A comparative study of AutoDock and PMF scoring performances, and SAR of 2-substituted pyrazolotriazolopyrimidines and 4-substituted pyrazolopyrimidines as potent xanthine oxidase inhibitors.

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.

Antitumor studies -- part 2: structure-activity relationship study for flavin analogs including investigations on their in vitro antitumor assay and docking simulation into protein tyrosine kinase.

Various analogs of flavins, 5-deazaflavins, and flavin-5-oxides were docked into the binding site of protein tyrosine kinase pp60(c-src), and some of them were assayed for their potential antitumor and PKC (protein kinase C) inhibitory activities in vitro. The results considering SAR (structure-activity relationship) revealed that the higher binding affinities obtained include compounds with the structure modifications on the flavin or 5-deazaflavin skeleton, namely, NH(2) or Ph (phenyl-) group at the C-2 position and so on. Computationally designed compounds 4a, 6a, b, 7, 11b, c, 12, 15, and 22c exhibited good docking results suggesting that they are potentially active antitumor agents. These compounds have 1-3 phenyl moieties, which are thought to be responsible for the planar aromatic fitting or electrostatic attraction onto the groove of the binding pocket.

A study on medicinal plants from Malaysia focused on Acalypha siamensis Oliv. ex Gage. isolation and structure of a new tetraterpene, acalyphaser A.

As a part of our chemical studies on Malaysian medicinal plants, five Malaysian plant species were evaluated by cytotoxicity assays using P388 murine leukemia cells. Since Acalypha siamensis exhibited the strongest growth inhibition, its constituents were studied as the object of search for bioactive materials. A novel tetraterpene, acalyphaser A (1), was isolated in the course of the purification. Its structure was elucidated on the basis of 1D- and 2D-NMR techniques, and mass spectrometry.

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.

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.

An innovative classification of, and a new structure-activity-relationship approach to degradation kinetics of cephalosporins: an attempt to enhance the therapeutic activity.

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.

[A study of pharmacists' consciousness toward separation of medical practice from pharmaceutical dispensing].

Separation of medical practice from pharmaceutical dispensing had been a system with just the notation without the reality even after Showa era, although its concept was brought into Japan along with European medicine in Meiji era. Since 1970's, its concept has been prevailing gradually, and the so-called separation rate currently has reached to 47 percent. Increasingly keen attention has been paid recently by the public toward medicine in general. Taking into consideration these facts, a questionnaire survey was conducted for dispensing pharmacists in order to find out where pharmacists stand at present. Most of pharmacists (98.3%) answered that they practice patient counseling either by documents or by verbal communication, and that they take patient profiles. They said that patients could enjoy a proper medical treatment (32.9%) as well as a rational prescribing (14.3%). For a question asking what pharmacists should do to promote the separation of medical practice from pharmaceutical dispensing, 40.3% of them answered that they should make progress in their knowledge on drug therapy.

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

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.

Structure-based drug design and AutoDock study of potential protein tyrosine kinase inhibitors.

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.

Studies on 16α-Hydroxylation of Steroid Molecules and Regioselective Binding Mode in Homology-Modeled Cytochrome P450-2C11.

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 (5ß-reduced), (2) C-3 α-hydroxyl group, (3) C-17ß-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°.

Reduction of lipophilicity at the lipophilic domain of RXR agonists enables production of subtype preference: RXRalpha-preferential agonist possessing a sulfonamide moiety.

Retinoid X receptor agonists (RXR agonists, rexinoids) are interesting candidates for the treatment of cancers such as tamoxifen-resistant breast cancer and taxol-resistant lung cancer. However, well-known RXR agonists possess a strong lipophilic character. In addition, although RXR has three subtypes, no subtype-selective RXR agonists are known. Thus we aimed to produce less-lipophilic and subtype-selective RXR agonists. By designing sulfonamide-type RXR agonists, 4-[N-methanesulfonyl-N-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-2-naphthyl)amino]benzoic acid (8 a) was found to prefer RXRalpha over RXRbeta and RXRgamma, although the potency is less than the potencies of well-known RXR pan-agonists. Moreover, our results suggest that the reduction of lipophilicity at the hydrophobic interaction region of RXR agonists enables production of RXR subtype preference. Our finding will be useful for the creation of more potent and less-lipophilic subtype-selective RXR agonists aimed at the reduction of undesirable side effects.

Analgesic agents without gastric damage: design and synthesis of structurally simple benzenesulfonanilide-type cyclooxygenase-1-selective inhibitors.

In order to create novel analgesic agents without gastric disturbance, structurally simple cyclooxygenase-1 (COX-1) inhibitors with a benzenesulfonanilide skeleton were designed and synthesized. As a result, compounds 11f and 15a, which possess a p-amino group on the benzenesulfonyl moiety and p-chloro group on the anilino moiety, showed COX-1-selective inhibition. Moreover compound 11f, which is the most potent compound in this study showed more potent analgesic activity than that of aspirin at 30 mg/kg by po. The anti-inflammatory activity and gastric damage, however, were very weak or not detectably different from aspirin. Since the structure of our COX-1 inhibitors are very simple, they may be useful as lead compounds for superior COX-1 inhibitors as analgesic agents without gastric disturbance.

Antitumor studies. Part 1: design, synthesis, antitumor activity, and AutoDock study of 2-deoxo-2-phenyl-5-deazaflavins and 2-deoxo-2-phenylflavin-5-oxides as a new class of antitumor agents.

Novel 2-deoxo-2-phenyl-5-deazaflavins and 2-deoxo-2-phenylflavin-5-oxides were prepared as a new class of antitumor agents and showed significant antitumor activities against NCI-H 460, HCT 116, A 431, CCRF-HSB-2, andKB cell lines. In vivo investigation, 2-deoxo-10-methyl-2-phenyl-5-deazaflavin exhibited the effective antitumor activity against A 431 human adenocarcinoma cells transplanted subcutaneously into nude mouse. Furthermore, AutoDock study has been done by binding of the flavin analogs into PTK pp60(c-src), where a good correlation between their IC(50) and AutoDock binding free energy was exhibited. In particular, 2-deoxo-2-phenylflavin-5-oxides exhibited the highest potential binding affinity within the binding pocket of PTK.

Evaluation of indole esters as inhibitors of p60(c-Src) receptor tyrosine kinase and investigation of the inhibition using receptor docking studies.

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.

A study on the interaction between p60 c-Src receptor tyrosine kinase and arylcarboxylic and arylacetic acid derivatives based on docking modes and in vitro activity.

The fundamental role that receptor tyrosine kinases play in cancer and other proliferative diseases has provided the impetus for an extensive effort on the part of both academic and pharmaceutical laboratories to develop highly specific inhibitors. In this study, inhibitory activity of previously synthesized arylacetic and arylcarboxylic acid derivatives were examined against substrate of tyrosine kinase. It can be assumed that the activity of compounds becomes higher when the -CH(2) linkage exist between aromatic ring and the amide group of the side chain. In addition, when the R(1) and R(2) substitutents are methyl group in both series, the higher activity observed. The data obtained from docking study (DOCK4.0) indicated that compounds 2, 4, 7, 8, 11 render satisfactory interaction with the active site of enzyme, Lys295 of p60(c-Src) tyrosine kinase. Comparison of this interaction and the evaluation of biological data showed that compound 4 is the most active among the entire derivatives.

A study of streptomycin blood level information of patients undergoing hemodialysis.

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.

Comparison of prescription reimbursement methodologies in Japan and the United States.

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.