CFP last date
20 December 2024
Call for Paper
January Edition
IJCA solicits high quality original research papers for the upcoming January edition of the journal. The last date of research paper submission is 20 December 2024

Submit your paper
Know more
The week's pick
Responsive image
Improved Shuffled Frog Leaping Algorithm with Self-Adaptive Shuffling for Fuzzy Logic PD+G Controller Optimization in Robotic Manipulators

Duc Hoang Nguyen
Random Articles
Reseach Article

Choke Point Analysis with Subtractive Proteomic Approach for Insilico Identification of Potential Drug Targets in Shigella Dysenteriae

by Manmohan Pandey, Anshul Tiwari, Shalini Maurya, Dipika Singh, Prachi Srivastava
journal cover thumbnail

International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 109 - Number 17
Year of Publication: 2015
Authors: Manmohan Pandey, Anshul Tiwari, Shalini Maurya, Dipika Singh, Prachi Srivastava
10.5120/19426-0455

Manmohan Pandey, Anshul Tiwari, Shalini Maurya, Dipika Singh, Prachi Srivastava . Choke Point Analysis with Subtractive Proteomic Approach for Insilico Identification of Potential Drug Targets in Shigella Dysenteriae. International Journal of Computer Applications. 109, 17 ( January 2015), 29-34. DOI=10.5120/19426-0455

@article{ 10.5120/19426-0455,
author = { Manmohan Pandey, Anshul Tiwari, Shalini Maurya, Dipika Singh, Prachi Srivastava },
title = { Choke Point Analysis with Subtractive Proteomic Approach for Insilico Identification of Potential Drug Targets in Shigella Dysenteriae },
journal = { International Journal of Computer Applications },
issue_date = { January 2015 },
volume = { 109 },
number = { 17 },
month = { January },
year = { 2015 },
issn = { 0975-8887 },
pages = { 29-34 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume109/number17/19426-0455/ },
doi = { 10.5120/19426-0455 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T22:45:06.057883+05:30
%A Manmohan Pandey
%A Anshul Tiwari
%A Shalini Maurya
%A Dipika Singh
%A Prachi Srivastava
%T Choke Point Analysis with Subtractive Proteomic Approach for Insilico Identification of Potential Drug Targets in Shigella Dysenteriae
%J International Journal of Computer Applications
%@ 0975-8887
%V 109
%N 17
%P 29-34
%D 2015
%I Foundation of Computer Science (FCS), NY, USA
Abstract

Shigellosis is an endemic disease prevalent in developing and poor countries due to fecal-oral transmission resulting a significant morbidity and mortality rate. Emergence of multi-drug resistant (MDR) in Shigella sp. reveals the inefficacy towards the first line antibiotics like quinolones, co-trimoxazole and ampicillin against it. There is continuous need to monitor the characteristics and antibiotic resistance patterns of this pathogen regarding the identification of new potential therapeutic drug targets. Availability of complete protein of different Shigella species viz flexneri, body, dysentery and son has made it possible to carry out the In-silico analysis of its protein for the identification of potential vaccine and drug targets. Subtractive proteomics approach is being used to mine the list of proteins present in different Shigella species which are non-homologous to human and essential for the survival of the pathogen. The metabolic chokepoint analysis also enriches the list of essential protein and adds those proteins in the list which are uniquely found in pathogenic pathway, catalyzed by single enzyme and involved in multi pathways. Screening of essential proteins against human gut flora and approved drug targets revealed the targets which are non-homologous to human gut flora and homologous to the approved drug targets. Broad spectrum drug targets screening revealed a list of highly conserved proteins of various pathogens including different Shigella species. Probably the drug developed against these targets may be useful in treating multiple diseases or diseases which results due to co-infection of different pathogens. Subcellular localization prediction revealed a list protein, which could be potential vaccine targets in different Shigella species. Virtual screening against these identified targets might be useful in the discovery of novel Drug against MDR Shigella species.

References
  1. Kotloff, K. L. , J. P. Winickoff, B. Ivanoff, J. D. Clemens, D. L. Swerdlow, P. J. Sansonetti, G. K. Adak, M. M. Levine, "Global burden of Shigella infections: implications for vaccine development and implementation of control strategies," Bulletin of the World Health Organization. vol. 77, pp. 651–666, 1999.
  2. Sur D. , T. Ramamurthy, J. Deen, S. K. Bhattacharya, "Shigellosis: challenges & management issues," Indian J Med Res. vol. 120, pp. 454–462, 2004.
  3. Legros D. , "Guidelines for the control of shigellosis, including epidemics due to Shigella dysenteriae type 1", Geneva: World Health Organization. 2005.
  4. Mehata S. , G. C. Duan, "Molecular mechanism of multi-drug resistance in Shigella isolates from rural China," Nepal Med Coll J. vol. 13, pp. 27-29, 2011.
  5. Watanabe T. , "Infective heredity of multiple drug resistance in bacteria," Bacteriol Rev. vol. 27, pp. 87–115, 1963.
  6. Sack R. B. , M. Rahman, M. Yunus, E. H. Khan, "Antimicrobial resistance in organisms causing diarrheal disease," Clin Infect Dis. vol. 24, pp. 102–105, 1997.
  7. Pazhani G. P. , S. K. Niyogi, A. K. Singh, B. Sen, N. Taneja, M. Kundu, S. Yamasaki, R. Thandavarayan, "Molecular characterization of multidrug-resistant Shigella species isolated from epidemic and endemic cases of shigellosis in India," J Med Microbiol. vol. 57, pp. 856–863, 2008.
  8. Ahamed J. , M. Kundu, "Molecular characterization of the SHV-11 Beta lactamase of Shigella dysenteriae," Antimicrob Agents Chemother. vol. 43, pp. 2081–2083, 1999.
  9. Varghese S. R. , A. Aggarwal, "Extended spectrum beta-lactamase production in Shigella isolates - A matter of concern. " Indian J Med Microbiol. vol. 29, pp. 76–78, 2011.
  10. Karthik R. , Y. Kalidas, C. Nagasuma, "targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. " BMC Systems Biology. vol. 2, pp. 109, 2008.
  11. Gasteiger E. , A. Gattiker, C. Hoogland, I. Ivanyi, R. D. Appel, A. Bairoch, "ExPASy: the proteomics server for in-depth protein knowledge and analysis," Nucleic Acids Res. vol. 31, pp. 3784-3788, 2003.
  12. Geer L. Y. , A. M. Bauer, R. C. Geer, et al. , "The NCBI BioSystems database. " Nucleic Acids Res. vol. 38, pp. 492-496, 2010.
  13. Weizhong Li. & G. Adam, (2006) "Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences," Bioinformatics. vol. 22, pp. 1658-1659, 2006.
  14. Altschul S. F. , T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, D. J. Lipman, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Research. vol. 25, pp. 3389-3402, 1997.
  15. Ren Z. , Y. O. Hong, T. Z. Chun, "DEG, a Database of Essential Genes," Nucleic Acids Research. vol. 32, pp. 271-272, 2004.
  16. Iwei Y. , H. Theodor, T. Sophia, D. K. Peter, B. Russ, "Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery," Genome Research. vol. 14, pp. 917, 2004.
  17. Caspi R. ,T. Altman, J. M. Dale, K. Dreher, C. A. Fulcher, F. Gilham, P. , Kaipa, A. S. Karthikeyan, A. Kothari, M. Krummenacker, "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases," Nucleic Acids Research. vol. 38, pp. 473-479, 2010.
  18. Knox C. , V. Law, T. Jewison, P. Liu, S. Ly, A. Frolkis, A. Pon, K. Banco, C. Mak, V. Neveu, Y. Djoumbou, R. Eisner, A. C. Guo, D. S. Wishart, "Drug Bank 3. 0: a comprehensive resource for 'omics' research on drugs. " Nucleic Acids Res. vol. 39, pp. 1035-1041, 2011.
  19. Marchler B. A. , C. Zheng, F. Chitsaz, M. K. Derbyshire, L. Y. Geer, R. C. Geer, et. al. , "CDD: conserved domains and protein three-dimensional structure. " Nucleic Acids Res. vol. 41, pp. 348-352, 2012.
  20. Telley I. A. I. Gáspár, A. Ephrussi, T. Surrey, "Aster migration determines the length scale of nuclear separation in the Drosophila syncytial embryo. " Journal of Cell Biology. vol. 197, pp. 887-895, 2012.
  21. Beifang Niu. , Fu. Limin, S. Shulei, Li. Weizhong, "Artificial and natural duplicates in Pyrosequencing read of metagenomic data. " BMC Bioinformatics. vol. 11, pp. 187, 2010.
  22. Bearson S. , B. Bearson, J. W. Foster, "Acid stress responses in enterobacteria. " FEMS Microbiol Lett. vol. 147, pp. 173–180, 1997.
  23. Foster J. W. , "Escherichia coli acid resistance: tales of an amateur acidophile. " Nat Rev Microbiol. vol. 2, pp. 898–907, 2004.
  24. Rembert P. , C. R. Fisher, S. Moo-Jin, S. T. Huang, P. Parmar, S. M. Payne, "Analysis of the proteome of intracellular Shigella flexneri reveals pathways important for intracellular growth". Infect Immune. vol. 81, pp. 4635-4648, 2013.
  25. Sharma, V. , S. Sharma, K. H. Bentrup, J. D. McKinney, D. G. W. Russell, R. Jacobs, J. C. Sacchettini, "Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. " Nat. Struct. Biol. vol. 7, pp. 663-668, 2000.
  26. Michael, C. L. and R. Gerald, "Fink: Life and Death in a Macrophage: Role of the Glyoxylate Cycle in Virulence. " Eukaryot Cell. vol. 1, pp. 657–662, 2002.
  27. Imlay J. A. , "Pathways of oxidative damage. " Annu Rev Microbiol. vol. 57, pp. 395–418, 2003.
  28. Imlay J. A. ,"Cellular defenses against superoxide and hydrogen peroxide". Annu Rev Biochem. vol. 77, pp. 755–776, 2008.
  29. Johnson J. R. , C. Clabots, H. Rosen, "Effect of inactivation of the global oxidative stress regulator oxyR on the colonization ability of Escherichia coli O1:K1:H7 in a mouse model of ascending urinary tract infection. " Infect Immun. vol. 74, pp. 461–468, 2006.
  30. Aaron D. , E. S. Akamol, R. J. Laura, "The Role of OxyR and SoxRS in oxidative stress survival in Shigella flexneri. " Microbiol Res. vol. 167, pp. 238–245, 2012.
  31. Yu, N. Y. , J. R. Wagner, M. R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, S. C. Sahinalp, M. Ester, L. J. Foster, F. S. L. Brinkman, "PSORTb 3. 0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes," Bioinformatics. vol. 26, pp. 1608-1615, 2010.
  32. Levy J. , "The effects of antibiotic use on gastrointestinal function". Am J Gastroenterol. vol. 95, pp. 8-10, 2000.
  33. Nicholson J. K. and I. D. Wilson, "Understanding 'global' systems biology: metabonomics and the continuum of metabolism. " Nat Rev Drug Discov. vol. 2, pp. 668-676, 2003.
  34. Nicholson J. K. , E. Holmes, I. D. Wilson, "Gut microorganisms, mammalian metabolism and personalized health care. " Nat Rev Microbiol. vol. 3, pp. 431-438, 2005.
Index Terms

Computer Science
Information Sciences

Keywords

Drug targets DEG metabolic choke point subtractive proteomic Shigella BioCyc.

Powered by PhDFocusTM