For many drug targets, such as GPCRs and kinases, their functions are modulated by endogenous ligands. Accordingly, most drugs bind receptors where the natural molecular activators (i.e. endogenous ligands) bind. In contrast, the binding site of voltage-gated ion channel activators is much more elusive since the activation of voltage-gated ion channels in the physiological environment is modulated by membrane potential rather than endogenous ligands. To date, there is only limited information about the binding site of activators to voltage-gated ion channels and structure-based drug design for voltage-gated ion channel activators is a challenge.

KCNQ2 channel is a low-threshold voltage-gated potassium (Kv) channel, activity reduction of which causes epilepsy. Researchers from Drug Discovery and Design Center and the International Scientist Working Station of Neuropharmacology, Shanghai Institute of Materia Medica (SIMM), reveal that the gating charge pathway of KCNQ2 channel can accommodate various small molecule ligands by combining mutagenesis, molecular simulation and electrophysiological recording.

A structure-based virtual screening assay targeting the defined ligand binding pocket was carried out. Nine activators with five new chemotypes were identified, and in vivo experiments showed three ligands binding to the gating charge pathway exhibit significant anti-epilepsy activity.

This study provides a good example to showcase the binding model of activators with ion channels and the feasibility for developing activators of ion channels by using structure-based approaches.

In addition, this study gains new insights into the structure and functionality of the gating charge pathways of Kv channels. Studies on Shaker and Kv1.2-2.1 chimeric channels suggest the pathway is occluded in the middle of the VSD. A conserved phenylalanine in the middle of S2, together with the nearby residues, was proposed to form the occluded site.

The occluded site separates the extracellular and intracellular hydrated crevices of the VSD and forms the charge transfer center that catalyzes movement of the gating charges. The activator binding pocket of KCNQ2 identified in this study partially overlaps with the corresponding regions of the gating charge pathways of Shaker and Kv1.2-2.1 chimera channels, and extends deeply into the intracellular side of the channel. This result indicates that the gating charge pathway of Kv channels might be structurally diverse.

On June 25, this study was released in Cell Research. This work was directed by Dr. Hualiang Jiang, Dr. Zhaobing Gao, and Dr. Huaiyu Yang. The first co-authors, Ping Li and Zhuxi Chen, are Phd candidates of SIMM. The study was supported by 973, NSFC, Shanghai Science and Technology Committee, and NIH.

Full text: http://www.nature.com/cr/journal/vaop/ncurrent/full/cr201382a.html

 

The binding mode of ztz240. (A and B) General (A) and detailed (B) views of the interactions between ztz240 and the VSD. (C) The structure of the binding pocket.

（IMAGE BY SIMM）