Virtual screening using protein-ligand docking: avoiding artificial enrichment

This study addresses a number of topical issues around the use of protein-ligand docking in virtual screening. We show that, for the validation of such methods, it is key to use focused libraries (containing compounds with one-dimensional properties, similar to the actives), rather than "random" or "drug-like" libraries to test the actives against. We also show that, to obtain good enrichments, the docking program needs to produce reliable binding modes. We demonstrate how pharmacophores can be used to guide the dockings and improve enrichments, and we compare the performance of three consensus-ranking protocols against ranking based on individual scoring functions. Finally, we show that protein-ligand docking can be an effective aid in the screening for weak, fragment-like binders, which has rapidly become a popular strategy for hit identification. All results presented are based on carefully constructed virtual screening experiments against four targets, using the protein-ligand docking program GOLD.     

Direct measurement of excited-state intervalence transfer in [(tpy)Ru(III)(tppz(*-))Ru(II)(tpy)](4+) by time-resolved near-infrared spectroscopy

Extension of time-resolved infrared (TRIR) measurements into the near-infrared region has allowed the first direct measurement of a mixed-valence band in the metal-to-ligand charge transfer (MLCT) excited state of a symmetrical ligand-bridged complex. Visible laser flash excitation of [(tpy)Ru(tppz)Ru(tpy)]4+ (tppz is 2,3,5,6-tetrakis(2-pyridyl)pyrazine; tpy is 2,2':6',6' '-terpyridine) produces the mixed-valence, MLCT excited state [(tpy)RuIII(tppz*-)RuII(tpy)]4+* with the excited electron localized on the bridging tppz ligand. A mixed-valence band appears at numax = 6300 cm-1 with a bandwidth-at-half- maximum, Deltanu1/2 = 1070 cm-1. In the analogous ground-state complex, [(tpy)Ru(tppz)Ru(tpy)]5+, a mixed-valence band appears at numax = 6550 cm-1 with Deltanu1/2 = 970 cm-1 which allows a comparison to be made of electronic coupling across tppz0 and tppz*- as bridging ligands.     

Generic dealkylation: a tool for increasing the hit‐rate of metabolite rationalization,and automatic customization of mass defect filters

The use of exact mass liquid chromatography/mass spectrometry (LC/MS) for drug metabolism studies has increased significantly in recent years. Firstly, exact mass measurements facilitate identification of standard biotransformations through the use of narrow window extracted ion chromatograms, which are typically highly selective relative to signals from matrix or dosing components. Secondly, novel metabolites can be characterized via elemental formula calculations and high‐resolution product ion spectra. Furthermore, biological background ions can be removed by the use of mass defect filters (MDFs) which filter out ions based on the decimal component of their m/z value. Here, we describe an approach which we term ‘generic dealkylation’ that in association with other data interpretation tools adds significant value to the assignment process. Generic dealkylation uses a simple strategy to identify those bonds which have the potential to be cleaved by metabolism. In combination with standard phase 1 and phase 2 biotransformations, this allows creation of a chemically intelligent MDF which balances the need to remove matrix background with the requirement of avoiding filtering true metabolites. Secondly, generic dealkylation increases the hit‐rate at which non‐trivial (i.e. not covered by simple phase 1 oxidations or direct phase 2 conjugations) metabolites can be directly rationalized. The value of the generic dealkylation approach is illustrated by its application to determination of in vitro metabolic routes for two commercial drugs, nefazodone and indinavir. Copyright © 2009 John Wiley & Sons, Ltd.     

FT-IR study of the effect of zinc exposure on the biochemical contents of the muscle of Labeo rohita

Heavy metal pollution is a major environmental problem in the modern world due to increasing human activities. Zinc is an essential element involved in a wide variety of cellular processes. However, it becomes toxic when elevated concentrations are introduced into the environment. The goal of the present study is to investigate the effect of zinc exposure on the biochemical contents of the muscle tissues of freshwater species Labeo rohita using Fourier transform infrared (FT-IR) spectroscopy. Since the muscle constitutes the greatest mass of the fish that is consumed, the present study has paid particular attention to muscle component. The result reveals that the zinc exposure causes significant changes in the biochemical contents of the L. rohita muscle tissues. In addition, it causes an alteration in the protein secondary structures by decreasing the α-helix and increasing the β-sheet contents of muscle tissues. Further, it has been observed that the administration of chelating agent D-penicillamine improves the protein and lipid contents in the muscle tissues compared to zinc exposed tissues. This result shows that D-penicillamine is the effective chelator of zinc in reducing the body burden of L. rohita fingerlings.     

Synthesis of gold nanoparticles using herbal Acorus calamus rhizome extract and coating on cotton fabric for antibacterial and UV blocking applications

Gold nanoparticles (AuNPs) have been synthesized by greener method using chloroauric acid as precursor and extract of Acorus calamus rhizome as reducing agent. Formation of AuNP was confirmed by the presence of Surface Plasmon Resonance (SPR) peak in UV–Visible spectral analysis. XRD and FT-IR spectral analyses were performed for characterization. SEM images show spherical morphology and HR-TEM images reveal nanosize of AuNPs. The AuNPs were then coated on cotton fabric by pad-dry-cure method and characterized by SEM with EDAX technique. The results reveal the deposition of AuNPs on the surface of cotton fabric. Uncoated cotton, neat extract coated cotton and extract containing AuNPs coated cotton fabrics were then tested for antibacterial activity against Gram positive (Staphylococcus aureus) and Gram negative (Escherichia coli) bacterial strains by AATCC 100 test method. It showed that the extract containing AuNPs coated cotton fabric had higher antibacterial activity than other test samples against E. coli. UV-DRS analysis performed on extract containing AuNPs coated cotton fabric showed improved UV-blocking property than uncoated cotton fabric and neat extract coated cotton fabric.     

Cyclopropane derivatives from the lithium aluminium hydride reduction of methoxyalkynols

Lithium aluminium hydride reduction of methoxyalkynol(1) yields cyclopropane derivatives (2) and (3), both formed by loss of a methoxy group; a reaction scheme for their formation is presented.     

Bayesian stratified random sampling using auxiliary information

Summary Smith (1976,J. R. Statist. Soc., A,139, 183–204) has argued that survey statisticians should attempt to model finite population structures in the same way that statisticians in other disciplines have to provide models of finite or infinite populations. Following this argument, we suggest in this paper that an obvious model for a stratified population when auxiliary information regarding variate values is available, is the one way analysis of covariance model with unequal variances and we consider the problem of estimating the finite population mean. Finally a possible extension of this result is discussed.