Discovery of Novel Small Molecule Inhibitors Disrupting the PCSK9-LDLR Interaction

Proprotein convertase subtilisin kexin 9 (PCSK9) has been identified as a reliable therapeutic target for hyper-cholesterolemia and coronary artery heart diseases since the monoclonal antibodies of PCSK9 have launched. Disrupting the protein-protein interaction (PPI) between PCSK9 and the lowdensity lipoprotein receptor (LDLR) has been considered as a promising approach for developing PCSK9 inhibitors. However, PPIs have been traditionally considered difficult to target by small molecules since the PPI surface is usually large, flat, featureless, and without a pocket or groove for ligand binding. The PCSK9LDLR PPI interface is such a typical case. In this study, a potential binding pocket was generated on the PCSK9-LDLR PPI surface of PCSK9 through induced-fit docking. On the basis of this induced binding pocket, virtual screening, molecular dynamics (MD) simulation, and biological evaluations have been applied for the identification of novel small molecule inhibitors of PCSK9-LDLR PPI. Among the selected compounds, compound 13 exhibited certain PCSK9-LDLR PPI inhibitory activity (IC50: 7.57 +/- 1.40 mu M). The direct binding affinity between 13 and PCSK9 was determined with a K-D value of 2.50 +/- 0.73 mu M. The LDLR uptake function could be also restored to a certain extent by 13 in HepG2 cells. This well-characterized hit compound will facilitate the further development of novel small molecule inhibitors of PCSK9-LDLR PPI.

Automated summary

A potential binding pocket was identified on the PCSK9-LDLR PPI surface by induced-fit docking, leading to the discovery of novel small molecule inhibitors through virtual screening and biological evaluations. Compound 13 showed inhibitory activity against PCSK9-LDLR PPI and restored LDLR uptake function in HepG2 cells, indicating its potential as a lead compound for further development of small molecule inhibitors targeting PCSK9-LDLR PPI.