X‐Ray Crystallography of Carbonic Anhydrase Inhibitors and Its Importance in Drug Design

Ureido-Substituted Benzenesulfonamides Potently Inhibit Carbonic Anhydrase IX and Show Antimetastatic Activity in a Model of Breast Cancer Metastasis

“…The CA isoforms have differing amino acid sequences in the external portion of their active sites; therefore, compounds with a better selectivity profile for the various isoforms will contain an R group moiety that can interact with this region. 13 This has been reported earlier by our group, 12 with Figure 1. Binding of ureido-substituted benzenesulfonamides to the hCA II active site.…”

“…Compounds such as 11,13,15,16,19,21,22,25,28, and 29 showed excellent hCA IX inhibiting properties, with K I in the range 0.3-7.3 nM. A few weak hCA IX inhibitors were detected (e.g., 4, 14, 18, and 27), with K I in the range 102-575 nM, whereas all other derivatives presented inhibition constants of <100 nM.…”

“…Another series of compounds showed medium potency hCA II inhibition, with K I in the range 15-96 nM. These compounds (7,12,13,21,23, and 25) also possess aromatic groups at the second nitrogen ureido group, such as 4-fluorophenyl, 3,5-di(trifluoromethyl)phenyl, pentafluorophenyl, 4-cyanophenyl, 4-phenoxyphenyl, or 3-nitrophenyl. The remaining derivatives showed lower hCA II inhibitory properties, with K I in the range 226-9600 nM.…”

“…These different linkers allow less flexibility for the inhibitor scaffold, and this is probably the reason why such sulfonamides bind in the cannonical hydrophobic pocket of hCA II. 13,14 They also generally do not show isoform selectivity. 10 In contrast, for derivatives incorporating the ureido linker (of type 4-30), it has been shown 10 that the tails (all of them well ordered in the crystal structures; see Figure 1) are found in various hydrophobic pockets of the CA II active site.…”

“…As seen from the crystallographic data (Figure 1), 10 the torsion angles between these two fragments of the scaffold were quite different for the five compounds investigated by X-ray crystallography (i.e., 7, 13, 16, 25, and 28). 10 This probably allows the flexibility of the inhibitor to select the hydrophobic subpocket in such a way to avoid steric clashes 10,13,14 and to make as many as possible favorable interactions with amino acid residues within the enzyme cavity.…”