Structural and ITC Characterization of Peptide‐Protein Binding: Thermodynamic Consequences of Cyclization Constraints, a Case Study on Vascular Endothelial Growth Factor Ligands

• Published in: Chemistry : a European journal Vol. 28; no. 48; pp. e202200465 - n/a
• Main Authors: Gaucher, Jean‐François, Reille‐Seroussi, Marie, Broussy, Sylvain
• Format: Journal Article
• Language: English
• Published: Germany Wiley Subscription Services, Inc 26.08.2022; Wiley-VCH Verlag
• Subjects: Affinity; Amides; Binding; Biochemistry, Molecular Biology; Biophysics; Calorimetry; Calorimetry - methods; Chemical Sciences; Chemistry; Constraints; Cyclization; drug design; Enthalpy; Entropy; Growth factors; helix stabilization; Life Sciences; Ligands; NMR; Nuclear magnetic resonance; Optimization; Organic chemistry; peptide folding thermodynamics; Peptides; Peptides - chemistry; Protein Binding; Proteins; Structural analysis; Structural Biology; Thermodynamics; Titration; Titration calorimetry; Vascular endothelial growth factor; Vascular Endothelial Growth Factor A; vibrational entropy; helix stabilization; drug design; peptide folding thermodynamics; vibrational entropy; lactam bridge; Macromolecular crystallography; NMR; Heat Capacity; macromolecular cristallography; Enthalpy-entropy compensation; peptide folding; Drug design; Isothermal Titration Calorimetry ITC
• ISSN: 0947-6539; 1521-3765; 1521-3765
• DOI: 10.1002/chem.202200465

Macrocyclization constraints are widely used in the design of protein ligands to stabilize their bioactive conformation and increase their affinities. However, the resulting changes in binding entropy can be puzzling and uncorrelated to affinity gains. Here, the thermodynamic (Isothermal Titration Calorimetry) and structural (X‐ray, NMR and CD) analysis of a complete series of lactam‐bridged peptide ligands of the vascular endothelial growth factor, and their unconstrained analogs are reported. It is shown that differences in thermodynamics arise mainly from the folding energy of the peptide upon binding. The systematic reduction in conformational entropy penalty due to helix pre‐organization can be counterbalanced by an unfavorable vibrational entropy change if the constraints are too rigid. The gain in configurational entropy partially escapes the enthalpy/entropy compensation and leads to an improvement in affinity. The precision of the analytical ITC method makes this study a possible benchmark for constrained peptides optimization. Does affinity come from constraint ? The thermodynamic and structural analysis of a series of constrained peptide ligands and unconstrained analogues accurately describes the binding process. It highlights how the variation in conformational and vibrational entropies associated with the constraints impacts the affinity.