been explored. The covered studies show that sample transformation facilitates faster reactions (e.g. several hours to minutes), reduces sample complexity, unlocks new sample dimensions (e.g. functional groups), provides correlations between multiple sample dimensions, and improves detectability. The article highlights the state-of-the-art and future prospects, focusing in particular on the characterization of protein and nucleic-acid therapeutics, nanoparticles, synthetic polymers, and small molecules.
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Affiliation(s)
- Annika A M van der Zon
- University of Amsterdam, van't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, Science Park 904, 1098 XH Amsterdam, The Netherlands.
- Centre of Analytical Sciences Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Joshka Verduin
- Centre of Analytical Sciences Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Vrije Universiteit Amsterdam, Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Rick S van den Hurk
- University of Amsterdam, van't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, Science Park 904, 1098 XH Amsterdam, The Netherlands.
- Centre of Analytical Sciences Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Andrea F G Gargano
- University of Amsterdam, van't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, Science Park 904, 1098 XH Amsterdam, The Netherlands.
- Centre of Analytical Sciences Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bob W J Pirok
- University of Amsterdam, van't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, Science Park 904, 1098 XH Amsterdam, The Netherlands.
- Centre of Analytical Sciences Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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31
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Karasawa K, Duchoslav E, Burton L, Kawakami J, Baba T. Sequencing of Morpholino Antisense Oligonucleotides Using Electron Capture Dissociation Mass Spectrometry. Anal Chem 2023; 95:16352-16358. [PMID: 37871344 DOI: 10.1021/acs.analchem.3c03621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
We report the first sequencing of morpholino antisense oligonucleotides (phosphorodiamidate morpholino oligomers, PMOs) using electron capture dissociation (ECD) mass spectrometry. In this research, we found dissociation of the backbone of 18- to 25-mer PMOs to produce d and z ions as the major ions, and 100% cleavage coverage (sequence coverage) was obtained with these ions. This is a critical contrast with beam-type collision-induced dissociation, which dominantly induces base loss, so it is difficult to obtain sequence information. The results showed that an electron beam energy (typically 15 eV) can be used universally for PMOs with different sequences, lengths, and charge states so that no detailed optimization is required for multiprecursor targeting liquid chromatography coupled with tandem mass spectrometry measurements. We also confirmed that the ECD reaction speed was compatible with the high-performance liquid chromatography time scale. Finally, we demonstrated a liquid chromatography electron capture dissociation tandem mass spectrometry workflow to survey the modification sites of the emulated PMO impurities.
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Affiliation(s)
- Kaoru Karasawa
- SCIEX, 4-7-35 Kitashinagawa, Shinagawa, Tokyo 140-0001, Japan
| | - Eva Duchoslav
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Lyle Burton
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Junji Kawakami
- Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe, Hyogo 658-8501, Japan
| | - Takashi Baba
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
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32
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Chen X, Xie L, Zhang C, Tian S, Tang Z, Tian W, Lu P, Yang X. A Convenient Method for the Synthesis of 2'-O-Cyanoethylated Nucleotides and Their Application in the Solid-Phase Synthesis of Related RNA Analogs. Curr Protoc 2023; 3:e923. [PMID: 37962485 DOI: 10.1002/cpz1.923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Although small interfering RNA (siRNA) is a key player among gene inhibition therapeutics, there are many obstacles to the development of siRNA drugs due to inherent properties of oligonucleotides, including the unsatisfactory stability of unmodified siRNA, poor pharmacokinetic distribution, and the toxicity induced by off-target effects. To maximize treatment potency, chemical modification of siRNA has undoubtedly been the most successful strategy by far. Widely applied modifications include phosphorothioate linkages, 2'-O-methyl modifications, and 2'-fluoro modifications, among others. To extend the family of chemical modifications for oligonucleotides, 2'-O-cyanoethylated RNA analogs were developed through the replacement of the 2'-hydroxyl group with a 2'-O-cyanoethyl group (-OCH2 CH2 CN). This modification can provide several advantages over unmodified RNA, such as increased stability, improved binding affinity to complementary DNA or RNA strands, and resistance to degradation by cellular nucleases. The 2'-O-cyanoethyl-modified RNAs not only are applied in RNA silencing machinery but also act as research tools for studying RNA structure and function or for developing RNA-based diagnostics. Therefore, the efficient synthesis, deprotection, purification, and characterization of 2'-O-cyanoethylated RNAs deserves more attention. This protocol describes the chemical synthesis of 2'-O-cyanoethylated nucleotides and the solid-phase synthesis, deprotection, and purification of 2'-O-cyanoethylated RNAs. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 6-N-dimethylformamidyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl adenosine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 2: Preparation of 4-N-acetyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl cytidine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 3: Preparation of 2-N-dimethylformamidyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl guanine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 4: Preparation of 5'-O-dimethoxytrityl-2'-O-2-cyanoethyl uridine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 5: Solid-phase synthesis of 2'-O-cyanoethylated RNA analogs Basic Protocol 6: Deprotection and purification of synthesized 2'-O-cyanoethyl-RNAs.
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Affiliation(s)
- Xuan Chen
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | - Long Xie
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | | | - Shen Tian
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | - Zeyu Tang
- Sirnaomics Ltd. Suzhou, Suzhou, China
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33
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Tabana Y, Babu D, Fahlman R, Siraki AG, Barakat K. Target identification of small molecules: an overview of the current applications in drug discovery. BMC Biotechnol 2023; 23:44. [PMID: 37817108 PMCID: PMC10566111 DOI: 10.1186/s12896-023-00815-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Target identification is an essential part of the drug discovery and development process, and its efficacy plays a crucial role in the success of any given therapy. Although protein target identification research can be challenging, two main approaches can help researchers make significant discoveries: affinity-based pull-down and label-free methods. Affinity-based pull-down methods use small molecules conjugated with tags to selectively isolate target proteins, while label-free methods utilize small molecules in their natural state to identify targets. Target identification strategy selection is essential to the success of any drug discovery process and must be carefully considered when determining how to best pursue a specific project. This paper provides an overview of the current target identification approaches in drug discovery related to experimental biological assays, focusing primarily on affinity-based pull-down and label-free approaches, and discusses their main limitations and advantages.
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Affiliation(s)
- Yasser Tabana
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Dinesh Babu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Arno G Siraki
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
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34
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Okamoto S, Echigoya Y, Tago A, Segawa T, Sato Y, Itou T. Antiviral Efficacy of RNase H-Dependent Gapmer Antisense Oligonucleotides against Japanese Encephalitis Virus. Int J Mol Sci 2023; 24:14846. [PMID: 37834294 PMCID: PMC10573891 DOI: 10.3390/ijms241914846] [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: 08/11/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
RNase H-dependent gapmer antisense oligonucleotides (ASOs) are a promising therapeutic approach via sequence-specific binding to and degrading target RNAs. However, the efficacy and mechanism of antiviral gapmer ASOs have remained unclear. Here, we investigated the inhibitory effects of gapmer ASOs containing locked nucleic acids (LNA gapmers) on proliferating a mosquito-borne flavivirus, Japanese encephalitis virus (JEV), with high mortality. We designed several LNA gapmers targeting the 3' untranslated region of JEV genomic RNAs. In vitro screening by plaque assay using Vero cells revealed that LNA gapmers targeting a stem-loop region effectively inhibit JEV proliferation. Cell-based and RNA cleavage assays using mismatched LNA gapmers exhibited an underlying mechanism where the inhibition of viral production results from JEV RNA degradation by LNA gapmers in a sequence- and modification-dependent manner. Encouragingly, LNA gapmers potently inhibited the proliferation of five JEV strains of predominant genotypes I and III in human neuroblastoma cells without apparent cytotoxicity. Database searching showed a low possibility of off-target binding of our LNA gapmers to human RNAs. The target viral RNA sequence conservation observed here highlighted their broad-spectrum antiviral potential against different JEV genotypes/strains. This work will facilitate the development of an antiviral LNA gapmer therapy for JEV and other flavivirus infections.
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Affiliation(s)
- Shunsuke Okamoto
- Laboratory of Preventive Veterinary Medicine and Animal Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan; (S.O.); (T.S.); (T.I.)
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
| | - Yusuke Echigoya
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Ayaka Tago
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Takao Segawa
- Laboratory of Preventive Veterinary Medicine and Animal Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan; (S.O.); (T.S.); (T.I.)
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
| | - Yukita Sato
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Takuya Itou
- Laboratory of Preventive Veterinary Medicine and Animal Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan; (S.O.); (T.S.); (T.I.)
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
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Weidner J, Kolosionek E, Holmila R, Ax E, Garreau M, Gnerlich F, Olsson H, Czechtizky W, Vollmer S, Rydzik AM. Gymnotic uptake of AntimiRs alter microRNA-34a levels in 2D and 3D epithelial cell culture. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:898-907. [PMID: 37680982 PMCID: PMC10480572 DOI: 10.1016/j.omtn.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023]
Abstract
MicroRNAs are attractive therapeutic targets in many diseases, including chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Among microRNA inhibitors antimiRs have been proven successful in lowering aberrant microRNA levels in the clinic. We present a set of antimiRs targeting miR-34a, which has been shown to be dysregulated in chronic lung diseases. The tool compounds were taken up by a bronchial epithelial cell line and primary human bronchial epithelial cells, followed by efficient knockdown of miR-34a. Similar results were observed in 3D differentiated primary human bronchial epithelial cells cultured at the air-liquid interface. Varying chemical properties of antimiRs had significant impact on cellular uptake and potency, resulting in effective tool compounds for use in lung-relevant cellular systems. This report demonstrates gymnotic antimiR uptake and activity in 3D epithelial cell culture after apical administration, mimicking inhalation conditions.
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Affiliation(s)
- Julie Weidner
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Ewa Kolosionek
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Reetta Holmila
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Elisabeth Ax
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Marion Garreau
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Felix Gnerlich
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Henric Olsson
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Stefan Vollmer
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Anna M. Rydzik
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
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Redhead C, Taye N, Hubmacher D. En route towards a personalized medicine approach: Innovative therapeutic modalities for connective tissue disorders. Matrix Biol 2023; 122:46-54. [PMID: 37657665 PMCID: PMC10529529 DOI: 10.1016/j.matbio.2023.08.005] [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: 06/28/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/03/2023]
Abstract
Connective tissue disorders can be caused by pathogenic variants (mutations) in genes encoding extracellular matrix (ECM) proteins. Such disorders typically manifest during development or postnatal growth and result in significant morbidity and mortality. The development of curative treatments for connective tissue disorders is hampered in part by the inability of many mature connective tissues to efficiently regenerate. To be most effective, therapeutic strategies designed to preserve or restore tissue function will likely need to be initiated during phases of significant endogenous connective tissue remodeling and organ sculpting postnatally and directly target the underlying ECM protein mutations. With recent advances in whole exome sequencing, in-vitro and in-vivo disease modeling, and the development of mutation-specific molecular therapeutic modalities, it is now feasible to directly correct disease-causing mutations underlying connective tissue disorders and ameliorate their pathogenic consequences. These technological advances may lead to potentially curative personalized medicine approaches for connective tissue disorders that have previously been considered incurable. In this review, we highlight innovative therapeutic modalities including gene replacement, exon skipping, DNA/mRNA editing, and pharmacological approaches that were used to preserve or restore tissue function in the context of connective tissue disorders. Inherent to a successful application of these approaches is the need to deepen the understanding of mechanisms that regulate ECM formation and homeostasis, and to decipher how individual mutations in ECM proteins compromise ECM and connective tissue development and function.
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Affiliation(s)
- Charlene Redhead
- Orthopedic Research Laboratories, Leni & Peter W. May Department of Orthopaedics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nandaraj Taye
- Orthopedic Research Laboratories, Leni & Peter W. May Department of Orthopaedics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dirk Hubmacher
- Orthopedic Research Laboratories, Leni & Peter W. May Department of Orthopaedics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Borsa BA, Hernandez LI, Jiménez T, Tellapragada C, Giske CG, Hernandez FJ. Therapeutic-oligonucleotides activated by nucleases (TOUCAN): A nanocarrier system for the specific delivery of clinical nucleoside analogues. J Control Release 2023; 361:260-269. [PMID: 37541593 DOI: 10.1016/j.jconrel.2023.07.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023]
Abstract
Nucleoside analogues have been in clinical use since 1960s and they are still used as the first therapeutic option for several cancers and viral infections, due to their high therapeutic efficacy. However, their wide clinical acceptance has been limited due to their high toxicity and severe side effects to patients. Herein, we report on a nanocarrier system that delivers nucleosides analogues in a target-specific manner, making nucleoside-based therapeutics safer and with the possibility to be used in other human conditions. This system, named, Therapeutic OligonUCleotides Activated by Nucleases" (TOUCAN) combines: i) the recognition power of oligonucleotides as substrates, ii) the use of nucleases as enzymatic biomarkers and iii) the clinical efficacy of nucleoside analogues, in a single approach. As a proof-of-concept, we report on a TOUCAN that is activated by a specific nuclease produced by bacteria and releases a therapeutic nucleoside, floxuridine. We demonstrate, for the first time, that, by incorporating a therapeutic nucleoside analogue into oligonucleotide probes, we can specifically inhibit bacterial growth in cultures. In this study, Staphylococcus aureus was selected as the targeted bacteria and the TOUCAN strategy successfully inhibited its growth with minimal inhibitory concentration (MIC) values ranging from 0.62 to 40 mg/L across all tested strains. Moreover, our results indicate that the intravenous administration of TOUCANs at a dose of 20 mg/kg over a 24-h period is a highly effective method for treating bacterial infections in a mouse model of pyomyositis. Importantly, no signs of toxicity were observed in our in vitro and in vivo studies. This work can significantly impact the current management of bacterial infections, laying the grounds for the development of a different class of antibiotics. Furthermore, it can provide a safer delivery platform for clinical nucleoside therapeutics in any human conditions, such as cancer and viral infection, where specific nuclease activity has been reported.
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Affiliation(s)
- Baris A Borsa
- Wallenberg Center for Molecular Medicine (WCMM), Linköping, Sweden; Department of Physics, Chemistry and Biology (IFM), Linköping University, Sweden; Nucleic Acid Technologies Laboratory (NAT-Lab), Linköping, Sweden
| | - Luiza I Hernandez
- Department of Clinical and Experimental Medicine (IKE), Linköping University, Sweden; SOMAprobes, Science and Technology Park of Gipuzkoa, Donostia-San Sebastian, Spain
| | - Tania Jiménez
- SOMAprobes, Science and Technology Park of Gipuzkoa, Donostia-San Sebastian, Spain
| | - Chaitanya Tellapragada
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Frank J Hernandez
- Wallenberg Center for Molecular Medicine (WCMM), Linköping, Sweden; Department of Physics, Chemistry and Biology (IFM), Linköping University, Sweden; Nucleic Acid Technologies Laboratory (NAT-Lab), Linköping, Sweden.
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Chander S, Bhatt S, Dua K, Jadhav H. Editorial: Recent trends and spotlight on nucleotide-based drugs: novel targets, their design, delivery, and clinical potential. Front Pharmacol 2023; 14:1245809. [PMID: 37521465 PMCID: PMC10374295 DOI: 10.3389/fphar.2023.1245809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Affiliation(s)
- Subhash Chander
- Amity Institute of Phytomedicine & Phytochemistry (AIP&P), Amity University Uttar Pradesh, Noida, Uttar Pradesh, India
| | - Shvetank Bhatt
- School of Health Sciences and Technology, Dr. Vishwanath Karad MIT World Peace University, Pune, Maharashtra, India
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology, Sydney, NSW, Australia
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology, Sydney, NSW, Australia
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Hemant Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Rajasthan, India
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Rosenqvist P, Saari V, Pajuniemi E, Gimenez Molina A, Ora M, Horvath A, Virta P. Stereo-Controlled Liquid Phase Synthesis of Phosphorothioate Oligonucleotides on a Soluble Support. J Org Chem 2023. [PMID: 37428953 PMCID: PMC10367069 DOI: 10.1021/acs.joc.3c01006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
5'-O-(2-Methoxyisopropyl) (MIP)-protected 2'-deoxynucleosides as chiral P(V)-building blocks, based on the limonene-derived oxathiaphospholane sulfide, were synthesized and used for the assembly of di-, tri-, and tetranucleotide phosphorothioates on a tetrapodal pentaerythritol-derived soluble support. The synthesis cycle consisted of two reactions and two precipitations: (1) the coupling under basic conditions, followed by neutralization and precipitation and (2) an acid catalyzed 5'-O-deacetalization, followed by neutralization and precipitation. The simple P(V) chemistry together with the facile 5'-O-MIP deprotection proved efficient in the liquid phase oligonucleotide synthesis (LPOS). Ammonolysis released nearly homogeneous Rp or Sp phosphorothioate diastereomers in ca. 80% yield/synthesis cycle.
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Affiliation(s)
- Petja Rosenqvist
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Verneri Saari
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Ella Pajuniemi
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Alejandro Gimenez Molina
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, 2340 Beerse, Belgium
| | - Mikko Ora
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Andras Horvath
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, 2340 Beerse, Belgium
| | - Pasi Virta
- Department of Chemistry, University of Turku, 20500 Turku, Finland
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Malecova B, Burke RS, Cochran M, Hood MD, Johns R, Kovach PR, Doppalapudi VR, Erdogan G, Arias JD, Darimont B, Miller CD, Huang H, Geall A, Younis H, Levin AA. Targeted tissue delivery of RNA therapeutics using antibody-oligonucleotide conjugates (AOCs). Nucleic Acids Res 2023; 51:5901-5910. [PMID: 37224533 PMCID: PMC10325888 DOI: 10.1093/nar/gkad415] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/05/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023] Open
Abstract
Although targeting TfR1 to deliver oligonucleotides to skeletal muscle has been demonstrated in rodents, effectiveness and pharmacokinetic/pharmacodynamic (PKPD) properties remained unknown in higher species. We developed antibody-oligonucleotide conjugates (AOCs) towards mice or monkeys utilizing anti-TfR1 monoclonal antibodies (αTfR1) conjugated to various classes of oligonucleotides (siRNA, ASOs and PMOs). αTfR1 AOCs delivered oligonucleotides to muscle tissue in both species. In mice, αTfR1 AOCs achieved a > 15-fold higher concentration to muscle tissue than unconjugated siRNA. A single dose of an αTfR1 conjugated to an siRNA against Ssb mRNA produced > 75% Ssb mRNA reduction in mice and monkeys, and mRNA silencing was greatest in skeletal and cardiac (striated) muscle with minimal to no activity in other major organs. In mice the EC50 for Ssb mRNA reduction in skeletal muscle was >75-fold less than in systemic tissues. Oligonucleotides conjugated to control antibodies or cholesterol produced no mRNA reduction or were 10-fold less potent, respectively. Tissue PKPD of AOCs demonstrated mRNA silencing activity primarily driven by receptor-mediated delivery in striated muscle for siRNA oligonucleotides. In mice, we show that AOC-mediated delivery is operable across various oligonucleotide modalities. AOC PKPD properties translated to higher species, providing promise for a new class of oligonucleotide therapeutics.
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Affiliation(s)
- Barbora Malecova
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Rob S Burke
- Seawolf Therapeutics, One Sansome Street Suite 3630, San Francisco, CA 94104, USA
| | - Michael Cochran
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Michael D Hood
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Rachel Johns
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Philip R Kovach
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Venkata R Doppalapudi
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Gulin Erdogan
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - J Danny Arias
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | | | - Christopher D Miller
- California Northstate University College of Medicine, 9700 W Taron Dr, Elk Grove, CA 95757, USA
| | - Hanhua Huang
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Andrew Geall
- Replicate Biosciences, 10210 Campus Point Dr, Suite 150, San Diego, CA 92121, USA
| | - Husam S Younis
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
| | - Arthur A Levin
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, CA 92121, USA
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Kasina V, Wahane A, Liu CH, Yang L, Nieh MP, Slack FJ, Bahal R. Next-generation poly-L-histidine formulations for miRNA mimic delivery. Mol Ther Methods Clin Dev 2023; 29:271-283. [PMID: 37123088 PMCID: PMC10133875 DOI: 10.1016/j.omtm.2023.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
Many diseases, especially cancer, are caused by the abnormal expression of non-coding microRNAs (miRNAs), which regulate gene expression, leading to the development of miRNA-based therapeutics. Synthetic miRNA inhibitors have shown promising efficacy in blocking the activity of aberrant miRNAs that are upregulated in disease-specific pathologies. On the other hand, miRNAs that aid in preventing certain diseases and are reduced in expression in the disease state need different strategies. To tackle this, miRNA mimics, which mimic the activity of endogenous miRNAs, can be delivered for those miRNAs downregulated in different disease states. However, the delivery of miRNA mimics remains a challenge. Here, we report a cationic polylactic-co-glycolic acid (PLGA)-poly-L-histidine delivery system to deliver miRNA mimics. We chose miR-34a mimics as a proof of concept for miRNA delivery. miR-34a-loaded PLGA-poly-L-histidine nanoparticles (NPs) were formulated and biophysically characterized to analyze the structural properties of miRNA mimic-loaded NPs. In vitro efficacy was determined by investigating miR-34a and downstream target levels and performing cell viability and apoptosis assays. We confirmed in vivo efficacy through prolonged survival of miR-34a NP-treated A549-derived xenograft mice treated intratumorally. The results of these studies establish PLGA-poly-L-histidine NPs as an effective delivery system for miRNA mimics for treating diseases characterized by downregulated miRNAs.
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Affiliation(s)
- Vishal Kasina
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Aniket Wahane
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Chung-Hao Liu
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mu-Ping Nieh
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Frank J. Slack
- Department of Pathology, HMS Initiative for RNA Medicine, BIDMC Cancer Center, Harvard Medical School, Boston, MA 02215, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
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Inagaki M, Abe N, Li Z, Nakashima Y, Acharyya S, Ogawa K, Kawaguchi D, Hiraoka H, Banno A, Meng Z, Tada M, Ishida T, Lyu P, Kokubo K, Murase H, Hashiya F, Kimura Y, Uchida S, Abe H. Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures. Nat Commun 2023; 14:2657. [PMID: 37169757 PMCID: PMC10175277 DOI: 10.1038/s41467-023-38244-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
Starting with the clinical application of two vaccines in 2020, mRNA therapeutics are currently being investigated for a variety of applications. Removing immunogenic uncapped mRNA from transcribed mRNA is critical in mRNA research and clinical applications. Commonly used capping methods provide maximum capping efficiency of around 80-90% for widely used Cap-0- and Cap-1-type mRNAs. However, uncapped and capped mRNA possesses almost identical physicochemical properties, posing challenges to their physical separation. In this work, we develop hydrophobic photocaged tag-modified cap analogs, which separate capped mRNA from uncapped mRNA by reversed-phase high-performance liquid chromatography. Subsequent photo-irradiation recovers footprint-free native capped mRNA. This approach provides 100% capping efficiency even in Cap-2-type mRNA with versatility applicable to 650 nt and 4,247 nt mRNA. We find that the Cap-2-type mRNA shows up to 3- to 4-fold higher translation activity in cultured cells and animals than the Cap-1-type mRNA prepared by the standard capping method.
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Affiliation(s)
- Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Zhenmin Li
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yuko Nakashima
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Susit Acharyya
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kazuya Ogawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Daisuke Kawaguchi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Haruka Hiraoka
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Ayaka Banno
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Zheyu Meng
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Mizuki Tada
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Tatsuma Ishida
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Pingxue Lyu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kengo Kokubo
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Hirotaka Murase
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Satoshi Uchida
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.
- CREST, Japan Science and Technology Agency, 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
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Thibonnier M, Ghosh S. Strategy for Pre-Clinical Development of Active Targeting MicroRNA Oligonucleotide Therapeutics for Unmet Medical Needs. Int J Mol Sci 2023; 24:ijms24087126. [PMID: 37108289 PMCID: PMC10138879 DOI: 10.3390/ijms24087126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
We present here an innovative modular and outsourced model of drug research and development for microRNA oligonucleotide therapeutics (miRNA ONTs). This model is being implemented by a biotechnology company, namely AptamiR Therapeutics, in collaboration with Centers of Excellence in Academic Institutions. Our aim is to develop safe, effective and convenient active targeting miRNA ONT agents for the metabolic pandemic of obesity and metabolic-associated fatty liver disease (MAFLD), as well as deadly ovarian cancer.
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Affiliation(s)
| | - Sujoy Ghosh
- Duke-NUS Medical School, Singapore and Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
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44
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Chen W, Liu X, Zhang S, Chen S. Artificial intelligence for drug discovery: Resources, methods, and applications. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:691-702. [PMID: 36923950 PMCID: PMC10009646 DOI: 10.1016/j.omtn.2023.02.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Conventional wet laboratory testing, validations, and synthetic procedures are costly and time-consuming for drug discovery. Advancements in artificial intelligence (AI) techniques have revolutionized their applications to drug discovery. Combined with accessible data resources, AI techniques are changing the landscape of drug discovery. In the past decades, a series of AI-based models have been developed for various steps of drug discovery. These models have been used as complements of conventional experiments and have accelerated the drug discovery process. In this review, we first introduced the widely used data resources in drug discovery, such as ChEMBL and DrugBank, followed by the molecular representation schemes that convert data into computer-readable formats. Meanwhile, we summarized the algorithms used to develop AI-based models for drug discovery. Subsequently, we discussed the applications of AI techniques in pharmaceutical analysis including predicting drug toxicity, drug bioactivity, and drug physicochemical property. Furthermore, we introduced the AI-based models for de novo drug design, drug-target structure prediction, drug-target interaction, and binding affinity prediction. Moreover, we also highlighted the advanced applications of AI in drug synergism/antagonism prediction and nanomedicine design. Finally, we discussed the challenges and future perspectives on the applications of AI to drug discovery.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.,Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xuesong Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sanyin Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.,Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shilin Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.,Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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45
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Hirsch E, Nacsa M, Pantea E, Szabó E, Vass P, Domján J, Farkas A, Nyíri Z, Eke Z, Vigh T, Andersen SK, Verreck G, Marosi GJ, Nagy ZK. Oligonucleotide Formulations Prepared by High-Speed Electrospinning: Maximizing Loading and Exploring Downstream Processability. Pharmaceutics 2023; 15:pharmaceutics15030855. [PMID: 36986716 PMCID: PMC10054037 DOI: 10.3390/pharmaceutics15030855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/16/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The aim of this study was to develop antisense oligonucleotide tablet formulations using high-speed electrospinning. Hydroxypropyl-beta-cyclodextrin (HPβCD) was used as a stabilizer and as an electrospinning matrix. In order to optimize the morphology of the fibers, electrospinning of various formulations was carried out using water, methanol/water (1:1), and methanol as solvents. The results showed that using methanol could be advantageous due to the lower viscosity threshold for fiber formation enabling higher potential drug loadings by using less excipient. To increase the productivity of electrospinning, high-speed electrospinning technology was utilized and HPβCD fibers containing 9.1% antisense oligonucleotide were prepared at a rate of ~330 g/h. Furthermore, to increase the drug content of the fibers, a formulation with a 50% drug loading was developed. The fibers had excellent grindability but poor flowability. The ground fibrous powder was mixed with excipients to improve its flowability, which enabled the automatic tableting of the mixture by direct compression. The fibrous HPβCD–antisense oligonucleotide formulations showed no sign of physical or chemical degradation over the 1-year stability study, which also shows the suitability of the HPβCD matrix for the formulation of biopharmaceuticals. The obtained results demonstrate possible solutions for the challenges of electrospinning such as scale-up and downstream processing of the fibers.
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Affiliation(s)
- Edit Hirsch
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Müegyetem rkp. 3, 1111 Budapest, Hungary
- Correspondence:
| | - Márió Nacsa
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Müegyetem rkp. 3, 1111 Budapest, Hungary
| | - Eszter Pantea
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Müegyetem rkp. 3, 1111 Budapest, Hungary
| | - Edina Szabó
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Müegyetem rkp. 3, 1111 Budapest, Hungary
| | - Panna Vass
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Müegyetem rkp. 3, 1111 Budapest, Hungary
| | - Júlia Domján
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Müegyetem rkp. 3, 1111 Budapest, Hungary
| | - Attila Farkas
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Müegyetem rkp. 3, 1111 Budapest, Hungary
| | - Zoltán Nyíri
- Joint Research and Training Laboratory on Separation Techniques, Eötvös Loránd University, Pázmány Péter stny. 1/A, 1117 Budapest, Hungary
| | - Zsuzsanna Eke
- Joint Research and Training Laboratory on Separation Techniques, Eötvös Loránd University, Pázmány Péter stny. 1/A, 1117 Budapest, Hungary
| | - Tamás Vigh
- Oral Solids Development, Janssen R&D, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Sune Klint Andersen
- Oral Solids Development, Janssen R&D, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Geert Verreck
- Oral Solids Development, Janssen R&D, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - György János Marosi
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Müegyetem rkp. 3, 1111 Budapest, Hungary
| | - Zsombor Kristóf Nagy
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Müegyetem rkp. 3, 1111 Budapest, Hungary
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46
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Pascual-Gilabert M, Artero R, López-Castel A. The myotonic dystrophy type 1 drug development pipeline: 2022 edition. Drug Discov Today 2023; 28:103489. [PMID: 36634841 DOI: 10.1016/j.drudis.2023.103489] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
The beginning of the 20th decade has witnessed an increase in drug development programs for myotonic dystrophy type 1 (DM1). We have collected nearly 20 candidate drugs with accomplished preclinical and clinical phases, updating our previous drug development pipeline review with new entries and relevant milestones for pre-existing candidates. Three interventional first-in-human clinical trials got underway with distinct drug classes, namely AOC 1001 and DYNE-101 nucleic acid-based therapies, and the small molecule pitolisant, which joins the race toward market authorization with other repurposed drugs, including tideglusib, metformin, or mexiletine, already in clinical evaluation. Furthermore, newly disclosed promising preclinical data for several additional nucleic-acid therapeutic candidates and a CRISPR-based approach, as well as the advent into the pipeline of novel therapeutic programs, increase the plausibility of success in the demanding task of providing valid treatments to patients with DM1.
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Affiliation(s)
| | - Ruben Artero
- University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain; Translational Genomics Group, Incliva Biomedical Research Institute, Valencia, Spain.
| | - Arturo López-Castel
- University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain; Translational Genomics Group, Incliva Biomedical Research Institute, Valencia, Spain.
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Guan B, Yan W, Stolee JA. Trace analysis of dimethoxytrityl alcohol (DMT-OH) in oligonucleotide matrices using liquid chromatography coupled with tandem mass spectrometry. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1054-1061. [PMID: 36722996 DOI: 10.1039/d2ay02020c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A liquid chromatography (LC) method with ultraviolet (UV) and tandem mass spectrometry (MS/MS) detection was developed to quantify dimethoxytrityl alcohol (DMT-OH), a small molecule byproduct generated during the detritylation reaction in oligonucleotide synthesis. The pros and cons of quantification via multiple analytical methods including LC coupled with UV, selected ion monitoring (SIM), and multiple reaction monitoring (MRM) were evaluated. The MRM method was ultimately selected for further qualification and exhibited good linearity (R2 = 0.997 from 0.5 to 64 ng mL-1), accuracy (recoveries ranging 75-90% with ≤ 2% RSD), repeatability (<5% RSD), and sensitivity (LOQ of 1.6 ng mL-1). The MRM method was further applied to analyze DMT-OH in various oligonucleotide intermediates and drug substances. Similar MRM methods for six other small molecule impurities (aniline, benzamide, isobutyramide, 2-phenylacetamide, succinamide, and uny-CTP) as well as their application are also presented.
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Affiliation(s)
- Bing Guan
- Biogen Inc., Cambridge, Massachusetts, USA
| | - Wuming Yan
- Biogen Inc., Cambridge, Massachusetts, USA
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Ghosh A, Akabane-Nakata M, Kundu J, Harp JM, Madaoui M, Egli M, Manoharan M, Sinha S. Synthesis and Biophysical Properties of Phosphorodiamidate Piperidino Oligomers. Org Lett 2023; 25:901-906. [PMID: 36734846 DOI: 10.1021/acs.orglett.2c04067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We report the synthesis of piperidino nucleoside phosphoramidates functionalized with uracil, cytosine, guanine, and adenine and their incorporation into oligomers. High-performance liquid chromatography analyses demonstrated that a phosphorodiamidate piperidino oligomer (PPO) is more lipophilic than a phosphorodiamidate morpholino oligomer (PMO) of the same tetrameric sequence. A PMO containing piperidino residues formed duplexes with both DNA and RNA, and the PPO had higher stability at endosomolytic pH and higher hydrophobicity than the PMO.
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Affiliation(s)
- Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | | | - Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Mimouna Madaoui
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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Das A, Ghosh A, Sinha S. C5-pyrimidine-functionalized morpholino oligonucleotides exhibit differential binding affinity, target specificity and lipophilicity. Org Biomol Chem 2023; 21:1242-1253. [PMID: 36633261 DOI: 10.1039/d2ob01759h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
C5-substituted uridine and cytidine morpholino chlorophosphoramidate monomers were synthesized and incorporated into a 12-mer Phosphorodiamidate Morpholino Oligonucleotide (PMO) using semi-automated solid phase synthesis. PMOs with most of the tested pyrimidine C5-substitutions have significantly increased thermal stability when bound to the complementary RNA strand relative to the PMO. They exhibit higher binding with RNA than DNA. CD-spectra show B-type helical conformation of duplexes. HPLC analysis indicates their greater lipophilicity compared to regular PMOs. These chemical modifications have significant potential towards the development of better antisense technologies.
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Affiliation(s)
- Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
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50
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A Novel Hybridization LC-MS/MS Methodology for Quantification of siRNA in Plasma, CSF and Tissue Samples. Molecules 2023; 28:molecules28041618. [PMID: 36838605 PMCID: PMC9967190 DOI: 10.3390/molecules28041618] [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: 01/18/2023] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/10/2023] Open
Abstract
Therapeutic oligonucleotides, such as antisense oligonucleotide (ASO) and small interfering RNA (siRNA), are a new class of therapeutics rapidly growing in drug discovery and development. A sensitive and reliable method to quantify oligonucleotides in biological samples is critical to study their pharmacokinetic and pharmacodynamic properties. Hybridization LC-MS/MS was recently established as a highly sensitive and specific methodology for the quantification of single-stranded oligonucleotides, e.g., ASOs, in various biological matrices. However, there is no report of this methodology for the bioanalysis of double-stranded oligonucleotides (e.g., siRNA). In this work, we investigated hybridization LC-MS/MS methodology for the quantification of double-stranded oligonucleotides in biological samples using an siRNA compound, siRNA-01, as the test compound. The commonly used DNA capture probe and a new peptide nucleic acid (PNA) probe were compared for the hybridization extraction of siRNA-01 under different conditions. The PNA probe achieved better extraction recovery than the DNA probe, especially for high concentration samples, which may be due to its stronger hybridization affinity. The optimized hybridization method using the PNA probe was successfully qualified for the quantitation of siRNA-01 in monkey plasma, cerebrospinal fluid (CSF), and tissue homogenates over the range of 2.00-1000 ng/mL. This work is the first report of the hybridization LC-MS/MS methodology for the quantification of double-stranded oligonucleotides. The developed methodology will be applied to pharmacokinetic and toxicokinetic studies of siRNA-01. This novel methodology can also be used for the quantitative bioanalysis of other double-stranded oligonucleotides.
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