Subunit rotation models activation of serotonin 5-HT<Subscript>3AB</Subscript> receptors by agonists

The N-terminal extracellular regions of heterooligomeric 3AB-type human 5-hydroxytryptamine receptors (5-HT3ABR) were modelled based on the crystal structure of snail acetylcholine binding protein AChBP. Stepwise rotation of subunit A by 5 degrees was performed between -10 degrees and 15 degrees to mimic agonist binding and receptor activation. Anticlockwise rotation reduced the size of the binding cavity in interface AB and reorganised the network of hydrogen bonds along the interface. AB subunit dimers with different rotations were applied for docking of ligands with different efficacies: 5-HT, m-chlorophenylbiguanide, SR 57227, quinolinyl piperazine and lerisetron derivatives. All ligands were docked into the dimer with -10 degrees rotation representing ligand-free, open binding cavities similarly, without pharmacological discrimination. Their ammonium ions were in hydrogen bonding distance to the backbone carbonyl of W183. Anticlockwise rotation and contraction of the binding cavity led to distinctive docking interactions of agonists with E129 and cation-pi interactions of their ammonium ions. Side chains of several further amino acids participating in docking (Y143, Y153, Y234 and E236) are in agreement with the effects of point mutations in the binding loops. Our model postulates that 5-HT binds to W183 in a hydrophobic cleft as well as to E236 in a hydrophilic vestibule. Then it elicits anticlockwise rotation to draw in loop C via pi-cation-pi interactions of its ammonium ion with W183 and Y234. Finally, closure of the binding cavity might end in rebinding of 5-HT to E129 in the hydrophilic vestibule.     

Synthesis and biological evaluation of <Superscript>99m</Superscript>Tc-HEDTA/HYNIC-MPP4 complex for 5-HT<Subscript>1A</Subscript> receptor imaging

5-HT_1A receptor is associated with a variety of pathophysiology of neuropsychiatric disorders. Accordingly, we have synthesized a new 5-HT_1A receptor ligand (HYNIC-MPP4) and labeled it with ^99mTc using N-(2-hydroxyethyl)ethylenediaminetriacetic acid (HEDTA) as coligand. ^99mTc-HEDTA/HYNIC-MPP4 was prepared under pH 6 at room temperature. Biodistribution of 99mTc-HEDTA/HYNIC-MPP4 in normal mice showed that this complex had moderate brain uptake (0.60% ID·g⁻¹ at 2 min p.i.) and good retention. The hippocampus had the highest radioactivity uptake at 2 min p.i. (1.84% ID⋆g⁻¹). The ratio of Hipp/CB was 3.1 at 2 min p.i. and increased to 4.4 at 60 min p.i. After blocking with 8-hydroxy-2-(dipropylamino) tetralin, the uptake of hippocampus was decreased significantly from 1.84% ID·g⁻¹ to 0.53% ID·g⁻¹ at 2 min p.i., while the cerebellum had no significant decrease. This ^99mTc complex could be a potent agent for 5-HT_1A receptor imaging. Supported by the National Natural Science Foundation of China (Grant No. 20401004) and the Analysis and Test fund of Beijing Normal University     

In search of novel ligands using a structure-based approach: a case study on the adenosine A<Subscript>2A</Subscript> receptor

In this work, we present a case study to explore the challenges associated with finding novel molecules for a receptor that has been studied in depth and has a wealth of chemical information available. Specifically, we apply a previously described protocol that incorporates explicit water molecules in the ligand binding site to prospectively screen over 2.5 million drug-like and lead-like compounds from the commercially available eMolecules database in search of novel binders to the adenosine A_2A receptor (A_2AAR). A total of seventy-one compounds were selected for purchase and biochemical assaying based on high ligand efficiency and high novelty (Tanimoto coefficient ≤0.25 to any A_2AAR tested compound). These molecules were then tested for their affinity to the adenosine A_2A receptor in a radioligand binding assay. We identified two hits that fulfilled the criterion of ~50 % radioligand displacement at a concentration of 10 μM. Next we selected an additional eight novel molecules that were predicted to make a bidentate interaction with Asn253^6.55, a key interacting residue in the binding pocket of the A_2AAR. None of these eight molecules were found to be active. Based on these results we discuss the advantages of structure-based methods and the challenges associated with finding chemically novel molecules for well-explored targets.     

Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A<Subscript>2A</Subscript> receptor

We report an investigation designed to explore alternative approaches for ranking of docking poses in the search for antagonists of the adenosine A_2A receptor, an attractive target for structure-based virtual screening. Calculation of 3D similarity of docking poses to crystallographic ligand(s) as well as similarity of receptor–ligand interaction patterns was consistently superior to conventional scoring functions for prioritizing antagonists over decoys. Moreover, the use of crystallographic antagonists and agonists, a core fragment of an antagonist, and a model of an agonist placed into the binding site of an antagonist-bound form of the receptor resulted in a significant early enrichment of antagonists in compound rankings. Taken together, these findings showed that the use of binding modes of agonists and/or antagonists, even if they were only approximate, for similarity assessment of docking poses or comparison of interaction patterns increased the odds of identifying new active compounds over conventional scoring.     

Theoretical studies on the pentacoordinate silylenoid PhCH<Subscript>2</Subscript>(NH<Subscript>2</Subscript>)CH<Subscript>3</Subscript>SiLiF

The structures of pentacoordinate silylenoid PhCH₂(NH₂)CH₃SiLiF were studied by density functional theory at the B3LYP/6-31G(d) level. Three equilibrium structures, the three-membered ring (1), the p-complex (2), and the σ-complex (3) structures, were located. Their energies are in the order of 2 > 1 > 3 both in vacuum and in THF. To exploit the stability of PhCH₂(NH₂)CH₃SiLiF, the insertion reactions of 1 and PhCH₂(NH₂)CH₃Si into C–F have been investigated, respectively. The results show that the insertion of PhCH₂(NH₂)CH₃Si is more favorable. To probe the influence of amine-coordination to the stability of PhCH₂(NH₂)CH₃SiLiF, the insertion reaction of PhCH₃CH₃SiLiF was also investigated. The calculations indicate that the insertion of PhCH₃CH₃SiLiF is more favorable than that of 1. So the N atom plays an important role on the stability of silylenoid PhCH₂(NH₂)CH₃SiLiF.     

Theoretical studies on model reaction pathways of prostaglandin H<Subscript>2</Subscript> isomerization to prostaglandin D<Subscript>2</Subscript>/E<Subscript>2</Subscript>

Model reaction mechanisms in the biosynthesis of prostaglandin D₂ (PGD₂) and prostaglandin E₂ (PGE₂) from prostaglandin H₂ with PGD₂/E₂ synthase were examined using the ab initio second-order Møller–Plesset perturbation method and density functional theory. The reaction was modeled similar to the isomerization of 2,3-dioxabicyclo[2.2.1]heptane to 3-hydroxycyclopentanone in the presence of MeS^?. An explicit solvation of two H₂O molecules was also considered, and two probable types of reaction mechanisms were demonstrated. One mechanism starts with proton abstraction from an oxygen-bound carbon at the endoperoxide by a thiolate ion and the other is stepwise and involves attack of a thiolate anion on an oxygen of the endoperoxide group in the first step with protonation of the other oxygen, followed by deprotonation from a carbon-attached oxygen to break an O–S bond to yield PGD₂ or PGE₂. We also found that the mPW1LYP hybrid method was superior to the B3LYP functional for systems with respect to the state-of-the-art CCSD(T) energetics.     

Side chain flexibility and the pore dimensions in the GABA<Subscript>A</Subscript> receptor

Permeation of ions through open channels and their accessibility to pore-targeting drugs depend on the pore cross-sectional dimensions, which are known only for static X-ray and cryo-EM structures. Here, we have built homology models of the closed, open and desensitized α₁β₂γ₂ GABA_A receptor (GABA_AR). The models are based, respectively, on the X-ray structure of α₃ glycine receptor (α₃ GlyR), cryo-EM structure of α₁ GlyR and X-ray structure of β₃ GABA_AR. We employed Monte Carlo energy minimizations to explore how the pore lumen may increase due to repulsions of flexible side chains from a variable-diameter electroneutral atom (an expanding sphere) pulled through the pore. The expanding sphere computations predicted that the pore diameter averaged along the permeation pathway is larger by approximately 3 Å than that computed for the models with fixed sidechains. Our models predict three major pore constrictions located at the levels of ?2′, 9′ and 20′ residues. Residues around the ?2′ and 9′ rings are known to form the desensitization and activation gates of GABA_AR. Our computations predict that the 20′ ring may also serve as GABA_AR gate whose physiological role is unclear. The side chain flexibility of residues ?2′, 9′ and 20′ and hence the dimensions of the constrictions depend on the GABA_AR functional state.     

Methodological approaches for the study of GABA<Subscript>A</Subscript> receptor pharmacology and functional responses

Inhibitory GABA_A receptor ion channels are the target for a wide range of clinically-used therapeutic agents. The complex structural diversity of these ligand-gated channels, revealed by molecular cloning studies, together with increasing requirements for higher-throughput functional assays in drug discovery, has led to the development of a wide range of techniques to examine GABA_A receptor pharmacology and function. In the current article we review some of the methodologies which have contributed to the expansion of knowledge in this field. The techniques include: molecular approaches, immunoprecipitation, and immunopurification to study receptor assembly, structure, and functional expression; in situ hybridization, immunocytochemistry, and autoradiography to examine receptor distribution in native tissues; radioligand binding, site-directed mutagenesis, and electrophysiology to examine pharmacology and allosteric modulation; and patch clamp, ion flux, microphysiometry, and a variety of novel fluorescence-based technologies to examine ion-channel function. The use of gene targetting approaches in transgenic mice has also provided important insights into the role of specific GABA_A receptor subtypes in vivo. The continuing evolution of novel technologies and assay approaches with appropriate sensitivity and resolution to measure subtle modulation of GABA_A ion channels will facilitate ongoing investigation of the physiological functions of these important inhibitory receptors.     

Bismuth in quaternary and quinary solid solutions based on A<Subscript>3</Subscript>B<Subscript>5</Subscript> compounds

The heterophase equilibria in the InBiAsSb and GaInBiAsSb systems are analyzed in the context of simple solutions. Linear interpolation is to determine the thermodynamic and crystal-chemical parameters for virtual GaBi compound. The boundaries of existence for InBiAsSb and GaInBiAsSb solid solutions are calculated and the thermodynamic limits that characterize their synthesis are determined for the temperature range of 650–780 K. Heteroepitaxial InBiAsSb/InSb structures are formed on the basis of our analysis by zone recrystallization according to temperature gradient (ZRTG).     

Glasses in the CuNbOF<Subscript>5</Subscript>-BaF<Subscript>2</Subscript> and CuNbOF<Subscript>5</Subscript>-PbF<Subscript>2</Subscript> systems

Nonhygroscopic, colored glasses have been synthesized in the CuNbOF₅-BaF₂ and CuNbOF₅-PbF₂ systems proceeding from crystals of the complex compound CuNbOF₅ · 4H₂O. The glasses have been studied structurally and thermally. The crystallization resistance of the glasses has been studied as a function of glass composition. Lead difluoride glasses are more stable than barium difluoride glasses of the same composition. These glasses have lower glass-transition temperatures than the binary glasses formed in the NbO₂F-BaF₂ system. The glass structure is built of Nb(O,F)₆ polyhedra, which are linked in glass networks through oxygen bridges. Modifier cations influence both the structure of glass networks and the linkage of polyhedra.     

Influence of ZrO<Subscript>5</Subscript> treatment temperature on the interaction with titanium tetrachloride

The data on phase and chemical transformations of nanosized zirconium dioxide upon annealing at 25–1300°С are presented. The in situ interaction of titanium tetrachloride with nanosized zirconia annealed at 200–800°С has been studied. The revealed regularities of the change of titanium content and the Cl/Ti ratio in the chemisorbed groups have confirmed that TiCl₄ predominantly reacts with zirconia treated at up to 400°С via the hydroxyl groups to yield the TiCl_4–n fragments. In the case of zirconia treated at higher temperature, the interaction with TiCl₄ involves the coordination-unsaturated Zr⁺ and Zr–O^– centers as well.     

Crystal structure of KPb<Subscript>2</Subscript>Cl<Subscript>5</Subscript> and KPb<Subscript>2</Subscript>Br<Subscript>5</Subscript>

The KPb₂Cl₅ and KPb₂Br₅ crystals are monoclinic (P2₁/c) with a microtwinned structure. X-ray analysis of chloride resulted in the parameters a = 8.854(2) Å, b = 7.927(2) Å, c = 12.485(3) Å; β = 90.05(3)°, d_calc = 4.78(1) g/cm³ (STOE STADI4, MoK_α, 2θ_max = 80°), R₁ = 0.0702 for 4094 F ≥ 4 σ(F) reflections. For bromide, a = 9.256(2) Å, b = 8.365(2) Å, c = 13.025(3) Å; β = 90.00(3)°, d_calc = 5.62(1) g/cm³ (Bruker P4, MoK_α, 2θ_max = 70°), R₁ = 0.0692 for 3076 F ≥ 4 (F) reflections.     

Subsolidus phase relations in the Al<Subscript>2</Subscript>O<Subscript>3</Subscript>-Li<Subscript>2</Subscript>O-Ta<Subscript>2</Subscript>O<Subscript>5</Subscript> (Nb<Subscript>2</Subscript>O<Subscript>5</Subscript>) systems

The phase composition has been studied and an equilibrium phase diagram has been designed for the Al₂O₃-Li₂O-R₂O₅ (R = Ta or Nb) systems in the subsolidus region up to 1000°C and 85 mol % Li₂O. New phases with the composition Li_1+x Al_1?x O_2?x , where x = 0–0.67, have been found.     

Modeling the active centers of V<Subscript>2</Subscript>O<Subscript>5</Subscript>/SiO<Subscript>2</Subscript> and V<Subscript>2</Subscript>O<Subscript>5</Subscript>/TiO<Subscript>2</Subscript> supported catalysts. DFT theoretical analysis of optical properties

Within the framework of the density functional theory (DFT), the electronic structure of monooxodioxovanadium functional groups in tetrahedral coordination, which model the active centers (ACs) of fine supported catalysts V₂O₅/SiO₂ and V₂O₅/TiO₂, has been analyzed. The optimal structures of three ACs as possible models of monomeric and polymeric oxovanadium forms on the carriers with low vanadium content were determined. The modified DFT method involving the time dependence of Kohn-Sham equation (TDDFT) was used for the adopted AC models to calculate the energies of the excited states, and optical spectra of the absorption in 25000–60000 cm^?1 region were reconstructed on their base. The spectrum in this region is due to O → V charge transfer. The features of electronic spectra with the charge transfer for V₂O₅/SiO₂ and V₂O₅/TiO₂ catalysts and the vibrational spectra of three AC models corresponding to the monomeric and dimeric oxovanadium forms of the supported catalysts V₂O₅/SiO₂ and V₂O₅/TiO₂ were defined. The detailed interpretation of normal vibration frequencies is given. The frequencies typical of the monomeric and dimeric oxovanadium forms on the carrier surface were identified.     

Prediction of new A<Subscript>3+</Subscript>B<Subscript>3+</Subscript>C<Subscript>2+</Subscript>O<Subscript>4</Subscript> compounds

Hitherto unprepared ABCO₄ compounds (where A and B stand for tervalent metals (r _A ≥ r _B) and C stands for a divalent metal) are predicted. Criteria are found to predict the possibility for these compounds to crystallize in some type of structure (K₂NiF₄, CaFe₂O₄, YbFe₂O₄, or spinel) at room temperature and atmospheric pressure. The prediction is based only on the properties of elements and simple oxides. A special software system for computer-aided analysis of information is used for calculations involving pattern recognition based on use case.     

Glass formation in the Li<Subscript>2</Subscript>O-Ta<Subscript>2</Subscript>O<Subscript>5</Subscript>-TeO<Subscript>2</Subscript> system

In the Li₂O-Ta₂O₅-TeO₂ system, the boundaries of the glass region have been determined. The electrical and spectral properties of glasses and crystalline materials have been investigated.     

Coefficients of thermal expansion of KPb<Subscript>2</Subscript>Cl<Subscript>5</Subscript> and RbPb<Subscript>2</Subscript>Br<Subscript>5</Subscript> crystals

The temperature dependence of unit cell parameters for monoclinic KPb₂Cl₅ and tetragonal RbPb₂Br₅ crystals was studied in the range of 100–298 K. Linear and volume thermal expansion coefficients were determined.     

Study of Li<Subscript>4</Subscript>Ti<Subscript>5</Subscript>O<Subscript>12</Subscript> interaction with solid lithium-containing electrolytes

Compatibility of the lithium-titanium spinel Li₄Ti₅O₁₂ in contact with precursors of lithium-conducting solid electrolytes of composition Li_1.3Al_0.3Ti_1.7(PO₄)₃ (LATP), Li_1.5Al_0.5Ge_1.5(PO₄)₃ (LAGP), Li_0.5La_0.5TiO₃ (LLT) was studied. It was found that, in sintering of Li₄Ti₅O₁₂ brought in contact with LATP and LAGP, a solid-phase reaction occurs to give nonconducting phases (TiO₂ and Li₃PO₄). The conductivity of the stable composite Li₄Ti₅O₁₂/LLT (10%) is higher than that of the starting Li₄Ti₅O₁₂, which makes it possible to regard the composite as a promising anode material for lithium-ion batteries.     

Phase formation in the V<Subscript>2</Subscript>O<Subscript>5</Subscript>-Nb<Subscript>2</Subscript>O<Subscript>5</Subscript>-MoO<Subscript>3</Subscript> system

The solid-phase interaction in the V₂O₅-Nb₂O₅-MoO₃ system has been investigated, and the formation of a solid solution bounded by the compositions MoNb₂V₄O_{18 ? δ}, Mo₂NbV₅O_{21 ? δ}, Mo₂Nb₃V₃O_{21 ? δ}, and Mo₄Nb₉V₉O_{57 ? δ} has been found (δ is nonstoichiometry). In the V₂O₅?Nb₂O₅ system, the formation of three compounds is verified, namely, VNbO₅ (tetragonal structure), VNb₉O₂₅, and V₂Nb₂₃O_62.5. The first two compounds are isostructural and form a continuous solid solution with tetragonal symmetry. A new compound of the composition Mo₃NbVO_{14 ? δ} has been synthesized. This compound is isostructural to the Mo₃Nb₂O₁₄ compound described in the literature and forms a tetragonal solid solution with it. The phase equilibria in the V₂O₅-Nb₂O₅-MoO₃ system in the subsolidus region have been determined.