Multiple e‑Pharmacophore Modeling, 3D-QSAR, and High-Throughput Virtual Screening of Hepatitis C Virus NS5B Polymerase Inhibitors

The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRP) is a crucial and unique component of the HCV RNA replication machinery and a validated target for drug discovery. Multiple crystal structures of NS5B inhibitor complexes have facilitated the identification of novel compound scaffolds through in silico analysis. With the goal of discovering new NS5B inhibitor leads, HCV NS5B crystal structures bound with inhibitors in the palm and thumb allosteric pockets in combination with ligands with known inhibitory potential were explored for a comparative pharmacophore analyses. The energy-based and 3D-QSAR-based pharmacophore models were validated using enrichment analysis, and the six models thus developed were employed for high-throughput virtual screening and docking to identify nonpeptidic leads. The hits derived at each stage were analyzed for diversity based on the six pharmacophore models, followed by molecular docking and filtering based on their interaction with amino acids in the NS5B allosteric pocket and 3D-QSAR predictions. The resulting 10 hits displaying diverse scaffold were then screened employing biochemical and cell-based NS5B and anti-HCV inhibition assays. Of these, two molecules H-5 and H-6 were the most promising, exhibiting IC₅₀ values of 28.8 and 47.3 μM against NS5B polymerase and anti-HCV inhibition of 96% and 86% at 50 μM, respectively. The identified leads comprised of benzimidazole (H-5) and pyridine (H-6) scaffolds thus constitute prototypical molecules for further optimization and development as NS5B inhibitors

Supplementary Tables 1-2 from Development of a Novel Multi-Isoform ALDH Inhibitor Effective as an Antimelanoma Agent

Supplementary table 1: RT-PCR analysis of the expression of ALDH isoforms in melanoma cell lines and isolated ALDH+ and ALDH- cells. Supplementary table 2: KS100 has no human off-target effects based on the Erebus algorithm.</p

Supplementary Figures 1-7 from Development of a Novel Multi-Isoform ALDH Inhibitor Effective as an Antimelanoma Agent

Supplementary Figure 1: KS100 is a multi-ALDH inhibitor. Supplementary Figure 2: Conformational arrangements of ALDH1A1, 2, and 3A1 are structurally identical. Supplementary Figure 3: Representative dot plots of Aldered staining of UACC 903 cells following ALDH inhibitor treatment. Supplementary Figure 4: Representative dot plots of Aldered staining of 1205 Lu cells following ALDH inhibitor treatment. Supplementary Figure 5: KS100 reduces enzymatic ALDH activity in cell lysates. Supplementary Figure 6: Representative dot plots of Annexin-V-PE/7-AAD staining of UACC 903 cells following ALDH inhibitor treatment. Supplementary Figure 7: Representative dot plots of Annexin-V-PE/7-AAD staining of 1205 Lu cells following ALDH inhibitor treatment.</p