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024 7 _ |a 10.1021/jacs.1c07591
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024 7 _ |a 1520-5126
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024 7 _ |a 1943-2984
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037 _ _ |a DZNE-2022-00161
041 _ _ |a English
082 _ _ |a 540
100 1 _ |a Robustelli, Paul
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245 _ _ |a Molecular Basis of Small-Molecule Binding to α-Synuclein.
260 _ _ |a Washington, DC
|c 2022
|b American Chemical Society
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520 _ _ |a 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-time-scale, 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.
536 _ _ |a 352 - Disease Mechanisms (POF4-352)
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650 _ 7 |a Intrinsically Disordered Proteins
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650 _ 7 |a Ligands
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650 _ 7 |a Small Molecule Libraries
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650 _ 7 |a alpha-Synuclein
|2 NLM Chemicals
650 _ 7 |a 1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine
|0 84477-87-2
|2 NLM Chemicals
650 _ 7 |a fasudil
|0 Q0CH43PGXS
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650 _ 2 |a 1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine: analogs & derivatives
|2 MeSH
650 _ 2 |a 1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine: chemistry
|2 MeSH
650 _ 2 |a 1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine: metabolism
|2 MeSH
650 _ 2 |a Amino Acid Sequence
|2 MeSH
650 _ 2 |a Hydrogen Bonding
|2 MeSH
650 _ 2 |a Intrinsically Disordered Proteins: chemistry
|2 MeSH
650 _ 2 |a Intrinsically Disordered Proteins: metabolism
|2 MeSH
650 _ 2 |a Ligands
|2 MeSH
650 _ 2 |a Molecular Conformation
|2 MeSH
650 _ 2 |a Molecular Dynamics Simulation
|2 MeSH
650 _ 2 |a Protein Binding
|2 MeSH
650 _ 2 |a Small Molecule Libraries: chemistry
|2 MeSH
650 _ 2 |a Small Molecule Libraries: metabolism
|2 MeSH
650 _ 2 |a alpha-Synuclein: metabolism
|2 MeSH
700 1 _ |a Ibanez de Opakua, Alain
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700 1 _ |a Campbell-Bezat, Cecily
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700 1 _ |a Giordanetto, Fabrizio
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700 1 _ |a Becker, Stefan
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700 1 _ |a Zweckstetter, Markus
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700 1 _ |a Pan, Albert C
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700 1 _ |a Shaw, David E
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773 _ _ |a 10.1021/jacs.1c07591
|g Vol. 144, no. 6, p. 2501 - 2510
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|t Journal of the American Chemical Society
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