Effect of N-o-nitrobenzylation on conformation and membrane permeability of linear peptides

In this study, we explored the potential of the photoremovable o-nitrobenzyl (oNB) group as a tool to manipulate the membrane permeability and regulate the conformation of linear peptides by means of experimental and computational studies. We found that the introduction of one or more oNB groups markedly increased the permeability and altered the conformation, as compared to the corresponding unmodified peptides. We thoroughly investigated the impact of peptide length, number of oNB group, oNB insertion position, and introduction of N- and C-terminal protecting groups on the passive membrane permeability by means of parallel artificial membrane permeability assay (PAMPA). Photoreaction of peptides containing one or two oNB groups proceeded cleanly in moderate to high yields, releasing the unprotected parent linear peptide. The oNB-modified peptides showed a cis/trans conformational equilibrium, while after photolysis, the unprotected linear peptides showed only the trans-amide conformation. Furthermore, a comprehensive comparison of oNB-modified peptides and N-methylated peptides was conducted, encompassing conformational analysis and physicochemical properties. N-Substituted peptides favored a folded-like structure, which may contribute to the improvement in permeability.

Stabilization of sp-Hybridized Nitrogen Cation by Lewis Acid-Base Complex Formation with Intramolecular Iodine

Here we show that the sp-hybridized nitrogen cation is strongly stabilized by a peri-iodine substituent in the tetralone system. The cation is captured by anionic species such as CF3 CO2 - , affording hypervalent iodine(III) compounds with a short nitrogen-iodine (N-I) bond, in which the cation serves as a Lewis acid. Notably, the O-I bond of the O-trifluoroacetate or O-acetate is intrinsically weaker than the N-I bond due to its more ionic character and is further weakened by protonation in trifluoroacetic acid. As a result, the oxygen ligand can dissociate in the presence of a Brønsted acid, affording a I+ cation intermediate that retains the N-I bond. We isolated the cation as the tetrafluoroborate, and characterized it experimentally by 1 H NMR spectroscopy and X-ray structure analysis, and theoretically by means of DFT calculation. The results suggest that the N-I bonded cation is intrinsically stable, and is weakly coordinated with water and the BF4 counter anion or trifluoroacetate anion. This cation can be employed as a reagent for α-oxidation of ketones.

Influence of CoFeB layer thickness on elastic parameters in CoFeB/MgO heterostructures

The surface acoustic waves, i.e., surface phonons may have huge potential for future spintronic devices, if coupled to other waves (e.g., spin waves) or quasiparticles. In order to understand the coupling of acoustic phonons with the spin degree of freedom, especially in magnetic thin film-based heterostructures, one needs to investigate the properties of phonons in those heterostructures. This also allows us to determine the elastic properties of individual magnetic layers and the effective elastic parameters of the whole stacks. Here, we study frequency versus wavevector dispersion of thermally excited SAWs in CoFeB/MgO heterostructures with varying CoFeB thickness by employing Brillouin light spectroscopy. The experimental results are corroborated by finite element method-based simulations. From the best agreement of simulation results with the experiments, we find out the elastic tensor parameters for CoFeB layer. Additionally, we estimate the effective elastic parameters (elastic tensors, Young's modulus, Poisson's ratio) of the whole stacks for varying CoFeB thickness. Interestingly, the simulation results, either considering elastic parameters of individual layers or considering effective elastic parameters of whole stacks, show good agreement with the experimental results. These extracted elastic parameters will be very useful to understand the interaction of phonons with other quasiparticles.

Isolation and Reactions of Imidoyl Fluorides Generated from Oxime Using the Diethylaminosulfur Trifluoride/Tetrahydrofuran (DAST-THF) System

Fluorination of oximes with the relatively mild diethylaminosulfur trifluoride/tetrahydrofuran (DAST-THF) system affords imidoyl fluorides. These compounds were isolated, and their structures were confirmed by X-ray single-crystal structure analysis. Reaction of imidoyl fluorides with various nucleophiles efficiently afforded amides, amidines, thioamides, and amine derivatives in high yields. Furthermore, one-pot reaction of in situ generated imidoyl fluorides from oximes was also applicable to efficient synthesis of these products. The oxime stereochemistry and acid-labile protecting group remained intact in this system.

Exploration of LPS2 agonist binding modes using the combination of a new hydrophobic scaffold and homology modeling

Lysophosphatidylserine (LysoPS) is an endogenous pan-agonist of three G-protein coupled receptors (GPCRs): LPS₁/GPR34, LPS₂/P2Y₁₀, and LPS₃/GPR174, and we previously reported a series of LysoPS-based agonists of these receptors. Interestingly, we found that LPS₁ agonist activity was very sensitive to structural change at the hydrophobic fatty acid moiety, whereas LPS₂ agonist activity was not. Here, to probe the molecular basis of LPS₂ agonist binding, we developed a new class of hydrophobic fatty acid surrogates having a biphenyl-ether scaffold. The LPS₂ agonist activity of these compounds proved sensitive to molecular modification of the hydrophobic skeleton. Thus, we next constructed an LPS₂ model by homology modeling and docking/molecular dynamics (MD) simulation, and validated it by means of SAR studies together with point mutations of selected receptor amino-acid residues. The putative ligand-binding site of LPS₂ is Γ-shaped, with a hydrophilic site horizontally embedded in the receptor transmembrane helix bundles and a perpendicular hydrophobic groove adjoining transmembrane domains 4 and 5 that is open to the membrane bilayer. The binding poses of LPS₂ agonists to this site are consistent with easy incorporation of various kinds of fatty acid surrogates. Structural development based on this model afforded a series of potent and selective LPS₂ full agonists, which showed enhanced in vitro actin stress fiber formation effect.

Isosteric Replacement of Ester Linkage of Lysophospholipids with Heteroaromatic Rings Retains Potency and Subtype Selectivity

Our group has reported various derivatives of lysophosphatidylserine (LysoPS) as potent and subtype-selective agonists for G-protein-coupled receptors (GPCRs). However, the ester linkage between the glycerol moiety and fatty acid or fatty acid surrogate is present in all of them. In order to develop these LysoPS analogs as drug candidates, appropriate pharmacokinetic consideration is essential. Here, we found that the ester bond of LysoPS is highly susceptible to metabolic degradation in mouse blood. Accordingly, we examined isosteric replacement of the ester linkage with heteroaromatic rings. The resulting compounds showed excellent retention of potency and receptor subtype selectivity, as well as increased metabolic stability in vitro.

Friedel-Crafts Acylation of Aminocarboxylic Acids in Strong Brønsted Acid Promoted by Lewis Base P4O10

The amino group in aminocarboxylic acids is sufficiently basic to be protonated in strong acids, and consequently, ionization of the carboxylic acid to an acylium ion is blocked due to charge-charge repulsion. Thus, acylation of aromatic compounds is significantly retarded in Friedel-Craft type reactions. We found that Friedel-Crafts acylation with aminocarboxylic acids can proceed smoothly even in a strong Brønsted acid (triflic acid, TfOH) if the Lewis base P₄O₁₀ is added. Here we describe the Friedel-Crafts acylation reactions of anthranilic acid and α- to δ-aminocarboxylic acids with benzene derivatives in the presence of P₄O₁₀. Non-amino-containing carboxylic acids as well as N-containing heteroaromatic carboxylic acids are available, and α-amino acids can be directly utilized without any protective group. Most substrates afford acylation products in high yields, although some epimerization/racemization may occur. Density functional theory (DFT) calculations suggested that P₄O₁₀ neutralizes the protonated amine, converting the N-H covalent bond to a N-hydrogen bond and allowing the carboxylic acid OH functionality to serve as a good leaving group.

Neighboring Group Participation of Nitrogen Cation to Form an Unusual Six-Membered Ring Intermediate During Oxime Rearrangement

Neighboring group participation involving a 6-membered ring structure is rare, despite the privilege of 6-membered ring transition structures in organic chemistry. We examined the putative role of a 6-membered cyclic intermediate with neighboring group participation of nitrogen cation in syn-migration of peri-ester indanone oximes. Direct observation of a peri-methyl ester-iminylium intermediate in solution by means of ¹H NMR supported the existence of the 6-membered cation intermediate. Density functional theory (DFT) calculations also supported the intervention of this intermediate in the rearrangement and indicated that it has a planar structure stabilized by electron delocalization.

Unexpectedly rigid short peptide foldamers in which NH-π and CH-π interactions are preserved in solution

NH-π and CH-π interactions, due to their weak character, are not easily identified in solution. We report a group of isolable short peptides with stable folds, in which NH-π and CH-π main chain-side chain interactions can be detected in solution by means of NMR and ATR-IR spectroscopy.

The 2021 Magnonics Roadmap

Magnonics is a budding research field in nanomagnetism and nanoscience that addresses the use of spin waves (magnons) to transmit, store, and process information. The rapid advancements of this field during last one decade in terms of upsurge in research papers, review articles, citations, proposals of devices as well as introduction of new sub-topics prompted us to present the first roadmap on magnonics. This is a collection of 22 sections written by leading experts in this field who review and discuss the current status besides presenting their vision of future perspectives. Today, the principal challenges in applied magnonics are the excitation of sub-100 nm wavelength magnons, their manipulation on the nanoscale and the creation of sub-micrometre devices using low-Gilbert damping magnetic materials and its interconnections to standard electronics. To this end, magnonics offers lower energy consumption, easier integrability and compatibility with CMOS structure, reprogrammability, shorter wavelength, smaller device features, anisotropic properties, negative group velocity, non-reciprocity and efficient tunability by various external stimuli to name a few. Hence, despite being a young research field, magnonics has come a long way since its early inception. This roadmap asserts a milestone for future emerging research directions in magnonics, and hopefully, it will inspire a series of exciting new articles on the same topic in the coming years.

Switching Lysophosphatidylserine G Protein-Coupled Receptor Agonists to Antagonists by Acylation of the Hydrophilic Serine Amine

Three human G protein-coupled receptors (GPCRs)-GPR34/LPS₁, P2Y10/LPS₂, and GPR174/LPS₃-are activated specifically by lysophosphatidylserine (LysoPS), an endogenous hydrolysis product of a cell membrane component, phosphatidylserine (PS). LysoPS consists of l-serine, glycerol, and fatty acid moieties connected by phosphodiester and ester linkages. We previously generated potent and selective GPCR agonists by modification of the three modules and the ester linkage. Here, we show that a novel modification of the hydrophilic serine moiety, that is, N-acylations of the serine amine, converted a GPR174 agonist to potent GPR174 antagonists. Structural exploration of the amide functionality provided access to a range of activities from agonist to partial agonist to antagonist. The present study would provide a new strategy for the development of lysophospholipid receptor antagonists.

Contribution of Solvents to Geometrical Preference in the Z/E Equilibrium of N-Phenylthioacetamide

We studied the Z/E preference of N-phenylthioacetamide (thioacetanilide) derivatives in various solvents by means of ¹H NMR spectroscopy, as well as molecular dynamics (MD) and other computational analyses. Our experimental results indicate that the Z/E isomer preference of secondary (NH)thioamides of N-phenylthioacetamides shows substantial solvent dependency, whereas the corresponding amides do not show solvent dependency of the Z/E isomer ratios. Detailed study of the solvent effects based on molecular dynamics simulations revealed that there are two main modes of hydrogen (H)-bond formation between solvent and (NH)thioacetamide, which influence the Z/E isomer preference of (NH)thioamides. DFT calculations of NH-thioamide in the presence of one or two explicit solvent molecules in the continuum solvent model can effectively mimic the solvation by multiple solvent molecules surrounding the thioamide in MD simulations and shed light on the precise nature of the interactions between thioamide and solvent. Orbital interaction analysis showed that, counterintuitively, the Z/E preference of NH-thioacetamides is mainly determined by steric repulsion, while that of sterically congested N-methylthioacetamides is mainly determined by thioamide conjugation.

Capsanthin Production in Escherichia coli by Overexpression of Capsanthin/Capsorubin Synthase from Capsicum annuum

Capsanthin, a characteristic red carotenoid found in the fruits of red pepper (Capsicum annuum), is widely consumed as a food and a functional coloring additive. An enzyme catalyzing capsanthin synthesis was identified as capsanthin/capsorubin synthase (CCS) in the 1990s, but no microbial production of capsanthin has been reported. We report here the first successful attempt to biosynthesize capsanthin in Escherichia coli by carotenoid-pathway engineering. Our initial attempt to coexpress eight enzyme genes required for capsanthin biosynthesis did not detect the desired product. The dual activity of CCS as a lycopene β-cyclase as well as a capsanthin/capsorubin synthase likely complicated the task. We demonstrated that a particularly high expression level of the CCS gene and the minimization of byproducts by regulating the seven upstream carotenogenic genes were crucial for capsanthin formation in E. coli. Our results provide a platform for further study of CCS activity and capsanthin production in microorganisms.

Elaboration of Non-naturally Occurring Helical Tripeptides as p53-MDM2/MDMX Interaction Inhibitors

Protein-protein interactions (PPIs) are often mediated by helical, strand and/or coil secondary structures at the interface regions. We previously showed that non-naturally occurring, stable helical trimers of bicyclic β-amino acids (Abh) with all-trans amide bonds can block the p53-MDM2/MDMX α-helix-helix interaction, which plays a role in regulating p53 function. Here, we conducted docking and molecular dynamics calculations to guide the structural optimization of our reported compounds, focusing on modifications of the C-terminal/N-terminal residues. We confirmed that the modified peptides directly bind to MDM2 by means of thermal shift assay, isothermal titration calorimetry, and enzyme-linked immunosorbent assay (ELISA) experiments. Biological activity assay in human osteosarcoma cell line SJSA-1, which has wild-type p53 and amplification of the Mdm2 gene, indicated that these peptides are membrane-permeable p53-MDM2/MDMX interaction antagonists that can rescue p53 function in the cells.

Non-naturally Occurring Regio Isomer of Lysophosphatidylserine Exhibits Potent Agonistic Activity toward G Protein-Coupled Receptors

Lysophosphatidylserine (LysoPS), an endogenous ligand of G protein-coupled receptors, consists of l-serine, glycerol, and fatty acid moieties connected by phosphodiester and ester linkages, respectively. An ester linkage of phosphatidylserine can be hydrolyzed at the 1-position or at the 2-position to give 2-acyl lysophospholipid or 1-acyl lysophospholipid, respectively. 2-Acyl lysophospholipid is in nonenzymatic equilibrium with 1-acyl lysophospholipid in vivo. On the other hand, 3-acyl lysophospholipid is not found, at least in mammals, raising the question of whether the reason for this might be that the 3-acyl isomer lacks the biological activities of the other isomers. Here, to test this idea, we designed and synthesized a series of new 3-acyl lysophospholipids. Structure-activity relationship studies of more than 100 "glycol surrogate" derivatives led to the identification of potent and selective agonists for LysoPS receptors GPR34 and P2Y10. Thus, the non-natural 3-acyl compounds are indeed active and appear to be biologically orthogonal with respect to the physiologically relevant 1- and 2-acyl lysophospholipids.

Conformational preference of bicyclic β-amino acid dipeptides

Bridged bicyclic amino acids have high potential applicability as self-organized, conformationally constrained synthetic building blocks that do not require assistance from hydrogen bond formation. We systematically investigated the intrinsic conformational propensities of dipeptides of bridged bicyclic β-amino acids by means of accelerated molecular dynamics simulation and density functional theory (DFT) calculations in methanol, chloroform, and water. While the main-chain conformation, represented by φ and θ values, is fixed by the nature of the bicyclic ring structure, rotation of the C-terminal carbonyl group (ψ) is also restricted, converging to one or two minima. In endo-type dipeptides, in which the two N- and C-terminal amides are spatially close to each other, the C-terminal amide plane is placed horizontally. In exo-type dipeptides, in which the two amides are on opposite sides of the ring plane, the C-terminal carbonyl group can take two types of positions: either parallel/antiparallel with the N-terminal carbonyl or beneath the bicyclic ring, forcing the amide NHMe moiety to lie outside of the ring. We also examined the cis-trans preference of model bicyclic amides. Although the parent amides exhibit cis-trans equilibrium without any preference, addition of a methyl group on one of the bridgehead positions tips the equilibrium towards trans.

Membrane Phospholipid Analogues as Molecular Rulers to Probe the Position of the Hydrophobic Contact Point of Lysophospholipid Ligands on the Surface of G-Protein-Coupled Receptor during Membrane Approach

When lipid mediators bind to G-protein-coupled receptors (GPCRs), the ligand first enters the lipid bilayer, then diffuses laterally in the cell membrane to make hydrophobic contact with the receptor protein, and finally enters the receptor's binding pocket. In this process, the location of the hydrophobic contact point on the surface of the receptor has been little discussed even in cases in which the crystal structure has been determined, because the ligand binding pocket is buried inside the transmembrane (TM) domains. Here, we coupled an activator ligand to a series of membrane phospholipid surrogates, which constrain the depth of entry of the ligand into the lipid bilayer. Consequently, via measurement of the receptor-activating activity as a function of the depth of entry into the membrane, these surrogates can be used as molecular rulers to estimate the location of the hydrophobic contact point on the surface of GPCR. We focused on lysophosphatidylserine (LysoPS) receptor GPR34 and prepared a series of simplified membrane-lipid-surrogate-conjugated lysophospholipid analogues by attaching alkoxy amine chains of varying lengths to the hydrophobic tail of a potent GPR34 agonist. As expected, the activity of these lipid-conjugated LysoPS analogues was dependent on chain length. The predicted contact position matches the position of the terminal benzene ring of a nonlipidic ligand that protrudes between TMs 4 and 5 of the receptor. We further found that the nature of the terminal hydrophilic functional group of the conjugated membrane lipid surrogate strongly influences the activity, suggesting that lateral hydrophilic contact of LysoPS analogues with the receptor's surface is also crucial for ligand-GPCR binding.

Peptide-based short single β-strand mimics without hydrogen bonding or aggregation

Generation of short peptides with a single β-strand structure in solution is difficult. Herein, we design a new class of single β-strand peptidic mimics that are stable without self-aggregation in protic and non-protic solvents. Introduction of one present β-strand mimic can induce and propagate the β-strand structure for at least a penta-peptide sequence.

Propagation dynamics of spin excitations along skyrmion strings

Magnetic skyrmions, topological solitons characterized by a two-dimensional swirling spin texture, have recently attracted attention as stable particle-like objects. In a three-dimensional system, a skyrmion can extend in the third dimension forming a robust and flexible string structure, whose unique topology and symmetry are anticipated to host nontrivial functional responses. Here we experimentally demonstrate the coherent propagation of spin excitations along skyrmion strings for the chiral-lattice magnet Cu₂OSeO₃. We find that this propagation is directionally non-reciprocal and the degree of non-reciprocity, as well as group velocity and decay length, are strongly dependent on the character of the excitation modes. These spin excitations can propagate over a distance exceeding 50 μm, demonstrating the excellent long-range ordered nature of the skyrmion-string structure. Our combined experimental and theoretical analyses offer a comprehensive account of the propagation dynamics of skyrmion-string excitations and suggest the possibility of unidirectional information transfer along such topologically protected strings.

Realization of Spin-dependent Functionality by Covering a Metal Surface with a Single Layer of Molecules

An interface of molecule and metal has attracted much attention in the research field of nanoelectronics because of their high degree of design freedom. Here, we demonstrate an efficient spin-to-charge current conversion at the metal surface covered by a single layer of molecules. Spin currents are injected into an interface between metal (Cu) and lead(II) phthalocyanine by means of the spin pumping method. An observed voltage signal is caused by the inverse Edelstein effect, i.e., spin-to-charge current conversion at the interface. The conversion coefficient, inverse Edelstein length, is estimated to be 0.40 ± 0.06 nm, comparable with the largest Rashba spin splitting of interfaces with heavy metals. Interestingly, the Edelstein length strongly depends on the thickness of the molecule and takes a maximum value when a single layer of molecules is formed on the Cu surface. Comparative analysis between scanning probe microscopy and first-principles calculations reveal that the formation of interface state with Rashba spin splitting causes the inverse Edelstein effect, whose magnitude is sensitive to the adsorption configuration of the molecules.

Non-naturally Occurring Helical Molecules Can Interfere with p53-MDM2 and p53-MDMX Protein-Protein Interactions

We have discovered that β-amino acid homooligomers with cis- or trans-amide conformation can fold themselves into highly ordered helices. Moreover, unlike α-amino acid peptides, which are significantly stabilized by intramolecular hydrogen bonding, these helical structures are autogenous conformations that are stable without the aid of hydrogen bonding and irrespective of solvent (protic/aprotic/halogenated) or temperature. A structural overlap comparison of helical cis/trans bicyclic β-proline homooligomers with typical α-helix structure of α-amino acid peptides reveals clear differences of pitch and diameter per turn. Bridgehead substituents of the present homooligomers point outwards from the helical surface. We were interested to know whether such non-naturally occurring divergent helical molecules could mimic α-helix structures. In this study, we show that bicyclic β-proline oligomer derivatives inhibit p53-MDM2 and p53-MDMX protein-protein interactions, exhibiting MDM2-antagonistic and MDMX-antagonistic activities.

Overall Shape Constraint of Alternating α/β-Hybrid Peptides Containing Bicyclic β-Proline

Our NMR, IR/Raman, CD spectroscopic, and X-ray crystallographic studies, as well as accelerated molecular dynamics simulations, showed that alternating hybrid α/β-peptides containing a bicyclic β-proline surrogate form unique extended curved folds, regardless of the peptide length and solvent environment. It is suggested that extended β/PPII structures are preferred in the insulating α-alanine moieties between the rigid bicyclic β-proline structures. These hybrid peptides inhibit p53-MDM2 and p53-MDMX protein-protein interactions.

Uncovering the Networks of Topological Neighborhoods in β-Strand and Amyloid β-Sheet Structures

Although multiple hydrophobic, aromatic π–π, and electrostatic interactions are proposed to be involved in amyloid fibril formation, the precise interactions within amyloid structures remain poorly understood. Here, we carried out detailed quantum theory of atoms-in-molecules (QTAIM) analysis to examine the hydrophobic core of amyloid parallel and antiparallel β-sheet structures, and found the presence of multiple inter-strand and intra-strand topological neighborhoods, represented by networks of through-space bond paths. Similar bond paths from side chain to side chain and from side chain to main chain were found in a single β-strand and in di- and tripeptides. Some of these bond-path networks were enhanced upon β-sheet formation. Overall, our results indicate that the cumulative network of weak interactions, including various types of hydrogen bonding (X-H—Y; X, Y = H, C, O, N, S), as well as non-H-non-H bond paths, is characteristic of amyloid β-sheet structure. The present study postulated that the presence of multiple through-space bond-paths, which are local and directional, can coincide with the attractive proximity effect in forming peptide assemblies. This is consistent with a new view of the van der Waals (vdW) interactions, one of the origins of hydrophobic interaction, which is updating to be a directional intermolecular force.

Nosocomial Mycobacterium tuberculosis transmission by brief casual contact identified using comparative genomics

This paper reports a case of nosocomial transmission of Mycobacterium tuberculosis by brief casual contact. Routine variable number tandem repeat typing in Yamagata Prefecture, Japan found that M. tuberculosis clinical isolates from two patients showed indistinguishable genotypes. The patients had an epidemiological relationship of sharing a waiting room in a hospital on the same day. As comparative genomics detected only two single nucleotide variants between the isolates, it was concluded that recent tuberculosis transmission occurred in the waiting room. These results indicate that the physical separation of infectious tuberculosis patients is an essential control measure for preventing unpredictable nosocomial transmission by casual contact.

A simple and effective preparation of quercetin pentamethyl ether from quercetin

Among the five hydroxy (OH) groups of quercetin (3,5,7,3',4'-pentahydroxyflavone), the OH group at 5 position is the most resistant to methylation due to its strong intramolecular hydrogen bonding with the carbonyl group at 4 position. Thus, it is generally difficult to synthesize the pentamethyl ether efficiently by conventional methylation. Here, we describe a simple and effective per-O-methylation of quercetin with dimethyl sulfate in potassium (or sodium) hydroxide/dimethyl sulfoxide at room temperature for about 2 hours, affording quercetin pentamethyl ether (QPE) quantitatively as a single product. When methyl iodide was used in place of dimethyl sulfate, the C-methylation product 6-methylquercetin pentamethyl ether was also formed. A computational study provided a rationale for the experimental results.

Elucidation of the E-Amide Preference of N-Acyl Azoles

The conformational properties of N-acyl azoles (imidazole, pyrazole, and triazole) were examined. The N-2',4',6'-trichlorobenzoyl azoles were stable in methanol at room temperature, and no hydrolyzed products were observed over 7 days in the presence of 5% trifluoroacetic acid or 5% triethylamine in CDCl₃. The high stability may be explained by the double-bond amide character caused by the steric hindrance due to the ortho-substituents in the benzoyl group. While specific E-amide preferences were observed in N-acyl pyrazoles/triazoles, the amides of the imidazoles gave a mixture of E and Z. One of the conceivable ideas to rationalize this conformational preference may be repulsive interaction between two sets of lone-pair electrons on the pyrazole 2-nitrogen (n_N) and the carbonyl oxygen atoms (n_O) in the Z-conformation of N-acyl pyrazoles/triazoles. However, analysis of orbital interactions suggested that in the case of the E-conformation of N-acyl pyrazoles, such electron repulsion is small because of distance. The interbond energy calculations suggested that the Z-conformer is involved in strong vicinal σ-σ repulsion along the amide linkage between the σ_N1N2 and σ_C1C2 orbitals in the anti-periplanar arrangement and between the σ_N1C5 and σ_C1C2 orbitals in the syn-periplanar arrangement, which lead to the overwhelming E-preference in N-acyl pyrazoles/triazoles. In the case of N-acyl imidazoles, similar vicinal σ-σ repulsions were counterbalanced, leading to a weak preference for the E-conformer over the Z-conformer. The chemically stable and E-preferring N-acyl azoles may be utilized as scaffolds in future drug design.

Revisiting secondary interactions in neighboring group participation, exemplified by reactivity changes of iminylium intermediates

Neighboring group participation is defined as the action of a substituent to stabilize a transition state or an intermediate by forming a bond or a partial bond with the reaction center. In addition to the primary interaction with the nearest neighboring group, secondary interactions involving another neighboring group(s) could also occur in principle. Here, we revisit this issue by examining the influence of secondary interactions on the stability and reactivity of the putative iminylium cation intermediates, formed by N-O bond cleavage of 1-tetralone oxime systems. A direct observation of a peri-bromo-iminylium intermediate in solution supported the involvement of iminylium cations and the stabilizing effect of secondary interactions arising from a distal tandem substituent. Both experimental and computational findings support the idea that secondary interactions of a tandem-neighboring group on the primary peri-heteroatom (Br, Cl, and O(Me))-iminylium bonding interaction, i.e., a weak halogen bonding interaction (ester (nitro) oxygen-halogen bonding) and an unprecedented hydrogen bonding interaction between a nitro oxygen atom and a CH₃O hydrogen atom, are crucial determinants of the reaction pathway, leading to either overwhelmingly selective syn-migration of the oxime functionality or covalent bond formation under acid-catalyzed Beckmann rearrangement conditions.

Synthesis, structure and N-N bonding character of 1,1-disubstituted indazolium hexafluorophosphate

1,1-Disubstituted indazolium hexafluorophosphates were synthesized via intramolecular electrophilic amination reactions under mild conditions. The crystal structures were determined and are consistent with the presence of a stable N-N bond, which can be cleaved by hydrogenation. Both experimental and computational studies suggest a covalent bonding character of the N-N bond, with diminished aromaticity of the newly formed pyrazolium ring due to the quaternary ammonium atom (N1), in contrast to the aromatic character of the parent indazole.

Contrasting C- and O-Atom Reactivities of Neutral Ketone and Enolate Forms of 3-Sulfonyloxyimino-2-methyl-1-phenyl-1-butanones

The mechanisms of intramolecular cyclization of 3-sulfonyloxyimino-2-methyl-1-phenyl-1-butanones (1) under basic (DABCO and t-BuOK) and acidic (AcOH and TFA) conditions were investigated by means of experimental and computational methods. The ketone, enol, and enolate forms of 1 can afford different intramolecular cyclization products (2, 3, 4), depending on the conditions. The results of the reaction of 1 under basic conditions suggest intermediacy of neutral enol (DABCO) and anionic enolate (t-BuOK), while the results under acidic conditions (AcOH and TFA) indicate involvement of neutral ketones, which exhibit reactivities arising from both the oxygen lone-pair electrons (O atom reactivity) and carbon σ-electrons (C atom reactivity). The neutral enol in DABCO afforded 2H-azirine 4. On the other hand, the products (isoxazole 2 and oxazole 3) generated from the ketone form and from the enolate form are the same, but the reaction mechanisms are apparently different. The results demonstrate ambident-like reactivity of neutral ketone in the 3-sulfonyloxyimino-2-methyl-1-phenyl-1-butanone system.

Facile synthesis of 2,3-benzodiazepines using one-pot two-step phosphate-assisted acylation–hydrazine cyclization reactions

We present a one-pot two-step methodology, in which an unprotected amino is tolerated, for rapidly synthesizing 2,3-benzodiazepines via phosphate-assisted acylation reaction and hydrazine cyclization reaction.

Electrophilic activation of aminocarboxylic acid by phosphate ester promotes Friedel-Crafts acylation by overcoming charge-charge repulsion

Friedel-Crafts acylation of aromatic compounds with aminocarboxylic acids proceeds efficiently in the presence of a tailored phosphate ester and a strong Brønsted acid, despite the strong charge-charge repulsion associated with acylium ion formation. Here, we investigate the mechanism of this electrophilic aromatic acylation reaction, focusing on how the aminocarboxylic acid is activated by the phosphate ester and how the charge-charge repulsion is overcome. In the first step of the reaction, an acyl phosphate is generated from the aminocarboxylic acid through the intervention of the phosphate ester, which possesses three methyl salicylate ester linkages. The o-methyl salicylates enhance the reactivity of the phosphate ester via a protonation-induced conformational change, thereby overwhelming the charge-charge repulsion associated with the acylium ion formation. Weakening of the resonance interaction in the C(O)-O(P) bond by the lone-pair electrons of the ether oxygen atom of the carboxylic acid functionality contributes to the rapid formation of the acylium ion. Thus, our results show that the formation of aromatic ketones from various carboxylic acids proceeds because the strong leaving ability of the acyl phosphate overwhelms the charge-charge repulsion associated with the formation of the acylium ion. This information will be helpful to improve the design of tailored phosphate reagents.

Fibroblast growth factor 13 regulates glioma cell invasion and is important for bevacizumab-induced glioma invasion

Glioblastoma has the poorest prognosis, and is characterized by excessive invasion and angiogenesis. To determine the invasive mechanisms, we previously used two glioma cell lines (J3T-1 and J3T-2) with different invasive phenotypes. The J3T-1 showed abundant angiogenesis and tumor cell invasion around neovasculature, while J3T-2 showed diffuse cell infiltration into surrounding healthy parenchyma. Microarray analyses were used to identify invasion-related genes in J3T-2 cells, and the expressed genes and their intracellular and intratumoral distribution patterns were evaluated in J3T-2 cell lines, human glioma cell lines, human glioblastoma stem cells and human glioblastoma specimens. To determine the role of the invasion-related genes, invasive activities were evaluated in vitro and in vivo. Fibroblast growth factor 13 (FGF13) was overexpressed in J3T-2 cells compared to J3T-1 cells, and in human glioma cell lines, human glioblastoma stem cells and human glioblastoma specimens, when compared to that of normal human astrocytes. Immunohistochemical staining and the RNA-seq (sequencing) data from the IVY Glioblastoma Atlas Project showed FGF13 expression in glioma cells in the invasive edges of tumor specimens. Also, the intracellular distribution was mainly in the cytoplasm of tumor cells and colocalized with tubulin. Overexpression of FGF13 stabilized tubulin dynamics in vitro and knockdown of FGF13 decreased glioma invasion both in vitro and in vivo and prolonged overall survival of several xenograft models. FGF13 was negatively regulated by hypoxic condition. Silencing of FGF13 also decreased in vivo bevacizumab-induced glioma invasion. In conclusion, FGF13 regulated glioma cell invasion and bevacizumab-induced glioma invasion, and could be a novel target for glioma treatment.

Current-Nonlinear Hall Effect and Spin-Orbit Torque Magnetization Switching in a Magnetic Topological Insulator

The current-nonlinear Hall effect or second harmonic Hall voltage is widely used as one of the methods for estimating charge-spin conversion efficiency, which is attributed to the magnetization oscillation by spin-orbit torque (SOT). Here, we argue the second harmonic Hall voltage under a large in-plane magnetic field with an in-plane magnetization configuration in magnetic-nonmagnetic topological insulator (TI) heterostructures, Cr_{x}(Bi_{1-y}Sb_{y})_{2-x}Te_{3}/(Bi_{1-y}Sb_{y})_{2}Te_{3}, where it is clearly shown that the large second harmonic voltage is governed not by SOT but mainly by asymmetric magnon scattering without macroscopic magnetization oscillation. Thus, this method does not allow an accurate estimation of charge-spin conversion efficiency in TI. Instead, the SOT contribution is exemplified by current pulse induced nonvolatile magnetization switching, which is realized with a current density of 2.5×10^{10}  A m^{-2}, showing its potential as a spintronic material.

Probing the Hydrophobic Binding Pocket of G-Protein-Coupled Lysophosphatidylserine Receptor GPR34/LPS1 by Docking-Aided Structure-Activity Analysis

The ligands of certain G-protein-coupled receptors (GPCRs) have been identified as endogenous lipids, such as lysophosphatidylserine (LysoPS). Here, we analyzed the molecular basis of the structure-activity relationship of ligands of GPR34, one of the LysoPS receptor subtypes, focusing on recognition of the long-chain fatty acid moiety by the hydrophobic pocket. By introducing benzene ring(s) into the fatty acid moiety of 2-deoxy-LysoPS, we explored the binding site's preference for the hydrophobic shape. A tribenzene-containing fatty acid surrogate with modifications of the terminal aromatic moiety showed potent agonistic activity toward GPR34. Computational docking of these derivatives with a homology modeling/molecular dynamics-based virtual binding site of GPR34 indicated that a kink in the benzene-based lipid surrogates matches the L-shaped hydrophobic pocket of GPR34. A tetrabenzene-based lipid analogue bearing a bulky tert-butyl group at the 4-position of the terminal benzene ring exhibited potent GPR34 agonistic activity, validating the present hydrophobic binding pocket model.

Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic β-Proline Oligomers: Length-Dependent Convergence to Organized Structures

In this study, the solution structures of the homooligomers of a conformationally constrained bicyclic proline-type β-amino acid were studied by means of molecular dynamics (MD) calculations in explicit methanol and water using the umbrella sampling method. The ratio of trans-amide and cis-amide was estimated by NMR and the rotational barrier of the amide of acetylated bicyclic amino acid monomer was estimated by two-dimensional (2D) exchange spectroscopy (EXSY) or line-shape analysis. A bias potential was introduced with respect to the amide torsion angle ω to enhance conformational exchange including isomerization of amide bonds by lowering the rotation energy barrier. After determination of reweighting parameters to best reproduce the experimental results of the monomer amide, the free energy profile around the amide torsion angle ω was obtained from the MD trajectory by reweighting of the biased probability density. The MD simulation results support the existence of invertomers of nitrogen-pyramidalized amide. Furthermore, extended structures with a high fraction of trans-amide conformation appear to be increasingly stabilized as the oligomer is elongated, both in methanol and in water. Our conformational analysis of natural and non-natural tertiary-amide-based peptide oligomers indicates that these oligomers preferentially adopt a limited number of conformations.

Chemoselective generation of acyl phosphates, acylium ion equivalents, from carboxylic acids and an organophosphate ester in the presence of a Brønsted acid

Reactions of an organophosphate ester with carboxylic acids proceeded smoothly and chemoselectively in the presence of a Brønsted acid, affording acyl phosphate intermediates, leading to formation of various functional aromatic ketones.

Development of beam emission spectroscopy for turbulence transport study in Heliotron J

This paper describes the development study of the beam emission spectroscopy (BES) for the turbulent transport study in Heliotron J. Modification of the sightlines (10 × 4 for edge and 10 × 2 for edge) enables us to obtain 2-dimensional BES imaging. The cooling effect on the reduction in the electrical noise of avalanche photodiode (APD) assembly has been investigated using a refrigerant cooling system. When the temperature of the APD element has set to be -20 °C, the electrical noise can be reduced more than 50%. The measurement error of the phase difference in the case of low signal level has been tested by two light-emitting diode lamps. The APD cooling has an effect to improve the measurement error at the low signal level of APD.

Identification of lysophosphatidylthreonine with an aromatic fatty acid surrogate as a potent inducer of mast cell degranulation

Upon various stimulations, mast cells (MCs) release a wide variety of chemical mediators stored in their cytoplasmic granules, which then initiates subsequent allergic reactions. Lysophosphatidylserine (LysoPS), a kind of lysophospholipid, potentiates the histamine release from MCs triggered by antigen stimulation. We previously showed through structure-activity studies of LysoPS analogs that LysoPS with a methyl group at the carbon of the serine residue, i.e., lysophosphatidylthreonine (LysoPT), is extremely potent in stimulating the MC degranulation. In this study, as our continuing study to identify more potent LysoPS analogs, we developed LysoPS analogs with fatty acid surrogates. We found that the substitution of oleic acid to an aromatic fatty acid surrogate (C3-pH-p-O-C11) in 2-deoxy-1-LysoPS resulted in significant increase in the ability to induce MCs degranulation compared with 2-deoxy-1-LysoPS with oleic acid. Conversion of the serine residue into the threonine residue further increased the activity of MC degranulation both in vitro and in vivo. The resulting super agonist, 2-deoxy-LysoPT with C3-pH-p-O-C11, will be a useful tool to elucidate the mechanisms of stimulatory effect of LysoPS on MC degranulation.

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Lysophosphatidylserine (LysoPS) stimulates degranulation of mast cell (MC).

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We evaluated various LysoPS analogs for their MC degranulation-stimulating activity.

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We identified a threonine containing LysoPS analogs as a super agonist.

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The MC LysoPS receptor is different from the known LysoPS receptors.

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The super agonist helps to identify the putative MC LysoPS receptor.