SIMULASI DINAMIKA MOLEKULER SENYAWA KOMPLEKS MOA-A DAN SAFROL SEBAGAI KANDIDAT ANTIDEPRESAN MENGGUNAKAN APLIKASI GROMACS

Abstract

Molecular dynamics (MDS) simulation of the complex compound of nutmeg (Myristica fragrans) with protein is very important to see the molecular interactions that occur, but so far no one has done it. Previous studies in docking and pharmacokinetics have concluded that safrole is an inhibitor that has no potential for MAO-A, but the docking interaction occurs in a static state and without solvent. This study aims to conduct MDS to see the dynamic interaction of the MAO-A complex and safrole in the presence of water as a solvent. MDS can be done using the GROMACS application which is run on the LINUX terminal on UBUNTU and the conformational changes and interactions that occur can be observed with BIOVIA Discovery Studio and PyMOL. The results of the MDS in the form of graph values of root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) which stated that the stability of the safrole complex was unsatisfactory when compared to native ligands and positive control. Changes in interaction occurred in all test ligands, but safrole did not have the same interaction with amino acid residues at the hydrophobic MAO-A active site as the positive control. The MDS results stated that safrole is a ligand that has no potential as an MAO-A inhibitor obtained from nutmeg based on the stability of the complex and the interaction at the active site, similar to the results of molecular docking under rigid conditions.