Beyond cysteine: recent developments in the area of targeted covalent inhibition
Abstract
Over the past decade targeted covalent inhibitors have undergone a renaissance due to the clinical validation and regulatory approval of several small molecule therapeutics that are designed to irreversibly modify their target protein. Invariably, these compounds rely on the serendipitous placement of a cysteine residue proximal to the small molecule binding site; while this strategy has afforded numerous successes, it necessarily limits the number of proteins that can be targeted by this approach. This drawback has led several research groups to develop novel methodologies that target non-cysteine residues for covalent modification. Herein, we survey the current literature of warheads that covalently modify non-cysteine amino acids in proteins.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
Covalent targeting of cysteine has not been successfully extended to other amino acids, making it questionable for KRAS mutants beyond G12C.
“The druggability advantage of covalently targeting the nucleophilic cysteine residue has thus far not materialized for other amino acids (31) and hence is questionable whether this strategy can be successfully applied to KRAS mutant oncoproteins beyond KRASG12C.”
From Expanding the Reach of Precision Oncology by Drugging All <i>KRAS</i> Mutants (2022) · cites this paper as [31]
Cites
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
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 1,404 · see citing works
Synthetic analogues of fumagillin that inhibit angiogenesis and suppress tumour growth
Ingber, D. E., Fujita, T., KISHIMOTO, S., Sudo, K., KANAMARU, T., Brem, H., & Folkman, J. (1990) · Nature · doi:10.1038/348555a0 · Cited by 1,292 · see citing works
ACETAMINOPHEN-INDUCED HEPATIC NECROSIS. II. ROLE OF COVALENT BINDING IN VIVO
Jollow, D. J., Mitchell, J. R., Potter, W. Z., Davis, D. C., Gillette, J. R., & Brodie, B. B. (1973) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1016/s0022-3565(25)29664-1 · Cited by 1,203 · see citing works
Proteasome inhibitors in cancer therapy
Manasanch, E. E., & Orlowski, R. Z. (2017) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2016.206 · Cited by 1,024 · see citing works
Acetylation of prostaglandin synthase by aspirin.
Roth, G. J., Stanford, N., & Majerus, P. W. (1975) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.72.8.3073 · Cited by 1,012 · see citing works
Finlay, M. R. V., Anderton, M., Ashton, S., Ballard, P., Bethel, P. A., Box, M. R., Bradbury, R. H., Brown, S. J., Butterworth, S., Campbell, A., et al. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm500973a · Cited by 636 · see citing works
Sin, N., Meng, L., Wang, M. Q. W., Wen, J., Bornmann, W. G., & Crews, C. M. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.12.6099 · Cited by 634 · see citing works
Bauer, R. A. (2015) · Drug Discovery Today · doi:10.1016/j.drudis.2015.05.005 · Cited by 534 · see citing works
Large shifts in pK a values of lysine residues buried inside a protein
Isom, D. G., Castañeda, C. A., Cannon, B. R., & Bertrand García‐Moreno, E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1010750108 · Cited by 468 · see citing works
Structure of Human Methionine Aminopeptidase-2 Complexed with Fumagillin
Liu, S., Widom, J., Kemp, C. W., Crews, C. M., & Clardy, J. (1998) · Science · doi:10.1126/science.282.5392.1324 · Cited by 440 · see citing works
Ligand-directed tosyl chemistry for protein labeling in vivo
Tsukiji, S., Miyagawa, M., Takaoka, Y., Tamura, T., & Hamachi, I. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.157 · Cited by 373 · see citing works
Tyrosine 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 · see citing works
Mortenson, D. E., Brighty, G. J., Plate, L., Bare, G. A. L., Chen, W., Li, S., Wang, H., Cravatt, B. F., Forli, S., Powers, E. T., et al. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b08366 · Cited by 301 · see citing works
Platzer, G., Okon, M., & McIntosh, L. P. (2014) · Journal of Biomolecular NMR · doi:10.1007/s10858-014-9862-y · Cited by 234 · see citing works
PI3K inhibitors as new cancer therapeutics: implications for clinical trial design
Massacesi, C., di Tomaso, E., Urban, P., Germa, C., Quadt, C., Trandafir, L., Aimone, P., Fretault, N., Dharan, B., Tavorath, R., et al. (2016) · OncoTargets and Therapy · doi:10.2147/ott.s89967 · Cited by 229 · see citing works
Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor
Davies, T. G., Bentley, J., Arris, C. E., Boyle, F. T., Curtin, N. J., Endicott, J., Gibson, A. E., Golding, B. T., Griffin, R. J., Hardcastle, I. R., et al. (2002) · Nature Structural Biology · doi:10.1038/nsb842 · Cited by 221 · see citing works
Inhibition of Mcl-1 through covalent modification of a noncatalytic lysine side chain
Akçay, G., Belmonte, M. A., Aquila, B., Chuaqui, C., Hird, A. W., Lamb, M. L., Rawlins, P. B., Su, N., Tentarelli, S., Grimster, N. P., et al. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2174 · Cited by 207 · see citing works
Self-citationDiscovery of PF-04457845: A Highly Potent, Orally Bioavailable, and Selective Urea FAAH Inhibitor
Johnson, D. S., Stiff, C. M., Lazerwith, S. E., Kesten, S. R., Fay, L. K., Morris, M. J., Beidler, D. R., Liimatta, M. B., Smith, S. E., Dudley, D. T., et al. (2010) · ACS Medicinal Chemistry Letters · doi:10.1021/ml100190t · Cited by 200 · see citing works
Rational Targeting of Active-Site Tyrosine Residues Using Sulfonyl Fluoride Probes
Hett, E. C., Xu, H., Geoghegan, K. F., Gopalsamy, A., Kyne, R. E., Menard, C. A., Narayanan, A., Parikh, M. D., Liu, S., Roberts, L. R., et al. (2015) · ACS Chemical Biology · doi:10.1021/cb5009475 · Cited by 192 · see citing works
Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity
Lonsdale, R., Burgess, J., Colclough, N., Davies, N. L., Lenz, E. M., Orton, A. L., & Ward, R. A. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00553 · Cited by 190 · see citing works
Grimster, N. P., Connelly, S., Baranczak, A., Dong, J., Krasnova, L. B., Sharpless, K. B., Powers, E. T., Wilson, I. A., & Kelly, J. W. (2013) · Journal of the American Chemical Society · doi:10.1021/ja311729d · Cited by 189 · see citing works
Self-citationBöttcher, T., & Sieber, S. A. (2008) · Angewandte Chemie International Edition · doi:10.1002/anie.200705768 · Cited by 181 · see citing works
Mukherjee, H., Debreczeni, J. E., Breed, J., Tentarelli, S., Aquila, B. M., Dowling, J. E., Whitty, A., & Grimster, N. P. (2017) · Organic & Biomolecular Chemistry · doi:10.1039/c7ob02028g · Cited by 171 · see citing works
Self-citationA Strategy for Functional Proteomic Analysis of Glycosidase Activity from Cell Lysates
Vocadlo, D. J., & Bertozzi, C. R. (2004) · Angewandte Chemie International Edition · doi:10.1002/anie.200454235 · Cited by 143 · see citing works
Covalent Enzyme Inhibition through Fluorosulfate Modification of a Noncatalytic Serine Residue
Fadeyi, O., Hoth, L. R., Choi, C., Feng, X., Gopalsamy, A., Hett, E. C., Kyne, R. E., Robinson, R. P., & Jones, L. H. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00403 · Cited by 137 · see citing works
Pal, P., Wechter, W. J., & Colman, R. W. (1975) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)40827-2 · Cited by 137 · see citing works
Identification and Characterization of an Irreversible Inhibitor of CDK2
Anscombe, E., Meschini, E., Mora-Vidal, R., Martin, M. P., Staunton, D., Geitmann, M., Danielson, U. H., Stanley, W. A., Wang, L.-Z., Reuillon, T. D., et al. (2015) · Chemistry & Biology · doi:10.1016/j.chembiol.2015.07.018 · Cited by 134 · see citing works
Dalton, S. E., Dittus, L., Thomas, D. A., Convery, M. A., Nunes, J., Bush, J. T., Evans, J. P., Werner, T., Bantscheff, M., Murphy, J. A., et al. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b08979 · Cited by 126 · see citing works
THE REACTION OF ISOXAZOLIUM SALTS WITH BASES
Woodward, R. B., & Olofson, R. A. (1961) · Journal of the American Chemical Society · doi:10.1021/ja01465a069 · Cited by 126 · see citing works
Relative Amino Acid Composition Signatures of Organisms and Environments
Moura, A., Savageau, M. A., & Alves, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077319 · Cited by 119 · see citing works
Staub, I., & Sieber, S. A. (2008) · Journal of the American Chemical Society · doi:10.1021/ja803349j · Cited by 117 · see citing works
Cheng, K., Lee, J., Hao, P., Yao, S. Q., Ding, K., & Li, Z. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201709584 · Cited by 110 · see citing works
Molecular Mechanism of Avibactam-Mediated β-Lactamase Inhibition
King, D. T., King, A. M., Lal, S. M., Wright, G. D., & Strynadka, N. C. J. (2015) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.5b00007 · Cited by 109 · see citing works
Baranczak, A., Liu, Y., Connelly, S., Han, W., Greiner, E. R., Genereux, J. C., Wiseman, R. L., Eisele, Y. S., Bradbury, N. C., Dong, J., et al. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b03042 · Cited by 108 · 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
Expanding the scope of electrophiles capable of targeting K-Ras oncogenes
McGregor, L. M., Jenkins, M. L., Kerwin, C., Burke, J. E., & Shokat, K. M. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00271 · Cited by 97 · 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
Chemoselective small molecules that covalently modify one lysine in a non-enzyme protein in plasma
Choi, S., Connelly, S., Reixach, N., Wilson, I. A., & Kelly, J. W. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.281 · Cited by 90 · see citing works
Bullough, D. A., & Allison, W. S. (1986) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)38442-9 · Cited by 87 · see citing works
Proximity-enabled bioreactivity to generate covalent peptide inhibitors of p53–Mdm4
Hoppmann, C., & Wang, L. (2016) · Chemical Communications · doi:10.1039/c6cc01226d · Cited by 81 · see citing works
Dahal, U. P., Gilbert, A. M., Obach, R. S., Flanagan, M. E., Chen, J. M., García-Irizarry, C. N., Starr, J. T., Schuff, B. P., Uccello, D. P., & Young, J. A. (2016) · MedChemComm · doi:10.1039/c6md00017g · Cited by 75 · see citing works
Cell-permeable probe for identification and imaging of sialidases
Tsai, C., Yen, H., Lin, M., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1222183110 · Cited by 73 · see citing works
An Irreversible Inhibitor of HSP72 that Unexpectedly Targets Lysine‐56
Pettinger, J., Bihan, Y. L., Widya, M., van Montfort, R. L. M., Jones, K., & Cheeseman, M. D. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201611907 · Cited by 72 · see citing works
11 Years of Cyanopyrrolidines as DPP-IV Inhibitors
Peters, J. (2007) · Current Topics in Medicinal Chemistry · doi:10.2174/156802607780091000 · Cited by 69 · see citing works
Hughes, T. E., Kim, D. D., Marjason, J. K., Proietto, J., Whitehead, J. P., & Vath, J. E. (2013) · Obesity · doi:10.1002/oby.20356 · Cited by 67 · see citing works
Chun, E., Han, C. K., Yoon, J. H., Sim, T. B., Kim, Y., & Lee, K. (2004) · International Journal of Cancer · doi:10.1002/ijc.20687 · Cited by 62 · see citing works
A covalent G-site inhibitor for glutathione S-transferase Pi (GSTP 1-1 )
Shishido, Y., Tomoike, F., Kimura, Y., Kuwata, K., Yano, T., Fukui, K., Fujikawa, H., Sekido, Y., Murakami‐Tonami, Y., Kameda, T., et al. (2017) · Chemical Communications · doi:10.1039/c7cc05829b · Cited by 59 · see citing works
Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions
Crichlow, G. V., Lubetsky, J. B., Leng, L., Bucala, R., & Lolis, E. (2008) · Biochemistry · doi:10.1021/bi8014423 · Cited by 54 · see citing works
Sinha, U., & Brewer, J. M. (1985) · Analytical Biochemistry · doi:10.1016/0003-2697(85)90183-6 · Cited by 53 · see citing works
Baker, B. R. (1969) · Accounts of Chemical Research · doi:10.1021/ar50017a001 · Cited by 47 · see citing works
Harlow, K. W., & Switzer, R. L. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)39388-3 · Cited by 40 · see citing works
[The properties of plasminogen activator from human blood plasma taken at sudden death].
Markova, O. A. (1983) · PubMed · Cited by 40 · see citing works
Reversible Lysine Modification on Proteins by Using Functionalized Boronic Acids
Cal, P. M. S. D., Frade, R. F. M., CORDEIRO, C. A., et al. (2015) · Chemistry - A European Journal · doi:10.1002/chem.201500127 · Cited by 40 · see citing works
Kolb, R., Bach, N. C., & Sieber, S. A. (2013) · Chemical Communications · doi:10.1039/c3cc46002a · Cited by 23 · see citing works
Jinno, F., Yoneyama, T., Morohashi, A., Kondo, T., & Asahi, S. (2011) · Biopharmaceutics & Drug Disposition · doi:10.1002/bdd.769 · Cited by 14 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Expanding the Reach of Precision Oncology by Drugging All <i>KRAS</i> Mutants
Hofmann, M. H., Gerlach, D., Misale, S., Petronczki, M., & Kraut, N. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-1331 · Cited by 336 · see citing works
Recent Advances in Selective and Irreversible Covalent Ligand Development and Validation
Zhang, T., Hatcher, J. M., Teng, M., Gray, N. S., & Kostic, M. (2019) · Cell Chemical Biology · doi:10.1016/j.chembiol.2019.09.012 · Cited by 178 · see citing works
Fragment-based covalent ligand discovery
Lu, W., Kostic, M., Zhang, T., Che, J., Patricelli, M. P., Jones, L. H., Chouchani, E. T., & Gray, N. S. (2021) · RSC Chemical Biology · doi:10.1039/d0cb00222d · Cited by 136 · 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
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
- Authors
- Mukherjee, H., & Grimster, N. P.
- Affiliations
- Arrakis Therapeutics (United States) (US)
- AstraZeneca (United States) (US)
- Corresponding author
- Grimster, Neil P
- ORCID
- Grimster, Neil P
- Venue
- Current Opinion in Chemical Biology
- Publisher
- Elsevier BV
- Published
- 2018-06
- Volume
- 44
- Pages
- 30-38
- ISSN
- 1367-5931 (ISSN-L)
- OpenAlex
- W2807112095
- Cited by
- 95
- References
- 57
- Citations by year
- 2026: 5 · 2025: 12 · 2024: 15 · 2023: 15 · 2022: 12 · 2021: 14 · 2020: 9 · 2019: 13
- FWCI
- 0.67
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Current Opinion in Chemical Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- AstraZeneca
- Topics
- Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- targeted covalent inhibitors, warheads, small molecule drugs
- MeSH terms
- Amino Acids, Animals, Cysteine, Humans, Pharmacology, Protein Conformation, Proteins, Drug Discovery, Molecular Targeted Therapy
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