Sulfonamide/Carboxylate Functionalized Acridinedione Derivatives: Design, Synthesis, and Carbonic Anhydrase Inhibition Profile.

Abstract

A new series of sulfonamide- and carboxylate-functionalized acridinedione derivatives 5a-n was designed through a pharmacophore-retention and simplification strategy that preserved the acridine core and zinc-binding motifs while systematically varying electronic and steric features on the aromatic rings. Targets 5a-n were synthesized from dimedone-based enaminones and aromatic aldehydes under acidic cyclization conditions and characterized by NMR, High-resolution mass spectrometry (HRMS), and elemental analysis. In vitro, all analogs inhibited cytosolic hCA I and II and membrane-bound hCA IX and XII with potencies spanning low micromolar to low nanomolar KI values, with sulfonamide derivatives consistently outperforming their carboxylate counterparts. Among the series, compounds 5j and 5n showed sub-10 nM inhibition of hCA II (KIs 6.3 and 7.8 nM), while 5i, 5h, 5k, and 5n exhibited high nanomolar activity against hCA IX and XII. Structure-based docking and GNINA CNN scoring confirmed that sulfonamide analogs adopt canonical Zn2+-coordinating poses with extensive hydrogen bonding to Thr199/Thr204 and hydrophobic engagement of the deep lipophilic pocket, correlating with the superior experimental inhibition. A 100 ns molecular dynamics study of lead compound 5k across hCA I, II, IX, and XII demonstrated stable metal-proximal binding, with particularly low ligand RMSD and persistent gatekeeper hydrogen bonding in hCA XII, supporting its promising inhibitory profile.

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