Structural Model for Phenylalkylamine Binding to L-type Calcium Channels

Abstract

Phenylalkylamines (PAAs), a major class of L-type calcium channel (LTCC) blockers, have two aromatic rings connected by a flexible chain with a nitrile substituent. Structural aspects of ligand-channel interactions remain unclear. We have built a KvAP-based model of LTCC and used Monte Carlo energy minimizations to dock devapamil, verapamil, gallopamil, and other PAAs. The PAA-LTCC models have the following common features: (i) the meta-methoxy group in ring A, which is proximal to the nitrile group, accepts an H-bond from a PAA-sensing Tyr_IIIS6; (ii) the meta-methoxy group in ring B accepts an H-bond from a PAA-sensing Tyr_IVS6; (iii) the ammonium group is stabilized at the focus of P-helices; and (iv) the nitrile group binds to a Ca 2؉ ion coordinated by the selectivity filter glutamates in repeats III and IV. The latter feature can explain Ca 2؉ potentiation of PAA action and the presence of an electronegative atom at a similar position of potent PAA analogs. Tyr substitution of a Thr in IIIS5 is known to enhance action of devapamil and verapamil. Our models predict that the para-methoxy group in ring A of devapamil and verapamil accepts an H-bond from this engineered Tyr. The model explains structure-activity relationships of PAAs, effects of LTCC mutations on PAA potency, data on PAA access to LTCC, and Ca 2؉ potentiation of PAA action. Common and class-specific aspects of action of PAAs, dihydropyridines, and benzothiazepines are discussed in view of the repeat interface concept.

Structural Basis for Pharmacology of Voltage-Gated Sodium and Calcium Channels

“…Molecular modeling suggested that these amino acid residues face the lumen of the pore and cooperate to form the drug-binding site (Cheng et al, 2009). In agreement with these prior molecular models, the three-dimensional structure of CavAb places these amino acid residues in positions to cooperate in forming a single drug-binding site in the central cavity of the pore (Fig.…”

“…Molecular modeling and ligand-docking methods have been used to predict the binding pose of the phenylalkylamines in their receptor site (Lipkind and Fozzard, 2003;Cheng et al, 2009). In the initial study, based on the structure of the KcsA potassium channel, the bound phenylakylamine was fit in a half-folded, L-shaped conformation, with the positively charged ammonium group projecting toward the negatively charged ion selectivity filter, aromatic ring A in the central cavity, and aromatic ring B projecting toward the interface between domains III and IV (Lipkind and Fozzard, 2003).…”

“…In the initial study, based on the structure of the KcsA potassium channel, the bound phenylakylamine was fit in a half-folded, L-shaped conformation, with the positively charged ammonium group projecting toward the negatively charged ion selectivity filter, aromatic ring A in the central cavity, and aromatic ring B projecting toward the interface between domains III and IV (Lipkind and Fozzard, 2003). In the second model, based on the KvAP structure, the elongated phenylalkylamine molecule is predicted to lie in a more extended conformation, with the conserved nitrile group projecting toward the ion selectivity filter with Ca 21 bound in it, the positively charged ammonium group placed at the axis of the pore in the focus of the helical dipole of the four P-helices, and the aromatic rings and methoxy groups making hydrophobic and hydrogen-binding interactions with amino acid side chains and the backbone of the S6 segments (Cheng et al, 2009). These models both satisfy many of the requirements derived from structure-function studies; therefore, studies of bound phenylalkylamines in crystal structures of calcium channels or their homologs will be required to precisely define the position of the bound drug and thereby determine the structural basis for state-dependent binding.…”

Why Does the Inner-Helix Mutation A413C Double the Stoichiometry of Kv1.3 Channel Block by Emopamil but Not by Verapamil?

“…Only the demethoxylated phenyl ring B of emopamil can penetrate the intersubunit niche of the mutant. In a model of devapamil in the Ca v 1.2 channel intra-and interdomain interfaces constitute binding loci for rings A and B, respectively (Cheng et al, 2009). Why does ring B of devapamil bind between helices 3P and 4S6 in Ca v 1.2, but does not bind between respective helices in Kv1.3?…”

“…S6s from neighboring subunits line four interfaces. 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).…”