Seeking the exclusive binding region of phenylalkylamine derivatives on human T-type calcium channels via homology modeling and molecular dynamics simulation approach.

Pharmaceutical features of phenylalkylamine derivatives (PAAs) binding to calcium channels have been studied extensively in the past decades. Only a few PAAs have the binding specificity on calcium channels, for example, NNC 55-0396. Here, we created the homology models of human Cav 3.2, Cav 3.3 and use them as a receptor on the rigid docking tests. The nonspecific calcium channel blocker mibefradil showed inconsistent docking preference across four domains; however, NNC 55-0396 had a unique binding pattern on domain II specifically. The subsequent molecular dynamics (MD) simulations identified that Cav 3.1, Cav 3.2, and Cav 3.3 share domain II when Ca2+ appearing in the neighbor region of selective filters (SFs). Moreover, free-energy perturbation analysis suggests single mutation of lysine at P-loop domain III, or threonine at the P-loop domain II largely reduced the total amount of hydration-free energy in the system. All these findings suggest that P-loop and segment six domain II in the T-type calcium channels (TCCs) are crucial for attracting the PAAs with specificity as the antagonist.