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

Abstract

The goal of rational drug design is to understand structure-thermodynamics correlations in order to predict the chemical structure of a drug that would exhibit excellent affinity and selectivity for a target protein. In this study we explored the contribution of added functionalities of benzenesulfonamide inhibitors to the intrinsic binding affinity, enthalpy, and entropy for recombinant human carbonic anhydrases (CA) CA I, CA II, CA VII, CA IX, CA XII, and CA XIII. The binding enthalpies of compounds possessing similar chemical structures and affinities were found to be very different, spanning a range from -90 to +10 kJ mol , and are compensated by a similar opposing entropy contribution. The intrinsic parameters of binding were determined by subtracting the linked protonation reactions. The sulfonamide group pK values of the compounds were measured spectrophotometrically, and the protonation enthalpies were measured by isothermal titration calorimetry (ITC). Herein we describe the development of meta- or ortho-substituted fluorinated benzenesulfonamides toward the highly potent compound 10 h, which exhibits an observed dissociation constant value of 43 pm and an intrinsic dissociation constant value of 1.1 pm toward CA IX, an anticancer target that is highly overexpressed in various tumors. Fluorescence thermal shift assays, ITC, and X-ray crystallography were all applied in this work.

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

“… Notes. 1- Zubrienė et al (2015) ; 2- Čapkauskaitė et al, (2012) ; 3- Čapkauskaitė et al (2013) ; 4- Dudutienė et al (2015) ; 5- Dudutienė et al (2014) ; 6- Zubrienė et al (2016) ; 7- This study; 8- Davis et al (2013) . a PDB ID entries of the crystal structures that are not analyzed in this article.…”

“…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) .…”

Engineered Carbonic Anhydrase VI-Mimic Enzyme Switched the Structure and Affinities of Inhibitors

“…Furthermore, substituents at ortho and para , but not meta positions were identified to be significant for the molecular recognition between the compound and CA VI. However, ortho and meta -substituted benzenesulfonamides have been recently shown to act as tight CA IX binders 32 . Therefore, such findings confirmed that intrinsic, but not observed parameters should be applied to analyze the dependence of binding efficiency on compound chemical structures, thereby allowing important structure-thermodynamics correlations to design CA-isoform selective inhibitors.…”

“…Therefore, protonation-deprotonation reactions are required to initiate the binding of inhibitor to CA. Only intrinsic values subtract energetic contribution of binding-linked protonation events and thus are relevant for the rational drug design 32–35 .…”

Sulfonamides incorporating ketene N,S‐acetal bioisosteres as potent carbonic anhydrase and acetylcholinesterase inhibitors

“…The crystal structures of the receptors, including h CA I (5E2M, resolution 1.41 Å, complex with V14), [ 75 ] h CA II (6H29, resolution 1.46 Å, complex with FK8), [ 76 ] and AChE (4M0E, resolution 2.00 Å, complex with 1YL), [ 77 ] which are downloaded from the RCSB PDB (http://rcsb.org), [ 78 ] were prepared using the Protein Preparation Wizard [ 79 ] in Schrödinger Suite 2019‐3. OPLS3e force field [ 80 ] was used for the optimization of both the synthesized ketene N,S ‐acetal sulfonamide analogs ( 7a–o ) and the receptors.…”