Hepatitis C VirusNS3 HSVNS3

Hepatitis C virus (HCV) is the main cause of both sporadic and post-transfusion non-A, non-B hepatitis (Kumar et al., 1997). The viral-encoded non-structural protein 3 (NS3) is a serine protease that has protease, nucleoside triphosphate, and helicase activities and therefore represents a good target for inhibition of HCV. A selection was performed with a library bearing a 120-nucleotide random region and after six rounds of selection, two aptamers were identified that bound to NS3 and inhibited its helicase and protease activities in vitro (Kumar et al., 1997). In order to identify an aptamer with specificity for the NS3 active site, Fukuda et al. (2000) performed a selection to the truncated polypeptide ANS3. Using a RNA library with a 30-nucleotide random region, they performed nine rounds of selection and identified 45 clones that bound to ANS3 (Fukuda et al., 2000).

While the aptamers were divided into three families based on their sequence similarity, they all retained a GA(A/U)UGGGAC conserved region. These aptamers bound to ANS3 with a Kd of 10 nmol/L and inhibited 90% of protease activity of ANS3 and of full-length NS3 fused with maltose-binding protein (MBP-NS3). In vivo, HCV non-structural proteins are processed by NS3 and cofactor NS4A and in order to recapitulate physiologic condition, the effect of the aptamers of NS3 protease activity was tested in the presence of P41 peptide, which enhances MBP-NS3 activity seven-fold. In this simulated physiologic state, the aptamers inhibited 70% of MBP-NS3 protease activity. The same group subsequently characterized the RNA aptamer-binding site of NS3 (Hwang et al., 2000).

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