2.4. Molecular Dynamics Simulations
This protocol is extracted from research article:
Computer-Aided Drug Discovery Identifies Alkaloid Inhibitors of Parkinson's Disease Associated Protein, Prolyl Oligopeptidase
Evid Based Complement Alternat Med, Apr 8, 2021; DOI: 10.1155/2021/6687572

To determine the reliability and consistency of the binding of the prospective drug candidates to the target protein, molecular dynamics (MD) simulations were performed using GROningen MAchine for Chemical Simulations (GROMACS) v5.0.6 package [24] and using CHARMm27 [25] as desired force field. Ligand topology was generated using SwissParam [26]. Dodecahedron system solvated with TIP3P water model was utilized for solvation. Na+ ions were added to neutralize the negative charge of the system. Steepest Descent was used for energy minimization. Equilibration of the system was carried out in two phases: constant number N, volume V, and temperature T (NVT) and constant number N, pressure P, and temperature T (NPT). NVT ensemble was performed at 300 K for 1 ns and NPT ensemble at 1 bar pressure for 1 ns with a Parrinello–Rahman barostat [27]. Once the system was well equilibrated, MD was carried out for 50 ns (metergoline) or 20 ns (other identified alkaloid inhibitors). MD analysis was performed using Visual Molecular Dynamics (VMD) and DS.

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