Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I, II, VII, XII, and XIII

Abstract

The early stage of drug discovery is often based on selecting the highest affinity lead compound. To this end the structural and energetic characterization of the binding reaction is important. The binding energetics can be resolved into enthalpic and entropic contributions to the binding Gibbs free energy. Most compound binding reactions are coupled to the absorption or release of protons by the protein or the compound. A distinction between the observed and intrinsic parameters of the binding energetics requires the dissection of the protonation/deprotonation processes. Since only the intrinsic parameters can be correlated with molecular structural perturbations associated with complex formation, it is these parameters that are required for rational drug design. Carbonic anhydrase (CA) isoforms are important therapeutic targets to treat a range of disorders including glaucoma, obesity, epilepsy, and cancer. For effective treatment isoform-specific inhibitors are needed. In this work we investigated the binding and protonation energetics of sixteen [(2-pyrimidinylthio)acetyl]benzenesulfonamide CA inhibitors using isothermal titration calorimetry and fluorescent thermal shift assay. The compounds were built by combining four sulfonamide headgroups with four tailgroups yielding 16 compounds. Their intrinsic binding thermodynamics showed the limitations of the functional group energetic additivity approach used in fragment-based drug design, especially at the level of enthalpies and entropies of binding. Combined with high resolution crystal structural data correlations were drawn between the chemical functional groups on selected inhibitors and intrinsic thermodynamic parameters of CA-inhibitor complex formation.

Intrinsic Thermodynamics and Structures of 2,4‐ and 3,4‐Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases

“…Thermodynamic parameters of protonation for the hydroxide bound to the Zn atom in the active center of CA I, CA II, CA VII, CA IX, CA XII, and CA XIII have been previously determined . CA I and CA XIII had similar p K a values (8.1 and 8.0, respectively, recalculated to T =37 °C) and Δ b_proton_CA H values (−38.5 and −41.5 kJ mol −1 , respectively, at T =37 °C), whereas the p K a values for CA II, CA VII, CA IX, and CA XII (6.9, 6.8, 6.6, and 6.8, respectively, at T =37 °C) were lower than those for CA I and CA XIII and the enthalpies of protonation (−23.5, −30.5, −21.5, and −25.5 kJ mol −1 , respectively, at T =37 °C) were noticeably less exothermic.…”

Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design

“…No H-bonds with 2 were evident in the structure. Recently several series of benzenesulfonamide-based inhibitors were analyzed bound in CA XIII in the search for isoform-specific ligands (Čapkauskaitė et al, 2013;Dudutienė et al, 2013Dudutienė et al, , 2015Kišonaitė et al, 2014). .…”

“…Chlorinated para-meta-benzenesulfonamides Four crystal structures of para-meta-substituted chlorinated benzenesulfonamides were presented in the comprehensive research trying to connect the intrinsic thermodynamic parameters of ligand binding to several CA isoforms with the structural information (Kišonaitė et al, 2014). The influence of chlorine in orthoposition and positions of the four different tails on the thermodynamic parameters of binding was analyzed.…”

Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding

“…It is important to dissect those linked reactions and calculate the intrinsic parameters that would be independent of the buffer and pH ( Krishnamurthy et al, 2008 ; Baranauskienė & Matulis, 2012 ; Jogaitė et al, 2013 ; Morkūnaitė et al, 2015 ). Here we correlate the thermodynamics of binding with the structures of a series of fluorinated and chlorinated benzenesulfonamides that have been previously described Kišonaitė et al (2014) , Zubrienė et al (2015) and Zubrienė et al (2016) .…”