Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it

Interdependence of Gemcitabine Treatment, Transporter Expression, and Resistance in Human Pancreatic Carcinoma Cells

(2015) Wolfgang Hagmann et al.   NEOPLASIA

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

The road from systems biology to systems medicine

(2013) Olaf Wolkenhauer et al.   PEDIATRIC RESEARCH

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

Human Equilibrative Nucleoside Transporter 1 Expression Predicts Survival of Advanced Cholangiocarcinoma Patients Treated With Gemcitabine-Based Adjuvant Chemotherapy After Surgical Resection

(2012) Hironori Kobayashi et al.   ANNALS OF SURGERY

Systems pharmacology of complex diseases

(2012) Jens Hansen et al.   Annals of the New York Academy of Sciences

Systems Pharmacology to Predict Drug Toxicity: Integration Across Levels of Biological Organization

(2012) Jane P.F. Bai et al.   Annual Review of Pharmacology and Toxicology

Towards Safer and More Predictable Drug Treatment - Reflections from Studies of the First BCPT Prize Awardee

(2012) Pertti J. Neuvonen   BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY

The prototypic pharmacogenetic drug debrisoquine is a substrate of the genetically polymorphic organic cation transporter OCT1

(2012) Ali R. Saadatmand et al.   BIOCHEMICAL PHARMACOLOGY

Scientific discovery as a combinatorial optimisation problem: How best to navigate the landscape of possible experiments?

(2012) Douglas B. Kell   BIOESSAYS

Absolute abundance and function of intestinal drug transporters: a prerequisite for fully mechanisticin vitro-in vivoextrapolation of oral drug absorption

(2012) M. D. Harwood et al.   BIOPHARMACEUTICS & DRUG DISPOSITION

Natural product-likeness score revisited: an open-source, open-data implementation

(2012) Kalai Vanii Jayaseelan et al.   BMC BIOINFORMATICS

Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast

(2012) Karin Lanthaler et al.   BMC BIOLOGY

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

Excision repair cross-complementing gene-1, ribonucleotide reductase subunit M1, ribonucleotide reductase subunit M2, and human equilibrative nucleoside transporter-1 expression and prognostic value in biliary tract malignancy

(2012) Sarah B. Fisher et al.   CANCER

Drug Trafficking: Recent Advances in Therapeutics and Disease

(2012) J A Sprowl et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Transporter-Mediated Drug–Drug Interactions Involving OATP Substrates: Predictions Based on In Vitro Inhibition Studies

(2012) K Yoshida et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Computational Modeling to Accelerate the Identification of Substrates and Inhibitors for Transporters That Affect Drug Disposition

(2012) S Ekins et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Prediction of Transporter-Mediated Drug–Drug Interactions Using Endogenous Compounds

(2012) M F Fromm   CLINICAL PHARMACOLOGY & THERAPEUTICS

Zebrafish as a Model to Study Drug Transporters at the Blood–Brain Barrier

(2012) R A Umans et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

The UCSF-FDA TransPortal: A Public Drug Transporter Database

(2012) K M Morrissey et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Physiologically Based Pharmacokinetics Joined With In Vitro–In Vivo Extrapolation of ADME: A Marriage Under the Arch of Systems Pharmacology

(2012) A Rostami-Hodjegan   CLINICAL PHARMACOLOGY & THERAPEUTICS

Highlights from the International Transporter Consortium Second Workshop

(2012) M J Zamek-Gliszczynski et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Phenotypic Screening Strategies for Neurodegenerative Diseases: A Pathway to Discover Novel Drug Candidates and Potential Disease Targets or Mechanisms

(2012) R. M. Pruss   CNS & Neurological Disorders-Drug Targets

The promise and challenge of personalized medicine: aging populations, complex diseases, and unmet medical need

(2012) Adriano M Henney   CROATIAN MEDICAL JOURNAL

Sodium Dependent Multivitamin Transporter (SMVT): A Potential Target for Drug Delivery

(2012) Aswani Dutt Vadlapudi et al.   CURRENT DRUG TARGETS

Ladostigil: A Novel Multimodal Neuroprotective Drug with Cholinesterase and Brain-Selective Monoamine Oxidase Inhibitory Activities for Alzheimers Disease Treatment

(2012) Orly Weinreb et al.   CURRENT DRUG TARGETS

Statins as Anti-Inflammatory Agents in Atherogenesis: Molecular Mechanisms and Lessons from the Recent Clinical Trials

(2012) Alexios S. Antonopoulos et al.   CURRENT PHARMACEUTICAL DESIGN

Expanding the medicinally relevant chemical space with compound libraries

(2012) Fabian López-Vallejo et al.   DRUG DISCOVERY TODAY

Can we discover pharmacological promiscuity early in the drug discovery process?

(2012) Jens-Uwe Peters et al.   DRUG DISCOVERY TODAY

Relevance of systems pharmacology in drug discovery

(2012) Lourdes Cucurull-Sanchez et al.   DRUG DISCOVERY TODAY

The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so

(2012) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

Contribution of tumoral and host solute carriers to clinical drug response

(2012) Jason A. Sprowl et al.   DRUG RESISTANCE UPDATES

Genetics or environment in drug transport: the case of organic anion transporting polypeptides and adverse drug reactions

(2012) John D Clarke et al.   Expert Opinion on Drug Metabolism & Toxicology

Novel models for assessing blood–brain barrier drug permeation

(2012) Werner J Geldenhuys et al.   Expert Opinion on Drug Metabolism & Toxicology

Fluoroquinolone disposition: identification of the contribution of renal secretory and reabsorptive drug transporters

(2012) Aditi Mulgaonkar et al.   Expert Opinion on Drug Metabolism & Toxicology

Impact of drug transporter pharmacogenomics on pharmacokinetic and pharmacodynamic variability – considerations for drug development

(2012) Yurong Lai et al.   Expert Opinion on Drug Metabolism & Toxicology

Pharmacogenomics of adverse drug reactions: implementing personalized medicine

(2012) C.-Y. Wei et al.   HUMAN MOLECULAR GENETICS

Implications of Promiscuous Pim-1 Kinase Fragment Inhibitor Hydrophobic Interactions for Fragment-Based Drug Design

(2012) Andrew C. Good et al.   JOURNAL OF MEDICINAL CHEMISTRY

Classification of Inhibitors of Hepatic Organic Anion Transporting Polypeptides (OATPs): Influence of Protein Expression on Drug–Drug Interactions

(2012) Maria Karlgren et al.   JOURNAL OF MEDICINAL CHEMISTRY

Effects of novel neuroprotective and neurorestorative multifunctional drugs on iron chelation and glucose metabolism

(2012) Yulia Pollak et al.   JOURNAL OF NEURAL TRANSMISSION

Neuroprotection by the multitarget iron chelator M30 on age-related alterations in mice

(2012) Lana Kupershmidt et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

(2012) Aarash Bordbar et al.   Molecular Systems Biology

Chemical genetic discovery of targets and anti-targets for cancer polypharmacology

(2012) Arvin C. Dar et al.   NATURE

Automated design of ligands to polypharmacological profiles

(2012) Jérémy Besnard et al.   NATURE

Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML

(2012) Georg E Winter et al.   Nature Chemical Biology

Systems metabolic engineering of microorganisms for natural and non-natural chemicals

(2012) Jeong Wook Lee et al.   Nature Chemical Biology

Quantifying the chemical beauty of drugs

(2012) G. Richard Bickerton et al.   Nature Chemistry

Finding the sweet spot: the role of nature and nurture in medicinal chemistry

(2012) Michael M. Hann et al.   NATURE REVIEWS DRUG DISCOVERY

Genetics and iron in the systems biology of Parkinson’s disease and some related disorders

(2012) Claudia Funke et al.   NEUROCHEMISTRY INTERNATIONAL

A personal view on systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized and participatory

(2012) Leroy Hood et al.   New Biotechnology

Physiologically Based Modeling of Pravastatin Transporter-Mediated Hepatobiliary Disposition and Drug-Drug Interactions

(2012) Manthena V. S. Varma et al.   PHARMACEUTICAL RESEARCH

Organic Anion and Cation SLC22 “Drug” Transporter (Oat1, Oat3, and Oct1) Regulation during Development and Maturation of the Kidney Proximal Tubule

(2012) Thomas F. Gallegos et al.   PLoS One

Fragment-based lead design

(2012) O A Filz et al.   RUSSIAN CHEMICAL REVIEWS

The Ancient Drug Salicylate Directly Activates AMP-Activated Protein Kinase

(2012) S. A. Hawley et al.   SCIENCE

Concise Review: A High-Content Screening Approach to Stem Cell Research and Drug Discovery

(2012) Xiaofeng Xia et al.   STEM CELLS

Epistemic and methodological iteration in scientific research

(2012) Kevin C. Elliott   STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE

The virtual liver: a multidisciplinary, multilevel challenge for systems biology

(2012) Hermann-Georg Holzhütter et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Systems pharmacology, pharmacogenetics, and clinical trial design in network medicine

(2012) Elliott Antman et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Ten Challenges for Systems Medicine

(2012) Enrico Capobianco   Frontiers in Genetics

Oral drug delivery utilizing intestinal OATP transporters

(2011) Ikumi Tamai   ADVANCED DRUG DELIVERY REVIEWS

Immunohistochemical Analysis of Human Equilibrative Nucleoside Transporter-1 (hENT1) Predicts Survival in Resected Pancreatic Cancer Patients Treated with Adjuvant Gemcitabine Monotherapy

(2011) Soichiro Morinaga et al.   ANNALS OF SURGICAL ONCOLOGY

Strategies to Discover Unexpected Targets for Drugs Active at G Protein–Coupled Receptors

(2011) John A. Allen et al.   Annual Review of Pharmacology and Toxicology

Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs

(2011) Lei Xie et al.   Annual Review of Pharmacology and Toxicology

Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action

(2011) Shan Zhao et al.   Annual Review of Pharmacology and Toxicology

The Expression and Function of Organic Anion Transporting Polypeptides in Normal Tissues and in Cancer

(2011) Amanda Obaidat et al.   Annual Review of Pharmacology and Toxicology

Drug Transporters in Drug Efficacy and Toxicity

(2011) M.K. DeGorter et al.   Annual Review of Pharmacology and Toxicology

Metabolites as global regulators: A new view of protein regulation

(2011) Xiyan Li et al.   BIOESSAYS

Softening the Rule of Five—where to draw the line?

(2011) Joachim Petit et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Metabolic network modeling and simulation for drug targeting and discovery

(2011) Hyun Uk Kim et al.   Biotechnology Journal

A Systems Biology Strategy for Predicting Similarities and Differences of Drug Effects: Evidence for Drug-specific Modulation of Inflammation in Atherosclerosis

(2011) Robert Kleemann et al.   BMC Systems Biology

Parameter estimation in systems biology models using spline approximation

(2011) Choujun Zhan et al.   BMC Systems Biology

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

Interaction of innovative small molecule drugs used for cancer therapy with drug transporters

(2011) K Mandery et al.   BRITISH JOURNAL OF PHARMACOLOGY

OATPs, OATs and OCTs: the organic anion and cation transporters of the SLCO and SLC22A gene superfamilies

(2011) Megan Roth et al.   BRITISH JOURNAL OF PHARMACOLOGY

Integration of Genotypic and Phenotypic Screening Reveals Molecular Mediators of Melanoma-Stromal Interaction

(2011) M. J. Stine et al.   CANCER RESEARCH

Improving Drug Candidates by Design: A Focus on Physicochemical Properties As a Means of Improving Compound Disposition and Safety

(2011) Nicholas A. Meanwell   CHEMICAL RESEARCH IN TOXICOLOGY

Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms

(2011) Iain M. Wallace et al.   CHEMISTRY & BIOLOGY

Revisiting the Rule of Five on the Basis of Pharmacokinetic Data from Rat

(2011) Lars Ridder et al.   ChemMedChem

Linking Pharmacology to Clinical Reports: Cyclobenzaprine and Its Possible Association With Serotonin Syndrome

(2011) J Mestres et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Transporter-Mediated Drug Uptake and Efflux: Important Determinants of Adverse Drug Reactions

(2011) O Zolk et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Mechanisms for the anti-inflammatory effects of statins

(2011) De-xiu Bu et al.   CURRENT OPINION IN LIPIDOLOGY

Structure-based systems biology for analyzing off-target binding

(2011) Lei Xie et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Synthetic and Natural Products as Iron Chelators

(2011) Philip C. Sharpe et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Integration not isolation: arguing the case for quantitative and systems pharmacology in drug discovery and development

(2011) Balaji M. Agoram et al.   DRUG DISCOVERY TODAY

Evolution of the physicochemical properties of marketed drugs: can history foretell the future?

(2011) Bernard Faller et al.   DRUG DISCOVERY TODAY

Pharmaceutical drug transport: the issues and the implications that it is essentially carrier-mediated only

(2011) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

Genetic Polymorphisms of OATP Transporters and Their Impact on Intestinal Absorption and Hepatic Disposition of Drugs

(2011) Takeo Nakanishi et al.   Drug Metabolism and Pharmacokinetics

Human equilibrative nucleoside transporter 1 (hENT1) expression is a potential predictive tool for response to gemcitabine in patients with advanced cholangiocarcinoma

(2011) I. Borbath et al.   EUROPEAN JOURNAL OF CANCER

2D MI-DRAGON: A new predictor for protein–ligands interactions and theoretic-experimental studies of US FDA drug-target network, oxoisoaporphine inhibitors for MAO-A and human parasite proteins

(2011) Francisco Prado-Prado et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Identifying and characterizing promiscuous targets: Implications for virtual screening

(2011) Violeta I Pérez-Nueno et al.   Expert Opinion on Drug Discovery

Environmental chemicals as substrates, inhibitors or inducers of drug transporters: implication for toxicokinetics, toxicity and pharmacokinetics

(2011) Olivier Fardel et al.   Expert Opinion on Drug Metabolism & Toxicology

Drug and metabolite concentrations in tissues in relationship to tissue adverse findings: a review

(2011) Mario Pellegatti et al.   Expert Opinion on Drug Metabolism & Toxicology

High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome

(2011) S. Alsford et al.   GENOME RESEARCH

The use of molecular-based risk stratification and pharmacogenomics for outcome prediction and personalized therapeutic management of multiple myeloma

(2011) Sarah K. Johnson et al.   INTERNATIONAL JOURNAL OF HEMATOLOGY

Looking to the Future: Biomarkers in the Management of Pancreatic Adenocarcinoma

(2011) Jennifer L. Spratlin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Strategies for bringing drug delivery tools into discovery

(2011) Elizabeth Kwong et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

Physiological and Pharmacological Roles of Vascular Nucleoside Transporters

(2011) Rachel W.S. Li et al.   JOURNAL OF CARDIOVASCULAR PHARMACOLOGY

Drug Effect Prediction by Polypharmacology-Based Interaction Profiling

(2011) Zoltán Simon et al.   Journal of Chemical Information and Modeling

Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening

(2011) Violeta I. Pérez-Nueno et al.   Journal of Chemical Information and Modeling

Human equilibrative nucleoside transporter 1 expression is a strong independent prognostic factor in UICC T3-T4 pancreatic cancer patients treated with preoperative gemcitabine-based chemoradiotherapy

(2011) Yasuhiro Murata et al.   Journal of Hepato-Biliary-Pancreatic Sciences

Using the reconstructed genome-scale human metabolic network to study physiology and pathology

(2011) A. Bordbar et al.   JOURNAL OF INTERNAL MEDICINE

Systems medicine and metabolic modelling

(2011) A. Mardinoglu et al.   JOURNAL OF INTERNAL MEDICINE

From zero to hero—Design-based systems metabolic engineering of Corynebacterium glutamicum for l-lysine production

(2011) Judith Becker et al.   METABOLIC ENGINEERING

The reconstruction and analysis of tissue specific human metabolic networks

(2011) Tong Hao et al.   Molecular BioSystems

In Silico Target Profiling of One Billion Molecules

(2011) Alfons Nonell-Canals et al.   Molecular Informatics

Ligand Efficiency Indices (LEIs): More than a Simple Efficiency Yardstick

(2011) Cele Abad-Zapatero et al.   Molecular Informatics

Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing

(2011) Tudor I. Oprea et al.   Molecular Informatics

Navigating the kinome

(2011) James T Metz et al.   Nature Chemical Biology

Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing

(2011) Ben G Small et al.   Nature Chemical Biology

How were new medicines discovered?

(2011) David C. Swinney et al.   NATURE REVIEWS DRUG DISCOVERY

The influence of the 'organizational factor' on compound quality in drug discovery

(2011) Paul D. Leeson et al.   NATURE REVIEWS DRUG DISCOVERY

Probing the links between in vitro potency, ADMET and physicochemical parameters

(2011) M. Paul Gleeson et al.   NATURE REVIEWS DRUG DISCOVERY

Novel molecular targets of the neuroprotective/neurorescue multimodal iron chelating drug M30 in the mouse brain

(2011) L. Kupershmidt et al.   NEUROSCIENCE

Systems Pharmacology: Bridging Systems Biology and Pharmacokinetics-Pharmacodynamics (PKPD) in Drug Discovery and Development

(2011) Piet H. van der Graaf et al.   PHARMACEUTICAL RESEARCH

Understanding and Classifying Metabolite Space and Metabolite-Likeness

(2011) Julio E. Peironcely et al.   PLoS One

Systems biology analysis of protein-drug interactions

(2011) Jacques Colinge et al.   Proteomics Clinical Applications

Systems metabolic engineering for chemicals and materials

(2011) Jeong Wook Lee et al.   TRENDS IN BIOTECHNOLOGY

Functions of OATP1A and 1B transporters in vivo: insights from mouse models

(2011) Dilek Iusuf et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Molecular obesity, potency and other addictions in drug discovery

(2011) Michael M. Hann   MedChemComm

A comparative analysis of the molecular topologies for drugs, clinical candidates, natural products, human metabolites and general bioactive compounds

(2011) Hongming Chen et al.   MedChemComm

Virtual Cell: computational tools for modeling in cell biology

(2011) Diana C. Resasco et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

RNAi screening: new approaches, understandings, and organisms

(2011) Stephanie E. Mohr et al.   Wiley Interdisciplinary Reviews-RNA

Chemical-protein interactome and its application in off-target identification

(2011) Lun Yang et al.   Interdisciplinary Sciences-Computational Life Sciences

The beautiful cell: high-content screening in drug discovery

(2010) Marc Bickle   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson’s, Huntington’s, Alzheimer’s, prions, bactericides, chemical toxicology and others as examples

(2010) Douglas B. Kell   ARCHIVES OF TOXICOLOGY

The Chemical Basis of Pharmacology

(2010) Michael J. Keiser et al.   BIOCHEMISTRY

iPHACE: integrative navigation in pharmacological space

(2010) Ricard Garcia-Serna et al.   BIOINFORMATICS

The prognostic significance of human equilibrative nucleoside transporter 1 expression in patients with metastatic bladder cancer treated with gemcitabine-cisplatin-based combination chemotherapy

(2010) Nagahide Matsumura et al.   BJU INTERNATIONAL

Compartmentalization of the Edinburgh Human Metabolic Network

(2010) Tong Hao et al.   BMC BIOINFORMATICS

Properties of the Proximate Parameter Tuning Regularization Algorithm

(2010) Martin Brown et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Gemcitabine metabolic and transporter gene polymorphisms are associated with drug toxicity and efficacy in patients with locally advanced pancreatic cancer

(2010) Motofumi Tanaka et al.   CANCER

Anti-inflammatory Agents: Present and Future

(2010) Charles A. Dinarello   CELL

Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

(2010) Xiyan Li et al.   CELL

Next-Generation Model-Based Drug Discovery and Development: Quantitative and Systems Pharmacology

(2010) S R B Allerheiligen   CLINICAL PHARMACOLOGY & THERAPEUTICS

Dissecting Variability in Responses to Cancer Chemotherapy Through Systems Pharmacology

(2010) R Yang et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Human Equilibrative Nucleoside Transporter 1 (hENT1) Levels Predict Response to Gemcitabine in Patients With Biliary Tract Cancer (BTC)

(2010) D. Santini et al.   CURRENT CANCER DRUG TARGETS

Rational approaches to targeted polypharmacology: creating and navigating protein–ligand interaction networks

(2010) James T Metz et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Expanding the range of ‘druggable’ targets with natural product-based libraries: an academic perspective

(2010) Renato A Bauer et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Kinetics of iron oxidation upon polyphenol binding

(2010) Nathan R. Perron et al.   DALTON TRANSACTIONS

Tissue Distribution and Characterization of Drug-Related Material in Rats and Dogs after Repeated Oral Administration of Casopitant

(2010) S. Pagliarusco et al.   DRUG METABOLISM AND DISPOSITION

Mapping of pharmacological space

(2010) Britta Nisius et al.   Expert Opinion on Drug Discovery

High-content screening for the discovery of pharmacological compounds: advantages, challenges and potential benefits of recent technological developments

(2010) Emmanuelle Soleilhac et al.   Expert Opinion on Drug Discovery

Lipophilicity in drug discovery

(2010) Michael J Waring   Expert Opinion on Drug Discovery

Anticipating drug side effects by comparative pharmacology

(2010) Ricard Garcia-Serna et al.   Expert Opinion on Drug Metabolism & Toxicology

Long evolutionary conservation and considerable tissue specificity of several atypical solute carrier transporters

(2010) Smitha Sreedharan et al.   GENE

Model-Free Drug-Likeness from Fragments

(2010) Oleg Ursu et al.   Journal of Chemical Information and Modeling

Polypharmacology Directed Compound Data Mining: Identification of Promiscuous Chemotypes with Different Activity Profiles and Comparison to Approved Drugs

(2010) Ye Hu et al.   Journal of Chemical Information and Modeling

Application of physiologically based pharmacokinetic modeling and clearance concept to drugs showing transporter-mediated distribution and clearance in humans

(2010) Takao Watanabe et al.   JOURNAL OF PHARMACOKINETICS AND PHARMACODYNAMICS

From structure to dynamics: Frequency tuning in the p53-Mdm2 network. II

(2010) Djomangan A. Ouattara et al.   JOURNAL OF THEORETICAL BIOLOGY

Mining metabolites: extracting the yeast metabolome from the literature

(2010) Chikashi Nobata et al.   Metabolomics

Genome-wide RNAi screens in African trypanosomes identify the nifurtimox activator NTR and the eflornithine transporter AAT6

(2010) Nicola Baker et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Genome-wide RNAi screens in bloodstream form trypanosomes identify drug transporters

(2010) Gabriela Schumann Burkard et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Reconstruction annotation jamborees: a community approach to systems biology

(2010) Ines Thiele et al.   Molecular Systems Biology

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

(2010) Christoph Gille et al.   Molecular Systems Biology

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Fishing for neuroactive compounds

(2010) Jeremy L Jenkins et al.   Nature Chemical Biology

A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans

(2010) Andrew R Burns et al.   Nature Chemical Biology

Rapid behavior-based identification of neuroactive small molecules in the zebrafish

(2010) David Kokel et al.   Nature Chemical Biology

Metabolites do social networking

(2010) Douglas B Kell   Nature Chemical Biology

ChemProt: a disease chemical biology database

(2010) O. Taboureau et al.   NUCLEIC ACIDS RESEARCH

PROMISCUOUS: a database for network-based drug-repositioning

(2010) J. von Eichborn et al.   NUCLEIC ACIDS RESEARCH

Chemical genetics approach to identify new small molecule modulators of cell growth by phenotypic screening of Saccharomyces cerevisiae strains with a library of morpholine-derived compounds

(2010) Andrea Trabocchi et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Realities and expectations of pharmacogenomics and personalized medicine: impact of translating genetic knowledge into clinical practice

(2010) Alessio Squassina et al.   PHARMACOGENOMICS

Natural products in modern life science

(2010) Lars Bohlin et al.   PHYTOCHEMISTRY REVIEWS

Anti-Inflammatory Effects of Resveratrol, Curcumin and Simvastatin in Acute Small Intestinal Inflammation

(2010) Stefan Bereswill et al.   PLoS One

Fourier analysis and systems identification of the p53 feedback loop

(2010) N. Geva-Zatorsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small molecules of different origins have distinct distributions of structural complexity that correlate with protein-binding profiles

(2010) P. A. Clemons et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population robustness arising from cellular heterogeneity

(2010) P. Paszek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Zebrafish Behavioral Profiling Links Drugs to Biological Targets and Rest/Wake Regulation

(2010) J. Rihel et al.   SCIENCE

Inferring Signaling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species

(2010) T.-R. Xu et al.   Science Signaling

The Application of Phenotypic High-Throughput Screening Techniques to Cardiovascular Research

(2010) Yoram Etzion et al.   TRENDS IN CARDIOVASCULAR MEDICINE

Impact of ion class and time on oral drug molecular properties

(2010) Paul D. Leeson et al.   MedChemComm

Small Molecule Screening in Zebrafish

(2010) David S. Peal et al.   Journal of Cardiovascular Translational Research

Role of systems pharmacology in understanding drug adverse events

(2010) Seth I. Berger et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Effects of Drug Transporters on Volume of Distribution

(2009) Anita Grover et al.   AAPS Journal

Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics

(2009) M. Brown et al.   ANALYST

Network analyses in systems pharmacology

(2009) S. I. Berger et al.   BIOINFORMATICS

Siderophore production by marine-derived fungi

(2009) Brian Holinsworth et al.   BIOMETALS

Physiochemical property space distribution among human metabolites, drugs and toxins

(2009) Varun Khanna et al.   BMC BIOINFORMATICS

Automated genome mining for natural products

(2009) Michael HT Li et al.   BMC BIOINFORMATICS

Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases

(2009) Douglas B Kell   BMC Medical Genomics

A Review of the Antioxidant Mechanisms of Polyphenol Compounds Related to Iron Binding

(2009) Nathan R. Perron et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Pharmacological Promiscuity: Dependence on Compound Properties and Target Specificity in a Set of Recent Roche Compounds

(2009) Jens-Uwe Peters et al.   ChemMedChem

Human Equilibrative Nucleoside Transporter 1 and Human Concentrative Nucleoside Transporter 3 Predict Survival after Adjuvant Gemcitabine Therapy in Resected Pancreatic Adenocarcinoma

(2009) R. Marechal et al.   CLINICAL CANCER RESEARCH

Applications of High Content Screening in Life Science Research

(2009) Joseph Zock   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Exploring the chemical space of microbial natural products

(2009) Hiroyuki Osada et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Implications of the Dominant Role of Transporters in Drug Uptake by Cells (Supplementary Material)

(2009) Paul Dobson et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Automation in high-content flow cytometry screening

(2009) U. Naumann et al.   CYTOMETRY PART A

Revealing promiscuous drug–target interactions by chemical proteomics

(2009) Marcus Bantscheff et al.   DRUG DISCOVERY TODAY

Role of membrane transporters in the safety profile of drugs

(2009) Edmund Jon Deoon Lee et al.   Expert Opinion on Drug Metabolism & Toxicology

Identification of interspecies difference in hepatobiliary transporters to improve extrapolation of human biliary secretion

(2009) Yurong Lai   Expert Opinion on Drug Metabolism & Toxicology

Physicochemical drug properties associated within vivotoxicological outcomes: a review

(2009) David A Price et al.   Expert Opinion on Drug Metabolism & Toxicology

Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products, and Molecular Libraries Small Molecule Repository

(2009) Narender Singh et al.   Journal of Chemical Information and Modeling

Novel Chemical Space Exploration via Natural Products

(2009) Josefin Rosén et al.   JOURNAL OF MEDICINAL CHEMISTRY

From structure to dynamics: Frequency tuning in the p53–Mdm2 network

(2009) Wassim Abou-Jaoudé et al.   JOURNAL OF THEORETICAL BIOLOGY

Predicting the multi-modal binding propensity of small molecules: towards an understanding of drug promiscuity

(2009) Keunwan Park et al.   Molecular BioSystems

The topology of drug–target interaction networks: implicit dependence on drug properties and target families

(2009) Jordi Mestres et al.   Molecular BioSystems

Molecular Pharmacology of Promiscuous Seven Transmembrane Receptors Sensing Organic Nutrients

(2009) P. Wellendorph et al.   MOLECULAR PHARMACOLOGY

Rapid and sustained nuclear–cytoplasmic ERK oscillations induced by epidermal growth factor

(2009) Harish Shankaran et al.   Molecular Systems Biology

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Predicting promiscuity

(2009) Andrew L. Hopkins   NATURE

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Synergistic drug combinations tend to improve therapeutically relevant selectivity

(2009) Joseph Lehár et al.   NATURE BIOTECHNOLOGY

A proteomics approach to discovering natural products and their biosynthetic pathways

(2009) Stefanie B Bumpus et al.   NATURE BIOTECHNOLOGY

Bioactivity-guided mapping and navigation of chemical space

(2009) Steffen Renner et al.   Nature Chemical Biology

Fulfilling the Promise of Personalized Medicine? Systematic Review and Field Synopsis of Pharmacogenetic Studies

(2009) Michael V. Holmes et al.   PLoS One

Pulsatile Stimulation Determines Timing and Specificity of NF- B-Dependent Transcription

(2009) L. Ashall et al.   SCIENCE

Drug Discovery and Natural Products: End of an Era or an Endless Frontier?

(2009) J. W.-H. Li et al.   SCIENCE

Update on statin-mediated anti-inflammatory activities in atherosclerosis

(2009) Fabrizio Montecucco et al.   Seminars in Immunopathology

Conciliating binding efficiency and polypharmacology

(2009) Jordi Mestres et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Systems pharmacology and genome medicine: a future perspective

(2009) Aislyn D Wist et al.   Genome Medicine

Systems medicine: the future of medical genomics and healthcare

(2009) Charles Auffray et al.   Genome Medicine

Identification of a Topological Characteristic Responsible for the Biological Robustness of Regulatory Networks

(2009) Yangle Wu et al.   PLoS Computational Biology

A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism

(2009) James Corey Adams et al.   PLoS Computational Biology

Drug Discovery for Schistosomiasis: Hit and Lead Compounds Identified in a Library of Known Drugs by Medium-Throughput Phenotypic Screening

(2009) Maha-Hamadien Abdulla et al.   PLoS Neglected Tropical Diseases

Immunomodulatory and Anti-Inflammatory Activities of Statins

(2009) Emilia Mira et al.   Endocrine Metabolic & Immune Disorders-Drug Targets

Natural Products as a Robust Source of New Drugs and Drug Leads: Past Successes and Present Day Issues

(2008) Gilbert M. Rishton   AMERICAN JOURNAL OF CARDIOLOGY

Adenoviral-mediated overexpression of human equilibrative nucleoside transporter 1 (hENT1) enhances gemcitabine response in human pancreatic cancer

(2008) Sandra Pérez-Torras et al.   BIOCHEMICAL PHARMACOLOGY

Genetic screening for novelDrosophilamutants with discrepancies in iron metabolism

(2008) Anuja Mehta et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

BioBayes: A software package for Bayesian inference in systems biology

(2008) V. Vyshemirsky et al.   BIOINFORMATICS

Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo

(2008) Bayu Jayawardhana et al.   BIOINFORMATICS

Pyridyl-phenyl ether monoamine reuptake inhibitors: Impact of lipophilicity on dual SNRI pharmacology and off-target promiscuity

(2008) Gavin A. Whitlock et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

The State of Innovation in Drug Development

(2008) I Kola   CLINICAL PHARMACOLOGY & THERAPEUTICS

A Ligand-Based Approach to Mining the Chemogenomic Space of Drugs

(2008) Elisabet Gregori-Puigjane et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Sloppiness, robustness, and evolvability in systems biology

(2008) Bryan C Daniels et al.   CURRENT OPINION IN BIOTECHNOLOGY

The impact of natural products upon modern drug discovery

(2008) A Ganesan   CURRENT OPINION IN CHEMICAL BIOLOGY

Human metabolic network reconstruction and its impact on drug discovery and development

(2008) Hongwu Ma et al.   DRUG DISCOVERY TODAY

Natural products in drug discovery

(2008) A HARVEY   DRUG DISCOVERY TODAY

‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries

(2008) Paul D. Dobson et al.   DRUG DISCOVERY TODAY

Interindividual variability in oral antidiabetic drug disposition and response: the role of drug transporter polymorphisms

(2008) Michael A Pacanowski et al.   Expert Opinion on Drug Metabolism & Toxicology

Human Equilibrative Nucleoside Transporter 1 Levels Predict Response to Gemcitabine in Patients With Pancreatic Cancer

(2008) James J. Farrell et al.   GASTROENTEROLOGY

Genome Mining for Novel Natural Product Discovery

(2008) Gregory L. Challis   JOURNAL OF MEDICINAL CHEMISTRY

High-order combination effects and biological robustness

(2008) Joseph Lehár et al.   Molecular Systems Biology

Scaffold diversity of natural products: inspiration for combinatorial library design

(2008) Kristina Grabowski et al.   NATURAL PRODUCT REPORTS

Natural products to drugs: natural product-derived compounds in clinical trials

(2008) Mark S. Butler   NATURAL PRODUCT REPORTS

A network solution

(2008) Adriano Henney et al.   NATURE

Frequency-modulated nuclear localization bursts coordinate gene regulation

(2008) Long Cai et al.   NATURE

Large-scale chemical dissection of mitochondrial function

(2008) Bridget K Wagner et al.   NATURE BIOTECHNOLOGY

A quantitative analysis of kinase inhibitor selectivity

(2008) Mazen W Karaman et al.   NATURE BIOTECHNOLOGY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Chemical biology and the limits of reductionism

(2008) Randall T Peterson   Nature Chemical Biology

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule?

(2008) Paul D. Dobson et al.   NATURE REVIEWS DRUG DISCOVERY

Rosuvastatin to Prevent Vascular Events in Men and Women with Elevated C-Reactive Protein

(2008) Paul M Ridker et al.   NEW ENGLAND JOURNAL OF MEDICINE

HMDB: a knowledgebase for the human metabolome

(2008) D. S. Wishart et al.   NUCLEIC ACIDS RESEARCH

Unfaithful neurotransmitter transporters: Focus on serotonin uptake and implications for antidepressant efficacy

(2008) Lynette C. Daws   PHARMACOLOGY & THERAPEUTICS

Editorial

(2008) G. Clapworthy et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Patient-specific simulation as a basis for clinical decision-making

(2008) S. K. Sadiq et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Protein area occupancy at the center of the red blood cell membrane

(2008) A. D. Dupuy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cholesterol Veers Off Script

(2008) J. Couzin   SCIENCE

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE

Caenorhabditis elegans: An Emerging Model in Biomedical and Environmental Toxicology

(2008) Maxwell C. K. Leung et al.   TOXICOLOGICAL SCIENCES

Application of systems biology for bioprocess development

(2008) Jin Hwan Park et al.   TRENDS IN BIOTECHNOLOGY

Role of transport proteins in drug discovery and development: a pharmaceutical perspective

(2008) A. Ayrton et al.   XENOBIOTICA

Fragment-Based Approach to Drug??Lead Discovery

(2008) Daniela Fattori et al.   Drugs in research & development

Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries

(2007) Peter Ertl et al.   Journal of Chemical Information and Modeling

Proximate parameter tuning for biochemical networks with uncertain kinetic parameters

(2007) Stephen J. Wilkinson et al.   Molecular BioSystems