3D-MOLECULAR SCREENING OF DIKETOPIPERAZINE DERIVATES ON Staphylococcus aureus DEHYDROSQUALENE SYNTHASE USING VINA
Abstract: Dehydrosqualene
synthase enzyme has been used as protein target model for exploring docking
simulation of pyrazoline analogues. One of diketopiperazine derivates that have
similar structure to pyrazoline has antibacterial activity against
Staphylococcus aureus (S. aureus). Vina is AutoDock- improved program that
capable for molecular screening based on free-energy and binding conformation
prediction between ligand and protein target. The aim of these studies is to
screen diketopiperazine derivates on dehydrosqualene synthase of S. aureus
using Vina. Diketopiperazine derivates, curcumin analogues, curcumin,
pentagammavunon derivates (PGV-0 and PGV-1) were calculated for their geometry
optimization energy using Gaussian-Density Functional Theory method.
3D-optimized ligands along with reference ligands were screened for their
binding energy with dehydrosqualene synthase (2ZCO) by docking using Vina. The
lowest values of binding energy were analyzed with statistic method. The
results showed that top thirteen ligands of docking binding energy with
receptor are diketopiperazine derivates (31%), curcumin analogues (31%), and
reference ligands (38%). The new compounds of diketopiperazine derivates and
curcumin analogues have better potency of binding energy than curcurmin as lead
compound.
Keywords: diketopiperazine,
Vina, docking, Staphylococcus aureus, curcumin
Penulis: Broto Santoso
Kode Jurnal: jpfarmasidd120263
