2025/12/02 by Sarfraz Ahmad, Muhammad Usman Mirza, Mamoona Nazir +4 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Enzyme function and inhibition #Mechanisms of cancer metastasis #Aldose Reductase and Taurine
paper · doi:10.1016/j.abb.2025.110682
openalex created_date 2025/12/02 · openalex publication_date 2025/12/02 · openalex updated_date 2026/07/30
Hypoxia in solid tumours induces carbonic anhydrases (CAs) upregulation, notably CA IX and CA XII, to sustain pH homeostasis. While sulfonamide-based zinc binders show high affinity for these targets, achieving the required selectivity versus the ubiquitous CA II remains challenging. Fortunately, the efforts of the community in obtaining experimental structures of ligand-protein complexes have now generated sufficient samples to rationalize isoform preferences. Herein, we provide our detailed structure-annotated meta-analysis of sulfonamide binding across CA II, CA IX, and CA XII that standardizes residue numbering and interaction taxonomy. We examine 130 X-ray cocrystal structures, CA II (47), CA IX (55), and CA XII (28), to quantify Zn-sulfonamide geometry, entrance-zone contacts (Arg60, Thr199/Thr200, His64 π-cation), conserved water mediation, and occupancy/orientation within the 130s subpocket (residues 131/132/135) that provide the best opportunities for delivering selectivity. From these data, we extract concrete, structure-derived design rules: (i) lowering sulfonamide pKa boosts affinity across isoforms but does not confer selectivity; (ii) directing steric/hydrophobic bulk into the 130s subpocket exploits Phe131/Gly132/Val135 (CA II) versus Val131/Asp132/Leu135 (CA IX) versus Ala131/Ser132/Ser135 (CA XII) differences; (iii) favourable entrance-zone interactions, e.g., salt bridging to Arg60 (IX), halogen bonding to Thr199, and occasional His64 π-cation, enhances IX/XII bias; and (iv) compact, highly polar heads without tailored tails tend to default to preferring CA II. This critical synthesis consolidates the dispersed structural evidence into an isoform-resolved map of selectivity-enabling interactions. This provides public access to a very useful tool for CA IX/XII-selective inhibitor design.