Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53

References

• Boike L, Henning NJ, Nomura DK. Advances in covalent drug discovery. Nat Rev Drug Discov. 2022;21(12):881–898. doi:10.1038/s41573-022-00542-z
   PubMed Web of Science ®Google Scholar
• Baillie TA. Targeted Covalent Inhibitors for Drug Design. Angew Chem Int Ed. 2016;55(43):13408–13421. doi:10.1002/anie.201601091
   PubMed Web of Science ®Google Scholar
• Singh J, Petter RC, Baillie TA, Whitty A. The resurgence of covalent drugs. Nat Rev Drug Discov. 2011;10(4):307–317. doi:10.1038/nrd3410
   PubMed Web of Science ®Google Scholar
• De Cesco S, Kurian J, Dufresne C, Mittermaier AK, Moitessier N. Covalent inhibitors design and discovery. Eur J Med Chem. 2017;138:96–114. doi:10.1016/j.ejmech.2017.06.019
   PubMed Web of Science ®Google Scholar
• Gehringer M, Laufer SA. Emerging and re-emerging warheads for targeted covalent inhibitors: applications in medicinal chemistry and chemical biology. J Med Chem. 2019;62(12):5673–5724. doi:10.1021/acs.jmedchem.8b01153
   PubMed Web of Science ®Google Scholar
• Chaikuad A, Koch P, Laufer SA, Knapp S. The cysteinome of protein kinases as a target in drug development. Angew Chem Int Ed Engl. 2018;57(16):4372–4385. doi:10.1002/anie.201707875
   PubMed Web of Science ®Google Scholar
• Keeley A, Petri L, Ábrányi-Balogh P, Keserű GM. Covalent fragment libraries in drug discovery. Drug Discov Today. 2020;25(6):983–996. doi:10.1016/j.drudis.2020.03.016
   PubMed Web of Science ®Google Scholar
• Butterworth S, Cross DAE, Finlay MRV, Ward RA, Waring MJ. The structure-guided discovery of osimertinib: the first U.S. FDA approved mutant selective inhibitor of EGFR T790M. . MedChemComm. 2017;8(5):820–822. doi:10.1039/C7MD90012K
   PubMed Web of Science ®Google Scholar
• Finlay MRV, Anderton M, Ashton S, et al. Discovery of a Potent and Selective EGFR Inhibitor (AZD9291) of Both Sensitizing and T790M Resistance Mutations That Spares the Wild Type Form of the Receptor. J Med Chem. 2014;57(20):8249–8267. doi:10.1021/jm500973a
   PubMed Web of Science ®Google Scholar
• Zhao Z, Bourne PE. Progress with covalent small-molecule kinase inhibitors. Drug Discov Today. 2018;23(3):727–735. doi:10.1016/j.drudis.2018.01.035
   PubMed Web of Science ®Google Scholar
• Lanman BA, Allen JR, Allen JG, et al. Discovery of a Covalent Inhibitor of KRASG12C (AMG 510) for the treatment of solid tumors. J Med Chem. 2020;63(1):52–65. doi:10.1021/acs.jmedchem.9b01180
   PubMed Web of Science ®Google Scholar
• Ostrem JM, Peters U, Sos ML, Wells JA, Shokat KM. K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature. 2013;503:7477):548–551. doi:10.1038/nature12796
   Web of Science ®Google Scholar
• Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and re-emerging warheads for targeted covalent inhibitors: an update. J Med Chem. 2024;67(10): 7668–7758. doi:10.1021/acs.jmedchem.3c01825
   PubMed Web of Science ®Google Scholar
• Uetrecht J. Idiosyncratic Drug Reactions: current Understanding. Annu Rev Pharmacol Toxicol. 2007;47(1):513–539. doi:10.1146/annurev.pharmtox.47.120505.105150
   PubMed Web of Science ®Google Scholar
• Baillie TA. Approaches to mitigate the risk of serious adverse reactions in covalent drug design. Expert Opin Drug Discov. 2021;16(3):275–287. doi:10.1080/17460441.2021.1832079
   PubMed Web of Science ®Google Scholar
• Bauer RA. Covalent inhibitors in drug discovery: from accidental discoveries to avoided liabilities and designed therapies. Drug Discov Today. 2015;20(9):1061–1073. doi:10.1016/j.drudis.2015.05.005
   PubMed Web of Science ®Google Scholar
• Lonsdale R, Ward RA. Structure-based design of targeted covalent inhibitors. Chem Soc Rev. 2018;47(11):3816–3830. doi:10.1039/c7cs00220c
   PubMed Web of Science ®Google Scholar
• Barf T, Kaptein A. Irreversible protein kinase inhibitors: balancing the benefits and risks. J Med Chem. 2012;55(14):6243–6262. doi:10.1021/jm3003203
   PubMed Web of Science ®Google Scholar
• McKenna SM, Fay EM, McGouran JF. Flipping the switch: innovations in inducible probes for protein profiling. ACS Chem Biol. 2021;16(12):2719–2730. doi:10.1021/acschembio.1c00572
   PubMed Web of Science ®Google Scholar
• Liu Q, Sabnis Y, Zhao Z, et al. Developing irreversible inhibitors of the protein kinase cysteinome. Chem Biol. 2013;20(2):146–159. doi:10.1016/j.chembiol.2012.12.006
   PubMed Web of Science ®Google Scholar
• Serafim RAM, Haarer L, Pedreira JGB, Gehringer M. Covalent chemical probes for protein kinases. Curr Res Chem Biol. 2023;100040. doi:10.1016/j.crchbi.2022.100040
   Google Scholar
• Lu X, Smaill JB, Patterson AV, Ding K. Discovery of cysteine-targeting covalent protein kinase inhibitors. J Med Chem. 2022;65(1):58–83. doi:10.1021/acs.jmedchem.1c01719
   PubMed Web of Science ®Google Scholar
• Hillebrand L, Gehringer M. Never gonna give you up – current developments in covalent protein kinase inhibitors. scientific articles. Chimia. 2022;76(5):435. doi:10.2533/chimia.2022.435
   PubMed Web of Science ®Google Scholar
• Strelow JM. A Perspective on the Kinetics of Covalent and Irreversible Inhibition. SLAS Discov. 2017;22(1):3–20. doi:10.1177/1087057116671509
   PubMed Web of Science ®Google Scholar
• Li KS, Quinn JG, Saabye MJ, et al. High-Throughput Kinetic Characterization of Irreversible Covalent Inhibitors of KRASG12C by Intact Protein MS and Targeted MRM. Anal Chem. 2022;94(2):1230–1239. doi:10.1021/acs.analchem.1c04463
   PubMed Web of Science ®Google Scholar
• Mons E, Roet S, Kim RQ, Mulder MPC. A comprehensive guide for assessing covalent inhibition in enzymatic assays illustrated with kinetic simulations. Curr Protoc. 2022;2(6):e419. doi:10.1002/cpz1.419
   PubMedGoogle Scholar
• Craven GB, Affron DP, Kösel T, et al. Multiparameter kinetic analysis for covalent fragment optimization by using quantitative irreversible tethering (qIT). ChemBioChem. 2020;21(23):3417–3422. doi:10.1002/cbic.202000457
   PubMed Web of Science ®Google Scholar
• McAulay K, Bilsland A, Bon M. Reactivity of covalent fragments and their role in fragment based drug discovery. Pharmaceuticals. 2022;15(11):1366. doi:10.3390/ph15111366
   Web of Science ®Google Scholar
• Flanagan ME, Abramite JA, Anderson DP, et al. Chemical and computational methods for the characterization of covalent reactive groups for the prospective design of irreversible inhibitors. J Med Chem. 2014;57(23):10072–10079. doi:10.1021/jm501412a
   PubMed Web of Science ®Google Scholar
• Forster M, Liang XJ, Schröder M, et al. Discovery of a novel class of covalent dual inhibitors targeting the protein kinases BMX and BTK. Int J Mol Sci. 2020;21(23):9269.
   PubMed Web of Science ®Google Scholar
• Zhang T, Inesta-Vaquera F, Niepel M, et al. Discovery of potent and selective covalent inhibitors of JNK. Chem Biol. 2012;19(1):140–154. doi:10.1016/j.chembiol.2011.11.010
   PubMed Web of Science ®Google Scholar
• Keeley A, Ábrányi-Balogh P, Keserű GM. Design and characterization of a heterocyclic electrophilic fragment library for the discovery of cysteine-targeted covalent inhibitors. MedChemComm. 2019;10(2):263–267. doi:10.1039/C8MD00327K
   PubMed Web of Science ®Google Scholar
• Jöst C, Nitsche C, Scholz T, Roux L, Klein CD. Promiscuity and selectivity in covalent enzyme inhibition: a systematic study of electrophilic fragments. J Med Chem. 2014;57(18):7590–7599. doi:10.1021/jm5006918
   PubMed Web of Science ®Google Scholar
• Resnick E, Bradley A, Gan J, et al. Rapid covalent-probe discovery by electrophile-fragment screening. J Am Chem Soc. 2019;141(22):8951–8968. doi:10.1021/jacs.9b02822
   PubMed Web of Science ®Google Scholar
• Zambaldo C, Daguer J-P, Saarbach J, Barluenga S, Winssinger N. Screening for covalent inhibitors using DNA-display of small molecule libraries functionalized with cysteine reactive moieties. MedChemComm. 2016;7(7):1340–1351.
   Web of Science ®Google Scholar
• Clark MA, Acharya RA, Arico-Muendel CC, et al. Design, synthesis and selection of DNA-encoded small-molecule libraries. Nat Chem Biol. 2009;5(9):647–654.
   PubMed Web of Science ®Google Scholar
• Zimmermann G, Rieder U, Bajic D, et al. A specific and covalent JNK-1 Ligand selected from an encoded self-assembling chemical library. Chemistry. 2017;23(34):8152–8155. doi:10.1002/chem.201701644
   PubMed Web of Science ®Google Scholar
• Scarpino A, Ferenczy GG, Keserű GM. Covalent docking in drug discovery: scope and limitations. Curr Pharm Des. 2020;26(44):5684–5699. doi:10.2174/1381612824999201105164942
   PubMed Web of Science ®Google Scholar
• Sotriffer C. Docking of covalent ligands: challenges and approaches. Mol Inform. 2018;37(9–10):1800062. doi:10.1002/minf.201800062
   Web of Science ®Google Scholar
• Scarpino A, Ferenczy GG, Keserű GM. Comparative evaluation of covalent docking tools. J Chem Inf Model. 2018;58(7):1441–1458. doi:10.1021/acs.jcim.8b00228
   PubMed Web of Science ®Google Scholar
• Shraga A, Resnick E, Gabizon R, London N. Chapter Eight - Covalent Fragment Screening. Ward RA, Grimster NP, eds.. Academic Press: 2021. 243–265.
   Google Scholar
• Murray CW, Rees DC. The rise of fragment-based drug discovery. Nat Chem. 2009;1(3):187–192. doi:10.1038/nchem.217
   PubMed Web of Science ®Google Scholar
• Kuntz ID, Chen K, Sharp KA, Kollman PA. The maximal affinity of ligands. Proc Natl Acad Sci U S A. 1999;96(18):9997–10002. doi:10.1073/pnas.96.18.9997
   PubMed Web of Science ®Google Scholar
• Hopkins AL, Groom CR, Alex A. Ligand efficiency: a useful metric for lead selection. Drug Discov Today. 2004;9(10):430–431. doi:10.1016/S1359-6446(04)03069-7
   PubMed Web of Science ®Google Scholar
• Heidrich J, Sperl LE, Boeckler FM. Embracing the diversity of halogen bonding motifs in fragment-based drug discovery-construction of a diversity-optimized halogen-enriched fragment library. Front Chem. 2019;7:9. doi:10.3389/fchem.2019.00009
   PubMed Web of Science ®Google Scholar
• Wilcken R, Liu X, Zimmermann MO, et al. Halogen-enriched fragment libraries as leads for drug rescue of mutant p53. J Am Chem Soc. 2012;134(15):6810–6818. doi:10.1021/ja301056a
   PubMed Web of Science ®Google Scholar
• Zimmermann MO, Lange A, Wilcken R, et al. Halogen-enriched fragment libraries as chemical probes for harnessing halogen bonding in fragment-based lead discovery. Future Med Chem. 2014;6(6):617–639. doi:10.4155/fmc.14.20
   PubMed Web of Science ®Google Scholar
• Wilcken R, Zimmermann MO, Lange A, Joerger AC, Boeckler FM. Principles and applications of halogen bonding in medicinal chemistry and chemical biology. J Med Chem. 2013;56(4):1363–1388. doi:10.1021/jm3012068
   PubMed Web of Science ®Google Scholar
• Lange A, Heidrich J, Zimmermann MO, Exner TE, Boeckler FM. Scaffold effects on halogen bonding strength. J Chem Inf Model. 2019;59(2):885–894. doi:10.1021/acs.jcim.8b00621
   PubMed Web of Science ®Google Scholar
• Dammann M, Kramer M, Zimmermann MO, Boeckler FM. Quadruple Target Evaluation of Diversity-Optimized Halogen-Enriched Fragments (HEFLibs) reveals substantial ligand efficiency for AP2-Associated Protein Kinase 1 (AAK1). Original Research. Front Chem. 2022;9:815567. doi:10.3389/fchem.2021.815567
   PubMed Web of Science ®Google Scholar
• Dammann M, Stahlecker J, Zimmermann MO, et al. Screening of a halogen-enriched fragment library leads to unconventional binding modes. J Med Chem. 2022;65(21):14539–14552. doi:10.1021/acs.jmedchem.2c00951
   PubMed Web of Science ®Google Scholar
• Stahlecker J, Klett T, Schwer M, et al. Revisiting a challenging p53 binding site: a diversity-optimized HEFLib reveals diverse binding modes in T-p53C-Y220C.. RSC Med Chem. 2022;13(12):1575–1586. doi:10.1039/D2MD00246A
   PubMedGoogle Scholar
• Congreve M, Carr R, Murray C, Jhoti H. A ‘Rule of Three’ for fragment-based lead discovery? Drug Discov Today. 2003;8(19):876–877. doi:10.1016/S1359-6446(03)02831-9
   PubMed Web of Science ®Google Scholar
• Martin JS, MacKenzie CJ, Fletcher D, Gilbert IH. Characterising covalent warhead reactivity. Biorg Med Chem. 2019;27(10):2066–2074. doi:10.1016/j.bmc.2019.04.002
   PubMed Web of Science ®Google Scholar
• Wildman SA, Crippen GM. Prediction of Physicochemical Parameters by Atomic Contributions. J Chem Inf Comput Sci. 1999;39(5):868–873. doi:10.1021/ci990307l
   Google Scholar
• Schrödinger, LCC. Schrödinger Release 2021-1: QikProp. New York: Schrödinger, LCC; 2021.
   Google Scholar
• Schrödinger, LCC. Schrödinger Release 2021-1: LigPrep. New York: Schrödinger, LCC; 2021.
   Google Scholar
• Lange A, Günther M, Büttner FM, et al. Targeting the Gatekeeper MET146 of C-Jun N-terminal kinase 3 induces a bivalent halogen/chalcogen bond. J Am Chem Soc. 2015;137(46):14640–14652. doi:10.1021/jacs.5b07090
   PubMed Web of Science ®Google Scholar
• Bauer MR, Joerger AC, Fersht AR. 2-Sulfonylpyrimidines: mild alkylating agents with anticancer activity toward p53-compromised cells. Proc Natl Acad Sci U S A. 2016;113(36):E5271–E5280. doi:10.1073/pnas.1610421113
   PubMed Web of Science ®Google Scholar
• Boeckler FM, Joerger AC, Jaggi G, Rutherford TJ, Veprintsev DB, Fersht AR. Targeted rescue of a destabilized mutant of p53 by an in silico screened drug. Proc Natl Acad Sci U S A. 2008;105(30):10360–10365. doi:10.1073/pnas.0805326105
   PubMed Web of Science ®Google Scholar
• Kaar JL, Basse N, Joerger AC, Stephens E, Rutherford TJ, Fersht AR. Stabilization of mutant p53 via alkylation of cysteines and effects on DNA binding. Protein Sci. 2010;19(12):2267–2278. doi:10.1002/pro.507
   PubMed Web of Science ®Google Scholar
• Jackson PA, Widen JC, Harki DA, Brummond KM. Covalent modifiers: a chemical perspective on the reactivity of α,β-unsaturated carbonyls with thiols via hetero-Michael addition reactions. J Med Chem. 2017;60(3):839–885. doi:10.1021/acs.jmedchem.6b00788
   PubMed Web of Science ®Google Scholar
• Kaur B, Singh P. Epoxides: developability as active pharmaceutical ingredients and biochemical probes. Bioorg Chem. 2022;125:105862. doi:10.1016/j.bioorg.2022.105862
   PubMed Web of Science ®Google Scholar
• Harshbarger W, Miller C, Diedrich C, Sacchettini J. Crystal structure of the human 20S proteasome in complex with carfilzomib. Structure. 2015;23(2):418–424. doi:10.1016/j.str.2014.11.017
   PubMed Web of Science ®Google Scholar
• Vitaku E, Smith DT, Njardarson JT. Analysis of the structural diversity, substitution patterns, and frequency of nitrogen heterocycles among U.S. FDA approved pharmaceuticals. J Med Chem. 2014;57(24):10257–10274. doi:10.1021/jm501100b
   PubMed Web of Science ®Google Scholar
• Heravi MM, Zadsirjan V. Prescribed drugs containing nitrogen heterocycles: an overview. RSC Adv. 2020;10(72):44247–44311. doi:10.1039/d0ra09198g
   PubMed Web of Science ®Google Scholar
• Wu Y-J. Chapter 1 - heterocycles and medicine: a survey of the heterocyclic drugs approved by the U.S. FDA from 2000 to present. In: Gribble GW, Joule JA, editors. Prog Heterocycl Chem. Elsevier; 2012:1–53.
   Google Scholar
• Hossain M, Habib I, Singha K, Kumar A. FDA-approved heterocyclic molecules for cancer treatment: synthesis, dosage, mechanism of action and their adverse effect. Heliyon. 2024;10(1):e23172. doi:10.1016/j.heliyon.2023.e23172
   PubMed Web of Science ®Google Scholar
• Jorgensen WL, Duffy EM. Prediction of drug solubility from structure. Adv Drug Deliv Rev. 2002;54(3):355–366. doi:10.1016/s0169-409x(02)00008-x
   PubMed Web of Science ®Google Scholar
• Ábrányi-balogh P, Petri L, Imre T, et al. A road map for prioritizing warheads for cysteine targeting covalent inhibitors. Eur J Med Chem. 2018;160:94–107. doi:10.1016/j.ejmech.2018.10.010
   PubMed Web of Science ®Google Scholar
• Grabrijan K, Hrast M, Proj M, et al. Covalent inhibitors of bacterial peptidoglycan biosynthesis enzyme MurA with chloroacetamide warhead. Eur J Med Chem. 2022;243:114752. doi:10.1016/j.ejmech.2022.114752
   PubMed Web of Science ®Google Scholar
• Proj M, Knez D, Sosič I, Gobec S. Redox active or thiol reactive? Optimization of rapid screens to identify less evident nuisance compounds. Drug Discov Today. 2022;27(6):1733–1742. doi:10.1016/j.drudis.2022.03.008
   PubMed Web of Science ®Google Scholar
• Cee VJ, Volak LP, Chen Y, et al. Systematic Study of the Glutathione (GSH) reactivity of N-Arylacrylamides: 1. Effects of aryl substitution. J Med Chem. 2015;58(23):9171–9178. doi:10.1021/acs.jmedchem.5b01018
   PubMed Web of Science ®Google Scholar
• Gerstenecker S, Haarer L, Schröder M, et al. Discovery of a potent and highly isoform-selective inhibitor of the neglected ribosomal protein S6 kinase beta 2 (S6K2). Cancers. 2021;13(20):1.
   Web of Science ®Google Scholar
• Porter NJ, Christianson DW. Binding of the microbial cyclic tetrapeptide trapoxin A to the class I histone deacetylase HDAC8. ACS Chem Biol. 2017;12(9):2281–2286. doi:10.1021/acschembio.7b00330
   PubMed Web of Science ®Google Scholar
• Pearson RG. Hard and soft acids and bases. J Am Chem Soc. 1963;85(22):3533–3539. doi:10.1021/ja00905a001
   Web of Science ®Google Scholar
• Vaas S, Zimmermann MO, Schollmeyer D, et al. Principles and applications of CF(2)X moieties as unconventional halogen bond donors in medicinal chemistry, chemical biology, and drug discovery. J Med Chem. 2023;66(15):10202–10225. doi:10.1021/acs.jmedchem.3c00634
   PubMed Web of Science ®Google Scholar
• Molland K, Zhou Q, Mesecar AD. A 2.2 Å resolution structure of the USP7 catalytic domain in a new space group elaborates upon structural rearrangements resulting from ubiquitin binding. Acta Crystallogr F Struct Biol Commun. 2014;70(Pt 3):283–287. doi:10.1107/s2053230x14002519
   PubMedGoogle Scholar
• Joerger AC, Allen MD, Fersht AR. Crystal structure of a superstable mutant of human p53 core domain. Insights into the mechanism of rescuing oncogenic mutations. J Biol Chem. 2004;279(2):1291–1296. doi:10.1074/jbc.M309732200
   PubMed Web of Science ®Google Scholar
• Cargnello M, Roux PP. Activation and function of the MAPKs and their substrates, the MAPK-activated protein kinases. Microbiol Mol Biol Rev. 2011;75(1):50–83. doi:10.1128/mmbr.00031-10
   PubMed Web of Science ®Google Scholar
• Barr RK, Bogoyevitch MA. The c-Jun N-terminal protein kinase family of mitogen-activated protein kinases (JNK MAPKs). Int J Biochem Cell Biol. 2001;33(11):1047–1063.
   PubMed Web of Science ®Google Scholar
• Davis RJ. Signal transduction by the JNK group of MAP kinases. Cell. 2000;103(2):239–252. doi:10.1016/s0092-8674(00)00116-1
   PubMed Web of Science ®Google Scholar
• Wada T, Penninger JM. Mitogen-activated protein kinases in apoptosis regulation. Oncogene. 2004;23(16):2838–2849. doi:10.1038/sj.onc.1207556
   PubMed Web of Science ®Google Scholar
• Bogoyevitch MA. The isoform‐specific functions of the c‐Jun N‐terminal Kinases (JNKs): differences revealed by gene targeting. Bioessays. 2006;28(9):923–934.
   PubMed Web of Science ®Google Scholar
• Cui J, Zhang M, Zhang YQ, Xu ZH. JNK pathway: diseases and therapeutic potential. Acta Pharmacol Sin. 2007;28(5):601–608. doi:10.1111/j.1745-7254.2007.00579.x
   PubMed Web of Science ®Google Scholar
• Antoniou X, Falconi M, Di Marino D, Borsello T. JNK3 as a therapeutic target for neurodegenerative diseases. J Alzheimers Dis. 2011;24(4):633–642. doi:10.3233/jad-2011-091567
   PubMed Web of Science ®Google Scholar
• Hunot S, Vila M, Teismann P, et al. JNK-mediated induction of cyclooxygenase 2 is required for neurodegeneration in a mouse model of Parkinson’s disease. Proc Natl Acad Sci U S A. 2004;101(2):665–670. doi:10.1073/pnas.0307453101
   PubMed Web of Science ®Google Scholar
• Wityak J, McGee KF, Conlon MP, et al. Lead optimization toward proof-of-concept tools for Huntington’s disease within a 4-(1H-pyrazol-4-yl)pyrimidine class of pan-JNK inhibitors. J Med Chem. 2015;58(7):2967–2987. doi:10.1021/jm5013598
   PubMed Web of Science ®Google Scholar
• Braithwaite SP, Schmid RS, He DN, et al. Inhibition of c-Jun kinase provides neuroprotection in a model of Alzheimer’s disease. Neurobiol Dis. 2010;39(3):311–317. doi:10.1016/j.nbd.2010.04.015
   PubMed Web of Science ®Google Scholar
• Zhang G-Y, Zhang Q-G. Agents targeting c-Jun N-terminal kinase pathway as potential neuroprotectants. Expert Opin Investig Drug. 2005;14(11):1373–1383. doi:10.1517/13543784.14.11.1373
   PubMed Web of Science ®Google Scholar
• Muth F, El-Gokha A, Ansideri F, et al. Tri- and tetrasubstituted pyridinylimidazoles as covalent inhibitors of c-Jun N-Terminal Kinase 3. J Med Chem. 2017;60(2):594–607. doi:10.1021/acs.jmedchem.6b01180
   PubMed Web of Science ®Google Scholar
• Hoffelner BS, Andreev S, Plank N, Koch P. Photocaging of pyridinylimidazole-based covalent JNK3 inhibitors affords spatiotemporal control of the binding affinity in live cells. Pharmaceuticals. 2023;16(2):264. doi:10.3390/ph16020264
   Web of Science ®Google Scholar
• Senkane K, Vinogradova EV, Suciu RM, et al. The proteome‐wide potential for reversible covalency at cysteine. Angew Chem. 2019;131(33):11507–11511. doi:10.1002/anie.201905829
   Google Scholar
• Liu R, Verma N, Henderson JA, Zhan S, Shen J. Profiling MAP kinase cysteines for targeted covalent inhibitor design. RSC Med Chem. 2022;13(1):54–63. doi:10.1039/d1md00277e
   PubMedGoogle Scholar
• Liu R, Zhan S, Che Y, Shen J. Reactivities of the FRONT POCket N-terminal cap cysteines in human kinases. J Med Chem. 2022;65(2):1525–1535. doi:10.1021/acs.jmedchem.1c01186
   PubMed Web of Science ®Google Scholar
• Tavana O, Gu W. Modulation of the p53/MDM2 interplay by HAUSP inhibitors. J Mol Cell Biol. 2017;9(1):45–52. doi:10.1093/jmcb/mjw049
   PubMed Web of Science ®Google Scholar
• Leger PR, Hu DX, Biannic B, et al. Discovery of potent, selective, and orally bioavailable inhibitors of USP7 with in vivo antitumor activity. J Med Chem. 2020;63(10):5398–5420. doi:10.1021/acs.jmedchem.0c00245
   PubMed Web of Science ®Google Scholar
• Reverdy C, Conrath S, Lopez R, et al. Discovery of specific inhibitors of human USP7/HAUSP deubiquitinating enzyme. Chem Biol. 2012;19(4):467–477. doi:10.1016/j.chembiol.2012.02.007
   PubMedGoogle Scholar
• Faesen AC, Dirac AM, Shanmugham A, Ovaa H, Perrakis A, Sixma TK. Mechanism of USP7/HAUSP activation by its C-terminal ubiquitin-like domain and allosteric regulation by GMP-synthetase. Mol Cell. 2011;44(1):147–159. doi:10.1016/j.molcel.2011.06.034
   PubMed Web of Science ®Google Scholar
• Reyes-Turcu FE, Ventii KH, Wilkinson KD. Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes. Annu Rev Biochem. 2009;78:363–397. doi:10.1146/annurev.biochem.78.082307.091526
   PubMed Web of Science ®Google Scholar
• Oliveira RI, Guedes RA, Salvador JAR. Highlights in USP7 inhibitors for cancer treatment. Front Chem. 2022;10:1005727. doi:10.3389/fchem.2022.1005727
   PubMed Web of Science ®Google Scholar
• Hu M, Li P, Li M, et al. Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell. 2002;111(7):1041–1054. doi:10.1016/s0092-8674(02)01199-6
   PubMed Web of Science ®Google Scholar
• Chauhan D, Tian Z, Nicholson B, et al. Deubiquitylating enzyme USP-7, a novel therapeutic target in multiple myeloma. Blood. 2009;114(22):610. doi:10.1182/blood.V114.22.610.610
   Google Scholar
• Li X, Kong L, Yang Q, et al. Parthenolide inhibits ubiquitin-specific peptidase 7 (USP7), Wnt signaling, and colorectal cancer cell growth. J Biol Chem. 2020;295(11):3576–3589. doi:10.1074/jbc.RA119.011396
   PubMed Web of Science ®Google Scholar
• Turnbull AP, Ioannidis S, Krajewski WW, et al. Molecular basis of USP7 inhibition by selective small-molecule inhibitors. Nature. 2017;550(7677):481–486. doi:10.1038/nature24451
   PubMed Web of Science ®Google Scholar
• Kategaya L, Di Lello P, Rougé L, et al. USP7 small-molecule inhibitors interfere with ubiquitin binding. Nature. 2017;550(7677):534–538. doi:10.1038/nature24006
   PubMed Web of Science ®Google Scholar
• Ohol YM, Sun MT, Cutler G, et al. Novel, selective inhibitors of USP7 uncover multiple mechanisms of antitumor activity in vitro and in vivo. Mol Cancer Ther. 2020;19(10):1970–1980. doi:10.1158/1535-7163.Mct-20-0184
   PubMed Web of Science ®Google Scholar
• Vogelstein B, Lane D, Levine AJ. Surfing the p53 network. Nature. 2000;408(6810):307–310. doi:10.1038/35042675
   PubMed Web of Science ®Google Scholar
• Lane DP. p53, guardian of the genome. Nature. 1992;358(6381):15–16. doi:10.1038/358015a0
   PubMed Web of Science ®Google Scholar
• Levine AJ, Hu W, Feng Z. The P53 pathway: what questions remain to be explored? Cell Death Differ. 2006;13(6):1027–1036. doi:10.1038/sj.cdd.4401910
   PubMed Web of Science ®Google Scholar
• Joerger AC, Fersht AR. Structural biology of the tumor suppressor p53. Annu Rev Biochem. 2008;77:557–582. doi:10.1146/annurev.biochem.77.060806.091238
   PubMed Web of Science ®Google Scholar
• Joerger AC, Fersht AR. The p53 pathway: origins, inactivation in cancer, and emerging therapeutic approaches. Annu Rev Biochem. 2016;85:375–404. doi:10.1146/annurev-biochem-060815-014710
   PubMed Web of Science ®Google Scholar
• Joerger AC, Fersht AR. Structure–function–rescue: the diverse nature of common p53 cancer mutants. Oncogene. 2007;26(15):2226–2242. doi:10.1038/sj.onc.1210291
   PubMed Web of Science ®Google Scholar
• Joerger AC, Ang HC, Fersht AR. Structural basis for understanding oncogenic p53 mutations and designing rescue drugs. Proc Natl Acad Sci U S A. 2006;103(41):15056. doi:10.1073/pnas.0607286103
   PubMed Web of Science ®Google Scholar
• Liu X, Wilcken R, Joerger AC, et al. Small molecule induced reactivation of mutant p53 in cancer cells. Nucleic Acids Res. 2013;41(12):6034–6044. doi:10.1093/nar/gkt305
   PubMed Web of Science ®Google Scholar
• Baud MGJ, Bauer MR, Verduci L, et al. Aminobenzothiazole derivatives stabilize the thermolabile p53 cancer mutant Y220C and show anticancer activity in p53-Y220C cell lines. Eur J Med Chem. 2018;152:101–114. doi:10.1016/j.ejmech.2018.04.035
   PubMed Web of Science ®Google Scholar
• Stephenson Clarke JR, Douglas LR, Duriez PJ, et al. Discovery of nanomolar-affinity pharmacological chaperones stabilizing the oncogenic p53 Mutant Y220C. ACS Pharmacol Transl Sci. 2022;5(11):1169–1180. doi:10.1021/acsptsci.2c00164
   PubMedGoogle Scholar
• Liang Y, Besch-Williford C, Hyder SM. PRIMA-1 inhibits growth of breast cancer cells by re-activating mutant p53 protein. Int J Oncol. 2009;35(5):1015–1023. doi:10.3892/ijo_00000416
   PubMed Web of Science ®Google Scholar
• Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsén L, Rozenberg H, Shakked Z. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Nat Commun. 2021;12(1):7057. doi:10.1038/s41467-021-27142-6
   PubMed Web of Science ®Google Scholar
• Wassman CD, Baronio R, Demir Ö, et al. Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53. Nat Commun. 2013;4(1):1407. doi:10.1038/ncomms2361
   PubMedGoogle Scholar
• Lambert JMR, Gorzov P, Veprintsev DB, et al. PRIMA-1 reactivates mutant p53 by covalent binding to the core domain. Cancer Cell. 2009;15(5):376–388. doi:10.1016/j.ccr.2009.03.003
   PubMed Web of Science ®Google Scholar
• Guiley KZ, Shokat KM. A small molecule reacts with the p53 somatic mutant Y220C to rescue wild-type thermal stability. Cancer Discov. 2023;13(1):56–69. doi:10.1158/2159-8290.Cd-22-0381
   PubMed Web of Science ®Google Scholar
• Scotcher J, Clarke DJ, Weidt SK, et al. Identification of two reactive cysteine residues in the tumor suppressor protein p53 using top-down FTICR mass spectrometry. J Am Soc Mass Spectrom. 2011;22(5):888–897. doi:10.1007/s13361-011-0088-x
   PubMed Web of Science ®Google Scholar
• Pichon MM, Drelinkiewicz D, Lozano D, et al. Structure–reactivity studies of 2-sulfonylpyrimidines allow selective protein arylation. Bioconjug Chem. 2023;34(9):1679–1687. doi:10.1021/acs.bioconjchem.3c00322
   PubMed Web of Science ®Google Scholar
• Zhang Q, Bykov VJN, Wiman KG, Zawacka-Pankau J. APR-246 reactivates mutant p53 by targeting cysteines 124 and 277. Cell Death Dis. 2018;9(5):439. doi:10.1038/s41419-018-0463-7
   PubMedGoogle Scholar
• Niesen FH, Berglund H, Vedadi M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc. 2007;2(9):2212–2221. doi:10.1038/nprot.2007.321
   PubMed Web of Science ®Google Scholar
• Gao K, Oerlemans R, Groves MR. Theory and applications of differential scanning fluorimetry in early-stage drug discovery. Biophys Rev. 2020;12(1):85–104. doi:10.1007/s12551-020-00619-2
   PubMedGoogle Scholar
• Huynh K, Partch CL. Analysis of protein stability and ligand interactions by thermal shift assay. Curr Protoc Protein Sci. 2015;79:28.29.21–28.29.14. doi:10.1002/0471140864.ps2809s79
   Google Scholar
• Huber K, Brault L, Fedorov O, et al. 7,8-Dichloro-1-oxo-β-carbolines as a versatile scaffold for the development of potent and selective kinase inhibitors with unusual binding modes. J Med Chem. 2012;55(1):403–413. doi:10.1021/jm201286z
   PubMed Web of Science ®Google Scholar
• Bullock AN, Debreczeni JÉ, Fedorov OY, Nelson A, Marsden BD, Knapp S. Structural basis of inhibitor specificity of the human protooncogene proviral insertion site in Moloney Murine Leukemia Virus (PIM-1) Kinase. J Med Chem. 2005;48(24):7604–7614. doi:10.1021/jm0504858
   PubMed Web of Science ®Google Scholar
• Fedorov O, Huber K, Eisenreich A, et al. Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing. Chem Biol. 2011;18(1):67–76. doi:10.1016/j.chembiol.2010.11.009
   PubMedGoogle Scholar
• Bullock AN, Henckel J, Fersht AR. Quantitative analysis of residual folding and DNA binding in mutant p53 core domain: definition of mutant states for rescue in cancer therapy. Oncogene. 2000;19(10):1245–1256. doi:10.1038/sj.onc.1203434
   PubMed Web of Science ®Google Scholar
• Baell JB, Nissink JWM. Seven Year Itch: pan-Assay Interference Compounds (PAINS) in 2017-Utility and Limitations. ACS Chem Biol. 2018;13(1):36–44. doi:10.1021/acschembio.7b00903
   PubMed Web of Science ®Google Scholar
• Sun C, Li Y, Yates EA, Fernig DG. SimpleDSFviewer: a tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions. Protein Sci. 2020;29(1):19–27. doi:10.1002/pro3703
   PubMed Web of Science ®Google Scholar
• Kharenko OA, Patel RG, Brown SD, et al. Design and Characterization of Novel Covalent Bromodomain and Extra-Terminal Domain (BET) Inhibitors Targeting a Methionine. J Med Chem. 2018;61(18):8202–8211. doi:10.1021/acs.jmedchem.8b00666
   PubMed Web of Science ®Google Scholar
• Cimmperman P, Baranauskiene L, Jachimoviciūte S, et al. A quantitative model of thermal stabilization and destabilization of proteins by ligands. Biophys J. 2008;95(7):3222–3231. doi:10.1529/biophysj.108.134973
   PubMed Web of Science ®Google Scholar
• Dai R, Wilson DJ, Geders TW, Aldrich CC, Finzel BC. Inhibition of Mycobacterium tuberculosis transaminase BioA by aryl hydrazines and hydrazides. ChemBioChem. 2014;15(4):575–586. doi:10.1002/cbic.201300748
   PubMed Web of Science ®Google Scholar
• Backus KM, Correia BE, Lum KM, et al. Proteome-wide covalent ligand discovery in native biological systems. Nature. 2016;534(7608):570–574. doi:10.1038/nature18002
   PubMed Web of Science ®Google Scholar
• Johansson H, Isabella Tsai Y-C, Fantom K, et al. Fragment-based covalent ligand screening enables rapid discovery of inhibitors for the RBR E3 Ubiquitin Ligase HOIP. J Am Chem Soc. 2019;141(6):2703–2712. doi:10.1021/jacs.8b13193
   PubMed Web of Science ®Google Scholar
• Tan L, Akahane K, McNally R, et al. Development of selective covalent janus kinase 3 inhibitors. J Med Chem. 2015;58(16):6589–6606. doi:10.1021/acs.jmedchem.5b00710
   PubMed Web of Science ®Google Scholar
• Serafimova IM, Pufall MA, Krishnan S, et al. Reversible targeting of noncatalytic cysteines with chemically tuned electrophiles. Nat Chem Biol. 2012;8(5):471–476. doi:10.1038/nchembio.925
   PubMed Web of Science ®Google Scholar
• Pettinger J, Jones K, Cheeseman MD. Lysine-Targeting Covalent Inhibitors. Angew Chem Int Ed. 2017;56(48):15200–15209. doi:10.1002/anie.201707630
   PubMed Web of Science ®Google Scholar