Small Molecule Alkoxy Oriented Selectiveness on Human Carbonic Anhydrase II and IX Inhibition

Abstract

We report aryl sulfonamide inhibitors of human carbonic anhydrase (hCA; EC 4.2.1.1) enzymes containing short ureido alkoxy tails. The inhibition potency of such compounds was investigated in vitro on the major hCA isoforms (i.e. I, II, IX, and XII). A selection of the most potent inhibitory derivatives against the hCA IX isoform (i.e. 5a, 5c, and 6c) was studied, and their binding modes on either hCA II and IX-mimic isoform were assessed by X-ray crystallography on the corresponding ligand/ protein adducts. This study adds to the field of developing hCA inhibitors at molecular level the critical interactions governing ligand selectivity.

New Insights into Conformationally Restricted Carbonic Anhydrase Inhibitors

“…Compound 3j was both weakly selective and had a similarly poor affinity for both CA II and CA IX at 280 nM and 215 nM, respectively ( Table 1 ). This is likely due to a similar phenomenon observed and discussed in our previous study [ 12 ]. The ureido-butyl linker-tail group is meta-substituted on the benzenesulfonamide and the substitution pattern on the benzenesulfonamide has been previously observed to have a steering effect on the tail region as a result of the rigid plane of the benzenesulfonamide.…”

“…The synthetic strategy adopted for the synthesis of the compounds reported in this manuscript was first introduced by researchers with the intent to decipher the details of the contribution onto CA isoform selectivity given from specific fragments connected to the ureido group in depth [ 12 ]. Such an approach became of large experimental applicability when the synthesis of compounds of the type in Scheme 1 bearing alkyl ureas endowed with differential rotational properties were accessed by means of nucleophilic attack of selected primary/secondary amines on the ad hoc prepared 2-oxo-2,3-dihydrobenzo[ d ]oxazole-5-sulfonamide 1 [ 1 , 12 , 13 ]. By making use of the structure activity relationship (SAR) knowledge acquired in the previous reports, herein we introduce ad hoc moieties able to afford highly potent and selective ligands for the tumor associated CA IX isoform ( Scheme 1 ).…”

“…These compounds are identical in the zinc-binding group composed of a multiply substituted benzenesulfonamide, with a para -substituted hydroxide and an ortho -substituted ureido-linker group attaching the head to the tail group, which is the variable region in this experiment. A naming convention similar to the one utilized in Bozdag et al, 2022 [ 12 ] is present in this work as well; however, the substitution pattern relative to the para -hydroxide is signified by the first character, the functional group by the second, and the number of carbons linking the two is the final digit [ 12 ].…”

“…The inhibition constants were obtained by non-linear least-squares methods using PRISM 3 and the Cheng–Prusoff equation, as reported earlier, and represent the mean from at least three different determinations. All CA isoforms were recombinant proteins obtained in house, as reported earlier [ 1 , 12 , 13 ].…”

Ibuprofen: a weak inhibitor of carbonic anhydrase II

“…A major hurdle in the development of effective CAIs is the similarity between the human CA isoforms, which leads to off-target binding. Thus, new isoformspecific CAIs that bind differentially depending on the amino acids that line the active sites are currently under development (Bozdag et al, 2022;Lomelino et al, 2016).…”