Design, anticancer activity, and mechanistic evaluation of a novel class of selective human carbonic anhydrase IX inhibitors featuring a trifluorodihydroxypropanone pharmacophore

: Carbonic anhydrases (CAs) have emerged as promising drug targets for cancer therapy. In particular, the human (h) CA IX (hCA IX) isoform is expressed in a wide variety of malignancies and appears tightly regulated by micro-environmental hypoxia. Ongoing efforts aim to identify novel classes of selective CA inhibitors (CAIs) by exploring molecular diversity and discovering original chemotypes and pharmacophores. Previously, we identified a new hit compound (TDP1) carrying a trifluorodihydroxypropanone (TDP) motif as an original zinc-binding function (ZBF), which has undergone structural optimization to generate derivatives with selective inhibition profile toward hCA IX. Herein, we report on the synthesis, biological evaluation, X-ray crystallographic analysis, and computational studies of a series of aromatic-substituted TDP derivatives as novel CAI-directed chemotypes. The most potent compounds selectively inhibited hCA IX, with KI values in the submicromolar to high nanomolar range and exhibited significant antiproliferative activity against representative normoxic and hypoxic pancreatic tumor cell lines. Ultrastructural studies indicated for TDPs a possible interference with the mitochondrial function or iron metabolism. Moreover, X-ray crystallography data provided insights into the CA inhibition mechanism, suggesting that these compounds behave similarly to classical CAIs. In summary, this original TDP pharmacophore effectively inhibits human CAs, with relative selectivity towards hCA IX over cytosolic isoforms, thus providing structural insights for the development of a new class of selective anticancer agents.