Crystal structures of the RNA-dependent RNA polymerase genotype 2a of hepatitis C virus (HCV) from two crystal forms have been determined. Similar to the three-dimensional structures of HCV polymerase genotype 1b and other known polymerases, the structures of the HCV polymerase genotype 2a in both crystal forms can be depicted in the classical right-hand arrangement with fingers, palm, and thumb domains. The main structural differences between the molecules in the two crystal forms lie at the interface of the fingers and thumb domains. The relative orientation of the thumb domain with respect to the fingers and palm domains and the ␤-flap region is altered. Structural analysis reveals that the NS5B polymerase in crystal form I adopts a "closed" conformation that is believed to be the active form, whereas NS5B in crystal form II adopts an "open" conformation and is thus in the inactive form. In addition, we have determined the structures of two NS5B polymerase/non-nucleoside inhibitor complexes. Both inhibitors bind at a common binding site, which is nearly 35 Å away from the polymerase active site and is located in the thumb domain. The binding pocket is predominantly hydrophobic in nature, and the enzyme inhibitor complexes are stabilized by hydrogen bonding and van der Waals interactions. Inhibitors can only be soaked in crystal form I and not in form II; examination of the enzyme-inhibitor complex reveals that the enzyme has undergone a dramatic conformational change from the form I (active) complex to the form II (inactive).

X-ray crystal structures of two non-nucleoside analogue inhibitors bound to hepatitis C virus NS5B RNAdependent RNA polymerase have been determined to 2.0 and 2.9 Å resolution. These noncompetitive inhibitors bind to the same site on the protein, ϳ35 Å from the active site. The common features of binding include a large hydrophobic region and two hydrogen bonds between both oxygen atoms of a carboxylate group on the inhibitor and two main chain amide nitrogen atoms of Ser 476 and Tyr 477 on NS5B. The inhibitor-binding site lies at the base of the thumb domain, near its interface with the C-terminal extension of NS5B. The location of this inhibitor-binding site suggests that the binding of these inhibitors interferes with a conformational change essential for the activity of the polymerase. Hepatitis C virus (HCV)1 infects about 3% of the world's human population. HCV infection can develop into chronic hepatitis, which, in some cases, causes cirrhosis of the liver, eventually leading to hepatocellular carcinoma (1). There is no vaccine against HCV currently, and no generally effective therapy for all genotypes of HCV is available. At the present time, the use of recombinant interferon ␣-2a, ␣-2b, "consensus" interferon, and pegylated interferon ␣-2b either in monotherapy or in combination with ribavirin is the only approved therapy available (2). However, limited efficacy and some adverse side effects are associated with these therapies (3). Therefore, the development of HCV-specific antiviral agents is needed urgently.Extensive studies have been done to understand the structures and functions of the individual components of the HCVencoded polyprotein (structural proteins C, E1, and E2 and nonstructural proteins NS2, NS3, NS4A, NS4B, NS5A, and NS5B) (4 -6). Among them, NS2, NS3 protease and helicase, and NS5B RNA-dependent RNA polymerase are essential enzymes for the replication of HCV. The high resolution crystal structures of NS3 protease (7-9) and helicase domains (10, 11) and NS5B polymerase (12-14) have been determined by crystallographic methods in the past 5 years. These enzymes are potential targets for structure-based drug design. The inhibitors of NS3 protease and, in some cases, corresponding structures of NS3 protease/inhibitor complexes have been reported recently (15). In the case of HCV NS5B polymerase, both nucleoside and non-nucleoside inhibitors have been discovered in recent years (16). 3TC (2Ј-deoxy-3Ј-thiacytidine proprietary compound lamivudine) triphosphate has been reported to have a weak inhibitory effect with a 50% inhibitory concentration (IC 50 ) of 180 M (17), whereas numerous non-nucleoside compounds have been documented to possess relatively potent anti-NS5B activity. Examples include specific rhodanines and barbituric acid derivatives, many of which were found to exhibit anti-NS5B activity with IC 50 values below 1 M (18, 19). Classes of dihydroxypyrimidine carboxylic acids and diketoacid derivatives were claimed as well with IC 50 values within the submicromolar range for the latt...

HCV NS5B polymerase is a validated target for the treatment of hepatitis C, known to be one of the most challenging enzymes for docking programs. In order to improve the low accuracy of existing docking methods observed with this challenging enzyme, we have significantly modified and updated F itted 1.0, a recently reported docking program, into F itted 1.5. This enhanced version is now applicable to the virtual screening of compound libraries and includes new features such as filters and pharmacophore- or interaction-site-oriented docking. As a first validation, F itted 1.5 was applied to the testing set previously developed for F itted 1.0 and extended to include hepatitis C virus (HCV) polymerase inhibitors. This first validation showed an increased accuracy as well as an increase in speed. It also shows that the accuracy toward HCV polymerase is better than previously observed with other programs. Next, application of F itted 1.5 to the virtual screening of the Maybridge library seeded with known HCV polymerase inhibitors revealed its ability to recover most of these actives in the top 5% of the hit list. As a third validation, further biological assays uncovered HCV polymerase inhibition for selected Maybridge compounds ranked in the top of the hit list.

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The HCV NS5B RNA dependent RNA polymerase plays an essential role in viral replication. The discovery of a novel class of inhibitors based on an N,N-disubstituted phenylalanine scaffold and structure-activity relationships studies to improve potency are described.