Background: Long-QT syndrome type-3 (LQT3) is a life-threatening disease caused by mutations in the cardiac sodium channel (NaV1.5). The class-Ib anti-arrhythmic mexiletine was proposed as an effective therapy for LQT3. However, clinical studies showed that LQT3 variants have distinct sensitivities to mexiletine. We hypothesized that altered voltage-sensing domain (VSD) function determines mutation-dependent mexiletine blockade. Methods: NaV1.5 contains four domains (DI-DIV), each with a VSD. We previously created four channel constructs that can track each VSD's conformation changes when tethered with a fluorophore. VSD-tracking fluorescence and ionic currents were recorded simultaneously for WT and LQT3-linked channels with or without mexiletine. Results: Mexiletine blockade of WT channel stabilized the DIII-VSD activated conformation. Among 14 common LQT mutations, 10 showed varied DIII-VSD activation voltage-dependence, despite distal locations of some, e.g. R1626P(DIV-VSD) and E1784K(C-terminus). DIII-VSD activation shifts correlate strongly with tonic block by mexiletine(R=0.91), suggesting that the DIII-VSD conformation determines mexiletine blockade at the cardiomyocyte resting potential. Decoupling the DIII-VSD from the pore eliminated mutation-specific mexiletine sensitivity, suggesting that the activated DIII-VSD facilitates mexiletine block by promoting pro-binding conformations within the DIII pore. Unlike WT, mexiletine blockade of the inactivation-impaired channel (F1486Q) did not shift the DIII-VSD, implying that during the action potential plateau, the DIII-VSD and inactivation gate coordinate to regulate mexiletine blockade. To predict use-dependent block (UDB) and QT-interval shortening (ΔQT) from channel gating parameters, we applied a machine learning approach, partial least-square regression(PLSR). Our PLSR model showed that changes in DIII-VSD activation, steady-state inactivation and slow recovery from inactivation parameters are strongly predictive of mexiletine-linked changes in UDB and ΔQT (RUDB=0.92, RΔQT=0.82). Conclusion: Traditional anti-arrhythmic block models have focused on the role of channel inactivation. We have revised this model to include an essential role of the DIII-VSD.
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