Selective Inhibitors For One of Six Ion Channel Isoforms

Background

The family of highly similar ion channel isoform.
Only one of which has to be targeted, specifically its open channel conformation.
The exact location of the most favorable binding pocket for achieving selectivity is unknown.
Achieving in vivo PoC was essential to confirm therapeutic efficacy.

Objective: To develop inhibitors that selectively target a specific ion channel isoform and specifically to the open channel conformation.

Three tentative binding sites were identified for each protein isoform by proprietary Receptor.AI pocket detection workflow: in the outer channel pore, inside the channel cavity, and between the functionally important transmembrane helices.
Selectivity assessment based on differential pocket pharmacophore’s representation combined with generative AI binding pose prediction was used.
Pre-filtered stock chemical space of 662K compounds was used as well as a custom focused diversity database of 50K compounds.

291 compounds were selected for experimental validation.

The similarity matrix of full-length isoforms

Fold increase of effect on target isoform in comparison to off-target isoforms.
UFD effect: the preference of the compound to block the active channel state relative to the resting state.
Peak blocking of the target channel at 120 μM of the compound relative to the vehicle.

40% hit rate: Out of 5 million compounds, 291 were identified as active hits.
5 selective compounds against all isoforms: The top compound exhibited 3.16 times selectivity, with the top 5 showing up to 5x selectivity across all isoforms, including effective targeting of both open and closed channel states.
Significant in vivo activity: 3 compounds demonstrated substantial in vivo activity (murine model) and were proven to be non-toxic, including one that was highly potent.

Novelty: Several compounds represent entirely new classes of chemical entities, showcasing the potential to design novel compounds.