Significance
We designed C6 peptide to address the absence of specific inhibitors of human voltage-gated proton channels (hHv1). Two C6 bind to the two hHv1 voltage sensors at the resting state, inhibiting activation on depolarization. Here, we identify the C6–hHv1 binding interface using tethered-toxin variants and channel mutants, unveil an important role for negatively charged lipids, and present a model of the C6–hHv1 complex. Inspired by nature, we create a peptide with two C6 epitopes (C6
2
) that binds to both channel subunits simultaneously, yielding picomolar affinity and significantly improved inhibition at high potentials. C6 and C6
2
are peptides designed to regulate hHv1, a channel involved in innate immune-system inflammatory pathophysiology, sperm capacitation, cancer-cell proliferation, and tissue damage in ischemic stroke.