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     

Universality of the Sodium Ion Binding Mechanism in Class A G‐Protein‐Coupled Receptors

The allosteric modulation of G‐protein‐coupled receptors (GPCRs) by sodium ions has received significant attention as crystal structures of several receptors show Na⁺ ions bound to the inactive conformations at the conserved Asp^2.50. To date, structures from 24 families of GPCRs have been determined, though mechanistic insights into Na⁺ binding to the allosteric site are limited. We performed hundreds‐of‐microsecond long simulations of 18 GPCRs and elucidated their Na⁺ binding mechanism. In class A GPCRs, the Na⁺ ion binds to the conserved residue 2.50 whereas in class B receptors, it binds at 3.43b, 6.53b, and 7.49b. Using Markov state models, we obtained the free energy profiles and kinetics of Na⁺ binding to the allosteric site, which reveal a conserved mechanism of Na⁺ binding for GPCRs and show the residues that act as major barriers for ion diffusion. Furthermore, we also show that the Na⁺ ion can bind to GPCRs from the intracellular side when the allosteric site is inaccessible from the extracellular side.     

Unwinding of the C‐Terminal Residues of Neuropeptide Y is critical for Y2 Receptor Binding and Activation

Despite recent breakthroughs in the structural characterization of G‐protein‐coupled receptors (GPCRs), there is only sparse data on how GPCRs recognize larger peptide ligands. NMR spectroscopy, molecular modeling, and double‐cycle mutagenesis studies were integrated to obtain a structural model of the peptide hormone neuropeptide Y (NPY) bound to its human G‐protein‐coupled Y₂ receptor (Y₂R). Solid‐state NMR measurements of specific isotope‐labeled NPY in complex with in vitro folded Y₂R reconstituted into phospholipid bicelles provided the bioactive structure of the peptide. Guided by solution NMR experiments, it could be shown that the ligand is tethered to the second extracellular loop by hydrophobic contacts. The C‐terminal α‐helix of NPY, which is formed in a membrane environment in the absence of the receptor, is unwound starting at T³² to provide optimal contacts in a deep binding pocket within the transmembrane bundle of the Y₂R.     

The Aminotriazole Antagonist Cmpd‐1 Stabilises a Distinct Inactive State of the Adenosine 2A Receptor

The widely expressed G‐protein coupled receptors (GPCRs) are versatile signal transducer proteins that are attractive drug targets but structurally challenging to study. GPCRs undergo a number of conformational rearrangements when transitioning from the inactive to the active state but have so far been believed to adopt a fairly conserved inactive conformation. Using ¹⁹F NMR spectroscopy and advanced molecular dynamics simulations we describe a novel inactive state of the adenosine 2A receptor which is stabilised by the aminotriazole antagonist Cmpd‐1. We demonstrate that the ligand stabilises a unique conformation of helix V and present data on the putative binding mode of the compound involving contacts to the transmembrane bundle as well as the extracellular loop 2.     

The Mechanism of Ligand‐Induced Activation or Inhibition of μ‐ and κ‐Opioid Receptors

G‐protein‐coupled receptors (GPCRs) are important targets for treating severe diseases. However why certain molecules act as activators whereas others, with similar structures, block GPCR activation, is poorly understood since the same molecule can activate one receptor subtype while blocking another closely related receptor. To shed light on these central questions, we used all‐atom, long‐time‐scale molecular dynamics simulations on the κ‐opioid and μ‐opioid receptors (κOR and μOR). We found that water molecules penetrating into the receptor interior mediate the activating versus blocking effects of a particular ligand–receptor interaction. Both the size and the flexibility of the bound ligand regulated water influx into the receptor. The solvent‐accessible inner surface area was found to be a parameter that can help predict the function of the bound ligand.     

In‐Membrane Chemical Modification (IMCM) for Site‐Specific Chromophore Labeling of GPCRs

We present in‐membrane chemical modification (IMCM) for obtaining selective chromophore labeling of intracellular surface cysteines in G‐protein‐coupled receptors (GPCRs) with minimal mutagenesis. This method takes advantage of the natural protection of most cysteines by the membrane environment. Practical use of IMCM is illustrated with the site‐specific introduction of chromophores for NMR and fluorescence spectroscopy in the human κ‐opioid receptor (KOR) and the human A_2A adenosine receptor (A_2AAR). IMCM is applicable to a wide range of in vitro studies of GPCRs, including single‐molecule spectroscopy, and is a promising platform for in‐cell spectroscopy experiments.     

Functional Dynamics of Deuterated β2‐Adrenergic Receptor in Lipid Bilayers Revealed by NMR Spectroscopy

G‐protein‐coupled receptors (GPCRs) exist in conformational equilibrium between active and inactive states, and the former population determines the efficacy of signaling. However, the conformational equilibrium of GPCRs in lipid bilayers is unknown owing to the low sensitivities of their NMR signals. To increase the signal intensities, a deuteration method was developed for GPCRs expressed in an insect cell/baculovirus expression system. The NMR sensitivities of the methionine methyl resonances from the β₂‐adrenergic receptor (β₂AR) in lipid bilayers of reconstituted high‐density lipoprotein (rHDL) increased by approximately 5‐fold upon deuteration. NMR analyses revealed that the exchange rates for the conformational equilibrium of β₂AR in rHDLs were remarkably different from those measured in detergents. The timescales of GPCR signaling, calculated from the exchange rates, are faster than those of receptor tyrosine kinases and thus enable rapid neurotransmission and sensory perception.     

Theoretical investigation on the spectroscopic properties of furylfulgide with different substituents and design of novel bis‐furylfulgimide photochromes

Density functional theory and time‐dependent density functional theory were employed to theoretically analyze the effect of different substituents on the spectroscopic properties of furylfulgide. The result shows that the absorption spectra of ring‐closed isomer which substituted by an electron‐donating group (NH₂) at the R₃‐position of furylfulgide has an evident bathochromic shift compared with the others. Due to the steric hindrance effect, the difference of absorption wavelength was evidently enlarged by introducing several representative electron‐withdrawing groups at the R₆‐position of furylfulgide. In addition, we also designed a series of novel dimers which combined two furylfulgimide monomers into one new molecule. The relevant frontier molecular orbitals, energy levels and absorption properties were analyzed in detail by the calculation of low‐lying excited states. Finally, taking BFF‐6 (bis‐furylfulgimide) for an example, we discussed the transformation mechanism of four stable isomers in the toluene solution. Our conclusions manifest that the asymmetrical BFF‐6 can act as a potential multifunctional molecular switch in consideration of its distinguishable absorption bands and reversible conversion process. We hope that this research will be beneficial to design more practical and efficient molecular switch for further applications.     

Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A<Subscript>2A</Subscript> adenosine receptor orthosteric binding site using a molecular docking approach? Insights from <Emphasis Type="Italic">Dockbench</Emphasis>

The allosteric modulation of G protein-coupled receptors (GPCRs) by sodium ions has received considerable attention as crystal structures of several receptors, in their inactive conformation, show a Na⁺ ion bound to specific residues which, in the human A_2A adenosine receptor (hA_2A AR), are Ser91^3.39, Trp246^6.48, Asn280^7.45, and Asn284^7.49. A cluster of water molecules completes the coordination of the sodium ion in the putative allosteric site. It is absolutely consolidated that the progress made in the field of GPCRs structural determination has increased the adoption of docking-driven approaches for the identification or the optimization of novel potent and selective ligands. Despite the extensive use of docking protocols in virtual screening approaches, to date, almost any of these studies have been carried out without taking into account the presence of the sodium cation and its first solvation shell in the putative allosteric binding site. In this study, we have focused our attention on determining how the presence of sodium ion binding and additionally its first hydration sphere, in hA_2AAR could influence the ligand positioning accuracy during molecular docking simulations for most of the available resting and activated hA_2A AR crystal structures, using DockBench as a comparative benchmarking tool and implementing a new correlation coefficient (EM). This work provides indications on the evidence that the posing performance (accuracy and/or precision) of the docking protocols in reproducing the crystallographic poses of different hA_2A AR antagonists is generally increased in the presence of the sodium cation and its first solvation shell, in agreement with experimental observations. Consequently, the inclusion of sodium ion and its first solvation shell should be considered in order to facilitate the selection of new potential ligands in all molecular docking-based virtual screening protocols that aim to find novel GPCRs antagonists and inverse agonists.     

Electrochemiluminescence Waveguide in Single Crystalline Molecular Wires

Here we report the first observation of active waveguide of electrochemiluminescence (ECL) in single crystalline molecular wires self‐assembled from cyclometalated iridium(III) complexes, namely tris(1‐phenylisoquinoline‐C², N) (Ir(piq)₃). Under dark conditions, the molecular wires deposited on the electrode surface can act as both ECL emitters and active waveguides. As revealed by ECL microscopy, they exhibit the typical characteristics of optical waveguides, transmitting ECL and generating much brighter ECL emission at their terminals. Moreover, self‐generated ECL can be confined inside the molecular wire and propagates along the longitudinal direction as far as ≈100 μm to the terminal out of touch with the electrode. Therefore, this one‐dimensional crystalline molecular wire‐based waveguide offers the opportunity to switch the electrochemically generated ECL to remote light emission in non‐conductive regions and is promising for contactless electrochemical analysis and study of (bio)chemical systems.     

GPCRs as therapeutic targets: a view on adenosine receptors structure and functions, and molecular modeling support

G-protein-coupled receptors (GPCRs) represent the largest known family of signal-transducing proteins and transmit signals for light and many extracellular regulatory molecules. GPCRs are dysfunctional or dysregulated in several human diseases and are estimated to be the targets of ～40% of the drugs used in clinical medicine today. Receptors for adenosine belong to this family, and so far four subtypes, the A₁, A_2A, A_2B, and A₃, have been recognized. The activation of adenosine receptors (ARs) is largely responsible for the variety of effects produced by adenosine throughout several organ systems. Based on the wide (and often beneficial) effects attributed to the accumulation of endogenously released adenosine, it has long been considered that regulation of ARs has considerable therapeutic potential. In this review, we focus on recent work on adenosine receptors as therapeutic targets and, in particular, on molecular modelling support to adenosine receptors targeting.     

Basal Histamine H4 Receptor Activation: Agonist Mimicry by the Diphenylalanine Motif

Histamine H₄ receptor (H₄R) orthologues are G-protein-coupled receptors (GPCRs) that exhibit species-dependent basal activity. In contrast to the basally inactive mouse H₄R (mH₄R), human H₄R (hH₄R) shows a high degree of basal activity. We have performed long-timescale molecular dynamics simulations and rigidity analyses on wild-type hH₄R, the experimentally characterized hH₄R variants S179M, F169V, F169V+S179M, F168A, and on mH₄R to investigate the molecular nature of the differential basal activity. H₄R variant-dependent differences between essential motifs of GPCR activation and structural stabilities correlate with experimentally determined basal activities and provide a molecular explanation for the differences in basal activation. Strikingly, during the MD simulations, F169^45.55 dips into the orthosteric binding pocket only in the case of hH₄R, thus adopting the role of an agonist and contributing to the stabilization of the active state. The results shed new light on the molecular mechanism of basal H₄R activation that are of importance for other GPCRs.     

Switchable Dielectric Phase Transition Triggered by Pendulum‐Like Motion in an Ionic Co‐crystal

Molecular‐based ionic co‐crystals, which have the merits of low‐cost/easy fabrication processes and flexible structure and functionality, have already exhibited tremendous potential in molecular memory switches and other electric devices. However, dipole (ON/OFF switching) triggering is a huge challenge. Here, we introduce a pendulum‐like dynamic strategy to induce the order–disorder transition of a co‐crystal [C₅H₇N₃Cl]₃[Sb₂Br₉] (compound 1 ). Here, the anion and cation act as a stator and a pendulum‐like rotor (the source of the dielectric switch), respectively. The temperature‐dependent dielectric and differential scanning calorimetry (DSC) analyses reveal that 1 undergoes a reversible phase transition, which stems from the order–disorder transition of the cations. The thermal ON/OFF switchable motions make 1 a promising candidate to promote the development of bulk crystals as artificial intelligent dielectric materials. In addition, the pendulum‐like molecular dynamics and distinct arrangements of two coexisting ions with a notable offset effect promotes/hinders dipolar reorientation after dielectric transition and provides a rarely observed but fairly useful and feasible strategy for understanding and modulating the dipole motion in crystalline electrically polarizable materials.     

Nanobody‐Enabled Reverse Pharmacology on G‐Protein‐Coupled Receptors

The conformational complexity of transmembrane signaling of G‐protein‐coupled receptors (GPCRs) is a central hurdle for the design of screens for receptor agonists. In their basal states, GPCRs have lower affinities for agonists compared to their G‐protein‐bound active state conformations. Moreover, different agonists can stabilize distinct active receptor conformations and do not uniformly activate all cellular signaling pathways linked to a given receptor (agonist bias). Comparative fragment screens were performed on a β₂‐adrenoreceptor–nanobody fusion locked in its active‐state conformation by a G‐protein‐mimicking nanobody, and the same receptor in its basal‐state conformation. This simple biophysical assay allowed the identification and ranking of multiple novel agonists and permitted classification of the efficacy of each hit in agonist, antagonist, or inverse agonist categories, thereby opening doors to nanobody‐enabled reverse pharmacology.     

Bimetallic Nanoparticles in Supported Ionic Liquid Phases as Multifunctional Catalysts for the Selective Hydrodeoxygenation of Aromatic Substrates

Bimetallic iron–ruthenium nanoparticles embedded in an acidic supported ionic liquid phase (FeRu@SILP+IL‐SO₃H) act as multifunctional catalysts for the selective hydrodeoxygenation of carbonyl groups in aromatic substrates. The catalyst material is assembled systematically from molecular components to combine the acid and metal sites that allow hydrogenolysis of the C=O bonds without hydrogenation of the aromatic ring. The resulting materials possess high activity and stability for the catalytic hydrodeoxygenation of C=O groups to CH₂ units in a variety of substituted aromatic ketones and, hence, provide an effective and benign alternative to traditional Clemmensen and Wolff–Kishner reductions, which require stoichiometric reagents. The molecular design of the FeRu@SILP+IL‐SO₃H materials opens a general approach to multifunctional catalytic systems (MM′@SILP+IL‐func).     

Nanodiscs for INPHARMA NMR Characterization of GPCRs: Ligand Binding to the Human A2A Adenosine Receptor

G-protein-coupled-receptors (GPCRs) are of fundamental importance for signal transduction through cell membranes. This makes them important drug targets, but structure-based drug design (SBDD) is still hampered by the limitations for structure determination of unmodified GPCRs. We show that the interligand NOEs for pharmacophore mapping (INPHARMA) method can provide valuable information on ligand poses inside the binding site of the unmodified human A_2A adenosine receptor reconstituted in nanodiscs. By comparing experimental INPHARMA spectra with back-calculated spectra based on ligand poses obtained from molecular dynamics simulations, a complex structure for A_2AR with the low-affinity ligand 3-pyrrolidin-1-ylquinoxalin-2-amine was determined based on the X-ray structure of ligand ZM-241,358 in complex with a modified A_2AR.     

Graphitic Silicon Nitride: A Metal‐Free Ferromagnet with Charge and Spin Current Rectification

As a first example, herein we show that g‐Si₄N₃ is expected to act as a metal‐free ferromagnet featuring both charge and spin current rectification simultaneously. Such rectification is crucial for envisioning devices that contain both logic and memory functionality on a single chip. The spin coherent quantum‐transport calculations on g‐Si₄N₃ reveal that the chosen system is a unique molecular spin filter, the current‐voltage characteristics of which is asymmetric in nature, which can create a perfect background for synchronous charge and spin current rectification. To shed light on this highly unusual in‐silico observation, we have meticulously inspected the bias‐dependent modulation of the spin‐polarized eigenstates. The results indicate that, whereas only the localized 2p orbitals of the outer‐ring (OR) Si atoms participate in the transmission process in the positive bias, both OR Si and N atoms contribute in the reverse bias. Furthermore, we have evaluated the spin‐polarized electron‐transfer rate in the tunneling regime, and the results demonstrate that the transfer rates are unequal in the positive and negative bias range, leading to the possible realization of a simultaneous logic–memory device.     

Molecular Simulations and Drug Discovery of Adenosine Receptors

G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins. Four subtypes of adenosine receptors (ARs), the A₁AR, A_2AAR, A_2BAR and A₃AR, each with a unique pharmacological profile and distribution within the tissues in the human body, mediate many physiological functions and serve as critical drug targets for treating numerous human diseases including cancer, neuropathic pain, cardiac ischemia, stroke and diabetes. The A₁AR and A₃AR preferentially couple to the G_i/o proteins, while the A_2AAR and A_2BAR prefer coupling to the G_s proteins. Adenosine receptors were the first subclass of GPCRs that had experimental structures determined in complex with distinct G proteins. Here, we will review recent studies in molecular simulations and computer-aided drug discovery of the adenosine receptors and also highlight their future research opportunities.     

A New Approach to Prepare Poly(ethylene terephthalate)/Silica Nanocomposites with Increased Molecular Weight and Fully Adjustable Branching or Crosslinking by SSP

Summary: In the present study, it has been unexpectedly found that solid‐state polycondensation (SSP) can act as a facile method to prepare poly(ethylene terephthalate)/silica (PET/SiO₂) nanocomposites with high molecular weight and an adjustable degree of branching or crosslinking. Fumed silica, with its surface silanol groups, seems to participate in some kind of reaction, probably esterification with the hydroxy end‐groups of PET, during SSP, to act as a multifunctional chain extender. Differential scanning calorimetry and FT‐IR spectroscopy reveal this ability of the silanol groups. The molecular weight increase depends on the used temperatures of SSP as well as on the amount of SiO₂ added. As the amount of silica increases the rate of increase of the intrinsic viscosity slows because of the higher extent of branching. At 5 wt.‐% SiO₂ the extensive branching produces a crosslinked polymeric material. Such polyesters with increased molecular weight and low silica content could be suitable for blown bottle production, while the high SiO₂ content and adjustable branching or crosslinking could make them ideal high‐melt‐strength resins suitable for the preparation of low‐density closed‐shell foams.

Schematic representation of PET/SiO₂ crosslinked macromolecules.     

Tetrahedron

Connecting a triangle base and an apex forms a simplest polyhedron—that is, a tetrahedron. On account of their structural simplicity and stability, two common classes of tetrahedra—namely, M₄L₄ and M₄L₆ (M indicates anions or metal cations, L indicates ligands with C₃ symmetry for M₄L₄ and C₂ symmetry for M₄L₆, respectively)—can be readily constructed from (i) six straight edges through an edge‐bridged strategy or (ii) four triangle faces through a face‐capped strategy, by means of supramolecular or coordination assembly. The intrinsic cavities inside tetrahedra enable them to act as versatile hosts for encapsulating a variety of guests, which leads to a wide range of applications including molecular recognition, catalysis, sensing and so on. In this review, we intend to summarize specifically the work carried out in the realm of porous tetrahedral cages. It includes representative synthetic strategies for the preparation of tetrahedra along with a general summary on their structural features. Thereafter, we will highlight the state‐of‐the‐art progress in various functions of tetrahedra, in addition to presenting a full overview of applications wherein we aim to provide new insights into the design and preparation of new topological geometric structures and functional materials on the basis of the simplest polyhedron—tetrahedron.