Login Register Cart 0
Generic placeholder image

Current Proteomics

Editor-in-Chief

ISSN (Print): 1570-1646
ISSN (Online): 1875-6247

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
General Research Article

In Silico Identification and Molecular Characterization of Extracellular Cathepsin L Proteases from Giardia duodenalis

Author(s): Sergio A. Durán-Pérez, José G. Rendón-Maldonado*, Lucio de Jesús Hernandez-Diaz, Annete I. Apodaca-Medina, Maribel Jiménez-Edeza and Julio Montes-Avila

Volume 17, Issue 4, 2020

Page: [342 - 351] Pages: 10

DOI: 10.2174/1570164617666191016170628

Price: $65

Abstract

Background: The protozoan Giardia duodenalis, which causes giardiasis, is an intestinal parasite that commonly affects humans, mainly pre-school children. Although there are asymptomatic cases, the main clinical features are chronic and acute diarrhea, nausea, abdominal pain, and malabsorption syndrome. Little is currently known about the virulence of the parasite, but some cases of chronic gastrointestinal alterations post-infection have been reported even when the infection was asymptomatic, suggesting that the cathepsin L proteases of the parasite may be involved in the damage at the level of the gastrointestinal mucosa.

Objective: The aim of this study was the in silico identification and characterization of extracellular cathepsin L proteases in the proteome of G. duodenalis.

Methods: The NP_001903 sequence of cathepsin L protease from Homo sapiens was searched against the Giardia duodenalis proteome. The subcellular localization of Giardia duodenalis cathepsin L proteases was performed in the DeepLoc-1.0 server. The construction of a phylogenetic tree of the extracellular proteins was carried out using the Molecular Evolutionary Genetics Analysis software (MEGA X). The Robetta server was used for the construction of the three-dimensional models. The search for possible inhibitors of the extracellular cathepsin L proteases of Giardia duodenalis was performed by entering the three-dimensional structures in the FINDSITEcomb drug discovery tool.

Results: Based on the amino acid sequence of cathepsin L from Homo sapiens, 8 protein sequences were identified that have in their modular structure the Pept_C1A domain characteristic of cathepsins and two of these proteins (XP_001704423 and XP_001704424) are located extracellularly. Threedimensional models were designed for both extracellular proteins and several inhibitory ligands with a score greater than 0.9 were identified. In vitro studies are required to corroborate if these two extracellular proteins play a role in the virulence of Giardia duodenalis and to discover ligands that may be useful as therapeutic targets that interfere in the mechanism of pathogenesis generated by the parasite.

Conclusion: In silico analysis identified two proteins in the Giardia duodenalis protein repertoire whose characteristics allowed them to be classified as cathepsin L proteases, which may be secreted into the extracellular medium to act as virulence factors. Three-dimensional models of both proteins allowed the identification of inhibitory ligands with a high score. The results suggest that administration of those compounds might be used to block the endopeptidase activity of the extracellular cathepsin L proteases, interfering with the mechanisms of pathogenesis of the protozoan parasite Giardia duodenalis.

Keywords: Giardia duodenalis, cathepsin L, virulence factor, inhibition, protease, protozoan.

« Previous
Graphical Abstract

[1]
Lalle, M.; Hanevik, K. Treatment-refractory giardiasis: challenges and solutions. Infect. Drug Resist., 2018, 11, 1921-1933.
[http://dx.doi.org/10.2147/IDR.S141468] [PMID: 30498364]
[2]
Tsui, C.K.; Miller, R.; Uyaguari-Diaz, M.; Tang, P.; Chauve, C.; Hsiao, W.; Isaac-Renton, J.; Prystajecky, N. Beaver fever: whole-genome characterization of waterborne outbreak and sporadic isolates to study the zoonotic transmission of Giardiasis. MSphere, 2018, 3(2), 3.
[http://dx.doi.org/10.1128/mSphere.00090-18] [PMID: 29695621]
[3]
Goudal, A.; Laude, A.; Valot, S.; Desoubeaux, G.; Argy, N.; Nourrisson, C.; Pomares, C.; Machouart, M.; Le Govic, Y.; Dalle, F.; Botterel, F.; Bourgeois, N.; Cateau, E.; Leterrier, M.; Lavergne, R.A.; Beser, J.; Le Pape, P.; Morio, F. Rapid diagnostic tests relying on antigen detection from stool as an efficient point of care testing strategy for giardiasis and cryptosporidiosis? Evaluation of a new immunochromatographic duplex assay. Diagn. Microbiol. Infect. Dis., 2019, 93(1), 33-36.
[http://dx.doi.org/10.1016/j.diagmicrobio.2018.07.012] [PMID: 30122511]
[4]
Hawrelak, J. Giardiasis: pathophysiology and management. Altern. Med. Rev., 2003, 8(2), 129-142.
[PMID: 12777159]
[5]
Zhen, Y.; Liao, L.; Zhang, H. Intestinal Giardiasis disguised as ulcerative colitis. Case Rep. Gastrointest. Med., 2018, 2018, 8968976
[http://dx.doi.org/10.1155/2018/8968976] [PMID: 29854495]
[6]
Halliez, M.C.M.; Buret, A.G. Extra-intestinal and long term consequences of Giardia duodenalis infections. World J. Gastroenterol., 2013, 19(47), 8974-8985.
[http://dx.doi.org/10.3748/wjg.v19.i47.8974] [PMID: 24379622]
[7]
Buret, A.G.; Amat, C.B.; Manko, A.; Beatty, J.K.; Halliez, M.C.M.; Bhargava, A.; Motta, J.P.; Cotton, J.A. Giardia duodenalis: new research developments in pathophysiology, pathogenesis, and virulence factors. Curr. Trop. Med. Rep., 2015, 2, 110-118.
[http://dx.doi.org/10.1007/s40475-015-0049-8]
[8]
Sahin Akkelle, B.; Tutar, E. O, K.S.; C,, A.C.; Ertem, D. A rare complication of giardiasis in children: protein losing enteropathy. Pediatr. Infect. Dis. J., 2018, 37(12), e345-e347.
[9]
Buret, A.; Hardin, J.A.; Olson, M.E.; Gall, D.G. Pathophysiology of small intestinal malabsorption in gerbils infected with Giardia lamblia. Gastroenterology, 1992, 103(2), 506-513.
[http://dx.doi.org/10.1016/0016-5085(92)90840-U] [PMID: 1634068]
[10]
Buret, A.G. Pathophysiology of enteric infections with Giardia duodenalius. Parasite, 2008, 15(3), 261-265.
[http://dx.doi.org/10.1051/parasite/2008153261] [PMID: 18814692]
[11]
Ma’ayeh, S.Y.; Liu, J.; Peirasmaki, D.; Hörnaeus, K.; Bergström Lind, S.; Grabherr, M.; Bergquist, J.; Svärd, S.G. Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells. The Impact On Host Cells, 2017, 11.
[12]
Cotton, J.A.; Beatty, J.K.; Buret, A.G. Host parasite interactions and pathophysiology in Giardia infections. Int. J. Parasitol., 2011, 41(9), 925-933.
[http://dx.doi.org/10.1016/j.ijpara.2011.05.002] [PMID: 21683702]
[13]
Emery, S.J.; van Sluyter, S.; Haynes, P.A. Proteomic analysis in Giardia duodenalis yields insights into strain virulence and antigenic variation. Proteomics, 2014, 14(21-22), 2523-2534.
[http://dx.doi.org/10.1002/pmic.201400144] [PMID: 25266764]
[14]
Turk, V.; Stoka, V.; Vasiljeva, O.; Renko, M.; Sun, T.; Turk, B.; Turk, D. Cysteine cathepsins: from structure, function and regulation to new frontiers. Biochim. Biophys. Acta, 2012, 1824(1), 68-88.
[http://dx.doi.org/10.1016/j.bbapap.2011.10.002] [PMID: 22024571]
[15]
Fonović, M.; Turk, B. Cysteine cathepsins and extracellular matrix degradation. Biochim. Biophys. Acta, 2014, 1840(8), 2560-2570.
[http://dx.doi.org/10.1016/j.bbagen.2014.03.017] [PMID: 24680817]
[16]
Robinson, M.W.; Tort, J.F.; Lowther, J.; Donnelly, S.M.; Wong, E.; Xu, W.; Stack, C.M.; Padula, M.; Herbert, B.; Dalton, J.P. Proteomics and phylogenetic analysis of the cathepsin L protease family of the helminth pathogen Fasciola hepatica: expansion of a repertoire of virulence-associated factors. Mol. Cell. Proteomics, 2008, 7(6), 1111-1123.
[http://dx.doi.org/10.1074/mcp.M700560-MCP200] [PMID: 18296439]
[17]
Steverding, D.; Sexton, D.W.; Wang, X.; Gehrke, S.S.; Wagner, G.K.; Caffrey, C.R. Trypanosoma brucei: chemical evidence that cathepsin L is essential for survival and a relevant drug target. Int. J. Parasitol., 2012, 42(5), 481-488.
[http://dx.doi.org/10.1016/j.ijpara.2012.03.009] [PMID: 22549023]
[18]
Siqueira-Neto, J.L.; Debnath, A.; McCall, L.I.; Bernatchez, J.A.; Ndao, M.; Reed, S.L.; Rosenthal, P.J. Cysteine proteases in protozoan parasites. PLoS Negl. Trop. Dis., 2018, 12(8) e0006512
[http://dx.doi.org/10.1371/journal.pntd.0006512] [PMID: 30138453]
[19]
Letunic, I.; Bork, P. 20 years of the SMART protein domain annotation resource. Nucleic Acids Res., 2018, 46(D1), D493-D496.
[http://dx.doi.org/10.1093/nar/gkx922] [PMID: 29040681]
[20]
Letunic, I.; Doerks, T.; Bork, P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Res., 2015, 43(Database issue), D257-D260.
[http://dx.doi.org/10.1093/nar/gku949] [PMID: 25300481]
[21]
Almagro Armenteros, J.J.; Sønderby, C.K.; Sønderby, S.K.; Nielsen, H.; Winther, O. DeepLoc: prediction of protein subcellular localization using deep learning. Bioinformatics, 2017, 33(21), 3387-3395.
[http://dx.doi.org/10.1093/bioinformatics/btx431] [PMID: 29036616]
[22]
Roy, A.; Zhang, Y. Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement. Structure, 2012, 20(6), 987-997.
[http://dx.doi.org/10.1016/j.str.2012.03.009] [PMID: 22560732]
[23]
Zhang, C.; Freddolino, P.L.; Zhang, Y. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Res., 2017, 45(W1), W291-W299.
[http://dx.doi.org/10.1093/nar/gkx366] [PMID: 28472402]
[24]
Roy, A.; Yang, J.; Zhang, Y. COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res., 2012, 40(Web Server issue), W471-7.
[http://dx.doi.org/10.1093/nar/gks372] [PMID: 22570420]
[25]
Song, J.; Li, F.; Leier, A.; Marquez-Lago, T.T.; Akutsu, T.; Haffari, G.; Chou, K.C.; Webb, G.I.; Pike, R.N.; Hancock, J. PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. Bioinformatics, 2018, 34(4), 684-687.
[http://dx.doi.org/10.1093/bioinformatics/btx670] [PMID: 29069280]
[26]
Kumar, S.; Stecher, G.; Li, M.; Knyaz, C.; Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol., 2018, 35(6), 1547-1549.
[http://dx.doi.org/10.1093/molbev/msy096] [PMID: 29722887]
[27]
Saitou, N.; Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 1987, 4(4), 406-425.
[PMID: 3447015]
[28]
Zuckerkandl, E.; Pauling, L. Evolutionary divergence and convergence in proteins BT - Evolving genes and proteins. Evol. Genes Proteins, 1965, 97-166.
[29]
Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 1985, 39(4), 783-791.
[http://dx.doi.org/10.1111/j.1558-5646.1985.tb00420.x] [PMID: 28561359]
[30]
Wilkins, M.R.; Gasteiger, E.; Bairoch, A.; Sanchez, J.C.; Williams, K.L.; Appel, R.D.; Hochstrasser, D.F. Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol., 1999, 112, 531-552.
[PMID: 10027275]
[31]
Kim, D.E.; Chivian, D.; Baker, D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res., 2004, 32(Web Server issue), W526-531.
[http://dx.doi.org/10.1093/nar/gkh468] [PMID: 15215442]
[32]
Laskowski, R.A.; MacArthur, M.W.; Moss, D.S.; Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 1993, 26, 283-291.
[http://dx.doi.org/10.1107/S0021889892009944]
[33]
Laskowski, R.A.; Rullmannn, J.A.; MacArthur, M.W.; Kaptein, R.; Thornton, J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR, 1996, 8(4), 477-486.
[http://dx.doi.org/10.1007/BF00228148] [PMID: 9008363]
[34]
Wiederstein, M.; Sippl, M.J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res., 2007, 35(Web Server issue), W407-410.
[http://dx.doi.org/10.1093/nar/gkm290] [PMID: 17517781]
[35]
Sippl, M.J. Recognition of errors in three-dimensional structures of proteins. Proteins, 1993, 17(4), 355-362.
[http://dx.doi.org/10.1002/prot.340170404] [PMID: 8108378]
[36]
Madeira, F.; Park, Y.M.; Lee, J.; Buso, N.; Gur, T.; Madhusoodanan, N.; Basutkar, P.; Tivey, A.R.N.; Potter, S.C.; Finn, R.D.; Lopez, R. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res., 2019, 47(W1), W636-W641.
[http://dx.doi.org/10.1093/nar/gkz268] [PMID: 30976793]
[37]
Ashkenazy, H.; Abadi, S.; Martz, E.; Chay, O.; Mayrose, I.; Pupko, T.; Ben-Tal, N. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res., 2016, 44(W1), W344-350.
[http://dx.doi.org/10.1093/nar/gkw408] [PMID: 27166375]
[38]
Celniker, G.; Nimrod, G.; Ashkenazy, H.; Glaser, F.; Martz, E.; Mayrose, I.; Pupko, T.; Ben-Tal, N. ConSurf: using evolutionary data to raise testable hypotheses about protein function. Isr. J. Chem., 2013, 53, 199-206.
[http://dx.doi.org/10.1002/ijch.201200096]
[39]
Ashkenazy, H.; Erez, E.; Martz, E.; Pupko, T.; Ben-Tal, N. Con- Surf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res., 2010, 38(Web Server issue), W529-533.
[http://dx.doi.org/10.1093/nar/gkq399] [PMID: 20478830]
[40]
Landau, M.; Mayrose, I.; Rosenberg, Y.; Glaser, F.; Martz, E.; Pupko, T.; Ben-Tal, N. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res., 2005, 33(Web Server issue), W299-302.
[http://dx.doi.org/10.1093/nar/gki370] [PMID: 15980475]
[41]
Glaser, F.; Pupko, T.; Paz, I.; Bell, R.E.; Bechor-Shental, D.; Martz, E.; Ben-Tal, N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 2003, 19(1), 163-164.
[http://dx.doi.org/10.1093/bioinformatics/19.1.163]] [PMID: 12499312]
[42]
Pettersen, E.F.; Goddard, T.D.; Huang, C.C.; Couch, G.S.; Greenblatt, D.M.; Meng, E.C.; Ferrin, T.E. UCSF Chimera--a visualization system for exploratory research and analysis. J. Comput. Chem., 2004, 25(13), 1605-1612.
[http://dx.doi.org/10.1002/jcc.20084] [PMID: 15264254]
[43]
Zhou, H.; Skolnick, J. FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach. J. Chem. Inf. Model., 2013, 53(1), 230-240.
[http://dx.doi.org/10.1021/ci300510n] [PMID: 23240691]
[44]
Stoka, V.; Turk, V.; Turk, B. Lysosomal cathepsins and their regulation in aging and neurodegeneration. Ageing Res. Rev., 2016, 32, 22-37.
[http://dx.doi.org/10.1016/j.arr.2016.04.010] [PMID: 27125852]
[45]
Touz, M.C.; Rivero, M.R.; Miras, S.L.; Bonifacino, J.S. Lysosomal protein trafficking in Giardia lamblia: common and distinct features. Front. Biosci. (Elite Ed.), 2012, 4, 1898-1909.
[http://dx.doi.org/10.2741/e511] [PMID: 22202006]
[46]
Evans-Osses, I.; Mojoli, A.; Monguió-Tortajada, M.; Marcilla, A.; Aran, V.; Amorim, M.; Inal, J.; Borràs, F.E.; Ramirez, M.I. Microvesicles released from Giardia intestinalis disturb host-pathogen response in vitro. Eur. J. Cell Biol., 2017, 96(2), 131-142.
[http://dx.doi.org/10.1016/j.ejcb.2017.01.005] [PMID: 28236495]
[47]
Fonte, L.; Fong, A.; Méndez, Y.; Moreira, Y. Patogenicidad de Blastocystis sp. Evidencias y mecanismos. Rev. Cubana Med. Trop., 2014, 66, 1-20.
[48]
Ikai, A. Thermostability and aliphatic index of globular proteins. J. Biochem., 1980, 88(6), 1895-1898.
[PMID: 7462208]
[49]
Eichacker, L.A.; Granvogl, B.; Mirus, O.; Müller, B.C.; Miess, C.; Schleiff, E. Hiding behind hydrophobicity. Transmembrane segments in mass spectrometry. J. Biol. Chem., 2004, 279(49), 50915-50922.
[http://dx.doi.org/10.1074/jbc.M405875200] [PMID: 15452135]
[50]
Zhang, M.; Wei, Z.; Chang, S.; Teng, M.; Gong, W. Crystal structure of a papain-fold protein without the catalytic residue: a novel member in the cysteine proteinase family. J. Mol. Biol., 2006, 358(1), 97-105.
[http://dx.doi.org/10.1016/j.jmb.2006.01.065] [PMID: 16497323]
[51]
Vega, M.C.; Martínez, J.C.; Serrano, L. Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II’ region of the Ramachandran plot. Protein Sci., 2000, 9(12), 2322-2328.
[http://dx.doi.org/10.1110/ps.9.12.2322] [PMID: 11206053]
[52]
Uddin, R.; Masood, F.; Azam, S.S.; Wadood, A. Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis. Microb. Pathog., 2019, 128, 28-35.
[http://dx.doi.org/10.1016/j.micpath.2018.12.015] [PMID: 30550846]
[53]
Verma, S.; Dixit, R.; Pandey, K.C. Cysteine proteases: Modes of activation and future prospects as pharmacological targets. Front. Pharmacol., 2016, 7, 107.
[http://dx.doi.org/10.3389/fphar.2016.00107] [PMID: 27199750]
[54]
Hardegger, L.A.; Kuhn, B.; Spinnler, B.; Anselm, L.; Ecabert, R.; Stihle, M.; Gsell, B.; Thoma, R.; Diez, J.; Benz, J.; Plancher, J.M.; Hartmann, G.; Banner, D.W.; Haap, W.; Diederich, F. Systematic investigation of halogen bonding in protein-ligand interactions. Angew. Chem. Int. Ed. Engl., 2011, 50(1), 314-318.
[http://dx.doi.org/10.1002/anie.201006781] [PMID: 21184410]
[55]
Kissoon-Singh, V.; Mortimer, L.; Chadee, K. Entamoeba histolytica cathepsin-like enzymes : interactions with the host gut. Adv. Exp. Med. Biol., 2011, 712, 62-83.
[http://dx.doi.org/10.1007/978-1-4419-8414-2_5] [PMID: 21660659]
[56]
Marquis, R.W.; Yamashita, D.S.; Ru, Y.; LoCastro, S.M.; Oh, H.J.; Erhard, K.F.; DesJarlais, R.L.; Head, M.S.; Smith, W.W.; Zhao, B.; Janson, C.A.; Abdel-Meguid, S.S.; Tomaszek, T.A.; Levy, M.A.; Veber, D.F. Conformationally constrained 1,3-diamino ketones: a series of potent inhibitors of the cysteine protease cathepsin K. J. Med. Chem., 1998, 41(19), 3563-3567.
[http://dx.doi.org/10.1021/jm980295f] [PMID: 9733481]
[57]
Lecaille, F.; Chowdhury, S.; Purisima, E.; Brömme, D.; Lalmanach, G. The S2 subsites of cathepsins K and L and their contribution to collagen degradation. Protein Sci., 2007, 16(4), 662-670.
[http://dx.doi.org/10.1110/ps.062666607] [PMID: 17384231]
[58]
Chowdhury, S.F.; Sivaraman, J.; Wang, J.; Devanathan, G.; Lachance, P.; Qi, H.; Ménard, R.; Lefebvre, J.; Konishi, Y.; Cygler, M.; Sulea, T.; Purisima, E.O. Design of noncovalent inhibitors of human cathepsin L. From the 96-residue proregion to optimized tripeptides. J. Med. Chem., 2002, 45(24), 5321-5329.
[http://dx.doi.org/10.1021/jm020238t] [PMID: 12431059]
[59]
Sudhan, D.R.; Siemann, D.W. HHS Public Access., 2016, 265-287.
[60]
Hashimoto, Y.; Kondo, C.; Katunuma, N. An active 32-kDa Cathepsin L is secreted directly from HT 1080 fibrosarcoma cells and not via lysosomal exocytosis. PLoS One, 2015, 10(12) e0145067
[http://dx.doi.org/10.1371/journal.pone.0145067] [PMID: 26674348]
[61]
Shah, P.P.; Wang, T.; Kaletsky, R.L.; Myers, M.C.; Purvis, J.E.; Jing, H.; Huryn, D.M.; Greenbaum, D.C.; Smith, A.B., III; Bates, P.; Diamond, S.L. A small-molecule oxocarbazate inhibitor of human cathepsin L blocks severe acute respiratory syndrome and ebola pseudotype virus infection into human embryonic kidney 293T cells. Mol. Pharmacol., 2010, 78(2), 319-324.
[http://dx.doi.org/10.1124/mol.110.064261] [PMID: 20466822]
[62]
Chaparro, J.D.; Cheng, T.; Tran, U.P.; Andrade, R.M.; Brenner, S.B.T.; Hwang, G.; Cohn, S.; Hirata, K.; McKerrow, J.H.; Reed, S.L. Two key cathepsins, TgCPB and TgCPL, are targeted by the vinyl sulfone inhibitor K11777 in in vitro and in vivo models of toxoplasmosis. PLoS One, 2018, 13(3) e0193982
[http://dx.doi.org/10.1371/journal.pone.0193982] [PMID: 29565998]

Rights & Permissions Print Cite
Article Metrics
12
1
© 2024 Bentham Science Publishers | Privacy Policy