Antivesiculation and Complete Unbinding of Tail-Tethered Lipids.

We report the effect of tail-tethering on vesiculation and complete unbinding of bilayered membranes. Amphiphilic molecules of a bolalipid, resembling the tail-tethered molecular structure of archaeal lipids, with two identical zwitterionic phosphatidylcholine headgroups self-assemble into a large flat lamellar membrane, in contrast to the multilamellar vesicles (MLVs) observed in its counterpart, monopolar nontethered zwitterionic lipids. The antivesiculation is confirmed by small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cyro-TEM). With the net charge of zero and higher bending rigidity of the membrane (confirmed by neutron spin echo (NSE) spectroscopy), the current membrane theory would predict that membranes should stack with each other (aka "bind") due to dominant van der Waals attraction, while the outcome of the nonstacking ("unbinding") membrane suggests that the theory needs to include entropic contribution for the nonvesicular structures. This report pioneers an understanding of how the tail-tethering of amphiphiles affects the structure, enabling better control over the final nanoscale morphology.

CH2 + O2: reaction mechanism, biradical and zwitterionic character, and formation of CH2OO, the simplest Criegee intermediate.

The singlet and triplet potential surfaces for the title reaction were investigated using the CBS-QB3 level of theory. The wave functions for some species exhibited multireference character and required the CASPT2/6-31+G(d,p) and CASPT2/aug-cc-pVTZ levels of theory to obtain accurate relative energies. A Natural Bond Orbital Analysis showed that triplet 3CH2OO (the simplest Criegee intermediate) and 3CH2O2 (dioxirane) have mostly polar biradical character, while singlet 1CH2OO has some zwitterionic character and a planar structure. Canonical variational transition state theory (CVTST) and master equation simulations were used to analyze the reaction system. CVTST predicts that the rate constant for reaction of 1CH2 + 3O2 is more than ten times as fast as the reaction of 3CH2 (X3B1) + 3O2 and the ratio remains almost independent of temperature from 900 K to 3000 K. The master equation simulations predict that at low pressures the 1CH2O + 3O product set is dominant at all temperatures and the primary yield of OH radicals is negligible below 600 K, due to competition with other primary reactions in this complex system.

Development of a robust crystallization platform for immune receptor TREM2 using a crystallization chaperone strategy.

TREM2 has been identified by genomic analysis as a potential and novel target for the treatment of Alzheimer's disease. To enable structure-based screening of potential small molecule therapeutics, we sought to develop a robust crystallization platform for the TREM2 Ig-like domain. A systematic set of constructs containing the structural chaperone, maltose binding protein (MBP), fused to the Ig domain of TREM2, were evaluated in parallel expression and purification, followed by crystallization studies. Using protein crystallization and high-resolution diffraction as a readout, a MBP-TREM2 Ig fusion construct was identified that generates reproducible protein crystals diffracting at 2.0 Å, which makes it suitable for soaking of potential ligands. Importantly, analysis of crystal packing interfaces indicates that most of the surface of the TREM2 Ig domain is available for small molecule binding. A proof of concept co-crystallization study with a small library of fragments validated potential utility of this system for the discovery of new TREM2 therapeutics.

Structure-based discovery of LpxC inhibitors.

The emergence and spread of multidrug-resistant (MDR) Gram negative bacteria presents a serious threat for public health. Novel antimicrobials that could overcome the resistance problems are urgently needed. UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase (LpxC) is a cytosolic zinc-based deacetylase that catalyzes the first committed step in the biosynthesis of lipid A, which is essential for the survival of Gram-negative bacteria. Our efforts toward the discovery of novel LpxC inhibitors are presented herein.

Fragment-based discovery of DNA gyrase inhibitors targeting the ATPase subunit of GyrB.

Inhibitors of the ATPase function of bacterial DNA gyrase, located in the GyrB subunit and its related ParE subunit in topoisomerase IV, have demonstrated antibacterial activity. In this study we describe an NMR fragment-based screening effort targeting Staphylococcus aureus GyrB that identified several attractive and novel starting points with good ligand efficiency. Fragment hits were further characterized using NMR binding studies against full-length S. aureus GyrB and Escherichia coli ParE. X-ray co-crystal structures of select fragment hits confirmed binding and suggested a path for medicinal chemistry optimization. The identification, characterization, and elaboration of one of these fragment series to a 0.265 µM inhibitor is described herein.

Predicted Chemical Activation Rate Constants for HO2 + CH2NH: The Dominant Role of a Hydrogen-Bonded Pre-reactive Complex.

The reaction of methanimine (CH2NH) with the hydroperoxy (HO2) radical has been investigated by using a combination of ab initio and density functional theory (CCSD(T)/CBSB7//B3LYP+Dispersion/CBSB7) and master equation calculations based on transition state theory (TST). Variational TST was used to compute both canonical (CVTST) and microcanonical (µVTST) rate constants for barrierless reactions. The title reaction starts with the reversible formation of a cyclic prereactive complex (PRC) that is bound by ∼11 kcal/mol and contains hydrogen bonds to both nitrogen and oxygen. The reaction path for the entrance channel was investigated by a series of constrained optimizations, which showed that the reaction is barrierless (i.e., no intrinsic energy barrier along the path). However, the variations in the potential energy, vibrational frequencies, and rotational constants reveal that the two hydrogen bonds are formed sequentially, producing two reaction flux bottlenecks (i.e., two transition states) along the reaction path, which were modeled using W. H. Miller's unified TST approach. The rate constant computed for the formation of the PRC is pressure-dependent and increases at lower temperatures. Under atmospheric conditions, the PRC dissociates rapidly and its lifetime is too short for it to undergo significant bimolecular reaction with other species. A small fraction isomerizes via a cyclic transition state and subsequent reactions lead to products normally expected from hydrogen abstraction reactions. The kinetics of the HO2 + CH2NH reaction system differs substantially from the analogous isoelectronic reaction systems involving C2H4 and CH2O, which have been the subjects of previous experimental and theoretical studies.

Comparison of Three Isoelectronic Multiple-Well Reaction Systems: OH + CH2O, OH + CH2CH2, and OH + CH2NH.

Methylenimine (CH2NH) has been predicted to be a product of the atmospheric photo-oxidation of methylamine, but its atmospheric reactions have not been measured. In this paper, we report potential energy surfaces (PESs) and rate constants for OH + CH2NH and its isoelectronic analogues OH + CH2O and OH + CH2CH2, which are more fully understood. The PESs were computed using the BHandHLYP/aug-cc-pVTZ and CCSD(T)/aug-cc-pVTZ levels of theory. Canonical variational transition state theory and Rice-Ramsperger-Kassel-Marcus and master equation modeling were used to calculate temperature- and pressure-dependent rate constants, with particular emphasis on the OH + reactant entrance channels and the effects of prereactive complexes. The computed results are in reasonable agreement with experimental data where they can be compared and also with the results of previous theoretical calculations. The results show that to some extent OH radicals both add to the carbon center double bond in CH2NH and abstract methylene hydrogen atoms, as in the OH + CH2O and OH + CH2CH2 reactions, respectively, but the dominant pathway is abstraction of the hydrogen from N-H. The computed rate constants are suitable for both atmospheric and combustion modeling.

HO + OClO Reaction System: Featuring a Barrierless Entrance Channel with Two Transition States.

Chlorine-containing compounds play a significant role in the troposphere and are key players in the stratosphere. The free radical compound OClO reacts with HO free radicals, but the existing experimental kinetics data are limited and uncertain. In the present theoretical investigation, the reaction mechanism, rate constants, and product branching ratios for the HO + OClO reaction system were computed over wide temperature and pressure ranges and compared with the existing experimental data. Stationary points on the singlet potential energy surface (PES) were calculated at high levels of theory, and the kinetics parameters were computed using several methods, including variational transition state theory (VTST) and RRKM/master equation techniques. The computed PES is in reasonable agreement with previous calculations, and the computed rate constants and branching ratio are in good agreement with the recent experiments. The results are used as the basis for recommendations for atmospheric chemistry modeling. The PES along the reaction path forming the peroxy bond has a steplike structure and only a very weakly bound prereactive complex, and yet it still supports two transition states along the reaction path. This feature may also be present in other reactions in which electrostatic forces align the approaching reactants in an unfavorable orientation at long distances, thus requiring a dramatic geometry change before reaction can take place.

When Rate Constants Are Not Enough.

Real-world chemical systems consisting of multiple isomers and multiple reaction channels often react significantly prior to attaining a steady state energy distribution (SED). Detailed elementary reaction models, which implicitly require SED conditions, may be invalid when non-steady-state energy distributions (NSED) exist. NSED conditions may result in reaction rates and product yields that are different from those expected for SED conditions, although this problem is to some extent reduced by using phenomenological models and rate constants. The present study defines pragmatic diagnostics useful for identifying NSED conditions in stochastic master equation simulations. A representative example is presented for each of four classes of common combustion species: RO2 radicals, aliphatic hydrocarbons, alkyl radicals, and polyaromatic radicals. An example selected from the seminal work of Tsang et al. demonstrates that stochastic simulations and eigenvalue methods for solving the master equation predict the same NSED effects. NSED effects are common under relatively moderate combustion conditions, and accurate simulations may require a master equation analysis.

Design, synthesis and structure-activity relationships of a novel class of sulfonylpyridine inhibitors of Interleukin-2 inducible T-cell kinase (ITK).

Starting from benzylpyrimidine 2, molecular modeling and X-ray crystallography were used to design highly potent inhibitors of Interleukin-2 inducible T-cell kinase (ITK). Sulfonylpyridine 4i showed sub-nanomolar affinity against ITK, was selective versus Lck and its activity in the Jurkat cell-based assay was greatly improved over 2.

Theoretical study on the kinetics of the reaction CH2Br + NO2.

The mechanism for the reaction CH2Br + NO2 was investigated by quantum chemical calculation, and the kinetic calculations were carried out by means of multichannel RRKM and variational transition-state theory method. Both singlet and triplet potential energy surfaces (PESs) were considered at the CCSD(T)/6-311++G(d,p)//B3LYP/6-311G(d,p) level. The results show that the singlet PES is preferred, and the initial association is a barrierless process (CH2Br + NO2 → CH2BrNO2), consistent with previous study, while the reaction occurring on the triplet PES is unfavorable due to the high barriers at the entrance channels. The calculated overall rate constants agree well with the experimental data within the measured temperature range of 221-363 K, fitted to the expression of k(T) = 2.61 × 10(-10)T(-0.76) exp(461/T) cm(3) molecule(-1) s(-1) over the temperature range of 200-2000 K. The product ratios were obtained by using master equation modeling and show that the formation of product CH2O + BrNO (P1) is dominant, in line with the experimental observation.

CH2NH2 + O2 and CH3CHNH2 + O2 reaction kinetics: photoionization mass spectrometry experiments and master equation calculations.

Two carbon centered amino radical (CH2NH2 and CH3CHNH2) reactions with O2 were scrutinized by means of laboratory gas kinetics experiments together with quantum chemical computations and master equation modeling. In the experiments, laser photolysis of alkylamine compounds at 193 nm was used for the radical production and photoionization mass spectrometry was employed for the time-resolved detection of the reactants and products. The investigations were performed in a tubular, uncoated borosilicate glass flow reactor. The rate coefficients obtained were high, ranging from 2.4 × 10(-11) to 3.5 × 10(-11) cm(3) molecule(-1) s(-1) in the CH2NH2 + O2 reaction and from 5.5 × 10(-11) to 7.5 × 10(-11) cm(3) molecule(-1) s(-1) in the CH3CHNH2 + O2 reaction, showed negative temperature dependence with no dependence on the helium bath gas pressure (0.5 to 2.5 Torr He). The measured rate coefficients can be expressed as a function of temperature with: k(CH2NH2 + O2) = (2.89 ± 0.13) × 10(-11) (T/300 K)(-(1.10±0.47)) cm(3) molecule(-1) s(-1) (267-363 K) and k(CH3CHNH2 + O2) = (5.92 ± 0.23) × 10(-11) (T/300 K)(-(0.50±0.42)) cm(3) molecule(-1) s(-1) (241-363 K). The reaction paths and mechanisms were characterized using quantum chemical calculations and master equation modeling. Master equation computations, constrained by experimental kinetic results, were employed to model pressure-dependencies of the reactions. The constrained modeling results reproduce the experimentally observed negative temperature dependence and the dominant CH2NH imine production in the CH2NH2 + O2 reaction at the low pressures of the present laboratory investigation. In the CH3CHNH2 + O2 reaction, similar qualitative behavior was observed both in the rate coefficients and in the product formation, although the fine details of the mechanism were observed to change according to the different energetics in this system. In conclusion, the constrained modeling results predict significant imine + HO2 production for both reactions even at atmospheric pressure.

What to do if you are referred to the NMC.

If you are subject to an investigation by a professional regulator, you need to be informed about the process and act quickly. This article outlines the process and offers some advice on how best to navigate it.

Accelerated flushing of contaminants from MSW landfill at the field scale using a fill-and-draw method.

A fill-and-draw flushing test on a landfill cell containing MSW waste was carried out to examine the operational viability of this method for accelerating the flushing of contaminants and landfill stabilisation. During the fill cycle, 800 m3 of water containing the tracer bromide was pumped into the base of a 0.44 ha landfill cell, resulting in the estimated saturation of 9,400 m3 of waste. Abstraction took place in two phases, during which 1,100 m3 of tracer/leachate was recovered. Samples of leachate were analysed for the tracer, electrical conductivity and indigenous solutes chloride and ammonia. Tracer recovery was between 63 and 72 % for bromide. An estimated 227 kg of ammonia and 575 kg of chloride were removed. Test data was used to calibrate a 1D, dual-porosity model involving advection in a mobile zone, and diffusion into 'blocks' of a less mobile zone. The model fitted well to the early time data, whereas later data appears to have been affected by recharge. The results of this trial demonstrate the possibilities of the 'fill-and-draw' concept using the basal leachate drainage system of landfills as a potential accelerated landfill remediation technique. However, modelling results suggest low contaminant removal efficiency. Including a pause between the fill and the draw cycles improves mass removal.

Discovery and Optimization of N-Heteroaryl Indazole LRRK2 Inhibitors.

Inhibition of leucine-rich repeat kinase 2 is a genetically supported mechanism for the treatment of Parkinson's disease. We previously disclosed the discovery of an indazole series lead that demonstrated both safety and translational risks. The safety risks were hypothesized to be of unknown origin, so structural diversity in subsequent chemical matter was prioritized. The translational risks were identified due to a low brain Kpu,u in nonhuman primate studies, which raised concern over the use of an established peripheral biomarker as a surrogate for central target engagement. Given these challenges, the team sought to leverage structure- and property-based drug design and expanded efflux transporter profiling to identify structurally distinct leads with enhanced CNS drug-likeness. Herein, we describe the discovery of a "reinvented" indazole series with improved physicochemical properties and efflux transporter profiles while maintaining excellent potency and off-target kinase selectivity, which resulted in advanced lead, compound 23.

Soluble epoxide hydrolase disruption as therapeutic target for wound healing.

BACKGROUND: Cytochrome P450 (CYP)-derived epoxyeicosatrienoic acids (EETs) possess angiogenic effects. However, the effect of CYP-derived EETs and soluble epoxide hydrolase (sEH) deletion on wound healing in vivo has not been rigorously investigated. In this study, we measured the effect of exogenous CYP-derived EETs and targeted disruption of sEH in an in vivo wound model. MATERIALS AND METHODS: Standardized full-thickness dermal wounds were created on the dorsum of mouse ears. Wound epithelialization was directly viewed and measured using intravital microscopy and computerized planimetry every second day until healing was complete. Wound sections were analyzed by immunostaining for metalloproteinase (MMP) 2, MMP7, MMP9, tissue inhibitor of metalloproteinases (TIMP) 1, and tumor necrosis factor (TNF) α on days 2, 4, and 12. RESULTS: Treatment with 11,12-EETs, 14,15-EETs, and sEH deletion significantly accelerated wound closure. This effect was attenuated by the EET antagonist 14,15-epoxyeicosa-5(Z)-enoic acid (14,15-EEZE) in sEH(-/-) mice. Neither 11,12- nor 14,15-EETs caused significant alterations in MMP9 expression in wounds. In contrast, MMP2 and MMP7 were significantly upregulated in the EET-treated groups, whereas TIMP1 and TNF-α were downregulated. CONCLUSIONS: Collectively, these data demonstrated that potentiation of the CYP epoxy-genase pathway by either exogenous CYP-derived EETs or sEH deletion significantly accelerated wound epithelialization in vivo. This beneficial effect might be due to downregulation of TNF-α production and, to a lesser degree, to the release of MMPs and could be used as a viable angiogenic therapeutic strategy.

HO + CO reaction rates and H/D kinetic isotope effects: master equation models with ab initio SCTST rate constants.

Ab initio microcanonical rate constants were computed using Semi-Classical Transition State Theory (SCTST) and used in two master equation formulations (1D, depending on active energy with centrifugal corrections, and 2D, depending on total energy and angular momentum) to compute temperature-dependent rate constants for the title reactions using a potential energy surface obtained by sophisticated ab initio calculations. The 2D master equation was used at the P = 0 and P = ∞ limits, while the 1D master equation with centrifugal corrections and an empirical energy transfer parameter could be used over the entire pressure range. Rate constants were computed for 75 K ≤ T ≤ 2500 K and 0 ≤ [He] ≤ 10(23) cm(-3). For all temperatures and pressures important for combustion and for the terrestrial atmosphere, the agreement with the experimental rate constants is very good, but at very high pressures and T ≤ 200 K, the theoretical rate constants are significantly smaller than the experimental values. This effect is possibly due to the presence in the experiments of dimers and prereactive complexes, which were not included in the model calculations. The computed H/D kinetic isotope effects are in acceptable agreement with experimental data, which show considerable scatter. Overall, the agreement between experimental and theoretical H/D kinetic isotope effects is much better than in previous work, and an assumption of non-RRKM behavior does not appear to be needed to reproduce experimental observations.

Human endothelial-like differentiated precursor cells maintain their endothelial characteristics when cocultured with mesenchymal stem cell and seeded onto human cancellous bone.

INTRODUCTION: Cancellous bone is frequently used for filling bone defects in a clinical setting. It provides favourable conditions for regenerative cells such as MSC and early EPC. The combination of MSC and EPC results in superior bone healing in experimental bone healing models. MATERIALS AND METHODS: We investigated the influence of osteogenic culture conditions on the endothelial properties of early EPC and the osteogenic properties of MSC when cocultured on cancellous bone. Additionally, cell adhesion, metabolic activity, and differentiation were assessed 2, 6, and 10 days after seeding. RESULTS: The number of adhering EPC and MSC decreased over time; however the cells remained metabolically active over the 10-day measurement period. In spite of a decline of lineage specific markers, cells maintained their differentiation to a reduced level. Osteogenic stimulation of EPC caused a decline but not abolishment of endothelial characteristics and did not induce osteogenic gene expression. Osteogenic stimulation of MSC significantly increased their metabolic activity whereas collagen-1α and alkaline phosphatase gene expressions declined. When cocultured with EPC, MSC's collagen-1α gene expression increased significantly. CONCLUSION: EPC and MSC can be cocultured in vitro on cancellous bone under osteogenic conditions, and coculturing EPC with MSC stabilizes the latter's collagen-1α gene expression.

Facile polymerization in a bicellar template to produce polymer nano-rings.

HYPOTHESIS: A well-defined discoidal bicelle composed of three lipids, specifically zwitterionic long-chain 1,2­dipalmitoyl phosphocholine (DPPC) and short-chain 1,2­dihexanoyl phosphocholine (DHPC) doped with anionic 1,2­dipalmitoyl phosphoglycerol (DPPG) provides a generalized template for the synthesis of hydrophobic polymer nano-rings. The lipid molar ratio of DPPC/DHPC/DPPG is 0.71/0.25/0.04. The detailed investigation and discussion were based on styrene but tested on three other vinyl monomers. EXPERIMENTS: The structure of nano-rings is identified through the detailed analysis of small angle X-ray/neutron scattering (SAXS and SANS) data and transmission electron micrographs (TEM), supported by the differential scanning calorimetric (DSC) data before and after polymerization. The investigation covers samples with a styrene-to-lipid ratio ranged varied from 1:50 to 1:10. FINDINGS: The styrene monomers are initially located at both the discoidal planar (long-chain lipid rich) and rim (short-chain lipid rich) regions. During polymerization, they migrate to the more fluid rim regionsection. The formation mechanism involves the interplay of hydrophobic interaction, mismatched miscibility of polystyrene between the ordered and disordered phases, and crystallinity of the long lipid acyl chains. This facile synthesis is proven applicable for several hydrophobic monomers. The well-defined nano-rings greatly enhance the interfacial area and have the potential to be the building blocks for functional materials, if monomers are incorporated with desirable functions, for future applications.

Pretreatment of Mesenchymal Stem Cells with Electrical Stimulation as a Strategy to Improve Bone Tissue Engineering Outcomes.

Electrical stimulation (EStim), whether used alone or in combination with bone tissue engineering (BTE) approaches, has been shown to promote bone healing. In our previous in vitro studies, mesenchymal stem cells (MSCs) were exposed to EStim and a sustained, long-lasting increase in osteogenic activity was observed. Based on these findings, we hypothesized that pretreating MSC with EStim, in 2D or 3D cultures, before using them to treat large bone defects would improve BTE treatments. Critical size femur defects were created in 120 Sprague-Dawley rats and treated with scaffold granules seeded with MSCs that were pre-exposed or not (control group) to EStim 1 h/day for 7 days in 2D (MSCs alone) or 3D culture (MSCs + scaffolds). Bone healing was assessed at 1, 4, and 8 weeks post-surgery. In all groups, the percentage of new bone increased, while fibrous tissue and CD68+ cell count decreased over time. However, these and other healing features, like mineral density, bending stiffness, the amount of new bone and cartilage, and the gene expression of osteogenic markers, did not significantly differ between groups. Based on these findings, it appears that the bone healing environment could counteract the long-term, pro-osteogenic effects of EStim seen in our in vitro studies. Thus, EStim seems to be more effective when administered directly and continuously at the defect site during bone healing, as indicated by our previous studies.