title: Biocomputational analysis of phosphoenolpyruvate carboxykinase from Raillietina echinobothrida, a cestode parasite, and its interaction with possible modulators.
abstract: 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.
authors.affiliation: Department of Zoology,North-Eastern Hill University,Shillong,Meghalaya-793022,India.
authors.forename: Asim Kumar
authors.initials: AK
authors.lastname: Dutta
authors.affiliation: Department of Zoology,North-Eastern Hill University,Shillong,Meghalaya-793022,India.
authors.lastname: Ramnath
authors.affiliation: Department of Zoology,North-Eastern Hill University,Shillong,Meghalaya-793022,India.
authors.forename: Veena
authors.initials: V
authors.lastname: Tandon
authors.affiliation: Department of Zoology,North-Eastern Hill University,Shillong,Meghalaya-793022,India.
authors.forename: Bidyadhar
authors.initials: B
authors.lastname: DAS
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001600:Berberine Alkaloids / Q000494:pharmacology; D002589:Cestoda / Q000187:drug effects* / Q000201:enzymology*; D019295:Computational Biology; D004789:Enzyme Activation / Q000187:drug effects; D004791:Enzyme Inhibitors / Q000494:pharmacology*; D007700:Kinetics; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D019764:Phosphoenolpyruvate Carboxykinase (ATP) / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D015203:Reproducibility of Results; D017421:Sequence Analysis
chemical_list: D001600:Berberine Alkaloids; D004791:Enzyme Inhibitors; C014215:tetrahydropalmatine; D019764:Phosphoenolpyruvate Carboxykinase (ATP)
keywords: Cestode; PEPCK (GTP); THP; enzyme kinetics; molecular docking