The internal ribosome entry site (IRES) in the 5′ untranslated region (UTR) of the hepatitis C virus (HCV) genome initiates translation of the viral polyprotein precursor. The unique structure and high sequence conservation of the 5′ UTR render the IRES RNA a potential target for the development of selective viral translation inhibitors. Here, we provide an overview of approaches to block HCV IRES function by nucleic acid, peptide and small molecule ligands. Emphasis will be given to the IRES subdomain IIa which currently is the most advanced target for small molecule inhibitors of HCV translation. The subdomain IIa behaves as an RNA conformational switch. Selective ligands act as translation inhibitors by locking the conformation of the RNA switch. We review synthetic procedures for inhibitors as well as structural and functional studies of the subdomain IIa target and its ligand complexes.

Thymidylate synthase (TS) is a key enzyme in the biosynthesis of thymidine. TS inhibitors, which are used in cancer chemotherapy, suffer from resistance development in tumors through upregulation of TS expression. Autoregulatory translation control has been implicated with TS overexpression. TS binding at its own mRNA, which leads to sequestration of the start codon, is abolished when the enzyme forms an inhibitor complex, thereby relieving translation suppression. We have used the protein binding site from the TS mRNA in the context of a bicistronic expression system to validate targeting the regulatory motif with stabilizing ligands that prevent ribosomal initiation. Stabilization of the RNA by mutations, which were studied as surrogates of ligand binding, suppresses translation of the TS protein. Compounds that stabilize the TS binding RNA motif and thereby inhibit ribosomal initiation might be used in combination with existing TS enzyme-targeting drugs to overcome resistance development during chemotherapy.

In this laboratory experiment, students were exposed to a real-world approach to science through learning about and simulating the processes by which drugs are designed and discovered. The students first synthesized oil of wintergreen from aspirin and analyzed the physical properties of both the starting material (aspirin) and product (oil of wintergreen) to validate that their reaction was successful. Second, unique to this lab experiment, students further scrutinized the synthesis by performing a biological assay investigating the antibacterial properties of their samples. Through the use of these analyses, students were able to play the roles of chemists, biologists, and team members involved in the drug-discovery pipeline. The results revealed to the students that small changes in molecular structure caused significant changes in medicinal activity. Through data analysis, discussion, and problem sets, students evaluated various steps of the experiment as they simulated the drug-discovery process.