NHS-Esters As Versatile Reactivity-Based Probes for Mapping Proteome-Wide Ligandable Hotspots
Open accessAbstract
Most of the proteome is considered undruggable, oftentimes hindering translational efforts for drug discovery. Identifying previously unknown druggable hotspots in proteins would enable strategies for pharmacologically interrogating these sites with small molecules. Activity-based protein profiling (ABPP) has arisen as a powerful chemoproteomic strategy that uses reactivity-based chemical probes to map reactive, functional, and ligandable hotspots in complex proteomes, which has enabled inhibitor discovery against various therapeutic protein targets. Here, we report an alkyne-functionalized N-hydroxysuccinimide-ester (NHS-ester) as a versatile reactivity-based probe for mapping the reactivity of a wide range of nucleophilic ligandable hotspots, including lysines, serines, threonines, and tyrosines, encompassing active sites, allosteric sites, post-translational modification sites, protein interaction sites, and previously uncharacterized potential binding sites. Surprisingly, we also show that fragment-based NHS-ester ligands can be made to confer selectivity for specific lysine hotspots on specific targets including Dpyd, Aldh2, and Gstt1. We thus put forth NHS-esters as promising reactivity-based probes and chemical scaffolds for covalent ligand discovery.
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IsoTOP-ABPP experiments using several lysine-directed probes have proved powerful in profiling lysine reactivity across the proteome.
“IsoTOP-ABPP experiments using several lysine-directed probes have proved powerful in profiling lysine reactivity across the proteome200,201.”
From Advances in covalent drug discovery (2022) · cites this paper as [201]
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Cites
Phthalimide conjugation as a strategy for in vivo target protein degradation
Winter, G. E., Buckley, D. L., Paulk, J., Roberts, J. M., Souza, A., Dhe-Paganon, S., & Bradner, J. E. (2015) · Science · doi:10.1126/science.aab1433 · Cited by 1,760 · see citing works
Quantitative reactivity profiling predicts functional cysteines in proteomes
Weerapana, E., Wang, C., Simon, G. M., Richter, F., Khare, S., Dillon, M. B. D., Bachovchin, D. A., Mowen, K., Baker, D., & Cravatt, B. F. (2010) · Nature · doi:10.1038/nature09472 · Cited by 1,684 · see citing works
SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways
Park, J., Chen, Y., Tishkoff, D. X., Peng, C., Tan, M., Dai, L., Xie, Z., Zhang, Y., Zwaans, B. M. M., Skinner, M. E., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.06.001 · Cited by 1,000 · see citing works
Proteome-wide covalent ligand discovery in native biological systems
Backus, K. M., Correia, B. E., Lum, K. M., Forli, S., Horning, B. D., González-Páez, G. E., Chatterjee, S., Lanning, B. R., Teijaro, J. R., Olson, A. J., et al. (2016) · Nature · doi:10.1038/nature18002 · Cited by 940 · see citing works
Selective blockade of 2-arachidonoylglycerol hydrolysis produces cannabinoid behavioral effects
Long, J. Z., Li, W., Booker, L., Burston, J. J., Kinsey, S. G., Schlosburg, J. E., Pavón, F. J., Serrano, A., Selley, D. E., Parsons, L. H., et al. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.129 · Cited by 938 · see citing works
Developing Irreversible Inhibitors of the Protein Kinase Cysteinome
Liu, Q., Sabnis, Y. A., Zhao, Z., Zhang, T., Buhrlage, S. J., Jones, L. H., & Gray, N. S. (2013) · Chemistry & Biology · doi:10.1016/j.chembiol.2012.12.006 · Cited by 662 · see citing works
Direct small-molecule inhibitors of KRAS: from structural insights to mechanism-based design
Ostrem, J. M. L., & Shokat, K. M. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.139 · Cited by 641 · see citing works
Modular PROTAC design for the degradation of oncogenic BCR-ABL
Lai, A. C., Toure, M., Hellerschmied, D., Salami, J., Jaime‐Figueroa, S., Ko, E., Hines, J., & Crews, C. M. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201507634 · Cited by 618 · see citing works
Targeted protein degradation by PROTACs
Neklesa, T. K., Winkler, J. D., & Crews, C. M. (2017) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2017.02.027 · Cited by 599 · see citing works
Mechanism-Based Profiling of Enzyme Families
Evans, M. J., & Cravatt, B. F. (2006) · Chemical Reviews · doi:10.1021/cr050288g · Cited by 568 · see citing works
The Aldo-Keto Reductase Superfamily and its Role in Drug Metabolism and Detoxification
Barski, O. A., Tipparaju, S. M., & Bhatnagar, A. (2008) · Drug Metabolism Reviews · doi:10.1080/03602530802431439 · Cited by 543 · see citing works
Activity-based protein profiling for biochemical pathway discovery in cancer
Nomura, D. K., Dix, M. M., & Cravatt, B. F. (2010) · Nature reviews. Cancer · doi:10.1038/nrc2901 · Cited by 342 · see citing works
Self-citationChemical cross‐linking with NHS esters: a systematic study on amino acid reactivities
Mädler, S., Bich, C., Touboul, D., & Zenobi, R. (2009) · Journal of Mass Spectrometry · doi:10.1002/jms.1544 · Cited by 306 · see citing works
Covalent docking of large libraries for the discovery of chemical probes
London, N., Miller, R. M., Krishnan, S., Uchida, K., Irwin, J. J., Eidam, O., Gibold, L., Cimermančič, P., Bonnet, R., Shoichet, B. K., et al. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1666 · Cited by 274 · see citing works
Disparate proteome reactivity profiles of carbon electrophiles
Weerapana, E., Simon, G. M., & Cravatt, B. F. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.91 · Cited by 246 · see citing works
Covalent protein modification: the current landscape of residue-specific electrophiles
Shannon, D. A., & Weerapana, E. (2014) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2014.10.021 · Cited by 234 · see citing works
Diverse Functional Roles of Reactive Cysteines
Pace, N. J., & Weerapana, E. (2012) · ACS Chemical Biology · doi:10.1021/cb3005269 · Cited by 205 · see citing works
Glycine N-Methyltransferase and Regulation of S-Adenosylmethionine Levels
Luka, Z., Mudd, S. H., & Wagner, C. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.r109.019273 · Cited by 192 · see citing works
Investigating the Proteome Reactivity and Selectivity of Aryl Halides
Shannon, D. A., Banerjee, R., Webster, E. R., Bak, D. W., Wang, C., & Weerapana, E. (2014) · Journal of the American Chemical Society · doi:10.1021/ja4116204 · Cited by 143 · see citing works
Review: Annexin-A5 and cell membrane repair
Bouter, A., Carmeille, R., Gounou, C., Bouvet, F., Degrelle, S. A., Evain‐Brion, D., & Brisson, A. R. (2015) · Placenta · doi:10.1016/j.placenta.2015.01.193 · Cited by 118 · see citing works
Identifying druggable disease-modifying gene products
Dixon, S. J., & Stockwell, B. R. (2009) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2009.08.003 · Cited by 117 · see citing works
Profilin1 biology and its mutation, actin(g) in disease
Alkam, D., Feldman, E. Z., Singh, A., & Kiaei, M. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2372-1 · Cited by 114 · see citing works
Chemoproteomic Screening of Covalent Ligands Reveals UBA5 As a Novel Pancreatic Cancer Target
Roberts, A. M., Miyamoto, D. K., Huffman, T. R., Bateman, L. A., Ives, A. N., Akopian, D., Heslin, M. J., Contreras, C. M., Rapé, M., Skibola, C. F., et al. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00020 · Cited by 113 · see citing works
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Chang, J. W., Nomura, D. K., & Cravatt, B. F. (2011) · Chemistry & Biology · doi:10.1016/j.chembiol.2011.02.008 · Cited by 98 · see citing works
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Cox, T. M. (1994) · The FASEB Journal · doi:10.1096/fasebj.8.1.8299892 · Cited by 98 · see citing works
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Ford, B., Bateman, L. A., Gutierrez-Palominos, L., Park, R., & Nomura, D. K. (2017) · Cell chemical biology · doi:10.1016/j.chembiol.2016.12.013 · Cited by 96 · see citing works
Self-citationLorentzen, E., Siebers, B., Hensel, R., et al. (2005) · Biochemistry · doi:10.1021/bi048192o · Cited by 75 · see citing works
Bateman, L. A., Nguyen, T., Roberts, A. M., Miyamoto, D. K., Ku, W.-M., Huffman, T. R., Petri, Y. D., Heslin, M. J., Contreras, C. M., Skibola, C. F., et al. (2017) · Chemical Communications · doi:10.1039/c7cc01480e · Cited by 73 · see citing works
Self-citationNucleoside diphosphate kinase as protein histidine kinase
Attwood, P. V., & Wieland, T. (2014) · Naunyn-Schmiedeberg s Archives of Pharmacology · doi:10.1007/s00210-014-1003-3 · Cited by 59 · see citing works
Chang, J. W., Zuhl, A. M., Speers, A. E., et al. (2015) · ACS Chemical Biology · doi:10.1021/cb500893q · Cited by 51 · see citing works
Medina-Cleghorn, D. A., Bateman, L. A., Ford, B., Heslin, A., Fisher, K. J., Dalvie, E. D., & Nomura, D. K. (2015) · Chemistry & Biology · doi:10.1016/j.chembiol.2015.09.008 · Cited by 49 · see citing works
Self-citationPeptide Biotinylation with Amine-Reactive Esters: Differential Side Chain Reactivity
Miller, B. T., Collins, T. J., Rogers, M. E., et al. (1997) · Peptides · doi:10.1016/s0196-9781(97)00225-8 · Cited by 44 · see citing works
Mapping proteome-wide interactions of reactive chemicals using chemoproteomic platforms
Counihan, J. L., Ford, B., & Nomura, D. K. (2015) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2015.11.007 · Cited by 40 · see citing works
Self-citationCounihan, J. L., Duckering, M., Dalvie, E. D., Ku, W.-M., Bateman, L. A., Fisher, K. J., & Nomura, D. K. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.6b01001 · Cited by 29 · see citing works
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Spradlin, J. N., Hu, X., Ward, C. C., Brittain, S. M., Jones, M. D., Ou, L., To, M., Proudfoot, A., Ornelas, E., Woldegiorgis, M., et al. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0304-8 · Cited by 432 · see citing works
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- Authors
- Ward, C. C., Kleinman, J. I., & Nomura, D. K.
- Affiliations
- University of California, Berkeley (US)
- Corresponding author
- Nomura, Daniel K.
- Venue
- ACS Chemical Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2017-05-01
- Volume
- 12
- Issue
- 6
- Pages
- 1478-1483
- ISSN
- 1554-8929 (ISSN-L)
- 1554-8937
- PMC
- PMC7771572
- OpenAlex
- W2609087524
- Cited by
- 158
- References
- 35
- Citations by year
- 2026: 16 · 2025: 16 · 2024: 25 · 2023: 25 · 2022: 10 · 2021: 27 · 2020: 11 · 2019: 14 · 2018: 8 · 2017: 6
- FWCI
- 4.45
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- ACS Chemical Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Cancer Institute (R01CA172667)
- U.S. Department of Defense (CDMRP W81XWH-15-1-0050)
- American Cancer Society (RSG14-242-01-TBE)
- Topics
- Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- NHS ester, activity-based protein profiling, chemoproteomics, lysine reactivity, covalent inhibitors, dihydropyrimidine dehydrogenase, ALDH2, GSTT1, post-translational modification sites, allosteric site
- MeSH terms
- Aldehyde Dehydrogenase, Mitochondrial, Alkynes, Binding Sites, Esters, Glutathione Transferase, Humans, Ligands, Lysine, Succinimides, Molecular Probes, Proteome
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