Cooperativity as quantification and optimization paradigm for nuclear receptor modulators

Nuclear Receptors (NRs) are highly relevant drug targets, for which small molecule modulation goes beyond a simple ligand/receptor interaction. NR–ligands modulate Protein–Protein Interactions (PPIs) with coregulator proteins. Here we bring forward a cooperativity mechanism for small molecule modulation of NR PPIs, using the Peroxisome Proliferator Activated Receptor γ (PPARγ), which describes NR–ligands as allosteric molecular glues. The cooperativity framework uses a thermodynamic model based on three-body binding events, to dissect and quantify reciprocal effects of NR–coregulator binding (K^I_D) and NR–ligand binding (K^II_D), jointly recapitulated in the cooperativity factor (α) for each specific ternary ligand·NR·coregulator complex formation. These fundamental thermodynamic parameters allow for a conceptually new way of thinking about structure–activity-relationships for NR–ligands and can steer NR modulator discovery and optimization via a completely novel approach.

A cooperativity framework describes the formation of nuclear receptor ternary complexes and deconvolutes ligand and cofactor binding into intrinsic affinities and a cooperativity factor, providing a conceptually new understanding of NR modulation.     

Direct determination of total mercury in phosphate rock using alkaline fusion digestion

The aim of this work was to develop a new method to determine the mercury (Hg) concentrations in phosphate rock using a dedicated analytical instrument (the DMA80 Tricell by Milestone) that employs an integrated sequence of thermal decomposition followed by catalyst conversion, amalgamation and atomic absorption spectrophotometry. However, this instrument underestimates Hg concentrations when phosphorite and apatite rocks are investigated with a classic thermal decomposition treatment that complies with US EPA method 7473.     

Characterization of a molecular sieve coating using ellipsometric porosimetry

Ellipsometric porosimetry was used to determine the adsorption isotherms of toluene, methanol, and water on b-oriented Silicalite-1 coatings with a thickness of less than ca. 250 nm and to obtain adsorption kinetics. The adsorption isotherms are of sufficient quality to reveal several aspects of the pore structure such as the adsorbate capacity and the adsorbate/framework affinity. The use of a combination of different molecular probes in ellipsometric porosimetry to elucidate the molecular accessibility of Silicalite-1 pores is demonstrated. It is shown that ellipsometric porosimetry is an appropriate technique for probing the influence of aging of the Silicalite-1 coating and of planarization polishing on the porosity, pore accessibility, and adsorbate/framework affinity.     

Phylogenetic analysis and homology modelling of <Emphasis Type=Italic>Paracentrotus lividus</Emphasis> nectin

The extracellular matrix protein Pl-nectin, a 210-kDa homodimer originally purified from sea urchin eggs, plays a crucial role in cell adhesion and embryonic morphogenesis. The compiled cDNA sequence, obtained by RT-PCR primer walking and 3′ RACE, identified a 984aa product containing a 23aa signal peptide and including all six internal peptides identified by protein microsequencing. The protein is a new member of the galactose-binding protein superfamily as it consists of six 151–156aa-long tandemly repeated domains (D1–D6), homologous to the discoidin-like domains, also known as F5/8-type C domains. Based on homology modelling, we present a three-dimensional structure (3D) for D5, identified as the prototype domain. The molecular modelling of the assembled Pl-nectin homodimer accounts for a Pl-nectin quaternary structure composed of two 105-kDa C-shaped monomers linked by a S–S bridge. The presence of an LDT motif between the first and the second exposed loops of the D2 domain suggests the binding of Pl-nectin to an integrin receptor. Altogether, the in silico analysis described here is consistent with previous biochemical reports and offers a basis for predictions to be experimentally tested.