L-selectin — a signalling receptor for lipopolysaccharide

The activation of leukocytes by bacterial cell-wall lipopolysaccharide contributes to the pathogenesis of septic shock. We propose that in neutrophils, and possibly other leukocytes, L-selectin can act as a low-affinity lipopolysaccharide receptor. Inhibitors of L-selectin may therefore be of therapeutic value in treating this life-threatening condition.     

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.     

Towards β-selectivity in functional estrogen receptor antagonists

Based on the benzo[b]naphtho[1,2-d]furan and benzo[b]naphtho[1,2-d]thiophene frameworks, a series of ligands with different basic side chains (BSCs) has been synthesized and pharmacologically evaluated. Also, their binding modes have been modelled using docking techniques. It was found that the introduction of a BSC in these systems brings about a decrease of affinity for both estrogen receptors α and β in an in vitro competitive binding assay. However, two full antagonists of the estrogen receptor β ( and ) have been discovered, with potency in the low micromolar concentration in a cell-based luciferase reporter assay, and completely devoid of activity against the α receptor at the same concentration range. Differences in the ERα/ERβ binding modes have also been rationalized with the help of molecular modelling techniques. This interesting functional profile could be used to elucidate the physiological role of each ER subtype.     

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.     

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.     

Pharmacophore development for antagonists at α1 adrenergic receptor subtypes

Summary Many receptors, including ₁ adrenergic receptors, have a range of subtypes. This offers possibilities for the development of highly selective antagonists with potentially fewer detrimental effects. Antagonists developed for _1A receptors, for example, would have potential in the treatment of benign prostatic hyperplasia. As part of the molecular design process, structural features necessary for the selective affinity for _1A and _1B adrenergic receptors have been investigated. The molecular modelling software (particularly the Apex module) of Molecular Simulations, Inc. was used to develop pharmacophore models for these two subtypes. Low-energy conformations of a set of known antagonists were used as input, together with a classification of the receptor affinity data. The biophores proposed by the program were evaluated and pharmacophores were proposed. The pharmacophore models were validated by testing the fit of known antagonists, not included in the training set. The critical structural feature for selectivity between the _1A and _1B adrenergic receptor sites is the distance between the basic nitrogen atom and the centre of an aromatic ring system. This will be exploited in the design and synthesis of structurally new selective antagonists for these sites.     

Protein–small molecule docking with receptor flexibility in iMOLSDOCK

We have earlier reported the iMOLSDOCK technique to perform ‘induced-fit’ peptide–protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLSs) technique to sample the conformation and the docking pose of the small molecule ligand and also the flexible residues of the receptor protein, and arrive at the optimum pose and conformation. In this paper we report the extension carried out in iMOLSDOCK to dock nonpeptide small molecule ligands to receptor proteins. We have benchmarked and validated iMOLSDOCK with a dataset of 34 protein–ligand complexes as well as with Astex Diverse dataset, with nonpeptide small molecules as ligands. We have also compared iMOLSDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time. The source code and binary of MOLS 2.0 (under a GNU Lesser General Public License) are freely available for download at https://sourceforge.net/projects/mols2-0/files/.     

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.     

Peroxisome proliferator-activated receptor �� agonist attenuates hepatic steatosis by anti-inflammatory mechanism

Although peroxisome proliferator receptor (PPAR)-α and PPAR-γ agonist have been developed as chemical tools to uncover biological roles for the PPARs such as lipid and carbohydrate metabolism, PPAR-δ has not been fully investigated. In this study, we examined the effects of the PPAR-δ agonist GW0742 on fatty liver changes and inflammatory markers. We investigated the effects of PPAR-δ agonist GW0742 on fatty liver changes in OLETF rats. Intrahepatic triglyceride contents and expression of inflammatory cytokines such as tumor necrosis factor-α (TNF-α) and monocyte chemo-attractant protein-1 (MCP-1) and also, PPAR-γ coactivator (PGC)-1α gene were evaluated in liver tissues of OLETF rats and HepG2 cells after GW0742 treatment. The level of TNF-α and MCP-1 was also examined in supernatant of Raw264. 7 cell culture. To address the effects of GW0742 on insulin signaling, we performed in vitro study with AML12 mouse hepatocytes. Rats treated with GW0742 (10 mg/kg/day) from 26 to 36 weeks showed improvement in fatty infiltration of the liver. In liver tissues, mRNA expressions of TNF-α, MCP-1, and PGC-1α were significantly decreased in diabetic rats treated with GW0742 compared to diabetic control rats. We also observed that GW0742 had inhibitory effects on palmitic acid-induced fatty accumulation and inflammatory markers in HepG2 and Raw264.7 cells. The expression level of Akt and IRS-1 was significantly increased by treatment with GW0742. The PPAR-δ agonist may attenuate hepatic fat accumulation through anti-inflammatory mechanism, reducing hepatic PGC-1α gene expression, and improvement of insulin signaling.     

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.     

New quinoxaline derivatives as potential MT₁ and MT₂ receptor ligands

Ever since the idea arose that melatonin might promote sleep and resynchronize circadian rhythms, many research groups have centered their efforts on obtaining new melatonin receptor ligands whose pharmacophores include an aliphatic chain of variable length united to an N-alkylamide and a methoxy group (or a bioisostere), linked to a central ring. Substitution of the indole ring found in melatonin with a naphthalene or quinoline ring leads to compounds of similar affinity. The next step in this structural approximation is to introduce a quinoxaline ring (a bioisostere of the quinoline and naphthalene rings) as the central nucleus of future melatoninergic ligands.     

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.     

A new anion receptor utilising aromatic and aliphatic C…H hydrogen bonds

We have synthesised 2, which bound weakly basic halide ions only with C–H…anion hydrogen bonds. Compound 2 utilised one aromatic C–H hydrogen bond and one benzylic C–H hydrogen bond to bind weakly halide ions such as chloride, bromide and iodide in solution. Ab initio calculations of binding energy values for these anions are in good agreement with experimental data. Although the binding affinities of 2 for these anions were low, 2 could be a unique example of host, which utilised only C–H hydrogen bonds to bind anion.     

3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

Close attention has been paid to estrogen compounds because these chemicals may pose a serious threat to the health of humans and wildlife. Estrogen receptor (ER) exists as two subtypes, ERα and ERβ. The difference in amino acids sequence of the binding sites of ERα and ERβ might lead to a result that some synthetic estrogens and naturally occurring steroidal ligands have different relative affinities and binding modes for ERα and ERβ. In this investigation, comparative molecular similarity indices analysis...     

Fading of a novel colorimetric receptor after recognizing H2PO4−

A novel selective and sensitive colorimetric receptor 1 (1, 10-phenanthroline-2, 9-dialdehyde bis-(-p-nitrophenylureasemicarbo-hydrazone)) based on urea showing distinctive color fading phenomenon towards H₂PO₄^? ion was reported. Fancifully, the recognition process of receptor 1 to H₂PO₄^? was not interfered by the existence of others anions. We have probed the binding mechanism of 1-H₂PO₄^? that H₂PO₄^? ion induced competitive hydrogen binding process via intramolecular hydrogen-bond by UV–vis, fluorescence, ¹H NMR titrations and ESI-MS experiments.     

Colorimetric ��naked-eye�� sensor for anions based on conformational flexible tripodal receptor

A new tripodal receptor for anion sensing based on amide-pyridinium as recognition site and nitro-benzene as signaling unit was designed and successfully synthesized. This receptor showed high selectivity and strong binding affinity toward AcO^? over the investigated anions, especially over H₂PO₄ ^?. Addition of AcO^? induced clear color change of solution from colorless to yellow, realizing the ??naked-eye?? detection. UV?CVis and ¹H NMR experiments indicated the selectivity might origin from the synergistic effects arising from hydrogen bonding, electrostatic interactions and conformational change.     

Computational studies of new potential antimalarial compounds – Stereoelectronic complementarity with the receptor

One of the most important pharmacological mechanisms of antimalarial action is the inhibition of the aggregation of hematin into hemozoin. We present a group of new potential antimalarial molecules for which we have performed a DFT study of their stereoelectronic properties. Additionally, the same calculations were carried out for the two putative drug receptors involved in the referred activity, i.e., hematin mu-oxo dimer and hemozoin. A complementarity between the structural and electronic profiles of the planned molecules and the receptors can be observed. A docking study of the new compounds in relation to the two putative receptors is also presented, providing a correlation with the defined electrostatic complementarity.