Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

Determination of trace amounts of cadmium and copper by atomic absorption spectrometry after simultaneous extraction and preconcentration using a new water-soluble polyacrylic acid/alumina sorbent

An analytical method using alumina modified with water-soluble polyacrylic acid polymer for the simultaneous separation and preconcentration of trace Cu and Cd in a column system, and their determination by flame atomic absorption spectrometry was developed. The conditions for coating Al₂O₃ with polyacrylic acid were optimized, then the column was packed with 50 mg of this sorbent. Cd and Cu solution was passed through a glass column at pH 4.5, and elution was carried out with 5 mL of 0.05 M HCl at a flow rate of 1 mL min⁻¹. A sorption capacity of 10 mg Cu and 12 mg Cd was obtained for 1 g sorbent. The detection limit was calculated as 4.5 μg L⁻¹ for Cu and 1.54 μg L⁻¹ for Cd in the final solution. Enrichment factors of 300 for Cd and 400 for Cu were obtained.     

Highly oxygenated triterpenes from the roots of Atropa acuminata

Two new oleanane triterpenes; 2alpha,3alpha,24-trihydroxyolean-12-ene-28,30-dioic acid ([structure: see text]) and 2alpha,3alpha,24,28-tetrahydroxyolean-12-ene ([structure: see text]) have been isolated from the roots of Atropa acuminata. Anti-oxidant p-hydroxyphenethyl trans-ferulate ([structure: see text]), beta-sitosterol-3-O-beta-D-glucopyranoside ([structure: see text]) and oleanolic acid ([structure: see text]) have also been reported for the first time from this species. The structures were determined by spectroscopic studies including 2D-NMR.     

4-(p-Chloro)phenyl-1,2,4-triazole-3,5-dione as a novel and reusable reagent for the oxidation of 1,3,5-trisubstituted pyrazolines under mild conditions

4-(p-Chloro)phenyl-1,3,4-triazole-3,5-dione is used as an effective oxidizing agent for the oxidation of 1,3,5-trisubstituted pyrazolines to their corresponding pyrazoles under mild conditions with moderate to good yields at room temperature.     

Aristoserratin,ein neues Indolalkaloid aus Aristotelia serrata W.R.B. OLIVER und A. peduncularis (LABILL.) HOOK. F. 178. Mitteilung über organische Naturstoffe

Aristoserratine, a New Indole Alkaloid from Aristotelia serrata W.R.B. OLIVER and from A. peduncularis (LABILL .) HOOK . F. The new indole alkaloid aristoserratine (2) has been isolated from Aristotelia. Its structure and absolute configuration were elucidated on the basis of spectroscopic data.     

Energetic and topological analyses of the oxidation reaction between Mo(n) (n = 1, 2) and N2O

The interaction between molybdenum, atom, and dimer, with nitrous oxide has been investigated using density functional theory. The analysis of the potential energy surfaces for both reactions has revealed that a single molybdenum atom can activate the N--O bond of N2O requiring a small activation energy. However, the presence of several intersystem crossings between three different spin states, namely, septet, quintet and triplet states, seems to be the major constraint to the Mo + N2O reaction. Contrarily, the low-lying excited states (triplet and quintet) do not participate in the reaction between the molybdenum dimer and N2O. The latter reaction fully evolves on the singlet spin surface. Three different regions have been distinguished along the pathway: formation of an adduct complex, formation of an inserted compound, and the N2 detachment. The connection between the two first regions has been characterized by the formation of a special complex in which the N--O bond is so weakened that it could be considered as a first step in the insertion process. It has been shown that the topological changes along the pathways provide a clear explanation for the geometrical changes that occur along the reaction pathway. In summary, the detachment of the N2 molecule is found to be kinetically an effective process for both reactions, owing to the high exothermicity and consequently to the high internal energy of the insertion intermediates. However, in the case of Mo atom, the reaction should be a slow process due to the presence of spin-forbidden transitions. These results fully agree with previous experimental works.     

Determination of phenols in water samples by single-drop microextraction followed by in-syringe derivatization and gas chromatography-mass spectrometric detection

Trace analysis of phenolic compounds in water was performed by coupling single-drop microextraction (SDME) with in-syringe derivatization of the analytes and GC-MS analysis. The analytes were extracted from a 3ml sample solution using 2.5microl of hexyl acetate. After extraction, derivatization was carried out in syringe barrel using 0.5microl of N,O-bis(trimethylsilyl)acetamide. The influence of derivatizing reagent volume, derivatization time and temperature on the yield of the in-syringe silylation was investigated. Derivatization reaction is completed in 5min at 50 degrees C. Experimental SDME parameters, such as selection of organic solvent, sample pH, addition of salt, extraction time and temperature of extraction were studied. Analytical parameters, such as enrichment factor, precision, linearity and detection limits were also determined. The limits of detection were in the range of 4-61ng/l (S/N=3). The relative standard deviations obtained were between 4.8 and 12% (n=5).     

Factors Contributing to Solubility Synergism of Some Basic Drugs with β-Cyclodextrin in Ternary Molecular Complexes

Ternary complexes exploiting solubility synergism (SSn) between basic drugs and β-cyclodextrin (β-CD) in the presence of an organic hydoxy acid have been reported to provide the pharmaceutical technology with highly soluble ternary complexes, even with the least soluble β-CD. In this work, phase solubility techniques were used to study factors affecting SSn in aqueous solution, which may help in understanding the mechanism involved in ternary complex formation in solution, under equilibrium conditions. The equilibrium solubility of both β-CD and each of 8 structurally unrelated drugs were measured in tandem in the presence of different acid types at low and high pHs, and at different time intervals over a period of 1–40 days. The results indicate that SSn is evident regardless of acid type (organic and inorganic) at low pH, but the extent of SSn is acid type dependant and is limited by the drug salt solubility product constant (pK _sp). Among different drugs, no apparent trend exists between drug salt solubility and the extent of SSn, but lowering drug salt solubility by increasing pH depresses SSn. The results also reveal no apparent trend between the magnitude of the complex formation constant (K _ij) and SSn. For example, drugs of low K _ij values such as astemizole, cisapride and sildenafil do not show any SSn, yet ketotifen and pizotifen, which also have low K _ij values, exhibit substantial SSn. However, the solublizing power of β-CD represented by the slope of phase solubility diagram can be used as a marker for SSn (slopes exceeding 0.4 induce SSn).     

Reaction of methyl tetronate with some amines. Synthesis of substituted 4-aminobut-2-enolides

A series of substituted 4-aminobut-2-enolide derivatives have been synthesized by reaction of a variety of substituted amines with methyl tetronate. The ¹H and ¹³C nmr spectral analysis of all compounds synthesized are given.     

Di­aqua­bis(4,5‐di­hydro‐1,2,4‐triazolo[1,5‐a]­pyrimidin‐5‐one‐N3)bis­(thiocyanato‐N)­nickel(II)

The title compound, [Ni(NCS)₂(C₅H₄N₄O)₂(H₂O)₂], crystallizes in the triclinic space group P. The molecular unit contains two neutral mol­ecules of 4,5‐di­hydro‐1,2,4‐triazolo[1,5‐a]­pyrimidin‐5‐one (5HtpO) coordinated through the N atom in position 3, two thio­cyanate ligands coordinated through their N atoms and two water mol­ecules completing an octahedral environment around the Ni^II ion, which lies on a centre of inversion. The structure is stabilized by hydrogen bonding. Distances in the coordination sphere are Ni—N3(5HtpO) 2.132 (2), Ni—O(water) 2.085 (2) and Ni—N(thio­cyanato) 2.040 (2) Å.