Magic of Alpha: The Chemistry of a Remarkable Bidentate Phosphine, 1,2-Bis(di-tert-butylphosphinomethyl)benzene.

The bidentate phosphine ligand 1,2-bis(di-tert-butylphosphinomethyl)benzene (1,2-DTBPMB) has been reported over the years as being one of, if not the, best ligands for achieving the alkoxycarbonylation of various unsaturated compounds. Bonded to palladium, the ligand provides the basis for the first step in the commercial (Alpha) production of methyl methacrylate as well as very high selectivity to linear esters and acids from terminal or internal double bonds. The present review is an overview covering the literature dealing with the 1,2-DTBPMB ligand: from its first reference, its catalysis, including the alkoxycarbonylation reaction and its mechanism, its isomerization abilities including the highly selective isomerizing methoxycarbonylation, other reactions such as cross-coupling, recycling approaches, and the development of improved, modified ligands, in which some tert-butyl ligands are replaced by 2-pyridyl moieties and which show exceptional rates for carbonylation reactions at low temperatures.

Molecular expression profiles of morphologically defined hippocampal neuron types: Empirical evidence and relational inferences.

Gene and protein expressions are key determinants of cellular function. Neurons are the building blocks of brain circuits, yet the relationship between their molecular identity and the spatial distribution of their dendritic inputs and axonal outputs remains incompletely understood. The open-source knowledge base Hippocampome.org amasses such transcriptomic data from the scientific literature for morphologically defined neuron types in the rodent hippocampal formation: dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex. Positive, negative, or mixed expression reports were initially obtained from published articles directly connecting molecular evidence to neurons with known axonal and dendritic patterns across hippocampal layers. Here, we supplement this information by collating, formalizing, and leveraging relational expression inferences that link a gene or protein expression or lack thereof to that of another molecule or to an anatomical location. With these additional interpretations, we freely release online a comprehensive human- and machine-readable molecular profile for more than 100 neuron types in Hippocampome.org. Analysis of these data ascertains the ability to distinguish unequivocally most neuron types in each of the major subdivisions of the hippocampus based on currently known biochemical markers. Moreover, grouping neuron types by expression similarity reveals eight superfamilies characterized by a few defining molecules.

Simple models of quantitative firing phenotypes in hippocampal neurons: Comprehensive coverage of intrinsic diversity.

Patterns of periodic voltage spikes elicited by a neuron help define its dynamical identity. Experimentally recorded spike trains from various neurons show qualitatively distinguishable features such as delayed spiking, spiking with or without frequency adaptation, and intrinsic bursting. Moreover, the input-dependent responses of a neuron not only show different quantitative features, such as higher spike frequency for a stronger input current injection, but can also exhibit qualitatively different responses, such as spiking and bursting under different input conditions, thus forming a complex phenotype of responses. In previous work, the comprehensive knowledge base of hippocampal neuron types Hippocampome.org systematically characterized various spike pattern phenotypes experimentally identified from 120 neuron types/subtypes. In this paper, we present a complete set of simple phenomenological models that quantitatively reproduce the diverse and complex phenotypes of hippocampal neurons. In addition to point-neuron models, we created compact multi-compartment models with up to four compartments, which will allow spatial segregation of synaptic integration in network simulations. Electrotonic compartmentalization observed in our compact multi-compartment models is qualitatively consistent with experimental observations. The models were created using an automated pipeline based on evolutionary algorithms. This work maps 120 neuron types/subtypes in the rodent hippocampus to a low-dimensional model space and adds another dimension to the knowledge accumulated in Hippocampome.org. Computationally efficient representations of intrinsic dynamics, along with other pieces of knowledge available in Hippocampome.org, provide a biologically realistic platform to explore the large-scale interactions of various neuron types at the mesoscopic level.

Escape from planarity in fragment-based drug discovery: A physicochemical and 3D property analysis of synthetic 3D fragment libraries.

Fragment-based drug discovery (FBDD) has grown into a well-established approach in the pursuit of new therapeutics. Key to the success of FBDD is the low molecular complexity of the initial hits and this has resulted in fragment libraries that mainly contain compounds with a two-dimensional (2D) shape. In an effort to increase the chemical diversity and explore the impact of increased molecular complexity on the hit rate of fragment library screening, several academic and industrial groups have designed and synthesised novel fragments with a three-dimensional (3D) shape. This review provides an overview of 25 synthetic 3D fragment libraries from the recent literature. We calculate and compare physicochemical properties and descriptors that are typically used to measure molecular three-dimensionality such as fraction sp3 (Fsp3), plane of best fit (PBF) scores and principal moment of inertia (PMI) plots. Although the libraries vary widely in structure and properties, some key common features can be identified which may have utility in designing the next generation of 3D fragment libraries.

The European Chemical Society (EuChemS).

The European Chemical Society (EuChemS) coordinates the work of almost all the European Chemical Societies. As an organization, it provides an independent and authoritative voice on all matters relating to chemistry, and try to place chemistry at the heart of policy in Europe. Furthermore, EuChemS seeks to develop its members through various activities, workshops and awards. Particularly, EuChemS has fostered growth in its young members through the European Young Chemists' Network. Beyond Europe, EuChemS has collaborated with various organizations in bringing chemistry out of the lab and into society in building a sustainable future for everyone.

Enterotoxigenic Escherichia coli EtpA mediates adhesion between flagella and host cells.

Adhesion to epithelial cells and flagella-mediated motility are critical virulence traits for many Gram-negative pathogens, including enterotoxigenic Escherichia coli (ETEC), a major cause of diarrhoea in travellers and children in developing countries. Many flagellated pathogens export putative adhesins belonging to the two-partner secretion (TPS) family. However, the actual function of these adhesins remains largely undefined. Here we demonstrate that EtpA, a TPS exoprotein adhesin of enterotoxigenic E. coli, mimics and interacts with highly conserved regions of flagellin, the major subunit of flagella, and that these interactions are critical for adherence and intestinal colonization. Although conserved regions of flagellin are mostly buried in the flagellar shaft, our results suggest that they are at least transiently exposed at the tips of flagella where they capture EtpA adhesin molecules for presentation to eukaryotic receptors. Similarity of EtpA to molecules encoded by other motile pathogens suggests a potential common pattern for bacterial adhesion, whereas participation of conserved regions of flagellin in adherence has implications for development of vaccines for Gram-negative pathogens.

Highly versatile catalytic hydrogenation of carboxylic and carbonic acid derivatives using a Ru-triphos complex: molecular control over selectivity and substrate scope.

The complex [Ru(Triphos)(TMM)] (Triphos = 1,1,1-tris(diphenylphosphinomethyl)ethane, TMM = trimethylene methane) provides an efficient catalytic system for the hydrogenation of a broad range of challenging functionalities encompassing carboxylic esters, amides, carboxylic acids, carbonates, and urea derivatives. The key control factor for this unique substrate scope results from selective activation to generate either the neutral species [Ru(Triphos)(Solvent)H2] or the cationic intermediate [Ru(Triphos)(Solvent)(H)(H2)](+) in the presence of an acid additive. Multinuclear NMR spectroscopic studies demonstrated together with DFT investigations that the neutral species generally provides lower energy pathways for the multistep reduction cascades comprising hydrogen transfer to C═O groups and C-O bond cleavage. Carboxylic esters, lactones, anhydrides, secondary amides, and carboxylic acids were hydrogenated in good to excellent yields under these conditions. The formation of the catalytically inactive complexes [Ru(Triphos)(CO)H2] and [Ru(Triphos)(µ-H)]2 was identified as major deactivation pathways. The former complex results from substrate-dependent decarbonylation and constitutes a major limitation for the substrate scope under the neutral conditions. The deactivation via the carbonyl complex can be suppressed by addition of catalytic amounts of acids comprising non-coordinating anions such as HNTf2 (bis(trifluoromethane)sulfonimide). Although the corresponding cationic cycle shows higher overall barriers of activation, it provides a powerful hydrogenation pathway at elevated temperatures, enabling the selective reduction of primary amides, carbonates, and ureas in high yields. Thus, the complex [Ru(Triphos)(TMM)] provides a unique platform for the rational selection of reaction conditions for the selective hydrogenation of challenging functional groups and opens novel synthetic pathways for the utilization of renewable carbon sources.

On the importance of decarbonylation as a side-reaction in the ruthenium-catalysed dehydrogenation of alcohols: a combined experimental and density functional study.

We report a density functional study (B97-D2 level) of the mechanism(s) operating in the alcohol decarbonylation that occurs as an important side-reaction during dehydrogenation catalysed by [RuH2(H2)(PPh3)3]. By using MeOH as the substrate, three distinct pathways have been fully characterised involving either neutral tris- or bis-phosphines or anionic bis-phosphine complexes after deprotonation. α-Agostic formaldehyde and formyl complexes are key intermediates, and the computed rate-limiting barriers are similar between the various decarbonylation and dehydrogenation paths. The key steps have also been studied for reactions involving EtOH and iPrOH as substrates, rationalising the known resistance of the latter towards decarbonylation. Kinetic isotope effects (KIEs) were predicted computationally for all pathways and studied experimentally for one specific decarbonylation path designed to start from [RuH(OCH3)(PPh3)3]. From the good agreement between computed and experimental KIEs (observed kH/kD =4), the rate-limiting step for methanol decarbonylation has been ascribed to the formation of the first agostic intermediate from a transient formaldehyde complex.

Mechanism of alkyne alkoxycarbonylation at a Pd catalyst with P,N hemilabile ligands: a density functional study.

A detailed mechanism for alkyne alkoxycarbonylation mediated by a palladium catalyst has been characterised at the B3PW91-D3/PCM level of density functional theory (including bulk solvation and dispersion corrections). This transformation, investigated via the methoxycarbonylation of propyne, involves a uniquely dual role for the P,N hemilabile ligand acting co-catalytically as both an in situ base and proton relay coupled with a Pd(0) centre, allowing for surmountable barriers (highest ΔG(≠) of 22.9 kcal mol(-1) for alcoholysis). This proton-shuffle between methanol and coordinated propyne accounts for experimental requirements (high acid concentration) and reproduces observed regioselectivities as a function of ligand structure. A simple ligand modification is proposed, which is predicted to improve catalytic turnover by three orders of magnitude.

Evaluation of a Novel Battery-Operated Tumbler Device for Use in the Detection of Mouse Pathogens for Rodent Health Monitoring.

The search for alternatives to live animal sentinels in rodent health monitoring programs is fundamental to the 3Rs (Reduction, Replacement, and Refinement) of animal research. We evaluated the efficacy of a novel battery-operated tumbler device that rotates soiled bedding in direct contact with sample media against the use of exhaust sample media and soiled bedding sentinel (SBS) mice. Four rodent racks were used, each with 3 test cages: a cage with a tumbler device that rotated for 10min twice a week (TUM10), a cage with a tumbler device that rotated for 60min twice a week (TUM60), and a cage housing 2 female Crl:CD1(ICR) mice. Every 2 wk, each test cage received soiled bedding collected from all cages on each respective rack. In addition to soiled bedding, the tumbler device contained various sample collection media: a contact Reemay filter (3mo-cRF) that remained in the tumbler for the duration of the study, a contact Reemay filter (1mo-cRF) that was replaced monthly, adhesive swabs (AS) that were added at every biweekly cage change, and an exhaust Reemay filter located at the exhaust outlet of the cage. All analyses were performed by direct PCR for both sample media in the animal-free methods, and fecal pellet, body swab, and oral swabs were collected from sentinel mice. Out of 16 total pathogens detected, assessment of 1mo-Crf from both TUM10 and TUM60 cages detected 84% and 79% of pathogens, respectively, while SBS samples detected only 47% of pathogens. AS in TUM60 and TUM10 cages detected the fewest pathogens (24% and 13%, respectively). These results indicate that the novel tumbler device is an effective and reliable tool for rodent health monitoring programs and a suitable replacement for live animal sentinels. In this study, 1mo-cRF in TUM10 cages detected the highest number of pathogens.

Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors.

Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery.  However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B  (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau  (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads.

Homogeneous catalytic hydrogenation of amides to amines.

Hydrogenation of amides in the presence of [Ru(acac)3] (acacH=2,4-pentanedione), triphos [1,1,1-tris- (diphenylphosphinomethyl)ethane] and methanesulfonic acid (MSA) produces secondary and tertiary amines with selectivities as high as 93% provided that there is at least one aromatic ring on N. The system is also active for the synthesis of primary amines. In an attempt to probe the role of MSA and the mechanism of the reaction, a range of methanesulfonato complexes has been prepared from [Ru(acac)3], triphos and MSA, or from reactions of [RuX(OAc)(triphos)] (X=H or OAc) or [RuH2(CO)(triphos)] with MSA. Crystallographically characterised complexes include: [Ru(OAc-κ(1)O)2(H2O)(triphos)], [Ru(OAc-κ(2)O,O')(CH3SO3-κ(1)O)(triphos)], [Ru(CH3SO3-κ(1)O)2(H2O)(triphos)] and [Ru2(µ-CH3SO3)3(triphos)2][CH3SO3], whereas other complexes, such as [Ru(OAc-κ(1)O)(OAc-κ(2)O,O')(triphos)], [Ru(CH3SO3-κ(1)O)(CH3SO3-κ(2)O,O')(triphos)], H[Ru(CH3SO3-κ(1)O)3(triphos)], [RuH(CH3SO3-κ(1)O)(CO)(triphos)] and [RuH(CH3SO3-κ(2)O,O')(triphos)] have been characterised spectroscopically. The interactions between these various complexes and their relevance to the catalytic reactions are discussed.

Adhesin degradation accelerates delivery of heat-labile toxin by enterotoxigenic Escherichia coli.

Many enteric pathogens, including enterotoxigenic Escherichia coli (ETEC), produce one or more serine proteases that are secreted via the autotransporter (or type V) bacterial secretion pathway. These molecules have collectively been referred to as SPATE proteins (serine protease autotransporter of the Enterobacteriaceae). EatA, an autotransporter previously identified in ETEC, possesses a functional serine protease motif within its secreted amino-terminal passenger domain. Although this protein is expressed by many ETEC strains and is highly immunogenic, its precise function is unknown. Here, we demonstrate that EatA degrades a recently characterized adhesin, EtpA, resulting in modulation of bacterial adhesion and accelerated delivery of the heat-labile toxin, a principal ETEC virulence determinant. Antibodies raised against the passenger domain of EatA impair ETEC delivery of labile toxin to epithelial cells suggesting that EatA may be an effective target for vaccine development.

Phosphorus containing mixed anhydrides--their preparation, labile behaviour and potential routes to their stabilisation.

Simple mixed anhydrides are known to pose synthetic difficulties relating to their thermal lability and ways to stabilise such mixed anhydride systems by relying on either electronic or steric effects were therefore explored. Thus, a series of acyloxyphosphines and acylphosphites derived from either propanoic acid or phenylacetic acid were prepared and their in solution stability assessed. These compounds were, where stability allowed, fully characterised using standard analytical techniques. NMR studies, in particular, unearthed interesting coupling behaviour for a number of the acyloxyphosphines and acylphosphites as well as their rearrangement products which could be linked to their chiral nature. Furthermore, the crystal structures for three of the prepared mixed anhydrides were determined using X-ray crystallography and are reported herein.

Escape from planarity in fragment-based drug discovery: A synthetic strategy analysis of synthetic 3D fragment libraries.

In fragment-based drug discovery (FBDD), there is a developing appreciation that 3D fragments could offer opportunities that are not provided by 2D fragments. This review provides an overview of the synthetic strategies that have been used to prepare 3D fragments, as discussed in 25 papers published from 2011 to mid-May 2020. Three distinct strategies are highlighted: (i) diversity-oriented synthesis; (ii) the synthesis and diversification of scaffolds; and (iii) computational design and synthesis (where 3D fragments were computationally enumerated and filtered on the basis of computationally generated 3D shape descriptors and other properties). We conclude that a workflow that combines computational design and one other strategy, together with a consideration of fragment properties, 3D shape and 'fragment sociability', could allow 3D fragments to feature more widely in fragment libraries and could facilitate fragment-to-lead optimisation.

Puckering the Planar Landscape of Fragments: Design and Synthesis of a 3D Cyclobutane Fragment Library.

Fragment-based drug discovery (FBDD) has a growing need for unique screening libraries. The cyclobutane moiety was identified as an underrepresented yet attractive three-dimensional (3D) scaffold. Synthetic strategies were developed via a key 3-azido-cyclobutanone intermediate, giving potential access to a range of functional groups with accessible growth vectors. A focused set of 33 novel 3D cyclobutane fragments was synthesised, comprising three functionalities: secondary amines, amides, and sulfonamides. This library was designed using Principal Component Analysis (PCA) and an expanded version of the rule of three (RO3), followed by Principal Moment of Inertia (PMI) analysis to achieve both chemical diversity and high 3D character. Cis and trans ring isomers of library members were generated to maximise the shape diversity obtained, while limiting molecular complexity through avoiding enantiomers. Property analyses of the cyclobutane library indicated that it fares favourably against existing synthetic 3D fragment libraries in terms of shape and physicochemical properties.

Evaluation of In-cage Filter Paper as a Replacement for Sentinel Mice in the Detection of Murine Pathogens.

Recent studies have evaluated alternatives to the use of live animals in colony health monitoring. Currently, an alternative method that is suitable for all rack types and that has been verified to detect the infectious agents most commonly excluded from mouse colonies is unavailable. We compared the use of filter paper placed on the inside floor of mouse cages to the traditional use of sentinel mice in the detection of several prevalent murine pathogens including mouse hepatitis virus (MHV), murine norovirus (MNV), minute virus of mice (MVM), mouse parvovirus (MPV), Theiler murine encephalomyelitis virus (TMEV), Helicobacter spp., Syphacia obvelata, and Aspiculuris tetraptera. Experimental groups comprised 7 cages containing either 2 pieces of filter paper on the cage floor or 2 ICR sentinel mice. Soiled bedding from pet-store mice was transferred to the experimental cages weekly for 8 wk. At 1 and 2 mo after bedding transfer, the filter papers were evaluated by PCR and sentinel mice were tested by serology and fecal PCR. Filter papers detected all pathogens as effectively (MHV, MNV, MPV, MVM, TMEV S. obvelata, and A. tetraptera) or more effectively (Helicobacter spp.) than sentinel mice at both time points. Filter papers more readily detected pathogens with a high copy number per RT-PCR analysis than a low copy number. Helicobacter spp. were not detected by sentinel mice at either time point. These results indicate that the use of filter paper placed on the interior floor of empty mouse cages and exposed to soiled bedding is efficient in detecting bacteria, endoparasites, and most of the common mouse viruses included in an animal health monitoring program.

Discovery of a Highly Selective and Potent TRPC3 Inhibitor with High Metabolic Stability and Low Toxicity.

The overactivation of transient receptor potential canonical 3 (TRPC3) is associated with neurodegenerative diseases and hypertension. Pyrazole 3 (Pyr3) is reported as the most selective TRPC3 inhibitor, but it has two inherent structural limitations: (1) the labile ester moiety leads to its rapid hydrolysis to the inactive Pyr8 in vivo, and (2) the alkylating trichloroacrylic amide moiety is known to be toxic. To circumvent these limitations, we designed a series of conformationally restricted Pyr3 analogues and reported that compound 20 maintains high potency and selectivity for human TRPC3 over its closely related TRP channels. It has significantly improved metabolic stability compared with Pyr3 and has a good safety profile. Preliminary evaluation of 20 demonstrated its ability to rescue Aß-induced neuron damage with similar potency to that of Pyr3 in vitro. Collectively, these results suggest that 20 represents a promising scaffold to potentially ameliorate the symptoms associated with TRPC3-mediated neurological and cardiovascular disorders.

Bromo-Cyclobutenaminones as New Covalent UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) Inhibitors.

Drug discovery programs against the antibacterial target UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) have already resulted in covalent inhibitors having small three- and five-membered heterocyclic rings. In the current study, the reactivity of four-membered rings was carefully modulated to obtain a novel family of covalent MurA inhibitors. Screening a small library of cyclobutenone derivatives led to the identification of bromo-cyclobutenaminones as new electrophilic warheads. The electrophilic reactivity and cysteine specificity have been determined in a glutathione (GSH) and an oligopeptide assay, respectively. Investigating the structure-activity relationship for MurA suggests a crucial role for the bromine atom in the ligand. In addition, MS/MS experiments have proven the covalent labelling of MurA at Cys115 and the observed loss of the bromine atom suggests a net nucleophilic substitution as the covalent reaction. This new set of compounds might be considered as a viable chemical starting point for the discovery of new MurA inhibitors.

Diazaphospholidine terminated polyhedral oligomeric silsesquioxanes in the hydroformylation of vinyl acetate.

The poorly active, monodentate SemiEsphos phosphine has been turned into an active ligand for rhodium catalysed vinyl acetate hydroformylation by attachment to the periphery of a polyhedral oligomeric silsesquioxane.