Ligand-based discovery of small molecules suppressing cancer cell proliferation via autophagic flux inhibition.

Autophagy is a conserved self-degradation system closely related to cancer progression. Small molecule inhibitors of autophagy have proven to be efficient tools in cancer therapy and are in high demand. Here we report the discovery of two compounds (LZ02/01) capable of suppressing cancer cell proliferation via inhibiting autophagy flux and promoting apoptosis. Potential autophagy inhibitors were selected based on the pharmacophore model derived from the structures of known autophagy inhibitors. LZ02/01-mediated autophagy flux disruption and apoptosis promotion in breast and hepatocellular carcinoma cells (MCF-7 and Hep3B) were examined using a combination of molecular methods in vitro and in vivo. The synergistic tumor-suppressing effects of LZ02 and chloroquine were validated by adopting a xenograft mice model of human breast cancer. Two potential inhibitors (LZ02/01) targeting an autophagy pathway were discovered from the Enamine database. In both MCF-7 and Hep3B cells, LZ02 and LZ01 had the effect of causing the co-occurrence of autophagic flux inhibition and apoptosis induction, robustly suppressing the growth, proliferation, and cell cycle progression. Further tests revealed that FoxO3a and its downstream target genes regulating autophagy, apoptosis, and cell cycle progression were activated and overexpressed, suggesting such effects of LZ02/01 on autophagy and apoptosis were associated with the activation and overexpression of FoxO3a. In addition, LZ02/01-mediated apoptosis is not independent; it was verified to be promoted by autophagic flux inhibition. Meanwhile, synergistic effects on tumor growth reduction were detected in the xenograft mice model of human breast cancer simultaneously treated with LZ02 and chloroquine. Our findings suggest that LZ01 and LZ02 are potent in suppressing cancer cell proliferation and tumor growth through autophagic flux inhibition and apoptosis promotion. The synergistic anti-cancer effects of LZ02 with chloroquine may provide a rational basis for prospective cancer therapy. KEY MESSAGES: A ligand-based pharmacophore model of high quality is constructed to query hits and two novel scaffold lead compounds LZ01/02 were identified by high-throughput virtual screening. LZ01/02 works to inhibit autophagic flux by attenuating lysosome function. LZ01/02 induces apoptosis through autophagic flux inhibition and apoptosis is the main mechanism to inhibit MCF-7 and Hep3B cancer cell proliferation. The synergistic antitumor growth effects of LZ02 and chloroquine are verified in human xenograft model.