A Global Map of Lipid-Binding Proteins and Their Ligandability in Cells

Cell

Volumn 161, Issue 7, 2015, Pages 1668-1680

  Niphakis, Micah J ^a   Lum, Kenneth M ^a   Cognetta, Armand B ^a   Correia, Bruno E ^a   Ichu, Taka Aki ^a   Olucha, Jose ^a   Brown, Steven J ^a   Kundu, Soumajit ^a   Piscitelli, Fabiana ^a   Rosen, Hugh ^a   Cravatt, Benjamin F ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENDOCANNABINOID; FATTY ACID; LIPID BINDING PROTEIN; NUCLEOBINDIN 1; UNCLASSIFIED DRUG; CALCIUM BINDING PROTEIN; DNA BINDING PROTEIN; ICOSANOID; MOLECULAR LIBRARY; NERVE PROTEIN; NUCLEOBINDIN; PROTEIN; PROTEOME;

AEROBIC METABOLISM; ARTICLE; CELL INTERACTION; CONTROLLED STUDY; DRUG ANALYSIS; DRUG MECHANISM; FLUOROSCOPY; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; ICOSANOID METABOLISM; MAMMAL CELL; PRIORITY JOURNAL; PROTEIN LIPID INTERACTION; PROTEOMICS; ULTRAVIOLET IRRADIATION; ULTRAVIOLET RADIATION; ANIMAL; DRUG EFFECTS; DRUG SCREENING; HEK293 CELL LINE; LIPID METABOLISM; METABOLISM; MOLECULAR LIBRARY; MOUSE; PHARMACOLOGY; TUMOR CELL LINE;

MAMMALIA;

ANIMALS; CALCIUM-BINDING PROTEINS; CELL LINE, TUMOR; DNA-BINDING PROTEINS; DRUG EVALUATION, PRECLINICAL; EICOSANOIDS; ENDOCANNABINOIDS; HEK293 CELLS; HUMANS; LIPID METABOLISM; MICE; NERVE TISSUE PROTEINS; PROTEINS; PROTEOME; SMALL MOLECULE LIBRARIES;

EID: 84935023329     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.05.045     Document Type: Article

References (45)

1. K. Ahn, S.E. Smith, M.B. Liimatta, D. Beidler, N. Sadagopan, D.T. Dudley, T. Young, P. Wren, Y. Zhang, and S. Swaney Mechanistic and pharmacological characterization of PF-04457845: a highly potent and selective fatty acid amide hydrolase inhibitor that reduces inflammatory and noninflammatory pain J. Pharmacol. Exp. Ther. 338 2011 114 124
2. B.A. Ballif, N.V. Mincek, J.T. Barratt, M.L. Wilson, and D.L. Simmons Interaction of cyclooxygenases with an apoptosis- and autoimmunity-associated protein Proc. Natl. Acad. Sci. USA 93 1996 5544 5549
3. F. Bartz, L. Kern, D. Erz, M. Zhu, D. Gilbert, T. Meinhof, U. Wirkner, H. Erfle, M. Muckenthaler, R. Pepperkok, and H. Runz Identification of cholesterol-regulating genes by targeted RNAi screening Cell Metab. 10 2009 63 75
4. M.S. Brown, and J.L. Goldstein Cholesterol feedback: from Schoenheimer's bottle to Scap's MELADL J. Lipid Res. 50 Suppl 2009 S15 S27
5. E. de Alba, and N. Tjandra Structural studies on the Ca2+-binding domain of human nucleobindin (calnuc) Biochemistry 43 2004 10039 10049
6. B. Díez-Dacal, J. Gayarre, S. Gharbi, J.F. Timms, C. Coderch, F. Gago, and D. Pérez-Sala Identification of aldo-keto reductase AKR1B10 as a selective target for modification and inhibition by prostaglandin A(1): implications for antitumoral activity Cancer Res. 71 2011 4161 4171
7. J.F. Evans, and J.H. Hutchinson Seeing the future of bioactive lipid drug targets Nat. Chem. Biol. 6 2010 476 479
8. R.M. Evans, and D.J. Mangelsdorf Nuclear receptors, RXR, and the Big Bang Cell 157 2014 255 266
9. J.F. Evans, A.D. Ferguson, R.T. Mosley, and J.H. Hutchinson What's all the FLAP about?: 5-lipoxygenase-activating protein inhibitors for inflammatory diseases Trends Pharmacol. Sci. 29 2008 72 78
10. O. Gallego, M.J. Betts, J. Gvozdenovic-Jeremic, K. Maeda, C. Matetzki, C. Aguilar-Gurrieri, P. Beltran-Alvarez, S. Bonn, C. Fernández-Tornero, and L.J. Jensen A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae Mol. Syst. Biol. 6 2010 430
11. J. Gubbens, E. Ruijter, L.E. de Fays, J.M. Damen, B. de Kruijff, M. Slijper, D.T. Rijkers, R.M. Liskamp, and A.I. de Kroon Photocrosslinking and click chemistry enable the specific detection of proteins interacting with phospholipids at the membrane interface Chem. Biol. 16 2009 3 14
12. P. Haberkant, R. Raijmakers, M. Wildwater, T. Sachsenheimer, B. Brügger, K. Maeda, M. Houweling, A.-C.C. Gavin, C. Schultz, and G. van Meer In vivo profiling and visualization of cellular protein-lipid interactions using bifunctional fatty acids Angew. Chem. Int. Ed. Engl. 52 2013 4033 4038
13. H. Harizi, J.B. Corcuff, and N. Gualde Arachidonic-acid-derived eicosanoids: roles in biology and immunopathology Trends Mol. Med. 14 2008 461 469
14. W.P. Heal, T.H. Dang, and E.W. Tate Activity-based probes: discovering new biology and new drug targets Chem. Soc. Rev. 40 2011 246 257
15. J.J. Hulce, A.B. Cognetta, M.J. Niphakis, S.E. Tully, and B.F. Cravatt Proteome-wide mapping of cholesterol-interacting proteins in mammalian cells Nat. Methods 10 2013 259 264
16. M. Kaczocha, S.T. Glaser, and D.G. Deutsch Identification of intracellular carriers for the endocannabinoid anandamide Proc. Natl. Acad. Sci. USA 106 2009 6375 6380
17. I. Kimura, Y. Nakayama, H. Yamauchi, M. Konishi, A. Miyake, M. Mori, M. Ohta, N. Itoh, and M. Fujimoto Neurotrophic activity of neudesin, a novel extracellular heme-binding protein, is dependent on the binding of heme to its cytochrome b5-like heme/steroid-binding domain J. Biol. Chem. 283 2008 4323 4331
18. C. Laggner, C. Schieferer, B. Fiechtner, G. Poles, R.D. Hoffmann, H. Glossmann, T. Langer, and F.F. Moebius Discovery of high-affinity ligands of sigma1 receptor, ERG2, and emopamil binding protein by pharmacophore modeling and virtual screening J. Med. Chem. 48 2005 4754 4764
19. P. Leclerc, J. Biarc, M. St-Onge, C. Gilbert, A.A. Dussault, C. Laflamme, and M. Pouliot Nucleobindin co-localizes and associates with cyclooxygenase (COX)-2 in human neutrophils PLoS ONE 3 2008 e2229
20. J. Lee, and M. Bogyo Target deconvolution techniques in modern phenotypic profiling Curr. Opin. Chem. Biol. 17 2013 118 126
21. Z. Li, P. Hao, L. Li, C.Y. Tan, X. Cheng, G.Y. Chen, S.K. Sze, H.M. Shen, and S.Q. Yao Design and synthesis of minimalist terminal alkyne-containing diazirine photo-crosslinkers and their incorporation into kinase inhibitors for cell- and tissue-based proteome profiling Angew. Chem. Int. Ed. Engl. 52 2013 8551 8556
22. B. Lomenick, R. Hao, N. Jonai, R.M. Chin, M. Aghajan, S. Warburton, J. Wang, R.P. Wu, F. Gomez, and J.A. Loo Target identification using drug affinity responsive target stability (DARTS) Proc. Natl. Acad. Sci. USA 106 2009 21984 21989
23. D. Martinez Molina, R. Jafari, M. Ignatushchenko, T. Seki, E.A. Larsson, C. Dan, L. Sreekumar, Y. Cao, and P. Nordlund Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay Science 341 2013 84 87
24. R. Mechoulam, E. Fride, and V. Di Marzo Endocannabinoids Eur. J. Pharmacol. 359 1998 1 18
25. M. Mileni, D.S. Johnson, Z. Wang, D.S. Everdeen, M. Liimatta, B. Pabst, K. Bhattacharya, R.A. Nugent, S. Kamtekar, and B.F. Cravatt Structure-guided inhibitor design for human FAAH by interspecies active site conversion Proc. Natl. Acad. Sci. USA 105 2008 12820 12824
26. E. Muro, G.E. Atilla-Gokcumen, and U.S. Eggert Lipids in cell biology: how can we understand them better? Mol. Biol. Cell 25 2014 1819 1823
27. T. Mutoh, R. Rivera, and J. Chun Insights into the pharmacological relevance of lysophospholipid receptors Br. J. Pharmacol. 165 2012 829 844
28. S. Oddi, F. Fezza, N. Pasquariello, A. D'Agostino, G. Catanzaro, C. De Simone, C. Rapino, A. Finazzi-Agrò, and M. Maccarrone Molecular identification of albumin and Hsp70 as cytosolic anandamide-binding proteins Chem. Biol. 16 2009 624 632
29. S.-E.E. Ong, B. Blagoev, I. Kratchmarova, D.B. Kristensen, H. Steen, A. Pandey, and M. Mann Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics 1 2002 376 386
30. V.V. Rostovtsev, L.G. Green, V.V. Fokin, and K.B. Sharpless A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective "ligation" of azides and terminal alkynes Angew. Chem. Int. Ed. Engl. 41 2002 2596 2599
31. C.A. Rouzer, and L.J. Marnett Endocannabinoid oxygenation by cyclooxygenases, lipoxygenases, and cytochromes P450: cross-talk between the eicosanoid and endocannabinoid signaling pathways Chem. Rev. 111 2011 5899 5921
32. M.M. Rowland, H.E. Bostic, D. Gong, A.E. Speers, N. Lucas, W. Cho, B.F. Cravatt, and M.D. Best Phosphatidylinositol 3,4,5-trisphosphate activity probes for the labeling and proteomic characterization of protein binding partners Biochemistry 50 2011 11143 11161
33. D.W. Russell Fifty years of advances in bile acid synthesis and metabolism J. Lipid Res. 50 Suppl 2009 S120 S125
34. A. Saghatelian, S.A. Trauger, E.J. Want, E.G. Hawkins, G. Siuzdak, and B.F. Cravatt Assignment of endogenous substrates to enzymes by global metabolite profiling Biochemistry 43 2004 14332 14339
35. A. Saghatelian, M.K. McKinney, M. Bandell, A. Patapoutian, and B.F. Cravatt A FAAH-regulated class of N-acyl taurines that activates TRP ion channels Biochemistry 45 2006 9007 9015
36. T.A. Samad, A. Sapirstein, and C.J. Woolf Prostanoids and pain: unraveling mechanisms and revealing therapeutic targets Trends Mol. Med. 8 2002 390 396
37. M.M. Savitski, F.B.M. Reinhard, H. Franken, T. Werner, M.F. Savitski, D. Eberhard, D. Martinez Molina, R. Jafari, R.B. Dovega, and S. Klaeger Tracking cancer drugs in living cells by thermal profiling of the proteome Science 346 2014 1255784
38. T. Shimizu Lipid mediators in health and disease: enzymes and receptors as therapeutic targets for the regulation of immunity and inflammation Annu. Rev. Pharmacol. Toxicol. 49 2009 123 150
39. G.M. Simon, M.J. Niphakis, and B.F. Cravatt Determining target engagement in living systems Nat. Chem. Biol. 9 2013 200 205
40. C.A. Smith, E.J. Want, G. O'Maille, R. Abagyan, and G. Siuzdak XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Anal. Chem. 78 2006 779 787
41. A.E. Speers, and B.F. Cravatt A tandem orthogonal proteolysis strategy for high-content chemical proteomics J. Am. Chem. Soc. 127 2005 10018 10019
42. Y. Su, J. Ge, B. Zhu, Y.G. Zheng, Q. Zhu, and S.Q. Yao Target identification of biologically active small molecules via in situ methods Curr. Opin. Chem. Biol. 17 2013 768 775
43. E.W. Tate, K.A. Kalesh, T. Lanyon-Hogg, E.M. Storck, and E. Thinon Global profiling of protein lipidation using chemical proteomic technologies Curr. Opin. Chem. Biol. 24 2015 48 57
44. L. Trapani, M. Segatto, P. Ascenzi, and V. Pallottini Potential role of nonstatin cholesterol lowering agents IUBMB Life 63 2011 964 971
45. M. Urbano, M. Guerrero, H. Rosen, and E. Roberts Modulators of the Sphingosine 1-phosphate receptor 1 Bioorg. Med. Chem. Lett. 23 2013 6377 6389