Enynones in organic synthesis. I. Spiroannulation by tandem oxy-cope rearrangement-electrocyclic ring closure

Bis-acetylenic alcohols of proper design undergo a facile oxy-Cope rearrangement to afford mixtures of E- and Z-enynones. These latter compounds afford methylenecyclopentenones upon enolization and electrocyclic ring closure.     

Gas hydrate single-crystal structure analyses

The first single-crystal diffraction studies on methane, propane, methane/propane, and adamantane gas hydrates SI, SII, and SH have been performed. To circumvent the problem of very slow crystal growth, a novel technique of in situ cocrystallization of gases and liquids resulting in oligocrystalline material in a capillary has been developed. With special data treatment, termed oligo diffractometry, structural data of the gas hydrates of methane, acetylene, propane, a propane/ethanol/methane-mixture and an adamantane/methane-mixture were obtained. Cell parameters are in accord with reported values. Host network and guest are subject to extensive disorder, reducing the reliability of structural information. It was found that most cages are fully occupied by a guest molecule with the exception of the dodecahedral cage in the acetylene hydrate which is only filled to 60%. For adamantane in the icosahedral cage a disordered model is proposed.     

Vessel effects in organic chemical reactions; a century-old,overlooked phenomenon

One of the most intriguing aspects of synthetic chemistry is the interplay of numerous dependent and independent variables en route to achieve a successful, high-yielding chemical transformation. The experienced synthetic chemist will probe many of these variables during reaction development and optimization, which will routinely involve investigation of reaction temperature, solvent, stoichiometry, concentration, time, choice of catalyst, addition sequence or quenching conditions just to name some commonly addressed variables. Remarkably, little attention is typically given to the choice of reaction vessel material as the surface of common laboratory borosilicate glassware is, incorrectly, assumed to be chemically inert. When reviewing the scientific literature, careful consideration of the vessel material is typically only given during the use of well-known glass-etching reagents such as HF, which is typically only handled in HF-resistant, polyfluorinated polymer vessels. However, there are examples of chemical transformations that do not involve such reagents but are still clearly influenced by the choice of reaction vessel material. In the following review, we wish to condense the most significant examples of vessel effects during chemical transformations as well as observations of container-dependent stability of certain molecules. While the primary focus is on synthetic organic chemistry, relevant examples from inorganic chemistry, polymerization reactions, atmospheric chemistry and prebiotic chemistry are also covered.

One of the most intriguing aspects of synthetic chemistry is the interplay of numerous dependent and independent variables en route to achieve a successful, high-yielding chemical transformation.     

Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides

Chemical probes for chromatin reader proteins are valuable tools for investigating epigenetic regulatory mechanisms and evaluating whether the target of interest holds therapeutic potential. Developing potent inhibitors for the plant homeodomain (PHD) family of methylation readers remains a difficult task due to the charged, shallow and extended nature of the histone binding site that precludes effective engagement of conventional small molecules. Herein, we describe the development of novel proximity-reactive cyclopeptide inhibitors for PHD3—a trimethyllysine reader domain of histone demethylase KDM5A. Guided by the PHD3–histone co-crystal structure, we designed a sidechain-to-sidechain linking strategy to improve peptide proteolytic stability whilst maintaining binding affinity. We have developed an operationally simple solid-phase macrocyclization pathway, capitalizing on the inherent reactivity of the dimethyllysine ε-amino group to generate scaffolds bearing charged tetraalkylammonium functionalities that effectively engage the shallow aromatic ‘groove’ of PHD3. Leveraging a surface-exposed lysine residue on PHD3 adjacent to the ligand binding site, cyclic peptides were rendered covalent through installation of an arylsulfonyl fluoride warhead. The resulting lysine-reactive cyclic peptides demonstrated rapid and efficient labeling of the PHD3 domain in HEK293T lysates, showcasing the feasibility of employing proximity-induced reactivity for covalent labeling of this challenging family of reader domains.

We describe the development of covalent cyclic peptide ligands which target a chromatin methylation reader domain using a proximity-reactive sulfonyl fluoride moiety.     

Flow goes forward and cells step backward: endothelial migration

Systemic and pulmonary circulations constitute a complex organ that serves multiple important biological functions. Consequently, any pathological processing affecting the vasculature can have profound systemic ramifications. Endothelial and smooth muscle are the two principal cell types composing blood vessels. Critically, endothelial proliferation and migration are central to the formation and expansion of the vasculature both during embryonic development and in adult tissues. Endothelial populations are quite heterogeneous and are both vasculature type- and organ-specific. There are profound molecular, functional, and phenotypic differences between arterial, venular and capillary endothelial cells and endothelial cells in different organs. Given this endothelial cell population diversity, it has been challenging to determine the origin of endothelial cells responsible for the angiogenic expansion of the vasculature. Recent technical advances, such as precise cell fate mapping, time-lapse imaging, genome editing, and single-cell RNA sequencing, have shed new light on the role of venous endothelial cells in angiogenesis under both normal and pathological conditions. Emerging data indicate that venous endothelial cells are unique in their ability to serve as the primary source of endothelial cellular mass during both developmental and pathological angiogenesis. Here, we review recent studies that have improved our understanding of angiogenesis and suggest an updated model of this process.Subject terms: Cell lineage, Chemotaxis     

An Integrated Mass Spectrometry-Based Glycomics-Driven Glycoproteomics Analytical Platform to Functionally Characterize Glycosylation Inhibitors

Cancer progression is linked to aberrant protein glycosylation due to the overexpression of several glycosylation enzymes. These enzymes are underexploited as potential anticancer drug targets and the development of rapid-screening methods and identification of glycosylation inhibitors are highly sought. An integrated bioinformatics and mass spectrometry-based glycomics-driven glycoproteomics analysis pipeline was performed to identify an N-glycan inhibitor against lung cancer cells. Combined network pharmacology and in silico screening approaches were used to identify a potential inhibitor, pictilisib, against several glycosylation-related proteins, such as Alpha1-6FucT, GlcNAcT-V, and Alpha2,6-ST-I. A glycomics assay of lung cancer cells treated with pictilisib showed a significant reduction in the fucosylation and sialylation of N-glycans, with an increase in high mannose-type glycans. Proteomics analysis and in vitro assays also showed significant upregulation of the proteins involved in apoptosis and cell adhesion, and the downregulation of proteins involved in cell cycle regulation, mRNA processing, and protein translation. Site-specific glycoproteomics analysis further showed that glycoproteins with reduced fucosylation and sialylation were involved in apoptosis, cell adhesion, DNA damage repair, and chemical response processes. To determine how the alterations in N-glycosylation impact glycoprotein dynamics, modeling of changes in glycan interactions of the ITGA5–ITGB1 (Integrin alpha 5-Integrin beta-1) complex revealed specific glycosites at the interface of these proteins that, when highly fucosylated and sialylated, such as in untreated A549 cells, form greater hydrogen bonding interactions compared to the high mannose-types in pictilisib-treated A549 cells. This study highlights the use of mass spectrometry to identify a potential glycosylation inhibitor and assessment of its impact on cell surface glycoprotein abundance and protein–protein interaction.     

Sensing the ortho Positions in C6Cl6 and C6H4Cl2 from Cl2− Formation upon Molecular Reduction

The geometrical effect of chlorine atom positions in polyatomic molecules after capturing a low-energy electron is shown to be a prevalent mechanism yielding Cl₂⁻. In this work, we investigated hexachlorobenzene reduction in electron transfer experiments to determine the role of chlorine atom positions around the aromatic ring, and compared our results with those using ortho-, meta- and para-dichlorobenzene molecules. This was achieved by combining gas-phase experiments to determine the reaction threshold by means of mass spectrometry together with quantum chemical calculations. We also observed that Cl₂⁻ formation can only occur in 1,2-C₆H₄Cl₂, where the two closest C–Cl bonds are cleaved while the chlorine atoms are brought together within the ring framework due to excess energy dissipation. These results show that a strong coupling between electronic and C–Cl bending motion is responsible for a positional isomeric effect, where molecular recognition is a determining factor in chlorine anion formation.     

Cationic molybdenum oxo alkylidenes stabilized by N-heterocyclic carbenes: from molecular systems to efficient supported metathesis catalysts

Cationic d⁰ group 6 olefin metathesis catalysts have been recently shown to display in most instances superior activity in comparison to their neutral congeners. Furthermore, their catalytic performance is greatly improved upon immobilization on silica. In this context, we have developed the new family of molecular cationic molybdenum oxo alkylidene complexes stabilized by N-heterocyclic carbenes of the general formula [Mo(O)(CHCMe₃)(IMes)(OR)[X⁻]] (IMes = 1,3-dimesitylimidazol-2-ylidene; R = 1,3-dimesityl-C₆H₃, C₆F₅; X⁻ = B(3,5-(CF₃)₂C₆H₃)₄⁻, B(Ar^F)₄, tetrakis(perfluoro-t-butoxy)aluminate (PFTA)). Immobilization of [Mo(O)(CHCMe₃)(IMes)(O-1,3-dimesityl-C₆H₃)⁺B(Ar^F)₄⁻] on silica via surface organometallic chemistry yields an active alkene metathesis catalyst that shows the highest productivity towards terminal olefins amongst all existing molybdenum oxo alkylidene catalysts.

The first cationic molybdenum oxo complexes were synthesized and immobilized on partially dehydroxylated silica. Vastly enhanced catalytic activity for terminal olefins was found compared to their neutral congeners.     

Pharmacomodulation of a ligand targeting the HBV capsid hydrophobic pocket

Hepatitis B virus (HBV) is a small enveloped retrotranscribing DNA virus and an important human pathogen. Its capsid-forming core protein (Cp) features a hydrophobic pocket proposed to be central notably in capsid envelopment. Indeed, mutations in and around this pocket can profoundly modulate, and even abolish, secretion of enveloped virions. We have recently shown that Triton X-100, a detergent used during Cp purification, binds to the hydrophobic pocket with micromolar affinity. We here performed pharmacomodulation of pocket binders through systematic modifications of the three distinct chemical moieties composing the Triton X-100 molecule. Using NMR and ITC, we found that the flat aromatic moiety is essential for binding, while the number of atoms of the aliphatic chain modulates binding affinity. The hydrophilic tail, in contrast, is highly tolerant to changes in both length and type. Our data provide essential information for designing a new class of HBV antivirals targeting capsid–envelope interactions.

Small-molecule binding to the Hepatitis B virus core protein hydrophobic pocket, a possible strategy for targeting viral particle assembly.     

A Method for Accurate Calculation ofB1Fields in Three Dimensions. Effects of Shield Geometry on Field Strength and Homogeneity in the Birdcage Coil

A method for calculatingB₁field strength and homogeneity as functions of radiofrequency shield geometry is presented. The method requires use of three-dimensional finite-element analysis, birdcage-coil theory, and antenna-array theory. Calculations were performed for a 12-element birdcage coil (19 cm diameter, 21 cm length) at 125 MHz. CalculatedB₁field strengths and homogeneities for the coil in 25 different shields and in no shield are given. For configurations where the shield is longer than the coil, bothB₁field strength and homogeneity decrease as shield diameter decreases or as shield length increases. In configurations where the shield is shorter than the coil and has a diameter of 25.6 cm,B₁homogeneity is greater than in an unshielded coil.B₁field strength was measured experimentally at 125 MHz in a birdcage coil of the same geometry as the model within shields of four different diameters. Calculated results very closely matched experimental measurement.