Ligand-Binding Sites in Vanilloid-Subtype TRP Channels

Abstract

Vanilloid-subfamily TRP channels TRPV1-6 play important roles in various physiological processes and are implicated in numerous human diseases. Advances in structural biology, particularly the “resolution revolution” in cryo-EM, have led to breakthroughs in molecular characterization of TRPV channels. Structures with continuously improving resolution uncover atomic details of TRPV channel interactions with small molecules and protein-binding partners. Here, we provide a classification of structurally characterized binding sites in TRPV channels and discuss the progress that has been made by structural biology combined with mutagenesis, functional recordings, and molecular dynamics simulations toward understanding of the molecular mechanisms of ligand action. Given the similarity in structural architecture of TRP channels, 16 unique sites identified in TRPV channels may be shared between TRP channel subfamilies, although the chemical identity of a particular ligand will likely depend on the local amino-acid composition. The characterized binding sites and molecular mechanisms of ligand action create a diversity of druggable targets to aid in the design of new molecules for tuning TRP channel function in disease conditions.

Human TRPV1 structure and inhibition by the analgesic SB-366791

“…The binding site located in the TMD region that faces the cytoplasmic leaflet of the membrane, in the crevice between S1-S4 and pore domains appears to be the vanilloid site, the same site that binds PI in the apo state as well as the agonists capsaicin, resiniferatoxin (RTX), and the competitive antagonist capsazepine (Supplementary Figs. 3 and 6 ) 17 , 19 , 33 , 34 , 36 , 41 . Binding of SB-366791 to the vanilloid site suggests that it acts as a competitive antagonist.…”

Structural mechanism of human oncochannel TRPV6 inhibition by the natural phytoestrogen genistein

“…So far, 14 unique ligand binding sites have been identified in TRPV channels 28 . Genistein binds to the intracellular pore entry site, which makes it a TRPV6 ion channel blocker.…”

“…What makes genistein a unique ion channel blocker of TRPV6? Among 14 types of TRPV ligands that were characterized structurally 28 , there are four types of ion channel blockers. TRPV6 can be blocked by trivalent cations, like Gd 3+ , which bind at the extracellular pore entry site formed by side chains of four D542 residues, each from four individual TRPV6 subunits.…”

“…The latter factor allows genistein to cause more damaging mechanistic changes in the structure of TRPV6 pore compared to any other ion channel blocker studied before. Due to the unprecedented character of genistein-induced conformational transformation of the channel, the mechanism of genistein block is also unique amongst all previously described mechanisms of TRP channel inhibition by various natural and synthetic antagonists 28 , including allosteric inhibition of hTRPV6 by 2-APB or econazole. With the potential to utilize various well-established chemical synthesis pathways for genistein and its derivatives 31 , 98 , 99 , the mechanism of ion channel block described here opens new avenues for the development of drugs targeting TRPV6 in pathological conditions.…”

“…While several synthetic inhibitors of TRPV6 have been making a slow progress towards clinical trials 1 – 3 , 26 – 28 , scientific exploration and pharmaceutical exploitation of natural TRPV6 inhibitors have been largely neglected despite their apparent benefits, such as pharmacokinetics optimized by nature in the course of evolution 29 . The natural isoflavone and phytoestrogen genistein (4′,5,7-trihydroxyisoflavone) was previously suggested to act as a TRPV6 inhibitor 30 .…”