Understanding binding behavior of human carbonic anhydrase II with aromatic benzenesulfonamides by molecular dynamics simulations and biophysical characterization

Human carbonic anhydrase II (HCAII) catalyzes the hydrolysis of carbon dioxide to form the bicarbonate ion and a proton. The active site of HCAII contains a Zn²⁺ ion and three histidine residues located between hydrophobic and hydrophilic pockets. Sulfonamides can bind to the active site zinc and inhibit the enzyme. We have investigated a series of new inhibitor-based benzenesulfonamides for HCAII inhibition. Molecular docking and molecular dynamics (MD) calculations were used to determine how the inhibitors interact with HCAII, and Molecular Mechanics-Generalized Born Surface Area (MM/GBSA) calculations were used to calculate binding free energies and important interactions. Circular dichroism data showed a notable change in the protein structure when para-aminobenzenesulfonamide and 2-nitroimidazole-benzenesulfonamide bind to zinc(II), which was explained by the root mean squared fluctuation and secondary structure elements analysis. The MM/GBSA calculations gave binding affinities that are much more negative but in the same relative order as the measured binding affinities. Among a series of new inhibitors, ortho-9-amino-4,5-diazafluorenebenzenesulfonamide, ortho-9-amino-4,5-diazafluorenebenzenesulfonamide, and PaQ exhibited the most significant binding affinity to HCAII, making them promising candidates for further research in drug discovery or catalysis.