Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods

In recent years, many virtual screening (VS) tools have been developed that employ different molecular representations and have different speed and accuracy characteristics. In this paper, we compare ten popular ligand-based VS tools using the publicly available Directory of Useful Decoys (DUD) data set comprising over 100?000 compounds distributed across 40 protein targets. The DUD was developed initially to evaluate docking algorithms, but our results from an operational correlation analysis show that it is also well suited for comparing ligand-based VS tools. Although it is conventional wisdom that 3D molecular shape is an important determinant of biological activity, our results based on permutational significance tests of several commonly used VS metrics show that the 2D fingerprint-based methods generally give better VS performance than the 3D shape-based approaches for surprisingly many of the DUD targets. To help understand this finding, we have analyzed the nature of the scoring functions used and the composition of the DUD data set itself. We propose that to improve the VS performance of current 3D methods, it will be necessary to devise screening queries that can represent multiple possible conformations and which can exploit knowledge of known actives that span multiple scaffold families.     

PubChemSR: A search and retrieval tool for PubChem

Background  

Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR.     

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.     

The molecular basis of electroporation

Background  

Electroporation is a common method to introduce foreign molecules into cells, but its molecular basis is poorly understood. Here I investigate the mechanism of pore formation by direct molecular dynamics simulations of phospholipid bilayers of a size of 256 and of more than 2000 lipids as well as simulations of simpler interface systems with applied electric fields of different strengths.     

DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0

Background  

Small-molecule docking is an important tool in studying receptor-ligand interactions and in identifying potential drug candidates. Previously, we developed a software tool (DOVIS) to perform large-scale virtual screening of small molecules in parallel on Linux clusters, using AutoDock 3.05 as the docking engine. DOVIS enables the seamless screening of millions of compounds on high-performance computing platforms. In this paper, we report significant advances in the software implementation of DOVIS 2.0, including enhanced screening capability, improved file system efficiency, and extended usability.     

Molecular docking studies and structural&electronic analysis of gefarnate

This study focused on the structural/electronic features of an anti-ulcer agent, gefarnate. The molecular geometry of the compound was calculated using Gaussian 09 W software and the structure was optimized using the DFT/B3LYP method with the 6–31++G(d,p) basis set ground state. Also, in silico studies like molecular docking studies and ADME/T estimation were carried out using web-based tools and software. The protein used in these calculations is the crystal structure of the 3U6J, VEGFR2 kinase domain in complex with a pyrazolone inhibitor. The binding energy for the gefarnate molecule-VEGFR2 kinase complex has been computed as −8.6 kcal/mol. The compound showed no toxicity properties including cytotoxic, mutagenic, carcinogenic, or immunogenic.     

Concise preparation of azenes by oxidation of aromatic amines with molecular oxygen in subcritical water

Abstract  

Reaction of organic substrates with molecular oxygen, the most abundant and accessible oxidant, has always been an attractive method for preparation of target molecules. In terms of green chemistry, non-metal-catalyzed oxidation of organic substrates is very attractive. This paper describes a general procedure for synthesis of azenes by oxidation of primary aromatic amines with molecular oxygen (³O₂) in subcritical water. The reactions afforded the corresponding azenes in moderate to good yield.     

STXMPy: a new software package for automated region of interest selection and statistical analysis of XANES data

Background  

Soft X-ray spectromicroscopy based absorption near-edge structure analysis, is a spectroscopic technique useful for investigating sample composition at a nanoscale of resolution. While the technique holds great promise for analysis of biological samples, current methodologies are challenged by a lack of automatic analysis software e. g. for selection of regions of interest and statistical comparisons of sample variability.     

Glutathionylation of beta-actin via a cysteinyl sulfenic acid intermediary

Background  

Cysteinyl residues in actin are glutathionylated, ie. form a mixed disulfide with glutathione, even in the absence of exogenous oxidative stress. Glutathionylation inhibits actin polymerization and reversible actin glutathionylation is a redox dependent mechanism for regulation of the cytoskeleton structure. The molecular mechanism that mediates actin glutathionylation in vivo is unclear.     

Synthesis and characterization of alternating fluorene–thiophene copolymers bearing ethylene glycol side-chains

Abstract  

New alternating fluorene–thiophene copolymers are introduced bearing polar ethylene glycol-carboxylate functionalities on the thiophene ring to achieve enhanced solubility in polar solvents. Suzuki polycondensation was applied to synthesize a set of three polymers with differing lengths of the ethylene glycol side-chains. The polymers are thermally stable up to temperatures of 300 °C. Solutions of the polymers in CHCl₃ show an absorption maximum at approximately 397 nm and a luminescence maximum of 472 nm in solutions with quantum yield of 30%. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) levels have been determined to be at −5.7 and −2.6 eV, respectively.     

Application of computational modeling to analyze reactive organotin(IV) species

Abstract  

Computational optimization modeling (COM) is a research method that uses advanced computers and specialized software (e.g., Gaussian) to generate extremely detailed analyses of molecular properties and structures with a goal of depicting models with values for molecular properties that match either (a) selected experimentally determined properties or (b) computationally determined conformers with lowest energies of formation over many properties. Determination and effects of various COM treatments on three series of medium-sized organotin(IV) molecules (a) (C₆H₄)S(CH₂)(Me)(Ph _x Cl _y Sn) (where x + y = 3), (b) three R₂SnCl₂ structures, where x + y = 2 and R = methyl or phenyl, and (c) MeSnCl₃ and Me₃SnCl, where Me = methyl were researched relative to X-ray crystallography and solid-state NMR. Also, a reliable COM was determined for a bimolecular organotin(IV) system to compute the energy reduction due to system formation. In summary, this research determined for organotin(IV) molecules: (a) reliable COMs, (b) validation methods, (c) complexities of creating reliable models, (d) comparative analyses of molecules in a series, (e) a substitution method to control intramolecularity and hypercoordination, and (f) pre-optimization COM treatments and pre-optimization conformation changes that may influence final conformations.     

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.     

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.     

Binding specificity of Bacillus thuringiensis Cry1Aa for purified, native Bombyx mori aminopeptidase N and cadherin-like receptors

Background  

To better understand the molecular interactions of Bt toxins with non-target insects, we have examined the real-time binding specificity and affinity of Cry1 toxins to native silkworm (Bombyx mori) midgut receptors. Previous studies on B. mori receptors utilized brush border membrane vesicles or purifed receptors in blot-type assays.     

An <Emphasis Type="Italic">ab initio</Emphasis>and AIM investigation into the hydration of 2-thioxanthine

Background  

Hydration is a universal phenomenon in nature. The interactions between biomolecules and water of hydration play a pivotal role in molecular biology. 2-Thioxanthine (2TX), a thio-modified nucleic acid base, is of significant interest as a DNA inhibitor yet its interactions with hydration water have not been investigated either computationally or experimentally. Here in, we reported an ab initio study of the hydration of 2TX, revealing water can form seven hydrated complexes.     

Identification, cloning and characterization of a novel 47 kDa murine PKA C subunit homologous to human and bovine Cβ2

Background  

Two main genes encoding the catalytic subunits Cα and Cβ of cyclic AMP dependent protein kinase (PKA) have been identified in all vertebrates examined. The murine, bovine and human Cβ genes encode several splice variants, including the splice variant Cβ2. In mouse Cβ2 has a relative molecular mass of 38 kDa and is only expressed in the brain. In human and bovine Cβ2 has a relative molecular mass of 47 kDa and is mainly expressed in lymphoid tissues.     

Secreted fungal sulfhydryl oxidases: sequence analysis and characterisation of a representative flavin-dependent enzyme from <Emphasis Type="Italic">Aspergillus oryzae</Emphasis>

Background  

Sulfhydryl oxidases are flavin-dependent enzymes that catalyse the formation of de novo disulfide bonds from free thiol groups, with the reduction of molecular oxygen to hydrogen peroxide. Sulfhydryl oxidases have been investigated in the food industry to remove the burnt flavour of ultraheat-treated milk and are currently studied as potential crosslinking enzymes, aiming at strengthening wheat dough and improving the overall bread quality.