Lead(II)-induced formation and coordination of 3,4-dihydro-3-thioxo-1,2,4-triazin-5(2H)-one

Cyclization of (n)butyl glyoxylate thiosemicarbazone (HBuTSC) under reflux in the presence of Pb(OAc)(2) led to tile formation of the complex [Pb(HTz)(2)] (H(2)Tz = 3,4-dihydro-3-thioxo-1,2,4-triazin-5(2H)-one), which after recrystallization from DMSO afforded the polymer [Pb(Tz)](n), the first example of a Tz(2-) metal complex. (C) 2008 Elsevier B.V. All rights reserved.

New insights on the Lewis acidity of diorganolead(IV) compounds: Diphenyllead(IV) complexes with N,O,S-chelating ligands

The reactions of PbPh2(OAC)(2) with alkylglyoxylate thiosemicarbazones (HRGTSC, R = Et, Bu) afforded complexes of the type [PbPh2(GTSC)] center dot H2O, [PbPh2(RGTSC)(2)] and [PbPh2Cl(BUGTSC)]. The structures of HRGTSC (R = Me, Et, Bu), [PbPh2(OAc)(RGTSC)](R = Me, Et, Bu), [PbPh2Cl(BuGTSC)] and [PbPh2(GTSC)] center dot H2O have been studied by X-ray diffraction. [PbPh2(OAc)(RGTSC)] and [PbPh2(GTSC)] center dot H2O have [PbC2NO3S] kernels and the coordination sphere of the metal is pentagonal bipyramidal. [PbPh2Cl(BuGTSC)] has a [PbC2NOSCI] kernel and the coordination geometry around lead is pentagonal bipyramidal with one vacant site. Analysis of the bond distances in [PbPh2(GTSC)] center dot H2O suggests a significant affinity between diphenyllead(IV) and carboxylate donor groups, supporting a borderline acidic character for this organometallic cation. H-1 and C-13 NMR spectra in DMSO-d(6) suggest the partial dissociation of the acetate in [PbPh2(OAc)(RGTSC)] solutions and indicate some differences in the coordination mode of the two RGTSC(-) ligands in [PbPh2(RGTSC)(2)] complexes. (C) 2007 Elsevier Ltd. All rights reserved.

New Pd(II) and Pt(II) complexes with N,S-chelated pyrazolonate ligands: Molecular and supramolecular structure and preliminary study of their in vitro antitumoral activity

New Pd(II) and Pt(II) complexes [ML2] (HL = a substituted 2,5-dihydro-5-oxo-1H-pyrazolone-1-carbothioamide) have been synthesized by reacting K2MCl4 (M = Pd, Pt) or Pd(OAc)(2) with beta-ketoester thiosemicarbazones. The structures of seven of these complexes were determined by X-ray diffraction. Although all exhibit a distorted square-planar coordination with trans- or (in one case) cis-[MN2S2] kernels, their supramolecular arrangements vary widely from isolated molecules to 3D-networks. The in vitro antitumoral assays performed with two HL ligands and their metal complexes showed significant cytostatic activity for the latter, with the most active [ML2] derivative (a palladium complex) being about sixteen times more active than cis-DDP against the cis-platinum-resistant cell line A2780cisR. (c) 2007 Elsevier Inc. All rights reserved.

The binding of synthetic triiodo L-thyronine analogs to human transthyretin: Molecular basis of cooperative and non-cooperative ligand recognition

Transthyretin (TTR) is a tetrameric beta-sheet-rich transporter protein directly involved in human amyloid diseases. Several classes of small molecules can bind to TTR delaying its amyloid fibril formation, thus being promising drug candidates to treat TTR amyloidoses. In the present study, we characterized the interactions of the synthetic triiodo L-thyronine analogs and thyroid hormone nuclear receptor TR beta-selecfive agonists GC-1 and GC-24 with the wild type and V30M variant of human transthyretin (TTR). To achieve this aim, we conducted in vitro TTR acid-mediated aggregation and isothermal titration calorimetry experiments and determined the TTR:GC-1 and TTR:GC-24 crystal structures. Our data indicate that both GC-1 and GC-24 bind to TTR in a non-cooperative manner and are good inhibitors of TTR aggregation, with dissociation constants for both hormone binding sites (HBS) in the low micromolar range. Analysis of the crystal structures of TTRwt:GC-1(24) complexes and their comparison with the TTRwt X-ray structure bound to its natural ligand thyroxine (T4) suggests, at the molecular level, the basis for the cooperative process displayed by T4 and the non-cooperative process provoked by both GC-1 and GC-24 during binding to TTR. (C) 2010 Elsevier Inc. All rights reserved.

Electronic Structure and Spectro-Structural Correlations of Fe(III)Zn(II) Biomimetics for Purple Acid Phosphatases: Relevance to DNA Cleavage and Cytotoxic Activity

Purple acid phosphatases (PAPs) are a group of metallohydrolases that contain a dinuclear Fe(II)M(II) center (M(II) = Fe, Mn, Zn) in the active site and are able to catalyze the hydrolysis of a variety of phosphoric acid esters. The dinuclear complex [(H(2)O)Fe(III)(mu-OH)Zn(II)(L-H)](CIO(4))(2) (2) with the ligand 2-[N-bis(2-pyridylmethyl)aminomethyl]-4-methyl-6-[N-(2-pyridylmethyl)(2-hydroxybenzyl) aminomethyl]phenol (H(2)L-H) has recently been prepared and is found to closely mimic the coordination environment of the Fe(III)Zn(II) active site found in red kidney bean PAP (Neves et al. J. Am. Chem. Soc. 2007, 129, 7486). The biomimetic shows significant catalytic activity in hydrolytic reactions. By using a variety of structural, spectroscopic, and computational techniques the electronic structure of the Fe(III) center of this biomimetic complex was determined. In the solid state the electronic ground state reflects the rhombically distorted Fe(III)N(2)O(4) octahedron with a dominant tetragonal compression align ad along the mu-OH-Fe-O(phenolate) direction. To probe the role of the Fe-O(phenolate) bond, the phenolate moiety was modified to contain electron-donating or -withdrawing groups (-CH(3), -H, -Br, -NO(2)) in the 5-position. Tie effects of the substituents on the electronic properties of the biomimetic complexes were studied with a range of experimental and computational techniques. This study establishes benchmarks against accurate crystallographic struck ral information using spectroscopic techniques that are not restricted to single crystals. Kinetic studies on the hydrolysis reaction revealed that the phosphodiesterase activity increases in the order -NO(2)<- Br <- H <- CH(3) when 2,4-bis(dinitrophenyl)phosphate (2,4-bdnpp) was used as substrate, and a linear free energy relationship is found when log(k(cat)/k(0)) is plotted against the Hammett parameter a. However, nuclease activity measurements in the cleavage of double stranded DNA showed that the complexes containing the electron-withdrawing -NO(2) and electron-donating CH3 groups are the most active while the cytotoxic activity of the biomimetics on leukemia and lung tumoral cells is highest for complexes with electron-donating groups.

Dithiocarbazate complexes with the [M(PPh(3))](2+) (M=Pd or Pt) moiety Synthesis, characterization and anti-Tripanosoma cruzi activity

New neutral Pd(II) and Pt(II) complexes of the type [M(L)(PPh(3))] (M Pd or Pt) were prepared in crystalline form in high-yield synthesis with the S-benzyldithiocarbazates and S-4-nitrobenzyldithiocarbazates derivatives from 2-hydroxyacetophenone, H(2)L(1a) and H(2)L(1b), and benzoylacetone, H(2)L(2a) and H(2)L(2b). The new complexes [Pt(L(1a))(PPh(3))] (1), [Pd(L(1a))(PPh(3))] (2), [Pt(L(1b))(PPh(3))] (3), [Pd(L(1b))(PPh(3))] (4), [Pt(L(2a))(PPh(3))] (5), [Pd(L(2a))(PPh(3))] (6), [Pt(L(2b))(PPh(3))] (7) and [Pd(L(2b))(PPh(3))] (8) were characterized on the basis of elemental analysis, conductivity measurements, UV-visible, IR, electrospray ionization mass spectrometry (ESI-MS), NMR ((1)H and (31)P) and by X-ray diffraction studies. The studies showed that differently from what was observed for the H(2)L(1a) and H(2)L(1b) ligands, H(2)L(2a) and H(2)L(2b) assume cyclic forms as 5-hydroxypyrazolinic. Upon coordination, H2L2a and H2L2b suffer ring-opening reaction, coordinating in the same manner as H(2)L(1a) and H(2)L(1b), deprotonated and in O,N,S-tridentate mode to the (MPPh(3))(2+) moiety. All complexes show a quite similar planar fourfold environment around the M(II) center. Furthermore, these complexes exhibited biological activity on extra and intracellular forms of Trypanosoma cruzi in a time- and concentration-dependent manner with IC(50) values ranging from 7.8 to 18.7 mu M, while the ligand H(2)L(2a) presented a trypanocidal activity on trypomastigote form better than the standard drug benznidazole. (C) 2010 Elsevier Inc. All rights reserved.

Structural relationships in the solid state of the anti-chagas agent (E)-phenylethenylbenzofuroxan

The crystal structure and the vibrational spectrum of a potential drug for Chagas`s disease treatment, the (E)-isomer of phenylethenylbenzofuroxan 1 (5(6)(E)-[(2-phenylethenyl)]benzo[1,2-c]1,2,5-oxadiazole N-oxide), are reported. In order to provide insights into structural relationships, quantum mechanical calculations were employed starting from crystal structure. These results have given theoretical support to state interesting structural features, such as the effect of some intermolecular contacts on the molecule conformation and the electronic delocalization decreasing through atoms of the benzofuroxan moiety. Furthermore, the MOGUL comparative analysis in the Cambridge Structural Database provided additional evidences on these structural behaviors of compound 1. Intermolecular contacts interfere on the intramolecular geometry, as, for instance, on the phenyl group orientation, which is twisted by 12.32(6)A degrees from the ethenylbenzofuroxan plane. The experimental Raman spectrum of compound 1 presents unexpected frequency shift and also anomalous Raman activities. At last, the molecule skeleton deformation and the characteristic vibrational modes were correlated by matching the experimental Raman spectrum to the calculated one.

Purification, and Biochemical and Biophysical Characterization of Cellobiohydrolase I from Trichoderma harzianum IOC 3844

Because of its elevated cellulolytic activity, the filamentous fungus Trichoderma harzianum has a considerable potential in biomass hydrolysis applications. Trichoderma harzianum cellobiohydrolase I (ThCBHI), an exoglucanase, is an important enzyme in the process of cellulose degradation. Here, we report an easy single-step ion-exchange chromatographic method for purification of ThCBHI and its initial biophysical and biochemical characterization. The ThCBHI produced by induction with microcrystalline cellulose under submerged fermentation was purified on DEAE-Sephadex A-50 media and its identity was confirmed by mass spectrometry. The ThCBHI biochemical characterization showed that the protein has a molecular mass of 66 kDa and pi of 5.23. As confirmed by small-angle X-ray scattering (SAXS), both full-length ThCBHI and its catalytic core domain (CCD) obtained by digestion with papain are monomeric in solution. Secondary structure analysis of ThCBHI by circular dichroism revealed alpha-helices and beta-strands contents in the 28% and 38% range, respectively. The intrinsic fluorescence emission maximum of 337 nm was accounted for as different degrees of exposure of ThCBHI tryptophan residues to water. Moreover, ThCBHI displayed maximum activity at pH 5.0 and temperature of 50 degrees C with specific activities against Avicel and p-nitrophenyl-beta-D-cellobioside of 1.25 U/mg and 1.53 U/mg, respectively.

A powder X-ray diffraction method for detection of polyprenylated benzophenones in plant extracts associated with HPLC for quantitative analysis

A robust, direct, rapid and non-destructive X-ray diffraction crystallography method to detect the polyprenylated benzophenones 7-epi-clusianone (1) and guttiferone A (2) in extracts from Garcinia brasiliensis is presented. Powder samples of benzophenones 1 and 2, dried hexane extracts from G. brasiliensis seeds and fruit`s pericarp, and the dried ethanolic extract from G. brasiliensis seeds were unambiguously characterized by powder X-ray diffractometry. The calculated X-ray diffraction peaks from crystal structures of analytes 1 and 2, previously determined by single-crystal X-ray diffraction technique, were overlaid to those of the experimental powder diffractograms, providing a practical identification of these compounds in the analyzed material and confirming the pure contents of the powder samples. Using the X-ray diffraction crystallography method, the studied polyprenylated benzophenones were selectively and simultaneously detected in the extracts which were mounted directly on sample holder. In addition, reference materials of the analytes were not required for analyses since the crystal structures of the compounds are known. High performance liquid chromatography analyses also were comparatively carried out to quantify the analytes in the same plant extracts showing to be in agreement with X-ray diffraction crystallography method. (C) 2010 Elsevier B.V. All rights reserved.

Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example

Alzheimer`s disease is an ultimately fatal neurodegenerative disease, and BACE-1 has become an attractive validated target for its therapy, with more than a hundred crystal structures deposited in the PDB. In the present study, we present a new methodology that integrates ligand-based methods with structural information derived from the receptor. 128 BACE-1 inhibitors recently disclosed by GlaxoSmithKline R&D were selected specifically because the crystal structures of 9 of these compounds complexed to BACE-1, as well as five closely related analogs, have been made available. A new fragment-guided approach was designed to incorporate this wealth of structural information into a CoMFA study, and the methodology was systematically compared to other popular approaches, such as docking, for generating a molecular alignment. The influence of the partial charges calculation method was also analyzed. Several consistent and predictive models are reported, including one with r (2) = 0.88, q (2) = 0.69 and r (pred) (2) = 0.72. The models obtained with the new methodology performed consistently better than those obtained by other methodologies, particularly in terms of external predictive power. The visual analyses of the contour maps in the context of the enzyme drew attention to a number of possible opportunities for the development of analogs with improved potency. These results suggest that 3D-QSAR studies may benefit from the additional structural information added by the presented methodology.

Flexibility and inhibitor binding in Cdc25 phosphatases

Cdc25 phosphatases involved in cell cycle checkpoints are now active targets for the development of anti-cancer therapies. Rational drug design would certainly benefit from detailed structural information for Cdc25s. However, only apo- or sulfate-bound crystal structures of the Cdc25 catalytic domain have been described so far. Together with previously available crystalographic data, results from molecular dynamics simulations, bioinformatic analysis, and computer-generated conformational ensembles shown here indicate that the last 30-40 residues in the C-terminus of Cdc25B are partially unfolded or disordered in solution. The effect of C-terminal flexibility upon binding of two potent small molecule inhibitors to Cdc25B is then analyzed by using three structural models with variable levels of flexibility, including an equilibrium distributed ensemble of Cdc25B backbone conformations. The three Cdc25B structural models are used in combination with flexible docking, clustering, and calculation of binding free energies by the linear interaction energy approximation to construct and validate Cdc25B-inhibitor complexes. Two binding sites are identified on top and beside the Cdc25B active site. The diversity of interaction modes found increases with receptor flexibility. Backbone flexibility allows the formation of transient cavities or compact hydrophobic units on the surface of the stable, folded protein core that are unexposed or unavailable for ligand binding in rigid and densely packed crystal structures. The present results may help to speculate on the mechanisms of small molecule complexation to partially unfolded or locally disordered proteins.

Structure, Dynamics, and RNA Interaction Analysis of the Human SBDS Protein

Shwachman-Bodian-Diamond syndrome is an autosomal recessive genetic syndrome with pleiotropic phenotypes, including pancreatic deficiencies, bone marrow dysfunctions with increased risk of myelodysplasia or leukemia, and skeletal abnormalities. This syndrome has been associated with mutations in the SBDS gene, which encodes a conserved protein showing orthologs in Archaea and eukaryotes. The Shwachman-Bodian-Diamond syndrome pleiotropic phenotypes may be an indication of different cell type requirements for a fully functional SBDS protein. RNA-binding activity has been predicted for archaeal and yeast SBDS orthologs, with the latter also being implicated in ribosome biogenesis. However, full-length SBDS orthologs function in a species-specific manner, indicating that the knowledge obtained from model systems may be of limited use in understanding major unresolved issues regarding SBDS function, namely, the effect of mutations in human SBDS on its biochemical function and the specificity of RNA interaction. We determined the solution structure and backbone dynamics of the human SBDS protein and describe its RNA binding site using NMR spectroscopy. Similarly to the crystal structures of Archaea, the overall structure of human SBDS comprises three well-folded domains. However, significant conformational exchange was observed in NMR dynamics experiments for the flexible linker between the N-terminal domain and the central domain, and these experiments also reflect the relative motions of the domains. RNA titrations monitored by heteronuclear correlation experiments and chemical shift mapping analysis identified a classic RNA binding site at the N-terminal FYSH (fungal, Yhr087wp, Shwachman) domain that concentrates most of the mutations described for the human SBDS. (C) 2010 Elsevier Ltd. All rights reserved.

PILZ Protein Structure and Interactions with PILB and the FIMX EAL Domain: Implications for Control of Type IV Pilus Biogenesis

The PilZ protein was originally identified as necessary for type IV pilus (T4P) biogenesis. Since then, a large and diverse family of bacterial PilZ homology domains have been identified, some of which have been implicated in signaling pathways that control important processes, including motility, virulence and biofilm formation. Furthermore, many PilZ homology domains, though not PilZ itself, have been shown to bind the important bacterial second messenger bis(3`-> 5`)cyclic diGMP (c-diGMP). The crystal structures of the PilZ orthologs from Xanthomonas axonopodis pv Citri (PilZ(XAC1133), this work) and from Xanthomonas campestris pv campestris (XC1028) present significant structural differences to other PilZ homologs that explain its failure to bind c-diGMP. NMR analysis of PilZ(XAC1133) shows that these structural differences are maintained in solution. In spite of their emerging importance in bacterial signaling, the means by which NZ proteins regulate specific processes is not clear. In this study, we show that PilZ(XAC1133) binds to PilB, an ATPase required for TV polymerization, and to the EAL domain of FiMX(XAC2398), which regulates TV biogenesis and localization in other bacterial species. These interactions were confirmed in NMR, two-hybrid and far-Western blot assays and are the first interactions observed between any PilZ domain and a target protein. While we were unable to detect phosphodiesterase activity for FimXX(AC2398) in vitro, we show that it binds c-diGMP both in the presence and in the absence of PilZ(XAC1133). Site-directed mutagenesis studies for conserved and exposed residues suggest that PilZ(XAC1133) interactions with FimX(XAC2398) and PilB(XAC3239) are mediated through a hydrophobic surface and an unstructured C-terminal extension conserved only in PilZ orthologs. The FimX-PilZ-PilB interactions involve a full set of ""degenerate"" GGDEF, EAL and PilZ domains and provide the first evidence of the means by which PilZ orthologs and FimX interact directly with the TP4 machinery. (C) 2009 Elsevier Ltd. All rights reserved.

Dinuclear Azide-Bridged Copper(II) Complex as Building Block for the Assembly of a 2D-Supramolecular Array

A novel Schiff base-copper(II) complex [Cu(2)L(2)(N(3))(2)](ClO(4))(2) 1, where L = (4-imidazolyl)ethylene-2-amino-1-ethylpyridine (apyhist), containing azide-bridges between adjacent copper ions in a dinuclear arrangement was isolated and characterized both in the solid state and in solution by X-ray crystallography and different spectroscopic techniques. Azide binding constants were estimated from titrations of the precursor [CuL(H(2)O)(2)](2+) solutions with sodium azide, giving rise to the azido-bridged species, [Cu(2)L(2)(N(3))(2)](2+). Raman spectra showed asymmetric stretching band at 2060 cm(-1), indicating the presence of azido ligands with a symmetric mu(1,) (1) binding geometry. EPA spectra, in frozen methanol/water solutions at 77 K, exhibited characteristic features of copper centers in tetragonal pyramidal coordination geometry, exhibiting magnetic interactions between them. Further, in solid state, two different values for magnetic coupling in this species were obtained, J/k = -(5.14 +/- 0.02) cm(-1) attributed to the mu(1, 1) azide-bridge mode, and J`z`/k = -(2.94 +/- 0.11) cm(-1) for the interaction between dinuclear moieties via water/perchorate bridges. Finally, an attempt was made to correlate structure and magnetic data for this dinuclear asymmetric end-on azido bridged-copper(II) 1 complex with those of another correlated dinuclear system, complex [Cu(2)L(2)Cl(2)](ClO(4))(2) 2, containing the same tridentate diimine ligand, but with chloro-bridged groups between the copper centres.

Formation of out of plane oxime metallacycles in [Cu(2)] and [Cu(4)] complexes

The reaction Of Cu(ClO(4))(2)center dot 6H(2)O with dimethylglyoxime (H(2)dmg) in a 1:1 mole ratio in aqueous methanol at room temperature affords the dinuclear complex [Cu(2)(mu-Hdmg)(4)] (1). Reaction of 1 with [Cu(bpy)(H(2)O)(2)](ClO(4))(2) (bpy = 2,2`-bipyridine) in a 1:1 mole ratio in aqueous methanol at room temperature yields the tetranuclear complex [Cu(2)(mu-HdMg)(2)(mu-dMg)(2)(bpy)(2)(H(2)O)(2)](ClO(4))(2) (2). The direct reaction of Cu(ClO(4))(2)center dot 6H(2)O with H(2)dmg and bpy in a 2:21 mole ratio in aqueous methanol at room temperature also yields 2 quantitatively. The complexes 1 and 2 were structurally characterized by X-ray crystallography. Unlike the binding in Ni/Co-dmg, two different types of N-O bridging modes during the oxime based metallacycle formation and stacking of square planar units have been identified in these complexes. The neutral dinuclear complex 1 has CuN(4)O coordination spheres and complex 2 consists of a dicationic [Cu(2)(mu-HdMg)(2)(mu-dMg)(2)(bpy)(2)(H(2)O)(2)](2+) unit and two uncoordinated ClO(4)(-) anions having CuN(4)O and CuN(2)O(3) coordination spheres. The two copper(II) ions are at a distance of 3.846(8) angstrom in 1 for the trans out of plane link and at 3.419(10) and 3.684(10) angstrom in 2 for the trans out of plane and cis in plane arrangements, respectively. The average Cu-N(oxime) distances are 1.953 and 1.935 angstrom, respectively. The average basal and apical Cu-N(oxime) distances are 1.945, 2.295 and 2.429 angstrom. The UV-Vis spectra of 2 is similar to the spectrum of the reaction mixture of 1 and [Cu(bpy)(H(2)O)(2)](2+). Variable temperature magnetic properties measurement shows that the interaction between the paramagnetic copper centers in complex I is antiferromagnetic in nature. The EPR spectra of frozen solution of the complexes at 77 K consist of axially symmetric fine-structure transitions (Delta M(S) = 1) and half-field signals (Delta M(S) = 2) at ca. 1600 G, suggesting the presence of appreciable Cu-Cu interactions. (C) 2009 Elsevier Ltd. All rights reserved.