Structure-based thermodynamic design of peptide ligands: Application to peptide inhibitors of the aspartic protease endothiapepsin

Abstract

The prediction of binding affinities from structure is a necessary requirement in the development of structure-based molecular design strategies. In this paper, a structural parameterization of the energetics previously developed in this laboratory has been incorporated into a molecular design algorithm aimed at identifying peptide conformations that minimize the Gibbs energy. This approach has been employed in the design of mutants of the aspartic protease inhibitor pepstatin A. The simplest design strategy involves mutation and/or chain length modification of the wild-type peptide inhibitor. The structural parameterization allows evaluation of the contribution of different amino acids to the Gibbs energy in the wild-type structure, and therefore the identification of potential targets for mutation in the original peptide. The structure of the wild-type complex is used as a template to generate families of conformational structures in which specific residues have been mutated. The most probable conformations of the mutated peptides are identified by systematically rotating around the side-chain and backbone torsional angles and calculating the Gibbs potential function of each conformation according to the structural parametrization. The accuracy of this approach has been tested by chemically synthesizing two different mutants of pepstatin A. In one mutant, the alanine at position five has been replaced by a phenylalanine, and in the second one a glutamate has been added at the carboxy terminus of pepstatin A. The thermodynamics of association of pepstatin A and the two mutants have been measured experimentally and the results compared with the predictions. The difference between experimental and predicted Gibbs energies for pepstatin A and the two mutants is 0.23 +/- 0.06 kcal/mol. The excellent agreement between experimental and predicted values demonstrates that this approach can be used in the optimization of peptide ligands.

The Regulatory Subunit of PKA-I Remains Partially Structured and Undergoes β-Aggregation upon Thermal Denaturation

“…A theoretical Δ H (Δ H calc ) value at the denaturation temperatures was calculated based on the crystal structure of the cAMP saturated protein (PDB 1RGS; [7]), using the structure-energetics relationships developed by Freire and co-workers [20], [21] (see [22] for specific equations). The Δ H calc -value of 236 kcal/mol (Table 1) lies within the range expected for a protein of this size.…”

“…The theoretical Δ H (Δ H calc ) based on crystal structures were obtained using well-known structure-energetics relationships [20], [21] as described previously [22].…”

Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation

“…A well‐known problem with molecular docking is that of false negatives, molecules that would inhibit the target but are not identified as hits. False negatives are often due to limitations or inaccuracies in the docking scoring function 38, 39. This problem is compounded because there is a large number of analogs in most databases, and the differences in scores between docking hits is often small.…”

Thermodynamic characterization of the interaction between TRAF2 and tumor necrosis factor receptor peptides by isothermal titration calorimetry

“…The current structural energetics formulations assume that the thermodynamic parameters, including ⌬H, ⌬S, and ⌬Cp, can be directly related to the surface area burial of polar and apolar groups (35,36). Unexpectedly, the calculation for the TRAF2-CD30 interaction showed a poor agreement with experimental data (Tables 1 and 2), even though these formulations have been successfully used in predicting energetics of ligand binding in many cases (44,45). The calculation suggests that the entropic change is the major contributor of the interaction.…”