Deciphering structural bases of intestinal and hepatic selectivity in targeting pregnane X receptor with indole-based microbial mimics.

Microbial metabolite mimicry is a new concept that promises to deliver compounds that have minimal liabilities and enhanced therapeutic effects in a host. In a previous publication, we have shown that microbial metabolites of L-tryptophan, indoles, when chemically altered, yielded potent anti-inflammatory pregnane X Receptor (PXR)-targeting lead compounds, FKK5 and FKK6, targeting intestinal inflammation. Our aim in this study was to further define structure-activity relationships between indole analogs and PXR, we removed the phenyl-sulfonyl group or replaced the pyridyl residue with imidazolopyridyl of FKK6. Our results showed that while removal of the phenyl-sulfonyl group from FKK6 (now called CVK003) shifts agonist activity away from PXR towards the aryl hydrocarbon receptor (AhR), the imidazolopyridyl addition preserves PXR activity in vitro. However, when these compounds are administered to mice, that unlike the parent molecule, FKK6, they exhibit poor induction of PXR target genes in the intestines and the liver. These data suggest that modifications of FKK6 specifically in the pyridyl moiety can result in compounds with weak PXR activity in vivo. These observations are a significant step forward for understanding the structure-activity relationships (SAR) between indole mimics and receptors, PXR and AhR.

Narrow-Spectrum Antibiotic Targeting of the Radical SAM Enzyme MqnE in Menaquinone Biosynthesis.

Antibiotic resistance continues to spread at an alarming rate, outpacing the introduction of new therapeutics and threatening to globally undermine health care. There is a crucial need for new strategies that selectively target specific pathogens while leaving the majority of the microbiome untouched, thus averting the debilitating and sometimes fatal occurrences of opportunistic infections. To address these challenges, we have adopted a unique strategy that focuses on oxygen-sensitive proteins, an untapped set of therapeutic targets. MqnE is a member of the radical S-adenosyl-l-methionine (RS) superfamily, all of which rely on an oxygen-sensitive [4Fe-4S] cluster for catalytic activity. MqnE catalyzes the conversion of didehydrochorismate to aminofutalosine in the essential menaquinone biosynthetic pathway present in a limited set of species, including the gut pathogen Helicobacter pylori (Hp), making it an attractive target for narrow-spectrum antibiotic development. Indeed, we show that MqnE is inhibited by the mechanism-derived 2-fluoro analogue of didehydrochorismate (2F-DHC) due to accumulation of a radical intermediate under turnover conditions. Structures of MqnE in the apo and product-bound states afford insight into its catalytic mechanism, and electron paramagnetic resonance approaches provide direct spectroscopic evidence consistent with the predicted structure of the radical intermediate. In addition, we demonstrate the essentiality of the menaquinone biosynthetic pathway and unambiguously validate 2F-DHC as a selective inhibitor of Hp growth that exclusively targets MqnE. These data provide the foundation for designing effective Hp therapies and demonstrate proof of principle that radical SAM proteins can be effectively leveraged as therapeutic targets.

Inhibition of Delta-induced Notch signaling using fucose analogs.

Notch is a cell-surface receptor that controls cell-fate decisions and is regulated by O-glycans attached to epidermal growth factor-like (EGF) repeats in its extracellular domain. Protein O-fucosyltransferase 1 (Pofut1) modifies EGF repeats with O-fucose and is essential for Notch signaling. Constitutive activation of Notch signaling has been associated with a variety of human malignancies. Therefore, tools that inhibit Notch activity are being developed as cancer therapeutics. To this end, we screened L-fucose analogs for their effects on Notch signaling. Two analogs, 6-alkynyl and 6-alkenyl fucose, were substrates of Pofut1 and were incorporated directly into Notch EGF repeats in cells. Both analogs were potent inhibitors of binding to and activation of Notch1 by Notch ligands Dll1 and Dll4, but not by Jag1. Mutagenesis and modeling studies suggest that incorporation of the analogs into EGF8 of Notch1 markedly reduces the ability of Delta ligands to bind and activate Notch1.

Lysosome Membrane Permeabilization and Disruption of the Molecular Target of Rapamycin (mTOR)-Lysosome Interaction Are Associated with the Inhibition of Lung Cancer Cell Proliferation by a Chloroquinoline Analog.

Lysosomes degrade cellular proteins and organelles and regulate cell signaling by providing a surface for the formation of critical protein complexes, notably molecular target of rapamycin (mTOR) complex 1 (mTORC1). Striking differences in the lysosomes of cancer versus normal cells suggest that they could be targets for drug development. Although the lysomotropic drugs chloroquine (CQ) and hydroxychloroquine (HCQ) have been widely investigated, studies have focused on their ability to inhibit autophagy. We synthesized a novel compound, called EAD1, which is structurally related to CQ but is a 14-fold more potent inhibitor of cell proliferation. Here we find that EAD1 causes rapid relocation, membrane permeabilization (LMP), and deacidification of lysosomes, and it induces apoptosis and irreversibly blocks proliferation of human lung cancer H460, H520, H1299, HCC827, and H1703 cells. EAD1 causes dissociation of mTOR from lysosomes and increases mTOR's perinuclear versus cytoplasmic localization, changes previously shown to inactivate mTORC1. The effect on mTOR was not seen with HCQ, even at >10-fold greater concentrations. Phosphorylation of a downstream target of mTORC1, ribosomal protein S6, was inhibited by EAD1. Although EAD1 also inhibited autophagy, it retained full antiproliferative activity in autophagy-deficient H1650 lung cancer cells, which have a biallelic deletion of Atg7, and in H460 Atg7-knockout cells. As Atg7 is critical for the canonical autophagy pathway, it is likely that inhibition of autophagy is not how EAD1 inhibits cell proliferation. Further studies are needed to determine the relationship of LMP to mTORC1 disruption and their relative contributions to drug-induced cell death. These studies support the lysosome as an underexplored target for new drug development.

Synthesis of stable azide and alkyne functionalized phosphoramidite nucleosides.

The use of CuAAC chemistry to crosslink and stabilize oligonucleotides has been limited by the incompatibility of azides with the phosphoramidites used in automated oligonucleotide synthesis. Herein we report optimized reaction conditions to synthesize azide derivatives of thymidine and cytidine phosphoramidites. Investigation of the stability of the novel phosphoramidites using 31P NMR at room temperature showed less than 10% degradation after 6 hours. The azide modified thymidine was successfully utilized as an internal modifier in the standard phosphoramidite synthesis of a DNA sequence. The synthesized azide and alkyne derivatives of pyrimidines will allow efficient incorporation of azide and alkyne click pairs into nucleic acids, thus widening the applicability of click chemistry in investigating the chemistry of nucleic acids.

Enolate-Forming Compounds as a Novel Approach to Cytoprotection.

Evidence from laboratory studies and clinical trials suggests that plant-derived polyphenolic compounds such as curcumin, resveratrol, or phloretin might be useful in the treatment of certain diseases (e.g., Alzheimer's disease) and acute tissue injury states (e.g., spinal cord trauma). However, despite this potential, the corresponding chemical instability, toxic potential, and low bioavailability of these compounds could limit their ultimate clinical relevance. We have shown that pharmacophores of curcumin (e.g., 2-acetylcyclopentanone) and phloretin (e.g., 2',4',6'-trihydroxyacetophenone; THA) can provide cytoprotection in cell culture and animal models of oxidative stress injury. These pharmacophores are 1,3-dicarbonyl and polyphenol derivatives, the enol groups of which can ionize in biological solutions to form an enolate. This carbanionic moiety can chelate metal ions and, as a nucleophile, can scavenge toxic electrophiles (e.g., acrolein, 4-hydroxy-2-nonenal, and N-acetyl-p-benzoquinone imine) involved in many pathogenic conditions. Aromatic derivatives such as THA can also trap free oxygen and nitrogen radicals and thereby provide another layer of cytoprotection. The multifunctional character of these enolate-forming compounds suggests an ability to block pathogenic processes (e.g., oxidative stress) at several steps. The purpose of this review is to discuss research supporting our theory that enolate formation is a significant cytoprotective property that represents a platform for development of pharmacotherapeutic approaches to a variety of toxic and pathogenic conditions. Our discussion will focus on mechanism and structure-activity studies that define enolate chemistry and their corresponding relationships to cytoprotection.

Chemical probing of glycans in cells and organisms.

Among the four major building blocks of life, glycans play essential roles in numerous physiological and pathological processes. Due to their non-templated biosynthesis, advances towards elucidating the molecular details of glycan functions are relatively slow compared with the pace of protein and nucleic acid research. Over the past 30 years, chemical tools have emerged as powerful allies to genetics and molecular biology in the study of glycans in their native environment. This tutorial review will provide an overview of the recent technological developments in the field, as well as the progress in the application of these techniques to probe glycans in cells and organisms.

Total synthesis, relay synthesis, and structural confirmation of the C18-norditerpenoid alkaloid neofinaconitine.

The first total synthesis of the C18-norditerpenoid aconitine alkaloid neofinaconitine and relay syntheses of neofinaconitine and 9-deoxylappaconitine from condelphine are reported. A modular, convergent synthetic approach involves initial Diels-Alder cycloaddition between two unstable components, cyclopropene 10 and cyclopentadiene 11. A second Diels-Alder reaction features the first use of an azepinone dienophile (8), with high diastereofacial selectivity achieved via rational design of siloxydiene component 36 with a sterically demanding bromine substituent. Subsequent Mannich-type N-acyliminium and radical cyclizations provide complete hexacyclic skeleton 33 of the aconitine alkaloids. Key endgame transformations include the installation of the C8-hydroxyl group via conjugate addition of water to a putative strained bridghead enone intermediate 45 and one-carbon oxidative truncation of the C4 side chain to afford racemic neofinaconitine. Complete structural confirmation was provided by a concise relay synthesis of (+)-neofinaconitine and (+)-9-deoxylappaconitine from condelphine, with X-ray crystallographic analysis of the former clarifying the NMR spectral discrepancy between neofinaconitine and delphicrispuline, which were previously assigned identical structures.

Neural Network Design for Impedance Modeling of Power Electronic Systems Based on Latent Features.

Data-driven approaches are promising to address the modeling issues of modern power electronics-based power systems, due to the black-box feature. Frequency-domain analysis has been applied to address the emerging small-signal oscillation issues caused by converter control interactions. However, the frequency-domain model of a power electronic system is linearized around a specific operating condition. It thus requires measurement or identification of frequency-domain models repeatedly at many operating points (OPs) due to the wide operation range of the power systems, which brings significant computation and data burden. This article addresses this challenge by developing a deep learning approach using multilayer feedforward neural networks (FNNs) to train the frequency-domain impedance model of power electronic systems that is continuous of OP. Distinguished from the prior neural network designs relying on trial-and-error and sufficient data size, this article proposes to design the FNN based on latent features of power electronic systems, i.e., the number of system poles and zeros. To further investigate the impacts of data quantity and quality, learning procedures from a small dataset are developed, and K-medoids clustering based on dynamic time warping is used to reveal insights into multivariable sensitivity, which helps improve the data quality. The proposed approaches for the FNN design and learning have been proven simple, effective, and optimal based on case studies on a power electronic converter, and future prospects in its industrial applications are also discussed.

Atomistic spin dynamic method with both damping and moment of inertia effects included from first principles.

We consider spin dynamics for implementation in an atomistic framework and we address the feasibility of capturing processes in the femtosecond regime by inclusion of moment of inertia. In the spirit of an s-d-like interaction between the magnetization and electron spin, we derive a generalized equation of motion for the magnetization dynamics in the semiclassical limit, which is nonlocal in both space and time. Using this result we retain a generalized Landau-Lifshitz-Gilbert equation, also including the moment of inertia, and demonstrate how the exchange interaction, damping, and moment of inertia, all can be calculated from first principles.

Co-targeting of BAX and BCL-XL proteins broadly overcomes resistance to apoptosis in cancer.

Deregulation of the BCL-2 family interaction network ensures cancer resistance to apoptosis and is a major challenge to current treatments. Cancer cells commonly evade apoptosis through upregulation of the BCL-2 anti-apoptotic proteins; however, more resistant cancers also downregulate or inactivate pro-apoptotic proteins to suppress apoptosis. Here, we find that apoptosis resistance in a diverse panel of solid and hematological malignancies is mediated by both overexpression of BCL-XL and an unprimed apoptotic state, limiting direct and indirect activation mechanisms of pro-apoptotic BAX. Both survival mechanisms can be overcome by the combination of an orally bioavailable BAX activator, BTSA1.2 with Navitoclax. The combination demonstrates synergistic efficacy in apoptosis-resistant cancer cells, xenografts, and patient-derived tumors while sparing healthy tissues. Additionally, functional assays and genomic markers are identified to predict sensitive tumors to the combination treatment. These findings advance the understanding of apoptosis resistance mechanisms and demonstrate a novel therapeutic strategy for cancer treatment.

Resonant inelastic soft x-ray scattering on LaPt2Si2.

X-ray absorption and resonant inelastic x-ray scattering spectra of LaPt2Si2single crystal at the Si 2pand La 4dedges are presented. The data are interpreted in terms of density functional theory, showing that the Si spectra can be described in terms of Sisanddlocal partial density of states (LPDOS), and the La spectra are due to quasi-atomic local 4fexcitations. Calculations show that Ptd-LPDOS dominates the occupied states, and a sharp localized Lafstate is found in the unoccupied states, in line with the observations.

Modulating mitofusins to control mitochondrial function and signaling.

Mitofusins reside on the outer mitochondrial membrane and regulate mitochondrial fusion, a physiological process that impacts diverse cellular processes. Mitofusins are activated by conformational changes and subsequently oligomerize to enable mitochondrial fusion. Here, we identify small molecules that directly increase or inhibit mitofusins activity by modulating mitofusin conformations and oligomerization. We use these small molecules to better understand the role of mitofusins activity in mitochondrial fusion, function, and signaling. We find that mitofusin activation increases, whereas mitofusin inhibition decreases mitochondrial fusion and functionality. Remarkably, mitofusin inhibition also induces minority mitochondrial outer membrane permeabilization followed by sub-lethal caspase-3/7 activation, which in turn induces DNA damage and upregulates DNA damage response genes. In this context, apoptotic death induced by a second mitochondria-derived activator of caspases (SMAC) mimetic is potentiated by mitofusin inhibition. These data provide mechanistic insights into the function and regulation of mitofusins as well as small molecules to pharmacologically target mitofusins.

Nature of the magnetic moment of cobalt in ordered FeCo alloy.

The magnets are typically classified into Stoner and Heisenberg type, depending on the itinerant or localized nature of the constituent magnetic moments. In this work, we investigate theoretically the behaviour of the magnetic moments of iron and cobalt in their B2-ordered alloy. The results based on local spin density approximation for the density functional theory (DFT) suggest that the Co magnetic moment strongly depends on the directions of the surrounding magnetic moments, which usually indicates the Stoner-type mechanism of magnetism. This is consistent with the disordered local moment picture of the paramagnetic state, where the magnetic moment of cobalt gets substantially suppressed. We argue that this is due to the lack of strong on-site electron correlations, which we take into account by employing a combination of DFT and dynamical mean-field theory (DMFT). Within LDA + DMFT, we find a substantial quasiparticle mass renormalization and a non Fermi-liquid behaviour of Fe-3dorbitals. The resulting spectral functions are in very good agreement with measured spin-resolved photoemission spectra. Our results suggest that local correlations play an essential role in stabilizing a robust local moment on Co in the absence of magnetic order at high temperatures.

Amide synthesis from alcohols and amines catalyzed by ruthenium N-heterocyclic carbene complexes.

The direct synthesis of amides from alcohols and amines is described with the simultaneous liberation of dihydrogen. The reaction does not require any stoichiometric additives or hydrogen acceptors and is catalyzed by ruthenium N-heterocyclic carbene complexes. Three different catalyst systems are presented that all employ 1,3-diisopropylimidazol-2-ylidene (IiPr) as the carbene ligand. In addition, potassium tert-butoxide and a tricycloalkylphosphine are required for the amidation to proceed. In the first system, the active catalyst is generated in situ from [RuCl(2)(cod)] (cod=1,5-cyclooctadiene), 1,3-diisopropylimidazolium chloride, tricyclopentylphosphonium tetrafluoroborate, and base. The second system uses the complex [RuCl(2)(IiPr)(p-cymene)] together with tricyclohexylphosphine and base, whereas the third system employs the Hoveyda-Grubbs 1st-generation metathesis catalyst together with 1,3-diisopropylimidazolium chloride and base. A range of different primary alcohols and amines have been coupled in the presence of the three catalyst systems to afford the corresponding amides in moderate to excellent yields. The best results are obtained with sterically unhindered alcohols and amines. The three catalyst systems do not show any significant differences in reactivity, which indicates that the same catalytically active species is operating. The reaction is believed to proceed by initial dehydrogenation of the primary alcohol to the aldehyde that stays coordinated to ruthenium and is not released into the reaction mixture. Addition of the amine forms the hemiaminal that undergoes dehydrogenation to the amide. A catalytic cycle is proposed with the {(IiPr)Ru(II)} species as the catalytically active components.

LTOT Patients' Experience of a Portable Oxygen Unit and Health-Related Quality of Life-A Cross-Sectional Study.

Background: The purpose of the present study was to elucidate the experiences of long-term oxygen therapy (LTOT) patients with a portable oxygen unit and to describe the patients' self-assessed health-related quality of life (HRQoL). Methods: The study employed a prospective cross-sectional design. Data collection entailed two questionnaires, namely the MedTech20 (patients' experience of the medical device in four areas) and EQ-5D (HRQoL). The informants consisted of patients (n = 148) treated with such a medical device and that were registered in Skåne University Hospital's database, Medusa. Results: In the domain Sense of security the informant felt the equipment reliable and safe to use and expressed a sense of control for the user. Regarding Social participation, the responses did not indicate the device to facilitate leisure activities, movement outside the homes, traveling or everyday tasks to a larger extent. The respondents did express a reduced sense of compromised integrity, with a minor effect on Intimacy. With regards to Convenience, the responses indicated the product to provide Adaptability to personal needs. Overall, a strongly affected HRQoL (Your current health condition, EQ-VAS Md = 50 (IQR 36-70)) with strong correlation with EQ-5D was seen. Conclusions: Informants experienced the portable oxygen unit as reliable and safe to use while giving a sense of control over the disease itself. A minor impact on social participation was reported, except for a reduced sense of compromised integrity. The patients also reported a strongly reduced HRQoL.

Self-induced spin glass state in elemental and crystalline neodymium.

Spin glasses are a highly complex magnetic state of matter intricately linked to spin frustration and structural disorder. They exhibit no long-range order and exude aging phenomena, distinguishing them from quantum spin liquids. We report a previously unknown type of spin glass state, the spin-Q glass, observable in bulk-like crystalline metallic neodymium thick films. Using spin-polarized scanning tunneling microscopy combined with ab initio calculations and atomistic spin-dynamics simulations, we visualized the variations in atomic-scale noncolinear order and its response to magnetic field and temperature. We quantified the aging phenomena relating the glassiness to crystalline symmetry and the energy landscape. This result not only resolves the long-standing debate of the magnetism of neodymium, but also suggests that glassiness may arise in other magnetic solids lacking extrinsic disorder.

Amide synthesis from alcohols and amines by the extrusion of dihydrogen.

An environmentally friendly method for synthesis of amides is presented where a simple ruthenium catalyst mediates the direct coupling between an alcohol and an amine with the liberation of two molecules of dihydrogen. The active catalyst is generated in situ from an easily available ruthenium complex, an N-heterocyclic carbene and a phosphine. The reaction allows primary alcohols to be coupled with primary alkylamines to afford the corresponding secondary amides in good yields. The amide formation presumably proceeds through a catalytic cycle where the intermediate aldehyde and hemiaminal are both coordinated to the metal catalyst.

Calculation of technologically important aspects of magnetism: anisotropy, critical temperatures and spin dependent transport (abstract only).

Magnetic materials, where the moments arising from the electron spins are ordered, have many potential applications of technological relevance. For instance, in recent years the focus has been on spintronics, a future technology where not only the electron's charge but also its spin will be utilized. In this presentation we will deal with a few of these applications from a microscopic theoretical view. The discussion is based on calculations of the electronic structure often within (spin) density functional methods. A large magnetic anisotropy, the fact that there are considerable energy differences between different magnetization directions, has considerable importance for e.g. magnetic storage and permanent magnet applications. We will discuss here how to calculate this quantity, which is exemplified by both a bulk system and a layered material, and the calculational accuracy and the method's predictability. One example of spin dependent transport is the so-called spin transfer torque, the fact that a current through a magnetic layer can rotate its magnetization. We will review its physical origin and present some recent calculations on naturally magnetic layered materials, so-called helical spin density waves. A crucial quantity for applications of the various spectacular magnetic effects is the Curie temperature, the temperature above which the magnetic order disappears. Many systems are limited by low Curie temperatures. A route to calculations of this quantity is described, and with the help of a few calculations we try to generalize what is needed to achieve significant magnetic ordering temperatures.

Tests of the efficiency of an augmented distorted planewave basis in electronic structure calculations.

An augmented distorted planewave plus local orbital basis set has been developed and implemented in a simple fashion in order to test its efficiency for electronic structure calculations. It is based on the idea of using distorted planewaves (Gygi 1993 Phys. Rev. B 48 11692) as basis functions in the interstitial region instead of ordinary planewaves, as in the usual linearized augmented planewave and augmented planewave plus local orbitals methods. This is shown to lead to a significantly more rapid convergence for open structures as well as a modestly improved convergence for close packed structures.