An automated system for the analysis of G protein-coupled receptor transmembrane binding pockets: alignment, receptor-based pharmacophores, and their application

G protein-coupled receptors (GPCRs) share a common architecture consisting of seven transmembrane (TM) domains. Various lines of evidence suggest that this fold provides a generic binding pocket within the TM region for hosting agonists, antagonists, and allosteric modulators. Here, a comprehensive and automated method allowing fast analysis and comparison of these putative binding pockets across the entire GPCR family is presented. The method relies on a robust alignment algorithm based on conservation indices, focusing on pharmacophore-like relationships between amino acids. Analysis of conservation patterns across the GPCR family and alignment to the rhodopsin X-ray structure allows the extraction of the amino acids lining the TM binding pocket in a so-called ligand binding pocket vector (LPV). In a second step, LPVs are translated to simple 3D receptor pharmacophore models, where each amino acid is represented by a single spherical pharmacophore feature and all atomic detail is omitted. Applications of the method include the assessment of selectivity issues, support of mutagenesis studies, and the derivation of rules for focused screening to identify chemical starting points in early drug discovery projects. Because of the coarseness of this 3D receptor pharmacophore model, however, meaningful scoring and ranking procedures of large sets of molecules are not justified. The LPV analysis of the trace amine-associated receptor family and its experimental validation is discussed as an example. The value of the 3D receptor model is demonstrated for a class C GPCR family, the metabotropic glutamate receptors.     

Syntheses and Crystal Structures of Rb2B2Se7, Tl2B2Se7, Cs3B3Se10, and Tl3B3Se10: New Perseleno‐selenoborates with Polymeric Anionic Chains

The perseleno‐selenoborates Rb₂B₂Se₇ and Cs₃B₃Se₁₀ were prepared from the metal selenides, amorphous boron and selenium, the thallium perseleno‐selenoborates Tl₂B₂Se₇ and Tl₃B₃Se₁₀ directly from the elements in evacuated carbon coated silica tubes by solid state reactions at temperatures between 920 K and 950 K. All structures were refined from single crystal X‐ray diffraction data. The isotypic perseleno‐selenoborates Rb₂B₂Se₇ and Tl₂B₂Se₇ crystallize in the monoclinic space group I 2/a (No. 15) with lattice parameters a = 12.414(3) Å, b = 7.314(2) Å, c = 14.092(3) Å, β = 107.30(3)°, and Z = 4 for Rb₂B₂Se₇ and a = 11.878(2) Å, b = 7.091(2) Å, c = 13.998(3) Å, β = 108.37(3)° with Z = 4 for Tl₂B₂Se₇. The isotypic perseleno‐selenoborates Cs₃B₃Se₁₀ and Tl₃B₃Se₁₀ crystallize in the triclinic space group P1 (Cs₃B₃Se₁₀: a = 7.583(2) Å, b = 8.464(2) Å, c = 15.276(3) Å, α = 107.03(3)°, β = 89.29(3)°, γ = 101.19(3)°, Z = 2, (non‐conventional setting); Tl₃B₃Se₁₀: a = 7.099(2) Å, b = 8.072(2) Å, c = 14.545(3) Å, α = 105.24(3)°, β = 95.82(3)°, γ = 92.79(3)°, and Z = 2). All crystal structures contain polymeric anionic chains of composition ([B₂Se₇]^2–)_n or ([B₃Se₁₀]^3–)_n formed by spirocyclically fused non‐planar five‐membered B₂Se₃ rings and six‐membered B₂Se₄ rings in a molar ratio of 1 : 1 or 2 : 1, respectively. All boron atoms have tetrahedral coordination with corner‐sharing BSe₄ tetrahedra additionally connected via Se–Se bridges. The cations are situated between three polymeric anionic chains leading to a nine‐fold coordination of the rubidium and thallium cations by selenium in M₂B₂Se₇ (M = Rb, Tl). Coordination numbers of Cs⁺ (Tl⁺) in Cs₃B₃Se₁₀ (Tl₃B₃Se₁₀) are 12(11) and 11(9).     

Novel Alkaline Earth Metal Chalcogenoborates: Syntheses and Crystal Structures of Sr4.2Ba2.8(BS3)4S and Ba7(BSe3)4Se

Systematic studies on quaternary thio‐ and selenoborates containing heavier alkaline earth metal cations led to the two new isotypic crystalline phases Sr_4.2Ba_2.8(BS₃)₄S and Ba₇(BSe₃)₄Se. Both compounds consist of trigonal‐planar BQ₃ (Q = S, Se) units, isolated Q^2– anions and the corresponding counter‐ions. The two new chalcogenoborates were prepared in solid state reactions from the metal sulfides (selenides), amorphous boron and sulfur (selenium). Evacuated carbon coated silica tubes were used as reaction vessels since temperatures up to 870 K were applied. Sr_4.2Ba_2.8(BS₃)₄S and Ba₇(BSe₃)₄Se crystallize in the monoclinic space group C2/c (no. 15) with a = 9.902(3) Å, b = 23.504(9) Å, c = 9.884(3) Å, β = 90.01(3)° and Z = 4 in the case of the thioborate, while for the selenoborate the lattice parameters a = 10.513(2) Å, b = 25.021(5) Å, c = 10.513(2) Å, β = 90.10(3)° were determined. X‐ray powder patterns are compared to calculated diffraction data obtained from single crystal X‐ray structure determination.     

Na6[B18Se17]: The First Selenoborato‐closo‐dodecaborate with a Polymeric Chain Anion

Systematic studies on selenoborates containing a B₁₂ cluster entity and alkali metal cations led to the new crystalline phase Na₆[B₁₈Se₁₇] which consists of a icosahedral B₁₂ cluster completely saturated with trigonal‐planar BSe₃ units and sodium counter‐ions. Neighbouring cluster entities are connected in one direction via exocyclic selenium atoms forming the infinite chain anion ([B₁₈Se₁₆Se_2/2]^6–)_∞. The new chalcogenoborate was prepared in a solid state reaction from sodium selenide, amorphous boron and selenium in evacuated carbon coated silica tubes at a temperature of 850 °C. Na₆[B₁₈Se₁₇] crystallizes in the monoclinic space group C2/c (no. 15) with a = 18.005(4) Å, b = 16.549(3) Å, c = 11.245(2) Å, β = 91.35(3)° and Z = 4.     

ChemInform Abstract: Novel Alkaline Earth Metal Chalcogenoborates: Syntheses and Crystal Structures of Sr4.2Ba2.8(BS3)4S and Ba7(BSe3)4Se.

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