Hepatitis C virus (HCV) infection is a serious cause of chronic liver disease worldwide with more than 170 million infected individuals at risk of developing significant morbidity and mortality. Current interferon-based therapies are suboptimal especially in patients infected with HCV genotype 1, and they are poorly tolerated, highlighting the unmet medical need for new therapeutics. The HCV-encoded NS3 protease is essential for viral replication and has long been considered an attractive target for therapeutic intervention in HCV-infected patients. Here we identify a class of specific and potent NS3 protease inhibitors and report the evaluation of BILN 2061, a small molecule inhibitor biologically available through oral ingestion and the first of its class in human trials. Administration of BILN 2061 to patients infected with HCV genotype 1 for 2 days resulted in an impressive reduction of HCV RNA plasma levels, and established proof-of-concept in humans for an HCV NS3 protease inhibitor. Our results further illustrate the potential of the viral-enzyme-targeted drug discovery approach for the development of new HCV therapeutics.

CommunicationsPotent and selective macrocyclic inhibitors of the hepatitis C virus NS3 serine protease based on the conformation of a enzyme-bound substratelike hexapeptide demonstrate many of the desirable properties of a druglike archetype, which could lead to an antiviral agent for the treatment of hepatitis C in man. For more details see the following communication by Tsantrizos et al.

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The interactions of the NS3 protease domain with inhibitors that are based on N-terminal cleavage products of peptide substrates were studied by NMR methods. Transferred nuclear Overhauser effect experiments showed that these inhibitors bind the protease in a well defined, extended conformation. Protease-induced linebroadening studies helped identify the segments of inhibitors which come into contact with the protease. A comparison of the NMR data of the free and proteasebound states suggests that these ligands undergo rigidification upon complexation. This work provides the first structure of an inhibitor when bound to NS3 protease and should be valuable for designing more potent inhibitors. Hepatitis C virus (HCV)1 infection is an important cause of chronic hepatitis, cirrhosis, hepatocellular carcinoma, and liver failure worldwide (1). Approved therapies with proven benefit for patients with chronic hepatitis C include various drug regimens of interferon-␣. These therapies have limited efficacy with a low sustained response rate and frequent side effects (1). Therefore, there is an urgent need for the development of new therapies for the treatment of HCV infections.HCV is a small enveloped virus containing a single-stranded RNA genome of positive polarity, which encodes a unique polyprotein of approximately 3000 amino acids (for reviews see Refs. 2 and 3). This polyprotein is the precursor of four structural and six nonstructural (NS) proteins (4 -10). The structural proteins are proteolytically processed by host signal peptidases, whereas two virally encoded proteases within the NS2 and NS3 regions process the remaining nonstructural proteins.The NS3 serine protease domain (20 kDa), located within the N-terminal portion of the NS3 protein, mediates the proteolysis at the NS3/4A, NS4A/4B, NS4B/5A, and NS5A/5B junctions (6 -11). We and others have recently reported that N-terminal cleavage products of peptide substrates are competitive inhibitors of NS3 protease activity (12, 13), which has served as the basis for designing substrate-based inhibitors (14, 15). To date, there have been no reports in the literature on the structure of substrates or inhibitors when bound to NS3 protease, which would certainly be valuable for inhibitor design efforts. However, x-ray crystal structures have been determined for NS3 protease alone (16) and for NS3 protease in the presence of an NS4A peptide cofactor (17,18). These structures show that NS3 protease adopts a chymotrypsin/trypsin-like fold.In this report we applied NMR methods to study the structure of peptides and inhibitors, based on N-terminal cleavage products of peptide substrates when bound to the NS3 protease domain of HCV. Transferred NOESY experiments were used to determine the conformation of ligands when bound to the protease, and differential line-broadening experiments were used to identify which segments of the ligands contact the protease. EXPERIMENTAL PROCEDURESPurification of NS3 Protease-A modification of a previously published procedure (19) was used ...

From the discovery of competitive hexapeptide inhibitors, potent and selective HCV NS3 protease macrocyclic inhibitors have been identified. Structure-activity relationship studies were performed focusing on optimizing the N-terminal carbamate and the aromatic substituent on the (4R)-hydroxyproline moiety. Inhibitors meeting the potency criteria in the cell-based assay and with improved oral bioavailability in rats were identified. BILN 2061 was selected as the best compound, the first NS3 protease inhibitor reported with antiviral activity in man.