The binding of agonists and antagonists to rat lung beta-adrenergic receptors as investigated by thermodynamics and structure-activity relationships

[Molecular docking: role of intermolecular contacts in formation of complexes of proteins with nucleotides and peptides]

Knowledge of 3D-structure of protein-ligand complex is a major prerequisite for understanding the functioning mechanism of cellular proteins and membrane receptors. This is also of a great help in rational drug design projects. In the present paper we briefly review the molecular docking approaches used to predict possible orientation of a ligand in the protein binding site. The recent trends to improve the accuracy and efficiency of docking algorithms are demonstrated with the results obtained in Laboratory of Biomolecular Modeling. Particular attention is paid to protein-ligand hydrophobic and stacking interactions responsible for molecular recognition of ligand fragments. Such type of interactions are not always adequately represented in scoring criteria of docking applications that leads to mismatch in 3D-structure complexes predictions. That is why further inquiry of methods to account for these interactions is now the area of active research.

Analysis of hydrophobic interactions of antagonists with the beta2-adrenergic receptor

The adrenergic receptors mediate a wide variety of physiological responses, including vasodilatation and vasoconstriction, heart rate modulation, and others. Beta-adrenergic antagonists ('beta-blockers') thus constitute a widely used class of drugs in cardiovascular medicine as well as in management of anxiety, migraine, and glaucoma. The importance of the hydrophobic effect has been evidenced for a wide range of beta-blocker properties. To better understand the role of the hydrophobic effect in recognition of beta-blockers by their receptor, we carried out a molecular docking study combined with an original approach to estimate receptor-ligand hydrophobic interactions. The proposed method is based on automatic detection of molecular fragments in ligands and the analysis of their interactions with receptors separately. A series of beta-blockers, based on phenylethanolamines and phenoxypropanolamines, were docked to the beta2-adrenoceptor binding site in the crystal structure. Hydrophobic complementarity between the ligand and the receptor was calculated using the PLATINUM web-server (http://model.nmr.ru/platinum). Based on the analysis of the hydrophobic match for molecular fragments of beta-blockers, we have developed a new scoring function which efficiently predicts dissociation constant (pKd) with strong correlations (r(2) approximately 0.8) with experimental data.

Entropic Trapping Binding Mechanism: Its Likely Role in Receptor−Ligand and Other Biochemical Systems

Entropy-driven binding continues to be discovered in receptor-ligand systems as well as in other important biochemical systems. In receptor-ligand systems the "thermodynamic agonist-antagonist discrimination" is often found: in some such receptor types the binding of antagonists is entropy-driven, in others this is a characteristic of the agonist binding. The interpretation of the entropy-driven binding mechanism in the systems in question is still rather elusive. Experimental findings clearly indicate that the entropic binding mechanisms which are usually considered cannot provide a consistent interpretation in these cases. Entropic trapping was therefore proposed in our earlier papers as a possible binding model which does not contradict the experimental facts. It is pointed out here that through the work which has appeared subsequently the existence of such a mechanism has been firmly established and that its role is strongly corroborated by the more recent data from several biochemical systems.

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.

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.

Temperature-nearly-independent binding constant in several biochemical systems. The underlying entropy-driven binding mechanism and its practical significance

Arguments are presented in this commentary to show that the model of temperature-nearly-independent binding that we proposed to rationalize the binding characteristics of beta-adrenergic antagonists (Miklavc et al., Biochem Pharmacol 40: 663-669, 1990) in fact provides a consistent interpretation of the temperature-nearly-independent binding constant in all other systems that have been reported in the literature: in the binding of coenzyme NADH to horse liver alcohol dehydrogenase and to octopine dehydrogenase and in the binding of an inhibitor to acetylcholinesterase No such consistent interpretation has been given thus far for any of these systems. It is characteristic of them that the binding takes place in a hydrophobic, sterically constrained environment. One can assume, therefore, that the underlying entropy-driven binding mechanism would reflect the existence and the properties of the steric bottleneck surrounding the binding pocket. We also explain why the temperature effects characteristic of hydrophobic interactions are not found experimentally in these systems, whereas in other, sometimes even structurally similar, systems such temperature effects are clearly present. Further work in necessary to establish more firmly the key features of the temperature-nearly-independent binding mechanism that has been disclosed through our analysis. The binding mechanism in question not only appears in important biochemical systems, but also has the interesting property of being relative unaffected by smaller structural changes.

Mechanism of ligand binding to alpha 1-acid glycoprotein (orosomucoid): correlated thermodynamic factors and molecular parameters of polarity

Eight ligands were used in this study, four basic, three neutral and one acidic. Their binding to serum alpha 1-acid glycoprotein (orosomucoid) was measured at several temperatures, and the data were analysed together by a general model with three unknowns, number of binding sites, delta H0 and delta S0. The partition coefficients of the ligands were measured in octanol/water and heptane/water systems (log Poct. and log Phep.), and their molecular volumes were calculated by molecular modelling techniques. These structural properties allow determination of polarity parameters (delta log Poct.-hep., lambda oct. and lambda hep.) which encode in different proportions the various polar interactions between the solute and the aqueous and organic phases, i.e. hydrogen-bonding capacity and dipolarity/polarizability. This study shows that good correlations exist between delta H0 or delta S0 and polarity parameters, such that the enthalpic contribution to binding increases with increasing polarity of the ligands, mainly hydrogen-bond-donor acidity, whereas their entropic contribution to binding decreases.

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.

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.

Partition and distribution coefficients of aryloxypropanolamine beta-adrenoceptor antagonists

n-Octanol/water partition and distribution coefficients of fifteen beta-blockers have been measured and the relationships between log P (neutral species), log Pi (fully ionized species) and log D7.4 have been examined. A strict correlation exists among these three parameters, suggesting that the ionization exerts similar effects on the partition behaviour of these drugs.

The specific binding of broxaterol, a new beta 2-selective agonist, to beta-adrenoceptors

The specific binding of broxaterol, a potent new orally active antiasthmatic drug, to beta 1- and beta 2-adrenoceptors was characterized by receptor binding studies with rat heart and lung membrane preparations. Broxaterol showed high affinity and selectivity for the beta 2-component of [3H]dihydroalprenolol binding in both lung (58% beta 2-sites, Ki = 130 nM) and heart membranes (19% beta 2-sites, Ki = 98 nM), whereas the binding to the beta 1-component was at lower affinity (42% beta 1-sites, Ki = 4100 nM in the lung and 81% beta 1-sites, Ki = 3460 mM in the heart). The influence of temperature changes on the binding properties of broxaterol towards beta-adrenoceptors was also investigated. A marked increase in the affinity of broxaterol for lung beta-receptors was observed on lowering the assay temperature, whereas the affinity for heart beta-receptors was little affected by temperature changes. Thermodynamic analysis of the binding data showed that the binding of broxaterol as well as isoproterenol to lung beta-receptors was associated with a large decrease in enthalpy, which correlates well with the full agonistic properties of this compound at beta 2-receptors.

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.

Asymmetric synthesis of a precursor for the automated radiosynthesis of S-(3'-t-butylamino-2'-hydroxypropoxy)-benzimidazol-2-[11C]one (S-[11C]CGP 12177) as a preferred radioligand for beta-adrenergic receptors

S-[1-(2,3-Diaminophenoxy)]-3'-(N-t-butylamino)propan-2'-ol has been synthesized in three steps from 2,3-dinitro-phenol and the chiral auxiliary, S-glycidyl-3-nitrobenzenesulphonate, to provide a precursor for labelling S-(3'-t-butylamino-2'-hydroxypropoxy)-benzimidazol-2-one (S-CGP 12177) with the short-lived positron-emitting radionuclide, carbon-11 (t 1/2 = 20.4 min; beta+ = 99.8%). Reaction of the diamine with [11C]phosgene, itself derived from no-carrier-added cyclotron-produced [11C]methane, provides radiochemically and chemically pure S-[carbonyl-11C]CGP 12177 in greater than 95% enantiomeric excess after HPLC. Automated apparatus is described for safely producing up to 5.9 GBq (160 mCi) of S-[11C]CGP 12177 with high sp. act. (20-40 GBq/mu mol or 0.54-1.08 Ci/mu mol) in a form suitable for human intravenous injection at only 30 min from the end of radionuclide production. S-[11C]CGP 12177 is preferred to the formerly described racemate as a radioligand for the study of beta-adrenergic receptors in vivo by positron emission tomography.

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.

Influence of lipophilicity and chirality on the selectivity of ligands for beta 1- and beta 2-adrenoceptors

Eudismic and QSAR analyses are reported for the beta 1- and beta 2-adrenoceptor affinities and beta 1-selectivity of 10 enantiomeric pairs of ligands with only N-isopropyl or N-t-butyl groups. For both receptors, the eudismic index (ratio of affinity) increases with the affinity of the eutomers. However, the affinity of the distomers for the beta 2-adrenoceptor is relatively high, suggesting additional hydrophobic interactions. This is confirmed by various correlations between affinities and lipophilicities, showing that the affinity for beta 2-adrenoceptors is slightly more dependent on lipophilicity than that for beta 1-adrenoceptors. As a result, the beta 1-selectivity of the investigated beta 1-adrenoceptor ligands is strongly and negatively correlated with their lipophilicity (r = -0.942).