Fagopyrins from Buckwheat Flowers: Structural and Stereochemical Characterization Through Combined NMR/CD Spectroscopy and Theoretical Calculations.

Fagopyrins are phenantroperylenequinones present in the flowers of Fagopyrum esculentum (buckwheat) endowed with photodynamic activity. It has been reported that fagopyrin extracts actually contain a complex mixture of closely related compounds, differing only on the nature of the perylenequinone substituents. We report our systematic and detailed study on the chemical composition of fagopyrin extracts by a combination of preparative and analytical techniques. The combined use of 1H-NMR and CD spectroscopy was found to be particularly suited to fully characterize all stereochemical aspects of the extracted fagopyrins. For the first time nine isomers have been structurally characterized and their stereochemistry fully elucidated. The presence of two different heterocyclic ring substituents, two stereogenic centers and the inherent axial chirality of the aromatic system provides a complex stereochemical relationships among isomers, thus giving account of the high level of molecular multiplicity found in the extract.

Polydisperse methyl ß-cyclodextrin-epichlorohydrin polymers: variable contact time (13)C CP-MAS solid-state NMR characterization.

The polymerization of partially methylated ß-cyclodextrin (CRYSMEB) with epichlorohydrin was carried out in the presence of a known amount of toluene as imprinting agent. Three different preparations (D1, D2 and D3) of imprinted polymers were obtained and characterized by solid-state (13)C NMR spectroscopy under cross-polarization magic angle spinning (CP-MAS) conditions. The polymers were prepared by using the same synthetic conditions but with different molar ratios of imprinting agent/monomer, leading to morphologically equivalent materials but with different absorption properties. The main purpose of the work was to find a suitable spectroscopic descriptor accounting for the different imprinting process in three homogeneous polymeric networks. The polymers were characterized by studying the kinetics of the cross-polarization process. This approach is based on variable contact time CP-MAS spectra, referred to as VCP-MAS. The analysis of the VCP-MAS spectra provided two relaxation parameters: T CH (the CP time constant) and T 1ρ (the proton spin-lattice relaxation time in the rotating frame). The results and the analysis presented in the paper pointed out that T CH is sensitive to the imprinting process, showing variations related to the toluene/cyclodextrin molar ratio used for the preparation of the materials. Conversely, the observed values of T 1ρ did not show dramatic variations with the imprinting protocol, but rather confirmed that the three polymers are morphologically similar. Thus the combined use of T CH and T 1ρ can be helpful for the characterization and fine tuning of imprinted polymeric matrices.

Chemoenzymatic deacylation of ramoplanin.

The chemoenzymatic deacylation of ramoplanin A2 is described for the first time: ramoplanin A2 was Boc-protected and hydrogenated to Boc-protected tetrahydroramoplanin, which was subsequently deacylated using an acylase from Actinoplanes utahensis NRRL 12052. The chemoenzymatic process proceeded with 80% overall yield, which favourably compares with the previously described chemical deacylation.

Synthesis, structural, and biological evaluation of bis-heteroarylmaleimides and bis-heterofused imides.

Bis-2,3-heteroarylmaleimides and polyheterocondensed imides joined through nitrogen atoms of the N,N'-bis(ethyl)-1,3-propanediamine linker were prepared from substituted maleic anhydrides and symmetrical diamines in good to satisfactory yields and short reaction times using microwave heating. The novel molecules were shown to inhibit proliferation of human tumor cells (NCI-H460 lung carcinoma) and rat aortic smooth muscle cells (SMCs) with variable potencies. Compound 11a, the most potent one of the series, showed IC(50) values comparable to those observed for the leading molecule elinafide in both cell lines, but with a higher selectivity toward human tumor cells. Compound 11a affected G1/S phase transition of the cell cycle, showed in vitro DNA intercalating activity and in vivo antitumor activity. A thorough structural analysis of the 11a-DNA complex was also made by mean of NMR and computational techniques.

PAMAM dendrimers for siRNA delivery: computational and experimental insights.

Short double-stranded RNAs, which are known as short interfering RNA (siRNA), can be used to specifically down-regulate the expression of the targeted gene in a process known as RNA interference (RNAi). However, the success of gene silencing applications based on the use of synthetic siRNA critically depends on efficient intracellular delivery. Polycationic branched macromolecules such as poly(amidoamine) (PAMAM) dendrimers show a strong binding affinity for RNA molecules and, hence, can provide an effective, reproducible, and relatively nontoxic method for transferring siRNAs into animal cells. Notwithstanding these perspectives, relatively few attempts have been made so far along these lines to study in detail the molecular mechanisms underlying the complexation process between PAMAMs and siRNAs. In this work we combine molecular simulation and experimental approaches to study the molecular requirements of the interaction of RNA-based therapeutics and PAMAM dendrimers of different generations. The dendrimers and their siRNA complexes were structurally characterized, and the free energy of binding between each dendrimer and a model siRNA was quantified by using the well-known MM/PBSA approach. DOSY NMR experiments confirmed the structural in silico prediction and yielded further information on both the complex structure and stoichiometry at low N/P ratio values. siRNA/PAMAM complex formation was monitored at different N/P ratios using gel retardation assays, and a simple model was proposed, which related the amount of siRNA complexed to the entropy variation upon complex formation obtained from the computer simulations.

Investigating the Role of Antioxidant Compounds in Riboflavin-Mediated Photo-Oxidation of Methionine: A 1H-NMR Approach.

Riboflavin (RF) is a well-known photosensitizer, responsible for the light-induced oxidation of methionine (Met) leading to the spoilage of wine. An NMR approach was used to investigate the role of gallic acid (GA) and sulfur dioxide (SO2) in the RF-mediated photo-oxidation of Met. Water solutions of RF and Met, with and without GA or SO2, were exposed to visible light for increasing time in both air and nitrogen atmospheres. Upon light exposure, a new signal appeared at 2.64 ppm that was assigned to the S(O)CH3 moiety of methionine sulfoxide. Its formation rate was lower in a nitrogen atmosphere and even lower in the presence of GA, supporting the ability of this compound in quenching the singlet oxygen. In contrast, SO2 caused relevant oxidation of Met, moderately observed even in the dark, making Met less available in donating electrons to RF. The competition of GA versus Met photo-oxidation was revealed, indicating effectiveness of this antioxidant against the light-dependent spoilage of wine. A pro-oxidant effect of SO2 toward Met was found as a possible consequence of radical pathways involving oxygen.

Magnetic Resonance Imaging and Molecular Dynamics Characterization of Ionic Liquid in Poly(ethylene oxide)-Based Polymer Electrolytes.

Ternary systems consisting of polymers, lithium salts, and ionic liquids (ILs) are promising materials for the development of next-generation lithium batteries. The ternary systems combine the advantages of polymer-salt and IL-salt systems, thus providing media with high ionic conductivity and solid-like mechanical properties. In this work, we apply nuclear magnetic resonance 1H microimaging [magnetic resonance imaging (MRI)] techniques and molecular dynamics (MD) simulations to study the translational and rotational dynamics of the N-butyl-N-methylpyrrolidinium (PYR14) cation in poly(ethylene oxide) (PEO) matrices containing the lithium bis(trifluoromethanesulfonyl) imide salt (LiTFSI) and the PYR14TFSI IL. The analysis of diffusion-weighted images in PEO/LiTFSI/PYR14TFSI samples with varying mole ratios (10:1:x, with x = 1, 2, 3, and 4) shows, in a wide range of temperatures, a spatially heterogeneous distribution of PYR14 diffusion coefficients. Their weight-averaged values increase with IL content but remain well below the values estimated for the neat IL. The analysis of T2 (spin-spin relaxation) parametric images shows that the PEO matrix significantly hinders PYR14 rotational freedom, which is only partially restored by increasing the IL content. The MD simulations, performed on IL-filled cavities within the PEO matrix, reveal that PYR14 diffusion is mainly affected by Li/TFSI coordination within the IL phase. In agreement with MRI experiments, increasing the IL content increases the PYR14 diffusion coefficients. Finally, the analysis of MD trajectories suggests that Li diffusion mostly develops within the IL phase, although a fraction of Li cations is strongly coordinated by PEO oxygen atoms.

Synthetic peptides of hepatitis G virus (GBV-C/HGV) in the selection of putative peptide inhibitors of the HIV-1 fusion peptide.

The GB virus C or hepatitis G virus (GBV-C/HGV) is a single-stranded positive sense RNA virus that belongs to the Flaviviridae family. Recent years have seen the publication of numerous works in which coinfection with GBV-C/HGV and HIV has been associated with slower progression of the illness and a higher survival rate of patients once AIDS has developed. The mechanism by which the GBV-C/HGV virus has a "protective effect" in patients with HIV has still not been defined. Study of the interaction of the GBV-C/HGV and HIV viruses could lead to the development of new therapeutic agents for the treatment of AIDS. Given that the mechanism responsible for the beneficial effect exercised by the GBV-C/HGV virus in the course of HIV infection has not been defined, the present work is intended as a study of the structure and interactions between the fusion peptide of HIV-1, gp41(1-23), and synthetic peptide sequences of the E2 envelope protein of GBV-C/HGV using biophysical techniques. Our results highlight that the E2(269-286) sequence interacts with the target fusion peptide of HIV-1 and modifies its conformation.

Interaction between double helix DNA fragments and a new topopyrone acting as human topoisomerase I poison.

A water soluble derivative (2) of topopyrones was selected for NMR studies directed to elucidate the mode of binding with specific oligonucleotides. Topopyrone 2 can intercalate into the CG base pairs, but the residence time into the double helix is very short and a fast chemical exchange averaging occurs at room temperature between the free and bound species. The equilibria involved become slow below room temperature, thus allowing to measure a mean lifetime of the complex of ca. 7 ms at 15 degrees C. Structural models of the complex with d(CGTACG)(2) were developed on the basis of DOSY, 2D NOESY and (31)P NMR experiments. Topopyrone 2 presents a strong tendency to self-associate. In the presence of oligonucleotide a certain number of ligand molecules are found to externally stack to the double-helix, in addition to a small fraction of the same ligand intercalated. The external binding to the ionic surface of the phosphoribose chains may thus represents the first step of the intercalation process.

Urinary TMAO Levels Are Associated with the Taxonomic Composition of the Gut Microbiota and with the Choline TMA-Lyase Gene (cutC) Harbored by Enterobacteriaceae.

Gut microbiota metabolization of dietary choline may promote atherosclerosis through trimethylamine (TMA), which is rapidly absorbed and converted in the liver to proatherogenic trimethylamine-N-oxide (TMAO). The aim of this study was to verify whether TMAO urinary levels may be associated with the fecal relative abundance of specific bacterial taxa and the bacterial choline TMA-lyase gene cutC. The analysis of sequences available in GenBank grouped the cutC gene into two main clusters, cut-Dd and cut-Kp. A quantitative real-time polymerase chain reaction (qPCR) protocol was developed to quantify cutC and was used with DNA isolated from three fecal samples collected weekly over the course of three consecutive weeks from 16 healthy adults. The same DNA was used for 16S rRNA gene profiling. Concomitantly, urine was used to quantify TMAO by ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). All samples were positive for cutC and TMAO. Correlation analysis showed that the cut-Kp gene cluster was significantly associated with Enterobacteriaceae. Linear mixed models revealed that urinary TMAO levels may be predicted by fecal cut-Kp and by 23 operational taxonomic units (OTUs). Most of the OTUs significantly associated with TMAO were also significantly associated with cut-Kp, confirming the possible relationship between these two factors. In conclusion, this preliminary method-development study suggests the existence of a relationship between TMAO excreted in urine, specific fecal bacterial OTUs, and a cutC subgroup ascribable to the choline-TMA conversion enzymes of Enterobacteriaceae.

Effect of processing conditions on water mobility and cooking quality of gluten-free pasta. A Magnetic Resonance Imaging study.

A new approach for producing gluten-free pasta from hydrated (50 °C, 20 min) rice kernels, skipping the grinding step, was explored. Magnetic Resonance Imaging (MRI) was used to study the hydration kinetics of rice, by monitoring the time evolution of both proton density and water transverse-relaxation rate during water diffusion. Results showed that the optimal water diffusion was reached after 180 min, allowing the extrusion of hydrated rice kernels into pasta. MRI analysis also highlighted in cooked pasta gradients of water distribution and mobility, in agreement with the high shear force that was measured using the Kramer cell (1066.5 vs 896.4 N). The high hydration in the external layers of pasta did not negatively affect the cooking quality (cooking loss, compression energy, firmness) of the product. MRI analysis provided experimental evidence for the optimization of early steps in the technological process of grains for the production of gluten-free pasta.

Stabilization of beta-lactoglobulin by polyols and sugars against temperature-induced denaturation involves diverse and specific structural regions of the protein.

Temperature sensitivity of bovine milk beta-lactoglobulin (BLG) was assessed in the presence/absence of non-reducing sugars (sucrose and trehalose) and polyols (glycerol and sorbitol). None of them affected the structural features of the protein at room temperature, where the only observed effect was an increased affinity towards hydrophobic probes in the presence of all co-solutes but glycerol. Although most of the observed effects in temperature-ramp experiments are due to entropic effects (fitting within the "preferential exclusion" theory of protein stabilization), this study indicates that each co-solute exhibit different efficacy at stabilizing specific regions of BLG, suggesting that each of them acts in a specific way on the solvent/protein system. The relevance of these observations with respect to systems of practical relevance is discussed, given the widespread use of heat-polymerizing proteins - such as BLG - in many food formulations that very often include significant amounts of sugars and/or polyols.

Streptococcus thermophilus urease activity boosts Lactobacillus delbrueckii subsp. bulgaricus homolactic fermentation.

The proto-cooperation between Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus in the yogurt consortium enhances the growth rate and size of each population. In contrast, the independent growth of the two species in milk leads to a slower growth rate and a smaller population size. In this study, we report the first evidence that the urease activity of S. thermophilus increases the intracellular pH of L. delbrueckii in the absence of carbon source. However, in milk, in the presence of lactose the alkalizing effect of urea-derived ammonia was not detectable. Nevertheless, based on glucose consumption and lactic acid production at different pHin, L. delbrueckii showed an optimum of glycolysis and homolactic fermentation at alkaline pH values. In milk, we observed that ammonia provided by urea hydrolysis boosted lactic acid production in S. thermophilus and in L. delbrueckii when the species were grown alone or in combination. Therefore, we propose that urease activity acts as an altruistic cooperative trait, which is costly for urease-positive individuals but provides a local benefit because other individuals can take advantage of urease-dependent ammonia release.

Macromolecular Traits in the African Rice Oryza glaberrima and in Glaberrima/Sativa Crosses, and Their Relevance to Processing.

Molecular properties of proteins and starch were investigated in 2 accessions of Oryza glaberrima and Oryza sativa, and in one NERICA cross between the 2 species, to assess traits that could be relevant to transformation into specific foods. Protein nature and organization in O. glaberrima were different from those in O. sativa and in NERICA. Despite the similar cysteine content in all samples, thiol accessibility in O. glaberrima proteins was higher than in NERICA or in O. sativa. Inter-protein disulphide bonds were important for the formation of protein aggregates in O. glaberrima, whereas non-covalent protein-protein interactions were relevant in NERICA and O. sativa. DSC and NMR studies indicated only minor differences in the structure of starch in these species, as also made evident by their microstructural features. Nevertheless, starch gelatinization in O. glaberrima was very different from what was observed in O. sativa and NERICA. The content of soluble species in gelatinized starch from the various species in the presence/absence of treatments with specific enzymes indicated that release of small starch breakdown products was lowest in O. glaberrima, in particular from the amylopectin component. These findings may explain the low glycemic index of O. glaberrima, and provide a rationale for extending the use of O. glaberrima in the production of specific rice-based products, thus improving the economic value and the market appeal of African crops. PRACTICAL APPLICATION: The structural features of proteins and starch in O. glaberrima are very different from those in O. sativa and in the NERICA cross. These results appear useful as for extending the use of O. glaberrima cultivars in the design and production of specific rice-based products (for example, pasta), that might, in turn, improve the economic value and the market appeal of locally sourced raw materials, by introducing added-value products on the African market.

Full spectroscopic characterization of two crystal pseudopolymorphic forms of the antiandrogen cortexolone 17α-propionate for topic application.

Cortexolone-17α-propionate (CP) is a topically active antiandrogen useful in the treatment of skin disorders. In the solid state, three anhydrous forms of this drug (CPI, CPII and CPIII) occur, together with one hydrated crystal (CPW). The single crystal structure of the monohydrated phase, CPW, compared with that of the anhydrous form CPIII, shows a markedly different solid state behavior. These latter pseudopolymorphic forms have also been fully characterized by spectroscopic methods.

Inhibitory properties and solution structure of a potent Bowman-Birk protease inhibitor from lentil (Lens culinaris, L) seeds.

Bowman-Birk serine protease inhibitors are a family of small plant proteins, whose physiological role has not been ascertained as yet, while chemopreventive anticarcinogenic properties have repeatedly been claimed. In this work we present data on the isolation of a lentil (Lens culinaris, L., var. Macrosperma) seed trypsin inhibitor (LCTI) and its functional and structural characterization. LCTI is a 7448 Da double-headed trypsin/chymotrypsin inhibitor with dissociation constants equal to 0.54 nM and 7.25 nM for the two proteases, respectively. The inhibitor is, however, hydrolysed by trypsin in a few minutes timescale, leading to a dramatic loss of its affinity for the enzyme. This is due to a substantial difference in the kon and k*on values (1.1 microM-1.s-1 vs. 0.002 microM-1.s-1), respectively, for the intact and modified inhibitor. A similar behaviour was not observed with chymotrypsin. The twenty best NMR structures concurrently showed a canonical Bowman-Birk inhibitor (BBI) conformation with two antipodal beta-hairpins containing the inhibitory domains. The tertiary structure is stabilized by ion pairs and hydrogen bonds involving the side chain and backbone of Asp10-Asp26-Arg28 and Asp36-Asp52 residues. At physiological pH, the final structure results in an asymmetric distribution of opposite charges with a negative electrostatic potential, centred on the C-terminus, and a highly positive potential, surrounding the antitryptic domain. The segment 53-55 lacks the anchoring capacity found in analogous BBIs, thus rendering the protein susceptible to hydrolysis. The inhibitory properties of LCTI, related to the simultaneous presence of two key amino acids (Gln18 and His54), render the molecule unusual within the natural Bowman-Birk inhibitor family.

Steroid hydroxylations with Botryodiplodia malorum and Colletotrichum lini.

An improved procedure for the microbial hydroxylations of dehydroepiandrosterone (DHEA, 1) and 15 beta,16 beta-methylene-dehydroepiandrosterone (2) was studied using whole cells of Botryodiplodia malorum and Colletotrichum lini. C. lini catalyzed 7 alpha- and 15 alpha-hydroxylation of 1 and 7 alpha-hydroxylation of 2, while B. malorum gave 7 beta-hydroxylation of both the substrates. The stability of the enzymatic activity was higher in the presence of co-substrates (i.e., glucose or mannitol) allowing for repeated batches of the biotransformations. The yields of 7 alpha,15 alpha-dihydroxy-1 production were improved obtaining 5.8 gl(-1) (recovered product) from 7.0 gl(-1) of substrate. The structures of the hydroxylated products were assigned by a combination of two-dimensional NMR proton-proton and proton-carbon correlation techniques.

Brostallicin, a novel anticancer agent whose activity is enhanced upon binding to glutathione.

Brostallicin (PNU-166196) is a synthetic alpha-bromoacrylic, second-generation DNA minor groove binder structurally related to distamycin A, presently in Phase II trials in Europe and the United States. The compound shows broad antitumor activity in preclinical models and dramatically reduced in vitro myelotoxicity in human hematopoietic progenitor cells compared with that of other minor groove binders. Brostallicin showed a 3-fold higher activity in melphalan-resistant L1210 murine leukemia cells than in the parental line (IC(50) = 0.46 and 1.45 ng/ml, respectively) under conditions in which the cytotoxicity of conventional antitumor agents was either unaffected or reduced. This melphalan-resistant cell line has increased levels of glutathione (GSH) in comparison with the parental cells. Conversely, GSH depletion by buthionine sulfoximine in a human ovarian carcinoma cell line (A2780) significantly decreased both the cytotoxic and the proapoptotic effects of brostallicin. In one experiment, human glutathione S-transferase pi (GST-pi) cDNA was transfected into A2780 cells, and four clones of A2780 with different expression levels of GST-pi were generated (i.e., two clones with high and two clones with low GST-pi expression). A 2-3-fold increase in GST-pi levels resulted in a 2-3-fold increase in cytotoxic activity of brostallicin. Similar results were obtained for GST-pi-transfected human breast carcinoma cells (MCF-7). Brostallicin showed 5.8-fold increased cytotoxicity in GST-pi-transfected versus empty vector-transfected cells with low GST-pi expression. In an in vivo experiment, A2780 clones were implanted into nude mice. The antitumor activity of brostallicin was higher in the GST-pi-overexpressing tumors without increased toxicity. Regarding the mechanism of action, brostallicin interacts reversibly with the DNA minor groove TA-rich sequences but appears unreactive in classical in vitro DNA alkylation assays. We speculated that an intracellular reactive nucleophilic species, e.g., GSH, could react with the alpha-bromoacrylamide moiety functions. Experiments on the interaction with plasmid DNA showed a change of the DNA topology from supercoiled to circular form (nicking) in the presence of GSH, whereas no change was found in its absence. In vitro incubations of brostallicin were performed with the human recombinant GST isoenzymes A1-1, M1-1, and P1-1 (alpha, mu and pi isoenzymes, respectively) in the presence of GSH. The decrease in brostallicin levels was monitored in these incubations; the rate of loss (and therefore brostallicin metabolism) was significantly higher for the M1-1 and P1-1 isoenzymes than for the A1-1 isoenzyme.

α-Synuclein is a Novel Microtubule Dynamase.

α-Synuclein is a presynaptic protein associated to Parkinson's disease, which is unstructured when free in the cytoplasm and adopts α helical conformation when bound to vesicles. After decades of intense studies, α-Synuclein physiology is still difficult to clear up due to its interaction with multiple partners and its involvement in a pletora of neuronal functions. Here, we looked at the remarkably neglected interplay between α-Synuclein and microtubules, which potentially impacts on synaptic functionality. In order to identify the mechanisms underlying these actions, we investigated the interaction between purified α-Synuclein and tubulin. We demonstrated that α-Synuclein binds to microtubules and tubulin α2ß2 tetramer; the latter interaction inducing the formation of helical segment(s) in the α-Synuclein polypeptide. This structural change seems to enable α-Synuclein to promote microtubule nucleation and to enhance microtubule growth rate and catastrophe frequency, both in vitro and in cell. We also showed that Parkinson's disease-linked α-Synuclein variants do not undergo tubulin-induced folding and cause tubulin aggregation rather than polymerization. Our data enable us to propose α-Synuclein as a novel, foldable, microtubule-dynamase, which influences microtubule organisation through its binding to tubulin and its regulating effects on microtubule nucleation and dynamics.

Studies on the structure-activity relationship of endostatin: synthesis of human endostatin peptides exhibiting potent antiangiogenic activities.

The aim of the present research was to study the relationship between chemical structure and antiangiogenic activity of endostatin. Four peptides, containing about 40 amino acid residues, designed to cover nearly the whole sequence of endostatin, were synthesized by the solid-phase method. They were termed Fragment I (sequence 6-49), II (sequence 50-92), III (sequence 93-133), and IV (sequence 134-178), with the latter bearing the original disulfide bond Cys135-Cys165. These peptides were tested for their ability to inhibit endothelial cell proliferation, migration, and both in vitro and in vivo angiogenesis assays in matrigel. Fragments I and IV inhibited cell proliferation and cell migration with a potency and an efficacy higher than that of the full length endostatin. Fragment I was also active in inhibiting in vitro the formation of tubules and in vivo the vascularization of the matrigel. Fragments II and III were devoid of antiangiogenic activity. We propose to use the peptides 6-49 and 134-178 as angiogenesis inhibitors in substitution of full length endostatin, in therapeutic applications for cancer, rheumatoid arthritis, and retinopathies.