Small Molecule Inhibitors of the PCSK9·LDLR Interaction

Abstract

The protein-protein interaction between proprotein convertase subtilisin/kexin type 9 (PCSK9) and low-density lipoprotein receptor (LDLR) is a relatively new, and extremely important, validated therapeutic target for treatment and prevention of heart disease. Experts in the area agree that the first small molecules to disrupt PCSK9·LDLR would represent a milestone in this field, yet few credible leads have been reported. This paper describes how side-chain orientations in preferred conformations of carefully designed chemotypes were compared with LDLR side chains at the PCSK9·LDLR interface to find molecules that would mimic interface regions of LDLR. This approach is an example of the procedure called EKO (Exploring Key Orientations). The guiding hypothesis on which EKO is based is that good matches indicate the chemotypes bearing the same side chains as the protein at the sites of overlay have the potential to disrupt the parent protein-protein interaction. In the event, the EKO procedure and one round of combinatorial fragment-based virtual docking led to the discovery of seven compounds that bound PCSK9 (SPR and ELISA) and had a favorable outcome in a cellular assay (hepatocyte uptake of fluorescently labeled low-density lipoprotein particles) and increased the expression LDLR on hepatocytes in culture. Three promising hit compounds in this series had dissociation constants for PCSK9 binding in the 20-40 μM range, and one of these was modified with a photoaffinity label and shown to form a covalent conjugate with PCSK9 on photolysis.

Biological Characterization of Computationally Designed Analogs of peptide TVFTSWEEYLDWV (Pep2-8) with Increased PCSK9 Antagonistic Activity

“…This tool has been optimized and validated in previous studies in which other PCSK9 inhibitors have been developed and characterized 11,12 . Initially, in agreement with recently published conditions 27 , a preliminary screening was performed at the fixed concentration of 100 µM. Figure 4A shows that [Y9A]Pep2-8 and [T4R,W12Y]Pep2-8 were able to decrease the PCSK9 / LDLR PPI much better than Pep2-8.…”

A small-molecule inhibitor of PCSK9 transcription ameliorates atherosclerosis through the modulation of FoxO1/3 and HNF1α

“…Gustafsen et al proposed that heparan sulfate (HS) mimetics directly interrupted the HS/PCSK9 interaction, which facilitated PCSK9 clustering to LDLR, but with low binding affinities [48]. A recent research on peptidomimetics was also performed to perturb the PCSK9-LDLR binding [49]. Last year, Hingez Therapeutics Inc. received a grant from the National Institutes of Health focusing on discovery of small molecules that block PCSK9-LDLR interactions using their novel high performance computing (HPC)-based platform.…”

Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations

“…The general conclusions from this work are, 1) it is difficult to impossible to break 3° PPI with high affinity using any conventional means of drug discovery such as HTS or FBDD, and 2) if the goal is to break a 3° PPI with a small molecule, then it is incumbent upon the investigators to determine a unique feature of the interaction that can be exploited. Finally, it is important to note that the Burgess[76] group successfully designed 20–40 μM small molecule PCSK9 inhibitors using the innovative computational procedure called Exploring Key Orientations, which creates scaffolds that present three side chains from the LDLR at critical interaction points with PCSK9. While these results are impressive, it confirms the great difficulty in breaking 3° PPI, because even achieving inhibition >20 μM requires careful design of a molecule the size of a tripeptide.…”