Molecular field analysis and 3D-quantitative structure-activity relationship study (MFA 3D-QSAR) unveil novel features of bile acid recognition at TGR5

Bile acids regulate nongenomic actions through the activation of TGR5, a membrane receptor that is G protein-coupled to the induction of adenylate cyclase. In this work, a training set of 43 bile acid derivatives is used to develop a molecular interaction field analysis (MFA) and a 3D-quantitative structure-activity relationship study (3D-QSAR) of TGR5 agonists. The predictive ability of the resulting model is evaluated using an external set of compounds with known TGR5 activity, and six bile acid derivatives whose unknown TGR5 activity is herein assessed with in vitro luciferase assay of cAMP formation. The results show a good predictive model and indicate a statistically relevant degree of correlation between the TGR5 activity and the molecular interaction fields produced by discrete positions of the bile acid scaffold. This information is instrumental to extend on a quantitative basis the current structure-activity relationships of bile acids as TGR5 modulators and will be fruitful to design new potent and selective agonists of the receptor.     

Purification of cellulases from Streptomyces strain A20 by electroendosmotic preparative electrophoresis

Five cellulase components were identified and purified in one step from Streptomyces strain A20 using electroendosmotic preparative electrophoresis. By this procedure up to 18 mg of protein mixture could be loaded on the column, with an estimated recovery of 60-70% of total activity; activity and protein recovery could be estimated 32% and 47% respectively, if only activity peaks were considered. In comparison to other purification methods, this technique results in high protein recovery and resolution of applied samples.     

An Efficient Algorithm for Bayesian Nearest Neighbours

K-Nearest Neighbours (k-NN) is a popular classification and regression algorithm, yet one of its main limitations is the difficulty in choosing the number of neighbours. We present a Bayesian algorithm to compute the posterior probability distribution for k given a target point within a data-set, efficiently and without the use of Markov Chain Monte Carlo (MCMC) methods or simulation—alongside an exact solution for distributions within the exponential family. The central idea is that data points around our target are generated by the same probability distribution, extending outwards over the appropriate, though unknown, number of neighbours. Once the data is projected onto a distance metric of choice, we can transform the choice of k into a change-point detection problem, for which there is an efficient solution: we recursively compute the probability of the last change-point as we move towards our target, and thus de facto compute the posterior probability distribution over k. Applying this approach to both a classification and a regression UCI data-sets, we compare favourably and, most importantly, by removing the need for simulation, we are able to compute the posterior probability of k exactly and rapidly. As an example, the computational time for the Ripley data-set is a few milliseconds compared to a few hours when using a MCMC approach.

     

Selectivity in the Ligand Functionalization of Photocatalytic Metal Oxide Nanoparticles for Phase Transfer and Self-Assembly Applications

The functionalization of photocatalytic metal oxide nanoparticles of TiO₂, ZnO, WO₃ and CuO with amine-terminated (oleylamine) and thiol-terminated (dodecane-1-thiol) alkyl-chain ligands was studied under ambient conditions. A high selectivity was observed in the binding specificity of a ligand towards nanoparticles of these different oxides. It was observed that oleylamine binds stably to only TiO₂ and WO₃, whereas dodecane-1-thiol binds stably only to ZnO and CuO. Similarly, polar-to-nonpolar solvent phase transfer of TiO₂ and WO₃ nanoparticles could be achieved by using oleylamine, but not dodecane-1-thiol, whereas the opposite holds for ZnO and CuO. The surface chemistry of ligand-functionalized nanoparticles was probed by attenuated total reflectance (ATR)-FTIR spectroscopy, which enabled the occupation of the ligands at the active sites to be elucidated. The photostability of the ligands on the nanoparticle surface was determined by the photocatalytic self-cleaning properties of the material. Although TiO₂ and WO₃ degrade the ligands within 24 h under both UV and visible light, ligands on ZnO and CuO remain unaffected. The gathered insights are also highly relevant from an application point of view. As an example, because the ligand-functionalized nanoparticles are hydrophobic in nature, they can be self-assembled at the air-water interface to give nanoparticle films with demonstrated photocatalytic as well as anti-fogging properties.     

Magnetic detection of crack initiation and propagation

Crack initiation and propagation in steel has been detected by measurements of magnetic flux variations.     

Identification of Broad-Spectrum MMP Inhibitors by Virtual Screening

Matrix metalloproteinases (MMPs) are the family of proteases that are mainly responsible for degrading extracellular matrix (ECM) components. In the skin, the overexpression of MMPs as a result of ultraviolet radiation triggers an imbalance in the ECM turnover in a process called photoaging, which ultimately results in skin wrinkling and premature skin ageing. Therefore, the inhibition of different enzymes of the MMP family at a topical level could have positive implications for photoaging. Considering that the MMP catalytic region is mostly conserved across different enzymes of the MMP family, in this study we aimed to design a virtual screening (VS) workflow to identify broad-spectrum MMP inhibitors that can be used to delay the development of photoaging. Our in silico approach was validated in vitro with 20 VS hits from the Specs library that were not only structurally different from one another but also from known MMP inhibitors. In this bioactivity assay, 18 of the 20 compounds inhibit at least one of the assayed MMPs at 100 μM (with 5 of them showing around 50% inhibition in all the tested MMPs at this concentration). Finally, this VS was used to identify natural products that have the potential to act as broad-spectrum MMP inhibitors and be used as a treatment for photoaging.     

Synthesis of new ribosylated Asn building blocks as useful tools for glycopeptide and glycoprotein synthesis

We performed the first synthesis of new Asn derivatives bearing α- or β-ribose as pure anomers, linked by an N-glycosidic bond, on the side chain of the Asn residue orthogonally protected for Fmoc/^tBu SPPS, by an efficient five-step strategy with a global yield of 73% starting from d-ribose. These building blocks are obtained in a large scale and can be useful tools for glycopeptide and glycoproteins synthesis.     

Analysis of human carbonic anhydrase II: docking reliability and receptor-based 3D-QSAR study

The ability of Gold software to predict the binding disposition of carbonic anhydrase (CA) inhibitors was evaluated using CA II as a case study. The best procedure was subsequently used for docking almost 300 CA II ligands, and the best poses were used as an alignment tool for the development of a 3D quantitative structure-activity relationship (QSAR) study. Evaluation of the resulting 3D-QSAR model allowed us to indicate the ligand properties and residues important for CA II inhibition. Since CAs are an important target involved in many pathologies such as glaucoma, obesity, and tumors, the results obtained could accurately predict the binding affinity of newly designed CA II inhibitors. Furthermore, it is reasonable that this strategy could be profitably used also for the investigation of other CAs.     

Hydration and hydrogen bonding of carbonyls in dimyristoyl-phosphatidylcholine bilayer

We combine two-color ultrafast infrared spectroscopy and molecular dynamics simulation to investigate the hydration of carbonyl moieties in a dimyristoyl-phosphatidylcholine bilayer. Excitation with femtosecond infrared pulses of the OD stretching mode of heavy water produces a time dependent change of the absorption band of the phospholipid carbonyl groups. This intermolecular vibrational coupling affects the entire C=O band, thus suggesting that the optical inhomogeneity of the infrared response of carbonyl in phospholipid membranes cannot be attributed to the variance in hydration. Both the experimental and the theoretical results demonstrate that sn-1 carbonyl has a higher propensity to form hydrogen bonds with water in comparison to sn-2. The time-resolved experiment allows following the evolution of the system from a nonequilibrium localization of energy in the OD stretching mode to a thermally equilibrated condition and provides the characteristic time constants of the process. The approach opens a new opportunity for investigation of intermolecular structural relations in complex systems, like membranes, polymers, proteins, and glasses.