Comparing pharmacophore models derived from crystallography and NMR ensembles

NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225–8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-γ (PPAR-γ). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their NMR counterparts. The crystal-based models exhibited optimum performance only when pharmacophore elements were dropped. This supports our assertion that the higher flexibility in NMR ensembles helps focus the models on the most essential interactions with the protein. Our studies suggest that the “extra” pharmacophore elements seen at the periphery in X-ray models arise as a result of decreased protein flexibility and make very little contribution to model performance.     

Temperature effect on the optical properties of two different triphenylamine-based organic dyes

In this paper, we present the absorption and photoluminescence (PL) spectra of conjugated, metal-free organic dyes, triphenylamine derivatives 3-(4-(bis(4-(5-(4-(hexyloxy)phenyl)thiophenyl)phenyl)amino)phenyl)-2-cyanoacrylic acid (OD3) and (E)-3-(5′-(4-(bis(4-(5-(4-hexyloxy)phenyl)thiophen-2-yl)phenyl)amino)phenyl)-2,2′-bithiophen-5-yl)-2-cyanoacrylic acid (OD3DT), with and without a π-conjugated bridge, respectively, in film at a temperature range from 13 to 400 K. We find that the intensities of absorption and PL of OD3 decrease gradually beyond 200 K, as well as the ratios of integral areas of absorption to PL spectra. However, the other compound, OD3DT, shows a very different behavior. An increase is discovered in the ratio of the absorption to PL integral area when the temperature is higher than 200 K. A π-conjugated bridge gives this compound a higher degree of symmetry, and therefore, a better alignment of the molecules in the film, which causes a stacking aggregation such that the temperature effect on this compound is different than OD3.     

Molden 2.0: quantum chemistry meets proteins

Since the first distribution of Molden in 1995 and the publication of the first article about this software in 2000 work on Molden has continued relentlessly. A few of the many improved or fully novel features such as improved and broadened support for quantum chemistry calculations, preparation of ligands for use in drug design related softwares, and working with proteins for the purpose of ligand docking.     

Facile synthesis of novel [1,3]oxazino[2,3-c][1,2,4] thiadiazin-12-one derivatives

Several novel fused heterocyclic systems which have rings containing N/O or N/S have been synthesized through a facile one-pot method by the treatment of substituted 2-(benzo[d]thiazol-2-yl)phenol and cyanogen bromide in THF and NEt₃. This one-pot method contains tough ring-opening of thiazole, special intermolecular rearrangement and ring-closing reactions. The newly synthesized compounds were characterized by HR-MS, ¹H-NMR, ¹³C-NMR spectral data and DFT calculation analysis. 2a was also determined by X-ray crystallographic analysis.     

An efficient synthesis of 3,4-dihydropyrimidin-2(1<Emphasis Type="Italic">H</Emphasis>)-one and 5,6-diphenylpyrimidine derivatives under solvent-free and base conditions

An efficient and convenient Biginelli-like reaction one-pot synthesis of a series of 4-aryl-5,6-diphenyl-3,4-dihydropyrimidin-2(1H)-one and 4-aryl-5,6-diphenylpyrimidine derivatives under solvent-free conditions from the reaction of aromatic aldehydes, 1,2-diphenylethanone, urea, guanidine carbonate or acetamidine hydrochloride has been reported. This methodology has the advantages of short reaction time, mild reaction conditions, easy work-up and environmental friendliness. Moreover, 4-aryl-5,6-diphenylpyrimidine derivatives were first reported in this process. The structures of the title compounds were further determined by X-ray diffraction. More importantly, different from general Biginelli reaction, this reported method was carried out under base conditions.     

Cholinesulfuric acid ionic liquid catalyzed an eco-friendly synthesis of 2,3-dihydroquinazolin-4(1H)-one in aqueous media

An efficient and straightforward approach to the synthesis of 2,3-dihydroquinazolin-4(1H)-one from 2-aminobenzamide and carbonyl compounds (aldehydes and ketones) using biocompatible choline sulfate-based acidic ionic liquid as a cheap and readily available catalyst in water has been developed. Various 2,3-dihydroquinazolin-4(1H)-one have been prepared using low-cost and environmental friendly solvent and catalyst in good to excellent yields in a shorter reaction time. The choline sulfate catalyst was prepared using a simple method from readily available starting material and was confirmed by ¹H NMR, FTIR, and TGA. The ease of the product separation without organic solvent and column chromatography and the reusability of the acidic ionic liquid catalyst makes this method economically affordable for large-scale synthesis.     

Polyhydroxyquinoline-carbon nanotube chelating resin for selective adsorption of lead ions: multivariate optimization,isothermic, and thermodynamic study

In this work a facile hydrothermal route has been employed to prepare a multiwall carbon nanotube wrapped in a chelating resin. 8-Hydroxyquinoline and p-formaldehyde were used as monomer and linker for polymer synthesis. The prepared composite was employed as an efficient adsorbent for lead adsorption and preconcentration from various matrices. Effective parameters on lead adsorption have been optimized by central composite design. Results showed that equilibrium adsorption was obtained at pH = 4, with a shacking time of 15 min and adsorbent dosage of 15 mg. Isotherm study showed that the sorbent has adsorbent capacity of 250 mg g^?1; moreover, the process followed a Langmuir isotherm model. Thermodynamic investigation confirmed that lead adsorption is spontaneous, as well as follows endothermic path.     

Application of carbon nanotubes as solid-phase extraction sorbent for analysis of chlorophenols in water samples

The aim of this work was to investigate the efficiency of various MWCNTs as SPE materials for the preconcentration of chlorophenols. The COOH-functionalized MWCNTs and MWCNTs were used as SPE sorbents. To evaluate the capability of MWCNTs for the preconcentration of chlorophenols from water samples, 2,4-chlorophenol, 4-chlorophenol, 2,4,6-chlorophenol, 2,6-chlorophenol, 3,4-chlorophenol, and 2-chlorophenol were used as model compounds. Chlorophenols were extracted with acetone, methanol, ethanol, and dichloromethane, and determined by gas chromatography–mass spectrometry. COOH-functionalized MWCNTs <8 nm were found to be the best sorbent for the tested chlorophenols. For COOH-functionalized MWCNTs <8 nm, the recovery rates for all chlorophenols were higher than 50% when acetone or ethanol was used as eluents. In the case of dichloromethane elution, recovery rates for chlorophenols were from 62.0% for 2,6-DCP to 116.8% for 2,4-DCP; only for 2,4,6-TCP was the recovery rate 30.6%. Similar percentage recoveries were achieved with methanol as the eluent.     

A practical and step-economic route to Favipiravir

A practical and step-economic route to Favipiravir, an antiviral drug, was developed. Favipiravir was synthesized in only six steps from 3-aminopyrazine-2-carboxylic acid with an overall yield of about 22.3%. Key intermediates 3 and 6 were obtained in excellent purity via recrystallization from optimized solvents, which was beneficial to large-scale production. In the key synthetic reaction, 3,6-dichloropyrazine-2-carbonitrile (6) was reacted sequentially, in one pot, with KF and 30% H₂O₂ to give (after crystallization from 95% EtOH) favipiravir as colorless crystals, with a 60% yield for this final step of the synthesis.     

Antimicrobial activity of newly synthesized thienoquinolizidines derivatives: inspired by natural plant alkaloids

The antimicrobial activity of 16 newly prepared quinolizidines derivatives using bacteria (Staphylococcus aureus, Staphylococcus epidermidis, Proteus sp., Escherichia coli) acid fast bacterium Mycobacterium smegmatis, yeasts (Candida albicans, Candida parapsilosis), and filamentous fungi (Fusarium culmorum, Microsporum gypseum, Aspergillus flavus, Botrytis cinerea, Alternaria alternata) was studied in this paper. The best antibacterial properties were demonstrated by derivatives 11Ba, trans10Bb and 11Bb, and the most sensitive microorganism was found to be the gram-positive bacterium S. epidermidis. The derivative 11Bb showed the best antifungal activity, while C. albicans was resistant to all tested derivatives, and C. parapsilosis was fully inhibited in the presence of the derivative 11Ba and 11Bb. Among the filamentous fungi, only the dermatophyte M. gypseum was partially inhibited. Biofilms represent the most prevalent type of microbial growth in nature and are crucial to the development of clinical infections. Newly synthesized derivatives were also added into the medium throughout the biofilm formation. We have observed a significant decrease of biofilm formation in the presence of quinolizidine derivatives, testifying to their significant antimicrobial activity. It seems that the relationship between antimicrobial activity and the structure is based on the alkaline character due to nitrogen, the saturated basic quinolizidine skeleton, and the position of sulfur in the molecule.