The effects of ligand charge, orientation and size on the binding of potential inhibitors for aldehyde dehydrogenase

Abstract

l-DOPA, used as a therapy for patients with Parkinson’s disease, is transformed into needed dopamine in the brain. This dopamine can then be deactivated via metabolism by a series of enzymes, including aldehyde dehydrogenase (ALDH). The targeted inhibition of the ALDH enzyme may help to prolong l-DOPA therapy. A series of potential inhibitors has been studied viaab initiomodels using a crystal-structure of the ALDH enzyme with an inhibitor bound in its active site (PDB ID: 4WP7). The positions of novel dopaminergic derivatives were optimized in the active site using M062X/6-31G with implicit solvation and relaxed amino-acid side-chains. This work examines different single molecule orientations, as well as double molecule configurations. Various sizes of ligands were also studied. Interaction energies between the ligands and the protein were calculated using M062X with the 6–311 + G* basis set. Some potential inhibitors show promising results such as the LP and CAM series.