Homology modeling and docking studies of Plasmodium falciparum telomerase reverse transcriptase with berberine and some of its derivatives

Authors

  • Pratap Parida Bioinformatics Infrastructure Facility, Centre for Studies in Biotechnology, Dibrugarh University, Assam
  • Samhita Kalita Bioinformatics Infrastructure Facility, Centre for Studies in Biotechnology, Dibrugarh University, Assam
  • R. N. S. Yadav Bioinformatics Infrastructure Facility, Centre for Studies in Biotechnology, Dibrugarh University, Assam
  • Brajesh Shankar Department of Pharmaceutical Sciences, Dibrugarh University, Assam

DOI:

https://doi.org/10.3329/bjp.v9i1.17535

Keywords:

AutoDock4.2, Berberine, Docking, Exome Horizon, Homology, pfTERT

Abstract

The telomerase reverse transcriptase (TERT) sequence from Plasmodium falciparum provides valuable information for the design of specific anti-telomerase drugs. The present study deals with the interaction of pfTERT against berberine derivatives to derive novel analogues. Berberine intercalates DNA, thereby inhibits DNA synthesis and PfTERT. This indicated that P. falciparum telomerase might be a potential target for malaria chemotherapy. The nature of the interactions between A three-dimensional structural model of PfTERT was constructed using multiple sequence alignment and homology modeling procedures, followed by extensive molecular dynamics calculations. The analogues of berberine were successfully docked into the binding pocket of the protein. The hydrogen bonds were analyzed along with the binding energy was observed. The binding energy were found to be -8.36, -8.36, -8.23, -11.34, -10.51, -3.56, +186.20, -5.99, -1.10 and -7.48 in Kcal/mol with reference drugs. The least binding energy was found to be -11.34 Kcal/mol which determines that the most effective analogue. As a result this can be used as antiplasmodial drug.

Downloads

Download data is not yet available.
Abstract
1969
Download
1090 Read
300

References

Achaz G, Netter P, Coissac E. Study of intrachromosomal duplications among the eukaryote genomes. Mol Biol Evol. 2001; 18: 2280-88.

Arnot DE, Gull K. The Plasmodium cell-cycle: Facts and questions. Ann Trop Med Parasitol. 1998; 92: 361-65.

Autexier C, Lue NF. The structure and function of telomerase reverse transcriptase. Ann Rev Biochem. 2006; 75: 493-517.

Bottius E, Bakhsis N, Scherf A. Plasmodium falciparum telomerease: De novo telomere addition to telomeric and non-telomeric sequences and role in chromosome healing. Mol Cell Biol. 1998; 18: 919-25.

Cong YS, Wright WE, Shay JW. Human telomerase and its regulation. Microbiol Mol Biol Rev. 2002; 66: 407-25.

Dutta NK, Panse MV. Usefulness of berberine (an alkaloid from Berberis aristata) in the treatment of cholera (experimental). Int J Med Res. 1962; 50: 732-36.

Figueiredo LM. The unusually large Plasmodium telomerase reverse transcriptase localizes in a discrete compartment associated with the nucleolus. Nucl Acids Res. 2005; 33: 1111-22.

Friedman KL, Cech TR. Essential functions of aminoterminal domains in the yeast telomerase catalytic subunit revealed by selection for viable mutants. Genes Develop. 1999; 13: 2863-74.

Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, Mcfadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B. 2002. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002; 419: 498-511.

Iwazaki RS, Endo EH, Ueda-Nakamura T, Nakamura CV, Garcia LB, Filho BP. In vitro antifungal activity of the berberine and its synergism with fluconazole. Antonie Van Leeuwenhoek. 2010; 97: 201-05.

Janbaz KH, Gilani AH. Studies on preventive and curative effects of berberine. Fitoterapia 2000; 71: 25-33.

Levinson G, Gutman GA. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol. 1997; 4: 203-21.

Lin JP, Yang JS, Wu CC, Lin SS, Hsieh WT, Lin ML, Yu FS, Yu CS, Chen GW, Chang YH, Chung JG. Berberine induced down-regulation of matrix metalloproteinase-1, -2 and -9 in human gastric cancer cells (SNU-5). In vivo. 2008; 22: 223-30.

Lingner J, Hughes TR, Shevchenko A, Mann M, Lundblad V, Cech TR. 1997. Reverse transcriptase motifs in the catalytic subunit of telomerase. Science 1997; 276: 561-67.

Malik HS, Burke WD, Eickbush TH. Putative telomerase catalytic subunits from Giardia lamblia and Caenorhabditis elegans. Gene 2000; 251: 101-08.

Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian Genetic Algorithm and empirical binding free energy function. J Comput Chem. 1998; 19: 1639-62.

Morris GM, Goodsell DS, Huey R, Olson AJ. Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. J Comput Aided Mol Design 1996; 10: 293-304.

Qi M, Feng Y, Dai DZ, Li N, Cheng YS, Dai Y. CPU86017, a berberine derivative, attenuates cardiac failure through normalizing calcium leakage and down regulated phospholamban and exerting antioxidant activity. Acta Pharmacologica Sinica 2010; 31: 165-74.

Ramachandran GN, Ramakrishnan C, Sasisekharan V. Sterochemistry of polypeptide chain configurations. Int J Mol Biol. 1963; 7: 95-99.

Rastelli G, Sirawaraporn W, Sompornpisut P, Vilaivan T, Kamchonwongpaisan S, Quarrell R, Lowe G, Thebtaranonth Y, Yuthavong Y. Interaction of pyrimethamine, cycloguanil, WR99210 and their analogues with Plasmodium falciparum dihydrofolate reductase: Structural basis of antifolate resistance. Bioorg Med Chem. 2000; 8: 1117-28.

Sharma K, Ranjan B, Neelam C, Birendra S, Kumar SN. Berberis aristata: A review. Int J Res Ayurveda Pharm. 2011; 2: 383-88.

Sheng WD, Jiddawi MS, Hong XQ, Abdulla SM. Treatment of chloroquine-resistant malaria using pyrimethamine in combination with berberine, tetracycline or cotrimoxazole. East Afr Med J. 1997; 74: 283-84.

Singh A, Duggal S, Kaur N, Singh J. Berberine: Alkaloid with wide spectrum of pharmacological activities. J Nat Prod. 2010; 3: 64-75.

Sinha R, Kumar GS. Interaction of isoquinoline alkaloids with an RNA triplex: Structural and thermodynamic studies of berberine, palmatine, and coralyne binding to Poly(U). Poly(A) (*)Poly(U). J Physical Chem. 2009; 113: 13410-20.

Sriwilaijareon N, Petmitr S, Mutirangura A, Ponglikitmongkol M, Wilairat P. Stage specificity of Plasmodium falciparum telomerase and its inhibition by berberine. Parasitol Int. 2002; 51: 99-103.

Vennerstrom JL, Klayman DL. Protoberberine alkaloids as antimalarials. J Med Chem. 1988. 31, 1084-87.

Wang YX, Wang YP, Zhang H, Kong WJ, Li YH, Liu F, Gao RM, Liu T, Jiang JD, Song DQ. Synthesis and biological evaluation of berberine analogues as novel up-regulators for both low-density-lipoprotein receptor and insulin receptor. Bioorg Med Chem Lett. 2009; 19: 6004-08.

Weinrich SL, Pruzan R, Ma L, Ouellette M, Tesmer VM, Holt SE, Bodnar AG, Lichtsteiner S, Kim NW, Trager JB, Taylor RD, Carlos R, Andrews WH, Wright WE, Shay JW, Harley CB, Morin GB. Reconstitution of human telomerase with the template RNA component hTR and the catalytic protein subunit hTRT. Nat Genetics. 1997; 17: 498-502.

Xia J, Peng Y, Mian IS, Lue NF. Identification of functionally important domains in the N-terminal region of telomerase reverse transcriptase. Mol Cell Biol. 2000; 20: 5196-207.

Yan D, Jin C, Xiao XH, Dongh XP. Antimicrobial properties of berberine alkaloids in CoPtis chinensis Franch by microcalorimetry. J Biochem Biophys Methods. 2007; 70: 845-49.

Zhang H, Wei J, Xue R, Wu JD, Zhao W, Wang ZZ, Wang SK, Zhou ZX, Song DQ, Wang YM, Pan HN, Kong WJ, Jiang JD. Berberine lowers blood glucose in type 2 diabetes mellitus patients through increasing insulin receptor expression. Metabolism 2010; 59: 285-92.

Downloads

Additional Files

Published

2014-02-25

How to Cite

Parida, P., S. Kalita, R. N. S. Yadav, and B. Shankar. “Homology Modeling and Docking Studies of Plasmodium Falciparum Telomerase Reverse Transcriptase With Berberine and Some of Its Derivatives”. Bangladesh Journal of Pharmacology, vol. 9, no. 1, Feb. 2014, pp. 96-104, doi:10.3329/bjp.v9i1.17535.

Issue

Vol. 9 No. 1 (2014)

Section

Research Articles

License

Authors who publish with this journal agree to the following terms:

  1. Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
  2. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
  3. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).