Atomic determinants of state-dependent block of sodium channels by charged local anesthetics and benzocaine

Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ont., Canada L8N 3Z5.
FEBS Letters (Impact Factor: 3.17). 12/2006; 580(26):6027-32. DOI: 10.1016/j.febslet.2006.10.035
Source: PubMed


Molecular modeling predicts that a local anesthetic (LA) lidocaine binds to the resting and open Na(v)1.5 in different modes, interacting with LA-sensing residues known from experiments. Besides the major pathway via the open activation gate, LAs can reach the inner pore via a "sidewalk" between D3S6, D4S6, and D3P. The ammonium group of a cationic LA binds in the focus of the pore-helices macrodipoles, which also stabilize a Na(+) ion chelated by two benzocaine molecules. The LA's cationic group and a Na(+) ion in the selectivity filter repel each other suggesting that the Na(+) depletion upon slow inactivation would stabilize a LA, while a LA would stabilize slow-inactivated states.

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    • "Besides the central cation-attractive cavity, which is lined by ligand-sensing residues, the pore module includes rather hydrophobic subunit interfaces lined by inner helices and the P-helix [1] (Fig. 2A and B). In calcium and sodium channels, the interface between repeat domains III and IV has been proposed to serve as a sidewalk access pathway to the inner pore [28] [29] [30]. Some ligand-sensing residues in potassium, sodium and calcium channels line these interfaces rather than the central cavity. "
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    ABSTRACT: The inner pore of potassium channels is targeted by many ligands of intriguingly different chemical structures. Previous studies revealed common and diverse characteristics of action of ligands including cooperativity of ligand binding, voltage- and use-dependencies, and patterns of ligand-sensing residues. Not all these data are rationalized in published models of ligand-channel complexes. Here we have used energy calculations with experimentally defined constraints to dock flecainide, ICAGEN-4, benzocaine, vernakalant, and AVE0118 into the inner pore of Kv1.5 channel. We arrived at ligand-binding models that suggest possible explanations for different values of the Hill coefficient, different voltage dependencies of ligands action, and effects of mutations of residues in subunit interfaces. Two concepts were crucial to build the models. First, the inner-pore block of a potassium channel requires a cationic "blocking particle". A ligand, which lacks a positively charged group, blocks the channel in a complex with a permeant ion. Second, hydrophobic moieties of a flexible ligand have a tendency to bind in hydrophobic subunit interfaces.
    Preview · Article · Dec 2013 · Biochimica et Biophysica Acta
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    • "In homology models of sodium and calcium channels, corresponding interfaces between domains III and IV contain residues whose mutations affect access and binding of different ligands (Zhorov and Tikhonov, 2004; Bruhova et al., 2008; Tikhonov and Zhorov, 2008; Cheng et al., 2009). Extracellularly applied permanently charged compounds, which cannot permeate the membrane , were proposed to reach their binding sites within the inner pore through the III/IV domain interface (Tikhonov et al., 2006; Bruhova et al., 2008; Tikhonov and Zhorov, 2008). Some ligands of the Kv1.5 channel were also proposed to reach their binding site via the intersubunit interface (Strutz-Seebohm et al., 2007). "
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    • "This concept allowed us to recently propose structural models that explain long-known effects of metal ions on L-type Ca 2ϩ channel ligands (Tikhonov and Zhorov, 2008; Cheng et al., 2009; Tikhonov and Zhorov, 2009). We also explained previously the observations that the cationic lidocaine and the uncharged benzocaine block Na ϩ channels with Hill coefficients of 1 and 2, respectively, by a model in which two benzocaine molecules coordinate an Na ϩ ion in the permeation pathway (Tikhonov et al., 2006). Based on the above-described experiments and the fact that the uncharged PAP-1 inhibits Kv1.3 with a Hill coefficient of 2 (Schmitz et al., 2005), we hypothesized that Kv1.3 is blocked by a tripartite complex consisting of two PAP-1 molecules and a K ϩ ion. "
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