On homology modeling of the M2 muscarinic acetylcholine receptor subtype

Twelve homology models of the human M₂ muscarinic receptor using different sets of templates have been designed using the Prime program or the modeller program and compared to crystallographic structure (PDB:3UON). The best models were obtained using single template of the closest published structure, the M₃ muscarinic receptor (PDB:4DAJ). Adding more (structurally distant) templates led to worse models. Data document a key role of the template in homology modeling. The models differ substantially. The quality checks built into the programs do not correlate with the RMSDs to the crystallographic structure and cannot be used to select the best model. Re-docking of the antagonists present in crystallographic structure and relative binding energy estimation by calculating MM/GBSA in Prime and the binding energy function in YASARA suggested it could be possible to evaluate the quality of the orthosteric binding site based on the prediction of relative binding energies. Although estimation of relative binding energies distinguishes between relatively good and bad models it does not indicate the best one. On the other hand, visual inspection of the models for known features and knowledge-based analysis of the intramolecular interactions allows an experimenter to select overall best models manually.     

A Three‐Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors

Molecular‐dynamics simulations with metadynamics enhanced sampling reveal three distinct binding sites for arginine vasopressin (AVP) within its V₂‐receptor (V₂R). Two of these, the vestibule and intermediate sites, block (antagonize) the receptor, and the third is the orthosteric activation (agonist) site. The contacts found for the orthosteric site satisfy all the requirements deduced from mutagenesis experiments. Metadynamics simulations for V₂R and its V_1aR‐analog give an excellent correlation with experimental binding free energies by assuming that the most stable binding site in the simulations corresponds to the experimental binding free energy in each case. The resulting three‐site mechanism separates agonists from antagonists and explains subtype selectivity.     

A Photoswitchable Dualsteric Ligand Controlling Receptor Efficacy

The investigation of the mode and time course of the activation of G-protein-coupled receptors (GPCRs), in particular muscarinic acetylcholine (mACh or M) receptors, is still in its infancy despite the tremendous therapeutic relevance of M receptors and GPCRs in general. We herein made use of a dualsteric ligand that can concomitantly interact with the orthosteric, that is, the neurotransmitter, binding site and an allosteric one. We synthetically incorporated a photoswitchable (photochromic) azobenzene moiety. We characterized the photophysical properties of this ligand called BQCAAI and investigated its applicability as a pharmacological tool compound with a set of FRET techniques at the M₁ receptor. BQCAAI proved to be an unprecedented molecular tool; it is the first photoswitchable dualsteric ligand, and its activity can be regulated by light. We also applied BQCCAI to investigate the time course of several receptor activation processes.     

Homology modelling of the human adenosine A2B receptor based on X-ray structures of bovine rhodopsin, the β2-adrenergic receptor and the human adenosine A2A receptor

A three-dimensional model of the human adenosine A_2B receptor was generated by means of homology modelling, using the crystal structures of bovine rhodopsin, the β₂-adrenergic receptor, and the human adenosine A_2A receptor as templates. In order to compare the three resulting models, the binding modes of the adenosine A_2B receptor antagonists theophylline, ZM241385, MRS1706, and PSB601 were investigated. The A_2A-based model was much better able to stabilize the ligands in the binding site than the other models reflecting the high degree of similarity between A_2A and A_2B receptors: while the A_2B receptor shares about 21% of the residues with rhodopsin, and 31% with the β₂-adrenergic receptor, it is 56% identical to the adenosine A_2A receptor. The A_2A-based model was used for further studies. The model included the transmembrane domains, the extracellular and the intracellular hydrophilic loops as well as the terminal domains. In order to validate the usefulness of this model, a docking analysis of several selective and nonselective agonists and antagonists was carried out including a study of binding affinities and selectivities of these ligands with respect to the adenosine A_2A and A_2B receptors. A common binding site is proposed for antagonists and agonists based on homology modelling combined with site-directed mutagenesis and a comparison between experimental and calculated affinity data. The new, validated A_2B receptor model may serve as a basis for developing more potent and selective drugs.     

The Antagonist pGlu-βGlu-Pro-NH2 Binds to an Allosteric Site of the Thyrotropin-Releasing Hormone Receptor

After we identified pGlu-βGlu-Pro-NH₂ as the first functional antagonist of the cholinergic central actions of the thyrotropin-releasing hormone (TRH, pGlu-His-Pro-NH₂), we became interested in finding the receptor-associated mechanism responsible for this antagonism. By utilizing a human TRH receptor (hTRH-R) homology model, we first refined the active binding site within the transmembrane bundle of this receptor to enhance TRH’s binding affinity. However, this binding site did not accommodate the TRH antagonist. This directed us to consider a potential allosteric binding site in the extracellular domain (ECD). Searches for ECD binding pockets prompted the remodeling of the extracellular loops and the N-terminus. We found that different trajectories of ECDs produced novel binding cavities that were then systematically probed with TRH, as well as its antagonist. This led us to establish not only a surface-recognition binding site for TRH, but also an allosteric site that exhibited a selective and high-affinity binding for pGlu-βGlu-Pro-NH₂. The allosteric binding of this TRH antagonist is more robust than TRH’s binding to its own active site. The findings reported here may shed light on the mechanisms and the multimodal roles by which the ECD of a TRH receptor is involved in agonist and/or antagonist actions.     

A homology-based model of the human 5-HT2A receptor derived from an in silico activated G-protein coupled receptor

A homology-based model of the 5-HT_2A receptor was produced utilizing an activated form of the bovine rhodopsin (Rh) crystal structure [1,2]. In silico activation of the Rh structure was accomplished by isomerization of the 11-cis-retinal (1) chromophore, followed by constrained molecular dynamics to relax the resultant high energy structure. The activated form of Rh was then used as a structural template for development of a human 5-HT_2A receptor model. Both the 5-HT_2A receptor and Rh are members of the G-protein coupled receptor (GPCR) super-family. The resulting homology model of the receptor was then used for docking studies of compounds representing a cross-section of structural classes that activate the 5-HT_2A receptor, including ergolines, tryptamines, and amphetamines. The ligand/receptor complexes that ensued were refined and the final binding orientations were observed to be compatible with much of the data acquired through both diversified ligand design and site directed mutagenesis.     

Synthesis,Biological Evaluation,and Docking Studies of Antagonistic Hydroxylated Arecaidine Esters Targeting mAChRs

The muscarinic acetylcholine receptor family is a highly sought-after target in drug and molecular imaging discovery efforts aimed at neurological disorders. Hampered by the structural similarity of the five subtypes’ orthosteric binding pockets, these efforts largely failed to deliver subtype-selective ligands. Building on our recent successes with arecaidine-derived ligands targeting M₁, herein we report the synthesis of a related series of 11 hydroxylated arecaidine esters. Their physicochemical property profiles, expressed in terms of their computationally calculated CNS MPO scores and HPLC-logD values, point towards blood–brain barrier permeability. By means of a competitive radioligand binding assay, the binding affinity values towards each of the individual human mAChR subtypes hM₁–hM₅ were determined. The most promising compound of this series 17b was shown to have a binding constant towards hM₁ in the single-digit nanomolar region (5.5 nM). Similar to our previously reported arecaidine-derived esters, the entire series was shown to act as hM1R antagonists in a calcium flux assay. Overall, this study greatly expanded our understanding of this recurring scaffolds’ structure–activity relationship and will guide the development towards highly selective mAChRs ligands.     

Parameterization of Org27569: An allosteric modulator of the cannabinoid CB1 G protein‐coupled receptor

The cannabinoid CB₁ receptor is a class A G protein‐coupled receptor (GPCR) that is the most widely expressed GPCR in the brain. Many GPCRs contain allosteric binding sites for endogenous and/or synthetic ligands, which are topographically distinct from the agonist‐binding site that is known as the orthosteric site. While both endogenous and synthetic ligands that act at the CB₁ orthosteric site have been known for some time, compounds that act at a CB₁ allosteric site have only recently been discovered. The most studied of these is 5‐chloro‐3‐ethyl‐1H‐indole‐2‐carboxylic acid [2‐(4‐piperidin‐1‐ylphenyl)ethyl]amide (Org27569). Because allosteric ligands are thought to act through conformational changes in the receptor that are transmitted from the allosteric to the orthosteric site, computational studies of the structural and dynamic interactions of Org27569 with the CB₁ receptor are crucial to achieve a molecular level understanding of the basis of action of this important new class of compounds. To date, such computational studies have not been possible due to the lack of a complete set of molecular mechanics force field parameters for Org27569. Here, we present the development of missing CHARMM force field parameters for Org27569 using previously published methods and the validation and application of these new parameters using normal mode analysis and molecular dynamics simulations combined with experimental infrared measurements. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Spectral and molecular docking studies of nucleic acids/protein binding interactions of a novel organometallic palladium (II) complex containing bioactive PTA ligands: Its synthesis,anticancer effects and encapsulation in albumin nanoparticles

The organometallic palladium complex with nitrogen-containing heterocycles is a potent antitumor agent. Coordination of phosphorus ligands to organometallic complexes increases their hydrophilicity, promotes ligand−DNA interactions and damage level to cancer cells, and blocks division in target cells. In this study, a phosphaadamantane palladium complex ([Pd{(C,N)- (C₁₂H₈NH₂)} (PTA) Cl], PTA = 1,3,5-Triaza-7-phosphaadamantane) ( 2 ) was synthesized via the reaction of biologically active PTA with binuclear palladacycles [Pd₂{(C,N)-(C₁₂H₈NH₂)}₂(μ-Cl)₂] ( 1 ). In vitro studies of the complex with DNA (calf-thymus) explored by UV–Vis, emission titration, circular dichroism and helix melting methods showed that the complex interacts with DNA via an intercalative mechanism. Furthermore, competitive binding studies using warfarin, digoxin and ibuprofen site markers containing definite binding sites revealed the binding of the complex to site I on bovine serum albumin. The in vitro release mechanism of the palladium complex exhibited a biphasic pattern characterized by an initial burst release followed by a slower sustained release. Ultimately, in vitro evaluation of cytotoxicity and cell death showed that the complexes were able to decrease the viability of human cancer cell lines (MCF-7 and Jurkat) in a dose-dependent manner, but lower decreases were observed in the viability of normal fibroblast cells ASF-4 at the dosages evaluated. Finally, the order of in vitro anticancer activities was found to be consistent with the DNA-binding affinities.     

Subtle Modification of Imine-linked Helical Receptors to Significantly Alter their Binding Affinities and Selectivities for Chiral Guests

Aromatic helical receptors P- 1 and P- 2 were slightly modified by aerobic oxidation to afford new receptors P- 7 and P- 8 with right-handed helical cavities. This subtle modification induced significant changes in the binding properties for chiral guests. Specifically, P- 1 was reported to bind d -tartaric acid (K_a=35500 M⁻¹), used as a template, much strongly than l -tartaric acid (326 M⁻¹). In contrast, its modified receptor P- 7 exhibited significantly reduced affinities for d -tartaric acid (3600 M⁻¹) and l -tartaric acid (125 M⁻¹). More dramatic changes in the affinities and selectivities were observed for P- 2 and P- 8 upon binding of polyol guests. P- 2 was determined to selectively bind d -sorbitol (52000 M⁻¹) over analogous guests, but P- 8 showed no binding selectivity: d -sorbitol (1890 M⁻¹), l -sorbitol (3330 M⁻¹), d -arabitol (959 M⁻¹), l -arabitol (4970 M⁻¹) and xylitol (4960 M⁻¹) in 5% (v/v) DMSO/CH₂Cl₂ at 25±1 °C. These results clearly demonstrate that even subtle post-modifications of synthetic receptors may significantly alter their binding affinities and selectivities, in particular for guests of long and flexible chains.     

Synthesis of N‐Substituted Piperidine Salts as Potential Muscarinic Ligands for Alzheimer's Applications

Several heterocyclic N‐piperidine substituted salts were synthesized that were found to inhibit the specific binding of the antagonist [³H] quinuclidinyl benzilate in radioligand muscarinic binding assays (³H‐QNB) in bioassays. One of the heterocyclic salts, compound 7 , met the significance criteria in these assays (>50% inhibition) at 10 μM of the nonselective muscarinic antagonist (³H‐QNB) in cells of the Wistar rat cerebral cortex. Furthermore, this compound displayed 61% inhibition at 10 μM of the antagonist (³H‐QNB) for the M₅ receptor (IC₅₀ 6.34 μM, K_i 3.93 μM, n_H = 0.996) in human recombinant CHO cell lines. These data obtained from Ricerca Biosciences suggested that compound 7 was selective for the M₅ receptor. Another study from the Czech Academy of Sciences demonstrated that compound 7 was 3 to 8 times more potent at M₂ than other subtypes of muscarinic receptors in competition with antagonist N‐methylscopolamine and selective for the M₁ receptors over M₃ and M₅ in antagonizing accumulation of inositol phosphates induced by muscarinic agonist carbachol.     

An ion pair receptor showing remarkable enhancement of anion-binding strengths in the presence of alkali metal cations

An ion pair receptor was prepared by coupling of a diazacrown ether and a rigid biindole scaffold bearing hydrogen bond donors of two indole NHs. The former serves as the cation-binding site and the latter functions as the anion-binding site. The anion-binding affinities to the receptor, determined by ¹H NMR titration experiments in 10% (v/v) DMSO-d₆/CD₃CN at 24 ± 1 °C, have been greatly improved when an alkali metal cation binds to the adjacent diazacrown ether. For example, the association constant between chloride and receptor alone is 7 M⁻¹, but the magnitudes increase into 120 M⁻¹, 14,000 M⁻¹, and 6200 M⁻¹ in the presence of lithium, sodium, and potassium ions, respectively. The enhanced binding affinities must be attributed to electrostatic interactions by possibly forming contact ion pairs.     

The interaction of dansyl amino acids with bovine serum albumin

The interaction of 5-dimethylaminonaphthalene-1-sulfonyl (DNS or dansyl) amino acids with bovine serum albumin (BSA) was investigated by means of fluorescence measurements. Fluorometric titrations revealed that BSA has one high affinity site (binding constant,K _a=10⁵10⁶ M^–1), and other sites of lower affinity (K _a=10³10⁴ M^–1) for the probes. Static excitation and emission spectra, lifetimes, time resolved emission spectra, and anisotropy data indicated that the binding is stabilized mainly through fixation by the high affinity binding site. The binding constant significantly decreased with the increase of the spacer distance between the dansyl and anionic groups of the probe molecule. This observation was explained by considering the change of the electrostatic interaction between the anionic group of the probe and a cationic residue in the vicinity of the site.     

Allosteric Modulation of the CB1 Cannabinoid Receptor by Cannabidiol—A Molecular Modeling Study of the N-Terminal Domain and the Allosteric-Orthosteric Coupling

The CB₁ cannabinoid receptor (CB₁R) contains one of the longest N termini among class A G protein-coupled receptors. Mutagenesis studies suggest that the allosteric binding site of cannabidiol (CBD) involves residues from the N terminal domain. In order to study the allosteric binding of CBD to CB₁R we modeled the whole N-terminus of this receptor using the replica exchange molecular dynamics with solute tempering (REST2) approach. Then, the obtained structures of CB₁R with the N terminus were used for ligand docking. A natural cannabinoid receptor agonist, Δ⁹-THC, was docked to the orthosteric site and a negative allosteric modulator, CBD, to the allosteric site positioned between extracellular ends of helices TM1 and TM2. The molecular dynamics simulations were then performed for CB₁R with ligands: (i) CBD together with THC, and (ii) THC-only. Analyses of the differences in the residue-residue interaction patterns between those two cases allowed us to elucidate the allosteric network responsible for the modulation of the CB₁R by CBD. In addition, we identified the changes in the orthosteric binding mode of Δ⁹-THC, as well as the changes in its binding energy, caused by the CBD allosteric binding. We have also found that the presence of a complete N-terminal domain is essential for a stable binding of CBD in the allosteric site of CB₁R as well as for the allosteric-orthosteric coupling mechanism.     

Antagonist binding in the rat muscarinic receptor A study by docking and X-ray crystallography

A series of agonists to the rat muscarinic receptor have been docked computationally to the active site of a homology model of rat M1 muscarinic receptor. The agonists were modelled on the X-ray crystal structure of atropine, which is reported here and the docking studies are shown to reproduce correctly the order of experimental binding affinities for the agonists as well as indicate where there appear to be inconsistencies in the experimental data. The crystal and molecular structure of atropine (tropine tropate; -[hydroxymethyl]benzeneacetic acid 8-methyl[3.2.1]oct-3-yl ester C₁₇H₂₃NO₃) has been determined by X-ray crystallography using an automated Patterson search method, and refined by full-matrix least-squares to a final R of 0.0452 for 2701 independent observed reflections and 192 parameters using Mo K radiation, λ = 0.71073 Å at 150 K. The compound crystallises in space group Fdd2 with Z = 16 molecules per unit cell.     

Dinucleosides with Non‐Natural Backbones: A New Class of Ribonuclease A and Angiogenin Inhibitors

Ribonuclease A (RNase A) serves as a convenient model enzyme in the identification and development of inhibitors of proteins that are members of the ribonuclease superfamily. This is principally because the biological activity of these proteins, such as angiogenin, is linked to their catalytic ribonucleolytic activity. In an attempt to inhibit the biological activity of angiogenin, which involves new blood vessel formation, we employed different dinucleosides with varied non‐natural backbones. These compounds were synthesized by coupling aminonucleosides with dicarboxylic acids and amino‐ and carboxynucleosides with an amino acid. These molecules show competitive inhibition with inhibition constant (K_i) values of (59±3) and (155±5) μM for RNase A. The compounds were also found to inhibit angiogenin in a competitive fashion with corresponding K_i values in the micromolar range. The presence of an additional polar group attached to the backbone of dinucleosides was found to be responsible for the tight binding with both proteins. The specificity of different ribonucleolytic subsites were found to be altered because of the incorporation of a non‐natural backbone in between the two nucleosidic moieties. In spite of the replacement of the phosphate group by non‐natural linkers, these molecules were found to selectively interact with the ribonucleolytic site residues of angiogenin, whereas the cell binding site and nuclear translocation site residues remain unperturbed. Docked conformations of the synthesized compounds with RNase A and angiogenin suggest a binding preference for the thymine–adenine pair over the thymine–thymine pair.     

Nucleotide/Protein Interaction: Energetic and Structural Features of Na,K-ATPase

Microcalorimetric titrations allow to recognize and investigate high-affinity ligand binding to Na,K-ATPase. Titrations with the cardiac glycoside Ouabain, which acts as a specific inhibitor of the enzyme, have provided not only the thermodynamic parameters of high-affinity binding with a stoichiometric coefficient of about 0.6 but also evidence for low-affinity binding to the lipid. The marked enthalpic contribution of -95 kJ mol^-1 at 298.2 K is partially compensated by a large negative entropy change, attributed to an increased interaction between water and the protein. The calorimetric ADP and ATP titrations at 298.2 K are indicative of high-affinity nucleotide binding either in 3 mM NaCl, 3 mM MgCl₂ or at high ionic strength such as 120 mM choline chloride. However, no binding is detected in the buffer solution alone at low ionic strength. The affinities for ADP and ATP are similar, around 10⁶ M^-1 and the stoichiometric coefficients are close to that of Ouabain binding. The exothermic binding of ADP is characterized by a ΔH and ΔS value of -65 kJ mol^-1 and -100 J mol^-1 K^-1, respectively. TheΔH value for ATP binding is larger than for ADP and is compensated by a larger, unfavorable ΔS value. This leads to an enthalpy/entropy compensation, which could express that H-bond formation represents the major type of interaction. As for Ouabain, the negative ΔS values that are also characteristic of nucleotide binding can indicate an increase of solvate interaction with the protein due to a conformational transition occurring subsequent to the binding process. The resulting binding constants are discussed with regard to the results of other studies employing different techniques. A molecular interaction model for nucleotide binding is suggested. This revised version was published online in July 2006 with corrections to the Cover Date.     

Relative binding orientations of adenosine A1 receptor ligands — A test case for Distributed Multipole Analysis in medicinal chemistry

Summary The electrostatic properties of adenosine-based agonists and xanthine-based antagonists for the adenosine A₁ receptor were used to assess various proposals for their relative orientation in the unknown binding site. The electrostatic properties were calculated from distributed multipole representations of SCF wavefunctions. A range of methods of assessing the electrostatic similarity of the ligands were used in the comparison. One of the methods, comparing the sign of the potential around the two molecules, gave inconclusive results. The other approaches, however, provided a mutually complementary and consistent picture of the electrostatic similarity and dissimilarity of the molecules in the three proposed relative orientations. This was significantly different from the results obtained previously with MOPAC AM1 point charges. In the standard model overlay, where the aromatic nitrogen atoms of both agonists and antagonists are in the same position relative to the binding site, the electrostatic potentials are so dissimilar that binding to the same receptor site is highly unlikely. Overlaying the N⁶-region of adenosine with that near C8 of theophylline (the N⁶-C8 model) produces the greatest similarity in electrostatic properties for these ligands. However, N⁶-cyclopentyladenosine (CPA) and 1,3-dipropyl-8-cyclopentylxanthine (DPCPX) show greater electrostatic similarity when the aromatic rings are superimposed according to the flipped model, in which the xanthine ring is rotated around its horizontal axis. This difference is mainly attributed to the change in conformation of N⁶-substituted adenosines and could result in a different orientation for theophylline and DPCPX within the receptor binding site. However, it is more likely that DPCPX also binds according to the N⁶-C8 model, as this model gives the best steric overlay and would be favoured by the lipophilic forces, provided that the binding site residues could accommodate the different electrostatic properties in the N⁶/N7-region. Finally, we have shown that Distributed Multipole Analysis (DMA) offers a new, feasible tool for the medicinal chemist, because it provides the use of reliable electrostatic models to determine plausible relative binding orientations.Abbreviations DMA distributed multipole analysis - SCF self-consistent field - CPA N⁶-cyclopentyladenosine - DPCPX 1,3-dipropyl-8-cyclopentylxanthine - R-PIA R-1-phenyl-2-propyladenosine - S-PIA S-1-phenyl-2-propyladenosine     

Cancer-Associated Mutations of the Adenosine A2A Receptor Have Diverse Influences on Ligand Binding and Receptor Functions

The adenosine A_2A receptor (A_2AAR) is a class A G-protein-coupled receptor (GPCR). It is an immune checkpoint in the tumor micro-environment and has become an emerging target for cancer treatment. In this study, we aimed to explore the effects of cancer-patient-derived A_2AAR mutations on ligand binding and receptor functions. The wild-type A_2AAR and 15 mutants identified by Genomic Data Commons (GDC) in human cancers were expressed in HEK293T cells. Firstly, we found that the binding affinity for agonist NECA was decreased in six mutants but increased for the V275A mutant. Mutations A165V and A265V decreased the binding affinity for antagonist ZM241385. Secondly, we found that the potency of NECA (EC₅₀) in an impedance-based cell-morphology assay was mostly correlated with the binding affinity for the different mutants. Moreover, S132L and H278N were found to shift the A_2AAR towards the inactive state. Importantly, we found that ZM241385 could not inhibit the activation of V275A and P285L stimulated by NECA. Taken together, the cancer-associated mutations of A_2AAR modulated ligand binding and receptor functions. This study provides fundamental insights into the structure–activity relationship of the A_2AAR and provides insights for A_2AAR-related personalized treatment in cancer.     

Molecular Alliance—From Orthosteric and Allosteric Ligands to Dualsteric/Bitopic Agonists at G Protein Coupled Receptors

Cell‐membrane‐spanning G protein coupled receptors (GPCRs) belong to the most important therapeutic target structures. Endogenous transmitters bind from the outer side of the membrane to the “orthosteric” binding site either deep in the binding pocket or at the extracellular N‐terminal end of the receptor protein. Exogenous modulators that utilize a different, “allosteric”, binding site unveil a pathway to receptor subtype‐selectivity. However, receptor activation through the orthosteric area is often more powerful. Recently there has been evidence that orthosteric/allosteric, in other words “dualsteric”, hybrid compounds unite subtype selectivity and receptor activation. These “bitopic” modulators channelreceptor activation and subsequent intracellular signaling into a subset of possible routes. This concept offers access to GPCR modulators with an unprecedented receptor‐subtype and signaling selectivity profile and, as a consequence, to drugs with fewer side effects.