An Integrated Machine Learning Approach Delineates an Entropic Expansion Mechanism for the Binding of a Small Molecule toα-Synuclein

The mis-folding and aggregation of intrinsically disordered proteins (IDPs) such asα-synuclein (αS) underlie the pathogenesis of various neurodegenerative disorders. However, targetingαS with small molecules faces challenges due to its lack of defined ligand-binding pockets in its disordered structure. Here, we implement a deep artificial neural network based machine learning approach, which is able to statistically distinguish fuzzy ensemble of conformational substates ofαS in neat water from those in aqueous fasudil (small molecule of interest) solution. In particular, the presence of fasudil in the solvent either modulates pre-existing states ofαS or gives rise to new conformational states ofαS, akin to an ensemble-expansion mechanism. The ensembles display strong conformation-dependence in residue-wise interaction with the small molecule. A thermodynamic analysis indicates that small-molecule modulates the structural repertoire ofαS by tuning protein backbone entropy, however entropy of the water remains unperturbed. Together, this study sheds light on the intricate interplay between small molecules and IDPs, offering insights into entropic modulation and ensemble expansion as key biophysical mechanisms driving potential therapeutics.