Discovery of a Potent Deubiquitinase (DUB) Small-Molecule Activity-Based Probe Enables Broad Spectrum DUB Activity Profiling in Living Cells**

Deubiquitinases (DUBs) are a family of >100 proteases that hydrolyze isopeptide bonds linking ubiquitin to protein substrates, often leading to reduced substrate degradation through the ubiquitin proteasome system. Deregulation of DUB activity has been implicated in many diseases, including cancer, neurodegeneration and auto-inflammation, and several have been recognized as attractive targets for therapeutic intervention. Ubiquitin-derived covalent activity-based probes (ABPs) provide a powerful tool for DUB activity profiling, but their large recognition element impedes cellular permeability and presents an unmet need for small molecule ABPs which can account for regulation of DUB activity in intact cells or organisms. Here, through comprehensive chemoproteomic warhead profiling, we identify cyanopyrrolidine (CNPy) probe IMP-2373 ( 12 ) as a small molecule pan-DUB ABP to monitor DUB activity in physiologically relevant live cells. Through proteomics and targeted assays, we demonstrate that IMP-2373 quantitatively engages more than 35 DUBs across a range of non-toxic concentrations in diverse cell lines. We further demonstrate its application to quantification of changes in intracellular DUB activity during pharmacological inhibition and during MYC deregulation in a model of B cell lymphoma. IMP-2373 thus offers a complementary tool to ubiquitin ABPs to monitor dynamic DUB activity in the context of disease-relevant phenotypes.     

Investigation of the copper binding site and the role of histidine as a ligand in riboflavin binding protein

Riboflavin Binding Protein (RBP) binds copper in a 1:1 molar ratio, forming a distinct well-ordered type II site. The nature of this site has been examined using X-ray absorption and pulsed electron paramagnetic resonance (EPR) spectroscopies, revealing a four coordinate oxygen/nitrogen rich environment. On the basis of analysis of the Cambridge Structural Database, the average protein bound copper-ligand bond length of 1.96 A, obtained by extended x-ray absorption fine structure (EXAFS), is consistent with four coordinate Cu(I) and Cu(II) models that utilize mixed oxygen and nitrogen ligand distributions. These data suggest a Cu-O 3N coordination state for copper bound to RBP. While pulsed EPR studies including hyperfine sublevel correlation spectroscopy and electron nuclear double resonance show clear spectroscopic evidence for a histidine bound to the copper, inclusion of a histidine in the EXAFS simulation did not lead to any significant improvement in the fit.     

Left division in the free left distributive algebra on many generators

Left distributive algebras arise in the study of classical structures such as groups, knots, and braids, as well as more exotic objects like large cardinals. A long-standing open question is whether the set of left divisors of every term in the free left distributive algebra on any number of generators is well-ordered. A conjecture of J. Moody describes a halting condition for descending sequences of left divisors in the free left distributive algebra on an arbitrary number of generators. In this paper we present progress toward an affirmative answer to the open question mentioned above, namely we prove that the many generator form of Moody’s conjecture holds if each member of the free left distributive algebra has a “division form” representation in an expanded algebra.     

Recent advances in the development and application of microemulsion EKC

Microemulsion EKC (MEEKC) is an electrodriven separation technique. Separations are typically achieved using oil-in-water microemulsions, which are composed of nanometre-sized oil droplets suspended in an aqueous buffer. The droplets are stabilised by a surfactant and a cosurfactant. The novel use of water-in-oil microemulsions has also been investigated. This review summarises the advances in the development of MEEKC separations and also the different areas of application including determination of log P values, pharmaceutical applications, chiral analysis, natural products and bioanalytical separations and the use of new methods such as multiplexed MEEKC and high speed MEEKC. Recent applications (2004-2006) are tabulated for each area with microemulsion composition details.     

Thermodynamics and kinetics of the nickel(II)-salicylhydroxamic acid system. Phenol rotation induced by metal ion binding

The kinetics and the equilibria of Ni(II) binding to p-hydroxybenzohydroxamic acid (PHBHA) and salicylhydroxamic acid (SHA) have been investigated in an aqueous solution at 25 degrees C and I=0.2 M by the stopped-flow method. Two reaction paths involving metal binding to the neutral acid and to its anion have been observed. Concerning PHBHA, the rate constants of the forward and reverse steps are k1=(1.9+/-0.1)x10(3) M-1 s-1 and k-1=(1.1+/-0.1)x10(2) s-1 for the step involving the undissociated PHBHA and k2=(3.2+/-0.2)x10(4) M-1 s-1 and k-2=1.2+/-0.2 s-1 for the step involving the anion. Concerning SHA, the analogous rate constants are k1=(2.6+/-0.1)x10(3) M-1 s-1, k-1=(1.3+/-0.1)x10(3) s-1, k2=(5.4+/-0.2)x10(3) M-1 s-1, and k-2=6.3+/-0.5 s-1. These values indicate that metal binding to the anions of the two acids concurs with the Eigen-Wilkins mechanism and that the phenol oxygen is not involved in the chelation. Moreover, a slow effect was observed in the SHA-Ni(II) system, which has been put down to rotation of the benzene ring around the C-C bond. Quantum mechanical calculations at the B3LYP/lanL2DZ level reveal that the phenol group in the most stable form of the Ni(II) chelate is in trans position relative to the carbonyl oxygen, contrary to the free SHA structure, where the phenol and carbonyl oxygen atoms both have cis configuration. These results bear out the idea that the complex formation is coupled with phenol rotation around the C-C bond.     

A Tetraferrocenyl‐Resorcinarene Cavitand as a Redox‐Switchable Host of Ammonium Salts

Tetraannulation of a resorcinarene‐octaamino cavitand with ferrocenecarboxaldehyde allows the preparation of a tetrabenzimidazole‐resorcinarene cavitand with four ferrocenyl moieties directly linked to the C2 atom of the imidazole units. Oxidation of the four ferrocenyl moieties produces important structural modifications of the molecule, as indicated by DFT calculations performed for the neutral and tetraoxidized forms of the cavitand. By means of ¹H NMR spectroscopic analysis, the encapsulating properties of the new tetraferrocenyl‐resorcinarene cavitand toward a series of ammonium salts were evaluated, and a clear cutoff point in binding affinity with respect to size was observed. Cyclic voltammetric studies allowed us to estimate the relative association constants for the neutral and oxidized forms of the cavitand, thus indicating that the guest was bound to the neutral (reduced) state of the cavitand and was released from the oxidized form. These redox‐addressable conformational and binding properties of the resorcinarene‐tetraferrocenyl cavitand constitute all the necessary features of a redox‐switchable molecular gripper. By means of mass‐spectrometric analysis, we could unambiguously confirm the molar stoichiometry of the host–guest complex (1:1) and assess the strong guest encapsulation, as indicated by triggering the covalent coupling between host and guest in the gas phase.     

Unveiling the Importance of π‐Stacking in Borrowing‐Hydrogen Processes Catalysed by Iridium Complexes with Pyrene Tags

This work describes the preparation of a series of pyrene‐tagged N‐heterocyclic carbene complexes of iridium, and their use in two benchmark borrowing hydrogen reactions: the reduction of ketones by transfer hydrogenation and the β‐alkylation of secondary alcohols with primary alcohols. The detailed study of these homogeneously catalysed reactions reveals several important implications regarding the strong influence of the pyrene tags in the catalysts. First, the catalytic activity is partially inhibited by addition of an external amount of pyrene, but only when pyrene‐tagged catalysts and aromatic substrates are used. Second, the rate order of the reaction is highly dependent on the nature of the substrates and the ligand. When pyrene‐tagged catalysts and aromatic substrates are used, the reaction follows a zero‐order dependence on the concentration of the substrate. All other combinations afford a second‐order rate in the substrates. And third, the presence or absence of the pyrene functionality in the catalyst also influences the reaction order with respect to the concentration of the catalyst. Pyrene‐containing catalysts display a fractional rate order of below 1. Finally, two pyrene‐tagged catalysts were supported onto reduced‐graphene oxide (rGO), and used as heterogeneous catalysts. While the dimetallic catalyst was effectively recycled 12 times, the monometallic catalyst maintained its activity for only three runs.     

Inorganic chemistry and IONiC: an online community bringing cutting-edge research into the classroom

This Viewpoint highlights creative ways that members of the Interactive Online Network of Inorganic Chemists (IONiC) are using journal articles from Inorganic Chemistry to engage undergraduate students in the classroom. We provide information about specific educational materials and networking features available free of charge to the inorganic community on IONiC's web home, the Virtual Inorganic Pedagogical Electronic Resource (VIPEr, www.ionicviper.org ) and describe the benefits of joining this community.     

Fluorescence energy transfer efficiency in labeled yeast cytochrome c: a rapid screen for ion biocompatibility in aqueous ionic liquids

A fluorescence energy transfer "de-quenching" assay was implemented to follow the equilibrium unfolding behaviour of site-specific tetramethylrhodamine-labelled yeast cytochrome c in aqueous ionic liquid solutions; additionally, this approach offers the prospect of naked eye screening for biocompatible ion combinations in hydrated ionic liquids.     

Effect of the irrigation with residual wastewaters on microbial soil activity of the ornamental flowers (<Emphasis Type="Italic">Dahlia pinnata)</Emphasis> cultures monitored by isothermal calorimetry

A microcalorimetric method was applied to study microbial soil activity of ornamental flower (Dahlia pinnata) plantations when irrigated with potable water and wastewaters. The samples were irrigated with potable water PW sample (reference) and treated wastewaters from Municipal Wastewater Treatment Station of Asa Norte in Brasilia City (Brazil). Three different water treatments were applied to irrigate soil samples, named TW1, TW2, and TW3 samples. The increase of the microbial soil activity observed in TW1 sample must have occurred because of the high amount of organic waste dissolved in wastewater used for irrigation. This rise indicates that the present treated wastewater can affect natural life cycle. However, only a low alteration in microbial soil activity was observed in the TW2 and TW3 samples, which suggests that these wastewater treatments can be normally used to irrigate soils without bringing environmental consequences, once they offer a great opportunity to upgrade and protect the environment.