- Paradoxically, Most Flexible Ligand Binds Most Entropy-Favored: Intriguing Impact of Ligand Flexibility and Solvation on Drug-Kinase Binding
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Biophysical parameters can accelerate drug development; e.g., rigid ligands may reduce entropic penalty and improve binding affinity. We studied systematically the impact of ligand rigidification on thermodynamics using a series of fasudil derivatives inhibiting protein kinase A by crystallography, isothermal titration calorimetry, nuclear magnetic resonance, and molecular dynamics simulations. The ligands varied in their internal degrees of freedom but conserve the number of heteroatoms. Counterintuitively, the most flexible ligand displays the entropically most favored binding. As experiment shows, this cannot be explained by higher residual flexibility of ligand, protein, or formed complex nor by a deviating or increased release of water molecules upon complex formation. NMR and crystal structures show no differences in flexibility and water release, although strong ligand-induced adaptations are observed. Instead, the flexible ligand entraps more efficiently water molecules in solution prior to protein binding, and by release of these waters, the favored entropic binding is observed.
- Wienen-Schmidt, Barbara,Jonker, Hendrik R. A.,Wulsdorf, Tobias,Gerber, Hans-Dieter,Saxena, Krishna,Kudlinzki, Denis,Sreeramulu, Sridhar,Parigi, Giacomo,Luchinat, Claudio,Heine, Andreas,Schwalbe, Harald,Klebe, Gerhard
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- Treatment of amyloidosis associated with Alzheimer disease using modulators of protein phosphorylation
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A method of regulating phosphorylation of proteins involved in controlling processing or function of key proteins found in intracellular neurofibrillary tangles and extracellular amyloid plaques associated with Alzheimer disease comprising introducing an effective amount of a kinase modulator or phosphatase modulator, the modulator capable of increasing or decreasing the rate of proteolytic processing, or modulating the function, of said key proteins.
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