Proteomics

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LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes, p2

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 leads. We have developed a drug target deconvolution approach with an automated data analysis pipeline, based on limited proteolysis coupled with mass spectrometry that works across species including in human cells (LiP-Quant). Here we demonstrate drug target identification by LiP-Quant across compound classes, including with drugs targeting kinases and phosphatases . We demonstrate that LiP-Quant identifies drug binding sites, a unique feature of this approach, and that it can be used to estimate drug EC50s 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.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Ilaria Piazza  

LAB HEAD: Dr. Lukas Reiter

PROVIDER: PXD018204 | Pride | 2020-09-09

REPOSITORIES: Pride

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Action DRS
20200115_110652_618-Exp1-15minRapa-ExpSpecLib-SparseNoImput.sne Other
20200116_131036_601-Exp5-ProscADR-Qvalue.sne Other
J_D190925_S601-Exp5-library01of12_MSG_R01_T0.raw Raw
J_D190925_S601-Exp5-library02of12_MSG_R01_T0.raw Raw
J_D190925_S601-Exp5-library03of12_MSG_R01_T0.raw Raw
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A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes.

Piazza Ilaria I   Beaton Nigel N   Bruderer Roland R   Knobloch Thomas T   Barbisan Crystel C   Chandat Lucie L   Sudau Alexander A   Siepe Isabella I   Rinner Oliver O   de Souza Natalie N   Picotti Paola P   Reiter Lukas L  

Nature communications 20200821 1

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 the development of optimized small-molecule compounds. Current approaches cannot identify the protein targets of a compound and also detect the interaction surfaces between ligands and protein targets without prior labeling or modification. To address this limitation, we here develop LiP-Quant, a drug target deconvolution pipeline based  ...[more]

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