Binding Of Agonist Ligands Research Articles

Graph-based algorithms to dissect long-distance water-mediated H-bond networks for conformational couplings in GPCRs.

Changes in structure and dynamics elicited by agonist ligand binding at the extracellular side of G protein coupled receptors (GPCRs) must be relayed to the cytoplasmic G protein binding side of the receptors. To decipher the role of water-mediated hydrogen-bond networks in this relay mechanism, we have developed graph-based algorithms and analysis methodologies applicable to datasets of static structures of distinct GPCRs. For a reference dataset of static structures of bovine rhodopsin solved at the same resolution, we show that graph analyses capture the internal protein-water hydrogen-bond network. The extended analyses of static structures of rhodopsins and opioid receptors suggest a relay mechanism whereby inactive receptors have in place much of the internal core hydrogen-bond network required for long-distance relay of structural change, with extensive local H-bond clusters observed in structures solved at high resolution and with internal water molecules.

Binding of de novo synthesized radiolabeled juvenile hormone (JH III) by JH receptors from the Cuban subterranean termite Prorhinotermes simplex and the German cockroach Blattella germanica

Juvenile hormone (JH) controls insect reproduction and development through an intracellular receptor complex comprising two bHLH-PAS proteins, the JH-binding Methoprene-tolerant (Met) and its partner Taiman (Tai). Many hemimetabolous insects including cockroaches strictly depend on JH for stimulation of vitellogenesis. In termites, the eusocial hemimetabolans, JH also regulates the development of caste polyphenism. Studies addressing the agonist ligand binding to recombinant JH receptors currently include three species belonging to two holometabolous insect orders, but none that would represent any of the hemimetabolous orders. Here, we examined JH receptors in two representatives of Blattodea, the cockroach Blattella germanica and the termite Prorhinotermes simplex. To test the JH-binding capacity of Met proteins from these species, we performed chemical synthesis and tritium labeling of the natural blattodean JH homolog, JH III. Our improved protocol increased the yield and specific activity of [10-3H]JH III relative to formerly available preparations. Met proteins from both species specifically bound [3H]JH III with high affinity, whereas Met variants mutated at a critical position within the ligand-binding domain were incapable of such binding. Furthermore, JH III and the synthetic JH mimic fenoxycarb stimulated dimerization between Met and Tai components of the respective JH receptors of both species. These data present primary evidence for agonist binding by JH receptors in any hemimetabolous species and provide a molecular basis for JH action in cockroaches and termites.

How does binding of agonist ligands control intrinsic molecular dynamics in human NMDA receptors?

NMDA-type glutamate receptors (NMDAR) are ligand-gated ion channels that contribute to excitatory neurotransmission in the central nervous system. NMDAR dysfunction has been found to be involved in various neurological disorders. Recent crystallographic and EM studies have shown the static structure of different states of the non-human NMDARs. Here we describe a model of a human NMDA receptor (hNMDAR) and its molecular dynamics (MD) before and after the binding of agonist ligands, glutamate and glycine. It is shown that the binding of ligands promotes a global reduction in molecular flexibility that produces a more tightly packed conformation than the unbound hNMDAR, and a higher cooperative regularity of moving. The ligand-induced synchronization of motion, identified on all structural levels of the modular hNMDA receptor is apparently a fundamental factor in channel gating. Although the time scale of the MD simulations (300 ns) was not sufficient to observe the complete gating event, the obtained data has shown the ligand-induced stabilization of hNMDAR that conforms the “going to be open state”. We propose a mechanistic dynamic model of the ligand-dependent gating mechanism in the hNMDA receptor. At the binding of the ligands, the differently twisted conformations of the highly flexible receptor are stabilized in unique conformation with a linear molecular axis, which is a condition that is optimal for pore development. By searching the receptor surface, we have identified three new pockets, which are different from the pockets described in the literature as the potential and known positive allosteric modulator binding sites. A successful docking of two NMDAR modulators to their binding sites validates the model of a human NMDA receptor as a biological relevant target.

Molecular interactions of agonist and inverse agonist ligands at serotonin 5-HT2C G protein-coupled receptors: computational ligand docking and molecular dynamics studies validated by experimental mutagenesis results

To understand molecular determinants for ligand activation of the serotonin 5-HT2C G protein-coupled receptor (GPCR), a drug target for obesity and neuropsychiatric disorders, a 5-HT2C homology model was built according to an adrenergic β2 GPCR (β2AR) structure and validated using a 5-HT2B GPCR crystal structure. The models were equilibrated in a simulated phosphatidyl choline membrane for ligand docking and molecular dynamics studies. Ligands included (2S, 4R)-(–)-trans-4-(3’-bromo- and trifluoro-phenyl)-N,N-dimethyl-1,2,3,4-tetrahydronaphthalene-2-amine (3’-Br-PAT and 3’-CF3-PAT), a 5-HT2C agonist and inverse agonist, respectively. Distinct interactions of 3’-Br-PAT and 3’-CF3-PAT at the wild-type (WT) 5-HT2C receptor model were observed and experimental 5-HT2C receptor mutagenesis studies were undertaken to validate the modelling results. For example, the inverse agonist 3’-CF3-PAT docked deeper in the WT 5-HT2C binding pocket and altered the orientation of transmembrane helices (TM) 6 in comparison to the agonist 3’-Br-PAT, suggesting that changes in TM orientation that result from ligand binding impact function. For both PATs, mutation of 5-HT2C residues S3.36, T3.37, and F5.47 to alanine resulted in significantly decreased affinity, as predicted from modelling results. It was concluded that upon PAT binding, 5-HT2C residues T3.37 and F5.47 in TMs 3 and 5, respectively, engage in inter-helical interactions with TMs 4 and 6, respectively. The movement of TMs 5 and 6 upon agonist and inverse agonist ligand binding observed in the 5-HT2C receptor modelling studies was similar to movements reported for the activation and deactivation of the β2AR, suggesting common mechanisms among aminergic neurotransmitter GPCRs.

Internalization of the chemokine receptor CCR4 can be evoked by orthosteric and allosteric receptor antagonists

The chemokine receptor CCR4 has at least two natural agonist ligands, MDC (CCL22) and TARC (CCL17) which bind to the same orthosteric site with a similar affinity. Both ligands are known to evoke chemotaxis of CCR4-bearing T cells and also elicit CCR4 receptor internalization. A series of small molecule allosteric antagonists have been described which displace the agonist ligand, and inhibit chemotaxis. The aim of this study was to determine which cellular coupling pathways are involved in internalization, and if antagonists binding to the CCR4 receptor could themselves evoke receptor internalization. CCL22 binding coupled CCR4 efficiently to β-arrestin and stimulated GTPγS binding however CCL17 did not couple to β-arrestin and only partially stimulated GTPγS binding. CCL22 potently induced internalization of almost all cell surface CCR4, while CCL17 showed only weak effects. We describe four small molecule antagonists that were demonstrated to bind to two distinct allosteric sites on the CCR4 receptor, and while both classes inhibited agonist ligand binding and chemotaxis, one of the allosteric sites also evoked receptor internalization. Furthermore, we also characterize an N-terminally truncated version of CCL22 which acts as a competitive antagonist at the orthosteric site, and surprisingly also evokes receptor internalization without demonstrating any agonist activity. Collectively this study demonstrates that orthosteric and allosteric antagonists of the CCR4 receptor are capable of evoking receptor internalization, providing a novel strategy for drug discovery against this class of target.

Molecular basis of peptide activation of the GLP-1 receptor

Molecular basis of peptide activation of the GLP-1 receptor

Role of saturability of noncovalent interactions in the analysis of the three-dimensional structure—opioid activity relationship

The effect of the saturability of noncovalent interactions on the character of opioid activity of opioid receptor ligands belonging to different structural classes was investigated. A three-dimensional model for an opiate pharmacophore was used to show that the involvement of pharmacophore elements, which are responsible for the agonist ligand binding to opioid receptors, in intramolecular interactions gives rise to antagonistic properties.

Intramolecular Fluorescence Resonance Energy Transfer (FRET) Sensors of the Orexin OX1 and OX2 Receptors Identify Slow Kinetics of Agonist Activation

Intramolecular fluorescence resonance energy transfer (FRET) sensors able to detect changes in distance or orientation between the 3rd intracellular loop and C-terminal tail of the human orexin OX(1) and OX(2) G protein-coupled receptors following binding of agonist ligands were produced and expressed stably. These were directed to the plasma membrane and, despite the substantial sequence alterations introduced, in each case were able to elevate [Ca(2+)](i), promote phosphorylation of the ERK1/2 MAP kinases and become internalized effectively upon addition of the native orexin peptides. Detailed characterization of the OX(1) sensor demonstrated that it was activated with rank order of potency orexin A > orexin B > orexin A 16-33, that it bound antagonist ligands with affinity similar to the wild-type receptor, and that mutation of a single residue, D203A, greatly reduced the binding and function of orexin A but not antagonist ligands. Addition of orexin A to individual cells expressing an OX(1) sensor resulted in a time- and concentration-dependent reduction in FRET signal consistent with mass-action and potency/affinity estimates for the peptide. Compared with the response kinetics of a muscarinic M(3) acetylcholine receptor sensor upon addition of agonist, response of the OX(1) and OX(2) sensors to orexin A was slow, consistent with a multistep binding and activation process. Such sensors provide means to assess the kinetics of receptor activation and how this may be altered by mutation and sequence variation of the receptors.

Agnostic about in Vivo Inverse Agonism of Agouti-Related Peptide

Agnostic about in Vivo Inverse Agonism of Agouti-Related Peptide

Molecular Basis of Glucagon-like Peptide 1 Docking to Its Intact Receptor Studied with Carboxyl-terminal Photolabile Probes

The glucagon-like peptide 1 (GLP1) receptor is a member of Family B G protein-coupled receptors and represents an important drug target for type 2 diabetes. Despite recent solution of the structure of the amino-terminal domain of this receptor and that of several close family members, understanding of the molecular basis of natural ligand GLP1 binding to its intact receptor remains limited. The goal of this study was to explore spatial approximations between specific receptor residues within the carboxyl terminus of GLP1 and its receptor as normally docked. Therefore, we developed and characterized two high affinity, full-agonist photolabile GLP1 probes having sites for covalent attachment in positions 24 and 35. Both probes labeled the receptor specifically and saturably. Subsequent peptide mapping using chemical and proteinase cleavages of purified wild-type and mutant GLP1 receptor identified that the Arg(131)-Lys(136) segment at the juxtamembrane region of the receptor amino terminus contained the site of labeling for the position 24 probe, and the specific receptor residue labeled by this probe was identified as Glu(133) by radiochemical sequencing. Similarly, nearby residue Glu(125) within the same region of the receptor amino-terminal domain was identified as the site of labeling by the position 35 probe. These data represent the first direct demonstration of spatial approximation between GLP1 and its intact receptor as docked, providing two important constraints for the modeling of this interaction. This should expand our understanding of the molecular basis of natural agonist ligand binding to the GLP1 receptor and may be relevant to other family members.

Structural Basis for Ligand Binding and Specificity in Adrenergic Receptors: Implications for GPCR-Targeted Drug Discovery

Crystal structures of engineered human beta 2-adrenergic receptors (ARs) in complex with an inverse agonist ligand, carazolol, provide three-dimensional snapshots of the disposition of seven transmembrane helices and the ligand-binding site of an important G protein-coupled receptor (GPCR). As expected, beta 2-AR shares substantial structural similarities with rhodopsin, the dim-light photoreceptor of the rod cell. However, although carazolol and the 11- cis-retinylidene moiety of rhodopsin are situated in the same general binding pocket, the second extracellular (E2) loop structures are quite distinct. E2 in rhodopsin shows beta-sheet structure and forms part of the chromophore-binding site. In the beta 2-AR, E2 is alpha-helical and seems to be distinct from the receptor's active site, allowing a potential entry pathway for diffusible ligands. The structures, together with extensive structure-activity relationship (SAR) data from earlier studies, provide insight about possible structural determinants of ligand specificity and how the binding of agonist ligands might alter receptor conformation. We review key features of the new beta 2-AR structures in the context of recent complementary work on the conformational dynamics of GPCRs. We also report 600 ns molecular dynamics simulations that quantified beta 2-AR receptor mobility in a membrane bilayer environment and show how the binding of an agonist ligand, adrenaline (epinephrine), causes conformational changes to the ligand-binding pocket and neighboring helices.

Specificity of receptor–ligand interactions and their effect on dimerisation as observed by electrospray mass spectrometry: bile acids form stable adducts to the RXRα

Electrospray (ES) mass spectrometry data is presented showing that agonist binding to the nuclear receptor (NR), retinoid X receptor alpha (RXRalpha), is competitive. The competitive nature of agonist binding can be used to discriminate between the specific and non-specific binding of small lipophilic molecules to NRs. Further, data is presented which show that high-affinity ligand binding to the RXRalpha ligand-binding domain (LBD) stabilises the domain homodimer. The results indicate that homodimerisation, a functional property of the receptor associated with the binding of agonist ligands, could be used to discriminate between specific and non-specific binding events. Additionally, we report on the remarkable stability of the gas-phase complex between the RXRalpha LBD protein and endogenous bile acids. Protein-bile acid interactions in the gas phase were found to be surprisingly strong, withstanding 'in-source' fragmentation in the ES interface, and, in the case of taurocholic acid (TCA) and lithocholic acid-3-sulphate (LCA-3-sulphate), collision-induced dissociation within the collision cell of a tandem mass spectrometer. Bile acids were found to be inactive towards RXRalpha in transfection assays, and have not been reported to be ligands for the RXRalpha, although lithocholic acid (LCA) has been found to be a competitor in the photoaffinity labelling of RXRbeta with 9-cis-retinoic acid (9-cis-RA). The observation of strong RXRalpha-bile acid non-covalent complexes in ES mass spectrometry highlight the danger of extrapolating gas-phase binding data to the solution phase and further to a possible biological activity, particularly when surface-active compounds such as bile acids are involved. The introduction of a competitive ligand-binding experiment can alleviate this problem and allow the differentiation between specific and non-specific binding.

Differential Effects of Modification of Membrane Cholesterol and Sphingolipids on the Conformation, Function, and Trafficking of the G Protein-coupled Cholecystokinin Receptor

The lipid microenvironment of receptors can influence their conformation, function, and regulation. Cholecystokinin (CCK)-stimulated signaling is abnormal in some forms of hyperlipidemia, suggesting the possibility of unique sensitivity to its lipid environment. Here we examined the influence of cholesterol and sphingolipids on CCK receptors in model Chinese hamster ovary cell systems having lipid levels modified. Cholesterol was modulated chemically or metabolically, and sphingolipids were modulated using a temperature-sensitive cell line (SPB-1). Receptor conformation was probed with a fluorescent full agonist ligand, Alexa 488-conjugated Gly-[Nle(28,31)]CCK-(26-33), shown previously to decrease in anisotropy and lifetime when occupying a receptor in the active conformation (Harikumar, K. G., Pinon, D. L., Wessels, W. S., Prendergast, F. G., and Miller, L. J. (2002) J. Biol. Chem. 277, 18552-18560). Anisotropy and lifetime of this probe were increased and prolonged with cholesterol enrichment, and decreased and shortened with depletion of cholesterol or sphingolipids. The increase in these parameters with cholesterol enrichment may reflect change in CCK receptor conformation toward its inactive, uncoupled state. Indeed, cholesterol enrichment resulted in nonproductive agonist ligand binding, with affinity of binding higher than normal and calcium signaling in response to this reduced. In cholesterol- and sphingolipid-depleted states, the receptor moved into conformations that were less than optimal. With cholesterol depletion, both ligand binding and signaling were decreased, yet internalization and trafficking were unperturbed. With sphingolipid depletion, ligand binding and signaling were normal, but internalization and trafficking were markedly inhibited. Of note, normal transferrin receptor trafficking through the same clathrin-dependent pathway was maintained under these conditions. Thus, lipid microenvironment of the CCK receptor is particularly important, with different lipids having distinct effects.

Peroxisome proliferator-activated receptor gamma agonist ligands stimulate a Th2 cytokine response and prevent acute colitis.

Peroxisome proliferator-activated receptor gamma (PPARgamma), a member of a nuclear transcription factor family, has been previously demonstrated to have antiinflammatory activity. The effects of PPARgamma activation in the development of an immune response are less well characterized. Through evaluation of PPARgamma heterozygote mice (PPARgamma(+/-) and specific PPARgamma agonist ligand binding, we evaluated the immunologic effects of PPARgamma activation in a well-described model of colitis. Increased susceptibility to dextran sodium sulfate (DSS)-induced colitis as defined by body weights, histologic injury, and survival was observed in the PPARgamma(+/-) mice in comparison to wild-type mice. Three different PPARgamma ligands (troglitazone, pioglitazone, and rosiglitazone) demonstrated beneficial dose-related treatment effects when administered prior to the onset of colitis. However, no protection was observed when PPARgamma ligand activation occurred after the onset of colitis. The reduction in DSS-induced inflammation noted with PPARgamma ligand treatment was associated with decreased interferon-gamma and tumor necrosis factor-alpha and increased interleukin (IL)-4 and IL- 10 levels as assessed by quantitative reverse transcriptase-polymerase chain reaction. Consistent with this shift towards a T helper (Th2) cytokine dominance, PPARgamma ligand treatment stimulated increased GATA-3 expression. These results indicate that the protective effects exhibited by PPARgamma ligands in intestinal inflammation may be due to immune deviation away from Th1 and towards Th2 cytokine production.

Coactivator peptides have a differential stabilizing effect on the binding of estrogens and antiestrogens with the estrogen receptor.

The effectiveness of estrogens in stimulating gene transcription mediated by the estrogen receptor (ER) appears to depend on ER interactions with coactivator proteins. These coactivators bind to ER when it is liganded with an estrogen agonist, but not when it is liganded with an estrogen antagonist. Because estrogen agonists are known to induce a conformation in ER that stabilizes coactivator binding, we asked whether coactivator binding to ER causes a reciprocal stabilization of agonist ligand binding. We used a fluorescent ligand for ER, tetrahydrochrysene-ketone, to monitor the rates of ligand dissociation from ERalpha and ERbeta, and to see how this process is affected by the p160-class coactivator, steroid receptor coactivator-1 (SRC-1). We used a 15-amino acid peptide corresponding to the second nuclear receptor box LXXLL motif in SRC-1 (NR-2 peptide), which is known to interact with the ER ligand-binding domain, a mutant peptide with an LXXAL sequence (NR-2A peptide), and a 203-amino acid fragment of SRC-1, termed the nuclear receptor domain (SRC1-NRD), embodying all three of the internal NR boxes of this protein. Both the NR-2 peptide and the SRC1-NRD fragment markedly slow the rate of dissociation of the agonist ligands tetrahydrochrysene-ketone, estradiol, and diethylstilbestrol, increasing the half-life of the ER-agonist complex by up to 50- to 60-fold. The SRC1-NRD has much higher potency in retarding ligand dissociation than does the NR-2 peptide; it is maximally effective at 30 nM, and it appears to bind with the stoichiometry of one SRC1-NRD per ER dimer. The peptides had little effect on the dissociation rate of antagonist ligands. Consistent with these results, we find that increasing the concentration of SRC-1 in cells by transfection of an expression plasmid encoding SRC-1 causes a 17-fold increase in the potency of estradiol in an estrogen-responsive reporter gene transcription assay. Thus, there is multifactorial control over receptor-coactivator interaction, its strength being determined by the agonist vs. antagonist nature of the ligand and the particular structure of the agonist ligand, and by the receptor subtype and the NR box sequence. The stabilizing effect of coactivator on ER-agonist ligand complexes may be important in determining the potency of estrogen agonists in a cell and may also underlie the tissue-selective pharmacology of certain synthetic estrogens.

Modulation of A1 adenosine receptor function in rat brain by the polyamine, spermine.

Studies on factors modulating the binding of agonist ligands to A1 adenosine receptors in rat forebrain membranes revealed that the reduction of [3H]cyclohexyladenosine [( 3H]CHA) binding, observed after removing Mg2+ by pretreatment with ethylene-dinitrilo-tetraacetic acid (EDTA), was restored by the polyamine, spermine (1mM). Parallel electrophysiological experiments performed on rat hippocampal slices in Mg(2+)-free medium indicated that spermine also led to a recovery of the depressive effect of 1 microM adenosine on stimulus train-evoked neuronal Ca2+ influx. These observations suggest that the polyamine, spermine is, like Mg2+, able to control the physiological adenosine-mediated modulation of synaptic transmission by changing the affinity state of A1 receptors.

Desensitization of adenosine A 2 receptors in the striatum of the rat following chronic treatment with diazepam

Following prolonged treatment (7 days) with diazepam (10 mg/kg/day, using ALZET mini-osmotic pumps) in rats, the function of adenosine receptors was assessed in specific structures of the brain, using both agonist ligand binding and adenylate cyclase assays. Binding to A 1 receptors was quantitified using [ 3 H]N 6-[( R)-1- methyl-2- phenylethyl] adenosine, a selective ligand at A 1 receptors. Differences in the binding of this ligand and that of [ 3 H]5'-N- ethylcarboxamide adenosine, which binds to both A 1 and A 2 subtypes of receptors with similar affinities, were used to quantify A 2 receptors. Treatment with diazepam failed to alter the binding of [ 3 H]-N 6-[( R)-1- methyl-2- phenylethyl] adenosine in all areas of the brain studied. However, the binding of A 2 receptors and A 2 receptor-mediated stimulation of adenylate-cyclase were significantly attenuated in striatal membranes from diazepam-treated rats. Thus, the present study indicated that functional adenosine A 2 receptors were desensitized after prolonged treatment with diazepam, since decreased agonist binding to A 2 receptors paralleled an attenuation in the stimulation by adenosine of the activity of adenylate cyclase, an effect mediated by the A 2 receptor. These results further indicate that the changes in adenosine A 2 receptors correlated with significant short-lasting alterations in the sleep-wake cycle during the withdrawal of diazepam. The alterations in sleep-wakefulness did not correlate with the effect of diazepam on benzodiazepine receptors since no changes were observed in the binding of benzodiazepine receptors.