Note: Measurement of synchrotron radiation phase-space beam properties to verify astigmatism compensation in Fresnel zone plate focusing optics.

The intensity distribution in phase space of an X-ray synchrotron radiation beamline was measured using a pinhole camera method, in order to verify astigmatism compensation by a Fresnel zone plate focusing optical system. The beamline is equipped with a silicon double crystal monochromator. The beam size and divergence at an arbitrary distance were estimated. It was found that the virtual source point was largely different between the vertical and horizontal directions, which is probably caused by thermal distortion of the monochromator crystal. The result is consistent with our astigmatism compensation by inclining a Fresnel zone plate.

From the chemistry of epoxy-sugar nucleosides to the discovery of anti-HIV agent 4'-ethynylstavudine-Festinavir.

Branched sugar nucleosides have attracted much attention due to their biological activities. We have demonstrated that epoxysugar nucleosides serve as versatile precursor for the stereo-defined synthesis of these nucleoside derivatives on the basis of its ring opening with organoaluminum or organosilicon reagents. In this review article, novel methods for the synthesis of nucleoside analogues branched at the 1' and 4'-position will be described. During this study, we could discover an anti-HIV agent, 4'-ethynylstavudine (Festinavir). Festinavir showed more potent anti-HIV activity than the parent compound stavudine (d4T). Other significant properties of Festinavir are as follows: 1) much less toxic to various cells and also to mitochondorial DNA synthesis than d4T, 2) better substrate for human thymidine kinase than d4T, 3) resistant not only to chemical glycosidic bond cleavage but also to catabolism by thymidine phosphorylase, 4) the activity improves in the presence of a major mutation, K103N, associated with resistance to non-nucleoside reverse transcriptase inhibitors. Detailed profile of the antiviral activities, biology and pharmacology of Festinavir are also described.

Synthetic use of epoxy-sugar nucleosides.

Preparation of 1',2 '-, 3 ',4 '-, and 4 ',5 '-epoxy derivatives of nucleosides and their use for the stereoselective synthesis of 1'- and 4 '-branched analogues are described.

Crystallinity estimation of thin silicon-on-insulator layers by means of diffractometry using a highly parallel X-ray microbeam.

An X-ray microbeam with a small angular divergence and a narrow energy bandwidth has been produced at BL24XU at SPring-8. The beam size was measured to be 3.1 microm and 1.6 microm in the horizontal and vertical directions, respectively, and the horizontal angular divergence was 4.0 arcsec. Using this microbeam the crystallinity estimation of thin layers on silicon-on-insulator (SOI) wafers is demonstrated. In reciprocal-space maps the lattice tilt variations were 80 arcsec and more than 220 arcsec in the SOI layers on bonded and SIMOX wafers, respectively. In equi-tilt maps, the typical equi-tilt areas of the SOI layers were 7 microm and 4 microm in size on the bonded and SIMOX wafers, respectively.

A new approach to the synthesis of 4'-carbon-substituted nucleosides: development of a highly active anti-HIV agent 2', 3'-didehydro-3'-deoxy-4'-ethynylthymidine.

Oxidation of 3'-O-TBDMS-4',5-unsaturated thymidine 3 with dimethyldioxirane (DMDO) allowed the isolation of the epoxide 4. Upon reacting with organosilicon reagents in the presence of SnCl4, 4 underwent stereoselective ring opening to give 4'-alpha-allyl (6), 4'-alpha-(2-bromoallyl) (7), 4'-alpha-(cyclopenten-3-yl) (8), and 4'-alpha-cyano (9) derivatives of thymidine. Reactions of the 3'-epimer 12 with organoaluminum reagents gave 4'-alpha-methyl (13), 4'-alpha-vinyl (14), and 4'-alpha-ethynyl (15) analogues. Compounds 13-15 were transformed into corresponding 2',3'-didehydro-3'-deoxy derivatives. Evaluation of their ability to inhibit the replication of HIV in cell culture showed that 4'-ethynyl-d4T (19) is more potent and less toxic than the parent compound d4T.

5-Exo versus 6-endo cyclization of nucleoside 2-sila-5-hexenyl radicals: reaction of 6-(bromomethyl)dimethylsilyl 1',2'-unsaturated uridines.

The mode of cyclization of 2-sila-5-hexen-1-yl radicals generated from 6-(bromomethyl)dimethylsilyl-1',2'-unsaturated uridines was investigated. In contrast to the case of the 2'-unsubstituted 6-silicon-tethered substrate (4), which undergoes exclusive 6-endo-cyclization, reactions of the 2'-substituted (Me, CO2Me, OBz, and Cl) derivatives (14, 20, 22, and 24) uniformly proceeded in preferential or exclusive 5-exo-mode. The Tamao oxidation of the resulting cyclized products was also carried out to synthesize the corresponding 1'-C-hydroxymethyl derivatives.

Synthesis and anti-HIV activity of 4'-cyano-2',3'-didehydro-3'-deoxythymidine.

A new anti-HIV agent 4'-cyano-2',3'-didehydro-3'-deoxythymidine (9) was synthesized by allylic substitution of the 3',4'-unsaturated nucleoside 14, having a leaving group at the 2'-position, with cyanotrimethylsilane in the presence of SnCl4. Evaluation of the anti-HIV activity of 9 showed that this compound is much less potent than the recently reported 2',3'-didehydro-3'-deoxy-4'-(ethynyl)thymidine (1).

Lithiation at the 6-position of uridine with lithium hexamethyldisilazide: crucial role of temporary silylation.

Lithium hexamethyldisilazide (LiHMDS) can mediate silylation at the 6-position of uridine, although LiHMDS alone is not able to generate the C-6-lithiated uridine. Experimental results showed that temporary silylation of O-4 (or N-3) of the uracil ring triggers the C-6 lithiation with LiHMDS. This finding allowed us to develop an efficient intramolecular alkylation of 5'-deoxy-5'-iodouridine to furnish 6,5'-C-cyclouridine. [reaction--see text]

Novel 4'-substituted stavudine analog with improved anti-human immunodeficiency virus activity and decreased cytotoxicity.

The antiviral drug 2',3'-didehydro-3'-deoxythymidine (D4T; also know as stavudine and Zerit), which is used against human immunodeficiency virus (HIV), causes delayed toxicity (peripheral neuropathy) in long-term use. After examining a series of 2',3'-didehydro-3'-deoxy-4'-substituted thymidine (4'-substituted D4T) analogs, 4'-ethynyl D4T was found to have a fivefold-better antiviral effect and to cause less cellular and mitochondrial toxicity than D4T. The antiviral activity of this compound can be reversed by dThd but not by dCyd. The compound acted synergistically with beta-L-2',3'-deoxy-3'-thiacytidine (also known as lamivudine) and beta-L-2',3'-dideoxy-2',3'-didehydro-5-fluorocytidine (also known as elvucitabine) and additively with 2',3'-dideoxyinosine (also known as didanosine and Videx) and 3'-azido-3'-deoxythymidine (also known as Retovir and zidovudine) against HIV. 4'-Ethynyl D4T is phosphorylated by purified human thymidine kinase 1 (TK-1) from CEM cells with a faster relative V(max) and a lower K(m) value than D4T. The efficiency of TK-1 in the phosphorylation of 4'-ethynyl D4T is fourfold better than that of D4T. While D4T is broken down by the catabolic enzyme thymidine phosphorylase, the level of breakdown of 4'-ethynyl D4T was below detection. Since 4'-ethynyl D4T has increased anti-HIV activity and decreased toxicity and interacts favorably with other currently used anti-HIV drugs, it should be considered for further development as an anti-HIV drug.

An alternative method suitable for a large scale synthesis of 4'-ethynyl-2',3'-didehydro-3'-deoxythymidine.

Reaction of 4', 5'-unsaturated thymine nucleoside 1 with Pb(OBz)4 gave the 4'-benzoyloxy derivative 9 as a diastereomeric mixture in 79% yield. When 9 was treated with Me3Al in CH2Cl2 at 0 degrees C, spiro-derivative 10 was formed as the major product in 76% yield. On the other hand, the use of Me2AlCl led to the formation of the 4'-chlorinated product 11, which was subjected to in situ treatment with Me3Al to give the 4'-alpha-methyl derivative 12 (15%) as well as the 4'-beta-methyl counterpart 13 (38%). Formation of 11 was also observed during the reaction between 9 and EtAl(Cl)C[triple bond]CTMS, prepared from EtAlCl2 and LiC[triple bond]CTMS. From this reaction, the 4'-ethynyl nucleoside 14 was obtained stereoselectively in 56% yield.

Architecture of a grid-enabled research platform with location-transparency for bioinformatics.

The recent advance in information technologies has bought about the borderlessness in every field of both science and business. The borderlessness has increasingly made activities in interdisciplinary field more important. This current situation produces a strong demand that people want to establish a virtual group, organization and society for their business and scientific purposes irrespective of the actual structure formed by organizations. Remarkably, bio sciences require a research platform that satisfies such demand for further development. In this paper, we present a research platform for bioinformatics in detail. The prominent feature of the research platform is the use of Grid and its location transparency, which means that bio scientists and researchers are able to utilize a large amount of computational power for their analysis and to access data of their interest without being aware of where data and computational resources are located. The usefulness and feasibility of the architecture of the research platform is shown as well as future issues to achieve toward the final goal of our research in this paper.

Synthesis of a highly active new anti-HIV agent 2',3'-didehydro-3'-deoxy-4'-ethynylthymidine.

Compounds having methyl, vinyl, and ethynyl groups at the 4'-position of stavudine (d4T: 2',3'-didehydro-3'-deoxythymidine) were synthesized. The compounds were assayed for their ability to inhibit the replication of HIV in cell culture. The 4'-ethynyl analogue (15) was found to be more potent and less toxic than the parent compound stavudine.

Study on the reaction mechanism of C-6 lithiation of pyrimidine nucleosides by using lithium hexamethyldisilazide as a base.

The reaction mechanism of C-6 lithiation of uridine mediated by lithium hexamethyldisilazide (LiHMDS) has been investigated. LiHMDS alone dose not lithiate at C-6 of uridine. However, in the presence of an appropriate silylating agent, e.g. trimethylsilyl chloride, the reaction of 1 with LiHMDS allowed to lithiate at C-6 and gave the corresponding C-6 silylated product 2. The experimental results shown below revealed that O-4 (N-3) of uracil moiety may be temporarily masked by silylation, which triggers the C-6 lithiation by lowering the pKa of H-6. The reaction could efficiently be applied to the synthesis of 6,5'-C-cyclouridine, a nucleoside analogue fixed in a specific glycosyl torsion angle by a carbon-carbon bridge.

Ring opening of 4',5'-epoxynucleosides: a novel stereoselective entry to 4'-C-branched nucleosides.

Stereoselective synthesis of 4'-alpha-carbon-substituted nucleosides has been accomplished through epoxidation of 4',5'-unsaturated nucleosides with dimethyldioxirane (DMDO) and successive SnCl(4)-promoted ring opening of the resulting 4',5'-epoxynucleosides with organosilicon reagents. [reaction: see text]

Reaction of 4',5'-epoxynucleosides with carbon nucleophiles: stereoselective synthesis of 4'-C-carbon-substituted nucleosides.

4',5'-Epoxythymidine (4) was obtained as a single diastereoisomer by oxidation of 3'-O-(t-butyldimethylsilyl)-4',5'-dehydrothymidine (3) with dimethyldioxirane. When the epoxide 4 was treated with allyltrimethylsilane in the presence of SnCl4, regio- (at the C4') and stereoselective (from the alpha-face) cleavage of the oxirane ring proceeded to afford a 4'-C-alpha-allylated derivative (5) as a sole product. In the reaction of 4 with trimethylaluminum, 4'-C-beta-methyl derivative (8) was obtained as a major product.