Targeting lysosomes with a novel chloroquine derivative induces irreversible lysosomal damage and disrupts autophagosome and lysosome assembly in cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) exhibits profound therapy resistance driven by lysosome dependent nutrient recycling, metabolic adaptation, and stress tolerance. Current lysosome-targeting agents such as chloroquine (CQ) and hydroxychloroquine (HCQ) show limited efficacy due to transient activity and dose-limiting toxicities. To overcome these limitations, we developed Lysostilbenes, a new class of hybrid small molecules combining the CQ pharmacophore with lysosome-disrupting trans -4,4′-dihydroxystilbene. Lysostilbene-4 emerged as the lead candidate, demonstrating ∼30–40-fold greater cytotoxicity against PDAC cells than parental compounds, while sparing non-malignant cells. At nanomolar concentrations, Lysostilbene-4 induced rapid, irreversible lysosomal membrane permeabilization (LMP), initiating a lysosome mitochondria apoptotic cascade via cathepsin-B release, BID cleavage, BAX activation, and caspase-mediated apoptosis. In parallel, it abrogated lysosomal recovery by impairing repair, lysophagy, autophagosome maturation, and uncoupling TFEB-driven transcriptional programs from effective lysosome biogenesis. TFEB knockout further sensitized PDAC cells, underscoring TFEB as a key determinant of lysosomal resilience and a potential predictive biomarker. Importantly, Lysostilbene-4 was well tolerated in preclinical mouse models at supra-therapeutic doses without systemic toxicity. These findings position Lysostilbene-4 as a first-in-class lysosome-targeting therapeutic that enforces sustained lysosomal collapse while disabling adaptive recovery mechanisms, providing a mechanistically precise and safe strategy against PDAC.