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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.
The crystal structure of C12H11N2SiCl3 (monoclinic, P21/m, Z = 2, with a: 9.284(4), b: 7.226(2), c: 10.832(5) Å, β = 115.14(3)°) was refined to R(F) =0.035 from 1228 independent reflections. A trigonal bipyramidal, pentacoordinate silicon is observed. The chelated complex shows two different Si−N bonds, a coordinative bond (1.984(2) Å) between Si and N on the axial position and a Si−N single bond (1.737(3) A, equatorial plane), introduced by chemical reaction. The coordinative bond is 14.2% longer than the Si−N single bond. The lengthening of the coordinative bond in the present case is compared with distances in other extracoordinated silicon compounds.