To Be or Not to Be an Ion Channel: Cryo-EM Structures Have a Say

Abstract

Ion channels are the second largest class of drug targets after G protein-coupled receptors. In addition to well-recognized ones like voltage-gated Na/K/Ca channels in the heart and neurons, novel ion channels are continuously discovered in both excitable and non-excitable cells and demonstrated to play important roles in many physiological processes and diseases such as developmental disorders, neurodegenerative diseases, and cancer. However, in the field of ion channel discovery, there are an unignorable number of published studies that are unsolid and misleading. Despite being the gold standard of a functional assay for ion channels, electrophysiological recordings are often accompanied by electrical noise, leak conductance, and background currents of the membrane system. These unwanted signals, if not treated properly, lead to the mischaracterization of proteins with seemingly unusual ion-conducting properties. In the recent ten years, the technical revolution of cryo-electron microscopy (cryo-EM) has greatly advanced our understanding of the structures and gating mechanisms of various ion channels and also raised concerns about the pore-forming ability of some previously identified channel proteins. In this review, we summarize cryo-EM findings on ion channels with molecular identities recognized or disputed in recent ten years and discuss current knowledge of proposed channel proteins awaiting cryo-EM analyses. We also present a classification of ion channels according to their architectures and evolutionary relationships and discuss the possibility and strategy of identifying more ion channels by analyzing structures of transmembrane proteins of unknown function. We propose that cross-validation by electrophysiological and structural analyses should be essentially required for determining molecular identities of novel ion channels.

Molecular Dynamics Simulations of Claudin-10a and -10b Ion Channels: With Similar Architecture, Different Pore Linings Determine the Opposite Charge Selectivity

“…In total, this MD simulation study provides the first atomic model of a complete and prototypic paracellular anion channel and suggests that CLDN10a anion and -10b cation channels share the same overall architecture but differ mainly in their pore-lining residues. This is of high interest since nearly all transcellular anion channels differ strongly from cation channels in their architecture [ 53 ]. However, one has to keep in mind that claudin-based paracellular channels differ strongly in structure from transmembrane channels since the ion pore runs parallel to instead of through the membrane.…”

“…In addition, free energy calculation can be used to analyze selectivity determinants in more detail [ 18 , 21 , 23 , 43 ]. Furthermore, progress in claudin complex structures resolved by cryo-electron microscopy [ 53 ] is expected to provide additional substantial insights into the structure of claudin channels and strands.…”

Targeting ion channels with ultra-large library screening for hit discovery

“…Examples include voltage-gated sodium channel blockers for the treatment of arrhythmia and local anesthesia, calcium channel blockers for the treatment of angina and hypertension, and ATPsensitive potassium channel blockers for the therapy of type II diabetes (Ford et al, 2016;Imbrici et al, 2016;Santos et al, 2016;Li et al, 2017;Wolkenberg et al, 2017;Hutchings et al, 2019;Chen et al, 2023). Despite this large number of existing drugs, ion channels remain relatively underexploited for therapeutic interventions.…”

“…The rapid growth in structural information of ion channels has fueled the use of computer-assisted drug discovery approaches. At the time of writing (as of October 2023), approximately 100 unique human ion channel protein structures have been deposited in the Protein Data Bank (PDB), ∼81% of these structures were determined by cryo-EM (Lau et al, 2018;Rao et al, 2019;Chen et al, 2023;mpstruc database, n.d.). In recent decades, the increasing numbers of high-quality ion channel structures, along with advances in computer-assisted drug discovery, have led to a number of successful virtual screening (VS) campaigns (Kang, 2001;Urbahns et al, 2003;Kenyon et al, 2006;Liu et al, 2007;Etkins, 2018;Llanos et al, 2022;Pasqualetto et al, 2023).…”