A Study of Energy Minimization Influence on the Molecular Docking of Acetylacetone-Based Oxindole Derivatives
Arif Fadlan (a*), Frans Josaphat (b)

(a*) Department of Chemistry, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Jl. Teknik Kimia, Surabaya 60111, Indonesia, *afadlan[at]chem.its.ac.id
(b) Department of Chemistry, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Jl. Teknik Kimia, Surabaya 60111, Indonesia

Abstract

Molecular docking plays an important role in the drugs discovery because it is more efficient and more affordable compared to traditional synthesis methods and biological assays. Molecular docking determines the conformation and affinity of non-covalent bonds between macromolecules (receptors) and small molecules (ligands) computationally. Molecular docking involves energy minimization producing ligands with the most stable conformation and lowest energy which is generally carried out by using the Merck Molecular Force Field 94 (MMFF94) force field. MarvinSketch and Open Babel for energy minimization were used in this molecular docking of acetylacetone-based oxindole derivatives to 2,3-dioxygenase indoleamine macromolecules (IDO-1, PDB: 2D0T). The results showed that MarvinSketch provides better binding energy compared to energy minimization with Open Babel. Molecular docking indicated different interactions between 2D0T macromolecule residues with ligands that have been prepared using MarvinSketch, Open Babel, and without energy minimization.

Keywords: Molecular docking, minimization energy, Merck Molecular Force Field 94 (MMFF94), IDO-1, Oxindole derivatives

Topic: Pharmacy