Hide and seek: Identification and confirmation of small molecule protein targets.

Target identification and confirmation for small molecules is often the rate limiting step in drug discovery. A robust method to identify proteins addressed by small molecules is affinity chromatography using chemical probes. These usually consist of the compound of interest equipped with a linker molecule and a proper tag. Recently, methods emerged that allow the identification of protein targets without prior functionalization of the small molecule of interest. The digest offers an update on the newest developments in the area of target identification with special focus on confirmation techniques.

[1]  Young-Hoon Ahn,et al.  Tagged small molecule library approach for facilitated chemical genetics. , 2007, Accounts of chemical research.

[2]  M. Bantscheff,et al.  High-resolution enabled TMT 8-plexing. , 2012, Analytical chemistry.

[3]  S. Yao,et al.  "Minimalist" cyclopropene-containing photo-cross-linkers suitable for live-cell imaging and affinity-based protein labeling. , 2014, Journal of the American Chemical Society.

[4]  Petra Schneider,et al.  Revealing the macromolecular targets of complex natural products. , 2014, Nature chemistry.

[5]  Simon G. Patching,et al.  Surface plasmon resonance spectroscopy for characterisation of membrane protein-ligand interactions and its potential for drug discovery. , 2014, Biochimica et biophysica acta.

[6]  P. Park,et al.  Atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands. , 2014, Biochimica et biophysica acta.

[7]  Michael C Fitzgerald,et al.  Thermodynamic analysis of protein-ligand binding interactions in complex biological mixtures using the stability of proteins from rates of oxidation , 2012, Nature Protocols.

[8]  S. Morimoto,et al.  An isotope-coded fluorogenic cross-linker for high-performance target identification based on photoaffinity labeling. , 2014, Angewandte Chemie.

[9]  I. Pang,et al.  Identification of PDE6D as a molecular target of anecortave acetate via a methotrexate-anchored yeast three-hybrid screen. , 2013, ACS chemical biology.

[10]  Y. Liu,et al.  Photoaffinity labeling of small-molecule-binding proteins by DNA-templated chemistry. , 2013, Angewandte Chemie.

[11]  E. Weerapana,et al.  1,3,5-Triazine as a modular scaffold for covalent inhibitors with streamlined target identification. , 2013, Journal of the American Chemical Society.

[12]  P. Bamborough,et al.  Discovery and characterization of small molecule inhibitors of the BET family bromodomains. , 2011, Journal of medicinal chemistry.

[13]  Olivier Elemento,et al.  DrugTargetSeqR: a genomics- and CRISPR/Cas9-based method to analyze drug targets , 2014, Nature chemical biology.

[14]  J. Irwin,et al.  Identifying mechanism-of-action targets for drugs and probes , 2012, Proceedings of the National Academy of Sciences.

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

[16]  Olivier Elemento,et al.  Using transcriptome sequencing to identify mechanisms of drug action and resistance , 2011, Nature chemical biology.

[17]  P. Nordlund,et al.  Monitoring Drug Target Engagement in Cells and Tissues Using the Cellular Thermal Shift Assay , 2013, Science.

[18]  Tiziana Bonaldi,et al.  Quantitative Chemical Proteomics Identifies Novel Targets of the Anti-cancer Multi-kinase Inhibitor E-3810 , 2014, Molecular & Cellular Proteomics.

[19]  Michael J. Keiser,et al.  Large Scale Prediction and Testing of Drug Activity on Side-Effect Targets , 2012, Nature.

[20]  M. D’Incalci,et al.  E-3810 is a potent dual inhibitor of VEGFR and FGFR that exerts antitumor activity in multiple preclinical models. , 2011, Cancer research.

[21]  Makoto Muroi,et al.  Target identification of small molecules based on chemical biology approaches. , 2013, Molecular bioSystems.

[22]  S. Seité,et al.  Vemurafenib: an unusual UVA‐induced photosensitivity , 2013, Experimental dermatology.

[23]  H. Osada,et al.  Affinity-based target identification for bioactive small molecules , 2014 .

[24]  George Papadatos,et al.  The ChEMBL bioactivity database: an update , 2013, Nucleic Acids Res..

[25]  Maria F. Sassano,et al.  Automated design of ligands to polypharmacological profiles , 2012, Nature.

[26]  Shin-ichi Sato,et al.  Biochemical target isolation for novices: affinity-based strategies. , 2010, Chemistry & biology.

[27]  Jeffry D. Sander,et al.  CRISPR-Cas systems for editing, regulating and targeting genomes , 2014, Nature Biotechnology.

[28]  R. Takeuchi,et al.  Identification of small molecule binding molecules by affinity purification using a specific ligand immobilized on PEGA resin. , 2008, Bioconjugate chemistry.

[29]  E. Mcwhinnie,et al.  DNA sequencing and CRISPR-Cas9 gene editing for target validation in mammalian cells. , 2014, Nature chemical biology.

[30]  M. Taussig,et al.  Protein microarrays: high-throughput tools for proteomics , 2009, Expert review of proteomics.

[31]  Matthias Mann,et al.  Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics , 2011, Nature Protocols.

[32]  G. Superti-Furga,et al.  A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies. , 2013, Journal of proteome research.

[33]  Steven J Brown,et al.  Confirming target engagement for reversible inhibitors in vivo by kinetically tuned activity-based probes. , 2012, Journal of the American Chemical Society.

[34]  M. Uesugi,et al.  Polyproline-rod approach to isolating protein targets of bioactive small molecules: isolation of a new target of indomethacin. , 2007, Journal of the American Chemical Society.

[35]  Jonathan D. Moore The impact of CRISPR-Cas9 on target identification and validation. , 2015, Drug discovery today.

[36]  Petra Schneider,et al.  Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus , 2014, Proceedings of the National Academy of Sciences.

[37]  G. Milligan,et al.  Structural and biophysical characterisation of G protein-coupled receptor ligand binding using resonance energy transfer and fluorescent labelling techniques. , 2014, Biochimica et biophysica acta.

[38]  B. Cravatt,et al.  Mapping the Protein Interaction Landscape for Fully Functionalized Small-Molecule Probes in Human Cells , 2014, Journal of the American Chemical Society.

[39]  Ruedi Aebersold,et al.  Direct identification of ligand-receptor interactions on living cells and tissues , 2012, Nature Biotechnology.

[40]  Steven A Carr,et al.  Identifying the proteins to which small-molecule probes and drugs bind in cells , 2009, Proceedings of the National Academy of Sciences.

[41]  S. Marqusee,et al.  Pulse proteolysis: A simple method for quantitative determination of protein stability and ligand binding , 2005, Nature Methods.

[42]  David S. Wishart,et al.  DrugBank 4.0: shedding new light on drug metabolism , 2013, Nucleic Acids Res..

[43]  Chiwook Park,et al.  Investigating protein unfolding kinetics by pulse proteolysis , 2009, Protein science : a publication of the Protein Society.

[44]  J. Cox,et al.  Proteomics strategy for quantitative protein interaction profiling in cell extracts , 2009, Nature Methods.

[45]  Jeffrey W. Clark,et al.  Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. , 2010, The New England journal of medicine.

[46]  G. Superti-Furga,et al.  Stereospecific targeting of MTH1 by (S)-crizotinib as anticancer strategy , 2014, Nature.

[47]  K. Johnsson,et al.  A yeast-based screen reveals that sulfasalazine inhibits tetrahydrobiopterin biosynthesis. , 2011, Nature chemical biology.

[48]  E. Lander,et al.  Development and Applications of CRISPR-Cas9 for Genome Engineering , 2014, Cell.

[49]  M. Fitzgerald,et al.  SILAC-Pulse Proteolysis: A Mass Spectrometry-Based Method for Discovery and Cross-Validation in Proteome-Wide Studies of Ligand Binding , 2014, Journal of The American Society for Mass Spectrometry.

[50]  H. Kung,et al.  SCH 51344 inhibits ras transformation by a novel mechanism. , 1995, Cancer research.

[51]  Kenichi Kato,et al.  Photochemical construction of coumarin fluorophore on affinity-anchored protein. , 2011, Bioconjugate chemistry.

[52]  Herbert Waldmann,et al.  Target identification for small bioactive molecules: finding the needle in the haystack. , 2013, Angewandte Chemie.

[53]  J. Christensen,et al.  Structure based drug design of crizotinib (PF-02341066), a potent and selective dual inhibitor of mesenchymal-epithelial transition factor (c-MET) kinase and anaplastic lymphoma kinase (ALK). , 2011, Journal of medicinal chemistry.

[54]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[55]  S. Morimoto,et al.  Structure-assisted ligand-binding analysis using fluorogenic photoaffinity labeling. , 2015, Bioorganic & medicinal chemistry letters.

[56]  D. Bar-Sagi,et al.  SCH 51344-induced reversal of RAS-transformation is accompanied by the specific inhibition of the RAS and RAC-dependent cell morphology pathway , 1997, Oncogene.

[57]  Marcus Bantscheff,et al.  Ion coalescence of neutron encoded TMT 10-plex reporter ions. , 2014, Analytical chemistry.

[58]  N. Brandon,et al.  Chemoproteomics demonstrates target engagement and exquisite selectivity of the clinical phosphodiesterase 10A inhibitor MP-10 in its native environment. , 2014, ACS chemical biology.

[59]  Y. Hatanaka,et al.  Affinity-based fluorogenic labeling of ATP-binding proteins with sequential photoactivatable cross-linkers. , 2013, Bioorganic & medicinal chemistry letters.

[60]  David Holmes Cancer drug's survivin suppression called into question , 2012, Nature Medicine.

[61]  M. Blanco,et al.  Target engagement in lead generation. , 2015, Bioorganic & medicinal chemistry letters.