Identification of Novel Drug Targets in Streptococcus pneumoniae using Subtractive Genomic Approach
DOI:
https://doi.org/10.30732/IJBBB.20190403002Keywords:
Streptococcus pneumoniae, Novel Drug Target, Antibiotics, Multidrug ResistanceAbstract
In today’s medical field, a major issue faced by the medical community is the increasing drug resistance capacity in the pathogenic microorganisms. Therefore, it becomes a necessity to either increase the dosage of currently available drugs or find potential drug targets and create new drugs according to the results. In the last few decades, with the advent of multidrug resistant capacity in various bacteria has caused concern for the researchers. With the assistance of computational tools in Bioinformatics and methods, the drug discovery process can be accelerated.
Streptococcus pneumoniae is a gram-positive extracellular pathogen having a capacity to resist multiple antibacterial drugs and cause a number of diseases.
This review paper will highlight the method of identifying new drug targets using Subtractive Genomic Approach and looks into the recent research done in the relation to Streptococcus pneumoniae.
References
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[12] Zhang, C., Ju, Y., Tang, N., Li, Y., Zhang, G., Song, Y., ... & Feng, J. (2019). Systematic analysis of supervised machine learning as an effective approach to predicate β-lactam resistance phenotype in Streptococcus pneumoniae. Briefings in bioinformatics.
[13] Bittaye, M., & Cash, P. (2015). Streptococcus pneumoniae proteomics: determinants of pathogenesis and vaccine development. Expert review of proteomics, 12(6), 607-621.
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[16] Haribalaganesh Ravinarayanan, Richard Coico and Krishnan Sundar, Identification of Putative Therapeutic Targets in Candida tropicalis: An in-silico Approach, 2015, Kalasalingam University, Krishnankoil
[17] Uddin, R., & Saeed, K. (2014). Identification and characterization of potential drug targets by subtractive genome analyses of methicillin resistant Staphylococcus aureus. Computational biology and chemistry, 48, 55-63.
[18] Sarangi, A. N., Aggarwal, R., Rahman, Q., & Trivedi, N. (2009). Subtractive genomics approach for in silico identification and characterization of novel drug targets in Neisseria Meningitides Serogroup B. J Comput Sci Syst Biol, 2(5), 255-258.
[19] Antibiotic Resistance Threat in United State, 2013, CDC, U.S. Department of Health and Human Services
[20] Hoskins, J., Alborn, W. E., Arnold, J., Blaszczak, L. C., Burgett, S., DeHoff, B. S., ... & Geringer, C. (2001). Genome of the bacterium Streptococcus pneumoniae strain R6. Journal of bacteriology, 183(19), 5709-5717.
[21] Wadood, A., Jamal, A., Riaz, M., Khan, A., Uddin, R., Jelani, M., & Azam, S. S. (2018). Subtractive genome analysis for in silico identification and characterization of novel drug targets in Streptococcus pneumonia strain JJA. Microbial pathogenesis, 115, 194-198.
[22] Nazir, Z., Afridi, S. G., Shah, M., Shams, S., & Khan, A. (2018). Reverse vaccinology and subtractive genomics-based putative vaccine targets identification for Burkholderia pseudomallei Bp1651. Microbial pathogenesis, 125, 219-229.
[23] Meshram, R. J., Goundge, M. B., Kolte, B. S., & Gacche, R. N. (2019). An in silico approach in identification of drug targets in Leishmania: A subtractive genomic and metabolic simulation analysis. Parasitology international, 69, 59-70. [24] Hossain, T., Kamruzzaman, M., Choudhury, T. Z., Mahmood, H. N., Nabi, A. H. M., & Hosen, M. (2017). Application of the subtractive genomics and molecular docking analysis for the identification of novel putative drug targets against Salmonella enterica subsp. enterica serovar Poona. BioMed research international, 2017.
[25] Jamal, S. B., Hassan, S. S., Tiwari, S., Viana, M. V., de Jesus Benevides, L., Ullah, A., ... & Silva, A. (2017). An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PLoS One, 12(10).
[26] Jacobsen, E. W., & Nordling, T. E. (2016). Robust Target Identification for Drug Discovery. IFAC-PapersOnLine, 49(7), 815-820.
Websites:
[1] India’s New Pneumonia Vaccine (https://everylifecounts.ndtv.com/know-indias-new-vaccine-pneumonia-13351)
[2] CDC website. http://www.cdc.gov/pneumococcal/
[3] Unipot Database, uniprot.org, National Institute of Health, EMBL-EBI, State Secretariat for Education Research and Innovation SERI (https://www.uniprot.org/)
[4] CD-Hit Suite, Ying Huang, Beifang Niu, Ying Gao, Limin Fu, Weizhong Li, CD-HIT Suite: a web server for clustering and comparing biological sequences, Bioinformatics, Volume 26, Issue 5, 1 March 2010, Pages 680–682 (http://weizhong-lab.ucsd.edu/cdhit_suite/cgi-bin/index.cgi?cmd=cd-hit)
[5] DEG: Database of Essential Genes, essentialgene.org, School of Science Tianjin University (http://www.essentialgene.org/)
[6] BLASTp, a registered trademark of the National Library of Medicine, National Centre for Biotechnology Information. (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins)
[7] KEGG Database, Bioinformatics Center, Kyoto University, Human Genome Centre, University of Tokyo
[2] O'Brien, K. L., Wolfson, L. J., Watt, J. P., Henkle, E., Deloria-Knoll, M., McCall, N., ... & Cherian, T. (2009). Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates. The Lancet, 374(9693), 893-902.
[3] Henriques-Normark, B., & Tuomanen, E. I. (2013). The pneumococcus: epidemiology, microbiology, and pathogenesis. Cold Spring Harbor perspectives in medicine, 3(7), a010215.
[4] Claudia Antonieta Nieves Prado, MD; Chief Editor: John L Brusch, Pneumococcal Infections (Streptococcus pneumoniae) Medication, 2018, Medscape.
[5] Catia Callioniz, Antoni Torres, Community-Acquired Pneumoniae 200-2015: What is new? 2016, University of Barcelona, Spain.
[6] Maharashtra Sees Rise in Infant Deaths in Three Years, The Hindu, 22nd June 2019
[7] Uttar Pradesh Facts, http://www.fightpneumoniae.org/up_facts
[8] The Borgen Project, Threefold strategy to fight pneumoniae in India, June 2017.
[9] Fritz CQ, Edwards KM, Self WH, Grijalva CG, Zhu Y, Arnold SR, McCullers JA et al, Prevalence, Risk Factors, and Outcomes of Bacteremic Pneumoniae in Children, 2019, Tennessee, Georgia.
[10] Arya BK, Bhattacharya SD, Harigovind G, Das RS, Khan T, Ganaie F, Niyogi SK et al, Streptococcus pneumoniaee Acquisition and Carriage in Vaccine Naïve Indian Children with HIV and their Parents: A Longitudinal Household Study, 2019, West Bengal.
[11] Lewnard, J. A., Givon-Lavi, N., & Dagan, R. (2019). Interaction With Nontypeable Haemophilus influenzae Alters Progression of Streptococcus pneumoniae From Colonization to Disease in a Site-Specific Manner. The Journal of infectious diseases, 220(8), 1367-1376.
[12] Zhang, C., Ju, Y., Tang, N., Li, Y., Zhang, G., Song, Y., ... & Feng, J. (2019). Systematic analysis of supervised machine learning as an effective approach to predicate β-lactam resistance phenotype in Streptococcus pneumoniae. Briefings in bioinformatics.
[13] Bittaye, M., & Cash, P. (2015). Streptococcus pneumoniae proteomics: determinants of pathogenesis and vaccine development. Expert review of proteomics, 12(6), 607-621.
[14] Vázquez, R., & García, P. (2019). Synergy between two chimeric lysins to kill Streptococcus pneumoniae. Frontiers in microbiology, 10, 1251. [15] Varghese, R., Jayaraman, R., & Veeraraghavan, B. (2017). Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era. Journal of microbiological methods, 141, 48-54.
[16] Haribalaganesh Ravinarayanan, Richard Coico and Krishnan Sundar, Identification of Putative Therapeutic Targets in Candida tropicalis: An in-silico Approach, 2015, Kalasalingam University, Krishnankoil
[17] Uddin, R., & Saeed, K. (2014). Identification and characterization of potential drug targets by subtractive genome analyses of methicillin resistant Staphylococcus aureus. Computational biology and chemistry, 48, 55-63.
[18] Sarangi, A. N., Aggarwal, R., Rahman, Q., & Trivedi, N. (2009). Subtractive genomics approach for in silico identification and characterization of novel drug targets in Neisseria Meningitides Serogroup B. J Comput Sci Syst Biol, 2(5), 255-258.
[19] Antibiotic Resistance Threat in United State, 2013, CDC, U.S. Department of Health and Human Services
[20] Hoskins, J., Alborn, W. E., Arnold, J., Blaszczak, L. C., Burgett, S., DeHoff, B. S., ... & Geringer, C. (2001). Genome of the bacterium Streptococcus pneumoniae strain R6. Journal of bacteriology, 183(19), 5709-5717.
[21] Wadood, A., Jamal, A., Riaz, M., Khan, A., Uddin, R., Jelani, M., & Azam, S. S. (2018). Subtractive genome analysis for in silico identification and characterization of novel drug targets in Streptococcus pneumonia strain JJA. Microbial pathogenesis, 115, 194-198.
[22] Nazir, Z., Afridi, S. G., Shah, M., Shams, S., & Khan, A. (2018). Reverse vaccinology and subtractive genomics-based putative vaccine targets identification for Burkholderia pseudomallei Bp1651. Microbial pathogenesis, 125, 219-229.
[23] Meshram, R. J., Goundge, M. B., Kolte, B. S., & Gacche, R. N. (2019). An in silico approach in identification of drug targets in Leishmania: A subtractive genomic and metabolic simulation analysis. Parasitology international, 69, 59-70. [24] Hossain, T., Kamruzzaman, M., Choudhury, T. Z., Mahmood, H. N., Nabi, A. H. M., & Hosen, M. (2017). Application of the subtractive genomics and molecular docking analysis for the identification of novel putative drug targets against Salmonella enterica subsp. enterica serovar Poona. BioMed research international, 2017.
[25] Jamal, S. B., Hassan, S. S., Tiwari, S., Viana, M. V., de Jesus Benevides, L., Ullah, A., ... & Silva, A. (2017). An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PLoS One, 12(10).
[26] Jacobsen, E. W., & Nordling, T. E. (2016). Robust Target Identification for Drug Discovery. IFAC-PapersOnLine, 49(7), 815-820.
Websites:
[1] India’s New Pneumonia Vaccine (https://everylifecounts.ndtv.com/know-indias-new-vaccine-pneumonia-13351)
[2] CDC website. http://www.cdc.gov/pneumococcal/
[3] Unipot Database, uniprot.org, National Institute of Health, EMBL-EBI, State Secretariat for Education Research and Innovation SERI (https://www.uniprot.org/)
[4] CD-Hit Suite, Ying Huang, Beifang Niu, Ying Gao, Limin Fu, Weizhong Li, CD-HIT Suite: a web server for clustering and comparing biological sequences, Bioinformatics, Volume 26, Issue 5, 1 March 2010, Pages 680–682 (http://weizhong-lab.ucsd.edu/cdhit_suite/cgi-bin/index.cgi?cmd=cd-hit)
[5] DEG: Database of Essential Genes, essentialgene.org, School of Science Tianjin University (http://www.essentialgene.org/)
[6] BLASTp, a registered trademark of the National Library of Medicine, National Centre for Biotechnology Information. (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins)
[7] KEGG Database, Bioinformatics Center, Kyoto University, Human Genome Centre, University of Tokyo
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Published
2020-01-27
How to Cite
Bhoi, P., Sahu, T. K., & Patel, A. (2020). Identification of Novel Drug Targets in Streptococcus pneumoniae using Subtractive Genomic Approach. CSVTU International Journal of Biotechnology, Bioinformatics and Biomedical, 4(3), 79–86. https://doi.org/10.30732/IJBBB.20190403002
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