Fig. 6

Contributions of thermodynamic affinity and association kinetics to the modulation of dissociation rate constants. a-d Logarithmic plots showing correlation of dissociation rate constant k _off (x axis) with the association rate constant, k _on, and the dissociation constant, K _D, (y axis) of compounds 1–20 determined by SPR for N-HSP90 WT (a, b) and L107A mutant (c, d). Points representing compounds assigned as loop-binders are colored black and compounds assigned as helix-binders are colored red. The black line is the linear regression with R ² representing the coefficient of determination and R the correlation coefficient. The gray lines represent the 99% upper and lower confidence intervals. The error bars represent the standard deviation of at least three measurements. The red and black shaded regions highlight the different kinetic profiles of helix- and loop-binders, respectively. k _off is not strongly correlated either with k _on or with K _D for N-HSP90 WT. Thus, an increase of residence time is driven by a combination of GS stabilization and TS destabilization. For the L107A mutant, k _off is strongly correlated with K _D (R=0.69 for WT and R=0.93 for L107A) and not correlated with k _on (R=0.48 for WT and R=0.017 for L107A), indicating that residence time is mainly driven by GS stabilization. These relations are shown on the right in schematic pseudo 1-step free energy profiles for the binding reaction of helix- and loop-binders (shown in red and black, respectively; the filled area indicates the energy distribution among the entire compound series) Red and black dashed lines indicate average free energy values for the helix-and loop-binders, respectively. e, f The binding pocket shape observed in the crystal structures of N-HSP90 WT and L107A mutant for loop- and helical- complexes (e, f, respectively). Two alternative conformations observed in the crystal structures are shown for the L107A mutant co-crystallized with compound 6 in e The molecular surface of the protein is colored from red to white indicating increasing hydrophobicity