In Silico Identification of Cholesterol Binding Sites in the Transient Potential Receptor Vanilloid 1 (TRPV1) Ion Channel

TRPV1 channels are activated by diverse physical and chemical stimuli, including natural products and inflammatory mediators, which often act on their transmembrane regions. Cholesterol, a key lipid in eukaryotic membranes, is known to influence ion channel activity both indirectly, by altering membrane properties, and directly, through specific binding interactions. Using in silico molecular docking and site identification by ligand competitive saturation (SILCS), multiple cholesterol binding sites on TRPV1 were systematically identified. These sites were further examined by comparing cholesterol to its stereoisomer epicholesterol, revealing differences in site specificity and interaction patterns. The results highlight structurally persistent cholesterol interaction hotspots that may stabilize channel structure, as well as state-dependent binding motifs potentially involved in functional modulation. This ensemble-based, high-resolution mapping of cholesterol-TRPV1 interactions underscores the need to account for protein conformational flexibility when studying lipid-protein interactions. The findings contribute to a deeper mechanistic understanding of how cholesterol regulates TRPV1 and similar membrane proteins, with broader implications for the modulation of ion channel function by membrane lipids.