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Article ; Online: VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform.

Baba, Natsumi / Akaho, Eiichi

2011 Volume 6, Issue 10, Page(s) 387–388

Abstract: ... pharm.kobegakuin.ac.jp/˜akaho/english_top.html. ...

Abstract	Unlabelled: Screening of ligand molecules to target proteins using computer-aided docking is a critical step in rational drug discovery. Based on this circumstance, we attempted to develop a virtual screening application system, named VSDK Virtual Screening by Docking, which can function under the Windows platform. This is a user-friendly, flexible, and versatile tool which can be used by users who are familiar with Windows OS. The virtual screening performance was tested for an arbitrarily-selected receptor, FGFR tyrosine kinase (pdb code: 1agw), by using ligands downloaded from ZINC database with its grid size of x,y,z = 30,30,30 and run number of 10. It took 90 minutes for 100 molecules for this virtual screening. VSDK is freely available at the designated URL, and a simplified manual can be downloaded from VSDK home page. This tool will have a more challenging scope and achievement as the computer speed and accuracy are increased and secured in the future. Availability: The database is available for free at http://www.pharm.kobegakuin.ac.jp/˜akaho/english_top.html.
Language	English
Publishing date	2011-08-02
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063 ; 0973-2063
ISSN (online)	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630006387
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structure-based drug design and AutoDock study of potential protein tyrosine kinase inhibitors.

Ali, Hamed Ismail / Nagamatsu, Tomofumi / Akaho, Eiichi

Bioinformation

2011 Volume 5, Issue 9, Page(s) 368–374

Abstract: Different classes of compounds were investigated for their binding affinities into different protein tyrosine kinases (PTKs) employing a novel flexible ligand docking approach by using AutoDock 3.05 and 4. These compounds include many flavin analogs, ... ...

Abstract	Different classes of compounds were investigated for their binding affinities into different protein tyrosine kinases (PTKs) employing a novel flexible ligand docking approach by using AutoDock 3.05 and 4. These compounds include many flavin analogs, which were developed in our group with varying degrees of cytotoxic activity (comparable or moderately superior to cisplatin and ara-c), and database selected analogs. They were docked onto twelve different families of PTKs retrieved from the Protein Data Bank. These proteins are representatives of plausible models of interactions with chemotherapeutic agents. A comparative study of the intact co-crystallized ligands of various types of PTKs was carried out. Results revealed that the new class of 5-deazapteridine and steroid hybrid compounds VIa,b, and d, and the vertical-type bispyridodipyrimidine with n-hexyl chain junction between its N-10 and N-10 atoms Xa, exhibited non-selective PTK binding capacities, with the lowest (Gb). On the other hand, 2-amino benzoic acid analog IIa, phenoxypyrido [3, 4-d]pyrimidine derivative IVc, tyrosine containing tripeptide Vd, and the one from Sumisho data base 831 are proposed to have selective PTK binding affinities to certain classes of tyrosine kinases, namely, HGFR (c-met), ZAP-70, insulin receptor kinase, EGFR, respectively. All These compounds of highest affinities were docked within the binding sites of PTKs with reasonable RMSD and 1-5 hydrogen bonds.
Language	English
Publishing date	2011-02-07
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063 ; 0973-2063
ISSN (online)	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630005368
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Article: An innovative classification of, and a new structure-activity-relationship approach to degradation kinetics of cephalosporins: an attempt to enhance the therapeutic activity.

Akaho, Eiichi / Nakayama, Hitomi

The Journal of antibiotics

2003 Volume 56, Issue 4, Page(s) 379–391

Abstract: Degradation kinetics of cephalosporins was innovatively classified into six groups according to its mechanism that is based on the attached functional and/or substituent groups. 3-Position plays an important role in the degradation kinetics, and they are ...

Abstract	Degradation kinetics of cephalosporins was innovatively classified into six groups according to its mechanism that is based on the attached functional and/or substituent groups. 3-Position plays an important role in the degradation kinetics, and they are classified into three major groups; one with a 3-acetoxy group, another with a 3-deacetoxy group, and the other without a 3-acetoxy group. Each group is further subdivided depending on whether it contains 7-x-amino group or not. The order of the alkaline hydrolysis of cephalosporins coincided with the order of the degree of their antibacterial activities. This provides an evidence to support the hypothesis that the biological activity of beta-lactam antibiotics depends upon the reactivity of the beta-lactam moiety. At the same time, the compound should be stable, and the stability is often related to the reactivity of 3-position. Combination products of biodegradable cephalosporins and acid-stable cephalosporins are desired products. An example of such products produced by chemical modifications stated above will be the one with a good leaving group at the 3-position that is not hydrolyzed.
MeSH term(s)	Animals ; Cephalosporins/chemistry ; Cephalosporins/classification ; Cephalosporins/pharmacology ; Humans ; Kinetics ; Structure-Activity Relationship
Chemical Substances	Cephalosporins
Language	English
Publishing date	2003-04
Publishing country	Japan
Document type	Journal Article ; Review
ZDB-ID	390800-8
ISSN	1881-1469 ; 0021-8820 ; 0368-3532
ISSN (online)	1881-1469
ISSN	0021-8820 ; 0368-3532
DOI	10.7164/antibiotics.56.379
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Article ; Online: A comparative study of AutoDock and PMF scoring performances, and SAR of 2-substituted pyrazolotriazolopyrimidines and 4-substituted pyrazolopyrimidines as potent xanthine oxidase inhibitors.

Ali, Hamed I / Fujita, Takayuki / Akaho, Eiichi / Nagamatsu, Tomohisa

Journal of computer-aided molecular design

2009 Volume 24, Issue 1, Page(s) 57–75

Abstract: 4-Alkylidenehydrazino-1H-pyrazolo[3,4-d]pyrimidines, 4-arylmethylidenehydrazino-1H-pyrazolo[3,4-d]pyrimidines, and 2-substituted 7H-pyrazolo[4,3-e]-1,2,4-triazolo-[1,5-c]-pyrimidines as potential xanthine oxidase inhibitors were docked into the active ... ...

Abstract	4-Alkylidenehydrazino-1H-pyrazolo[3,4-d]pyrimidines, 4-arylmethylidenehydrazino-1H-pyrazolo[3,4-d]pyrimidines, and 2-substituted 7H-pyrazolo[4,3-e]-1,2,4-triazolo-[1,5-c]-pyrimidines as potential xanthine oxidase inhibitors were docked into the active site of the bovine milk xanthine dehydrogenase using two scoring functions involved in AutoDock 3.05 and the CAChe 6.1.10. The correlation coefficiency obtained between the AutoDock binding energy and IC(50) of the inhibitors was better than that obtained by the CAChe-PMF docking score. Many ligands exhibited one to four hydrogen bonds within the active site, where the detected hydrogen bonds by CAChe was identified quantitatively in the docked conformation by using MOPAC 2002. These ligands were docked into a long, narrow channel of the enzyme leading to the molybdopterin active moiety, with hydrogen bonding and electrostatic interaction between the planar aromatic moiety of the ligand and the enzyme. Furthermore, SAR among inhibitors was investigated, which revealed that the oxo group of pyrazolopyrimidine analogs is essential for its activity and the tricyclic derivatives are shown to be more potent than bicyclic ones. The mode of interaction of the docked inhibitors was described in details.
MeSH term(s)	Animals ; Catalytic Domain ; Cattle ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Models, Molecular ; Protein Binding ; Pyrazoles/chemistry ; Pyrazoles/pharmacology ; Pyrimidines/chemistry ; Pyrimidines/pharmacology ; Structure-Activity Relationship ; Xanthine Oxidase/antagonists & inhibitors ; Xanthine Oxidase/metabolism
Chemical Substances	Enzyme Inhibitors ; Pyrazoles ; Pyrimidines ; pyrazole (3QD5KJZ7ZJ) ; Xanthine Oxidase (EC 1.17.3.2) ; pyrimidine (K8CXK5Q32L)
Language	English
Publishing date	2009-12-29
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	808166-9
ISSN	1573-4951 ; 0920-654X
ISSN (online)	1573-4951
ISSN	0920-654X
DOI	10.1007/s10822-009-9314-z
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Article ; Online: Studies on 16α-Hydroxylation of Steroid Molecules and Regioselective Binding Mode in Homology-Modeled Cytochrome P450-2C11

Hamed I. Ali / Morio Yamada / Yukihisa Fujita / Mitsuko Maeda / Eiichi Akaho

International Journal of Medicinal Chemistry , Vol

2011 Volume 2011

Keywords	Therapeutics. Pharmacology ; RM1-950 ; Medicine ; R ; DOAJ:Therapeutics ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
Language	English
Publishing date	2011-01-01T00:00:00Z
Publisher	Hindawi Publishing Corporation
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Synthesis and anti-tyrosine kinase activity of 3-(substituted-benzylidene)-1, 3-dihydro-indolin derivatives: investigation of their role against p60c-Src receptor tyrosine kinase with the application of receptor docking studies.

Olgen, Sureyya / Akaho, Eiichi / Nebioglu, Dogu

Farmaco (Societa chimica italiana : 1989)

2005 Volume 60, Issue 6-7, Page(s) 497–506

Abstract: A series of 3-(substituted-benzylidene)-1, 3-dihydro-indolin-2-thione derivatives were synthesized as modified congeners of 3-(substituted-benzylidene)-1, 3-dihydro-indolin-2-one series. All the synthesized compounds were examined for their in vitro anti- ...

Abstract	A series of 3-(substituted-benzylidene)-1, 3-dihydro-indolin-2-thione derivatives were synthesized as modified congeners of 3-(substituted-benzylidene)-1, 3-dihydro-indolin-2-one series. All the synthesized compounds were examined for their in vitro anti-tyrosine kinase activity against p60c-Src. The activity results revealed that compounds (Z)-3-(4'-Dimethylamino-benzylidene)-1, 3-dihydro-indolin-2-thione (12) (E)-3-(2', 6'-Dichloro-benzylidene)-1, 3-dihydro-indolin-2-thione (13) and (E)-3-(3'-Hydroxy-4'-methoxy-benzylidene)-1, 3-dihydro-indolin-2-thione (19) exhibited anti-tyrosine kinase activity with IC50 value of 21.91, 21.20 and 30.92 microM, respectively. These results are comparable to PP1 [1-tert-Butyl-3-p-tolyl-1H-pyrazolo[3, 4-d]pyrimidine-4-yl-amine] (IC50=0.17 microM), which is reported as a potent and selective p60c-Src tyrosine kinase inhibitor. Some thio congeners are found to be more potent than oxo derivatives; however, no significant correlation was observed between the activity profiles of these two series. Docking program was used to investigate the docking mode of each compound at the active site. Among all of the compounds, only (Z)-3-(2'-Chloro-benzylidene)-1, 3-dihydro-indolin-2-one (8) and (E)-3-(3'-Nitro-benzylidene)-1, 3-dihydro-indolin-2-thione (16) were docked at the active site where the PP1 was embedded.
MeSH term(s)	Amino Acid Sequence ; Benzylidene Compounds/chemistry ; Binding, Competitive ; Indoles/chemical synthesis ; Indoles/metabolism ; Indoles/pharmacology ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Protein-Tyrosine Kinases/antagonists & inhibitors ; Protein-Tyrosine Kinases/metabolism ; Proto-Oncogene Proteins pp60(c-src)/antagonists & inhibitors ; Proto-Oncogene Proteins pp60(c-src)/metabolism ; Receptor Protein-Tyrosine Kinases/antagonists & inhibitors ; Receptor Protein-Tyrosine Kinases/metabolism ; Structure-Activity Relationship ; src-Family Kinases/antagonists & inhibitors ; src-Family Kinases/metabolism
Chemical Substances	Benzylidene Compounds ; Indoles ; Protein-Tyrosine Kinases (EC 2.7.10.1) ; Receptor Protein-Tyrosine Kinases (EC 2.7.10.1) ; Proto-Oncogene Proteins pp60(c-src) (EC 2.7.10.2) ; src-Family Kinases (EC 2.7.10.2)
Language	English
Publishing date	2005-06
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	130072-6
ISSN	1879-0569 ; 0014-827X
ISSN (online)	1879-0569
ISSN	0014-827X
DOI	10.1016/j.farmac.2005.01.015
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Article: Studies on 16α-Hydroxylation of Steroid Molecules and Regioselective Binding Mode in Homology-Modeled Cytochrome P450-2C11.

Ali, Hamed I / Yamada, Morio / Fujita, Yukihisa / Maeda, Mitsuko / Akaho, Eiichi

International journal of medicinal chemistry

2010 Volume 2011, Page(s) 918168

Abstract: We investigated the 16α-hydroxylation of steroid molecules and regioselective binding mode in homology-modeled cytochrome P450-2C11 to correlate the biological study with the computational molecular modeling. It revealed that there was a positive ... ...

Abstract	We investigated the 16α-hydroxylation of steroid molecules and regioselective binding mode in homology-modeled cytochrome P450-2C11 to correlate the biological study with the computational molecular modeling. It revealed that there was a positive relationship between the observed inhibitory potencies and the binding free energies. Docking of steroid molecules into this homology-modeled CYP2C11 indicated that 16α-hydroxylation is favored with steroidal molecules possessing the following components, (1) a bent A-B ring configuration (5β-reduced), (2) C-3 α-hydroxyl group, (3) C-17β-acetyl group, and (4) methyl group at both the C-18 and C-19. These respective steroid components requirements were defined as the inhibitory contribution factor. Overall studies of the male rat CYP2C11 metabolism revealed that the above-mentioned steroid components requirements were essential to induce an effective inhibition of [(3)H]progesterone 16α-hydroxylation. As far as docking of homology-modeled CYP2C11 against investigated steroids is concerned, they are docked at the active site superimposed with flurbiprofen. It was also found that the distance between heme iron and C16α-H was between 4 to 6 Å and that the related angle was in the range of 180 ± 45°.
Language	English
Publishing date	2010-07-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2582356-5
ISSN	2090-2077 ; 2090-2069
ISSN (online)	2090-2077
ISSN	2090-2069
DOI	10.1155/2011/918168
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Article: Evaluation of indole esters as inhibitors of p60(c-Src) receptor tyrosine kinase and investigation of the inhibition using receptor docking studies.

Olgen, Sureyya / Akaho, Eiichi / Nebioglu, Dogu

Journal of enzyme inhibition and medicinal chemistry

2004 Volume 18, Issue 6, Page(s) 485–490

Abstract: Several indole esters were tested as inhibitors of tyrosine kinase p60(c-Src). Compound (4) was found fairly active against the enzyme with IC50 = 1.34 microM. DOCK methodology was used to asses our inhibitors for their inhibitory potency against ... ...

Abstract	Several indole esters were tested as inhibitors of tyrosine kinase p60(c-Src). Compound (4) was found fairly active against the enzyme with IC50 = 1.34 microM. DOCK methodology was used to asses our inhibitors for their inhibitory potency against tyrosine kinase. The docking results showed that compounds (4), (25) and (26) were bound to the active site of the enzyme Lys 295 of p60(c-Src) tyrosine kinase. Both activity and docking studies showed a parallel result, with compound (4) having a better interaction with the enzyme active site and also greater activity than the other compounds, indicating a potential role as new lead inhibitor.
MeSH term(s)	Amino Acid Sequence ; Animals ; Chickens ; Enzyme Inhibitors/metabolism ; Enzyme Inhibitors/pharmacology ; Esters ; Indoles/metabolism ; Indoles/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Proto-Oncogene Proteins pp60(c-src)/antagonists & inhibitors ; Proto-Oncogene Proteins pp60(c-src)/metabolism ; Software ; Structure-Activity Relationship ; Substrate Specificity
Chemical Substances	Enzyme Inhibitors ; Esters ; Indoles ; Proto-Oncogene Proteins pp60(c-src) (EC 2.7.10.2)
Language	English
Publishing date	2004-05-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2082578-X
ISSN	1475-6366
ISSN	1475-6366
DOI	10.1080/14756360310001612211
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Article: A study of streptomycin blood level information of patients undergoing hemodialysis.

Akaho, Eiichi / Maekawa, Takashi / Uchinashi, Masako / Kanamori, Ryuichi

Biopharmaceutics & drug disposition

2003 Volume 23, Issue 2, Page(s) 47–52

Abstract: Pharmacokinetic feature of streptomycin (SM) was investigated before and during hemodialysis (HD) in four patients with renal failure undergoing HD. SM concentrations were assayed by using TDX SM KIT (DAINABOT). Patients received 10 mg/kg of SM by ... ...

Abstract	Pharmacokinetic feature of streptomycin (SM) was investigated before and during hemodialysis (HD) in four patients with renal failure undergoing HD. SM concentrations were assayed by using TDX SM KIT (DAINABOT). Patients received 10 mg/kg of SM by intramuscular injection before HD. Pharmacokinetic parameters of SM intramuscular injection before HD were k(a)=2.38+/-0.53 h(-1); k(e)=0.0130+/-0.0025 h(-1); V(d)=0.313+/-0.026l/kg and t(1/2)=55.6+/-10.4 h. The maximum concentration (C(max)) of SM was observed at about 2 h after the SM administration and the mean serum concentration of SM was 30.4 microg/ml; even 4 h after the SM injection, the concentration still remained in a range over 30 microg/ml. The data suggest that a possible toxicity might have appeared in the patients. During the hemodialysis an average t(1/2) value was 3.32 h. This value is close to the value of a healthy person. The k(e) value of patient A during the hemodialysis became 24 times as large as that observed before the hemodialysis. On the average it was 17 times as large as that observed before the hemodialysis. Thus, it was found that the values of pharmacokinetics parameters such as k(e) and t(1/2) during the hemodialysis were similar to those of a healthy person, although there are some variations.
MeSH term(s)	Adult ; Algorithms ; Anti-Bacterial Agents/administration & dosage ; Anti-Bacterial Agents/blood ; Anti-Bacterial Agents/pharmacokinetics ; Computer Simulation ; Female ; Humans ; Injections, Intravenous ; Male ; Middle Aged ; Renal Dialysis ; Renal Insufficiency/metabolism ; Streptomycin/administration & dosage ; Streptomycin/blood ; Streptomycin/pharmacokinetics
Chemical Substances	Anti-Bacterial Agents ; Streptomycin (Y45QSO73OB)
Language	English
Publishing date	2003-02-21
Publishing country	England
Document type	Clinical Trial ; Journal Article
ZDB-ID	603014-2
ISSN	1099-081X ; 0142-2782
ISSN (online)	1099-081X
ISSN	0142-2782
DOI	10.1002/bdd.293
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Article: Comparison of prescription reimbursement methodologies in Japan and the United States.

Akaho, Eiichi / MacLaughlin, Eric J / Takeuchi, Yoshikazu

Journal of the American Pharmacists Association : JAPhA

2003 Volume 43, Issue 4, Page(s) 519–526

Abstract: Objectives: To compare methods of prescription reimbursement in Japan and the United States.: Data sources: Data were obtained through interviews and a search of the pharmacy literature using MEDLINE, International Pharmaceutical Abstracts, the Iowa ... ...

Abstract	Objectives: To compare methods of prescription reimbursement in Japan and the United States. Data sources: Data were obtained through interviews and a search of the pharmacy literature using MEDLINE, International Pharmaceutical Abstracts, the Iowa Drug Information Service, and the Internet. Search terms were pharmacy, dispensing fee, reimbursement, prescriptions, Japan, United States, and average wholesale price (AWP). A comprehensive search was done (i.e., no year limits were observed). Study selection and data extraction: Performed manually by the authors. Data synthesis: The reimbursement systems for prescriptions differ widely between Japan and the United States. The reimbursement system in the United States is fairly straightforward and easy to understand; it is generally based on product cost (e.g., AWP minus a percentage) plus a small dispensing fee. The system in Japan is extremely complex. Reimbursement formulae have four components, including fees for professional dispensing, drug cost, counseling and administration, and medication supplies and devices. Additionally, various adjustments to the final amount are made based on dosage form, length of therapy, number of prescriptions dispensed by the pharmacy per month, and when the prescription is filled (e.g., after hours, on Sundays or holidays). In Japan, each pharmacist is limited to filling 40 prescriptions per day, but each "prescription" can involve several medication orders, making it difficult to compare Japanese pharmacists' workloads with those of their counterparts in the United States. In addition, Japanese pharmacists are provided remuneration for providing various cognitive services, such as taking a patient history, counseling a patient, consulting with a physician, and identifying drug-related problems. Conclusion: Japan and the United States have very different methods of reimbursing pharmacists for dispensing prescriptions, each with positive and negative features. Based on the features of pharmacy reimbursement systems in each country, perhaps the optimal pharmacy practice system would have workload limits that reflect safety standards and amount of support staff available, provide a fair and standardized method for determining drug cost, are relatively straightforward, pay for cognitive services, and provide care for all of citizens through of some type of national health care system.
MeSH term(s)	Costs and Cost Analysis ; Data Collection ; Drug Costs ; Drug Prescriptions/economics ; Humans ; Japan ; Legislation, Pharmacy ; Pharmaceutical Services/economics ; Pharmaceutical Services/legislation & jurisprudence ; Prescription Fees ; Reimbursement Mechanisms/economics ; Reimbursement Mechanisms/legislation & jurisprudence ; United States
Language	English
Publishing date	2003-08-25
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Review
ZDB-ID	2118585-2
ISSN	1544-3450 ; 1544-3191 ; 1086-5802
ISSN (online)	1544-3450
ISSN	1544-3191 ; 1086-5802
DOI	10.1331/154434503322226275
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