Novel strategy for medicinal chemistry utilizing protein knockdown

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We have developed a method that induces selective degradation of target proteins by small molecules consisting of cIAP1 ligand linked to a ligand of the target protein (protein knockdown). In this study, protein knockdown was applied to target identification of bioactive small molecules, and degradation of misfolded proteins which would cause neurodegenerative disorders. As a proof of concept, a known target protein was identified with a proteome analysis using a linked molecule consisting of cIAP1 ligand and a small molecule which binds to a protein. On the other hand, molecules consisting of dyes bound to the misfolded proteins linked to cIAP1 ligand were designed and synthesized. The molecule was proved to bind a poly glutamine (polyQ) peptide, a major component of misfoled proteins, and decrease proteins which were immunostained with anti-polyQ antibody in living cells.