3D-QSAR study for the development of chalcone-based inhibitors targeting ovarian cancer cells with experimental validation

Abstract

Background: Ovarian cancer remains one of the most lethal gynecological malignancies, mainly due to late-stage diagnosis and frequent chemoresistance. Purpose: This study sought to develop 3D-QSAR models—Comparative Molecular Field and Similarity Index Analysis (CoMFA and CoMSIA)—to predict the antiproliferative activity of synthetic chalcone derivatives against A2780 ovarian cancer cells and to explore potential mechanisms of action through antioxidant response biomarkers. Materials and methods: CoMFA and CoMSIA models were developed using a dataset of 64 chalcone derivatives and validated using q2, r2ncv, and other statistical metrics. Twelve chalcones predicted as active were synthesized and characterized by FT-IR and NMR spectroscopy. Their antiproliferative effects were evaluated using MTT assays, complemented by clonogenic testing, intracellular glutathione quantification, and analysis of biomarkers, including nuclear factor erythroid 2-related factor 2 (Nrf2), heme oxygenase-1 (HO-1), and NAD(P)H: quinone oxidoreductase 1 (NQO1). The most active compounds were further assessed in a cisplatin-resistant A2780 subline, with N-acetylcysteine (NAC) used to probe reactive oxygen species (ROS)-dependent mechanisms. Results and discussion: The CoMFA and CoMSIA models demonstrated strong predictive performance (q2 = 0.763/0.789; r2ncv = 0.963/0.920). Contour maps highlighted steric and electrostatic features linked to enhanced antiproliferative activity. The twelve synthesized chalcones exhibited experimental pIC50 values that strongly correlated with model predictions. Compounds 065, 066, and 072 showed the highest potency, with compound 072 also reducing clonogenic survival. Active derivatives increased intracellular glutathione and upregulated HO-1 without activating canonical Nrf2 signaling. In cisplatin-resistant A2780 cells, compounds 072 and 074 displayed markedly higher potency (IC50 = 6.50 and 10.22 μM) than cisplatin (93.4 μM). Their cytotoxicity was abrogated by NAC, indicating a ROS-dependent mode of action. Conclusions: CoMFA and CoMSIA models accurately predicted the activity of synthetic chalcones, and the biological findings identify these derivatives as promising candidates for the treatment of ovarian cancer, including chemoresistant forms.