Prediction of binding modes and affinities of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide inhibitors to the carbonic anhydrase receptor by docking and ONIOM calculations

Abstract

Inhibition activities of a series of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamides against the human carbonic anhydrase II (HCAII) enzyme have been explored by employing molecular docking and hybrid QM/MM methods. The docking protocol has been employed to assess the best pose of each ligand in the active site cavity of the enzyme, and probe the interactions with the amino acid residues. The docking calculations reveal that the inhibitor binds to the catalytic Zn2+ site through the deprotonated sulfonamide nitrogen atom by making several hydrophobic and hydrogen bond interactions with the side chain residues depending on the substituted moiety. A cross-docking approach has been adopted prior to the hybrid QM/MM calculation to validate the docked poses. A correlation between the experimental dissociation constants and the docked free energies for the enzyme-inhibitor complexes has been established. Two-layered ONIOM calculations based on QM/MM approach have been performed to evaluate the binding efficacy of the inhibitors. The inhibitor potency has been predicted from the computed binding energies after taking into account of the electronic phenomena associated with enzyme-inhibitor interactions. Both the hybrid (B3LYP) and meta-hybrid (M06-2X) functionals are used for the description of the QM region. To improve the correlation between the experimental biological activity and the theoretical results, a three-layered ONIOM calculation has been carried out and verified for some of the selected inhibitors. The charge transfer stabilization energies are calculated via natural bond orbital analysis to recognize the donor-acceptor interaction in the binding pocket of the enzyme. The nature of binding between the inhibitors and HCAII active site is further analyzed from the electron density distribution maps.