







Vol.2 , No. 2, Publication Date: Feb. 12, 2018, Page: 7-14
[1] | Alejandro Soto Ospina, Faculty of Medicine, University of Antioquia, Medellín, Colombia. |
[2] | Pedronel Araque Marín, Basic Sciences Department, University EIA (University School of Antioquia Engineering), Envigado, Colombia. |
American trypanosomiasis, commonly known as Chagas disease, is a desease with the highest prevalence in the tropics and is caused by the parasite Trypanosoma cruzi, whose vector is an insect from the Rhodnius prolixus family. The pathology of this disease is characterized by the presence of cardiopathies and gastrointestinal problems in patients during chronic phases. It should be noted that an approach of a structure of the orthosteric site that allows to explain the functionality and the plausible mechanism of reaction is important in order to understand the design of molecular targets or possible resistance generated in chronic phases of the disease. This is why the structural biology has tools such as the homology modelling and the structural assembly by sequence-based fold recognition to construct a model. Besides, the proposed models obtained by comparison with the reported structures are validated through energetic and stereochemical softwares that produce quantitative data, which characterize the structural models. The previous validation would allow to compare two predictive and structural refinement methods to generate the best methodology of elucidation.
Keywords
Structure, Trypanosoma-cruzi, Enzyme, Chagas Disease
Reference
[01] | C. Bern, “Chagas’ Disease,” N. Engl. J. Med., vol. 373, no. 5, pp. 456-466, 2015. |
[02] | G. A. Schmunis and Z. E. Yadon, “Chagas disease: A Latin American health problem becoming a world health problem,” Acta Trop., vol. 115, no. 1–2, pp. 14-21, 2010. |
[03] | A. Rassi, A. Rassi, and J. A. Marin-Neto, “Chagas disease,” Lancet, vol. 375, no. 9723, pp. 1388-1402, 2010. |
[04] | C. J. Schofield, J. Jannin, and R. Salvatella, “The future of Chagas disease control,” Trends Parasitol., vol. 22, no. 12, pp. 583-588, 2006. |
[05] | J. A. Pérez-Molina and I. Molina, “Chagas disease,” Lancet, vol. 6736, no. 17, pp. 1-13, 2017. |
[06] | J. Murillo et al., “Congenital Chagas’ disease transmission in the United States: Diagnosis in adulthood,” IDCases, vol. 5, pp. 72-75, 2016. |
[07] | G. A. Vallejo, Y. Suárez, J. L. Olaya, S. A. Gutiérrez, and J. C. Carranza, “Trypanosoma rangeli : un protozoo infectivo y no patógeno para el humano que contribuye al entendimiento de la transmisión vectorial y la infección por Trypanosoma cruzi, agente causal de la enfermedad de Chagas.,” Rev. Acad. Colomb. Ciencias Exactas, Físicas y Nat., vol. 39, no. 150, pp. 111-122, 2015. |
[08] | D. Silva-dos-Santos et al., “Unraveling Chagas disease transmission through the oral route: Gateways to Trypanosoma cruzi infection and target tissues,” PLoS Negl. Trop. Dis., vol. 11, no. 4, pp. 1-26, 2017. |
[09] | M. Ray et al., “Analysis of Alzheimer’s disease severity across brain regions by topological analysis of gene co-expression networks,” BMC Syst. Biol., vol. 4, no. 1, p. 136, 2010. |
[10] | S. F. Cui, L. P. Peng, H. Z. Zhang, S. Rasheed, K. Vijaya Kumar, and C. H. Zhou, “Novel hybrids of metronidazole and quinolones: Synthesis, bioactive evaluation, cytotoxicity, preliminary antimicrobial mechanism and effect of metal ions on their transportation by human serum albumin,” Eur. J. Med. Chem., vol. 86, pp. 318-334, 2014. |
[11] | J. Gascon et al., “[Diagnosis, management and treatment of chronic Chagas’ heart disease in areas where Trypanosoma cruzi infection is not endemic],” Rev Esp Cardiol, vol. 60, no. 3, pp. 285-293, 2007. |
[12] | J. R. Coura, “The main sceneries of chagas disease transmission. The vectors, blood and oral transmissions - A comprehensive review,” Mem. Inst. Oswaldo Cruz, vol. 110, no. 3, pp. 277-282, 2015. |
[13] | E. Chatelain, “Chagas disease research and development: Is there light at the end of the tunnel?,” Comput. Struct. Biotechnol. J., vol. 15, pp. 98-103, 2017. |
[14] | C. A. Haynes, R. L. Koder, A. F. Miller, and D. W. Rodgers, “Structures of nitroreductase in three states. Effects of inhibitor binding and reduction,” J. Biol. Chem., vol. 277, no. 13, pp. 11513-11520, 2002. |
[15] | S. G. Mayhew, “The effects of pH and semiquinone formation on the oxidation-reduction potentials of flavin mononucleotide. A reappraisal,” Eur. J. Biochem., vol. 265, no. 2, pp. 698-702, 1999. |
[16] | L. Hu et al., “Synthesis and structure-activity relationships of nitrobenzyl phosphoramide mustards as nitroreductase-activated prodrugs,” Bioorganic Med. Chem. Lett., vol. 21, no. 13, pp. 3986-3991, 2011. |
[17] | C. Bern, “A New Epoch in Antitrypanosomal Treatment for Chagas Disease,” J. Am. Coll. Cardiol., vol. 69, no. 8, pp. 948-950, 2017. |
[18] | A. H. Romero and S. E. López, “In silico molecular docking studies of new potential 4-phthalazinyl-hydrazones on selected Trypanosoma cruzi and Leishmania enzyme targets,” J. Mol. Graph. Model., vol. 76, pp. 313-329, 2017. |
[19] | B. S. Hall, C. Bot, and S. R. Wilkinson, “Nifurtimox activation by trypanosomal type I nitroreductases generates cytotoxic nitrile metabolites,” J. Biol. Chem., vol. 286, no. 15, pp. 13088-13095, 2011. |
[20] | Nature, “Structural biology definition,” Subjects-Nature, 2017. [Online]. Available: https://www.nature.com/subjects/structural-biology. [Accessed: 24-Oct-2017]. |
[21] | (NIH), “Structural Biology Fact Sheet,” National Institute of medical general sciences-Science education, 2017. [Online]. Available: https://www.nigms.nih.gov/education/pages/factsheet_structuralbiology.aspx. [Accessed: 24-Oct-2017]. |
[22] | M. K. Higgins and S. M. Lea, “On the state of crystallography at the dawn of the electron microscopy revolution,” Curr. Opin. Struct. Biol., vol. 46, pp. 95-101, 2017. |
[23] | N. Soni and M. S. Madhusudhan, “Computational modeling of protein assemblies,” Curr. Opin. Struct. Biol., vol. 44, pp. 179-189, 2017. |
[24] | J. Vonck and D. J. Mills, “Advances in high-resolution cryo-EM of oligomeric enzymes,” Curr. Opin. Struct. Biol., vol. 46, pp. 48-54, 2017. |
[25] | M. J. Bower, F. E. Cohen, and R. L. Dunbrack, “Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool,” J. Mol. Biol., vol. 267, no. 5, pp. 1268-1282, 1997. |
[26] | C. N. Cavasotto and S. S. Phatak, “Homology modeling in drug discovery: current trends and applications,” Drug Discov. Today, vol. 14, no. 13–14, pp. 676-683, 2009. |
[27] | R. Rodriguez, G. Chinea, N. Lopez, T. Pons, and G. Vriend, “Homology modeling, model and software evaluation: three related resources.,” Bioinformatics, vol. 14, no. 6, pp. 523-528, 1998. |
[28] | E. Krieger et al., “Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8,” Proteins Struct. Funct. Bioinforma., vol. 77, no. SUPPL. 9, pp. 114-122, 2009. |
[29] | D. Petrey et al., “Using Multiple Structure Alignments, Fast Model Building, and Energetic Analysis in Fold Recognition and Homology Modeling,” Proteins Struct. Funct. Genet., vol. 53, no. SUPPL. 6, pp. 430-435, 2003. |
[30] | UniProt, “The Universal Protein Resource,” vol. 2010, no. November 2007, pp. 190-195, 2010. |
[31] | R. D. Finn et al., “Pfam: The protein families database,” Nucleic Acids Res., vol. 42, no. D1, pp. 222-230, 2014. |
[32] | G. N. Parkinson, J. V. Skelly, and S. Neidle, “Crystal structure of FMN-dependent nitroreductase from Escherichia coli B: A prodrug-activating enzyme,” J. Med. Chem., vol. 43, no. 20, pp. 3624-3631, 2000. |
[33] | A. Roy, A. Kucukural, and Y. Zhang, “I-TASSER: a unified platform for automated protein structure and function prediction,” Nat. Protoc., vol. 5, no. 4, pp. 725-738, 2010. |
[34] | J. Yang, R. Yan, A. Roy, D. Xu, P. J, and Y. Zhang, “The I-TASSER Suite: Protein structure and function prediction,” Nat Methods, vol. 12, no. 1, pp. 7-8, 2015. |
[35] | Y. Zhang, “I-TASSER server for protein 3D structure prediction.,” BMC Bioinformatics, vol. 9, p. 40, 2008. |
[36] | L. A. Kelly, S. Mezulis, C. Yates, M. Wass, and M. Sternberg, “The Phyre2 web portal for protein modelling, prediction, and analysis,” Nat. Protoc., vol. 10, no. 6, pp. 845-858, 2015. |
[37] | L. a Kelley, S. Mezulis, C. M. Yates, M. N. Wass, and M. J. E. Sternberg, “The Phyre2 web portal for protein modeling, prediction and analysis.,” Nat. Protoc., vol. 10, no. 6, pp. 845-58, Jun. 2015. |
[38] | L. A. Kelley and M. J. E. Sternberg, “Protein structure prediction on the Web: a case study using the Phyre server.,” Nat. Protoc., vol. 4, no. 3, pp. 363-371, 2009. |
[39] | J. Zhang, Y. Liang, and Y. Zhang, “Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling,” Structure, vol. 19, no. 12, pp. 1784-1795, 2011. |
[40] | D. Xu and Y. Zhang, “Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization,” Biophys. J., vol. 101, no. 10, pp. 2525-2534, 2011. |
[41] | P. Artimo et al., “ExPASy: SIB bioinformatics resource portal,” Nucleic Acids Res., vol. 40, no. W1, pp. 597-603, 2012. |
[42] | E. F. Pettersen et al., “UCSF Chimera - A visualization system for exploratory research and analysis,” J. Comput. Chem., vol. 25, no. 13, pp. 1605-1612, 2004. |
[43] | N. Guex and M. C. Peitsch, “SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling,” Electrophoresis, vol. 18, no. 15, pp. 2714-2723, 1997. |
[44] | W. Humphrey, A. Dalke, and K. Schulten, “VMD- Visual molecular dynamics,” J. Mol. Graph., vol. 14, no. 1, pp. 33-38, 1996. |
[45] | J. C. Phillips et al., “Scalable molecular dynamics with NAMD,” J. Comput. Chem., vol. 26, no. 16, pp. 1781–1802, 2005. |
[46] | A. maria Mejia, G. Fernández, and O. Triana-chávez, Trypanosoma cruzi strains resistant to benznidazole occurring in Colombia, vol. 32, no. 3. 2012. |
[47] | A. M. Mejia et al., “Benznidazole-resistance in trypanosoma cruzi is a readily acquired trait that can arise independently in a single population,” J. Infect. Dis., vol. 206, no. 2, pp. 220-228, 2012. |
[48] | A. M. Waterhouse, J. B. Procter, D. M. A. Martin, M. Clamp, and G. J. Barton, “Jalview Version 2-A multiple sequence alignment editor and analysis workbench,” Bioinformatics, vol. 25, no. 9, pp. 1189-1191, 2009. |