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Figure 6 | BMC Bioinformatics

Figure 6

From: Multiple virtual screening approaches for finding new Hepatitis c virus RNA-dependent RNA polymerase inhibitors: Structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors

Figure 6

A) Overlay of docked and PDB coordinates of 2JC1 ligand for the Palm I site (original ligand pose coloured blue, docked ligand pose coloured pink); B) docked pose of DB05039 it shows a very good placement of the diethyl-indanyl group into the deep pocket. A salt bridge strengthens the binding with ARG394. Similarly, hydrogen bonding with ARG386 and TYR415, and Pi stacking with TYR415; C) docked pose of DB01940 forming a HB inside the deep hydrophobic pocket (as with one of benzodiazepines) in addition to a HB with GLN446 (just four atoms away along the backbone's TYR448 amidic nitrogen); D) docked pose of DB04142.(red dotted lines represent salt bridges, green dotted lines represent hydrogen bonds, orange solid lines represent π-interactions, backbone shown as curved purple lines, protein transparent surface with interpolated charges; bluish(+ve), reddish(-ve)). The furan ring show similar interaction with TYR448. These three hits preserved these binding modalities after molecular dynamics simulations.

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BMC Bioinformatics

ISSN: 1471-2105

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