Advertisement

Journal of Computer-Aided Molecular Design

, Volume 30, Issue 4, pp 305–321 | Cite as

Discovery of novel polyamine analogs with anti-protozoal activity by computer guided drug repositioning

  • Lucas N. Alberca
  • María L. Sbaraglini
  • Darío Balcazar
  • Laura Fraccaroli
  • Carolina Carrillo
  • Andrea Medeiros
  • Diego Benitez
  • Marcelo Comini
  • Alan Talevi
Article

Abstract

Chagas disease is a parasitic infection caused by the protozoa Trypanosoma cruzi that affects about 6 million people in Latin America. Despite its sanitary importance, there are currently only two drugs available for treatment: benznidazole and nifurtimox, both exhibiting serious adverse effects and limited efficacy in the chronic stage of the disease. Polyamines are ubiquitous to all living organisms where they participate in multiple basic functions such as biosynthesis of nucleic acids and proteins, proliferation and cell differentiation. T. cruzi is auxotroph for polyamines, which are taken up from the extracellular medium by efficient transporters and, to a large extent, incorporated into trypanothione (bis-glutathionylspermidine), the major redox cosubstrate of trypanosomatids. From a 268-compound database containing polyamine analogs with and without inhibitory effect on T. cruzi we have inferred classificatory models that were later applied in a virtual screening campaign to identify anti-trypanosomal compounds among drugs already used for other therapeutic indications (i.e. computer-guided drug repositioning) compiled in the DrugBank and Sweetlead databases. Five of the candidates identified with this strategy were evaluated in cellular models from different pathogenic trypanosomatids (T. cruzi wt, T. cruzi PAT12, T. brucei and Leishmania infantum), and in vitro models of aminoacid/polyamine transport assays and trypanothione synthetase inhibition assay. Triclabendazole, sertaconazole and paroxetine displayed inhibitory effects on the proliferation of T. cruzi (epimastigotes) and the uptake of putrescine by the parasite. They also interfered with the uptake of others aminoacids and the proliferation of infective T. brucei and L. infantum (promastigotes). Trypanothione synthetase was ruled out as molecular target for the anti-parasitic activity of these compounds.

Keywords

Chagas disease Drug repositioning Polyamines Trypanosomatids virtual screening Paroxetine Triclabendazole 

Notes

Acknowledgments

The authors would like to thank the following public and non-profit organizations: National University of La Plata and Exact Sciences Faculty PIRPS. National University of La Plata Travel Grants and Incentivos X-730, Argentinean National Agency of Scientific and Technical Research(ANPCyT), PICT 2013-0520, CONICET. DB and MAC acknowledge the support of ANII for postgraduate fellowship (POS_NAC_2013_1_114477) and FOCEM (MERCOSUR Structural Convergence Fund, COF 03/11), respectively.

Supplementary material

10822_2016_9903_MOESM1_ESM.pdf (3.9 mb)
Supplementary material 1 (PDF 4013 kb)
10822_2016_9903_MOESM2_ESM.pdf (43 kb)
Supplementary material 2 (PDF 43 kb)

References

  1. 1.
    Rodrigues Coura J, de Castro SL (2002) A critical review on Chagas disease chemotherapy. Mem Inst Oswaldo Cruz 97:3–24CrossRefGoogle Scholar
  2. 2.
    Rodrigues Coura J, Pinto Dias JC (2009) Epidemiology, control and surveillance of Chagas disease—100 years after its discovery. Mem Inst Oswaldo Cruz 104:31–40Google Scholar
  3. 3.
    Bustamante JM, Tarleton RL (2014) Potential new clinical therapies for Chagas disease. Expert Rev Clin Pharmacol 7:317–325CrossRefGoogle Scholar
  4. 4.
    Nunes MC, Dones W, Morillo CA, Encina JJ, Ribeiro AL (2013) Chagas disease: an overview of clinical and epidemiological aspects. J Am Coll Cardiol 62:767–776CrossRefGoogle Scholar
  5. 5.
    World Health Organization (2015) Chagas disease in Latin America: an epidemiological update based on 2010 estimates. Wkly Epidemiol Rec 90:33–44Google Scholar
  6. 6.
    Croft SL, Barret MP, Urbina JA (2005) Chemotherapy of trypanosomiases and leishmaniasis. TRENDS in Parasitol 21:508–512CrossRefGoogle Scholar
  7. 7.
    Morillo CA, Marin-Neto JA, Avenzum A, Sosa-Estani S, Rassi A, Rosas F, Villena E, Quiroz R, Bonilla R, Britto C, Guhl F, Velazquez E, Bonilla L, Meeks B, Rao-Melacini R, Pogue J, Mattos A, Lazdins J, Rassi A, Connolly SJ, Yusuf S (2015) Randomized trial of benznidazole for chronic Chagas’ cardiomyopathy. N Engl J Med 373:1295–1306CrossRefGoogle Scholar
  8. 8.
    Comini MA, Flohé L (2013) In: Flohé L, Jäger T, Koch O (eds) Drug discovery for trypanosomatid diseases. Oxford, WileyGoogle Scholar
  9. 9.
    Carrillo C, Cejas S, González NS, Algranati ID (1999) Trypanosoma cruzi epimastigotes lack ornithine decarboxylase but can express a foreign gene encoding this enzyme. FEBS Lett 454:192–196CrossRefGoogle Scholar
  10. 10.
    Carrillo C, Cejas S, Huber A, González NS, Algranati ID (2003) Lack of arginine decarboxylase in Trypanosoma cruzi epimastigotes. EukaryotMicrobiol 50:312–316Google Scholar
  11. 11.
    Algranati ID, Serra MP, Carrillo C, González NS (2005) Biología molecular del metabolismo de poliaminas en parásitos tripanosomátidos. Expresión de genes heterólogos de ornitina y arginina decarboxilasa en Trypanosoma cruzi. Química Viva 2:78–94Google Scholar
  12. 12.
    Carrillo C, Canepa GE, Algranati ID, Pereira CA (2006) Molecular and functional characterization of a spermidine transporter (TcPAT12) from Trypanosoma cruzi. Biochem Biophys Res Commun 334:936–940CrossRefGoogle Scholar
  13. 13.
    Hasne MP, Coppens I, Soysa R, Ullman B (2010) A high-affinity putrescine-cadaverine transporter from Trypanosoma cruzi. Mol Microbiol 76:78–91CrossRefGoogle Scholar
  14. 14.
    Pereyra CA, Carrillo C, Miranda MR, Bouvier LA, Canepa GE (2008) Trypanosoma cruzi: transporte de metabolitos esenciales obtenidos del hospedador. Medicina 68:398–404Google Scholar
  15. 15.
    Comini MA, Guerrero SA, Haile S, Menge U, Lünsdorf H, Flohé L (2004) Validation of Trypanosoma brucei trypanothione synthetase as drug target. Free Radic Biol Med 36(10):1289–1302CrossRefGoogle Scholar
  16. 16.
    Sousa AF, Gomes-Alves AG, Benítez D, Comini MA, Flohé L, Jaeger T, Passos J, Stuhlmann F, Tomás AM, Castro H (2014) Genetic and chemical analyses reveal that trypanothione synthetase but not glutathionylspermidine synthetase is essential for Leishmania infantum. Free Randic Biol Med 73:229–238CrossRefGoogle Scholar
  17. 17.
    Liu Z, Fang H, Reagan K, Xu X, Mendrick DL, Slikker W Jr, Tong W (2013) In silico drug repositioning—what we need to know. Drug Discov Today 18:110–115CrossRefGoogle Scholar
  18. 18.
    Allarakhia M (2013) Open-source approaches for the repurposing of existing or failed candidate drugs: learning from and applying the lessons across diseases. Drug Des Dev Ther 2013:753–766CrossRefGoogle Scholar
  19. 19.
    Ashburn TT, Thor KB (2004) Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 3:673–683CrossRefGoogle Scholar
  20. 20.
    Bellera CL, Balcazar DE, Vanrell MC, Casassa AF, Palestro PH, Gavernet L, Labriola CA, Gálvez J, Bruno-Blanch LE, Romano PS, Carrillo C, Talevi A (2015) Computer-guided drug repurposing: identification of trypanocidal activity of clofazimine, benidipine and saquinavir. Eur J Med Chem 93:338–348CrossRefGoogle Scholar
  21. 21.
    Ekins S, Williams AJ, Krasowski MD, Freundlich JS (2011) In silico repositioning of approved drugs for rare and neglected diseases. Drug Discov Today 16:298–310CrossRefGoogle Scholar
  22. 22.
    Sbaraglini ML, Vanrell MC, Bellera CL, Benaim G, Carrillo C, Talevi A, Romano PS (2016) Neglected tropical protozoan diseases: drug repositioning as a rational option. Curr Top Med Chem 16Google Scholar
  23. 23.
    Díaz MV, Miranda MR, Campos-Estrada C, Reigada C, Maya JD, Pereira CA, López-Muñoz R (2014) Pentamidine exerts in vitro and in vivo anti Trypanosoma cruzi activity and inhibits the polyamine transport in Trypanosoma cruzi. Acta Trop 134:1–9CrossRefGoogle Scholar
  24. 24.
    Silva CF, Batista MM, Alves Mota R, Mello de Souza E, Stephens CE, Som P, Boykin DW, Soeiro MNC (2007) Activity of ‘‘reversed’’ diamidines against Trypanosoma cruzi ‘‘in vitro’’. Biochem Pharm 73:939–946CrossRefGoogle Scholar
  25. 25.
    Liew LPP, Kaiser M, Copp BR (2013) Discovery and preliminary structure–activity relationship analysis of 1,14-sperminediphenylacetamides as potent and selective antimalarial lead compounds. Bioorg Med Chem Lett 23:452–454CrossRefGoogle Scholar
  26. 26.
    Da Silva CF, Da Silva PB, Batista MM, Daliry A, Tidwell RR, Soeiro MNC (2010) The biological in vitro effect and selectivity of aromatic dicationic compounds on Trypanosoma cruzi. Mem Inst Oswaldo Cruz 105(3):239–245CrossRefGoogle Scholar
  27. 27.
    Daliry A, Da Silva PB, Da Silva CF, Batista MM, De Castro SL, Tidwell RR, Soeiro MNC (2009) In vitro analyses of the effect of aromatic diamidines upon Trypanosoma cruzi. J Antimicrob Chemother 64:747–750CrossRefGoogle Scholar
  28. 28.
    Stephens CE, Brun R, Salem MM, Werbovetz KA, Tanious F, Wilson WD, Boykin DW (2003) The Activity of Diguanidino and ‘Reversed’ Diamidino 2,5-Diarylfurans versus Trypanosoma cruzi and Leishmania donovani. Bioorg Med Chem Lett 13:2065–2069CrossRefGoogle Scholar
  29. 29.
    Gonzales JL, Stephens CE, Wenzler T, Brun R, Tanious FA, Wilson WD, Barszcz T, Werbovetz KA, Boykin DW (2007) Synthesis and antiparasitic evaluation of bis-2,5-[4-guanidinophenyl]thiophenes. Eur J Med Chem 42:552–557CrossRefGoogle Scholar
  30. 30.
    De Oliveira Pacheco MG, Da Silva CF, De Souza CF, Batista MM, Da Silva PB, Kumar A, Stephens CE, Boykin DW, Soeiro MNC (2009) Trypanosoma cruzi: activity of heterocyclic cationic molecules in vitro. Exp Parasitol 123:73–80CrossRefGoogle Scholar
  31. 31.
    Da Silva CF, Batista MM, Batista DGJ, De Souza EM, Da Silva PB, De Oliveira GM, Meuser AS, Shareef AR, Boykin DW, Soeiro MNC (2008) In vitro and in vivo studies of the trypanocidal activity of a diarylthiophene diamidine against Trypanosoma cruzi. Antimicrob Agents Chemother 52(9):3307–3314CrossRefGoogle Scholar
  32. 32.
    Patrick DA, Ismail MA, Arafa RK, Wenzler T, Zhu X, Pandharkar T, Jones SK, Werbovetz KA, Brun R, Boykin DW, Tidwell RR (2013) Synthesis and antiprotozoal activity of dicationic m-terphenyl and 1,3-dipyridylbenzene derivatives. J Med Chem 56(13):5473–5494CrossRefGoogle Scholar
  33. 33.
    Menezes D, Valentim C, Oliveira MF, Vannier-Santos MA (2006) Putrescine analogue cytotoxicity against Trypanosoma cruzi. Parasitol Res 98:99–105CrossRefGoogle Scholar
  34. 34.
    Daliry A, Pires MQ, Silva CF, Pacheco RS, Munde M, Stephens CE, Kumar A, Ismail MA, Liu Z, Farahat AA, Akay S, Som P, Hu Q, Boykin DW, Wilson WD, De Castro SL, Soeiro MNC (2011) The trypanocidal activity of amidine compounds does not correlate with their binding affinity to Trypanosoma cruzi kinetoplast DNA. Antimicrob Agents Chemother 55(10):4765–4773CrossRefGoogle Scholar
  35. 35.
    Birkholtz LM, Williams M, Niemand J, Louw AI, Persson L, Heby O (2011) Polyamine homoeostasis as a drug target in pathogenic protozoa: peculiarities and possibilities. Biochem J 438:229–244CrossRefGoogle Scholar
  36. 36.
    Lizzi F, Veronesi G, Belluti F, Bergamini C, López-Sánchez A, Kaiser M, Brun R, Krauth-Siegel RL, Hall DG, Rivas L, Bolognesi ML (2012) Conjugation of quinones with natural polyamines: toward an expanded antitrypanosomatid profile. J Med Chem 55(23):10490–10500CrossRefGoogle Scholar
  37. 37.
    De Souza EM, Da Silva PB, Nefertiti ASG, Ismail MA, Arafa RK, Tao B, Nixon-Smith CK, Boykin DW, Soeiro MNC (2011) Trypanocidal activity and selectivity in vitro of aromatic amidine compounds upon bloodstream and intracellular forms of Trypanosoma cruzi. Exp Parasitol 127:429–435CrossRefGoogle Scholar
  38. 38.
    Borges MN, Messeder JC, Figueroa-Villar JD (2004) Synthesis, anti-Trypanosoma cruzi activity and micelle interaction studies of bisguanylhydrazones analogous to pentamidine. Eur J Med Chem 39:925–929CrossRefGoogle Scholar
  39. 39.
    Majumder S, Kierszenbaum F (1993) Inhibition of host cell invasion and intracellular replication of Trypanosoma cruzi by N, N′-Bis(Benzyl)-substituted polyamine analogs. Antimicrob Agents Chemother 37(10):2235–2238CrossRefGoogle Scholar
  40. 40.
    Zhu X, Liu Q, Yang S, Parman T, Green CE, Mirsalis JC, Soeiro MNC, De Souza EM, Da Silva CF, Batista DGJ, Stephens CE, Banerjee M, Farahat AA, Munde M, Wilson WD, Boykin DW, Wang MZ, Werbovetz KA (2012) Evaluation of Arylimidamides DB1955 and DB1960 as candidates against Visceral Leishmaniasis and Chagas’ disease: in vivo efficacy, acute toxicity, pharmacokinetics, and toxicology studies. Antimicrob Agents Chemother 56(7):3690–3699CrossRefGoogle Scholar
  41. 41.
    Klenke B, Stewart M, Barret MP, Brun R, Gilbert IH (2001) Synthesis and biological evaluation of s-triazine substituted polyamines as potential new anti-trypanosomal drugs. J Med Chem 44:3440–3452CrossRefGoogle Scholar
  42. 42.
    Braga SFP, Alves EVP, Ferreira RS, Fradico JRB, Lage PS, Duarte MC, Ribeiro TG, Júnior PAS, Romanha AJ, Tonini ML, Steindel M, Coelho EF, De Oliveira RB (2014) Synthesis and evaluation of the antiparasitic activity of bis-(arylmethylidene) cycloalkanones. Eur J Med Chem 71:282–289CrossRefGoogle Scholar
  43. 43.
    Caterina MC, Perillo IA, Boiani L, Pezaroglo H, Cerecetto H, González M, Salerno A (2008) Imidazolidines as new anti-Trypanosoma cruzi agents: biological evaluation and structure–activity relationships. Bioorg Med Chem 16:2226–2234CrossRefGoogle Scholar
  44. 44.
    Perez-Lamas C, Lopez-Bigas N (2011) Gitools: analysis and visualization of genomic data using interactive heat-maps. PLoS One 6:e19541CrossRefGoogle Scholar
  45. 45.
    Stahl M, Mauser H (2005) Database clustering with a combination of fingerprint and maximum common substructure methods. J Chem Inf Model 45(3):542–548CrossRefGoogle Scholar
  46. 46.
    Böcker A (2008) Toward an improved clustering of large data sets using maximum common substructures and topological fingerprints. J Chem Inf Model 48(11):2097–2107CrossRefGoogle Scholar
  47. 47.
    Hariharan R, Janakiraman A, Nilakantan R, Singh B, Varghese S, Landrum G, Schuffenhauer A (2011) MultiMCS: a fast algorithm for the maximum common substructure problem on multiple molecules. J Chem Inf Model 51(4):788–806CrossRefGoogle Scholar
  48. 48.
    Herhaus C (2014) Introducing fuzziness into maximum common substructures for meaningful cluster characterization. J Cheminform 6(Suppl 1):17CrossRefGoogle Scholar
  49. 49.
    Talevi A, Bellera CL, Di Ianni M, Duchowicz PR, Bruno-Blanch LE, Castro EA (2012) An integrated drug development approach applying topological descriptors. Curr Comput Aided Drug Des 8:172–181CrossRefGoogle Scholar
  50. 50.
    Yasri A, Hartsough D (2001) Toward an optimal procedure for variable selection and QSAR model building. J Chem Inf Comput Sci 41:3–6CrossRefGoogle Scholar
  51. 51.
    Mysinger MM, Carchia M, Irwin JJ, Shoichet BK (2012) Directory of Useful Decoys, Enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem 55:6582–6594CrossRefGoogle Scholar
  52. 52.
    Irwin JJ, Shoichet BK (2005) ZINC–a free database of commercially available compounds for virtual screening. J Chem Inf Model 45(1):177–182CrossRefGoogle Scholar
  53. 53.
    Yang Y, Hongming C, Nilsson I, Muresan S, Engkvist O (2010) Investigation of the relationship between topology and selectivity for druglike molecules. J Med Chem 53:7709–7714CrossRefGoogle Scholar
  54. 54.
    Yang Y, Engkvist O, Llinas A, Chen H (2012) Beyond size, ionization state, and lipophilicity: influence of molecular topology on absorption, distribution, metabolism, excretion, and toxicity for druglike compounds. J Med Chem 55:3667–3677CrossRefGoogle Scholar
  55. 55.
    Triballeau N, Acher F, Brabet I, Pin JP, Bertrand HO (2005) Virtual screening workflow development guided by the “receiver operating characteristic” curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. J Med Chem 48(7):2534–2547CrossRefGoogle Scholar
  56. 56.
    DeLong ER, DeLong DM, Clarke-Pearson DL (1988) Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics 44(3):837–845CrossRefGoogle Scholar
  57. 57.
    Li L, Hu Q, Wu X, Yu D (2014) Exploration of classification confidence in ensemble learning. Pattern Recogn 47:3120–3131CrossRefGoogle Scholar
  58. 58.
    Zhang Q, Muegge I (2006) Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: ranking, voting, and consensus scoring. J Med Chem 49:1536–1548CrossRefGoogle Scholar
  59. 59.
    Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS (2011) DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs. NucleicAcids Res 39:1035–1041CrossRefGoogle Scholar
  60. 60.
    Novick PA, Ortiz OF, Poelman J, Abdulhay AY, Pande VS (2013) SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discovery. PLoS One 8(11):e79568CrossRefGoogle Scholar
  61. 61.
    Bellera CL, Balcazar DE, Alberca LN, Labriola CA, Talevi A, Carrillo C (2013) Application of computer-aided drug repurposing in the search of New Cruzipain inhibitors: discovery of amiodarone and bromocriptine inhibitory effects. J Chem Inf Model 53(9):2402–2408CrossRefGoogle Scholar
  62. 62.
    Biebinger S, Wirtz LE, Lorenz P, Clayton C (1997) Vectors for inducible expression of toxic gene products in bloodstream and procyclic Trypanosoma brucei. Mol Biochem Parasitol 85(1):99–112CrossRefGoogle Scholar
  63. 63.
    Fernández M, Becco L, Correia I, Benítez J, Piro OE, Echeverria GA, Medeiros A, Comini M, Lavaggi ML, González M, Cerecetto H, Moreno V, Pessoa JC, Garat B, Gambino D (2013) Oxidovanadium(IV) and dioxidovanadium(V) complexes of tridentate salicylaldehyde semicarbazones: searching for prospective antitrypanosomal agents. J Inorg Biochem 127:150–160CrossRefGoogle Scholar
  64. 64.
    Mosmann T (1983) Rapid colorimetric assay for cellular growth and survival: application to proliferation and cytotoxicity assays. J Immunol Methods 65:55–63CrossRefGoogle Scholar
  65. 65.
    Sousa AF, Gomes-Alves AG, Benítez D, Comini MA, Flohé L, Jaeger T, Passos J, Stuhlmann F, Tomás AM, Castro H (2014) Genetic and chemical analyses reveal that trypanothione synthetase but not glutathionylspermidine synthetase is essential for Leishmania infantum. Free Radic Biol Med 73:229–238CrossRefGoogle Scholar
  66. 66.
    Maiwald F, Benítez D, Charquero D, Dar MA, Erdmann H, Preu L, Koch O, Hölscher C, Loaëc N, Meijer L, Comini MA, Kunick C (2014) 9- and 11-substituted 4-azapaullones are potent and selective inhibitors of African trypanosoma. Eur J Med Chem 83:274–283CrossRefGoogle Scholar
  67. 67.
    Oprea TI, Overington JP (2015) Computational and practical aspects of drug repositioning. Assay Drug Dev Technol 13(6):299–306CrossRefGoogle Scholar
  68. 68.
    Schumacher SM, Gao E, Zhu W, Chen X, Chuprun JK, Feldman AM, Tesmer JJG, Koch WJ (2015) Paroxetine-mediated GRK2 inhibition reverses cardiac dysfunction and remodeling after myocardial infarction. Sci Transl Med 7(277):277ra31CrossRefGoogle Scholar
  69. 69.
    Taylor MC, Kaur H, Blessington B, Kelly JM, Wilkinson SR (2008) Validation of spermidine synthase as a drug target in African trypanosomes. Biochem J 409(2):563–569CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Lucas N. Alberca
    • 1
  • María L. Sbaraglini
    • 1
  • Darío Balcazar
    • 2
  • Laura Fraccaroli
    • 2
  • Carolina Carrillo
    • 2
  • Andrea Medeiros
    • 3
  • Diego Benitez
    • 3
  • Marcelo Comini
    • 3
  • Alan Talevi
    • 1
  1. 1.Laboratory of Bioactive Compounds Research and Development (LIDeB), Medicinal Chemistry, Department of Biological Science, Exact Sciences CollegeNational University of La Plata (UNLP), ArgentinaLa PlataArgentina
  2. 2.Instituto de Ciencias y Tecnología Dr. César Milstein (ICT Milstein)Argentinean National Council of Scientific and Technical Research (CONICET)Buenos AiresArgentina
  3. 3.Laboratory Redox Biology of TrypanosomesInstitut Pasteur de MontevideoMontevideoUruguay

Personalised recommendations