Fast Methods for Prediction of Aldehyde Oxidase-Mediated Site-of-Metabolism

Abstract

Aldehyde Oxidase (AO) is an enzyme involved in the metabolism of aldehydes and N-containing heterocyclic compounds. Many drug compounds contain heterocyclic moieties, and AO metabolism has lead to failure of several late-stage drug candidates. Therefore, it is important to take AO-mediated metabolism into account early in the drug discovery process, and thus, to have fast and reliable models to predict the site of metabolism (SOM). We have collected a dataset of 78 substrates of human AO with a total of 89 SOMs and 347 non-SOMs and determined atomic descriptors for each compound. The descriptors comprise NMR shielding and ESP charges from density functional theory (DFT), NMR chemical shift from ChemBioDraw, and Gasteiger charges from RDKit. Additionally, atomic accessibility was considered using 2D-SASA and relative span descriptors from SMARTCyp. Finally, stability of the product, the metabolite, was determined with DFT and also used as a descriptor. All descriptors have AUC larger than 0.75. In particular, descriptors related to the chemical shielding and chemical shift (AUC = 0.96) and ESP charges (AUC = 0.96) proved to be good descriptors. We recommend two simple methods to identify the SOM for a given molecule: 1) use ChemBioDraw to calculate the chemical shift or 2) calculate ESP charges or chemical shift using DFT. The first approach is fast but somewhat difficult to automate, while the second is more time-consuming, but can easily be automated. The two methods predict correctly 93% and 91%, respectively, of the 89 experimentally observed SOMs.