A Set of Novel Capsaicin Analogs as Molecular Ruler for Conformational Change of the TRPV1 Ligand-Binding Pocket

Abstract

Capsaicin activates TRPV1 by inducing a conformational change of the ligand-binding pocket. Comparison between cryo-EM structures in the apo and capsaicin-bound states suggests that the S4-S5 linker swings up towards S4. This movement is mediated by two H-bonds formed between capsaicin's neck and head to T551 (mTRPV1) in S4 and E571 in the S4-S5 linker, respectively. The distance between T551 and E571 (measured from H-bond forming polar groups) is shortened by 1.3 Å, from 9.1 to 7.8. To validate the significance of this movement for channel activation, we designed a set of capsaicin analogs with a shortened or lengthened neck. Functional tests revealed these analogs retained agonist activities but exhibited a reduced potency, due to a reduction in both binding affinity and efficacy. Computational modeling indicated weaker binding and alternation of the binding pose. The study confirmed the existence of an optimal ligand-binding pocket conformation for activation gating, and revealed structural details for ligand-channel interactions.