Structural Model for Dihydropyridine Binding to L-type Calcium Channels

Abstract

1,4-Dihydropyridines (DHPs) constitute a major class of ligands for L-type Ca 2؉ channels (LTCC). The DHPs have a boat-like, six-membered ring with an NH group at the stern, an aromatic moiety at the bow, and substituents at the port and starboard sides. Various DHPs exhibit antagonistic or agonistic activities, which were previously explained as stabilization or destabilization, respectively, of the closed activation gate by the portside substituents. Here we report a novel structural model in which agonist and antagonist activities are determined by different parts of the DHP molecule and have different mechanisms. In our model, which is based on Monte Carlo minimizations of DHP-LTCC complexes, the DHP moieties at the stern, bow, and starboard form H-bonds with side chains of the key DHP-sensing residues Tyr_IIIS6, Tyr_IVS6, and Gln_IIIS5, respectively. We propose that these H-bonds, which are common for agonists and antagonists, stabilize the LTCC conformation with the open activation gate. This explains why both agonists and antagonists increase probability of the long lasting channel openings and why even partial disruption of the contacts eliminates the agonistic action. In our model, the portside approaches the selectivity filter. Hydrophobic portside of antagonists may induce long lasting channel closings by destabilizing Ca 2؉ binding to the selectivity filter glutamates. Agonists have either hydrophilic substituents or a hydrogen atom at their portside, and thus lack this destabilizing effect. The predicted orientation of the DHP core allows accommodation of long substituents in the domain interface or in the inner pore. Our model may be useful for developing novel clinically relevant LTCC blockers. 1,4-Dihydropyridines (DHPs)2 form a major class of L-type Ca 2ϩ channel (LTCC) ligands. DHPs can operate as agonists or antagonists depending on their chemical structure. Importantly, activity of some DHP derivatives may shift from agonism to antagonism (and vice versa) upon site-specific mutation of the channel or modified experimental conditions (for reviews, see Refs. 1 and 2). It has been the dual nature of DHP activity (agonism and antagonism), which has made it challenging for interpretation in structural terms. The other major classes of LTCC ligands, the phenylalkylamines and benzothiazepines, are strictly antagonists.Despite a number of studies, the molecular mechanism for the activity of DHPs on LTCC remains unclear. In the present work we have addressed this problem by combining a molecular modeling approach with analyses of relevant published data. We employed a method of multiple Monte Carlo energy minimizations for docking various DHPs in our earlier reported homology model of LTCC (3), which is based on the crystal structure of the KvAP K ϩ channel (4). We constrained our analyses to potential ligand-binding modes that would be consistent with the features of the ligand-channel activity relationship described in published experiments. These include the structure-activity relationship of the m...

Structural Model for Phenylalkylamine Binding to L-type Calcium Channels

“…However, it should be emphasized that we did not modify the template structure to satisfy the proposed interactions. The same model based on the same sequence alignment was used previously for analyses of binding of DHPs and BTZs to LTCC (19,20). It should be noted that despite the obvious differences in the structure and mechanism of action of these three classes of LTCC ligands, two important features of ligand-channel interactions are common in our models.…”

“…However, E 3p50 and E 4p50 , whose mutations significantly affect the PAA block (10), are bound in our model to the Ca 2ϩ ion that directly interacts with the nitrile group of potent PAAs. Calcium coordination by E 3p50 and E 4p50 is not an ad hoc feature of the current model; it is also proposed in our LTCC models with BTZs (19) and DHPs (20).…”

“…Fig. 7A shows the superimposed LTCC models with a DHP (20) and a PAA. The bulky core of the DHP ligand occurs in the repeat interface, and only a small moiety protrudes into the pore.…”

“…In the DHP-LTCC models (20), the ligands also bind in the interface between repeats III and IV, whereas the moieties that differ between agonist and antagonists extend to the pore. Both models suggest direct interactions between the ligands and a Ca 2ϩ ion bound to the selectivity filter glutamates in repeats III and IV.…”

Unveiling (−)‐Englerin A as a Modulator of L‐Type Calcium Channels

“…Considering the fact that there are no reported crystal structures for these channels, we used the open‐state Ca v 1.2 homology model reported by Zhorov et al 17. and performed molecular docking of (−)‐EA into the dihydropyridine binding site with AutoDock Vina 18.…”