Does the sequence of a disordered protein encode small molecule binding paths?

Abstract

Ligand binding to intrinsically disordered proteins resists description in terms of conventional binding pockets, yet it can be analysed as a dynamic process in which ligands move across transient surface interaction sites. Here we characterise a pathway-based representation in which ligand binding is described as a sequence of transitions between residue-defined microstates, enabling ligand-specific effects to be distinguished from intrinsic properties of the peptide conformational ensemble. Using all-atom molecular dynamics simulations of A{beta}42 and the C-terminal region of -synuclein in complex with chemically diverse small molecules, we construct transition matrices that encode ligand movement across the peptide surface and use Markov state models to identify dominant binding pathways and relative binding propensities. Pairwise enrichment-factor and AUC analyses reveal strong conservation of the highest-ranked pathways across chemically diverse ligands, with enrichment factors of 15-45 for the top-ranked states and AUC values typically [≥]0.75, well above random expectation. These dominant pathways are also preserved across changes in pH and temperature, whereas a urea control, included as a non-specific binder, shows reduced enrichment, indicating that ligands primarily modulate pathway weights rather than define the underlying network topology. Ensemble docking across chemically diverse libraries further supports the presence of recurrent ligand-accessible hotspots within the peptide conformational ensemble. Building on this framework, we apply a prospective screening pipeline to A{beta}42, combining MSM-derived hotspots with sequence-based Ligand-Transformer scoring and Gnina docking across 1.66 million compounds, to nominate 19 candidates for prospective experimental evaluation. Together, these results indicate that disordered protein sequences give rise to conformational ensembles that exhibit characteristic binding pathways for small molecules.