Superstolide A : a potent cytotoxic macrolide of a new type from the New Caledonian deep water marine sponge Neosiphonia superstes

A highly cytotoxic macrolide, superstolide A (1), has been isolated from the deep water marine sponge Neosiphonia superstes, collected off New Caledonia. The gross structure was determined by extensive 2D NMR experiments on the lactone 1 and on its opened-ring-derived methyl esters 2 and 3. The relative stereochemistries of the decaline moiety and of the C22-C26 fragment were determined by a combination of NMR data and acetonide analysis on 2. Absolute stereostructure of the decaline portion of 1 has been determined on the basis of GLC-modified Horeau's methodology applied to 4, whereas the results of the application of the modified Mosher's method to 1 and 3 allowed us to propose for the C22-C26 fragment the 22R, 23R, 24R, 25S, 26R configuration. We also propose the solution conformations of superstolide A (1) based on molecular dynamics and mechanics calculations using NMR-derived constraints

Computational approaches to shed light on molecular mechanisms in biological processes

Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines. © Springer-Verlag 2007

The Importance of Stereochemically Active Lone Pairs For Influencing Pb II and As III Protein Binding

The toxicity of heavy metals, which is associated with the high affinity of the metals for thiolate rich proteins, constitutes a problem worldwide. However, despite this tremendous toxicity concern, the binding mode of As III and Pb II to proteins is poorly understood. To clarify the requirements for toxic metal binding to metalloregulatory sensor proteins such as As III in ArsR/ArsD and Pb II in PbrR or replacing Zn II in δ‐aminolevulinc acid dehydratase (ALAD), we have employed computational and experimental methods examining the binding of these heavy metals to designed peptide models. The computational results show that the mode of coordination of As III and Pb II is greatly influenced by the steric bulk within the second coordination environment of the metal. The proposed basis of this selectivity is the large size of the ion and, most important, the influence of the stereochemically active lone pair in hemidirected complexes of the metal ion as being crucial. The experimental data show that switching a bulky leucine layer above the metal binding site by a smaller alanine residue enhances the Pb II  binding affinity by a factor of five, thus supporting experimentally the hypothesis of lone pair steric hindrance. These complementary approaches demonstrate the potential importance of a stereochemically active lone pair as a metal recognition mode in proteins and, specifically, how the second coordination sphere environment affects the affinity and selectivity of protein targets by certain toxic ions. Experimental and computational methods have been employed to study the influence of the lone pair of As III and Pb II for the binding of these ions in proteins using designed peptide models. The results show that the mode of coordination of As III and Pb II is greatly influenced by the steric bulk within the second coordination environment of the metals (see figure).Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90414/1/chem_201102786_sm_miscellaneous_information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/90414/2/2040_ftp.pd

Metabolites of the new Caledonian sponge Cladocroce incurvata

The deep-water New Caledonian sponge #Cladocroce incurvata$ contains two "polyketide" metabolites. Cladocrocin A (1) appears to be derived from fatty acid with ethyl side chains, thus incorporating butyrate units. Cladocroic acid (2) is a straight chain fatty acid which incorporates a terminal enyne functionality and a cycloproprane ring directly attached to the carboxylic acid function. The structures were elucidated by interpretation of spectral data, and the cis stereochemistry of the cyclopropane ring in cladocroic acid (2) was derived after the synthesis of cis - and trans - 2, 3 - methanohexanoic acid models and nmr spectral comparisons. (Résumé d'auteur

Three new potent cytotoxic macrolides closely related to sphinxolide from the New Caledonia sponge Neosiphonia superstes

Three new macrolides 2-4 have been isolated with sphinxolide 1 from the marine sponge #N. superstes$ collected off New Caledonia. The structures of the new compounds were determined by interpretation of NMR spectral data as well as comparison of spectral data with those of 1. These compounds were highly cytotoxic against various human carcinoma cells. (Résumé d'auteur

Mechanistic Analysis of Nucleophilic Substrates Oxidation by Functional Models of Vanadium-Dependent Haloperoxidases: A Density Functional Theory Study

Density functional theory has been used to investigate the structural, electronic, and reactivity properties of an established functional model for vanadium-dependent haloperoxidases, K[VO(O 2 )Hheida] (Hheida 2– = 2,2′-[(2-hydroxyethyl)imino]diacetate). Possible solution species were determined on the basis of potential exogenous donors present under the conditions necessary for reactivity. The energetically favored solution-state species is a 1:1 complex of Hheida and vanadium with a coordinated hydroxyethyl donor trans to the vanadium–oxido bond which is in agreement with the reported solid-state structure for K[VO(O 2 )Hheida]. Transition states of the oxidation reaction were located for four substrates: chloride, bromide, iodide, and dimethyl sulfide. The role of protonation and its effects on reactivity were examined for each substrate. Protonation of the peroxido moiety leads to a significant drop in the activation barrier for oxidation. In contrast no transition states could be located for an oxido-transfer process involving the oxido ligand. Barriers of activation calculated for halide oxidation were similar, providing support to the hypothesis that the p K a of the halide in acetonitrile is responsible for the decrease in reactivity between I – , Br – , and Cl – . The results presented herein provide a mechanistic correlation between a functional model and the enzyme, making K[VO(O 2 )Hheida] a “complete” functional model for vanadium-dependent haloperoxidase.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55972/1/515_ftp.pd

1H-NMR metabolite fingerprinting analysis reveals a disease biomarker and a field treatment response in xylella fastidiosa subsp. Pauca-infected olive trees

Xylella fastidiosa subsp. pauca is a xylem-limited bacterial phytopathogen currently found associated on many hectares with the “olive quick decline syndrome” in the Apulia region (Southern Italy), and the cultivars Ogliarola salentina and Cellina di Nardò result in being particularly sensitive to the disease. In order to find compounds showing the capability of reducing the population cell density of the pathogen within the leaves, we tested, in some olive orchards naturally-infected by the bacterium, a zinc-copper-citric acid biocomplex, namely Dentamet®, by spraying it to the crown, once per month, during spring and summer. The occurrence of the pathogen in the four olive orchards chosen for the trial was molecularly assessed. A 1H NMR metabolomic approach, in conjunction with a multivariate statistical analysis, was applied to investigate the metabolic pattern of both infected and treated adult olive cultivars, Ogliarola salentina and Cellina di Nardò trees, in two sampling periods, performed during the first year of the trial. For both cultivars and sampling periods, the orthogonal partial least squares discriminant analysis (OPLS-DA) gave good models of separation according to the treatment application. In both cultivars, some metabolites such as quinic acid, the aldehydic form of oleoeuropein, ligstroside and phenolic compounds, were consistently found as discriminative for the untreated olive trees in comparison with the Dentamet®-treated trees. Quinic acid, a precursor of lignin, was confirmed as a disease biomarker for the olive trees infected by X. fastidiosa subsp. pauca. When treated with Dentamet®, the two cultivars showed a distinct response. A consistent increase in malic acid was observed for the Ogliarola salentina trees, whereas in the Cellina di Nardò trees the treatments attenuate the metabolic response to the infection. To note that in Cellina di Nardò trees at the first sampling, an increase in γ-aminobutyric acid (GABA) was observed. This study highlights how the infection incited by X. fastidiosa subsp. pauca strongly modifies the overall metabolism of olive trees, and how a zinc-copper-citric acid biocomplex can induce an early re-programming of the metabolic pathways in the infected trees