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Inhibition mechanism of cathepsin L-specific inhibitors based on the crystal structure of papain-CLIK148 complex.

Tsuge H, Nishimura T, Tada Y, Asao T, Turk D, Turk V, Katunuma N
Biochem Biophys Res Commun 266 411-6 (1999)
Cited: 48 times
EuropePMC logo PMID: 10600517

Abstract

Papain was used as an experimental model structure to understand the inhibition mechanism of newly developed specific inhibitors of cathepsin L, the papain superfamily. Recently, we developed a series of cathepsin L-specific inhibitors which are called the CLIK series [(1999) FEBS Lett. 458, 6-10]. Here, we report the complex structure of papain with CLIK148, which is a representative inhibitor from the CLIK series. The inhibitor complex structure was solved at 1.7 A resolution with conventional R 0.177. Unlike other epoxisuccinate inhibitors (E64, CA030, and CA074), CLIK148 uses both prime and nonprime sites, which are important for the specific inhibitory effect on cathepsin L. Also, the specificity for cathepsin L could be explained by the existence of Phe in the P2 site and hydrophobic interaction of N-terminal pyridine ring.

Reviews - 1cvz mentioned but not cited (1)

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Articles - 1cvz mentioned but not cited (10)

  1. Crystal structure of NS-134 in complex with bovine cathepsin B: a two-headed epoxysuccinyl inhibitor extends along the entire active-site cleft. Stern I, Schaschke N, Moroder L, Turk D. Biochem J 381 511-517 (2004)
  2. Kinetic characterization and molecular docking of a novel, potent, and selective slow-binding inhibitor of human cathepsin L. Shah PP, Myers MC, Beavers MP, Purvis JE, Jing H, Grieser HJ, Sharlow ER, Napper AD, Huryn DM, Cooperman BS, Smith AB, Diamond SL. Mol Pharmacol 74 34-41 (2008)
  3. A comparison of the membrane binding properties of C1B domains of PKCgamma, PKCdelta, and PKCepsilon. Sánchez-Bautista S, Corbalán-García S, Pérez-Lara A, Gómez-Fernández JC. Biophys J 96 3638-3647 (2009)
  4. Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through In Silico Approaches. Hernández Alvarez L, Naranjo Feliciano D, Hernández González JE, Soares RO, Barreto Gomes DE, Pascutti PG. PLoS Negl Trop Dis 9 e0003759 (2015)
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  6. Fluorescent Probes for Studying Thioamide Positional Effects on Proteolysis Reveal Insight into Resistance to Cysteine Proteases. Liu C, Barrett TM, Chen X, Ferrie JJ, Petersson EJ. Chembiochem 20 2059-2062 (2019)
  7. High-resolution complex of papain with remnants of a cysteine protease inhibitor derived from Trypanosoma brucei. Alphey MS, Hunter WN. Acta Crystallogr Sect F Struct Biol Cryst Commun 62 504-508 (2006)
  8. An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius oreades agglutinin (MOA) with a Caspase Inhibitor. Cordara G, van Eerde A, Grahn EM, Winter HC, Goldstein IJ, Krengel U. PLoS One 11 e0149407 (2016)
  9. Letter Covalent docking in CDOCKER. Wu Y, Brooks Iii CL. J Comput Aided Mol Des 36 563-574 (2022)
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Reviews citing this publication (10)

  1. Cysteine cathepsins: from structure, function and regulation to new frontiers. Turk V, Stoka V, Vasiljeva O, Renko M, Sun T, Turk B, Turk D. Biochim Biophys Acta 1824 68-88 (2012)
  2. Lysosomal cathepsins and their regulation in aging and neurodegeneration. Stoka V, Turk V, Turk B. Ageing Res Rev 32 22-37 (2016)
  3. Insights into the roles of cathepsins in antigen processing and presentation revealed by specific inhibitors. Katunuma N, Matsunaga Y, Himeno K, Hayashi Y. Biol Chem 384 883-890 (2003)
  4. A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L. Dana D, Pathak SK. Molecules 25 E698 (2020)
  5. Structure-based development of specific inhibitors for individual cathepsins and their medical applications. Katunuma N. Proc Jpn Acad Ser B Phys Biol Sci 87 29-39 (2011)
  6. Peptidase inhibitors in the MEROPS database. Rawlings ND. Biochimie 92 1463-1483 (2010)
  7. Proteolysis and antigen presentation by MHC class II molecules. Bryant PW, Lennon-Duménil AM, Fiebiger E, Lagaudrière-Gesbert C, Ploegh HL. Adv Immunol 80 71-114 (2002)
  8. Microbial inhibitors of cysteine proteases. Kędzior M, Seredyński R, Gutowicz J. Med Microbiol Immunol 205 275-296 (2016)
  9. The identification, characterization and optimization of small molecule probes of cysteine proteases: experiences of the Penn Center for Molecular Discovery with cathepsin B and cathepsin L. Huryn DM, Smith AB. Curr Top Med Chem 9 1206-1216 (2009)
  10. Papaya (Carica papaya L.) Flavour Profiling. Zhou Z, Ford R, Bar I, Kanchana-Udomkan C. Genes (Basel) 12 1416 (2021)

Articles citing this publication (27)

  1. IL-6-STAT3 controls intracellular MHC class II alphabeta dimer level through cathepsin S activity in dendritic cells. Kitamura H, Kamon H, Sawa S, Park SJ, Katunuma N, Ishihara K, Murakami M, Hirano T. Immunity 23 491-502 (2005)
  2. Lysosomal cathepsins: structure, role in antigen processing and presentation, and cancer. Turk V, Turk B, Guncar G, Turk D, Kos J. Adv Enzyme Regul 42 285-303 (2002)
  3. Carboxypeptidase cathepsin X mediates beta2-integrin-dependent adhesion of differentiated U-937 cells. Obermajer N, Premzl A, Zavasnik Bergant T, Turk B, Kos J. Exp Cell Res 312 2515-2527 (2006)
  4. Structural basis for the recognition and cleavage of histone H3 by cathepsin L. Adams-Cioaba MA, Krupa JC, Xu C, Mort JS, Min J. Nat Commun 2 197 (2011)
  5. CD4-independent human immunodeficiency virus infection involves participation of endocytosis and cathepsin B. Yoshii H, Kamiyama H, Goto K, Oishi K, Katunuma N, Tanaka Y, Hayashi H, Matsuyama T, Sato H, Yamamoto N, Kubo Y. PLoS One 6 e19352 (2011)
  6. Cathepsin L inhibition prevents murine autoimmune diabetes via suppression of CD8(+) T cell activity. Yamada A, Ishimaru N, Arakaki R, Katunuma N, Hayashi Y. PLoS One 5 e12894 (2010)
  7. Caging the uncageable: using metal complex release for photochemical control over irreversible inhibition. Huisman M, White JK, Lewalski VG, Podgorski I, Turro C, Kodanko JJ. Chem Commun (Camb) 52 12590-12593 (2016)
  8. Characterization of CAA0225, a novel inhibitor specific for cathepsin L, as a probe for autophagic proteolysis. Takahashi K, Ueno T, Tanida I, Minematsu-Ikeguchi N, Murata M, Kominami E. Biol Pharm Bull 32 475-479 (2009)
  9. Design, synthesis, and evaluation of inhibitors of cathepsin L: Exploiting a unique thiocarbazate chemotype. Myers MC, Shah PP, Beavers MP, Napper AD, Diamond SL, Smith AB, Huryn DM. Bioorg Med Chem Lett 18 3646-3651 (2008)
  10. Marasmius oreades agglutinin (MOA) is a chimerolectin with proteolytic activity. Cordara G, Egge-Jacobsen W, Johansen HT, Winter HC, Goldstein IJ, Sandvig K, Krengel U. Biochem Biophys Res Commun 408 405-410 (2011)
  11. Cathepsin L is required for ecotropic murine leukemia virus infection in NIH3T3 cells. Yoshii H, Kamiyama H, Minematsu K, Goto K, Mizota T, Oishi K, Katunuma N, Yamamoto N, Kubo Y. Virology 394 227-234 (2009)
  12. Small-molecule inhibitors of cathepsin L incorporating functionalized ring-fused molecular frameworks. Song J, Jones LM, Chavarria GE, Charlton-Sevcik AK, Jantz A, Johansen A, Bayeh L, Soeung V, Snyder LK, Lade SD, Chaplin DJ, Trawick ML, Pinney KG. Bioorg Med Chem Lett 23 2801-2807 (2013)
  13. Quantifying the protein core flexibility through analysis of cavity formation. Pereira B, Jain S, Garde S. J Chem Phys 124 74704 (2006)
  14. Crystal Structure of the Salmonella Typhimurium Effector GtgE. Xu C, Kozlov G, Wong K, Gehring K, Cygler M. PLoS One 11 e0166643 (2016)
  15. Structure-function relationship of Chikungunya nsP2 protease: A comparative study with papain. Ramakrishnan C, Kutumbarao NHV, Suhitha S, Velmurugan D. Chem Biol Drug Des 89 772-782 (2017)
  16. Catalytic Enantioselective Synthesis of Heterocyclic Vicinal Fluoroamines by Using Asymmetric Protonation: Method Development and Mechanistic Study. Ashford MW, Xu C, Molloy JJ, Carpenter-Warren C, Slawin AMZ, Leach AG, Watson AJB, Watson AJB. Chemistry 26 12249-12255 (2020)
  17. Cysteine protease-mediated cytoskeleton interactions with LFA-1 promote T-cell morphological changes. Jevnikar Z, Obermajer N, Kos J. Cell Motil Cytoskeleton 66 1030-1040 (2009)
  18. Oxidative and antioxidative responses in the wheat-Azospirillum brasilense interaction. Méndez-Gómez M, Castro-Mercado E, Alexandre G, García-Pineda E. Protoplasma 253 477-486 (2016)
  19. Affinity-Enhanced Luminescent Re(I)- and Ru(II)-Based Inhibitors of the Cysteine Protease Cathepsin L. Huisman M, Kodanko JP, Arora K, Herroon M, Alnaed M, Endicott J, Podgorski I, Kodanko JJ. Inorg Chem 57 7881-7891 (2018)
  20. An assessment of protein-ligand binding site polarizability. Nayeem A, Krystek S, Stouch T. Biopolymers 70 201-211 (2003)
  21. Optimization of dipeptidic inhibitors of cathepsin L for improved Toxoplasma gondii selectivity and CNS permeability. Zwicker JD, Diaz NA, Guerra AJ, Kirchhoff PD, Wen B, Sun D, Carruthers VB, Larsen SD. Bioorg Med Chem Lett 28 1972-1980 (2018)
  22. Papain Loaded Poly(ε-Caprolactone) Nanoparticles: In-silico and In-Vitro Studies. Budama-Kilinc Y, Cakir-Koc R, Kecel-Gunduz S, Zorlu T, Kokcu Y, Bicak B, Karavelioglu Z, Ozel AE. J Fluoresc 28 1127-1142 (2018)
  23. Effect of Er:YAG, Co2 lasers, papain, and bromelain enzymes dentin treatment on shear bond strength of composite resin. Sharafeddin F, Maroufi S. Clin Exp Dent Res 8 1575-1581 (2022)
  24. Nobuhiko Katunuma: an outstanding scientist in the field of proteolysis and warm-hearted 'Kendo Fighter' biochemist. Kido H, Ishidoh K. J Biochem 148 527-531 (2010)
  25. Probing of primed and unprimed sites of calpains: Design, synthesis and evaluation of epoxysuccinyl-peptide derivatives as selective inhibitors. Dókus LE, Menyhárd DK, Tantos Á, Hudecz F, Bánóczi Z. Eur J Med Chem 82 274-280 (2014)
  26. Identifying and characterizing the biological targets of metallotherapeutics: Two approaches using Au(I)-protein interactions as model systems. Karver MR, Barrios AM. Anal Biochem 382 63-65 (2008)
  27. Historical Article Vito Turk--30 years of research on cysteine proteases and their inhibitors. Turk B, Fritz H. Biol Chem 384 833-836 (2003)


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