Vol. 63, Issue 3, 499-511, March 2003

Molecular Modeling of Interactions of Dihydropyridines and Phenylalkylamines with the Inner Pore of the L-Type Ca²⁺ Channel

Gregory M. Lipkind and Harry A. Fozzard

Cardiac Electrophysiology Labs, Departments of Biochemistry & Molecular Biology and Medicine, the University of Chicago, Chicago, Illinois

Domains IIIS5, IIIS6, and IVS6 transmembrane segments of L-type Ca²⁺ channels participate in dihydropyridine (DHP) and phenylalkylamine (PAA) binding. The inner pore structure of the Ca_v1.2 channel was reconstructed from coordinates of the transmembrane -helices of the KcsA channel. S6s were aligned with M2 by comparative analysis of the pore-facing M2 side chains and those required for drug binding. Two neighboring tilted S6 helices of domains III and IV below the selectivity filter formed an interdomain crevice. Docking of DHPs inside this crevice located the DHP ring between Phe-1159 of IIIS6 and Ala-1467 of IVS6, parallel to the pore axis, whereas the 4-aryl ring participated in aromatic and polar interactions with the side chains of Tyr-1152 and Tyr-1463. Nonpolar interactions of the port side ester group with hydrophobic side chains of Ile-1156, Ile-1163, and Ile-1471 on the bottom of the binding cavity, formed by the crossover of IIIS6 and IVS6, could stabilize the channel's closed/inactivated state. Similar arrangements were found for DHP agonist drugs, except for the absence of hydrophobic interactions with the helical crossing. In this arrangement, DHPs do not physically block the pore. Locating the central amine group of desmethoxyverapamil near the selectivity filter domain III glutamic acid allows one aromatic ring through its CH₂CH₂ linker to interact with the side chain of Tyr-1463 inside the DHP binding site, whereas the opposite aromatic ring is in contact with the side chain of Ile-1470 of IVS6, blocking the pore.