Design of Rigid Compounds to Enhance Selectivity for Carbonic Anhydrase IX

Abstract High affinity and selectivity for intended targets is an important goal of small molecule design in drug discovery, yet balancing molecular flexibility and rigidity remains a challenge. While flexible compounds can increase target affinity, they often result in non‐specific interactions and reduced selectivity. In contrast, rigid compounds may recognize their target more precisely and have lower off‐target effects. In this study, we incorporated a 1,1‐dioxido‐1,4‐thiazine ring into fluorinated benzenesulfonamide derivatives with bulky meta ‐substituents to enhance selectivity for human carbonic anhydrase IX (CAIX), an important cancer‐associated target. Due to the structural similarities of CAIX with other carbonic anhydrase isozymes, selective inhibition remains a significant challenge. A series of 3,4‐substituted trifluorobenzenesulfonamides containing oxidized thiazine rings were synthesized using a novel synthetic pathway. Although the potency against CAIX was modestly reduced compared to more flexible analogs, selectivity increased significantly, with lead compounds 7 d and 7 e exhibiting over 1000‐fold selectivity for CAIX over most other isozymes. X‐ray crystallography revealed the structural basis for this selectivity, confirming the advantageous positioning of rigidified compounds within some CA isozyme active sites. These findings highlight the potential of molecular rigidity in the design of highly selective inhibitors for therapeutic applications.