A fragment-based method to discover irreversible covalent inhibitors of cysteine proteases

Journal of Medicinal Chemistry

Volumn 57, Issue 11, 2014, Pages 4969-4974

  Kathman, Stefan G ^a   Xu, Ziyang ^a   Statsyuk, Alexander V ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACRYLIC ACID; CYSTEINE PROTEASE INHIBITOR; CYSTEINE PROTEINASE; DEUBIQUITINASE; ELECTROPHILE; ENZYME INHIBITOR; PAPAIN; UBIQUITIN CONJUGATING ENZYME E2; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; CATALYSIS; CONTROLLED STUDY; DRUG PROTEIN BINDING; DRUG SCREENING; DRUG SPECIFICITY; DRUG STRUCTURE; DRUG SYNTHESIS; ENZYME ACTIVE SITE; ENZYME INHIBITION; FRAGMENT BASED DRUG DISCOVERY; HUMAN; MASS SPECTROMETRY; PROCEDURES;

ACRYLAMIDES; ACRYLATES; ANTIPARASITIC AGENTS; CYSTEINE PROTEINASE INHIBITORS; DRUG DESIGN; HUMANS; MODELS, MOLECULAR; PAPAIN; RHINOVIRUS; SMALL MOLECULE LIBRARIES; STRUCTURE-ACTIVITY RELATIONSHIP; SULFONAMIDES; SULFONES; UBIQUITIN-CONJUGATING ENZYMES; UBIQUITIN-SPECIFIC PROTEASES; VINYL COMPOUNDS; VIRAL PROTEINS;

EID: 84902438455     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm500345q     Document Type: Article

References (24)

1. Scott, D. E.; Coyne, A. G.; Hudson, S. A.; Abell, C. Fragment-Based Approaches in Drug Discovery and Chemical Biology Biochemistry 2012, 51, 4990-5003
2. Erlanson, D. A.; Braisted, A. C.; Raphael, D. R.; Randal, M.; Stroud, R. M.; Gordon, E. M.; Wells, J. A. Site-directed ligand discovery Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 9367-9372 (Pubitemid 30650781)
3. Erlanson, D. A.; Wells, J. A.; Braisted, A. C. Tethering: fragment-based drug discovery Annu. Rev. Biophys. Biomol. Struct. 2004, 33, 199-223 (Pubitemid 38829958)
4. Miller, R. M.; Paavilainen, V. O.; Krishnan, S.; Serafimova, I. M.; Taunton, J. Electrophilic fragment-based design of reversible covalent kinase inhibitors J. Am. Chem. Soc. 2013, 135, 5298-5301
5. Singh, J.; Petter, R. C.; Baillie, T. A.; Whitty, A. The resurgence of covalent drugs Nature Rev. Drug Discovery 2011, 10, 307-317
6. Zartler, E.; Shapiro, M. Fragment-Based Drug Discovery: A Practical Approach; Wiley: New York, 2008.
7. Cardoso, R.; Love, R.; Nilsson, C. L.; Bergqvist, S.; Nowlin, D.; Yan, J.; Liu, K. K.; Zhu, J.; Chen, P.; Deng, Y. L.; Dyson, H. J.; Greig, M. J.; Brooun, A. Identification of Cys255 in HIF-1α as a novel site for development of covalent inhibitors of HIF-1α/ARNT PasB domain protein-protein interaction Protein Sci. 2012, 21, 1885-1896
8. Weerapana, E.; Wang, C.; Simon, G. M.; Richter, F.; Khare, S.; Dillon, M. B.; Bachovchin, D. A.; Mowen, K.; Baker, D.; Cravatt, B. F. Quantitative reactivity profiling predicts functional cysteines in proteomes Nature 2010, 468, 790-795
9. Nonoo, R. H.; Armstrong, A.; Mann, D. J. Kinetic Template-Guided Tethering of Fragments ChemMedChem 2012, 7, 2082-2086
10. Rosenthal, P. J. Falcipains and other cysteine proteases of malaria parasites Adv. Exp. Med. Biol. 2011, 712, 30-48
11. Reddick, J. J.; Cheng, J.; Roush, W. R. Relative Rates of Michael Reactions of 2′-(Phenethyl)thiol with Vinyl Sulfones, Vinyl Sulfonate Esters, and Vinyl Sulfonamides Relevant to Vinyl Sulfonyl Cysteine Protease Inhibitors Org. Lett. 2003, 5, 1967-1970 (Pubitemid 37161970)
12. Chen, G.; Heim, A.; Riether, D.; Yee, D.; Milgrom, Y.; Gawinowicz, M. A.; Sames, D. Reactivity of Functional Groups on the Protein Surface: Development of Epoxide Probes for Protein Labeling J. Am. Chem. Soc. 2003, 125, 8130-8133 (Pubitemid 36828576)
13. Hanzlik, R. P.; Thompson, S. A. Vinylogous Amino Acid Esters: A New Class of Inactivators for Thiol Proteases J. Med. Chem. 1984, 27, 711-712 (Pubitemid 14082800)
14. Ettari, R.; Micale, N.; Schirmeister, T.; Gelhaus, C.; Leippe, M.; Nizi, E.; Di Francesco, M. E.; Grasso, S.; Zappalà, M. Novel Peptidomimetics Containing a Vinyl Ester Moiety as Highly Potent and Selective Falcipain-2 Inhibitors J. Med. Chem. 2009, 52, 2157-60
15. Patick, A. K.; Brothers, M. A.; Maldonado, F.; Binford, S.; Maldonado, O.; Fuhrman, S.; Petersen, A.; Smith, G. J., III; Zalman, L. S.; Burns-Naas, L. A.; Tran, J. Q. In Vitro Antiviral Activity and Single-Dose Pharmacokinetics in Humans of a Novel, Orally Bioavailable Inhibitor of Human Rhinovirus 3C Protease Antimicrob. Agents Chemother. 2005, 49, 2267-2275 (Pubitemid 40734453)
16. Congreve, M.; Carr, R.; Murray, C.; Jhoti, H. A. Drug Discovery Today 2003, 8, 876-877
17. Rosenthal, P. J. Falcipains and other cysteine proteases of malaria parasites Adv. Exp. Med. Biol. 2011, 712, 30-48
18. Liu, S.; Hanzlik, R. P. Structure-activity relationships for inhibition of papain by peptide Michael acceptors J. Med. Chem. 1992, 35, 1067-1075
19. 50 Values J. Biomol. Screening 2009, 14, 913-23
20. Powers, J. C.; Asgian, J. L.; Ekici, O. D.; James, K. E. Irreversible Inhibitors of Serine, Cysteine, and Threonine Proteases Chem. Rev. 2002, 102, 4639-4750
21. Renukuntla, J.; Vadlapudi, A. D.; Patel, A.; Boddu, S. H.; Mitra, A. K. Approaches for enhancing oral bioavailability of peptides and proteins Int. J. Pharm. 2013, 447, 75-93
22. Byun, S.; Lee, S. Y.; Lee, J.; Jeong, C. H.; Farrand, L.; Lim, S.; Reddy, K.; Kim, J. Y.; Lee, M. H.; Lee, H. J.; Bode, A. M.; Lee, K. W.; Dong, Z. USP8 is a novel target for overcoming gefitinib-resistance in lung cancer Clin. Cancer Res. 2013, 19, 3894-904
23. Whitcomb, E. A.; Dudek, E. J.; Liu, Q.; Taylor, A. Novel control of S phase of the cell cycle by ubiquitin-conjugating enzyme H7 Mol. Biol. Cell 2009, 20, 1-9
24. Kitz, R.; Wilson, I. B. Esters of Methanesulfonic Acid as Irreversible Inhibitors of Acetylcholinesterase J. Biol. Chem. 1962, 237, 3245-3249