文章基本信息

标题：On the role of water density fluctuations in the inhibition of a proton channel
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作者：Eleonora Gianti ; Lucie Delemotte ; Michael L. Klein 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2016
卷号：113
期号：52
页码：E8359-E8368
DOI：10.1073/pnas.1609964114
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceHv1, a voltage-gated proton channel, is an emerging pharmacological target implicated in many pathological conditions, including cancer and ischemic brain damage. We used the recently published experimental structure of Hv1 to generate structural models of relevant conformational states. Thermodynamic analyses of pore waters shed light on the molecular underpinnings of Hv1 druggability. We exploit this information to suggest possible optimizations of known inhibitors and identify a potential binding site located at the exit of the proton path. The resulting molecular picture paves the way for the discovery of novel Hv1 inhibitors and outlines a general approach for identifying druggable binding sites in ion channels. Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently solved crystal structure of Hv1, we used structural modeling and molecular dynamics simulations to characterize the channels most relevant conformations along the activation cycle. We then performed computational docking of known Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI) and analogs. Although salt-bridge patterns and electrostatic potential profiles are well-defined and distinctive features of activated versus nonactivated states, the water distribution along the channel lumen is dynamic and reflects a conformational heterogeneity inherent to each state. In fact, pore waters assemble into intermittent hydrogen-bonded clusters that are replaced by the inhibitor moieties upon ligand binding. The entropic gain resulting from releasing these conformationally restrained waters to the bulk solvent is likely a major contributor to the binding free energy. Accordingly, we mapped the water density fluctuations inside the pore of the channel and identified the regions of maximum fluctuation within putative binding sites. Two sites appear as outstanding: One is the already known binding pocket of 2GBI, which is accessible to ligands from the intracellular side; the other is a site located at the exit of the proton permeation pathway. Our analysis of the waters confined in the hydrophobic cavities of Hv1 suggests a general strategy for drug discovery that can be applied to any ion channel.
关键词：Hv1 ; drug design ; pore waters ; binding site discovery ; confined waters