Computational discovery and molecular modelling of small-molecule modulators of GDNF

Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuronal loss and motor dysfunction. Glial cell line-derived neurotrophic factor (GDNF) is essential for neuronal maintenance; however, its pathological overexpression has been linked to neuroinflammation and PD progression. This study presents an integrative in silico strategy to identify novel small-molecule inhibitors targeting GDNF to mitigate its pro-inflammatory effects. A structure-based virtual screening workflow in Maestro v13.4 evaluated 28.5 million compounds using HTVS, SP, and XP docking protocols. Five lead molecules displayed stronger binding affinities than the reference inhibitor SOS (-6.678 kcal/mol), forming stable hydrogen-bond and hydrophobic interactions with key GDNF residues. Molecular dynamics simulations over 300 ns confirmed the structural stability of the GDNF-ligand complexes, supported by consistent RMSD/RMSF profiles and favourable MMGB/PBSA binding free energies. Additionally, DFT and PCA/FEL analyses indicated optimal electronic properties and stable conformational dynamics of the identified compounds. Among them, GDNF000064 emerged as the most promising inhibitor capable of modulating GDNF overexpression, suggesting its potential to reduce neuroinflammation and protect dopaminergic neurons. Overall, this computational framework provides valuable insights for the rational design of GDNF-targeted therapeutics for PD.