Chem-Bio Informatics Journal最新文献_第10页

Physicochemical properties of GPCR amino acid sequences for understanding GPCR-G-protein coupling GPCR氨基酸序列的理化性质为了解GPCR- g -蛋白偶联提供依据

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.49

Ganga D. Ghimire, Hideki Tanizawa, M. Sonoyama, S. Mitaku

引用次数: 1

Solvent Site-Dipole Field Accompanying Protein-Ligand Approach Process 溶剂位偶极子场伴随蛋白质配体接近过程

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.14

N. Takano, K. Umezawa, Jinzen Ikebe, Yuki Sonobe, Ryosuke Yagisawa, Ito Junichi, N. Hamasaki, D. Mitomo, H. Miyagawa, A. Yamagishi, J. Higo

引用次数: 7

Functional genomics analysis of n-alkyl sulfates toxicity in the yeast Saccharomyces cerevisiae 正烷基硫酸盐对酿酒酵母毒性的功能基因组学分析

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Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.69

S. Sirisattha, E. Kitagawa, M. Yonekura, H. Iwahashi

{"title":"Functional genomics analysis of n-alkyl sulfates toxicity in the yeast Saccharomyces cerevisiae","authors":"S. Sirisattha, E. Kitagawa, M. Yonekura, H. Iwahashi","doi":"10.1273/CBIJ.8.69","DOIUrl":"https://doi.org/10.1273/CBIJ.8.69","url":null,"abstract":"The n-alkyl sulfates (AS) are a class of anionic surfactants that are widely used in industry and in consumer products. In this study, the effects of AS on yeast growth and genome wide transcriptional profiles were analysed by DNA microarray technology. Induced genes were categorized by localization of gene products and by function according to accepted gene ontologies using the MIPS database. A number of genes whose products localized to the cell wall and peroxisome were significantly induced. Genes involved in energy metabolism (i.e., fatty acid β-oxidation pathway) were also significantly induced. To confirm the role of these functions, the sensitivity of selected single gene deletion strains to sodium dodecyl sulfate (SDS) was tested. Deletion strains of cell wall maintenance genes (ΔGAS1, ΔKRE6, and ΔCHS5) were found to be highly sensitive. Interestingly, mutants deleted for genes in the fatty acid β-oxidation pathway were not found to be sensitive. However, regulating genes in the fatty acid β-oxidation pathway were found to respond to SDS exposure in a dose-dependent manner and to be involved in H2O2 production. Here, we report a functional genomics analysis of genome-wide expression data to screen and evaluate AS toxicity in yeast. While the approach begins with a determination of highly-induced genes, its power lies in then determining the most relevant functions targeted by AS, and then assessing loss of key genes by evaluating AS sensitivity in the corresponding deletion mutants.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80373713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Application of Rough Set Theory to High Throughput Screening Data for Rational Selection of Lead Compounds 粗集理论在高通量筛选数据中合理选择先导化合物的应用

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.85

Michio Koyama, K. Hasegawa, Masamoto Arakawa, K. Funatsu

{"title":"Application of Rough Set Theory to High Throughput Screening Data for Rational Selection of Lead Compounds","authors":"Michio Koyama, K. Hasegawa, Masamoto Arakawa, K. Funatsu","doi":"10.1273/CBIJ.8.85","DOIUrl":"https://doi.org/10.1273/CBIJ.8.85","url":null,"abstract":"In the field of drug discovery, high-throughput screening (HTS) is widely used to identify new lead compounds. A considerable number of hit compounds, however, will subsequently be found to have low activities when their inhibitory activities are measured more precisely. Such compounds are called false positives. For a more efficient selection of lead compounds, virtual screening methods with QSAR models have been investigated, but no definitive solutions have been found. In this study, we propose an effective method to identify lead compounds. The proposed method is based on rough set theory (RST), which is a mathematical tool for depicting the uncertainty and vagueness of knowledge. The essential parts of RST are the construction of reducts, which are minimal subsets of variables to distinguish samples, and the extraction of rules using their reducts. By applying RST to the QSAR study of monoamine oxidase (MAO) inhibitors, we extracted several rules for identifying lead compounds. First, 3D-structures of MAO inhibitors were generated uniformly by CORINA, and chemical descriptors were calculated by the Volsurf method. Finally, three unique rules were extracted by using RST. It is found that the each rule is chemically reasonable and compatible with previous studies. Furthermore, the predictive power of RST was also proved by comparison with partial least squares (PLS) and decision tree (DT). These results demonstrate the usefulness of our method.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81100203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Integrated pharmacokinetic assessment and strategy for orally effective prodrugs overcoming luminal degradation and biological membrane barriers 口服有效前药克服腔内降解和生物膜屏障的综合药代动力学评价与策略

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.58

T. Mizuma

{"title":"Integrated pharmacokinetic assessment and strategy for orally effective prodrugs overcoming luminal degradation and biological membrane barriers","authors":"T. Mizuma","doi":"10.1273/CBIJ.8.58","DOIUrl":"https://doi.org/10.1273/CBIJ.8.58","url":null,"abstract":"Because no kinetic principles have been proposed for designing orally effective prodrugs, the author recently reported a kinetic model for membrane transport of prodrugs (Chem-Bio Informatics Journal, 8, 25-32 (2008)), and proposed the kinetic classification and criteria for effective membrane-permeable prodrugs (KCCEMP). The present study addressed more practical conditions, where a prodrug is metabolized/degraded to a drug in the luminal tract after oral administration. Primary factors in orally effective prodrugs are luminal degradation/metabolism and absorption clearance (permeability), which includes the mechanism of membrane transport and metabolism in intestinal cells. The fraction of absorbed prodrug is expressed by the functions of these parameters. Based on the required improvement ratio of the absorption clearance, the kinetic classification and criteria of orally effective prodrugs (KCCOEP) are proposed as a decision tree with conditional equations for guiding kinetic assessment and strategy for the rational development of prodrugs. The assessment of lenampicillin, which was selected as an example of successful prodrugs, according to the procedure indicated a significant impact of luminal degradation/metabolism on the absorbed fraction, and suggests that most ester-type prodrugs on the market degrade in the luminal tract. Thus, a comprehensive study on the fraction of luminal degradation/metabolism and the absorption clearance (permeability) should be conducted to develop orally effective prodrugs, in particular, quantitative assessment of the fraction of contribution (fc,dd) of the drug formed from the prodrug in the luminal tract to the absorption following oral administration of the prodrug is emphasized.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87866516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Density, Diffusion, and Site-Dipole Field of Solvent around Four Types of Flavonoid Studid by Molecular Dynamics 分子动力学研究了四类黄酮类化合物周围溶剂的密度、扩散和位偶极子场

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2008-01-01 DOI: 10.1273/CBIJ.8.33

丸山慶一朗, 成敏神谷, 永淑尹, 彰功刀, 剛横溝, 順一肥後

{"title":"Density, Diffusion, and Site-Dipole Field of Solvent around Four Types of Flavonoid Studid by Molecular Dynamics","authors":"丸山慶一朗, 成敏神谷, 永淑尹, 彰功刀, 剛横溝, 順一肥後","doi":"10.1273/CBIJ.8.33","DOIUrl":"https://doi.org/10.1273/CBIJ.8.33","url":null,"abstract":"We studied hydration of four types of small nonpeptidic molecule, flavonoid, by molecular dynamics simulations at 300 K with focusing on three physical quantities: solvent density, solvent site-dipole field, and solvent diffusion. The solvent site-dipole field is a quantity recently introduced by us to study directional ordering of water molecules around solute. The spatial patterns of these quantities showed strong site-dependency around the flavonoids. Common to the four flavonoids, high solvent-density sites around hydrophilic solute atoms were characterized by strong directional ordering of water molecule and by depressed solvent diffusive motions. Contrarily, high solvent-density sites around hydrophobic solute surface were characterized by weak directional ordering. The solvent site-dipole field showed specific ordering patterns of water molecules not only in the first solvent layer but also in the second solvent layer. The spatial patterns of the three quantities were conservative among the four flavonoids whether the intra-flavonoid flexibility was large or not. Thus, an adiabatic approximation, which has been assumed in various theoretical hydration studies, was satisfied well. The hydration at a site in the vicinity of solute was determined mainly by the physico-chemical property of the solute atom group nearest to the solvent site, which supports a phenomenological theorem that the solvent accessible surface area of a solute is proportional to the solvation free energy.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74996294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Nuclear localization of proteins with a charge periodicity of 28 residues 具有28个残基电荷周期的蛋白质的核定位

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2007-01-01 DOI: 10.1273/CBIJ.7.35

N. Sakiyama, R. Ke, R. Sawada, M. Sonoyama, S. Mitaku

引用次数: 5

Compound-Transporter Interaction Studies using Canonical Correlation Analysis 使用典型相关分析的化合物-转运体相互作用研究

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2007-01-01 DOI: 10.1273/CBIJ.7.24

M. Kitajima, Yohsuke Minowa, H. Matsuda, Y. Okuno

引用次数: 0

Implementation of the blue moon ensemble method 实现蓝月亮集合法

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Chem-Bio Informatics Journal Pub Date : 2007-01-01 DOI: 10.1273/CBIJ.7.12

Y. Komeiji

引用次数: 15

Nuclear proteins with charge periodicity of 28 residues are specifically increased in vertebrate genomes 具有28个残基电荷周期性的核蛋白在脊椎动物基因组中特异性增加

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2007-01-01 DOI: 10.1273/CBIJ.7.69

N. Sakiyama, R. Ke, R. Sawada, M. Sonoyama, S. Mitaku

{"title":"Nuclear proteins with charge periodicity of 28 residues are specifically increased in vertebrate genomes","authors":"N. Sakiyama, R. Ke, R. Sawada, M. Sonoyama, S. Mitaku","doi":"10.1273/CBIJ.7.69","DOIUrl":"https://doi.org/10.1273/CBIJ.7.69","url":null,"abstract":"More than 36,000 open reading frames (ORFs) from the human genome were previously analyzed by the autocorrelation function of electric charge distribution, revealing the existence of many proteins with a charge periodicity of 28 residues (PCP28) (Ke et al., Jpn. J. Appl. Phys. 2007). The major component of PCP28 was located in the nucleus, and the nuclear PCP28 of ten vertebrate and seven invertebrate organisms were predicted with a novel software system (Sakiyama et al., CBI Journal 2007) for revealing the biological significance of nuclear PCP28. Retrieval of the features of the human nuclear PCP28 in Swiss-Prot revealed that almost 90% of nuclear PCP28 functions in transcriptional regulation, including hypothetical transcription factors. To study how nuclear PCP28 is increased in eukaryote genomes, we compared the number of all nuclear PCP28 in vertebrate and invertebrate genomes. The results showed that nuclear PCP28 is specifically increased in vertebrate genomes and that the ratio of other types of PCP28 is almost constant in all eukaryote genomes. These findings strongly suggest that nuclear PCP28 is an essential protein for vertebrate organisms.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74685206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1