Drug repositioning for personalized medicine

[1]  M. Goetz,et al.  Tamoxifen Pharmacogenomics: The Role of CYP2D6 as a Predictor of Drug Response , 2008, Clinical pharmacology and therapeutics.

[2]  David Bryant,et al.  DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists , 2007, Nucleic Acids Res..

[3]  L. Kuller,et al.  The Heterogeneity of Diabetes , 2007, Diabetes.

[4]  Michael A. Choti,et al.  DAXX/ATRX, MEN1, and mTOR Pathway Genes Are Frequently Altered in Pancreatic Neuroendocrine Tumors , 2011, Science.

[5]  J. Apperley,et al.  Mechanisms of Resistance to Imatinib and Second-Generation Tyrosine Inhibitors in Chronic Myeloid Leukemia , 2009, Clinical Cancer Research.

[6]  B. Schuessler What do we know about duloxetine's mode of action? Evidence from animals to humans , 2006, BJOG : an international journal of obstetrics and gynaecology.

[7]  Y.Z. Chen,et al.  Ligand–protein inverse docking and its potential use in the computer search of protein targets of a small molecule , 2001, Proteins.

[8]  Robert B. Russell,et al.  SuperTarget and Matador: resources for exploring drug-target relationships , 2007, Nucleic Acids Res..

[9]  Zhaowei Zhong,et al.  Quantitative analysis on the characteristics of targets with FDA approved drugs , 2007, International journal of biological sciences.

[10]  Y. Shin Glycogen storage disease: clinical, biochemical, and molecular heterogeneity. , 2006, Seminars in pediatric neurology.

[11]  Charles C. Persinger,et al.  How to improve R&D productivity: the pharmaceutical industry's grand challenge , 2010, Nature Reviews Drug Discovery.

[12]  W. Yung,et al.  An integrated in vitro and in vivo high-throughput screen identifies treatment leads for ependymoma. , 2011, Cancer cell.

[13]  Chantal Dreyer,et al.  Sunitinib in advanced pancreatic neuroendocrine tumors: latest evidence and clinical potential , 2012, Therapeutic advances in medical oncology.

[14]  Michael Gross Riding the wave of biological data , 2011, Current Biology.

[15]  M Day The bitterest pill , 2007, BMJ : British Medical Journal.

[16]  C. Chong,et al.  New uses for old drugs , 2007, Nature.

[17]  T. Paravar,et al.  Thalidomide: Mechanisms of Action , 2008, International reviews of immunology.

[18]  B. Druker,et al.  Comparison of imatinib mesylate, dasatinib (BMS-354825), and nilotinib (AMN107) in an N-ethyl-N-nitrosourea (ENU)-based mutagenesis screen: high efficacy of drug combinations. , 2006, Blood.

[19]  Lee T. Sam,et al.  Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study , 2011, Science Translational Medicine.

[20]  S. Nelson,et al.  Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation , 2010, Nature.

[21]  R. Solé,et al.  The topology of drug-target interaction networks: implicit dependence on drug properties and target families. , 2009, Molecular bioSystems.

[22]  G. Klebe Virtual ligand screening: strategies, perspectives and limitations , 2006, Drug Discovery Today.

[23]  Min Guan,et al.  Anti-HIV drugs for cancer therapeutics: back to the future? , 2009, The Lancet. Oncology.

[24]  R. Tibshirani,et al.  Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[25]  D. Marcus Duloxetine use in painful conditions , 2011, Expert opinion on pharmacotherapy.

[26]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[27]  Joel Dudley,et al.  Exploiting drug-disease relationships for computational drug repositioning , 2011, Briefings Bioinform..

[28]  B. Roth,et al.  Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia , 2004, Nature Reviews Drug Discovery.

[29]  R. Tagliaferri,et al.  Discovery of drug mode of action and drug repositioning from transcriptional responses , 2010, Proceedings of the National Academy of Sciences.

[30]  D. Tuveson,et al.  Effect of the tyrosine kinase inhibitor STI571 in a patient with a metastatic gastrointestinal stromal tumor. , 2001, The New England journal of medicine.

[31]  T. Hunter,et al.  The Protein Kinase Complement of the Human Genome , 2002, Science.

[32]  Laurence Choulier,et al.  Validation of surface plasmon resonance screening of a diverse chemical library for the discovery of protein tyrosine phosphatase 1b binders. , 2012, Analytical biochemistry.

[33]  G. Sinha Academia's $1,000 genome , 2011, Nature Biotechnology.

[34]  Richard B. Smith,et al.  Repositioned drugs: integrating intellectual property and regulatory strategies , 2011 .

[35]  Steven J. M. Jones,et al.  A new frontier in personalized cancer therapy: mapping molecular changes. , 2011, Future oncology.

[36]  Lupei Du,et al.  A novel structure-based virtual screening model for the hERG channel blockers. , 2007, Biochemical and biophysical research communications.

[37]  J. Arrowsmith Trial watch: Phase II failures: 2008–2010 , 2011, Nature Reviews Drug Discovery.

[38]  J. Mesirov,et al.  Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. , 1999, Science.

[39]  L. Staudt,et al.  Stromal gene signatures in large-B-cell lymphomas. , 2008, The New England journal of medicine.

[40]  S. Giordano,et al.  From single- to multi-target drugs in cancer therapy: when aspecificity becomes an advantage. , 2008, Current medicinal chemistry.

[41]  P. Jänne,et al.  The biology and treatment of EML4-ALK non-small cell lung cancer. , 2010, European journal of cancer.

[42]  L. Mueller-Kuhrt,et al.  Revisiting old drugs as novel agents for retinoblastoma: in vitro and in vivo antitumor activity of cardenolides. , 2009, Investigative ophthalmology & visual science.

[43]  Steven J. M. Jones,et al.  A Computational Approach to Finding Novel Targets for Existing Drugs , 2011, PLoS Comput. Biol..

[44]  Kui Xu,et al.  Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases , 2011, Briefings Bioinform..

[45]  Leming Shi,et al.  Identifying Unexpected Therapeutic Targets via Chemical-Protein Interactome , 2010, PloS one.

[46]  黄亚明 MedScape , 2009 .

[47]  L. Wodicka,et al.  A small molecule–kinase interaction map for clinical kinase inhibitors , 2005, Nature Biotechnology.

[48]  T. Bekaii-Saab,et al.  New developments in the treatment of metastatic gastric cancer: focus on trastuzumab , 2011, OncoTargets and therapy.

[49]  David P Bick,et al.  Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease , 2011, Genetics in Medicine.

[50]  P. Mease Further strategies for treating fibromyalgia: the role of serotonin and norepinephrine reuptake inhibitors. , 2009, The American journal of medicine.

[51]  Ruili Huang,et al.  The NCGC Pharmaceutical Collection: A Comprehensive Resource of Clinically Approved Drugs Enabling Repurposing and Chemical Genomics , 2011, Science Translational Medicine.

[52]  R. Pazdur,et al.  Approval summary: imatinib mesylate in the treatment of metastatic and/or unresectable malignant gastrointestinal stromal tumors. , 2009, The oncologist.

[53]  R. Plodkowski,et al.  Bupropion and naltrexone: a review of their use individually and in combination for the treatment of obesity , 2009 .

[54]  R. Palmer,et al.  Crizotinib--latest champion in the cancer wars? , 2010, The New England journal of medicine.

[55]  S. Broder,et al.  The development of antiretroviral therapy and its impact on the HIV-1/AIDS pandemic. , 2010, Antiviral research.

[56]  Ken Chen,et al.  Recurring mutations found by sequencing an acute myeloid leukemia genome. , 2009, The New England journal of medicine.

[57]  Christian A. Rees,et al.  Molecular portraits of human breast tumours , 2000, Nature.

[58]  J. Ross,et al.  Saving lives with accurate HER2 testing. , 2010, American journal of clinical pathology.

[59]  T. Ashburn,et al.  Drug repositioning: identifying and developing new uses for existing drugs , 2004, Nature Reviews Drug Discovery.

[60]  Liwei Li,et al.  BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome , 2010, Nucleic Acids Res..

[61]  G. V. Paolini,et al.  Global mapping of pharmacological space , 2006, Nature Biotechnology.

[62]  S. Lawrence Drug output slows in 2006 , 2007, Nature Biotechnology.

[63]  David Bradley,et al.  Why big pharma needs to learn the three 'R's , 2005, Nature Reviews Drug Discovery.

[64]  R. Nahta,et al.  HER2 therapy: Molecular mechanisms of trastuzumab resistance , 2006, Breast Cancer Research.

[65]  Yang Song,et al.  Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery , 2011, Nucleic Acids Res..

[66]  J. Kauh,et al.  Chemotherapy in the Treatment of Metastatic Gastric Cancer: Is There a Global Standard? , 2011, Current treatment options in oncology.

[67]  E. Van Cutsem,et al.  Cetuximab plus irinotecan, fluorouracil, and leucovorin as first-line treatment for metastatic colorectal cancer: updated analysis of overall survival according to tumor KRAS and BRAF mutation status. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[68]  Tom Misteli,et al.  RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E) , 2011, Nature.

[69]  M. Stratton Exploring the Genomes of Cancer Cells: Progress and Promise , 2011, Science.

[70]  Robert Nadon,et al.  Statistical practice in high-throughput screening data analysis , 2006, Nature Biotechnology.

[71]  Min-Seok Kwon,et al.  IDMap: facilitating the detection of potential leads with therapeutic targets , 2008, Bioinform..

[72]  Robert H. Shoemaker,et al.  Nelfinavir, A Lead HIV Protease Inhibitor, Is a Broad-Spectrum, Anticancer Agent that Induces Endoplasmic Reticulum Stress, Autophagy, and Apoptosis In vitro and In vivo , 2007, Clinical Cancer Research.

[73]  György Kéri,et al.  Cellular targets of gefitinib. , 2005, Cancer research.

[74]  Alexander A. Morgan,et al.  Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease , 2011, Science Translational Medicine.

[75]  L. Gourgiotis,et al.  Pharmaceutical interventions for obesity: a public health perspective , 2011, Diabetes, obesity & metabolism.

[76]  M. Ladanyi,et al.  KRAS mutation detection: a new look at an old gene. , 2010, Clinical chemistry.

[77]  E. Tambuyzer,et al.  Rare diseases, orphan drugs and their regulation: questions and misconceptions , 2010, Nature Reviews Drug Discovery.

[78]  Anton Yuryev,et al.  Computational Approaches for Drug Repositioning and Combination Therapy Design , 2010, J. Bioinform. Comput. Biol..

[79]  D. Kerr,et al.  Predictive biomarkers: a paradigm shift towards personalized cancer medicine , 2011, Nature Reviews Clinical Oncology.

[80]  Philip E. Bourne,et al.  Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis , 2009, PLoS Comput. Biol..

[81]  Russ B Altman,et al.  PharmGKB: a logical home for knowledge relating genotype to drug response phenotype , 2007, Nature Genetics.

[82]  W. Miller,et al.  Resistance to Cancer Treatment: The Role of Somatic Genetic Events and the Challenges for Targeted Therapies , 2011, Front. Pharmacol..

[83]  J. Arrowsmith Trial watch: Phase III and submission failures: 2007–2010 , 2011, Nature Reviews Drug Discovery.

[84]  Z. Estrov,et al.  The biology of chronic myeloid leukemia. , 1999, The New England journal of medicine.

[85]  Trial watch: Adaptive BATTLE trial uses biomarkers to guide lung cancer treatment , 2010, Nature Reviews Drug Discovery.

[86]  H. Aburatani,et al.  Identification of the transforming EML4–ALK fusion gene in non-small-cell lung cancer , 2007, Nature.

[87]  J. Melo,et al.  The presence of a BCR-ABL mutant allele in CML does not always explain clinical resistance to imatinib , 2006, Leukemia.

[88]  H. McLeod,et al.  The thiopurine S-methyltransferase gene locus -- implications for clinical pharmacogenomics. , 2002, Pharmacogenomics.

[89]  D. Light,et al.  Demythologizing the high costs of pharmaceutical research , 2011 .

[90]  A. Iafrate,et al.  Mechanisms of Acquired Crizotinib Resistance in ALK-Rearranged Lung Cancers , 2012, Science Translational Medicine.

[91]  Andreas Bender,et al.  Understanding False Positives in Reporter Gene Assays: in Silico Chemogenomics Approaches To Prioritize Cell-Based HTS Data , 2007, J. Chem. Inf. Model..

[92]  Jacob de Vlieg,et al.  Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases , 2010, PLoS Comput. Biol..

[93]  Joshua F. McMichael,et al.  Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing , 2011, Nature.

[94]  O. Kallioniemi,et al.  High-Throughput Cell-Based Screening of 4910 Known Drugs and Drug-like Small Molecules Identifies Disulfiram as an Inhibitor of Prostate Cancer Cell Growth , 2009, Clinical Cancer Research.

[95]  Steven J. M. Jones,et al.  Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors , 2010, Genome Biology.

[96]  Wenqing Cai,et al.  Small molecule regulators of autophagy identified by an image-based high-throughput screen , 2007, Proceedings of the National Academy of Sciences.

[97]  J. Drews Drug discovery: a historical perspective. , 2000, Science.

[98]  B. Shoichet Screening in a spirit haunted world. , 2006, Drug discovery today.

[99]  B. Druker Imatinib as a paradigm of targeted therapies , 2003 .

[100]  M. Relling,et al.  Pharmacogenomics: translating functional genomics into rational therapeutics. , 1999, Science.

[101]  B. Padhy,et al.  Drug repositioning: re-investigating existing drugs for new therapeutic indications. , 2011, Journal of postgraduate medicine.

[102]  Jürgen Bajorath,et al.  Towards Unified Compound Screening Strategies: A Critical Evaluation of Error Sources in Experimental and Virtual High‐Throughput Screening , 2006 .

[103]  R Voelker,et al.  International group seeks to dispel incontinence "taboo". , 1998, JAMA.

[104]  B. Munos Lessons from 60 years of pharmaceutical innovation , 2009, Nature Reviews Drug Discovery.

[105]  P. Bork,et al.  Drug Target Identification Using Side-Effect Similarity , 2008, Science.

[106]  E. Tobinick The value of drug repositioning in the current pharmaceutical market. , 2009, Drug news & perspectives.

[107]  D. Solit,et al.  Drug discovery: How melanomas bypass new therapy , 2010, Nature.

[108]  F. Sharom ABC multidrug transporters: structure, function and role in chemoresistance. , 2008, Pharmacogenomics.

[109]  David S. Wishart,et al.  DrugBank: a comprehensive resource for in silico drug discovery and exploration , 2005, Nucleic Acids Res..

[110]  Cheng Zhu,et al.  Drug repositioning for orphan diseases , 2011, Briefings Bioinform..

[111]  Bin Chen,et al.  PubChem as a Source of Polypharmacology , 2009, J. Chem. Inf. Model..

[112]  Michael Schroeder,et al.  Old friends in new guise: repositioning of known drugs with structural bioinformatics , 2011, Briefings Bioinform..

[113]  Ara Darzi,et al.  Preparing for precision medicine. , 2012, The New England journal of medicine.

[114]  Ken Chen,et al.  Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. , 2011, JAMA.

[115]  S. Roman,et al.  Medullary thyroid cancer: early detection and novel treatments , 2009, Current opinion in oncology.

[116]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[117]  L. Borish,et al.  Asthma: a syndrome composed of heterogeneous diseases. , 2008, Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology.

[118]  Mindy I. Davis,et al.  A quantitative analysis of kinase inhibitor selectivity , 2008, Nature Biotechnology.

[119]  Xiaomin Luo,et al.  TarFisDock: a web server for identifying drug targets with docking approach , 2006, Nucleic Acids Res..

[120]  I. Kola,et al.  Can the pharmaceutical industry reduce attrition rates? , 2004, Nature Reviews Drug Discovery.

[121]  S. Frantz Drug discovery: Playing dirty , 2005, Nature.

[122]  Michael J. Keiser,et al.  Predicting new molecular targets for known drugs , 2009, Nature.

[123]  H. Ghofrani,et al.  Sildenafil: from angina to erectile dysfunction to pulmonary hypertension and beyond , 2006, Nature Reviews Drug Discovery.

[124]  M. Haffner Adopting orphan drugs--two dozen years of treating rare diseases. , 2006, The New England journal of medicine.

[125]  P. Aloy,et al.  Unveiling the role of network and systems biology in drug discovery. , 2010, Trends in pharmacological sciences.

[126]  A. Ullrich,et al.  Paul Ehrlich's magic bullet concept: 100 years of progress , 2008, Nature Reviews Cancer.

[127]  Timothy R. Coté,et al.  Accelerating orphan drug development , 2010, Nature Reviews Drug Discovery.

[128]  Lyndsay N Harris,et al.  Efficacy and safety of trastuzumab as a single agent in first-line treatment of HER2-overexpressing metastatic breast cancer. , 2002, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.