Monoacidic Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1:NRF2) Protein–Protein Interaction with High Cell Potency Identified by Fragment-Based Discovery
Abstract
KEAP1 is the key regulator of the NRF2-mediated cytoprotective response, and increasingly recognized as a target for diseases involving oxidative stress. Pharmacological intervention has focused on molecules that decrease NRF2-ubiquitination through covalent modification of KEAP1 cysteine residues, but such electrophilic compounds lack selectivity and may be associated with off-target toxicity. We report here the first use of a fragment-based approach to directly target the KEAP1 Kelch-NRF2 interaction. X-ray crystallographic screening identified three distinct "hot-spots" for fragment binding within the NRF2 binding pocket of KEAP1, allowing progression of a weak fragment hit to molecules with nanomolar affinity for KEAP1 while maintaining drug-like properties. This work resulted in a promising lead compound which exhibits tight and selective binding to KEAP1, and activates the NRF2 antioxidant response in cellular and in vivo models, thereby providing a high quality chemical probe to explore the therapeutic potential of disrupting the KEAP1-NRF2 interaction.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The text we found for this paper looks like another document, so the self-check wasn’t run.
Cites
Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method
Livak, K. J., & Schmittgen, T. D. (2001) · Methods · doi:10.1006/meth.2001.1262 · Cited by 180,860 · see citing works
<i>Coot</i> : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571 · see citing works
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
Murshudov, G. N., Vagin, A. A., & Dodson, E. J. (1997) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444996012255 · Cited by 14,671 · see citing works
Itoh, K., Chiba, T., Takahashi, S., Ishii, T., Igarashi, K., Katoh, Y., Oyake, T., Hayashi, N., Satoh, K., Hatayama, I., et al. (1997) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.1997.6943 · Cited by 3,999 · see citing works
Cell Survival Responses to Environmental Stresses Via the Keap1-Nrf2-ARE Pathway
Kensler, T. W., Wakabayashi, N., & Biswal, S. (2007) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.46.120604.141046 · Cited by 3,630 · see citing works
Dinkova-Kostova, A. T., Holtzclaw, W. D., Cole, R. N., Itoh, K., Wakabayashi, N., Katoh, Y., Yamamoto, M., & Talalay, P. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.172398899 · Cited by 1,947 · see citing works
Zhang, D. D., & Hannink, M. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.22.8137-8151.2003 · Cited by 1,480 · see citing works
Keap1 Is a Redox-Regulated Substrate Adaptor Protein for a Cul3-Dependent Ubiquitin Ligase Complex
Zhang, D. D., Lo, S., Cross, J. V., Templeton, D. J., & Hannink, M. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.24.10941-10953.2004 · Cited by 1,262 · see citing works
Linker, R. A., Lee, D.-H., Ryan, S., van Dam, A. M., Conrad, R., Bista, P., Zeng, W., Hronowsky, X., Buko, A., Chollate, S., et al. (2011) · Brain · doi:10.1093/brain/awq386 · Cited by 1,155 · see citing works
Genetic ablation of Nrf2 enhances susceptibility to cigarette smoke–induced emphysema in mice
Rangasamy, T., Cho, C. Y., Thimmulappa, R. K., Zhen, L., Srisuma, S., Kensler, T. W., Yamamoto, M. P., Petrache, I., Tuder, R. M., & Biswal, S. S. (2004) · Journal of Clinical Investigation · doi:10.1172/jci21146 · Cited by 993 · see citing works
Wakabayashi, N., Dinkova-Kostova, A. T., Holtzclaw, W. D., Kang, M.-I., Kobayashi, A., Yamamoto, M., Kensler, T. W., & Talalay, P. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307301101 · Cited by 986 · see citing works
Cullinan, S. B., Gordan, J. D., Jin, J., Harper, J. W., & Diehl, J. A. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.19.8477-8486.2004 · Cited by 986 · see citing works
Bardoxolone Methyl and Kidney Function in CKD with Type 2 Diabetes
Pergola, P. E., Raskin, P., Toto, R. D., Meyer, C. J., Huff, J. W., Grossman, E. B., Krauth, M., Ruiz, S., Audhya, P., Christ-Schmidt, H., et al. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1105351 · Cited by 890 · see citing works
Tong, K. I., Katoh, Y., Kusunoki, H., Itoh, K., Tanaka, T., & Yamamoto, M. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.26.8.2887-2900.2006 · Cited by 759 · see citing works
Structural basis for defects of Keap1 activity provoked by its point mutations in lung cancer
Padmanabhan, B., Tong, K. I., Ohta, T., Nakamura, Y., Scharlock, M., Ohtsuji, M., Kang, M.-I., Kobayashi, A., Yokoyama, S., & Yamamoto, M. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.01.013 · Cited by 735 · see citing works
Functional antioxidant responsive elements
Wasserman, W. W., & Fahl, W. E. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.10.5361 · Cited by 705 · see citing works
Emerging roles of Nrf2 and phase II antioxidant enzymes in neuroprotection
Zhang, M., An, C., Gao, Y., Leak, R. K., Chen, J., & Zhang, F. (2012) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2012.09.003 · Cited by 622 · see citing works
Structure of the Keap1:Nrf2 interface provides mechanistic insight into Nrf2 signaling
Lo, S., Li, X., Henzl, M. T., Beamer, L. J., & Hannink, M. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601243 · Cited by 604 · see citing works
Prochaska, H. J., & Santamaria, A. B. (1988) · Analytical Biochemistry · doi:10.1016/0003-2697(88)90292-8 · Cited by 495 · see citing works
Tong, K. I., Padmanabhan, B., Kobayashi, A., Shang, C., Hirotsu, Y., Yokoyama, S., & Yamamoto, M. P. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00753-07 · Cited by 447 · see citing works
The Nrf2/ARE Pathway as a Potential Therapeutic Target in Neurodegenerative Disease
Calkins, M. J., Johnson, D. A., Townsend, J. A., Vargas, M. R., Dowell, J. A., Williamson, T. P., Kraft, A. D., Lee, J., Li, J., & Johnson, J. A. (2008) · Antioxidants and Redox Signaling · doi:10.1089/ars.2008.2242 · Cited by 440 · see citing works
Sussan, T. E., Rangasamy, T., Blake, D. J., Malhotra, D., El-Haddad, H., Bedja, D., Yates, M. S., Kombairaju, P., Yamamoto, M., Liby, K. T., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804333106 · Cited by 346 · see citing works
Nrf2‐deficient mice are highly susceptible to cigarette smoke‐induced emphysema
Iizuka, T., Ishii, Y., Itoh, K., Kiwamoto, T., Kimura, T., Matsuno, Y., Morishima, Y., Hegab, A. E., Homma, S., Nomura, A., et al. (2005) · Genes to Cells · doi:10.1111/j.1365-2443.2005.00905.x · Cited by 336 · see citing works
Modification of Keap1 Cysteine Residues by Sulforaphane
Hu, C., Eggler, A. L., Mesecar, A. D., & van Breemen, R. B. (2011) · Chemical Research in Toxicology · doi:10.1021/tx100389r · Cited by 312 · see citing works
Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases
Canning, P., Cooper, C. D. O., Krojer, T., Murray, J. W., Pike, A. C. W., Chaikuad, A., Keates, T., Thangaratnarajah, C., Hojzan, V., Marsden, B. D., et al. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.437996 · Cited by 284 · see citing works
Structure of the BTB Domain of Keap1 and Its Interaction with the Triterpenoid Antagonist CDDO
Cleasby, A., Yon, J. R., Day, P. J., Richardson, C. J., Tickle, I. J., Williams, P. A., Callahan, J. F., Carr, R. A. E., Concha, N. O., Kerns, J. K., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0098896 · Cited by 265 · see citing works
Self-citationJiang, Z., Lu, M., Xu, L., Yang, T., Xi, M., Xu, X., Guo, X., Zhang, X., You, Q., & Sun, H.-P. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm5000529 · Cited by 263 · see citing works
Crystal Structure of the Kelch Domain of Human Keap1
Li, X., Zhang, D. D., Hannink, M., & Beamer, L. J. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m410073200 · Cited by 249 · see citing works
Marcotte, D. J., Zeng, W., Hus, J., McKenzie, A., Hession, C., Jin, P., Bergeron, C., Lugovskoy, A. A., Enyedy, I. J., Cuervo, H., et al. (2013) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2013.04.019 · Cited by 245 · see citing works
Nrf2 protects against airway disorders
Cho, H., & Kleeberger, S. R. (2009) · Toxicology and Applied Pharmacology · doi:10.1016/j.taap.2009.07.024 · Cited by 237 · see citing works
NRF2 targeting: a promising therapeutic strategy in chronic obstructive pulmonary disease
Boutten, A., Goven, D., Artaud-Macari, É., Boczkowski, J., & Bonay, M. (2011) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2011.02.006 · Cited by 223 · see citing works
Fragment-based lead discovery grows up
Baker, M. (2012) · Nature Reviews Drug Discovery · doi:10.1038/nrd3926 · Cited by 214 · see citing works
Rachakonda, G., Xiong, Y., Sekhar, K. R., Stamer, S. L., Liebler, D. C., & Freeman, M. L. (2008) · Chemical Research in Toxicology · doi:10.1021/tx700302s · Cited by 210 · see citing works
Discovery of a small-molecule inhibitor and cellular probe of Keap1–Nrf2 protein–protein interaction
Hu, L., Magesh, S., Chen, L., Wang, L., Lewis, T. A., Chen, Y., Khodier, C., Inoyama, D., Beamer, L. J., Emge, T. J., et al. (2013) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2013.03.013 · Cited by 206 · see citing works
Binding Mode and Structure–Activity Relationships around Direct Inhibitors of the Nrf2–Keap1 Complex
Jnoff, E., Albrecht, C., Barker, J. J., Barker, O., Beaumont, E., Bromidge, S. M., Brookfield, F. A., Brooks, M., Bubert, C., Ceska, T., et al. (2014) · ChemMedChem · doi:10.1002/cmdc.201300525 · Cited by 180 · see citing works
Eggler, A. L., Small, E., Hannink, M., & Mesecar, A. D. (2009) · Biochemical Journal · doi:10.1042/bj20090471 · Cited by 178 · see citing works
Keap Calm, and Carry on Covalently
Wilson, A. J., Kerns, J. K., Callahan, J. F., & Moody, C. J. (2013) · Journal of Medicinal Chemistry · doi:10.1021/jm400224q · Cited by 171 · see citing works
Self-citationTargeting the Nrf2 pathway against cardiovascular disease
Li, J., Ichikawa, T., Janicki, J. S., & Cui, T. (2009) · Expert Opinion on Therapeutic Targets · doi:10.1517/14728220903025762 · Cited by 168 · see citing works
Zhuang, C., Narayanapillai, S. C., Zhang, W., Sham, Y. Y., & Xing, C. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm4017174 · Cited by 156 · see citing works
AstexViewerTM †: a visualisation aid for structure-based drug design
Hartshorn, M. J. (2002) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1023813504011 · Cited by 145 · see citing works
Shimozono, R., Asaoka, Y., Yoshizawa, Y., Aoki, T., Noda, H., Yamada, M., Kaino, M., & Mochizuki, H. (2013) · Molecular Pharmacology · doi:10.1124/mol.112.084269 · Cited by 131 · see citing works
Anti-inflammatory Effect of a Cell-Penetrating Peptide Targeting the Nrf2/Keap1 Interaction
Steel, R., Cowan, J., Payerne, E., O'Connell, M. A., & Searcey, M. (2012) · ACS Medicinal Chemistry Letters · doi:10.1021/ml300041g · Cited by 111 · see citing works
Wasilko, D. J., Lee, S. E., Stutzman-Engwall, K. J., Reitz, B. A., Emmons, T. L., Mathis, K. J., Bienkowski, M. J., Tomasselli, A. G., & Fischer, H. (2009) · Protein Expression and Purification · doi:10.1016/j.pep.2009.01.002 · Cited by 101 · see citing works
Winkel, A. F., Engel, C. K., Margerie, D., Kannt, A., Szillat, H., Glombik, H., Kallus, C., Ruf, S. G., Güssregen, S., Riedel, J., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.678136 · Cited by 101 · see citing works
Proteomic Analysis Shows Synthetic Oleanane Triterpenoid Binds to mTOR
Yore, M. M., Kettenbach, A. N., Sporn, M. B., Gerber, S. A., & Liby, K. T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022862 · Cited by 99 · see citing works
Kargl, J., Brown, A. J., Andersen, L., Dorn, G., Schicho, R., Waldhoer, M., & Heinemann, Á. (2013) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1124/jpet.113.204180 · Cited by 98 · see citing works
Automated Protein–Ligand Crystallography for Structure‐Based Drug Design
Mooij, W. T. M., Hartshorn, M. J., Tickle, I. J., Sharff, A., Verdonk, M. L., & Jhoti, H. (2006) · ChemMedChem · doi:10.1002/cmdc.200600074 · Cited by 96 · see citing works
Jiang, Z., Xu, L., Lu, M., Chen, Z., Yuan, Z., Xu, X., Guo, X., Zhang, X., Sun, H.-P., & You, Q. (2015) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b00185 · Cited by 94 · see citing works
Chessari, G., Buck, I. M., Day, J. E. H., Day, P. J., Iqbal, A., Johnson, C. N., Lewis, E. J., Martins, V., Miller, D., Reader, M., et al. (2015) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b00706 · Cited by 90 · see citing works
Self-citationFragment Screening Using X-Ray Crystallography
Davies, T. G., & Tickle, I. J. (2011) · Topics in current chemistry · doi:10.1007/128_2011_179 · Cited by 82 · see citing works
Self-citationPadmanabhan, B., Tong, K. I., Kobayashi, A., Yamamoto, M. P., & Yokoyama, S. (2008) · Journal of Synchrotron Radiation · doi:10.1107/s090904950705114x · Cited by 31 · see citing works
Nishida, K., Ohta, Y., & Ishiguro, I. (1997) · Free Radical Biology and Medicine · doi:10.1016/s0891-5849(97)00116-0 · Cited by 21 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Twenty years on: the impact of fragments on drug discovery
Erlanson, D. A., Fesik, S. W., Hubbard, R. E., Jahnke, W., & Jhoti, H. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.109 · Cited by 1,000 · see citing works
Lu, H., Zhou, Q., He, J., Jiang, Z., Peng, C., Tong, R., & Shi, J. (2020) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-020-00315-3 · Cited by 891 · see citing works
Targeted protein degradation: expanding the toolbox
Schapira, M., Calabrese, M. F., Bullock, A. N., & Crews, C. M. (2019) · Nature Reviews Drug Discovery · doi:10.1038/s41573-019-0047-y · Cited by 960 · see citing works
Nrf2 Activation Promotes Lung Cancer Metastasis by Inhibiting the Degradation of Bach1
Lignitto, L., LeBoeuf, S. E., Homer, H., Jiang, S., Askenazi, M., Karakousi, T. R., Pass, H. I., Bhutkar, A. J., Tsirigos, A., Ueberheide, B., et al. (2019) · Cell · doi:10.1016/j.cell.2019.06.003 · Cited by 573 · see citing works
WD40 repeat domain proteins: a novel target class?
Schapira, M., Tyers, M., Torrent, M., & Arrowsmith, C. H. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2017.179 · Cited by 335 · see citing works
Muir, A., Danai, L. V., Gui, D. Y., Waingarten, C. Y., Lewis, C. A., & Vander Heiden, M. G. (2017) · eLife · doi:10.7554/elife.27713 · Cited by 311 · see citing works
Maniaci, C., Hughes, S. J., Testa, A., Chen, W., Lamont, D. J., Rocha, S., Alessi, D. R., Romeo, R., & Ciulli, A. (2017) · Nature Communications · doi:10.1038/s41467-017-00954-1 · Cited by 245 · see citing works
Sayin, V. I., LeBoeuf, S. E., Singh, S. X., Davidson, S. M., Biancur, D., Guzelhan, B. S., Alvarez, S. W., Wu, W. L., Karakousi, T. R., Zavitsanou, A. M., et al. (2017) · eLife · doi:10.7554/elife.28083 · Cited by 231 · see citing works
LeBoeuf, S. E., Wu, W. L., Karakousi, T. R., Karadal, B., Jackson, S. R., Davidson, S. M., Wong, K.-K., Koralov, S. B., Sayin, V. I., & Papagiannakopoulos, T. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2019.11.012 · Cited by 150 · see citing works
Harnessing the E3 Ligase KEAP1 for Targeted Protein Degradation
Wei, J., Meng, F., Park, K.-S., Yim, H., Velez, J., Kumar, P., Wang, L., Xie, L., Chen, H., Shen, Y., et al. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c04841 · Cited by 154 · see citing works
Zhuang, C., Wu, Z., Xing, C., & Miao, Z. (2017) · MedChemComm · doi:10.1039/c6md00500d · Cited by 84 · see citing works
Small molecules targeting protein–protein interactions for cancer therapy
Wu, D., Li, Y., Zheng, L., Xiao, H., Ouyang, L., Wang, G., & Sun, Q. (2023) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2023.05.035 · Cited by 71 · see citing works
Georgakopoulos, N., Talapatra, S., Dikovskaya, D., Dayalan Naidu, S., Higgins, M., Gatliff, J., Ayhan, A., Nikoloudaki, R., Schaap, M., Valko, K., et al. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.2c00457 · Cited by 33 · see citing works
Cuadrado, A., Cazalla, E., Bach, A., Bathish, B., Naidu, S. D., DeNicola, G. M., Dinkova-Kostova, A. T., Fernández-Ginés, R., Grochot-Przeczek, A., Hayes, J. D., et al. (2025) · Redox Biology · doi:10.1016/j.redox.2025.103569 · Cited by 28 · see citing works
- Authors
- Davies, T. G., Wixted, W. E., Coyle, J. E., Griffiths-Jones, C., Hearn, K., McMenamin, R., Norton, D., Rich, S. J., Richardson, C., Saxty, G., Willems, H. M. G., Woolford, A. J.-A., Cottom, J. E., Kou, J.-P., Yonchuk, J. G., Feldser, H. G., Sanchez, Y., Foley, J. P., Bolognese, B. J., Logan, G., Podolin, P. L., Yan, H., Callahan, J. F., Heightman, T. D., & Kerns, J. K.
- Affiliations
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K.
- GlaxoSmithKline (United States) (US)
- Corresponding author
- Heightman, Tom D.
- Kerns, Jeffrey K.
- ORCID
- Venue
- Journal of Medicinal Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2016-04-12
- Volume
- 59
- Issue
- 8
- Pages
- 3991-4006
- ISSN
- 0022-2623 (ISSN-L)
- 1520-4804
- OpenAlex
- W2327865165
- Cited by
- 322
- References
- 52
- Citations by year
- 2026: 34 · 2025: 38 · 2024: 37 · 2023: 35 · 2022: 34 · 2021: 31 · 2020: 36 · 2019: 26 · 2018: 14 · 2017: 28 · 2016: 9
- FWCI
- 13.86
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Medicinal Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics, phytochemicals, and oxidative stress
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Keywords
- Keap1, Nrf2, Keap1-Nrf2 interaction, protein-protein interaction inhibitors, fragment-based drug discovery, oxidative stress, antioxidant response, chemical probes, binding hot spots, lead optimization, cysteine modification
- MeSH terms
- Kelch-Like ECH-Associated Protein 1, Animals, Cells, Cultured, Humans, Protein Binding, Crystallography, X-Ray, NF-E2-Related Factor 2, Mice, Drug Discovery
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