The virally encoded
serine protease NS3/NS4A is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing
chronic hepatitis,
cirrhosis of the liver, and
hepatocellular carcinoma. Until very recently, the design of inhibitors for the HCV NS3
protease was limited to large
peptidomimetic compounds with poor pharmacokinetic properties, making
drug discovery an extremely challenging endeavor. In our quest for the discovery of a small-molecule lead that could block replication of the hepatitis C virus by binding to the HCV NS3
protease, the critical
protein-
polypeptide interactions between the virally encoded NS3
serine protease and its
polyprotein substrate were investigated. Lead optimization of a substrate-based hexapeptide, guided by structural data, led to the understanding of the molecular dynamics and electronic effects that modulate the affinity of
peptidomimetic ligands for the active site of this
enzyme. Macrocyclic beta-strand scaffolds were designed that allowed the discovery of potent, highly selective, and orally bioavailable compounds. These molecules were the first HCV NS3
protease inhibitors reported that inhibit replication of HCV
subgenomic RNA in a cell-based replicon assay at low nanomolar concentrations. Optimization of their
biopharmaceutical properties led to the discovery of the clinical candidate
BILN 2061.
Oral administration of
BILN 2061 to patients infected with the
hepatitis C genotype 1 virus resulted in an impressive reduction of
viral RNA levels, establishing proof-of-concept for HCV NS3
protease inhibitors as therapeutic agents in humans.