Development of a Nanoscale Protein–Protein Mapping of PDE4 Interface-Disrupting Peptides

Spatially confined β-adrenergic receptor-cAMP nanodomain signaling depends on scaffolded protein-protein interactions (PPIs), yet converting such nanointerfaces into cell-active disruptor peptides remains challenging. Here, we identify a previously unrecognized phosphodiesterase 4A (PDE4A)-filamin A complex in human cardiac tissue that is disrupted in dilated cardiomyopathy. To target this interaction, we developed a nanodomain-resolved AlphaFold3 workflow integrating interface-recurrence filtering, orthogonal docking, and peptide-binding site inference to define a tractable binding region. This approach identified a filamin A docking sequence spanning R2520-H2528, which was optimized to RLVSNHSLH and rendered cell-permeant by N-terminal polyarginine tagging. In ventricular cardiomyocytes, the peptide reduced PDE4A-filamin A proximity and selectively attenuated β-adrenergic cAMP signaling in cytosolic and sarcolemmal compartments, measured by FRET biosensors. This work establishes a potential transferable strategy for translating predicted scaffolded PPI nanointerfaces into functional disruptor peptides and highlights compartmentalized signaling complexes as actionable targets for selective cellular modulation.