Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 7, 2014, Pages 2518-2523

  Kasperkiewicz, Paulina ^a   Poreba, Marcin ^a   Snipas, Scott J ^b   Parker, Heather ^c   Winterbourn, Christine C ^c   Salvesen, Guy S ^b,c   Drag, Marcin ^a,b  

^a WROCLAW UNIVERSITY OF TECHNOLOGY   (Poland)

^b BURNHAM INSTITUTE   (United States)

^c UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING SITES; COMBINATORIAL CHEMISTRY TECHNIQUES; GENE LIBRARY; HUMANS; KINETICS; LEUKOCYTE ELASTASE; MOLECULAR PROBES; MOLECULAR STRUCTURE; SUBSTRATE SPECIFICITY;

EID: 84894352703     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1318548111     Document Type: Article

References (35)

1. Drag M, Salvesen GS (2010) Emerging principles in protease-based drug discovery. Nat Rev Drug Discov 9(9):690-701.
2. Turk B (2006) Targeting proteases: Successes, failures and future prospects. Nat Rev Drug Discov 5(9):785-799.
3. Poreba M, Drag M (2010) Current strategies for probing substrate specificity of proteases. Curr Med Chem 17(33):3968-3995.
4. Lim MD, Craik CS (2009) Using specificity to strategically target proteases. Bioorg Med Chem 17(3):1094-1100.
5. Choe Y, et al. (2006) Substrate profiling of cysteine proteases using a combinatorial peptide library identifies functionally unique specificities. J Biol Chem 281(18): 12824-12832.
6. Harris JL, et al. (2000) Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries. Proc Natl Acad Sci USA 97(14): 7754-7759.
7. Kasperkiewicz P, Gajda AD, Dra̧ g M (2012) Current and prospective applications of non-proteinogenic amino acids in profiling of proteases substrate specificity. Biol Chem 393(9):843-851.
8. Deu E, Verdoes M, Bogyo M (2012) New approaches for dissecting protease functions to improve probe development and drug discovery. Nat Struct Mol Biol 19(1):9-16.
9. Rano TA, et al. (1997) A combinatorial approach for determining protease specificities: Application to interleukin-1beta converting enzyme (ICE). Chem Biol 4(2): 149-155.
10. Schechter I, Berger A (1967) On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun 27(2):157-162.
11. Drag M, Bogyo M, Ellman JA, Salvesen GS (2010) Aminopeptidase fingerprints, an integrated approach for identification of good substrates and optimal inhibitors. J Biol Chem 285(5):3310-3318.
12. Zervoudi E, et al. (2011) Probing the S1 specificity pocket of the aminopeptidases that generate antigenic peptides. Biochem J 435(2):411-420.
13. Poreba M, et al. (2012) Fingerprinting the substrate specificity of M1 and M17 aminopeptidases of human malaria, Plasmodium falciparum. PLoS ONE 7(2):e31938.
14. Korkmaz B, Horwitz MS, Jenne DE, Gauthier F (2010) Neutrophil elastase, proteinase 3, and cathepsin G as therapeutic targets in human diseases. Pharmacol Rev 62(4): 726-759.
15. Moroy G, Alix AJ, Sapi J, Hornebeck W, Bourguet E (2012) Neutrophil elastase as a target in lung cancer. Anticancer Agents Med Chem 12(6):565-579.
16. Rawlings ND, Barrett AJ, Bateman A (2012) MEROPS: The database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 40(Database issue): D343-D350.
17. Korkmaz B, et al. (2012) Measurement of neutrophil elastase, proteinase 3, and cathepsin G activities using intramolecularly quenched fluorogenic substrates. Methods Mol Biol 844:125-138.
18. Maly DJ, et al. (2002) Expedient solid-phase synthesis of fluorogenic protease substrates using the 7-amino-4-carbamoylmethylcoumarin (ACC) fluorophore. J Org Chem 67(3):910-915.
19. Schilling O, Overall CM (2008) Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites. Nat Biotechnol 26(6):685-694.
20. Castillo MJ, Nakajima K, Zimmerman M, Powers JC (1979) Sensitive substrates for human leukocyte and porcine pancreatic elastase: A study of the merits of various chromophoric and fluorogenic leaving groups in assays for serine proteases. Anal Biochem 99(1):53-64.
21. Rao NV, Hoidal JR (2013) Myeloblastin. Handbook of Proteolytic Enzymes, ed Rawlings ND, Salvesen G (Academic Press, London), 3rd Ed, pp 2666-2675.
22. Soroka M, Goldeman W (2007) Polish Patent PL 196222.
23. Salvesen GS, Nagase H (2001) Inhibition of proteolytic enzymes. Proteolytic Enzymes: A Practical Approach, ed Bond JS, Beynon RJ (Oxford University Press, Oxford), 2nd Ed, pp 105-130.
24. Watorek W, Farley D, Salvesen G, Travis J (1988) Neutrophil elastase and cathepsin G: Structure, function, and biological control. Adv Exp Med Biol 240:23-31.
25. Parker H, Dragunow M, Hampton MB, Kettle AJ, Winterbourn CC (2012) Requirements for NADPH oxidase and myeloperoxidase in neutrophil extracellular trap formation differ depending on the stimulus. J Leukoc Biol 92(4):841-849.
26. Urban CF, et al. (2009) Neutrophil extracellular traps contain calprotectin, a cytosolic protein complex involved in host defense against Candida albicans. PLoS Pathog 5(10):e1000639.
27. Fuchs TA, et al. (2007) Novel cell death program leads to neutrophil extracellular traps. J Cell Biol 176(2):231-241.
28. Sexton KB, Witte MD, Blum G, Bogyo M (2007) Design of cell-permeable, fluorescent activity-based probes for the lysosomal cysteine protease asparaginyl endopeptidase (AEP)/legumain. Bioorg Med Chem Lett 17(3):649-653.
29. Bogyo M, et al. (2004) Applications for chemical probes of proteolytic activity. Curr Protoc Protein Sci Chapter 21:Unit 21.17.
30. Liu Y, Patricelli MP, Cravatt BF (1999) Activity-based protein profiling: The serine hydrolases. Proc Natl Acad Sci USA 96(26):14694-14699.
31. Brinkmann V, Zychlinsky A (2012) Neutrophil extracellular traps: Is immunity the second function of chromatin? J Cell Biol 198(5):773-783.
32. Barrientos L, et al. (2013) An improved strategy to recover large fragments of functional human neutrophil extracellular traps. Front Immunol, 24;4:166-175.
33. Papayannopoulos V, Metzler KD, Hakkim A, Zychlinsky A (2010) Neutrophil elastase and myeloperoxidase regulate the formation of neutrophil extracellular traps. J Cell Biol 191(3):677-691.
34. Bode W, et al. (1986) X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor. EMBO J 5(10):2453-2458.
35. Sie-nczyk M, Oleksyszyn J (2009) Irreversible inhibition of serine proteases-design and in vivo activity of diaryl alpha-aminophosphonate derivatives. Curr Med Chem 16(13): 1673-1687.