Compounds and methods for inhibiting hepatitis C virus replication

Abstract

The inventors have discovered that an ATPase-deficient dominant-negative mutant NS3 protein of hepatitis C virus inhibits activity of the wild-type NS3 protein and inhibits replication of hepatitis C virus (HCV). The solved crystal structure of a multi-enzyme NS3 complex on a DNA substrate is also provided. The inventors have tested a peptide matching the sequence of a portion of NS3 that interacts with another NS3 molecule for inhibiting HCV replication. The peptide inhibits HCV replication. Accordingly, the invention provides a method of inhibiting HCV replication in cells infected with HCV involving transforming the cells with a vector expressing a dominant-negative mutant NS3 gene. The invention also provides a method of inhibiting HCV replication in cells infected with HCV involving administering to the cells a dominant-negative mutant NS3 protein. The invention also provides peptides and agents that inhibit HCV replication and methods of identifying agents that inhibit HCV replication.

1 - 9 . (canceled) 
     
     
         10 . A compound of molecular weight 10,000 or less,
 wherein the compound interacts with NS3 to inhibit NS3 oligomerization and wherein the compound inhibits hepatitis C virus (HCV) replication.   
     
     
         11 . The compound of  claim 10  wherein the compound comprises an inhibitory peptide comprising 4 or more contiguous residues of SEQ ID NO:1. 
     
     
         12 . The compound of  claim 11  wherein the inhibitory peptide comprises 6 or more contiguous residues of SEQ ID NO:1. 
     
     
         13 . The compound of  claim 12  wherein the inhibitory peptide comprises 8 or more contiguous residues of SEQ ID NO:1. 
     
     
         14 . The compound of  claim 13  wherein the inhibitory peptide comprises SEQ ID NO:1. 
     
     
         15 . The compound of  claim 14  wherein the inhibitory peptide comprises SEQ ID NO:2. 
     
     
         16 . The compound of  claim 11  wherein the compound further comprises a cell-entry vehicle coupled to the inhibitor peptide. 
     
     
         17 . The compound of  claim 10  wherein the structure of the compound fits a molecular interface of NS3 such that a free energy calculation predicts the compound is expected to bind to the molecular interface of NS3. 
     
     
         18 . The compound of  claim 10  wherein the surface of NS3 which the compound fits includes at least one amino acid residue selected from residues 541-553, 584-591, 435-453, 477-488, and 524-536 of SEQ ID NO:3. 
     
     
         19 - 31 . (canceled) 
     
     
         32 . The compound of  claim 10  wherein the compound comprises an inhibitory peptide comprising at least 4 contiguous residues of reverse D sequence of SEQ ID NO:1.