STUDY OF MOLECULAR DOCKING IN SILKWORM ODORANT BINDING PROTEIN

Abstract

In many insect species, it is believed that odorant binding proteins (OBPs) are responsible for transport of pheromones and other semiochemicals through the sensory lymph to the olfactory receptors (Ors) within the antenna sensilla. The present study was aimed to use the technique of molecular docking to obtain the connection-free energies between the natural ligand and similar ligands of the BMori GOBP protein (General Odorant Binding Protein), 2WC5 (PDB code) obtained from the Protein Data Bank. Protein residues, such as water molecules, magnesium and the hexadeca10,12-dien-1-ol, were removed by using the software Chimera 1.10.2. Polar hydrogens were added to the general odorant binding protein and the protein ligand-based search space was constructed, in which the coordinates of the binding site were determined using the AutoDock Tools software. Nevertheless, through the software AutoDock Tools the PDB file was converted to the PDBQT format. With AutoDock Vina 1.1.2 and ArgusLab 4.0.1 software, simulations of re-docking, docking and molecular cross-docking of the hexadeca-10,12-dien-1-ol ligand were performedto the protein to obtain the ranking of ligand poses and binding affinity energies. For docking and cross-docking, the choice of ligands was done through the similarity of the structural molecular formula in The Pherobase database. Hence, it was possible to demonstrate that, for the proposed ligands, the most stable protein-ligand binding energies obtained in the dockings were of ligands that had cyclic structures, although the energy of these ligands were lower than the original ligand.