An entropic expansion mechanism modulates small-molecule recognition by alpha-synuclein.

Abstract

Aberrant misfolding and progressive aggregation of the intrinsically disordered protein, alpha-synuclein, is associated with the etiology of several neurodegenerative diseases. However, the structurally heterogeneous ensemble of alpha-synuclein precludes the implementation of conventional structure-based drug discovery methods with small molecules targeted to interact with a well-defined binding pocket. Here, by harnessing powerful framework of Markov State Models on unprecedentedly long millisecond atomistic simulation trajectories of monomeric alpha-synuclein interacting with the small-molecule drug fasudil, we identify exhaustive sets of metastable binding-competent states of alpha-synuclein. Characterisation and comparison of the metastable states in the presence and absence of the small molecule in the system indicate that interaction with the small molecule facilitates the protein to explore both more compact and more extended conformational states hitherto undetectable in neat water, thereby broadening the structural repertoire via an ‘entropy expansion’ mechanism. These states exhibit diverse modes of interaction with the small molecule involving the entirety of the protein, albeit the predominant interactions lie in the negatively charged C-terminal region. Subsequent simulation of dimerization process shows that fasudil can retard the self-aggregation propensity of the alpha-synuclein via creating multiple distinct states using similar entropic-expansion mechanism. In particular, due to presence of small molecules, conformations featuring aggregation-resistant long-range interactions are populated that has an inhibitory effect on the early dimerisation propensity of alpha-synuclein. This demonstrated ability of small-molecule illustrates its ensemble-modulatory effect on IDPs that can be effectively utilised for therapeutic strategies probing aggregation-related diseases.