Synthesis of Unprecedented Sulfonylated Phosphono‐exo‐Glycals Designed as Inhibitors of the Three Mycobacterial Galactofuranose Processing Enzymes

This study reports a new methodology to synthesize exo‐glycals bearing both a sulfone and a phosphonate. This synthetic strategy provides a way to generate exo‐glycals displaying two electron‐withdrawing groups and was applied to eight different carbohydrates from the furanose and pyranose series. The Z/E configurations of these tetrasubstituted enol ethers could be ascertained using NMR spectroscopic techniques. Deprotection of an exo‐glycal followed by an UMP (uridine monophosphate) coupling generated two new UDP (uridine diphosphate)‐galactofuranose analogues. These two Z/E isomers were evaluated as inhibitors of UGM, GlfT1, and GlfT2, the three mycobacterial galactofuranose processing enzymes. Molecule 46‐(E) is the first characterized inhibitor of GlfT1 reported to date and was also found to efficiently inhibit UGM in a reversible manner. Interestingly, GlfT2 showed a better affinity for the (Z) isomer. The three enzymes studied in the present work are not only interesting because, mechanistically, they are still the topic of intense investigations, but also because they constitute very important targets for the development of novel antimycobacterial agents.     

Structural Distortion of the Epoxy Groups in Norbornanes: A Rotational Study of exo‐2,3‐Epoxynorbornane

Exo‐2,3‐epoxynorbornane is studied in the gas phase by pulsed jet Fourier transform microwave spectroscopy in the 4–18 GHz region. Six isotopologues were observed and characterized in their natural abundance. The experimental substitution and effective structures were obtained. Comparison with the structure of norbornane shows significant differences in several bond lengths and valence angles upon introduction of the epoxy group. All the work is supported by quantum chemical calculations.     

Synthesis and Characterization of 2‐Mono‐ and 1,2‐Diaminocarba‐closo‐dodecaborates M[1‐R‐2‐H2N‐closo‐CB11H10] (R=H,Ph, H2N,CyHN)

The first primary 2‐aminocarba‐closo‐dodecaborates [1‐R‐2‐H₂N‐closo‐CB₁₁H₁₀]^? (R=H ( 1 ), Ph ( 2 )) have been synthesized by insertion reactions of (Me₃Si)₂NBCl₂ into the trianions [7‐R‐7‐nido‐CB₁₀H₁₀]^3?. The difunctionalized species [1,2‐(H₂N)₂‐closo‐CB₁₁H₁₀] ( 3 ) and 1‐CyHN‐2‐H₃N‐closo‐CB₁₁H₁₀ (H‐ 4 ) have been prepared analogously from (Me₃Si)₂NBCl₂ and 7‐H₃N‐7‐nido‐CB₁₀H₁₂. In addition, the preparation of [Et₄N][1‐H₂N‐2‐Ph‐closo‐CB₁₁H₁₀] ([Et₄N]‐ 5 ) starting from PhBCl₂ and 7‐H₃N‐7‐nido‐CB₁₀H₁₂ is described. Methylation of the [1‐Ph‐2‐H₂N‐closo‐CB₁₁H₁₀]^? ion ( 2 ) to produce 1‐Ph‐2‐Me₃N‐closo‐CB₁₁H₁₀ ( 6 ) is reported. The crystal structures of [Et₄N]‐ 2 , [Et₄N]‐ 5 , and 6 were determined and the geometric parameters were compared to theoretical values derived from DFT and ab initio calculations. All new compounds were studied by NMR, IR, and Raman spectroscopy, MALDI mass spectrometry, and elemental analysis. The discussion of the experimental NMR chemical shifts and of selected vibrational band positions is supported by theoretical data. The thermal properties were investigated by differential scanning calorimetry (DSC). The pK_a values of 2‐H₃N‐closo‐CB₁₁H₁₁ (H‐ 1 ), 1‐H₃N‐closo‐CB₁₁H₁₀ (H‐ 7 ), and 1,2‐(H₃N)₂‐closo‐CB₁₁H₁₀ (H₂‐ 3 ) were determined by potentiometric titration and by NMR studies. The experimental results are compared to theoretical data (DFT and ab initio). The basicities of the aminocarba‐closo‐dodecaborates agree well with the spectroscopic and structural properties.     

HyperBIRD: A Sensitivity‐Enhanced Approach to Collecting Homonuclear‐Decoupled Proton NMR Spectra

Samples prepared following dissolution dynamic nuclear polarization (DNP) enable the detection of NMR spectra from low‐γ nuclei with outstanding sensitivity, yet have limited use for the enhancement of abundant species like ¹H nuclei. Small‐ and intermediate‐sized molecules, however, show strong heteronuclear cross‐relaxation effects: spontaneous processes with an inherent isotopic selectivity, whereby only the ¹³C‐bonded protons receive a polarization enhancement. These effects are here combined with a recently developed method that delivers homonuclear‐decoupled ¹H spectra in natural abundance samples based on heteronuclear couplings to these same, ¹³C‐bonded nuclei. This results in the HyperBIRD methodology; a single‐shot combination of these two effects that can simultaneously simplify and resolve complex, congested ¹H NMR spectra with many overlapping spin multiplets, while achieving 50–100 times sensitivity enhancements over conventional thermal counterparts.     

Stereoselective Fluorination Alters the Geometry of a Cyclic Peptide: Exploration of Backbone‐Fluorinated Analogues of Unguisin A

New methods for enhancing the efficiency of peptide cyclization, and for fine‐tuning the conformations of cyclic peptides, are valuable from a drug development perspective. Herein stereoselective fluorination is investigated as a new strategy for achieving these goals. Four vicinal difluorinated analogues of the natural cyclic heptapeptide unguisin A have been efficiently synthesized. The analogues are found to adopt dramatically different secondary structures, controlled by the fluorine stereochemistry.     

A Molecular Paddlewheel with a Sliding Organometallic Latch: Syntheses,X‐Ray Crystal Structures and Dynamic Behaviour of [Cr(CO)3{η6‐2‐(9‐triptycyl)indene}], and of [M(CO)3{η5‐2‐(9‐triptycyl)indenyl}] (M=Mn,Re)

Metal clamping in operation! Deprotonation of [η⁶‐2‐(9‐triptycyl)indene]tricarbonylchromium induces a haptotropic shift of the organometallic fragment from the six‐membered to the five‐membered ring, as in a→b . In the anion, rotation of the molecular paddlewheel is blocked by the bulky tripod. X‐ray crystal structures provide pictures of the system in both its “ON” and “OFF” states.

     

Solventless and Metal‐Free Synthesis of High‐Molecular‐Mass Polyaminoboranes from Diisopropylaminoborane and Primary Amines

The solventless reaction of diisopropylaminoborane with n‐butylamine, at room temperature, leads to a mixture of B_(sp2)H‐, B_(sp3)H₂‐, and B_(sp3)H₃‐containing species. At low temperature, the reaction outcome is completely modified, thus leading selectively to the formation of high‐mass polybutylaminoborane. When extended to a variety of primary amines, under solventless conditions and at low temperature, this reaction provides a new, efficient, and direct metal‐free access to high‐molecular‐mass polyaminoboranes in good to high yields under mild reaction conditions.     

Tetrafluorination of Sugars as Strategy for Enhancing Protein–Carbohydrate Affinity: Application to UDP‐Galp Mutase Inhibition

Tetrafluorinated analogues of both UDP‐galactopyranose and UDP‐galactofuranose have been synthesized and assayed against UDP‐galactopyranose mutase, a key enzyme for Mycobacterium tuberculosis cell wall biosynthesis. Competition assays and STD‐NMR spectroscopy techniques have evidenced not only the first unambiguous case of affinity enhancement through local sugar polyfluorination, but also showed that tetrafluorination can still have a beneficial effect on binding when monofluorination at the same position does not.     

NMR Structure of a Triangulenium‐Based Long‐Lived Fluorescence Probe Bound to a G‐Quadruplex

An NMR structural study of the interaction between a small‐molecule optical probe (DAOTA‐M2) and a G‐quadruplex from the promoter region of the c‐myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR‐restrained structural calculations show that binding of DAOTA‐M2 occurs mainly through π–π stacking between the polyaromatic core of the ligand and guanine residues of the outer G‐quartets. Interestingly, the binding affinities of DAOTA‐M2 differ by a factor of two for the outer G‐quartets of the unimolecular parallel G‐quadruplex under study. Unrestrained MD calculations indicate that DAOTA‐M2 displays significant dynamic behavior when stacked on a G‐quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G‐quadruplexes.     

Scalar Coupling Constants—Their Analysis and Their Application for the Elucidation of Structures

Since their discovery in the early fifties, scalar/coupling constants have been of great interest to the NMR spectroscopist. Their impact on structure determination by NMR spectroscopy is founded on the fact that the size of the coupling constant is directly related to molecular conformation. Today, for most chemical substances the parameters for the Karplus relationship, which relates the vicinial (3-bond) coupling constant to the dihedral angle, have been determined. In addition to proton–proton distances, the application of coupling constants in modern conformational analysis is indispensable. In the study of larger molecules which are of current interest, more and more involved experiments are necessary in order to overcome signal overlap and increasing line widths. A large number of experimental techniques for the determination of coupling constants has been developed; however, for this reason the choice of the most appropriate experiment to use has become more difficult. This decision must be made carefully to maximize instrument usage and obtain the largest number of couplings with the greatest accuracy possible. Many of the computer programs used in structure calculations can directly apply coupling constant restraints, similar to proton–proton distances developed from NOEs. Therefore, not only is the quality of the structure improved, but the molecular motions (internal dynamics) are better described. In this article, we review the techniques that exist today with particular attention paid to helping the non-expert to choose the appropriate experiment for the problem at hand. In addition, the use of coupling constants in computer simulations are discussed.     

Characterization of the Core Oligosaccharide and the O‐Antigen Biological Repeating Unit from Halomonas stevensii Lipopolysaccharide: The First Case of O‐Antigen Linked to the Inner Core

A novel core structure among bacterial lipopolysaccharides (LPS) that belong to the genus Halomonas has been characterized. H. stevensii is a moderately halophilic microorganism, as are the majority of the Halomonadaceae. It brought to light the pathogenic potential of this genus. On account of their role in immune system elicitation, elucidation of LPS structure is the mandatory starting point for a deeper understanding of the interaction mechanisms between host and pathogen. In this paper we report the structure of the complete saccharidic portion of the LPS from H. stevensii. In contrast to the finding that the O‐antigen is usually covalently linked to the outer core oligosaccharide, we could demonstrate that the O‐polysaccharide of H. stevensii is linked to the inner core of an LPS. By means of high‐performance anion‐exchange chromatography with pulsed amperometric detection we were able to isolate the core decasaccharide as well as a tridecasaccharide constituted by the core region plus one O‐repeating unit after alkaline degradation of the LPS. The structure was elucidated by one‐ and two‐dimensional NMR spectroscopy, ESI Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometry, and chemical analysis.     

A Designed Three‐Stranded β‐Sheet in an α/β Hybrid Peptide

The incorporation of β‐amino acid residues into the antiparallel β‐strand segments of a multi‐stranded β‐sheet peptide is demonstrated for a 19‐residue peptide, Boc‐LV^βFV^DPGL^βFVVL^DPGLVL^βFVV‐OMe (BBH19). Two centrally positioned ^DPro–Gly segments facilitate formation of a stable three‐stranded β‐sheet, in which β‐phenylalanine (^βPhe) residues occur at facing positions 3, 8 and 17. Structure determination in methanol solution is accomplished by using NMR‐derived restraints obtained from NOEs, temperature dependence of amide NH chemical shifts, rates of H/D exchange of amide protons and vicinal coupling constants. The data are consistent with a conformationally well‐defined three‐stranded β‐sheet structure in solution. Cross‐strand interactions between ^βPhe3/^βPhe17 and ^βPhe3/Val15 residues define orientations of these side‐chains. The observation of close contact distances between the side‐chains on the N‐ and C‐terminal strands of the three‐stranded β‐sheet provides strong support for the designed structure. Evidence is presented for multiple side‐chain conformations from an analysis of NOE data. An unusual observation of the disappearance of the Gly NH resonances upon prolonged storage in methanol is rationalised on the basis of a slow aggregation step, resulting in stacking of three‐stranded β‐sheet structures, which in turn influences the conformational interconversion between type I′ and type II′ β‐turns at the two ^DPro–Gly segments. Experimental evidence for these processes is presented. The decapeptide fragment Boc‐LV^βFV^DPGL^βFVV‐OMe (BBH10), which has been previously characterized as a type I′ β‐turn nucleated hairpin, is shown to favour a type II′ β‐turn conformation in solution, supporting the occurrence of conformational interconversion at the turn segments in these hairpin and sheet structures.     

1H NMR‐Guided Isolation of Formyl‐Phloroglucinol Meroterpenoids from the Leaves of Eucalyptus robusta

Nine formyl‐phloroglucinolmeroterpenoids (FPMs), namely, eucalrobusones A–I ( 1 – 9 ), were isolated from the leaves of Eucalyptus robusta by tracking the phenolic hydroxyl ¹H NMR peaks. The Snatzke helicity rules for the Cotton effects of twisted benzene rings were applied to elucidate the absolute configurations of the FPMs. These findings, along with NMR spectroscopy, the circular dichroism (CD) exciton chirality method, and CD calculations, allowed complete structures for the FPMs to be assigned. Eucalrobusones A–F ( 1 – 6 ) are novel adducts formed between a formyl‐derived carbon atom on the phloroglucinol ring and monoterpene and sesquiterpene components. Eucalrobusones G–I ( 7 – 9 ) are the first examples of FPMs with cubebane part structures connected by an unusual 1‐oxaspiro[5.5]undecane subunit. Among these isolates, eucalrobusone C ( 3 ) showed significant cytotoxicity against HepG2, MCF‐7, and U2OS cancer cell lines, with IC₅₀ values less than 10 μm . Compound 3 significantly blocks cell proliferation in MCF‐7 cells and induces MCF‐7 cell death through apoptosis.     

Dendrimer‐Type Peptoid‐Decorated Hexaphenylxylenes and Tetraphenylmethanes: Synthesis and Structure in Solution and in the Gas Phase

Branched organic nanostructures are useful scaffolds that find multiple applications in a variety of fields. Here, we present a novel approach to dendrimer‐like structures. Our design contains a rigid hydrocarbon‐based core (hexaphenylxylylene/tetraethynylphenylmethane) combined with a library of N‐substituted oligoglycines (so‐called peptoids) providing a flexible shell. The use of click chemistry allows rapid assembly of the nanostructures. The possibility of tuning the size and the solubility of this new type of nanostructure will be advantageous for future applications such as heterogeneous catalysis.     

Enhancing NMR Sensitivity of Natural‐Abundance Low‐γ Nuclei by Ultrafast Magic‐Angle‐Spinning Solid‐State NMR Spectroscopy

Although magic‐angle‐spinning (MAS) solid‐state NMR spectroscopy has been able to provide piercing atomic‐level insights into the structure and dynamics of various solids, the poor sensitivity has limited its widespread application, especially when the sample amount is limited. Herein, we demonstrate the feasibility of acquiring high S/N ratio natural‐abundance ¹³C NMR spectrum of a small amount of sample (≈2.0 mg) by using multiple‐contact cross polarization (MCP) under ultrafast MAS. As shown by our data from pharmaceutical compounds, the signal enhancement achieved depends on the number of CP contacts employed within a single scan, which depends on the T_1ρ of protons. The use of MCP for fast 2D ¹H/¹³C heteronuclear correlation experiments is also demonstrated. The significant signal enhancement can be greatly beneficial for the atomic‐resolution characterization of many types of crystalline solids including polymorphic drugs and nanomaterials.     

Atomic‐Resolution Three‐Dimensional Structure of Amyloid β Fibrils Bearing the Osaka Mutation

Despite its central importance for understanding the molecular basis of Alzheimer's disease (AD), high‐resolution structural information on amyloid β‐peptide (Aβ) fibrils, which are intimately linked with AD, is scarce. We report an atomic‐resolution fibril structure of the Aβ1‐40 peptide with the Osaka mutation (E22Δ), associated with early‐onset AD. The structure, which differs substantially from all previously proposed models, is based on a large number of unambiguous intra‐ and intermolecular solid‐state NMR distance restraints.     

Structure and Metabolic‐Flow Analysis of Molecular Complexity in a 13C‐Labeled Tree by 2D and 3D NMR

Improved signal identification for biological small molecules (BSMs) in a mixture was demonstrated by using multidimensional NMR on samples from ¹³C‐enriched Rhododendron japonicum (59.5 atom%) cultivated in air containing ¹³C‐labeled carbon dioxide for 14 weeks. The resonance assignment of 386 carbon atoms and 380 hydrogen atoms in the mixture was achieved. 42 BSMs, including eight that were unlisted in the spectral databases, were identified. Comparisons between the experimental values and the ¹³C chemical shift values calculated by density functional theory supported the identifications of unlisted BSMs. Tracing the ¹³C/¹²C ratio by multidimensional NMR spectra revealed faster and slower turnover ratios of BSMs involved in central metabolism and those categorized as secondary metabolites, respectively. The identification of BSMs and subsequent flow analysis provided insight into the metabolic systems of the plant.