PT  - JOURNAL ARTICLE
AU  - Robustelli, Paul
AU  - Ibanez-de-Opakua, Alain
AU  - Campbell-Bezat, Cecily
AU  - Giordanetto, Fabrizio
AU  - Becker, Stefan
AU  - Zweckstetter, Markus
AU  - Pan, Albert C.
AU  - Shaw, David E.
TI  - Molecular basis of small-molecule binding to α-synuclein
AID  - 10.1101/2021.01.22.426549
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.22.426549
4099  - http://biorxiv.org/content/early/2021/01/24/2021.01.22.426549.short
4100  - http://biorxiv.org/content/early/2021/01/24/2021.01.22.426549.full
AB  - Intrinsically disordered proteins (IDPs) are implicated in many human diseases. They have generally not been amenable to conventional structure-based drug design, however, because their intrinsic conformational variability has precluded an atomic-level understanding of their binding to small molecules. Here we present long-timescale, atomic-level molecular dynamics (MD) simulations of monomeric α-synuclein (an IDP whose aggregation is associated with Parkinson’s disease) binding the small-molecule drug fasudil in which the observed protein-ligand interactions were found to be in good agreement with previously reported NMR chemical shift data. In our simulations, fasudil, when bound, favored certain charge-charge and π-stacking interactions near the C terminus of α-synuclein, but tended not to form these interactions simultaneously, rather breaking one of these interactions and forming another nearby (a mechanism we term dynamic shuttling). Further simulations with small molecules chosen to modify these interactions yielded binding affinities and key structural features of binding consistent with subsequent NMR experiments, suggesting the potential for MD-based strategies to facilitate the rational design of small molecules that bind with disordered proteins.Competing Interest StatementThe authors have declared no competing interest.