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.
