Structure of an unsaturated fatty acid with unique vicinal dimethyl branches isolated from the Okinawan soft coral of the genus Sinularia

A new unsaturated fatty acid with unique vicinal dimethyl branches was isolated from the Okinawan soft coral of the genus Sinularia. The structure of the compound was determined based on the results of spectroscopic analysis and chemical conversion. The absolute configuration was deduced by applying the Ohrui-Akasaka method.     

Peroxy radicals as motional probes at the end of isolated polystyrene chains and on the cellulose surfaces in vacuum

The isolated polystyrene chains spin-labeled with peroxide radical at the free end (IPSOO) in which the chain roots were covalently bonded to the surface of microcrystalline cellulose (MCC) powder were produced by mechanochemical polymerization of styrene initiated by MCC mechanoradicals. The IPSOO was used as motional probes at the ends of isolated polystyrene chains tethered on the surface of MCC powder. Two modes for the molecular motion of IPSOO were observed. One was a tumbling motion of IPSOO on the MCC surface, defined as a train state, and another was a free rotational motion of IPSOO protruding out from the MCC surface, defined as a tail state. The temperature of tumbling motion (T _tum ) of IPSOO at the train state was at 90 K with anisotropic correlation times. T _tum (90 K) is extremely low compared to the glass transition temperature (T _g ^b ; 373 K) of polystyrene in the bulk. At temperatures above 219 K, the IPSOO was protruded out from the MCC surface, and freely rotated at the tail state. The train–tail transition temperature (T _train–tail ) was estimated to be 222 K. T _tum (90 K) and T _train–tail (222 K) are due to the extremely low chain segmental density of IPSOO on the MCC surface under vacuum. The interaction between IPSOO and the MCC surface is a minor contributing factor in the mobility of IPSOO on the surface under vacuum. It was found that peroxy radicals are useful probes to characterize the chain mobility reflecting their environmental conditions.     

Synthesis of 6-formylpterin nucleoside analogs and their ROS generation activities in the presence of NADH in the dark

We demonstrated previously that 3-position-modified 6-formylpterin (6FP) derivatives produce reactive oxygen species (ROS) such as hydrogen peroxide (H(2)O(2)) from oxygen in the presence of NADH in the dark. It has been shown that 6FP derivatives markedly generate ROS, which gives rise to their particular physiological activities, such as induction of apoptosis in cellular and living systems, suggesting that such compounds provide a hint for the design of a ROS controlling agent in vivo. However, it is not well understood why such unique activities appear on chemical modification. In the present study, in order to see the effect on ROS generation activity in the dark by the modification of the 1-position in 6FP, we have developed a new synthetic procedure for nucleoside analogs of 6FP and prepared 1-(beta-d-ribofuranosyl)-2-(N,N-diethylaminomethyleneamino)-6-formylpteridin-4-one (RDEF) and 1-(beta-d-ribofuranosyl)-2-(piperidine-1-ylmethyleneamino)-6-formylpteridin-4-one (RPIF) in which the 1-position of 6FP is glycosylated. At pH 7.4, NADH was spontaneously oxidized to NAD(+) in the presence of RDEF in the dark. Using electron paramagnetic resonance analysis coupled with the spin trapping technique, we show that O(2) was converted to H(2)O(2)via superoxide anion radical ( O(2)(-)) during this reaction. The modification of the 1-position of 6FP did not cancel ROS generation activities, which were demonstrated in 3-position-modified 6FPs. Since the 6FP derivatives developed in the present study have a ribose moiety, these compounds can be subjected to further derivatization, such as incorporation into oligonucleotides, oligosaccharides, proteins, or any other compounds that recognize and interact with specific biomolecules, and therefore would be useful in pharmaceutical investigations that need generation of appropriate and controllable amounts of ROS in vivo.     

Efficient preparation of amine-modified oligodeoxynucleotide using modified H-phosphonate chemistry for DNA microarray fabrication

Amine-modified oligodeoxynucleotides (AMO) are commonly used probe oligodeoxynucleotides for DNA microarray preparation. Two methods are currently used for AMO preparation—use of amine phosphoramidites protected by acid-labile monomethoxytrityl (MMT) groups or alkali-labile trifluoroacetyl (TFA) groups. Because conventional AMO preparation procedures have defects, for example stringent acidic conditions are required for deprotection of MMT and hydrophobic purification cannot be used for TFA-protected amino groups, conventional preparation of AMO is unlikely to result in the expected outcome. In this paper a method of AMO synthesis using modified H-phosphonate chemistry is suggested. An aliphatic diamine is coupled with a phosphonate group forming a phosphoramidate linkage to the last internucleotide phosphate of oligodeoxynucleotides. In this method dimethoxytrityl (DMT) purification steps are used and stringent acid deprotection is not required to obtain the AMO. Although the method could lead to formation of AMO diastereomers, melting-temperature and CD analysis showed for two AMO that DNA duplex formation was the same as when normal oligodeoxynucleotides were used. Also, when these AMO were used as probes for DNA microarrays the immobilization efficiency was similar to that for AMO probes prepared by conventional means using an amino-modifier unit. The hybridization performance of these AMO was better than for those prepared conventionally. The procedures suggested would be useful for preparation of efficient AMO for fabrication of DNA microarrays and DNA-based nanoparticle systems. Nagendra Kumar Kamisetty and Seung Pil Pack have equally contributed to this work.     

ELECT++: Faster conformational search method for docking flexible molecules using molecular similarity

We have developed a program, ELECT++ (Effective LEssening of Conformations by Template molecules in C++), to speed up the conformational search for small flexible molecules using the similar property principle. We apply this principle to molecular shape and, importantly, to molecular flexibility. After molecules in a database are clustered according to flexibility and shape (FCLUST++), additional reagents are generated to screen the conformational space of molecules in each cluster (TEMPLATE++). We call these representative reagents of each cluster template reagents. Template reagents and clustered reagents produce, after reaction, template molecules and clustered molecules, respectively (tREACT++). The conformations of a template molecule are searched in the context of a macromolecular target. Acceptable conformational choices are then applied to all molecules in its cluster, thus effectively biasing conformational space to speed up conformational searches (tSEARCH++). In our incremental search method, it is necessary to calculate the root-mean-square deviations (RMSD) matrix of distances between different conformations of the same molecule to reduce the number of conformations. Instead of calculating the RMSD matrix for all molecules in a cluster, the RMSD matrix of a template molecule is chosen as a reference and applied to all the molecules in its cluster. We demonstrate that FCLUST++ clusters the primary amine reagents from the Available Chemicals Directory (ACD) successfully. The program tSEARCH++ was applied to dihydrofolate reductase with virtual molecules generated by tREACT++ using clustered primary amine reagents. The conformational search by the program tSEARCH++ was about 4.8 times faster than by SEARCH++, with an acceptable range of errors. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1834–1852, 1998     

Aromaticity and diatropicity of <Emphasis Type="Italic">p</Emphasis>-polyphenyl-α,ω-quinododimethides

p-Polyphenyl-α,ω-quinododimethides were predicted to be moderately aromatic and diatropic, although they exist only in a single classical resonance structure with no aromatic conjugated circuits. Such a dichotomy was resolved using our graph theory of aromaticity and ring-current diamagnetism. Six-site non-conjugated circuits were found to contribute appreciably to aromaticity and ring-current diamagnetism. Within each quinododimethide molecule, local aromaticity increases on going from the outermost to inner phenylene rings.     

Total Synthesis and Biological Evaluation of (+)‐Neopeltolide and Its Analogues

The stereocontrolled total synthesis of the originally proposed ( 1 ) and correct ( 2 ) structures of (+)‐neopeltolide, a novel marine macrolide natural product with highly potent antiproliferative activity against several cancer cell lines as well as potent antifungal activity, has been achieved by exploiting a newly developed Suzuki–Miyaura coupling/ring‐closing metathesis strategy. Alkylborate 44 , which was generated in situ from iodide 34 , was coupled with enol phosphate 8 by a Suzuki–Miyaura coupling. Ring‐closing metathesis of the derived diene 45 followed by stereoselective hydrogenation afforded tetrahydropyran 47 as a single stereoisomer in high overall yield from 34 . Our convergent strategy enabled us to construct the 14‐membered macrolactone core structure of 2 in a rapid and efficient manner. Total synthesis and biological evaluation of synthetic intermediates and designed synthetic analogues, performed to establish the structure–activity relationships of 2 , led to the discovery of a structurally simple yet potent cytotoxic analogue, 9‐demethylneopeltolide ( 54 ).     

Simultaneous determination of tetracyclines and their degradation products in environmental waters by liquid chromatography–electrospray tandem mass spectrometry

A sensitive method was developed for the trace determination of six tetracyclines and ten of their degradation products in influent, effluent, and river waters using liquid chromatography–electrospray tandem mass spectrometry detection, combined with Oasis hydrophilic–lipophilic balance (HLB) cartridge extraction and Oasis mixed-mode strong anion exchange (MAX) cartridge cleanup. Tetracyclines and their products were separated by liquid chromatography in 9.5 min, and the instrument detection limits were generally between 0.03 and 0.1 μg/L except for minocycline (0.5 μg/L). The chromatograms were improved through the MAX cleanup and no apparent matrix effect was found. The recoveries of all the target compounds except for 4-epianhydrochlortetracycline and anhydrochlortetracycline (34–52%) were 75–120% for influent, 61–103% for effluent, and 64–113% for river waters. The method detection limits (MDLs) of the analytes varied in the range of 0.8–17.5 ng/L in all studied matrices. The method was applied for the determination of tetracyclines and their products in a sewage treatment plant (STP) and surface waters in Beijing, China. Oxytetracycline (3.8–72.5 ng/L), tetracycline (1.9–16.5 ng/L), and five products including 4-epitetracycline, 4-epioxytetracycline, isochlortetracycline, anhydrotetracycline, and 4-epianhydrochlortetracycline (5.7–25.3 ng/L) were detected in wastewater, while only oxytetracycline and tetracycline (2.2 and 2.1 ng/L) were detected in surface water samples.