The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
Proteome-wide covalent ligand discovery in native biological systems
Open accessAbstract
Small molecules are powerful tools for investigating protein function and can serve as leads for new therapeutics. Most human proteins, however, lack small-molecule ligands, and entire protein classes are considered 'undruggable'. Fragment-based ligand discovery can identify small-molecule probes for proteins that have proven difficult to target using high-throughput screening of complex compound libraries. Although reversibly binding ligands are commonly pursued, covalent fragments provide an alternative route to small-molecule probes, including those that can access regions of proteins that are difficult to target through binding affinity alone. Here we report a quantitative analysis of cysteine-reactive small-molecule fragments screened against thousands of proteins in human proteomes and cells. Covalent ligands were identified for >700 cysteines found in both druggable proteins and proteins deficient in chemical probes, including transcription factors, adaptor/scaffolding proteins, and uncharacterized proteins. Among the atypical ligand-protein interactions discovered were compounds that react preferentially with pro- (inactive) caspases. We used these ligands to distinguish extrinsic apoptosis pathways in human cell lines versus primary human T cells, showing that the former is largely mediated by caspase-8 while the latter depends on both caspase-8 and -10. Fragment-based covalent ligand discovery provides a greatly expanded portrait of the ligandable proteome and furnishes compounds that can illuminate protein functions in native biological systems.
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In the citing paper
“Although human CASP10 shares some degree of substrate specificity with CASP8 [317] and possibly contributes to extrinsic apoptosis in primary T cells [318]”
From Molecular mechanisms of cell death: recommendations of the nomenclature committee on cell death 2018. (2018) · cites this paper as [318]
In the citing paper
“Covalent inhibitors have been reported to achieve high efficiency through forming covalent bonds with cysteine or other nucleophilic residues in the target protein.”
From The design and development of covalent protein-protein interaction inhibitors for cancer treatment (2020) · cites this paper as [53]
In the citing paper
“Reactive cysteine residues on proteins have high nucleophilicity, which enables covalent binding with electrophilic small molecules [53, 54].”
From The design and development of covalent protein-protein interaction inhibitors for cancer treatment (2020) · cites this paper as [53]
In the citing paper
“In this study, more than 700 ligandable cysteines were identified, and information was provided about the proteome-wide selectivity of each covalent fragment in the library.”
From Advances in covalent drug discovery (2022) · cites this paper as [180]
In the citing paper
“The use of competitive isoTOP-ABPP was expanded to identify proteome-wide targets of a small covalent fragment library by competing individual acrylamide and chloroacetamide fragments against an iodoacetamide–alkyne probe180.”
From Advances in covalent drug discovery (2022) · cites this paper as [180]
In the citing paper
“showing that this approach can rapidly identify compounds that target proteins of biological interest.”
From Advances in covalent drug discovery (2022) · cites this paper as [180]
In the citing paper
“The covalent ligands discovered with this approach and their corresponding ligandable sites were used to help elucidate the role of caspase 8 and caspase 10 in extrinsic apoptosis in T cells”
From Advances in covalent drug discovery (2022) · cites this paper as [180]
In the citing paper
“We finally observed limited overlap of enantioprobe targets with proteins that demonstrated ligandability in previous chemical proteomic studies using cysteine-26,27 or lysine-reactive28 electrophilic fragments (Fig. 3b)”
From Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs (2019) · cites this paper as [26]
In the citing paper
“prior to further processing using a well-validated method for covalent ligand target identification—isotopic tandem orthogonal proteolysis ABPP (isoTOP-ABPP) 2,17,26.”
From Manumycin polyketides act as molecular glues between UBR7 and P53 (2020) · cites this paper as [2]
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Citations
Cites
NIH Image to ImageJ: 25 years of image analysis
Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012) · Nature Methods · doi:10.1038/nmeth.2089 · Cited by 64,638
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21256 · Cited by 26,294
Self-citationBLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Open Babel: An open chemical toolbox
O'Boyle, N. M., Banck, M. S., James, C. A. J., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011) · Journal of Cheminformatics · doi:10.1186/1758-2946-3-33 · Cited by 10,745
The I-TASSER Suite: protein structure and function prediction
Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015) · Nature Methods · doi:10.1038/nmeth.3213 · Cited by 5,596
UniProt: a hub for protein information
The UniProt Consortium (2015) · Nucleic Acids Research · doi:10.1093/nar/gku989 · Cited by 5,106
Hopkins, A. L., & Groom, C. R. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd892 · Cited by 3,305
K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions
Ostrem, J. M., Peters, U., Sos, M. L., Wells, J. A., & Shokat, K. M. (2013) · Nature · doi:10.1038/nature12796 · Cited by 2,557
DrugBank 4.0: shedding new light on drug metabolism
Law, V., Knox, C., Djoumbou-Feunang, Y., Jewison, T., Guo, A. C., Liu, Y., Maciejewski, A., Arndt, D., Wilson, M., Neveu, V., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1068 · Cited by 1,995
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Items 901–953 of 953
Kamoshita, S., & Sakurai, K. (2026) · ChemistryEurope · doi:10.1002/ceur.70328
“Recently, their use has expanded to include proximity - dependent crosslinking in covalent drug discovery [10–14], fragment - based screening [15], ligand - directed chemistry [2, 16], and reactivity - based protein profiling [11, 17, 18].”
Waters, J. E., Wilders, H., Biggs, G. S., Kintzel, M., Cawood, E. E., Bailey, J., Maslen, S., Yip, Y. M., Wakley, M., Riziotis, I. G., et al. (2026) · Angewandte Chemie · doi:10.1002/ange.8867549
Sobral, P. J. M., Oliveira, R., Marín, S., Cascante, M., & Salvador, J. A. R. (2026) · RSC Medicinal Chemistry · doi:10.1039/d6md00432f
Zeng, Q., Yang, J., & He, D. (2026) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2026.102732
Liu, Y., Zi, Y., Jiang, Z., Xin, L., Zhang, Y., Wang, Y., Lü, J., & Chen, Z. (2026) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2026.110316
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Sadagopan, A., Sodhi, A., & Gibson, W. J. (2026) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6c00249
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Ren, Y., Mou, M., 朱怡淼, Pan, Z., Zhang, K., Qian, Y., Zhang, Y., Li, J., Fu, T., & Zhu, F. (2026) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6c01911
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Huang, Y., Hou, L., Zhu, L., Xi, Y., & Li, G. (2026) · STAR Protocols · doi:10.1016/j.xpro.2026.104786
Zhang, X., Zhang, W., You, J., Xing, X., & Shao, X. (2026) · Environmental Science & Technology · doi:10.1021/acs.est.6c02754
Li, Z., Ware, M. L., Gingrich, P. W., Al‐Lazikani, B., & Hsu, K. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.6c07487
Hsu, C.-P., Desgagné, M., Rössler, S. L., Grob, N. M., Farquhar, C. E., Loas, A., Jensvold, Z. D., Baddock, H. T., Bratkowski, M. A., Nile, A. H., et al. (2026) · Chemical Science · doi:10.1039/d6sc05323h
Shuken, S. R., Frere, G. A., Beard, C. R., McGann, C. D., Canterbury, J. D., Zuniga, N. R., Gassaway, B. M., Dawson, S. L., Ooi, K. H., Paulo, J. A., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-76929-y · Cited by 1
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Kim, J., Correy, G. J., Hall, B. W., Rachman, M. M., Mailhot, O., Togo, T., Gonciarz, R. L., Jaishankar, P., Neitz, R. J., Hantz, E. R., et al. (2026) · eLife · doi:10.7554/elife.110475.2
Pan, Z., Qin, Z., Qian, Z., Han, G., Sun, M., Bian, Y., 金廷橞, Yin, Y., Zhang, Y., Wang, Z., et al. (2026) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6c02041
Chemoproteomics in covalent cancer drug discovery
Ong, J.-P., Dalziel, M., Johns, D., Zhu, J., & Bertoldo, J. B. (2026) · Drug Discovery Today · doi:10.1016/j.drudis.2026.104817
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El-sagheir, A. M. K. (2026) · ChemMedChem · doi:10.1002/cmdc.70516
Kamiyama, H., Onizawa, Y., Kubara, K., Matsumoto, Y., Sagane, K., Gotoda, M., Miyazaki, T., Suzuki, Y., Kotake, Y., Takase, Y., et al. (2026) · ChemBioChem · doi:10.1002/cbic.70556
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Liu, K., Wang, M., Sun, L., Li, N., Chen, W., Tian, C., Chen, Y., Bai, Y., Jiang, P., Fu, L., et al. (2026) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2026.09.030
Altahla, R., Wang, Z., Rong, S., Li, C., Jadgal, N., Mehran, M. J., Bolideei, M., & Alshorman, J. (2026) · Clinical and Translational Discovery · doi:10.1002/ctd2.70223
Shi, X., & Zhang, J. (2026) · Nature Chemical Biology · doi:10.1038/s41589-026-02326-7
Adekola, P. A., Edo, G. I., Akpo, M. O., Orogu, J. O., Makia, R. S., Oghroro, E. E. A., Akpoghelie, P. O., Owheruo, J. O., Yousif, E., Jikah, A. N., et al. (2026) · Ecological Genetics and Genomics · doi:10.1016/j.egg.2026.100551
Long, Y., Yu, T., Sun, J., Hu, J., & Bai, W. (2026) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.6c07262
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Ting, Y. U., & Mingliang, Y. E. (2026) · Analysis and Testing Technology and Instruments · doi:10.3724/j.1006-3757.2026.05.003
BindingDB Entry 50017954: PROTACs to address the challenges facing small molecule inhibitors.
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BindingDB (2021) · UC San Diego · doi:10.7270/q2028vtf
BindingDB Entry 50010106: Fragment-to-Lead Medicinal Chemistry Publications in 2017.
BindingDB (2021) · UC San Diego · doi:10.7270/q22b92hn
BindingDB Entry 50015871: Advanced approaches of developing targeted covalent drugs.
BindingDB (2023) · UC San Diego · doi:10.7270/q2df6w53
BindingDB (2024) · UC San Diego · doi:10.7270/q2vq374f
BindingDB Entry 50023340: Size-Dependent Target Engagement of Covalent Probes.
BindingDB (2026) · UC San Diego · doi:10.7270/q2cr609x
BindingDB (2024) · UC San Diego · doi:10.7270/q2dv1q4t
BindingDB (2024) · UC San Diego · doi:10.7270/q2t72nnm
BindingDB (2024) · UC San Diego · doi:10.7270/q2zk5n38
Xiao, J., Mu, L., Zang, Y., & Zhang, D.-M. (2026) · Journal of Asian Natural Products Research · doi:10.1080/10286020.2026.2748980
Metadata
- Authors
- 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., Wolan, D. W., & Cravatt, B. F.
- Affiliations
- Scripps Research Institute (US)
- Corresponding author
- Backus, Keriann M.
- Cravatt, Benjamin F.
- ORCID
- Venue
- Nature
- Published
- 2016-06-15
- Volume
- 534
- Issue
- 7608
- Pages
- 570-574
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4919207
- OpenAlex
- W2430132928
- Cited by
- 940
- References
- 43
- Citations by year
- 2026: 109 · 2025: 114 · 2024: 114 · 2023: 134 · 2022: 82 · 2021: 94 · 2020: 87 · 2019: 69 · 2018: 61 · 2017: 54 · 2016: 18
- FWCI
- 31.01
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Cancer Institute (CA-087660, R37CA087660, R01CA087660)
- National Institute of General Medical Sciences (GM069832, GM-090294, GM108208, R01GM090294, F32GM108208, R01GM069832)
- 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 ligands, chemical probes, undruggable proteins, transcription factors, caspase-8, caspase-10, extrinsic apoptotic pathway, T cells, protein function
- MeSH terms
- Cells, Cultured, Cysteine, Drug Evaluation, Preclinical, Enzyme Precursors, Humans, Ligands, Peptide Fragments, T-Lymphocytes, Transcription Factors, Apoptosis, Proteome, Caspase 8, Caspase 10, Small Molecule Libraries
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