Hepatitis C virus (HCV) infection is a major health problem that leads
to cirrhosis and hepatocellular carcinoma in a substantial number of
infected individuals, estimated to be 100-200 million worldwide. Unfor
tunately, immunotherapy or other effective treatments fbr HCV infectio
n are not yet available, and interferon administration has limited eff
icacy. Different approaches to HCV therapy are being explored, and the
se include inhibition of the viral proteinase, helicase, and RNA-depen
dent RNA polymerase and development of a vaccine. Here we present the
design of selective inhibitors with nanomolar potencies of HCV NS3 pro
teinase based on eglin c, These eglin c mutants were generated by resh
aping the inhibitor active site-binding loop, and the results emphasiz
e the role played by residues P5-P4' in enzyme recognition. In additio
n, alanine scanning experiments provide evidence that the N terminus o
f eglin c also contributes to NS3 binding. These eglin inhibitors offe
r a unique tool for accurately assessing the requirements for effectiv
e inhibition of the enzymatic activity of NS3 and at the same time can
be considered lead compounds for the identification of other NS3 inhi
bitors in targeted design efforts.