Study on the uranium (U(⠥)) adsorption stability of high-dose γ-ray-irradiated clay.

The Alxa region (Inner Mongolia, China) is one of the areas preselected for use as a geological repository of high-level radioactive waste in China. Radioactive waste produces radioactive rays during long-term storage, and the cumulative absorbed dose in 1000 years can significantly exceed the maximum of 0.7 MGy, thereby challenging the long-term adsorption stability of clay. This study employed 60Co gamma (γ)-rays to irradiate clay in air under a dose rate of 10 kGy/h. The changes in the internal structure and mechanisms of clay under different gamma radiation doses (1, 2, and 3 MGy) were investigated. Additionally, the adsorption properties of irradiated clay for U(Ⅵ) were tested under different conditions. The clay samples underwent minimal structural changes following high-dose irradiation, and the interlayer spacing was altered due to the fractured framework, dehydroxylation, and radiolysis of water. After irradiation, the Fe (Ⅱ) content in clay was significantly increased, unlike Fe (Ⅲ) content. The adsorption mechanisms of clay before and after the experiments were verified, revealing that the adsorption capacity of irradiated clay to U(Ⅵ) is reduced.

Biochemical Screening of Five Protein Kinases from Plasmodium falciparum against 14,000 Cell-Active Compounds.

In 2010 the identities of thousands of anti-Plasmodium compounds were released publicly to facilitate malaria drug development. Understanding these compounds' mechanisms of action--i.e., the specific molecular targets by which they kill the parasite--would further facilitate the drug development process. Given that kinases are promising anti-malaria targets, we screened ~14,000 cell-active compounds for activity against five different protein kinases. Collections of cell-active compounds from GlaxoSmithKline (the ~13,000-compound Tres Cantos Antimalarial Set, or TCAMS), St. Jude Children's Research Hospital (260 compounds), and the Medicines for Malaria Venture (the 400-compound Malaria Box) were screened in biochemical assays of Plasmodium falciparum calcium-dependent protein kinases 1 and 4 (CDPK1 and CDPK4), mitogen-associated protein kinase 2 (MAPK2/MAP2), protein kinase 6 (PK6), and protein kinase 7 (PK7). Novel potent inhibitors (IC50 < 1 µM) were discovered for three of the kinases: CDPK1, CDPK4, and PK6. The PK6 inhibitors are the most potent yet discovered for this enzyme and deserve further scrutiny. Additionally, kinome-wide competition assays revealed a compound that inhibits CDPK4 with few effects on ~150 human kinases, and several related compounds that inhibit CDPK1 and CDPK4 yet have limited cytotoxicity to human (HepG2) cells. Our data suggest that inhibiting multiple Plasmodium kinase targets without harming human cells is challenging but feasible.

High-throughput screening against thioredoxin glutathione reductase identifies novel inhibitors with potential therapeutic value for schistosomiasis.

BACKGROUND: Schistosomiasis, a parasitic disease also known as bilharzia and snail fever, is caused by different species of flatworms, such as Schistosoma mansoni (S. mansoni). Thioredoxin glutathione reductase (TGR) from S. mansoni (SmTGR) is a well-characterized drug target for schistosomiasis, yet no anti-SmTGR compounds have reached clinical trials, suggesting that therapeutic development against schistosomiasis might benefit from additional scaffolds targeting this enzyme. METHODS: A high-throughput screening (HTS) assay in vitro against SmTGR was developed and applied to a diverse compound library. SmTGR activity was quantified with ThioGlo®, a reagent that fluoresces upon binding to the free sulfhydryl groups of the reaction product GSH (reduced glutathione). RESULTS: We implemented an HTS effort against 59,360 synthetic compounds. In the primary screening, initial hits (928 or 1.56 %) showing greater than 90 % inhibition on SmTGR activity at a final concentration of 10 µM for each compound were identified. Further tests were carried out to confirm the effects of these hits and to explore the concentration-dependent response characteristics. As a result, 74 of them (0.12 %) representing 17 chemical scaffolds were confirmed and showed a great concentration-dependent inhibitory trend against SmTGR, including structures previously shown to be lethal to schistosomal growth. Of these, two scaffolds displayed a limited structure-activity relationship. When tested in cultured larvae, 39 compounds had cidal activity in 48 h, and five of them killed larvae completely at 3.125 µM. Of these, three compounds also killed adult worms ex vivo at concentrations between 5 µM and 10 µM. CONCLUSION: These confirmed hits may serve as starting points for the development of novel therapeutics to combat schistosomiasis.

Biosurfactant produced by novel Pseudomonas sp. WJ6 with biodegradation of n-alkanes and polycyclic aromatic hydrocarbons.

Alkanes and polycyclic aromatic hydrocarbons (PAHs) have threatened the environment due to toxicity and poor bioavailability. Interest in degradation of these hazardous materials by biosurfactant-producing bacteria has been steadily increasing in recent years. In this work, a novel biosurfactant-producing Pseudomonas sp. WJ6 was isolated to degrade a wide range of n-alkanes and polycyclic aromatic hydrocarbons. Production of lipopeptide biosurfactant was observed in all biodegradable studies. These lipopeptides were purified and identified by C18 RP-HPLC system and electrospray ionization-mass spectrometry. Results of structural analysis showed that these lipopeptides generated from different hydrocarbons were classified to be surfactin, fengycin and lichenysin. Heavy-oil sludge washing experiments demonstrated that lipopeptides produced by Pseudomonas sp. WJ6 have 92.46% of heavy-oil washing efficiency. The obtained results indicate that this novel bacterial strain and its lipopeptides have great potentials in the environmental remediation and petroleum recovery.

Cofactor-independent phosphoglycerate mutase from nematodes has limited druggability, as revealed by two high-throughput screens.

Cofactor-independent phosphoglycerate mutase (iPGAM) is essential for the growth of C. elegans but is absent from humans, suggesting its potential as a drug target in parasitic nematodes such as Brugia malayi, a cause of lymphatic filariasis (LF). iPGAM's active site is small and hydrophilic, implying that it may not be druggable, but another binding site might permit allosteric inhibition. As a comprehensive assessment of iPGAM's druggability, high-throughput screening (HTS) was conducted at two different locations: ∼220,000 compounds were tested against the C. elegans iPGAM by Genzyme Corporation, and ∼160,000 compounds were screened against the B. malayi iPGAM at the National Center for Drug Screening in Shanghai. iPGAM's catalytic activity was coupled to downstream glycolytic enzymes, resulting in NADH consumption, as monitored by a decline in visible-light absorbance at 340 nm. This assay performed well in both screens (Z'-factor >0.50) and identified two novel inhibitors that may be useful as chemical probes. However, these compounds have very modest potency against the B. malayi iPGAM (IC50 >10 µM) and represent isolated singleton hits rather than members of a common scaffold. Thus, despite the other appealing properties of the nematode iPGAMs, their low druggability makes them challenging to pursue as drug targets. This study illustrates a "druggability paradox" of target-based drug discovery: proteins are generally unsuitable for resource-intensive HTS unless they are considered druggable, yet druggability is often difficult to predict in the absence of HTS data.

Development of Toxoplasma gondii calcium-dependent protein kinase 1 (TgCDPK1) inhibitors with potent anti-toxoplasma activity.

Toxoplasmosis is a disease of prominent health concern that is caused by the protozoan parasite Toxoplasma gondii. Proliferation of T. gondii is dependent on its ability to invade host cells, which is mediated in part by calcium-dependent protein kinase 1 (CDPK1). We have developed ATP competitive inhibitors of TgCDPK1 that block invasion of parasites into host cells, preventing their proliferation. The presence of a unique glycine gatekeeper residue in TgCDPK1 permits selective inhibition of the parasite enzyme over human kinases. These potent TgCDPK1 inhibitors do not inhibit the growth of human cell lines and represent promising candidates as toxoplasmosis therapeutics.

Structural and mechanistic comparisons of the metal-binding members of the vicinal oxygen chelate (VOC) superfamily.

The vicinal oxygen chelate family of enzymes catalyzes a highly diverse set of chemistries that derives from one common mechanistic trait: bidentate coordination to a divalent metal center by a substrate or intermediate or transition state through vicinal oxygen atoms. The array of reactions catalyzed by this family is mediated structurally by a common fold and protein-chelating residues that secure and localize a metal ion. The common fold has topological symmetry being comprised of two ßαßßß units that form an incompletely closed barrel of ß-sheet about the metal ion. Interestingly, despite the diversity of the reactions catalyzed and the large number of metals observed to bind and promote the chemistry, this semi-symmetrical open barrel extends metal liganding side chains inward from a highly positionally conserved constellation of amino acid residues within the structure. Moreover, the core barrel fold arises from an array of possible intra/inter domain and subunit arrangements of the individual ßαßßß units that are universally observed to stack side-by-side contacting along the first ß-strand of each. While there are examples of enzymes that use this fold and do not bind a metal ion, this review is concerned with summarizing the key structural and mechanistic correlations that can be made for the metal-dependent vicinal oxygen chelate enzyme family members.

The rate-limiting catalytic steps of hydroxymandelate synthase from Amycolatopsis orientalis.

Hydroxymandelate synthase (HMS) catalyzes the committed step in the formation of p-hydroxyphenylglycine, a recurrent substructure of polycyclic nonribosomal peptide antibiotics such as vancomycin. HMS has the same structural fold as and uses the same substrates as 4-hydroxyphenylpyruvate dioxygenase (HPPD) (4-hydroxyphenylpyruvate (HPP) and O(2)). Moreover, HMS catalyzes a very similar dioxygenation reaction to that of HPPD, adding the second oxygen atom to the benzylic position, rather than the aromatic C1 carbon of the substrate. The dissociation constant for HPP (59 microM) was measured under anaerobic conditions by titrating substrate with enzyme and monitoring the intensity of the weak (epsilon(475nm ) approximately 250 M(-1) cm(-1)) charge-transfer absorption band of the HMS.Fe(II).HPP complex. Pre-steady-state analysis indicates that evidence exists for the accumulation of three intermediates in a single turnover and the decay of the third is rate-limiting in multiple turnovers. The rate constants used to fit the data were k(1) = 1 x 10(5) M(-1) s(-1), k(2) = 250 s(-1), k(3) = 5 s(-1), and k(4) = 0.3 s(-1). However, the values for k(1) and k(2) could not be accurately measured due to both a prolonged mixing time for the HMS system that obscures observation at the early times (<10 ms) and the apparent high relative value of k(2). The third phase, k(3), is attributed to the formation of the product complex, and no kinetic isotope effect was observed on this step when the protons of the substrate's benzylic carbon were substituted with deuteriums, suggesting that hydroxylation is fast relative to the steps observed. The final and predominantly rate-limiting step shows a 3-fold decrease in the magnitude of the rate constant in deuterium oxide solvent, and a proton inventory for this step suggests the contribution of a single proton from the solvent environment.

Use of thermal melt curves to assess the quality of enzyme preparations.

This study sought to determine whether the quality of enzyme preparations can be determined from their melting curves, which may easily be obtained using a fluorescent probe and a standard reverse transcription-polymerase chain reaction (RT-PCR) machine. Thermal melt data on 31 recombinant enzymes from Plasmodium parasites were acquired by incrementally heating them to 90 degrees C and measuring unfolding with a fluorescent dye. Activity assays specific to each enzyme were also performed. Four of the enzymes were denatured to varying degrees with heat and sodium dodecyl sulfate (SDS) prior to the thermal melt and activity assays. In general, melting curve quality was correlated with enzyme activity; enzymes with high-quality curves were found almost uniformly to be active, whereas those with lower quality curves were more varied in their catalytic performance. Inspection of melting curves of bovine xanthine oxidase and Entamoeba histolytica cysteine protease 1 allowed active stocks to be distinguished from inactive stocks, implying that a relationship between melting curve quality and activity persists over a wide range of experimental conditions and species. Our data suggest that melting curves can help to distinguish properly folded proteins from denatured ones and, therefore, may be useful in selecting stocks for further study and in optimizing purification procedures for specific proteins.

We two alone will sing: the two-substrate alpha-keto acid-dependent oxygenases.

4-Hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate synthase (HMS) are the only two known members of the alpha-keto acid-dependent oxygenases that adopt the fold common to the vicinal oxygen chelate superfamily of enzymes. All other oxygenases of this type have a jellyroll fold. Despite a clearly different ancestry, the salient details of HPPD and HMS catalysis are the same as all alpha-keto acid-dependent oxygenases. All alpha-keto acid-dependent oxygenases use reducing equivalents from an alpha-keto acid to reduce dioxygen via an active site ferrous ion mediator and then catalyze decarboxylation of the alpha-keto acid to promote the formation of a high valence iron-oxo species. The most common purpose of which is to then hydroxylate the substrate. This mini-review summarizes the structural and mechanistic data assembled in recent years for HPPD and HMS in the context of both their roles in nature and the vicinal oxygen chelate and alpha-keto acid-dependent oxygenases superfamilies.

Two roads diverged: the structure of hydroxymandelate synthase from Amycolatopsis orientalis in complex with 4-hydroxymandelate.

The crystal structure of the hydroxymandelate synthase (HMS).Co2+.hydroxymandelate (HMA) complex determined to a resolution of 2.3 A reveals an overall fold that consists of two similar beta-barrel domains, one of which contains the characteristic His/His/acid metal-coordination motif (facial triad) found in the majority of Fe2+-dependent oxygenases. The fold of the alpha-carbon backbone closely resembles that of the evolutionarily related enzyme 4-hydroxyphenylpyruvate dioxygenase (HPPD) in its closed conformation with a root-mean-square deviation of 1.85 A. HPPD uses the same substrates as HMS but forms instead homogentisate (HG). The active site of HMS is significantly smaller than that observed in HPPD, reflecting the relative changes in shape that occur in the conversion of the common HPP substrate to the respective HMA or HG products. The HMA benzylic hydroxyl and carboxylate oxygens coordinate to the Co2+ ion, and three other potential H-bonding interactions to active site residue side chains are observed. Additionally, it is noted that there is a buried well-ordered water molecule 3.2 A from the distal carboxylate oxygen. The p-hydroxyl group of HMA is within hydrogen-bonding distance of the side chain hydroxyl of a serine residue (Ser201) that is conserved in both HMS and HPPD. This potential hydrogen bond and the known geometry of iron ligation for the substrate allowed us to model 4-hydroxyphenylpyruvate (HPP) in the active sites of both HMS and HPPD. These models suggest that the position of the HPP substrate differs between the two enzymes. In HMS, HPP binds analogously to HMA, while in HPPD, the p-hydroxyl group of HPP acts as a hydrogen-bond donor and acceptor to Ser201 and Asn216, respectively. It is suggested that this difference in the ring orientation of the substrate and the corresponding intermediates influences the site of hydroxylation.

Burkholderia cenocepacia C5424 produces a pigment with antioxidant properties using a homogentisate intermediate.

Burkholderia cenocepacia is a gram-negative opportunistic pathogen that belongs to the Burkholderia cepacia complex. B. cenocepacia can survive intracellularly within phagocytic cells, and some epidemic strains produce a brown melanin-like pigment that can scavenge free radicals, resulting in the attenuation of the host cell oxidative burst. In this work, we demonstrate that the brown pigment produced by B. cenocepacia C5424 is synthesized from a homogentisate (HGA) precursor. The disruption of BCAL0207 (hppD) by insertional inactivation resulted in loss of pigmentation. Steady-state kinetic analysis of the BCAL0207 gene product demonstrated that it has 4-hydroxyphenylpyruvic acid dioxygenase (HppD) activity. Pigmentation could be restored by complementation providing hppD in trans. The hppD mutant was resistant to paraquat challenge but sensitive to H2O2 and to extracellularly generated superoxide anions. Infection experiments in RAW 264.7 murine macrophages showed that the nonpigmented bacteria colocalized in a dextran-positive vacuole, suggesting that they are being trafficked to the lysosome. In contrast, the wild-type strain did not localize with dextran. Colocalization of the nonpigmented strain with dextran was reduced in the presence of the NADPH oxidase inhibitor diphenyleneiodonium, and also the inducible nitric oxide inhibitor aminoguanidine. Together, these observations suggest that the brown pigment produced by B. cenocepacia C5424 is a pyomelanin synthesized from an HGA intermediate that is capable of protecting the organism from in vitro and in vivo sources of oxidative stress.