Systems, methods, and compositions to identify new protein targets of a chemical compound or its derivatives

A method for a detection of novel binding proteins of a pharmaceutical chemical compound or its derivatives performed with lysates from cultured human cells, comprising following steps:

• (a) generating a detection agent raised by a complex of the pharmaceutical chemical compound conjugated with a protein carrier, wherein the pharmaceutical chemical compound is protein tyrosine kinase inhibitor or protein tyrosine phosphatase inhibitor;
• wherein the protein tyrosine kinase inhibitor is afatinib, or its derivatives erlotinib or gefitinib;
• and wherein the protein tyrosine phosphatase inhibitor is phenyl vinyl sulfone (PVS), or its derivatives phenyl vinyl sulfonate (PVSN) or Bay 11-7082;
• the detection agent is antiserum, single-chain variable fragment binding protein, monoclonal antibody in any immunoglobulin format, or a combination thereof, which is against the pharmaceutical chemical compound;
• (b) generating cellular lysates after the pharmaceutical chemical compound treatment from cultured human cells;
• (c) executing an immunoprecipitation performed with the cellular lysates and the detection agent to immunoprecipitate a complex of the pharmaceutical chemical compound and its target binding proteins;
• (d) executing a proteomic analysis to identify the target binding proteins of the pharmaceutical chemical compound.