Rosetta modeling of the inner KCa3.1 pore, a hotspot for small molecule modulation

Abstract

The intermediate‐conductance KCa3.1 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 channels that could be used for structure‐assisted drug design. Using the Rosetta modeling method we constructed a model of the KCa3.1 pore and energy minimized it in the presence of the KCa3.1 blocker TRAM‐34. The lowest energy confirmation of the KCa3.1 complex with TRAM‐34 identified Thr250 and Val275 as interaction sites, two residues which had been previously demonstrated to completely abolish triarylmethane sensitivity when mutated to the corresponding residues in KCa2.3. The model further correctly identified the interaction of the benzothiazinone‐type KCa3.1 blocker NS6180 with Thr250 and Val275 in KCa3.1 and modeled binding of the negative KCa2 channel gating modulator NS8593 to a KCa3.1‐Thr250Ser‐ Val275Ala mutant channel, which is blocked more potently by NS8593 than the WT‐KCa2.3 channel. The Rosetta KCa3.1 model can be used to understand the molecular mechanism of action of KCa2/3 channel modulators and assist with drug design of blockers and gating modulators.Supported by RO1 GM076063 (to H.W.) and UC Davis startup (to V.Y.).