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bioRxiv · 10.1101/860072

LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes

Piazza, I.·Beaton, N.·Bruderer, R.·Knobloch, T.·Barbisan, C.·Siepe, I.·Rinner, O.·de Souza, N.·Picotti, P.·Reiter, L.
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Abstract

Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in developing optimized small-molecule compounds. Current unbiased approaches cannot directly pinpoint the interaction surfaces between ligands and protein targets. To address his limitation we have developed a new drug target deconvolution approach based on limited proteolysis coupled with mass spectrometry that works across species including human cells (LiP-Quant). LiP-Quant features an automated data analysis pipeline and peptide-level resolution for the identification of any small-molecule binding sites, Here we demonstrate drug target identification by LiP-Quant across compound classes, including compounds targeting kinases and phosphatases. We demonstrate that LiP-Quant estimates the half maximal effective concentration (EC50) of compound binding sites in whole cell lysates. LiP-Quant identifies targets of both selective and promiscuous drugs and correctly discriminates drug binding to homologous proteins. We finally show that the LiP-Quant technology identifies targets of a novel research compound of biotechnological interest.

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Piazza, I., Beaton, N., Bruderer, R., Knobloch, T., Barbisan, C., Siepe, I., Rinner, O., de Souza, N., Picotti, P., Reiter, L.. 2019-12-01. LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes. https://doi.org/10.1101/860072

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