Journal of Computer-Aided Molecular Design

, Volume 30, Issue 12, pp 1165–1174 | Cite as

Identification of novel Trypanosoma cruzi prolyl oligopeptidase inhibitors by structure-based virtual screening

  • Hugo de Almeida
  • Vincent Leroux
  • Flávia Nader Motta
  • Philippe Grellier
  • Bernard Maigret
  • Jaime M. Santana
  • Izabela Marques Dourado Bastos


We have previously demonstrated that the secreted prolyl oligopeptidase of Trypanosoma cruzi (POPTc80) is involved in the infection process by facilitating parasite migration through the extracellular matrix. We have built a 3D structural model where POPTc80 is formed by a catalytic α/β-hydrolase domain and a β-propeller domain, and in which the substrate docks at the inter-domain interface, suggesting a “jaw opening” gating access mechanism. This preliminary model was refined by molecular dynamics simulations and next used for a virtual screening campaign, whose predictions were tested by standard binding assays. This strategy was successful as all 13 tested molecules suggested from the in silico calculations were found out to be active POPTc80 inhibitors in the micromolar range (lowest Ki at 667 nM). This work paves the way for future development of innovative drugs against Chagas disease.


Chagas disease Trypanosoma cruzi Prolyl oligopeptidase POPTc80 Homology modeling Catalytic mechanism Binding assays Structure-based drug design Virtual screening Docking GOLD Molecular dynamics NAMD 

Supplementary material

10822_2016_9985_MOESM1_ESM.pdf (8.4 mb)
Supplementary material 1 (PDF 8592 kb)


  1. 1.
    Haberland A et al (2013) Chronic Chagas disease: from basics to laboratory medicine. Clin Chem Lab Med 51:271–294CrossRefGoogle Scholar
  2. 2.
    Nunes MCP et al (2013) Chagas disease: an overview of clinical and epidemiological aspects. J Am Coll Cardiol 62:767–776CrossRefGoogle Scholar
  3. 3.
    Dias JCP, Silveira AC, Schofield CJ (2002) The impact of Chagas disease control in Latin America: a review. Mem Inst Oswaldo Cruz 97:603–612CrossRefGoogle Scholar
  4. 4.
    de Castro SL (1993) The challenge of Chagas’ disease chemotherapy: an update of drugs assayed against Trypanosoma cruzi. Acta Trop 53:83–98CrossRefGoogle Scholar
  5. 5.
    Rodriques Coura J, de Castro SL (2002) A critical review on Chagas disease chemotherapy. Mem Inst Oswaldo Cruz 97:3–24CrossRefGoogle Scholar
  6. 6.
    Urbina JA, Docampo R (2003) Specific chemotherapy of Chagas disease: controversies and advances. Trends Parasitol 19:495–501CrossRefGoogle Scholar
  7. 7.
    Croft SL, Barrett MP, Urbina JA (2005) Chemotherapy of trypanosomiases and leishmaniasis. Trends Parasitol 21:508–512CrossRefGoogle Scholar
  8. 8.
    Savioli L et al (2010) Working to overcome the global impact of neglected tropical diseases: first WHO report on neglected tropical diseases. World Health Organization Geneva, SwitzerlandGoogle Scholar
  9. 9.
    Santana J et al (1997) A Trypanosoma cruzi-secreted 80 kDa proteinase with specificity for human collagen types I and IV. Biochem J 137:129–137CrossRefGoogle Scholar
  10. 10.
    Grellier P et al (2001) Trypanosoma cruzi prolyl oligopeptidase Tc80 is involved in nonphagocytic mammalian cell invasion by trypomastigotes. J Biol Chem 276:47078–47086CrossRefGoogle Scholar
  11. 11.
    Dourado Bastos IM et al (2005) Molecular, functional and structural properties of the prolyl oligopeptidase of Trypanosoma cruzi (POP Tc80), which is required for parasite entry into mammalian cells. Biochem J 388:29–38CrossRefGoogle Scholar
  12. 12.
    Vendeville S et al (1999) Identification of inhibitors of an 80 kDa protease from Trypanosoma cruzi through the screening of a combinatorial peptide library. Chem Pharm Bull 47:194–198CrossRefGoogle Scholar
  13. 13.
    Joyeau R et al (2000) Synthesis and activity of pyrrolidinyl- and thiazolidinyl-dipeptide derivatives as inhibitors of the Tc80 prolyl oligopeptidase from Trypanosoma cruzi. Eur J Med Chem 35:257–266CrossRefGoogle Scholar
  14. 14.
    Bal G et al (2003) Prolylisoxazoles: potent inhibitors of prolyloligopeptidase with antitrypanosomal activity. Bioorg Med Chem Lett 13:2875–2878CrossRefGoogle Scholar
  15. 15.
    Choe Y et al (2005) Development of alpha-keto-based inhibitors of cruzain, a cysteine protease implicated in Chagas disease. Bioorg Med Chem 13:2141–2156CrossRefGoogle Scholar
  16. 16.
    Dourado Bastos IM et al (2013) Parasite prolyl oligopeptidases and the challenge of designing chemotherapeuticals for Chagas disease, leishmaniasis and African trypanosomiasis. Curr Med Chem 20:3103–3115CrossRefGoogle Scholar
  17. 17.
    Maluf FV et al (2013) A pharmacophore-based virtual screening approach for the discovery of Trypanosoma cruzi GAPDH inhibitors. Future Med Chem 5:2019–2035CrossRefGoogle Scholar
  18. 18.
    Meiering S et al (2005) Inhibitors of Trypanosoma cruzi trypanothione reductase revealed by virtual screening and parallel synthesis. J Med Chem 48:4793–4802CrossRefGoogle Scholar
  19. 19.
    Cavasotto CN, Phatak SS (2009) Homology modeling in drug discovery: current trends and applications. Drug Discov Today 14:676–683CrossRefGoogle Scholar
  20. 20.
    Du H et al (2015) Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening. Methods 71:77–84CrossRefGoogle Scholar
  21. 21.
    Fülöp V, Böcskei Z, Polgár L (1998) Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis. Cell 94:161–170CrossRefGoogle Scholar
  22. 22.
    Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38CrossRefGoogle Scholar
  23. 23.
    Phillips JC et al (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802CrossRefGoogle Scholar
  24. 24.
    MacKerell AD et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616CrossRefGoogle Scholar
  25. 25.
    Iturrioz X et al (2010) By interacting with the C-terminal Phe of apelin, Phe255 and Trp259 in helix VI of the apelin receptor are critical for internalization. J Biol Chem 285:32627–32637CrossRefGoogle Scholar
  26. 26.
    Cai W, Shao X, Maigret B (2002) Protein–ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening. J Mol Graph Model 20:313–328CrossRefGoogle Scholar
  27. 27.
    Cai W et al (2008) SHEF: a vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces. J Mol Model 14:393–401CrossRefGoogle Scholar
  28. 28.
    Weidel E et al (2014) Composing compound libraries for hit discovery—rationality-driven preselection or random choice by structural diversity? Future Med Chem 6:2057–2072CrossRefGoogle Scholar
  29. 29.
    López A, Tarragó T, Giralt E (2011) Low molecular weight inhibitors of prolyl oligopeptidase: a review of compounds patented from 2003 to 2010. Expert Opin Ther Pat 21:1023–1044CrossRefGoogle Scholar
  30. 30.
    Pripp AH (2006) Quantitative structure—activity relationship of prolyl oligopeptidase inhibitory peptides derived from β-casein using simple amino acid descriptors. J Agric Food Chem 54:224–228CrossRefGoogle Scholar
  31. 31.
    Sadowski J, Gasteiger J (1993) From atoms and bonds to three-dimensional atomic coordinates: automatic model builders. Chem Rev 93:2567–2581CrossRefGoogle Scholar
  32. 32.
    Sadowski J, Gasteiger J, Klebe G (1994) Comparison of automatic three-dimensional model builders using 639 X-ray structures. J Chem Inf Model 34:1000–1008CrossRefGoogle Scholar
  33. 33.
    Verdonk ML et al (2003) Improved protein–ligand docking using GOLD. Proteins 52:609–623CrossRefGoogle Scholar
  34. 34.
    Cornish-Bowden A (1976) Principles of enzyme kinetics. Butterworths, LondonGoogle Scholar
  35. 35.
    Salvesen G, Nagase H (1989) Inhibition of proteolytic enzymes. In: Bond JS, Beynon RJ (eds) Proteolytic enzymes: a practical approach. IRL Press, Oxford, pp 83–104Google Scholar
  36. 36.
    Haffner CD et al (2008) Pyrrolidinyl pyridone and pyrazinone analogues as potent inhibitors of prolyl oligopeptidase (POP). Bioorg Med Chem Lett 18:4360–4363CrossRefGoogle Scholar
  37. 37.
    Devine SM et al (2015) Promiscuous 2-aminothiazoles (PrATs): a frequent hitting scaffold. J Med Chem 58:1205–1214CrossRefGoogle Scholar
  38. 38.
    Baell J, Walters MA (2014) Chemical con artists foil drug discovery. Nature 513:481–483CrossRefGoogle Scholar
  39. 39.
    Irwin JJ et al (2015) An aggregation advisor for ligand discovery. J Med Chem 58:7076–7087CrossRefGoogle Scholar
  40. 40.
    Ferreira RS et al (2010) Complementarity between a docking and a high-throughput screen in discovering new Cruzain inhibitors. J Med Chem 53:4891–4905CrossRefGoogle Scholar
  41. 41.
    Feng BY, Shoichet BK (2006) A detergent-based assay for the detection of promiscuous inhibitors. Nat Protoc 1:550–553CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Hugo de Almeida
    • 1
  • Vincent Leroux
    • 2
  • Flávia Nader Motta
    • 1
    • 3
  • Philippe Grellier
    • 4
  • Bernard Maigret
    • 2
  • Jaime M. Santana
    • 1
  • Izabela Marques Dourado Bastos
    • 1
  1. 1.Department of Cellular Biology, Laboratory of Host-Pathogen InterfaceThe University of BrasíliaBrasíliaBrazil
  2. 2.LORIA, CNRS UMR 7503, INRIA Grand Est, CAPSID teamUniversity of LorraineVandœuvre-lès-NancyFrance
  3. 3.Faculty of CeilândiaThe University of BrasíliaBrasíliaBrazil
  4. 4.UMR 7245 CNRS, Équipe APE, CP52Muséum National d’Histoire NaturelleParisFrance

Personalised recommendations