Allosteric inhibition of the PCSK9–LDLR interaction: structural insights for small molecule design

Abstract

Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates plasma LDL cholesterol levels through direct interaction with the LDL receptor (LDLR), making it a clinically validated target for lipid-lowering therapy. While monoclonal antibodies have demonstrated efficacy, orally available small-molecule inhibitors remain scarce due to the challenging, flat protein–protein interaction (PPI) surface. In this study, we elucidate the mechanism of allosteric PCSK9 inhibition using molecular dynamics (MD) simulations and mutual information (MI) analysis across a congeneric series of tetrahydroisoquinoline-based compounds (cpd). High-affinity compounds, such as cpd9 and cpd6, simultaneously engage key polar residues R357 (catalytic domain), R458, and R476 (C-terminal domain), forming a stable electrostatic network that anchors the ligand via persistent hydrogen bonds and salt bridges. In contrast, low-affinity analogues lack substituents to engage R476, resulting in shallow binding and reduced enthalpic stabilization. Notably, D360 consistently provides strong Coulombic interactions across all compounds and serves as an essential electrostatic anchor, although it does not explain potency differences. Per-pair enthalpy and distance analyses reveal localized energetic redistribution at the LDLR interface, where the D310^L–R194^P salt bridge is weakened and the N295^L–D238^P contact is modestly reinforced upon ligand binding. MI-based dynamic mapping shows that potent inhibitors preserve long-range coupling between the allosteric pocket and the LDLR-binding segment D374–C378, whereas weak inhibitors fail to maintain this communication pathway, similar to the inhibitor-free form. Together, these results define a structural dynamic axis that links localized interfacial modulation to long-range allosteric communication and provide a mechanistic framework for the design of next-generation allosteric PCSK9 inhibitors with enhanced potency and efficacy.