Structure Assisted Design of Small Molecule KCa Channel Modulators

Abstract

Pharmacological modulation of ion channels offers tremendous opportunities for the design of new drugs for neurological and cardiovascular diseases. However, in contrast to other therapeutic targets such as protein kinases, ion channels have not been popular with medicinal chemists in the pharmaceutical industry. One reason is the absence of co‐crystals of medically relevant channels with bound drug molecules, a prerequisite for structure based drug design. Using the Rosetta molecular modeling suite we generated homology models of the pore of the Ca2+‐activated K+ channel KCa3.1 and tested the models by first confirming previously mapped binding sites and visualizing the mechanism of TRAM‐34, senicapoc and NS6180 inhibition at the atomistic level. All three compounds block ion conduction directly by fully or partially occupying the site that would normally be occupied by K+ before it enters the selectivity filter. We then challenged the model to predict the receptor sites and mechanisms of action of the dihydropyridine nifedipine and an isosteric 4‐phenyl‐pyran. Rosetta predicted receptor sites for nifedipine in the fenestration region and for the 4‐phenyl‐pyran in the pore lumen, which could both be confirmed by site‐directed mutagenesis and electrophysiology. We further used Rosetta modeling to explain the KCa3.1 selectivity of the positive allosteric gating modulator SKA‐121, a compound that binds at the interface of the calmodulin N‐lobe and the calmodulin binding domain of these voltage‐independent Ca2+‐activated channels, where it “facilitates” mechanical opening (= increase open channel probability) at a given Ca2+ concentration. Rosetta Ligand provides a plausible explanation for why KCa channel activators in general are 5–10‐fold more potent in activating KCa3.1 than KCa2 channels. The presence of R362 creates an extensive “background” hydrogen‐bond network in the KCa3.1 interface pocket that stabilizes the main contacts NH2‐substituted KCa activators make with M51 and E54 in calmodulin. The three KCa2 channels have shorter N or S residues in the corresponding position and therefore cannot form this hydrogen‐bond network.Overall these examples illustrate that ion channels are highly accessible to small molecule drugs and we suggest that both the KCa3.1 pore and KCa3.1‐CaM‐BD/CaM model could be used for structure assisted drug design.Support or Funding InformationThis work was supported by the CounterACT Program, National Institutes of Health Office of the Director (NIH OD), and the National Institute of Neurological Disorders and Stroke (NINDS), Grant Number U54NS079202 and R21NS101876 (to H.W.).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.