Analysis of conformational equilibria in aplidine using selective excitation 2D NMR spectroscopy and molecular mechanics/dynamics calculations

Aplidine (dehydrodidemnin B), a natural product with potent antitumor activity currently in multicenter phase II clinical trials, exists in DMSO as a mixture of four slowly interconverting conformations in a ratio of 47:33:13:7. NMR spectroscopy shows that these arise as a consequence of cis/trans isomerization about the NMe-Leu(7)-Pro(8) and Pro(8)-Pyr amide bonds of the molecule's side chain. Two major conformations account for 47% and 33% of the total population, a ratio of 60:40 between the two. They correspond to the cis- and trans-isomers, respectively, about the Pro(8)-Pyr amide bond. Two minor conformers arise as a consequence of similar isomerism about the Pro(8)-Pyr amide bond, but in structures in which the NMe-Leu(7)-Pro(8) amide bond is cis rather than trans. These account for approximately 13% and 7% of the total population, corresponding to a ratio of 65:35 cis/trans, respectively. Molecular dynamics simulations show that the three-dimensional structures of all four conformational isomers are similar in the macrocycle and that all are essentially unchanged with respect to the macrocycle of didemnin B. Significant differences in the conformation of the molecule's side chain are, however, observed between major and minor pairs. Analysis of hydrogen-bonding patterns shows that each major conformer exhibits a beta-turn like structure and is stabilized by hydrogen bonding between a different carbonyl group of the pyruvyl unit of the molecule's side chain and the NH of the Thr(6) residue. The minor isomers have a cis-amide bond between the NMe-Leu(7) and Pro(8) residues that obliges the side chain to adopt an extended disposition where hydrogen bonding to the macrocycle is absent. These results suggest that the ability of the molecule's side chain to adopt a beta-turn-like conformation may not be a prerequisite for biological activity in the didemnins and that conformations having an extended side-chain may play a role in the biological activity of aplidine.     

Evaluation of the Use of Elicitors for the Production of Antioxidant Compounds in Liquid Cultures of Ganoderma curtisii from Costa Rica

The use of substances or conditions as elicitors can significantly increase the production of secondary metabolites. In this research, the effects of different elicitors on the production of antioxidant secondary metabolites were evaluated in a strain of Ganoderma sp. The elicitors tested were pH changes in different growth phases of the fungus (pH 3, 5.5 and 8), different concentrations of peptone as a nitrogen source (1 g/L and 10 g/L), and the addition of chemical agents to the culture medium (ethanol, growth regulators, and salts). The alkaline pH during the stationary phase and the high availability of nitrogen were effective elicitors, producing cultures with higher antioxidant activity (37.87 g/L and 43.13 g/L dry biomass) although there were no significant differences with other treatments.     

Enantioselective 1,3-Dipolar Cycloaddition Using (Z)-α-Amidonitroalkenes as a Key Step to the Access to Chiral cis-3,4-Diaminopyrrolidines

The enantioselective 1,3-dipolar cycloaddition between imino esters and (Z)-nitroalkenes bearing a masked amino group in the β-position was studied using several chiral ligands and silver salts. The optimized reaction conditions were directly applied to the study of the scope of the reaction. The determination of the absolute configuration was evaluated using NMR experiments and electronic circular dichroism (ECD). The reduction and hydrolysis of both groups was performed to generate in an excellent enantiomeric ratio the corresponding cis-2,3-diaminoprolinate.     

PET Imaging of the Neuropeptide Y System: A Systematic Review

Neuropeptide Y (NPY) is a vastly studied biological peptide with numerous physiological functions that activate the NPY receptor family (Y₁, Y₂, Y₄ and Y₅). Moreover, these receptors are correlated with the pathophysiology of several diseases such as feeding disorders, anxiety, metabolic diseases, neurodegenerative diseases, some types of cancers and others. In order to deepen the knowledge of NPY receptors’ functions and molecular mechanisms, neuroimaging techniques such as positron emission tomography (PET) have been used. The development of new radiotracers for the different NPY receptors and their subsequent PET studies have led to significant insights into molecular mechanisms involving NPY receptors. This article provides a systematic review of the imaging biomarkers that have been developed as PET tracers in order to study the NPY receptor family.     

Directed ortho-lithiation of unprotected diphenylphosphinic acids

Directed ortho lithiation of diphenylphosphinic acid and subsequent electrophilic trapping provides mono ortho-functionalized derivatives including enantiopure γ-aminophosphinic acids in moderate yields. Copper catalyzed coupling of the ortho anion leads to biphenyl-2,2′-diylbis(phenylphosphinic acid), a phosphorus analogue of biphenyl-2,2′-dicarboxylic acid. Preliminary studies of the metal-binding abilities of this O,O-chelating ligand towards a series of metal cations are included.     

Toward the computer-aided discovery of FabH inhibitors. Do predictive QSAR models ensure high quality virtual screening performance?

Antibiotic resistance has increased over the past two decades. New approaches for the discovery of novel antibacterials are required and innovative strategies will be necessary to identify novel and effective candidates. Related to this problem, the exploration of bacterial targets that remain unexploited by the current antibiotics in clinical use is required. One of such targets is the \(\beta \) -ketoacyl-acyl carrier protein synthase III (FabH). Here, we report a ligand-based modeling methodology for the virtual-screening of large collections of chemical compounds in the search of potential FabH inhibitors. QSAR models are developed for a diverse dataset of 296 FabH inhibitors using an in-house modeling framework. All models showed high fitting, robustness, and generalization capabilities. We further investigated the performance of the developed models in a virtual screening scenario. To carry out this investigation, we implemented a desirability-based algorithm for decoys selection that was shown effective in the selection of high quality decoys sets. Once the QSAR models were validated in the context of a virtual screening experiment their limitations arise. For this reason, we explored the potential of ensemble modeling to overcome the limitations associated to the use of single classifiers. Through a detailed evaluation of the virtual screening performance of ensemble models it was evidenced, for the first time to our knowledge, the benefits of this approach in a virtual screening scenario. From all the obtained results, we could arrive to a significant main conclusion: at least for FabH inhibitors, virtual screening performance is not guaranteed by predictive QSAR models.     

Synthesis and characterization of nanostructured iron compounds prepared from the decomposition of iron pentacarbonyl dispersed into carbon materials with varying porosities

This work describes the production and characterization of carbon-iron nanocomposites obtained from the decomposition of iron pentacarbonyl (Fe(CO)₅) mixed with different carbon materials: a high surface area activated carbon (AC), powdered graphite (G), milled graphite (MG), and carbon black (CB). The nanocomposites were prepared either under argon or in ambient atmosphere, with a fixed ratio of Fe(CO)₅ (4.0 mL) to carbon precursor (2.0 g). The images of scanning electron microscopy and the analysis of textural properties indicated the presence of nanostructured Fe compounds homogeneously dispersed into the different classes of pores of the carbon matrices. The elemental Fe content was always larger for samples prepared in ambient atmosphere, reaching values in the range of 20–32 wt%. On the other hand, samples prepared under argon showed reduced Fe content, with values in the range 5–10 wt% for samples prepared from precursors with low surface area (G, MG, and CB) and a much higher value (~19 wt%) for samples prepared from the precursor of high surface area (AC). Mössbauer spectroscopy and X-ray diffractometry showed that the nanoparticles were mostly composed of iron oxides in the case of the samples prepared in oxygen-rich ambient atmosphere and also for the AC-derived nanocomposite prepared under argon, which is consistent with the large oxygen content of this precursor. For the other precursors, with reduced or no oxygen content, metallic iron and iron carbides were found to be the dominant phases in samples prepared under oxygen-free atmosphere. The samples prepared in ambient atmosphere and the AC-derived sample prepared under argon exhibited superparamagnetic behavior at room temperature, as revealed by temperature-dependent magnetization curves and Mössbauer spectroscopy.