Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

New approaches for dissecting protease functions to improve probe development and drug discovery

Nature Structural & Molecular Biology volume 19, pages 9–16 (2012)Cite this article

Subjects

Abstract

Proteases are well-established targets for pharmaceutical development because of their known enzymatic mechanism and their regulatory roles in many pathologies. However, many potent clinical lead compounds have been unsuccessful either because of a lack of specificity or because of our limited understanding of the biological roles of the targeted protease. In order to successfully develop protease inhibitors as drugs, it is necessary to understand protease functions and to expand the platform of inhibitor development beyond active site–directed design and in vitro optimization. Several newly developed technologies will enhance assessment of drug selectivity in living cells and animal models, allowing researchers to focus on compounds with high specificity and minimal side effects in vivo. In this review, we highlight advances in the development of chemical probes, proteomic methods and screening tools that we feel will help facilitate this paradigm shift in drug discovery.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Mechanism of substrate hydrolysis by the primary families of proteases.
Figure 2: Schematic presentation of the hit-to-lead process.
Figure 3: Activity-based probes report on tightly regulated protease activity.
Figure 4: Chemical tools to study protease function and to measure target inhibition.

Similar content being viewed by others

References

  1. Drag, M. & Salvesen, G.S. Emerging principles in protease-based drug discovery. Nat. Rev. Drug Discov. 9, 690–701 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Rawlings, N.D., Barrett, A.J. & Bateman, A. Asparagine peptide lyases: a seventh catalytic type of proteolytic enzymes. J. Biol. Chem. 286, 38321–38328 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Powers, J.C., Asgian, J.L., Ekici, O.D. & James, K.E. Irreversible inhibitors of serine, cysteine, and threonine proteases. Chem. Rev. 102, 4639–4750 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Johnson, S.L. & Pellecchia, M. Structure- and fragment-based approaches to protease inhibition. Curr. Top. Med. Chem. 6, 317–329 (2006).

    Article  CAS  PubMed  Google Scholar 

  5. Turk, B. Targeting proteases: successes, failures and future prospects. Nat. Rev. Drug Discov. 5, 785–799 (2006).

    Article  CAS  PubMed  Google Scholar 

  6. Shen, A. Allosteric regulation of protease activity by small molecules. Mol. Biosyst. 6, 1431–1443 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Bock, P.E., Panizzi, P. & Verhamme, I.M. Exosites in the substrate specificity of blood coagulation reactions. J. Thromb. Haemost. 5 (suppl. 1), 81–94 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Conus, S. & Simon, H.U. Cathepsins and their involvement in immune responses. Swiss Med. Wkly. 140, w13042 (2010).

    PubMed  Google Scholar 

  9. Lupardus, P.J., Shen, A., Bogyo, M. & Garcia, K.C. Small molecule-induced allosteric activation of the Vibrio cholerae RTX cysteine protease domain. Science 322, 265–268 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Bauernfeind, F. et al. Inflammasomes: current understanding and open questions. Cell Mol. Life Sci. 68, 765–783 (2011).

    Article  CAS  PubMed  Google Scholar 

  11. Edgington, L.E. et al. Noninvasive optical imaging of apoptosis by caspase-targeted activity-based probes. Nat. Med. 15, 967–973 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Mason, S.D. & Joyce, J.A. Proteolytic networks in cancer. Trends Cell Biol. 21, 228–237 (2011).

    Article  CAS  PubMed  Google Scholar 

  13. López-Otín, C. & Hunter, T. The regulatory crosstalk between kinases and proteases in cancer. Nat. Rev. Cancer 10, 278–292 (2010).

    Article  PubMed  CAS  Google Scholar 

  14. Smith, D.M., Fraga, H., Reis, C., Kafri, G. & Goldberg, A.L. ATP binds to proteasomal ATPases in pairs with distinct functional effects, implying an ordered reaction cycle. Cell 144, 526–538 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Palermo, C. & Joyce, J.A. Cysteine cathepsin proteases as pharmacological targets in cancer. Trends Pharmacol. Sci. 29, 22–28 (2008).

    Article  CAS  PubMed  Google Scholar 

  16. Overall, C.M. & Kleifeld, O. Tumour microenvironment - opinion: validating matrix metalloproteinases as drug targets and anti-targets for cancer therapy. Nat. Rev. Cancer 6, 227–239 (2006).

    Article  CAS  PubMed  Google Scholar 

  17. Omara-Opyene, A.L. et al. Genetic disruption of the Plasmodium falciparum digestive vacuole plasmepsins demonstrates their functional redundancy. J. Biol. Chem. 279, 54088–54096 (2004).

    Article  CAS  PubMed  Google Scholar 

  18. Deu, E. et al. Functional studies of Plasmodium falciparum dipeptidyl aminopeptidase I using small molecule inhibitors and active site probes. Chem. Biol. 17, 808–819 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Klemba, M., Gluzman, I. & Goldberg, D.E. A Plasmodium falciparum dipeptidyl aminopeptidase I participates in vacuolar hemoglobin degradation. J. Biol. Chem. 279, 43000–43007 (2004).

    Article  CAS  PubMed  Google Scholar 

  20. Dalal, S. & Klemba, M. Roles for two aminopeptidases in vacuolar hemoglobin catabolism in Plasmodium falciparum. J. Biol. Chem. 282, 35978–35987 (2007).

    Article  CAS  PubMed  Google Scholar 

  21. Sadaghiani, A.M., Verhelst, S.H. & Bogyo, M. Tagging and detection strategies for activity-based proteomics. Curr. Opin. Chem. Biol. 11, 20–28 (2007).

    Article  CAS  PubMed  Google Scholar 

  22. Cravatt, B.F., Wright, A.T. & Kozarich, J.W. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem. 77, 383–414 (2008).

    Article  CAS  PubMed  Google Scholar 

  23. Desmarais, S., Masse, F. & Percival, M.D. Pharmacological inhibitors to identify roles of cathepsin K in cell-based studies: a comparison of available tools. Biol. Chem. 390, 941–948 (2009).

    Article  CAS  PubMed  Google Scholar 

  24. Paulick, M.G. & Bogyo, M. Application of activity-based probes to the study of enzymes involved in cancer progression. Curr. Opin. Genet. Dev. 18, 97–106 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Blum, G. Use of fluorescent imaging to investigate pathological protease activity. Curr. Opin. Drug Discov. Devel. 11, 708–716 (2008).

    CAS  PubMed  Google Scholar 

  26. Meng, L., Kwok, B.H., Sin, N. & Crews, C.M. Eponemycin exerts its antitumor effect through the inhibition of proteasome function. Cancer Res. 59, 2798–2801 (1999).

    CAS  PubMed  Google Scholar 

  27. Sin, N. et al. Total synthesis of the potent proteasome inhibitor epoxomicin: a useful tool for understanding proteasome biology. Bioorg. Med. Chem. Lett. 9, 2283–2288 (1999).

    Article  CAS  PubMed  Google Scholar 

  28. Arastu-Kapur, S. et al. Identification of proteases that regulate erythrocyte rupture by the malaria parasite Plasmodium falciparum. Nat. Chem. Biol. 4, 203–213 (2008).

    Article  CAS  PubMed  Google Scholar 

  29. Chang, J.W., Nomura, D.K. & Cravatt, B.F. A potent and selective inhibitor of KIAA1363/AADACL1 that impairs prostate cancer pathogenesis. Chem. Biol. 18, 476–484 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Ahn, K. et al. Discovery and characterization of a highly selective FAAH inhibitor that reduces inflammatory pain. Chem. Biol. 16, 411–420 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Staub, I. & Sieber, S.A. Beta-lactam probes as selective chemical-proteomic tools for the identification and functional characterization of resistance associated enzymes in MRSA. J. Am. Chem. Soc. 131, 6271–6276 (2009).

    Article  CAS  PubMed  Google Scholar 

  32. Adibekian, A. et al. Click-generated triazole ureas as ultrapotent in vivo-active serine hydrolase inhibitors. Nat. Chem. Biol. 7, 469–478 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Jain, S., Diefenbach, C., Zain, J. & O'Connor, O.A. Emerging role of carfilzomib in treatment of relapsed and refractory lymphoid neoplasms and multiple myeloma. Core Evid. 6, 43–57 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hall, C.I. et al. Chemical genetic screen identifies Toxoplasma DJ-1 as a regulator of parasite secretion, attachment, and invasion. Proc. Natl. Acad. Sci. USA 108, 10568–10573 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Chandramohanadas, R. et al. Apicomplexan parasites co-opt host calpains to facilitate their escape from infected cells. Science 324, 794–797 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Gocheva, V. et al. IL-4 induces cathepsin protease activity in tumor-associated macrophages to promote cancer growth and invasion. Genes Dev. 24, 241–255 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Berger, A.B. et al. Identification of early intermediates of caspase activation using selective inhibitors and activity-based probes. Mol. Cell 23, 509–521 (2006).

    Article  CAS  PubMed  Google Scholar 

  38. Méthot, N. et al. In vivo inhibition of serine protease processing requires a high fractional inhibition of cathepsin C. Mol. Pharmacol. 73, 1857–1865 (2008).

    Article  PubMed  CAS  Google Scholar 

  39. Blum, G., von Degenfeld, G., Merchant, M.J., Blau, H.M. & Bogyo, M. Noninvasive optical imaging of cysteine protease activity using fluorescently quenched activity-based probes. Nat. Chem. Biol. 3, 668–677 (2007).

    Article  CAS  PubMed  Google Scholar 

  40. Blum, G., Weimer, R.M., Edgington, L.E., Adams, W. & Bogyo, M. Comparative assessment of substrates and activity based probes as tools for non-invasive optical imaging of cysteine protease activity. PLoS ONE 4, e6374 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Hagel, M. et al. Selective irreversible inhibition of a protease by targeting a noncatalytic cysteine. Nat. Chem. Biol. 7, 22–24 (2011).

    Article  CAS  PubMed  Google Scholar 

  42. Blair, J.A. et al. Structure-guided development of affinity probes for tyrosine kinases using chemical genetics. Nat. Chem. Biol. 3, 229–238 (2007).

    Article  CAS  PubMed  Google Scholar 

  43. Agard, N.J., Maltby, D. & Wells, J.A. Inflammatory stimuli regulate caspase substrate profiles. Mol. Cell. Proteomics 9, 880–893 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. auf dem Keller, U. et al. Novel matrix metalloproteinase inhibitor [18F]marimastat-aryltrifluoroborate as a probe for in vivo positron emission tomography imaging in cancer. Cancer Res. 70, 7562–7569 (2010).

    Article  CAS  PubMed  Google Scholar 

  45. Bowyer, P.W., Simon, G.M., Cravatt, B.F. & Bogyo, M. Global profiling of proteolysis during rupture of Plasmodium falciparum from the host erythrocyte. Mol. Cell Proteomics 10, M110.001636 (2011).

    Article  PubMed  CAS  Google Scholar 

  46. Enoksson, M. et al. Identification of proteolytic cleavage sites by quantitative proteomics. J. Proteome Res. 6, 2850–2858 (2007).

    Article  CAS  PubMed  Google Scholar 

  47. Kleifeld, O. et al. Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat. Biotechnol. 28, 281–288 (2010).

    Article  CAS  PubMed  Google Scholar 

  48. Mahrus, S. et al. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 134, 866–876 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. auf dem Keller, U., Prudova, A., Gioia, M., Butler, G.S. & Overall, C.M. A statistics-based platform for quantitative N-terminome analysis and identification of protease cleavage products. Mol. Cell Proteomics 9, 912–927 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Simon, G.M., Dix, M.M. & Cravatt, B.F. Comparative assessment of large-scale proteomic studies of apoptotic proteolysis. ACS Chem. Biol. 4, 401–408 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Wildes, D. & Wells, J.A. Sampling the N-terminal proteome of human blood. Proc. Natl. Acad. Sci. USA 107, 4561–4566 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Staes, A. et al. Selecting protein N-terminal peptides by combined fractional diagonal chromatography. Nat. Protoc. 6, 1130–1141 (2011).

    Article  CAS  PubMed  Google Scholar 

  53. Prudova, A., auf dem Keller, U., Butler, G.S. & Overall, C.M. Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics. Mol. Cell Proteomics 9, 894–911 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Schilling, O., Barre, O., Huesgen, P.F. & Overall, C.M. Proteome-wide analysis of protein carboxy termini: C terminomics. Nat. Methods 7, 508–511 (2010).

    Article  CAS  PubMed  Google Scholar 

  55. Timmer, J.C. et al. Profiling constitutive proteolytic events in vivo. Biochem. J. 407, 41–48 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Gray, D.C., Mahrus, S. & Wells, J.A. Activation of specific apoptotic caspases with an engineered small-molecule-activated protease. Cell 142, 637–646 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Truebestein, L. et al. Substrate-induced remodeling of the active site regulates human HTRA1 activity. Nat. Struct. Mol. Biol. 18, 386–388 (2011).

    Article  CAS  PubMed  Google Scholar 

  58. Vaidya, S., Velazquez-Delgado, E.M., Abbruzzese, G. & Hardy, J.A. Substrate-induced conformational changes occur in all cleaved forms of caspase-6. J. Mol. Biol. 406, 75–91 (2011).

    Article  CAS  PubMed  Google Scholar 

  59. Hardy, J.A. & Wells, J.A. Dissecting an allosteric switch in caspase-7 using chemical and mutational probes. J. Biol. Chem. 284, 26063–26069 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Scheer, J.M., Romanowski, M.J. & Wells, J.A. A common allosteric site and mechanism in caspases. Proc. Natl. Acad. Sci. USA 103, 7595–7600 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Schneck, J.L. et al. Chemical mechanism of a cysteine protease, cathepsin C, as revealed by integration of both steady-state and pre-steady-state solvent kinetic isotope effects. Biochemistry 47, 8697–8710 (2008).

    Article  CAS  PubMed  Google Scholar 

  62. Patricelli, M.P. et al. In situ kinase profiling reveals functionally relevant properties of native kinases. Chem. Biol. 18, 699–710 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Sheahan, K.L., Cordero, C.L. & Satchell, K.J. Autoprocessing of the Vibrio cholerae RTX toxin by the cysteine protease domain. EMBO J. 26, 2552–2561 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Shen, A. et al. Mechanistic and structural insights into the proteolytic activation of Vibrio cholerae MARTX toxin. Nat. Chem. Biol. 5, 469–478 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Puri, A.W. et al. Rational design of inhibitors and activity-based probes targeting Clostridium difficile virulence factor TcdB. Chem. Biol. 17, 1201–1211 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Falgueyret, J.P. et al. Lysosomotropism of basic cathepsin K inhibitors contributes to increased cellular potencies against off-target cathepsins and reduced functional selectivity. J. Med. Chem. 48, 7535–7543 (2005).

    Article  CAS  PubMed  Google Scholar 

  67. Deu, E., Yang, Z., Wang, F., Klemba, M. & Bogyo, M. Use of activity-based probes to develop high throughput screening assays that can be performed in complex cell extracts. PLoS ONE 5, e11985 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  68. Thong, B., Pilling, J., Ainscow, E., Beri, R. & Unitt, J. Development and validation of a simple cell-based fluorescence assay for dipeptidyl peptidase 1 (DPP1) activity. J. Biomol. Screen. 16, 36–43 (2011).

    Article  CAS  PubMed  Google Scholar 

  69. Wakata, A. et al. Simultaneous fluorescent monitoring of proteasomal subunit catalysis. J. Am. Chem. Soc. 132, 1578–1582 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Poreba, M. & Drag, M. Current strategies for probing substrate specificity of proteases. Curr. Med. Chem. 17, 3968–3995 (2010).

    Article  CAS  PubMed  Google Scholar 

  71. Whitney, M. et al. Parallel in vivo and in vitro selection using phage display identifies protease-dependent tumor-targeting peptides. J. Biol. Chem. 285, 22532–22541 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Greenbaum, D.C. et al. A role for the protease falcipain 1 in host cell invasion by the human malaria parasite. Science 298, 2002–2006 (2002).

    Article  CAS  PubMed  Google Scholar 

  73. Sadaghiani, A.M. et al. Design, synthesis, and evaluation of in vivo potency and selectivity of epoxysuccinyl-based inhibitors of papain-family cysteine proteases. Chem. Biol. 14, 499–511 (2007).

    Article  CAS  PubMed  Google Scholar 

  74. Albrow, V.E. et al. Development of small molecule inhibitors and probes of human SUMO deconjugating proteases. Chem. Biol. 18, 722–732 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Ponder, E.L. et al. Functional characterization of a SUMO deconjugating protease of Plasmodium falciparum using newly identified small molecule inhibitors. Chem. Biol. 18, 711–721 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Patterson, A.W., Wood, W.J. & Ellman, J.A. Substrate activity screening (SAS): a general procedure for the preparation and screening of a fragment-based non-peptidic protease substrate library for inhibitor discovery. Nat. Protoc. 2, 424–433 (2007).

    Article  CAS  PubMed  Google Scholar 

  77. Patterson, A.W. et al. Identification of selective, nonpeptidic nitrile inhibitors of cathepsin s using the substrate activity screening method. J. Med. Chem. 49, 6298–6307 (2006).

    Article  CAS  PubMed  Google Scholar 

  78. Brak, K., Doyle, P.S., McKerrow, J.H. & Ellman, J.A. Identification of a new class of nonpeptidic inhibitors of cruzain. J. Am. Chem. Soc. 130, 6404–6410 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Brak, K. et al. Nonpeptidic tetrafluorophenoxymethyl ketone cruzain inhibitors as promising new leads for Chagas disease chemotherapy. J. Med. Chem. 53, 1763–1773 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Bachovchin, D.A. et al. Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening. Proc. Natl. Acad. Sci. USA 107, 20941–20946 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Ahn, K. et al. Novel mechanistic class of fatty acid amide hydrolase inhibitors with remarkable selectivity. Biochemistry 46, 13019–13030 (2007).

    Article  CAS  PubMed  Google Scholar 

  82. Speers, A.E. & Cravatt, B.F. Profiling enzyme activities in vivo using click chemistry methods. Chem. Biol. 11, 535–546 (2004).

    Article  CAS  PubMed  Google Scholar 

  83. Berkers, C.R. et al. Activity probe for in vivo profiling of the specificity of proteasome inhibitor bortezomib. Nat. Methods 2, 357–362 (2005).

    Article  CAS  PubMed  Google Scholar 

  84. Arastu-Kapur, S. et al. Nonproteasomal targets of the proteasome inhibitors bortezomib and carfilzomib: a link to clinical adverse events. Clin. Cancer Res. 17, 2734–2743 (2011).

    Article  CAS  PubMed  Google Scholar 

  85. Desmarais, S. et al. Effect of cathepsin k inhibitor basicity on in vivo off-target activities. Mol. Pharmacol. 73, 147–156 (2008).

    Article  CAS  PubMed  Google Scholar 

  86. Gauthier, J.Y. et al. The discovery of odanacatib (MK-0822), a selective inhibitor of cathepsin K. Bioorg. Med. Chem. Lett. 18, 923–928 (2008).

    Article  CAS  PubMed  Google Scholar 

  87. Geurink, P. et al. A peptide hydroxamate library for enrichment of metalloproteinases: towards an affinity-based metalloproteinase profiling protocol. Org. Biomol. Chem. 6, 1244–1250 (2008).

    Article  CAS  PubMed  Google Scholar 

  88. Saghatelian, A., Jessani, N., Joseph, A., Humphrey, M. & Cravatt, B.F. Activity-based probes for the proteomic profiling of metalloproteases. Proc. Natl. Acad. Sci. USA 101, 10000–10005 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Harbut, M.B. et al. Bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases. Proc. Natl. Acad. Sci. USA 108, E526–E534 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Sieber, S.A., Niessen, S., Hoover, H.S. & Cravatt, B.F. Proteomic profiling of metalloprotease activities with cocktails of active-site probes. Nat. Chem. Biol. 2, 274–281 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Nakai, R., Salisbury, C.M., Rosen, H. & Cravatt, B.F. Ranking the selectivity of PubChem screening hits by activity-based protein profiling: MMP13 as a case study. Bioorg. Med. Chem. 17, 1101–1108 (2009).

    Article  CAS  PubMed  Google Scholar 

  92. Li, Y.M. et al. Photoactivated gamma-secretase inhibitors directed to the active site covalently label presenilin 1. Nature 405, 689–694 (2000).

    Article  CAS  PubMed  Google Scholar 

  93. Weerapana, E. et al. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature 468, 790–795 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors thank Dr. Christopher Kirk for his comments and suggestions. This work was funded by NIH grants R01 EB005011 and R01 AI078947 (to M.B.) and a Rubicon grant from The Netherlands Organization for Scientific Research (NWO) (to M.V.).

Author information

Authors and Affiliations

  1. Department of Pathology, Stanford University School of Medicine, Stanford, California, USA

    Edgar Deu, Martijn Verdoes & Matthew Bogyo

  2. Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA

    Matthew Bogyo

Authors
  1. Edgar Deu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martijn Verdoes
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Matthew Bogyo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Matthew Bogyo.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Box 1 (PDF 70 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Deu, E., Verdoes, M. & Bogyo, M. New approaches for dissecting protease functions to improve probe development and drug discovery. Nat Struct Mol Biol 19, 9–16 (2012). https://doi.org/10.1038/nsmb.2203

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.2203

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing