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PubMedDate not supplied

NIPALSTREE: a new hierarchical clustering approach for large compound libraries and its application to virtual screening.

A hierarchical clustering algorithm--NIPALSTREE--was developed that is able to analyze large data sets in high-dimensional space. The result can be displayed as a dendrogram. At each tree level the algorithm projects a data set via principle component analysis onto one dimension. The data set is sorted according to this one dimension and split at the median position. To avoid distortion of clusters at the median position, the algorithm identifies a potentially more suited split point left or right of the median. The procedure is recursively applied on the resulting subsets until the maximal distance between cluster members exceeds a user-defined threshold. The approach was validated in a retrospective screening study for angiotensin converting enzyme (ACE) inhibitors. The resulting clusters were assessed for their purity and enrichment in actives belonging to this ligand class. Enrichment was observed in individual branches of the dendrogram. In further retrospective virtual screening studies employing the MDL Drug Data Report (MDDR), COBRA, and the SPECS catalog, NIPALSTREE was compared with the hierarchical k-means clustering approach. Results show that both algorithms can be used in the context of virtual screening. Intersecting the result lists obtained with both algorithms improved enrichment factors while losing only few chemotypes.

Algorithms↗
PubMedDate not supplied

Comparison of the NCI open database with seven large chemical structural databases.

Eight large chemical databases have been analyzed and compared to each other. Central to this comparison is the open National Cancer Institute (NCI) database, consisting of approximately 250 000 structures. The other databases analyzed are the Available Chemicals Directory ("ACD," from MDL, release 1.99, 3D-version); the ChemACX ("ACX," from CamSoft, Version 4.5); the Maybridge Catalog and the Asinex database (both as distributed by CamSoft as part of ChemInfo 4.5); the Sigma-Aldrich Catalog (CD-ROM, 1999 Version); the World Drug Index ("WDI," Derwent, version 1999.03); and the organic part of the Cambridge Crystallographic Database ("CSD," from Cambridge Crystallographic Data Center, 1999 Version 5.18). The database properties analyzed are internal duplication rates; compounds unique to each database; cumulative occurrence of compounds in an increasing number of databases; overlap of identical compounds between two databases; similarity overlap; diversity; and others. The crystallographic database CSD and the WDI show somewhat less overlap with the other databases than those with each other. In particular the collections of commercial compounds and compilations of vendor catalogs have a substantial degree of overlap among each other. Still, no database is completely a subset of any other, and each appears to have its own niche and thus "raison d'être". The NCI database has by far the highest number of compounds that are unique to it. Approximately 200 000 of the NCI structures were not found in any of the other analyzed databases.

Cluster Analysis↗
PubMed2001

The legacy of pharmacogenetics and potential applications.

Some 40 years of pharmacogenetic research indicates that knowledge of human genetic diversity is essential to a broader understanding of variation in human drug response, and suggests that drug therapy tailored to the genetic characteristics of the individual may be a realistic goal. Aided by new technologies, molecular studies of genetic polymorphisms of many human enzymes, receptors, and other proteins indicate that only a limited number of important protein variants account for the diversity in drug response, raising the prospect that these variants may be cataloged relatively soon for many human populations. The next great challenge of pharmacogenetics is to pin down the cellular location and effect of these variant proteins on the pathways and networks that govern individual variation in responses to drugs and other exogenous chemicals. In this paper, we will discuss some the current challenges to progress in pharmacogenetics and newer strategies that might be used to improve prospects of drug design and personalized therapy.

Animals↗
PubMed2005

American Diabetes Association. Resource guide 2005. Insulin delivery.

Syringes...pumps...jet injectors...pens...infusers...they all do the same basic thing--deliver insulin. These items carry insulin through the outermost layer of skin and into fatty tissue so it can be used by the body. This section will also cover injection aids, products design to make injecting easier.

Catalogs, Commercial as Topic↗
PubMedDate not supplied

Framework for pharmacy services quality improvement--a bridge to cross the quality chasm. Part I. The opportunity and the tool.

OBJECTIVE: To review the literature on the subject of quality improvement principles and methods applied to pharmacy services and to describe a framework for current and future efforts in pharmacy services quality improvement and effective drug therapy management. BACKGROUND: The Academy of Managed Care Pharmacy produced the Catalog of Pharmacy Quality Indicators in 1997, followed by the Summary of National Pharmacy Quality Measures in February 1999. In April 2002, AMCP introduced Pharmacy's Framework for Drug Therapy Management in the 21st Century. The Framework documents include a self-assessment tool that details more than 250 specific "components" that describe tasks, behaviors, skills, functions, duties, and responsibilities that contribute to meeting customer expectations for effective drug therapy management. FINDINGS: There are many opportunities for quality improvement in clinical, service, and cost outcomes related to drug therapy management. These may include patient safety; incidence of medical errors; adverse drug events; patient adherence to therapy; attainment of target goals of blood pressure, glucose, and lipid levels; risk reduction for adverse cardiac events and osteoporotic-related fractures; patient satisfaction; risk of hospitalization or mortality; and cost of care. Health care practitioners can measure improvements in health care quality in several ways including (a) a better patient outcome at the same cost, (b) the same patient outcome at lower cost, (c) a better patient outcome at lower cost, or (d) a significantly better patient outcome at moderately higher cost. Measurement makes effective management possible. A framework of component factors (e.g., tasks) is necessary to facilitate changes in the key processes and critical factors that will help individual practitioners and health care systems meet customer expectations in regard to drug therapy, thus improving these outcomes. CONCLUSIONS: Quality improvement in health care services in the United States will be made in incremental changes that rely on a structure-process-outcome model. The structure is provided by evidence created from controlled randomized trials and other studies of care and system outcomes that are based on the scientific method. The process portion is created by the application of evidence in the form of clinical practice guidelines, clinical practice models, and self-assessment tools such as Pharmacy's Framework for Drug Therapy Management. Incremental changes in structure and process will result in the desirable outcome of meeting customer needs for more effective drug therapy and disease management.

Guidelines as Topic↗
PubMed2005

Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations.

The structure of the complex between the minor groove binder netropsin and d(GGCCAATTGG) was determined via single-crystal X-ray techniques. The structure was refined to completion using refmac5.1.24, resulting in a residual R-factor of 20.0% (including 68 water molecules). Using crystal engineering and cryocooling techniques, the resolution could be enhanced to 1.75 A, resulting in an unambiguous determination of the drug conformation and orientation. As previously noticed, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and the N3 and O2 atoms of A and T base pairs, respectively, clearly cataloging the structure to class I. As the bulky NH2 group on guanine was believed to prevent binding of the drug in the minor groove, the detailed nature of several of the amidinium and guanidinium end contacts were further investigated by ab initio quantum chemical methods.

Base Sequence↗
PubMed2005

A comprehensive listing of bioactivation pathways of organic functional groups.

The occurrence of idiosyncratic adverse drug reactions during late clinical trials or after a drug has been released can lead to a severe restriction in its use and even in its withdrawal. Metabolic activation of relatively inert functional groups to reactive electrophilic intermediates is considered to be an obligatory event in the etiology of many drug-induced adverse reactions. Therefore, a thorough examination of the biochemical reactivity of functional groups/structural motifs in all new drug candidates is essential from a safety standpoint. A major theme attempted in this review is the comprehensive cataloging of all of the known bioactivation pathways of functional groups or structural motifs commonly utilized in drug design efforts. Potential strategies in the detection of reactive intermediates in biochemical systems are also discussed. The intention of this review is not to "black list" functional groups or to immediately discard compounds based on their potential to form reactive metabolites, but rather to serve as a resource describing the structural diversity of these functionalities as well as experimental approaches that could be taken to evaluate whether a "structural alert" in a new drug candidate undergoes bioactivation to reactive metabolites.

Animals↗
PubMed2005

Usability of the kink parameters for nucleic acid structure in database.

DNA/RNA molecules with the specific three-dimensional structure, express the specific structural and biological functions. The knowledge integration based on three dimensional structures can be used to explain biochemical observations, to predict biological functions and to design drugs specific to a given complex system. The database cataloging the interaction motifs of nucleic acid moieties has been developed. Skew matrix, a kind of kink parameter, affords the structural description between the adjacent moieties. The proper values in skew matrix have the good properties, i.e., impregnable and flexible presentation. The geometrical parameters about hydrogen bond and base stacking would also provide the tolerant aspect for stereochemical bioinformatics. The tentative database including these parameters with the species and physical properties of the surrounding nucleic acid components and amino acids has been constructed.

Amino Acids↗
PubMed1999

Racial and ethnic factors in the genetic pathogenesis of colorectal cancer.

Colorectal cancer can develop by two distinct pathogenic mechanisms: one involving chromosomal breakage and aneuploidy (called chromosomal instability) and one involving mutations at DNA micro-satellite sequences (termed micro-satellite instability). Relatively few reports consider these mechanisms of colorectal cancer development across racial or ethnic groups. Available data indicate a moderate increase in colorectal cancer risk among Ashkenazi Jews who have a mutational polymorphism at codon 1307 in the APC gene. In American blacks, there is evidence for a higher prevalence of right-sided colonic tumors and an earlier age of onset of colorectal cancer. In addition, blacks have the highest colon cancer incidence in the United States among ethnic groups and have poorer 5-year survival rates compared with whites. While some differences may be attributed to health care access and socioeconomic differences, these do not completely explain all the variances. In the chromosomal instability pathway, there are polymorphisms within the P53 gene that are more prevalent in blacks, but the significance of these polymorphisms is not fully known. Blacks are more likely to demonstrate micro-satellite instability in their tumors; however, the mechanism for this phenomenon in blacks is unexplored. Differences in diet among racial and ethnic groups and polymorphic variations in drug metabolizing or acetylation genes have not been adequately cataloged. Identification of genetic and environmental factors among racial and ethnic groups should offer some insights into the observed epidemiologic data and advance opportunities to better understand the control and development of colorectal cancer.

Adenoma↗
PubMed1997

Migraine prophylactic drugs: proof of efficacy, utilization and cost.

OBJECTIVES: In order to understand the pattern of utilization of migraine prophylactic drugs by US physicians, we reviewed the scientific rigor of published trials of anti-migraine medications, assessed their cost, and tested the correlation, if any, between utilization, scientific rigor and cost. MATERIALS AND METHODS: Scientific rigor of published reports. We identified all placebo-controlled, randomized, double-blind trials of migraine prophylactic agents through Medline search, major Headache textbooks and proceedings of major scientific meetings where headache-related topics are discussed. We excluded trials that did not include placebo treatment during the active phase of the study. The trials were reviewed and rated for scientific rigor using a 5-point scale (scientific score [ss]; 1 = low, 5 = good), blinded to the physicians' utilization data and cost of the drugs. Studies that did not show benefit of the active drug over placebo were scored -1 to -5, thus allowing for the reverse logic of negative studies. US physicians utilization. Neurologists and primary care physicians (PCP) completed phone-mail-phone questionnaires which inquired about first and second choices of migraine prophylaxis. These choices were averaged to obtain a weighted average percent usage of each drug. Cost. The average wholesale price (AWP) of each drug was obtained from data published by Adelman and Von Seggern, and from the Amerisource (7/9/96) catalog. STATISTICAL ANALYSIS: Spearman's correlation coefficient was used to assess the relationship between the average ss, physician use, and cost of each drug. RESULTS: Propranolol (ss = 1.44), amitriptyline (ss = 2.33) and verapamil (ss = 1.00) were the three preferred migraine prophylactic drugs by both neurologists and PCPs. Approximately 10% of neurologists said that divalproex (ss = 3.75) would be their first or second choice. The selective serotonin reuptake blockers were favored by 13.21% of PCPs. All other prophylactic drugs were felt to be first or second line of treatment by less than 10% of either neurologists or PCPs. Except for one study (ss = 1) that showed that propranolol reduced the migraine frequency by 76% over placebo, trials of the three most preferred medications failed to demonstrate that the active drug is > 50% better than placebo, i.e. the difference in headache frequency when on placebo vs active drug is > 50%. Of the drugs available in the United States, flurbiprofen and metoprolol achieved the best ss (5.00 and 4.33, respectively) but their efficacy over placebo (23% and 14-33%, respectively) and cost ($67.2 and $65.6) were unfavorable. Neurologists and PCPs chose migraine prophylaxis on the basis of scientific merit (r = 0.644, p = 0.018; r = 0.576, p = 0.05, respectively) but not cost (r = -0.254, p = 0.45; r = -0.255, p = 0.455). CONCLUSION: The three most commonly chosen migraine prophylactic agents have not been shown irrefutably to prevent migraine. Furthermore, their benefit, if any, does not exceed 50% over placebo. The well-conducted recent trials that demonstrated the efficacy of divalproex in migraine prevention are steps in the right direction of finding the "ideal migraine preventative agent". Until that drug is discovered, it is difficult to argue that one migraine prophylactic medication is superior to another and accordingly should be used as a first line of treatment.

Adult↗
PubMed2003

Novel aspects of renal organic anion transporters.

PURPOSE OF REVIEW: Organic anion transporters, transmembrane proteins present in the renal proximal tubule, are a critical component of the human drug excretion machinery. Recent advances have clarified the function of these transporters, with broad clinical implications for pharmacogenetics, drug interactions and adverse reactions. Here, we discuss these issues in the context of the basic biology of the transporters. RECENT FINDINGS: Understanding of organic anion transporter function has proceeded on several fronts. The continued cataloging of organic anion transporter substrates has revealed that the transporters' activity likely underlies many common drug interactions and nephrotoxic adverse reactions. Meanwhile, immunohistochemical and physiological studies suggest their potential involvement in the apical as well as basolateral steps of renal organic anion secretion. In addition, studies of the genomic organization of these transporters reveal that they are found in pairs of similar and similarly expressed genes, suggesting that pair members are coordinately regulated. Finally, we hypothesize here that organic anion transporters might impact renal susceptibility to ischemia and toxic injury, because their uptake of substrates can result in the efflux of Krebs cycle intermediates, an important nutrient source for the proximal tubule. SUMMARY: The study of these transporters will likely have a significant impact on renal pharmacology and pharmacogenetics. In this regard, the generation of organic anion transporter gene knockout mice could provide invaluable models for defects in renal drug-handling. Ultimately, detailed knowledge of organic anion transporter function will assist in the choice of optimum pharmacological therapies.

Animals↗
PubMed2001

Pharmacological studies of prepulse inhibition models of sensorimotor gating deficits in schizophrenia: a decade in review.

RATIONALE: Patients with schizophrenia exhibit deficits in an operational measure of sensorimotor gating: prepulse inhibition (PPI) of startle. Similar deficits in PPI are produced in rats by pharmacological or developmental manipulations. These experimentally induced PPI deficits in rats are clearly not animal models of schizophrenia per se, but appear to provide models of sensorimotor gating deficits in schizophrenia patients that have face, predictive, and construct validity. In rodents, disruptions in PPI of startle are produced by: stimulation of D2 dopamine (DA) receptors, produced by amphetamine or apomorphine; activation of serotonergic systems, produced by serotonin (5-HT) releasers or direct agonists at multiple serotonin receptors; and blockade of N-methyl-D-aspartate (NMDA) receptors, produced by drugs such as phencyclidine (PCP). Accordingly, dopaminergic, serotonergic, and glutamatergic models of disrupted PPI have evolved and have been applied to the identification of potential antipsychotic treatments. In addition, some developmental manipulations, such as isolation rearing, have provided non-pharmacological animal models of the PPI deficits seen in schizophrenia. OBJECTIVE: This review summarizes and evaluates studies assessing the effects of systemic drug administrations on PPI in rats. METHODS: Studies examining systemic drug effects on PPI in rats prior to January 15, 2001 were compiled and organized into six annotated appendices. Based on this catalog of studies, the specific advantages and disadvantages of each of the four main PPI models used in the study of antipsychotic drugs were critically evaluated. RESULTS: Despite some notable inconsistencies, the literature provides strong support for significant disruptions in PPI in rats produced by DA agonists, 5-HT2 agonists, NMDA antagonists, and isolation rearing. Each of these models exhibits sensitivity to at least some antipsychotic medications. While the PPI model based on the effects of direct DA agonists is the most well-validated for the identification of known antipsychotics, the isolation rearing model also appears to be sensitive to both typical and atypical antipsychotics. The 5-HT PPI model is less generally sensitive to antipsychotic medications, but can provide insight into the contribution of serotonergic systems to the actions of newer antipsychotics that act upon multiple receptors. The deficits in PPI produced by NMDA antagonists appear to be more sensitive to clozapine-like atypical antipsychotics than to typical antipsychotics. Hence, despite some exceptions to this generalization, the NMDA PPI model might aid in the identification of novel or atypical antipsychotic medications. CONCLUSIONS: Studies of drug effects on PPI in rats have generated four distinctive models that have utility in the identification of antipsychotic medications. Because each of these models has specific advantages and disadvantages, the choice of model to be used depends upon the question being addressed. This review should help to guide such decisions.

Animals↗
PubMed2002

A catalogue of polymorphisms related to xenobiotic metabolism and cancer susceptibility.

High-throughput genotyping technology of multiple genes based on large samples of cases and controls are likely to be important in identifying common genes which have a moderate effect on the development of specific diseases. We present here a comprehensive list of 313 known experimentally confirmed polymorphisms in 54 genes which are particularly relevant for metabolism of drugs, alcohol, tobacco, and other potential carcinogens. We have compiled a catalog with a standardized format that summarizes the genetic and biochemical properties of the selected polymorphisms. We have also confirmed or redesigned experimental conditions for simplex or multiplex PCR amplification of a subset of 168 SNPs of particular interest, which will provide the basis for the design of assays compatible with high-throughput genotyping.

Cytochrome P-450 Enzyme System↗