Real-time visualization of drug-target interactions in native subcellular microenvironments for lysosome-targeted...

Conventional ex vivo drug screening platforms struggle to recapitulate native subcellular microenvironments, leading to high off-target rates and compromised discovery of bioactive compounds. To address this, we developed subcellular target-tracking fluorescent-visualization-based interaction screening (SubTrack-FVIS), a platform combining super-resolution imaging with target-specific fluorescent tagging. SubTrack-FVIS first maps nanoscale spatial distributions of drug targets within living cells, then screens compound libraries to identify molecules specifically binding to target-enriched domains, and finally quantifies drug-target interactions through super-resolution imaging tracking. Compared to traditional toolbox, SubTrack-FVIS reduces off-target effects by evaluating compound binding within native subcellular architectures. When applied to the lysosomal vacuolar H⁺-ATPases (V-ATPase) subunit, ATP6V1A, a validated anti-cancer target, this approach identified for lysosomal alkalization fluorescent drug (LAFD) as a potent inhibitor. Super-resolution imaging revealed LAFD's dynamic binding to ATP6V1A clusters, enabling real-time visualization of V-ATPase inhibition and subsequent lysosomal destabilization. Crucially, SubTrack-FVIS uncovered LAFD's unique mechanism of blocking autophagosome-lysosome fusion, resolving autophagic flux obstruction at sub-100 nm resolution. This platform establishes a visualization framework for discovering drugs within physiological subcellular contexts while simultaneously decoding their mechanistic impacts, offering application potential for target-centric drug development.