Molecular dynamics simulations of a nucleoside analogue of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid synthesized as a potential antiviral agent: Conformational studies in vacuum and in water

Conformational analysis of nucleosides may have direct applications to the structure–activity relationship (SAR) studies and in the design of new drug candidates. Although conformational analysis may be accessed in many different ways, in this work it was performed using molecular dynamics (MD) simulation in order to study the dynamic behavior of a nucleoside derivative of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid, synthesized by our group as a potential antiviral agent. The MD simulation was carried out during 10 ns in vacuum and in a box of water at two different temperatures (i.e., 300 and 600 K) using the AMBER force field. The in vacuum MD simulation results are in agreement with the crystallographic structure and with the DFT calculations of the nucleoside, revealing the anti conformer as the more stable one. The simulation in water, however, shows that both conformers may exist at 300 K, the temperature of the in vivo and in vitro assays, revealing that both the syn and anti conformers should be considered in a MD simulation study of the inhibitor–enzyme complex. Simulations are also in agreement with the NOE experiment, which shows that the anti conformer is the preferential one in DMSO-d6 solution at 298 K.     

Construction of 4D-QSAR Models for Use in the Design of Novel p38-MAPK Inhibitors

The p38-mitogen-activated protein kinase (p38-MAPK) plays a key role in lipopolysaccharide-induced tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1) release during the inflammatory process, emerging as an attractive target for new anti-inflammatory agents. Four-dimensional quantitative structure-activity relationship (4D-QSAR) analysis [Hopfinger et al., J. Am. Chem. Soc., 119 (1997) 10509] was applied to a series of 33 (a training set of 28 and a test set of 5) pyridinyl-imidazole and pyrimidinyl-imidazole inhibitors of p38-MAPK, with IC50 ranging from 0.11 to 2100 nM [Liverton et al., J. Med. Chem., 42 (1999) 2180]. Five thousand conformations of each analogue were sampled from a molecular dynamics simulation (MDS) during 50 ps at a constant temperature of 303 K. Each conformation was placed in a 2 angstroms grid cell lattice for each of three trial alignments. 4D-QSAR models were constructed by genetic algorithm (GA) optimization and partial least squares (PLS) fitting, and evaluated by leave-one-out cross-validation technique. In the best models, with three to six terms, the adjusted cross-validated squared correlation coefficients, Q2adj, ranged from 0.67 to 0.85. Model D (Q2adj = 0.84) was identified as the most robust model from alignment 1, and it is representative of the other best models. This model encompasses new molecular regions as containing pharmacophore sites, such as the amino-benzyl moiety of pyrimidine analogs and the N1-substituent in the imidazole ring. These regions of the ligands should be further explored to identify better anti-inflammatory inhibitors of p38-MAPK.     

Ultra‐high pressure LC for astaxanthin determination in shrimp by‐products and active food packaging

Nowadays, there is increasing interest in natural antioxidants from food by‐products. Astaxanthin is a potent antioxidant and one of the major carotenoids in crustaceans and salmonids. An ultra‐high pressure liquid chromatographic method was developed and validated for the determination of astaxanthin in shrimp by‐products, and its migration from new packaging materials to food simulants was also studied. The method uses an UPLC® BEH guard‐column (2.1 × 5 mm, 1.7 µm particle size) and an UPLC® BEH analytical column (2.1 × 50 mm, 1.7 µm particle size). Chromatographic separation was achieved using a programmed gradient mobile phase consisting of (A) acetonitrile–methanol (containing 0.05 m ammonium acetate)–dichloromethane (75:20:5, v/v/v) and (B) ultrapure water. This method was evaluated with respect to validation parameters such as linearity, precision, limit of detection, limit of quantification and recovery. Low‐density polyethylene films were prepared with different amounts of the lipid fraction of fermented shrimp waste by extrusion, and migration was evaluated into food simulants (isooctane and ethanol 95%, v/v). Migration was not detected under the tested conditions. Copyright © 2012 John Wiley & Sons, Ltd.     

Control over the Self‐Assembly Modes of PtII Complexes by Alkyl Chain Variation: From Slipped to Parallel π‐Stacks

We report the self‐assembly of a new family of hydrophobic, bis(pyridyl) Pt^II complexes featuring an extended oligophenyleneethynylene‐derived π‐surface appended with six long (dodecyloxy ( 2 )) or short (methoxy ( 3 )) side groups. Complex 2 , containing dodecyloxy chains, forms fibrous assemblies with a slipped arrangement of the monomer units (d_Pt???Pt≈14 Å) in both nonpolar solvents and the solid state. Dispersion‐corrected PM6 calculations suggest that this organization is driven by cooperative π–π, C?H???Cl and π–Pt interactions, which is supported by EXAFS and 2D NMR spectroscopic analysis. In contrast, nearly parallel π‐stacks (d_Pt???Pt≈4.4 Å) stabilized by multiple π–π and C?H???Cl contacts are obtained in the crystalline state for 3 lacking long side chains, as shown by X‐ray analysis and PM6 calculations. Our results reveal not only the key role of alkyl chain length in controlling self‐assembly modes but also show the relevance of Pt‐bound chlorine ligands as new supramolecular synthons.     

Tablet of Spondias mombin L. Developed from Nebulized Extract Prevents Gastric Ulcers in Mice via Cytoprotective and Antisecretory Effects

Spondias mombin L. (Anacardiaceae) has a worldwide distribution and is present in all regions of Brazil. Its leaves, flowers and bark are used as teas in folk medicine to treat diseases of the digestive system. This study aimed to evaluate the acute non-clinical toxicity, gastroprotective activity, and the related mechanisms of action of nebulized extract and tablets based on dried Spondias mombin (SmNE). SmNE screening showed the presence of flavonoids (0.65%), polyphenols (25.50%), where the major compound is gallic acid. In the acute oral toxicity assay, a dose of 2000 mg/kg of SmNE administered orally in Swiss mice did not induce any behavioral changes. SmNE (250 or 500 mg/kg p.o) significantly reduced the ulcerative lesion area when compared to the control group in ethanol and non-steroidal anti-inflammatory drug (NSAIDs) models. Results showed that treatment with SmNE (250 mg/kg) reduced acid secretion and gastric content, accompanied with an increase in pH. Previous administration of indomethacin and glibenclamide reversed the protection provided by SmNE, confirming the participation of prostaglandins (PGs) and ATP-sensitive potassium channels (KATP) in its gastroprotective effect. The SmNE tablets met the pharmacopeial quality requirements with gastroprotective activity and similar protection in comparison to the isolated extract administrated. In conclusion, SmNe has a gastroprotective activity related to cytoprotective mechanisms, such as the participation of endogenous prostaglandins and KATP channels, having an anti-secretory effect with systemic action. The formulation obtained presented gastroprotective effects similar to the administration of the extract, the tablets showed favorable compression characteristics by the direct route and met the pharmacopeial quality requirements.     

Spin waves propagation in Fibonacci quasiperiodic metamagnet superlattices

In this work we present a fractal analysis of the spin wave modes propagating in a Fibonacci quasiperiodic metamagnetic superlattices consisting of a ferromagnetic material (layer A being Fe) and a metamagnetic material (layer B being FeBr₂). The spin wave modes are obtained in the exchange regime, using the transfer matrix technique. Our numerical results show that the power law for this system is independent of the dimensionless in-plane wavevector kxa$k_{x}a$, and that the spectrum present a multifractal characteristic, exhibiting several scale invariant windows for a fixed value of the in-plane wavevector. The results reported here can be experimentally observed by light scattering techniques.