QSAR-Guided Virtual Screening and Molecular Dynamics Reveal Olaparib as a Repurposing Lead Against α-Synuclein Aggregation

Abstract

Parkinson's disease (PD) is characterised by the pathological aggregation of α-synuclein (α-syn) into Lewy body inclusions, yet no disease-modifying therapy exists. To address this, we developed an integrated computational pipeline combining quantitative structure-activity relationship (QSAR) modelling, structure-based virtual screening, molecular dynamics (MD) simulation, and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations to repurpose FDA-approved drugs as α-syn fibril inhibitors. Two complementary QSAR model families were trained on 501 α-syn binding affinity records from BindingDB: Morgan extended-connectivity fingerprint (ECFP4) classifiers and a frozen ChemBERTa-77M-MLM transformer encoder, each using Random Forest and Logistic Regression. The applicability domain (AD) was assessed using Morgan-Tanimoto similarity (Tc ≥ 0.40) and calibrated ChemBERTa cosine distance (θ ≤ 0.367). A three-stage funnel applying central nervous system (CNS) permeability filters, a consensus QSAR probability threshold (≥0.80), and AD gating reduced 2241 FDA-approved drugs to 205 candidates for AutoDock Vina 1.2.6 docking against two sites on the cryo-electron microscopy (cryo-EM) α-syn fibril structure, PDB 6SSX: the inter-protofilament cleft (Site 1) and the non-amyloid-beta component (NAC) groove (Site 2). The Morgan fingerprint models achieved an area under the receiver operating characteristic curve (AUROC) of up to 0.940 and a balanced accuracy of 0.810; the ChemBERTa models achieved an AUROC of 0.785 and a balanced accuracy of 0.728. Notably, ChemBERTa AD covered 76.8% of the FDA drugs versus only 5.5% for Morgan-Tanimoto, enabling broad-spectrum screening. The top docking candidates were Olaparib (-7.91 kcal/mol), Paliperidone (-7.75 kcal/mol), Niraparib (-7.18 kcal/mol), Dordaviprone (-7.06 kcal/mol), and Parecoxib (-6.89 kcal/mol). The MD simulations over 200 ns across three independent replicates confirmed stable NAC groove binding, and replicate-averaged MM-PBSA calculations yielded ΔG = -20.6 ± 1.9 kcal/mol for Olaparib at Site 2, -17.1 ± 0.9 kcal/mol for Risperidone, and -16.9 ± 0.8 kcal/mol for Paliperidone, reported as the mean ± standard error of the mean (SEM) across replicates. Olaparib additionally formed five hydrogen bonds in the representative pose, while MD trajectories maintained approximately 2-5 hydrogen bonds, together with a halogen bond within the NAC groove, the largest contact count of any screened compound. These findings identify Olaparib as a novel high-affinity repurposing lead, while Paliperidone and Risperidone are reported as chemically informative secondary NAC-groove binders rather than proposed antiparkinsonian therapeutics, given that their dopamine D2-antagonist pharmacology is clinically associated with drug-induced parkinsonism. All of the candidates warrant experimental validation via thioflavin-T fluorescence or nuclear magnetic resonance (NMR) spectroscopy.