Thermodynamic evaluation of torsional strain in peptide backbones : studies on constrained tripeptide Grb2 adaptor protein inhibitors

Abstract

A substantial challenge in ligand design for protein-ligand interactions is the accurate prediction of changes in binding energy associated with small structural variations in ligands. In a previous study analyzing the binding energetics of varied hydrophobic surface area in peptide mimics, we observed an unfavorable gauche conformation in the pY+3 sidechain of an inhibitor of growth receptor bound protein 2 (Grb2) SH2 domain. To investigate the change in binding energy from alleviating of torsional strain in the protein-ligand complex, constrained ligand analogues containing a cyclopropane ring were designed to reduce the energetic penalty associated with adopting a gauche conformation, potentially enhancing binding enthalpy. Additionally, the cyclopropane ring serves to preorganize the ligand by positioning the terminal substituent in a similar fashion to the bound state of the flexible control, potentially enhancing binding entropy. Thus, the proposed constrained ligands present a unique opportunity to enhance both binding enthalpy and entropy with a single modification. The synthesis of three constrained peptide mimics will be discussed. Additionally, optimization of the growth and expression of Grb2 SH2 for binding analysis with the prepared ligands will be discussed.