Exploration of stilbenoid trimers as potential inhibitors of sirtuin1 enzyme using a molecular docking and molecular dynamics simulation approach

Figures

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  Fig. 1. Chemical structure of stilbenoid trimers isolated from the tree bark of Dryobalanops oblongifolia and Vitis labrusca, where the atomic label and ring region are marked.

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  Fig. 2. Active site determination: (A) cluster sphere selected within radius 10 Å from the native ligand, (B) the ligand native is represented by a crystal conformation (cyan), a minimized conformation (blue), and a flexible conformation (magenta), (C) the active site interaction between 1NS (flexible conformation) and amino acid residues, (D) the interaction types shown in 2D-diagram.

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  Fig. 3. Molecular docking result of the candidate-receptor shows closer on the pocket area of the active site.

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  Fig. 4. Trajectories analysis: the root-mean-square displacement of each system plotted along the 250 ns of MD simulation.

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  Fig. 5. Flexibility analysis: the B-factor (top) and the root-mean-square fluctuation (bottom).

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  Fig. 6. Trajectories analysis during the simulation over the last 50 ns: atom contacts within radius 3.5 Å (top), the radius of gyration (middle), and the solvent-accessible surface area (bottom).

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  Fig. 7. Percentage of hydrogen bond over the last 50 ns of MD simulation.

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  Fig. 8. Visualization of hydrogen bond interaction between candidate and receptor on the active site. Hydrogen bond data are represented by a green line with the average value of distance in the angstroms unit (Å).