In silico, design, synthesis and evaluation of new naphthyridine-dione analogues as potential candidates for carbonic anhydrase inhibitors

Abstract: Hypoxia in many kinds of solid tumours represent the main factor to induce Carbonic anhydrase IX (CAIX) and thus supports tumour pH homeostasis under low-oxygen condition. In mouse models, pharmacological CAIX inhibition has been shown to delay tumour growth, reduce metastatic spread, and restrain cancer stem cell expansion. Accordingly, targeting carbonic anhydrase overexpression—especially CAIX—represents a promising anticancer approach. Based on this premise, a new series of naphthyridinedione derivatives (5a to 5c) was designed, synthesised, and evaluated in cell lines (HCT116 and MCF-7), with acetazolamide (ACZ) used as a control compound. To prioritise the most promising candidates, molecular docking (Schrödinger Maestro 2021-1 and PyMOL) was performed prior to synthesis to select compounds with the highest predicted binding. Antiproliferative effects were then measured using an MTT assay in both cell models. Relative to acetazolamide, compound 5c demonstrated substantially greater antiproliferative potency in HCT116 (IC₅₀ = 1.08 μM) and MCF-7 cells (IC₅₀ = 1.49 μM) compared with acetazolamide (IC₅₀ = 1.79 μM and 2.55 μM, respectively). In contrast, compounds 5a and 5b exhibited cytotoxicity broadly comparable to acetazolamide. Collectively, these findings suggest that naphthyridinedione derivatives (5a–c) provide a useful starting scaffold for further anticancer drug development. Docking analyses further indicated that 5c achieved more favourable S-scores than acetazolamide, consistent with stronger predicted binding to the CAIX active site. The methoxy substituent and the naphthyridinedione core may contribute to increased conformational flexibility and improved receptor interactions. Overall, these naphthyridinedione derivatives (5a–c) show notable CAIX-related inhibitory potential alongside measurable cytotoxicity, supporting continued evaluation as anticancer lead compounds.