Simple 1,4-benzoquinones with antibacterial activity from stems and leaves of Gunnera perpensa

From the dichloromethane extract of the leaves and stems of Gunnera perpensa two new, simple 1,4-benzoquinones and a known benzopyran-6-ol were isolated. From the methanol extract phytol was obtained. The two benzoquinones, 2-methyl-6-(-3-methyl-2-butenyl)benzo-1,4-quinone (1) and 3-hydroxy-2-methyl-5-(3-methyl-2-butenyl)benzo-1,4-quinone (2) and the benzopyran, 6-hydroxy-8-methyl-2,2-dimethyl-2H-benzopyran (3) were examined for antimicrobial properties together with the crude stem, leaf and root extracts. Minimum inhibitory concentration (MIC) assays were used to quantify antimicrobial activity and the MIC values for the crude extracts of stems, roots and leaves ranged between 100 microg and >16 mg/ml against the eight microorganisms investigated. Compound 1 showed significant antimicrobial activity with the most sensitive organism being Staphylococcus epidermidis with an MIC of 9.8 microg/ml. For compound 2, no activity was noted. Compound 3 exhibited good activity against the yeasts Cryptococcus neoformans (75 microg/ml) and Candida albicans (37.5 microg/ml).     

Minor pyrano-isoflavones from Eriosema kraussianum: activity-, structure-, and chemical reaction studies

The isolation and identification of two minor pyrano-isoflavones from Eriosema kraussianum is described. New studies on the original pyrano-isoflavones shows that: (i) kraussianone 2 (a major compound in the plant) can be cyclised under acid conditions, (ii) kraussianones 3 and 5 cause contraction (not relaxation as anticipated) of corpus cavernosum tissue and (iii) the structures proposed previously for 4 and 5 are confirmed by the data obtained from an X-ray study of 5.     

Crystal structure of exo-inulinase from Aspergillus awamori: the enzyme fold and structural determinants of substrate recognition

Exo-inulinases hydrolyze terminal, non-reducing 2,1-linked and 2,6-linked beta-d-fructofuranose residues in inulin, levan and sucrose releasing beta-d-fructose. We present the X-ray structure at 1.55A resolution of exo-inulinase from Aspergillus awamori, a member of glycoside hydrolase family 32, solved by single isomorphous replacement with the anomalous scattering method using the heavy-atom sites derived from a quick cryo-soaking technique. The tertiary structure of this enzyme folds into two domains: the N-terminal catalytic domain of an unusual five-bladed beta-propeller fold and the C-terminal domain folded into a beta-sandwich-like structure. Its structural architecture is very similar to that of another member of glycoside hydrolase family 32, invertase (beta-fructosidase) from Thermotoga maritima, determined recently by X-ray crystallography The exo-inulinase is a glycoprotein containing five N-linked oligosaccharides. Two crystal forms obtained under similar crystallization conditions differ by the degree of protein glycosylation. The X-ray structure of the enzyme:fructose complex, at a resolution of 1.87A, reveals two catalytically important residues: Asp41 and Glu241, a nucleophile and a catalytic acid/base, respectively. The distance between the side-chains of these residues is consistent with a double displacement mechanism of reaction. Asp189, which is part of the Arg-Asp-Pro motif, provides hydrogen bonds important for substrate recognition.     

Fucoidans from the brown seaweed Adenocystis utricularis: extraction methods,antiviral activity and structural studies

The brown seaweed Adenocystis utricularis (family Adenocystaceae, order Ectocarpales sensu lato) was extracted in parallel with three solvents usually utilized for obtaining fucoidans: distilled water, 2% calcium chloride solution and diluted hydrochloric acid (pH 2) solution. In each case, the extraction was effected at room temperature and then at 70 degrees C. The extraction yields and characteristics of the products were similar in the three cases, with only minor differences. The analytical features of the products indicate that two different types of fucoidans are present in this seaweed. One of them, mostly extracted at room temperature, is composed mainly of L-fucose, D-galactose and ester sulfate (the 'galactofucan'). The other product (the 'uronofucoidan') is the major component of the extracts obtained at 70 degrees C. It is composed mainly of fucose, accompanied by other monosaccharides (mostly Man, but also Glc, Xyl, Rha and Gal), significant amounts of uronic acids and low proportions of sulfate ester. Fractionation with the cationic detergent cetrimide has allowed achieving a better separation of the galactofucan and uronofucoidan components. The galactofucans show a high inhibitory activity against herpes simplex virus 1 and 2, with no cytotoxicity, whereas the uronofucoidans carry no antiviral activity. Structural studies on the galactofucan fractions were carried out by methylation analysis, desulfation and NMR spectroscopy. The fucan constituent is mainly composed of 3-linked alpha-L-fucopyranosyl backbone, mostly sulfated at C-4, and branched at C-2 with non-sulfated fucofuranosyl and fucopyranosyl units, and 2-sulfated fucopyranosyl units. The galactan moiety is more heterogeneous, with predominant D-galactopyranose units linked on C-3 and C-6, and sulfation mostly on C-4, even in terminal non-reducing units. It may be inferred that at least some of these galactose units carry the alpha-configuration.     

Comparative structural analysis of oxidized and reduced thioredoxin from Drosophila melanogaster

Thioredoxins (Trx) participate in essential antioxidant and redox-regulatory processes via a pair of conserved cysteine residues. In dipteran insects like Drosophila and Anopheles, which lack a genuine glutathione reductase (GR), thioredoxins fuel the glutathione system with reducing equivalents. Thus, characterizing Trxs from these organisms contributes to our understanding of redox control in GR-free systems and provides information on novel targets for insect control. Cytosolic Trx of Drosophila melanogaster (DmTrx) is the first thioredoxin that was crystallized for X-ray diffraction analysis in the reduced and in the oxidized form. Comparison of the resulting structures shows rearrangements in the active-site regions. Formation of the C32-C35 disulfide bridge leads to a rotation of the side-chain of C32 away from C35 in the reduced form. This is similar to the situation in human Trx and Trx m from spinach chloroplasts but differs from Escherichia coli Trx, where it is C35 that moves upon change of the redox state. In all four crystal forms that were analysed, DmTrx molecules are engaged in a non-covalent dimer interaction. However, as demonstrated by gel-filtration analyses, DmTrx does not dimerize under quasi in vivo conditions and there is no redox control of a putative monomer/dimer equilibrium. The dimer dissociation constants K(d) were found to be 2.2mM for reduced DmTrx and above 10mM for oxidized DmTrx as well as for the protein in the presence of reduced glutathione. In human Trx, oxidative dimerization has been demonstrated in vitro. Therefore, this finding may indicate a difference in redox control of GR-free and GR-containing organisms.     

Biochemical and structural studies of a l-haloacid dehalogenase from the thermophilic archaeon Sulfolobus tokodaii

Haloacid dehalogenases have potential applications in the pharmaceutical and fine chemical industry as well as in the remediation of contaminated land. The l-2-haloacid dehalogenase from the thermophilic archaeon Sulfolobus tokodaii has been cloned and over-expressed in Escherichia coli and successfully purified to homogeneity. Here we report the structure of the recombinant dehalogenase solved by molecular replacement in two different crystal forms. The enzyme is a homodimer with each monomer being composed of a core-domain of a β-sheet bundle surrounded by α-helices and an α-helical sub-domain. This fold is similar to previously solved mesophilic l-haloacid dehalogenase structures. The monoclinic crystal form contains a putative inhibitor l-lactate in the active site. The enzyme displays haloacid dehalogenase activity towards carboxylic acids with the halide attached at the C2 position with the highest activity towards chloropropionic acid. The enzyme is thermostable with maximum activity at 60°C and a half-life of over 1 h at 70°C. The enzyme is relatively stable to solvents with 25% activity lost when incubated for 1 h in 20% v/v DMSO.     

Magnetic and structural studies of novel tetranickel hydroxamates

The dinickel(II) compound [Ni₂(μ-OAc)₂(OAc)₂(μ-H₂O)(asy·dmen)₂]·2.5H₂O, 1; undergoes facile reaction in a 1:2 molar ratio with benzohydroxamic acid (BHA) in ethanol to give the novel nickel(II) tetranuclear hydroxamate complex [Ni₄(μ-OAc)₃(μ-BA)₃(asy·dmen)₃][OTf]₂·H₂O, 2, in which the bridging acetates, bridging two nickel atoms in 1, undergo a carboxylate shift from the μ₂-η¹:η¹ bridging mode of binding to the μ₃-η¹:η² bridging three nickel atoms in the tetramer. The structure of complex 2 was determined by single-crystal X-ray crystallography. The two monodentate acetates, water and two bidentate bridging acetates of two moles of complex 1 are replaced by three monodentate bridging acetates and three benzohydroxamates. Three nickel atoms in the tetramer, Ni(2), Ni(3) and Ni(4) are in a N₂O₄ octahedral environment, while the fourth nickel atom Ni(1) is in an O(6) octahedral environment. The Ni-Ni separations are Ni(1)-Ni(2) = 3.108 Å, Ni(1)-Ni(3) = 3.104 Å and Ni(1)-Ni(4) = 3.110 Å, which are longer than previously studied in dinuclear urease inhibited models but shorter than in the nickel(II) tetrameric glutarohydroxamate complex [Ni₄(μ-OAc)₂(μ-gluA₂)₂(tmen)₄][OTf]₂, isolated and characterized previously in this laboratory. Magnetic studies of the tetrameric complex show that the four Ni(II) ions are ferromagnetically coupled, leading to a total ground spin state S_T = 4. Three analogous tetranuclear nickel hydroxamates were prepared from AHA and BHA and the appropriate dinuclear complex with either sy·dmen or asy·dmen as capping ligands.     

Palladium(II) complexes of a bis-2-aminobiphenyl N-heterocyclic carbene: Synthesis, structural studies and catalytic activity

A new imidazolinium [(SIBiphen)H](BF₄) was synthesized in three steps from 2-aminobiphenyl. The reaction of the salt with Pd(OAc)₂, NaI and t-BuOK gave a dimeric Pd(II) complex [(SIBiphen)PdI₂]₂, which was analyzed by an X-ray diffraction study. The reaction of [Pd(allyl)Cl]₂, the imidazolinium salt and t-BuOK in THF at −78 °C gave the monomeric Pd complex, in which the N-heterocyclic carbene was bound to the metal centre, as confirmed by a single-crystal X-ray diffraction study. A preliminary catalytic study showed that these new systems were moderately active in the Suzuki-Miyaura coupling of aryl halides.     

The structural basis for exopolygalacturonase activity in a family 28 glycoside hydrolase

Family 28 glycoside hydrolases (polygalacturonases) are found in organisms across the plant, fungal and bacterial kingdoms, where they are central to diverse biological functions such as fruit ripening, biomass recycling and plant pathogenesis. The structures of several polygalacturonases have been reported; however, all of these enzymes utilize an endo-mode of digestion, which generates a spectrum of oligosaccharide products with varying degrees of polymerization. The structure of a complementary exo-acting polygalacturonase and an accompanying explanation of the molecular determinants for its specialized activity have been noticeably lacking. We present the structure of an exopolygalacturonase from Yersinia enterocolitica, YeGH28 in a native form (solved to 2.19 A resolution) and a digalacturonic acid product complex (solved to 2.10 A resolution). The activity of YeGH28 is due to inserted stretches of amino acid residues that transform the active site from the open-ended channel observed in the endopolygalacturonases to a closed pocket that restricts the enzyme to the exclusive attack of the non-reducing end of oligogalacturonide substrates. In addition, YeGH28 possesses a fused FN3 domain with unknown function, the first such structure described in pectin active enzymes.     

Easy access to various natural keto polyunsaturated fatty acids and their corresponding racemic alcohols

Various optically active hydroxy derivatives of polyunsaturated fatty acids were easily oxidised to their corresponding keto derivatives using Dess-Martin periodinane. The reaction was run on the millimolar scale with good yields and without appreciable isomerisation of the surrounding double bonds. Reduction of these keto compounds to yield back the starting alcohols, but now as racemic mixtures, was also conducted using CeCl(3)-NaBH(4), once again without noticeable modification of the stereochemistry of the double bonds. These reactions proved the usefulness of the chemoenzymatic access to oxylipins through the use of lipoxygenases with various regiospecificity, combined with chemical transformations of the formed hydro(pero)xides.     

Isolation and structural characterisation of two antibacterial free fatty acids from the marine diatom, <Emphasis Type="Italic">Phaeodactylum tricornutum</Emphasis>

One solution to the global crisis of antibiotic resistance is the discovery of novel antimicrobial compounds for clinical application. Marine organisms are an attractive and, as yet, relatively untapped resource of new natural products. Cell extracts from the marine diatom, Phaeodactylum tricornutum, have antibacterial activity and the fatty acid, eicosapentaenoic acid (EPA), has been identified as one compound responsible for this activity. During the isolation of EPA, it became apparent that the extracts contained further antibacterial compounds. The present study was undertaken to isolate these additional antibacterial factors using silica column chromatography and reverse-phase high-performance liquid chromatography. Two antibacterial fractions, each containing a pure compound, were isolated and their chemical structures were investigated by mass spectrometry and nuclear magnetic resonance spectroscopy. The antibacterial compounds were identified as the monounsaturated fatty acid (9Z)-hexadecenoic acid (palmitoleic acid; C16:1 n-7) and the relatively unusual polyunsaturated fatty acid (6Z, 9Z, 12Z)-hexadecatrienoic acid (HTA; C16:3 n-4). Both are active against Gram-positive bacteria with HTA further inhibitory to the growth of the Gram-negative marine pathogen, Listonella anguillarum. Palmitoleic acid is active at micro-molar concentrations, kills bacteria rapidly, and is highly active against multidrug-resistant Staphylococcus aureus. These free fatty acids warrant further investigation as a new potential therapy for drug-resistant infections.     

Functional and structural characterization of Spl proteases from Staphylococcus aureus

Staphylococcus aureus is the major cause of nosocomial infections world-wide, with increasing prevalence of community-acquired diseases. The recent dramatic increase in multi-antibiotic resistance, including resistance to the last-resort drug, vancomycin, together with the lack of an effective vaccine highlight the need for better understanding of S.aureus pathogenicity. Comparative analysis of available bacterial genomes allows for the identification of previously uncharacterized S.aureus genes with potential roles in pathogenicity. A good example is a cluster of six serine protease-like (spl) genes encompassed in one operon, which encode for putative proteases with similarity to staphylococcal glutamylendopeptidase (V8 protease). Here, we describe an efficient expression system for the production of recombinant SplB and SplC proteases in Escherichia coli, together with structural and functional characterization of the purified enzymes. A unique mechanism of cytoplasm protection against activity of misdirected SplB was uncovered. Apparently, the co-translated signal peptide maintains protease latency until it is cleaved by the signal peptidase during protein secretion. Furthermore, the crystal structure of the SplC protease revealed a fold resembling that of the V8 protease and epidermolytic toxins. Arrangement of the active site cleft and substrate-binding pocket of SplC explains the mechanism of enzyme latency and suggests that some Spl proteases possess restricted substrate specificity similar to that of the V8 protease and epidermolytic toxins.     

New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D3 with conformationally restricted side chains: evaluation of biological activity and structural determination of VDR-bound conformations

We have successfully prepared E- and Z- isomers of 17-20 dehydro analogs of 2-methylene-19-nor-(20S)-1alpha,25-dihydroxyvitamin D3 (2MD). Both isomers bind to the recombinant rat vitamin D receptor (VDR) with high affinity. The Z-isomer (Vit-III 17-20Z) displays activity in vivo and in vitro that is similar to 2MD. The in vitro activity of the E-isomer (Vit-III 17-20E) is comparable to the natural hormone, though in vivo this analog is significantly less calcemic. Crystal structures of the rat VDR ligand binding domain complexed with the analogs demonstrate that the Vit-III 17-20Z analog is oriented almost identically to 2MD, with only minor differences induced by the planar configuration around the C17-C20 double bond. The Vit-III 17-20E analog is oriented in a conformation distinct from both 2MD and the natural hormone. The structural comparisons suggest that the position of C21 in the ligand binding site may be an important determinant of biological activity.     

Synchrotron SAXS studies on the structural stability of Carcinus aestuarii hemocyanin in solution

The effect of GuHCl and of NaCl on the structural properties of the hemocyanin (Hc) from Carcinus aestuarii has been studied by small angle x-ray scattering (SAXS) using synchrotron radiation. SAXS data collected as a function of perturbant concentration have been used to analyze conformational states of hexameric holo and apoHc as well as the holo and apoforms of the monomeric subunit CaeSS2. In the case of the holoprotein in GuHCl, two concentration domains were identified: at lower concentration, the perturbant induces aggregation of Hc molecules, whereas at higher concentration the aggregates dissociate with concomitant denaturation of the protein. In contrast, with apoHc the denaturation occurs at rather low GuHCl, pointing to an important effect of the active site bound copper for the stabilization of Hc tertiary structure. The effects of NaCl are similar to those of GuHCl as far as CaeSS2 is concerned, namely oligomerization precedes denaturation, whereas in the case of the hexameric form no aggregation occurs. To improve data analysis, on the basis of the current models for Hc monomers and oligomers, the fraction of each aggregation state and/or unfolded protein has been determined by fitting experimental SAXS curves with form factors calculated from Monte Carlo methods. In addition, a global analysis has been carried out on the basis of a thermodynamic model involving an equilibrium between a monomer in a nativelike and denatured form as well as a class of equilibria among the monomer and other aggregates.     

Cassia grandis Linn. f. seed galactomannan: structural and crystallographical studies

Cassia grandis is a small or medium sized tree, found in abundance throughout India. The seeds contain about 50% endosperm gum and possess the characteristics of becoming a potential source of seed gum. The purified polysaccharide has been characterized as a pure galactomannan having a mannose-galactose ratio of 3.15; molecular weight (Mw) 80,200; polydispersity (Mw/Mn), 1.35 and intrinsic viscosity [eta], 848 mL/g. Methylation, periodate oxidation, Smith degradation and 13C NMR studies confirm that the polysaccharide has the basic structure of legume galactomannans consisting of a beta-(1-->4)-linked main mannan backbone to which galactose units are attached at O-6. The orthorhombic lattice constants of the hydrated gum are as follows: a=9.00, b=24.81, c=10.30 A. The crystallographic data establish that the probable space group symmetry of the unit cell is P2(1)2(1)2. The results are in contradiction to earlier reports (Indian J. Chem. 16B (1978) 966; J. Indian Chem. Soc. 55 (1978) 1216) in which a non-galactomannan polysaccharide structure has been assigned having a main chain of (1-->4)-linked galactose and mannose units in the molar ratio 6:3, where 50% of the galactose units branched with two galactose and one mannose through 1-->3 linkage.     

Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes

We have determined the crystal structure, at 1.4A, of the Nudix hydrolase DR1025 from the extremely radiation resistant bacterium Deinococcus radiodurans. The protein forms an intertwined homodimer by exchanging N-terminal segments between chains. We have identified additional conserved elements of the Nudix fold, including the metal-binding motif, a kinked beta-strand characterized by a proline two positions upstream of the Nudix consensus sequence, and participation of the N-terminal extension in the formation of the substrate-binding pocket. Crystal structures were also solved of DR1025 crystallized in the presence of magnesium and either a GTP analog or Ap(4)A (both at 1.6A resolution). In the Ap(4)A co-crystal, the electron density indicated that the product of asymmetric hydrolysis, ATP, was bound to the enzyme. The GTP analog bound structure showed that GTP was bound almost identically as ATP. Neither nucleoside triphosphate was further cleaved.     

First total synthesis and antiprotozoal activity of (Z)-17-methyl-13-octadecenoic acid, a new marine fatty acid from the sponge Polymastia penicillus

The first total synthesis for the (Z)-17-methyl-13-octadecenoic acid was accomplished in seven steps and in a 45% overall yield. The use of (trimethylsilyl)acetylene was key in the synthesis. Based on a previous developed strategy in our laboratory the best synthetic route towards the title compound was first acetylide coupling of (trimethylsilyl)acetylene to the long-chain protected 12-bromo-1-dodecanol followed by a second acetylide coupling to the short-chain 3-methyl-1-bromobutane, which resulted in higher yields. Complete spectral data is also presented for the first time for this recently discovered fatty acid. The title compound displayed antiprotozoal activity against Leishmania donovani (EC₅₀ = 19.8 μg/ml) and inhibited the leishmania DNA topoisomerase IB at concentrations of 50 μM.     

Molecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies

Human NUDT5 (hNUDT5) is an ADP-ribose (ADPR) pyrophosphatase (ADPRase) that plays important roles in controlling the intracellular levels of ADPR and preventing non-enzymatic ADP-ribosylation of proteins by hydrolyzing ADPR to AMP and ribose 5′-phosphate. We report the crystal structure of hNUDT5 in complex with a non-hydrolyzable ADPR analogue, α,β-methyleneadenosine diphosphoribose, and three Mg^2 + ions representing the transition state of the enzyme during catalysis. Analysis of this structure and comparison with previously reported hNUDT5 structures identify key residues involved in substrate binding and catalysis. In the transition-state structure, three metal ions are bound at the active site and are coordinated by surrounding residues and water molecules. A conserved water molecule is at an ideal position for nucleophilic attack on the α-phosphate of ADPR. The side chain of Glu166 on loop L9 changes its conformation to interact with the conserved water molecule compared with that in the substrate-bound structure and appears to function as a catalytic base. Mutagenesis and kinetic studies show that Trp28 and Trp46 are important for the substrate binding; Arg51 is involved in both the substrate binding and the catalysis; and Glu112 and Glu116 of the Nudix motif, Glu166 on loop L9, and Arg111 are critical for the catalysis. The structural and biochemical data together reveal the molecular basis of the catalytic mechanism of ADPR hydrolysis by hNUDT5. Specifically, Glu166 functions as a catalytic base to deprotonate a conserved water molecule that acts as a nucleophile to attack the α-phosphate of ADPR, and three Mg^2 + ions are involved in the activation of the nucleophile and the binding of the substrate. Structural comparison of different ADPRases also suggests that most dimeric ADPRases may share a similar catalytic mechanism of ADPR hydrolysis.