4 billion molecule virtual screen against alpha-synuclein for an inhibitor of prion propagation

Intro: Alpha-synuclein is an intrinsically disordered protein that forms prions in a variety of neurodegenerative diseases. Prion conformation is context specific. This study is a structure-based virtual screen against alpha-synuclein prions from patients with Multiple Systems Atrophy (MSA). The same ultra-large library was screened against MSA Type A and MSA Type B fibrils.

Objective: The objective of this study is to identify ligands that inhibit prion propagation of alpha-synuclein MSA Type A and MSA Type B fibrils.

Methods: The study employs molecular docking software SymDOCK to virtually screen over 4-billion molecules from the ZINC22 database of commercially available compounds. A physics-based scoring function is used to rank each molecule according to its computed binding energy. SymDOCK only scores poses that can form a symmetric stack matching the symmetry of the prion fibril. A cell-based prion propagation assay detects inhibition with fluorescence microscopy. HEK293T cells expressing YFP-tagged alpha-synuclein are incubated with patient-derived MSA prion transfection complexes and ligand. If the ligand fails to inhibit prion propagation, fluorescent puncta form.

Results: Computed binding energy and predicted non-covalent interactions for billions of molecules guide the selection of molecules to purchase for testing. The assay has demonstrated dozens of molecules that can inhibit prion propagation with EC50 values in the two-digit nanomolar range.

Conclusion: Molecular docking can help identify molecules that inhibit prion propagation.