Thermodynamic analysis of the drug-receptor interaction

3D-RISM-AI: A Machine Learning Approach to Predict Protein-Ligand Binding Affinity Using 3D-RISM

Hydration free energy (HFE) is a key factor in improving protein-ligand binding free energy (BFE) prediction accuracy. The HFE itself can be calculated using the three-dimensional reference interaction model (3D-RISM); however, the BFE predictions solely evaluated using 3D-RISM are not correlated to the experimental BFE for abundant protein-ligand pairs. In this study, to predict the BFE for multiple sets of protein-ligand pairs, we propose a machine learning approach incorporating the HFEs obtained using 3D-RISM, termed 3D-RISM-AI. In the learning process, structural metrics, intra-/intermolecular energies, and HFEs obtained via 3D-RISM of ∼4000 complexes in the PDBbind database (ver. 2018) were used. The BFEs predicted using 3D-RISM-AI were well correlated to the experimental data (Pearson's correlation coefficient of 0.80 and root-mean-square error of 1.91 kcal/mol). As important factors for the prediction, the difference in the solvent accessible surface area between the bound and unbound structures and the hydration properties of the ligands were detected during the learning process.

Thermodynamics and kinetics of inhibitor binding to human equilibrative nucleoside transporter subtype-1

Many nucleoside transport inhibitors are in clinical use as anti-cancer, vasodilator and cardioprotective drugs. However, little is known about the binding energetics of these inhibitors to nucleoside transporters (NTs) due to their low endogenous expression levels and difficulties in the biophysical characterization of purified protein with ligands. Here, we present kinetics and thermodynamic analyses of inhibitor binding to the human equilibrative nucleoside transporter-1 (hENT1), also known as SLC29A1. Using a radioligand binding assay, we obtained equilibrium binding and kinetic rate constants of well-known NT inhibitors--[(3)H]nitrobenzylmercaptopurine ribonucleoside ([(3)H]NBMPR), dilazep, and dipyridamole--and the native permeant, adenosine, to hENT1. We observed that the equilibrium binding affinities for all inhibitors decreased whereas, the kinetic rate constants increased with increasing temperature. Furthermore, we found that binding is enthalpy driven and thus, an exothermic reaction, implying that the transporter does not discriminate between its inhibitors and substrates thermodynamically. This predominantly enthalpy-driven binding by four chemically distinct ligands suggests that the transporter may not tolerate diversity in the type of interactions that lead to high affinity binding. Consistent with this, the measured activation energy of [(3)H]NBMPR association was relatively large (20 kcal mol(-1)) suggesting a conformational change upon inhibitor binding. For all three inhibitors the enthalpy (ΔH°) and entropy (ΔS°) contributions to the reaction energetics were determined by van't Hoff analysis to be roughly similar (25-75% ΔG°). Gains in enthalpy with increasing polar surface area of inhibitors suggest that the binding is favored by electrostatic or polar interactions between the ligands and the transporter.

Thermodynamics of A2B adenosine receptor binding discriminates agonistic from antagonistic behaviour

Thermodynamic parameters DeltaG degrees , DeltaH degrees and DeltaS degrees of the binding equilibrium of 12 ligands (six agonists and six antagonists) to the A(2B) adenosine receptor subtype have been determined by affinity measurements carried out on HEK 293 cells stably transfected with human A(2B) adenosine receptors at six different temperatures (4, 10, 15, 20, 25, 30 degrees C) and van't Hoff plot analysis have been performed. Affinity constants were obtained from saturation experiments of [(3)H]MRE 2029-F20 or by its displacement in inhibition assays for the other compounds. van't Hoff plots were essentially linear in the temperature range investigated, showing that the DeltaC(p) degrees of the binding equilibrium is nearly zero. Thermodynamic parameters are in the range 7< or =DeltaH degrees < or =23 kJ mol(-1)and 123< or =DeltaS degrees < or =219 JK(-1)mol(-1) for agonists and -40 < or =DeltaH degrees < or =-20 kJ mol(-1) and 10< or =DeltaS degrees < or =91 JK(-1)mol(-1) for antagonists indicating that agonistic binding is always totally entropy-driven while antagonistic binding is enthalpy and entropy-driven. In the -TDeltaS degrees versus DeltaH degrees plot the thermodynamic data are clearly arranged in separate clusters for agonists and antagonists, which, therefore, turn out to be thermodynamically discriminated.

Thermodynamic analysis of ligands at cholecystokinin CCK2 receptors in rat cerebral cortex

BACKGROUND AND PURPOSE

Several studies using radioligand binding assays, have shown that measurement of thermodynamic parameters can allow discrimination of agonists and antagonists (Weiland et al., 1979; Borea et al., 1996a). Here we investigate whether agonists and antagonists can be thermodynamically discriminated at CCK(2) receptors in rat cerebral cortex.

EXPERIMENTAL APPROACH

The pK(L) of [(3)H]-JB93182 in rat cerebral cortex membranes was determined at 4, 12, 21 and 37 degrees C in 50 mM Tris-HCl buffer (buffer B pH 6.96; containing 0.089 mM bacitracin). pK(I) values of ligands of diverse chemical structure and with differing intrinsic activity (alpha), as defined by the lumen-perfused rat and mouse stomach bioassays, were determined in buffer B at 4, 12, 21 and 37 degrees C.

KEY RESULTS

[(3)H]-JB93182 labelled a homogeneous population of receptors in rat cerebral cortex at 4, 12, 21 and 37 degrees C and the pK(L) and B(max) were not altered by incubation temperature. [(3)H]-JB93182 binding reached equilibrium after 10, 50, 90 and 220 min at 37, 21, 12 and 4 degrees C, respectively. pK(I) values for R-L-365,260, R-L-740,093, YM220, PD134,308 and JB95008 were higher at 4 degrees C than at 37 degrees C. There was no effect of temperature on pK(I) values for pentagastrin, CCK-8S, S-L-365,260, YM022, PD140,376 and JB93242.

CONCLUSIONS AND IMPLICATIONS

CCK(2) receptor agonists and antagonists at rat CCK(2) receptors cannot be discriminated by thermodynamic analysis using [(3)H]-JB93182 as the radioligand.

Histamine H3-receptor agonists and imidazole-based H3-receptor antagonists can be thermodynamically discriminated

BACKGROUND AND PURPOSE

Studies suggest that measurement of thermodynamic parameters can allow discrimination of agonists and antagonists. Here we investigate whether agonists and antagonists can be thermodynamically discriminated at histamine H(3) receptors.

EXPERIMENTAL APPROACH

The pK(L) of the antagonist radioligand, [(3)H]-clobenpropit, in guinea-pig cortex membranes was estimated at 4, 12, 21 and 30 degrees C in 20 mM HEPES-NaOH buffer (buffer A), or buffer A containing 300 mM CaCl(2), (buffer A(Ca)). pK(I)' values for ligands with varying intrinsic activity were determined in buffer A and A(Ca) at 4, 12, 21 and 30 degrees C.

KEY RESULTS

In buffer A, the pK(L) of [(3)H]-clobenpropit increased with decreasing temperature while it did not change in buffer A(Ca). The Bmax was not affected by temperature or buffer and n (H) values were not different from unity. In buffer A, pK(I)' values for agonists remained unchanged or decreased with decreasing temperature, while antagonist pK(I) values increased with decreasing temperature; agonist binding was entropy-driven while antagonist binding was enthalpy and entropy-driven. In buffer A(Ca), temperature had no effect on antagonist and agonist pK(I) values; both agonist and antagonist binding were enthalpy and entropy-driven.

CONCLUSIONS AND IMPLICATIONS

The binding of H(3)-receptor agonists and antagonists can be thermodynamically discriminated under conditions where agonist pK(I)' values are over-estimated (pK(I)' not = pK(app)). However, under conditions when agonist pK(I) approximately pK(app), the thermodynamics underlying the binding of agonists are not different to those of antagonists.

Designing allosteric peptide ligands targeting a globular protein

Patented signal analytic algorithms applied to hydrophobically transformed, numerical amino acid sequences have previously been used to design short, protein-targeted, L or D retro-inverso peptides. These peptides have demonstrated allosteric and/or indirect agonist effects on a variety of G-protein and tyrosine kinase coupled membrane receptors with 30% to over 80% hit rates. Here we extend these approaches to a globular protein target. We designed eight peptide ligands targeting an ELISA antibody responsive protein, beta-galactosidase, betaGAL. Three of the eight 14mer peptides allosterically activated betaGAL with ELISA methodology. Using Bayesian statistics, this 38% hit rate would have occurred 2 x 10(-9) by chance. These peptides demonstrated binding site competitive or noncompetitive interactions, suggesting allosteric site multiplicity with respect to their betaGAL binding-mediated ELISA signal. Kinetic studies demonstrated the temperature dependence of the betaGAL peptide binding functions. Using the van't Hoff relation, we found evidence for enthalpy-entropy compensation. This relation is often found for hydrophobic interactions in aqueous media, and is consistent with the postulated hydrophobic series encoding underlying our protein-targeted, peptide design methods. It appears that our algorithmic, hydrophobic autocovariance eigenvector template approach to the design of allosteric peptides targeting membrane receptors may also be applicable to the design of peptide ligands targeting nonmembrane involved globular proteins.

Binding thermodynamics at the human A(3) adenosine receptor

The thermodynamic parameters DeltaG , DeltaH and DeltaS of the binding equilibrium of six adenosine receptor agonists and five antagonists at adenosine A(3) receptors were determined by means of affinity measurements at six different temperatures (4, 10, 15, 20, 25 and 30) and van't Hoff plots were constructed. Affinity constants were measured on Chinese hamster ovary (CHO) cells transfected with the human A(3) receptors by inhibition assays of the binding of the selective A(3) antagonist [3H]MRE 3008F20. van't Hoff plots were linear for agonists and antagonists in the temperature range 4-30 degree. Their thermodynamic parameters fall in the ranges 21 < or = DeltaH < or = 67kJmol(-1) and 208 < or = DeltaS < or =410 J(Kmol)(-1) for agonists and -52 < or = DeltaH < or = -9 kJmol(-1) and 16 < or = DeltaS < or =81 J(K/mol)(-1) for antagonists, showing that agonist binding is always totally entropy-driven while antagonist binding is enthalpy- and entropy-driven. The results are discussed with the aim of obtaining new details on the nature of the forces driving the A(3) binding at a molecular level.

(Extra)thermodynamics of the drug-receptor interaction

A core concept in pharmacology is drug-receptor affinity, i.e., the tendency of a drug molecule to bind to one or more receptors due to the collective influence of multiple molecular forces. The estimation of affinity as a dissociation constant (reciprocal of the equilibrium constant) is extraordinarily valuable. However, elucidation of the nature of the underlying concept--i.e., what accounts for affinity--is not achievable using such a static measure. Observing how the system responds to a perturbation (e.g., to a change in temperature) reveals more fundamental information. The present review summarizes the general concepts of thermodynamic analysis applied to drug-receptor interactions and discusses 'extrathermodynamic' phenomena, such as enthalpy-entropy 'compensation'. Together, these concepts may provide insight into the nature of drug-receptor interactions, begin to elucidate the forces that underlie such interactions--and begin to define and refine more nebulous terms such as affinity.

Apparent thermodynamic parameters of ligand binding to the cloned rat mu-opioid receptor

The apparent thermodynamic parameters of binding of ten ligands to the cloned rat mu-opioid receptor stably expressed in Chinese hamster ovary (CHO) cells were investigated. For every ligand, the Kd or Ki values at 0 degrees C, 12 degrees C, 25 degrees C and 37 degrees C were determined, a van't Hoff plot was generated and deltaH degrees' , deltaS degrees' and -TdeltaS degrees' and deltaG degrees' were calculated. Changes in free energy (deltaG degrees') ranged from -10.35 to -15.65 kcal/mol. The binding of sufentanil, ohmefentanyl, diprenorphine and D-Phe-Cys-Tyr-D-Trp-Arg-Thr-penicillamineThr-NH2 (CTAP) was endothermic (deltaH degrees' > 0) and driven by an increase in entropy (-TdeltaS degrees' = -13.08 to -18.57 kcal/mol). The binding of naltrexone was exothermic (deltaH degrees' = -12.56 kcal/mol) and essentially enthalpy-driven. The binding of morphine, methadone, pentazocine, [D-Ala2, NMePhe4, Gly-ol]enkephalin (DAMGO) and Tyr-Pro-NMePhe-D-Pro-NH2 (PL017) was exothermic (deltaH degrees' = -3.53 to -9.95 kcal/mol) and occurred with an increase in entropy (-TdeltaS degrees' = -2.48 to -7.92 kcal/mol). Plots of enthalpy versus entropy and enthalpy versus free energy were linear, although enthalpy-entropy compensation was not evident. The entropy changes were not correlated with apparent lipophilicity of the compounds. These results suggest that: (1) opioid ligands bind to the mu receptor by specific mechanisms, unrelated to lipid solubility; (2) the mechanism of binding is not universally different for peptide and non-peptide ligands; (3) the nature of binding does not a priori determine intrinsic activity. The results reveal a novel differentiation of opioid ligands into two groups (group 1: ohmefentanyl, sufentanil, diprenorphine, CTAP and PL017; group 2: naltrexone, morphine, methadone, DAMGO, pentazocine), based on two distinct relationships between enthalpy versus free energy of binding, the details of which are yet to be elucidated.

Receptor binding thermodynamics as a tool for linking drug efficacy and affinity

Determination of drug-receptor binding constants (association, KA, or dissociation, KD = l/KA) by radiochemical specific binding assays has proved to be an invaluable tool for screening of potential active drugs. Simple determination of KA (or KD) values makes it possible, however, to calculate the standard free energy delta G degree = -RTln KA = RTln KD (T = 298.15 K) of the binding equilibrium but not that of its two components as defined by the Gibbs equation delta G degree = delta H degree - T delta S degree, where delta H degree and delta S degree are the equilibrium standard enthalpy and entropy, respectively. This incomplete knowledge is highly inconvenient from a pure thermodynamic point of view as delta H degree and delta S degree carry much information on the details of the drug-receptor interaction and the interplay of both reaction partners with the solvent. In recent times it has been shown that the relative delta H degree and delta S degree magnitudes can often give a simple 'in vitro' way for discriminating 'the effect', that is the manner in which the drug interferes with the signal transduction pathways. This particular effect, called 'thermodynamic discrimination', results from the fact that binding of antagonists may be enthalpy-driven and that of agonists entropy-driven, or vice versa. The first case of thermodynamic discrimination was reported for the beta-adrenergic G-protein coupled receptor (GPCR) and only recently has it been confirmed for adenosine A1 and A2a receptors. Only very recently has the binding thermodynamics of ligand-gated ion channel receptors (LGICR) been investigated and data for four receptors have been reported showing that all of them are thermodynamically discriminated. While it seems difficult at present to find a reasonable explanation for the thermodynamic discrimination phenomenon in GPCR, some hypotheses can be suggested for LGICR. Since global delta H degree and delta S degree values of the binding process are expected to be heavily affected by rearrangements occurring in the solvent, thermodynamic discrimination in LGICR is at least logically understandable admitting that the observed delta H degree (and then delta S degree) values are determined by both specific binding and abrupt variation of water-accessible receptor surfaces consequent to the setting up of the channel opening.

Thermodynamics of ligand binding to the cloned delta-opioid receptor

The goal of this study was to determine the relative contribution of entropy and enthalpy to the free energies of binding to recombinant mouse delta-opioid receptors for the peptide agonist, DPDPE ([D-Pen2,D-Pen5]enkephalin), the peptide antagonist, TIPP(psi) (Tyr-Tic(psi)[CH2NH]Phe-Phe-OH), the nonpeptide agonist, SNC80 ((+)-4-[(alphaR)-alpha-((2S,5R)-4-allyl-2,5-dimethyl-1-piperazinyl )-3-methoxybenzyl]-N,N-diethylbenzamide), and the nonpeptide antagonist, naltrindole. Competitive binding studies were carried out using [3H]naltrindole at 0 degrees C, 12 degrees C, 25 degrees C and 37 degrees C, the affinities calculated and van't Hoff plots constructed for each ligand. The temperature dependence of binding and van't Hoff plots indicated that the entropy contribution is the major component of the free energy, for all four ligands, independent of its activity or chemical nature.

Binding thermodynamics at A1 and A2A adenosine receptors

Only recently the binding equilibrium of a number of ligands at adenosine A1 and A2a receptors has been analyzed from a thermodynamic point of view. This approach presents the advantage, with respect to usual affinity constant measurements, of a greater capability to give information about the molecular mechanisms underlying the binding process. All available data agree in indicating that, for both A1 and A2a receptors, agonist binding of adenosine derivatives was totally entropy-driven, while xanthine antagonist binding was essentially enthalpy-driven. The differences in thermodynamic behaviour of A1 and A2a agonists and antagonists could be interpreted in terms of a simplified general model of drug-receptor interaction, which accounted for the role played by the ribose moiety and N6-substituents of adenosinic drugs in determining both affinity and intrinsic activity properties. In the frame of this model, measurements of thermodynamic parameters of N6-monosubstituted agonists allowed to hypothesize, for the first time, the existence of partial agonists to adenosine A1 receptors, as now confirmed experimentally. All thermodynamic data concerning the interaction of all ligands studied with A1 and A2a receptors are briefly discussed in terms of the enthalpy-entropy compensation phenomenon which appears to be widely determined by the reorganization of solvent molecules in the binding process.

Thermodynamic parameters of opioid binding in the presence and absence of G-protein coupling

We have investigated the thermodynamic parameters of various opioid ligands interacting with their receptors in rat brain membranes. Affinity constants (Ka), enthalpy and entropy values were obtained from homologous displacement experiments performed at 0, 24 and 33 degrees C. It was found that all the opioid agonists tested ([3H]dihydromorphine (DHM) mu alkaloid; [3H]DAMGO mu peptide; [3H]deltorphin-B delta peptide) display endothermic binding accompanied with a large entropy increase, regardless of their chemical structure (alkaloid or peptide), or of their mu or delta receptor selectivity. In contrast, binding of the antagonist naloxone is exothermic, mainly enthalpy driven. Na+ or Mg2+ results only in quantitative changes of the thermodynamic parameters. In the presence of the GTP-analog Gpp(NH)p; or Gpp(NH)p + Na+; or Gpp(NH)p + Na- + Mg2+ the affinity of DHM binding dramatically decreases which might reflect functional uncoupling of the receptor-ligand complex and G-proteins. This altered molecular interactions are also indicated by curvilinear van't Hoff plot and entropy increase. It is concluded that the thermodynamic analysis provides means of determining the underlying driving forces of ligand binding and helps to delineate its mechanism.

Receptor discrimination and control of agonist-antagonist binding

The law of mass action is the common model for the interaction of agonist and antagonist compounds with cellular receptors. Parameters of the interaction, obtained from functional and radioligand-binding studies, allow discrimination and subtyping of receptors and aid in understanding specific mechanisms. This article reviews the theory and associated mathematical models and graphical transformations of data that underlie the determination of receptor parameters. The main theory assumes that agonist and antagonist compounds bind to cells that have a fixed number of receptors and provides the framework for obtaining drug-receptor parameters from data and their graphical transformations. Conditions that produce a change in receptor number, a newer concept in pharmacology, can have an important effect on the parameter values derived in the usual way. This review concludes with a discussion of the quantitative study of receptor-mediated feedback control of endogenous ligands, a very new topic with potentially important implications for understanding antagonist effectiveness, loss of control, and chaos in regulated mass action binding.

Thermodynamic studies with acetylthiocholine on nicotinic receptors of mammalian skeletal muscle in vitro

The temperature dependency of binding of acetylthiocholine, a specific nicotinic agonist, to the nicotinic receptor of mammalian skeletal muscle was studied using isotonic contractions of the rat denervated diaphragm preparation in vitro. The dissociation constants at different temperatures (22-39 degrees) were determined by the Furchgott method using alpha-bungarotoxin as an irreversible antagonist. Both free energy of association (delta G zero = -22.93 kJ/mol at 37 degrees) and enthalpy of binding (delta H zero = -58.35 kJ/mol) calculated from Kd (dissociation constant) and slope of lnKd versus 1/T (van't Hoff plot) respectively were found to be negative. The negative entropy value (delta S zero = -0.113 kJ/mol/deg) obtained from the intercept of this van't Hoff plot differs from the large positive value obtained earlier employing radioligand binding studies of the nicotinic receptor of Electrophorus electricus.

Binding thermodynamics of adenosine A2a receptor ligands

The thermodynamic parameters delta G degree, delta H degree, and delta S degree of the binding equilibrium of seven adenosine agonists and five xanthine antagonists binding specifically to adenosine A2a receptors were determined by means of affinity measurements at six different temperatures (0, 10, 20, 25, 30 and 35 degrees) and van't Hoff plots. Affinity constants were measured on rat striatum membranes by saturation experiments for the selective A2a agonist 2-[p-(carboxy-ethyl)-phenethylamino-]5'-(N-ethyl)carboxamidoadenos ine ([3H]CGS 21680) and by inhibition assays of [3H]CGS 21680 binding for all other compounds. Scatchard plots were monophasic in the full range of temperatures, indicating a single class of high affinity binding sites whose receptor density, BMAX, is essentially temperature independent. Van't Hoff plots were linear in the temperature range 0-30 degrees for agonists and 0-35 degrees for antagonists; their thermodynamic parameters fall, respectively, in the ranges 7 < or = delta H degree < or = 50 kJ/mol and 177 < or = delta S degree < or = 278 J K-1 mol-1 and -36 < or = delta H degree < or = -7 kJ/mol and -33 < or = delta S degree < or = 94 J K-1 mol-1, showing that agonist binding is entropy-driven while antagonist binding is enthalpy-driven. The results are compared with those already reported for the binding of the same compounds to rat brain minus striatum adenosine A1 receptors obtained by displacing [3H]CHA as A1 selective radioligand (Borea PA et al., Mol Neuropharmacol 2: 273-281, 1992). The comparison suggests that the two receptors are very similar as far as their binding sites are concerned and possibly philogenetically related. The analysis of thermodynamical data makes it possible to propose an analogical model of drug-receptor interaction which may account for both affinity and intrinsic activity properties.

Differentiation of receptor subtypes by thermodynamic analysis: application to opioid delta receptors

The temperature dependence of the dissociation constant for the interaction of an opioid delta selective ligand and its receptor was evaluated in three tissues. The change in free energy of this interaction was similar in mouse brain, mouse spinal cord, and NG 108-15 mouse neuroblastoma-rat glioma hybrid cells (delta G(o)' = -13.44, -13.34, and -13.66 kcal.mol-1, respectively). However, the reaction was endothermic and occurred with an increase in entropy in mouse brain and NG 108-15 cells, but it was exothermic and occurred with a negligible change in entropy in mouse spinal cord. These data are consistent with the existence of multiple subtypes of opioid delta receptor, and they further suggest that the opioid delta receptor recently cloned from the NG 108-15 cell line is of the brain subtype. Subtypes of opioid delta receptors may mediate analgesia, but not side-effects, of opiates and thus could be targets for future drug design.

Thermodynamics of inhibitor binding to the catalytic site of glucoamylase from Aspergillus niger determined by displacement titration calorimetry

The binding of different inhibitors to glucoamylase G2 from Aspergillus niger and its temperature and pH dependencies have been studied by titration calorimetry. The enzyme binds the inhibitors 1-deoxynojirimycin and the pseudo-tetrasaccharide acarbose with association constants of 3 x 10(4) and 9 x 10(11) M-1, respectively, at 27 degrees C. The binding free energy for both ligands is remarkably temperature-invariant in the interval from 9 to 54 degrees C as the result of large compensating changes in enthalpy and entropy. Acarbose and 1-deoxynojirimycin bound with slightly different free energy-pH profiles, with optima at 5.5 and 5.5-7.0, respectively. Variations in delta H degrees and T delta S degrees as a function of pH were substantially larger than variations in delta G degrees in a partly compensatory manner. Two titratable groups at or near subsite 1 of the catalytic site were found to change their pKa slightly upon binding. The hydrogenated forms of acarbose, D-gluco- and L-ido-dihydroacarbose, bind with greatly reduced association constants of 3 x 10(7) and 2 x 10(5) M-1, respectively, and the pseudo-disaccharide methyl acarviosinide, lacking the two glucose units at the reducing end compared to acarbose, has a binding constant of 8 x 10(6) M-1; these values all result from losses in both enthalpy and entropy compared to acarbose. Three thio analogues of the substrate maltose, methyl alpha- and beta-4-thiomaltoside and methyl alpha-4,5'-dithiomaltoside, bind with affinities from 3 x 10(3) to 6 x 10(4) M-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterization of the binding of [3H]SR 33805 to the slow Ca2+ channel in rat heart sarcolemmal membrane

SR 33805 is a representative of a new class of compounds (indole sulfone) that inhibits L-type Ca2+ channels. [3H]SR 33805 has been shown to bind with a high affinity (Kd approximately 20 pM calculated from saturation isotherms and association/dissociation kinetics) to a single site in a purified preparation of rat cardiac sarcolemmal membranes. The binding was found to be saturable and reversible. The maximal binding capacity was in approximately 1:1 stoichiometry with that of other Ca2+ channel antagonists. Various cations (Na+, Ca2+, Cd2+, and La3+) were shown to inhibit specific [3H]SR 33805 binding, with La3+ being the most potent. Using a range of receptor or channel ligands (including omega-conotoxin and Na+ and K+ channel modulators), only the L-type Ca2+ channel antagonists were found to displace [3H]SR 33805. However, dihydropyridines, phenylalkylamines, benzothiazepines, and diphenyl-butylpiperidines were found to inhibit [3H]SR 33805 in a non-competitive manner as demonstrated by displacement experiments in addition to dissociation kinetics. In contrast, the interaction of SR 33805 with fantofarone has been found to be competitive. Binding of [3H]SR 33805 (and [3H]fantofarone) is entropy driven as opposed to that of the [3H]nitrendipine which is enthalpy driven. From these results we suggest that SR 33805 binds with a high affinity to a unique site on the L-type Ca2+ channel found in rat cardiac sarcolemmal membranes. This site is equivalent to that of fantofarone and in allosteric interaction with that of the dihydropyridines, phenylalkylamines and benzothiazepines.

Thermodynamic analysis of isoproterenol binding to beta-adrenoceptors in rat lung membranes

The thermodynamic properties of the binding of the beta-adrenoceptor agonist isoproterenol and of the antagonist propranolol to beta-adrenoceptors of rat lung were investigated. We found that in our experimental conditions, the high- and low-affinity binding sites for the agonist displayed different properties: the binding to the high-affinity binding site was entropy-driven with a small increase in enthalpy, while agonist binding to the low-affinity binding site was enthalpy-driven. Binding of isoproterenol in the presence of GTP or its non-hydrolyzable analogue GppNHp, and the binding of propranolol were enthalpy-driven with a small increase in entropy.

Thermodynamic analysis of agonist and antagonist binding to the chicken brain melatonin receptor

1. The binding of 2-[125I]-iodomelatonin to chicken brain membranes, and the inhibition of binding by melatonin, N-acetyltryptamine and luzindole, were examined at temperatures between 4 degrees C and 37 degrees C. 2. At all temperatures studied, the binding affinity (Kd or Ki) for 2-[125I]-iodomelatonin, melatonin (both agonists) and, to a lesser extent, N-acetyltryptamine (a partial agonist) was reduced by inclusion of guanosine triphosphate (GTP, 1 mM) in the assay. GTP did not affect the Ki for luzindole, a melatonin receptor antagonist. 3. The maximal density of binding sites (Bmax) was not affected by temperature but the Kd showed a peak at 21 degrees C with lower values at both higher and lower temperatures giving curvilinear van't Hoff plots (lnKA vs l/temperature). 4. Derived changes in entropy (delta S degree) and enthalpy (delta H degree) of binding for all of the melatonin ligands decreased as temperature increased. 5. The affinity, and thus the free energy of binding, delta G degree, of these ligands at the melatonin receptor have identical values at several temperatures yet at these temperatures delta S degree and delta H degree were very different, implying that more than one intermolecular force must be involved in the binding of ligand and receptor. 6. Conceivably, the large positive delta S degree observed at low temperatures, perhaps as a result of hydrophobic interactions, is compensated by a corresponding, but opposite, change in enthalpy at higher temperatures. However, it is not clear what type of binding force(s) would show such a temperature-dependence. 7. These studies suggest that caution must be exercised in the molecular interpretation of derived measures of delta S degree and delta H degree obtained from direct measurements of delta G degree.

Temperature dependence of unitary properties of an ATP-dependent potassium channel in cardiac myocytes

The temperature dependence of the properties of unitary currents in cultured rat ventricular myocytes has been studied. Currents flowing through an ATP-dependent K+ channel were recorded from inside-out patches with the bath temperature varied from 10 degrees to 30 degrees C. The channel conductance was 56 pS at room temperature (22 degrees C), and the amplitudes of unitary currents and the channel conductance exhibited a relatively weak (Q10 from 1.4 to 1.6) dependence on temperature. The temperature dependence of channel mean open times was biphasic with the low temperature (10-20 degrees C) range showing a relatively stronger temperature dependence (Q10 of 2.3) than the high temperature (20-30 degrees C) range (Q10 of 1.6). The activation energies for the two regions were determined from an Arrhenius plot with the activation energy, corresponding to the lower temperature range, near 16 kcal/mol. Thermodynamic analysis, using transition rate theory, indicated that the formation of a transition state prior to channel closure to be associated with a positive entropy component for the high Q10 region.

Thermodynamics of antagonist binding to rat muscarinic M2 receptors: antimuscarinics of the pridinol, sila-pridinol, diphenidol and sila-diphenidol type

1. We studied the effect of temperature on the binding to rat heart M2 muscarinic receptors of antagonists related to the carbon/silicon pairs pridinol/sila-pridinol and diphenidol/sila-diphenidol (including three germanium compounds) and six structurally related pairs of enantiomers [(R)- and (S)-procyclidine, (R)- and (S)-trihexyphenidyl, (R)- and (S)-tricyclamol, (R)- and (S)-trihexyphenidyl methiodide, (R)- and (S)-hexahydro-diphenidol and (R)- and (S)-hexbutinol]. Binding affinities were determined in competition experiments using [3H]-N-methyl-scopolamine chloride as radioligand. The reference drugs were scopolamine and N-methyl-scopolamine bromide. 2. The affinity of the antagonists either increased or decreased with temperature. van't Hoff plots were linear in the 278-310 degrees K temperature range. Binding of all antagonists was entropy driven. Enthalpy changes varied from large negative values (down to -29 kJ mol-1) to large positive values (up to +30 kJ mol-1). 3. (R)-configurated drugs had a 10 to 100 fold greater affinity for M2 receptors than the corresponding (S)-enantiomers. Enthalpy and entropy changes of the respective enantiomers were different but no consistent pattern was observed. 4. When silanols (R3SiOH) were compared to carbinols (R3COH), the affinity increase caused by C/Si exchange varied between 3 and 10 fold for achiral drugs but was negligible in the case of chiral drugs. Silanols induced more favourable enthalpy and less favourable entropy changes than the corresponding carbinols when binding. Organogermanium compounds (R4Ge) when compared to their silicon counterparts (R4Si) showed no significant difference in affinity as well as in enthalpy and entropy changes. 5. Exchange of a cyclohexyl by a phenyl moiety was associated with an increase or a decrease in drug affinity (depending on the absolute configuration in the case of chiral drugs) and generally also with a more favourable enthalpy change and a less favourable entropy change of drug binding. 6. Replacement of a pyrrolidino by a piperidino group and increasing the length of the alkylene chain bridging the amino group and the central carbon or silicon atom were associated with either an increase or a decrease of entropy and enthalpy changes of drug binding. However, there was no clear correlation between these structural variations and the thermodynamic effects. 7. Taken together, these results suggest that hydrogen bond-forming OH groups and, to a lesser extent, polarizable phenyl groups contribute significantly to the thermodynamics of interactions between these classes of muscarinic antagonists and M2 muscarinic receptors.

Thermodynamics of anesthetic/protein interactions. Temperature studies on firefly luciferase

Firefly luciferase is a soluble enzyme which is unusually sensitive to general anesthetics. The inhibition of the highly purified enzyme by three inhalational and three alcohol general anesthetics has been studied as a function of temperature, in the range from 5 to 20 degrees C. Inhibition constants Ki were determined at different temperatures, and van't Hoff plots of ln (Ki) versus reciprocal absolute temperature were found to be linear for all agents. Analysis of these plots gave values for the standard Gibbs free energy, enthalpy and entropy changes for transferring each anesthetic from water to the anesthetic-binding pocket on the protein. The most striking finding was that the enthalpy changes were much more negative for anesthetics binding to the protein than for binding to lipids or simple solvents. Furthermore, amongst the set of anesthetics studied, it was found that increasing potency correlated with favorable enthalpy rather than entropy changes. We discuss our results with respect to the molecular mechanisms underlying general anesthesia.

Thermodynamic parameters for [D-Pen2,5]enkephalin at delta-opioid receptors in the mouse isolated vas deferens

Dissociation constants (KA) for [D-Pen2,5]enkephalin (DPDPE) inhibition of the electrically evoked twitch of the mouse isolated vas deferens preparation (MVD) were calculated at five temperatures (25, 30, 34, 37 and 40 degrees C). These values were determined from the equiactive concentrations obtained before (A) and after (A') partial irreversible blockade of a fraction of the receptor population by beta-chlornaltrexamine (beta-CNA) plotted as (1/A') where KA = (slope -1)/intercept. The values of KA tended to increase (approximately doubled) over this temperature range, indicating that the affinity of DPDPE for the opioid delta receptor is an inverse function of temperature. From these results, thermodynamic parameters were calculated from a Van't Hoff plot of 1n(KA) against 1/T. The relative magnitudes of the change in enthalpy (delta Ho' = -6.67 kcal mol-1), the change in entropy (delta So' = +0.009 kcal mol-1 degrees K-1) and the change in free energy (delta Go' = -9.43 kcal mol-1) suggest that the interaction between DPDPE and the delta-opioid receptor in MVD is an exothermic exergonic reaction, predominantly enthalpy-driven and results in an increase in the entropy of the system.

Thermodynamic analysis of binding to the cerebellar type I benzodiazepine receptor

The temperature dependence of binding to the type I benzodiazepine receptor in rat cerebellum was determined using [3H]Ro15-1788 and regression analysis techniques. The ligands chosen were from diverse chemical families and display different pharmacological properties. Included were the agonists flunitrazepam, CL 218,872, zolpidem and alpidem; the antagonists Ro15-1788 and propyl-beta-carboline-3-carboxylate (beta-CCP); the inverse agonists ethyl-beta-carboline-3-carboxylate (beta-CCE) and methyl-6,7-dimethoxy-beta-carboline-3-carboxylate (DMCM); and the selective muscle relaxant AHR-11797. Assays were performed at 0 degrees C, 20 degrees C and 37 degrees C and the K(i) at each temperature was used to construct a van't Hoff plot for each compound. The binding of all ligands, with the exception of DMCM, was enthalpy-driven. However, enthalpy alone does not determine the rank order of affinity. There was no relationship between the thermodynamic behavior of binding and the observation of agonism, antagonism or inverse agonism, indicating that activation and recognition are distinct steps in this receptor system.

Biochemical and thermodynamic aspects of the binding of [3H]glycine to its strychnine-insensitive recognition site associated with the N-methyl-D-aspartate receptor complex

The molecular mechanism of interaction between glycine and its strychnine-insensitive binding site linked to the N-methyl-D-aspartate receptor was investigated by examining on the one hand the thermodynamic properties of glycine binding, and, on the other hand, the effects of various functional group modifying agents on ligand binding. Raising the incubation temperature from 0 degrees to 37 degrees resulted in a consistent decrease of glycine binding affinity. Calculation of thermodynamic parameters from the corresponding Van't Hoff plot showed that the binding of glycine was mainly entropy-driven, the change in enthalpy contributing only little (25-30%) to the change in Gibbs free energy. Chemical modification with the sulfhydryl-directed agents p-hydroxy-mercuribenzoate and N-ethyl-maleimide showed free -SH groups to be critical for ligand binding to the receptor site. Furthermore, guanidino groups on arginyl residues, sensitive to 2,3-butanedione, were also found to participate in glycine binding. Both the -SH and the guanidino groups could be protected against their inactivation by co-incubation with glycine, indicating a direct involvement of these functional groups in the binding process. Dithiothreitol, a disulfide-reducing agent, likewise prevented [3H]glycine binding, suggesting that the glycine recognition site is stabilized by at least one disulfide bridge. It is concluded that the binding of glycine probably involves a strong ion-ion interaction between its carboxyl group and a positively charged guanidino group at the receptor site, resulting in a thermodynamically favorable increase in entropy by displacement of water molecules from the latter and a concomitant decrease in enthalpy. Furthermore, at least one free sulfhydryl group seems to participate in the binding process.

Kinetics of haloperidol binding to monoclonal antibodies as measured by direct fluorescence quenching

Monoclonal antibodies which bind small neurogenic ligands may mimic certain aspects of the stereospecific binding present in the natural biological receptor, and may prove useful in designing engineered protein receptors, provided their interactions are correctly understood. We report here the kinetic and equilibrium characteristics of ligand-antibody complexes of haloperidol, a dopaminergic antagonist, with three of its monoclonal antibodies as studied by fluorescence quenching techniques. These antibodies possessed moderate to high affinity constants, ranging from 10(5) to 10(9) M-1, and caused fluorescence quenching of a fluorescein-labeled haloperidol as well as quenching (40-60%) of the internal tryptophan fluorescence. The dissociation rates of the ligand from the complexes were measured at different conditions of temperature, pH and ionic strength. The results provide important information regarding the kinetic and thermodynamic parameters of the binding pockets of these antibodies.

Effects of pentobarbital tolerance and dependence on convulsant and GABAA receptor antagonist binding

Experiments were performed which examined the effects of pentobarbital tolerance and dependence on GABAA receptor antagonist binding. In rats implanted with pentobarbital pellets for 7 days, followed by 24 hours of withdrawal, there was a significant decrease in the latency of TBPS-induced seizures and an increase in [35S]TBPS binding in the frontal cortex. The pentobarbital tolerant rats had a significant increase in the low affinity KD of [3H]SR95531 binding. Removal of the pellets for 24 hours caused a reversal of the effect on the low affinity KD and caused a decrease in the number of low affinity binding sites. In vitro addition of pentobarbital to binding assays produced a decrease in the number of high affinity [3H]SR95531 binding sites without changing low affinity binding. In the cerebellum, the binding in none of the treatment groups was significantly different from placebo. These observations suggest that pentobarbital tolerance and withdrawal cause changes in the properties of the GABAA receptor antagonist binding site which are different from those caused by in vitro exposure to the drug.

Temperature dependence of drug blockade of a calcium-dependent potassium channel in cultured hippocampal neurons

The temperature dependence of drug blockade of a calcium-dependent potassium channel K(Ca) has been studied in cultured CA1 hippocampal neurons. Channel openings from a 70-pS K+ channel were recorded when inside-out patches were exposed to a bath solution containing 140 mM K+ and 0.2 mM Ca2+. The mean open times of channel events were not significantly altered when the bath temperature was lowered from 24 degrees to 14 degrees C (Q10 = 1.2). Introduction of the drug RP-62719 into the bath solution (at 5 microM) resulted in the mean open time of the K(Ca) channel to be diminished by 85% (at 24 degrees C) with no change in the amplitudes of the unitary currents. Over the same temperature range of 24 degrees to 14 degrees C, in the presence of RP-62719, the mean open times were significantly prolonged (Q10 = 2.2). A simple open channel block scheme was used to determine the temperature dependence of the onward- (blocking) and off- (unblocking) rate constants. Thermodynamic analysis, using transition rate theory, showed that the blocking rate constant was associated with a large increase in entropy. The relatively high temperature dependence for channel blockade is not consistent with a rate-limiting process established by simple diffusion of the agent to a channel blocking site. Channel block may involve conformational changes in the channel protein as a consequence of hydrophobic interactions between drug and channel sites.

Thermodynamic and kinetic aspects of agonist and antagonist binding to 1,4-dihydropyridine receptors

The kinetic and equilibrium binding properties of the 1,4-dihydropyridine activator [3H](-)-S-Bay K 8644 and the antagonist [3H](+)-PN 200-110 were determined in rat heart membrane particulate preparations at temperatures between 4 and 37 degrees C. The binding of [3H](-)-S-Bay K 8644 was temperature-dependent with a single binding site with KD = 3.57 nM and Bmax = 330 fmol/mg.protein at 25 degrees C. The association and dissociation rate constants were 3.4 x 10(7) min-1 M-1 and 0.095 min-1 respectively at 25 degrees C and decreased slightly at lower temperatures. In contrast, [3H](+)-PN 200-110 bound to high (KD(H) = 0.032 nM, Bmax(H) = 316 fmol/mg.protein) and low affinity sites (KD(L) = 27.6 nM and Bmax(L) = 6432 fmol/mg.protein) at 25 degrees C in rat heart preparation. A similar two-site binding of [3H](+)-PN 200-110 was found in rat brain preparation, but only a single binding site was detected in rat skeletal muscle. Binding of [3H](+)-PN 200-110 to the high and low affinity sites in cardiac membranes was sensitive and insensitive respectively to temperature. Association and dissociation rates of [3H](+)-PN 200-110 at the high affinity binding sites were best fitted as mono-exponential functions. Association and dissociation rates of [3H](+)-PN 200-110 were 3.94 x 10(8) min-1 M-1 and 7.86 x 10(-3) min-1 at 25 degrees C. The association rate varied only slightly (3-fold), but the rate of dissociation decreased significantly (200-fold) with temperature from 37 to 4 degrees C. Thermodynamic analysis of equilibrium binding showed that the binding of activator was enthalpy driven, whereas the binding of antagonist to the high affinity site was both entropy- and enthalpy-driven and to the low affinity site was totally entropy-driven.

Temperature dependence of [3H]PAF binding to washed human platelets

Our results indicate that the binding of [3H]PAF to a single class of high affinity sites on human platelets is endothermic and largely entropy-driven. The increase in entropy can be attributed to the disorganization of water molecules bound to both receptor and ligand during the binding process.

Effect of age on the kinetics of the binding of iodocyanopindolol to a membrane preparation of rat lungs

The association (k+1) and dissociation (k-1) rate constants, and the equilibrium thermodynamic binding parameters (delta G0, delta H0 and delta S0) of the beta-adrenergic ligand [125Iodo]cyanopindolol (ICYP) were studied in a crude lung membrane preparation of rats of different ages. There was no difference in k+1-values for the different age groups, while the k-1-values were in all cases difficult to measure: almost no dissociation of ICYP from its binding site occurs. The thermodynamic properties were not affected by age. It is concluded that, in these experimental conditions, age has no effect on the kinetic parameters of the binding of ICYP to the beta-adrenoceptors in rat lung.