Computational docking showed physiological anions robustly bind the Na1301-centered pocket of human NBCn1, while inhibitors S0859 and DIDS failed to generate compatible poses.
Computational docking demonstrates that the Na1301-centered pocket of human NBCn1 robustly accommodates physiological anions but not bulky pharmacological inhibitors like S0859 and DIDS.
The electroneutral Na + /HCO 3 - cotransporter NBCn1 (SLC4A7) is a key regulator of intracellular pH in excitable and nonexcitable cells and has been implicated in cardiovascular and neurological disease as well as cancer. However, the structural determinants of Na + and anion binding in human NBCn1 remain incompletely defined. We hypothesized that recent cryo-electron microscopy structures of human NBCn1 could be used to construct a physically plausible Na + /anion binding-site model and to establish a docking workflow suitable for future inhibitor discovery. Using the outward-facing NBCn1 structure (PDB 9OVR), we identified a single Na + density (Na1301) and its associated carbonate density as the primary Na + /anion site by analogy with other SLC4 transporters. A local binding pocket surrounding Na1301 was extracted and subjected to restrained energy minimization with OpenMM, and AutoDock4 was used to dock physiological and control anions (carbonate, bicarbonate, formate, acetate) into the Na-loaded pocket. Docked poses were then filtered using geometric criteria requiring realistic Na–O coordination and hydrogen bonding to conserved polar residues. Preliminary results show that all tested anions yield top-ranked poses localized to the Na1301-centered pocket, with carbonate and bicarbonate adopting closely related binding geometries compatible with the cryo-EM density, whereas non-native anions exhibit more variable orientations and weaker geometric agreement with the coordination shell. In contrast, when the larger small-molecule inhibitors S0859 and the stilbene disulfonate DIDS were docked into the same Na + -loaded pocket, they failed to generate poses that simultaneously coordinated the Na + ion and satisfied our hydrogen-bonding criteria, despite sampling the pocket region. These negative docking results, together with prior evidence that stilbene reagents primarily act from the extracellular vestibule rather than as simple competitive ligands at the ion site, suggest that S0859 and DIDS are unlikely to act as Scenario 1 Na-site blockers in this outward-facing conformation. We conclude that the Na1301-centered pocket provides a physically plausible Na + /anion binding site that robustly accommodates physiological anions, and that our docking pipeline can discriminate between native anions and bulky pharmacological inhibitors. This framework provides a computational foundation for extending the analysis to Na + -free states, additional NBCn1 conformations and extracellular vestibule models to probe state-dependent inhibition and guide rational design of more selective NBCn1 modulators. This abstract was presented at the American Physiology Summit 2026 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.
Yang et al. (Fri,) reported a other. Computational docking was evaluated on Binding geometries and coordination of anions and inhibitors in the Na1301-centered pocket. Computational docking showed physiological anions robustly bind the Na1301-centered pocket of human NBCn1, while inhibitors S0859 and DIDS failed to generate compatible poses.