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Biocomputational analysis of phosphoenolpyruvate carboxykinase from Raillietina echinobothrida, a cestode parasite, and its interaction with possible modulators

Published online by Cambridge University Press:  22 December 2015

ASIM KUMAR DUTTA ,
RAMNATH ,
VEENA TANDON  and
BIDYADHAR DAS
ASIM KUMAR DUTTA
Affiliation:
Department of Zoology, North-Eastern Hill University, Shillong, Meghalaya-793022, India
RAMNATH
Affiliation:
Department of Zoology, North-Eastern Hill University, Shillong, Meghalaya-793022, India
VEENA TANDON
Affiliation:
Department of Zoology, North-Eastern Hill University, Shillong, Meghalaya-793022, India
BIDYADHAR DAS*
Affiliation:
Department of Zoology, North-Eastern Hill University, Shillong, Meghalaya-793022, India
*
*Corresponding author: Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong-793022, Meghalaya, India. E-mail: [email protected]
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Summary

Phosphoenolpyruvate carboxykinase (PEPCK) involved in gluconeogenesis in higher vertebrates opposedly plays a significant role in glucose oxidation of the cestode parasite, Raillietina echinobothrida. Considering the importance of the enzyme in the parasite and lack of its structural details, there exists an urgent need for understanding the molecular details and development of possible modulators. Hence, in this study, PEPCK gene was obtained using rapid amplification of cDNA ends, and various biocomputational analyses were performed. Homology model of the enzyme was generated, and docking simulations were executed with its substrate, co-factor, and modulators. Computer hits were generated after structure- and ligand-based screening using Discovery Studio 4.1 software; the predicted interactions were compared with those of the existing structural information of PEPCK. In order to evaluate the docking simulation results of the modulators, PEPCK gene was cloned and the overexpressed protein was purified for kinetic studies. Enzyme kinetics and in vitro studies revealed that out of the modulators tested, tetrahydropalmatine (THP) inhibited the enzyme with lowest inhibition constant value of 93 nm. Taking the results together, we conclude that THP could be a potential inhibitor for PEPCK in the parasite.

Keywords

CestodePEPCK (GTP)molecular dockingTHPenzyme kinetics
Type
Research Article
Information
Parasitology , Volume 143 , Issue 3 , March 2016 , pp. 300 - 313
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Copyright
Copyright © Cambridge University Press 2015 

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References

REFERENCES

Ahmad, M. and Nizami, W. A. (1987). In vitro effects of mebendazole on the carbohydrate metabolism of Avitellina lahorea (Cestoda). Journal of Helminthology 61, 247–252.Google Scholar
Baker, D. and Sali, A. (2001). Protein structure prediction and structural genomics. Science 294, 93–96.Google Scholar
Bradford, M. M. (1976). A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein dye binding. Analytical Biochemistry 72, 248–254.CrossRefGoogle Scholar
Carlson, G. M. and Holyoak, T. (2009). Structural insights into the mechanism of phosphoenolpyruvate carboxykinase catalysis. Journal of Biological Chemistry 284, 27037–27041.CrossRefGoogle ScholarPubMed
Chan, J. D., Zarowiecki, M. and Marchant, J. S. (2013). Ca2+ channels and Praziquantel: a view from the free world. Parasitology International 62, 619–628.Google Scholar
Cheek, S., Zhang, H. and Grishin, N. V. (2002). Sequence and classification of kinases. Journal of Molecular Biology 320, 855–881.Google Scholar
Cheng, K. C. and Nowak, T. (1989). Arginine residues at the active site of avian liver phosphoenolpyruvate carboxykinase. Journal of Biological Chemistry 264, 3317–3324.CrossRefGoogle ScholarPubMed
Cook, J. S., Weldon, S. L., Garcia-Ruiz, J. P., Hod, Y. and Hanson, R. W. (1986). Nucleotide sequence of the mRNA encoding the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) from the chicken. Proceedings of the National Academy of Sciences of USA 83, 7583–7587.Google Scholar
Das, B., Tandon, V. and Saha, N. (2004). Effects of phytochemicals of Flemingia vestita (Fabaceae) on glucose 6-phosphate dehydrogenase and enzymes of gluconeogenesis in a cestode (Raillietina echinobothrida). Comparative Biochemistry and Physiology – Part C 139, 141–146.Google Scholar
Das, B., Tandon, V., Saxena, J. K., Joshi, S. and Singh, A. R. (2013). Purification and characterization of phosphoenolpyruvate carboxykinase from Raillietina echinobothrida, a cestode parasite of the domestic fowl. Parasitology 140, 136–146.Google Scholar
Ghedin, E., Wang, S., Spiro, D., Caler, E., Zhao, Q., Crabtree, J., Allen, J. E., Delcher, A. L., Guiliano, D. B., Miranda-Saavedra, D., Angiuoli, S. V., Creasy, T., Amedeo, P., Haas, B., El-Sayed, N. M., Wortman, J. R., Feldblyum, T., Tallon, L., Schatz, M., Shumway, M., Koo, H., Salzberg, S. L., Schobel, S., Pertea, M., Pop, M., White, O., Barton, G. J., Carlow, C. K., Crawford, M. J., Daub, J., Dimmic, M. W., Estes, C. F., Foster, J. M., Ganatra, M., Gregory, W. F., Johnson, N. M., Jin, J., Komuniecki, R., Korf, I., Kumar, S., Laney, S., Li, B. W., Li, W., Lindblom, T. H., Lustigman, S., Ma, D., Maina, C. V., Martin, D. M., McCarter, J. P., McReynolds, L., Mitreva, M., Nutman, T. B., Parkinson, J., Peregrín-Alvarez, J. M., Poole, C., Ren, Q., Saunders, L., Sluder, A. E., Smith, K., Stanke, M., Unnasch, T. R., Ware, J., Wei, A. D., Weil, G., Williams, D. J., Zhang, Y., Williams, S. A., Fraser-Liggett, C., Slatko, B., Blaxter, M. L. and Scott, A. L. (2007). Draft genome of the filarial nematode parasite Brugia malayi . Science 317, 1756–1760.CrossRefGoogle ScholarPubMed
Guruprasad, K., Reddy, B. V. B. and Pandit, M. W. (1990). Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering 4, 155–161.Google Scholar
Hammes, G. G. (2002). Multiple conformational changes in enzyme catalysis. Biochemistry 41, 8221–8228.Google Scholar
Hanson, R. W. (2009). Thematic minireview series: a perspective on the biology of phosphoenolpyruvate carboxykinase 55 years after its discovery. Journal of Biological Chemistry 284, 27021–27023.Google Scholar
Hlavaty, J. J. and Nowak, T. (1997). Affinity cleavage at the metal-binding site of phosphoenolpyruvate carboxykinase. Biochemistry 36, 15514–15525.Google Scholar
Holyoak, T., Sullivan, S. M. and Nowak, T. (2006). Structural insights into the mechanism of PEPCK catalysis. Biochemistry 45, 8254–8263.Google Scholar
Huang, S. Y., Grinter, S. Z. and Zou, X. (2010). Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Physical Chemistry Chemical Physics 12, 12899–12908.CrossRefGoogle ScholarPubMed
Jabalquinto, A. M., Laivenieks, M., González-Nilo, F. D., Yévenes, A., Encinas, M. V., Zeikus, J. G. and Cardemil, E. (2002). Evaluation by site-directed mutagenesis of active site amino acid residues of Anaerobiospirillum succiniciproducens phosphoenolpyruvate carboxykinase. Journal of Protein Chemistry 21, 393–400.Google Scholar
Jo, J. S., Ishihara, N. and Kikuchi, G. (1974). Occurrence and properties of four forms of phosphoenolpyruvate carboxykinase in the chicken liver. Archives of Biochemistry and Biophysics 160, 246–254.Google Scholar
Johnson, T. A. and Holyoak, T. (2012). The Ω-loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function. Biochemistry 51, 9547–9559.CrossRefGoogle ScholarPubMed
Klein, R. D., Winterrowd, C. A., Hatzenbuhler, N. T., Shea, M. H., Favreau, M. A., Nulf, S. C. and Geary, T. G. (1992). Cloning of a cDNA encoding phosphoenolpyruvate carboxykinase from Haemonchus contortus . Molecular and Biochemical Parasitology 50, 285–294.Google Scholar
Knapp, J., Nakao, M., Yanagida, T., Okamoto, M., Saarma, U., Lavikainen, A. and Ito, A. (2011). Phylogenetic relationships within Echinococcus and Taenia tapeworms (Cestoda: Taeniidae): an inference from nuclear protein-coding genes. Molecular Phylogenetics and Evolution 61, 628–638.Google Scholar
Kyte, J. and Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology 157, 105–132.Google Scholar
Lewis, C. T., Haley, B. E. and Carlson, G. M. (1989). Formation of an intramolecular cystine disulfide during the reaction of 8-azidoguanosine 5′-triphosphate with cytosolic phosphoenolpyruvate carboxykinase (GTP) causes inactivation without photolabeling. Biochemistry 28, 9248–9255.Google Scholar
Lewis, C. T., Seyer, J. M., Cassell, R. G. and Carlson, G. M. (1993). Identification of vicinal thiols of phosphoenolpyruvate carboxykinase (GTP). Journal of Biological Chemistry 268, 1628–1636.CrossRefGoogle ScholarPubMed
Lipinski, C. A., Lombardo, F., Dominy, B. W. and Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews 46, 3–26.Google Scholar
Liu, F., Lu, J., Hu, W., Wang, S. Y., Cui, S. J., Chi, M., Yan, Q., Wang, X. R., Song, H. D., Xu, X. N., Wang, J. J., Zhang, X. L., Zhang, X., Wang, Z. Q., Xue, C. L., Brindley, P. J., McManus, D. P., Yang, P. Y., Feng, Z., Chen, Z. and Han, Z. G. (2006). New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum . PLoS Pathogens 2, e29.Google Scholar
Makinen, A. L. and Nowak, T. (1989). A reactive cysteine in avian liver phosphoenolpyruvate carboxykinase. Journal of Biological Chemistry 264, 12148–12157.Google Scholar
Marhefka, C. A., Moore, B. M., Bishop, T. C., Kirkovsky, L., Mukherjee, A., Dalton, J. T. and Miller, D. D. (2001). Homology modeling using multiple molecular dynamics simulations and docking studies of the human androgen receptor ligand binding domain bound to testosterone and nonsteroidal ligands. Journal of Medicinal Chemistry 44, 1729–1740.Google Scholar
Matte, A., Tari, L. W., Goldie, H. and Delbaere, L. T. J. (1997). Structure and mechanism of phosphoenolpyruvate carboxykinase. Journal of Biological Chemistry 272, 8105–8108.Google Scholar
Mommsen, T. P., Patrick, J. W. and Moon, T. W. (1985). Gluconeogenesis in hepatocytes and kidney of Atlantic salmon. Molecular Physiology 8, 89–100.Google Scholar
Reynolds, C. H. (1980). Phosphoenolpyruvate carboxykinase from the rat and from the tapeworm, Hymenolepis diminuta . Comparative Biochemistry and Physiology 65, 481–487.Google Scholar
Ríos, S. E. and Nowak, T. (2002). Role of cysteine 306 in the catalytic mechanism of Ascaris suum phosphoenolpyruvate carboxykinase. Archives of Biochemistry and Biophysics 404, 25–37.Google Scholar
Rollinger, J. M., Stuppner, H. and Langer, T. (2008). Virtual screening for the discovery of bioactive natural products. Progress in Drug Research 65, 213–249.Google ScholarPubMed
Smith, A. A. and Caruso, A. (2013). In silico characterization and homology modeling of a cyanobacterial phosphoenolpyruvate carboxykinase enzyme. Structural Biology, Article ID 370820, 10.Google Scholar
Smyth, J. D. and McManus, D. P. (1989). The Physiology and Biochemistry of Cestodes. Cambridge University Press, Cambridge, UK.Google Scholar
Soulsby, E. J. L. (1982). Helminths, Arthropods and Protozoa of Domesticated Animals, 7th Edn, ELBS and Bailliere Tindall, London.Google Scholar
Swargiary, A., Verma, A. K. and Sarma, K. (2013). Homology modeling and docking studies of phosphoenolpyruvate carboxykinase in Schistosoma mansoni . Medicinal Chemistry Research 22, 2870–2878.Google Scholar
Tandon, V. and Das, B. (2007). In vitro testing of anthelmintic efficacy of Flemingia vestita (Fabaceae) on carbohydrate metabolism in Raillietina echinobothrida . Methods 42, 330–338.Google Scholar
Utter, M. F. and Kurahashi, K. (1954). Purification of oxalacetic carboxylase from chicken liver. Journal of Biological Chemistry 207, 787–802.Google Scholar
Verma, A. K., Swargiary, A., Prasad, S. B. and Arjun, J. (2012). Homology modeling of phosphoenolpyruvate carboxykinase of Ascaris suum . Journal of Pharmacy Research 5, 1248–1255.Google Scholar
Villarreal, J. M., Bueno, C., Arenas, F., Jabalquinto, A. M., González-Nilo, F. D., Encinas, M. V. and Cardemil, E. (2006). Nucleotide specificity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase kinetics, fluorescence spectroscopy, and molecular simulation studies. International Journal of Biochemistry and Cell Biology 38, 576–588.Google Scholar
Wang, X., Chen, W., Huang, Y., Sun, J., Men, J., Liu, H., Luo, F., Guo, L., Lv, X., Deng, C., Zhou, C., Fan, Y., Li, X., Huang, L., Hu, Y., Liang, C., Hu, X., Xu, J. and Yu, X. (2011). The draft genome of the carcinogenic human liver fluke Clonorchis sinensis . Genome Biology 12, R107.Google Scholar
Weldon, S. L., Rando, A., Matathias, A. S., Hod, Y., Kalonick, P. A., Savon, S., Cook, J. S. and Hanson, R. W. (1990). Mitochondrial phosphoenolpyruvate carboxykinase from the chicken. Comparison of the cDNA and protein sequences with the cytosolic isozyme. Journal of Biological Chemistry 265, 7308–7317.Google Scholar
Yang, J., Kalhan, S. C. and Hanson, R. W. (2009). What is the metabolic role of phosphoenolpyruvate carboxykinase? Journal of Biological Chemistry 284, 27025–27029.Google Scholar
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