Spectrum structures and biological functions of 8-mers in the human genome

The spectra of k-mer frequencies can reveal the structures and evolution of genome sequences. We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We conjectured that (1) nucleosome binding motifs are mainly characterized by CG1 8-mers and (2) the core structural units of CpG island sequences are predominantly characterized by CG2 8-mers. To validate our conjectures, nucleosome occupied sequences and CGI sequences were extracted, then the sequence parameters were constructed through the information of the three CG 8-mer sets respectively. ROC analysis showed that CG1 8-mers are more preference in nucleosome occupied segments (AUC > 0.7) and CG2 8-mers are more preference in CGI sequences (AUC > 0.99). This validates our conjecture in principle.     

Cyclopentene dialdehydes from Tabebuia impetiginosa

The isolation of two cyclopentene dialdehydes, 2-formyl-5-(4'-methoxybenzoyloxy)-3-methyl-2-cyclopentene-1-acetal dehyde, and 2-formyl-5-(3', 4'-dimethoxybenzoyloxy)-3-methyl-2-cyclopentene-1-acetaldehyde, from the bark of Tabebuia impetiginosa is reported. The structures were established by analysis of spectroscopic data. These compounds showed anti-inflammatory activity.     

Organization of model helical peptides in lipid bilayers: insight into the behavior of single-span protein transmembrane domains

Selectively deuterated transmembrane peptides comprising alternating leucine-alanine subunits were examined in fluid bilayer membranes by solid-state nuclear magnetic resonance (NMR) spectroscopy in an effort to gain insight into the behavior of membrane proteins. Two groups of peptides were studied: 21-mers having a 17-amino-acid hydrophobic domain calculated to be close in length to the hydrophobic thickness of 1-palmitoyl-2-oleoyl phosphatidylcholine and 26-mers having a 22-amino-acid hydrophobic domain calculated to exceed the membrane hydrophobic thickness. (2)H NMR spectral features similar to ones observed for transmembrane peptides from single-span receptors of higher animal cells were identified which apparently correspond to effectively monomeric peptide. Spectral observations suggested significant distortion of the transmembrane alpha-helix, and/or potential for restriction of rotation about the tilted helix long axis for even simple peptides. Quadrupole splittings arising from the 26-mer were consistent with greater peptide "tilt" than were those of the analogous 21-mer. Quadrupole splittings associated with monomeric peptide were relatively insensitive to concentration and temperature over the range studied, indicating stable average conformations, and a well-ordered rotation axis. At high peptide concentration (6 mol% relative to phospholipid) it appeared that the peptide predicted to be longer than the membrane thickness had a particular tendency toward reversible peptide-peptide interactions occurring on a timescale comparable with or faster than approximately 10(-5) s. This interaction may be direct or lipid-mediated and was manifest as line broadening. Peptide rotational diffusion rates within the membrane, calculated from quadrupolar relaxation times, T(2e), were consistent with such interactions. In the case of the peptide predicted to be equal to the membrane thickness, at low peptide concentration spectral lineshape indicated the additional presence of a population of peptide having rotational motion that was restricted on a timescale of 10(-5) s.     

Biologically active oligodeoxyribonucleotides. Part 11: The least phosphate-modification of quadruplex-forming hexadeoxyribonucleotide TGGGAG, bearing 3′- and 5′-end-modification, with anti-HIV-1 activity

We have found that a hexadeoxyribonucleotide (5′TGGGAG3′, R-95288), Koizumi, M. et al. Bioorganic & Medicinal Chemistry, 1997, 5, 2235, bearing a 3,4-dibenzyloxybenzyl (3,4-DBB) group at the 5′-end and a 2-hydroxyethylphosphate at the 3′-end, has high anti-HIV-1 activity and the least cytotoxicity in vitro and in vivo. In order to synthesize more potent hexadeoxyribonucleotides, we substituted phosphodiester (P---O) bonds in the 6-mer with the least phosphorothioate (P---S), phosphoramidate (P---N), or methylphosphonate (P---Me) bonds. When more than two P---N or P---Me bonds were introduced into a 6-mer, the phosphate-modified 6-mers had weak or no anti-HIV-1 activity, in spite of quadruplex structure formation. However, when P---S bonds were substituted for P---O bonds, anti-HIV-1 activity of their 6-mers did not dramatically decrease, compared with compounds substituted with P---N or P---Me bonds. The results suggest that the formation of a quadruplex structure is not always sufficient for anti-HIV-1 activity of the 6-mer, and that net negative charges derived from P---O or P---S bonds in the quadruplex are important for anti-HIV-1 activity. Moreover, among various phosphate-modified ODNs, we found that the anti-HIV-1 activity of ODN PS7 with only one P---S bond was the same as that of R-95288, both having a high stability in human plasma.     

Modified chitosans carrying sulfonic acid groups

The sulfonic acid function was introduced into chitosan by reacting it with 5-formyl-2-furansulfonic acid, sodium salt, under the mild conditions of the Schiff reaction, thus avoiding polymer degradation and O-substitution. The reaction of chitosan (degree of deacetylation 0·58) with 5-formyl-2-furansulfonic acid, sodium salt produced a viscous solution that, upon hydrogenation, yielded N-sulfofurfuryl chitosan sodium salt. Infrared spectrometry, alkalimetry and elemental analysis provided evidence that the degree of substitution was 0·26. Circular dichroism measurements on solutions showed multiple Cotton bands in the pH interval 7·1–8·3, while at lower and higher pH values just one negative band was observed, thus providing indication of the polyampholyte nature of N-sulfofurfuryl chitosan. The ¹³C-NMR and FTIR spectra showed typical signals of furane carbons. Metal ion solutions at concentrations in the range 0·1–5·0 m , pH 6, promoted precipitation of metal ion complexes of N-sulfofurfuryl chitosan, with most effective removal from the solutions for Cu(II), Pb(II) and Ni(II). Sulfoethyl N-carboxymethyl chitosan was also synthesized from 2-chloroethanesulfonic acid in organic media: the sulfur content was similar (3·7%) in both polymers.     

Alkaloids from Corydalis saxicola and their anti-hepatitis B virus activity

Eight protoberberine-type alkaloids and two indole alkaloids were isolated from the MeOH extracts of the herb Corydalis saxicola Bunting (Papaveraceae). Their structures were identified as dehydrocavidine (1), dehydroapocavidine (2), dehydroisoapocavidine (3), berberine (4), dehydroisocorypalmine (5), coptisine (6), tetradehydroscoulerine (7), berbinium (8), 1-formyl-5-methoxy-6-methylindoline (9), and 1-formyl-2-hydroxy-5-methoxy-6-methylindoline (10). Compounds 3, 9, and 10 are new alkaloids. All compounds were tested for anti-HBV activity against the 2.2.15 cell line in vitro. Dehydrocavidine (1), dehydroapocavidine (2), and dehydroisoapocavidine (3) exhibited inhibitory activity against HBsAg and HBeAg, but no cytotoxicity against the 2.2.15 cell line.     

Immunodominant epitopes in herpes simplex virus type 2 glycoprotein D are recognized by CD4 lymphocytes from both HSV-1 and HSV-2 seropositive subjects

In human recurrent cutaneous herpes simplex, there is a sequential infiltrate of CD4 and then CD8 lymphocytes into lesions. CD4 lymphocytes are the major producers of the key cytokine IFN-gamma in lesions. They recognize mainly structural proteins and especially glycoproteins D and B (gD and gB) when restimulated in vitro. Recent human vaccine trials using recombinant gD showed partial protection of HSV seronegative women against genital herpes disease and also, in placebo recipients, showed protection by prior HSV1 infection. In this study, we have defined immunodominant peptide epitopes recognized by 8 HSV1(+) and/or 16 HSV2(+) patients using (51)Cr-release cytotoxicity and IFN-gamma ELISPOT assays. Using a set of 39 overlapping 20-mer peptides, more than six immunodominant epitopes were defined in gD2 (two to six peptide epitopes were recognized for each subject). Further fine mapping of these responses for 4 of the 20-mers, using a panel of 9 internal 12-mers for each 20-mers, combined with MHC II typing and also direct in vitro binding assay of these peptides to individual DR molecules, showed more than one epitope per 20-mers and promiscuous binding of individual 20-mers and 12-mers to multiple DR types. All four 20-mer peptides were cross-recognized by both HSV1(+)/HSV2(-) and HSV1(-)/HSV2(+) subjects, but the sites of recognition differed within the 20-mers where their sequences were divergent. This work provides a basis for CD4 lymphocyte cross-recognition of gD2 and possibly cross-protection observed in previous clinical studies and in vaccine trials.     

Pentamers not found in the universal proteome can enhance antigen specific immune responses and adjuvant vaccines

Certain short peptides do not occur in humans and are rare or non-existent in the universal proteome. Antigens that contain rare amino acid sequences are in general highly immunogenic and may activate different arms of the immune system. We first generated a list of rare, semi-common, and common 5-mer peptides using bioinformatics tools to analyze the UniProtKB database. Experimental observations indicated that rare and semi-common 5-mers generated stronger cellular responses in comparison with common-occurring sequences. We hypothesized that the biological process responsible for this enhanced immunogenicity could be used to positively modulate immune responses with potential application for vaccine development. Initially, twelve rare 5-mers, 9-mers, and 13-mers were incorporated in frame at the end of an H5N1 hemagglutinin (HA) antigen and expressed from a DNA vaccine. The presence of some 5-mer peptides induced improved immune responses. Adding one 5-mer peptide exogenously also offered improved clinical outcome and/or survival against a lethal H5N1 or H1N1 influenza virus challenge in BALB/c mice and ferrets, respectively. Interestingly, enhanced anti-HBsAg antibody production by up to 25-fold in combination with a commercial Hepatitis B vaccine (Engerix-B, GSK) was also observed in BALB/c mice. Mechanistically, NK cell activation and dependency was observed with enhancing peptides ex vivo and in NK-depleted mice. Overall, the data suggest that rare or non-existent oligopeptides can be developed as immunomodulators and supports the further evaluation of some 5-mer peptides as potential vaccine adjuvants.     

Analysis of the sequence motifs responsible for the interactions of peroxins 14 and 5, which are involved in glycosome biogenesis in Trypanosoma brucei

Glycosome biogenesis in trypanosomatids occurs via a process that is homologous to peroxisome biogenesis in other eukaryotes. Glycosomal matrix proteins are synthesized in the cytosol and imported posttranslationally. The import process involves a series of protein-protein interactions starting by recognition of glycosomal matrix proteins by a receptor in the cytosol. Most proteins to be imported contain so-called PTS-1 or PTS-2 targeting sequences recognized by, respectively, the receptor proteins PEX5 and PEX7. PEX14, a protein associated with the peroxisomal membrane, has been identified as a component of the docking complex and a point of convergence of the PEX5- and PEX7-dependent import pathways. In this paper, the strength of the interactions between Trypanosoma brucei PEX14 and PEX5 was studied by a fluorescence assay, using (i) a panel of N-terminal regions of TbPEX14 protein variants and (ii) a series of different peptides derived from TbPEX5, each containing one of the three WXXXF/Y motifs present in this receptor protein. On the PEX14 side, the N-terminal region of TbPEX14 including residues 1-84 appeared to be responsible for TbPEX5 binding. The results from PEX14 mutants identified specific residues in the N-terminal region of TbPEX14 involved in PEX5 binding and showed that in particular hydrophobic residues F35 and F52 are critical. On the PEX5 side, 13-mer peptides incorporating the first or the third WXXXF/Y motif bind to PEX14 with an affinity in the nanomolar range. However, the second WXXXF/Y motif peptide did not show any detectable affinity. Studies using variants of second and third motif peptides suggest that the alpha-helical content of the peptides as well as the charge of a residue at position 9 in the motif may be important for PEX14 binding. Assays with 7-, 10-, 13-, and 16-mer third motif peptides showed that 16-mers and 13-mers have comparable binding affinity for PEX14, whereas 10-mers and 7-mers have about 10- and 100-fold lower affinity than the 16-mers, respectively. The low sequence identities of PEX14 and PEX5 between parasite and its human host, and the vital importance of proper glycosome biogenesis to the parasite, render these peroxins highly promising drug targets.     

Refined peptide HLA-B*3501 binding motif reveals differences in 9-mer to 11-mer peptide binding

 HLA-B^*3501 is associated with subacute thyroiditis and fast progression of AIDS. An important prerequisite to investigate the T-cell recognition of HLA-B^*3501-restricted antigens is the characterization of peptide-HLA-B^*3501 interactions. In this study, peptide-HLA-B^*3501 interactions were determined in quantitative peptide binding assays. The results were statistically analyzed to evaluate the influence of both anchor and nonanchor positions and the predictability of peptide binding. The binding data demonstrated that all anchor residues at position 2 and the C-terminus found in 9-mers functioned equally as anchors in 10-mers and 11-mers. These minimum requirements of peptide binding were refined by assessing positive and negative effects of nonanchor residues. Aliphatic hydrophobic residues at positions 3, 5, and 8 of 10-mers and position 3 of 11-mers significantly enhanced HLA-B^*3501 binding. Similar effects rendered aromatic, bulky residues, acidic or polar residues of 11-mers at position 1 as well as at positions 4, 8, and 10, respectively. Negative effects were observed for residues carrying positively charged side-chains at position 7 of 11-mers. The refined HLA-B^*3501 peptide binding motifs enhanced the identification of potential T-cell epitopes. The disparity between positive effects at the middle and C-terminal part (positions 5 – 8 and 10) of 11-mers and shorter peptides supports the extrusion of 11-mer residues at positions 5, 6, and 7, away from the HLA-B^*3501 binding cleft. Received: 29 May 1996 / Revised: 5 August 1996     

Nucleosides and nucleotides. 126. Incorporation of a mutagenic nucleoside, 5-formyl-2′-deoxyuridine, into an oligodeoxyribonucleotide

An oligodeoxyribonucleotide containing 5-formyl-2′-deoxyuridine (1) was synthesized using a new protecting group of the formyl group.     

The Synthesis of 5-Substituted-2, 4-dimethoxypyrimidines and Some Related Nucleoside Analogues

Abstract

The reaction of 5-formyl-2,4-dimethoxypyrimidine with active methylene compounds in the Knoevenagel reaction and the subsequent nucleoside formation reactions of some of the products was investigated. A new synthesis of (E)-5-(2-bromovinyl)uracil and an improved synthesis of 5-formyl-2′,3′-isopropylidene uridine are reported.     

A contribution to the chemistry of pyrazole-type dianhydrophenylosazones

3,4,5,6-Tetra-O-acetyl-d-lyxo-hexosulose 1-acetylphenylhydrazone 2-phenylhydrazone (10) was transformed into 5-(d-glycero-1,2-diacetoxyethyl)-3-formyl-1-phenylpyrazole acetylphenylhydrazone (d-4, n = 3) in boiling acetic anhydride containing anhydrous sodium acetate. Racemic 3,4,6-tri-O-acetyl-5-deoxyhex-4-enos-2-ulose 1-acetylphenylhydrazone 2-phenylhydrazone (11) was isolated as an intermediate in the reaction performed in the absence of sodium acetate. The cyclisation of 11, via allylic rearrangement, into dl-4 (n = 3) and 5-(dl-glycero-1,2-dihydroxyethyl)-3-formyl-1-phenylpyrazole acetylphenylhydrazone (dl-3, n = 3) in acidic, neutral, and basic media is described.     

Structure and cytotoxic activity of enzymatic hydrolysis products of secoiridoid glucosides, isoligustroside and isooleuropein

Hydrolysis of isoligustroside (1) and isooleuropein (2), secoiridoid glucosides, in the presence of β-glucosidase provided 2-(4-hydroxyphenyl)methyl (2R,3S,4S)-3-formyl-3,4-dihydro-4-(2-methoxy-2-oxoethyl)-2-methyl-2H-pyran-5-carboxylate (3) and 2-(3,4-dihydroxyphenyl)methyl (2R,3S,4S)-3-formyl-3,4-dihydro-4-(2-methoxy-2-oxoethyl)-2-methyl-2H-pyran-5-carboxylate (4), respectively. The structures of 3 and 4 were elucidated on the basis of extensive spectral analyses, including 2D-NMR experiments. Compounds 3 and 4 were found to be new rearrangement products of the aglycones of 1 and 2. The cytotoxic activities of 3 and 4 were evaluated using a disease-oriented panel of 39 human cancer cell lines and showed moderate cytotoxic activity for 4, while 3 exhibited weaker activity compared to that of 4.     

Biologically Active Oligodeoxyribonucleotides - IV: Anti-HIV-1 Activity of Tgggag Having Hydrophobic Substituent at Its 5′-End via Phosphodiester Linkage

Abstract

Hexadeoxyribonucleotides (6-mers) having a 5′-TGGGAG-3′ sequence bearing hydrophobic substituents at their 5′-ends via phosphodiester linkages were prepared and evaluated for anti-HIV-1 activity in vitro. Some of these modified 6-mers showed weak anti-HIV-1 activities and they were less potent than the 6-mer having a DMTr group directly attached at its 5′-terminus.

     

Lignin degradation byPhanerochaete chrysosporium: Metabolism of a phenolic phenylcoumaran substructure model compound

The degradation of a lignin substructure model compound, 5-formyl-3-hydroxymethyl-2-(4-hydroxy-3,5-dimethoxyphenyl)-7-methoxycoumaran (I), in ligninolytic culture of a white-rot wood decay fungus,Phanerochaete chrysosporium, was investigated. It was found that I was hydroxylated or dehydrogenated in its coumaran ring to give 2-(5-formyl-2-hydroxy-3-methoxyphenyl)-3-hydroxypropiosyringone (II) and two coumarones, 5-formyl-3-hydroxymethyl-2-(4-hydroxy-3,5-dimethyoxyphenyl)-7-methoxycoumarone (V) and 3,5-diformyl-2-(4-hydroxy-3,5-dimethoxyphenyl)-7-methoxycoumarone (VI), II was further converted to 2,6-dimethoxy-p-benzoquinone (IV), syringic acid (III), and 5-carboxyvanillic acid (VIII). These metabolic products were identified by mass spectrometric comparison with the authentic compounds. A proposed pathway for the degradation of I is presented on the basis of these metabolic products. The degradation could be catalyzed mainly by phenol-oxidizing enzymes.Non-Standard Abbreviations TLC thin layer chromatography     

Alumina-supported synthesis of antibacterial quinolines using microwaves

7-(5'-Alkyl-1',3',4'-thiadiazol/oxadiazol-2'-ylthio)-6 -fluoro-2,4-dimethylquinolines and 3-formyl-2-(2'-hydroxy- 1',4'-naphthoquinon-3'-yl)-4-methyl/6-methyl/7-quinolines have been synthesised by the reaction of 5-alkyl-1,3,4-thiadiazol/oxadiazol-2-thiols with 7-chloro-6-fluoro-2,4-dimethylquinoline and by the reaction of 2-hydroxy-1,4-naphthoquinone with 2-chloro-3-formyl-4-methyl/6-methyl/7-methyl/8-methylquinolines respectively on basic alumina using microwaves, the reaction time has been brought down from hours to seconds with improved yield as compared to conventional heating. The compounds were tested for their in vitro antibacterial activity. All compounds showed promising antibacterial activity. The best activity was observed by compounds 3a and 3f.     

Unusual chromenes from Peperomia blanda

From the methanol extract of the aerial parts of Peperomia blanda (Piperaceae), two chromenes were isolated and characterized mainly through application of 2D-NMR spectroscopy. The structures were 2S-(4-methyl-3-pentenyl)-6-formyl-8-hydroxy-2,7-dimethyl-2H-chromene and 2S-(4-methyl-3-pentenyl)-5-hydroxy-6-formyl-2,7-dimethyl-2H-chromene named as blandachromenes I and II, respectively.