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

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.Protein misfolding and aggregation are involved in many diseases, such as Alzheimer's disease, Parkinson's disease and Prion disease, and such proteins accumulate as inclusion bodies in the brain. Lewy bodies are inclusion bodies observed in Parkinson's-disease patients. The major component of the Lewy body is amyloid-like fibrils of α-synuclein [1]. The familial mutants of α-synuclein A53T, A30P and E46K accelerate α-synuclein aggregation and/or fibrillation and cause autosomal-dominant Parkinson's disease [2-4]. These results strongly support the idea that α-synuclein is the pathogenic protein of Parkinson's disease. It is known that α-synuclein is one of the natively unfolded proteins which have little or no ordered secondary structure under physiological condition. However, changes in various environmental factors (e.g., pH, ion strength, agitation) induce the formation of α-synuclein aggregates and amyloid-like fibrils in vitro [5]. Especially, the aggregates called "protofibrils," an intermediate in the fibrillogenesis process, have more cytotoxicity than the amyloid-like fibrils of most of the proteins which generate fibrils [6]. Therefore, aggregation inhibitors are expected to serve as therap