Protein target identification of CL16 in HCT116 cells by an alkyne probe, CL16-alkyne

By coupling activity-based protein profiling (ABPP) with covalent ligand screening experiment, we have identified a cysteine-reactive covalent ligand, CL16, which can bind strongly and selectively with RhoA in vitro. In this experiment, we investigated the protein targets of CL16 in colorectal cancer HCT116 cells by a molecular probe of CL16, CL16-alkyne. HCT116 cells were pretreated with solvent vehicle or CL16, followed by CL16-alkyne. The cells were lysed, and the CL16-alkyne-labeled proteins were then installed with desthiobiotin through copper-catalyzed azide-alkyne cycloaddition (CuAAC), enriched, tryptic digested and profiled by LC-MS/MS. Peptides with fold change (Control/CL16)>4 and p<0.05 (i.e. at least 75% occupancy and statistical significance) were considered as targets bound with CL16.