Abstract
High-throughput screening has led to the identification of small-molecule blockers of the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel, but the structural basis of blocker binding remains to be defined. We developed molecular models of the CFTR channel on the basis of homology to the bacterial transporter Sav1866, which could permit blocker binding to be analyzed in silico. The models accurately predicted the existence of a narrow region in the pore that is a likely candidate for the binding site of an open-channel pore blocker such as N-(2-naphthalenyl)-[(3,5-dibromo-2,4-dihydroxyphenyl)methylene]glycine hydrazide (GlyH-101), which is thought to act by entering the channel from the extracellular side. As a more-stringent test of predictions of the CFTR pore model, we applied induced-fit, virtual, ligand-docking techniques to identify potential binding sites for GlyH-101 within the CFTR pore. The highest-scoring docked position was near two pore-lining residues, Phe337 and Thr338, and the rates of reactions of anionic, thiol-directed reagents with cysteines substituted at these positions were slowed in the presence of the blocker, consistent with the predicted repulsive effect of the net negative charge on GlyH-101. When a bulky phenylalanine that forms part of the predicted binding pocket (Phe342) was replaced with alanine, the apparent affinity of the blocker was increased ∼200-fold. A molecular mechanics-generalized Born/surface area analysis of GlyH-101 binding predicted that substitution of Phe342 with alanine would substantially increase blocker affinity, primarily because of decreased intramolecular strain within the blocker-protein complex. This study suggests that GlyH-101 blocks the CFTR channel by binding within the pore bottleneck.
Footnotes
↵ The online version of this article (available at http://molpharm.aspetjournals.org) contains supplemental material.
This work was supported by the National Institutes of Health National Institute of Diabetes and Digestive and Kidney Diseases [Grant DK45880]; the Cystic Fibrosis Foundation [Grant DAWSON08G0]; and the American Lung Association [Grant RT-7962-N]. The laboratory of M.S.P.S. was supported by the Wellcome Trust and the Biotechnology and Biological Sciences Research Council.
Article, publication date, and citation information can be found at http://molpharm.aspetjournals.org.
ABBREVIATIONS:
- CFTR
- cystic fibrosis transmembrane conductance regulator
- 2-ME
- 2-mercaptoethanol
- DTT
- dithiothreitol
- MD
- molecular dynamics
- IFD
- induced-fit docking
- EC50(0)
- EC50 at 0 mV
- MM-GB/SA
- molecular mechanics-generalized Born/surface area
- IBMX
- 3-isobutyl-1-methylxanthine
- MTSET+
- [2-(trimethylammonium)ethyl]methanethiosulfonate
- MTSES−
- [2-sulfonatoethyl]methanethiosulfonate
- NEM
- N-ethyl maleimide
- wt
- wild-type
- PDB
- Protein Data Bank
- TM
- transmembrane segment
- GlyH-101
- N-(2-naphthalenyl)-[(3,5-dibromo-2,4-dihydroxyphenyl)methylene]glycine hydrazide
- iOWH032
- 3-(3,5-dibromo-4-hydroxyphenyl)-N-(4-phenoxybenzyl)-1,2,4-oxadiazole-5-carboxamide.
- Received May 28, 2012.
- Accepted August 24, 2012.
- Copyright © 2012 The American Society for Pharmacology and Experimental Therapeutics
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