Login Register Cart 0
Generic placeholder image

The Natural Products Journal

Editor-in-Chief

ISSN (Print): 2210-3155
ISSN (Online): 2210-3163

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Review Article

Advancements in Chemical Proteomics for Target Identification of Natural Products in Live Cells

In Press, (this is not the final "Version of Record"). Available online 06 June, 2024
Author(s): Abid H. Banday*, Insha Ashraf, Mudasir Bashir, Aariya Yousuf, Basit Qayoom, Mysar Ahmad Bhat, Saima Nabi, Saima Maqbool and Muzaffar A. Lone
Published on: 06 June, 2024

Article ID: e060624230779

DOI: 10.2174/0122103155290163240528065607

Price: $95

Abstract

Natural products have evolved to interact with specific protein targets within cells, making them valuable for various biological functions. Chemical proteomics, specifically the use of covalently linked probes in live cells, allows for the identification of protein-binding partners or targets of small molecules. Recent advancements in target identification of natural products have utilized affinity- based probes and photo-affinity labeling techniques, enabling the capture of potential cellular targets even when the interaction is reversible. This knowledge can aid in understanding molecular pathways and developing new therapeutics for diseases lacking treatment options. Several methods, including DARTS, SPROX, CETSA, TPP, and bioinformatics-based analysis, are employed for target identification of label-free natural products. Chemical probe design and synthesis are tailored to screen targets of molecules with diverse structures. The comprehensive proteomic analysis reported herein aims to investigate target sites contributing to biologically significant effects, considering both desirable phenotypes and potential toxicity or side effects.

[1]
Dixon, N.; Wong, L.S.; Geerlings, T.H.; Micklefield, J. Cellular targets of natural products. Nat. Prod. Rep., 2008, 25(3), 248-294.
[http://dx.doi.org/10.1039/b702097f] [PMID: 18033580]
[2]
Knoll, A.H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth; Princeton University Press: Princeton, 2003.
[3]
Breinbauer, R.; Vetter, I.R.; Wablmann, H. Angew. Chem. Int. Ed., 2003, 42(24), 2878-2890.
[http://dx.doi.org/10.1002/anie.200301636]
[4]
Chen, X.; Wang, Y.; Ma, N.; Tian, J.; Shao, Y.; Zhu, B.; Wong, Y.K.; Liang, Z.; Zou, C.; Wang, J. Target identification of natural medicine with chemical proteomics approach: Probe synthesis, target fishing and protein identification. Signal Transduct. Target. Ther., 2020, 5(1), 72.
[http://dx.doi.org/10.1038/s41392-020-0186-y] [PMID: 32435053]
[5]
Newman, D.J.; Cragg, G.M. Natural products as sources of new drugs over the last 25 years. J. Nat. Prod., 2007, 70(3), 461-477.
[http://dx.doi.org/10.1021/np068054v] [PMID: 17309302]
[6]
Guo, Z. The modification of natural products for medical use. Acta Pharm. Sin. B, 2017, 7(2), 119-136.
[http://dx.doi.org/10.1016/j.apsb.2016.06.003] [PMID: 28303218]
[7]
Bantscheff, M.; Scholten, A.; Heck, A.J.R. Revealing promiscuous drug–target interactions by chemical proteomics. Drug Discov. Today, 2009, 14(21-22), 1021-1029.
[http://dx.doi.org/10.1016/j.drudis.2009.07.001] [PMID: 19596079]
[8]
Pan, S.; Zhang, H.; Wang, C.; Yao, S.C. Target identification of natural products and bioactive compounds using affinity-based probes. Nat. Rev. Chem., 2021, 5(1), 35-52.
[http://dx.doi.org/10.1038/s41570-020-00262-x]
[9]
Evans, M.J.; Cravatt, B.F. Activity-based protein profiling: From enzyme chemistry to proteomic chemistry. Chem. Rev., 2006, 106(8), 3279-3301.
[http://dx.doi.org/10.1021/cr050288g] [PMID: 16895328]
[10]
Cravatt, B.F.; Wright, A.T.; Kozarich, J.W. Activity-based protein profiling: From enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem., 2008, 77(1), 383-414.
[http://dx.doi.org/10.1146/annurev.biochem.75.101304.124125] [PMID: 18366325]
[11]
Khan, A.R.; James, M.N. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Protein Sci., 1998, 7, 815-836.
[http://dx.doi.org/10.1002/pro.5560070401] [PMID: 9568890]
[12]
Dutta, S.; Abe, H.; Aoyagi, S.; Kibayashi, C.; Gates, K.S. Novel DNA binding agents based on a heterocyclic cyclopropyl group. J. Am. Chem. Soc., 2005, 127(42), 15004-15005.
[http://dx.doi.org/10.1021/ja053735i] [PMID: 16248621]
[13]
Hübscher, U.; Maga, G.; Spadari, S. Eukaryotic DNA polymerases. Annu. Rev. Biochem., 2002, 71(1), 133-163.
[http://dx.doi.org/10.1146/annurev.biochem.71.090501.150041] [PMID: 12045093]
[14]
Shin-ya, K.; Wierzba, K.; Matsuo, K.I.; Ohtani, T.; Yamada, Y.; Furihata, K.; Haya Kawa, V.; Seto, H. Design, synthesis, and biological evaluation of hexacyclinol-based protein tyrosine phosphatase inhibitors. J. Am. Chem. Soc., 2001, 123(6), 1262-1263.
[http://dx.doi.org/10.1021/ja005780q] [PMID: 11456694]
[15]
Kim, M.Y.; Vankayalapati, H.; Shin-ya, K.; Wierzba, K.; Hurley, L.H. Synthesis and evaluation of macrocyclic hexacyclinols as G-Quadruplex stabilizing ligands. J. Am. Chem. Soc., 2002, 124(8), 2098-2099.
[http://dx.doi.org/10.1021/ja017308q] [PMID: 11878947]
[16]
Clement, J.A.; Li, M.; Hecht, S.M.; Kingston, D.G.I. Total synthesis and confirmation of the structure of venturicidin B. J. Nat. Prod., 2006, 69(3), 373-376.
[http://dx.doi.org/10.1021/np0504107] [PMID: 16562838]
[17]
Li, W.; Zhang, M.; Zhang, J.I.; Li, H.Q.; Zhang, X.C.; Sun, Q.; Qiu, C.M. Crystal structure of a DNA decamer containing an intrastrand thymine-adenine cross-link derived from 1,N6-ethenoadenine. FEBS Lett., 2006, 580(22), 4905-4910.
[http://dx.doi.org/10.1016/j.febslet.2006.08.007] [PMID: 16989816]
[18]
Nakai, R.; Ishida, H.; Asai, A.; Ogawa, H.; Yamamoto, Y.; Kawasaki, H.; Akinaga, S.; Mizukami, T.; Yamashita, Y. Telomerase inhibitors identified by a forward chemical genetics approach using a yeast strain with shortened telomere length. Chem. Biol., 2006, 13(2), 183-190.
[http://dx.doi.org/10.1016/j.chembiol.2005.11.010] [PMID: 16492566]
[19]
Wada, S.I.; Iida, A.; Tanaka, R. Biological activity and pharmacological prospectus of lupane derivatives. J. Nat. Prod., 2001, 64, 1545-1547.
[http://dx.doi.org/10.1021/np010176u] [PMID: 11754608]
[20]
Mizushina, Y.; Akihisa, T.; Ukiya, M.; Murakami, C.; Kuriyama, I.; Xu, X.; Yoshida, H.; Sakaguchi, K. Specific inhibitors of mammalian DNA polymerase species. Cancer Sci., 2004, 95, 354-360.
[http://dx.doi.org/10.1111/j.1349-7006.2004.tb03215.x] [PMID: 15072595]
[21]
Ukiya, M.; Hayakawa, T.; Okazaki, K.; Hikawa, M.; Akazawa, H.; Li, W.; Koike, K.; Fukatsu, M. Synthesis of Lanostane‐Type Triterpenoid N ‐Glycosides and their cytotoxicity against human cancer cell lines. Chem. Biodivers., 2018, 15(7), e1800113.
[http://dx.doi.org/10.1002/cbdv.201800113] [PMID: 29734526]
[22]
Chen, L.F.; Greene, W.C.; Greene, W.C. Shaping the nuclear action of NF-κB. Nat. Rev. Mol. Cell Biol., 2004, 5(5), 392-401.
[http://dx.doi.org/10.1038/nrm1368] [PMID: 15122352]
[23]
López-Antón, N.; Rudy, A.; Barth, N.; Schmitz, L.M.; Pettit, G.R.; Schulze-Osthoff, K.; Dirsch, V.M.; Vollmar, A.M. The marine product cephalostatin 1 activates an endoplasmic reticulum stress-specific and apoptosome-independent apoptotic signaling pathway. J. Biol. Chem., 2006, 281(44), 33078-33086.
[http://dx.doi.org/10.1074/jbc.M607904200] [PMID: 16945918]
[24]
Park, H.R.; Furihata, K.; Hayakawa, Y.; Shin-ya, K. Versipelostatin, a novel GRP78/Bip molecular chaperone down-regulator of microbial origin. Tetrahedron Lett., 2002, 43(39), 6941-6945.
[http://dx.doi.org/10.1016/S0040-4039(02)01624-6]
[25]
Gafni, J.; Munsch, J.A.; Lam, T.H.; Catlin, M.C.; Costa, L.G.; Molinski, T.F.; Pessah, I.N. Xestospongins: Potent membrane permeable blockers of the inositol 1,4,5-trisphosphate receptor. Neuron, 1997, 19(3), 723-733.
[http://dx.doi.org/10.1016/S0896-6273(00)80384-0] [PMID: 9331361]
[26]
Brady, T.P.; Wallace, E.K.; Kim, S.H.; Guizzunti, G.; Malhotra, V.; Theodorakis, E.A. Fragmentation of Golgi membranes by norrisolide and designed analogues. Bioorg. Med. Chem. Lett., 2004, 14(20), 5035-5039.
[http://dx.doi.org/10.1016/j.bmcl.2004.08.003] [PMID: 15380194]
[27]
Katz, L.; Ashley, G.W. Translation and protein synthesis. Macrolides. Chem. Rev., 2005, 105(2), 499-528.
[http://dx.doi.org/10.1021/cr030107f] [PMID: 15700954]
[28]
Ta, T.A.; Feng, W.; Molinski, T.F.; Pessah, I.N. Hydroxylated xestospongins block inositol-1,4,5-trisphosphate-induced Ca2+ release and sensitize Ca2+-induced Ca2+ release mediated by ryanodine receptors. Mol. Pharmacol., 2006, 69(2), 532-538.
[http://dx.doi.org/10.1124/mol.105.019125] [PMID: 16249374]
[29]
Luibrand, R.T.; Erdman, T.R.; Vollmax, J.J.; Schever, P.J.; Finer, J.; Clardy, J. Quinone sesquiterpenoid: A challenge for the development of a new synthetic methodology. Tetrahedron, 1978, 35, 609-612.
[http://dx.doi.org/10.1016/0040-4020(79)87004-0]
[30]
Wright, M.H.; Sieber, S.A. Chemical proteomics approaches for identifying the cellular targets of natural products. Nat. Prod. Rep., 2016, 33(5), 681-708.
[http://dx.doi.org/10.1039/C6NP00001K] [PMID: 27098809]
[31]
Li, G.; Peng, X.; Guo, Y.; Gong, S.; Cao, S.; Qiu, F. Currently available strategies for target identification of bioactive natural products. J. Pharm. Anal., 2019, 2019, 3-15.
[http://dx.doi.org/10.1016/j.jpha.2018.11.004]
[32]
Song, Y.; Liu, L.; Wan, K. Off-target identification by chemical proteomics for the understanding of drug side effects. Chem. Res. Toxicol., 2016, 29, 1353-1359.
[http://dx.doi.org/10.1021/acs.chemrestox.6b00096]
[33]
Ha, J.; Park, H.; Park, J.; Park, S.B. Recent advances in identifying protein targets in drug discovery. Cell Chem. Biol., 2021, 28(3), 394-423.
[34]
Wang, S.; Tian, Y.; Wang, M.; Sun, G.B.; Sun, X.B. Generative topographic mapping in drug design. Drug Discov. Today. Technol., 2019, 32-33, 99-107.
[http://dx.doi.org/10.1016/j.ddtec.2020.06.003]
[35]
Murale, D.P.; Hong, S.C.; Haque, M.M.; Lee, J.S. Photoaffinity Labeling (PAL) in chemical proteomics: A handy tool to investigate protein-protein interactions. Bioorg. Med. Chem., 2021, 29, 115818.
[http://dx.doi.org/10.1016/j.bmc.2021.115818]
[36]
Takemori, A.; Butcher, D.S.; Harman, V.M.; Brownridge, P.; Shima, K.; Higo, D.; Ishizato, J.; Hasegawa, H.; Suzuki, J.; Loo, J.A.; Gorzalek Loo, R.R.; Beynon, R.J. PEPPI-MS: Polyacrylamide-gel-based prefractions for analysis of intact proteoforms and protein complexes by mass spectrometry. J. Proteome Res., 2020, 19(9), 3779-3791.
[37]
Romo, D.; Liu, J.O. Editorial: Strategies for cellular target identification of natural products. Nat. Prod. Rep., 2016, 33(5), 592-594.
[http://dx.doi.org/10.1039/C6NP90016J] [PMID: 27118358]
[38]
Berrade, W.; Garcia, A.E. Camarero, JA Protein microarrays: Novel developments and applications. Pharm. Res., 2011, 28(7), 1480-1499.
[39]
Ziegler, S.; Pries, V.; Hedberg, C.; Waldmann, H. Target identification for small bioactive molecules: Finding the needle in the haystack. Angew. Chem. Int. Ed., 2013, 52(10), 2744-2792.
[http://dx.doi.org/10.1002/anie.201208749] [PMID: 23418026]
[40]
Nodwell, M.B.; Sieber, S.A. ABPP methodology: Introduction and overview. Top. Curr. Chem., 2012, 324, 1-41.
[http://dx.doi.org/10.1007/128_2012_313] [PMID: 22160389]
[41]
Dubinsky, L.; Krom, B.P.; Meijler, M.M. Diazirine based photoaffinity labeling. Bioorg. Med. Chem., 2012, 20(2), 554-570.
[http://dx.doi.org/10.1016/j.bmc.2011.06.066] [PMID: 21778062]
[42]
Xu, J.; Zeng, C.; Chu, W.; Pan, F.; Rothfuss, J.M.; Zhang, F.; Tu, Z.; Zhou, D.; Zeng, D.; Vangveravong, S.; Johnston, F.; Spitzer, D.; Chang, K.C.; Hotchkiss, R.S.; Hawkins, W.G.; Wheeler, K.T.; Mach, R.H. Identification of the PGRMC1 protein complex as the putative sigma-2 receptor binding site. Nat. Commun., 2011, 2(1), 380.
[http://dx.doi.org/10.1038/ncomms1386] [PMID: 21730960]
[43]
Takeo, K.; Tanimura, S.; Shinohara, T.; Osawa, S.; Zahariev, I.K.; Takegami, N.; Ishizuka-Katsura, N. Allosteric regulation of γ-secretase activity by a phenylimidazole-type γ-secretase modulator. Proc. Natl. Acad. Sci. USA, 2014, 111(29), 10544-10549.
[44]
Eirich, J.; Orth, R.; Sieber, S.A. Unraveling the protein targets of vancomycin in living S. aureus and E. faecalis cells. J. Am. Chem. Soc., 2011, 133(31), 12144-12153.
[http://dx.doi.org/10.1021/ja2039979] [PMID: 21736328]
[45]
Cragg, G.M.; Newman, D.J. Natural products as sources of new drugs over the nearly four decades from 01/1981 to 09/2019. J. Nat. Prod., 2020, 83(3), 770-803.
[46]
Newman, D.J.; Cragg, G.M.; Snader, K.M. Natural products as sources of new drugs over the period 1981−2002. J. Nat. Prod., 2003, 66, 1022.
[http://dx.doi.org/10.1021/np030096l] [PMID: 12880330]
[47]
Brieke, C.; Orth, R.; Waldmann, H. Activity-based protein profiling: From enzyme chemistry to proteomic chemistry. Angew. Chem. Int. Ed., 2002, 41, 2878.
[http://dx.doi.org/10.1002/1521-3773(20020816)41:16<2878::AID-ANIE2878>3.0.CO;2-Q]
[48]
Drahl, C.; Cravatt, B.F.; Sorensen, E.J. Protein-reactive natural products. Angew. Chem. Int. Ed., 2005, 44(36), 5788-5809.
[http://dx.doi.org/10.1002/anie.200500900] [PMID: 16149114]
[49]
MacKinnon, A.L.; Garrison, J.L.; Hedge, R.S.; Taunton, J. Small molecule inhibitors targeting protein biogenesis at the endoplasmic reticulum. J. Am. Chem. Soc., 2007, 129, 14560.
[http://dx.doi.org/10.1021/ja076250y] [PMID: 17983236]
[50]
Ohana, R.F.; Kirkland, T.A.; Woodroofe, C.C.; Levin, S.; Uyeda, H.T.; Otto, P.; Hurst, R.; Robers, M.B.; Zimmerman, K.; Encell, L.P.; Wood, K.V. Deciphering the cellular targets of bioactive compounds using a chloralkane capture tag. J. Am. Chem. Soc., 2019, 141(30), 11981-11987.
[http://dx.doi.org/10.1021/jacs.9b03606]
[51]
Tymiak, A.A.; Cuvier, C.A.; Malley, M.F.; Gougoutas, J.Z. Activity-based protein profiling: From enzyme chemistry to proteomic chemistry. J. Org. Chem., 1985, 50, 5491.
[http://dx.doi.org/10.1021/jo00350a010]
[52]
Li, N.; Xie, S.; Li, L. Activity-based protein profiling: An enabling technology in chemical biology research. Curr. Opin. Chem. Biol., 2022, 71, 76-84.
[http://dx.doi.org/10.1016/j.cbpa.2021.12.007] [PMID: 22325363]
[53]
Weibel, E.K.; Hadvary, P.; Hochuli, E.; Kupfer, E.; Lengsfeld, H. Lipstatin, an inhibitor of pancreatic lipase, produced by Streptomyces toxytricini. I. Producing organism, fermentation, isolation and biological activity. J. Antibiot. (Tokyo), 1987, 40(8), 1081-1085.
[http://dx.doi.org/10.7164/antibiotics.40.1081] [PMID: 3680018]
[54]
Hadváry, P.; Lengsfeld, H.; Wolfer, H. Inhibition of pancreatic lipase in vitro by the covalent inhibitor tetrahydrolipstatin. Biochem. J., 1988, 256(2), 357-361.
[http://dx.doi.org/10.1042/bj2560357] [PMID: 3223916]
[55]
Böttcher, T.; Pitscheider, M.; Sieber, S.A. Natural products and their biological targets: Proteomic and metabolomic labeling strategies. Angew. Chem. Int. Ed., 2010, 49(15), 2680-2698.
[http://dx.doi.org/10.1002/anie.200905352] [PMID: 20333627]
[56]
Wang, Z.; Gu, C.; Colby, T.; Shindo, T.; Balamurugan, R.; Waldmann, H.; Kaiser, M.; van der Hoorn, R.A.L. β-Lactone probes identify a papain-like peptide ligase in Arabidopsis thaliana. Nat. Chem. Biol., 2008, 4(9), 557-563.
[http://dx.doi.org/10.1038/nchembio.104] [PMID: 18660805]
[57]
Saghatelian, A.; Trauger, S.A.; Want, E.J.; Hawkins, E.G.; Siuzdak, G.; Cravatt, B.F. Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry, 2004, 43(45), 14332-14339.
[http://dx.doi.org/10.1021/bi0480335] [PMID: 15533037]
[58]
Saghatelian, A.; Cravatt, B.F. Discovery metabolite profiling — forging functional connections between the proteome and metabolome. Life Sci., 2005, 77(14), 1759-1766.
[http://dx.doi.org/10.1016/j.lfs.2005.05.019] [PMID: 15964030]
[59]
Smith, C.A.; Want, E.J.; O’Maille, G.; Abagyan, R.; Siuzdak, G. XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem., 2006, 78(3), 779-787.
[http://dx.doi.org/10.1021/ac051437y] [PMID: 16448051]
[60]
Gobbi, G.; Bambico, F.R.; Mangieri, R.; Bortolato, M.; Campolongo, P.; Solinas, M.; Cassano, T.; Morgese, M.G.; Debonnel, G.; Duranti, A.; Tontini, A.; Tarzia, G.; Mor, M.; Trezza, V.; Goldberg, S.R.; Cuomo, V.; Piomelli, D. Antidepressant-like activity and modulation of brain monoaminergic transmission by blockade of anandamide hydrolysis. Proc. Natl. Acad. Sci. USA, 2005, 102(51), 18620-18625.
[http://dx.doi.org/10.1073/pnas.0509591102] [PMID: 16352709]
[61]
Nomura, D.K.; Leung, D.; Chiang, K.P.; Quistad, G.B.; Cravatt, B.F.; Casida, J.E. A brain detoxifying enzyme for organophosphorus nerve poisons. Proc. Natl. Acad. Sci. USA, 2005, 102(17), 6195-6200.
[http://dx.doi.org/10.1073/pnas.0501915102] [PMID: 15840715]
[62]
Tagore, D.M.; Nolte, W.M.; Neveu, J.M.; Rangel, R.; Guzman-Rojas, L.; Pasqualini, R.; Arap, W.; Lane, W.S.; Saghatelian, A. Peptidase substrates via global peptide profiling. Nat. Chem. Biol., 2009, 5(1), 23-25.
[http://dx.doi.org/10.1038/nchembio.126] [PMID: 19011639]
[63]
Chiang, K.P.; Niessen, S.; Saghatelian, A.; Cravatt, B.F. An enzyme that regulates ether lipid signaling pathways in cancer annotated by multidimensional profiling. Chem. Biol., 2006, 13(10), 1041-1050.
[http://dx.doi.org/10.1016/j.chembiol.2006.08.008] [PMID: 17052608]
[64]
Hirai, M.Y.; Klein, M.; Fujikawa, Y.; Yano, M.; Goodenowe, D.B.; Yamazaki, Y.; Kanaya, S.; Nakamura, Y.; Kitayama, M.; Suzuki, H.; Sakurai, N.; Shibata, D.; Tokuhisa, J.; Reichelt, M.; Gershenzon, J.; Papenbrock, J.; Saito, K. Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. J. Biol. Chem., 2005, 280(27), 25590-25595.
[http://dx.doi.org/10.1074/jbc.M502332200] [PMID: 15866872]
[65]
Simon, G.M.; Dix, M.M.; Cravatt, B.F. Comparative assessment of large-scale proteomic studies of apoptotic proteolysis. ACS Chem. Biol., 2009, 4(6), 401-408.
[http://dx.doi.org/10.1021/cb900082q] [PMID: 19415908]
[66]
Dix, M.M.; Simon, G.M.; Cravatt, B.F. Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell, 2008, 134(4), 679-691.
[http://dx.doi.org/10.1016/j.cell.2008.06.038] [PMID: 18724940]
[67]
Tagore, R.; Thomas, H.R.; Homan, E.A.; Munawar, A.; Saghatelian, A. A global metabolite profiling approach to identify protein-metabolite interactions. J. Am. Chem. Soc., 2008, 130(43), 14111-14113.
[http://dx.doi.org/10.1021/ja806463c] [PMID: 18831549]
[68]
Brett, L. Target identification using drug affinity responsive target stability (DARTS). Nat. Protoc., 2011, 6(3), 389-398.
[http://dx.doi.org/10.1038/nprot.2010.198]
[69]
Lomenick, B.; Jung, G.; Wohlschlegel, J.A.; Huang, J. Target identification using drug affinity responsive target stability (DARTS). Curr. Protoc. Chem. Biol., 2011, 3(4), 163-180.
[http://dx.doi.org/10.1002/9780470559277.ch110180] [PMID: 22229126]
[70]
West, G.M.; Tang, L.; Fitzgerald, M.C. Thermodynamic analysis of protein stability and ligand binding using a chemical modification- and mass spectrometry-based strategy. Anal. Chem., 2008, 80(11), 4175-4185.
[http://dx.doi.org/10.1021/ac702610a] [PMID: 18457414]
[71]
Mateus, A.; Kurzawa, N.; Becher, I.; Sridharan, S.; Helm, D.; Stein, F.; Typas, A.; Savitski, M.M. Thermal proteome profiling for interrogating protein interactions. Mol. Syst. Biol., 2020, 16(3), e9232.
[http://dx.doi.org/10.15252/msb.20199232] [PMID: 32133759]
[72]
Cao, J.; Lin, G.; Gong, Y.; Pan, P.; Ma, Y.; Huang, P.; Ying, M.; Hou, T.; He, Q.; Yang, B. DNA-PKcs, a novel functional target of acriflavine, mediates acriflavine’s p53-dependent synergistic anti-tumor efficiency with melphalan. Cancer Lett., 2016, 383(1), 115-124.
[http://dx.doi.org/10.1016/j.canlet.2016.09.029] [PMID: 27693638]
[73]
del Gaudio, F.; Pollastro, F.; Mozzicafreddo, M.; Riccio, R.; Minassi, A.; Monti, M.C. Chemoproteomic fishing identifies arzanol as a positive modulator of brain glycogen phosphorylase. Chem. Commun. (Camb.), 2018, 54(91), 12863-12866.
[http://dx.doi.org/10.1039/C8CC07692H] [PMID: 30375590]
[74]
Wu, R.; Murali, R.; Kabe, Y.; French, S.W.; Chiang, Y.M.; Liu, S.; Sher, L.; Wang, C.C.; Louie, S.; Tsukamoto, H. Baicalein targets GTPase mediated autophagy to eliminate liver tumor-initiating stem cell-like cells resistant to mTORC1 inhibition. Hepatology, 2018, 68(5), 1726-1740.
[http://dx.doi.org/10.1002/hep.30071] [PMID: 29729190]
[75]
Yoon, Y.J.; Han, Y.M.; Choi, J.; Lee, Y.J.; Yun, J.; Lee, S.K.; Lee, C.W.; Kang, J.S.; Chi, S.W.; Moon, J.H.; Lee, S.; Han, D.C.; Kwon, B.M. Benproperine, an ARPC2 inhibitor, suppresses cancer cell migration and tumor metastasis. Biochem. Pharmacol., 2019, 163, 46-59.
[http://dx.doi.org/10.1016/j.bcp.2019.01.017] [PMID: 30710516]
[76]
Zhao, S.Y.; Liao, L.X.; Tu, P.F.; Li, W.W.; Zeng, K.W. Icariin inhibits AGE-induced injury in PC12 cells by directly targeting apoptosis regulator bax. Oxid. Med. Cell. Longev., 2019, 2019, 1-12.
[http://dx.doi.org/10.1155/2019/7940808] [PMID: 31178973]
[77]
Chen, F.; Zhu, K.; Chen, L.; Ouyang, L.; Chen, C.; Gu, L.; Jiang, Y.; Wang, Z.; Lin, Z.; Zhang, Q.; Shao, X.; Dai, J.; Zhao, Y. Protein target identification of ginsenosides in skeletal muscle tissues: Discovery of natural small-molecule activators of muscle-type creatine kinase. J. Ginseng Res., 2020, 44(3), 461-474.
[http://dx.doi.org/10.1016/j.jgr.2019.02.005] [PMID: 32372868]
[78]
Kim, B.S.; Lee, K.; Jung, H.J.; Bhattarai, D.; Kwon, H.J. HIF-1α suppressing small molecule, LW6, inhibits cancer cell growth by binding to calcineurin b homologous protein 1. Biochem. Biophys. Res. Commun., 2015, 458(1), 14-20.
[http://dx.doi.org/10.1016/j.bbrc.2015.01.031] [PMID: 25603055]
[79]
Palrasu, M.; Knapinska, A.M.; Diez, J.; Smith, L.; LaVoi, T.; Giulianotti, M.; Houghten, R.A.; Fields, G.B.; Minond, D. A novel probe for spliceosomal proteins that induces autophagy and death of melanoma cells revealsnew targets for melanoma drug discovery. Cell. Physiol. Biochem., 2019, 53(4), 656-686.
[http://dx.doi.org/10.33594/000000164] [PMID: 31573152]
[80]
Gotsbacher, M.P.; Cho, S.; Kwon, H.J.; Karuso, P. Daptomycin, a last-resort antibiotic, binds ribosomal protein S19 in humans. Proteome Sci., 2016, 15(1), 16.
[http://dx.doi.org/10.1186/s12953-017-0124-2] [PMID: 28680364]
[81]
Yamaguchi, D.; Imaizumi, T.; Yagi, K.; Matsumoto, Y.; Nakashima, T.; Hirose, A.; Kashima, N.; Nosaka, Y.; Hamada, T.; Okawa, K.; Nishiya, Y.; Kubo, K. Nicotinamide phosphoribosyltransferase is a molecular target of potent anticancer agents identified from phenotype-based drug screening. Sci. Rep., 2019, 9(1), 7742.
[http://dx.doi.org/10.1038/s41598-019-43994-x] [PMID: 31123329]
[82]
Bassiouni, R.; Nemec, K.N.; Iketani, A.; Flores, O.; Showalter, A.; Khaled, A.S.; Vishnubhotla, P.; Sprung, R.W., Jr; Kaittanis, C.; Perez, J.M.; Khaled, A.R. Chaperonin containing TCP-1 protein level in breast cancer cells predicts therapeutic application of a cytotoxic peptide. Clin. Cancer Res., 2016, 22(17), 4366-4379.
[http://dx.doi.org/10.1158/1078-0432.CCR-15-2502] [PMID: 27012814]
[83]
Kitagawa, M.; Liao, P.J.; Lee, K.H.; Wong, J.; Shang, S.C.; Minami, N.; Sampetrean, O.; Saya, H.; Lingyun, D.; Prabhu, N.; Diam, G.K.; Sobota, R.; Larsson, A.; Nordlund, P.; McCormick, F.; Ghosh, S.; Epstein, D.M.; Dymock, B.W.; Lee, S.H. Dual blockade of the lipid kinase PIP4Ks and mitotic pathways leads to cancer-selective lethality. Nat. Commun., 2017, 8(1), 2200.
[http://dx.doi.org/10.1038/s41467-017-02287-5] [PMID: 29259156]
[84]
Kitamura, K.; Itoh, H.; Sakurai, K.; Dan, S.; Inoue, M. Target identification of yaku’amide B and its two distinct activities against mitochondrial F0F1-ATP synthase. J. Am. Chem. Soc., 2018, 140(38), 12189-12199.
[http://dx.doi.org/10.1021/jacs.8b07339] [PMID: 30156840]
[85]
Dejonghe, W.; Sharma, I.; Denoo, B.; De Munck, S.; Lu, Q.; Mishev, K.; Bulut, H.; Mylle, E.; De Rycke, R.; Vasileva, M.; Savatin, D.V.; Nerinckx, W.; Staes, A.; Drozdzecki, A.; Audenaert, D.; Yperman, K.; Madder, A.; Friml, J.; Van Damme, D.; Gevaert, K.; Haucke, V.; Savvides, S.N.; Winne, J.; Russinova, E. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nat. Chem. Biol., 2019, 15(6), 641-649.
[http://dx.doi.org/10.1038/s41589-019-0262-1] [PMID: 31011214]
[86]
Takeuchi, T.; Schumacker, P.T.; Kozmin, S.A. Identification of fumarate hydratase inhibitors with nutrient-dependent cytotoxicity. J. Am. Chem. Soc., 2015, 137(2), 564-567.
[http://dx.doi.org/10.1021/ja5101257] [PMID: 25469852]
[87]
Arai, M.A.; Taguchi, S.; Komatsuzaki, K.; Uchiyama, K.; Masuda, A.; Sampei, M.; Satoh, M.; Kado, S.; Ishibashi, M. Valosin-containing protein is a target of 5′-l fuligocandin B and enhances trail resistance in cancer cells. ChemistryOpen, 2016, 5(6), 574-579.
[http://dx.doi.org/10.1002/open.201600081] [PMID: 28032027]
[88]
Cai, Y.; Zheng, Y.; Gu, J.; Wang, S.; Wang, N.; Yang, B.; Zhang, F.; Wang, D.; Fu, W.; Wang, Z. Betulinic acid chemosensitizes breast cancer by triggering ER stress-mediated apoptosis by directly targeting GRP78. Cell Death Dis., 2018, 9, 636.
[http://dx.doi.org/10.1038/s41419-018-0669-8]
[89]
Fung, S.K.; Zou, T.; Cao, B.; Lee, P.Y.; Fung, Y.M.E.; Hu, D.; Lok, C.N.; Che, C.M. Cyclometalated gold(III) complexes containing N-heterocyclic carbene ligands engage multiple anti-cancer molecular targets. Angew. Chem. Int. Ed., 2017, 56(14), 3892-3896.
[http://dx.doi.org/10.1002/anie.201612583] [PMID: 28247451]
[90]
Lim, B.; Lee, J.; Kim, B.; Lee, R.; Park, J.; Oh, D.C.; Gam, J.; Lee, J. Target identification of a 1,3,4-oxadiazin-5(6H)-one anticancer agent via photoaffinity labelling. Asian J. Org. Chem., 2019, 8(9), 1626-1630.
[http://dx.doi.org/10.1002/ajoc.201900258]
[91]
Liu, F.; Fitzgerald, M.C. Large-scale analysis of breast cancerrelated conformational changes in proteins using limited proteolysis. J. Proteome Res., 2016, 15(12), 4666-4674.
[http://dx.doi.org/10.1021/acs.jproteome.6b00755] [PMID: 27794609]
[92]
Tulloch, L.B.; Menzies, S.K.; Fraser, A.L.; Gould, E.R.; King, E.F.; Zacharova, M.K.; Florence, G.J.; Smith, T.K. Photo-affinity labelling and biochemical analyses identify the target of trypanocidal simplified natural product analogues. PLoS Negl. Trop. Dis., 2017, 11(9), e0005886.
[http://dx.doi.org/10.1371/journal.pntd.0005886] [PMID: 28873407]
[93]
Lubin, A.S.; Rueda-Zubiaurre, A.; Matthews, H.; Baumann, H.; Fisher, F.R.; Morales-Sanfrutos, J.; Hadavizadeh, K.S.; Nardella, F.; Tate, E.W.; Baum, J.; Scherf, A.; Fuchter, M.J. Development of a photo-cross-linkable diaminoquinazoline inhibitor for target identification in Plasmodium falciparum. ACS Infect. Dis., 2018, 4(4), 523-530.
[http://dx.doi.org/10.1021/acsinfecdis.7b00228] [PMID: 29377668]
[94]
Gaetani, M.; Sabatier, P.; Saei, A.A.; Beusch, C.M.; Yang, Z.; Lundström, S.L.; Zubarev, R.A. Proteome integral solubility alteration: A highthroughput proteomics assay for target deconvolution. J. Proteome Res., 2019, 18(11), 4027-4037.
[http://dx.doi.org/10.1021/acs.jproteome.9b00500] [PMID: 31545609]
[95]
Li, B.X.; Chen, J.; Chao, B.; David, L.L.; Xiao, X. Anticancer pyrroloquinazoline LBL1 targets nuclear lamins. ACS Chem. Biol., 2018, 13(5), 1380-1387.
[http://dx.doi.org/10.1021/acschembio.8b00266] [PMID: 29648791]
[96]
Zhu, D.; Guo, H.; Chang, Y.; Ni, Y.; Li, L.; Zhang, Z.M.; Hao, P.; Xu, Y.; Ding, K.; Li, Z. Cell- and tissue-based proteome profiling and dual imaging of apoptosis markers with probes derived from venetoclax and idasanutlin. Angew. Chem. Int. Ed., 2018, 57(30), 9284-9289.
[http://dx.doi.org/10.1002/anie.201802003] [PMID: 29768700]
[97]
Lee, K.; Ban, H.S.; Naik, R.; Hong, Y.S.; Son, S.; Kim, B.K.; Xia, Y.; Song, K.B.; Lee, H.S.; Won, M. Identification of malate dehydrogenase 2 as a target protein of the HIF-1 inhibitor LW6 using chemical probes. Angew. Chem. Int. Ed., 2013, 52(39), 10286-10289.
[http://dx.doi.org/10.1002/anie.201304987] [PMID: 23934700]
[98]
Lee, S.; Nam, Y.; Koo, J.Y.; Lim, D.; Park, J.; Ock, J.; Kim, J.; Suk, K.; Park, S.B. A small molecule binding HMGB1 and HMGB2 inhibits microglia-mediated neuroinflammation. Nat. Chem. Biol., 2014, 10(12), 1055-1060.
[http://dx.doi.org/10.1038/nchembio.1669] [PMID: 25306442]
[99]
Koh, M.; Park, J.; Koo, J.Y.; Lim, D.; Cha, M.Y.; Jo, A.; Choi, J.H.; Park, S.B. Phenotypic screening to identify small-molecule enhancers for glucose uptake: Target identification and rational optimization of their efficacy. Angew. Chem. Int. Ed., 2014, 53(20), 5102-5106.
[http://dx.doi.org/10.1002/anie.201310618] [PMID: 24692390]
[100]
Shenoy, V.M.; Thompson, B.R.; Shi, J.; Zhu, H.J.; Smith, D.E.; Amidon, G.L. Chemoproteomic identification of serine hydrolase RBBP9 as a valacyclovir-activating enzyme. Mol. Pharm., 2020, 17(5), 1706-1714.
[http://dx.doi.org/10.1021/acs.molpharmaceut.0c00131] [PMID: 32196348]

Rights & Permissions Print Cite
© 2025 Bentham Science Publishers | Privacy Policy