title: On the role of water density fluctuations in the inhibition of a proton channel.
abstract: 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 channel's 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.
authors.affiliation: Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122.
authors.forename: Eleonora
authors.initials: E
authors.lastname: Gianti
authors.affiliation: Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Lucie
authors.initials: L
authors.lastname: Delemotte
authors.affiliation: Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122; mlklein@temple.edu vincenzo.carnevale@temple.edu.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Klein
authors.affiliation: Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122; mlklein@temple.edu vincenzo.carnevale@temple.edu.
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Carnevale
mesh_terms: D000818:Animals; D001665:Binding Sites; D006859:Hydrogen / Q000378:metabolism; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D015640:Ion Channel Gating; D007473:Ion Channels / Q000502:physiology*; D051379:Mice; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011522:Protons; D017382:Reactive Oxygen Species / Q000378:metabolism; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: C540876:Hv1 proton channel, mouse; D007473:Ion Channels; D011522:Protons; D017382:Reactive Oxygen Species; D014867:Water; D006859:Hydrogen
keywords: Hv1; binding site discovery; confined waters; drug design; pore waters