Mechanism of gating and isoform-specific inhibition in renal CLC chloride channels
- Chih-Ta Chien
- Briana L. Sobecks-Doherty
- Alexander S. Powers
- Anindita Das
- Jürgen Kreiter
- Chloe N. Barry
- Muyuan Chen
- Andrew Hinman
- Camille F. Petrakian
- Brianna Williams
- Chase A. P. Wood
- Mengyuan Xu
- Ron O. Dror
- Wah Chiu
- Merritt Maduke
2026-09-01
Hyponatremia is a prevalent disorder marked by excess water retention and substantial morbidity, motivating interest in the chloride channel CLC-Ka as a therapeutic target. Selectively inhibiting CLC-Ka without affecting the closely related CLC-Kb is essential for preventing serious side effects. However, developing isoform-selective inhibitors has been challenging because most small molecules do not distinguish between CLC-Ka and CLC-Kb, and the basis for selectivity in the few known exceptions remains unclear. The small molecule BIM1 preferentially inhibits CLC-Ka over CLC-Kb, providing an opportunity to dissect isoform-specific pharmacology. To investigate this mechanism, we determined cryo-EM structures of BIM1 and BIM15, a related nonselective analog, bound to a CLC-K variant engineered to match the human CLC-Ka binding pocket. Structural and computational analyses reveal that inhibition and isoform selectivity are anchored by interactions with a conserved lysine, with surrounding binding-site residues subtly tuning the local electrostatic environment to promote or disfavor these contacts. These analyses further identify a dynamic extracellular loop that intermittently occludes the shared pathway accessing the inhibitor-binding site and pore. Bound BIM15 engages this gating loop more extensively than BIM1, suggesting that differential loop engagement contributes to inhibitor selectivity, a prediction validated by mutagenesis. Because loop dynamics block the pore, we examined the structural impact of Ca 2+ , which favors opening, and found the gating loop ordered and withdrawn from the pathway. Together, these findings define how binding-site microenvironments and gating-loop dynamics shape isoform-specific inhibition and pore access in CLC-K channels.