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Publications from the Center on Proteolytic Pathways

 

1. Chehade, K.A.H., Baruch, A., Verhelst, S.H.L., and Bogyo, M. (2005) An improved preparation of the activity-based probe JPM-OEt and in situ applications. Synthesis, 2, pp. 240-244.

2. Soulié P., Carrozzino F., Pepper M.S., Strongin A.Y., Poupon M-F, Montesano R (2005) Membrane-type-1 matrix metalloproteinase confers tumorigenicity on non-malignant epithelial cells. Oncogene, 24, 1689-1697.

3. Kato, D., Boatright, K.M., Berger, A.B., Nazif, T., Blum, G., Ryan, C., Chehade, K.A.H., Salvesen, G., and Bogyo, M. (2005) Activity based probes that target diverse cysteine protease families. Nature Chemical Biology.1. Published online.

4. Verhelst, S.H.L., and Bogyo, M. (2005) Solid Phase Synthesis of double headed epoxysuccinyl activity based probes for selective targeting of papain family cysteine proteases. ChemBioChem, 6, 824-827.

5. Visser, K.E., Korets, L.V., and Coussens, L.M. (2005) De novo carcinogenesis promoted by chronic inflammation is B lymphocyte dependent. Cancer Cell, 7 (May), 411-423.

6. Mai, J., Demchik, L., Roshy, S., Rudy, D., Dosecu, J., Linebaugh, B.E., Sameni, M., Moin, K., Soane, B.F. (2005) Roles of the propeptide domain in trafficking and processing of calthepsin B.

7. Shiryaev, S.A., Ratnikov, B.I., Chekanov, A.V., Sikora, S., Rozanov, D.V., Wang, J., Smith, J.W., Huang, Z., Lindberg, I., Samuel, M.A., Diamond, M.S., Strongin, A.Y. (2005) Structural and functional analysis identifies the inhibitors and the cleavage targets of the West Nile virus NS3 processing proteinase. J. Biol. Chem.

8. Sloane, B.F., Sameni, M., Podgorski, I., Cavallo-Medved, D., and Moin, K., (2006) Functional Imaging of Tumor Proteolysis. Annual Review of Pharmacology and Toxicology, 46.

9. Blum, G., Mullins, S.R., Keren, K., Fonovic, Jedeszko, C., Rice, M.J., Sloane, B.F., and Bogyo, M. (2005) Dynamic imaging of protease activity with fluorescently quenched activity-based probes. Nature Chemical Biology, 1, 203-209.*

10. Golubkov VS, Boyd S, Savinov AY, Chekanov AV, Osterman AL, Remacle A., Rozanov DV, Doxsey SJ, Strongin AY (2005) Membrane type-1 matrix metalloproteinase (MT1-MMP) exhibits an important intracellular cleavage function and causes chromosome instability. J. Biol. Chem. 280, 25079-25086*

11. Golubkov VS, Chekanov AV, Doxsey SJ, Strongin AY (2005) Centrosomal pericentrin is a direct cleavage target of membrane type-1 matrix metalloproteinase in humans but not in mice: potential implications for tumorigenesis. J. Biol. Chem. 280, 42237-42241*

12. Kato, D., Verhelst, S.H.L., Sexton, K.B. and Bogyo, M. (2005) A General Solid Phase Method for the Preparation of Diverse Azapeptide Probes Directed Against Cysteine Proteases. Organic Letters, 7, 5649-5652.*

13. Pan Z, Jeffery DA, Chehade K, Beltman J, Clark JM, Grothaus P, Bogyo M, Baruch A. (2006) Development of activity-based probes for trypsin-family serine proteases. Bioorg. Med. Chem. Lett. 16, 2882-2885.*

14. Remacle, AG, Rozanov, DV, Baciu, PC, Chekanov, AV, Golubkov, VS, Strongin, AY (2005) The transmembrane domain is essential for the microtubular trafficking of membrane type-1 matrix metalloproteinase (MT1-MMP). J. Cell Sci. 118, 4975-4984.

15. Savinov AY, Rozanov DV, Golubkov VS, Wong FS, Strongin AY (2005) Inhibition of MT1-MMP by cancer drugs interferes with the homing of diabetogenic T cells into the pancreas. J. Biol. Chem. 280, 27755-27758.

16. Shiryaev SA, Ratnikov BI, Chekanov AV, Sikora S, Rozanov DV, Godzik A, Wang J, Smith JW, Huang Z, Lindberg I, Samuel MA, Diamond MS, Strongin AY (2006) The cleavage targets and the (D)-arginine-based inhibitors of the West Nile virus NS3 processing proteinase. Biochem. J. 393, 503-511

17. Sloane, B.F., Sameni, M., Podgoski, I., Cavallo-Medved, D. and Moin K.: Functional imaging of tumor proteolysis. Annu. Rev. Pharmacol. Toxicol. 46: 301-315, 2006).

18. Strongin AY (2006) Mislocalization and unconventional functions of cellular MMPs in cancer. Cancer Metastasis Rev. 25, 87-98.

19. Verhelst, S.H.L., Witte, M.D., Arastu-Kapur, S., Fonovic M., and Bogyo, M. (2006) Novel aza peptide inhibitors and active site probes of papain family cysteine proteases. Chem BioChem.

20. Yuan, F., Verhelst, S., Blum, G., Coussens, L., and Bogyo, M. (2006) A selective activity-based probe for the papain family cysteine protease dipeptidyl peptidase I/cathepsin C. J. Am. Chem. Soc. 128.

21. Berger A., Witte M., Sadaghiani A.M., Sexton K.M.B., Denault J.B., Salvesen G.S., and Bogyo, M. (2006) Identification of early intermediates of caspase activation during intrinsic apoptosis using selective inhibitors and activity based probes. Molecular Cell.

22. Browne, C.D., Hindmarsh, E.J., and Smith, J.W. (2006) Inhibition of Endothelial Cell Proliferation and Angiogenesis oy Orlistat, a Fatty Acid Synthase Inhibitor. FASEB.

23. Denault, J.B., Bekes M., Scott, F.L., Sexton K.M.B., Bogyo M. and Salvesen G.S., Engineered Hybrid Dimers: Tracking the Activation pathway of Caspase-7. Molecular Cell.

24. Enoksson, M, Li, J., Ivancic, M., Timmer, J., Wildfang, E., Eroshkin, A.M., Salvensen, G.S. Identification of Proteolytic Cleavage Sites by Quantitative Proteomics. Mol. Cell Bio.

25. Ivanisenko, VA, Eroshkin, A.M., Kolchanov, N.A. WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families. Nucleic Acids Res. 2005 Jul 1;33 (Web Server issue): W99-104. 

26. Jedeszko, C., Sameni, M., Olive, M., Moin, K. and Sloane, B.F.:  Visualizing Protease Activity in Living Cells: From 2D to 4D.  In:  Current Protocols Cell Biol.

27. Moin, K., Sloane, B.F.: Fluorescent imaging in tumors. In: In vivo Imaging of Cancer Therapy. A. Shield and P. Price, eds. Humana Press, Totowa, NJ USA.

28. Nooh, M., Aziz, R.K., Kotb, M., Eroshkin, A.M., Chaung, W.J., Proft, T., Kansa, R. Streptococcal Mitogenic Exotoxin, SmeZ, is the Most Susceptible M1T1 Streptococccal Superantigen to Degradation by the Streptococcal Cysteine Protease, SpeB. J. Bacteriol.

29. Remacle AG., Chekanov AV, Golubkov VS, Savinov, AY, Rozanov, DV, Strongin, AY (2006) O-glycosylation regulates autolysis of cellular membrane type-1 matrix metalloproteinase (MT1-MMP). J. Biol. Chem.

30. Remacle AG, Rozanov DV, Fugere M, Day R, Strongin AY (2006) Furin regulates the intracellular activation and the uptake rate of cell surface-associated MT1-MMP. Oncogene.

31. Rozanov, DV, Savinov, AY, Golubkov, VS, Tomlinson, S, Strongin AY (2006) Interference with the complement system by tumor cell MT1-MMP plays a significant role in promoting metastasis in mice. Cancer Res.

32. Savinov, AY, Rozanov DV, Strongin AY (2006) Mechanistic insights into targeting T cell membrane proteinase to promote islet β-cell rejuvenation in type 1 diabetes. FASEB J.

33. Sexton, K.B., Kato, D., Berger, A., Fonovic, M., Verhelst, S., and Bogyo, M. Selectivity versus potency: application of aza peptide activity based probes for profiling caspase, legumain and cathepsin activity

34. Yooseph, S., Li, W., Jaroszewski, L., Cieplak, P., Godzik, A., Venter, J.C. (2006) The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. In revision PloS Biology.

35. Berger A..B., Witte M., Sadaghiani A.M., Sexton K.M.B., Denault J.B., Salvesen G.S., and Bogyo, M. (2006) Identification of early intermediates of caspase activation during intrinsic apoptosis using selective inhibitors and activity based probes. Molecular Cell, 23, 509-521.

36. Berger, A.B., Sexton, K.B., and Bogyo, M. (2006) Commonly used caspase inhibitors designed based on substrate specificity profiles lack selectivity. Cell Research, 16, 961-963.

37. Sojka D, Hajdusek O, Dvorak J, Sajid M, Franta Z, Schneider EL, Craik CS, Vancova M, Buresova V, Bogyo M, Sexton KB, McKerrow JH, Caffrey CR, Kopacek P. IrAE - An asparaginyl endopeptidase (legumain) in the gut of the hard tick Ixodes ricinus. Int J Parasitol. 2007 Jan 30; [Epub ahead of print]

38. Sexton, K.B., Kato, D., Berger, A.B., Fonovic, M., Verhelst, S.H.L., and Bogyo, M. (2007) Specificity if aza-peptide electrophile activity based probes of caspases. Cell Death and Differentiation. 14, 727-732.

39. Sexton, K.B., Witte, M.D., Blum, G., and Bogyo, M. (2007) Design of cell permeable, fluorescent activity based probes of the lysosomal cysteine protease asparaginyl endopeptidase (AEP)/legumain. Bioorg. Med. Chem. 17, 649-653.

40. Denault, J.B., Bekes M., Sexton K.M.B., Scott F.L., Bogyo M., and Salvesen G.S. (2006) Conformational mobility in the activation of executioner caspases. Molecular Cell, 23, 523-533.

41. Sadaghiani, M., Verhelst, S.H.L., and Bogyo, M. (2006) Solid phase methods for the preparation of epoxysuccinate-based inhibitors of cysteine proteases. J. Comb. Chem. 8, 802-804.

42. Cuerrier, D., Moldoveanu, T., Campbell, R.L., Kelly, J., Yoruk, B., Verhelst, S.H., Greenbaum, D., Bogyo, M., Davies, P.L. (2007) Development of calpain-specific inactivators by screening of positional-scanning epoxide libraries. J Biol Chem. 282, 9600- 9611.

43. Verhelst, S.H.L., Fonovic, M. and Bogyo, M. (2007) A mild Chemically Cleavable linker for proteomic applications Agnew. Chem. 46, 1284-1286.

44. Teo CF, Zhou XW, Bogyo, M, Carruthers VB. (2007) Cysteine protease inhibitors block Toxoplasma gondii microneme secretion and cell invasion. Antimicrob Agents Chemother. 51, 679-88.

45. Sloane, B.F., Gillies, R.J., Mohla, S., Sogn, J.A., Menkens, A.E. and Sullivan, D.C.: I2 imaging: cancer biology and the tumor microenvironment. Cancer Res. 66: 11097-11099, 2006. 

46. Podgorski, I. and Sloane, B.F.: Loss of caspase-8 in tumor cells: mechanism to overcome integrin-mediated death? Mol. Interventions 6: 132-136, 2006

47. Cavallo-Medved, D. and Sloane, B.F.: Proteases and inhibitors. In: Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine. Birchmeier, W., ed. (Springer-Verlag, Berlin) 1: 1469-1473, 2006.

48. Mohamed, M.M. and Sloane, B.F.: Cysteine cathepsins: multifunctional enzymes in cancer. Nature Rev. Cancer 6: 764-775, 2006

49. Aleshin AE, Shiryaev SA, Strongin AY, Liddington RC (2007) Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold. Protein Sci. 16, 795-806

50. Golubkov VS, Chekanov AV, Savinov AY, Rozanov DV, Golubkova NV, Strongin AY (2006) MT1-MMP confers aneuploidy and tumorigenicity on mammary epithelial cells. Cancer Res.66, 10460-5

51. Golubkov VS, Strongin AY (2007) Proteolysis-driven oncogenesis. Cell Cycle 6, 147-50

52. Remacle AG, Rozanov DV, Fugere M, Day R, Strongin AY (2006) Furin regulates the intracellular activation and the uptake rate of cell surface-associated MT1-MMP. Oncogene 25, 5648-55

53. Remacle AG., Chekanov AV, Golubkov VS, Savinov, AY, Rozanov, DV, Strongin, AY (2006) O-glycosylation regulates autolysis of cellular membrane type-1 matrix metalloproteinase (MT1-MMP). J. Biol. Chem. 281, 16897-905

54. Rozanov DV, Savinov AY, Golubkov VS, Tomlinson S, Strongin AY (2006) Interference with the complement system by tumor cell MT1-MMP plays a significant role in promoting metastasis in mice. Cancer Res. 66, 6258-63

55. Savinov AY, Rozanov DV, Strongin AY (2006) Mechanistic insights into targeting T cell membrane proteinase to promote islet beta-cell rejuvenation in type 1 diabetes. FASEB J. 20, 1793-801.

56. Savinov AY, Remacle AG, Golubkov VS, Krajewska M, Kennedy S, Duffy MJ, Rozanov DV, Krajewski S, Strongin AY. (2006) MMP-26 proteolysis of the N-terminal domain of the estrogen receptor-beta correlates with the survival of breast cancer patients. Cancer Res. 66, 2716-24

57. Shiryaev SA, Kozlov IA, Ratnikov BI, Smith JW, Lebl M, Strongin AY (2007) Cleavage preference distinguishes the two-component NS2B-NS3 serine proteinases of Dengue and West Nile viruses. Biochem. J. 401, 743-52

58. Shiryaev SA, Ratnikov BI, Aleshin AE, Kozlov IA, Nelson NA, Lebl M, Smith JW, Liddington RC, Strongin AY (2007) Switching the substrate specificity of the two-component NS2B-NS3 flaviviral proteinase by structure-based mutagenesis. J. Virol. 81, 4501-9

59. Shiryaev SA, Aleshin AE, Ratnikov BI, Smith JW, Liddington RC, Strongin AY (2007) Expression and purification of a two-component flaviviral proteinase resistant to autocleavage at the NS2B-NS3 junction region. Protein Expr. Purif. 52, 334-9

60. Strongin AY (2006) Mislocalization and unconventional functions of cellular MMPs in cancer. Cancer Metastasis Rev. 25, 87-98.

61. Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, Godzik A., CutDB: a proteolytic event database. Nucleic Acids Res. 2007 Jan;35 (Database issue):D546-9. Epub 2006 Nov 16. PMID: 17142225.

62. Furmonaviciene R, Ghaemmaghami AM, Boyd SE, Jones NS, Nailey K, Willis AC, Sewell HF, Mitchell DA, Shakib F., The protease allergen Der p 1 cleaves cell surface DC-SIGN and DC-SIGNR: experimental analysis of in silico substrate identification and implications in allergic responses. Clin. Exp. Allergy. 2007 Feb; 37(2):231-42.

63. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC., The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families., PLoS Biol. 2007 Mar 13;5(3):e16.

64. Sadaghiani, A.M.,.Verhelst, S.H.L., Gocheva, V., Hill, K., Majerova, E., Stinson, S. Joyce, J.A. and Bogyo, M. (2007) Design, Synthesis and Evaluation of in vivo Potency and Selectivity of Epoxysuccinyl-Based Inhibitors of Papain Family Cysteine Proteases. Chem. Biol.

65. Moin, K., McIntyre, O. J., Matrisian, L. M., and Sloane, B.F.: Fluorescent imaging in tumors. In: In vivo Imaging of Cancer Therapy. A. Shield and Price, P. eds. (Humana Press, Totowa, NJ USA).

66. Jedeszko, C., Sameni, M., Olive, M., Moin, K. and Sloane, B.F.: Visualizing protease activity in living cells: from 2D to 4D. Curr. Protocols Cell Biol.

67. Enoksson, M., Li, J., Ivancic, M.M., Timmer, J.C., Wildfang, E., Eroshkin, A., Salvesen, G.S., and Tao, W.A. (2007) Identification of Proteolytic Cleavage Sites by Quantitative Proteomics. Journal of Proteome Research.

68. Rozanov DV, Savinov AY, Williams R, Liu K, Golubkov VS, Krajewski S, Strongin AY (2008) Molecular signature of MT1-MMP: transactivation of the downstream universal gene network in cancer. Cancer Res. (in press)

69. Day R, Strongin AY (2008) Furin in "Encyclopedia of Cancer" (Ed. Manfred Schwab), Springer, Berlin-Heidelberg-New York (in press)

70. Radichev I, Shiryaev SA, Aleshin AE, Ratnikov BI, Smith JW, Liddington RC, Strongin AY (2008) Structure-based mutagenesis identifies important novel determinants of the NS2B cofactor of the West Nile virus two-component NS2B-NS3 proteinase. J. Gen. Virol. 89, 636-641

71. D’Alessio S, Ferrari G, Cinnante K, Scheerer W, Galloway AC, Roses DF, Rozanov DV, Remacle AG, Oh E-S, Shiryaev AS, Strongin A, Pintucci G, Mignatti P. (2008) TIMP-2 binding to MT1-MMP induces MAP kinase activation and cell growth by a non-proteolytic mechanism. J. Biol. Chem. 283, 87-99

72. Johnston PA, Phillips J, Shun TY, Shinde S, Lazo JS, Huryn DM, Myers MC¶, Ratnikov BI, Smith JW, Su Y, Dahl R, Cosford NDP, Shiryaev SA, Strongin AY (2007) High throughput screening (HTS) identifies novel and specific uncompetitive inhibitors of the two-component NS2B-NS3 proteinase of West Nile virus. Assay and Drug Dev. Technol. 5, 737-750

73. Golubkov VS, Chekanov AV, Shiryaev SA, Aleshin AE, Ratnikov BI, Gawlik K, Radichev I, Motamedchaboki K, Smith JW, Strongin AY (2007) Proteolysis of the membrane type-1 matrix metalloproteinase prodomain: Implications for a two-step proteolytic processing and activation. J. Biol. Chem. 282, 36283–36291

74. Savinov AY, Dmitri V. Rozanov DV, Strongin AY (2007) Specific inhibition of autoimmune T cell transmigration contributes to b-cell functionality and insulin synthesis in non-obese diabetic (NOD) mice. J. Biol. Chem. 282, 32106-32111

75. Shiryaev SA, Remacle AG, Ratnikov BI, Nelson NA, Savinov AY, Wei G, Bottini M, Rega MF, Parent A, Desjardins R, Fugere M, Day R, Sabet M, Pellecchia M, Liddington RC, Smith JW, Mustelin T, Guiney DG, Lebl, M, Strongin AY (2007) Targeting host cell furin proprotein convertases as a therapeutic strategy against bacterial toxins and viral pathogens. J. Biol. Chem. 282, 20847-20853

76. Savinov AY, Strongin AY (2007) Defining the roles of T cell membrane proteinase and CD44 in type 1 diabetes. IUBMB Life 59, 6-13

 

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