Analysis of aplidine (dehydrodidemnin B), a new marine-derived depsipeptide, in rat biological fluids by liquid chromatography–tandem mass spectrometry

Aplidine (dehydrodidemnin B) is a new marine-derived depsipeptide with a powerful cytotoxic activity, which is under early clinical investigation in Europe and in the US. In order to investigate the pharmacokinetic properties of this novel drug, an HPLC–tandem mass spectrometry method was developed for the determination of aplidine in biological samples. Didemnin B, a hydroxy analogue, was used as internal standard. After protein precipitation with acetonitrile and extraction with chloroform, aplidine was chromatographed with a RP octadecylsilica column using a water–acetonitrile linear gradient in the presence of formic acid at the flow-rate of 500 μl/min. The method was linear over a 5–100 ng/ml range (LOD=0.5 ng/ml) in plasma and over a 1.25–125 ng/ml range (LOD=0.2 ng/ml) in urine with precision and accuracy below 14.0%. The intra- and inter-day precision and accuracy were below 12.5%. The extraction procedure recoveries for aplidine and didemnin B were 69% and 68%, respectively in plasma and 91% and 87%, respectively in urine. Differences in linearity, LOQ, LOD and recoveries between plasma and urine samples seem to be matrix-dependent. The applicability of the method was tested by measuring aplidine in rat plasma and urine after intravenous treatment.     

Kluyveromyces wickerhamii killer toxin: purification and activity towards Brettanomyces/Dekkera yeasts in grape must

Brettanomyces/Dekkera yeasts have been identified as part of the grape yeast flora. They are well known for colonizing the cellar environmental and spoiling wines, causing haze, turbidity and strong off-flavours in wines and enhancing the volatile acidity. As the general practices applied to combat Brettanomyces/Dekkera yeasts are not particularly appropriate during wine ageing and storage, a biological alternative to curtailing their growth would be welcomed in winemaking. In this study, we investigated the Kluyveromyces wickerhamii killer toxin (Kwkt) that is active against Brettanomyces/Dekkera spoilage yeasts. Purification procedures allowed the identification of Kwkt as a protein with an apparent molecular mass of 72 kDa and without any glycosyl residue. Interestingly, purified Kwkt has fungicidal effects at low concentrations under the physicochemical conditions of winemaking. The addition of 40 and 80 mg L(-1) purified Kwkt showed efficient antispoilage effects, controlling both growth and metabolic activity of sensitive spoilage yeasts. At these two killer toxin concentrations, compounds known to contribute to the 'Brett' character of wines, such as ethyl phenols, were not produced. Thus, purified Kwkt appears to be a suitable biological strategy to control Brettanomyces/Dekkera yeasts during fermentation, wine ageing and storage.     

Australin: a chromosomal passenger protein required specifically for Drosophila melanogaster male meiosis

The chromosomal passenger complex (CPC), which is composed of conserved proteins aurora B, inner centromere protein (INCENP), survivin, and Borealin/DASRA, localizes to chromatin, kinetochores, microtubules, and the cell cortex in a cell cycle-dependent manner. The CPC is required for multiple aspects of cell division. Here we find that Drosophila melanogaster encodes two Borealin paralogues, Borealin-related (Borr) and Australin (Aust). Although Borr is a passenger in all mitotic tissues studied, it is specifically replaced by Aust for the two male meiotic divisions. We analyzed aust mutant spermatocytes to assess the effects of fully inactivating the Aust-dependent functions of the CPC. Our results indicate that Aust is required for sister chromatid cohesion, recruitment of the CPC to kinetochores, and chromosome alignment and segregation but not for meiotic histone phosphorylation or spindle formation. Furthermore, we show that the CPC is required earlier in cytokinesis than previously thought; cells lacking Aust do not initiate central spindle formation, accumulate anillin or actin at the cell equator, or undergo equatorial constriction.     

Ancient hemes for ancient catalysts

Tetrapyrroles are essential molecules in living organisms and perform a multitude of functions in all kingdoms. Their synthesis is achieved in cells via a complex biosynthetic machinery which is unlikely to be maintained, if unnecessary. Here we propose that ancient hemes, such as the d₁-heme of cd₁ nitrite reductase or the siroheme of bacterial and plant nitrite and sulphite reductases, are molecular fossils which have survived the evolutionary pressure because their role is strategic for the organism where they are found today. The peculiar NO-releasing propensity of the d₁-heme of P. aeruginosa NIR, recently shown by our group is, in our opinion, an example of this strategy. The hypothesis is that the d₁-heme structure might be a pre-requisite for the fast rate of NO dissociation from the ferrous form, a property which is crucial to enzymatic activity and cannot be achieved with a more common b-type heme.Key words: d1-heme, porphyrin, siroheme, nitrite reductase, sulphite reductase, nitric oxide, evolutionPseudomonas aeruginosa is a Gram-negative bacterium commonly found in soil and water, well known for its metabolic versatility; under anaerobic conditions it can use nitrate and nitrite to produce energy via the denitrification pathway. In natural environments, denitrification is the part of the biological nitrogen cycle in which nitrate is transformed into nitrogen gas; reduction of nitrate occurs in four stages each catalyzed by a specific metalloenzyme.^1,2 P. aeruginosa is also an opportunistic pathogen, capable of causing serious infections in several hosts, such as humans and plants^3,4; pathogenesis, NO metabolism and denitrification are strictly related.^5,6The conversion of nitrite (NO₂^-) to nitric oxide (NO) is catalyzed in denitrifying bacteria by the periplasmic nitrite reductases (NIR).⁷ In P. aeruginosa NIR is a heme-containing enzyme (cd₁NIR) which produces NO in the active site where the unique d₁-heme cofactor (Fig. 1) is bound. This peculiar heme is synthesized from iron-protoporphyrin IX and belongs to the isobacteriochlorines subgroup;¹ it is exclusively found in this type of bacterial NIR.Open in a separate windowFigure 1Chemical structure of the d₁-heme.Reduction of nitrite involves binding of this molecule to the reduced d₁-heme, followed by dehydration to yield NO; release of NO and re-reduction of the enzyme close the cycle. An high affinity for nitrite (and anions) of the ferrous d₁-heme is a peculiar feature of cd₁NIR.⁷ However since the product NO is a powerful inhibitor of ferrous hemeproteins, enzymatic turnover demands the quick release of NO. In our recent paper⁸ we have shown that NO dissociates rapidly from the reduced form of the specialized d₁-heme of P. aeruginosa cd₁NIR. This unexpected result indicates that cd₁NIR behaves differently from other hemeproteins, since the rate of NO dissociation is by far faster (more than 100-fold) than that measured for any other heme in the ferrous state.^8–11Our hypothesis is that the d₁-heme structure might be a prerequisite for the fast rate of NO dissociation from the ferrous form, a property which cannot be achieved with a standard b-type heme.A major consequence of our finding is that this property of the d₁-heme is essential to avoid quasi-irreversible binding of NO to the reduced heme, which would jeopardize the physiological function of the enzyme evolved to scavenge nitrite, the toxic product of nitrate reduction. From the bioenergetic view-point, the main energy-generating step in denitrification is nitrate reduction (with a net H⁺ traslocation of 2H⁺/2e^-); thus, although a complex electron transfer chain is often present, the major biological role of the reductive steps downstream of nitrate reduction is likely to be nitrite scavenging.² If the complex of NO with reduced cd₁NIR was very long lived it would hamper further reaction cycles thus resulting in the accumulation of nitrite which is toxic for the bacterium. In line with this interpretation, we have also shown very recently¹² that nitrite is able to displace NO from the ferrous enzyme; thus substrate availability is the key factor that controls the enzyme turnover.From the standpoint of molecular evolution it is accepted that bacterial denitrification is an ancient metabolic pathway which existed even before oxygen became abundant in the athmosphere. Several reports pointed out that the enzymes involved in aerobic respiration derive from those involved in the denitrification pathway. Primitive denitrifying bacteria (similar to the extant Paracoccus denitrificans) can be considered as a common ancestral symbiotic prototype of the eukaryotic mitochondrion. Indeed there is compelling evidence that modern eukaryotic oxidases evolved from bacterial NO-reductase once oxygen became available as a major oxidant.^13,14In microrganisms, other “ancient” metabolisms are represented by sulphite and nitrite reduction pathways, which were well suited for a prebiotic photoreducing environment.¹⁵ Also in these pathways several enzymes are heme-containing proteins in which modified hemes, such as siroheme, are used as cofactors.¹⁶ Interestingly also in plants siroheme is a relevant porphyrin group,¹⁷ being the cofactor of plant nitrite and sulphite reductases, required for the assimilation of inorganic nitrogen and sulphur from the environment.Tetrapyrroles are essential molecules in living organisms and perform a multitude of functions in all kingdoms. Their biosynthesis is achieved in cells via branched pathways which are expensive in terms of energy consumption.^16–18 The single pathways are tightly regulated and often activated only “on demand” when the specific heme group is required. Therefore, parsimony suggests that a complex biosynthetic machinery is unlikely to be maintained, if unnecessary.We thus propose that these ancient hemes (such as the d₁-heme or the siroheme) are molecular fossils which have survived the evolutionary pressure because their role is strategic only for the organism where they are found today. The peculiar NO-releasing propensity of the d₁-heme of P. aeruginosa NIR shown by our group could be, in our opinion, an example of this strategy. A major challenge for the future is to unveil other uncommon features of these hemes.     

Astroglial cells in the central nervous system of the adult brown anole lizard, Anolis sagrei, revealed by intermediate filament immunohistochemistry

We analyzed the distribution of intermediate filament molecular markers, glial fibrillary acidic protein (GFAP), and vimentin in the brain and spinal cord of the adult brown anole lizard, Anolis sagrei. The GFAP immunoreactivity is strong and the positive structures are basically represented by fibers of different lengths and thicknesses which are arranged in a regular radial pattern throughout the central nervous system. In the brain regions that have a thicker neural wall, the radial orientation is not so evident as in the thinner areas. These fibers emerge from radial ependymoglia (tanycytes) whose cell bodies are generally GFAP-immunopositive. The glial fibers give rise to endfeet that are apposed to the subpial surface and to blood vessel walls. In the spinal cord, the optic tectum and the lateroventral regions of the mesencephalon and medulla oblongata, star-shaped astrocytes coexist with radial structures. Vimentin-immunoreactive structures are absent in the brain and spinal cord. In A. sagrei the immunohistochemical response of the astroglial intermediate filaments appears typical of a mature astroglial cell lineage, since they fundamentally express GFAP immunoreactivity. A Western-blot analysis reveals a GFAP-positive single band, common to the different nervous areas. This immunohistochemical study shows that the star-shaped astrocytes have a different distribution in saurians and while the glial pattern of A. sagrei is more evolved than in urodeles it remains immature as compared with crocodilians, avians, and mammals. This condition suggests that reptiles represent a fundamental step in the phylogenetic evolution of the vertebrate glial cells.     

Thermodynamic and spectroscopic investigation on the role of Met residues in Cu(II) binding to the non-octarepeat site of the human prion protein

Among the common features shared by neurodegenerative diseases there is the central role played by specific proteins or peptides which accumulate in neurons as insoluble plaques or tangles, containing abnormal amounts of redox-active metal ions, like copper and iron. In the case of transmissible spongiform encephalopathies (TSE), the involved protein is known as "prion protein" (PrP(C)) since "prions" (proteinaceous and infectious) are the agents which make TSE transmissible. It is widely accepted that PrP(C), in its wild-type form, can bind up to six Cu(II) ions, four of them in the so-called "octarepeat domain" and the others in the "fifth (non-octarepeat) binding-site". The latter domain contains two His residues, acting as anchoring sites for Cu(II) ions, and other potential binding residues, such as Lys and Met. While it is widely accepted that Lys residues do not take part in complex-formation, the role of methionines is still debated. In order to shed light on this issue, some peptides have been synthesized, either directly mimicking the sequence of the second half of the fifth binding site of human-PrP(C) (apo-form) or analogues where Met residues have been substituted by n-leucine. In addition, a series of short peptides, containing both His and Met residues in different relative positions, have been investigated, for the sake of comparison. Spectroscopic results, including NMR spectra of systems containing Ni(II) as a probe for the paramagnetic Cu(II) ion, agree on the exclusion of any direct interaction between the sulphur atom of Met residues and the Cu(II) ion already bound to His-imidazole side-chains. However, thermodynamic data show that Met-109 somewhat contributes to stability of complex species and this can be attributed to different electronic and steric effects.     

Discovery of the first small molecule inhibitor of human DDX3 specifically designed to target the RNA binding site: towards the next generation HIV-1 inhibitors

Efficacy of currently approved anti-HIV drugs is hampered by mutations of the viral enzymes, leading invariably to drug resistance and chemotherapy failure. Recent data suggest that cellular co-factors also represent useful targets for anti-HIV therapy. Here we describe the identification of the first small molecules specifically designed to inhibit the HIV-1 replication by targeting the RNA binding site of the human DEAD-Box RNA helicase DDX3. Optimization of a easily synthetically accessible hit (1) identified by application of a high-throughput docking approach afforded the promising compounds 6 and 8 which proved to inhibit both the helicase and ATPase activity of DDX3 and to reduce the viral load of peripheral blood mononuclear cells (PBMC) infected with HIV-1.     

Cytochalasins from Phoma exigua var. Heteromorpha

Three further cytochalasins fromPhoma exigua var. heteromorpha, grown on wheat, were isolated and characterized by spectroscopic methods and by chemical correlation with cytochalasin B. They were identified as cytochalasin T, a new 24-oxa[14]cytochalasan, cytochalasin F and 7-O-acetylcytochalasin B, both isolated for the first time from this fungus. Cytochalasin F showed significant activity in the brine shrimp assay and on tomato seedling growth.