2.5 Molecular Dynamics Simulation
In order to verify the stability of the compound-protein complexes from the docking study, in this study, we used GROMACS41,42to do Molecular dynamic simulation (MD). Firstly, from Swissparam web server43, we obtained topology files and parameters for the ligands. Placed in a periodic cubic bos with a 1.2nm edge, the protein-ligand complex was solvated with TIP3P water molecules and 0.145 M NaCl ions. The complex systems was minimized for 5000 steps by the steepest descent algorithm. The temperature was set at 310K in canonical ensemble (NVT) and isothermal-isobaric ensemble (NPT). The NVT balance simulation is a total of 20 ns with a time step of 2 fs. The Lincs algorithm constrains all keys and 310K temperature settings, similar to the physiological environment. The NPT operates in balance for 20 ns and sets the temperature coupling during the simulation. To describe the chemical scaffold of the protein-ligand complex, the charmm27 was applied. Neighbor searching cutoff and 3-D PBC for periodic boundary conditions was performed with Verlet scheme in this 100ns dynamic simulation. For analyzing the stability of the compound-protein complexes, we calculate root mean square deviation (RMSD), total energy, radius of gyrate, solvent accessible solvent area (SASA), root mean square fluctuation (RMSF), mean square deviation (MSD).