Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases.

MutY adenine glycosylases prevent DNA mutations by excising adenine from promutagenic 8-oxo-7,8-dihydroguanine (OG):A mismatches. Here, we describe structural features of the MutY active site bound to an azaribose transition state analog which indicate a catalytic role for Tyr126 and approach of the water nucleophile on the same side as the departing adenine base. The idea that Tyr126 participates in catalysis, recently predicted by modeling calculations, is strongly supported by mutagenesis and by seeing close contact between the hydroxyl group of this residue and the azaribose moiety of the transition state analog. NMR analysis of MutY methanolysis products corroborates a mechanism for adenine removal with retention of stereochemistry. Based on these results, we propose a revised mechanism for MutY that involves two nucleophilic displacement steps akin to the mechanisms accepted for 'retaining' O-glycosidases. This new-for-MutY yet familiar mechanism may also be operative in related base excision repair glycosylases and provides a critical framework for analysis of human MutY (MUTYH) variants associated with inherited colorectal cancer

Fast method for the determination of short-chain-length polyhydroxyalkanoates (scl-PHAs) in bacterial samples by In Vial-Thermolysis (IVT)

none8siA new method based on the GC–MS analysis of thermolysis products obtained by treating bacterial samples at a high temperature (above 270 C) has been developed. This method, here named “In-Vial- Thermolysis” (IVT), allowed for the simultaneous determination of short-chain-length polyhydrox- yalkanoates (scl-PHA) content and composition. The method was applied to both single strains and microbial mixed cultures (MMC) fed with different carbon sources. The IVT procedure provided similar analytical performances compared to previous Py-GC–MS and Py- GC-FID methods, suggesting a similar application for PHA quantitation in bacterial cells. Results from the IVT procedure and the traditional methanolysis method were compared; the correlation between the two datasets was fit for the purpose, giving a R2 of 0.975. In search of further simplification, the rationale of IVT was exploited for the development of a “field method” based on the titration of thermolyzed samples with sodium hydrogen carbonate to quantify PHA inside bacterial cells. The accuracy of the IVT method was fit for the purpose. These results lead to the possibility for the on-line measurement of PHA productivity. Moreover, they allow for the fast and inexpensive quantification/characterization of PHA for biotechnological process control, as well as investigation over various bacterial communities and/or feeding strategies.mixedF. Abbondanzi; G. Biscaro; G. Carvalho; L. Favaro; P. Lemos; M. Paglione; C. Samorì; C. TorriF. Abbondanzi; G. Biscaro; G. Carvalho; L. Favaro; P. Lemos; M. Paglione; C. Samorì; C. Torr

Lactose as an inexpensive starting material for the preparation of aldohexos-5-uloses: synthesis of L-ribo and D-lyxo derivatives

SUMMARY: Partially protected derivatives of L-ribo- and D-lyxo-aldohexos-5-ulose have been prepared starting from triacetonlactose dimethyl acetal derivatives. Key steps of the synthetic sequences are a) the synthesis of 4'-deoxy-4'-eno- and 6'-deoxy-5'-eno lactose derivatives, and b) the epoxidation-methanolysis of the above enol ethers to give 1,5-bis-glycopyranosides, masked form of the target 1,5-dicarbonyl hexoses

Recent progress in the synthesis of six-membered aminocyclitols (2008-2017)

Aminocyclitols are of interest as glucosidase inhibitors, as probes for the study of pseudoglycosyltransferases, and as potential therapeutics for the treatment of Gaucher’s disease. The synthesis of these targets was reviewed in early 2008, and the aim of this review is to cover material relevant to the synthesis of aminocyclitols since that time. While not a focus of this review, biological evaluation of compounds will be presented where it is recorded in the literature

Automated access to well-defined ionic oligosaccharides

Ionic polysaccharides are part of many biological events, but lack structural characterisation due to challenging purifications and complex synthesis. Four monosaccharides bearing modifications not found in nature are used for the automated synthesis of a collection of ionic oligosaccharides. Structural analysis reveals how the charge pattern affects glycan conformation

Modelling the kinetics of transesterification reaction of sunflower oil with ethanol in microreactors

Transesterification reaction of vegetable oil with ethanol leads to ethyl esters, used to date for applications principally in food and cosmetic industry. To open the application field to biofuels (to substitute current fuels resulting from fossil resources), the process efficiency has to be developed to be economically profitable. In this work, the sunflower oil ethanolysis was performed in a micro-scaled continuous device, inducing better control for heat and mass transfer in comparison with batch processes. Moreover, this device ensures kinetic data acquisition at the first seconds of the reaction, which was not feasible in a conventional batch process. These data were used to model occurring phenomena and to determine kinetic constants and mass transfer coefficients. A single set of these parameters is able to represent the evolution of the reaction media composition function of time for five ethanol to oil molar ratios (6.0, 9.0, 16.2, 22.7 and 45.4). The model was validated in reaction and diffusion mode. Finally, it was subsequently used to simulate reactions with other operational conditions and to propose other process implementation

Systematic Hydrogen‐Bond Manipulations To Establish Polysaccharide Structure–Property Correlations

A dense hydrogen‐bond network is responsible for the mechanical and structural properties of polysaccharides. Random derivatization alters the properties of the bulk material by disrupting the hydrogen bonds, but obstructs detailed structure–function correlations. We have prepared well‐defined unnatural oligosaccharides including methylated, deoxygenated, deoxyfluorinated, as well as carboxymethylated cellulose and chitin analogues with full control over the degree and pattern of substitution. Molecular dynamics simulations and crystallographic analysis show how distinct hydrogen‐bond modifications drastically affect the solubility, aggregation behavior, and crystallinity of carbohydrate materials. This systematic approach to establishing detailed structure–property correlations will guide the synthesis of novel, tailor‐made carbohydrate materials

A platform for the discovery of new macrolide antibiotics.

The chemical modification of structurally complex fermentation products, a process known as semisynthesis, has been an important tool in the discovery and manufacture of antibiotics for the treatment of various infectious diseases. However, many of the therapeutics obtained in this way are no longer effective, because bacterial resistance to these compounds has developed. Here we present a practical, fully synthetic route to macrolide antibiotics by the convergent assembly of simple chemical building blocks, enabling the synthesis of diverse structures not accessible by traditional semisynthetic approaches. More than 300 new macrolide antibiotic candidates, as well as the clinical candidate solithromycin, have been synthesized using our convergent approach. Evaluation of these compounds against a panel of pathogenic bacteria revealed that the majority of these structures had antibiotic activity, some efficacious against strains resistant to macrolides in current use. The chemistry we describe here provides a platform for the discovery of new macrolide antibiotics and may also serve as the basis for their manufacture