The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors

Metabolism of drugs affects their absorption, distribution, efficacy, excretion, and toxicity profiles. Metabolism is routinely assessed experimentally using recombinant enzymes, human liver microsome, and animal models. Unfortunately, these experiments are expensive, time-consuming, and often extrapolate poorly to humans because they fail to capture the full breadth of metabolic reactions observed in vivo. As a result, metabolic pathways leading to the formation of toxic metabolites are often missed during drug development, giving rise to costly failures. To address some of these limitations, computational metabolism models can rapidly and cost-effectively predict sites of metabolism-the atoms or bonds which undergo enzymatic modifications-on thousands of drug candidates, thereby improving the likelihood of discovering metabolic transformations forming toxic metabolites. However, current computational metabolism models are often unable to predict the specific metabolites formed by metabolism at certain sites. Identification of reaction type is a key step toward metabolite prediction. Phase I enzymes, which are responsible for the metabolism of more than 90% of FDA approved drugs, catalyze highly diverse types of reactions and produce metabolites with substantial structural variability. Without knowledge of potential metabolite structures, medicinal chemists cannot differentiate harmful metabolic transformations from beneficial ones. To address this shortcoming, we propose a system for simultaneously labeling sites of metabolism and reaction types, by classifying them into five key reaction classes: stable and unstable oxidations, dehydrogenation, hydrolysis, and reduction. These classes unambiguously identify 21 types of phase I reactions, which cover 92.3% of known reactions in our database. We used this labeling system to train a neural network model of phase I metabolism on a literature-derived data set encompassing 20 736 human phase I metabolic reactions. Our model, Rainbow XenoSite, was able to identify reaction-type specific sites of metabolism with a cross-validated accuracy of 97.1% area under the receiver operator curve. Rainbow XenoSite with five-color and combined output is available for use free and online through our secure server at http://swami.wustl.edu/xenosite/p/phase1_rainbow.