Three-dimensional models for beta-adrenergic receptor complexes with agonists and antagonists

Structural Basis and Mechanism of Chiral Benzedrine Molecules Interacting With Third Dopamine Receptor

In order to investigate the chiral benzedrine molecules corresponding to their different characteristics in biochemical systems, we studied their interaction with D3 R using the docking method, molecular dynamic simulation, and quantum chemistry. The obtained results indicate that the active residues for R-benzedrine (RAT) bound with D3 R are Ala132, Asp133, and Tyr55, while Asn57, Asp133, Asp168, Cys172, Gly54, Trp24, and Vall136 act as the active residues for S-benzedrine (SAT). The different active pockets are observed for ART or SAT because they possess different active residues. The binding energies between RAT and SAT with D3 R were determined to be -44.0 kJ.mol(-1) and -71.2 kJ.mol(-1) , respectively. These results demonstrate that SAT within the studied pocket of D3 R has a stronger capability of binding with D3 R, while it is more feasible for RAT to leave from the interior positions of D3 R. In addition, the results suggest that the D3 R protein can recognize chiral benzedrine molecules and influence their different addictive and pharmacological effects in biochemical systems. Chirality 28:674-685, 2016. © 2016 Wiley Periodicals, Inc.

Computational study on the different ligands induced conformation change of β2 adrenergic receptor-Gs protein complex

β₂ adrenergic receptor (β₂AR) regulated many key physiological processes by activation of a heterotrimeric GTP binding protein (Gs protein). This process could be modulated by different types of ligands. But the details about this modulation process were still not depicted. Here, we performed molecular dynamics (MD) simulations on the structures of β₂AR-Gs protein in complex with different types of ligands. The simulation results demonstrated that the agonist BI-167107 could form hydrogen bonds with Ser203^5.42, Ser207^5.46 and Asn293^6.55 more than the inverse agonist ICI 118,551. The different binding modes of ligands further affected the conformation of β₂AR. The energy landscape profiled the energy contour map of the stable and dissociated conformation of Gαs and Gβγ when different types of ligands bound to β₂AR. It also showed the minimum energy pathway about the conformational change of Gαs and Gβγ along the reaction coordinates. By using interactive essential dynamics analysis, we found that Gαs and Gβγ domain of Gs protein had the tendency to separate when the inverse agonist ICI 118,551 bound to β₂AR. The α5-helix had a relatively quick movement with respect to transmembrane segments of β₂AR when the inverse agonist ICI 118,551 bound to β₂AR. Besides, the analysis of the centroid distance of Gαs and Gβγ showed that the Gαs was separated from Gβγ during the MD simulations. Our results not only could provide details about the different types of ligands that induced conformational change of β₂AR and Gs protein, but also supplied more information for different efficacies of drug design of β₂AR.

Docking studies of novel pyrazinopyridoindoles class of antihistamines with the homology modelled H(1)-receptor

Histamine is an important neurotransmitter as it controls a multitude of physiological functions by activating specific receptors on target cells. It exerts its effects by binding to four different histamine receptors (H(1)-H(4)), which all belong to the large family of G protein-coupled receptors (GPCRs). Research and development of H(1) ligand has largely focused on antagonists which are used for their anti-allergy effects in the periphery. Recent understanding of the clinical importance of H(1) receptors in brain, however, suggests the pharmacotherapeutic potential of H(1) agonists in neurodegenerative and neuropsychiatric disorders. Despite the therapeutic importance of the H(1) receptor, for many years the molecular features of the H(1) receptor protein had been unknown. In view of the recently reported crystal structure of human H(1) receptor and in continuation of our work on 3D-pharmacophore on antihistamine H(1) and homology model of histamine H(1) receptor, docking studies have been carried out on some promising pyrazinopyridoindole class of antihistamine H(1), including two outliers, to validate our earlier reported models/hypotheses on H(1)-receptor, where a good explanation between estimated and observed activities has been obtained. In addition, the docking study also provided insights about the optimal activity of the outliers, for which no explanation was reported previously.

Do crystal structures obviate the need for theoretical models of GPCRs for structure-based virtual screening?

Recent highly expected structural characterizations of agonist-bound and antagonist-bound beta-2 adrenoreceptor (β2AR) by X-ray crystallography have been widely regarded as critical advances to enable more effective structure-based discovery of GPCRs ligands. It appears that this very important development may have undermined many previous efforts to develop 3D theoretical models of GPCRs. To address this question directly, we have compared several historical β2AR models versus the inactive state and nanobody-stabilized active state of β2AR crystal structures in terms of their structural similarity and effectiveness of use in virtual screening for β2AR specific agonists and antagonists. Theoretical models, incluing both homology and de novo types, were collected from five different groups who have published extensively in the field of GPCRs modeling. All models were built before X-ray structures became available. In general, β2AR theoretical models differ significantly from the crystal structure in terms of TMH definition and the global packing. Nevertheless, surprisingly, several models afforded hit rates resulting from virtual screening of large chemical library enriched by known β2AR ligands that exceeded those using X-ray structures. The hit rates were particularly higher for agonists. Furthemore, the screening performance of models is associated with local structural quality, such as the RMSDs for binding pocket residues and the ability to capture accurately, most if not all critical protein/ligand interactions. These results suggest that carefully built models of GPCRs could capture critical chemical and structural features of the binding pocket, and thus may be even more useful for practical structure-based drug discovery than X-ray structures.

β(3)-Adrenoceptor agonists and (antagonists as) inverse agonists history, perspective, constitutive activity, and stereospecific binding

β(3)-Adrenergic receptor (β(3)-AR) is expressed in several tissues and is considered a drug target for the treatment of several pathologies such as obesity, type 2 diabetes, cachexia, metabolic syndrome, heart failure, anxiety and depressive disorders, preterm labor, overactive bladder, control colon motility, and of coadjuvants in colon cancer therapy. It is a seven-transmembrane domain (7TD) G-protein coupled receptor and is usually coupled to a Gs-protein (Gi-protein in very few cases), and its stimulation increases the production of cAMP. A lot of β(3)-AR agonists have been uncovered and extensively characterized. Conversely, very little is known about β(3)-AR inverse agonists that would suppress the agonist-independent activity (constitutive activity) of the receptor by stabilizing it in its inactive state. This chapter attempts to outline (a) the importance of the β(3)-AR as a therapeutic target through the disquisition of its role in human health (physiology) and disease (pathology); (b) the description of β(3)-AR structure [amino acid sequence and 7TD organization]; (c) the medicinal chemistry of β(3)-AR: 7TD amino acid-ligand specific interactions, β-adrenoreceptor subtype selectivity, stereospecific interactions and biological activity relationships, inverse agonism and blockage of β(3)-adrenoceptor constitutive activity; and (d) β(3)-AR inverse agonists. The detailed procedure to prepare and assess the biological activity/selectivity of the more potent and selective β(3)-AR inverse agonists (SP-1e and SP-1g) up to now known is also described.

An efficient asymmetric synthesis of the potent beta-blocker ICI-118,551 allows the determination of enantiomer dependency on biological activity

A highly efficient, practical and flexible two-step asymmetric synthesis of the beta(2)-selective beta-blocker ICI 118,551 is reported, allowing an unambiguous determination of the dependency of biological activity with optical activity, revealing the S,S-enantiomer to be the most potent.

Molecular docking and molecular dynamics simulation studies of GPR40 receptor-agonist interactions

In order to explore the agonistic activity of small-molecule agonists to GPR40, AutoDock and GROMACS software were used for docking and molecular dynamics studies. A molecular docking of eight structurally diverse agonists (six carboxylic acids (CAs) agonist, and two non-carboxylic acids (non-CAs) agonist) was performed and the differences in their binding modes were investigated. Moreover, a good linear relationship based on the predicted binding affinities (pK(i)) determined by using AutoDock and experimental activity values (pEC50) was obtained. Then, the 10ns molecular dynamics (MD) simulations of three obtained ligand-receptor complexes embedded into the phospholipid bilayer were carried out. The position fluctuations of the ligands located inside the transmembrane domain were explored, and the stable binding modes of the three studied agonists were determined. Furthermore, the residue-based decomposition of interaction energies in three systems identified several critical residues for ligand binding.

Comparative molecular field analysis of fenoterol derivatives: A platform towards highly selective and effective beta(2)-adrenergic receptor agonists

PURPOSE

To use a previously developed CoMFA model to design a series of new structures of high selectivity and efficacy towards the beta(2)-adrenergic receptor.

RESULTS

Out of 21 computationally designed structures 6 compounds were synthesized and characterized for beta(2)-AR binding affinities, subtype selectivities and functional activities.

CONCLUSION

the best compound is (R,R)-4-methoxy-1-naphthylfelnoterol with K(i)beta(2)-AR=0.28microm, K(i)beta(1)-AR/K(i)beta(2)-AR=573, EC(50cAMP)=3.9nm, EC(50cardio)=16nm. The CoMFA model appears to be an effective predictor of the cardiomocyte contractility of the studied compounds which are targeted for use in congestive heart failure.

Comparative 3D QSAR study on β(1)-, β(2)-, and β(3)-adrenoceptor agonists

A quantitative structure–activity relationship study of tryptamine-based derivatives of β₁-, β₂-, and β₃-adrenoceptor agonists was conducted using comparative molecular field analysis (CoMFA). Correlation coefficients (cross-validated r²) of 0.578, 0.595, and 0.558 were obtained for the three subtypes, respectively, in three different CoMFA models. All three CoMFA models have different steric and electrostatic contributions, implying different requirements inside the binding cavity. The CoMFA coefficient contour plots of the three models and comparisons among these plots provide clues regarding the main chemical features responsible for the biological activity variations and also result in predictions which correlate very well with the observed biological activity. Based on the analysis, a summary regeospecific description of the requirements for improving β-adrenoceptor subtype selectivity is given.

Biological evaluation of 10-(diphenylmethylene)- 4-azatricyclo[5.2.1.02,6]dec-8-ene-3,5-dione derivatives

Antibacterial and antifungal activity of 10-(diphenylmethylene)-4-azatricyclo[5.2.1.02,6]dec-8-ene-3,5-dione derivatives were examined by the disc-diffusion method (growth inhibition zone diameter in agar medium). The MIC’s for the most active agents were determined. Title compounds were also evaluated in vitro against representatives of different virus classes. Most of the tested compounds exhibit activity against CVB-2 virus.

Sweet taste in man: a review

A greater understanding of the molecular mechanisms of sweet taste has profound significance for the food industry as well as for consumers. Understanding the mechanism by which sweet taste is elicited by saccharides, peptides, and proteins will assist science and industry in their search for sweet substances with fewer negative health effects. The original AH-B theories have been supplanted by detailed structural models. Recent identification of the human sweet receptor as a dimeric G-protein coupled receptor comprising T1R2 and T1R3 subunits has greatly increased the understanding of the mechanisms involved in sweet molecule binding and sweet taste transduction. This review discusses early theories of the sweet receptor, recent research of sweetener chemoreception of nonprotein and protein ligands, homology modeling, the transduction pathway, the possibility of the sweet receptor functioning allosterically, as well as the implications of allelic variation.

Discovery of novel human histamine H4 receptor ligands by large-scale structure-based virtual screening

A structure-based virtual screening (SBVS) was conducted on a ligand-supported homology model of the human histamine H4 receptor (hH4R). More than 8.7 million 3D structures derived from different vendor databases were investigated by docking to the hH4R binding site using FlexX. A total of 255 selected compounds were tested by radioligand binding assay and 16 of them possessed significant [(3)H]histamine displacement. Several novel scaffolds were identified that can be used to develop selective H4 ligands in the future. As far as we know, this is the first SBVS reported on H4R, representing one of the largest virtual screens validated by the biological evaluation of the virtual hits.

Use of the X-ray structure of the Beta2-adrenergic receptor for drug discovery

The recently reported X-ray structure of the Beta2-adrenergic receptor, the first reported crystal structure of a ligand-mediated GPCR, is used to explore its utility in computer-aided drug design. Validations were conducted with known beta blockers. This was followed by high-throughput docking studies with proprietary and commercial databases to further validate the X-ray structure's usefulness as a design tool and to explore the potential for discovery of novel chemical classes acting as Beta2 inhibitors. Our results include the finding of ligands with traditional beta-blocker motifs as well as new motifs, thereby serving to both validate the approach and project its usefulness in the finding and design of novel compounds.

High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor

Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors constitute the largest family of eukaryotic signal transduction proteins that communicate across the membrane. We report the crystal structure of a human beta2-adrenergic receptor-T4 lysozyme fusion protein bound to the partial inverse agonist carazolol at 2.4 angstrom resolution. The structure provides a high-resolution view of a human G protein-coupled receptor bound to a diffusible ligand. Ligand-binding site accessibility is enabled by the second extracellular loop, which is held out of the binding cavity by a pair of closely spaced disulfide bridges and a short helical segment within the loop. Cholesterol, a necessary component for crystallization, mediates an intriguing parallel association of receptor molecules in the crystal lattice. Although the location of carazolol in the beta2-adrenergic receptor is very similar to that of retinal in rhodopsin, structural differences in the ligand-binding site and other regions highlight the challenges in using rhodopsin as a template model for this large receptor family.

Comparative Molecular Field Analysis of the Binding of the Stereoisomers of Fenoterol and Fenoterol Derivatives to the β2Adrenergic Receptor

Stereoisomers of fenoterol and six fenoterol derivatives have been synthesized and their binding affinities for the beta2 adrenergic receptor (Kibeta2-AR), the subtype selectivity relative to the beta1-AR (Kibeta1-AR/Kibeta2-AR) and their functional activities were determined. Of the 26 compounds synthesized in the study, submicromolar binding affinities were observed for (R,R)-fenoterol, the (R,R)-isomer of the p-methoxy, and (R,R)- and (R,S)-isomers of 1-naphthyl derivatives and all of these compounds were active at submicromolar concentrations in cardiomyocyte contractility tests. The Kibeta1-AR/Kibeta2-AR ratios were >40 for (R,R)-fenoterol and the (R,R)-p-methoxy and (R,S)-1-naphthyl derivatives and 14 for the (R,R)-1-napthyl derivative. The binding data was analyzed using comparative molecular field analysis (CoMFA), and the resulting model indicated that the fenoterol derivatives interacted with two separate binding sites and one steric restricted site on the pseudo-receptor and that the chirality of the second stereogenic center affected Kibeta2 and subtype selectivity.

Structural determinants for ligand-receptor conformational selection in a peptide G protein-coupled receptor

G protein coupled receptors (GPCRs) modulate the majority of physiological processes through specific intermolecular interactions with structurally diverse ligands and activation of differential intracellular signaling. A key issue yet to be resolved is how GPCRs developed selectivity and diversity of ligand binding and intracellular signaling during evolution. We have explored the structural basis of selectivity of naturally occurring gonadotropin-releasing hormones (GnRHs) from different species in the single functional human GnRH receptor. We found that the highly variable amino acids in position 8 of the naturally occurring isoforms of GnRH play a discriminating role in selecting receptor conformational states. The human GnRH receptor has a higher affinity for the cognate GnRH I but a lower affinity for GnRH II and GnRHs from other species possessing substitutions for Arg(8). The latter were partial agonists in the human GnRH receptor. Mutation of Asn(7.45) in transmembrane domain (TM) 7 had no effect on GnRH I affinity but specifically increased affinity for other GnRHs and converted them to full agonists. Using molecular modeling and site-directed mutagenesis, we demonstrated that the highly conserved Asn(7.45) makes intramolecular interactions with a highly conserved Cys(6.47) in TM 6, suggesting that disruption of this intramolecular interaction induces a receptor conformational change which allosterically alters ligand specific binding sites and changes ligand selectivity and signaling efficacy. These results reveal GnRH ligand and receptor structural elements for conformational selection, and support co-evolution of GnRH ligand and receptor conformations.

Role of group-conserved residues in the helical core of beta2-adrenergic receptor

G protein-coupled receptors (GPCRs) belonging to class A contain several highly conserved (>90%) amino acids in their transmembrane helices. Results of mutational studies of these highly conserved residues suggest a common mechanism for locking GPCRs in an inactive conformation and for their subsequent activation upon ligand binding. Recently, a second set of sites in the transmembrane helices has been identified in which amino acids with small side chains, such as Gly, Ala, Ser, Thr, and Cys, are highly conserved (>90%) when considered as a group. These group-conserved residues have not been recognized as having essential structural or functional roles. To determine the role of group-conserved residues in the beta(2)-adrenergic receptor (beta(2)-AR), amino acid replacements guided by molecular modeling were carried out at key positions in transmembrane helices H2-H4. The most significant changes in receptor expression and activity were observed upon replacement of the amino acids Ser-161 and Ser-165 in H4. Substitution at these sites by larger residues lowered the expression and activity of the receptor but did not affect specific binding to the antagonist ligand dihydroalprenolol. A second site mutation, V114A, rescued the low expression of the S165V mutant. Substitution of other group-conserved residues in H2-H4 by larger amino acids lowered receptor activity in the order Ala-128, Ala-76, Ser-120, and Ala-78. Together these data provide comprehensive analysis of group-conserved residues in a class A GPCR and allow insights into the roles of these residues in GPCR structure and function.

Novel chiral isoxazole derivatives: Synthesis and pharmacological characterization at human β-adrenergic receptor subtypes

Isoxazole derivative (+/-)-4 and the three pairs of stereoisomeric 3-bromo-isoxazolyl amino alcohols (S,R)-(-)-7a/(R,R)-(+)-7b, (S,R)-(-)-8a/(R,R)-(+)-8b, and (S,R)-(-)-9a/(R,R)-(+)-9b were synthesized and assayed for their affinity and efficacy at human beta(1)-, beta(2)-, and beta(3)-adrenergic receptors (beta-ARs) in membranes from Chinese hamster ovary (CHO) cells stably transfected with the respective receptor subtype. Whereas derivative (+/-)-4 did not bind at all three beta-ARs, stereoisomers (S,R)-7a-(S,R)-9a behaved as high-affinity ligands at beta(1)- and, particularly, at beta(2)-ARs (K(i) 2.82-66.7 nM). The K(i) values of isomers (R,R)-7b-(R,R)-9b at beta(1)- and beta(2)-subtypes were about 30-100 times higher than those of their (S,R)-7a-9a counterparts, indicating a sizable stereochemical effect. The affinity at beta(3)-ARs was negligible for all the investigated compounds. When submitted to a functional assay, the three stereoisomeric pairs showed a comparable pattern of efficacy at all three beta-AR subtypes. The highest value of efficacy (75-90%) was observed at beta(2)-ARs, whereas all compounds behaved as partial agonists (30-60%) at the beta(3)-subtype. The lowest degree of efficacy (15-35%) was found at beta(1)-ARs. The affinity/efficacy profile of the derivatives under study has been compared with that of the two model compounds, Broxaterol [(+/-)-1] and BRL 37344 [(+/-)-6].

Modeling and active site refinement for G protein-coupled receptors: application to the β-2 adrenergic receptor

It is well known that G protein-coupled receptors are prime targets for drug discovery. At the present time there is only one protein from this class that has an X-ray crystal structure, bovine rhodopsin. Crystal structures of rhodopsin have become invaluable templates for the modeling of class-A G protein-coupled receptors as they likely represent the overall topology of this family of proteins. However, because of low sequence homology within the class and the inherent mobility of integral membrane proteins, it is unlikely that this single structural template reflects the ensemble of conformations accessible for any given receptor. We have devised a procedure based upon comparative modeling that uses induced fit modeling coupled with binding site expansion. The modeling protocol enables an ensemble approach to binding mode prediction. The utility of models for beta-2 adrenergic receptor will be discussed.

I want a new drug: G-protein-coupled receptors in drug development

Huey Lewis and the News summed it up nicely in their 1980s hit record: 'I want a new drug, one that won't make me sick, one that won't make me crash my car, or make me feel three feet thick'. The song could be an anthem for drug discovery in the pharmaceutical industry. We all want new and better drugs with fewer side effects, which are effective for combating the major diseases of our time: cancer, heart disease, obesity and autoimmune diseases. How do we get these new drugs? There are currently some new ideas in drug discovery, centered on that staple diet of the pharmaceutical industry, the G-protein-coupled receptor (GPCR) superfamily. In silico methods, employing receptor-based modeling, offer a more rational approach in the design of drugs targeting GPCRs. These approaches can be used to understand receptor selectivity and species specificity of drugs that interact with GPCRs. In addition, there are various novel approaches, such as the design and potential utility of drugs that target more than one GPCR ('dual specificity' drugs).

Three-dimensional models of histamine H3 receptor antagonist complexes and their pharmacophore

Molecular modeling was used to analyze the binding mode and activities of histamine H3 receptor antagonists. A model of the H3 receptor was constructed through homology modeling methods based on the crystal structure of bovine rhodopsin. Known H3 antagonists were interactively docked into the putative antagonist binding pocket and the resultant model was subjected to molecular mechanics energy minimization and molecular dynamics simulations which included a continuum model of the lipid bilayer and intra- and extracellular aqueous environments surrounding the transmembrane helices. The transmembrane helices stayed well embedded in the dielectric slab representing the lipid bilayer and the intra- and extracellular loops remain situated in the aqueous solvent region of the model during molecular dynamics simulations of up to 200 ps in duration. A pharmacophore model was calculated by mapping the features common to three active compounds three-dimensionally in space. The 3D pharmacophore model complements our atomistic receptor/ligand modeling. The H3 antagonist pharmacophore consists of two protonation sites (i.e. basic centers) connected by a central aromatic ring or hydrophobic region. These two basic sites can simultaneously interact with Asp 114 (3.32) in helix III and a Glu 206 (5.46) in helix V which are believed to be the key residues that histamine interacts with to stabilize the receptor in the active state. The interaction with Glu 206 is consistent with the enhanced activity resulting from the additional basic site. In addition to these two salt bridging interactions, the central region of these antagonists contains a lipophilic group, usually an aromatic ring, that is found to interact with several nearby hydrophobic side chains. The picture of antagonist binding provided by these models is consistent with earlier pharmacophore models for H3 antagonists with some exceptions.

Molecular evolution of adrenoceptors and dopamine receptors: implications for the binding of catecholamines

We derived homology models for all human catecholamine-binding GPCRs (CABRs; the alpha-1, alpha-2, and beta-adrenoceptors and the D1-type and D2-type dopamine receptor) using the bovine rhodopsin-11-cis-retinal X-ray structure. Interactions were predicted from the endogenous ligands norepinephrine or dopamine and from the binding site and were used to optimize receptor-ligand interactions. Similar binding modes in the complexes agree with a large "binding core" conserved across the CABRs, that is, D3.32, V(I)3.33, T3.37, S5.42, S(A/C)5.43, S5.46, F6.51, F6.52, and W6.48. Model structures and docking simulations suggest that extracellular loop 2 could provide a common attachment point for the ligands' beta-hydroxyl via a hydrogen bond donated by the main-chain NH group of residue xl2.52. The modeled CABRs and docking modes are in good agreement with published experimental studies. Complementarity between the ligand and the binding site suggests that the bovine rhodopsin structure is a suitable template for modeling agonist-bound CABRs.

Virtual screening of biogenic amine-binding G-protein coupled receptors: comparative evaluation of protein- and ligand-based virtual screening protocols

In this paper, we compare protein- and ligand-based virtual screening techniques for identifying the ligands of four biogenic amine-binding G-protein coupled receptors (GPCRs). For the screening of the virtual compound libraries, we used (1) molecular docking into GPCR homology models, (2) ligand-based pharmacophore and Feature Tree models, (3) three-dimensional (3D)-similarity searches, and (4) statistical methods [partial least squares (PLS) and partial least squares discriminant analysis (PLS-DA) models] based on two-dimensional (2D) molecular descriptors. The comparison of the different methods in retrieving known antagonists from virtual libraries shows that in our study the ligand-based pharmacophore-, Feature Tree-, and 2D quantitative structure-activity relationship (QSAR)-based screening techniques provide enrichment factors that are higher than those provided by molecular docking into the GPCR homology models. Nevertheless, the hit rates achieved when docking with GOLD and ranking the ligands with GoldScore (up to 60% among the top-ranked 1% of the screened databases) are still satisfying. These results suggest that docking into GPCR homology models can be a useful approach for lead finding by virtual screening when either little or no information about the active ligands is available.

Identification of Determinants of Ligand Binding Affinity and Selectivity in the Prostaglandin D2 Receptor CRTH2

The chemoattractant receptor-homologous molecule expressed on Th2 cells (CRTH2) is a G protein-coupled receptor that mediates the pro-inflammatory effects of prostaglandin D(2) (PGD(2)) generated in allergic inflammation. The CRTH2 receptor shares greatest sequence similarity with chemoattractant receptors compared with prostanoid receptors. To investigate the structural determinants of CRTH2 ligand binding, we performed site-directed mutagenesis of putative mCRTH2 ligand-binding residues, and we evaluated mutant receptor ligand binding and functional properties. Substitution of alanine at each of three residues in the transmembrane (TM) helical domains (His-106, TM III; Lys-209, TM V; and Glu-268, TM VI) and one in extracellular loop II (Arg-178) decreased PGD(2) binding affinity, suggesting that these residues play a role in binding PGD(2). In contrast, the H106A and E268A mutants bound indomethacin, a nonsteroidal anti-inflammatory drug, with an affinity similar to the wild-type receptor. HEK293 cells expressing the H106A, K209A, and E268A mutants displayed reduced inhibition of intracellular cAMP and chemotaxis in response to PGD(2), whereas the H106A and E268A mutants had functional responses to indomethacin similar to the wild-type receptor. Binding of PGE(2) by the E268A mutant was enhanced compared with the wild-type receptor, suggesting that Glu-268 plays a role in determining prostanoid ligand selectivity. Replacement of Tyr-261 with phenylalanine did not affect PGD(2) binding but decreased the binding affinity for indomethacin. These results provided the first details of the ligand binding pocket of an eicosanoid-binding chemoattractant receptor.

Long-chain formoterol analogues: an investigation into the effect of increasing amino-substituent chain length on the beta2-adrenoceptor activity

The synthesis of a series of long-chain formoterol analogues in which the terminal ether residue of the beta-phenethyl-amino-substituent has been extended beyond the methyl ether residue present in the parent compound are described. Evaluation of these analogues as beta(2)-adrenoceptor agonists was used to provide an insight into the factors controlling the magnitude and duration of receptor activation.

Site-directed mutagenesis of the rat beta1-adrenoceptor. Involvement of Tyr356 (7.43) in (+/-)cyanopindolol but not (+/-)[125Iodo]cyanopindolol binding

To determine the role played by Tyr(356 (7.43)) in the rat beta(1)-adrenoceptor in binding the antagonists (+/-)cyanopindolol (4-[3-(t-butylamino]-3-(2'-cyano-indoloxy)-2-propanolol) and its iodinated analogue (+/-)[(125)Iodo]cyanopindolol (1-(t-butylamino]-3-(2'-cyano-3'-iodo-indoloxy)-2-propanolol), Tyr(356 (7.43)) was mutated to either Phe or Ala and binding affinities determined for wild type and mutant rat beta(1)-adrenoceptors. Our results indicate that Tyr(356 (7.43)) is important for (+/-)cyanopindolol, but not (+/-)[(125)Iodo]cyanopindolol, binding and that (+/-)cyanopindolol adopts a "reverse" binding orientation whereas (+/-)[(125)Iodo]cyanopindolol cannot be accommodated in this binding mode. We define a "reverse" antagonist binding mode as one where the aryloxy moiety interacts with residues on transmembrane helices 1, 2, 3 and 7. The beta(1)-adrenoceptor site-directed mutagenesis results are the first to support a "reverse" antagonist binding orientation and the involvement of Tyr(356 (7.43)) in this binding mode.

Structure-based Drug Discovery Using GPCR Homology Modeling: Successful Virtual Screening for Antagonists of the Alpha1A Adrenergic Receptor

In this paper, we describe homology modeling of the alpha1A receptor based on the X-ray structure of bovine rhodopsin. The protein model has been generated by applying ligand-supported homology modeling, using mutational and ligand SAR data to guide the protein modeling procedure. We performed a virtual screening of the company's compound collection to test how well this model is suited to identify alpha1A antagonists. We applied a hierarchical virtual screening procedure guided by 2D filters and three-dimensional pharmacophore models. The ca. 23,000 filtered compounds were docked into the alpha1A homology model with GOLD and scored with PMF. From the top-ranked compounds, 80 diverse compounds were tested in a radioligand displacement assay. 37 compounds revealed K(i) values better than 10 microM; the most active compound binds with 1.4 nM to the alpha1A receptor. Our findings suggest that rhodopsin-based homology models may be used as the structural basis for GPCR lead finding and compound optimization.

Characterization of β3-adrenergic receptor: determination of pharmacophore and 3D QSAR model for β3 adrenergic receptor agonism

The beta3-adrenoreceptor (beta3-AR) has been shown to mediate various pharmacological and physiological effects such as lipolysis, thermogenesis, and intestinal smooth muscle relaxation. It also plays an important role in glucose homeostasis and energy balance. Molecular modeling studies were undertaken to develop predictive pharmacophoric hypothesis and 3D-QSAR model, which may explain variations in beta3-AR agonistic activity in terms of chemical features and physicochemical properties. The two softwares, CATALYST for pharmacophoric alignment and APEX-3D for 3D-QSAR modeling were used to establish the structure activity relationships for beta3-AR agonistic activity. Among the several statistically significant models, the selection of the best pharmacophore and 3D-QSAR model was based on its ability to estimate the activity of external test sets of similar and different structural types along with the reasonable consistency of the model with the limited information of the active site of beta3-AR. The final 3D-QSAR model was derived using the pharmacophoric alignments from the hypothesis which consisted of four chemical features: basic or positive ionizable feature on the nitrogen of the aryloxypropylamino group, two ring aromatic features corresponding to the phenyl ring of the phenoxide and the benzenesulphonamido groups and a hydrogen-bond donor (HBD) in the vicinity of the nitrogen atom of the benzenesulphonamido group with the most active molecule mapping in an energetically favorable extended conformation. This hypothesis was in agreement with the site directed mutagenesis studies on human beta3-AR and correlated well the observed and estimated activity both in, training and both the external test sets. It also mapped reasonably well to six beta3-AR agonists of different structural classes under clinical development and thus this hypothesis may have a universal applicability in providing a powerful template for virtual screening and also for designing new chemical entities (NCEs) as beta3-AR agonists.

Purine receptors: GPCR structure and agonist design

An integrated approach to the study of drug-receptor interactions has been applied to adenosine receptors (ARs) and P2Y nucleotide receptors. This approach includes probing the receptor structure through site-directed mutagenesis and molecular modeling, in concert with altering the structure of the agonist ligands. Goals of this structural approach are to generate a testable hypothesis for location of the binding site and subsequently to enable the rational design of new agonists and antagonists. In this manner, receptor subtype selectivity has been increased, and agonists have been converted into partial agonists and antagonists. An approach to receptor engineering (neoceptors) has been explored, in which synthetic small molecule agonists (neoligands) are specifically tailored to activate only receptors in which the putative binding sites have been modified. This orthogonal approach to receptor activation, intended for eventual gene therapy, has been demonstrated for A3 and A2A ARs.

Structural determinants of arylacetic acid nonsteroidal anti-inflammatory drugs necessary for binding and activation of the prostaglandin D2 receptor CRTH2

The chemoattractant receptor-homologous molecule expressed on Th2 cells (CRTH2) receptor, a G protein-coupled receptor that mediates chemotaxis of inflammatory cells in response to prostaglandin D2 (PGD2), is hypothesized to play a role in Th2-mediated allergic disease. In addition to PGD2, CRTH2 can be activated by indomethacin, a nonselective cyclooxygenase inhibitor and widely used nonsteroidal anti-inflammatory drug (NSAID). To evaluate the structural features that confer CRTH2 binding selectivity, structure-activity relationship analysis of arylacetic acid class NSAIDs as CRTH2 receptor ligands was performed. Indomethacin, sulindac sulfide, and zomepirac displaced [3H]PGD2 binding at the mouse CRTH2 receptor (mCRTH2) with comparable affinity (Ki = 1.5 +/- 0.1, 2.5 +/- 0.4, and 3.3 +/- 0.3 microM, respectively). The indomethacin metabolite 5'-O-desmethyl indomethacin (5'-DMI) possessed binding affinity similar to indomethacin; however, elimination of the 2-methyl substituent on the indole ring resulted in a 10-fold decrease in binding affinity. No binding was detected for indole acetic acid and indole derivatives such as tryptophan, serotonin, and 5-hydroxy indole acetic acid, demonstrating the importance of the N-acyl moiety of indomethacin. Neutral derivatives of indomethacin also failed to bind to mCRTH2, suggesting that the negatively charged carboxylate moiety participates in a key ligand-receptor interaction. Despite similar binding affinities, NSAID-type mCRTH2 ligands exhibited variable potencies as mCRTH2 agonists. Sulindac sulfide and 5'-DMI inhibited intracellular cyclic AMP ([cAMP]i) generation and stimulated cell migration comparable with indomethacin. In contrast, zomepirac did not inhibit [cAMP]i generation or stimulate cell migration but weakly antagonized the effects of indomethacin on [cAMP]i. Together, these results reveal structural features of arylacetic acid NSAIDs that may be exploited for the development of selective CRTH2 ligands.

Agonist binding and activation of the rat beta(1)-adrenergic receptor: role of Trp(134(3.28)), Ser(190(4.57)) and Tyr(356(7.43))

We investigated the role of Trp(134(3.28)), Ser(190(4.57)) and Tyr(356(7.43)) in agonist binding to, and activation of, the rat beta(1)-adrenergic receptor by comparing pK(i)s and functional responses of W134A, S190A and Y356F mutant receptors to wild type, all stably expressed in CHO cells. All three mutations significantly (P < 0.05) reduced adenylyl cyclase intrinsic activity (IA) compared to wild type in response to stimulation with both (-)-isoprenaline (53-88%) and (-)-RO363 (46-61%), and there was no significant correlation either between IA or pD(2) and pK(i) (P > 0.4), suggesting that changes in pK(i) were not sufficient to explain the fall in adenylyl cyclase activity. The most pronounced reduction in affinity (126-fold, P < 0.01) was displayed by xamoterol for the Y356F mutation, suggesting that xamoterol is able to directly interact with Tyr(356(7.43)). For the other agonists, the change in pK(i) values for the mutant receptors ranged from a 20-fold decrease to a 2-fold increase compared to the wild type. In a three-dimensional model of the rat beta(1)-adrenergic receptor, Trp(134(3.28)) and Tyr(356(7.43)) form part of a hydrophobic binding pocket involving residues in transmembrane helices 1, 2, 3 and 7. Our results suggest that Trp(134(3.28)) and Tyr(356(7.43)), together with Trp(353(7.40)), are able to interact via pi-pi interactions to stabilize the extracellular ends of transmembrane helices 3 and 7. Ser(190(4.57)) appears to be involved in a hydrogen bonding network, which maintains the spatial relationship between transmembrane helices 3 and 4. These interhelical interactions suggest that the three mutated residues stabilize the active receptor state by maintaining the proper packing of their respective transmembrane helix within the helix bundle, facilitating the appropriate movement and rotation of the transmembrane regions during the activation process.

Ligand-Binding Modes in Cationic Biogenic Amine Receptors

The binding site in G protein-coupled cationic biogenic amine receptors is formed in the cleft of the seven transmembrane segments. Upon binding the ligand, the receptors are activated or inactivated through the conformational changes of the transmembrane segments. G protein-coupled receptors bind four functionally distinct ligands; inverse agonists, antagonists, partial agonists, and full agonists. Hence, putative structural models for biogenic amine receptors corresponding to the ligand function (inverse agonist-, antagonist-, partial agonist-, and full agonist-bound receptor models) were built by using photointermediate models in the rhodopsin photocascade (M. Ishiguro et al. ChemBioChem. 2004, 5, 298-310). The ligand-receptor recognition of each was examined by modeling receptor-ligand complexes with functional ligands. The complex models suggested that each functional ligand binds the corresponding receptor structure and that ligand-specific interactions contribute to stabilization of the corresponding receptor structure.

A virtual screening approach to finding novel and potent antagonists at the melanin-concentrating hormone 1 receptor

Melanin-concentrating hormone (MCH) has been known to be an appetite-stimulating peptide for a number of years. However, it is only recently that MCH has been discovered to be the natural ligand for a previously "orphan" G-protein-coupled receptor, now designated MCH-1R. This receptor has been shown to mediate the effects of MCH on appetite and body weight, and consequently, drug discovery programs have begun to exploit this information in the search for MCH-1R antagonists for the treatment of obesity. In this paper, we report the rapid discovery of multiple, structurally distinct series of MCH-1R antagonists using a variety of virtual screening techniques. The most potent of these compounds (12) demonstrated an IC(50) value of 55 nM in the primary screen and exhibited antagonist properties in a functional cellular assay measuring Ca(2+) release. More potent compounds were identified by follow-up searches around the initial hit. A proposed binding mode for compound 12 in a homology model of the MCH-1R is also presented.