Akiyoshi Hirata

A facile synthesis of cyclic bis(3'→5')diguanylic acid

Abstract This paper describes a new method for synthesizing biologically important cyclic bis(3′→5′)diguanylic acid (cGpGp) in a higher yield than that of the existing synthetic method. In the new synthesis, the following two means, in place of those used in the existing synthesis are employed as main strategies to cause the increase in product yield. One of these distinctive strategies in the new synthesis is that the phosphoramidite method is used for the preparation of a key synthetic intermediate of a linear guanylyl(3′→5′)guanylic acid derivative. This method allowed higher-yield formation of the intermediate than that by the triester method used in the existing synthesis. The second distinctive strategy used in the new synthesis is that allyloxycarbonyl and allyl groups are used for the protection of two guanine bases and two internucleotide bonds, respectively. These four allylic protectors can be removed all at once by the organopalladium-catalyzed reaction under neutral conditions. Thus, deprotection of the protected cGpGp precursor was achieved in the present synthesis in a shorter step and under milder conditions than the deprotection achieved in the existing synthesis, which uses diphenylacetyl and o-chlorophenyl groups as protectors for two guanine bases and two internucleotide bonds, respectively, whose full removal requires two different procedures including rather harsh basic treatment. As a result, technical loss and decomposition of the target product in the new synthesis is remarkably reduced.

Structural Evaluation of Tandem Hairpin Pyrrole–Imidazole Polyamides Recognizing Human Telomeres

A polyamide containing N-methylpyrrole (Py) and N-methylimidazole (Im), designated PIPA, binds with high affinity and specificity to specific nucleotide sequences in the minor groove of double-helical DNA. Based on a recent report of the synthesis of PIPA for telomere visualization, the present paper focused on the size of the connecting part (hinge region) of two PIPA segments of the tandem hairpin PIPA, Dab(Im-Im-Py)-Py-Py-Py-Im-[Hinge]-Dab(Im-Im-Py)-Py-Py-Py-Im-βAla-NH(CH2)3N(CH3)-(CH2)3NH-[Dye]. The present paper also describes the characterization of binding by measuring the thermal melting temperature and surface plasmon resonance and by specific staining of telomeres (TTAGGG)n in human cells. Microheterogeneity was also investigated by high-resolution mass spectrometry. We found that the optimal compound as the hinge segment for telomere staining was [-NH(C2H4O)2(C2H4)CO-] with tetramethylrhodamine as the fluorescent dye.

Effect of molecular sieves in the liquid-phase synthesis of nucleotides via the phosphoramidite method

Abstract It is demonstrated that the reaction of a nucleoside phosphoramidite and a nucleoside aided by a suitable promoter in the presence of molecular sieves 3A or 4A in a liquid phase is efficiently performed by the use of stoichiometric amounts of the reactants to give the desired coupling product in an excellent yield.

Preparative scale isolation, purification and derivatization of mimosine, a non-proteinogenic amino acid

Focusing on drug discovery non-proteinogenic amino acids have often been used as important building blocks for construction of compound libraries in the filed of combinatorial chemistry and chemical biology. Highly homogeneous l-mimosine, α-amino-β-(3-hydoxy-4-oxo-1,4-dihydropyridin-1-yl)-propanoic acid, a non-proteinogenic amino acid, has been successfully isolated and purified on an industrial scale from wild leaves of Leucaena (Leucaena leucocephala de Wit) which is a widely distributed legume in Okinawa, a sub-tropical island in Japan. Optical purity determinations used for quality control have been established through diastereomer formation. Physico-chemical properties and biological properties of purified mimosine have been clarified. Mimosine is sparingly soluble in water and organic solvents but can be dissolved in aqueous alkaline solution. The tyrosinase pathway is of particular interest in the cosmetic field, since mimosine is an analog of tyrosine. Thus the present purified mimosine have been tested in tyrosinase inhibitory assays. The IC50 for tyrosinase inhibitory activity of purified Mim was compared with kojic acid. Mimosine shows significant inhibition of melanin production in murine melanoma cells. The derivatization of mimosine has been investigated with a focus on its use in conventional peptide syntheses to generate mimosyl peptides. N-(9-Fluorenylmethoxycarbonyloxy)-mimosine and resin-bound mimosine for solid-phase syntheses have also been performed. Highly homogeneous Mim is a useful material for the development of functional cosmetics or active pharmaceutical ingredients.

Novel assay with fluorescence-labelled PrP peptides for differentiating L-type atypical and classical BSEs, and scrapie

PrP‐peptides HPP01, 02, 03, 06, 11 physically interact with PrPSc of L‐type atypical and classical BSEs, and scrapie by pull down

Structural Conversion Rate Changes of Recombinant Bovine Prion by Designed Synthetic Peptides

An understanding of structural changes and self-assembly of proteins, which are thought to involve specific peptide–peptide interactions, will contribute to the development of therapeutic agents and diagnosis for the detection of conformational diseases. We hypothesize that certain peptides may contribute to the conformational change of prion proteins. The present paper describes the discovery of prion-related synthetic peptides which influence structural conversion of recombinant bovine prion protein. The peptides designed are prion-protein fragments containing core domains consisting of α-helical (human prion protein fragment 180–195) and known β-sheet (human prion protein fragment 169–175) structures. Additionally several reported known β-sheet breaker peptides and a conjugate consisting of β-sheet and α-helix segments based on the secondary structures of human prion protein, designated HPPSH, have been chemically synthesized by the conventional Fmoc solid-phase method and characterized by circular dichroism and the Thioflavin T fluorescence method. Our data indicated that the co-existence of peptides, HPPSH or other prion fragment peptides involving toxic core sequence (the fragment 106–126), influenced the kinetic rate of aggregation and the lag-time of fibril formation of recombinant bovine prion protein except the core sequence itself. The method will be used for discovery of responsible material from natural resources. And designed peptides can be also used for bio-detection.

Telomere Visualization in Tissue Sections using Pyrrole–Imidazole Polyamide Probes

Pyrrole–Imidazole (PI) polyamides bind to specific DNA sequences in the minor groove with high affinity. Specific DNA labeling by PI polyamides does not require DNA denaturation with harsh treatments of heat and formamide and has the advantages of rapid and less disruptive processing. Previously, we developed tandem hairpin PI polyamide probes (TH59 series), which label telomeres in cultured cell lines more efficiently than conventional methods, such as fluorescence in situ hybridization (FISH). Here, we demonstrate that a TH59 derivative, HPTH59-b, along with immunostaining for specifying cell types in the tissues, visualizes telomeres in mouse and human tissue sections. Quantitative measurements of telomere length with single-cell resolution suggested shorter telomeres in the proliferating cell fractions of tumor than in non-tumor tissues. Thus, PI polyamides are a promising alternative for telomere labeling in clinical research, as well as in cell biology.

Peptidoglycan microarray as a novel tool to explore protein–ligand recognition

Peptidoglycan is a giant bag‐shaped molecule essential for bacterial cell shape and resistance to osmotic stresses. The activity of a large number of bacterial surface proteins involved in cell growth and division requires binding to this macromolecule. Recognition of peptidoglycan by immune effectors is also crucial for the establishment of the immune response against pathogens. The availability of pure and chemically defined peptidoglycan fragments is a major technical bottleneck that has precluded systematic studies of the mechanisms underpinning protein‐mediated peptidoglycan recognition. Here, we report a microarray strategy suitable to carry out comprehensive studies to characterize proteins–peptidoglycan interactions. We describe a method to introduce a functional group on peptidoglycan fragments allowing their stable immobilization on amorphous carbon chip plates to minimize nonspecific binding. Such peptidoglycan microarrays were used with a model peptidoglycan binding protein—the human peptidoglycan recognition protein‐S (hPGRP‐S). We propose that this strategy could be implemented to carry out high‐throughput analyses to study peptidoglycan binding proteins.

Recognition of a monoclonal antibody against a small molecular weight antigen by monitoring the antigen-antibody reaction using fluorescence labeled structured peptides.

Interaction between proteins (as analytes) and de novo designed structured peptides as capture molecules cause structural changes, which are reflected in fluorescent-intensity changes of labeled peptides in a dose dependent manner. In contrast to conventional detection methods our detection system does not involve the detection of specific molecules themselves in a 1:1 manner, but uses the principle of the differences in fluorescent intensity changes of capture peptides upon addition of analytes. Instead of the use of secondary antibodies we have attempted monitoring these structural changes by an array of de novo designed synthetic and structured peptides. In the present study we have focused on a recognition system, 5-fluorouracil, as a low molecular antigen and a monoclonal antibody against 5-FU. The fluorescent intensity changes of fluorescent labeled peptides have been measured after incubation with a monoclonal antibody and again after further incubation with the antigen, 5-FU. Unique intensity changes were found for several peptides in the fluorescent peptide library that allowed the visualization as a color-coded protein fingerprint. The peptide screen used in the present study offers a useful detection system as capture molecules for peptide-based microarrays.

SEPARATION OF PEPTIDES HAVING STRUCTURES AND DERIVATIVES OF MIMOSINE, A NONPROTEINOGENIC AMINO ACID, BY A NOVEL REVERSE-PHASE HPLC COLUMN PACKED WITH WIDE-PORE SILICA

To elucidate the mechanisms of the self-assembly and understand the molecular basis of the pathogenesis of conformational changes of proteins, β-amyloid or prion protein related peptides are indispensable materials. Hence, these peptides are known to have β-sheet rich structures that tend to cause difficulty in syntheses, as well as characterization by the conventional solid-phase assembly with reversed-phase columns. In general, reversed-phase HPLC combined with on-line mass spectrometry (LCMS) is routinely used for analyses and purification of resulting crude peptides and is carried out using preparative scale HPLC-columns. However, for such peptides, conventional C18 columns often give broad-peaks. We have improved separation procedures using a novel column packed with wide-pore silica having hydrophilic properties that gave separation of structural conformers with improved profiles. Thus, we have prepared several peptides for conformational studies. The same column also offers advantages for the chiral analysis of mimosine, a nonproteinogenic amino acid, which cannot be separated by the conventional C18 columns. Supplemental materials are available for this article. Go to the publishers online edition of the Journal of Liquid Chromatography and Related Technologies to view the supplemental file.