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Small Interfering RNAs, Antisense Drugs and Therapeutic Oligonucleotide Analogues

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pharmacology".

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 3111

Special Issue Editor


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Guest Editor
Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
Interests: nucleic acid-based diagnostics and therapeutics; supramolecular functional biomaterials with controlled chemical and biological properties

Special Issue Information

Dear Colleagues,

One of the major biomedical and pharmaceutical challenges is a highly selective therapy against abnormal gene expression in disease states. Most conventional small-molecule drugs confront downstream cellular components, when disease is already established in cell components at the level of expressed pathogenic proteins. Although successful at treating or alleviating symptoms for some disease states, these approaches often suffer from off-target effects and severe toxicity, typical for chemotherapy and anti-viral drugs. Small interfering RNAs, antisense oligonucleotides and therapeutic nucleic acid analogues offer a powerful platform for the development of novel therapeutic strategies for the selective inhibition of disease states via the controlled translational arrest of disease-relevant proteins by targeting upstream cellular components (e.g. DNA, messenger RNA, microRNA or viral genomic RNA). Therapeutic nucleic acids and their functional analogues use the most sophisticated and elegant 3D molecular design and offer high efficacy, remarkable selectivity, and fewer side effects due to their unique shape, precision in molecular recognition and action. These therapeutic strategies need to be developed further, optimized, tested in pre-clinical models, and translated into future clinical applications. For this Special Issue, we invite manuscripts addressing one or several of the following aspects:

  1. New synthetic strategies for the fabrication of innovative nucleic acid analogues to improve their potency, precision in sequence-specific recognition, biological stability, resistance to cellular nucleases and/or intracellular delivery.
  2. Mechanistic studies on such nucleic acid therapeutics, including but not limited to the investigation of their mechanisms of action responsible for the observed effects and/or therapeutic responses at the molecular, cellular, or physiological levels.
  3. Development of therapeutic siRNAs or antisense oligonucleotides and/or their functional derivatives that provide means for cell-specific or tissue-selective targeting.
  4. Experimental evidence of the substantial transformative potential of nucleic acid therapeutics through the manipulation of gene expression, demonstrated at the tissue or cellular level, and/or in pre-clinical animal models.
  5. Study of toxicological and immune responses to treatments with siRNAs, antisense drugs, or therapeutic nucleic acids, with evaluation of potential toxicity and off-target effects.

Dr. Elena V. Bichenkova
Guest Editor

Manuscript Submission Information

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Keywords

  • nucleic acid therapeutics
  • RNA
  • antisense DNA
  • cellular delivery
  • hybridisation
  • sequence specificity
  • knockdown
  • substrate turnover
  • gene silencing
  • translational arrest

Published Papers (2 papers)

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Research

12 pages, 2551 KiB  
Article
Fork- and Comb-like Lipophilic Structures: Different Chemical Approaches to the Synthesis of Oligonucleotides with Multiple Dodecyl Residues
by Timofey D. Zharkov, Ekaterina M. Mironova, Oleg V. Markov, Sergey A. Zhukov, Svetlana N. Khodyreva and Maxim S. Kupryushkin
Int. J. Mol. Sci. 2023, 24(19), 14637; https://doi.org/10.3390/ijms241914637 - 27 Sep 2023
Cited by 2 | Viewed by 973
Abstract
Lipophilic oligonucleotide conjugates represent a powerful tool for nucleic acid cellular delivery, and many methods for their synthesis have been developed over the past few decades. In the present study, a number of chemical approaches for the synthesis of different fork- and comb-like [...] Read more.
Lipophilic oligonucleotide conjugates represent a powerful tool for nucleic acid cellular delivery, and many methods for their synthesis have been developed over the past few decades. In the present study, a number of chemical approaches for the synthesis of different fork- and comb-like dodecyl-containing oligonucleotide structures were performed, including use of non-nucleotide units and different types of phosphate modifications such as alkyl phosphoramidate, phosphoryl guanidine, and triazinyl phosphoramidate. The influence of the number of introduced lipophilic residues, their mutual arrangement, and the type of formed modification backbone on cell penetration was evaluated. The results obtained indicate great potential in the developed chemical approaches, not only for the synthesis of complex oligonucleotide structures but also for the fine-tuning of their properties. Full article
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19 pages, 1614 KiB  
Article
Cholesterol Stationary Phase in the Separation and Identification of siRNA Impurities by Two-Dimensional Liquid Chromatography-Mass Spectrometry
by Sylwia Studzińska, Feiyang Li, Michał Szumski, Bogusław Buszewski and Michael Lämmerhofer
Int. J. Mol. Sci. 2022, 23(23), 14960; https://doi.org/10.3390/ijms232314960 - 29 Nov 2022
Cited by 6 | Viewed by 1599
Abstract
The aim of this research was to develop a simple and efficient ion-pair reagent-free chromatographic method for the separation and qualitative determination of oligonucleotide impurities, exemplified by synthesis of raw products of the two single strands of patisiran siRNA. The stationary phases with [...] Read more.
The aim of this research was to develop a simple and efficient ion-pair reagent-free chromatographic method for the separation and qualitative determination of oligonucleotide impurities, exemplified by synthesis of raw products of the two single strands of patisiran siRNA. The stationary phases with mixed hydrophobic/hydrophilic properties (cholesterol and alkylamide) were firstly used for this purpose with reversed-phased high-performance liquid chromatography. Several different chromatographic parameters were tested for their impact on impurities separation: type, concentration, pH of salt, as well as organic solvent type in the mobile phase. The pH was the most influential factor on the separation and signal intensities in mass spectrometry detection. Finally, the optimized method included the application of cholesterol stationary phase, with mobile phase containing 20 mM ammonium formate (pH 6.5) and methanol. It allowed good separation and the identification of most impurities within 25 min. Since not all closely related impurities could be fully resolved from the main peak in this oligonucleotide impurity profiling, two-dimensional liquid chromatography was used for peak purity determination of the target oligonucleotides. The Ethylene Bridged Hybrid (BEH) Amide column in hydrophilic interaction liquid chromatography was applied in the second dimension, allowing additional separation of three closely related impurities. Full article
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