Updated Prediction of Aggregators and Assay-Interfering Substructures in Food Compounds

Positive outcomes in biochemical and biological assays of food compounds may appear due to the well-described capacity of some compounds to form colloidal aggregates that adsorb proteins, resulting in their denaturation and loss of function. This phenomenon can lead to wrongly ascribing mechanisms of biological action for these compounds (false positives) as the effect is nonspecific and promiscuous. Similar false positives can show up due to chemical (photo)reactivity, redox cycling, metal chelation, interferences with the assay technology, membrane disruption, etc., which are more frequently observed when the tested molecule has some definite interfering substructures. Although discarding false positives can be achieved experimentally, it would be very useful to have in advance a prognostic value for possible aggregation and/or interference based only in the chemical structure of the compound tested in order to be aware of possible issues, help in prioritization of compounds to test, design of appropriate assays, etc. Previously, we applied cheminformatic tools derived from the drug discovery field to identify putative aggregators and interfering substructures in a database of food compounds, the FooDB, comprising 26,457 molecules at that time. Here, we provide an updated account of that analysis based on a current, much-expanded version of the FooDB, comprising a total of 70,855 compounds. In addition, we also apply a novel machine learning model (SCAM Detective) to predict aggregators with 46-53% increased accuracies over previous models. In this way, we expect to provide the researchers in the mode of action of food compounds with a much improved, robust, and widened set of putative aggregators and interfering substructures of food compounds.

Automated summary

False positive outcomes in biochemical and biological assays of food compounds may occur due to the ability of some compounds to form colloidal aggregates that adsorb proteins, resulting in denaturation and loss of function. This is especially observed when the tested molecule has interfering substructures, leading to more frequent false positives.