Thermodynamic analysis of the drug-receptor interaction

Thermodynamic analysis of pharmacologic data potentially offers an insight into the molecular events underlying drug-receptor interactions not obtainable by other techniques. Embodied in thermodynamics are the laws governing the interconvertibility of heat and work and, hence, it is a particularly apt framework for the analysis of the transduction of information from ligand to biological tissue during the initiation of a drug effect. Implicit in thermodynamic analysis of pharmacologic data is quantitative measurement of the driving forces involved in the drug-receptor interaction (in place of less precise terms such as "affinity"). In addition, the cautious interpretation of thermodynamic analysis can give clues to the underlying mechanisms of the drug-receptor interaction that is beyond the resolving power of other parameters, such as the dissociation constant. The present review is an attempt to identify representative reports that have overtly analyzed pharmacologic data with thermodynamic analysis, to summarize the findings within and across studies (particularly regarding enthalpy- versus entropy-driven binding of agonists and antagonists), to point out and address some apparent inconsistencies that can arise, and to consider the application of thermodynamic analysis to data obtained using isolated tissue preparations.     

Hydrophobic salts markedly diminish viscosity of concentrated protein solutions

Reducing viscosities of concentrated solutions of therapeutic proteins is important for their subcutaneous and intravenous delivery. Although inorganic salts and optimizing the pH were previously reported to dramatically lower the viscosity of a monoclonal antibody solution, herein we have determined these effects not to be general. Separately, we have found that hydrophobic ionic excipients, both anionic and cationic, substantially decrease the viscosity of concentrated (300–400 mg/mL) aqueous solutions of bovine serum albumin and γ‐globulin. The more hydrophobic the excipient, the greater its viscosity‐lowering effect is. With cationic ones, the concomitant contribution of the counter‐ion broadly follows the chaotropic order. The most potent excipients lower the viscosity over fourfold to levels far below the 50 cP threshold for subcutaneous injections. The observed viscosity reductions are rationalized in terms of three‐dimensional transient protein networks formed in concentrated solutions due to hydrophobic and, to a lesser extent, ionic interactions. These reversible protein aggregates are responsible for strong resistance to flow in concentrated protein solutions and hence their high viscosity; hydrophobic ions apparently effectively compete for these interprotein interactions, thereby giving rise to less viscous solutions. Biotechnol. Bioeng. 2011; 108:632–636. © 2010 Wiley Periodicals, Inc.     

Modelling and simulation of the adsorption of the lipase from Geotrichum sp. on hydrophobic interaction columns

The Langmuir model fitted well the adsorption isotherms of lipase on the hydrophobic resin. The model parameters, Q _m and k _d, were affected by NaCl concentration: Q _m increased from 31 to 80 U g^–1 resin, and k _d changed from 9.4 to 3 U ml^–1. Column modelling and the simulation data were compared with the experimental data with good agreement. The highest achieved column efficiency was 71%.     

Thermodynamic characterization of the interaction of mutant UvrB protein with damaged DNA

During the DNA damage recognition of nucleotide excision repair in Escherichia coli the interaction of UvrB protein with damaged DNA ensures the recognition of differences in the intrinsic chemical structures of a variety of adduct molecules in DNA double helix. Our earlier study indicated that a single tyrosine-to-tryptophan mutation at residue 95 converted the UvrB to a protein [UvrB(Y95W)] that is able to bind to a structure-specific bubble DNA substrate, even in the absence of UvrA. Fluorescence spectroscopy therefore was adopted to investigate the biochemical properties and thermodynamics of DNA damage recognition by the mutant protein. We examined the binding of the UvrB(Y95W) mutant protein to a structure-specific 30 bp DNA substrate containing a single fluorescein which serves as both an adduct and a fluorophore. Binding of the protein to the substrate results in a significant reduction in fluorescence. By monitoring the fluorescence changes, binding isotherms were generated from a series of titration experiments at various physiological temperatures, and dissociation constants were determined. Analysis of our data indicate that interaction of UvrB(Y95W) protein with the adduct incurred a large negative change in heat capacity DeltaC(p)(o)(obs) (-1.1 kcal mol(-1) K(-1)), while the DeltaG(o)(obs) was relatively unchanged with temperature. Further study of the binding at various concentrations of KCl showed that on average only about 1.5 ion pairs were involved in formation of the UvrB-DNA complex. Together, these results suggested that hydrophobic interactions are the main driving forces for the recognition of DNA damage by UvrB protein.     

Thermodynamic analysis of quadruplex DNA-drug interaction

This work studies the binding properties of distamycin and its carbamoyl analog, containing four pyrrole units, with the [d(TGGGGT)](4) quadruplex by means of isothermal titration calorimetry (ITC). Analysis of the ITC data reveals that drug/quadruplex binding stoichiometry is 1:1 for both interactions and that distamycin analog gives approximately a 10-fold increase in the quadruplex affinity.     

Prediction of protein retention in hydrophobic interaction chromatography

Hydrophobic interaction chromatography (HIC) is a powerful technique for protein separation. This review examines methodologies for predicting protein retention time in HIC involving elution with salt gradients. The methodologies discussed consider three-dimensional structure data of the protein and its surface hydrophobicity. Despite their limitations, the methods discussed are useful in designing purification processes for proteins and easing the tedious experimental work that is currently required for developing purification protocols.     

Thermodynamic analysis of the lactose repressor-operator DNA interaction

Kinetic and equilibrium constants for lactose repressor-operator DNA interaction have been examined as a function of salt concentration, size and sequence context of the operator DNA, and temperature. Significant salt effects were observed on kinetic and equilibrium parameters for pLA 322-8, an operator-containing derivative of pBR 322, and pIQ, an operator and pseudooperator-containing derivative of pBR 322. The association rate constant and equilibrium constant for the 40 base pair operator fragment were also salt dependent. Data for all the DNAs were consistent with a sliding mechanism for repressor-operator association/dissociation [Berg, O. G., & Blomberg, C. (1978) Biophys. Chem. 8, 271-280]. Calculation of the number of ionic interactions based on salt dependence yielded a value of approximately 8 for repressor binding to pIQ and pLA 322-8 vs. approximately 6 for the repressor-40 base pair fragment. These data and the differences in binding parameters for the plasmids vs. the 40 base pair operator are consistent with the formation of an intramolecular ternary complex in the plasmid DNAs. Unusual biphasic temperature dependence was observed in the equilibrium and dissociation rate constants for pLA 322-8, pIQ, and the 40 base pair fragment. These observations coupled with a discontinuity found in the inducer association rate constant as a function of temperature suggest a structural change in the protein. The large positive entropy contributions associated with repressor binding to all the DNAs examined provide the significant driving force for the reaction and are consistent with involvement of ionic and apolar interactions in complex formation.     

Thermodynamic analysis of protein interactions with biosensor technology

A methodology using biosensor technology for combined kinetic and thermodynamic analysis of biomolecular interactions is described. Rate and affinity constants are determined with BIAcore. Thermodynamics parameters, changes in free energy, enthalpy and entropy, are evaluated from equilibrium data and by using rate constants and transition state theory. The methodology using van't Hoff theory gives complementary information to microcalorimetry, since only the direct binding is measured with BIAcore whereas microcalorimetry measures all components, including e.g. hydration effects. Furthermore, BIAcore gives possibilities to gain new information by thermodynamic analysis of the rate constants.     

Thermodynamic analysis of the interaction of factor VIII with von Willebrand factor

Factor VIII (FVIII) is a glycoprotein that plays an important role in the intrinsic pathway of coagulation. In circulation, FVIII is protected upon binding to von Willebrand factor (VWF), a chaperone molecule that regulates its half-life, distribution, and activity. Despite the biological significance of this interaction, its molecular mechanisms are not fully characterized. We determined the equilibrium and activation thermodynamics of the interaction between FVIII and VWF. The equilibrium affinity determined by surface plasmon resonance was temperature-dependent with a value of 0.8 nM at 35 °C. The FVIII-VWF interaction was characterized by very fast association (8.56 × 10(6) M(-1) s(-1)) and fast dissociation (6.89 × 10(-3) s(-1)) rates. Both the equilibrium association and association rate constants, but not the dissociation rate constant, were dependent on temperature. Binding of FVIII to VWF was characterized by favorable changes in the equilibrium and activation entropy (TΔS° = 89.4 kJ/mol, and -TΔS(++) = -8.9 kJ/mol) and unfavorable changes in the equilibrium and activation enthalpy (ΔH° = 39.1 kJ/mol, and ΔH(++) = 44.1 kJ/mol), yielding a negative change in the equilibrium Gibbs energy. Binding of FVIII to VWF in solid-phase assays demonstrated a high sensitivity to acidic pH and a sensitivity to ionic strength. Our data indicate that the interaction between FVIII and VWF is mediated mainly by electrostatic forces, and that it is not accompanied by entropic constraints, suggesting the absence of conformational adaptation but the presence of rigid "pre-optimized" binding surfaces.     

The interaction between cytoplasmic prion protein and the hydrophobic lipid core of membrane correlates with neurotoxicity

Prion protein (PrP), normally a cell surface protein, has been detected in the cytosol of a subset of neurons. The appearance of PrP in the cytosol could result from either retro-translocation of misfolded PrP from the endoplasmic reticulum (ER) or impaired import of PrP into the ER. Transgenic mice expressing cytoplasmic PrP (cyPrP) developed neurodegeneration in cerebellar granular neurons, although no detectable pathology was observed in other brain regions. In order to understand why granular neurons in the cerebellum were most susceptible to cyPrP-induced degeneration, we investigated the subcellular localization of cyPrP. Interestingly, we found that cyPrP is membrane-bound. In transfected cells, it binds to the ER and plasma/endocytic vesicular membranes. In transgenic mice, it is associated with synaptic and microsomal membranes. Furthermore, the cerebellar neurodegeneration in transgenic mice correlates with the interaction between cyPrP and the hydrophobic lipid core of the membrane but not with either the aggregation status or the dosage of cyPrP. These results suggest that lipid membrane perturbation could be a cellular mechanism for cyPrP-induced neurotoxicity and explain the seemingly conflicting results concerning cyPrP.     

Urea effects on protein stability: Hydrogen bonding and the hydrophobic effect

The effects of urea on protein stability have been studied using a model system in which we have determined the energetics of dissolution of a homologous series of cyclic dipeptides into aqueous urea solutions of varying concentration at 25°C using calorimetry. The data support a model in which urea denatures proteins by decreasing the hydrophobic effect and by directly binding to the amide units via hydrogen bonds. The data indicate also that the enthalpy of amide hydrogen bond formation in water is considerably higher than previously estimated. Previous estimates included the contribution of hydrophobic transfer of the α-carbon resulting in an overestimate of the binding between urea and the amide unit of the backbone and an underestimate of the binding enthalpy. Proteins 31:107–115, 1998. © 1998 Wiley-Liss, Inc.     

Yeast mitochondrial inner membrane 30 kd hydrophobic protein: properties and interaction with phospholipids

A 30 kd hydrophobic protein is extracted from yeast mitochondrial inner membrane. It is present in wild yeast strains but absent in mitochondrial DNA lacking mutants. The isoelectric point of the protein and its solubility in various organic solvents are determined. The fluorescence of a tryptophan residue near the surface of the 30 kd protein dissolved in butanol-1, can be quenched by phospholipids containing unsaturated fatty acids. Results are in accordance with the 30 kd protein being an integral protein of the yeast mitochondrial inner membrane.     

Purification of human plasma retinol-binding protein by hydrophobic interaction chromatography

Human plasma retinol-binding protein has been purified to homogeneity by a simple method that requires an ammonium sulfate fractionation, a hydrophobic interaction chromatography on phenyl-Sepharose, which dissociates the complex between retinol-binding protein and its carrier, transthyretin, and a gel filtration on Sephadex G-50. The yield of pure protein is comparable or higher than that obtained with the more complex procedures previously reported.     

Thermodynamic analysis of rat brain opioid mu-receptor-ligand interaction

Opioid mu-receptors are membrane bound receptors. The mechanism by which they transduce their biological effect into the inner compartment of the postsynaptic cell is still not fully understood. The present study was attempted to the measurement of changes of the thermodynamic parameters of the receptor--agonist/antagonist interaction. We have set up the binding assays of a mu-receptor agonist (3H-dihydromorphine) as well as an antagonist (3H-naloxone). The saturation isotherms of both ligands have been assayed at various temperatures and from the resulting KD values the standard changes of Gibbs energy, enthalpy and entropy have been calculated. While the binding of the mu-receptor agonist 3H-dihydromorphine appears to be entropy driven (delta S0 = 230 J mol-1 K-1) and endothermic (delta H0 = 19 kJ mol-1), the binding of the mu-receptor antagonist 3H-naloxone is apparently driven by a decrease of standard enthalpy (delta H0 = -27 kJ mol-1; i.e. the reaction is exothermic) and is also characterized by an increase of standard entropy (delta S0 = 76 J mol-1 K-1). The maximal number of 3H-naloxone binding sites has to be determined by incubation at 0-4 degrees C. The present data to not support the view that opioid mu-receptors transduce their biological signal through the adenylatecyclase system by a mechanism similar to beta-adrenergically stimulated adenylatecyclase.     

The effect of hydrophobic interaction on endotoxin adsorption by polymeric affinity matrix

Endotoxin, a major pyrogen of concern to the biological industry, is a lipopolysaccharide containing a highly hydrophobic region, lipid A, in its structure. The effect of hydrophobic interaction on endotoxin adsorption from an aqueous solution was studied by covalently bonding aminoalkyl groups with varying hydrocarbon lengths to a cellulose and acrylic composite matrix. The amount of endotoxin adsorbed on the matrix increased with the increasing length of alkyl groups, demonstrating the contribution of hydrophobic interaction between endotoxin and the solid matrix. Both the hydrophobic and the charge interaction prove to be effective for endotoxin adsorption, and a synergistic effect from the dual chemical forces is achievable under specified conditions. The effect of solvent, pH and salts on endotoxin adsorption provides further evidence for the importance of hydrophobic force as a means of removing endotoxin from aqueous solutions.     

The displacement effect of phenylalanine on lysozyme elution in hydrophobic interaction chromatography

The volume, retention time, and shape of the lysozyme peak eluted from a hydrophobic interaction chromatography column (TosoHaas 650 M Phenyl) was influenced by the presence and concentration of phenylalanine in the elution buffer. Lysozyme peak retention time decreased by a factor of 2.5 with the addition of 86 mM phenylalanine to the elution buffer.     

Thermodynamic analysis of the interaction of the antibiotic teicoplanin and its aglycone with cell-wall peptides.

The thermodynamics of the interaction of the glycopeptidic antibiotic teicoplanin and its peptidic moiety with analogues of bacterial cell-wall peptides were studied by means of calorimetric and spectrophotometric techniques. The analysis of the thermodynamic data has allowed us to evaluate the contributions of the different peptide groups to the binding process. The nature of the primary binding forces is also discussed for each interacting group, on the basis of their enthalpic and entropic contribution and in connection with the detailed structural information available for these antibiotics from n.m.r. data. Similar analyses for the case of vancomycin and ristocetin are also reported.