Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies

J Med Chem. 2016 May 12;59(9):4245-56. doi: 10.1021/acs.jmedchem.5b01643. Epub 2016 Jan 12.


The binding of sulfonamides to human carbonic anhydrase II (hCAII) is a complex and long-debated example of protein-ligand recognition and interaction. In this study, we investigate the para-substituted n-alkyl and hydroxyethylene-benzenesulfonamides, providing a complete reconstruction of their binding pathway to hCAII by means of large-scale molecular dynamics simulations, density functional calculations, surface plasmon resonance (SPR) measurements, and X-ray crystallography experiments. Our analysis shows that the protein-ligand association rate (kon) dramatically increases with the ligand's hydrophobicity, pointing to the existence of a prebinding stage largely stabilized by a favorable packing of the ligand's apolar moieties with the hCAII "hydrophobic wall". The characterization of the binding pathway allows an unprecedented understanding of the structure-kinetic relationship in hCAII/benzenesulfonamide complexes, depicting a paradigmatic scenario for the multistep binding process in protein-ligand systems.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carbonic Anhydrase II / metabolism*
  • Crystallography, X-Ray
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Kinetics
  • Molecular Structure
  • Protein Binding
  • Sulfonamides / metabolism*
  • Zinc / chemistry


  • Sulfonamides
  • Carbonic Anhydrase II
  • Zinc