In this study, synthesis and docking studies of a series of new benzimidazole derivatives linked to substituted pyrimidines either through the methylenethio linkage or its bioisosteric methylene amino bridge were carried out. All the synthesized compounds were evaluated for their hepatitis C virus (HCV) RNA replication-inhibitory activity. Compounds 4d, 4f, and 4h were found to be more potent than VX-950 (IC 50/ Key words synthesis; benzimidazole; pyrimidine; hepatitis C virus; viral RNA replication inhibitor As estimated by WHO, 170 million persons worldwide are infected with hepatitis C virus (HCV) which causes chronic liver disease. HCV is a positive stranded RNA virus and is a member of the Flaviviridae family of viruses.1,2) Combined therapy of HCV infections with pegylated alpha interferon (IFN-α) and ribavirin is only effective in 50-60% of infected individuals and is associated with serious side effects such as depression, flu-like symptoms, fatigue and hemolytic anemia caused by ribavirin.
3,4)There is an unmet need for potent and selective inhibitors of HCV replication. Significant research efforts are currently directed towards targeting viral enzymes especially NS3-4A serine protease [5][6][7][8] and NS5B RNA-dependent RNA polymerase which are both required for virus propagation.
9-11)The NS3-4A serine protease has been an attractive target in the development of new antivirals with activities against HCV since it is essential for viral replication.9-11) The serine protease activity of NS3 in complex with the NS4A cofactor is responsible for the proteolytic cleavage at four junctions of the HCV polyprotein precursor: NS3-NS4A (self cleavage), NS4A-NS4B, NS4B-NS5A, and NS5A-NS5B. 7,[12][13][14][15][16][17] Crystal structure of the serine protease domain of the NS3, with its essential cofactor NS4A, 18,19) revealed that the NS3-4A complex adopts a chymotrypsin/trypsin-like fold with structurally conserved regions typical of small chymotrypsin-like proteases. 20,21) The N-terminal region of NS3-4A (residues 1-93 of NS3 and residues 21-34 of NS4A) contains an eightstranded β-barrel motif, with one of the strands contributed by the NS4A cofactor.20) The C-terminal region (residues 94-175) contains a six-stranded-barrel that ends with a helix. The active site (His: 57, Asp: 81, and Ser: 139) is located between these two regions and is formed by a shallow solvent exposed pocket to which the inhibitors bind in an extended conformation.
18-21)Sofosbuvir (GS-7977), a uridine nucleotide analogue, and an inhibitor of HCV NS5B polymerase is effective against HCV genotypes 1, 2, 3, 4, and 6. Sofosbuvir, especially in interferon-free combinations, represents a very promising option in the treatment of chronic hepatitis C.
22)Currently, different anti-HCV treatments depend on the inhibition of HCV NS3-4A serine protease. Telaprevir (VX-950), boceprevir and BILN 2061 (Fig. 1) are examples of well known HCV NS3-4A serine protease inhibtors. 23,24) Telaprevir, a small molecule peptidomimetic, forms a covalent but revers...