The Effect of Energy Minimization on the Molecular Docking Study of Acetone-Based Oxindole Derivatives Arif Fadlan (a*), Yesaya Reformyada Nusantoro (b)
a) Chemistry Department, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Jl. Teknik Kimia, Surabaya 60111, Indonesia, Email: afadlan[at]chem.its.ac.id (corresponding author)
b) Chemistry Department, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Jl. Teknik Kimia, Surabaya 60111, Indonesia
Abstract
In silico study by molecular docking are useful in the drug discovery and virtual screening for obtaining compounds with promising biological activity. The merck molecular force field 94 (MMFF94) is the prevalent function for energy minimization in molecular docking for better geometry estimation and ligand-receptor affinity. The two programs namely MarvinSketch and Open Babel for energy minimization were used in this molecular docking study of acetone-based oxindole derivatives. The results showed that the binding energy produced by MarvinSketch was generally better than the binding energy obtained with Open Babel. The visualization of molecular docking results indicated that the poses and hydrogen bonding, halogen bonding and --- interactions are different between MarvinSketch, Open Babel, and with no energy minimization. The results revealed that energy minimization affects the molecular docking results.
Keywords: Molecular Docking- Energy minimization- Merck molecular force field 94- Oxindole- IDO1
