Rotaxane Formation from Borate Ion-Containing Crown Ether and Ammonium Ion: Enhancement of Their Association through Ion-Pairing.

We synthesized [2]rotaxanes featuring a catechol borate ion-containing crown ether and secondary ammonium ions. These rotaxane components show both ion-ion interactions and hydrogen bonds. X-ray crystallography and NMR spectroscopy allowed elucidation of the rotaxane structure.

Acid-base responsive molecular switching of a [2]rotaxane incorporating two different stations in an axle component.

Interlocked compounds such as rotaxanes and catenanes exhibit unique kinetic properties in response to external chemical or physical stimuli and are therefore expected to be applied to molecular machines and molecular sensors. To develop a novel rotaxane for this application, an isophthalamide macrocycle and a neutral phenanthroline axle were used. Stable pseudorotaxanes are known to be formed using hydrogen bonds and π-π interactions.

Affinity-directed substrate/H-antiport by a MATE transporter.

Multidrug and toxin extrusion (MATE) family transporters excrete toxic compounds coupled to Na/H influx. Although structures of MATE transporters are available, the mechanism by which substrate export is coupled to ion influx remains unknown. To address this issue, we conducted a structural analysis of Pyrococcus furiosus MATE (PfMATE) using solution nuclear magnetic resonance (NMR).

Synthesis of Cross-Chain Bridging Cryptands and Induction of Molecular Chirality.

In this study, we synthesized two cryptands featuring entangled tri- and tetra(ethylene glycol) linkers. The cryptand bearing short linkers was chiral without any asymmetric carbon atoms. After chiral high-performance liquid chromatography was used to separate the enantiomers, the absolute configuration of each cryptand was determined through single-crystal X-ray and circular dichroism analyses.

The oxidative folding of nascent polypeptides provides electrons for reductive reactions in the ER.

The endoplasmic reticulum (ER) maintains an oxidative redox environment that is advantageous for the oxidative folding of nascent polypeptides entering the ER. Reductive reactions within the ER are also crucial for maintaining ER homeostasis. However, the mechanism by which electrons are supplied for the reductase activity within the ER remains unknown.

Repetitive DNA symmetry elements negatively regulate gene expression in embryonic stem cells.

Transcription factor (TF) binding to genomic DNA elements constitutes one of the key mechanisms that regulates gene expression program in cells. Both consensus and nonconsensus DNA sequence elements influence the recognition specificity of TFs. Based on the analysis of experimentally determined c-Myc binding preferences to genomic DNA, here we statistically predict that certain repetitive, nonconsensus DNA symmetry elements can relatively reduce TF-DNA binding preferences.

Monitoring and Predicting the Size of Fine Particles Prepared in a Fluidized-Bed Granulator Using a Handheld-Type Raman Spectrometer.

We prepared two kinds of fine particles by treating lactose monohydrate (Lac) with the same formulation in a fluidized-bed granulator, which differed in the spraying air pressure. Raman intensities of treated Lac during processing were measured using a handheld-type Raman spectrometer and plotted against particle size. As particle size increased, Raman intensity decreased in both operating conditions.

Base-induced multi-state fluorescence of a trefoil-shaped salicylaldehyde azine derivative.

A trefoil-shaped salicylaldehyde azine derivative bearing multiple acidic protons displays base-induced multi-state luminescence. The azine was prepared through the reaction of 1,3,5-triformylphloroglucinol with 4-methoxysalicylaldehyde hydrazone. H NMR spectroscopy revealed that the azine existed in solution at room temperature as an equilibrium mixture of two geometric isomers.

Development of Low Molecular Weight Ligands for Integrin αβ.

We designed and synthesized non-peptide organic molecular ligands for integrin αβ. Candidate ligands featured amidino analog and carboxy groups as binding sites on either side of a spacer, which consisted of benzophenone or an analog, such as diphenyl sulfide, diphenyl sulfoxide, diphenyl sulfone, or diphenyl ether. Competitive binding assays to integrin αβ with respect to [I]echistatin were used to determine inhibitory activity of the synthetic ligands.

Four- and two-armed hetero porphyrin dimers: their specific recognition and self-sorting behaviours.

In this study we self-assembled the four-armed porphyrin hetero dimer capsule Cap4, stabilized through amidinium-carboxylate salt bridges, in CHCl and CHCl. The dimer capsule Cap4 was kinetically and thermodynamically more stable than the corresponding two-armed dimer Cap2. The number of arms strongly influenced their recognition behaviour; guests possessing small aromatic faces (, 1,3,5-trinitrobenzene) preferred residing in the cavity of the two-armed capsule Cap2, rather than in Cap4, both thermodynamically and kinetically; in contrast, large aromatic guests (, 9,10-dibromoanthracene) were encapsulated predominantly by Cap4 because of favourable entropic effects.

Quantitative Difference in Solubility of Diastereomeric (H/H)-Isotopomers.

Many achiral organic compounds become chiral by an isotopic substitution of one of the enantiotopic moieties in their structures. Although spectroscopic methods can recognize the molecular chirality due to an isotopic substitution, the effects of isotopically chiral compounds in enantioselective reactions have remained unsolved because the small chirality arises only from the difference between the number of neutrons in the atomic nuclei. The difference between the diastereomeric isotopomers of reactive sources should be the key to these effects.

Synthesis of a Mechanically Planar Chiral and Axially Chiral [2]Rotaxane.

In this study, we synthesized a [2]rotaxane that was both mechanically planar chiral and axially chiral, comprising a symmetrical bis-crown ether featuring a biphenyl moiety (as the macrocyclic component) and a symmetrical bis-ammonium salt (as the dumbbell-shaped component).

Function-Related Dynamics in Multi-Spanning Helical Membrane Proteins Revealed by Solution NMR.

A primary biological function of multi-spanning membrane proteins is to transfer information and/or materials through a membrane by changing their conformations. Therefore, particular dynamics of the membrane proteins are tightly associated with their function. The semi-atomic resolution dynamics information revealed by NMR is able to discriminate function-related dynamics from random fluctuations.

Potential pharmacokinetic interaction between orally administered drug and osmotically active excipients in pediatric polypharmacy.

Poorly absorbable sugar alcohols (e.g., mannitol, sorbitol, and maltitol) are the excipients frequently contained in pediatric dosage forms.

Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin.

Water dynamics in the hydration layers of biomolecules play crucial roles in a wide range of biological functions. A hydrated protein contains multiple components of diffusional and vibrational dynamics of water and protein, which may be coupled at ∼0.1-THz frequency (10-ps timescale) at room temperature.

A Chiral [3]Rotaxane Comprising Achiral Bis-macrocyclic and Dumbbell-Shaped Components.

In this study, we synthesized a molecularly chiral [3]rotaxane comprising a calix-bis-crown ether (as the macrocyclic component) and two unsymmetrical dialkylammonium salts (as dumbbell-shaped components) without any chirality in any of the individual components. Chiral high-performance liquid chromatography was used to separate the enantiomers, which were characterized by circular dichroism spectroscopy. Density functional theory calculations gave an insight into the absolute configuration of each [3]rotaxane.

Conformational Plasticity of Cyclic Ras-Inhibitor Peptides Defines Cell Permeabilization Activity.

Cyclorasins 9A5 and 9A54 are 11-mer cyclic peptides that inhibit the Ras-Raf protein interaction. The peptides share a cell-penetrating peptide (CPP)-like motif; however, only cyclorasin 9A5 can permeabilize cells to exhibit strong cell-based activity. To unveil the structural origin underlying their distinct cellular permeabilization activities, we compared the three-dimensional structures of cyclorasins 9A5 and 9A54 in water and in the less polar solvent dimethyl sulfoxide (DMSO) by solution NMR.

Role of NMR in High Ordered Structure Characterization of Monoclonal Antibodies.

Obtaining high ordered structure (HOS) information is of importance to guarantee the efficacy and safety of monoclonal antibodies (mAbs) in clinical application. Assessment of HOS should ideally be performed in a non-invasive manner under their formulated storage conditions, as any perturbation can introduce unexpected detritions. However, most of the currently available techniques only indirectly report HOS of mAbs and/or require a certain condition to conduct the analyses.

Locking the Dynamic Axial Chirality of Biphenyl Crown Ethers through Threading.

This paper describes the syntheses of [2]rotaxanes comprising 23- and 26-membered biphenyl crown ethers as the macrocyclic components and secondary ammonium ions as the dumbbell-shaped components, and the locking of the dynamic axial chirality of the biphenyl moieties in these structures. Chiral high-performance liquid chromatography (HPLC) revealed that our [2]rotaxane featuring the 26-membered crown ether racemized at room temperature, but the racemization of the [2]rotaxane featuring the 23-membered crown ether did not proceed at room temperature over a period of three days. After separation of the enantiomers of the [2]rotaxane incorporating the 23-membered crown ether through chiral HPLC, we studied its racemization at elevated temperature.

Targeting the cryptic sites: NMR-based strategy to improve protein druggability by controlling the conformational equilibrium.

Cryptic ligand binding sites, which are not evident in the unligated structures, are beneficial in tackling with difficult but attractive drug targets, such as protein-protein interactions (PPIs). However, cryptic sites have thus far not been rationally pursued in the early stages of drug development. Here, we demonstrated by nuclear magnetic resonance that the cryptic site in Bcl-xL exists in a conformational equilibrium between the open and closed conformations under the unligated condition.

Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences.

In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on the sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by RNA polymerase at a genome-wide level.

Utilization of a Crown Ether/Amine-Type Rotaxane as a Probe for the Versatile Detection of Anions and Acids by Thin-Layer Chromatography.

A crown ether/amine-type [2]rotaxane was synthesized and utilized as a probe for the detection of acids and anions. The addition of acids to the amine-type [2]rotaxane solution generated corresponding crown ether/ammonium-type [2]rotaxanes, which were purified by silica gel column chromatography as ammonium salts. The isolated yields of the [2]rotaxanes, possessing a variety of anions, depended on the acidity and polarity of the counter anions.

A Five-layer π-Aromatic Structure Formed through Self-assembly of a Porphyrin Trimer and Two Aromatic Guests.

In this study we synthesized two- and four-armed porphyrins - bearing two carboxyl and four 2-aminoquinolino functionalities, respectively, at their meso positions - as a complementary hydrogen bonding pair for the self-assembly of a D -symmetric porphyrin trimer host. Two units of the two-armed porphyrin and one unit of the four-armed porphyrin self-assembled quantitatively into the D -symmetric porphyrin trimer, stabilized through ammidinium-carboxylate salt bridge formation, in CH Cl and CHCl . The porphyrin trimer host gradually bound two units of 1,3,5-trinitrobenzene between the pair of porphyrin units, forming a five-layer aromatic structure.

The Provisional No-Effect Threshold of Sugar Alcohols on Oral Drug Absorption Estimated by Physiologically Based Biopharmaceutics Model.

Sugar alcohols reduce oral drug bioavailability by osmotic effects, but the magnitude of these effects differs among different drugs. This study aimed to identify the drug-related critical attributes of osmotic effects and estimate the impact of a "practical" sugar alcohol dose on the pharmacokinetics of various molecules using modeling and simulation approaches. We developed a physiologically based biopharmaceutics model that considers the dose-dependent effects of sugar alcohols on the gastrointestinal physiology.