1. Interrogating the Druggability of the 2-Oxoglutarate-Dependent Dioxygenase Target Class by Chemical Proteomics.

    ACS Chemical Biology 11(7):2002 (2016) PMID 27197014

    The 2-oxoglutarate-dependent dioxygenase target class comprises around 60 enzymes including several subfamilies with relevance to human disease, such as the prolyl hydroxylases and the Jumonji-type lysine demethylases. Current drug discovery approaches are largely based on small molecule inhibit...
  2. Chemical Proteomics Reveals Ferrochelatase as a Common Off-target of Kinase Inhibitors.

    ACS Chemical Biology 11(5):1245 (2016) PMID 26863403

    Many protein kinases are valid drug targets in oncology because they are key components of signal transduction pathways. The number of clinical kinase inhibitors is on the rise, but these molecules often exhibit polypharmacology, potentially eliciting desired and toxic effects. Therefore, a comp...
  3. Mutational Analysis of Glycogen Synthase Kinase 3β Protein Kinase Together with Kinome-Wide Binding and Stability Studies Suggests Context-Dependent Recognition of Kinases by the Chaperone Heat Shock Protein 90.

    Molecular and Cellular Biology 36(6):1007 (2016) PMID 26755559 PMCID PMC4810477

    The heat shock protein 90 (HSP90) and cell division cycle 37 (CDC37) chaperones are key regulators of protein kinase folding and maturation. Recent evidence suggests that thermodynamic properties of kinases, rather than primary sequences, are recognized by the chaperones. In concordance, we obse...
  4. Discovery and Characterization of GSK2801, a Selective Chemical Probe for the Bromodomains BAZ2A and BAZ2B.

    Journal of medicinal and pharmaceutical chemistry 59(4):1410 (2016) PMID 25799074 PMCID PMC4770311

    Bromodomains are acetyl-lysine specific protein interaction domains that have recently emerged as a new target class for the development of inhibitors that modulate gene transcription. The two closely related bromodomain containing proteins BAZ2A and BAZ2B constitute the central scaffolding prot...
  5. Discovery of Novel Small Molecules that Activate Satellite Cell Proliferation and Enhance Repair of Damaged Muscle.

    ACS Chemical Biology 11(2):518 (2016) PMID 26696218

    Skeletal muscle progenitor stem cells (referred to as satellite cells) represent the primary pool of stem cells in adult skeletal muscle responsible for the generation of new skeletal muscle in response to injury. Satellite cells derived from aged muscle display a significant reduction in regene...
  6. Thermal proteome profiling monitors ligand interactions with cellular membrane proteins.

    Nature Methods 12(12):1129 (2015) PMID 26524241

    We extended thermal proteome profiling to detect transmembrane protein-small molecule interactions in cultured human cells. When we assessed the effects of detergents on ATP-binding profiles, we observed shifts in denaturation temperature for ATP-binding transmembrane proteins. We also observed ...
  7. New IDH1 mutant inhibitors for treatment of acute myeloid leukemia.

    Nature Chemical Biology 11(11):878 (2015) PMID 26436839

    Neomorphic mutations in isocitrate dehydrogenase 1 (IDH1) are driver mutations in acute myeloid leukemia (AML) and other cancers. We report the development of new allosteric inhibitors of mutant IDH1. Crystallographic and biochemical results demonstrated that compounds of this chemical series bi...
  8. Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.

    Nature Protocols 10(10):1567 (2015) PMID 26379230

    The direct detection of drug-protein interactions in living cells is a major challenge in drug discovery research. Recently, we introduced an approach termed thermal proteome profiling (TPP), which enables the monitoring of changes in protein thermal stability across the proteome using quantitat...
  9. A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets.

    Molecular & Cellular Proteomics 14(9):2394 (2015) PMID 25987413 PMCID PMC4563723

    Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there ...
  10. Catalytic in vivo protein knockdown by small-molecule PROTACs.

    Nature Chemical Biology 11(8):611 (2015) PMID 26075522 PMCID PMC4629852

    The current predominant therapeutic paradigm is based on maximizing drug-receptor occupancy to achieve clinical benefit. This strategy, however, generally requires excessive drug concentrations to ensure sufficient occupancy, often leading to adverse side effects. Here, we describe major improve...
  11. Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics.

    Molecular & Cellular Proteomics 13(12):3709 (2014) PMID 25106551 PMCID PMC4256517

    One of the limiting factors in determining the sensitivity of tandem mass spectrometry using hybrid quadrupole orthogonal acceleration time-of-flight instruments is the duty cycle of the orthogonal ion injection system. As a consequence, only a fraction of the generated fragment ion beam is coll...
  12. Kruidenier et al. reply.

    Nature 514(7520):E2 (2014) PMID 25279927

  13. Chemoproteomics reveals time-dependent binding of histone deacetylase inhibitors to endogenous repressor complexes.

    ACS Chemical Biology 9(8):1736 (2014) PMID 24877719

    Class I histone deacetylases (HDACs) are attractive drug targets in oncology and inflammation. However, the development of selective inhibitors is complicated by the characteristic that the localization, activity, and selectivity of class I HDACs are regulated by association in megadalton repres...
  14. Mass-spectrometry-based draft of the human proteome.

    Nature 509(7502):582 (2014) PMID 24870543

    Proteomes are characterized by large protein-abundance differences, cell-type- and time-dependent expression patterns and post-translational modifications, all of which carry biological information that is not accessible by genomics or transcriptomics. Here we present a mass-spectrometry-based d...
  15. Ion coalescence of neutron encoded TMT 10-plex reporter ions.

    Analytical chemistry 86(7):3594 (2014) PMID 24579773

    Isobaric mass tag-based quantitative proteomics strategies such as iTRAQ and TMT utilize reporter ions in the low mass range of tandem MS spectra for relative quantification. The recent extension of TMT multiplexing to 10 conditions has been enabled by utilizing neutron encoded tags with reporte...
  16. The commonly used PI3-kinase probe LY294002 is an inhibitor of BET bromodomains.

    ACS Chemical Biology 9(2):495 (2014) PMID 24533473

    A commonly used small-molecule probe in cell-signaling research is the phosphoinositide 3-kinase inhibitor LY294002. Quantitative chemoproteomic profiling shows that LY294002 and LY303511, a close analogue devoid of PI3K activity, inhibit the BET bromodomain proteins BRD2, BRD3, and BRD4 that co...
  17. Quantifying small molecule-induced changes in cellular protein expression and posttranslational modifications using isobaric mass tags.

    Methods in Molecular Biology 1156:431 (2014) PMID 24792006

    Proteomics enables the comprehensive analysis of cellular perturbations induced by bioactive small molecules and contributes to our understanding of the mechanisms by which drugs elicit their activity in disease situations. Here we describe a quantitative proteomics approach to study dose-depend...
  18. Mapping protein complexes using covalently linked antibodies and isobaric mass tags.

    Methods in Molecular Biology 1156:279 (2014) PMID 24791996

    Affinity enrichment techniques in combination with quantitative proteomics enable the unbiased identification of protein-protein interaction, and thus the delineation of protein complexes and interaction networks. Here, we describe an immunoaffinity enrichment approach that employs covalently im...
  19. Measuring and managing ratio compression for accurate iTRAQ/TMT quantification.

    Journal of Proteome Research 12(8):3586 (2013) PMID 23768245

    Isobaric mass tagging (e.g., TMT and iTRAQ) is a precise and sensitive multiplexed peptide/protein quantification technique in mass spectrometry. However, accurate quantification of complex proteomic samples is impaired by cofragmentation of peptides, leading to systematic underestimation of qua...
  20. Affinity profiling of the cellular kinome for the nucleotide cofactors ATP, ADP, and GTP.

    ACS Chemical Biology 8(3):599 (2013) PMID 23215245

    Most kinase inhibitor drugs target the binding site of the nucleotide cosubstrate ATP. The high intracellular concentration of ATP can strongly affect inhibitor potency and selectivity depending on the affinity of the target kinase for ATP. Here we used a defined chemoproteomics system based on ...