We have previously reported that pyrroloquinoline quinone (PQQ) prevents the amyloid formation of alpha-synuclein, amyloid beta(1-42) (A beta(1-42)), and mouse prion protein. Moreover, PQQ-modified alpha-synuclein and a proteolytic fragment of the PQQ-modified alpha-synuclein are able to inhibit the amyloid formation of alpha-synuclein. Here, we identified the peptide sequences that play an important role as PQQ-modified specific peptide inhibitors of alpha-synuclein. We demonstrate that the PQQ-modified alpha-Syn(36-46) peptide, which is a partial sequence of alpha-synuclein, prevented alpha-synuclein amyloid fibril formation but did not inhibit A beta(1-42) fibril formation. In addition, the alpha-synuclein partial peptide modified with other small-molecule inhibitors, Baicalein and epigallocatechin gallate (EGCG), prevented alpha-synuclein fibril formation. Currently reported quinone amyloid inhibitors do not have selectivity toward protein molecules. Therefore, our achievements provide a novel strategy for the development of targeted specific amyloid formation inhibitors: the combination of quinone compounds with specific peptide sequence from target proteins involved in amyloid formation.