A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase

We report a new structure-based strategy for the identification of novel inhibitors. This approach has been applied to Bacillus stearothermophilus alanine racemase (AlaR), an enzyme implicated in the biosynthesis of the bacterial cell wall. The enzyme catalyzes the racemization of l- and d-alanine using pyridoxal 5-phosphate (PLP) as a cofactor. The restriction of AlaR to bacteria and some fungi and the absolute requirement for d-alanine in peptidoglycan biosynthesis make alanine racemase a suitable target for drug design. Unfortunately, known inhibitors of alanine racemase are not specific and inhibit the activity of other PLP-dependent enzymes, leading to neurological and other side effects.This article describes the development of a receptor-based pharmacophore model for AlaR, taking into account receptor flexibility (i.e. a `dynamic' pharmacophore model). In order to accomplish this, molecular dynamics (MD) simulations were performed on the full AlaR dimer from Bacillus stearothermophilus (PDB entry, 1sft) with a d-alanine molecule in one active site and the non-covalent inhibitor, propionate, in the second active site of this homodimer. The basic strategy followed in this study was to utilize conformations of the protein obtained during MD simulations to generate a dynamic pharmacophore model using the property mapping capability of the LigBuilder program. Compounds from the Available Chemicals Directory that fit the pharmacophore model were identified and have been submitted for experimental testing.The approach described here can be used as a valuable tool for the design of novel inhibitors of other biomolecular targets.     

A New Ent-Kaurane from the Roots of Lasianthaea aurea

Chemistry of Natural Compounds - A known kaurenoic acid (1), together with a new kaurane derivative named 3α-isobutyryloxykaurenoic acid (2), was isolated from the roots of Lasianthaea aurea,...     

Synthesis and Biological Evaluation of New N-Acyl-α-amino Ketones and 1,3-Oxazoles Derivatives

In order to develop novel bioactive substances with potent activities, some new valine-derived compounds incorporating a 4-(phenylsulfonyl)phenyl fragment, namely, acyclic precursors from N-acyl-α-amino acids and N-acyl-α-amino ketones classes, and heterocycles from the large family of 1,3-oxazole-based compounds, were synthesized. The structures of the new compounds were established using elemental analysis and spectral (UV-Vis, FT-IR, MS, NMR) data, and their purity was checked by reversed-phase HPLC. The newly synthesized compounds were evaluated for their antimicrobial and antibiofilm activities, for toxicity on D. magna, and by in silico studies regarding their potential mechanism of action and toxicity. The 2-aza-3-isopropyl-1-[4-(phenylsulfonyl)phenyl]-1,4-butanedione 4b bearing a p-tolyl group in 4-position exhibited the best antibacterial activity against the planktonic growth of both Gram-positive and Gram-negative strains, while the N-acyl-α-amino acid 2 and 1,3-oxazol-5(4H)-one 3 inhibited the Enterococcus faecium biofilms. Despite not all newly synthesized compounds showing significant biological activity, the general scaffold allows several future optimizations for obtaining better novel antimicrobial agents by the introduction of various substituents on the phenyl moiety at position 5 of the 1,3-oxazole nucleus.     

Polyphenolic QTOF-ESI MS Characterization and the Antioxidant and Cytotoxic Activities of Prunus domestica Commercial Cultivars from Costa Rica

There is an increased interest in plum research because of their metabolites’ potential bioactivities. In this study, the phenolic profiles of Prunus domestica commercial cultivars (Methley, Pisardii and Satsuma) in Costa Rica were determined by Ultra Performance Liquid Chromatography coupled with High Resolution Mass Spectrometry using a quadrupole-time-of-flight analyzer (UPLC-ESI-QTOF MS) on enriched phenolic extracts obtained through Pressurized Liquid Extraction (PLE) under acidic and neutral extraction conditions. In total, 41 different phenolic compounds were identified in the skin and flesh extracts, comprising 11 flavan-3-ols, 14 flavonoids and 16 hydroxycinnamic acids and derivatives. Neutral extractions for the skins and flesh from all of the cultivars yielded a larger number of compounds, and were particularly rich in the number of procyanidin trimers and tetramers when compared to the acid extractions. The total phenolic content (TPC) and antioxidant potential using the DPPH and ORAC methods exhibited better results for neutral extracts with Satsuma skins and Methley flesh, which showed the best values (685.0 and 801.6 mg GAE/g extract; IC₅₀ = 4.85 and 4.39 µg/mL; and 12.55 and 12.22 mmol TE/g extract, respectively). A Two-Way ANOVA for cytotoxicity towards AGS gastric adenocarcinoma and SW620 colon adenocarcinoma indicated a significant difference (p < 0.05) for PLE conditions, with better results for neutral extractions, with Satsuma skin delivering the best results (IC₅₀ = 60.7 and 46.7 µg/mL respectively) along with Methley flesh (IC₅₀ = 76.3 and 60.9 µg/mL, respectively). In addition, a significant positive correlation was found between TPC and ORAC (r = 0.929, p < 0.05), as well as a significant negative correlation (p < 0.05) between TPC and cytotoxicity towards AGS and SW620 cell lines (r = −0.776, and −0.751, respectively). A particularly high, significant, negative correlation (p < 0.05) was found between the number of procyanidins and cytotoxicity against the AGS (r = −0.868) and SW620 (r = −0.855) cell lines. Finally, the PCA clearly corroborated that neutral extracts are a more homogenous group exhibiting higher antioxidant and cytotoxic results regardless of the part or cultivar; therefore, our findings suggest that PLE extracts under neutral conditions would be of interest for further studies on their potential health benefits.     

“Surface water” and “strong-bonded water” in cyclodextrins: a Karl Fischer titration approach

Cyclodextrins are some of the most used carriers for bioactive compounds (as host–guest complex) and many factors influence the association–dissociation of this complex, some of them being related to hydrophobicity. In the solid state, cyclodextrins contain two types of water molecules: “surface” water molecules (especially close to the crystal surface) and “strong-bonded” water molecules (especially from the cyclodextrin cavity), but the classification is hard to do, and the concentration of these water molecules are relatively difficult to estimate by simple methods. In the present study we used the volumetric Karl Fischer titration to estimate these types of water molecules in cyclodextrins by means of the rate of water reaction (related to diffusion from cyclodextrin crystals). “Surface” water molecules are titrated with rates between 1.8–2.8 mM/s for α-cyclodextrin, while for β-cyclodextrin these rates are little bit higher (2.9–3.4 mM/s). The rates corresponding to “strong-bonded” water molecules are approximately tens fold lower (0.05–0.3 mM/s for α-cyclodextrin and 0.15–0.33 mM/s for β-cyclodextrin). The approximate ratio between “surface” and “strong-bonded” water molecules could also be estimated by this simple and rapid method.     

Removal of heavy metal ions from aqueous solutions using low-cost sorbents obtained from ash

This study’s main objective was the development of effective low-cost sorbents for the removal of heavy metal ions from aqueous solutions. The influence of different factors on the sorption capacity of ash and modified ash as low-cost sorbents obtained by different methods was investigated. The synthesis of new ash-based materials was carried out at ambient temperature (20°C), 70°C, and 90°C, respectively, in an alkaline medium with NaOH concentrations of 2 M and 5 M, respectively, corresponding to a mixture with solid/liquid ratios of 1: 3 and 1: 5, respectively. The prepared materials (sorbents) were characterised by scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDAX), X-ray diffraction, and BET surface measurement. Adsorption isotherms were determined using the batch equilibrium method. The results showed that these types of new materials displayed a good capacity to remove copper, nickel, and lead ions (29.97 mg of Cu²⁺ per g of sorbent, 303 mg of Ni²⁺ per g of sorbent, and 1111 mg of Pb²⁺ per g of sorbent) from aqueous solutions. The modified materials were prepared using an alkaline attack (a recognised method used in previous studies), but Romanian ash from a thermal power plant was studied for the above purpose for the first time. Hence, the factors which affect the sorption capacity of the prepared low-cost sorbents were determined and their behaviour was explained, taking into account the composition and structure of the new materials.     

Thermal decomposition of the [Pt(NH3)4]2+ complex in NaX zeolite

The effect of the calcination procedure on the decomposition of the [Pt(NH₃)₄]²⁺ complex in a cesium-containing NaX zeolite was studied by thermal decomposition accompanied by mass spectrometry and diffuse reflectance spectroscopy, as well as electron paramagnetic resonance and infrared spectroscopy. The decomposition of the complex took place in two steps. Under oxygen, the [Pt(NH₃)₄]²⁺ complex was first converted into the [Pt(NH₃)₂]²⁺ complex in the first step, with predominant nitrogen release. In the second step, corresponding to the decomposition of the remaining two amine ligands, NO was also formed and adsorbed. Oxygen paramagnetic species were also observed. Under He, the decomposition also occurred in two steps with H₂ release.     

Comparative study of the oxidative and thermal stability of vegetable oils to be used as lubricant bases

Demand for lubricating oils is increasing in the growing Brazilian economy. The use of vegetable bases in exchange of minerals can bring socio-economic and environmental benefits for Brazil. The purpose of this study is to compare the thermal and oxidative stability of vegetable oils related to the bases commonly used as lubricants. In this study, thermogravimetric analysis of castor oil, cotton oil, macauba’s almond oil, passion oil, paraffinic mineral oil, naphthenic oil (NH-140) and synthetic oil (Etro) was performed in inert and oxidative atmosphere to study the thermal and oxidative degradation of the vegetable oils related to the most common lubricants’ oils base. These oils’ oxidation stability were determined by standard procedures (ISO 6886). The use of mineral oil’s additives in these vegetable oils was tested to verify the viability of these additives to improve the oxidative stability of the vegetable oils. The castor oil and the cotton oil presented results of thermal analysis similar to the mineral and synthetic bases values. The castor oil was the only vegetable oil that showed a great oxidative stability. All other vegetable oils had their oxidative stability significantly increased by the additives.     

Planar Chromatographic and Electrophoretic Study of Thermally Induced Conformational Modifications of Protein Structure

JPC – Journal of Planar Chromatography – Modern TLC -