The structures of macbecin I and II : New antitumor antibiotics

Macbecin I 1, C₃₀H₄₂N₂O₈, and macbecin II 2, C₃₀H₄₄N₂O₈, were shown to be 2,6-disubstituted benzoquinone and hydroquinone derivatives by an oxidation-reduction relationship, UV. ¹H and ¹³C NMR spectra. Alkaline methanolysis of 1 gave a 2-aminobenzoquinone derivative 5, suggesting an ansa-structure for 1, and acid hydrolysis of 1 gave decarbamoyl products 9,10 and 11, indicative of the location of carbamoyloxy group in allylic position. Spin decoupling studies on 1,3 and 5clarified the partial structures [A], [B], [C] and [D]. From their mutual disposition two structures 1a and 1b, were proposed out of which 1a has been selected for the structure of 1 on the basis of the structure of oxidative degradation product 12. X-Ray analysis of the bromoacetyl derivative of 1 confirmed the above proposed structure and determined the absolute stereochemistry of 1 and 2.     

Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase

Two molecular dynamics (MD) simulations totaling 25 ns of simulation time of monomeric scytalone dehydratase (SD) were performed. The enzyme has a ligand-binding pocket containing a cone-shaped alpha+beta barrel, and the C-terminal region covers the binding pocket. Our simulations clarified the difference in protein dynamics and conformation between the liganded protein and the unliganded protein. The liganded protein held the ligand molecule tightly and the initial structure was maintained during the simulation. The unliganded protein, on the other hand, fluctuated dynamically and its structure changed largely from the initial structure. In the equilibrium state, the binding pocket was fully solvated by opening of the C-terminal region, and the protein dynamics was connected with hydration water molecules entry into and release from the binding pocket. In addition, the cooperative motions of the unliganded protein and the hydration water molecules produced the path through the protein interior for ligand binding.     

Resistance properties of a macroporous silica-based N,N,N′,N′-tetraoctyl-3-oxapentane-1,5-diamide-impregnated polymeric adsorption material against nitric acid, temperature and γ-irradiation

The resistance of a novel silica-based N,N,N′,N′-tetraoctyl-3-oxapentane-1,5-diamide (TODGA) polymeric adsorption material (TODGA/SiO₂-P) against nitric acid, temperature and γ-irradiation had been investigated. The adsorption property of the treated TODGA/SiO₂-P was evaluated by a 3 M HNO₃ solution containing 0.01 M Nd(III). It was found that both 3 and 0.01 M HNO₃ concentrations did not decrease the stability of TODGA/SiO₂-P at 25°C. The quantity of TODGA leaked from TODGA/SiO₂-P was equivalent to its solubility in the corresponding HNO₃ aqueous solution. The effect of 3 M HNO₃ on the leakage of TODGA at 80°C was significantly higher than that in 0.01 M HNO₃ as well as in all cases at 25°C. The amount of Nd(III) adsorbed towards the treated TODGA/SiO₂-P was determined in the range of 0.143–0.148 mmol/g for the HNO₃ concentration effect and 0.142–0.0506 mmol/g for the temperature effect. γ-Irradiation showed a more noticeable destruction effect on TODGA/SiO₂-P. The content of TODGA leaked increased with an increase in the γ-irradiation dose (ID) from 1.06 to 3.72 MGy in terms of the linear equation [TODGA]=794.5ID+84.0. The amount of Nd(III) adsorbed onto the irradiated TODGA/SiO₂-P decreased rapidly from 0.134 to 0.0438 mmol/g, which was lower than 0.153 mmol/g, the adsorption of fresh TODGA/SiO₂-P for Nd(III), according to the equation Q_Nd(III)=−0.0301ID+0.160, showing that a large quantity of TODGA leaked from TODGA/SiO₂-P. The adsorbed amount of Nd(III) decreased obviously in this order: the HNO₃ concentration effect, temperature effect and γ-irradiation.     

Poly(ethylene glycol)-lipase complexes that are highly active and enantioselective in ionic liquids

Lipase-catalyzed alcoholysis between vinyl acetate and 2-phenyl-1-propanol was investigated in dialkylimidazolium-based ionic liquids. Although native lipase powder exhibited very low activity in an ionic liquid, forming a poly(ethylene glycol)(PEG)-lipase complex improved the lipase activity in the ionic liquid. The activity of the PEG-lipase complex was higher in ionic liquids than in common organic solvents (n-hexane, isooctane and dimethylsulfoxide). Fluorescence measurements using 4-aminophthalimide revealed that the ionic liquids were more hydrophilic than the organic solvents used for non-aqueous enzymology. A kinetic study of lipase-catalyzed alcoholysis in an ionic liquid ([Bmim][PF6]) revealed that the Michaelis constant (Km) for 2-phenyl-1-propanol in the ionic liquid was half that in n-hexane, suggesting that the ionic liquid stabilized the enzyme-substrate complex. Finally, we carried out enantioselective alcoholysis of 1-phenylethanol in ionic liquids employing the PEG-lipase complex, and obtained high enantioselectivity, comparable to that in n-hexane.     

Direct Introduction of a Dimesitylboryl Group Using Base‐Mediated Substitution of Aryl Halides with Silyldimesitylborane

The first dimesitylboryl substitution of aryl halides with a silylborane bearing a dimesitylboryl group in the presence of alkali‐metal alkoxides is described. The reactions of aryl bromides or iodides with Ph₂MeSi?BMes₂ and Na(OtBu) afforded the desired aryl dimesitylboranes in good to high yields and with high borylation/silylation ratios. Selective reaction of the sterically less‐hindered C?Br bond of dibromoarenes provided monoborylated products. This reaction was used to rapidly construct a D‐π‐A aryl dimesityl borane with a non‐symmetrical biphenyl spacer.     

A novel condition for capillary electrophoretic analysis of reductively aminated saccharides without removal of excess reagents

We have identified novel CE conditions for the separation of 7‐amino‐4‐methylcoumarin‐labeled monosaccharides and oligosaccharides from glycoproteins. Using a neutrally coated capillary and alkaline borate buffer containing hydroxypropylcellulose and ACN, saccharide derivatives form anionic borate complexes, which move from the cathode to the anode in an electric field and are detected near the anodic end. Excess labeling reagents and other fluorescent products remain at the cathodic end. Fluorimetric detection using an LED as a light source enables determination of monosaccharide derivatives with good linearity between at least 0.4 and 400 μM, may correspond to 140 amol to 140 fmol. The lower LOD (S/N = 5) is only 80 nM in the sample solution (ca. 28 amol). The results were comparable to reported values using fluorometric detection LC. The method was also applied to the analysis of oligosaccharides that were enzymatically released from glycoproteins. Fine resolution enables profiling of glycans in glycoproteins. The applicability of the method was examined by applying it to other derivatives labeled with nonacidic tags such as ethyl p‐aminobenzoate‐ and 2‐aminoacridone‐labeled saccharides.     

A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model

The Poisson–Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N‐ and C‐terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules. © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Acidic‐pH‐Activatable Fluorescence Probes for Visualizing Exocytosis Dynamics

Live imaging of exocytosis dynamics is crucial for a precise spatiotemporal understanding of secretion phenomena, but current approaches have serious limitations. We designed and synthesized small‐molecular fluorescent probes that were chemically optimized for sensing acidic intravesicular pH values, and established that they can be used to sensitively and reliably visualize vesicular dynamics following stimulation. This straightforward technique for the visualization of exocytosis as well as endocytosis/reacidification processes with high spatiotemporal precision is expected to be a powerful tool for investigating dynamic cellular phenomena involving changes in the pH value.     

Dehydration‐fragmentation mechanism of cathinones and their metabolites in ESI‐CID

Various cathinone‐derived designer drugs (CATs) have recently appeared on the drug market. This study examined the mechanism for the generation of dehydrated ions for CATs during electrospray ionization collision‐induced dissociation (ESI‐CID). The generation mechanism of dehydrated ions is dependent on the amine classification in the cathinone skeleton, which is used in the identification of CATs. The two hydrogen atoms eliminated during the dehydration of cathinone (primary amine) and methcathinone (secondary amine) were determined, and the reaction mechanism was elucidated through the deuterium labeling experiments. The hydrogen atom bonded to the amine nitrogen was eliminated with the proton added during ESI, in both of the tested compounds. This provided evidence that CATs with tertiary amine structures (such as dimethylcathinone and α‐pyrrolidinophenones [α‐PPs]) do not undergo dehydration. However, it was shown that the two major tertiary amine metabolites (1‐OH and 2″‐oxo) of CATs generate dehydrated ions in ESI‐CID. The dehydration mechanisms of the metabolites of α‐pyrrolidinobutiophenone (α‐PBP) belongs to α‐PPs were also investigated. Stable‐isotope labeling showed the dehydration of the 1‐OH metabolite following a simple mechanism where the hydroxy group was eliminated together with the proton added during ESI. In contrast, the dehydration mechanism of the 2″‐oxo metabolite involved hydrogen atoms in three or more locations along with the carbonyl group oxygen, indicating that dehydration occurred via multiple mechanisms likely including the rearrangement reaction of hydrogen atoms. These findings presented herein indicate that the dehydrated ions in ESI‐CID can be used for the structural identification of CATs.