Design, Synthesis And Biological Evaluation Of Novel Indole Derivatives As HCV Non-Nucleoside NS5B Inhibitors

Hepatitis C virus (HCV) RNA-depended-RNA-polymerase (NS5B) plays a vital role in HCV life cycle. The development of novel NS5B inhibitors with high affinity, low toxicity and high potency for the mutated NS5B has been a very active research field during recent years.Three non-nucleoside binding pockets have been reported on NS5B, that is, Thumb Site I, Thumb Site II and Palm Site. Thumb Site I is the first reported site among these binding pockets and indole analogues are the most important NS5B Thumb Site I inhibitors. Prompted by the analyses of the crystal structures of these series of compounds with NS5B, molecular simulation and the 3D-QSAR model, the pocket which is filled by cyclohexyl still have enough space for further modification. Moreover, some hydrophilic residues in this pocket also promote the modification of this site. According to the structure-activity relationship as well as the co-crystal structure of NS5B-ligand, a series of novel indole analogues are synthesized. The cyclohexyl motif is replaced by a series of substituents with different sizes and different polarity.The synthetic route started with the commercially available methyl indole-6-carboxylate. The methyl indole-6-carboxylate was alkylated and brominated, affording methyl 2,3-dibromo-1-(2-morpholino-2-oxoethyl)-1H-indole-6-carboxylate (c01).c01 was reacted with different boronic acids by Suzuki reaction, affording different products, then the methyl ester was hydrolyzed, affording the final products.The biological evaluation was carried out by testing the affinity between ligands and NS5B. Some of the indole analogues demonstrated remarkable affinity against NS5B. Especially compounds a10 and b13 showed higher binding affinity against NS5B compared to the positive compound, which are worthy to be further optimized.In vitro anti-HCV assay was carried out by testing the inhibition of HCV replication. Compounds a02, a10, b13 exhibited potency against HCV replication with the IC50 value of 8.09μM,1.33μM and 4.59μM, respectively. While compound 121 showed 48% inhibition against HCV replication under 50μM.To sum up, based on the the available structural information, revealing binding modes for HCV NS5B inhibitors, and the structure-activity relationships, a series of novel indole analogues were designed. All the synthesized compounds were identified by MS,’H NMR and 13C NMR. Several compounds showed activity against NS5B in SPR-based affinity assays, which paved the way for further optimizations of novel HCV NS5B inhibitors.