Nanosensing of Fcγ receptors on macrophages

Determining the distribution of specific binding sites on biological samples with high spatial accuracy (in the order of several nanometer) is an important challenge in many fields of biological science. Combination of high-resolution atomic force microscope (AFM) topography imaging with single-molecule force spectroscopy provides a unique possibility for the detection of specific molecular recognition events. The identification and localization of specific receptor binding sites on complex heterogeneous biosurfaces such as cells and membranes are of particular interest in this context. Simultaneous topography and recognition imaging was used to unravel the nanolandscape of cells of the immune system such as macrophages. The most studied phagocytic receptors include the Fc receptors that bind to the Fc portion of immunoglobulins. Here, nanomapping of FcγRs (Fc receptors for immunoglobulin G (IgG)) was performed on fixed J774.A1 mouse macrophage cell surfaces with magnetically coated AFM tips functionalized with Fc fragments of mouse IgG via long and flexible poly(ethylene glycol) linkers. Because of possible AFM tip engulfment on living macrophages, appropriate cell fixation procedure leaving the binding activity of FcγRs practically intact was elaborated. The recognition maps revealed prominent spots (microdomains) more or less homogeneously distributed on the macrophage surface with the sizes from 4 to 300 nm. Typical recognition image contained about ∼4% of large clusters (>200 nm), which were surrounded by a massive number (∼50%) of small-size (4–30 nm) and the rest by middle-size (50, 150 nm) domains. These spots were detected from the decrease of oscillation amplitude during specific binding between Fc-coated tip and FcγRs on macrophage surfaces. In addition, the effect of osmotic swelling on the topographical landscape of macrophage surfaces and on the reorganization of FcγRs was investigated.     

Structure Analysis of Streptococcal Protein G Fc Binding Domain

The gene fragment (191 bp) encoding protein G IgG Fc binding domain was isolated by PCR from group G streptococcus (CMCC32138), and a clone containing this gene fragment was found to give fine reactivity to human IgG when expressed in Escherichia coli. The complete nucleotide sequence of the gene fragment was determined. One base pair differs from previously reported protein Gnucleotide sequences, and resultsin an amino acid change (Ala-Thr), but this variation makes no difference in binding to the IgG Fc part by ELISA.The secondary structure of the protein G IgG Fc binding domain has been estimated by circular dichroism and assigned by computer algorithm.It shows a typical α-helix region in this domain.By breaking this α-helix region with recombinant DNA techniques, a 44 peptide, which contained the N-terminal 27 amino acid residues of this domain, was expressed in E. coli and showed no reactivity to IgG.The hydropathicity of this domain was also analyzed and compared with that of protein A relevant     

Engineered Bacterial Fc Receptors

Five new-type Fc receptor molecules were constructed based on streptococcal protein G (SpG) and staphylococcal protein A (SpA). These protein molecules contain one to six Fc binding domains to immunoglobulins which are structurally different from native SpG or SpA. Their expression levels reached 17-30% of the total bacterial proteins after heat induction in E. colt. Immunodiffusion and ELISA results showed that the engineered protein TG (184 amino acid residues) composed of three SpG C3 domain could bind more broadly and efficiently than the native SpG to the IgGs of human, goat, rabbit, etc. , and its optimal pH for binding became wider (pH5-8) compared with the SpG (pH5) ; and the protein TGA (357AA), fused by protein TG and the A, B, C domains of SpA, displayed both the binding pattern of SpG and SpA.     

Importance of inter-residue interactions in ligand—receptor binding

In the present study, the role of inter-residue interactions in ligand binding and the ligand—receptor interactions were examined. Computational chemistry methods of ligand docking and molecular dynamics simulations were used to study the binding of β-funaltrexamine (β-FNA) and N-methyl-β-funaltrexamine (N-methyl-β-FNA) to μ- and κ-opioid receptors and to the μ-receptor with Lys303^6.58Glu mutation. It was found that inter-residue interactions Lys233^5.39—Glu303^6.58 in the mutant receptor and Lys227^5.39—Asp223^5.35 in the κ-receptor are more likely to prevent covalent bond formation between β-FNA and the receptor than the ligand-receptor interactions. This emphasizes the importance of inter-residue interactions in ligand binding as well as the effects of point-mutations.     

Selective detection of F− by chromogenic tetrazole receptor

A chromogenic anion host 4, containing two amide functionalities linked to azo dye and tetrazole rings, was synthesised and its complexes with various anions were investigated. The results show that receptor 4 can recognise selectively biologically important F^?  ion. The binding affinity for F^?  was investigated by naked-eye colour change, UV–vis and ¹H NMR spectroscopy. Addition of F^?  ion in CH₃CN and Dimethyl sulfoxide to receptor 4 causes a change in colour of the solution from colourless to yellow. The stoichiometry for host:anion is 1:1. Furthermore, receptor 4 was used as an ion carrier in ion-selective membrane electrodes. Selectivity of this membrane was studied towards various anions in water solution. Binding behaviour of receptor 4 towards several anions (Cl^? , F^? , Br^? , I^? ) has been investigated using density functional theory calculations.     

Free energy calculations offer insights into the influence of receptor flexibility on ligand–receptor binding affinities

Docking algorithms for computer-aided drug discovery and design often ignore or restrain the flexibility of the receptor, which may lead to a loss of accuracy of the relative free enthalpies of binding. In order to evaluate the contribution of receptor flexibility to relative binding free enthalpies, two host–guest systems have been examined: inclusion complexes of α-cyclodextrin (αCD) with 1-chlorobenzene (ClBn), 1-bromobenzene (BrBn) and toluene (MeBn), and complexes of DNA with the minor-groove binding ligands netropsin (Net) and distamycin (Dist). Molecular dynamics simulations and free energy calculations reveal that restraining of the flexibility of the receptor can have a significant influence on the estimated relative ligand–receptor binding affinities as well as on the predicted structures of the biomolecular complexes. The influence is particularly pronounced in the case of flexible receptors such as DNA, where a 50% contribution of DNA flexibility towards the relative ligand–DNA binding affinities is observed. The differences in the free enthalpy of binding do not arise only from the changes in ligand–DNA interactions but also from changes in ligand–solvent interactions as well as from the loss of DNA configurational entropy upon restraining.     

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.     

Single-molecule imaging reveals the stoichiometry change of epidermal growth factor receptor during transactivation by β_2-adrenergic receptor

Stimulation of G protein-coupled receptors(GPCRs) can lead to the transactivation of the epidermal growth factor receptors(EGFR). The cross-communication between the two signaling pathways regulates several important physiological or pathological processes. However, the molecule mechanism underlying EGFR transactivation remains poorly understood. Here, we aim to study the GPCR-mediated EGFR transactivation process using the single-molecule fluorescence imaging and tracking approach.We found that although EGFR existed as monomers at the plasma membrane of resting cells, they became dimers and thus diffused slower following the activation of β2-adrenergic receptor(β2-AR) by isoproterenol(ISO). We further proved thatβ2-AR-mediated changes of EGFR in stoichiometry and dynamics were mediated by Src kinase. Thus, the observations obtained via the single-molecule imaging and tracking methods shed new insights into the molecular mechanism of EGFR transactivation at single molecule level.     

A chemoenzymatic approach to the synthesis of the stereoisomers of a β-adrenergic receptor antagonist

The four stereoisomers of Δ²-isoxazoline 2, a β-adrenergic receptor antagonist structurally related to Falintolol 1, were prepared by an enzyme-catalyzed kinetic resolution of the unsaturated secondary alcohol (±)-7 followed by its cycloaddition to pyruvonitrile oxide. Through this strategy, diastereomeric aminoalcohols (+)-2a/(−)-2b and (−)-2a/(+)-2b were obtained in 99 and 92% enantiomeric excess, respectively. The absolute configuration to the target compounds was assigned via chemical correlation to the enantiomers of epoxides 4a and 4b, whose stereochemistry had been previously established.     

Molecular modeling of neurokinin B and tachykinin NK₃ receptor complex

The tachykinin receptor NK? is a member of the rhodopsin family of G-protein coupled receptors. The NK? receptor has been regarded as an important drug target due to diverse physiological functions and its possible role in the pathophysiology of psychiatric disorders, including schizophrenia. The NK3 receptor is primarily activated by the tachykinin peptide hormone neurokinin B (NKB) which is the most potent natural agonist for the NK? receptor. NKB has been reported to play a vital role in the normal human reproduction pathway and in potentially life threatening diseases such as pre-eclampsia and as a neuroprotective agent in the case of neurodegenerative diseases. Agonist binding to the receptor is a critical event in initiating signaling, and therefore a characterization of the structural features of the agonists can reveal the molecular basis of receptor activation and help in rational design of novel therapeutics. In this study a molecular model for the interaction of the primary ligand NKB with its G-protein coupled receptor NK? has been developed. A three-dimensional model for the NK? receptor has been generated by homology modeling using rhodopsin as a template. A knowledge based docking of the NMR derived bioactive conformation of NKB to the receptor has been performed utilizing limited ligand binding data obtained from photoaffinity labeling and site-directed mutagenesis studies. A molecular model for the NKB-NK? receptor complex obtained sheds light on the topographical features of the binding pocket of the receptor and provides insight into the biochemical data currently available for the receptor.     

Synthesis of CJ-15,208, a novel κ-opioid receptor antagonist

The tryptophan isomers of the cyclic tetrapeptide CJ-15,208, reported to be a kappa opioid receptor (KOR) antagonist [Saito, T.; Hirai, H.; Kim, Y. J.; Kojima, Y.; Matsunaga, Y.; Nishida, H.; Sakakibara, T.; Suga, O.; Sujaku, T.; Kojima, N. J. Antibiot. (Tokyo)2002, 55, 847-854.], were synthesized to determine the tryptophan stereochemistry in the natural product. A strategy was developed to select linear precursor peptides that favor cyclization using molecular modeling, and optimized cyclization conditions are reported. The optical rotation of the l-Trp isomer is consistent with that of the natural product. Unexpectedly both isomers exhibit similar nanomolar affinity for KOR.     

Analysis of Fas–ligand interactions using a molecular model of the receptor–ligand interface

A molecular model of the complex between Fas and its ligand was generated to better understand the location and putative effects of site-specific mutations, analyze interactions at the Fas–FasL interface, and identify contact residues. The modeling study was conservative in the sense that regions in Fas and its ligand which could not be predicted with confidence were omitted from the model to ensure accuracy of the analysis. Using the model, it was possible to map four of five N-linked glycosylation sites in Fas and FasL and to study 10 of 11 residues previously identified by mutagenesis as important for binding. Interactions involving six of these residues could be analyzed in detail and their importance for binding was rationalized based on the model. The predicted structure of the Fas–FasL interface was consistent with the experimentally established importance of these residues for binding. In addition, five previously not targeted residues were identified and predicted to contribute to binding via electrostatic interactions. Despite its limitations, the study provided a much improved basis to understand the role of Fas and FasL residues for binding compared to previous residue mapping studies using only a molecular model of Fas.     

“In silico” study of the binding of two novel antagonists to the nociceptin receptor

Antagonists of the nociceptin receptor (NOP) are raising interest for their possible clinical use as antidepressant drugs. Recently, the structure of NOP in complex with some piperidine-based antagonists has been revealed by X-ray crystallography. In this study, a multi-flexible docking (MF-docking) procedure, i.e. docking to multiple receptor conformations extracted by preliminary molecular dynamics trajectories, together with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have been carried out to provide the binding mode of two novel NOP antagonists, one of them selective (BTRX-246040, formerly named LY-2940094) and one non selective (AT-076), i.e. able to inactivate NOP as well as the classical µ- k- and δ-opioid receptors (MOP KOP and DOP). According to our results, the pivotal role of residue D130^3,32 (upper indexes are Ballesteros–Weinstein notations) is analogous to that enlighten by the already known X-ray structures of opioid receptors: binding of the molecules are predicted to require a slight readjustment of the hydrophobic pocket (residues Y131^3,33, M134^3,36, I219^5,43, Q280^6,52 and V283^6,55) in the orthosteric site of NOP, accommodating either the pyridine–pyrazole (BTRX-246040) or the isoquinoline (AT-076) moiety of the ligand, in turn allowing the protonated piperidine nitrogen to maximize interaction (salt-bridge) with residue D130^3,32 of the NOP, and the aromatic head to be sandwiched in optimal π-stacking between Y131^3,33 and M134^3,36. The QM/MM optimization after the MF-docking procedure has provided the more likely conformations for the binding to the NOP receptor of BTRX-246040 and AT-076, based on different pharmacophores and exhibiting different selectivity profiles. While the high selectivity for NOP of BTRX-246040 can be explained by interactions with NOP specific residues, the lack of selectivity of AT-076 could be associated to its ability to penetrate into the deep hydrophobic pocket of NOP, while retaining a conformation very similar to the one assumed by the antagonist JDTic into the K-opioid receptor. The proposed binding geometries fit better the binding pocket environment providing clues for experimental studies aimed to design selective or multifunctional opioid drugs.     

Encapsulation of trivalent phosphate anion within a rigidified π-stacked dimeric capsular assembly of tripodal receptor

The tris(thiourea) receptor, L, in the presence of excess H(2)PO(4)(-) has been found to encapsulate a trivalent phosphate ion within a π-stacked dimeric capsular assembly of the receptor with twelve strong H-bonds via deprotonation, as evident from the origin of a new set of signals in the (1)H NMR titration experiments.     

Synthesis of RGD analogues containing α-Tfm-arginine as potential fibrinogen receptor antagonists

The synthesis of two peptide mimetics of RGD, α-Tfm-Arg-Gly-Asp-Phe-NH₂ 9 and α-Tfm-Arg-Gly-Asp-NH-(CH₂)₂-C₆H₅ 13, is described. The precursor of α-Tfm-ornithine was obtained in two synthetic steps from 2-N-Cbz-2-Tfm-hexanediacid-1-alkyl ester and introduced into the peptide chain by α-carboxy-group activation via oxazolone. The introduction of the guanidine residue led to the final peptides as mixtures of the two diastereomers. Configurationally pure peptides were obtained in good yields by RP-HPLC.     

The agonistic binding site at the histamine H2 receptor. II. Theoretical investigations of histamine binding to receptor models of the seven α-helical transmembrane domain

Summary In the first part (pp. 461–478 in this issue) of this study regarding the histamine H₂ receptor agonistic binding site, the best possible interactions of histamine with an -helical oligopeptide, mimicking a part of the fifth transmembrane -helical domain (TM5) of the histamine H₂ receptor, were considered. It was established that histamine can only bind via two H-bonds with a pure -helical TM5, when the binding site consists of Tyr¹⁸²/Asp¹⁸⁶ and not of the Asp¹⁸⁶/Thr¹⁹⁰ couple. In this second part, two particular three-dimensional models of G-protein-coupled receptors previously reported in the literature are compared in relation to agonist binding at the histamine H₂ receptor. The differences between these two receptor models are discussed in relation to the general benefits and limitations of such receptor models. Also the pros and cons of simplifying receptor models to a relatively easy-to-deal-with oligopeptide for mimicking agonistic binding to an agonistic binding site are addressed. Within complete receptor models, the simultaneous interaction of histamine with both TM3 and TM5 can be analysed. The earlier suggested three-point interaction of histamine with the histamine H₂ receptor can be explored. Our results demonstrate that a three-point interaction cannot be established for the Asp⁹⁸/Asp¹⁸⁶/Thr¹⁹⁰ binding site in either of the investigated receptor models, whereas histamine can form three H-bonds in case the agonistic binding site is constituted by the Asp⁹⁸/Tyr¹⁸²/Asp¹⁸⁶ triplet. Furthermore this latter triplet is seen to be able to accommodate a series of substituted histamine analogues with known histamine H₂ agonistic activity as well.     

Discovery of α7-nicotinic receptor ligands by virtual screening of the chemical universe database GDB-13

The chemical universe database GDB-13 enumerates 977 million organic molecules up to 13 atoms of C, N, O, Cl, and S that are virtually possible following simple rules for chemical stability and synthetic feasibility. Analogs of nicotine were identified in GDB-13 using the city-block distance in MQN-space (CBD(MQN)) as a similarity measure, combined with a restriction eliminating problematic structural elements. The search was carried out with a Web browser available at www.gdb.unibe.ch . This virtual screening procedure selected 31?504 analogs of nicotine from GDB-13, from which 48 were known nicotinic ligands reported in Chembl. An additional 60 virtual screening hits were purchased and tested for modulation of the acetylcholine signal at the human α7 nAChR expressed in Xenopus oocytes, which led to the identification of three previously unknown inhibitors. These experiments demonstrate for the first time the use of GDB-13 for ligand discovery.