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Profiling the Proteome-Wide Selectivity of Diverse Electrophiles
Open accessPreprint — published as 10.1038/s41557-025-01902-z
Abstract
Targeted covalent inhibitors are powerful entities in drug discovery, but their application has so far mainly been limited to addressing cysteine residues. The development of cysteine-directed covalent inhibitors has largely profited from determining their proteome-wide selectivity using competitive residue-specific proteomics. Several probes have recently been described to monitor other amino acids using this technology and many more electrophiles exist to modify proteins. Nevertheless, a direct, proteome‑wide comparison of the selectivity of diverse probes is still entirely missing. Here, we developed a completely unbiased workflow to analyse electrophile selectivity proteome‑wide and applied it to directly compare 54 alkyne probes containing diverse reactive groups. In this way, we verified and newly identified probes to monitor a total of nine different amino acids as well as the N ‑terminus proteome‑wide. This selection includes the first probes to globally monitor tryptophans, histidines and arginines as well as novel tailored probes for methionines, aspartates and glutamates.
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“A recent preprint reported the use of a chemoproteomic approach to profile the amino acid reactivity preference of 54 different electrophiles, which will prove to be a great resource for covalent ligand discovery210.”
From Advances in covalent drug discovery (2022) · cites this paper as [210]
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Cites
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
Pérez-Riverol, Y., Csordas, A., Bai, J.-W., Bernal-Llinares, M., Hewapathirana, S., Kundu, D. J., Inuganti, A., Griss, J., Mayer, G., Eisenacher, M., et al. (2018) · Nucleic Acids Res. · doi:10.1093/nar/gky1106 · Cited by 6,216
Keller, A., Nesvizhskii, A., Kolker, E., & Aebersold, R. (2002) · Analytical Chemistry · doi:10.1021/ac025747h · Cited by 4,970
Self-citationA statistical model for identifying proteins by tandem mass spectrometry.
Nesvizhskii, A., Keller, A., Kolker, E., & Aebersold, R. (2003) · Analytical Chemistry · doi:10.1021/ac0341261 · Cited by 4,902
Self-citationMSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
Kong, A. T., Leprevost, F. D. V., Avtonomov, D. M., Mellacheruvu, D., & Nesvizhskii, A. I. (2017) · Nature Methods · doi:10.1038/nmeth.4256 · Cited by 2,406
Self-citationThe resurgence of covalent drugs
Singh, J., Petter, R. C., Baillie, T. A., & Whitty, A. (2011) · Nature Reviews Drug Discovery · doi:10.1038/nrd3410 · Cited by 1,873
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
Sulfur(VI) Fluoride Exchange (SuFEx): Another Good Reaction for Click Chemistry
Dong, J., Krasnova, L. B., Finn, M. G., & Sharpless, K. B. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201309399 · Cited by 1,431
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
Gehringer, M., & Laufer, S. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b01153 · Cited by 772
Horsburgh, M. J., Aish, J., White, I. J., Shaw, L., Lithgow, J. K., & Foster, S. J. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.19.5457-5467.2002 · Cited by 699
Philosopher: a versatile toolkit for shotgun proteomics data analysis
Leprevost, F. D. V., Haynes, S. E., Avtonomov, D. M., Chang, H.-Y., Shanmugam, A. K., Mellacheruvu, D., Kong, A. T., & Nesvizhskii, A. I. (2020) · Nature Methods · doi:10.1038/s41592-020-0912-y · Cited by 635
Self-citationRedox-based reagents for chemoselective methionine bioconjugation
Lin, S., Yang, X., Jia, S., Weeks, A. M., Hornsby, M. J., Lee, P. S., Nichiporuk, R. V., Iavarone, A. T., Wells, J. A., Toste, F. D., et al. (2017) · Science · doi:10.1126/science.aal3316 · Cited by 520
Self-citationpLogo: a probabilistic approach to visualizing sequence motifs
O'Shea, J. P., Chou, M. F., Quader, S., Ryan, J. K., Church, G. M., & Schwartz, D. (2013) · Nature Methods · doi:10.1038/nmeth.2646 · Cited by 491
Global profiling of lysine reactivity and ligandability in the human proteome
Hacker, S. M., Backus, K. M., Lazear, M. R., Forli, S., Correia, B. E., & Cravatt, B. F. (2017) · Nature Chemistry · doi:10.1038/nchem.2826 · Cited by 485
Self-citationChi, H., Liu, C., Yang, H., Zeng, W., Wu, L., Zhou, W., Wang, R., Niu, X.-N., Ding, Y., Zhang, Y., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4236 · Cited by 430
Click Chemistry in Proteomic Investigations
Parker, C. G., & Pratt, M. R. (2020) · Cell · doi:10.1016/j.cell.2020.01.025 · Cited by 392
Covalent inhibitors: a rational approach to drug discovery
Sutanto, F., Konstantinidou, M., & Dömling, A. (2020) · RSC Medicinal Chemistry · doi:10.1039/d0md00154f · Cited by 389
Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant
Yu, F., Haynes, S. E., Teo, G. C., Avtonomov, D. M., Polasky, D. A., & Nesvizhskii, A. I. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir120.002048 · Cited by 377
Self-citationTyrosine Bioconjugation through Aqueous Ene-Type Reactions: A Click-Like Reaction for Tyrosine
Ban, H., Gavrilyuk, J. I., & Barbas, C. F. (2010) · Journal of the American Chemical Society · doi:10.1021/ja909062q · Cited by 341
One-step site-specific modification of native proteins with 2-pyridinecarboxyaldehydes
MacDonald, J. I., Munch, H. K., Moore, T., & Francis, M. B. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1792 · Cited by 323
Unlocking P(V): Reagents for chiral phosphorothioate synthesis
Knouse, K. W., deGruyter, J. N., Schmidt, M. A., Zheng, B., Vantourout, J. C., Kingston, C., Mercer, S. E., McDonald, I. M., Olson, R. E., Zhu, Y., et al. (2018) · Science · doi:10.1126/science.aau3369 · Cited by 314
Chaudhuri, R. R., Allen, A. G., Owen, P., Shalom, G., Stone, K. M., Harrison, M., Burgis, T. A., Lockyer, M. J., Garcı́a-Lara, J., Foster, S. J., et al. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-291 · Cited by 309
Identification of modified peptides using localization-aware open search
Yu, F., Teo, G. C., Kong, A. T., Haynes, S. E., Avtonomov, D. M., Geiszler, D., & Nesvizhskii, A. I. (2020) · Nature Communications · doi:10.1038/s41467-020-17921-y · Cited by 289
Self-citationA protein functionalization platform based on selective reactions at methionine residues
Taylor, M. T., Nelson, J. E., Suero, M. G., & Gaunt, M. J. (2018) · Nature · doi:10.1038/s41586-018-0608-y · Cited by 288
Lysine‐Targeting Covalent Inhibitors
Pettinger, J., Jones, K., & Cheeseman, M. D. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201707630 · Cited by 250
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
Tamura, T., Ueda, T., Goto, T., Tsukidate, T., Shapira, Y., Nishikawa, Y., Fujisawa, A., & Hamachi, I. (2018) · Nature Communications · doi:10.1038/s41467-018-04343-0 · Cited by 242
Global targeting of functional tyrosines using sulfur-triazole exchange chemistry
Hahm, H. S., Toroitich, E. K., Borne, A. L., Brulet, J. W., Libby, A. H., Yuan, K., Ware, T. B., McCloud, R. L., Ciancone, A. M., & Hsu, K. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0404-5 · Cited by 232
Frei, R., Wodrich, M. D., Hari, D. P., Borin, P., Chauvier, C., & Waser, J. (2014) · Journal of the American Chemical Society · doi:10.1021/ja5083014 · Cited by 229
Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine
Teo, G. C., Polasky, D. A., Yu, F., & Nesvizhskii, A. I. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00544 · Cited by 217
Self-citationBan, H., Nagano, M., Gavrilyuk, J. I., Hakamata, W., Inokuma, T., & Barbas, C. F. (2013) · Bioconjugate Chemistry · doi:10.1021/bc300665t · Cited by 206
Rostovtsev, V. V., Green, L. G., Fokin, V. V., et al. (2002) · ChemInform · doi:10.1002/chin.200243045 · Cited by 159
Abegg, D., Frei, R., Cerato, L., Hari, D. P., Wang, C., Waser, J., & Adibekian, A. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201505641 · Cited by 158
NHS-Esters As Versatile Reactivity-Based Probes for Mapping Proteome-Wide Ligandable Hotspots
Ward, C. C., Kleinman, J. I., & Nomura, D. K. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00125 · Cited by 158
2H-Azirine-Based Reagents for Chemoselective Bioconjugation at Carboxyl Residues Inside Live Cells
Ma, N., Hu, J., Zhang, Z., Liu, W., Huang, M., Fan, Y., Yin, X., Wang, J., Ding, K., Ye, W., et al. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.9b12116 · Cited by 157
Tower, S. J., Hetcher, W. J., Myers, T. E., Kuehl, N. J., & Taylor, M. T. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.0c03039 · Cited by 154
Bioinspired Thiophosphorodichloridate Reagents for Chemoselective Histidine Bioconjugation
Jia, S., He, D., & Chang, C. J. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.8b11912 · Cited by 153
Self-citationGeiszler, D., Kong, A. T., Avtonomov, D. M., Yu, F., Leprevost, F. D. V., & Nesvizhskii, A. I. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir120.002216 · Cited by 152
Self-citationTunable Heteroaromatic Sulfones Enhance in-Cell Cysteine Profiling
Motiwala, H. F., Kuo, Y.-H., Stinger, B. L., Palfey, B. A., & Martin, B. R. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b08831 · Cited by 126
“Doubly Orthogonal” Labeling of Peptides and Proteins
Tessier, R., Ceballos, J., Guidotti, N., Simonet‐Davin, R., Fierz, B., & Waser, J. (2019) · Chem · doi:10.1016/j.chempr.2019.06.022 · Cited by 118
Guo, A., Wei, D., Nie, H., Hu, H., Peng, C., Li, S., Yan, K., Zhou, B.-S., Feng, L., Fang, C., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19274-y · Cited by 117
Zanon, P. R. A., Lewald, L., & Hacker, S. M. (2019) · Angewandte Chemie International Edition · doi:10.1002/anie.201912075 · Cited by 114
Self-citationBenns, H. J., Wincott, C. J., Tate, E. W., & Child, M. A. (2020) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2020.06.011 · Cited by 112
Liganding Functional Tyrosine Sites on Proteins Using Sulfur–Triazole Exchange Chemistry
Brulet, J. W., Borne, A. L., Yuan, K., Libby, A. H., & Hsu, K. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.0c00648 · Cited by 107
A Caged Electrophilic Probe for Global Analysis of Cysteine Reactivity in Living Cells
Abo, M., & Weerapana, E. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b04350 · Cited by 105
A Physical Organic Approach to Tuning Reagents for Selective and Stable Methionine Bioconjugation
Christian, A. H., Jia, S., Cao, W., Zhang, P., Meza, A. T., Sigman, M. S., Chang, C. J., & Toste, F. D. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b04744 · Cited by 102
Self-citationSerine-Selective Bioconjugation
Vantourout, J. C., Adusumalli, S. R., Knouse, K. W., Flood, D. T., Ramı́rez, A., Padial, N. M., Istrate, A., Maziarz, K., deGruyter, J. N., Merchant, R. R., et al. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.0c05595 · Cited by 99
Fu, L., Li, Z., Liu, K., Tian, C., He, J.-X., He, J., He, F., Xu, P., & Yang, J. H. (2020) · Nature Protocols · doi:10.1038/s41596-020-0352-2 · Cited by 88
Jones, A. X., Cao, Y., Tang, Y., Wang, J., Ding, Y., Tan, H., Chen, Z., Fang, R.-Q., Yin, J., Chen, R., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11917-z · Cited by 84
Ethynylation of Cysteine Residues: From Peptides to Proteins in Vitro and in Living Cells
Tessier, R., Nandi, R. K., Dwyer, B. G., et al. (2020) · Angewandte Chemie International Edition · doi:10.1002/anie.202002626 · Cited by 81
Rational Tuning of Fluorobenzene Probes for Cysteine‐Selective Protein Modification
Embaby, A. M., Schoffelen, S., Kofoed, C., Meldal, M., & Diness, F. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201712589 · Cited by 77
Bacterial Redox Potential Powers Controlled Radical Polymerization
Nothling, M. D., Cao, H., McKenzie, T. G., et al. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.0c10673 · Cited by 72
N-Terminal selective modification of peptides and proteins using 2-ethynylbenzaldehydes
Deng, J., Lai, N. C., Kung, K. K., et al. (2020) · Communications Chemistry · doi:10.1038/s42004-020-0309-y · Cited by 64
The Proteome‐Wide Potential for Reversible Covalency at Cysteine
Senkane, K., Vinogradova, E. V., Suciu, R. M., Crowley, V. M., Zaro, B. W., Bradshaw, J. M., Brameld, K. A., & Cravatt, B. F. (2019) · Angewandte Chemie International Edition · doi:10.1002/anie.201905829 · Cited by 56
Hirata, T., Kogiso, H., Morimoto, K., et al. (1998) · Bioorganic & Medicinal Chemistry · doi:10.1016/s0968-0896(98)00156-4 · Cited by 50
Dovgan, I., Erb, S., Hessmann, S., Ursuegui, S., Michel, C., Muller, C. D., Chaubet, G., Cianférani, S., & Wagner, A. (2018) · Organic & Biomolecular Chemistry · doi:10.1039/c7ob02844j · Cited by 49
Ivancová, I., Pohl, R., Hubálek, M., et al. (2019) · Angewandte Chemie International Edition · doi:10.1002/anie.201906737 · Cited by 49
Multiplexed CuAAC Suzuki–Miyaura Labeling for Tandem Activity-Based Chemoproteomic Profiling
Cao, J. X., Boatner, L. M., Desai, H. S., Burton, N. R., Armenta, E., Chan, N. J., Castellón, J. O., & Backus, K. M. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.0c04726 · Cited by 48
Crystal-C: A Computational Tool for Refinement of Open Search Results
Chang, H.-Y., Kong, A. T., Leprevost, F. D. V., Avtonomov, D. M., Haynes, S. E., & Nesvizhskii, A. I. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00119 · Cited by 47
Self-citationArginine selective reagents for ligation to peptides and proteins
Thompson, D. A., Ng, R., & Dawson, P. E. (2016) · Journal of Peptide Science · doi:10.1002/psc.2867 · Cited by 45
Dissolving Peptides in 0.1% Formic Acid Brings Risk of Artificial Formylation
Lenčo, J., Khalikova, M. A., & Švec, F. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00823 · Cited by 43
Abegg, D., Frei, R., Cerato, L., Hari, D. P., Wang, C., Waser, J., & Adibekian, A. (2015) · Angewandte Chemie · doi:10.1002/ange.201505641 · Cited by 40
Triazolecarbaldehyde Reagents for One‐Step N‐Terminal Protein Modification
Onoda, A., Inoue, N., Sumiyoshi, E., et al. (2019) · ChemBioChem · doi:10.1002/cbic.201900692 · Cited by 32
Co-opting a Bioorthogonal Reaction for Oncometabolite Detection
Zengeya, T. T., Garlick, J. M., Kulkarni, R. A., Miley, M., Roberts, A. M., Yang, Y., Crooks, D. R., Sourbier, C., Linehan, W. M., & Meier, J. L. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b09706 · Cited by 30
Zanon, P. R. A., Lewald, L., & Hacker, S. M. (2019) · Angewandte Chemie · doi:10.1002/ange.201912075 · Cited by 29
Self-citationAn efficient reagent for covalent introduction of alkynes into proteins
Zhang, J., Ma, D., Du, D., et al. (2014) · Organic & Biomolecular Chemistry · doi:10.1039/c4ob01873g · Cited by 28
Rational Tuning of Fluorobenzene Probes for Cysteine‐Selective Protein Modification
Embaby, A. M., Schoffelen, S., Kofoed, C., Meldal, M., & Diness, F. (2018) · Angewandte Chemie · doi:10.1002/ange.201712589 · Cited by 20
Lee, K. M., Le, P., Sieber, S. A., & Hacker, S. M. (2020) · Chemical Communications · doi:10.1039/c9cc09204h · Cited by 17
Self-citationThe Proteome‐Wide Potential for Reversible Covalency at Cysteine
Senkane, K., Vinogradova, E. V., Suciu, R. M., Crowley, V. M., Zaro, B. W., Bradshaw, J. M., Brameld, K. A., & Cravatt, B. F. (2019) · Angewandte Chemie · doi:10.1002/ange.201905829 · Cited by 16
A Physical Organic Approach to Tuning Reagents for Selective and Stable Methionine BioconjugationPreprint
Christian, A. H., Jia, S., Zhang, P., et al. (2019) · ChemRxiv · doi:10.26434/chemrxiv.8176823 · Cited by 10
Bach, K., Beerkens, B. L. H., Zanon, P. R. A., et al. (2019) · ChemRxiv · doi:10.26434/chemrxiv.11352101 · Cited by 7
Self-citationGeiszler, D. J., Kong, A. T., Avtonomov, D. M., et al. (2020) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.4042961 · Cited by 7
Rostovtsev, V. V., Green, L. G., Fokin, V. V., & Sharpless, K. B. (2002) · Angewandte Chemie International Edition · doi:10.1002/1521-3773(20020715)41:14
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Advances in covalent drug discovery
Boike, L., Henning, N. J., & Nomura, D. K. (2022) · Nature Reviews Drug Discovery · doi:10.1038/s41573-022-00542-z · Cited by 823
Metadata
- Authors
- Zanon, P. R. A., Yu, F., Musacchio, P., Lewald, L., Zollo, M., Krauskopf, K., Mrdović, D., Raunft, P., Maher, T. E., Cigler, M., Chang, C., Lang, K., Toste, F. D., Nesvizhskii, A. I., & Hacker, S. M.
- Affiliations
- Technical University of Munich (DE)
- University of Michigan (US)
- University of California, Berkeley (US)
- ORCID
- Venue
- ChemRxiv
- Publisher
- American Chemical Society (ACS)
- Published
- 2021-03-10
- ISSN
- 2573-2293 (ISSN-L)
- OpenAlex
- W3138203650
- Cited by
- 35
- References
- 74
- Citations by year
- 2025: 6 · 2024: 6 · 2023: 10 · 2022: 5 · 2021: 8
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- Royal College of Surgeons in Ireland (submittedVersion, cc-by-nc-nd)
- Funders
- American Cancer Society (PF-18-132-01-CDD)
- Deutsche Forschungsgemeinschaft (SFB 1035, Project B10, 201302640)
- École Polytechnique Fédérale de Lausanne
- Studienstiftung des Deutschen Volkes
- Technische Universität München
- National Institutes of Health
- Novartis Institutes for BioMedical Research
- National Cancer Institute (U24CA210967)
- National Institute of General Medical Sciences (R01GM139245, R01GM094231)
- National Institute of Environmental Health Sciences (R01ES028096)
- Topics
- Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
- Keywords
- covalent inhibitors, targeted covalent inhibitors, proteome-wide profiling, tryptophan, histidine, L-arginine, methionine, aspartic acid, glutamate, N-terminus, protein modification
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