Structural Modeling of KCa3.1 Channel Interaction with Small Molecules

Abstract

The intermediate-conductance KCa3.1 channel and the related small-conductance KCa2 channels constitute potential pharmacological targets for immunosuppression, fibroproliferative disorders, hypertension and various neurological diseases. However, there currently is no available crystal structure or molecular model of these medically relevant targets that could be used for structure-assisted drug design. We used the Kv1.2-Kv2.1 channel structure (pdb id: 2R9R) as a template to generate a homology model of the KCa3.1 channel transmembrane region with the Rosetta modeling method. Docking of small molecules that are known to block KCa3.1 channel currents using Rosetta Dock generated structural channel - drug complexes that can be validated using experimental approaches. The lowest energy confirmation of the KCa3.1 channel complex with TRAM-34 identified T250 and V275 as interaction sites, two residues which had been previously demonstrated to completely abolish triarylmethane sensitivity when mutated to the corresponding residues in KCa2.3 channel. The model further correctly identified the interaction of the benzothiazinone-type KCa3.1 channel blocker NS6180 with T250 and V275 in KCa3.1 channel and modeled binding of the negative KCa2 channel gating modulator NS8593 to a KCa3.1-T250S- V275A mutant channel, which is blocked more potently by NS8593 than the WT-KCa2.3 channel. For the dihydropyridine nifedipine, which blocks KCa3.1 channels with low micromolar activity, the Rosetta model suggested a receptor site located between the pore lining S5 and S6 segment in agreement with available experimental data showing that nifedipine does not interact with T250 in the selectivity filter. The Rosetta KCa2/3 channel models can be used to understand the molecular mechanism of action of KCa channel blockers and gating modulators and assist with drug design efforts. Supported by RO1 GM076063 (to H.W.) and UC Davis startup (to V.Y-Y.).