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

Abstract

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.

KinITC—One Method Supports both Thermodynamic and Kinetic SARs as Exemplified on FimH Antagonists

“…This finding is in excellent agreement with previous observations from Gaspari et al. for the interaction of hCAII with hydrophobic ligands . In general, initial hydrophobic interactions to stabilize protein–ligand interactions established before the final binding mode is reached might facilitate ligand recruitment from solution.…”

“…Only then the protein–ligand complex relaxes from the TS ≠ to the bound state B by a successful completion of the hydrogen bond network within the binding site. A similar effect was described for the human carbonic anhydrase II (hCAII), where the on‐rate increased in parallel with the chain length of interacting alkyl benzenesulfonamides, that is, in a pre‐binding state, an interaction with a hydrophobic patch of the enzymatic cavity is formed …”

Discovery of a small molecule targeting ULK1-modulated cell death of triple negative breast cancer in vitro and in vivo

“…47 The measurements were performed on a Biacore S51 device (GE Healthcare, Uppsala). For immobilization, PBS with 0.05% Tween 20 and pH 7.4, was used as a background buffer.…”

Water‐Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase

“…While one might expect free energy and enthalpy to be correlated in any system with H/S compensation, the nature of the correlation in this system (positive), and our ability to attribute it primarily to the influence of mutations on local water networks, has a specific implication: Enthalpically favorable rearrangements of water within the binding pocket of HCAII give rise to stronger protein-ligand association than entropically favorable rearrangements of water. (The differential influence of such rearrangements on HCAII-ligand association rate-which, in light of recent evidence [34] , might correlate with ligand hydrophobicity-represents an interesting direction for a future study).…”