• P-ISSN 0974-6846 E-ISSN 0974-5645

Indian Journal of Science and Technology


Indian Journal of Science and Technology

Year: 2020, Volume: 13, Issue: 43, Pages: 4434-4445

Original Article

New insight into the In-Silico prediction and molecular docking of Giardia intestinalis protease resistance to nitroimidazole

Received Date:01 February 2020, Accepted Date:17 November 2020, Published Date:08 December 2020


Background/Objective. Giardia intestinalis is a flagella protozoan residing in human intestine causing diarrhea that affecting most common among the children. Usually metronidazole and nitroimidazole were used for the treatment of giardiasis worldwide. Pyruvate Ferredoxin oxidoreductase (PFeO) protease enzyme may play a role inactivation of these drugs that may lead to resistance. Studies regarding drug resistance are very less. Therefore, present study was carried out to predict the structure and characterize them structurally as well as functionally by using appropriate in-silico methods. Methods: The proteins sequences of wild type and mutant strain i.e. Pyruvate Ferredoxin oxidoreductase (PFeO) and Pyruvate flavodoxin oxidoreductase (PFIO) were retracted from the NCBI and aligned using ClustalW. Bioinformatic tools were carried out like molecular dynamics simulations and docking to understand the three-dimensional (3D) conformational structure and interaction behavior of mutant and wild types with the ligand. Findings: The wild complex maintained an approximate 4H-bonds during simulation while the mutant complex could hardly maintain single H-bond by the end of the simulation, suggesting that 4-nitroimidazole is highly stable in the wild complex. Since the compound occupies this binding site by making stable H-bond with key interacting residues, the function of mutant may be affected. For the very reason, the mutant may be resistant to the nitroimidazole. Applications: Molecular dynamic simulation and docking results have increased our understanding of resistance mechanisms and may also help for the design derivatives of nitroimidazole that inhibit protein function more efficiently.

Keywords: Molecular dynamic simulation; Nitroimidazole resistance; Pyruvate Ferredoxin Oxidoreductase (PFeO) mutant type; Pyruvate Flavodoxin Oxidoreductase (PFIO) wild type; Giardia intestinalis


  1. Ansell BRE, McConville MJ, Ma'ayeh SY, Dagley MJ, Gasser RB, Svärd SG, et al. Drug resistance in Giardia duodenalis. Biotechnology Advances. 2015;33:888–901. Available from: https://dx.doi.org/10.1016/j.biotechadv.2015.04.009
  2. Lane S, Lloyd D. Current Trends in Research into the Waterborne Parasite Giardia. Critical Reviews in Microbiology. 2002;28:123–147. Available from: https://dx.doi.org/10.1080/1040-840291046713
  3. Kosek M, Bern C, Guerrant RL. The global burden of diarrhoeal disease. Bulletin of the world health organization. 1992;81:197–204. Available from: https://www.scielosp.org/article/bwho/2003.v81n3/197-204/pt/
  4. Savioli L, Smith H, Thompson A. Giardia and Cryptosporidium join the ‘Neglected Diseases Initiative’. Trends in Parasitology. 2006;22(5):203–208. Available from: https://dx.doi.org/10.1016/j.pt.2006.02.015
  5. Tian W, Chen C, Lei X, Zhao J, Liang J. CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Research. 2018;46(W1):W363–W367. Available from: https://dx.doi.org/10.1093/nar/gky473
  6. Verdu EF, Riddle MS. Chronic gastrointestinal consequences of acute infectious diarrhea: Evolving concepts in epidemiology and pathogenesis. American Journal of Gastroenterology. 2012;107(7):981–989. Available from: https://dx.doi.org/10.1038/ajg.2012.65
  7. Mørch K, Hanevik K, Rivenes AC, Bødtker JE, Næss H, Stubhaug B, et al. Chronic fatigue syndrome 5 years after giardiasis: differential diagnoses, characteristics and natural course. BMC Gastroenterology. 2013;13(1). Available from: https://dx.doi.org/10.1186/1471-230x-13-28
  8. Escobedo AA, Cimerman S. Giardiasis: a pharmacotherapy review. Expert Opinion on Pharmacotherapy. 2007;8:1885–1902. Available from: https://dx.doi.org/10.1517/14656566.8.12.1885
  9. Boreham PFL, Phillips RE, Shepherd RW. The sensitivity of Giardia intestinalis to drugs in vitro. Journal of Antimicrobial Chemotherapy. 1984;14(5):449–461. Available from: https://dx.doi.org/10.1093/jac/14.5.449
  10. McIntyre P, Boreham PFL, Phillips RE, Shepherd RW. Chemotherapy in giardiasis: Clinical responses and in vitro drug sensitivity of human isolates in axenic culture. The Journal of Pediatrics. 1986;108:1005–1010. Available from: https://dx.doi.org/10.1016/s0022-3476(86)80950-7
  11. Escobedo AA, Lalle M, Hrastnik NI, Rodríguez-Morales AJ, Castro-Sánchez E, Cimerman S, et al. Combination therapy in the management of giardiasis: What laboratory and clinical studies tell us, so far. Acta Tropica. 2016;162:196–205. Available from: https://dx.doi.org/10.1016/j.actatropica.2016.06.026
  12. Boreham PFL, Phillips RE, Shepherd RW. A comparison of the in-vitro activity of some 5-nitroimidazoles and other compounds against Giardia intestinalis. Journal of Antimicrobial Chemotherapy. 1985;16(5):589–595. Available from: https://dx.doi.org/10.1093/jac/16.5.589
  13. Čerkasovová A, Čerkasov J, Kulda J. Metabolic differences between metronidazole resistant and susceptible strains of Tritrichomonas foetus. Molecular and Biochemical Parasitology. 1984;11:105–118. Available from: https://dx.doi.org/10.1016/0166-6851(84)90058-6
  14. Edwards DI. Nitroimidazole drugs-action and resistance mechanisms I. Mechanism of action. Journal of Antimicrobial Chemotherapy. 1993;31(1):9–20. Available from: https://dx.doi.org/10.1093/jac/31.1.9
  15. Leitsch D, Schlosser S, Burgess A, Duchêne M. Nitroimidazole drugs vary in their mode of action in the human parasite Giardia lamblia. International Journal for Parasitology: Drugs and Drug Resistance. 2012;2:166–170. Available from: https://dx.doi.org/10.1016/j.ijpddr.2012.04.002
  16. Müller J, Rout S, Leitsch D, Vaithilingam J, Hehl A, Müller N. Comparative characterisation of two nitroreductases from Giardia lamblia as potential activators of nitro compounds. International Journal for Parasitology: Drugs and Drug Resistance. 2015;5(2):37–43. Available from: https://dx.doi.org/10.1016/j.ijpddr.2015.03.001
  17. Müller J, Braga S, Heller M, Müller N. Resistance formation to nitro drugs in Giardia lamblia: No common markers identified by comparative proteomics. International Journal for Parasitology: Drugs and Drug Resistance. 2019;9:112–119. Available from: https://dx.doi.org/10.1016/j.ijpddr.2019.03.002
  18. Paget TA, Kelly ML, Jarroll EL, Lindmark DG, Lloyd D. The effects of oxygen on fermentation in Giardia lamblia. Molecular and Biochemical Parasitology. 1993;57:65–71. Available from: https://dx.doi.org/10.1016/0166-6851(93)90244-r
  19. Müller J, Ley S, Felger I, Hemphill A, Müller N. Identification of differentially expressed genes in a Giardia lamblia WB C6 clone resistant to nitazoxanide and metronidazole. Journal of Antimicrobial Chemotherapy. 2008;62(1):72–82. Available from: https://dx.doi.org/10.1093/jac/dkn142
  20. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology. 1990;215(3):403–410. Available from: https://dx.doi.org/10.1016/s0022-2836(05)80360-2
  21. Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. Current Protocols in Bioinformatics. 2016;54(1):5–6. Available from: https://dx.doi.org/10.1002/cpbi.3
  22. Lovell SC, Davis IW, Arendall I, Wb D, Bakker PI, Word JM, et al. Structure validation by Cα geometry: ϕ, ψ and Cβ deviation. Proteins: Structure, Function, and Bioinformatics. 2003;15(50(3)):437–450. Available from: https://doi.org/10.1002/prot.10286
  23. Spoel DVD, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC. GROMACS: Fast, flexible, and free. Journal of Computational Chemistry. 2005;26(16):1701–1718. Available from: https://dx.doi.org/10.1002/jcc.20291
  24. Hess B, P-Lincs. A parallel linear constraint solver for molecular simulation. Journal of chemical theory and computation. 2008;4(1):116–122. Available from: https://doi.org/10.1021/ct700200b
  25. Wang H, Dommert F, Holm C. Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency. The Journal of Chemical Physics. 2010;133. Available from: https://dx.doi.org/10.1063/1.3446812
  26. Zoete V, Cuendet MA, Grosdidier A, Michielin O. SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry. 2011;32(11):2359–2368. Available from: https://dx.doi.org/10.1002/jcc.21816
  27. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry. 2009;30(16):2785–2791. Available from: https://dx.doi.org/10.1002/jcc.21256
  28. Goodsell DS, Morris GM, Olson AJ. Automated docking of flexible ligands: Applications of autodock. Journal of Molecular Recognition. 1996;9:1–5. Available from: https://dx.doi.org/10.1002/(sici)1099-1352(199601)9:1<1::aid-jmr241>3.0.co;2-6
  29. Morris GM, Huey R, Olson AJ. Using AutoDock for Ligand‐Receptor Docking. Current Protocols in Bioinformatics. 2008;24:8–14. Available from: https://dx.doi.org/10.1002/0471250953.bi0814s24


© 2020 Langbang et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Published By Indian Society for Education and Environment (iSee)


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