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Special Report

Cell Permeable Affinity- and Activity-Based Probes

Pages 2131-2141 | Published online: 29 Oct 2015

References

  • Bunnage ME , CheklerELP, JonesLH. Target validation using chemical probes. Nat. Chem. Biol.9, 195–199 (2013).
  • Moellering RE , CravattBF. How chemoproteomics can enable drug discovery and development. Chem. Biol.19, 11–22 (2012).
  • Hett EC , XuH, GeogheganKFet al. Rational targeting of active site tyrosine residues using sulfonyl fluoride probes. ACS Chem. Biol.10, 1094–1098 (2015).
  • Narayanan A , JonesLH. Sulfonyl fluorides as privileged warheads in chemical biology. Chem. Sci.10 (4), 1094–1098 (2015).
  • Barglow KT , CravattBF. Activity-based protein profiling for the functional annotation of enzymes. Nat. Methods4, 822–827 (2007).
  • Ghosh B , JonesLH. Target validation using in-cell small molecule clickable imaging probes. Med. Chem. Commun.5, 247–254 (2014).
  • Jones LH , BealDM, SelbyMDet al. In-cell click labelling of small molecules to determine subcellular localisation. J. Chem. Biol.4, 49–53 (2011).
  • Torn⊘e CW , ChristensenC, MeldalM. Peptidotriazoles on solid phase: [1,2,3]-triazoles by regiospecific copper(I)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem.67, 3057–3064 (2002).
  • Rostovtsev VV , GreenLG, FokinVV, SharplessKB. A stepwise Huisgen cycloaddition process: copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angew. Chem. Int. Ed. Engl. Engl.41, 2596–2599 (2002).
  • Martell J , WeerapanaE. Applications of copper-catalyzed click chemistry in activity-based protein profiling. Molecules19, 1378–1393 (2014).
  • McKay CS , FinnMG. Click chemistry in complex mixtures: bioorthogonal bioconjugation. Chem. Biol.21, 1075–1101 (2014).
  • Willems LI , van der LindenWA, LiNet al. Bioorthogonal chemistry: applications in activity-based protein profiling. Acc. Chem. Res.44, 718–729 (2011).
  • Patricelli MP , NomanbhoyTK, WuJet al. In situ kinase profiling reveals functionally relevant properties of native kinases. Chem. Biol.18, 699–710 (2011).
  • Bantscheff M , EberhardD, AbrahamYet al. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotech.25, 1035–1044 (2007).
  • Yee M-C , FasSC, StohlmeyerMM, WandlessTJ, CimprichKA. A cell-permeable, activity-based probe for protein and lipid kinases. J. Biol. Chem.280, 29053–29059 (2005).
  • Sherratt AR , NasheriN, McKayCSet al. A new chemical probe for phosphatidylinositol kinase activity. ChemBioChem15, 1253–1256 (2014).
  • Shi H , ChengX, SzeSK, YaoSQ. Proteome profiling reveals potential cellular targets of staurosporine using a clickable cell-permeable probe. Chem. Commun.47, 11306–11308 (2011).
  • Shi H , ZhangC-J, ChenGYJ, YaoSQ. Cell-based proteome profiling of potential dasatinib targets by use of affinity-based probes. J. Am. Chem. Soc.134, 3001–3014 (2012).
  • Ranjitkar P , PereraBGK, SwaneyDLet al. Affinity-based probes based on type II kinase inhibitors. J. Am. Chem. Soc.134, 19017–19025 (2012).
  • Liu Q , SabnisY, ZhaoZet al. Developing irreversible inhibitors of the protein kinase cysteinome. Chem. Biol.20, 146–159 (2013).
  • Honigberg LA , SmithAM, SirisawadMet al. The Bruton tyrosine kinase inhibitor PCI-32765 blocks B-cell activation and is efficacious in models of autoimmune disease and B-cell malignancy. Proc. Natl Acad. Sci. USA107, 13075–13080 (2010).
  • Lanning BR , WhitbyLR, DixMMet al. A road map to evaluate the proteome-wide selectivity of covalent kinase inhibitors. Nat. Chem. Biol.10, 760–767 (2014).
  • Cohen MS , HadjivassiliouH, TauntonJ. A clickable inhibitor reveals context-dependent autoactivation of p90 RSK. Nat. Chem. Biol.3, 156–160 (2007).
  • Nishino M , ChoyJW, GushwaNNet al. Hypothemycin, a fungal natural product, identifies therapeutic targets in Trypanosoma brucei. eLife2, e00712 (2013).
  • Dong J , KrasnovaL, FinnMG, SharplessKB. Sulfur(VI) fluoride exchange (SuFEx): another good reaction for click chemistry. Angew. Chem. Int. Ed. Engl.53, 9430–9448 (2014).
  • Gushwa NN , KangS, ChenJ, TauntonJ. Selective targeting of distinct active site nucleophiles by irreversible Src-family kinase inhibitors. J. Am. Chem. Soc.134, 20214–20217 (2012).
  • Sanman LE , BogyoM. Activity-based profiling of proteases. Annu. Rev. Biochem.83, 249–273 (2014).
  • Gillet LCJ , NamotoK, RuchtiAet al. In-cell selectivity profiling of serine protease inhibitors by activity-based proteomics. Mol. Cell. Proteomics7, 1241–1253 (2008).
  • Adibekian A , MartinBR, ChangJWet al. Confirming target engagement for reversible inhibitors in vivo by kinetically tuned activity-based probes. J. Am. Chem. Soc.134, 10345–10348 (2012).
  • Ahn K , JohnsonDS, MileniMet al. Discovery and characterization of a highly selective FAAH inhibitor that reduces inflammatory pain. Chem. Biol.16, 411–420 (2009).
  • Chang JW , CognettaABIII, NiphakisMJ, CravattBF. Proteome-wide reactivity profiling identifies diverse carbamate chemotypes tuned for serine hydrolase inhibition. ACS Chem. Biol.8, 1590–1599 (2013).
  • Verdoes M , EdgingtonLE, ScheerenFAet al. A non-peptidic cathepsin S activity-based probe for noninvasive optical imaging of tumor-associated macrophages. Chem. Biol.19, 619–628 (2012).
  • Reich M , Van SwietenPF, SommandasVet al. Endocytosis targets exogenous material selectively to cathepsin S in live human dendritic cells, while cell-penetrating peptides mediate nonselective transport to cysteine cathepsins. J. Leukoc. Biol.81, 990–1001 (2007).
  • Ovaa H , van SwietenPF, KesslerBMet al. Chemistry in living cells: detection of active proteasomes by a two-step labeling strategy. Angew. Chem. Int. Ed. Engl.42, 3626–3629 (2003).
  • Carmony KC , LeeD-M, WuYet al. A bright approach to the immunoproteasome: development of LMP2/b1i-specific imaging probes. Bioorg. Med. Chem.20, 607–613 (2012).
  • Wright AT , CravattBF. Chemical proteomic probes for profiling cytochrome P450 activities and drug interactions in vivo. Chem. Biol.14, 1043–1051 (2007).
  • Krysiak JM , KreuzerJ, MacherouxP, HermetterA, SieberSA, BreinbauerR. Activity-based probes for studying the activity of flavin-dependent oxidases and for the protein target profiling of monoamine oxidase inhibitors. Angew. Chem. Int. Ed. Engl.51, 7035–7040 (2012).
  • Tsai C-S , YenH-Y, LinM-Iet al. Cell-permeable probe for identification and imaging of sialidases. Proc. Natl Acad. Sci. USA110, 2466–2471 (2013).
  • Witte MD , KallemeijnWW, AtenJet al. Ultrasensitive in situ visualization of active glucocerebrosidase molecules. Nat. Chem. Biol.6, 907–913 (2010).
  • An H , StatsyukAV. Development of activity-based probes for ubiquitin and ubiquitin-like protein signaling pathways. J. Am. Chem. Soc.135, 16948–16962 (2013).
  • Slack JL , CauseyCP, LuoY, ThompsonPR. Development and use of clickable activity-based protein profiling agents for protein arginine deiminase 4. ACS Chem. Biol.6, 466–476 (2011).
  • Salisbury CM , CravattBF. Activity-based probes for proteomic profiling of histone deacetylase complexes. Proc. Natl Acad. Sci. USA104, 1171–1176 (2007).
  • Paulsen CE , TruongTH, GarciaFJet al. Peroxide-dependent sulfenylation of the EGFR catalytic site enhances kinase activity. Nat. Chem. Biol.8, 57–64 (2011).
  • Yang J , GuptaV, CarrollKS, LieblerDC. Site-specific mapping and quantification of protein S-sulfenylation in cells. Nat. Commun.5, 4776 (2014).
  • Kalesh KA , ClulowJA, TateEW. Target profiling of zerumbone using a novel cell-permeable clickable probe and quantitative chemical proteomics. Chem. Commun.51, 5497–5500 (2015).
  • Yang PY , LiuK, NgaiMH, LearMJ, WenkMR, YaoSQ. Activity-based proteome profiling of potential cellular targets of Orlistat - an FDA-approved drug with anti-tumor activities. J. Am. Chem. Soc.132, 656–666 (2010).
  • Böttcher T , SieberSA. Showdomycin as a versatile chemical tool for the detection of pathogenesis-associated enzymes in bacteria. J. Am. Chem. Soc.132, 6964–6972 (2010).
  • Hulce JJ , CognettaAB, NiphakisMJ, TullySE, CravattBF. Proteome-wide mapping of cholesterol-interacting proteins in mammalian cells. Nat. Methods10, 259–264 (2013).
  • Tantama M , LinWC, LichtS. An activity-based protein profiling probe for the nicotinic acetylcholine receptor. J. Am. Chem. Soc.130, 15766–15767 (2008).
  • Xu F , ZhaoH, FengXet al. Single-cell chemical proteomics with an activity-based probe: identification of low-copy membrane proteins on primary neurons. Angew. Chem. Int. Ed. Engl.53, 6730–6733 (2014).
  • Kambe T , CorreiaBE, NiphakisMJ, CravattBF. Mapping the protein interaction landscape for fully functionalized small-molecule probes in human cells. J. Am. Chem. Soc.136, 10777–10782 (2014).
  • Shannon DA , WeerapanaE. Covalent protein modification: the current landscape of residue-specific electrophiles. Curr. Opin. Chem. Biol.24, 18–26 (2015).

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