Design and Development of Pi-Pi Staple Peptides Targeting Alpha-Synuclein for Parkinson’s Treatment
Primary Investigator (PI) Name
Mohammad Halim
Department
CSM – Chemistry and Biochemistry
Abstract
Parkinson’s disease (PD) is a progressive neurodegenerative disorder marked by pathological aggregation of α-synuclein, an intrinsically disordered protein. Peptide-based inhibitors offer a promising therapeutic strategy to block α-synuclein aggregation. This study aimed to design, synthesize, and evaluate peptide candidates with inhibitory potential. Twelve peptides were initially screened from SynPEP-DB using molecular docking to predict binding interactions with α-synuclein. Five top candidates with favorable docking scores were synthesized via solid-phase peptide synthesis (SPPS) and characterized by LC-MS. Binding affinities were quantified using selected ion monitoring mass spectrometry (SIM-MS), which confirmed strong peptide–protein interactions. Three peptides showed nanomolar affinity with dissociation constants (Kd) of 22.98, 63.53, and 65.57 nM. Structural analogs were also evaluated, and an α-methylated peptide exhibited the strongest binding (Kd = 21.49 nM). On the other hand, α-synuclein fibril reduction was evaluated using the Thioflavin T fluorescence assay. The α-methylated analogue exhibited a significant 89.2% reduction in fibril formation, compared to other top candidates showing reductions ranging from 66.6% to 87.8%. These findings validate computational predictions and demonstrate that methylation effectively enhances peptide activity. This integrated computational–experimental approach provides a rational framework for peptide drug discovery targeting α-synuclein aggregation. The combined SIM-MS and ThT fluorescence results offer proof-of-concept that α-methylation improves fibril reduction, supporting the potential of pi-pi staple peptides as inhibitors of α-synuclein aggregation for Parkinson’s disease (PD)Treatment. Future work will aim to further enhance peptide stability and activity through structural modifications such as cyclization and targeted methylation.
Disciplines
Medicinal-Pharmaceutical Chemistry | Organic Chemistry
Design and Development of Pi-Pi Staple Peptides Targeting Alpha-Synuclein for Parkinson’s Treatment
Parkinson’s disease (PD) is a progressive neurodegenerative disorder marked by pathological aggregation of α-synuclein, an intrinsically disordered protein. Peptide-based inhibitors offer a promising therapeutic strategy to block α-synuclein aggregation. This study aimed to design, synthesize, and evaluate peptide candidates with inhibitory potential. Twelve peptides were initially screened from SynPEP-DB using molecular docking to predict binding interactions with α-synuclein. Five top candidates with favorable docking scores were synthesized via solid-phase peptide synthesis (SPPS) and characterized by LC-MS. Binding affinities were quantified using selected ion monitoring mass spectrometry (SIM-MS), which confirmed strong peptide–protein interactions. Three peptides showed nanomolar affinity with dissociation constants (Kd) of 22.98, 63.53, and 65.57 nM. Structural analogs were also evaluated, and an α-methylated peptide exhibited the strongest binding (Kd = 21.49 nM). On the other hand, α-synuclein fibril reduction was evaluated using the Thioflavin T fluorescence assay. The α-methylated analogue exhibited a significant 89.2% reduction in fibril formation, compared to other top candidates showing reductions ranging from 66.6% to 87.8%. These findings validate computational predictions and demonstrate that methylation effectively enhances peptide activity. This integrated computational–experimental approach provides a rational framework for peptide drug discovery targeting α-synuclein aggregation. The combined SIM-MS and ThT fluorescence results offer proof-of-concept that α-methylation improves fibril reduction, supporting the potential of pi-pi staple peptides as inhibitors of α-synuclein aggregation for Parkinson’s disease (PD)Treatment. Future work will aim to further enhance peptide stability and activity through structural modifications such as cyclization and targeted methylation.