K. Fukuda et al., Isolation and characterization of RNA aptamers specific for the hepatitis C virus nonstructural protein 3 protease, EUR J BIOCH, 267(12), 2000, pp. 3685-3694
Nonstructural protein 3 (NS3) from hepatitis C virus (HCV) is a serine prot
ease that provides an essential function in maturation of the virus by clea
ving the nonstructural regions of the viral polyprotein. The goal of this w
ork was to isolate RNA aptamers that bind specifically to the NS3 protease
active site in the truncated polypeptide Delta NS3. RNA aptamers were selec
ted in vitro by systematic evolution of ligands by exponential enrichment (
SELEX). The RNA pool for SELEX had a 30-nucleotide randomized core region.
After nine selection cycles, a pool of Delta NS3-specific RNA aptamers were
obtained. This RNA pool included 45 clones that divided into three main cl
asses (G9-I, II and III). These classes include the conserved sequence GA(A
/U)UGGGAC. These aptamers bind to Delta NS3 with a binding constant of abou
t 10 nM and inhibit approximately 90% of the protease activity of Delta NS3
and MBP-NS3 (full-length of NS3 fused with maltose binding protein). In ad
dition, these aptamers inhibited approximately 70% of the MBP-NS3 protease
activity in the presence of the NS4A peptide P41. G9-I aptamer appeared to
be a noncompetitive inhibitor for Delta NS3 with a K-i approximate to 100 n
M in the presence of P41. These results suggest that the pool of selected a
ptamers have potential as anti-HCV compounds. Mutational analysis of the G9
-I aptamer demonstrated that the sequences required for protease inhibition
are in stem I, stem III and loop III of the aptamer. These regions include
the conserved sequence GA(A/U)UGGGAC.