References
- Williamson R. On the tretment of glycosuria and diabetes mellitus with Aspirin. Bmj. 1902;2:1946–1948.
- Roth G, Stanford N, Majerus P. Acetylation of prostaglandin synthase by aspirin. Proc Nat Acad Sci. 1975;72:3073–3076.
- Lavergne S, Park B, Naisbitt D. The roles of drug metabolism in the pathogenesis of T-cell-mediated drug hypersensitivity. Curr Opin Allergy Clin Immunol. 2008;8:299–307.
- Uetrecht J. Idiosyncratic drug reactions: past, present, and future. Chem Res Toxicol. 2008;21:84–92.
- Nakayama S, Atsumi R, Takakusa H, et al. A zone classification system for risk assessment of idiosyncratic drug toxicity using daily dose and covalent binding. Drug Metab Dispos. 2009;37:1970–1977.
- Pichler W. The p-i concept: pharmacological interaction of drugs with immune receptors. World Allergy Org. J. 2008;1:96–102.
- Johnson D, Weerapana E, Cravatt B. Strategies for discovering and derisking covalent, irreversible enzyme inhibitors. Future Med Chem. 2010;2:949–964.
- Lipton S. Paradigm shift in neuroprotection by NMDA receptor blockade: memantine and beyond. Nat Rev Drug Discov. 2006;5:160–170.
- Ohlson S. Designing transient binding drugs: a new concept for drug discovery. Drug Disc Today. 2008;13:433–439.
- Zhang R, Monsma F. The importance of drug-target residence time. Curr Opin Drug Discov Dev. 2009;12:488–496.
- Smith A, Zhang X, Leach A, et al. Beyond picomolar affinities: quantitative aspects of noncovalent and covalent binding of drugs to proteins. J Med Chem. 2009;52:225–233.
- Jann M. Rivastigmine, a new-generation cholinesterase inhibitor for the treatment of Alzheimer’s disease. Pharmacotherapy. 2000;20:1–12.
- Davids M, Brown J. Ibrutinib: a first in class covalent inhibitor of Bruton’s tyrosine kinase. Future Oncol. 2014;10:957–967.
- Holohan C, van Schaeybroeck S, Longley D, et al. Cancer drug resistance: an evolving paradigm. Nat Rev Cancer. 2013;13:714–726.
- Tan L, Wang J, Tanizaki J, et al. Development of covalent inhibitors that can overcome resistance to first-generation FGFR kinase inhibitors. Proc Nat Acad Sci U.S.A. 2014;111:E4869–E4877.
- Lagoutte R, Patouret R, Winssinger N. Covalent inhibitors: an opportunity for rational target selectivity. Curr Opin Chem Biol. 2017;39:54–63.
- Ferguson F, Gray N. Kinase inhibitors: the road ahead. Nat Rev Drug Discov. 2018;17:353–376.
- Vita E. 10 years into the resurgence of covalent drugs. Future Med Chem. 2021;13:193–210. **Useful review of covalent drugs that contains the complete list of FDA approved drugs as supplementary table.
- Du J, Yan X, Liu Z, et al. cBinderDB: a covalent binding agent database. Bioinformatics. 2016;49:1258–1260.
- Du H, Gao J, Weng G, et al. CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. Nucleic Acids Res. 2021;49:D1122–D1129. *A comprehensive database of warheads and its targets based on the literature.
- Gao M, Moumbock A, and Qaseem A, et al. CovPDB: a high-resolution coverage of the covalent protein–ligand interactome. Nucleic Acids Res. 2022;50(1):D445–D450.
- Sardi F, Manta B, Portillo-Ledesma S, et al. Determination of acidity and nucleophilicity in thiols by reaction with monobromobimane and fluorescence detection. Anal Biochem. 2013;435:74–82.
- Isom D, Castaneda C, Cannon B, et al. Large shifts in pKa values of lysine residues buried inside a protein. Proc Nat Acad Sci. 2011;108:5260–5265.
- Platzer G, Okon M, McIntosh L. PH-dependent random coil 1H, 13C, and 15N chemical shifts of the ionizable amino acids: a guide for protein pK a measurements. J Biomol NMR. 2014;60:109–129.
- Wheless J, Ramsay R, Collins S. Vigabatrin. Neurotherapeutics. 2007;4:163–172.
- Long J, Cravatt B. The metabolic serine hydrolases and their functions in mammalian physiology and disease. Chem Rev. 2011;111:6022–6063.
- Schwans J, Sunden F, Gonzalez A, et al. Uncovering the determinants of a highly perturbed tyrosine pka in the active site of ketosteroid isomerase. Biochemistry. 2013;52:7840–7855.
- Elledge S, Tran H, Christian A, et al. Systematic identification of engineered methionines and oxaziridines for efficient, stable, and site-specific antibody bioconjugation. Proc Nat Acad Sci. 2020;117:5733–5740.
- Gehringer M, Laufer S. Emerging and re-emerging warheads for targeted covalent inhibitors: applications in medicinal chemistry and chemical biology. J Med Chem. 2019;62:5673–5724. *A comprehensive review of warheads available for many amino acids.
- Hamarsheh S, Osswald L, Saller B, et al. Oncogenic KrasG12D causes myeloproliferation via NLRP3 inflammasome activation. Nat Commun. 2020;11:1659.
- Smith E, Collins I. Photoaffinity labeling in target-and binding-site identification. Future Med Chem. 2015;7:159–183. *A comprehensive review on photoaffinity labeling.
- Fleming S A. Chemical reagents in photoaffinity labeling. Tetrahedron. 1995;51:12479–12520.
- Sakurai K, Ozawa S, Yamada R, et al. Comparison of the reactivity of carbohydrate photoaffinity probes with different photoreactive groups. Chem Bio Chem. 2014;15:1399–1403.
- Dzubak P, Hajduch M, Vydra D, et al. Pharmacological activities of natural triterpenoids and their therapeutic implications. Nat Prod Rep. 2006;23:394–411.
- Shi H, Zhang C, Chen G, et al. Cell-based proteome profiling of potential Dasatinib targets by use of affinity-based probes. J Am Chem Soc. 2012;134:3001–3014.
- Hamouda A, Stewart D, Husain S, et al. Multiple transmembrane binding sites for p-trifluoromethyldiazirinyl- etomidate, a photoreactive Torpedo nicotinic acetylcholine receptor allosteric inhibitor. J Biol Chem. 2011;286:20466–20477.
- Hamouda A, Stewart D, Chiara D, et al. Identifying barbiturate binding sites in a nicotinic acetylcholine receptor with [3H]allyl m-trifluoromethyldiazirine mephobarbital, a photoreactive barbiturate. Mol Pharmacol. 2014;85:735–746.
- Chiara D, Jayakar S, Zhou X, et al. Specificity of intersubunit general anesthetic-binding sites in the transmembrane domain of the human α1β3γ2 α-aminobutyric acid type A (GABAA) receptor. J Biol Chem. 2013;288:19343–19357.
- Balaratnam S, Rhodes C, Bume D, et al. A chemical probe based on the PreQ1 metabolite enables transcriptome-wide mapping of binding sites. Nat Commun. 2021;12:5856.
- Browne CM, Jiang B, Ficarro SB, et al. A chemoproteomic strategy for direct and proteome-wide covalent inhibitor target-site identification. J Am Chem Soc. 2019;141:191–203.
- Kuljanin M, Mitchell DC, Schweppe DK, et al. Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries. Nat Biotechnol. 2021;39:630–641.
- Ohata J, Miller M, Mountain C, et al. A three‐component organometallic tyrosine bioconjugation. Angew Chem Int Ed. 2018;130:2877–2880.
- Seki Y, Ishiyama T, Sasaki D, et al. Transition metal-free tryptophan-selective bioconjugation of proteins. J Am Chem Soc. 2016;138:10798–10801.
- Tower S, Hetcher W, Myers T, et al. Selective modification of tryptophan residues in peptides and proteins using a biomimetic electron transfer process. J Am Chem Soc. 2020;142:9112–9118.
- Chen X, Ye F, Luo X, et al. Histidine-Specific peptide modification via visible-light-promoted C-H alkylation. J Am Chem Soc. 2019;141:18230–18237.
- Taylor MT, Nelson JE, Suero MG, et al. A protein functionalization platform based on selective reactions at methionine residues. Nature. 2018;562:563–568.
- Klimánková I, Hubálek M, Matoušek V, et al. Synthesis of water-soluble hypervalent iodine reagents for fluoroalkylation of biological thiols. Org Biomol Chem. 2019;17:10097–10102.
- Powers JC, Asgian JL, Ekici ÖD, et al. Irreversible inhibitors of serine, cysteine, and threonine proteases. Chem Rev. 2002;102:4639–4750.
- Hoch DG, Abegg D, Adibekian A. Cysteine-reactive probes and their use in chemical proteomics. Chem Commun. 2018;54:4501–4512.
- 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.
- Zhao Z, Bourne PE. Progress with covalent small-molecule kinase inhibitors. Drug Disc Today. 2018;23:727–735.
- Macegoniuk K, Grela E, Palus J, et al. 1,2-Benzisoselenazol-3(2H)-one derivatives as a new class of bacterial urease inhibitors. J Med Chem. 2016;59:8125–8133.
- Fuller S, Denyer S, Hugo W, et al. The mode of action of 1,2-benzisothiazolin-3-one on Staphylococcus aureus. Lett Appl Microbiol. 1985;1:13–15.
- Bornstein S. Action of penicillin on enterococci and other streptococci. J Bacteriol. 1940;39:383–387.
- Charalambous A, Schwarzbich M, Witzens-Harig M. Ibrutinib. Recent Results Cancer Res. 2018;212:133–168.
- Wecker H, Waller C. Afatinib. Recent Results Cancer Res. 2018;211:199–215.
- Cambray S, Gao J. Versatile bioconjugation chemistries of ortho-boronyl aryl ketones and aldehydes. Acc Chem Res. 2018;51:2198–2206.
- Miller RM, Paavilainen VO, Krishnan S, et al. Electrophilic fragment-based design of reversible covalent kinase inhibitors. J Am Chem Soc. 2013;135:5298–5301.
- Luo YL. Mechanism-Based and computational-driven covalent drug design. J Chem Inf Model. 2021;61:5307–5311.
- Świderek K, Moliner V. Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 Mproby QM/MM computational methods. Chem Sci. 2020;11:10626–10630.
- Arafet K, Serrano-Aparicio N, Lodola A, et al. Mechanism of inhibition of SARS-CoV-2 MprobyN3peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity. Chem Sci. 2021;12:1433–1444.
- Mihalovits LM, Ferenczy GG, and Keserű GM. The role of quantum chemistry in covalent inhibitor design. Int J Quantum Chem. 2021;121:1–17.
- Lonsdale R, Burgess J, Colclough N, et al. Expanding the armory: predicting and tuning covalent warhead reactivity. J Chem Inf Model. 2017;57:3124–3137.
- Mihalovits LM, Ferenczy GG, Keserü GM. Affinity and selectivity assessment of covalent inhibitors by free energy calculations. J Chem Inf Model. 2020;60:6579–6594.
- Awoonor-Williams E, Abu-Saleh AAAA. Covalent and non-covalent binding free energy calculations for peptidomimetic inhibitors of SARS-CoV-2 main protease. Phys Chem Chem Phys. 2021;23:6746–6757.
- Scarpino A, Ferenczy GG, Keserü GM. Comparative evaluation of covalent docking tools. J Chem Inf Model. 2018;58:1441–1458.
- Martin JS, MacKenzie CJ, Fletcher D, et al. Characterising covalent warhead reactivity. Bioorg Med Chem. 2019;27:2066–2074.
- 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;57:10072–10079. **A robust and general protocol for the systematic investigation of covalent inhibitors.
- Petri L, Ábrányi-Balogh P, Varga PR, et al. Comparative reactivity analysis of small-molecule thiol surrogates. Bioorg Med Chem. 2020;22:743–753.
- Mukherjee H, Debreczeni J, Breed J, et al. A study of the reactivity of S(VI)-F containing warheads with nucleophilic amino-acid side chains under physiological conditions. Org Biomol Chem. 2017;15:9685–9695.
- Petri L, Ábrányi-Balogh P, Tímea I, et al. Assessment of tractable cysteines for covalent targeting by screening covalent fragments. Chem Bio Chem. 2021;22:743–753.
- Petri L, Egyed A, Bajusz D, et al. An electrophilic warhead library for mapping the reactivity and accessibility of tractable cysteines in protein kinases. Eur J Med Chem. 2020;207:112836.
- Backus KM, Correia BE, Lum KM, et al. Proteome-wide covalent ligand discovery in native biological systems. Nature. 2016;534:570–574. **Proteome-wide screening of covalent fragments.
- Abbasov M, Kavanagh M, Ichu T, et al. A proteome-wide atlas of lysine-reactive chemistry. Nat Chem. 2021;13:1081–1092.
- Cheng K, Lee J, Hao P, et al. Tetrazole-Based probes for integrated phenotypic screening, affinity-based proteome profiling, and sensitive detection of a cancer biomarker. Angew Chem Int Ed. 2017;56:15044–15048.
- Bach K, Beerkens B, Zanon P, et al. Light-Activatable, 2,5-Disubstituted tetrazoles for the proteome-wide profiling of aspartates and glutamates in living bacteria. ACS Cent Sci. 2020;6:546–554.
- Ma N, Hu J, Zhang Z, et al. 2 H-Azirine-Based reagents for chemoselective bioconjugation at carboxyl residues inside live cells. J Am Chem Soc. 2020;142:6051–6059.
- Lin S, Yang X, Jia S, et al. Redox-based reagents for chemoselective methionine bioconjugation. Science. 2017;355:597–602.
- Hahm H, Toroitich E, Borne A, et al. Global targeting of functional tyrosines using sulfur-triazole exchange chemistry. Nat Chem Biol. 2020;16:150–159.