Thermodynamic and Structural Effects of Macrocyclization as a Constraining Method in Protein-Ligand Interactions.

The thermodynamic and structural effects of macrocyclization as a tactic for stabilizing the biologically active conformation of Grb2 SH2 binding peptides were investigated using isothermal titration calorimetry and X-ray crystallography. 23-Membered macrocycles containing the sequence pYVN were slightly more potent than their linear controls; however, preorganization did not necessarily eventuate in a more favorable binding entropy. Structures of complexes of macrocycle 7 and its acyclic control 8 are similar except for differences in relative orientations of corresponding atoms in the linking moieties of 7 and 8. There are no differences in the number of direct or water-mediated protein−ligand contacts that might account for the less favorable binding enthalpy of 7; however, an intramolecular hydrogen bond between the pY and the pY+3 residues in 8 that is absent in 7 may be a factor. These studies highlight the difficulties associated with correlating energetics and structure in protein−ligand interactions.