Modeling L-type Calcium Channel with Phenylalkylamines

Abstract

Phenylalkylamines (PAAs), a major class of L-type calcium channel (LCC) blockers, have aromatic rings A and B connected by a flexible chain with cyano and ammonium groups proximal to rings A and B, respectively. Structural aspects of ligand-channel interactions remain unclear. We have built LCC models as in (Tikhonov and Zhorov, 2008) with KvAP, MthK, Kv1.2 and KcsA as templates and used Monte Carlo energy-minimizations to dock devapamil, verapamil, and gallopamil, which have three, four, and five methoxy groups, respectively. The PAA-LCC models have the following common features: meta-methoxy group in ring A accepts an H-bond from Y1179(3i10) in domain 3 inner-helix position 10, the ammonium group is stabilized at the focus of P-helices, and the cyano group coordinates a Ca2+ ion bound to the selectivity-filter glutamates in domains 3 and 4. The latter feature can explain the well-known effect of Ca2+ potentiation of PAA action. Our models are also consistent with structure-activity and mutational studies. For instance, mutation of Y1490(4i11) affects action of devapamil, but not verapamil and gallopamil (Johnson et al., 1996). In our models, the single meta-methoxy group in ring B of devapamil accepts an H-bond from Y1490(4i11), while meta- and para-methoxy groups in ring B of verapamil and gallopamil chelate the Ca2+ ion. Mutation T1066(3o14)Y in domain 3 outer-helix position 14 enhances action of devapamil and verapamil, but not gallopamil (Huber et al., 2004). Our models predict that para-methoxy group in ring A of devapamil and verapamil accepts an H-bond from Y3o14, while tri-methoxylated ring A of gallopamil is too bulky to approach Y3o14. Docking of devapamil in different models shows that the Kv1.2 template is most consistent with the experimental data. The closed (KcsA-based) model has the same ligand-channel contacts, but with weaker interaction energy. Supported by CIHR.