Virtual screening of selective inhibitors of phosphopantetheine adenylyltransferase from <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis>

Bacterial phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis (PPAT Mt) is a convenient target protein for the directed search for selective inhibitors as potent antituberculosis drugs. Four compounds suitable for the detailed investigation of their interactions with PPAT Mt were found by virtual screening. The active-site region of the enzyme was chosen as the ligand-binding site. The positions of the ligands found by the docking were refined by molecular dynamics simulation. The nearest environment of the ligands, the positions of which in the active site of the enzyme were found in a computational experiment, was analyzed. The compounds under consideration were shown to directly interact with functionally important active-site amino-acid residues and block access of substrates to the active site. Therefore, these compounds can be used for the design of selective inhibitors of PPAT Mt as potent antituberculosis drugs.     

The Fe<Superscript>2+</Superscript>/Fe<Superscript>3+</Superscript> ratio in natural and heat-treated iron-rich eudialytes

The structures of natural iron-rich eudialyte (specimen 3458 from the Khibiny massif, the Kola Peninsula) and two heat-treated samples of this mineral calcined at 700 and 800°C were determined by X-ray diffraction. The trigonal unit-cell parameters (sp. gr. R3m) are as follows: a = 14.2645(1) Å, c = 29.9635(5) Å; a = 14.1307(1) Å, c = 30.1229(3) Å; a = 14.1921(2) Å, c = 30.2417(5) Å, respectively. It was found that Fe³⁺ ions in the calcined eudialytes, as well as impurities in the starting specimen, occupy the square-pyramidal Fe³⁺(V) sites, whereas Fe²⁺ ions are in the planar-tetragonal Fe²⁺(IV) sites.     

Structure of a new crystal modification of the bacterial NAD-dependent formate dehydrogenase with a resolution of 2.1 Å

Formate dehydrogenase (FDG) from methylotrophic bacteria Pseudomonas sp. 101 catalyzes the reaction of oxidation of the formate ion to carbon dioxide, which is accompanied by the reduction of nicotinamid adenine dinucleotide (NAD⁺). The structures of the apo and holo (enzyme-NAD-azide triple complex) forms of the enzyme were determined earlier. In an attempt to prepare a complex of FDG with the product of the enzymatic reaction (NADH), a new crystal modification of FDG is obtained (space group P4₂2₁2, a = b = 93.3 Å, c = 103.05 Å). The FDG structure is solved by the molecular replacement method and refined to R = 20.7%. The asymmetric part of the unit cell contains one FDG molecule. In contrast to the previously studied FDG structures, the biologically active dimer is formed by the crystallographic rotation axis. A comparative structural analysis of the studied form with the apo and holo forms of the enzyme is performed. The influence of the molecular structure on the environment in the crystal is investigated.     

Synthesis and structure of oxovanadium(IV) complexes [VO(<Emphasis Type="Italic">Acac</Emphasis>)<Subscript>2</Subscript>] and [VO(<Emphasis Type="Italic">Sal</Emphasis>: <Emphasis Type="Italic">L</Emphasis>-alanine)(H<Subscript>2</Subscript>O)]

Bis(acetylacetonato)oxovanadium C₁₀H₁₄O₅V (I) and (S)-[2-(N-salicylidene)aminopropionate]oxovanadium monohydrate C₁₀H₉NO₅V (II) are synthesized. The crystal structures of compounds I and II are determined using single-crystal X-ray diffraction. Crystals of compound I are triclinic, a = 7.4997(19) Å, b = 8.2015(15) Å, c = 11.339(3) Å, α = 91.37(2)°, β = 110.36(2)°, γ = 113.33(2)°, Z = 2, and space group \(P\bar 1\). Crystals of compound II are monoclinic, a = 8.5106(16) Å, b = 7.373(2) Å, c = 9.1941(16) Å, β = 101.88(1)°, Z = 2, and space group P2₁. The structures of compounds I and II are solved by direct methods and refined to R₁ = 0.0382 and 0.0386, respectively. The oxovanadium complexes synthesized are investigated by vibrational spectroscopy.     

Comparative analysis of spatial organization of laccases from <Emphasis Type="Italic">Cerrena maxima</Emphasis> and <Emphasis Type="Italic">Coriolus zonatus</Emphasis>

Laccase (oxygen oxidoreductase, EC 1.10.3.2) belongs to the multicopper oxidase family. The main function of this enzyme is to perform electron transfer from the oxidized substrate through the mononuclear copper-containing site T1 to the oxygen molecule bound to the site T3 in the trinuclear T2/T3 cluster. The structures of two new fungal laccases from C. maxima and C. zonatus were solved on the basis of synchrotron X-ray diffraction data. Both laccases show high structural homology with laccases from other sources. The role of the carbohydrate component of laccases in structure stabilization and formation of ordered protein crystals was demonstrated. In the structures of C. maxima and C. zonatus laccases, two water channels of functional importance were found and characterized. The structural results reported in the present study characterize one of the functional states of the enzyme fixed in the crystal structure.     

Gosset helicoids: I. 8D crystallographic lattice <Emphasis Type="Italic">E</Emphasis><Subscript>8</Subscript> and crystallographic,quasi-crystallographic,and fractional helicoidal axes determined by this lattice

It is shown that mapping of substructures of a semiregular Gosset polytope, whose 240 vertices form the first coordination sphere of a 8D lattice E ₈, determines the orders of p/d axes of helicoids that are set only by invariants of (sub)algebras. Axes of such (Gosset) helicoids are derived. These axes perform rotation by an angle (360°/p(d; can be crystallographic, quasi-crystallographic (p = 2, 3, 4, 5, 6, …; d = 1), or fractional (1 < d < p/2); and may belong to regular polytopes (conventional, starlike, etc.). Formation of ordered structures is considered as a formation of Gosset helicoids (rods) with their subsequent assembly. Helicoids with axes 15/4 and 15/7 are considered as examples. They correspond to crystallographic approximants—helicoids with axes 4₁ and 2₁ composed of deformed icosahedra (dodecahedra)—in a β-Mn crystal (clathrate IX).     

Synthesis and Molecular Structures of (3-Hydroxy, 3-Chloro, 3-Arylamino)-<Emphasis Type="Italic">N</Emphasis>-acetyl-3-arylaminotropones

The structures of 5,7-di(tert-butyl)-2-(5,8-dimethyl-4-piperidinoquinolin-2-yl)-3-hydroxytropone, 5,7-di(tert-butyl)-3-chloro-2-(5,8-dimethyl-4-piperidinoquinolin-2-yl)tropone, 5,7-di(tert-butyl)- 3-(3,5-dimethylphenylamino)-2-(5,8-dimethyl-4-piperidinoquinolin-2-yl)tropone, and 3-(N-acetyl-3,5- dimethylphenylamino)-5,7-di(tert-butyl)-2-(5,8-dimethyl-4-piperidinoquinolin-2-yl)tropone were determined by X-ray diffraction. These compounds were synthesized through a series of transformations, including the nucleophilic substitution of the chlorine atom by piperidine in the starting 5,7-di(tert-butyl)-2-(4- chloroquinolin-2-yl)-3-hydroxytropone followed by the three-step functionalization of the 3-position in 3-hydroxytropone. The nature of dynamic processes in a solution of N-acetyl-3-arylaminotropone associated with the rotation of the N-acetyl group was revealed by the PCM/PBE0/6-31G(d,p) method.     

Specific stereochemical features of metallochelate complexes with tridentate <Emphasis Type="Italic">N,N,N</Emphasis>(<Emphasis Type="Italic">N,N</Emphasis>,O)-donating ligands

Earlier X-ray diffraction studies of a series of 12 adducts (I–XII) between metallochelate complexes [M = Co(II), Ni(II), and Cu(II)] with tridentate N,N,N(N,N,O)-donating Schiff bases (L) and monodentate or bidentate ligands (L′) revealed a similarity in the stereochemistry of these compounds. The coordination polyhedron of metal atoms in compounds I–XII is a tetragonal pyramid (bipyramid) with two vertices occupied competitively. The L ligand occupies three coordination sites in the base of the pyramid. The L′ ligand approaches the metal atom, as a rule, in a direction perpendicular to the basal plane. The fourth site in the base of the pyramid and the apical vertex are occupied competitively. Different patterns of occupation of these positions are observed: they include the donor atoms of both the L and L′ ligands.     

Crystal structure of Rb<Subscript>2</Subscript>Mn<Subscript>3</Subscript>(H<Subscript>2</Subscript>O)<Subscript>2</Subscript>[P<Subscript>2</Subscript>O<Subscript>7</Subscript>]<Subscript>2</Subscript>, a new representative of the family of hydrated diphosphates

The crystal structure of Rb₂Mn₃(H₂O)₂[P₂O₇]₂, a new phase obtained in the form of single crystals under hydrothermal conditions in the MnCl₂–Rb₃PO₄–H₂O system, is determined by X-ray diffraction (Xcalibur-S-CCD diffractometer, R = 0.0270): a = 9.374(2), b = 8.367(2), c = 9.437(2) Å, ß = 99.12(2)°, space group P2₁/c, Z = 2, D_x = 3.27 g/cm³. A correlation between the unit-cell parameters and the size of cations forming the crystal structures of isostructural A₂M₃(H₂O)₂[P₂O₇]₂ diphosphates (A = K, NH₄, Rb, or Na; _M = Mn, Fe, Co, or Ni) is revealed. It is shown that, due to the topological similarity, the structures of diphosphates and orthophosphates of the farringtonite structural type can undergo mutual transformations.     

Growth and structure of La<Subscript>3</Subscript>Zr<Subscript>0.5</Subscript>Ga<Subscript>5</Subscript>Si<Subscript>0.5</Subscript>O<Subscript>14</Subscript> crystals

The complete X-ray structure determination of Czochralski grown La₃Zr_0.5Ga₅Si_0.5O₁₄ single crystals with the Ca₃Ga₂Ge₄O₁₄ structure is performed (sp. gr. P321, a = 8.226(1) Å, c = 5.1374(6) Å, Z = 1, Mo K_α1 radiation, 1920 crystallographically independent reflections, R = 0.0166, R_w = 0.0192). The absolute structure is determined. It is shown that possible transition of some of La atoms (～1.2%) from the 3e to 6g position may give rise to the formation of structural defects.     

Crystallographic analysis of the structure of livingstonite HgSb<Subscript>4</Subscript>S<Subscript>8</Subscript> from refined data

An X-ray diffraction study of mineral livingstonite (HgSb₄S₈) from Khaydarkan (Kyrgyzstan) has been performed on a Bruker Nonius X8Apex diffractometer with a 4K CCD detector (R = 0.031). The unit-cell parameters were found to be a = 30.1543(10) Å, b = 3.9953(2) Å, c = 21.4262(13) Å, β = 104.265(1)°, V = 2501.7(2) ų, Z = 8, d _calcd = 5.013 g/cm³, and sp. gr. A2/a. It was confirmed that livingstonite belongs to rod-layers structures. In one type of layer, two double Sb₂S₄ chains are bound by disulfide groups [S₂]^2? (S-S 2.078(2) Å); in the other type, these chains are bound via Hg²⁺ cations. A crystallographic analysis confirmed the existence of independent pseudotranslational ordering in the cation and anion matrices, which is characteristic of the lozenge-like structures of sulfides and sulfosalts.     

Crystal chemistry of KCuMn<Subscript>3</Subscript>(VO<Subscript>4</Subscript>)<Subscript>3</Subscript> in the context of detailed systematics of the alluaudite family

The crystal structure of new manganese potassium copper vanadate KCuMn₃(VO₄)₃, which was prepared by the hydrothermal synthesis in the K₂CO₃–CuO–MnCl₂–V₂O₅–H₂O system, was studied by X-ray diffraction (R = 0.0355): a = 12.396(1) Å, b = 12.944(1) Å, c = 6.9786(5) Å, β = 112.723(1)°, sp. gr. C2/c, Z = 4, ρ_calc = 3.938 g/cm³. A comparative analysis of the crystal-chemical features of the new representative of the alluaudite family and related structures of minerals and synthetic phosphates, arsenates, and vanadates of the general formula A(1)A(1)′A(1)″A(2)A(2)′M(1)M(2)₂(TO₄)₃ (where A are sites in the channels of the framework composed of MО₆ octahedra and TО₄ tetrahedra) was performed. A classification of these structures into subgroups according to the occupancy of A sites is suggested.     

Cluster self-organization of <Emphasis Type="Italic">TR</Emphasis>-containing germanate systems: Suprapolyhedral precursors and self-assembly of the crystal structures of the LiNdGeO<Subscript>4</Subscript> and CeGeO<Subscript>4</Subscript> compounds

A combinatorial-topological analysis of the orthogermanates LiNdGeO₄ (space group Pbcn) and CeGeO₄ (space group I 4₁/a, the scheelite structure type), which have MT frameworks composed of polyhedral structural units in the form of M dodecahedra (NdO₈ and CeO₈) and T tetrahedra (GeO₄), is performed using the method of coordination sequences with the TOPOS program package. It is established that the structures of both orthogermanates are characterized by equivalent crystal-forming nets 4444. The cluster precursors of the M ₂ T ₂ cyclic type are identified by the method of two-color decomposition. The local symmetry of four-polyhedral clusters corresponds to the point group 2. In the precursor of the LiNdGeO₄ orthogermanate, the Li atom is located above the M ₂ T ₂ ring. The number of Li-O bonds in this precursor is 4. The cluster precursors M ₂ T ₂ and LiM ₂ T ₂ are responsible for the formation of crystal-forming clusters of a higher level according to the mechanism of matrix self-assembly. The coordination numbers of the cluster precursors in two-dimensional nets for these structures are found to be equal to 4. The equivalent bilayer TR,Ge stacks that consist of eight cluster precursors are revealed in the structures under investigation. It is demonstrated that there exist three types of translational interlayer arrangements of cluster precursors upon the formation of macrostructures of the orthogermanates.     

Synthesis and structure of (Rb<Subscript>0.50</Subscript>Ba<Subscript>0.25</Subscript>)[UO<Subscript>2</Subscript>(CH<Subscript>3</Subscript>COO)<Subscript>3</Subscript>]

A new compound (Rb_0.50Ba_0.25)[UO₂(CH₃COO)₃] is synthesized and its crystal structure is studied by X-ray diffraction. The compound crystallizes in the form of yellow plates belonging to the cubic crystal system. The unit cell parameter a = 17.0367(1) Å, V = 4944.89(5) ų, space group I \(\bar 4\)3d, Z = 16, and R = 0.0182. The coordination polyhedron of the uranium atom is a hexagonal bipyramid with oxygen atoms of three acetate groups and the uranyl group in the vertices. The crystal chemical formula of the uranium-containing group is AB ₃ ⁰¹ (A = UO ₂ ²⁺ , B ⁰¹ = CH₃COO^?). The oxygen atoms of the acetate groups that enter the coordination polyhedron of uranium are bound to barium and rubidium atoms.     

Complexes of Ambidentate N,O-Donor Ligands with Rhenium(I) and -(V)

The reaction of the potentially bidentate ambidentate N,O-donor ligands 3-hydroxy-2-pyridinecarboxylic acid (Hhpc) and 3-hydroxy-2-(hydroxymethyl)pyridine (Hhhp) with trans-[ReOCl₃(PPh₃)₂] led to the isolation of the products [ReOCl(hpc)₂] (1) (from acetonitrile) and [ReOCl₂(hhp)(PPh₃)] (2) (from ethanol) respectively. In both complexes hpc and hhp are coordinated as bidentate N,O-donor chelates, rather than as O,O-donor ligands. From the reaction of [Re(CO)₅Cl] and Hhhp·HCl in ethanol the neutral complex fac-[Re(CO)₃Cl(Hhhp)] (3) was obtained, with N,O-coordination of Hhhp. Complex 1 crystallizes in the monoclinic space group P2₁/n with a?=?6.8782(3), b?=?20.0647(8), c?=?10.8692(4) Å, β?=?107.545(1)°, and Z?=?4. Complex 2 crystallizes in the triclinic space group P-1 with a?=?7.3523(4), b?=?8.1047(5), c?=?19.591(1) Å, α?=?91.133(2)°, β?=?93.656(2)°, γ?=?93.074(2)° and Z?=?2. Complex 3 has monoclinic P2₁/c symmetry with the cell parameters a?=?10.6452(5), b?=?11.1372(5), c?=?9.7229(5) Å, β?=?106.107(2)°, and Z?=?4.

Graphical Abstract

The reaction of the potentially bidentate ambidentate N,O-donor ligands 3-hydroxy-2-pyridinecarboxylic acid (Hhpc) and 3-hydroxy-2-(hydroxymethyl)pyridine (Hhhp) with trans-[ReOCl₃(PPh₃)₂] led to the isolation of the products [ReOCl(hpc)₂] (from acetonitrile) and [ReOCl₂(hhp)(PPh₃)] (from ethanol) respectively. In both complexes hpc and hhp are coordinated as bidentate N,O-donor chelates, rather than as O,O-donor ligands. From the reaction of [Re(CO)₅Cl] and Hhhp·HCl in ethanol the neutral complex fac-[Re(CO)₃Cl(Hhhp)] was obtained, with N,O-coordination of Hhhp. Spectroscopic data and the X-ray crystal structures of the complexes are reported.

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Multicell model of La<Subscript>3</Subscript>Ga<Subscript>5</Subscript>GeO<Subscript>14</Subscript> crystal: A new approach to the description of the short-range order of atoms

The multicell model alternative to the model of mixed atomic sites used now is proposed for a single crystal of La₃Ga₅GeO₁₄ belonging to the langasite family. The multicell consists of four unit cells. In three identical cells of the structure, atoms adapt to the Ge atom occupying one of the two 2d positions on the threefold symmetry axis. In the fourth cell, atoms surround the Ge atom located at the 1a position. The multicell model allows one to study the short-range order of atoms by the methods of classical structure analysis based on Bragg scattering. Four high-resolution data sets measured at 295 and 111.5 K are used in the study. The results are obtained with high relative precision (space group P321, Z = 1; at 295 K a = 8.2020(6) Å and c = 5.1065(6) Å, R/wR = 0.81/0.73% for 3829 unique ref lections; at 111.5 K a = 8.1939(1) Å and c = 5.1022(4) Å, R/wR = 0.85/0.76% for 3880 reflections).     

Ionic Conductivity of KTiOPO<Subscript>4</Subscript> Single Crystals Grown by Flux Crystallization under Different Conditions

The ionic conductivity of three KTiOPO₄ crystals grown from high-temperature solution–melts in combination with the Czochralski technique under different conditions has been investigated. The first crystal was obtained at a cooling rate V_g = 0.2–0.5 mm/day and a ratio of potassium and phosphorus concentrations in the solution–melt [K]/[P] = 2. The other two crystals were grown at a much higher velocity (V_g = 3–7 mm/day) from solution–melts with [K]/[P] = 1.5 and 1. It is shown that the crystal grown upon slow cooling at [K]/[P] = 2 has the lowest ionic conductivity: σ_||c = 1.0 × 10^–5 and 3 × 10^–11 S/cm at 573 and 293 K, respectively.     

X-ray crystal structures of two polymorphic forms,monoclinic and triclinic,of: 1-[(<Emphasis Type="Italic">E</Emphasis>)-2-(4-bromophenyl)1-diazenyl]-3-({3-[(<Emphasis Type="Italic">E</Emphasis>)-2-(4-bromophenyl)-1-diazenyl]-6-ethylhexahydro-1-pyrimidinyl}methyl)-4-ethylhexahydropyrimidine

1-[(E)-2-(4-bromophenyl)-1-diazenyl]-3-({3-[(E)-2-(4-bromophenyl)-1-diazenyl]-6-ethylhexahydro-1-pyrimidinyl}methyl)-4-ethylhexahydropyrimidine (1) has been synthesized by reaction of a mixture of formaldehyde and 1,3-pentanediamine{DYTEK^®EPdiamine} with p-bromobenzenediazonium chloride. This compound crystallizes in two polymorphic forms 1-α and 1-β whose crystal structures have been determined by single crystal X-ray diffraction analysis. Both polymorphs 1-α and 1-β display crystallographic disorder within the hexahydropyrimidine rings. The molecule of 1 is built up of two equivalent 3-(aryldiazenyl)-6-ethylhexahydro-1-pyrimidinyl groups in the s-trans orientation around the central methylene group (C13). In both structures the triazene moieties adopt the anti configuration around the N=N bonds, displaying significant π-conjugation. The crystal packings are determined only by van der Waals interactions. The crystal structures of 1-α and 1-β are compared with the previously reported structure of the 5,5-dimethylhexahydropyrimidine analogue 3. Compounds 1 and 3 are isomeric with respect to the hexahydropyrimidine moiety. The structures of 1 and 3 are very different in one respect; in 1 the aryldiazenyl-hexahydropyrimidinyl groups are in the s-trans orientation around the central methylene group, whereas in 3 the arrangement of the aryldiazenylhexahydropyrimidinyl groups is the s-cis orientation. Crystal data: 1-α C₂₅H₃₄N₈Br₂, monoclinic, space group P2(1)/c, a = 9.2150(3), b = 19.4059(6), c = 15.4324(5) Å, β = 98.738(1)^°, V = 2727.7(2) ų, for Z = 4; 1-β C₂₅H₃₄N₈Br₂, triclinic, space group P-1, a = 9.6009(3), b = 10.7509(4), c = 14.2169(5) Å, α = 99.830(2), β = 105.973(3), γ = 95.578(1)^°, V = 1373.9(1) ų, for Z = 2.     

Crystal structures of oxalate-bearing cancrinite with an unusual arrangement of CO<Subscript>3</Subscript> groups and sulfate-rich davyne

The crystal structures of two unusual varieties of cancrinite-group minerals—oxalate-bearing cancrinite from the Kovdor massif (Kola Peninsula) and the sulfate end member of the davyne series from the Sar-e Sang mine (Badakhshan, Afghanistan)—were studied by single-crystal X-ray diffraction. The unit-cell parameters of the hexagonal cells are a = 12.688(4) Å, c = 5.189(1) Å and a = 12.773(1) Å, c = 5.334(1) Å, sp. gr. P6₃; the R factors are 0.034 and 0.035, respectively. The presence of oxalate groups in cancrinite as admixtures is one of the factors responsible for the shift of CO₃ groups in wide channels.     

X-Ray Structure Investigation of Sr<Subscript>3</Subscript>NbGa<Subscript>3</Subscript>Si<Subscript>2</Subscript>O<Subscript>14</Subscript> Langasite Family Crystal

An accurate structure analysis of Sr₃NbGa₃Si₂O₁₄ single crystals, belonging to the langasite family, has been performed. Two datasets are obtained on an Xcalibur S diffractometer equipped with a CCD detector. The structure is been refined using an averaged dataset: sp. gr. P 321, Z = 1, 295 K, sin θ/λ ≤ 1.35 Å^–1, a = 8.2797(3) Å, c = 5.0774(5) Å; the agreement factors between the model and experiment are found to be R/wR = 0.76/0.64% and Δρ_min/Δρ_max =–0.21/0.17 e/ų for 3820 independent ref lections. The Sr₃NbGa₃Si₂O₁₄ and Sr₃NbFe₃Si₂O₁₄ structures are compared, and the role of magnetic ions in the predicted P321 → P3 phase transition is analyzed.