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RNA as a target for small-molecule therapeutics

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Pages 49-62 | Published online: 22 Apr 2005

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Efrat Kligun & Yael Mandel-Gutfreund. (2013) Conformational readout of RNA by small ligands. RNA Biology 10:6, pages 981-989.
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Li-Zhen Sun, Yangwei Jiang, Yuanzhe Zhou & Shi-Jie Chen. (2020) RLDOCK: A New Method for Predicting RNA–Ligand Interactions. Journal of Chemical Theory and Computation 16:11, pages 7173-7183.
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Klara Aradi, Audrey Di Giorgio & Maria Duca. (2020) Aminoglycoside Conjugation for RNA Targeting: Antimicrobials and Beyond. Chemistry – A European Journal 26:54, pages 12273-12309.
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Víctor Díaz-García & Gerardo Retamal-Morales. 2020. Antibiotic Materials in Healthcare. Antibiotic Materials in Healthcare 231 247 .
Amanda L Garner. (2019) RNA-targeted drug discovery: moving beyond promiscuous small-molecule scaffolds. Future Medicinal Chemistry 11:19, pages 2487-2490.
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Roya Pournejati, Ronald Gust & Hamid Reza Karbalaei-Heidari. (2019) An Aminoglycoside Antibacterial Substance, S-137-R, Produced by Newly Isolated Bacillus velezensis Strain RP137 from the Persian Gulf. Current Microbiology 76:9, pages 1028-1037.
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Christopher S. Eubanks & Amanda E. Hargrove. (2018) RNA Structural Differentiation: Opportunities with Pattern Recognition. Biochemistry 58:4, pages 199-213.
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Anita Donlic & Amanda E. Hargrove. (2018) Targeting RNA in mammalian systems with small molecules. WIREs RNA 9:4.
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Christopher S. Eubanks, Jordan E. Forte, Gary J. Kapral & Amanda E. Hargrove. (2016) Small Molecule-Based Pattern Recognition To Classify RNA Structure. Journal of the American Chemical Society 139:1, pages 409-416.
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David W. Crawford, Brett D. Blakeley, Po-Han Chen, Chringma Sherpa, Stuart F.J. Le Grice, Ite A. Laird-Offringa & Brian R. McNaughton. (2016) An Evolved RNA Recognition Motif That Suppresses HIV-1 Tat/TAR-Dependent Transcription. ACS Chemical Biology 11:8, pages 2206-2215.
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Brett D. Blakeley & Brian R. McNaughton. (2014) Synthetic RNA Recognition Motifs That Selectively Recognize HIV-1 Trans-Activation Response Element Hairpin RNA. ACS Chemical Biology 9:6, pages 1320-1329.
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Déborah Perez-Fernandez, Dmitri Shcherbakov, Tanja Matt, Ng Chyan Leong, Iwona Kudyba, Stefan Duscha, Heithem Boukari, Rashmi Patak, Srinivas Reddy Dubbaka, Kathrin Lang, Martin Meyer, Rashid Akbergenov, Pietro Freihofer, Swapna Vaddi, Pia Thommes, V. Ramakrishnan, Andrea Vasella & Erik C. Böttger. (2014) 4′-O-substitutions determine selectivity of aminoglycoside antibiotics. Nature Communications 5:1.
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Maroti G. Pawar, Ashok Nuthanakanti & Seergazhi G. Srivatsan. (2013) Heavy Atom Containing Fluorescent Ribonucleoside Analog Probe for the Fluorescence Detection of RNA-Ligand Binding. Bioconjugate Chemistry 24:8, pages 1367-1377.
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Trang N. Do, Paolo Carloni, Gabriele Varani & Giovanni Bussi. (2013) RNA/Peptide Binding Driven by Electrostatics—Insight from Bidirectional Pulling Simulations. Journal of Chemical Theory and Computation 9:3, pages 1720-1730.
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Ludmila Frolov, Andrew Dix, Yitzhak Tor, Alexander B. Tesler, Yulia Chaikin, Alexander Vaskevich & Israel Rubinstein. (2013) Direct Observation of Aminoglycoside–RNA Binding by Localized Surface Plasmon Resonance Spectroscopy. Analytical Chemistry 85:4, pages 2200-2207.
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Richard J. Fair, Mary E. Hensler, Wdee Thienphrapa, Quang N. Dam, Victor Nizet & Yitzhak Tor. (2012) Selectively Guanidinylated Aminoglycosides as Antibiotics. ChemMedChem 7:7, pages 1237-1244.
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Trang N. Do, Emiliano Ippoliti, Paolo Carloni, Gabriele Varani & Michele Parrinello. (2012) Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. Journal of Chemical Theory and Computation 8:2, pages 688-694.
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Katherine E. Deigan & Adrian R. FerrÉ-D’AmarÉ. (2011) Riboswitches: Discovery of Drugs That Target Bacterial Gene-Regulatory RNAs. Accounts of Chemical Research 44:12, pages 1329-1338.
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Lisa S. McCoy, Yun Xie & Yitzhak Tor. (2011) Antibiotics that target protein synthesis. Wiley Interdisciplinary Reviews: RNA 2:2, pages 209-232.
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Oriana Tabarrini, Serena Massari & Violetta Cecchetti. (2010) 6-desfluoroquinolones as HIV-1 Tat-mediated transcription inhibitors. Future Medicinal Chemistry 2:7, pages 1161-1180.
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Yun Xie, Victor K. Tam & Yitzhak Tor. 2010. The Chemical Biology of Nucleic Acids. The Chemical Biology of Nucleic Acids 115 140 .
Yun Xie, Andrew V. Dix & Yitzhak Tor. (2009) FRET Enabled Real Time Detection of RNA-Small Molecule Binding. Journal of the American Chemical Society 131:48, pages 17605-17614.
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Alexander Serganov & Dinshaw J. Patel. (2009) Amino acid recognition and gene regulation by riboswitches. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1789:9-10, pages 592-611.
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Alethia A. Hostetter, Erich G. Chapman & Victoria J. DeRose. (2009) Rapid Cross-Linking of an RNA Internal Loop by the Anticancer Drug Cisplatin. Journal of the American Chemical Society 131:26, pages 9250-9257.
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Seergazhi G. Srivatsan & Yitzhak Tor. (2009) Enzymatic Incorporation of Emissive Pyrimidine Ribonucleotides. Chemistry - An Asian Journal 4:3, pages 419-427.
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Yitzhak Tor. (2009) Exploring RNA-ligand interactions. Pure and Applied Chemistry 81:2, pages 263-272.
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Matthew J. Belousoff, Bim Graham, Leone Spiccia & Yitzhak Tor. (2009) Cleavage of RNA oligonucleotides by aminoglycosides. Org. Biomol. Chem. 7:1, pages 30-33.
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Steven A. Kawamoto, Christopher G. Sudhahar, Cynthia L. Hatfield, Jing Sun, Edward J. Behrman & Venkat Gopalan. (2008) Studies on the mechanism of inhibition of bacterial ribonuclease P by aminoglycoside derivatives. Nucleic Acids Research 36:2, pages 697-704.
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Mariana Hainrichson, Igor Nudelman & Timor Baasov. (2008) Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases. Org. Biomol. Chem. 6:2, pages 227-239.
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Patrick Pfeffer & Holger Gohlke. (2007) DrugScore RNA Knowledge-Based Scoring Function To Predict RNA−Ligand Interactions . Journal of Chemical Information and Modeling 47:5, pages 1868-1876.
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Victor K. Tam, Denise Kwong & Yitzhak Tor. (2007) Fluorescent HIV-1 Dimerization Initiation Site:  Design, Properties, and Use for Ligand Discovery. Journal of the American Chemical Society 129:11, pages 3257-3266.
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Seergazhi G. Srivatsan & Yitzhak Tor. (2007) Fluorescent Pyrimidine Ribonucleotide:  Synthesis, Enzymatic Incorporation, and Utilization. Journal of the American Chemical Society 129:7, pages 2044-2053.
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Kenneth F Blount & Ronald R Breaker. (2006) Riboswitches as antibacterial drug targets. Nature Biotechnology 24:12, pages 1558-1564.
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Kenneth F. Blount & Yitzhak Tor. (2006) A Tale of Two Targets: Differential RNA Selectivity of Nucleobase-Aminoglycoside Conjugates. ChemBioChem 7:10, pages 1612-1621.
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Yuefen Zhou, Zhongxiang Sun, Jamie M. Froelich, Thomas Hermann & Daniel Wall. (2006) Structure–activity relationships of novel antibacterial translation inhibitors: 3,5-Diamino-piperidinyl triazines. Bioorganic & Medicinal Chemistry Letters 16:20, pages 5451-5456.
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Yuefen Zhou, Vlad E. Gregor, Zhongxiang Sun, Benjamin K. Ayida, Geoffrey C. Winters, Douglas Murphy, Klaus B. Simonsen, Dionisios Vourloumis, Sarah Fish, Jamie M. Froelich, Daniel Wall & Thomas Hermann. (2005) Structure-Guided Discovery of Novel Aminoglycoside Mimetics as Antibacterial Translation Inhibitors. Antimicrobial Agents and Chemotherapy 49:12, pages 4942-4949.
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Thomas Hermann. (2005) Drugs targeting the ribosome. Current Opinion in Structural Biology 15:3, pages 355-366.
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Qing Han, Qiang Zhao, Sarah Fish, Klaus B. Simonsen, Dionisios Vourloumis, Jamie M. Froelich, Daniel Wall & Thomas Hermann. (2005) Molecular Recognition by Glycoside Pseudo Base Pairs and Triples in an Apramycin–RNA Complex. Angewandte Chemie International Edition 44:18, pages 2694-2700.
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Qing Han, Qiang Zhao, Sarah Fish, Klaus B. Simonsen, Dionisios Vourloumis, Jamie M. Froelich, Daniel Wall & Thomas Hermann. (2005) Molecular Recognition by Glycoside Pseudo Base Pairs and Triples in an Apramycin–RNA Complex. Angewandte Chemie 117:18, pages 2754-2760.
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