Figure 6.

Ligand-protein analysis and conformation changes during MD simulation. (A) Chart shows the type of interaction fraction time (Shown in different colors for each interaction) of protein containing amino acid during the 500 ns MD simulations. However, As the MD simulation began and gradually increased, the hydrogen bond decreased. The highest contact times are shown by residues such as Phe469, Ile204, and Arg656, which suggest important roles. (B) OATP1A2 RMSF calculations illustrate the flexibility during MD simulation, A connecting amino acids from 100-150 in OATP1A2 protein revealed the highest fluctuation above the 8 Å. This suggests the extracellular loop is important for ligand transportation (C) The RMSD values for the protein-ligand complex were shown in the figure during 500ns MD simulation. The analysis revealed stability throughout the simulation period, with the protein stabilized around6 Å and ligand 1.5 Å, followed by RMSD values remained consistent. After 100ns figure represented the structural integrity and reliability of the protein-ligand interactions over the MD simulation. (D) The left side: the figure shows the types of interaction before MD simulation (Docking protein-ligand complex). The hydrogen bond with amino acid Arg⁶⁵⁶ and Gly⁵⁶⁰was observed and the other is hydrophobic interaction. The right side: After MD which shows only hydrophobic interaction over 500ns. Which was reflects the changes in the interaction bond after 500 ns.