This study focuses on the structure-guided design and synthesis of small molecules that target hepatitis C virus internal ribosome entry site subdomain IIa RNA - a structural element that plays a key role in the viral protein translation initiation process. A series of aryl- substituted benzimidazole molecules was designed using guidance from a shape-similarity screening that utilized the structure of a known subdomain IIa RNA-binding benzimidazole translation inhibitor as the query molecule. The syntheses of the designed aryl-substituted benzimidazole molecules were described. Their binding affinities towards the target RNA were assessed by a FRET assay. The structure-binding relationship of these molecules was analyzed. The second part of the study explores the design and synthetic development of 2- aminoquinazolin-4-one and 2-amino-lin-benzoguanine molecules, whose design were guided by the ligand-bound subdomain IIa RNA crystal structur
