Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery

Impressive progress in genome sequencing, protein expression and high-throughput crystallography and NMR has radically transformed the opportunities to use protein three-dimensional structures to accelerate drug discovery, but the quantity and complexity of the data have ensured a central place for informatics. Structural biology and bioinformatics have assisted in lead optimization and target identification where they have well established roles; they can now contribute to lead discovery, exploiting high-throughput methods of structure determination that provide powerful approaches to screening of fragment binding.     

Reduction of N<Subscript>2</Subscript> by Fe<Superscript>2+</Superscript> via Homogeneous and Heterogeneous Reactions Part 2: The Role of Metal Binding in Activating N<Subscript>2</Subscript> for Reduction; a Requirement for Both Pre-biotic and Biological Mechanisms

Nitrogen reduction by ferrous iron has been suggested as an important mechanism in the formation of ammonia on pre-biotic Earth. This paper examines the effects of adsorption of ferrous iron onto a goethite (alpha-FeOOH) substrate on the thermodynamic driving force and rate of a ferrous iron-mediated reduction of N2 as compared with the homogeneous aqueous reaction. Utilizing density functional theory and Marcus Theory of proton coupled electron transfer reactions, the following two reactions were studied: Fe2+aq + N2aq + H2Oaq --> N2H* + FeOH2+aq and triple bond Fe2+ads + N2aq + 2H2Oaq --> N2H* + alpha-FeOOHs + 2H+aq. Although the rates of both reactions were calculated to be approximately zero at 298 K, the model results suggest that adsorption alters the thermodynamic driving force for the reaction but has no other effect on the direct electron transfer kinetics. Given that simply altering the thermodynamic driving force will not reduce dinitrogen, we can make mechanistic connections between possible prebiotic pathways and biological N2 reduction. The key to reduction in both cases is N2 adsorption to multiple transition metal centers with competitive H2 production.     

Chemical-ionization mass spectrometry of carbohydrates: behavior of the antibiotic celesticetin under various conditions of ionization

The chemical-ionization mass spectrum of the polyfunctional carbohydrate antibiotic, celesticetin, is remarkably simple, in contrast to its electron-impact mass spectrum. With ammonia as the ionizing gas the protonated molecular ion is the principal species, and simple fragmentation modes reflect eleavage between principal moietics of the molecule. Substantial modifications of the fragmentation pathway are observed when isobutane is used as the ionizing gas. The different pathways of fragmentation according to the mode of ionization are interpreted in terms of differential reactivity of various heteroatomic centers in the molecule toward each of the ionizing agents. Use of a combination of ionizing modes may provide a useful general method for identification on a micro scale of complex carbohydrates isolated from fermentation or other mixtures.     

Analysis of sugar derivatives by chemical-ionization mass-spectrometry

D-Glucose diethyl dithioacetal (1), its penta-O-acetyl derivative (2), penta-O-acetyl-aldehydo-D-glucose (3), L-xylo-hexulose phenylosotriazole (4), 1,2:5,6-di-O-isopropylidene-D-mannitol (5), 1,2:4,5-di-O-isopropylidene-β-D-fructopyranose (6), 1,2-O-isopropylidene-α-D-glucofuranose (7) and its triacetate (8), 1,6-anhydro-β-D-galactopyranose (9) and its triacetate (10), D-glucopyranose (11), methyl β-D-glucopyranoside tetraacetate (12), 1-thio-β-D-glucopyranose pentaacetate (13), β-D-fructofuranose pentaacetate (14), and raffinose hendecaacetate (15) have been examined by chemical-ionization mass-spectrometry with both isobutane and ammonia as ionizing intermediates. Extreme simplicity characterizes these spectra, and, in most instances, molecular-weight data are available from intact, protonor NH₄⁺capture ions; the limited fragmentation that occurs corresponds in large measure to simple dehydration or substituent-cleavage processes, and is strongly dependent upon the groups present, so that considerable information about the substituent groups in the sugar molecule may be inferred.     

Gradient fit functions for two-body potential energy surfaces based upon a harmonic series

While force-field development has been discussed extensively in the literature, the question of what analytical expressions make the best function choices, particularly in the context of matching quantum mechanic potential energy surfaces (PES), is less explored. Traditional forms based upon harmonic oscillators and Lennard-Jones types have dominated the field owing to the focus on fitting properties. However, with the advent of gradient-fitting approaches, it is now possible with the correct force-field expressions to achieve consistent high-accuracy results with molecular dynamics calculations. Using the general principle that power series can fit surfaces of any shape well, we have utilised harmonic series functions to fit a two-body PES represented by a Morse function. The harmonic functions are fast because they have only integer exponents, and they fit accurately with a limited number of terms.     

Characterization of reaerosolization from impingers in an effort to improve airborne virus sampling

Aims:  To assess the impact of reaerosolization from liquid impingement methods on airborne virus sampling.
Methods and Results:  An AGI-30 impinger containing particles [MS2 bacteriophage or 30-nm polystyrene latex (PSL)] of known concentration was operated with sterile air. Reaerosolized particles as a function of sampling flow rate and particle concentration in the impinger collection liquid were characterized using a scanning mobility particle sizer. Reaerosolization from the impinger was also compared to that from a BioSampler. Results show that reaerosolization increases as flow rate increases. While the increased particle concentration in the impinger collection liquid leads to an increase in the reaerosolization of PSL particles, it does not necessarily lead to an increase in the reaerosolization of virus particles. Reaerosolization of virus particles begins to decrease as the particle concentration in the impinger collection liquid rises above 10⁶ PFU ml⁻¹. This phenomenon results from aggregation of viral particles at high concentrations. Compared with micron-sized particles, nanosized virus particles are easier to aerosolize because of reduced inertia. Reaerosolization from the BioSampler is demonstrated to be significantly less than that from the impinger.
Conclusions:  Reaerosolization from impingement sampling methods is a mode of loss in airborne virus sampling, although it is not as significant a limitation as the primary particle size of the aerosol. Utilizing a BioSampler coupled with short sampling periods to prevent high accumulative concentrations can minimize the impact of reaerosolization.
Significance and Impact of the Study:  This study confirms reaerosolization of virus particles to be a mode of loss in impingement sampling and identifies methods to minimize the loss.     

5-Lipoxygenase is a key determinant of acute myocardial inflammation and mortality during Trypanosoma cruzi infection

This study provides evidence supporting the idea that although inflammatory cells migration to the cardiac tissue is necessary to control the growth of Trypanosoma cruzi, the excessive influx of such cells during acute myocarditis may be deleterious to the host. Production of lipid mediators of inflammation like leukotrienes (LTs) along with cytokines and chemokines largely influences the severity of inflammatory injury in response to tissue parasitism. T. cruzi infection in mice deficient in 5-lipoxygenase (5-LO), the enzyme responsible for the synthesis of LTs and other lipid inflammatory mediators, resulted in transiently increased parasitemia, and improved survival rate compared with WT mice. Myocardia from 5-LO^?/? mice exhibited reduced inflammation, collagen deposition, and migration of CD4⁺, CD8⁺, and IFN-γ-producer cells compared with WT littermates. Moreover, decreased amounts of TNF-α, IFN-γ, and nitric oxide synthase were found in the hearts of 5-LO^?/? mice. Interestingly, despite of early higher parasitic load, 5-LO^?/? mice survived, and controlled T. cruzi infection. These results show that efficient parasite clearance is possible in a context of moderate inflammatory response, as occurred in 5-LO^?/? mice, in which reduced myocarditis protects the animals during T. cruzi infection.