Affinity purification in target identification: the specificity challenge

HIF-1α suppressing small molecule, LW6, inhibits cancer cell growth by binding to calcineurin b homologous protein 1

(2015) Beom Seok Kim et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Global Analysis of Protein Folding Thermodynamics for Disease State Characterization

(2015) Jagat Adhikari et al.   JOURNAL OF PROTEOME RESEARCH

Photoaffinity labeling of transcription factors by DNA-templated crosslinking

(2015) Ying Liu et al.   Chemical Science

Multiplex Imaging and Cellular Target Identification of Kinase Inhibitors via an Affinity-Based Proteome Profiling Approach

(2015) Ying Su et al.   Scientific Reports

Thermodynamic Analysis of Protein Folding and Stability Using a Tryptophan Modification Protocol

(2014) Yingrong Xu et al.   ANALYTICAL CHEMISTRY

Probing the Anticancer Mechanism of (−)-Ainsliatrimer A through Diverted Total Synthesis and Bioorthogonal Ligation

(2014) Chao Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enzyme Inhibitor Discovery by Activity-Based Protein Profiling

(2014) Micah J. Niphakis et al.   Annual Review of Biochemistry

Multivalent Photoaffinity Probe for Labeling Small Molecule Binding Proteins

(2014) Gang Li et al.   BIOCONJUGATE CHEMISTRY

LDAI-Based Chemical Labeling of Intact Membrane Proteins and Its Pulse-Chase Analysis under Live Cell Conditions

(2014) Takayuki Miki et al.   CHEMISTRY & BIOLOGY

Chemical biology approaches to target validation in cancer

(2014) Julian Blagg et al.   CURRENT OPINION IN PHARMACOLOGY

“Minimalist” Cyclopropene-Containing Photo-Cross-Linkers Suitable for Live-Cell Imaging and Affinity-Based Protein Labeling

(2014) Zhengqiu Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mapping the Protein Interaction Landscape for Fully Functionalized Small-Molecule Probes in Human Cells

(2014) Tohru Kambe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SILAC-Pulse Proteolysis: A Mass Spectrometry-Based Method for Discovery and Cross-Validation in Proteome-Wide Studies of Ligand Binding

(2014) Jagat Adhikari et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Terazosin activates Pgk1 and Hsp90 to promote stress resistance

(2014) Xinping Chen et al.   Nature Chemical Biology

A more rapid route to target deconvolution

(2014) Charlotte Harrison   NATURE REVIEWS DRUG DISCOVERY

Phenotypic screening in cancer drug discovery — past, present and future

(2014) John G. Moffat et al.   NATURE REVIEWS DRUG DISCOVERY

Subchronic atrazine exposure changes defensive behaviour profile and disrupts brain acetylcholinesterase activity of zebrafish

(2014) Ademir J. Schmidel et al.   NEUROTOXICOLOGY AND TERATOLOGY

Ribosome Display and Photo-Cross-Linking Techniques for In Vitro Identification of Target Proteins of Bioactive Small Molecules

(2013) Akira Wada et al.   ANALYTICAL CHEMISTRY

Design and Synthesis of Minimalist Terminal Alkyne-Containing Diazirine Photo-Crosslinkers and Their Incorporation into Kinase Inhibitors for Cell- and Tissue-Based Proteome Profiling

(2013) Zhengqiu Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Photoaffinity Labeling of Small-Molecule-Binding Proteins by DNA-Templated Chemistry

(2013) Gang Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Target Identification for Small Bioactive Molecules: Finding the Needle in the Haystack

(2013) Slava Ziegler et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Selective Fluorescence Detection of Small-Molecule-Binding Proteins by Using a Dual Photoaffinity Labeling System

(2013) Kaori Sakurai et al.   CHEMBIOCHEM

Specific Detection and Imaging of Enzyme Activity by Signal-Amplifiable Self-Assembling19F MRI Probes

(2013) Kazuya Matsuo et al.   CHEMISTRY-A EUROPEAN JOURNAL

Target identification of biologically active small molecules via in situ methods

(2013) Ying Su et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Target deconvolution techniques in modern phenotypic profiling

(2013) Jiyoun Lee et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

A Bioorthogonal Ligation Enabled by Click Cycloaddition of o-Quinolinone Quinone Methide and Vinyl Thioether

(2013) Qiang Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Target identification of small molecules based on chemical biology approaches

(2013) Yushi Futamura et al.   Molecular BioSystems

Recent Advances in Target Characterization and Identification by Photoaffinity Probes

(2013) Jitapa Sumranjit et al.   MOLECULES

The why and how of phenotypic small-molecule screens

(2013) Ulrike S Eggert   Nature Chemical Biology

Target identification and mechanism of action in chemical biology and drug discovery

(2013) Monica Schenone et al.   Nature Chemical Biology

Lenalidomide Causes Selective Degradation of IKZF1 and IKZF3 in Multiple Myeloma Cells

(2013) J. Kronke et al.   SCIENCE

Affinity-based target identification for bioactive small molecules

(2013) Makoto Kawatani et al.   MedChemComm

Traceless Affinity Labeling of Endogenous Proteins for Functional Analysis in Living Cells

(2012) Takahiro Hayashi et al.   ACCOUNTS OF CHEMICAL RESEARCH

Xanthohumol Impairs Autophagosome Maturation through Direct Inhibition of Valosin-Containing Protein

(2012) Yukiko Sasazawa et al.   ACS Chemical Biology

A Natural Product Inspired Tetrahydropyran Collection Yields Mitosis Modulators that Synergistically Target CSE1L and Tubulin

(2012) Tobias Voigt et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Activity-Based Probes for Studying the Activity of Flavin-Dependent Oxidases and for the Protein Target Profiling of Monoamine Oxidase Inhibitors

(2012) Joanna M. Krysiak et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Triple Bioorthogonal Ligation Strategy for Simultaneous Labeling of Multiple Enzymatic Activities

(2012) Lianne I. Willems et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Discovery and Target Identification of an Antiproliferative Agent in Live Cells Using Fluorescence Difference in Two-Dimensional Gel Electrophoresis

(2012) Jongmin Park et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Aptamer-Based Affinity Labeling of Proteins

(2012) Jan L. Vinkenborg et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Identification of Regulators of Polyploidization Presents Therapeutic Targets for Treatment of AMKL

(2012) Qiang Wen et al.   CELL

Active/Inactive Dual-Probe System for Selective Photoaffinity Labeling of Small Molecule-Binding Proteins

(2012) Kaori Sakurai et al.   Chemistry-An Asian Journal

Identification of NIPSNAP1 as a Nocistatin-interacting Protein Involving Pain Transmission

(2012) Emiko Okuda-Ashitaka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Affinity-Based Probes Based on Type II Kinase Inhibitors

(2012) Pratistha Ranjitkar et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cell-Based Proteome Profiling of Potential Dasatinib Targets by Use of Affinity-Based Probes

(2012) Haibin Shi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ligand-Directed Acyl Imidazole Chemistry for Labeling of Membrane-Bound Proteins on Live Cells

(2012) Sho-hei Fujishima et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fully Functionalized Small-Molecule Probes for Integrated Phenotypic Screening and Target Identification

(2012) Justin S. Cisar et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Native FKBP12 Engineering by Ligand-Directed Tosyl Chemistry: Labeling Properties and Application to Photo-Cross-Linking of Protein Complexes in Vitro and in Living Cells

(2012) Tomonori Tamura et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

From noncovalent to covalent bonds: a paradigm shift in target protein identification

(2012) Jongmin Park et al.   Molecular BioSystems

Active site profiling reveals coupling between domains in SRC-family kinases

(2012) Ratika Krishnamurty et al.   Nature Chemical Biology

Thermodynamic analysis of protein-ligand binding interactions in complex biological mixtures using the stability of proteins from rates of oxidation

(2012) Erin C Strickland et al.   Nature Protocols

Identification of DNA-Dependent Protein Kinase Catalytic Subunit (DNA-PKcs) as a Novel Target of Bisphenol A

(2012) Yuki Ito et al.   PLoS One

Simplified proteomics approach to discover protein-ligand interactions

(2012) Youngil Chang et al.   PROTEIN SCIENCE

Bioorthogonal Chemistry: Applications in Activity-Based Protein Profiling

(2011) Lianne I. Willems et al.   ACCOUNTS OF CHEMICAL RESEARCH

Chemical Genetics–Based Target Identification in Drug Discovery

(2011) Feng Cong et al.   Annual Review of Pharmacology and Toxicology

Identification and validation of bioactive small molecule target through phenotypic screening

(2011) Yoon Sun Cho et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Tools and methodologies capable of isolating and identifying a target molecule for a bioactive compound

(2011) Satoshi Sakamoto et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Diazirine based photoaffinity labeling

(2011) Luba Dubinsky et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Construction of a 19F-lectin biosensor for glycoprotein imaging by using affinity-guided DMAP chemistry

(2011) Yedi Sun et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Aliphatic Diazirines as Photoaffinity Probes for Proteins: Recent Developments

(2011) Joydip Das   CHEMICAL REVIEWS

Marine Natural Product Aurilide Activates the OPA1-Mediated Apoptosis by Binding to Prohibitin

(2011) Shin-ichi Sato et al.   CHEMISTRY & BIOLOGY

Searching for the Protein Targets of Bioactive Molecules

(2011) Christopher Chidley et al.   CHIMIA

Drug target deconvolution by chemical proteomics

(2011) Manfred Raida   CURRENT OPINION IN CHEMICAL BIOLOGY

Vipirinin, a Coumarin-based HIV-1 Vpr Inhibitor, Interacts with a Hydrophobic Region of VPR

(2011) Eugene Boon Beng Ong et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mapping the Subcellular Protein Distribution in Three Human Cell Lines

(2011) Linn Fagerberg et al.   JOURNAL OF PROTEOME RESEARCH

Thermodynamic Analysis of Protein–Ligand Interactions in Complex Biological Mixtures using a Shotgun Proteomics Approach

(2011) Patrick D. DeArmond et al.   JOURNAL OF PROTEOME RESEARCH

Probing small molecule–protein interactions: A new perspective for functional proteomics

(2011) Thomas Lenz et al.   Journal of Proteomics

Examining the Mechanism of Action of a Kinesin Inhibitor Using Stable Isotope Labeled Inhibitors for Cross-Linking (SILIC)

(2011) Sarah A. Wacker et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Chemical Cell-Surface Receptor Engineering Using Affinity-Guided, Multivalent Organocatalysts

(2011) Hangxiang Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Peptide Aldehyde Microarray for High-Throughput Profiling of Cellular Events

(2011) Hao Wu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Unraveling the Protein Targets of Vancomycin in Living S. aureus and E. faecalis Cells

(2011) Jürgen Eirich et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Selective killing of cancer cells by a small molecule targeting the stress response to ROS

(2011) Lakshmi Raj et al.   NATURE

Natural product–inspired cascade synthesis yields modulators of centrosome integrity

(2011) Heiko Dückert et al.   Nature Chemical Biology

A yeast-based screen reveals that sulfasalazine inhibits tetrahydrobiopterin biosynthesis

(2011) Christopher Chidley et al.   Nature Chemical Biology

Natural products reveal cancer cell dependence on oxysterol-binding proteins

(2011) Anthony W G Burgett et al.   Nature Chemical Biology

How were new medicines discovered?

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

Impact of high-throughput screening in biomedical research

(2011) Ricardo Macarron et al.   NATURE REVIEWS DRUG DISCOVERY

Identification of Direct Protein Targets of Small Molecules

(2010) Brett Lomenick et al.   ACS Chemical Biology

Natural Products and Their Biological Targets: Proteomic and Metabolomic Labeling Strategies

(2010) Thomas Böttcher et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Identification of a novel Vpr-binding compound that inhibits HIV-1 multiplication in macrophages by chemical array

(2010) Kyoji Hagiwara et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Biochemical Target Isolation for Novices: Affinity-Based Strategies

(2010) Shin-ichi Sato et al.   CHEMISTRY & BIOLOGY

Chemical Proteomics Identifies Nampt as the Target of CB30865, An Orphan Cytotoxic Compound

(2010) Tracey C. Fleischer et al.   CHEMISTRY & BIOLOGY

Proteomics accelerating the identification of the target molecule of bioactive small molecules

(2010) Konstanty Wierzba et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Use of phage display technology for the determination of the targets for small-molecule therapeutics

(2010) Yoichi Takakusagi et al.   Expert Opinion on Drug Discovery

Terpestacin Inhibits Tumor Angiogenesis by Targeting UQCRB of Mitochondrial Complex III and Suppressing Hypoxia-induced Reactive Oxygen Species Production and Cellular Oxygen Sensing

(2010) Hye Jin Jung et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of HSP60 as a Primary Target ofo-Carboranylphenoxyacetanilide, an HIF-1α Inhibitor

(2010) Hyun Seung Ban et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Chemical proteomics reveals bolinaquinone as a clathrin-mediated endocytosis inhibitor

(2010) Luigi Margarucci et al.   Molecular BioSystems

Gamma-secretase activating protein is a therapeutic target for Alzheimer’s disease

(2010) Gen He et al.   NATURE

A vancomycin photoprobe identifies the histidine kinase VanSsc as a vancomycin receptor

(2010) Kalinka Koteva et al.   Nature Chemical Biology

A small molecule accelerates neuronal differentiation in the adult rat

(2010) H. Wurdak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements

(2010) G. M. West et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a Primary Target of Thalidomide Teratogenicity

(2010) T. Ito et al.   SCIENCE

cDNA phage display as a novel tool to screen for cellular targets of chemical compounds

(2010) Bieke Van Dorst et al.   TOXICOLOGY IN VITRO

The identification of cellular targets of 17β estradiol using a lytic (T7) cDNA phage display approach

(2010) Bieke Van Dorst et al.   TOXICOLOGY IN VITRO

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

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

Photoaffinity labeling the agonist binding domain of α4β4 and α4β2 neuronal nicotinic acetylcholine receptors with [125I]epibatidine and 5[125I]A-85380

(2009) Ayman K. Hamouda et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Cleavable Linker for Photo-Cross-Linked Small-Molecule Affinity Matrix

(2009) Naoki Kanoh et al.   BIOCONJUGATE CHEMISTRY

Preparation of conophylline affinity nano-beads and identification of a target protein

(2009) Eriko Suzuki et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Design and synthesis of an all-in-one 3-(1,1-difluoroprop-2-ynyl)-3H-diazirin-3-yl functional group for photo-affinity labeling

(2009) Nag S. Kumar et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Revealing promiscuous drug–target interactions by chemical proteomics

(2009) Marcus Bantscheff et al.   DRUG DISCOVERY TODAY

Isothermal Microcalorimetry to Investigate Non Specific Interactions in Biophysical Chemistry

(2009) Vincent Ball et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Quenched Ligand-Directed Tosylate Reagents for One-Step Construction of Turn-On Fluorescent Biosensors

(2009) Shinya Tsukiji et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Marinopyrrole A Target Elucidation by Acyl Dye Transfer

(2009) Chambers C. Hughes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling

(2009) Shih-Min A. Huang et al.   NATURE

Target profiling of small molecules by chemical proteomics

(2009) Uwe Rix et al.   Nature Chemical Biology

Ligand-directed tosyl chemistry for protein labeling in vivo

(2009) Shinya Tsukiji et al.   Nature Chemical Biology

Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds

(2009) Yan Feng et al.   NATURE REVIEWS DRUG DISCOVERY

Identifying the proteins to which small-molecule probes and drugs bind in cells

(2009) S.-E. Ong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Target identification using drug affinity responsive target stability (DARTS)

(2009) B. Lomenick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and validation of calmodulin as a binding protein of an anti-proliferative small molecule 3,4-dihydroisoquinolinium salt

(2009) Hye Jin Jung et al.   Proteomics Clinical Applications

Recent advances and method development for drug target identification

(2009) Janet N.Y. Chan et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Adenosine Kinase of T. b. rhodesiense Identified as the Putative Target of 4-[5-(4-phenoxyphenyl)-2H-pyrazol-3-yl]morpholine Using Chemical Proteomics

(2009) Sabine Kuettel et al.   PLoS Neglected Tropical Diseases

Thermodynamic Analysis of Protein Stability and Ligand Binding Using a Chemical Modification- and Mass Spectrometry-Based Strategy

(2008) Graham M. West et al.   ANALYTICAL CHEMISTRY

Enantiodifferential Approach for the Detection of the Target Membrane Protein of the Jasmonate Glycoside that Controls the Leaf Movement ofAlbizzia saman

(2008) Yoko Nakamura et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Activity-Based Protein Profiling: From Enzyme Chemistry to Proteomic Chemistry

(2008) Benjamin F. Cravatt et al.   Annual Review of Biochemistry

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou et al.   Annual Review of Biophysics

Binding is not enough: Flexibility is needed for photocrosslinking of Lck kinase by benzophenone photoligands

(2008) Akira Kawamura et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Activity-Based Protein Profiling: New Developments and Directions in Functional Proteomics

(2008) Mahesh Uttamchandani et al.   CHEMBIOCHEM

Identification of the cellular targets of bioactive small organic molecules using affinity reagents

(2008) Benjamin J. Leslie et al.   CHEMICAL SOCIETY REVIEWS

Proteomic methods for drug target discovery

(2008) Lekha Sleno et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Mass spectrometry for proteomics

(2008) Xuemei Han et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Optimization of Activity-Based Probes for Proteomic Profiling of Histone Deacetylase Complexes

(2008) Cleo M. Salisbury et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Photocrosslinkers illuminate interactions in living cells

(2008) Yoshihito Tanaka et al.   Molecular BioSystems

The identification of an osteoclastogenesis inhibitor through the inhibition of glyoxalase I

(2008) M. Kawatani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Target-Specific Chemical Acylation of Lectins by Ligand-Tethered DMAP Catalysts

(2007) Yoichiro Koshi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY