Crystal structure of NS-134 in complex with bovine cathepsin B: A two-headed epoxysuccinyl inhibitor extends along the entire active-site cleft

Biochemical Journal

Volumn 381, Issue 2, 2004, Pages 511-517

  Štern, Igor ^a   Schaschke, Norbert ^b   Moroder, Luis ^b   Turk, Dušan ^a  

^a JO EF STEFAN INSTITUTE   (Slovenia)

^b MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

Cathepsin B; Cysteine protease; Epoxysuccinyl inhibitor; Inhibitor design; NS 134

Indexed keywords

CRYSTAL STRUCTURE; ENZYME INHIBITION; ENZYMES;

ACTIVE-SITE CLEFT; PRIMED BINDING SITES;

BIOCHEMICAL ENGINEERING;

1 [2 [[3 [1 [[(METHOXYCARBONYLMETHYLCARBAMOYL)METHYL]CARBAMOYL] 3 METHYLBUTYLCARBAMOYL]OXIRANECARBONYL]AMINO] 4 METHYLPENTANOYL]PYRROLIDINE 2 CARBOXYLIC ACID; CARBOXYLIC ACID DERIVATIVE; CATHEPSIN B; FUNCTIONAL GROUP; GLYCINE; HISTIDINE; HYDROXYL GROUP; LEUCINE; METHYL GROUP; NS 134; PROLINE; PROTEIN INHIBITOR; SUCCINIC ACID DERIVATIVE; UNCLASSIFIED DRUG;

AMINO ACID ANALYSIS; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; COMPARATIVE STUDY; CRYSTAL STRUCTURE; DRUG STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; RESIDUE ANALYSIS;

ANIMALS; BINDING SITES; CATHEPSIN B; CATTLE; CRYSTALLOGRAPHY, X-RAY; CYSTEINE PROTEINASE INHIBITORS; DIPEPTIDES; EPOXY COMPOUNDS; KIDNEY; LEUCINE; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; OLIGOPEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, QUATERNARY; PYRIDINES; PYRROLES;

BOVINAE;

EID: 3242794877     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20040237     Document Type: Article

References (47)

1. Turk, B., Turk, D. and Turk, V. (2000) Lysosomal cysteine proteases: more than scavengers. Biochim. Biophys. Acta 1477, 98-111
2. Turk, B., Stoka, V., Rozman-Pungercar, J., Cirman, T., Droga-Mazovec, G., Orešić, K. and Turk, V. (2002) Apoptotic pathways: involvement of lysosomal proteases. Biol. Chem. 383, 1035-1044
3. Balaji, K. N., Schaschke, N., Machleidt, W., Calfamo, M. and Henkert, P. A. (2002) Surface cathepsin B protects cytotoxic lymphocytes from self-destruction after degranulation. J. Exp. Med. 196, 493-503
4. Aisa, M. C., Beccari, T., Costanzi, E. and Maggio, D. (2003) Cathepsin B in osteoblasts. Biochim. Biophys. Acta 1621, 149-159
5. Keppler, D., Walter, R., Perez, C. and Sierra, F. (2000) Increased expression of mature cathepsin B in aging rats. Cell Tissue Res. 320, 181-188
6. Hashimoto, Y., Kakegawa, H., Narita, Y., Hachiya, Y., Hayakawa, T., Kos, J., Turk, V. and Katunuma, N. (2001) Significance of cathepsin B accumulation in synovial fluid of rheumatoid arthritis. Biochem. Biophys. Res. Commun. 283, 334-339
7. Lang, A., Horler, D. and Baici, A. (2000) The relative importance of cysteine peptidases in osteoarthritis. J. Rheumatol. 27, 1970-1979
8. Koblinski, J. E., Ahram, M. and Sloane, B. F. (2000) Unraveling the role of proteases in cancer. Clin. Chim. Acta 291, 113-135
9. Podgorski, I. and Sloane, B. F. (2003) Cathepsin B and its role(s) in cancer progression. Biochem. Soc. Symp. 70, 263-276
10. Kostoulas, G., Lang, A., Nagase, H. and Baici, A. (1999) Stimulation of angiogenesis trough cathepsin B inactivation of the tissue inhibitors matrix metalloproteinases. FEBS Lett. 455, 286-290
11. Cavallo-Medved, D. and Sloane, B. F. (2003) Cell surface cathepsin B: understanding its functional significance. Curr. Top. Dev. Biol. 54, 313-341
12. Kukor, Z., Mayerle, J., Krüger, B., Tóth, M., Steed, P. M., Halangk, W., Lerch, M. M. and Sahin-Tóth, M. (2002) Presence of cathepsin B in the human pancreatic secretory pathway and its role in trypsinogen activation during hereditary pancreatitis. J. Biol. Chem. 277, 21389-21396
13. Musil, D., Zucic, D., Engh, R. A., Mayr, I., Huber, R., Popovič, T., Turk, V., Towatari, T. and Katunuma, N. (1991) The refined 2.15 Å X-ray crystal structure of human liver cathepsin B: the structural basis for its specificity. EMBO J. 10, 2321-2330
14. Turk, D., Podobnik, M., Popovič, T., Katunuma, N., Bode, W., Huber, R. and Turk, V. (1995) Crystal structure of cathepsin B inhibited with CA030 at 2.0-Å resolution: a basis for the design of specific epoxysuccinyl inhibitors. Biochemistry 34, 4791-4797
15. Towatari, T., Nikawa, T., Murata, M., Yokoo, C., Tamai, M., Hanada, K. and Katunuma, N. (1991) Novel epoxysuccinyl peptides. A selective inhibitor of cathepsin B, in vivo. FEBS Lett. 280, 311-315
16. Murata, M., Miyashita, S., Yokoo, C., Tamai, M., Kanada, K., Hatayama, K., Towatari, T., Nikawa, T. and Katunuma, N. (1991) Novel epoxysuccinyl peptides. Selective inhibitors of cathepsin B, in vitro. FEBS Lett. 280, 307-310
17. Hanada, K., Tamai, M., Yamagishi, M., Ohmura, S., Sawada, J. and Tanaka, I. (1978) Isolation and characterization of E-64, a new thiol protease inhibitor. Agric. Biol. Chem. 42, 523-528
18. Varughese, K. I., Ahmed, F. R., Carey, P. R., Hasnain, S., Huber, C. P. and Storer, A. C. (1989) Crystal structure of a papain-E-64 complex. Biochemistry 28, 1330-1332
19. Yamamoto, D., Matsumoto, K., Ohishi, H., Ishida, T., Inoue, M., Kitamura, K. and Mizuno, H. (1991) Retined X-ray structure ot papain-E-64-c complex at 2.1 Å resolution. J. Biol. Chem. 266, 14771-14777
20. Kim, M. J., Yamamoto, D., Matsumoto, K., Inoue, M., Ishida, T., Mizuno, H., Sumiya, S. and Kitamura, K. (1992) Crystal structure ot papain-E-64-c complex. Biochem. J. 287, 797-803
21. Cygler, M., Sivaraman, J., Grochulski, P., Coulombe, R., Storer, A. C. and Mort, J. S. (1996) Structure of rat procathepsin B: model for inhibition of cysteine protease activity by the proregion. Structure 4, 405-416
22. Turk, D., Podobnik, M., Kuhelj, R., Dolinar, M. and Turk, V. (1996) Crystal structures of human procathepsin B at 3.2 and 3.3 Å resolution reveal an interaction motif between a papain-like cysteine protease and its propeptide. FEBS Lett. 384, 211-214
23. Schascnke, N., Assfalg-Machleidt, I., Machleidt, W., Turk, D. and Moroder, L. (1997) E-64 analogues as inhibitors of cathepsin B. On the role of the absolute configuration of the epoxysuccinyl group. Bioorg. Med. Chem. 5, 1789-1797
24. Scnascnke, N., Assfalg-Machleidt, I., Machleidt, W. and Moroder, L. (1998) Substrate/propeptide-derived endo-epoxysuccinyl peptides as highly potent and selective cathepsin B inhibitors. FEBS Lett. 421, 80-82
25. Katunuma, N., Murata, E., Kakegawa, H., Matsui, A., Tsuzuki, H., Tsuge, H., Turk, D., Turk, V., Fukushima, M., Tada, Y. et al. (1999) Structure based development of novel specific inhibitors for cathepsin L and cathepsin S in vitro and in vivo. FEBS Lett. 458, 6-10
26. Tsuge, H., Nishimura, T., Tada, Y., Asao, T., Turk, D., Turk, V. and Katunuma, N. (1999) Inhibition mechanism of cathepsin L-specific inhibitors based on the crystal structure of papain-CLIK148 complex. Biochem. Biophys. Res. Commun. 266, 411-416
27. Zvonar-Popovič, T., Lah, T., Kregar, I. and Turk, V. (1980) Some characteristics of cathepsin B and α-N-benzoylarginine-β- naphthylamide hydrolase from bovine lymph nodes. Croat. Chem. Acta 53, 509-517
28. Barrett, A. J. and Kirschke, H. (1981) Cathepsin B, cathepsin H, and cathepsin L. Methods Enzymol. 80, 535-561
29. Pace, C. N., Vajdos, F., Fee, L., Frimsley, G. and Gray, T. (1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411-2423
30. Turk, B., Križaj, I., Kralj, B., Dolenc, I., Popovič, T. Bieth, J. G. and Turk, V. (1993) Bovine stefin C, a new member of the stefin family. J. Biol. Chem. 268, 7323-7329
31. Yamamoto, A., Kaji, T., Tomoo, K., Ishida, T., Inoue, M., Kitamura, K. and Murata, M. (1992) Crystallization and preliminary X-ray study of the cathepsin B complexed with CA074, a selective inhibitor. J. Mol. Biol. 227, 942-944
32. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326
33. Kissinger, C. R., Gehlhaar, D. K. and Fogel, D. B. (1999) Rapid automated molecular replacement by evolutionary search. Acta Crystallogr. D 55, 484-491
34. Turk, D. (1992) Weiterntwicklung eines Programms für Molekülgraphik und Elektronendichte-Manipulation und seine Anwendung auf verschiedene Protein-Strukturaufklärungen. Ph.D. thesis, Technische Universität München, München
35. Laskowski, R. A., MacArthur, M. W., Moss, D. S. and Thornton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291
36. Yamamoto, A., Hara, T., Tomoo, K., Ishida, T., Fujii, T., Hata, Y., Murata, M. and Kitamura, K. (1997) Binding mode of CA074, a specific irreversible inhibitor, to bovine cathepsin B as determined by X-ray crystal analysis of the complex. J. Biochem. (Tokyo) 121, 974-977
37. Schechter, I. and Berger, A. (1967) On the size of the active site in proteases. I. Papain. Biochem. Biophys. Res. Commun. 27, 157-162
38. Varughese, K. I., Su, Y., Cromwell, D., Hasnain, S. and Xoung, N. H. (1992) Crystal structure of actinidin-E-64 complex. Biochemistry 31, 5172-5176
39. Zhao, B., Janson, C. A., Amegadzie, B. Y., D'Alessio, K., Griffin, C., Hanning, C. R., Jones, C., Kurdyla, J., McQueney, M., Qiu, X. et al. (1997) Crystal structure of human osteoclast cathepsin K complex with E-64. Nat. Struct. Biol. 4, 109-111
40. Coulombe, R., Grochulski, P., Sivaraman, J., Menard, R., Mort, J. S. and Cygler, M. (1996) Structure of human procathepsin L reveals the molecular basis of inhibition by the prosegment. EMBO J. 15, 5492-5503
41. LaLonde, J. M., Zhao, B., Janson, C. A., D'Alessio, K. J., McQueney, M. S., Orsini, M. J., Debouck, C. M. and Smith, W. W. (1999) The crystal structure of human procathepsin K. Biochemistry 38, 862-869
42. Sivaraman, J., Nägler, D. K., Zhang, R., Menard, R. and Cygler, M. (2000) Crystal structure of human procathepsin X: a cysteine protease with the proregion covalently linked to the active site cysteine. J. Mol. Biol. 295, 939-951
43. Schaschke, N., Assfalg-Machleidt, I., Lassleben, Th., Sommerhof, C. P., Moroder, L. and Machleidt, W. (2000) Epoxysuccinyl peptide-derived affinity labels for cathepsin B. FEBS Lett. 482, 91-96
44. Schaschke, N., Assfalg-Machleidt, I., Machleidt, W., Lassleben, T., Sommerhot, C. P. and Moroder, L. (2000) β-Cyclodextrin-epoxysuccinyl peptide conjugates: a new drug targeting system for tumor cells. Bioorg. Med. Chem. Lett. 10, 677-680
45. Thompson, S. K., Halbert, S. M., Bossard, M. J., Thaddeus, A. T., Ley, M. A., Zhao, B., Smith, W. W., Abdel-Meguid, A. A., Janson, C. A., D'Alessio, K. J. et al. (1997) Design of potent and selective human cathepsin K inhibitors that span the active site. Proc. Natl. Acad. Sci. U.S.A. 94, 14249-14254
46. Merritt, E. A. and Bacon, D. J. (1997) Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505-524
47. Nicholls, A., Sharp, K. A. and Honig, B. (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Gen. 11, 281-296