Novel fluorinated carbonic anhydrase IX inhibitors reduce hypoxia-induced acidification and clonogenic survival of cancer cells

Human carbonic anhydrase (CA) IX has emerged as a promising anticancertarget and a diagnostic biomarker for solid hypoxic tumors. Novel fluorinated CAIX inhibitors exhibited up to 50 pM affinity towards the recombinant human CA IX,selectivity over other CAs, and direct binding to Zn(II) in the active site of CA IXinducing novel conformational changes as determined by X-ray crystallography. Massspectrometric gas-analysis confirmed the CA IX-based mechanism of the inhibitors ina CRISPR/Cas9-mediated CA IX knockout in HeLa cells. Hypoxia-induced extracellularacidification was significantly reduced in HeLa, H460, MDA-MB-231, and A549 cellsexposed to the compounds, with the IC50 values up to 1.29 nM. A decreased clonogenicsurvival was observed when hypoxic H460 3D spheroids were incubated with ourlead compound. These novel compounds are therefore promising agents for CA IXspecifictherapy.