Influence of Neighboring Groups on the Thermodynamics of Hydrophobic Binding: An Added Complex Facet to the Hydrophobic Effect (original) (raw)
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Angewandte Chemie International Edition, 2013
is grateful to the EU for providing an ERC Advanced Grant (DrugProfilBind 268145). We thank the beamline support staff at the Helmholtz-Zentrum Berlin, Bessy II for radiation time and their advice during data collection. We thank the HZB for financial support of travel costs. Supporting information for this article (experimental procedures for the crystallization and soaking of the ligands, data collection and processing, crystal structure determination and refinement, kinetic assay, isothermal titration calorimetry, and the synthesis of ligands 1-8) is available on the WWW under http://dx.doi.org/10.1002/ anie.201208561. .
Water Networks Contribute to Enthalpy/Entropy Compensation in Protein–Ligand Binding
Journal of the American Chemical Society, 2013
The mechanism (or mechanisms) of enthalpy− entropy (H/S) compensation in protein−ligand binding remains controversial, and there are still no predictive models (theoretical or experimental) in which hypotheses of ligand binding can be readily tested. Here we describe a particularly well-defined system of protein and ligandshuman carbonic anhydrase (HCA) and a series of benzothiazole sulfonamide ligands with different patterns of fluorinationthat we use to define enthalpy/entropy (H/S) compensation in this system thermodynamically and structurally. The binding affinities of these ligands (with the exception of one ligand, in which the deviation is understood) to HCA are, despite differences in fluorination pattern, indistinguishable; they nonetheless reflect significant and compensating changes in enthalpy and entropy of binding. Analysis reveals that differences in the structure and thermodynamic properties of the waters surrounding the bound ligands are an important contributor to the observed H/S compensation. These results support the hypothesis that the molecules of water filling the active site of a protein, and surrounding the ligand, are as important as the contact interactions between the protein and the ligand for biomolecular recognition, and in determining the thermodynamics of binding.
Journal of Molecular Biology, 2006
Here, we examine the thermodynamic penalty arising from burial of a polar group in a hydrophobic pocket that forms part of the binding-site of the major urinary protein (MUP-I). X-ray crystal structures of the complexes of octanol, nonanol and 1,8 octan-diol indicate that these ligands bind with similar orientations in the binding pocket. Each complex is characterised by a bridging water molecule between the hydroxyl group of Tyr120 and the hydroxyl group of each ligand. The additional hydroxyl group of 1,8 octandiol is thereby forced to reside in a hydrophobic pocket, and isothermal titration calorimetry experiments indicate that this is accompanied by a standard free energy penalty of + 21 kJ/mol with respect to octanol and + 18 kJ/mol with respect to nonanol. Consideration of the solvation thermodynamics of each ligand enables the "intrinsic" (solute-solute) interaction energy to be determined, which indicates a favourable enthalpic component and an entropic component that is small or zero. These data indicate that the thermodynamic penalty to binding derived from the unfavourable desolvation of 1,8 octan-diol is partially offset by a favourable intrinsic contribution. Quantum chemical calculations suggest that this latter contribution derives from favourable solute-solute dispersion interactions.
Effector-modulated subunit associations in a model hydrophobic system
Journal of Molecular Biology, 1974
To study the binding of apolar ligands to hydrophobic sites, which contain water that must be displaced, the interaction of oyclohexane and n-heptane with c(and /3-oyclodextrins was investigated. The j3 complexes are in every way normal. Both ligands form strict 1: 1 complexes. Cyclohexane binds more strongly than n-heptane, as expected from the geometry. The AGO, AHO, AS0 and ACpo of dissociation are typical of transfers of these ligands from a hydrophobic medium to water (e.g. for oyclohexane at 25'C : 7.45 kcal, 1.3 kcal,-21 gibbs, 75 gibbs, in mole fraction units). The interior of fi is thus large enough to approximate bulk water, so that the behavior reflects the decrease of interface between hydrophobes and bulk water, which iu this case happens to come only partly from the ligand, and partly from /I. The 01 complexes are anomalous. The binding isotherms show, and ultracentrifuge studies confbm, that two equilibria, aL = cc + L, and crzL = 2a + L, are important. The K1 for cr-heptane, /I-heptane, and ,!I-cyclohexane dissociation are roughly comparable, with Kl for cc-cyclohexane ten times greater, but the monomeric dc complexes are still not "normal". Except for AC,O, the thermodynamic parameters are atypical: AH,O is 3 kcal (cyclohexane) and 5 kcal (heptane) larger than for the "normal" dissociation of ,!?-ligand; compensating increases in the entropies of dissociation keep the AG,O more or less the same. The reaction MEL = 2a + L is even more temperature dependent (the fraction of ligand bound to dimers decreases from 50 to 80% at 0°C to 15 to 30% at 5O'C). At 25"C, AH,O for cyolohexane and heptane is 10.9 and 11.8 koal, respectively. Entropies of dissociation are less negative than normal by 15 to 20 gibbs for both ligands. These data suggest that the dimer, stabilized as much by displacement of suboptimal water as by the usual hydrophobic contributions, has a hydrogen bond-surrounded cage analogous to the gas hydrates.
Biochimica Et Biophysica Acta-general Subjects, 2010
Background: Prerequisite for the design of tight binding protein inhibitors and prediction of their properties is an in-depth understanding of the structural and thermodynamic details of the binding process. A series of closely related phosphonamidates was studied to elucidate the forces underlying their binding affinity to thermolysin. The investigated inhibitors are identical except for the parts penetrating into the hydrophobic S 1 '-pocket. Methods: A correlation of structural, kinetic and thermodynamic data was carried out by X-ray crystallography, kinetic inhibition assay and isothermal titration calorimetry. Results and conclusions: Binding affinity increases with larger ligand hydrophobic P 1 '-moieties accommodating the S 1 '-pocket. Surprisingly, larger P 1 '-side chain modifications are accompanied by an increase in the enthalpic contribution to binding. In agreement with other studies, it is suggested that the release of largely disordered waters from an imperfectly hydrated pocket results in an enthalpically favourable integration of these water molecules into bulk water upon inhibitor binding. This enthalpically favourable process contributes more strongly to the binding energetics than the entropy increase resulting from the release of water molecules from the S 1 '-pocket or the formation of apolar interactions between protein and inhibitor. General significance: Displacement of highly disordered water molecules from a rather imperfectly hydrated and hydrophobic specificity pocket can reveal an enthalpic signature of inhibitor binding.
Thermodynamics of Protein–Ligand Interactions: History, Presence, and Future Aspects
Journal of Receptors and Signal Transduction, 2004
The understanding of molecular recognition processes of small ligands and biological macromolecules requires a complete characterization of the binding energetics and correlation of thermodynamic data with interacting structures involved. A quantitative description of the forces that govern molecular associations requires determination of changes of all thermodynamic parameters, including free energy of binding (deltaG), enthalpy (deltaH), and entropy (deltaS) of binding and the heat capacity change (deltaCp). A close insight into the binding process is of significant and practical interest, since it provides the fundamental know-how for development of structure-based molecular design-strategies. The only direct method to measure the heat change during complex formation at constant temperature is provided by isothermal titration calorimetry (ITC). With this method one binding partner is titrated into a solution containing the interaction partner, thereby generating or absorbing heat. This heat is the direct observable that can be quantified by the calorimeter. The use of ITC has been limited due to the lack of sensitivity, but recent developments in instrument design permit to measure heat effects generated by nanomol (typically 10-100) amounts of reactants. ITC has emerged as the primary tool for characterizing interactions in terms of thermodynamic parameters. Because heat changes occur in almost all chemical and biochemical processes, ITC can be used for numerous applications, e.g., binding studies of antibody-antigen, protein-peptide, protein-protein, enzyme-inhibitor or enzyme-substrate, carbohydrate-protein, DNA-protein (and many more) interactions as well as enzyme kinetics. Under appropriate conditions data analysis from a single experiment yields deltaH, K(B), the stoichiometry (n), deltaG and deltaS of binding. Moreover, ITC experiments performed at different temperatures yield the heat capacity change (deltaCp). The informational content of thermodynamic data is large, and it has been shown that it plays an important role in the elucidation of binding mechanisms and, through the link to structural data, also in rational drug design. In this review we will present a comprehensive overview to ITC by giving some historical background to calorimetry, outline some critical experimental and data analysis aspects, discuss the latest developments, and give three recent examples of studies published with respect to macromolecule-ligand interactions that have utilized ITC technology.
Molecular driving forces of the pocket–ligand hydrophobic association
Chemical Physics Letters, 2012
Molecular dynamics simulations have shown that the concave pocket-convex ligand hydrophobic association is enthalpy-driven due to water reorganisation [11]. A different theoretical analysis is provided, grounded on the basic notion that the Gibbs energy gain upon association is mainly due to the decrease in the solvent-excluded volume, that translates in a gain of configurational-translational entropy of water molecules. It is also underscored that the reorganisation of water-water H-bonds is characterised by an almost complete enthalpy-entropy compensation and cannot affect the Gibbs energy change.
Thermodynamic aspects of hydrophobicity and biological QSAR
2001
A protein contains a large amount of water molecules, and the nature of the interactions of the water molecules with a protein play an important role in the thermodynamics of the ligand binding process. In this paper, thermodynamic aspects of drug-receptor interactions, enthalpy-entropy compensation or reinforcement, hydrophobicity, and biological 2D-and 3D-QSAR are discussed. Comparisons of the thermodynamic QSAR of phenyl esters of N-benzoyl L-alanine in phosphate buffer and pentanol provide useful insight for the ligand-enzyme interactions.
Protein-Ligand Interactions: Thermodynamic Effects Associated with Increasing Nonpolar Surface Area
Journal of the …, 2011
Thermodynamic parameters were determined for complex formation between the Grb2 SH2 domain and Ac-pTyr-Xaa-Asn derived tripeptides in which the Xaa residue is an α,αcycloaliphatic amino acid that varies in ring size from 3-to 7-membered. Although the 6-and 7membered ring analogs are approximately equipotent, binding affinities of those having 3-to 6membered rings increase incrementally with ring size because increasingly more favorable binding enthalpies dominate increasingly unfavorable binding entropies, a finding consistent with an enthalpy-driven hydrophobic effect. Crystallographic analysis reveals that the only significant differences in structures of the complexes are in the number of van der Waals contacts between the domain and the methylene groups in the Xaa residues. There is a positive correlation between buried nonpolar surface area and binding free energy and enthalpy, but not with ΔC p . Displacing a water molecule from a protein-ligand interface is not necessarily reflected in a favorable change in binding entropy. These findings highlight some of the fallibilities associated with commonly held views of relationships of structure and energetics in protein-ligand interactions and have significant implications for ligand design.