Expanding the application of a novel proteomics tool for drug target and mechanism identification

Abstract: In drug discovery and development, characterization of the drug targets and mechanisms of action is an essential step. ProTargetMiner is a publicly available proteome signature library of anticancer molecules and its automated bioinformatics platform can be used for drug target and mechanism deconvolution. The possibility of expanding ProTargetMiner to treatments that are non-anticancer is investigated in this project. A new proteome signature library was built for 15 versatile drugs with diverse indications, e.g. against allergies, hypertension, and depression. To comprehensively cover the proteome response to these treatments, deep expression profiling was performed in human fibroblast, breast cancer MCF7, and neuron-like SHSY5Y cells using multiplexed LC-MS/MS analysis at an optimized duration of 48h. Here, each collected proteome signature is contrasted against other signatures using OPLS-DA models to deconvolute drug targets, similar to the approach devised in the original ProTargetMiner platform. Furthermore, the drugs are further profiled by a validation technique called Proteome Integral Solubility Alteration (PISA) assay to identify the protein targets that are directly engaged by the molecules. Several known targets and mechanistic proteins are identified in the deep expression profiling experiment and are further verified by the PISA assay. Further testing and literature research could uncover novel targets for the treatments. This platform is expandable to novel drugs and provides a resource for target deconvolution of compounds in preclinical and clinical testing.