Affinity and Selectivity of Protein–Ligand Recognition: A Minor Chemical Modification Changes Carbonic Anhydrase Binding Profile

Discovery of small-molecule drugs relies on their strong
binding
affinity compared to nontarget proteins, thus possessing selectivity.
Minor chemical structure changes usually exhibit little change in
the compound efficacy, with rare exceptions. We developed a series
of nearly 50 ortho-substituted benzenesulfonamides
and experimentally measured their interactions with the 12 catalytically
active human carbonic anhydrase (CA) isozymes. Inhibitors were designed
using seven different substituent groups, including 4-sulfanyl-substituted 3-sulfamoyl benzoates and benzamides, 4-sulfinyl-substituted 3-sulfamoyl benzoates and benzamides, 4-sulfonyl-substituted 3-sulfamoyl benzoates and benzamides, and 4-amino-substituted
benzamides. The oxidation state of sulfur at the ortho position significantly influenced the compound’s affinity
for CAIX, a target for anticancer drugs, demonstrating affinities
hundreds of thousands of times stronger than related compounds. Coupled
with X-ray crystal structures and molecular docking, the relationship
between structure and thermodynamics offers insights into how small
changes in the structure lead to significant changes in affinity for
drug design.