- 著者
- Tomohisa Takagi Yuji Naito Ryo Inoue Saori Kashiwagi Kazuhiko Uchiyama Katsura Mizushima Saeko Tsuchiya Tetsuya Okayama Osamu Dohi Naohisa Yoshida Kazuhiro Kamada Takeshi Ishikawa Osamu Handa Hideyuki Konishi Kayo Okuda Yoshimasa Tsujimoto Hiromu Ohnogi Yoshito Itoh
- 出版者
- SOCIETY FOR FREE RADICAL RESEARCH JAPAN
- 雑誌
- Journal of Clinical Biochemistry and Nutrition (ISSN:09120009)
- 巻号頁・発行日
- vol.62, no.1, pp.100-105, 2018 (Released:2018-01-01)
- 参考文献数
- 23
- 被引用文献数
- 86
Proton pump inhibitors (PPIs) are widely used to treat gastro-esophageal reflux and prevent gastric ulcers, and have been considered as low risk. However, recent studies have identified possible associations between PPI use and gut microbiota, suggesting that PPIs use increases the risk of enteric infections, including Clostridium difficile infection. To investigate gut microbiota in Japanese PPIs users, we conducted 16S metagenomics analysis of fecal samples collected from PPI users and healthy adults. In total, 36 PPI users and 36 PPI non-users (as control subjects) matched by age and sex were recruited and fecal samples were obtained to analyze the gut microbiome using 16S rRNA gene sequencing. There were significant differences in the microbial structure between PPI non-users and PPI users. In contrast, the analysis of α-diversity revealed no significant differences between PPI non-users and PPI users. When comparing in genus level between these two groups, the genera Streptococcus was significantly abundant and the genera Faecalibacterium was significantly decreased in PPI users. Our findings indicate a probable association between PPI use and the alternation of microbiota. These alterations might provide a mechanism by which PPIs predispose enteric infection such as Clostridium difficile infection.
- 著者
- Norihito Kawashita Hiroyuki Yamasaki Tomoyuki Miyao Kentaro Kawai Yoshitake Sakae Takeshi Ishikawa Kenichi Mori Shinya Nakamura Hiromasa Kaneko
- 出版者
- 公益社団法人 日本化学会・情報化学部会
- 雑誌
- Journal of Computer Aided Chemistry (ISSN:13458647)
- 巻号頁・発行日
- vol.16, pp.15-29, 2015 (Released:2015-10-29)
- 参考文献数
- 192
- 被引用文献数
- 3 6
We have reviewed chemoinformatics approaches for drug discovery such as aromatic interactions, aromatic clusters, structure generation, virtual screening, de novo design, evolutionary algorithm, inverse-QSPR/QSAR, Monte Carlo, molecular dynamics, fragment molecular orbital method and matched molecular pair analysis from the viewpoint of young researchers. We intend to introduce various fields of chemoinformatics for non-expert researchers. The structure of this review is given as follows: 1. Introduction, 2. Analysis of Aromatic Interactions, 2.1 Aromatic Interactions, 2.2 Aromatic Clusters, 3. Ligand Based Structure Generation, 3.1 Virtual Screening, 3.2 De Novo Ligand Design, 3.3 Combinatorial Explosion, 3.4 Inverse-QSPR/QSAR, 4. Trends in Chemoinformatics-Based De Novo Drug Design, 5. Conformational Search Method Using Genetic Crossover for Bimolecular Systems, 6. Interaction Analysis using Fragment Molecular Orbital Method for Drug Discovery, 7. Matched Molecular Pair Analysis and SAR Analysis by Fragment Molecular Orbital Method, 8. Chemoinformatics Approach in Pharmaceutical Processes, 9. Conclusion.
- 著者
- Tomohisa Takagi Yuji Naito Ryo Inoue Saori Kashiwagi Kazuhiko Uchiyama Katsura Mizushima Saeko Tsuchiya Tetsuya Okayama Osamu Dohi Naohisa Yoshida Kazuhiro Kamada Takeshi Ishikawa Osamu Handa Hideyuki Konishi Kayo Okuda Yoshimasa Tsujimoto Hiromu Ohnogi Yoshito Itoh
- 出版者
- SOCIETY FOR FREE RADICAL RESEARCH JAPAN
- 雑誌
- Journal of Clinical Biochemistry and Nutrition (ISSN:09120009)
- 巻号頁・発行日
- pp.17-78, (Released:2017-12-12)
- 参考文献数
- 23
- 被引用文献数
- 86
Proton pump inhibitors (PPIs) are widely used to treat gastro-esophageal reflux and prevent gastric ulcers, and have been considered as low risk. However, recent studies have identified possible associations between PPI use and gut microbiota, suggesting that PPIs use increases the risk of enteric infections, including Clostridium difficile infection. To investigate gut microbiota in Japanese PPIs users, we conducted 16S metagenomics analysis of fecal samples collected from PPI users and healthy adults. In total, 36 PPI users and 36 PPI non-users (as control subjects) matched by age and sex were recruited and fecal samples were obtained to analyze the gut microbiome using 16S rRNA gene sequencing. There were significant differences in the microbial structure between PPI non-users and PPI users. In contrast, the analysis of α-diversity revealed no significant differences between PPI non-users and PPI users. When comparing in genus level between these two groups, the genera Streptococcus was significantly abundant and the genera Faecalibacterium was significantly decreased in PPI users. Our findings indicate a probable association between PPI use and the alternation of microbiota. These alterations might provide a mechanism by which PPIs predispose enteric infection such as Clostridium difficile infection.
- 著者
- Takuya Okamoto Takeshi Ishikawa Yoshiyuki Koyano Norifumi Yamamoto Kazuo Kuwata Masataka Nagaoka
- 出版者
- (社)日本化学会
- 雑誌
- Bulletin of the Chemical Society of Japan (ISSN:00092673)
- 巻号頁・発行日
- vol.86, no.2, pp.210-222, 2013-02-15 (Released:2013-02-15)
- 参考文献数
- 95
- 被引用文献数
- 20 4
For the purpose of providing a realistic description of the reaction mechanisms in large molecular systems, we propose a quantum mechanical/molecular mechanical (QM/MM) method combined with the ab initio fragment molecular orbital (FMO) method, i.e., the ab initio FMO-QM/MM method. By connecting a molecular dynamics (MD) program AMBER with an FMO program PAICS, we have implemented an AMBER-PAICS interface (AP-IF). Using the AP-IF, we demonstrate three example applications: (a) a hydrogen fluoride and water molecular clusters, (b) an alanine dipeptide in aqueous solution, and (c) a prion protein–GN8 complex. From these results, it is confirmed that the FMO-QM/MM method offers a good compromise between chemical accuracy and computational cost and enables us to obtain in ab initio quality the inter- and intramolecular interaction energies between molecules or residues in large molecular systems such as solution and biomolecule, by using the dynamics-based interfragment interaction energy (IFIE) analysis.