Replica sub-permutation method for molecular dynamics and monte carlo simulations

We propose an improvement of the replica-exchange and replica-permutation methods, which we call the replica sub-permutation method (RSPM). Instead of considering all permutations, this method uses a new algorithm referred to as sub-permutation to perform parameter transition. The RSPM succeeds in reducing the number of combinations between replicas and parameters without the loss of sampling efficiency. For comparison, we applied the replica sub-permutation, replica-permutation, and replica-exchange methods to a β-hairpin mini protein, chignolin, in explicit water. We calculated the transition ratio and number of tunneling events in the parameter space, the number of folding–unfolding events, the autocorrelation function, and the autocorrelation time as measures of sampling efficiency. The results indicate that among the three methods, the proposed RSPM is the most efficient in both parameter and conformational spaces. © 2019 Wiley Periodicals, Inc.     

Biomimetic Peptide Catalytic Bond-Forming Utilizing a Mild Brønsted Acid

Since the global peptide drug market demand has been predicted to increase, highly efficient and inexpensive mass scale peptides are required. However, the production process raises questions about the cost of energy input, scale-up production, raw materials, and solvents treatment. This paper introduces 2 methods for the 2–4 mer oligopeptides bond formation for batch reaction utilizing 50–100 mol% of a mild Brønsted acid under the mild condition. One of the methods has been capably adapted to flow synthesis at room temperature using organic solvents with boiling points below 100 °C. The method applies the tert-butoxycarbonyl amino methoxy group, forming the desired dipeptide without solvent at mild temperatures. Furthermore, the conversion of the carboxylic acid leaving the group to phenyl ester promotes peptide bond formation, and the reaction were applied to di, tri, and tetrapeptide bond formation in excellent yield without notable racemization at ambient temperature (up to >99 % yield and 99 : 1 dr). Finally, this study proposes this new production method to overcome the limited scale-up production by reaction device scale: liquid phase biomimetic catalytic peptide flow synthesis utilizing a mild Brønsted acid.     

In vivo time‐resolved X‐ray fluorescence mapping measurements of Egeria densa immersed in Cr(VI) aqueous solution

In vivo time‐resolved Cr and Ca X‐ray fluorescence (XRF) mapping measurements were performed in a laboratory over a period of 69 days on a living common aquatic plant Egeria densa that was immersed in 5 mM K₂CrO₄ aqueous solution. The time and spatial resolution for each time‐resolved XRF map were ~1.6 days and 1 × 1 mm², respectively. The obtained XRF maps exhibited characteristic localized Cr and Ca areas where the XRF signals were especially strong (‘hot spots’), and this indicated the necessity of preliminary millimeter‐resolution surveying in XRF microscopy. Ca hot spots were detected prior to Cr(VI) immersion and nearly disappeared after immersion in deionized water for 2 weeks and the Cr(VI) solution for 1 week. After these immersions, a Cr hot spot was formed at approximately the same location of the missing Ca hot spot, which suggests that the original Ca‐accumulated regions were substituted for the isolation of Cr species when they were introduced. The sizes and intensity distributions of the Cr hot spots were sensitive to the Cr(VI) exposure approximately 1 week prior to each XRF measurement. This sensitivity suggests potential applications of E. densa as a Cr(VI) biomonitor in aquatic environments. Copyright © 2014 John Wiley & Sons, Ltd.     

Enantioselective total synthesis of (+)-sarcodictyenone

The first enantioselective total synthesis of (+)-sarcodictyenone is described [4.3% overall yield from (5R,6R)-6-methyl-5-trimethylsily-2-cyclohexenone]. This work establishes the absolute stereochemistry of the natural product.     

Synthesis of selenylfullerene with selenium-containing dibenzo[b,g]cyclooctane moiety

The photochemical reaction of C₆₀ with selenium-containing bicyclooctanes affords for the first time the selenylfullerenes. The derivatives were characterized by mass, UV-vis absorption, NMR spectroscopy, and X-ray crystallographic analysis.     

Kinetic analysis of superoxide anion radical-scavenging and hydroxyl radical-scavenging activities of platinum nanoparticles

There are few reports on the physiological effects of metal nanoparticles (nps), especially with respect to their functions as scavengers for superoxide anion radical (O2(.-)) and hydroxyl radical (.OH). We tried to detect the scavenging activity of Pt nps using a hypoxanthine-xanthine oxidase system for O2(.-) and using a Fenton and a UV/H2O2 system for .OH. Electron spin resonance analysis revealed that 2 nm particle size Pt nps have the ability to scavenge O2(.-) and .OH. The calculated rate constant for the O2(.-)-scavenging reaction was 5.03 +/- 0.03 x 10(7) M (-1) s (-1). However, the analysis of the Fenton and UV/H 2O 2 system in the presence of Pt nps suggested that the .OH-scavenging reaction cannot be determined in both systems. Among particle sizes tested from 1 to 5 nm, 1 nm Pt nps showed the highest O2(.-)-scavenging ability. Almost no cytotoxicity was observed even after adherent cells (TIG-1, HeLa, HepG2, WI-38, and MRC-5) were exposed to Pt nps at concentrations as high as 50 mg/L. Pt nps scavenged intrinsically generated reactive oxygen species (ROS) in HeLa cells. Additionally, Pt nps significantly reduced the levels of intracellular O2(.-) generated by UVA irradiation and subsequently protected HeLa cells from ROS damage-induced cell death. These findings suggest that Pt nps may be a new type of antioxidant capable of circumventing the paradoxical effects of conventional antioxidants.     

Polymer-like polyphenols of black tea and their lipase and amylase inhibitory activities

Lipase and amylase inhibitory activities of black tea were examined. After solvent partitioning of a black tea extract with the ethyl acetate and n-butanol, the two soluble fractions showed comparable inhibitory activities. Activity in the ethyl acetate fraction was mainly attributable to polyphenols with low-molecular weights, such as theaflavin gallates. On the other hand, the active substance in the n-butanol layer was ascertained to be a polymer-like substance. 1H- and 13C-NMR spectra showed signals arising from the flavan A-ring and galloyl groups, although signals due to flavan B-rings were not detected, suggesting that the polymer-like substances were generated by oxidative condensation of flavan B-rings, a result which was previously deduced from our results of in vitro catechin oxidation experiments. Enzymatic oxidation of epicatechin 3-O-gallate produced a similar polymer-like substance and suggested that condensation between a B-ring and galloyl groups was involved in the polymerization reaction.     

Medicinal foodstuffs. XXXIV. Structures of new prenylchalcones and prenylflavanones with TNF-alpha and aminopeptidase N inhibitory activities from Boesenbergia rotunda

The methanolic extract from the rhizomes of Boesenbergia rotunda (Zingiberaceae) was found to show inhibitory effect on tumor necrosis factor-alpha (TNF-alpha)-induced cytotoxicity in L929 cells (IC(50)=6.1 microg/ml). By bioassay-guided separation, four new prenylcalcones, (+)-krachaizin A (1a), (-)-krachaizin A (1b), (+)-krachaizin B (2a), and (-)-krachaizin B (2b), and four new prenylflavanones, rotundaflavones Ia (3a), Ib (3b), IIa (4a), and IIb (4b), were isolated together with 18 known constituents (5a-7b and 8-19). The structures of eight new compounds were elucidated on the basis of physicochemical evidence. Among them, (+)-krachaizin B (2a), (-)-krachaizin B (2b), (+)-4-hydroxypanduratin A (6a), (-)-4-hydroxypanduratin A (6b), (+)-isopanduratin A (7a), (-)-isopanduratin A (7b), alpinetin (10), cardamonin (14), and 2,6-dihydroxy-4-methoxydihydrochalcone (15) significantly inhibited TNF-alpha-induced cytotoxicity in L929 cells at 10 microM. In addition, 2a, 2b, (+)-panduratins A (5a), (-)-panduratin A (5b), 6a, 7b, and geranyl-2,4-dihydroxy-6-phenylbenzoate (17) were found to show strong inhibitory effects on aminopeptidase N activity.     

Bioactive constituents from Chinese natural medicines. XXXII. aminopeptidase N and aldose reductase inhibitors from Sinocrassula indica: structures of sinocrassosides B(4), B(5), C(1), and D(1)-D(3)

From the methanolic extract of the whole plant of Sinocrassula indica (Crassulaceae), six new flavonol glycosides, sinocrassosides B(4) (1), B(5) (2), C(1) (3), D(1) (4), D(2) (5), and D(3) (6), were isolated together with 30 compounds. The structures of 1-6 were elucidated on the basis of chemical and physicochemical evidence. In addition, several constituents were found to show inhibitory effects on aminopeptidase N and aldose reductase.