Molecular basis of small-molecule binding to α-synuclein
| Autor: | David E. Shaw, Markus Zweckstetter, Fabrizio Giordanetto, Cecily K. Campbell-Bezat, Paul Robustelli, Ibanez-de-Opakua A, Stefan Becker, Albert C. Pan |
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| Rok vydání: | 2021 |
| Předmět: |
0303 health sciences
010304 chemical physics Chemistry C-terminus Chemical shift Rational design Intrinsically disordered proteins 01 natural sciences Small molecule 3. Good health 03 medical and health sciences chemistry.chemical_compound Molecular dynamics Monomer 0103 physical sciences Biophysics Small molecule binding 030304 developmental biology |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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