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Background  Identification of the target proteins of bioactive compounds is critical for elucidating the mode of action; however, target identification has been difficult in general, mostly due to the low sensitivity of detection using affinity chromatography followed by CBB staining and MS/MS analysis.    Results  We applied our protocol of predicting target proteins combining  in silico  screening and experimental verification for incednine, which inhibits the anti-apoptotic function of Bcl-xL by an unknown mechanism. One hundred eighty-two target protein candidates were computationally predicted to bind to incednine by the statistical prediction method, and the predictions were verified by  in vitro  binding of incednine to seven proteins, whose expression can be confirmed in our cell system.  As a result, 40% accuracy of the computational predictions was achieved successfully, and we newly found 3 incednine-binding proteins.    Conclusions  This study revealed that our proposed protocol of predicting target protein combining  in silico  screening and experimental verification is useful, and provides new insight into a strategy for identifying target proteins of small molecules.

Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications