Streamlined Proteome-Wide Identification of Drug Targets Indicates Organ-Specific Engagement

Abstract

Proteins are the primary targets of almost all small molecule drugs. However, even the most selectively designed drugs can potentially target several unknown proteins. Identification of potential drug targets can facilitate design of new drugs and repurposing of existing ones. Current state-of-the-art proteomics methodologies enable screening of thousands of proteins against a limited number of drug molecules. Here we report the development of a label-free quantitative proteomics approach that enables proteome-wide screening of small organic molecules in a scalable, reproducible, and rapid manner by streamlining the proteome integral solubility alteration (PISA) assay. We used rat organs ex-vivo to determine organ specific targets of medical drugs and enzyme inhibitors to identify novel drug targets for common drugs such as Ibuprofen. Finally, global drug profiling revealed overarching trends of how small molecules affect the proteome through either direct or indirect protein interactions.

ThermoTargetMiner as a proteome integral solubility alteration target database for prospective drugs against lung cancer

“…Two research groups have tried to push PISA to large-scale experiments. Olsen group used q-value ≤ 0.05 and an absolute log2transformed fold-change ≥ 0.5 as the cut-offs 66 . Alternatively, Gygi group acquired data from two replicates and chose cut-offs based on log2-transformed fold-changes and standard deviations 67 .…”

“…The fold-changes were then calculated as the ratios of the protein abundances in treated samples vs those of the controls. Batch effects among three biological replicates were removed using Limma package 66 . For each protein, the median fold-change was used for further analysis, and the p-values were calculated by the two-sided Student's t-test on the normalized abundances in treated samples vs those in controls.…”