Predicting olfactory receptor neuron responses from odorant structure

Background  

Olfactory receptors work at the interface between the chemical world of volatile molecules and the perception of scent in the brain. Their main purpose is to translate chemical space into information that can be processed by neural circuits. Assuming that these receptors have evolved to cope with this task, the analysis of their coding strategy promises to yield valuable insight in how to encode chemical information in an efficient way.     

Automated extraction of chemical structure information from digital raster images

Background  

To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated.     

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

Background  

Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit.     

Interplay of thermochemistry and Structural Chemistry, the journal (volume 17, 2006) and the discipline

Abstract  

In the current study we relate the contents of the journal of “Structural Chemistry” for the calendar year 2006 to thermochemistry. Each paper is briefly summarized and supplemented by a comment which explicitly interrelates the content of the study to chemical energetics.     

Synthesis and pharmacological activity of some synthesized polyazacyclopenta[a]naphthalenes and pyrazolo[3,4-b]pyridines using 2-amino-6-methyl-4-phenylnicotinonitrile as synthon

Abstract  

A series of pyridines, pyrimidines, and their derivatives were synthesized using 2-amino-6-methyl-4-phenylnicotinonitrile as starting material. Thirteen new heterocyclics containing a pyridine ring were thus prepared. Pharmacological screening showed that many of these compounds have good anti-inflammatory and analgesic activity comparable with those of diclofenac potassium and valdecoxib as reference drugs. Assignment of the structures of the new compounds was based on chemical and spectroscopic evidence. Synthesis, spectroscopic data, and pharmacological properties of the compounds are reported in detail.     

Fast 3D shape screening of large chemical databases through alignment-recycling

Background  

Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes.     

Facile solution-phase synthesis of γ-Mn3O4 hierarchical structures

Background  

A lot of effort has been focused on the integration of nanorods/nanowire as building blocks into three-dimensional (3D) complex superstructures. But, the development of simple and effective methods for creating novel assemblies of self-supported patterns of hierarchical architectures to designed materials using a suitable chemical method is important to technology and remains an attractive, but elusive goal.     

Charting calcium-regulated apoptosis pathways using chemical biology: role of calmodulin kinase II

Background  

Intracellular free calcium ([Ca²⁺]_i) is a key element in apoptotic signaling and a number of calcium-dependent apoptosis pathways have been described. We here used a chemical biology strategy to elucidate the relative importance of such different pathways.     

Chemogenetic fingerprinting by analysis of cellular growth dynamics

Background  

A fundamental goal in chemical biology is the elucidation of on- and off-target effects of drugs and biocides. To this aim chemogenetic screens that quantify drug induced changes in cellular fitness, typically taken as changes in composite growth, is commonly applied.     

Calculation of chemical shielding in C-doped zigzag BN nanotubes

Abstract  

Chemical shielding tensors at the sites of various ¹¹B and ¹⁵N nuclei were calculated to study the electronic structure properties of carbon-doped boron nitride nanotubes. The chemical shielding tensors were converted to isotropic and anisotropic chemical shielding parameters. The results reveal the significant effect of C-doping on the chemical shielding tensors at the sites of those ¹¹B and ¹⁵N nuclei located in the nearest neighborhood of the C-doped ring. The isotropic and anisotropic chemical shielding tensors of those B atoms directly bonded to C atoms reach values observed for B atoms placed at the B-mouth of the nanotube.     

Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study)

Background  

Molecular mechanics (MM) and quantum chemical (QM) calculations are widely applied and powerful tools for the stereochemical and conformational investigations of molecules. The same methods have been extensively used to probe the conformational profile of Taxol (Figure 1) both in solution and at the β-tubulin protein binding site.     

Synthesis, complete NMR spectral assignments, and antifungal screening of new 2,4-diaryl-3-azabicyclo[3.3.1]nonan-9-one oxime derivatives

Abstract  

A series of differently substituted 2,4-diaryl-3-azabicyclo[3.3.1]nonan-9-one oximes have been synthesized and their ¹H and ¹³C NMR chemical shifts have been unambiguously assigned using H,H-COSY, NOESY, HSQC, and HMBC spectral data. On the basis of the NMR studies, irrespective of the nature and position of the substituents, all reported compounds exist in twin-chair conformation with equatorial disposition of the phenyl groups at C-2 and C-4 of the 3-azabicyclononane moiety. Among the synthesized oxime derivatives, compounds with halo-substituents at ortho/para positions of the phenyl showed good antifungal profile against all tested organisms.     

Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model

Abstract  

A series of 27 benzamidine inhibitors covering a wide range of biological activity and chemical diversity was analysed to derive a Linear Interaction Energy in Continuum Electrostatics (LIECE) model for analysing the thrombin inhibitory activity. The main interactions occurring at the thrombin binding site and the preferred binding conformations of inhibitors were explicitly biased by including into the LIECE model 10 compounds extracted from X-ray solved thrombin-inhibitor complexes available from the Protein Data Bank (PDB). Supported by a robust statistics (r ² = 0.698; q ² = 0.662), the LIECE model was successful in predicting the inhibitory activity for about 76% of compounds (r _ext² ≥ 0.600) from a larger external test set encompassing 88 known thrombin inhibitors and, more importantly, in retrieving, at high sensitivity and with better performance than docking and shape-based methods, active compounds from a thrombin combinatorial library of 10240 mimetic chemical products. The herein proposed LIECE model has the potential for successfully driving the design of novel thrombin inhibitors with benzamidine and/or benzamidine-like chemical structure.     

Enhancement of intracellular γ-tocopherol levels in cytokine-stimulated C3H 10T1/2 fibroblasts: relation to NO synthesis,isoprostane formation,and tocopherol oxidation

Background  

Stimulation of C3H 10T1/2 murine fibroblasts with interferon-γ(IFN) and bacterial lipopolysaccharide (LPS) generates reactive oxygen and nitrogen species leading to DNA damage, lipid oxidation, and tocopherol oxidation. The tocopherols possess unique chemical and biological properties that suggest they have important roles related to intracellular defense against radical-mediated damage.     

DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

Background  

Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats.     

Core charge distribution and self assembly of columnar phases: the case of triphenylenes and azatriphenylenes

Background  

The relation betweeen the structure of discotic molecules and columnar properties, a crucial point for the realization of new advanced materials, is still largely unknown. A paradigmatic case is that hexa-alkyl-thio substituted triphenylenes present mesogenic behavior while the corresponding azatriphenylenes, similar in shape and chemical structure, but with a different core charge distribution, do not form any liquid crystalline mesophase. This study is aimed at investigating, with the help of computer simulations techniques, the effects on phase behaviour of changes of the charge distribution in the discotic core.     

The effect of ultrasonic pre-treatment on the catalytic activity of lipases in aqueous and non-aqueous media

Background  

Ultrasound has been used to accelerate the rates of numerous chemical reactions, however its effects on enzymatic reactions have been less extensively studied. While known to result in the acceleration of enzyme-catalysed reactions, ultrasonication has also been shown to induce enzyme inactivation. In this study we investigated the effects of ultrasonic pretreatment on lipases in both aqueous and non-aqueous media.     

A one-pot synthesis of alkyl acylcarbamodithioates from acid chlorides, thiols, and ammonium thiocyanate

Abstract  

An efficient synthesis of alkyl acylcarbamodithioates by reaction of acid chlorides with ammonium thiocyanate in the presence of thiols is described. The unusually large values of ⁵ J _FH = 12–15 Hz, observed for alkyl (2-fluorobenzoyl)carbamodithioates provide information about Ar–C–N–H torsion in these compounds.     

Study of the structural and electronic origin of the sandalwood odor of some terpenylcyclohexanols

Abstract  

The correlation between structural and electronic features and the sandalwood odor of some terpenylcyclohexanols is established on the basis of quantum chemical calculation methods. A definite structural fragment with electronic properties determining the origin of the odor is revealed. The effects of HOMO–LUMO energy gaps and total energies of some terpenylcyclohexanols on their odor intensity are investigated.     

Identification of archaeal proteins that affect the exosome function in vitro

Background  

The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors.