It has been estimated that at least 1 percent of the world's population is chronically infected with hepatitis C virus (HCV). Infection by this virus can cause acute or chronic hepatitis, as well as liver cirrhosis which can lead to hepatocellular carcinoma. Only 50 percent of HCV infected patients respond to alpha-interferon and fewer than 25 percent of treated patients will have long term remission. In addition, the lack of protective immunity after HCV infection has impaired the development of effective antiviral therapies and vaccines. Although there is genetic diversity among different HCV isolates, there is a significant restriction on the sequence diversity within the 5' noncoding regions (5'NCR) of these RNA genomes. This conservation can be attributed to the presence of RNA elements that are involved in viral genome replication and translation. Distinct structural elements in the viral 5' NCR, especially a pseudoknot structure located near the start site AUG codon, are required to permit the translation of the viral genome by an unusual mechanism of internal ribosome entry which is used by all picornaviral and certain cellular mRNAs. However, the internal ribosome entry site (IRES) in HCV has functional features that are different from those of any other known IRES element or 5'NCR. All eukaryotic mRNAs studied to date recruit 43S ribosomal subunits, 40S ribosomal subunits that carry factors eIF3 and eIF2-tRNAinit. In contrast, the HCV IRES can bind """"""""empty"""""""" 40S subunits directly at the translational initiation start codon, very much like prokaryotic mRNAs which are known to recruit 30S subunits directly. Thus, the HCV IRES is an ideal target for the design of antiviral therapeutics, because such therapeutics may not affect other cellular functions. Molecular genetic approaches are proposed to select and to characterize conformationally constrained peptides, expressed from combinatorial libraries, that selectively inhibit the HCV IRES in living cells. Furthermore, three-dimensional structures of domains of the HCV IRES RNA, including the pseudoknot structure, will be determined by NMR. The use of a combination of molecular, biochemical and structural approachers to study the HCV IRES, will greatly assist in more rational design of antiviral reagents.
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