SAR by shape: towards small molecules that target RNA Public Deposited

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  • March 21, 2019
  • Grawoig, David
    • Affiliation: College of Arts and Sciences, Department of Chemistry
  • RNA plays critical roles in diverse biological processes but has proven to be a difficult target for small molecule drug development. I addressed this challenge by developing automated SAR by SHAPE (structure-activity-relationships by selective 2'-hydroxyl acylation analyzed by primer extension), a powerful approach for rapid and generic RNA screening against small molecule libraries. I incorporated three innovations in automated SAR by SHAPE that, together, permit effective small molecule screening campaigns against diverse RNA targets. First, I developed and programmed a magnetic bead-based SHAPE protocol on a liquid handling robot. Second, I created an automated SHAPE analysis pipeline by combining reference-based analysis and novel error-correcting algorithms. Third, I applied single-nucleotide resolution statistical hit detection to identify novel RNA ligands. In a successful proof-of-concept for automated SAR by SHAPE, I screened nearly 500 small molecules against the Hepatitis C Virus Internal Ribosome Entry Site (HCV IRES), a large, highly structured RNA crucial for viral translation and replication. This screen identified more than 80 previously unknown IRES ligands. Significantly, several of these ligands also inhibited IRES-mediated translation in a dual luciferase assay.
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  • In Copyright
  • Weeks, Kevin
  • Doctor of Philosophy
Graduation year
  • 2014

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