Molecular Docking of Substituted Oxindole Derivatives with MMFF94 Energy Minimization by Using MarvinSketch and Open Babel PyRx Arif Fadlan (a*), Atika Umi Hanif (b)
a) Assistant Professor, Department of Chemistry, Sepuluh Nopember Institute of Technology, Jl. Teknik Kimia, Surabaya 60111, Indonesia, Email : afadlan[at]chem.its.ac.id (Corresponding author)
b) Student, Department of Chemistry, Sepuluh Nopember Institute of Technology, Indonesia
Abstract
In silico technique is widely used for drug discovery because it can predict the conformation of ligands in protein macromolecules and is able to calculate the binding affinity. The energy minimization is carried out to make the ligand more stable near the initial state during molecular docking process. The Merck Molecular Force Field (MMFF94) is one type of energy minimization process often used in organic compounds. The molecular docking of substituted oxindole derivatives on indoleamine macromolecules 2,3-dioxygenase (IDO-1, PDB: 2D0T) by using MMFF94 minimization operated by MarvinSketch and Open Babel showed different results. The binding affinity energy obtained was also quite different, but the ligands have the same conformation and bind the same residue with slightly different bond distances.
Keywords: Molecular Docking; Energy Minimization; Oxindole; IDO-1; Merck Molecular Force Field 94
