Nonpeptide inhibitors of cathepsin G: optimization of a novel beta-ketophosphonic acid lead by structure-based drug design

The serine protease cathepsin G (EC 3.4.21.20; Cat G), which is stored in the azurophilic granules of neutrophils (polymorphonuclear leukocytes) and released on degranulation, has been implicated in various pathological conditions associated with inflammation. By employing high-throughput screening, we identified beta-ketophosphonic acid 1 as a moderate inhibitor of Cat G (IC(50) = 4.1 microM). We were fortunate to obtain a cocrystal of 1 with Cat G and solve its structure by X-ray crystallography (3.5 A). Structural details from the X-ray analysis of 1.Cat G served as a platform for optimization of this lead compound by structure-based drug design. With the aid of molecular modeling, substituents were attached to the 3-position of the 2-naphthyl ring of 1, which occupies the S1 pocket of Cat G, to provide an extension into the hydrophobic S3 region. Thus, we arrived at analogue 7 with an 80-fold potency improvement over 1 (IC(50) = 53 nM). From these results, it is evident that the beta-ketophosphonic acid unit can form the basis for a novel class of serine protease inhibitors.     

The different steric environments of the 5-exo- and 5-endo- substituent for a pair of isomeric tricarbonyl(methoxycyclohexa-1,-diene)irons

A shift reagent has been employed to demonstrate the sterically-hindered environment of the methoxy group in tricarbonyl(5-endo-methoxycyclohexa-1,-diene)iron relative to that of the methoxy group in the 5-exo analogue.     

Protein structure determination using long-distance constraints from double-quantum coherence ESR: study of T4 lysozyme

We report the use of a novel pulsed ESR technique for distance measurement, based on the detection of double quantum coherence (DQC), which yields high quality dipolar spectra, to significantly extend the range of measurable distances in proteins using nitroxide spin-labels. Eight T4 lysozyme (T4L) mutants, doubly labeled with methanethiosulfonate spin-label (MTSSL), have been studied using DQC-ESR at 9 and 17 GHz. The distances span the range from 20 A for the 65/76 mutant to 47 A for the 61/135 mutant. The high quality of the dipolar spectra also allows the determination of the distance distributions, the width of which can be used to set upper and lower bounds in future computational strategy. It is also demonstrated that the shape of these distributions can reveal the presence of multiple conformations of the spin-label, an issue of critical relevance to the structural interpretation of the distances. The distances and distributions found in this study are readily rationalized in terms of the known crystal structure, the characteristic conformers of the nitroxide side chains, and molecular modeling. This study sets the stage for the use of DQC-ESR for determining the tertiary structure of large proteins with just a small number of long-distance constraints.     

Control over calcium carbonate phase formation by dendrimer/surfactant templates

Poly(propylene imine) dendrimers that are modified with long alkyl chains self-assemble to form well-defined aggregates. The geometry and surface chemistry of the dendrimer assemblies can be varied through the addition of surfactants. These dendrimer/surfactant aggregates can be tuned to template the formation of the different phases of calcium carbonate. The use of octadecylamine results in the formation of polyhedral aggregates that become embedded within an amorphous calcium carbonate phase that persists in competition with the thermodynamic product, calcite. In combination with hexadecyltrimethylammonium bromide, small spherical aggregates are formed that induce the formation of vaterite. The use of the negatively charged surfactant SDS results in growth retardation by the Ca(2+)-induced agglomeration of dendrimer/surfactant aggregates into giant spherical particles. Eventually these particles become overgrown by rhombohedral calcite.     

Organolithium-mediated diversification of peptide thiazoles

[Reaction: see text] We report a one-step, racemization-free method for the diversification of peptide thiazoles via direct lithiation of the thiazole ring. The method is compatible with N-Boc, N-trityl, carboxylic ester, and carboxamide protecting groups and has been used to directly functionalize the thiazole ring of cyclopeptide natural products.     

A quantitative method for dual‐pass electrostatic force microscopy phase measurements

Electrostatic force microscopy (EFM) has become a powerful tool for investigating charges on surfaces. The use of phase measurement in EFM is a direct and fast way to detect electrostatic force gradients, but only qualitatively. With the dual‐pass scheme, the phase signal at lifted height is often assumed to exclude any influences from the topography, but it does not. We report the collection of both topography and phase data by EFM on charged, micron‐sized metal wires. In order to quantify the electrostatic force, a cone model and finite element analysis are provided to integrate the force gradient from the phase signal. Copyright © 2007 John Wiley & Sons, Ltd.     

Strategies to enhance the enzymatic hydrolysis of pretreated softwood with high residual lignin content

Pretreatment of Douglas-fir by steam explosion produces a substrate containing approx 43% lignin. Two strategies were investigated for reducing the effect of this residual lignin on enzymatic hydrolysis of cellulose: mild alkali extraction and protein addition. Extraction with cold 1% NaOH reduced the lignin content by only approx 7%, but cellulose to glucose conversion was enhanced by about 30%. Before alkali extraction, addition of exogenous protein resulted in a significant improvement in cellulose hydrolysis, but this protein effect was substantially diminished after alkali treatment. Lignin appears to reduce cellulose hydrolysis by two distinct mechanisms: by forming a physical barrier that prevents enzyme access and by non-productively binding cellulolytic enzymes. Cold alkali appears to selectively remove a fraction of lignin from steam-exploded Douglas-fir with high affinity for protein. Corresponding data for mixed softwood pretreated by organosolv extraction indicates that the relative importance of the two mechanisms by which residual lignin affects hydrolysis is different according to the pre- and post-treatment method used.