Molecular Docking and Dynamics Simulation Studies to Predict Multiple Medicinal Plants’ Bioactive Compounds Interaction and Its Behavior on the Surface of DENV-2 E Protein

The envelope protein (E) is a fusion class II protein that is essential for DENV fusion. We use two active compounds derived from commonly used plants in Indonesia: galangin and kaempferide. We ran a docking and 1000 ps molecular dynamic analysis with normal physiological parameters. During the simulation, galangin and kaempferide binding sites fluctuated. But chloroquine has lesser ligand mobility, hence keeping contact with fusion loops, whereas both drugs lose contact with hydrophobic pockets. However, the two active compounds have a more stable ligand configuration. Less than 2 Å alterations were seen in the RMSF simulation of the protein E residues. In a 1000 ps simulation, all tested compounds form stable complex with protein E, demonstrating that the two active compounds may be predicted as DENV-2 E protein fusion inhibitors, despite chloroquine inhibiting in a unique manner linked to its interaction domains.