Combinatorial Design of Isoform-Selective N-Alkylated Benzimidazole-Based Inhibitors of Carbonic Anhydrases

Abstract

Human carbonic anhydrases comprise a family of isoforms that form structurally similar active site and thus it is difficult to design inhibitors that would selectively inhibit the targeted isoform and leave uninhibited all remaining ones. Most common inhibitors are aromatic sulfonamides that strongly bind and inhibit CAs, but usually with limited selectivity towards a targeted isoform. However, sometimes seemingly minor changes in the inhibitor structure may cause significant increase or decrease in affinity towards a CA isoform. Here, the affinities of previously designed N‐alkylated benzimidazoles were determined to all active human CA isoforms. This combinatorial approach yielded several compounds that were highly selective for CA VA. Intrinsic affinities were determined by subtraction of the binding‐linked protonation reactions that, together with the X‐ray crystallographic structures revealing the arrangement of the inhibitors in the active site, help in the design of inhibitors exhibiting subnanomolar affinities and improved selectivities towards a particular CA isoform.

Engineered Carbonic Anhydrase VI-Mimic Enzyme Switched the Structure and Affinities of Inhibitors

“…The standard error of K d measurements is ±2-fold. The p K a values of applied sulfonamide amino group (p K a _SA ) and inhibitor affinities towards CA II and CA VI have been already reported 58,86 . Dissociation constants K d s of selected compounds were confirmed by SFA (pH 7.5).…”

Methyl 2-Halo-4-Substituted-5-Sulfamoyl-Benzoates as High Affinity and Selective Inhibitors of Carbonic Anhydrase IX

“…These compounds differ structurally by meta -substituents; EA3-3 has a longer and more flexible substituent (-NH(CH 2 ) 2 OH), but both meta - groups were mostly exposed to the solvent, so they did not contribute much to the positioning in the active site. Both compounds are chlorinated at the ortho - position of the benzenesulfonamide, and chlorine is known to restrict the position of the ligand in the active site [ 11 , 20 ]. In addition, the para -cyclooctyl groups of both compounds occupied the same position.…”