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.     

Spectroscopic evidence for the unusual stereochemical configuration of an endosome-specific lipid

At a glance: The stereochemical configuration of the diglycerophosphate backbone of the endosome-specific lipid bis(monoacylglycero)phosphate (BMP, see picture) was determined by (1)H?NMR spectroscopy. Enantiomeric discrimination was facilitated by introduction of D-camphor ketals as chiral shift reagents, and enantiopure synthetic BMP analogues were prepared as reference materials. Natural BMP exhibited the unusual sn-1,1' diglycerophosphate backbone.     

Magnetization reversal in a preferred oriented (111) L1(0) FePt grown on a soft magnetic metallic glass for tilted magnetic recording

L1(0) FePt is an important material for the fabrication of high density perpendicular recording media, but the ultrahigh coercivity of L1(0) FePt restricts its use. Tilting of the magnetic easy axis and the introduction of a soft magnetic underlayer can solve this problem. However, high temperature processing and the requirement of epitaxial growth conditions for obtaining an L1(0) FePt phase are the main hurdles to be overcome. Here, we introduce a bilayered magnetic structure ((111) L1(0) FePt/glassy Fe(71)Nb(4)Hf(3)Y(2)B(20)/SiO(2)/Si) in which the magnetic easy axis of L1(0) FePt is tilted by ~36° from the film plane and epitaxial growth conditions are not required. The soft magnetic underlayer not only promotes the growth of L1(0) FePt with the preferred orientation but also provides an easy cost-effective micro/nanopatterning of recording bits. A detailed magnetic characterization of the bilayered structure in which the thickness of (111) L1(0) FePt with the soft magnetic Fe(71)Nb(4)Hf(3)Y(2)B(20) glassy underlayer varied from 5 to 60 nm is carried out in an effort to understand the magnetization switching mechanism. The magnetization switching behavior is almost the same for bilayered structures in which FePt layer thickness is >10 nm (greater than the domain wall thickness of FePt). For FePt film ~10 nm thick, magnetization reversal takes place in a very narrow field range. Magnetization reversal first takes place in the soft magnetic underlayer. On further increase in the reverse magnetic field, the domain wall in the soft magnetic layer compresses at the interface of the hard and soft layers. Once the domain wall energy becomes sufficiently large to overcome the nucleation energy of the domain wall in L1(0) FePt, the magnetization of the whole bilayer is reversed. This process takes place quickly because the domain walls in the hard layer do not need to move, and the formation of a narrower domain wall may not be favorable energetically. Our results showed that the present bilayered structure is very promising for the fabrication of tilted bit-patterned magnetic recording media.     

Syntheses and reactions of functional polymers. XCIII. Syntheses of polymers containing the N-(4-hydroxy-3-nitrophenyl)succinimide structure in the chain and the use of these activated polymer esters of N-blocked amino acids or peptides

Polymers containing the N-(4-hydroxy-3-nitrophenyl)succinimide residue were designed in order to achieve acyl activation of a reacting carboxylic acid in the solid phase. These polymers were prepared through the following three routes: (a) styrene was allowed to copolymerize with N-(4-hydroxy-3-nitrophenyl)- or N-(4-acetoxy-3-nitrophenyl)maleimide, (b) styrene was copolymerized with N-(4-acetoxyphenyl)maleimide in the presence of divinylbenzene (DVB), and the copolymer obtained was hydrolyzed and nitrated, (c) a copolymer of maleic anhydride and styrene was reacted with p-aminophenol, followed by nitration. The polymers prepared by routes b and c were converted to the activated polymer esters of N-blocked amino acids and peptides by using dicyclohexylcarbodiimide (DCC). The acylated polymers thus obtained were treated with amino acid esters and found to give peptides quantitatively without racemization.