Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

An unexpected P-cluster like intermediate en route to the nitrogenase FeMo-co

The nitrogenase MoFe protein contains two different FeS centers, the P-cluster and the iron–molybdenum cofactor (FeMo-co). The former is a [Fe₈S₇] center responsible for conveying electrons to the latter, a [MoFe₇S₉C-(R)-homocitrate] species, where N₂ reduction takes place. NifB is arguably the key enzyme in FeMo-co assembly as it catalyzes the fusion of two [Fe₄S₄] clusters and the insertion of carbide and sulfide ions to build NifB-co, a [Fe₈S₉C] precursor to FeMo-co. Recently, two crystal structures of NifB proteins were reported, one containing two out of three [Fe₄S₄] clusters coordinated by the protein which is likely to correspond to an early stage of the reaction mechanism. The other one was fully complemented with the three [Fe₄S₄] clusters (RS, K1 and K2), but was obtained at lower resolution and a satisfactory model was not obtained. Here we report improved processing of this crystallographic data. At odds with what was previously reported, this structure contains a unique [Fe₈S₈] cluster, likely to be a NifB-co precursor resulting from the fusion of K1- and K2-clusters. Strikingly, this new [Fe₈S₈] cluster has both a structure and coordination sphere geometry reminiscent of the fully reduced P-cluster (P^N-state) with an additional μ²-bridging sulfide ion pointing toward the RS cluster. Comparison of available NifB structures further unveils the plasticity of this protein and suggests how ligand reorganization would accommodate cluster loading and fusion in the time-course of NifB-co synthesis.

The K-cluster of NifB as a key intermediate in the synthesis of the nitrogenase active site supports [Fe₄S₄] cluster fusion occurs before carbide and sulfide insertion and displays ligand spatial arrangement reminiscent to that of the P-cluster.     

Synthesis, crystal structure, magnetic properties, and electronic structure of the new ternary vanadate CuMnVO4

A new magnetic oxide, CuMnVO4, was prepared, and its crystal structure was determined by single-crystal X-ray diffraction. The magnetic properties of CuMnVO4 were characterized by magnetic susceptibility and specific heat measurements, and the spin exchange interactions of CuMnVO4 were analyzed on the basis of spin-polarized electronic band structure calculations. CuMnVO4 contains MnO4 chains made up of edge-sharing MnO6 octahedra containing high-spin Mn2+ cations. Our work shows that CuMnVO4 undergoes a three-dimensional antiferromagnetic transition at approximately 20 K. Both the intrachain and interchain spin exchanges are antiferromagnetic, and the interchain spin exchange is not negligible compared to the intrachain spin exchange.     

Isotropic hard core dumbell fluid: Equation of state

A monte-Carlo calculation has been made for 108 hard core dumbbells of the compressibility factor in the isotropic density range. These compressibility factors are compared to several approximate theories, and comments are made on the utility of these approximate theories.     

EPR evidence for 17O− on molybdenum oxide supported by silica-gel

The EPR spectrum of ¹⁷O^? on partially reduced molybdenum oxide supported on silica-gel has been observed following adsorption of N₂O at room temperature. The spectrum is chracterized by g_⊥=2.019 and g_|=2.002 with a_|¹⁷O^?=96±1 G and a_|⁹⁵MO,⁹⁷MO=7.5±0.5 G. The O ^?ion appears to undergo exchange with oxide ions at the surface.     

Characteristics of immunosorbents used as a new approach to selective solid-phase extraction in environmental analysis

Summary The trace-level determination of organic pollutants in complex matrices is difficult and often not reliable because theccurrent extraction procedures are non-selective. New extraction sorbents involving antigen-antibody interactions, called immunosorbents (ISs), have been synthesised in order to trap a group of structurally related pollutants. The IS capacity is always high for the analyte-antigen used to make the antibodies, but can be low for some related compounds. In this work, we show the relationship that exists between capacity, break-through volume and recovery of analytes because of the competition between the structurally related compounds for antibody sites. Breakthrough due to the overloading of the column should be avoided because calibration curves are no longer linear. The capacity of two ISs, one made for trapping the triazine pesticide group and the second for the phenylurea, group, have been optimised by selecting silica with 50 nm pore size. Calibration curves are linear for all the compounds in a mixture of ten phenylureas up to a concentration of 5 to 10 μg L⁻¹ for each compound when handling 50 mL water samples through a precolumn packed with 0.22 g of IS. Under these conditions, reliable quantitative results are obtained because calibration curves are similar when compounds are alone or in a mixture. Application to the clean-up of soil extracts illustrates the high selectivity and the high potential of these new sorbents in environmental analysis. Presented at the 21^st ISC held in Stuttgart, Germany, 15^th–20^th September, 1996     

Quantitative effect of nonionic surfactant partitioning on the hydrophile-lipophile balance temperature

Phase behaviors of water/nonionic surfactants/isooctane systems are determined experimentally in temperature-global surfactant concentration diagrams. The surfactants are monodistributed polyoxyethylene glycol n-dodecyl ether. They are used as model mixtures of two, three, or five compounds or as constituents of a commercial surfactant. It is found that the phase diagrams of these systems are bent gradually toward the highest temperatures as the global surfactant concentration decreases. Each phase diagram is well-characterized by the curve of the HLB (hydrophile-lipophile balance) temperature versus the global surfactant concentration. For any fixed global surfactant concentration, this temperature is the middle temperature of the three-phase region; it can be calculated from an additive rule of the HLB temperatures of the surfactants weighted by their mole fractions at the water/oil interface. These mole fractions are determined through the pseudophase model using surfactant partitioning. Calculations require the knowledge of the critical micelle concentration, the partition coefficient between water and oil, and the HLB temperature of each surfactant of the mixture. This treatment can be used to correctly predict the variation of the HLB temperatures of the surfactant mixtures studied versus the global surfactant concentration. Furthermore, these calculations show that the observed curvature of the phase diagrams at the lowest global concentrations is due to the most favorable partitioning toward the oil of the lowest ethoxylated surfactant molecules.     

Tracking the optical mass centroid of single electroactive nanoparticles reveals the electrochemically inactive zone

The inevitable microstructural defects, including cracks, grain boundaries and cavities, make a portion of the material inaccessible to electrons and ions, becoming the incentives for electrochemically inactive zones in single entity. Herein, we introduced dark field microscopy to study the variation of scattering spectrum and optical mass centroid (OMC) of single Prussian blue nanoparticles during electrochemical reaction. The “dark zone” embedded in a single electroactive nanoparticle resulted in the incomplete reaction, and consequently led to the misalignment of OMC for different electrochemical intermediate states. We further revealed the dark zones such as lattice defects in the same entity, which were externally manifested as the fixed pathway for OMC for the migration of potassium ions. This method opens up enormous potentiality to optically access the heterogeneous intraparticle dark zones, with implications for evaluating the crystallinity and electrochemical recyclability of single electroactive nano-objects.

The schematic of single cubic-shaped Prussian blue (PB) mesocrystals formed by the oriented aggregation of small nanocrystals. The dark-field images of single PB nanoparticle at PB and Prussian white (PW) states, respectively.     

4,4′‐Bipyridyl N,N′‐dioxide–3‐hydroxy‐2‐naphthoic acid (1/2)

4,4′‐Bipyridyl N,N′‐dioxide crystallizes with 3‐hydr­oxy‐2‐naphthoic acid to give a centrosymmetric three‐component adduct, C₁₀H₈N₂O₂·2C₁₁H₈O₃, which is engineered into a two‐dimensional layer structure by two kinds of π–π inter­actions. Weak C—H⋯O inter­actions further link the two‐dimensional structure into a three‐dimensional structure.     

Etude de phosphates condenses diagramme d’equilibre du systeme AgPO3−Pr(PO3)3 Données sur AgPr(PO3)4

The AgPO₃?Pr(PO₃)₃ system has been studied for the first time by differential thermal analysis, X-ray diffraction and IR spectroscopy. The system shows one compound AgPr(PO₃)₄ which melts in a peritectic decomposition at 1069 K. An eutectic appears at 761 K. AgPr(PO₃)₄ belongs to the monoclinic system with space group P2_t/c,Z=4. The parameters of the unit cell are:a=12.000(9),b=13.177(4),c=7.046(5) Å and β=123^o,81(6),Z=4. Its IR absorption spectrum is typical of chain phosphates.