Mechanisms
Hydrocarbon-stapled peptides jam the self-binding switch of CETP more than fivefold better, a new route to blocking the protein (J Mol Graph Model 2020)
Original title: Molecular modeling and rational design of hydrocarbon-stapled/halogenated helical peptides targeting CETP self-binding site: Therapeutic implication for atherosclerosis
The C-terminal amphipathic alpha-helix of CETP acts as a self-binding peptide that reversibly binds its own cognate site within the protein to carry out lipid transfer, making that self-binding site a druggable target. Earlier work derived a halogenated version of this helical peptide to competitively disrupt self-binding, but it achieved only a roughly threefold affinity gain and modest potency. This study used hydrocarbon-stapling to reduce the large intrinsic conformational disorder of the peptide in its unbound state, which otherwise imposes an entropy penalty on rebinding. Molecular dynamics simulations and circular dichroism confirmed the stapled peptides were less disordered when free, and energetics calculations plus fluorescence assays showed stapled and halogenated peptides improved binding affinity for the self-binding site by more than fivefold over the native peptide, without altering the underlying binding mode. A computational and biophysical proof-of-concept for a distinct CETP-inhibition mechanism, with no animal or clinical testing.
Original abstract
The human plasma cholesteryl ester transfer protein (CETP) collects triglycerides from very-/low-density lipoproteins (V/LDL) and exchanges them for cholesteryl esters from high-density lipoproteins (HDL), which has recognized as an important therapeutic target for atherosclerosis. The protein has a C-terminal amphipathic α-helix that serves as self-binding peptide to fulfill biological function by dynamically binding to/unbinding from its cognate site (termed self-binding site) in the same protein. Previously, we successfully derived and halogenated the helical peptide to competitively disrupt the self-binding behavior of CETP C-terminal tail. However, the halogenated peptides have only a limited affinity increase as compared to native helical peptide (∼3-fold), thus exhibiting only a moderate competitive potency. Here, instead of optimizing the direct intermolecular interaction of peptide with CETP self-binding site we attempt to further improve the peptide competitive potency by reducing its conformational flexibility with hydrocarbon-stapling technique. Computational analysis reveals that the helical peptide has large intrinsic disorder in unbound free state, which would incur a considerable entropy penalty upon rebinding to the self-binding site. All-hydrocarbon bridge is designed and optimized on native and halogenated peptides in terms of the helical pattern and binding mode of self-binding peptide. Dynamics simulation and circular dichroism indicate that the stapling can considerably reduce peptide disorder in free state. Energetics calculation and fluorescence assay conform that the binding affinity of stapled/halogenated peptides is improved substantially (by > 5-fold), thus exhibiting an effective competition potency with native peptide for the self-binding site. Structural examination suggests that the binding modes and nonbonded interactions of native and halogenated peptides are not influenced essentially due to the stapling.
Summary written by cetpinhibition.org from the published abstract; figures as published. Page updated 18 August 2026. Methods.