Discovery of Novel Hepatitis C Virus NS5B Polymerase Inhibitors by Combining Random Forest, Multiple e-Pharmacophore Modeling and Docking

Abstract

The NS5B polymerase is one of the most attractive targets for developing new drugs to block Hepatitis C virus (HCV) infection. We describe the discovery of novel potent HCV NS5B polymerase inhibitors by employing a virtual screening (VS) approach, which is based on random forest (RB-VS), e-pharmacophore (PB-VS), and docking (DB-VS) methods. In the RB-VS stage, after feature selection, a model with 16 descriptors was used. In the PB-VS stage, six energy-based pharmacophore (e-pharmacophore) models from different crystal structures of the NS5B polymerase with ligands binding at the palm I, thumb I and thumb II regions were used. In the DB-VS stage, the Glide SP and XP docking protocols with default parameters were employed. In the virtual screening approach, the RB-VS, PB-VS and DB-VS methods were applied in increasing order of complexity to screen the InterBioScreen database. From the final hits, we selected 5 compounds for further anti-HCV activity and cellular cytotoxicity assay. All 5 compounds were found to inhibit NS5B polymerase with IC50 values of 2.01-23.84 μM and displayed anti-HCV activities with EC50 values ranging from 1.61 to 21.88 μM, and all compounds displayed no cellular cytotoxicity (CC50 > 100 μM) except compound N2, which displayed weak cytotoxicity with a CC50 value of 51.3 μM. The hit compound N2 had the best antiviral activity against HCV, with a selective index of 32.1. The 5 hit compounds with new scaffolds could potentially serve as NS5B polymerase inhibitors through further optimization and development.

Fig 1. A chart for the virtual screen targeting HCV NS5B polymerase.

Fig 2. Redocked binding modes of the co-crystalized inhibitors in the active site of NS5B polymerase.

(A-B) the palm I region, (C-D) the thumb I region, (E-F) the thumb II region.

Fig 3. E-pharmacophore hypotheses with energetically favorable sites from the six crystal structures.

Pink sphere represents hydrogen-bond acceptor (A); orange ring represents aromatic ring (R); blue sphere represents hydrogen-bond donor (D); red sphere represents negatively ionizable (N); green spheres represent hydrophobic (H).

Fig 4. Structures of the 5 hit compounds.

Fig 5. The structures of known NS5B inhibitors (K1 –K5).

These inhibitors have the highest Tcs with N1 –N5, respectively.

Fig 6. The binding poses of compound N1 –N5 in the respective binding pocket of NS5B polymerase.

(A) N1; (B) N2; (C) N3; (D) N4; (E) N5. Potential hydrogen bonding interaction are shown as dashed lines.