Expanding the scope of electrophiles capable of targeting K-Ras oncogenes
Open accessAbstract
There is growing interest in reversible and irreversible covalent inhibitors that target noncatalytic amino acids in target proteins. With a goal of targeting oncogenic K-Ras variants (e.g., G12D) by expanding the types of amino acids that can be targeted by covalent inhibitors, we survey a set of electrophiles for their ability to label carboxylates. We functionalized an optimized ligand for the K-Ras switch II pocket with a set of electrophiles previously reported to react with carboxylates and characterized the ability of these compounds to react with model nucleophiles and oncogenic K-Ras proteins. Here, we report that aziridines and stabilized diazo groups preferentially react with free carboxylates over thiols. Although we did not identify a warhead that potently labels K-Ras G12D, we were able to study the interactions of many electrophiles with K-Ras, as most of the electrophiles rapidly label K-Ras G12C. We characterized the resulting complexes by crystallography, hydrogen/deuterium exchange, and differential scanning fluorimetry. Our results both demonstrate the ability of a noncatalytic cysteine to react with a diverse set of electrophiles and emphasize the importance of proper spatial arrangements between a covalent inhibitor and its intended nucleophile. We hope that these results can expand the range of electrophiles and nucleophiles of use in covalent protein modulation.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
KRAS G12D has a low GTP hydrolysis rate, which keeps it continuously active.
“Biologically, this mutation has a low GTP hydrolysis rate, which keeps it continuously active.”
From RAS Mutations in Advanced Colorectal Cancer: Mechanisms, Clinical Implications, and Novel Therapeutic Approaches (2025) · cites this paper as [96]
The Switch II pocket of KRAS G12D lacks the reactive residues required to form a strong covalent bond, making it difficult to target.
“In addition, the Switch II pocket of KRAS G12D lacks the reactive residues required to form a strong covalent bond, making it difficult to target [96].”
From RAS Mutations in Advanced Colorectal Cancer: Mechanisms, Clinical Implications, and Novel Therapeutic Approaches (2025) · cites this paper as [96]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
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 · see citing works
Self-citationHaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis
Los, G. V., Encell, L. P., McDougall, M. G., Hartzell, D., Karassina, N., Zimprich, C., Wood, M. G., Learish, R., Ohana, R. F., Urh, M., et al. (2008) · ACS Chemical Biology · doi:10.1021/cb800025k · Cited by 2,527 · see citing works
Niesen, F., Berglund, H., & Vedadi, M. (2007) · Nature Protocols · doi:10.1038/nprot.2007.321 · Cited by 2,420 · see citing works
A Comprehensive Survey of Ras Mutations in Cancer
Prior, I. A., Lewis, P. D., & Mattos, C. (2012) · Cancer Research · doi:10.1158/0008-5472.can-11-2612 · Cited by 2,063 · see citing works
The 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 · 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 inhibition of oncogenic KRAS output with small molecules targeting the inactive state
Patricelli, M. P., Janes, M. R., Li, L.-S., Hansen, R., Peters, U., Kessler, L. V., Chen, Y., Kucharski, J. M., Feng, J., Ely, T., et al. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-15-1105 · Cited by 759 · 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
Self-citationMaurer, T., Garrenton, L. S., Oh, A., Pitts, K., Anderson, D. J., Skelton, N. J., Fauber, B. P., Pan, B., Malek, S., Stokoe, D., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116510109 · Cited by 618 · see citing works
Targeted Covalent Inhibitors for Drug Design
Baillie, T. A. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201601091 · Cited by 578 · see citing works
Sulfonyl fluorides as privileged warheads in chemical biology
Narayanan, A., & Jones, L. H. (2015) · Chemical Science · doi:10.1039/c5sc00408j · Cited by 557 · see citing works
Redox-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 511 · see citing works
Discovery of Small Molecules that Bind to K‐Ras and Inhibit Sos‐Mediated Activation
Sun, Q., Burke, J. P., Phan, J., Burns, M. C., Olejniczak, E. T., Waterson, A. G., Lee, T., Rossanese, O. W., & Fesik, S. W. (2012) · Angewandte Chemie International Edition · doi:10.1002/anie.201201358 · Cited by 490 · see citing works
Self-citationTherapeutic Targeting of Oncogenic K‐Ras by a Covalent Catalytic Site Inhibitor
Lim, S. M., Westover, K. D., Ficarro, S. B., Harrison, R. A., Choi, H. G., Pacold, M. E., Carrasco, M., Hunter, J., Kim, N. D., Xie, T., et al. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201307387 · Cited by 300 · see citing works
An orthosteric inhibitor of the Ras-Sos interaction
Patgiri, A., Yadav, K. K., Arora, P. S., & Bar‐Sagi, D. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.612 · Cited by 294 · see citing works
Multivalent Small-Molecule Pan-RAS Inhibitors
Welsch, M., Kaplan, A. R., Chambers, J. M., Stokes, M. E., Bos, P. H., Zask, A., Zhang, Y., Sánchez-Martín, M., Badgley, M. A., Huang, C., et al. (2017) · Cell · doi:10.1016/j.cell.2017.02.006 · Cited by 273 · 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
Ligand-Directed Acyl Imidazole Chemistry for Labeling of Membrane-Bound Proteins on Live Cells
Fujishima, S., Yasui, R., Miki, T., et al. (2012) · Journal of the American Chemical Society · doi:10.1021/ja2108855 · Cited by 210 · see citing works
Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange
Burns, M. C., Sun, Q., Daniels, R. N., Camper, D., Kennedy, J. P., Phan, J., Olejniczak, E. T., Lee, T., Waterson, A. G., Rossanese, O. W., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1315798111 · Cited by 199 · see citing works
Drug discovery considerations in the development of covalent inhibitors
Mah, R., Thomas, J. R., & Shafer, C. M. (2013) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2013.10.003 · Cited by 197 · see citing works
Targeting biomolecules with reversible covalent chemistry
Bandyopadhyay, A., & Gao, J. (2016) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2016.08.011 · Cited by 143 · see citing works
Covalent Protein Labeling at Glutamic Acids
Martín‐Gago, P., Fansa, E. K., Winzker, M., Murarka, S., Janning, P., Schultz‐Fademrecht, C., Baumann, M., Wittinghofer, A., & Waldmann, H. (2017) · Cell chemical biology · doi:10.1016/j.chembiol.2017.03.015 · Cited by 100 · see citing works
Diazo compounds for the bioreversible esterification of proteins
McGrath, N. A., Andersen, K. A., Davis, A. K. F., Lomax, J. E., & Raines, R. T. (2014) · Chemical Science · doi:10.1039/c4sc01768d · Cited by 97 · see citing works
Covalent targeting of acquired cysteines in cancer
Visscher, M., Arkin, M. R., & Dansen, T. B. (2016) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2015.11.004 · Cited by 95 · see citing works
Optimized Diazo Scaffold for Protein Esterification
Mix, K. A., & Raines, R. T. (2015) · Organic Letters · doi:10.1021/acs.orglett.5b00840 · Cited by 91 · see citing works
Gallagher, E. S., & Hudgens, J. W. (2015) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2015.08.010 · Cited by 65 · see citing works
Structural Dynamics in Ras and Related Proteins upon Nucleotide Switching
Harrison, R. A., Lu, J., Carrasco, M. A., Hunter, J., Manandhar, A., Gondi, S. R., Westover, K. D., & Engen, J. R. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.10.017 · Cited by 37 · see citing works
Spontaneous formation of PMB esters using 4-methoxybenzyl-2,2,2-trichloroacetimidate
Shah, J. P., Russo, C. M., Howard, K. T., et al. (2014) · Tetrahedron Letters · doi:10.1016/j.tetlet.2014.01.097 · Cited by 23 · see citing works
Trzeciakiewicz, A., Fortin, S., Moreau, E., et al. (2011) · Biochemical Pharmacology · doi:10.1016/j.bcp.2011.02.014 · Cited by 2 · see citing works
Benedetti, F. M., Berti, F., Campaner, P., et al. (2014) · ACS Medicinal Chemistry Letters · doi:10.1021/ml500092e · Cited by 2 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Identification of MRTX1133, a Noncovalent, Potent, and Selective KRAS <sup>G12D</sup> Inhibitor
Wang, X., Allen, S., Blake, J. F., Bowcut, V., Briere, D. M., Calinisan, A., Dahlke, J. R., Fell, J. B., Fischer, J. P., Gunn, R. J., et al. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c01688 · Cited by 769 · see citing works
Structure-based design of targeted covalent inhibitors
Lonsdale, R., & Ward, R. A. (2018) · Chemical Society Reviews · doi:10.1039/c7cs00220c · Cited by 344 · see citing works
New Electrophiles and Strategies for Mechanism-Based and Targeted Covalent Inhibitor Design
Ray, S., & Murkin, A. S. (2019) · Biochemistry · doi:10.1021/acs.biochem.9b00293 · Cited by 108 · see citing works
Beyond cysteine: recent developments in the area of targeted covalent inhibition
Mukherjee, H., & Grimster, N. P. (2018) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2018.05.011 · Cited by 95 · see citing works
Sakamoto, K., Masutani, T., & Hirokawa, T. (2020) · Scientific Reports · doi:10.1038/s41598-020-78712-5 · Cited by 85 · see citing works
Development of covalent inhibitors: Principle, design, and application in cancer
Zheng, L., Li, Y., Wu, D., Xiao, H., Zheng, S., Wang, G., & Sun, Q. (2023) · MedComm – Oncology · doi:10.1002/mog2.56 · Cited by 71 · see citing works
Sakamoto, K., Qi, Y., & Miyako, E. (2023) · Scientific Reports · doi:10.1038/s41598-023-27825-8 · Cited by 14 · see citing works
Sütcüoğlu, O., Yıldırım, H. Ç., Almuradova, E., Günenç, D., & Yalçın, Ş. (2025) · Medicina · doi:10.3390/medicina61071202 · Cited by 10 · see citing works
- Authors
- McGregor, L. M., Jenkins, M. L., Kerwin, C., Burke, J. E., & Shokat, K. M.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of Victoria (CA)
- Corresponding author
- Shokat, Kevan M.
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2017-06-16
- Volume
- 56
- Issue
- 25
- Pages
- 3178-3183
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- PMC
- PMC5665167
- OpenAlex
- W2626406025
- Cited by
- 97
- References
- 31
- Citations by year
- 2026: 10 · 2025: 14 · 2024: 15 · 2023: 8 · 2022: 12 · 2021: 8 · 2020: 15 · 2019: 7 · 2018: 6 · 2017: 2
- FWCI
- 3.35
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Biochemistry (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- U.S. Department of Health and Human Services (5R01CA190408)
- Entertainment Industry Foundation (SU2C-AACR-DT17-15)
- American Cancer Society (PF-15-104-01-CDD)
- Government of Canada (NSERC-2014-05218)
- Pancreatic Cancer Action Network, NCI Frederick National Laboratory for Cancer Research KRAS Fellowship (15-25-40-McGregor)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
- Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- KRAS, G12D mutation, covalent inhibitors, electrophiles, aziridines, diazo group, switch-II pocket, reversible covalent inhibitors, protein-ligand interactions, hydrogen-deuterium exchange
- MeSH terms
- Aziridines, Carboxylic Acids, Humans, Oncogenes, Protein Conformation, Sulfhydryl Compounds, Proto-Oncogene Proteins p21(ras)
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
