- 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
- Keiji Nishiwaki Shinya Nakamura Kenji Yoshioka Eri Nakagawa Shiori Nakatani Masato Tsuyuguchi Takayoshi Kinoshita Isao Nakanishi
- 出版者
- The Pharmaceutical Society of Japan
- 雑誌
- Chemical and Pharmaceutical Bulletin (ISSN:00092363)
- 巻号頁・発行日
- vol.71, no.7, pp.558-565, 2023-07-01 (Released:2023-07-01)
- 参考文献数
- 47
- 被引用文献数
- 2
Protein kinase CK2 (CK2) is involved in the suppression of gene expression, protein synthesis, cell proliferation, and apoptosis, thus making it a target protein for the development of therapeutics toward cancer, nephritis, and coronavirus disease 2019. Using the solvent dipole ordering-based method for virtual screening, we identified and designed new candidate CK2α inhibitors containing purine scaffolds. Virtual docking experiments supported by experimental structure–activity relationship studies identified the importance of the 4-carboxyphenyl group at the 2-position, a carboxamide group at the 6-position, and an electron-rich phenyl group at the 9-position of the purine scaffold. Docking studies based on the crystal structures of CK2α and inhibitor (PDBID: 5B0X) successfully predicted the binding mode of 4-(6-carbamoyl-8-oxo-9-phenyl-8,9-dihydro-7H-purin-2-yl) benzoic acid (11), and the results were used to design stronger small molecule targets for CK2α inhibition. Interaction energy analysis suggested that 11 bound around the hinge region without the water molecule (W1) near Trp176 and Glu81 that is frequently reported in crystal structures of CK2α inhibitor complexes. X-ray crystallographic data for 11 bound to CK2α was in very good agreement with the docking experiments, and consistent with activity. From the structure–activity relationship (SAR) studies presented here, 4-(6-Carbamoyl-9-(4-(dimethylamino)phenyl)-8-oxo-8,9-dihydro-7H-purin-2-yl) benzoic acid (12) was identified as an improved active purine-based CK2α inhibitor with an IC50 of 4.3 µM. These active compounds with an unusual binding mode are expected to inspire new CK2α inhibitors and the development of therapeutics targeting CK2 inhibition.
- 著者
- Tatsuo Akaki Shinya Nakamura Keiji Nishiwaki Isao Nakanishi
- 出版者
- The Pharmaceutical Society of Japan
- 雑誌
- Chemical and Pharmaceutical Bulletin (ISSN:00092363)
- 巻号頁・発行日
- pp.c22-00866, (Released:2023-02-02)
- 参考文献数
- 52
- 被引用文献数
- 2
The fragment molecular orbital (FMO) method is a fast quantum-mechanics method that divides systems into pieces of fragments and performs ab initio calculations. The method has been expected to improve the accuracy of describing protein-ligand interactions by incorporating electronic effects. In this article, FMO calculation with solvation methods were applied to the affinity prediction at the ATP-binding site of PDHK4. As the ionized aspartic acid lies at the center and is involved in the complex hydrogen bond networks, this system has turned out to be a difficult target to describe by traditional molecular-mechanics method. In the FMO calculation with the polarizable continuum model (PCM) solvation method, a considerable amount of charge (-0.27e) was transferred from the ionized aspartate to the surrounding residues. We found that using FMO with the PCM solvation method was important to increase the correlation, and by incorporating the ligand deformation energy, the correlation was improved to R = 0.81 for whole twelve compounds and R= 0.91 without one outlier compound.
- 著者
- Masato Nakamura Takanari Kitazono Ken Kozuma Toru Sekine Shinya Nakamura Kazuhito Shiosakai Ayumi Tanabe Tomoko Iizuka
- 出版者
- The Japanese Circulation Society
- 雑誌
- Circulation Journal (ISSN:13469843)
- 巻号頁・発行日
- vol.84, no.11, pp.1981-1989, 2020-10-23 (Released:2020-10-23)
- 参考文献数
- 20
- 被引用文献数
- 4
Background:PRASFIT-Practice II is a postmarketing observational study conducted in 4,155 Japanese patients with ischemic heart disease (IHD) who received long-term prasugrel. The data were used to assess the utility of Academic Research Consortium for High Bleeding Risk (ARC-HBR) criteria.Methods and Results:Patients in PRASFIT-practice II were clinically followed for 2 years. The primary endpoint was the cumulative incidence of major adverse cardiovascular events (MACE) and Thrombolysis in Myocardial Infarction (TIMI) major/minor bleeding. Patients were divided into 2 groups based on ARC-HBR criteria (HBR (40.1% of patients) and non-HBR (59.9%)) and the effect of HBR on the primary endpoint was assessed. The median duration of dual antiplatelet therapy with prasugrel was 391.0 days. At 2 years, the cumulative incidence of MACE was 3.3%, and of TIMI major/minor bleeding was 2.7%. At 1 year, MACE and TIMI major/minor bleeding in the HBR group (4.0% and 3.4%, respectively) were higher than that in the non-HBR group (1.3% for both). Landmark analysis at 3 months and 1 year showed that the higher risk of MACE or TIMI major/minor bleeding in the HBR group persisted through 2 years.Conclusions:The results of this study confirmed the safety and effectiveness of long-term treatment with prasugrel, and demonstrated that the ARC-HBR criteria for bleeding risk are applicable in Japanese IHD patients treated with prasugrel.