Trends in Pharmaceutical Sciences and Technologies

Trends in Pharmaceutical Sciences and Technologies

In silico evaluation of rare codons and their positions in the structure of cytosine deaminase and substrate docking studies

Document Type : Research(Original) Article

Authors
Mojtaba Mortazavi 1
Navid Nezafat 2
Manica Negahdaripour 3
Ahmad Gholami 3
Masoud Torkzadeh-Mahani 1
Safa Lotfi 1
Younes Ghasemi 4
1 Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
2 Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran
3 Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran and Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
4 Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
Abstract
Cytosine deaminase (CDase) is used with 5-fluorocytosine (5FC) for genetic cancer treatment. This approach has several undesirable features, such as a relatively poor turnover of 5FC and low prodrug conversion activities, thus limiting the overall therapeutic response. We previously reported the molecular cloning of a new type of CDase in E. coli AGH09. Here, we describe the hidden layer of information of rare codons in this gene, which can help in problem solving of protein expression. With the help of several web servers, some rare codons in different locations of CDase gene were identified. By in silico modelling of CDase in I-TASSER server, the three rare codons of Arg242, Arg286 and Arg360 were evaluated. All of these rare codons were located at special positions that seem to have a critical role in proper folding of CDase. In silico docking of the substrate binding site simulation with AutoDock Vina showed that Glu218 is involved in substrate binding site, but the others residues were incompatible. Structural analysis showed that rare codon of Arg286 is located adjacent to Glu218 in binding site, which may have a critical role in ensuring the correct formation of the binding site structure. Investigation of this hidden information can enhance our understanding of CDase folding. Moreover, studies of these rare codons help to clarify their role in rational design of new and effective drugs.
Keywords
AutoDock
Bioinformatics analysis
CDase
Rare codon
  1. Negroni L, Samson M, Guigonis J-M, Rossi B, Pierrefite-Carle V, Baudoin C. Treatment of colon cancer cells using the cytosine deaminase/5-fluorocytosine suicide system induces apoptosis, modulation of the proteome, and Hsp90β phosphorylation. Molecular cancer therapeutics. 2007;6(10):2747-56.
  2. Miyagi T, Koshida K, Hori O, Konaka H, Katoh H, Kitagawa Y, et al. Gene therapy for prostate cancer using the cytosine deaminase/uracil phosphoribosyltransferase suicide system. The journal of gene medicine. 2003;5(1):30-7.
  3. Kaliberov S, Chiz S, Kaliberova L, Krendelchtchikova V, Della Manna D, Zhou T, et al. Combination of cytosine deaminase suicide gene expression with DR5 antibody treatment increases cancer cell cytotoxicity. Cancer gene therapy. 2006;13(2):203-14.
  4. OH N. The conversion of 5-methyldeoxycytidine to thymidine in vitro and in vivo. 1957.
  5. Mullen CA, Kilstrup M, Blaese RM. Transfer of the bacterial gene for cytosine deaminase to mammalian cells confers lethal sensitivity to 5-fluorocytosine: a negative selection system. Proceedings of the National Academy of Sciences. 1992;89(1):33-7.
  6. Mahan SD, Ireton GC, Knoeber C, Stoddard BL, Black ME. Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy. Protein Engineering Design and Selection. 2004;17(8):625-33.
  7. Gholami A, Shahin S, Mohkam M, Nezafat N, Ghasemi Y. Cloning, Characterization and Bioinformatics Analysis of Novel Cytosine Deaminase from Escherichia coli AGH09. International Journal of Peptide Research and Therapeutics.1-10.
  8. Ireton GC, Black ME, Stoddard BL. The 1.14 Å crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy. Structure. 2003;11(8):961-72.
  9. Fuchita M, Ardiani A, Zhao L, Serve K, Stoddard BL, Black ME. Bacterial Cytosine Deaminase Mutants Created by Molecular Engineering Show Improved 5-Fluorocytosine–Mediated Cell Killing In vitro and In vivo. Cancer research. 2009;69(11):4791-9.
  10. Dix DB, Thompson RC. Codon choice and gene expression: synonymous codons differ in translational accuracy. Proceedings of the National Academy of Sciences. 1989;86(18):6888-92.
  11. Kane JF. Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Current opinion in biotechnology. 1995;6(5):494-500.
  12. Muhlrad D, Parker R. Premature translational termination triggers mRNA decapping. 1994.
  13. Nakamura Y, Gojobori T, Ikemura T. Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic acids research. 2000;28(1):292-.
  14. Chartier M, Gaudreault F, Najmanovich R. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. Bioinformatics. 2012;28(11):1438-45.
  15. Widmann M, Clairo M, Dippon J, Pleiss J. Analysis of the distribution of functionally relevant rare codons. BMC genomics. 2008;9(1):207.
  16. Thanaraj T, Argos P. Protein secondary structural types are differentially coded on messenger RNA. Protein science. 1996;5(10):1973-83.
  17. Goodluck U. ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization. BMC Bioinformatics. 2015;16:303.
  18. Theodosiou A, Promponas VJ. LaTcOm: a web server for visualizing rare codon clusters in coding sequences. Bioinformatics. 2012;28(4):591-2.
  19. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC bioinformatics. 2008;9(1):40.
  20. Kaplan W, Littlejohn TG. Swiss-PDB viewer (deep view). Briefings in Bioinformatics. 2001;2(2):195-7.
  21. DeLano WL. The PyMOL molecular graphics system. 2002.
  22. Clarke TF, Clark PL. Rare codons cluster. PLoS One. 2008;3(10):e3412.
  23. Varenne S, Baty D, Verheij H, Shire D, Lazdunski C. The maximum rate of gene expression is dependent in the downstream context of unfavourable codons. Biochimie. 1989;71(11):1221-9.
  24. Varenne S, Lazdunski C. Effect of distribution of unfavourable codons on the maximum rate of gene expression by an heterologous organism. Journal of theoretical biology. 1986;120(1):99-110.
  25. Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins-Structure Function and Genetics. 1997;28(3):405-20.
  26. Dong H, Nilsson L, Kurland CG. Co-variation of trna abundance and codon usage inescherichia coliat different growth rates. Journal of molecular biology. 1996;260(5):649-63.
  27. Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic acids research. 2007;35(10):3375-82.
  28. Guex N, Peitsch M. Swiss-PdbViewer: a fast and easy-to-use PDB viewer for Macintosh and PC. Protein Data Bank Quaterly Newsletter. 1996;77(7).
  29. Vriend G. WHAT IF: a molecular modeling and drug design program. Journal of molecular graphics. 1990;8(1):52-6.
  30. Tina K, Bhadra R, Srinivasan N. Nucleic Acids Res 35. Web Server issue) W473–W476. 2007.
  31. Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry. 2010;31(2):455-61.
  32. 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):2785-91.
  33. OLBoyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminf. 2011;3:33.
  34. Hall RS, Fedorov AA, Xu C, Fedorov EV, Almo SC, Raushel FM. Three-dimensional structure and catalytic mechanism of cytosine deaminase. Biochemistry. 2011;50(22):5077-85.
  35. Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein engineering. 1995;8(2):127-34.
  36. Shahbazi M, Haghkhah M, Rahbar MR, Nezafat N, Ghasemi Y. In Silico Sub-unit Hexavalent Peptide Vaccine Against an Staphylococcus aureus Biofilm-Related Infection. International Journal of Peptide Research and Therapeutics. 2015:1-17.
  37. Zamani M, Nezafat N, Negahdaripour M, Dabbagh F, Ghasemi Y. In silico evaluation of different signal peptides for the secretory production of human growth hormone in E. coli. International Journal of Peptide Research and Therapeutics. 2015:1-8.
  38. Fattahi M, Malekpour A, Mortazavi M, Safarpour A, Naseri N. The Characteristics of Rare Codon Clusters in the Genome and Proteins of Hepatitis C Virus; a Bioinformatics Look. Middle East journal of digestive diseases. 2014;6(4):214.
  39. Cheng T, Li Q, Zhou Z, Wang Y, Bryant SH. Structure-based virtual screening for drug discovery: a problem-centric review. The AAPS journal. 2012;14(1):133-41.