Intrinsic thermodynamics of inhibitor binding to human carbonic anhydrase IX

• Published in: Biochimica et biophysica acta 2016-04, Vol.1860 (4), p.708-718
• Main Authors: Linkuvienė, Vaida, Matulienė, Jurgita, Juozapaitienė, Vaida, Michailovienė, Vilma, Jachno, Jelena, Matulis, Daumantas
• Format: Article
• Language: English
• Subjects: Antigens, Neoplasm - chemistry; Antigens, Neoplasm - metabolism; Benzenesulfonamide inhibitors; Carbonic anhydrase; Carbonic Anhydrase Inhibitors - chemistry; Carbonic Anhydrase Inhibitors - metabolism; Carbonic Anhydrase IX; Carbonic Anhydrases - chemistry; Carbonic Anhydrases - metabolism; Drug design; Fluorescent thermal shift assay; Humans; Intrinsic thermodynamics of protein-ligand binding; Isothermal titration calorimetry; Protein Binding; Thermodynamics
• ISSN: 0304-4165; 0006-3002; 1872-8006
• DOI: 10.1016/j.bbagen.2016.01.007

Human carbonic anhydrase 9th isoform (CA IX) is an important marker of numerous cancers and is increasingly interesting as a potential anticancer drug target. Various synthetic aromatic sulfonamide-bearing compounds are being designed as potent inhibitors of CA IX. However, sulfonamide compound binding to CA IX is linked to several reactions, the deprotonation of the sulfonamide amino group and the protonation of the CA active site Zn(II)-bound hydroxide. These linked reactions significantly affect the affinities and other thermodynamic parameters such as enthalpies and entropies of binding. The observed and intrinsic affinities of compound binding to CA IX were determined by the fluorescent thermal shift assay. The enthalpies and entropies of binding were determined by the isothermal titration calorimetry. The pKa of CA IX was determined to be 6.8 and the enthalpy of CA IX-Zn(II)-bound hydroxide protonation was −24kJ/mol. These values enabled the analysis of intrinsic thermodynamics of a library of compounds binding to CA IX. The most strongly binding compounds exhibited the intrinsic affinity of 0.01nM and the observed affinity of 2nM. The intrinsic thermodynamic parameters of compound binding to CA IX helped to draw the compound structure to thermodynamics relationship. It is important to distinguish the intrinsic from observed parameters of any disease target protein interaction with its inhibitors as drug candidates when drawing detailed compound structure to thermodynamics correlations. •The pKa of CA IX was determined to be 6.8, the enthalpy of protonation of CA IX was −24 kJ/mol at 25 °C.•Intrinsic binding thermodynamics – structure correlations were drawn for 40 novel CA IX inhibitors.•Affinities of the CA IX inhibitors achieved the Kd_intr of 0.01 nM and the Kd_obs of 2nM.