An Integrated Machine Learning Approach Delineates an Entropic Expansion Mechanism for the Binding of a Small Molecule to α-synuclein

The mis-folding and aggregation of intrinsically disordered proteins (IDPs) such as -synuclein (S) underlie the pathogenesis of various neurodegenerative disorders. However, targeting S 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 of S 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 of S or gives rise to new conformational states of S, 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 of S 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.