Target proteins are functional biomolecules that are addressed and controlled by biologically active compounds. The identification of target proteins is a key element of
understanding molecular mechanism of action of ligands, since the interaction with target proteins is particular important for molecular biology, molecular pharmacy. To identify target proteins, new technologies are being developed. In this protocol, we developed a new system to identify target proteins in PC-3 cells of natural compound, Ganoderic acid DM (1). Ganoderic acid DM (1) is a naturally occurring triterpenoid of Ganoderma which exhibits distinct pharmacological effects. We used ganoderic acid DM-conjugated magnetic beads as a probe, and Tublin was identified as a ganoderic acid DM-binding protein using LC-MS/MS. Ganoderic acid DM should exert its cytotoxicity by binding with tubulin, and showed the microtubule-stabilizing activity comparable to the well-established antimitotic chemotherapeutic drug, paclitaxel. We also show that this technique is capable of detecting different target proteins of other compounds among cells. The whole protocol, starting from bead conjugation can be completed within 4 days.