Investigation of some benzoquinazoline and quinazoline derivatives as novel inhibitors of HCV-NS3/4A protease: biological, molecular docking and QSAR studies

Abstract

Morbidity and mortality due to hepatitis C virus (HCV) is a globe health concern. Hence, there is a persistent demand to design and optimize current HCV therapy and develop novel agents. HCV NS3/A4 protease plays an essential role in HCV life cycle and replication. Thus, HCV NS3/A4 protease inhibitors are one of the best therapeutic targets for the identification of novel candidate drugs. Recent studies have shown some benzoquinazolines as potent antiviral agents and promising HAV-3C protease inhibitors. In the present study, a series of benzo[g]quinazolines (1-13) and their quinazoline analogues (14-17) were evaluated for their HCV-NS3/4A inhibitory activities using in vitro assay. Our results revealed that the target compounds inhibited the activity of the NS3/4A enzyme, (IC₅₀ = 6.41 ± 0.12 to 78.80 ± 1.70 μM) in comparison to telaprevir (IC₅₀ = 1.72 ± 0.03 μM) as a reference drug. Compounds 1, 2, 3, 9, 10 and 13 showed the highest activity (IC₅₀ = 11.02 ± 0.25, 6.41 ± 0.12, 9.35 ± 0.19, 9.08 ± 0.20, 16.03 ± 0.34 and 7.21 ± 0.15 μM, respectively). Molecular docking was performed to study the binding modes of the docked-chosen benzo[g]quinazolines, hydrogen bonding, and amino acid residues at the catalytic triad of the NS3/4A enzyme of HCV. The QSAR was determined to explore the relationships between the molecular structures of the targets and their biological activities by developing prediction models among the known HCV NS3/A4 inhibitors and then to predict the inhibitory activity of the target molecules synthesized.

Fig. 1. Schematic of the HCV polyprotein with cleavage sites of the two proteases, NS2 and NS3.

Fig. 2. Structure of the NS3/4A serine protease, with the NS3 protease domain coloured in cyan, helicase domain coloured in brown and allosteric pocket coloured in green, the active site residues, Ser139, His57 and Asp81, sit on the protein–protein interaction surface and are shown as stick figures in black.

Fig. 3. The reported and designed HCV-NS3/4A inhibitors.

Fig. 4. (A) 3D structural representation of NS3/4A complexed with telaprevir and binding site divided at S1′ (green; Gln1041, Thr1042, Phe1043 and Gly1137), S1 (yellow; Leu1135, Lys1136, Ser1139 and Phe1154), S2 (brown; His1057, Arg1155, Ala1156 and Asp1168), S3 (Pink; Ile1132 and Ala1157), S4 (red; Arg1123 and Val1158) and S5 (blue; Ser1159) subsites. (B) 3D structural representation of NS3/4A complexed with superposing selected synthesized compounds (1–10), with binding site divided at S1′, S1, S2, S3, S4 and S5.

Scheme 1. Synthetic routes for the target benzoquinazolines and quinazolines 1–17.

Fig. 5. 3D Interaction of reference compound (telaprevir) with active site of HCV NS3/4A enzyme. Telaprevir shows four hydrogen bonds with Ser1159, Ala1157, Arg1155, His1057, Ser1159, Gly1137 and Ser1139 of the target protein active site residue.

Fig. 6. 3D Interaction of compound 3 with active site of HCV NS3/4A enzyme. Compound 3 shows four hydrogen bonds with Gln1041 and Gly1137 and two π-bonds with Lys1136 of the target protein active site residue.

Fig. 7. 3D Interaction of compound 9 with active site of HCV NS3/4A enzyme. Compound 9 shows four hydrogen bonds with Gly1137 and two π-bonds with Lys1136 of the target protein active site residue.

Fig. 8. 3D interaction of compound 13 with active site of HCV NS3/4A enzyme. Compound 13 shows four hydrogen bonds with Gly1137 and two π-bonds with Lys1136 of the target protein active site residue.

Fig. 9. Experimental versus predicted (LOO) inhibitory potency pIC₅₀ values of the HCV NS3/4A serine protease inhibitors. The data points in red circle and blue square represent training and test set compounds, respectively.

Fig. 10. PCA plots of training set compounds for data obtained for the HCV NS3/4A serine protease. The 3D graphical plot was constructed with three eigenvectors PCA1, PCA2 and PCA3 in the range of +3 to −3 and coordinate value for each compound has represented with colored spots.