Harnessing oligonucleotide architecture for potent multivalent inhibition of human carbonic anhydrases

Abstract

This study presents the design and synthesis of a novel class of carbonic anhydrase inhibitors (CAIs) using oligonucleotides as an original multivalent platform. Single-stranded oligonucleotides bearing one to four terminal alkyne moieties were prepared by solid-phase synthesis using the commercially available 2'-O-propargyl uridine phosphoramidite. In parallel, four different azide-functionalized CA inhibitor derivatives were generated from established coumarin and benzenesulfonamide pharmacophores. The resulting components were introduced into the oligonucleotides through Cu-catalyzed azide-alkyne cycloaddition (CuAAC), yielding a library of 17 oligonucleotide-based CA inhibitors with defined mono- to tetravalent architectures. This modular approach highlights the versatility of oligonucleotides as programmable platforms for the spatially controlled presentation of pharmacophores, opening new avenues for the development of potent and selective multivalent enzyme inhibitors. Among the resulting constructs, the divalent benzenesulfonamide conjugate 19 exhibited the most pronounced multivalency effect, showing a 3.5-fold increase in potency (r _p = 3.5) against the tumor-associated isoform hCA IX, with a K _i of 69 nM compared to its monovalent analogue 12 (K _i = 245 nM).

Scheme 1. Synthesis of modified oligonucleotide sequences.

Scheme 2. Synthesis of azide derivatives 6–9 based on CA inhibitors.

Scheme 3. CuAAC click ligation between the modified sequences and the azides of CAs inhibitors.