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Publications
DrugBank: a knowledgebase for drugs, drug actions and drug targetsDavid S Wishart
Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
Nucleic Acids Res 36:D901-6. 2008..DrugBank has also significantly improved the power and simplicity of its structure query and text query searches. DrugBank is available at http://www.drugbank.ca...
Predicting new molecular targets for known drugsMichael J Keiser
Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94143 2550, USA
Nature 462:175-81. 2009..The chemical similarity approach is systematic and comprehensive, and may suggest side-effects and new indications for many drugs...
PubChem: a public information system for analyzing bioactivities of small moleculesYanli Wang
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 37:W623-33. 2009..Most of the tools described in this work can be directly accessed at http://pubchem.ncbi.nlm.nih.gov/assay/. URLs for accessing other tools described in this work are specified individually...
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settingsC A Lipinski
Central Research Division, Pfizer Inc, Groton, CT 06340, USA
Adv Drug Deliv Rev 46:3-26. 2001..Recent work on linear free energy relationships and Log P approaches are critically reviewed. Useful predictions are possible in closely related analog series when coupled with experimental thermodynamic solubility measurements...
STITCH 2: an interaction network database for small molecules and proteinsMichael Kuhn
Biotechnology Center, TU Dresden, 01062 Dresden, Germany
Nucleic Acids Res 38:D552-6. 2010..STITCH 2.0 connects proteins from 630 organisms to over 74,000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/...
Drug target identification using side-effect similarityMonica Campillos
European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Science 321:263-6. 2008..Nine of these were tested and confirmed in cell assays, documenting the feasibility of using phenotypic information to infer molecular interactions and hinting at new uses of marketed drugs...
Benchmarking sets for molecular dockingNiu Huang
Department of Pharmaceutical Chemistry, University of California San Francisco, QB3 Building, 1700 4th Street, Box 2550, San Francisco, California 94143-2550, USA
J Med Chem 49:6789-801. 2006..DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/...
Update of TTD: Therapeutic Target DatabaseFeng Zhu
Department of Pharmacy and Computation and Systems Biology, Center for Computational Science and Engineering, Singapore MIT Alliance, National University of Singapore, Singapore
Nucleic Acids Res 38:D787-91. 2010..This database can be accessed at http://bidd.nus.edu.sg/group/cjttd/TTD.asp...
ADMET in silico modelling: towards prediction paradise?Han van de Waterbeemd
Pfizer Global Research and Development, PDM, Sandwich, Kent CT13 9NJ, UK
Nat Rev Drug Discov 2:192-204. 2003..Here, we describe how in silico approaches will further increase our ability to predict and model the most relevant pharmacokinetic, metabolic and toxicity endpoints, thereby accelerating the drug discovery process...
Global mapping of pharmacological spaceGaia V Paolini
The Department of Knowledge Discovery, Pfizer Global Research and Development, Sandwich, Kent CT13 9NJ, UK
Nat Biotechnol 24:805-15. 2006..The relationships between proteins, chemical structures and drug-like properties provide a framework for developing a probabilistic approach to drug discovery that can be exploited to increase research productivity...
Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformaticsChristoph Steinbeck
Cologne University Bioinformatics Center CUBIC, Germany
Curr Pharm Des 12:2111-20. 2006..This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software...
SuperTarget and Matador: resources for exploring drug-target relationshipsStefan Günther
Structural Bioinformatics Group, Institute of Molecular Biology and Bioinformatics, Charite University Medicine Berlin, Arnimallee 22, 14195 Berlin, Germany
Nucleic Acids Res 36:D919-22. 2008..SuperTarget and Matador are available at http://insilico.charite.de/supertarget and http://matador.embl.de...
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated frameworkYoshihiro Yamanishi
Mines ParisTech, Centre for Computational Biology, 35 rue Saint Honore, F 77305 Fontainebleau Cedex, Institut Curie, F 75248, INSERM U900, F 75248, Paris, France
Bioinformatics 26:i246-54. 2010..There is therefore a strong incentive to develop new methods capable of detecting these potential drug-target interactions efficiently...
A side effect resource to capture phenotypic effects of drugsMichael Kuhn
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Mol Syst Biol 6:343. 2010..We illustrate the potential of SIDER with a number of analyses. The resource is freely available for academic research at http://sideeffects.embl.de...
KEGG for linking genomes to life and the environmentMinoru Kanehisa
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
Nucleic Acids Res 36:D480-4. 2008..KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers...
Systematic evaluation of drug-disease relationships to identify leads for novel drug usesA P Chiang
Department of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
Clin Pharmacol Ther 86:507-10. 2009..When compared with a control group of drug uses, the suggested novel drug uses generated by this approach were significantly enriched with respect to previous and ongoing clinical trials...
Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeastAinslie B Parsons
Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
Cell 126:611-25. 2006..This compendium should serve as a valuable key for interpreting cellular effects of novel compounds with similar activities...
Identifying the proteins to which small-molecule probes and drugs bind in cellsShao En Ong
Proteomics Platform, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 106:4617-22. 2009..Here, we describe in full detail the application of the method to identify targets of kinase inhibitors and immunophilin binders...
Virtual screening of chemical librariesBrian K Shoichet
Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143 2240, USA
Nature 432:862-5. 2004....
DrugBank: a comprehensive resource for in silico drug discovery and explorationDavid S Wishart
Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
Nucleic Acids Res 34:D668-72. 2006..DrugBank is available at http://redpoll.pharmacy.ualberta.ca/drugbank/...
Relating protein pharmacology by ligand chemistryMichael J Keiser
Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St, San Francisco California 94143 2550, USA
Nat Biotechnol 25:197-206. 2007..These predictions were subsequently confirmed experimentally. Relating receptors by ligand chemistry organizes biology to reveal unexpected relationships that may be assayed using the ligands themselves...
The many roles of computation in drug discoveryWilliam L Jorgensen
Department of Chemistry, Yale University, New Haven, CT 06520 8107, USA
Science 303:1813-8. 2004..Particular emphasis is placed on virtual screening, de novo design, evaluation of drug-likeness, and advanced methods for determining protein-ligand binding...
Medication errors and adverse drug events in pediatric inpatientsR Kaushal
Children's Hospital, Enders 609, Longwood Avenue, Boston, MA 02115, USA
JAMA 285:2114-20. 2001..CONCLUSIONS: Medication errors are common in pediatric inpatient settings, and further efforts are needed to reduce them...
Pharmaceuticals, hormones, and other organic wastewater contaminants in U.S. streams, 1999-2000: a national reconnaissanceDana W Kolpin
US Geological Survey, Iowa City, Iowa 52244, USA
Environ Sci Technol 36:1202-11. 2002....
A robustness-based approach to systems-oriented drug designHiroaki Kitano
Sony Computer Science Laboratories Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
Nat Rev Drug Discov 6:202-10. 2007....
'Metabolite-likeness' as a criterion in the design and selection of pharmaceutical drug librariesPaul D Dobson
School of Chemistry and The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
Drug Discov Today 14:31-40. 2009....
Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport propertiesP Ertl
Cheminformatics, Novartis Pharma AG, WKL 490 4 35, CH 4002 Basel, Switzerland
J Med Chem 43:3714-7. 2000..This article describes the new methodology and shows the results of validation studies based on sets of published absorption data, including intestinal absorption, Caco-2 monolayer penetration, and blood-brain barrier penetration...
From genomics to chemical genomics: new developments in KEGGMinoru Kanehisa
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 34:D354-7. 2006..Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps...
Drug-related problems in hospitals: a review of the recent literatureAnita Krähenbühl Melcher
Hospital Pharmacy, Regionalspital Emmental, Burgdorf, Switzerland
Drug Saf 30:379-407. 2007....
STITCH: interaction networks of chemicals and proteinsMichael Kuhn
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nucleic Acids Res 36:D684-8. 2008..5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.de/...
Comparison of support vector machine and artificial neural network systems for drug/nondrug classificationEvgeny Byvatov
, , Marie-Curie-Strasse 11, D-60439 Frankfurt, Germany
J Chem Inf Comput Sci 43:1882-9. 2003..The theory of SVM and ANN training is briefly reviewed...
ChEBI: a database and ontology for chemical entities of biological interestKirill Degtyarenko
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nucleic Acids Res 36:D344-50. 2008..ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/..
Extracting medication information from clinical textOzlem Uzuner
Department of Information Studies, University at Albany, State University of New York, Albany, NY, USA
J Am Med Inform Assoc 17:514-8. 2010..However, they are limited in recognizing duration and reason fields and would benefit from future research...
Supervised prediction of drug-target interactions using bipartite local modelsKevin Bleakley
Mines ParisTech, Centre for Computational Biology, Fontainebleau, France
Bioinformatics 25:2397-403. 2009..This, however, remains extremely challenging due to, amongst other things, the rarity of known drug-target interactions...
Stability of protein pharmaceuticals: an updateMark Cornell Manning
Legacy BioDesign LLC, Johnstown, Colorado 80534, USA
Pharm Res 27:544-75. 2010....
The chemical basis of pharmacologyMichael J Keiser
Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158 2558, USA
Biochemistry 49:10267-76. 2010..The bases for these new methods, some of their successes and liabilities, and new opportunities for their use are described...
Predicting drug disposition via application of BCS: transport/absorption/ elimination interplay and development of a biopharmaceutics drug disposition classification systemChi-Yuan Wu
Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California 94143, USA
Pharm Res 22:11-23. 2005....
Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstractsJiao Li
State Key Laboratory of Intelligent Technology and Systems, Tsinghua National Laboratory for Information Science and Technology, Department of Computer Science and Technology, Tsinghua University, Beijing, China
PLoS Comput Biol 5:e1000450. 2009....
Graphic rule for drug metabolism systemsKuo Chen Chou
Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130, USA
Curr Drug Metab 11:369-78. 2010..g., according to their directed graphs, the metabolism of seliciclib and the metabolism of vildagliptin can be categorized as 0-->5 mechanism while that of AG-024322 as 0-->4-->3 mechanism...
Searching for safety: addressing search engine, website, and provider accountability for illicit online drug salesBryan A Liang
Institute of Health Law Studies, California Western School of Law, San Diego, CA, USA
Am J Law Med 35:125-84. 2009....
Micellar solubilization of drugsCarlota Oliveira Rangel-Yagui
Department of Biochemical and Pharmaceutical Technology FCF, University of Sao Paulo, Sao Paulo, Brazil
J Pharm Pharm Sci 8:147-65. 2005..Micellar solubilization is a powerful alternative for dissolving hydrophobic drugs in aqueous environments. In this work, we provide an insight into this subject...
Chemiluminescence detection in liquid chromatography: applications to clinical, pharmaceutical, environmental and food analysis--a reviewLaura Gámiz-Gracia
Department of Analytical Chemistry, Faculty of Sciences, Campus Fuentenueva, University of Granada, E 18071 Granada, Spain
Anal Chim Acta 640:7-28. 2009..The review covers the literature from 2000 until the end of 2008...
An evaluation of the utility of physiologically based models of pharmacokinetics in early drug discoveryNeil Parrott
F Hoffmann La Roche AG, Pharmaceuticals Division, CH 4070 Bl, Switzerland
J Pharm Sci 94:2327-43. 2005..However verification of the simulations with in vivo data for a few compounds of each compound class is recommended since recent discovery compounds may have properties beyond the scope of the current generic models...
Modelling and PBPK simulation in drug discoveryHannah M Jones
Pfizer Global R and D, Department of Pharmacokinetics, Dynamics and Metabolism, IPC 654, Ramsgate Road, Sandwich, Kent, CT13 9NJ, UK
AAPS J 11:155-66. 2009....
Sex differences in pharmacokinetics and pharmacodynamicsOffie P Soldin
Departments of Medicine, Oncology and Physiology, Center for the Study of Sex Differences, Georgetown University Medical Center, Washington, DC, USA
Clin Pharmacokinet 48:143-57. 2009..Since this is a rapidly evolving area, it is essential for the practitioner to review drug prescribing information and recent literature in order to fully understand the impact of these differences on clinical therapeutics...
Drug effects viewed from a signal transduction network perspectiveAnton F Fliri
Pfizer Global Research and Development, CT, USA
J Med Chem 52:8038-46. 2009..These protein network topology models reveal that drugs having similar pharmacology profiles reach similar discrete positions in cellular protein network systems and provide a network view of medicine cause-effect relationships...
Observational study of potential risk factors of medication administration errorsEdgar Tissot
Pharmacy Department, , Boulevard Fleming, , France
Pharm World Sci 25:264-8. 2003..CONCLUSION: According to these data, the quality of the medication administration process needs to be optimized in hospitals in order to minimize the incidence of iatrogenic preventable diseases...
Physiologically-based pharmacokinetic simulation modellingGeorge M Grass
LION Bioscience, 9880 Campus Point Drive, San Diego, CA 92121, USA
Adv Drug Deliv Rev 54:433-51. 2002....
Data-driven methods to discover molecular determinants of serious adverse drug eventsA P Chiang
Department of Medicine, Stanford Center for Biomedical Informatics, Stanford University School of Medicine, Stanford, California, USA
Clin Pharmacol Ther 85:259-68. 2009..We also describe recent examples of how bioinformatics methods coupled with data repositories can advance the science of SADRs...
Polar molecular surface as a dominating determinant for oral absorption and brain penetration of drugsJ Kelder
Department of Molecular Design and Informatics, NV Organon, Oss, The Netherlands
Pharm Res 16:1514-9. 1999..To study oral absorption and brain penetration as a function of polar molecular surface area...
A topological substructural approach for the prediction of P-glycoprotein substratesMiguel Angel Cabrera
Department of Drug Design, Centre of Chemical Bioactive, Central University of Las Villas, Santa Clara, Villa Clara, Cuba
J Pharm Sci 95:589-606. 2006....
Mathematical modeling of drug deliveryJ Siepmann
College of Pharmacy, JE 2491, University of Lille, 3 rue du Professeur Laguesse, 59006 Lille, France
Int J Pharm 364:328-43. 2008..Ideally, the effects of the design parameters of the dosage form on the resulting drug concentration time profiles at the site of action and the pharmacodynamic effects will become predictable...
SMPDB: The Small Molecule Pathway DatabaseAlex Frolkis
Department of Computing Science, University of Alberta, Edmonton, AB, Canada
Nucleic Acids Res 38:D480-7. 2010..Gene, metabolite and protein concentration data can also be visualized through SMPDB's mapping interface. All of SMPDB's images, image maps, descriptions and tables are downloadable. SMPDB is available at: http://www.smpdb.ca...
Computation of octanol-water partition coefficients by guiding an additive model with knowledgeTiejun Cheng
State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Road, Shanghai, P R China
J Chem Inf Model 47:2140-8. 2007..It is also able to utilize the ever-increasing experimentally measured logP data more effectively...
Timing of new black box warnings and withdrawals for prescription medicationsKaren E Lasser
Department of Medicine, Cambridge Hospital, Cambridge, MA 02139, USA
JAMA 287:2215-20. 2002..Recently approved drugs may be more likely to have unrecognized adverse drug reactions (ADRs) than established drugs, but no recent studies have examined how frequently postmarketing surveillance identifies important ADRs...
Structure-based virtual screening: an overviewPaul D Lyne
AstraZeneca R and D Boston, Waltham, MA 02451, USA
Drug Discov Today 7:1047-55. 2002..Here, the current strengths and weaknesses of the technology are discussed, and emphasis is placed on aspects of the work-flow of a virtual screening campaign, from preparation through to post-screening analysis...
Large-scale prediction of drug-target relationshipsMichael Kuhn
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
FEBS Lett 582:1283-90. 2008..We finally discuss how phenotypic data could help to expand our understanding of the complex mechanisms of drug action...
Drugs behave as substrates, inhibitors and inducers of human cytochrome P450 3A4Shu Feng Zhou
Division of Chinese Medicine, School of Health Sciences, WHO Collaborating Center for Traditional Medicine, RMIT University, Victoria, Australia
Curr Drug Metab 9:310-22. 2008....
Primary hepatocytes: current understanding of the regulation of metabolic enzymes and transporter proteins, and pharmaceutical practice for the use of hepatocytes in metabolism, enzyme induction, transporter, clearance, and hepatotoxicity studiesNicola J Hewitt
Scientific Writing Services, Wingertstrasse, Erzhausen, Germany
Drug Metab Rev 39:159-234. 2007..We also report pharmaceutical perspectives of these topics and compare methods and interpretations for the drug development process...
SuperToxic: a comprehensive database of toxic compoundsUlrike Schmidt
Structural Bioinformatics Group, Institute of Molecular Biology and Bioinformatics, Charite University Medicine Berlin, Arnimallee 22, 14195 Berlin, Germany
Nucleic Acids Res 37:D295-9. 2009..This database is available online at: http://bioinformatics.charite.de/supertoxic...
Passive permeability and P-glycoprotein-mediated efflux differentiate central nervous system (CNS) and non-CNS marketed drugsKelly M Mahar Doan
Preclinical Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Research Triangle Park, North Carolina 27709, USA
J Pharmacol Exp Ther 303:1029-37. 2002..For CNS delivery, a drug should ideally have an in vitro passive permeability >150 nm/s and not be a good (B --> A/A --> B ratio <2.5) Pgp substrate...
Overriding of drug safety alerts in computerized physician order entryHeleen van der Sijs
Department of Hospital Pharmacy, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
J Am Med Inform Assoc 13:138-47. 2006..Studies on cognitive processes playing a role in overriding drug safety alerts are lacking...
PROMISCUOUS: a database for network-based drug-repositioningJoachim von Eichborn
Charite Universitatsmedizin Berlin, Institute for Physiology, Structural Bioinformatics Group, Lindenberger Weg 80, 13125 Berlin, Germany
Nucleic Acids Res 39:D1060-6. 2011..This network-based approach can provide a starting point for drug-repositioning. PROMISCUOUS is publicly available at http://bioinformatics.charite.de/promiscuous...
Mitochondrial abnormalities--a link to idiosyncratic drug hepatotoxicity?Urs A Boelsterli
Molecular Toxicology Lab, Department of Pharmacology, Yong Loo Lin School of Medicine, Singapore
Toxicol Appl Pharmacol 220:92-107. 2007..New animal models (e.g., the Sod2(+/-) mouse) provide supporting evidence for this concept. However, genetic analyses of DILI patient samples are needed to ultimately provide the proof-of-concept...
EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilitiesKun Yi Hsin
The Centre for Translational and Chemical Biology, The University of Edinburgh, King s Buildings, Edinburgh, UK
Nucleic Acids Res 39:D1042-8. 2011..Two ligand searching applications are given to demonstrate how EDULISS can be used to extract families of molecules with selected structural and biophysical features...
Simulation and prediction of in vivo drug metabolism in human populations from in vitro dataAmin Rostami-Hodjegan
Academic Unit of Clinical Pharmacology, Floor M, The Royal Hallamshire Hospital, Sheffield S10 2JF, and Simcyp Ltd, The Blades Enterprise Centre, John Street, Sheffield S2 4SU, UK
Nat Rev Drug Discov 6:140-8. 2007..An effort to build virtual populations using extensive demographic, physiological, genomic and in vitro biochemical data to simulate and predict drug disposition from routinely collected in vitro data is outlined...
Computational prediction of human drug metabolismSean Ekins
GeneGo, Inc, 500 Renaissance Drive, Suite 106, St Joseph, MI 49085, USA
Expert Opin Drug Metab Toxicol 1:303-24. 2005..This will ultimately aid in hypothesis generation and the early triaging of molecules likely to have undesirable predicted properties or measured effects on key proteins and cellular functions...
The influence of drug-like concepts on decision-making in medicinal chemistryPaul D Leeson
AstraZeneca R and D Charnwood, Bakewell Road, Loughborough LE15 5RH, UK
Nat Rev Drug Discov 6:881-90. 2007..Tackling the threat of compound-related toxicological attrition needs to move to the mainstream of medicinal chemistry decision-making...
The incidence and nature of prescribing and medication administration errors in paediatric inpatientsMaisoon Abdullah Ghaleb
Department of Practice and Policy, The School of Pharmacy, University of Hertfordshire, Hatfield AL10 9AB, UK
Arch Dis Child 95:113-8. 2010..To determine the incidence and nature of prescribing and medication administration errors in paediatric inpatients...
Prediction of passive blood-brain partitioning: straightforward and effective classification models based on in silico derived physicochemical descriptorsSantiago Vilar
Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
J Mol Graph Model 28:899-903. 2010....
Consumer reporting of adverse drug reactions: a retrospective analysis of the Danish adverse drug reaction database from 2004 to 2006Lise Aagaard
Department of Pharmacology and Pharmacotherapy, Section for Social Pharmacy, Faculty of Pharmaceutical Sciences, University of Copenhagen, Copenhagen, Denmark
Drug Saf 32:1067-74. 2009..The objective of this study was to compare ADRs reported by consumers with ADRs reported from other sources, in terms of their type, seriousness and the suspected medicines involved...
Predicting drug side-effects by chemical systems biologyNicholas P Tatonetti
Training Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA
Genome Biol 10:238. 2009..New approaches to predicting ligand similarity and protein interactions can explain unexpected observations of drug inefficacy or side-effects...
Utilising atomic force microscopy for the characterisation of nanoscale drug delivery systemsJohannes Sitterberg
Department of Pharmaceutical Technology and Biopharmacy, Philipps Universitat Marburg, Marburg, Germany
Eur J Pharm Biopharm 74:2-13. 2010....
Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactomeLun Yang
Bio X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
PLoS Comput Biol 5:e1000441. 2009..In conclusion, SADR targets and the patient-specific off-targets could be identified through a systematic investigation of the CPI, generating important hypotheses for prospective experimental validation of the candidate genes...
Detecting drug targets with minimum side effects in metabolic networksZ Li
Beijing Wuzi University, School of Information, Beijing, People s Republic of China
IET Syst Biol 3:523-33. 2009..The results show that our approach can identify the optimal drug targets in an exact and efficient manner. In particular, it can be applied to large-scale networks including the whole metabolic networks from most organisms...
SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactomeLun Yang
Bio X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, PR China
Nucleic Acids Res 37:W406-12. 2009..The server is freely available at http://SePreSA.Bio-X.cn/...
Pharmaceutical applications of confocal laser scanning microscopy: the physical characterisation of pharmaceutical systemsSamuel R Pygall
Formulation Insights, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
Adv Drug Deliv Rev 59:1434-52. 2007..In the future, there is continuing scope for wider exploitation of existing techniques, and continuing advancements in instrumentation...
The role of drug transporters at the blood-brain barrierA G de Boer
Blood Brain Barrier Research Group, Division of Pharmacology, Leiden Amsterdam Center for Drug Research, University of Leiden, The Netherlands
Annu Rev Pharmacol Toxicol 43:629-56. 2003....
Balancing early market access to new drugs with the need for benefit/risk data: a mounting dilemmaHans Georg Eichler
European Medicines Agency, Canary Wharf, London, UK
Nat Rev Drug Discov 7:818-26. 2008....
Functional role of P-glycoprotein in limiting intestinal absorption of drugs: contribution of passive permeability to P-glycoprotein mediated efflux transportManthena V S Varma
Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Sector No. 67, SAS Nagar 160 062, Punjab, India
Mol Pharm 2:12-21. 2005..Thus, integrating these factors with drug characteristics of the Biopharmaceutics Classification System (BCS) class better predicts the functional role of P-gp in limiting intestinal drug absorption...
The use of questionnaires for measuring patient-reported side effects of drugs: its importance and methodological challengesJuliet M Foster
Department of General Practice, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
Pharmacoepidemiol Drug Saf 17:278-96. 2008....
Hyperkalemia in the elderly: drugs exacerbate impaired potassium homeostasisM A Perazella
Department of Medicine, Yale University School of Medicine, New Haven, Conn 06520 8029, USA
J Gen Intern Med 12:646-56. 1997....
Liver function and phase I drug metabolism in the elderly: a paradoxD L Schmucker
Cell Biology and Aging Section 151E, Veterans Affairs Medical Center, San Francisco, California 94121, USA
Drugs Aging 18:837-51. 2001....
Effect of computer order entry on prevention of serious medication errors in hospitalized childrenKathleen E Walsh
Department of Pediatrics, University of Massachusetts Medical School UMass Memorial Medical Center, Worcester, Massachusetts 01655, USA
Pediatrics 121:e421-7. 2008..Our objective was to evaluate comprehensively the effect of computerized physician order entry on the rate of inpatient pediatric medication errors...
Immunogenicity of therapeutic proteins. Part 1: impact of product handlingBasant Sharma
Pharmaceutical Technology, Global Biologics Supply Chain LLC, HTD 6 2, Horsham, PA 19044, USA
Biotechnol Adv 25:310-7. 2007....
Using computerized data to identify adverse drug events in outpatientsB Honigman
University of Colorado Health Sciences Center, Denver, USA
J Am Med Inform Assoc 8:254-66. 2001....
Sex differences in drug metabolism: cytochrome P-450 and uridine diphosphate glucuronosyltransferaseGail D Anderson
Department of Pharmacy, Box 357630, University of Washington, Seattle, WA 98195, USA
J Gend Specif Med 5:25-33. 2002..However, genetics also controls the amount (or activity) of the enzymes. Sex-dependent differences have been demonstrated for several CYP isoenzymes and for UGT. Ethnicity also appears to play a role in the activity of these enzymes...
Hormonal regulation of hepatic drug-metabolizing enzyme activity during adolescenceMj Kennedy
Kosair Charities Pediatric Clinical Research Unit, Department of Pediatrics, School of Medicine, University of Louisville, Louisville, Kentucky, USA
Clin Pharmacol Ther 84:662-73. 2008....
Quality assessment of internet pharmaceutical products using traditional and non-traditional analytical techniquesBenjamin J Westenberger
Food and Drug Administration, Division of Pharmaceutical Analysis, 1114 Market Street, St Louis, MO 63101, USA
Int J Pharm 306:56-70. 2005..For example, these methods detected suspect manufacturing issues (such as blending), which were not evident from traditional testing alone...
Influence of drugs and comorbidity on serum potassium in 15 000 consecutive hospital admissionsSamuel Henz
Department of Internal Medicine, Kantonsspital, CH 9007 St Gallen, Switzerland
Nephrol Dial Transplant 23:3939-45. 2008..Nevertheless, after approval, these drugs will be prescribed to a much broader collective. Our goal was to quantify the impact of drugs and comorbidity on serum potassium in unselected patients admitted to the hospital...
Prediction of P-glycoprotein substrates by a support vector machine approachY Xue
Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543
J Chem Inf Comput Sci 44:1497-505. 2004..5 decision tree, that use the same sets of data and molecular descriptors. Our study indicates the potential of SVM in facilitating the prediction of P-gp substrates...
Predicting drug-drug interactions: an FDA perspectiveLei Zhang
Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Rm 3188, Bldg 51, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA
AAPS J 11:300-6. 2009..This report summarizes critical elements in the in vitro evaluation of drug interaction potential during drug development and uses a case study to highlight the impact of in vitro information on drug labeling...
The properties of known drugs. 1. Molecular frameworksG W Bemis
Vertex Pharmaceuticals, Cambridge, Massachusetts 02139 4242, USA
J Med Chem 39:2887-93. 1996..We discuss the possible interpretations of these findings and the way they may be used to guide future drug discovery research...
SuperPred: drug classification and target predictionMathias Dunkel
Institute of Molecular Biology and Bioinformatics, Charite University Medicine Berlin, Arnimallee 22, 14195 Berlin, Germany
Nucleic Acids Res 36:W55-9. 2008..Availability: the system is freely accessible at http://bioinformatics.charite.de/superpred. SuperPred can be obtained via a Creative Commons Attribution Noncommercial-Share Alike 3.0 License...
Frequency of and risk factors for preventable medication-related hospital admissions in the NetherlandsAnne J Leendertse
Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Division of Pharmacoepidemiology and Pharmacotherapy, Utrecht University, Utrecht, The Netherlands
Arch Intern Med 168:1890-6. 2008..Furthermore, little information exists on potential risk factors associated with preventable medication-related hospitalizations...
Investigating drug-induced mitochondrial toxicity: a biosensor to increase drug safety?Cláudia V Pereira
Center for Neurosciences and Cell Biology, Department of Zoology, University of Coimbra, Coimbra, Portugal
Curr Drug Saf 4:34-54. 2009....
Large-scale production of pharmaceuticals by marine sponges: sea, cell, or synthesis?Detmer Sipkema
Food and Bioprocess Engineering Group, Wageningen University, P O Box 8129, 6700 EV Wageningen, The Netherlands
Biotechnol Bioeng 90:201-22. 2005..It was concluded that the latter two approaches could prove to be valuable methods for the production of pharmaceuticals, based on chemical structures of secondary metabolites present in trace amounts in marine sponges...
A European study of HLA-B in Stevens-Johnson syndrome and toxic epidermal necrolysis related to five high-risk drugsChristine Lonjou
INSERM, U563 Paul Sabatier University III, Toulouse, France
Pharmacogenet Genomics 18:99-107. 2008..Recently, a strong association between carbamazepine and allopurinol induced SJS or TEN has been described with respectively, HLA-B*1502 and HLA-B*5801 in a Han Chinese population from Taiwan and other Asian countries...
Enhancing the effectiveness of virtual screening by fusing nearest neighbor lists: a comparison of similarity coefficientsMartin Whittle
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, U K
J Chem Inf Comput Sci 44:1840-8. 2004..The use of group recall can lead to improved enrichment in database searches and virtual screening...
Random forest models to predict aqueous solubilityDavid S Palmer
Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
J Chem Inf Model 47:150-8. 2007..Finally, the diversity of the training and test sets are compared to the chemical space occupied by molecules in the MDL drug data report, on the basis of molecular descriptors selected by the regression analysis...
Nanostructured bacterial materials for innovative medicinesEscarlata Rodríguez-Carmona
Institute for Biotechnology and Biomedicine, Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain
Trends Microbiol 18:423-30. 2010....
Research Grants
- Mechanisms of Manganese NeurotoxicityANUMANTHA GOUNDER KANTHASAMY; Fiscal Year: 2010..problem resulting from the use of Mn as a gasoline additive, and its use in welding rods, pesticides, pharmaceutical preparations, alloy manufacturing, and in dry cell battery production, for instance...
- Mechanisms of Manganese NeurotoxicityANUMANTHA GOUNDER KANTHASAMY; Fiscal Year: 2010..problem resulting from the use of Mn as a gasoline additive, and its use in welding rods, pesticides, pharmaceutical preparations, alloy manufacturing, and in dry cell battery production, for instance...
- TARGETED METAL CHELATORS FOR DIAGNOSTIC IMAGINGMichael Welch; Fiscal Year: 2001..The synthesis characterization and physicochemical studies will be carried out at Texas A&M University while the in vitro and in vivo evaluation of the pharmaceutical preparations will be undertaken at Washington University.
- TARGETED METAL CHELATORS FOR DIAGNOSTIC IMAGINGMichael Welch; Fiscal Year: 1993..and physicochemical studies will be carried out at Texas A&M University with non-radioactive isotopes while in vitro and in vivo evaluation of the pharmaceutical preparations will be carried out at Washington University.
- Bi(III)-Initiated Chemistry: Mechanistic Investigations of Catalytic ActivityRobert Hinkle; Fiscal Year: 2007..In fact, bismuth compounds have been widely utilized in pharmaceutical preparations for over 400 years...
- Label Free Pharmaceutical Anticounterfeiting TechnologyROBERT HAUSHALTER; Fiscal Year: 2007..However, an anticounterfeiting method to protect pharmaceutical preparations directly at the pill level presents a singularly stringent set of requirements in terms of employing a ..
- CONTROLLED RELEASE OF MACROMOLECULESRobert Langer; Fiscal Year: 2003..The stabilization of DNA in viable long-term pharmaceutical preparations is one critical part toward the advance of gene therapy to the clinic...
- Pharmaceutical Anticounterfeiting TechnologyROBERT HAUSHALTER; Fiscal Year: 2005..has prevented any of these techniques from evolving into a widely used and effective system to protect pharmaceutical preparations. Parallel Synthesis Technologies proposes the use of an inexpensive and easy to use encoding technology,..
- ACYL GLUCURONIDES: COVALENT BINDING & PHARMACOKINETICSLeslie Benet; Fiscal Year: 1993..investigate the relationship between irreversible binding in vivo and immunological toxicity...
- Metabolism of Carcinogens and Drugs by Human P450sF Guengerich; Fiscal Year: 2007....
- ACYLCOA FORMATION--COVALENT BINDING, PHARMACOKINETICSLeslie Benet; Fiscal Year: 2002....
- BIOACTIVATION OF HALOGENATED HYDROCARBONSF Guengerich; Fiscal Year: 2005..These experiments involving enzymatic oxidation and conjugation reactions are intended to help define important concepts that can be applied to other halogenated hydrocarbons and to other cancer suspect chemicals as well. ..
- Novel Approaches to Blood Brain Barrier FunctionAlex Avdeef; Fiscal Year: 2007....
- Polymerase Interactions with Carcinogen-modified DNAF Peter Guengerich; Fiscal Year: 2010..The goals of this project involve understanding how the DNA polymerases make such mistakes. ..
- Physics-based Simulation of Biological Structures(RMI)Russ Altman; Fiscal Year: 2007..It will thus provide a critical piece of a national biomedical computing infrastructure. ..
- Annotating functional sites in 3D biological structuresRUSS BIAGIO ALTMAN; Fiscal Year: 2010..In particular, we will focus our new capabilities on three difficult function annotation challenges: ATP binding sites, phosphorylation sites, and metabolizing enzyme active sites. ..
- Design and Characterization of DNA Interactive AgentsJennifer Brodbelt; Fiscal Year: 2005..The anticancer and antibacterial effects of UK-1 and A-62176 analogs will be examined in a range of human cancer cell lines and Gram negative and Gram positive bacteria. ..
- POLYMERASE INTERACTIONS WITH CARCINOGEN MODIFIED DNAF Guengerich; Fiscal Year: 2004..The overall goal is understanding molecular mechanisms of mutagenesis as a part of chemical carcinogenesis. ..
- Hyopthyroidism Treatment in Aging and Thyroid CancerOffie P Soldin; Fiscal Year: 2010..This will help in setting therapeutic goals and help millions in diagnosis, treatment and management of thyroid disease in aging. ..
- CHROMATOGRAPHIC STUDIES OF FUNCTIONAL PROTEOMICSDAVID HAGE; Fiscal Year: 2007..This, in turn, should allow an improved description of how the transport, metabolism, and effective dose of a drug will differ between a diabetic patient and an individual without diabetes. ..
- CHROMATOGRAPHIC AUTOMATION OF IMMUNOASSAYSDAVID HAGE; Fiscal Year: 2004..The result of this work should be the creation of new, more rapid tools for determining free drug or hormone levels, providing a better means for studying how such compounds behave and interact within our bodies. ..
- Analysis of Phenolic Phytochemical by ESI-MSJennifer Brodbelt; Fiscal Year: 2003....
- MECHANISMS OF TOXICITY GORDON CONFERENCERONALD HINES; Fiscal Year: 2002..There also is substantial involvement of new personnel as Chairs and co-Chairs. Thus, the Mechanism of Toxicity GRC is poised to continue its growth as the single leading small conference on Molecular Toxicology. ..
- Physiological functions of G-alpha-i/o and control by regulators of G protein sigRichard R Neubig; Fiscal Year: 2010..By improving those therapeutically useful signals at the expense of signals leading to side effects, we can produce better medicines or can make existing medicines better tolerated. ..
- Design of Small Molecules Acting at Regulators of G Protein SignalingRichard R Neubig; Fiscal Year: 2010..This project will provide the initial steps and proof of principle for medications development targeting RGS proteins - a key modulator of signaling related to drug abuse. ..
- Design of Small Molecules Acting at Regulators of G Protein SignalingRichard Neubig; Fiscal Year: 2007..This project will provide the initial steps and proof of principle for medications development targeting RGS proteins - a key modulator of signaling related to drug abuse. ..
- Super-persistent cells and the paradox of untreatable infectionsKim Lewis; Fiscal Year: 2009..Our findings are likely to change the way we view infectious diseases and will provide rational approaches for discovering drugs that completely eradicate the infection. ..
- PEPTIDE MODULATORS OF G PROTEIN FUNCTIONRichard Neubig; Fiscal Year: 2000..The specificity of these "drugs" will be tested in cell culture with the aim of future use in gene therapy approaches to cardiovascular disease. ..
- PEPTIDE MODULATORS OF G PROTEIN FUNCTIONRichard Neubig; Fiscal Year: 1993....
- Biosensors for metabolic engineeringJay Keasling; Fiscal Year: 2006..abstract_text> ..
- SCREEN DEVELOPMENT FOR ANTIMICROBIAL PRODRUGSKim Lewis; Fiscal Year: 2007....
- Contraceptive Services/Primary Care to Prevent Birth DefectsEleanor Schwarz; Fiscal Year: 2007....
