Thermodynamic Optimisation in Drug Discovery: A Case Study using Carbonic Anhydrase Inhibitors

Abstract

Historically the early stages of drug discovery have been based on finding the highest affinity compounds that bind to the target of interest, with little consideration for the forces driving the binding event. The association constant (K a ) can be defined by the equation DG = ÀRTln K a , with DG = DHÀTDS. To fully describe K a it would therefore be beneficial to characterize both of the thermodynamic terms (DH and DS) that drive this affinity for binding. The importance of separating affinity into its thermodynamic components is emphasized by the ubiquitous "enthalpy/entropy compensation effect", where large changes in DH and DS tend to be of similar but opposite signs and there is no net change in affinity, despite potentially very different binding mode.[1] It has been proposed by Freire, [2] and Ward & Holdgate [3] that it is advantageous, in terms of both potency and selectivity, to start from an enthalpically-driven lead. It can also be argued that choosing compounds with different binding modes increases the variety of chemical substrate for optimization, therefore reducing the risk of all the compounds encountering the same side effects. These points emphasize the need to measure thermodynamic signatures of lead compounds as early in the drug discovery process as possible.The only method that directly measures the thermodynamics of a binding event in solution is isothermal titration calorimetry (ITC).[4] Even though ITC can give a full thermodynamic signature (DG obs , DH obs , DS obs and K B, obs ) from a single experiment, the full utilization of the technique for lead optimization has been hampered by technical limitations requiring substantial quantities of reagents. In addition, data have frequently been collected from optimized, but varied, experimental conditions for a particular system, and without appropriate controls the interpretation of results between studies is difficult. Here, we demonstrate that with recent advances in ITC technology [5] and comparing subtly modified ligands against the same target, under identical conditions, and with X-ray data support, thermodynamic measurements can provide medicinal chemists with another differentiator in their quest to discover the best lead compounds. Moreover, these data are informative to medicinal chemists as they are applicable to situations where a less complete biophysical analysis is possible.We chose human carbonic anhydrase (hCA II) as a favorable system for this investigation as there is already a wealth of both 3D structures and calorimetric data available, which has established this protein as the leading model system. [6][7][8][9][10][11] Additionally, the protein binds benzene sulfonamides (BSAs) with a 1:1 stoichiometry and does not undergo gross conformational changes upon binding, providing an essentially thermodynamically closed system that will therefore not complicate interpretation of the binding thermodynamics. The binding of BSA to hCA II is driven mainly through four H bonds from the sulfonamide, two H bonds to the Zn co-...

Thermodynamic Evaluation of the Binding of Bisphosphonates to Human Farnesyl Pyrophosphate Synthase

“…Our results demonstrate the same trend for BPs: newer, more potent drugs are enthalpically more optimized. Altogether, as has been suggested previously, [29][30][31]33,40) our results argue the importance of monitoring thermodynamics balance of the drug/target interaction to efficiently produce best-in-class compounds.…”

“…27,28) Such thermodynamic profiles of the binding are helpful in drug discovery. [29][30][31][32][33] Recent studies have also suggested the importance of enthalpy-driven optimization when exploring drug candidates. 29) For example, Freire et al have examined the complete thermodynamics information of two drug classes: statins and human immunodeficiency virus-1 (HIV-1) protease inhibitors.…”

Effect of mutation in active site residue Trp209 to Val, Leu, Ile and Pro on the catalytic activity and affinity for some benzenesulfonamides of human carbonic anhydrase II

“…Inhibition effects of the compounds (3,4-diamino-benzenesulfonamide 1, 3-amino-4-chlorobenzenesulfonamide 2, 5-amino-2-methylbenzenesulfonamide 3, and acetazolamide 4) on SUMO fusion the wt and mutant enzymes were analyzed in their different concentrations. The Cheng-Prusoff equation was used to determine the K i values of each compound (Scott et al, 2009). …”

The Impact of Binding Thermodynamics on Medicinal Chemistry Optimizations

“…Owing to their low affinity, compounds have to be screened at high concentration that requires high solubility. In line with their small size and polarity that allows fragments to form few, good quality polar interactions without significant contribution from apolar desolvation fragment hits typically bind with favorable enthalpy [17,30,31,32,33,34,35] ( Figure 5). The few compounds in Figure 5 that bind with unfavorable enthalpy are all anionic species with highly unfavourable desolvation profile.…”