Polyphenols as novel NPC1L1 inhibitors: A computational study of natural cholesterol uptake blockers

Niemann-Pick C1-Like 1 (NPC1L1) is the primary intestinal transporter responsible for dietary cholesterol absorption and a validated therapeutic target for hypercholesterolemia; however, the long-term use of the FDA-approved inhibitor ezetimibe is limited by its adverse effects, motivating the search for safer alternatives. In this study, an integrated in silico strategy combining molecular docking, lipid-embedded all-atom molecular dynamics simulations, principal component analysis, and MM/PBSA binding free-energy calculations was employed to evaluate plant-derived polyphenols as potential NPC1L1 inhibitors under physiologically relevant conditions. Four compounds, cis-resveratroloside, eriodictyol-7-O-glucoside, luteolin-7-O-glucoside, and 3,4-dicaffeoylquinic acid, exhibited superior binding affinity toward the NPC1L1 neck region compared to ezetimibe. Unlike ezetimibe, which occupied the deep binding cleft, these polyphenols preferentially localized to the upper-mid channel region and formed conserved π-π interactions with Phe1101/Tyr1102 and hydrogen bonds with Gln873/Leu877. Molecular dynamics analyses revealed enhanced complex stability, favorable binding energetics, and pronounced modulation of lipid-protein interactions near the TM7-TM8 loop, a critical cholesterol transport domain; notably, luteolin-7-O-glucoside and 3,4-dicaffeoylquinic acid displayed high lipid occupancy in this region, suggesting a steric blockade mechanism that may impede cholesterol internalization. Collectively, these findings provide molecular-level evidence that selected plant-derived polyphenols inhibit NPC1L1 via mechanisms distinct from ezetimibe, highlighting their potential as safer, next-generation cholesterol absorption inhibitors.