Relevant bibliographies by topics / RNA-Targeted small molecules

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'RNA-Targeted small molecules'

Author: Grafiati
Published: 20 July 2024
Last updated: 31 July 2025

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Journal articles on the topic "RNA-Targeted small molecules"

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Chen, Shi-Jie, and Yuanzhe Zhou. "Harnessing Computational Approaches for RNA-Targeted Drug Discovery." RNA NanoMed 1, no. 1 (2024): 1–15. https://doi.org/10.59566/isrnn.2024.0101001.

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RNA molecules have emerged as promising therapeutic targets due to their diverse functional and regulatory roles within cells. Computational modeling in RNA-targeted drug discovery presents a significant opportunity to expedite the discovery of novel small molecule compounds. However, this field encounters unique challenges compared to protein-targeted drug design, primarily due to limited experimental data availability and current models’ inability to adequately address RNA’s conformational flexibility during ligand recognition. Despite these challenges, several studies have successfully iden
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Xu, Ling, Kevin Chung, Tianshuo Liu, and Anna Marie Pyle. "Structural insights into RNA targeting with de novo small molecule." Structural Dynamics 12, no. 2_Supplement (2025): A41. https://doi.org/10.1063/4.0000350.

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Targeting RNA with small molecules has emerged as a promising approach in drug development, offering the potential to expand the druggable genome and enable pharmacological targeting of non-coding genes or difficult-to-target gene products. However, the identification of functionally active RNA binders faces low hit rates in routine chemical space exploration and lacks robust high-throughput screening assays. The visualization of atomic details of RNA-small molecule interactions also poses a challenge due to the dynamic nature of RNA molecules. To address these challenges, we targeted a struct
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Costales, Matthew G., Haruo Aikawa, Yue Li, et al. "Small-molecule targeted recruitment of a nuclease to cleave an oncogenic RNA in a mouse model of metastatic cancer." Proceedings of the National Academy of Sciences 117, no. 5 (2020): 2406–11. http://dx.doi.org/10.1073/pnas.1914286117.

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As the area of small molecules interacting with RNA advances, general routes to provide bioactive compounds are needed as ligands can bind RNA avidly to sites that will not affect function. Small-molecule targeted RNA degradation will thus provide a general route to affect RNA biology. A non–oligonucleotide-containing compound was designed from sequence to target the precursor to oncogenic microRNA-21 (pre–miR-21) for enzymatic destruction with selectivity that can exceed that for protein-targeted medicines. The compound specifically binds the target and contains a heterocycle that recruits an
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Nagano, Konami, Takashi Kamimura, and Gota Kawai. "Interaction between a fluoroquinolone derivative and RNAs with a single bulge." Journal of Biochemistry 171, no. 2 (2021): 239–44. http://dx.doi.org/10.1093/jb/mvab124.

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Abstract Interaction analysis between small molecules and RNA as well as structure determination of RNA–small molecule complexes will be the clues to search for compounds that bind to specific mRNA or non-coding RNA in drug discovery. In this study, the RNA-binding ability of a fluoroquinolone derivative, KG022, was examined against single-residue bulge-containing hairpin RNAs as RNA models. Nuclear magnetic resonance analysis indicated that KG022 interacts with the RNAs in the vicinity of the bulge residue, with preferring C and G as the bulge residues. The solution structures of the RNA–KG02
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Sun, Saisai, Jianyi Yang, and Zhaolei Zhang. "RNALigands: a database and web server for RNA–ligand interactions." RNA 28, no. 2 (2021): 115–22. http://dx.doi.org/10.1261/rna.078889.121.

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RNA molecules can fold into complex and stable 3D structures, allowing them to carry out important genetic, structural, and regulatory roles inside the cell. These complex structures often contain 3D pockets made up of secondary structural motifs that can be potentially targeted by small molecule ligands. Indeed, many RNA structures in PDB contain bound small molecules, and high-throughput experimental studies have generated a large number of interacting RNA and ligand pairs. There is considerable interest in developing small molecule lead compounds targeting viral RNAs or those RNAs implicate
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Tadesse, Kisanet, and Raphael I. Benhamou. "Targeting MicroRNAs with Small Molecules." Non-Coding RNA 10, no. 2 (2024): 17. http://dx.doi.org/10.3390/ncrna10020017.

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MicroRNAs (miRs) have been implicated in numerous diseases, presenting an attractive target for the development of novel therapeutics. The various regulatory roles of miRs in cellular processes underscore the need for precise strategies. Recent advances in RNA research offer hope by enabling the identification of small molecules capable of selectively targeting specific disease-associated miRs. This understanding paves the way for developing small molecules that can modulate the activity of disease-associated miRs. Herein, we discuss the progress made in the field of drug discovery processes,
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Angelbello, Alicia J., Suzanne G. Rzuczek, Kendra K. Mckee, et al. "Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model." Proceedings of the National Academy of Sciences 116, no. 16 (2019): 7799–804. http://dx.doi.org/10.1073/pnas.1901484116.

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Myotonic dystrophy type 1 (DM1) is an incurable neuromuscular disorder caused by an expanded CTG repeat that is transcribed into r(CUG)exp. The RNA repeat expansion sequesters regulatory proteins such as Muscleblind-like protein 1 (MBNL1), which causes pre-mRNA splicing defects. The disease-causing r(CUG)exp has been targeted by antisense oligonucleotides, CRISPR-based approaches, and RNA-targeting small molecules. Herein, we describe a designer small molecule, Cugamycin, that recognizes the structure of r(CUG)exp and cleaves it in both DM1 patient-derived myotubes and a DM1 mouse model, leavi
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Wu, Liping, Jing Pan, Vala Thoroddsen, et al. "Novel Small-Molecule Inhibitors of RNA Polymerase III." Eukaryotic Cell 2, no. 2 (2003): 256–64. http://dx.doi.org/10.1128/ec.2.2.256-264.2003.

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ABSTRACT A genetic approach utilizing the yeast Saccharomyces cerevisiae was used to identify the target of antifungal compounds. This analysis led to the identification of small molecule inhibitors of RNA polymerase (Pol) III from Saccharomyces cerevisiae. Three lines of evidence show that UK-118005 inhibits cell growth by targeting RNA Pol III in yeast. First, a dominant mutation in the g domain of Rpo31p, the largest subunit of RNA Pol III, confers resistance to the compound. Second, UK-118005 rapidly inhibits tRNA synthesis in wild-type cells but not in UK-118005 resistant mutants. Third,
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Alagia, Adele, Jana Tereňová, Ruth F. Ketley, Arianna Di Fazio, Irina Chelysheva, and Monika Gullerova. "Small vault RNA1-2 modulates expression of cell membrane proteins through nascent RNA silencing." Life Science Alliance 6, no. 6 (2023): e202302054. http://dx.doi.org/10.26508/lsa.202302054.

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Gene expression can be regulated by transcriptional or post-transcriptional gene silencing. Recently, we described nuclear nascent RNA silencing that is mediated by Dicer-dependent tRNA-derived small RNA molecules. In addition to tRNA, RNA polymerase III also transcribes vault RNA, a component of the ribonucleoprotein complex vault. Here, we show that Dicer-dependent small vault RNA1-2 (svtRNA1-2) associates with Argonaute 2 (Ago2). Although endogenous vtRNA1-2 is present mostly in the cytoplasm, svtRNA1-2 localises predominantly in the nucleus. Furthermore, in Ago2 and Dicer knockdown cells,
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Francois-Moutal, Liberty, David Donald Scott, and May Khanna. "Direct targeting of TDP-43, from small molecules to biologics: the therapeutic landscape." RSC Chemical Biology 2, no. 4 (2021): 1158–66. http://dx.doi.org/10.1039/d1cb00110h.

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Given the therapeutic interest of targeting TDP-43, this review focuses on the current landscape of strategies, ranging from biologics to small molecules, that directly target TDP-43. Regions targeted are shown on the 3D structure of RNA-bound TDP-43.
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Dissertations / Theses on the topic "RNA-Targeted small molecules"

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Panei, Francesco Paolo. "Advanced computational techniques to aid the rational design of small molecules targeting RNA." Electronic Thesis or Diss., Sorbonne université, 2024. http://www.theses.fr/2024SORUS106.

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Les molécules d'ARN sont devenues des cibles thérapeutiques majeures, et le ciblage par petites molécules se révèle particulièrement prometteur. Cependant, malgré leur potentiel, le domaine est encore en développement, avec un nombre limité de médicaments spécifiquement conçus pour l'ARN. La flexibilité intrinsèque de l'ARN, bien qu'elle constitue un obstacle, introduit des opportunités thérapeutiques que les outils computationnels actuels ne parviennent pas pleinement à exploiter malgré leur prédisposition. Le projet de cette thèse est de construire un cadre computationnel plus complet pour l
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Chung, Janet. "Investigation of small molecule - SL1 RNA interactions and implications in drug design targeted at HIV-1 genomic dimer maturation." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3390040.

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Books on the topic "RNA-Targeted small molecules"

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Slabý, Ondřej. MicroRNAs in solid cancer: From biomarkers to therapeutic targets. Nova Science, 2011.

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Book chapters on the topic "RNA-Targeted small molecules"

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Fladung, Matthias, Hely Häggman, and Suvi Sutela. "Application of RNAi technology in forest trees." In RNAi for plant improvement and protection. CABI, 2021. http://dx.doi.org/10.1079/9781789248890.0007.

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Abstract A diverse set of small RNAs is involved in the regulation of genome organization and gene expression in plants. These regulatory sRNAs play a central role for RNA in evolution and ontogeny in complex organisms, including forest tree species, providers of indispensable ecosystem services. RNA interference is a process that inhibits gene expression by double-stranded RNA and thus causes the degradation of target messenger RNA molecules. Targeted gene silencing by RNAi has been utilized in various crop plants in order to enhance their characteristics. For forest tree species, most of the
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Fladung, Matthias, Hely Häggman, and Suvi Sutela. "Application of RNAi technology in forest trees." In RNAi for plant improvement and protection. CABI, 2021. http://dx.doi.org/10.1079/9781789248890.0054.

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Abstract A diverse set of small RNAs is involved in the regulation of genome organization and gene expression in plants. These regulatory sRNAs play a central role for RNA in evolution and ontogeny in complex organisms, including forest tree species, providers of indispensable ecosystem services. RNA interference is a process that inhibits gene expression by double-stranded RNA and thus causes the degradation of target messenger RNA molecules. Targeted gene silencing by RNAi has been utilized in various crop plants in order to enhance their characteristics. For forest tree species, most of the
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Ursu, Andrei, Matthew G. Costales, Jessica L. Childs-Disney, and Matthew D. Disney. "Chapter 15. Small-molecule Targeted Degradation of RNA." In Protein Degradation with New Chemical Modalities. Royal Society of Chemistry, 2020. http://dx.doi.org/10.1039/9781839160691-00317.

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Damski, Caio, and Kevin V. Morris. "Targeted Small Noncoding RNA-Directed Gene Activation in Human Cells." In Methods in Molecular Biology. Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0931-5_1.

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Wilson, W. David, and Ananya Paul. "Reversible Small Molecule–Nucleic Acid Interactions." In Nucleic Acids in Chemistry and Biology. The Royal Society of Chemistry, 2022. http://dx.doi.org/10.1039/9781837671328-00477.

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Historically, small molecules have targeted double helical DNA through intercalation and minor groove complexes. Initially, small molecules to target RNA were focused on RNAs involved in protein biosynthesis. Now, many more compounds to target diverse RNA structures have been designed or discovered. This coincides with the exciting discovery that, while only a small amount of the genome is transcribed into RNA for protein synthesis, much of the genome is used to synthesize a variety of non-coding RNAs (ncRNAs). These have important cell functions, including the involvement of ncRNAs in disease
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Oktay, Yavuz. "Metabolomiks ve Uygulamaları." In Moleküler Biyoloji ve Genetik. Türkiye Bilimler Akademisi, 2023. http://dx.doi.org/10.53478/tuba.978-625-8352-48-1.ch12.

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Small molecules that enter chemical reactions as a substrate inside or outside the cell, or that emerge as a result of the reactions are known as metabolites. So far, only a fraction of the existing metabolites, numbering in the millions, have yet been identified, and even a smaller portion have been measured. Two main technologies are commonly used for metabolite analysis: analytes, which are usually separated by liquid or gas chromatography, are examined with the aid of either mass spectrometry or nuclear magnetic resonance. With the understanding that metabolites play roles in gene regulati
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Hampson, Ian, Gavin Batman, and Thomas Walker. "RNA interference technology." In Tools and Techniques in Biomolecular Science. Oxford University Press, 2013. http://dx.doi.org/10.1093/hesc/9780199695560.003.0006.

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This chapter explains the RNA interference (RNAi) machinery that regulates post-transcriptional gene silencing. The RNAi technology is considered a vital tool in basic molecular and cellular genetic research, functional genomics, gene expression profiling, drug discovery, prospective disease targeting, and therapies. The chapter describes how the two main classes of small regulatory RNAs-short interfering RNA (siRNA) and microRNA (miRNA)-are generated and how they silence gene expression. It gives an overview of the RNAi pathway and looks at the two main approaches currently used to silence ge
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Iqbal, Nashra, Priyanka Vishwakarma, and Vidya Meenakshi. "NEXT GENERATION SEQUENCING FOR CANCER DIAGNOSIS." In Futuristic Trends in Biotechnology Volume 3 Book 21. Iterative International Publishers, Selfypage Developers Pvt Ltd, 2024. http://dx.doi.org/10.58532/v3bkbt21p1ch11.

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The development of sequencing of the next generation (NGS) technology has facilitated the study of cancer. Massive parallel sequencing made possible by NGS provides for the most thorough genomic analysis of tumors. Different NGS methods focus on DNA and RNA analysis. Genome on the whole part, whole-exome, and targeted DNA sequencing are several classes of sequencing that concentrate on a subdivision of genetic factors that may be related to a certain condition. Alternative gene-spliced transcripts, small and long non-coding RNAs, mutations/single-nucleotide polymorphisms, post-transcriptional
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Scarpino, Stefania, and Umberto Malapelle. "Liquid Biopsy: A New Diagnostic Strategy and Not Only for Lung Cancer?" In Histopathology and Liquid Biopsy [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.94838.

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Targeted molecular therapies have significantly improved the therapeutic management of advanced lung cancer. The possibility of detecting lung cancer at an early stage is surely an important event in order to improve patient survival. Liquid biopsy has recently demonstrated its clinical utility in advanced non-small cell lung cancer (NSCLC) as a possible alternative to tissue biopsy for non-invasive evaluation of specific genomic alterations, thus providing prognostic and predictive information when the tissue is difficult to find or the material is not sufficient for the numerous investigatio
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Conference papers on the topic "RNA-Targeted small molecules"

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Kahen, Elliot J., Darcy Welch, Jamie Teer, et al. "Abstract 3010: Osteosarcoma cell lines display both shared and unique vulnerabilities to 140 targeted small molecules with RNA-seq revealing putative mechanisms." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-3010.

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Kahen, Elliot J., Darcy Welch, Jamie Teer, et al. "Abstract 3010: Osteosarcoma cell lines display both shared and unique vulnerabilities to 140 targeted small molecules with RNA-seq revealing putative mechanisms." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-3010.

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