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Open Access Highly Accessed Research article

Peptide ligand screening of α-synuclein aggregation modulators by in silico panning

Koichi Abe, Natsuki Kobayashi, Koji Sode and Kazunori Ikebukuro*

Author Affiliations

Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-13 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan

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BMC Bioinformatics 2007, 8:451  doi:10.1186/1471-2105-8-451

Published: 16 November 2007



α-Synuclein is a Parkinson's-disease-related protein. It forms aggregates in vivo, and these aggregates cause cell cytotoxicity. Aggregation inhibitors are expected to reduce α-synuclein cytotoxicity, and an aggregation accelerator has recently been reported to reduce α-synuclein cytotoxicity. Therefore, amyloid aggregation modulating ligands are expected to serve as therapeutic medicines.


We screened peptide ligands against α-synuclein by in silico panning, a method which we have proposed previously. In this study, we selected as the target a very hydrophobic region known as the amyloid-core-forming region. Since this region cannot be dissolved in water, it is difficult to carry out the in vitro screening of its peptide ligand. We carried out 6 rounds of in silico panning using a genetic algorithm and a docking simulation. After the in silico panning, we evaluated the top peptides screened in silico by in vitro assay. These peptides were capable of binding to α-synuclein.


We demonstrated that it is possible to screen α-synuclein-binding peptides by in silico panning. The screened peptides bind to α-synuclein, thus affecting the aggregation of α-synuclein.