Crystal structure of Schistosoma purine nucleoside phosphorylase complexed with a novel monocyclic inhibitor

A novel inhibitor of Schistosoma PNP was identified using an ""in silico"" approach allied to enzyme inhibition assays. The compound has a monocyclic structure which has not been previously described for PNP inhibitors The crystallographic structure of the complex was determined and used to elucidate the binding mode within the active site Furthermore, the predicted pose was very similar to that determined crystallographically, validating the methodology The compound Sm_VS1, despite its low molecular weight, possesses an IC(50) of 1 3 mu M, surprisingly low when compared with purine analogues This is presumably due to the formation of eight hydrogen bonds with key residues in the active site E203, N245 and T244. The results of this study highlight the importance of the use of multiple conformations for the target during virtual screening. Indeed the Sm_VS1 compound was only identified after flipping the N245 side chain It is expected that the structure will be of use in the development of new highly active non-purine based compounds against the Sclustosoma enzyme. (c) 2010 Elsevier B V. All rights reserved

Pt(II) and Ag(I) complexes with acesulfame: Crystal structure and a study of their antitumoral, antimicrobial and antiviral activities

Two new complexes of platinum(II) and silver(I) with acesulfame were synthesized. Acesulfame is in the anionic form acesulfamate (ace). The structures of both complexes were determined by X-ray crystallography. For K(2)[PtCl(2)(ace)(2)] the platinum atom is coordinated to two Cl(-) and two N-acesulfamate atoms forming a trans-square planar geometry. Each K(+) ion interacts with two oxygen atoms of the S(=O)(2) group of each acesulfamate. For the polymeric complex [Ag(ace)](n) the water molecule bridges between two crystallographic equivalent Agl atoms which are related each other by a twofold symmetry axis. Two Agl atoms, related to each other by a symmetry centre, make bond contact with two equivalent oxygen atoms. These bonds give rise to infinite chains along the unit cell diagonal in the ac plane. The in vitro cytotoxic analyses for the platinum complex using HeLa (human cervix cancer) cells show its low activity when compared to the vehicle-treated cells. The Ag(I) complex submitted to in vitro antimycobacterial tests, using the Microplate Alamar Blue (MABA) method, showed a good activity against Mycobacterium tuberculosis, responsible for tuberculosis, with a minimal inhibitory concentration (MIC) value of 11.6 mu M. The Ag(I) complex also presented a promising activity against Gram negative (Escherichia colt and Pseudomonas aeruginosa) and Gram positive (Enterococcus faecalis) microorganisms. The complex K(2)[PtCl(2)(ace)(2)] was also evaluated for antiviral properties against dengue virus type 2 (New Guinea C strain) in Vero cells and showed a good inhibition of dengue virus type 2 (New Guinea G strain) replication at 200 mu M, when compared to vehicle-treated cells. (C) 2010 Elsevier Inc. All rights reserved.

Synthesis, molecular structure and physicochemical properties of bis(3 `-azido-3 `-deoxythymidin-5 `-yl) carbonate

3`-Azido-3`-deoxythymidine (zidovudine, AZT), a synthetic analog of natural nucleoside thymidine, has been used extensively in AIDS treatments. We report here the synthesis. X-ray crystal and molecular structure, NMR, IR and Raman spectra and the thermal behavior of a novel carbonate of AZT [(AZT-O)(2)C=O], prepared by the reaction of zidovudine with carbonyldiimidazole. The carbonate compound, C(21)H(24)N(10)O(9), crystallizes in the tetragonal space group P4(1)2(1)2 with a = b = 15.284(1), c = 21.695(1) angstrom, and Z = 8 molecules per unit cell. It consists of two AZT moieties of closely related conformations which are bridged by a carbonyl group to adopt a folded Z-like shape. (C) 2010 Elsevier B.V. All rights reserved.

Synthesis, Structure, and Phosphatase-Like Activity of a New Trinuclear Gd Complex with the Unsymmetrical Ligand H(3)L As a Model for Nucleases

The new trinuclear gadolinium complex [Gd(3)L(2)(NO(3))(2)(H(2)O)(4)]NO(3)center dot 8H(2)O (1) with the unsymmetrical ligand 2-[N-bis-(2-pyridylmethyl)aminomethyl]-4-methyl-6-[N-bis(2-hydroxy-2-oxoethyl)aminomethyl] phenol (H(3)L) was synthesized and characterized. The new ligand H(3)L was obtained in good yield. Complex I crystallizes in an orthorhombic cell, space group Pcab. Kinetic studies show that complex 1 is highly active in the hydrolysis of the substrate 2,4-bis(dinitrophenyl)phosphate (K(m) = 4.09 mM, V(max) = 2.68 x 10(-2) mM s(-1), and k(cat) = V(max)/[1] = 0.67 s(-1)). Through a potentiometric study and determination of the kinetic behavior of 1 in acetonitrile/water solution, the species present in solution could be identified, and a trinuclear monohydroxo species appears to be the most prominent catalyst under mild conditions. Complex 1 displays high efficiency in DNA hydrolytic cleavage, and complete kinetic studies were carried out (K(m) = 4.57 x 10(-4) M, K(cat)` = 3.42 h(-1), and k(cat)`/K(m) = 7.48 x 10(3) M(-1) h(-1)). Studies with a radical scavenger (dimethyl sulfoxide, DMSO) showed that it did not inhibit the activity, indicating the hydrolytic action of 1 in the cleavage of DNA, and studies on the incubation of distamycin with plasmid DNA suggest that 1 is regio-specific, interacting with the minor groove of DNA.

Synthesis, Infrared Spectroscopy and Crystal Structure Determination of a New Decavanadate

Synthesis, infrared spectroscopy and crystal structure of a new potassium decavanadate decahydrate, K(6)[V(10)O(28)] 10H(2)O, has been reported The infrared spectrum is dominated by decavanadate polyanion and water bands The X-ray crystallography analysis found the compound crystallizes in a triclinic system with the parameters a = 10 5334 (4) angstrom, b = 10 6600 (4) angstrom, c = 17 7351 (5) angstrom, alpha = 76 940 (2)degrees, beta = 75 836 (2)degrees, gamma = 64 776 (2)degrees, V = 1,729 86 (11) A(3), Z = 2, space group P (1) over bar The polyanion consists of ten [VO(6)] octahedra sharing edges, in which the V-O distances are in good agreement with those reported for other decavanadates The crystal structure is stabilized by potassium cations and water molecules forming a complex pattern of hydrogen bonding and short contact ionic interactions

Experimental and theoretical investigation of molecular structure and conformation of the 4-isopropylthioxanthone

In this study, the molecular structure and conformational analyses of the 4-isopropylthioxanthone (4-ITX) are reported according to experimental and theoretical results. The compound crystallizes in the centrosymmetric P (1) over bar space group with only one molecule in the asymmetric unit, presenting the most stable conformation, in which the three fused-rings adopt a planar geometry, and the isopropyl group assumes a torsional angle with less sterical hindrance. The structural and conformational analyses were performed using theoretical calculations such as Hartree-Fock (HF), DFT method in combination with 6-311G(d,p) and 6-31++G(d,p) and the results were compared with infrared spectroscopy (FT-IR) and X-ray diffraction (XRD). The supramolecular assembly of 4-ITX is kept by non-classical C-H center dot center dot center dot O hydrogen bonds and weak interactions such as pi-pi stacking. 4-ITX was also studied by (1)H and (13)C NMR spectroscopy. UV-Vis absorption spectroscopic properties of the 4-ITX showed the long-wavelength maximum shifts towards high energy when the solvent polarity increases. (C) 2011 Elsevier B.V. All rights reserved.

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

Crystal structure of a soluble decoy receptor IL-22BP bound to interleukin-22

Interleukin-22 (IL-22) plays an important role in the regulation of immune and inflammatory responses in mammals. The IL-22 binding protein (IL-22BP), a soluble receptor that specifically binds IL-22, prevents the IL-22/interleukin-22 receptor 1 (IL-22R1)/interleukin-10 receptor 2 (IL-10R2) complex assembly and blocks IL-22 biological activity. Here we present the crystal structure of the IL-22/IL-22BP complex at 2.75 angstrom resolution. The structure reveals IL-22BP residues critical for IL-22 binding, which were confirmed by site-directed mutagenesis and functional studies. Comparison of IL-22/IL-22BP and IL-22/IL-22R1 crystal structures shows that both receptors display an overlapping IL-22 binding surface, which is consistent with the inhibitory role played by IL-22 binding protein.

Synthesis, characterization, and single crystal X-ray structure of the 1-furoyl-3-cyclohexylthiourea cadmium chloride complex, Cd[C4H3OC(O)NHC(S)NHC6H11]4Cl2

Cadmium chloride complex of 1-furoyl-3-cyclohexylthiourea (CyTu) was prepared and characterized by elemental analysis, IR, and Raman spectroscopy. The structure of the complex was determined by single crystal X-ray methods (space group Bbab, a = 20.918(1), b = 23.532(1), c = 23.571(1) angstrom, = = , Z = 8). Each cadmium has distorted octahedral geometry, coordinated by two chlorides and the thiocarbonyl sulfurs from four CyTu molecules. All the spectroscopic data are consistent with coordination of CyTu by sulfur to cadmium.

Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 angstrom resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis, for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting beta-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

Structure and thermal reactivity of Zn(II) salts of isocinchomeronic acid (2,5-pyridinedicarboxylic acid)

The synthesis, an improved refined crystal and molecular structure re-determination, and the thermal decomposition behavior of two Zn(II) derivatives of isocinchomeronic acid (2,5-pyridinedicarboxylic acid or H(2)2,5-pydc) are presented. [Zn(2,5-pydc)(H(2)O)(3)Zn(2,5-pydc)(H(2)O)(2)](2) (1) crystallizes in the triclinic P-1 space group with a = 7.106(2), b = 11.450(2), c = 11.869(1) angstrom, alpha = 107.29(1), beta = 104.08(1), gamma = 90.32(2)degrees, and Z = 2. [Zn(2,5-pydc)(H(2)O)(2)] center dot H(2)O (2) is orthorhombic (P2(1)2(1)2(1) space group), with a = 7.342(1), b = 9.430(1), c = 13.834(2) angstrom, and Z = 4. The structures were refined to agreement R(1)-factors of 0.0315 (1) and 0.0336 (2). Complex (1) is arranged as molecular Zn(4)(2,5-pydc)(4)(H(2)O)(10) tetramers, the cages of which define channels that remain unblocked by anions. Compound (2) is polymeric with Zn(2,5-pydc)(H(2)O)(2) and Zn(2,5-pydc)(H(2)O)(3) units linked through bridging ligands. Both compounds were synthesized under mild conditions in aqueous media, without need to resort to hydrothermal media. Changing the pH from 4.51 to 5.75 suffices to direct the chemical processes toward the orthorhombic compound rather than to the triclinic one.

Mode of operation and low-resolution structure of a multi-domain and hyperthermophilic endo-beta-1,3-glucanase from Thermotoga petrophila

1,3-beta-Glucan depolymerizing enzymes have considerable biotechnological applications including biofuel production, feedstock-chemicals and pharmaceuticals. Here we describe a comprehensive functional characterization and low-resolution structure of a hyperthermophilic laminarinase from Thermotoga petrophila (TpLam). We determine TpLam enzymatic mode of operation, which specifically cleaves internal beta-1,3-glucosidic bonds. The enzyme most frequently attacks the bond between the 3rd and 4th residue from the non-reducing end, producing glucose, laminaribiose and laminaritriose as major products. Far-UV circular dichroism demonstrates that TpLam is formed mainly by beta structural elements, and the secondary structure is maintained after incubation at 90 degrees C. The structure resolved by small angle X-ray scattering, reveals a multi-domain structural architecture of a V-shape envelope with a catalytic domain flanked by two carbohydrate-binding modules. Crown Copyright (C) 2011 Published by Elsevier Inc. All rights reserved.

Crystal structure of the (Mg,Fe)[UO2(P,As)O-4](2) center dot 10H(2)O solid solution - A novel mineral variety of saleeite

The crystal structure of a novel variety {[(Mg0.81Fe0.19)(H2O)(6)](H2O)(4)}{(UO2)[(P0.67As0.33)O-4]}(2) of the mineral saleeite is determined using X-ray diffraction (Bruker Smart diffractometer, lambda MoK alpha, graphite monochromator, 2 theta(max) = 56.62 degrees, R = 0.0321 for 2317 reflections, T = 100 K). The main crystal data are as follows: a = 6.952(6) angstrom, b = 19.865(5) , angstrom, c = 6.969(2) angstrom, beta = 90.806(4)degrees, space group P12(l)/n1, Z = 2, and P-calcd = 3.34 g/cm(3). It is shown that the structure is formed by alternating (along the [010] direction) anionic layers, which are composed of uranium bipyramids and T(P,As) tetrahedra, and cation layers consisting of M(Mg, Fe) octahedra and water molecules, which are joined through a system of asymmetric hydrogen bonds. The hydrogen atoms are located, the scheme of hydrogen bonds is established, and their geometric characteristics are calculated.

Menezesite, the first natural heteropolyniobate, from Cajati, Sao Paulo, Brazil: Description and crystal structure

Menezesite, ideally Ba2MgZr4(BaNb12O42)center dot 12H(2)O, occurs as a vug mineral in the contact zone between dolomite carbonatite and ""jacupirangite"" (=a pyroxenite) at the Jacupiranga mine, in Cajati county, Sao Paulo state, Brazil, associated with dolomite, calcite, magnetite, clinohumite, phlogopite, ancylite-(Ce), strontianite, pyrite, and tochilinite. This is also the type locality for quintinite-2H. The mineral forms rhombododecahedra up to I mm, isolated or in aggregates. Menezesite is transparent and displays a vitreous luster; it is reddish brown with a white streak. It is non-fluorescent. Mohs hardness is about 4. Calculated density derived from the empirical formula is 4.181 g/cm(3). It is isotropic, 1.93(1) (white light); n(calc) = 2.034. Menezesite exhibits weak anomalous birefringence. The empirical formula is (Ba1.47K0.53Ca0.3,Ce0.17Nd0.10Na0.06La0.02)(Sigma 2.66)(Mg0.94Mn0.23Fe0.23Al0.03)(Sigma 1.43)(Zr2.75Ti0.96Th0.29)(Sigma 4.00)[(Ba0.72Th0.26U0.02)(Sigma 1.00)(Nb9.23Ti2.29Ta0.36Si0.12)Sigma O-12.00(42)]center dot 12H(2)O. The mineral is cubic, space group 10 (204), a = 13.017(1) angstrom, V = 2206(1) angstrom(3), Z = 2. Menezesite is isostructural with the synthetic compound Mg-7[MgW12O42](OH)(4)center dot 8H(2)O. The mineral was named in honor of Luiz Alberto Dias Menezes Filho (born 1950), mining engineer, mineral collector and merchant. Both the description and the name were approved by the CNMMN-IMA (Nomenclature Proposal 2005-023). Menezesite is the first natural heteropolyniobate. Heteropolyanions have been employed in a range of applications that include virus-binding inorganic drugs (including the AIDs virus), homogeneous and heterogeneous catalysts, electro-optic and electrochromic materials, metal and protein binding, and as building blocks for nanostructuring of materials.

Footemineite, the Mn-analog of atencioite, from the Foote mine, Kings Mountain, Cleveland County, North Carolina, USA, and its relationship with other roscherite-group minerals

Footemineite, ideally Ca2Mn2+square Mn22+Be4(PO4)(6)(OH)(4)-6H(2)O, triclinic, is a new member of the roscherite group. It occurs on thin fractures crossing quartz-microcline-spodumene pegmatite at the Foote mine, Kings Mountain, Cleveland County, North Carolina, U.S.A. Associated minerals are albite, analcime, eosphorite, siderite/rhodochrosite, fairfieldite, fluorapatite, quartz, milarite, and pyrite. Footemineite forms prismatic to bladed generally rough to barrel-shaped crystals up to about 1.5 mm long and I mm in diameter. Its color is yellow, the streak is white, and the luster is vitreous to slightly pearly. Footemineite is transparent and non-fluorescent. Twinning is simple, by reflection, with twin boundaries across the length of the crystals. Cleavage is good on {0 (1) over bar1}) and {100}. Density (calc.) is 2.873 g/cm(3). Footemineite is biaxial (-), n(alpha) = 1.620(2), n(beta) = 1.627(2), n(gamma) = 1.634(2) (white light). 2V(obs) = 80 degrees, 2V(calc) = 89.6 degrees. Orientation: X boolean AND b similar to 12 degrees, Y boolean AND c similar to 15 degrees, Z boolean AND a similar to 15 degrees. Elongation direction is c, dispersion: r > v or r < v, weak. Pleochroism: beta (brownish yellow) > alpha = gamma (yellow). Mossbauer and IR spectra are given. The chemical composition is (EDS mode electron microprobe, Li and Be by ICP-OES, Fe3+:Fe2+ y Mossbauer, H2O by TG data, wt%): Li2O 0.23, BeO 9.54, CaO 9.43, SrO 0.23, BaO 0.24, MgO 0.18, MnO 26.16, FeO 2.77, Fe2O3 0.62, Al2O3 0.14, P2O5 36.58, SiO2 0.42, H2O 13.1, total 99.64. The empirical formula is (Ca1.89Sr0.03Ba0.02)Sigma(1.94)(Mn-0.90(2+)square(0.10))Sigma(1.00)(square 0.78Li0.17Mg0.05) Sigma(1.00)(Mn3.252+Fe0.432+ Fe0.093+Al0.03)Sigma(3.80) Be-4.30(P5.81Si0.08O24)[(OH)3.64(H2O)0.36]Sigma(4.00)center dot 6.00H(2)O . The strongest reflection peaks of the powder diffraction pattern [d, angstrom (1, %) (hkl)] are 9.575 (53) (010), 5.998 (100) (0 (1) over bar1), 4.848 (26) (021), 3.192 (44) (210), 3.003 (14) (0 (2) over bar2), 2.803 (38) ((1) over bar 03), 2.650 (29) ((2) over bar 02), 2.424 (14) (231). Single-crystal unit-cell parameters are a = 6.788(2), b = 9.972(3), c = 10.014(2) A, (x = 73.84(2), beta = 85.34(2), gamma = 87.44(2)degrees,V = 648.74 angstrom(3), Z = 1. The space group is P (1) over bar. Crystal structure was refined to R = 0.0347 with 1273 independent reflections (F > 2(5). Footemineite is dimorphous with roscherite, and isostructural with atencioite. It is identical with the mineral from Foote mine described as ""triclinic roscherite."" The name is for the Foote mine, type locality for this and several other minerals.