Evaluation of a Pooling Chemoproteomics Strategy with an FDA-approved Drug Library

ABSTRACT: Chemoproteomics is a key platform for characterizing the mode of action (MoA) for compounds, especially for targeted protein degraders such as proteolysis targeting chimerics (PROTACs) and molecular glues. With deep proteome coverage, multiplexed tandem mass tag-mass spectrometry (TMT-MS) can tackle up to 18 samples in a single experiment. Here, we present a pooling strategy to further enhance the throughput, and apply the strategy to an FDA-approved drug library (95 best-in-class compounds). The TMT-MS-based pooling strategy was evaluated in the following steps. First, we demonstrated the capability of TMT-MS by analyzing over 15,000 unique proteins (>12,000 gene products) in HEK293 cells treated with five PROTACs (two BRD/BET degraders and three degraders for FAK, ALK, and BTK kinases). We then introduced a rationalized pooling strategy to separate structurally similar compounds in different pools, and identified the proteomic response to 14 pools from the drug library. Finally, we validated the proteomic response from one pool by re-profiling the cells under individual drug treatment with sufficient replicates. Interestingly, numerous proteins were found to change upon drug treatment, including AMD1, ODC1, PRKX, PRKY, EXO1, AEN and LRRC58 by 7-Hydroxystaurosporine; C6orf64, HMGCR and RRM2 by Sorafenib; SYS1 and ALAS1 by Venetoclax; and ATF3, CLK1 and CLK4 by Palbocilib. Thus, the pooling chemoproteomics screening provides an efficient method for dissecting the molecular targets of compound libraries.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Embryonic Stem Cell

DISEASE(S): Kidney Cancer

SUBMITTER: huan sun  

LAB HEAD: Junmin Peng

PROVIDER: PXD033780 | Pride | 2023-03-11

REPOSITORIES: Pride