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. Author manuscript; available in PMC: 2015 Jul 15.
Published in final edited form as: Bioorg Med Chem Lett. 2014 May 14;24(14):3113–3117. doi: 10.1016/j.bmcl.2014.05.009

Figure 1.

Figure 1

Ligand design for the internal ribosome entry site (IRES) target of hepatitis C virus (HCV). A) The IRES element comprises the first 342 nucleotides in the 5′ untranslated region (UTR) of the HCV RNA genome. The boxed region highlights the subdomain IIa target whose secondary structure is shown in on the right. B) Structures of a 2-aminobenzimidazole translation inhibitor 1 which was previously co-crystallized in complex with the subdomain IIa RNA, and aryl-substituted 2-aminobenzimidazoles 2 which were designed using guidance by the co-crystal structure of the IIa RNA in complex with 1. C) Model of the 1-phenyl-2-aminobenzimidazole core of 2 (light blue) docked at the binding site of 1 (yellow) in the subdomain IIa RNA co-crystal structure.17 Hydrogen bonds and nucleotides participating in intramolecular contacts are indicated.