In silico systems biology approaches for the identification of antimicrobial targets

Methods in Molecular Biology

Volumn 993, Issue , 2013, Pages 13-30

  Sarker, Malabika ^a   Talcott, Carolyn ^a   Galande, Amit K ^a  

^a SRI INTERNATIONAL   (United States)

Author keywords

Antimicrobials; Database; Metabolites; Omics; Software tools; Systems biology; Targets

Indexed keywords

ANTIBIOTIC AGENT; BACTERIAL ENZYME; BACTERIAL PROTEIN; ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; ARTICLE; ASPERGILLUS; BACILLUS SUBTILIS; COMPUTER MODEL; COMPUTER PROGRAM; DATA ANALYSIS; DATA BASE; DRUG SCREENING; DRUG TARGETING; ESCHERICHIA COLI; FRANCISELLA TULARENSIS; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; HELICOBACTER PYLORI; HUMAN IMMUNODEFICIENCY VIRUS; INFLUENZA VIRUS; INTERNET; MACHINE LEARNING; METABOLITE; METABOLOMICS; MICROARRAY ANALYSIS; MOLECULAR LIBRARY; MYCOBACTERIUM LEPRAE; MYCOBACTERIUM TUBERCULOSIS; MYCOPLASMA PULMONIS; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA; SACCHAROMYCES CEREVISIAE; SIMULATION; SYSTEMS BIOLOGY; VIBRIO CHOLERAE; ANIMAL; FACTUAL DATABASE; HUMAN; METHODOLOGY; MICROBIOLOGY; REVIEW;

ANIMALS; ANTI-INFECTIVE AGENTS; DATABASES, FACTUAL; DRUG EVALUATION, PRECLINICAL; HUMANS; MICROBIOLOGY; SOFTWARE; SYSTEMS BIOLOGY;

EID: 84884256409     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-342-8_2     Document Type: Article

References (37)

1. Bevan P, Ryder H, Shaw I (1995) Identifying small-molecule lead compounds: the screening approach to drug discovery. Trends Biotechnol 13:115-121
2. Kitano H (2002) Systems biology: a brief overview. Science 295:1662-1664
3. Gwynn MN, Portnoy A, Rittenhouse SF et al (2010) Challenges of antibacterial discovery revisited. Ann N Y Acad Sci 1213:5-19
4. Westerhoff HV, Palsson BO (2004) The evolution of molecular biology into systems biology. Nat Biotechnol 22:1249-1252
5. Butcher EC, Berg EL, Kunkel EJ (2004) Systems biology in drug discovery. Nat Biotechnol 22:1253-1259
6. Davidov E, Holland J, Marple E et al (2003) Advancing drug discovery through systems biology. Drug Discov Today 8:175-183
7. Aderem A (2005) Systems biology: its practice and challenges. Cell 121:511-513
8. Palsson B (2000) The challenges of in silico biology. Nat Biotechnol 18:1147-1150
9. Kitano H (2002) Computational systems biology. Nature 420:206-210
10. Raman K, Yeturu K, Chandra N (2008) TargetTB: a target identi fication pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC Syst Biol 2:109
11. Gu S, Chen J, Dobos KM et al (2003) Comprehensive proteomic pro filing of the membrane constituents of a Mycobacterium tuberculosis strain. Mol Cell Proteomics 2:1284-1296
12. Bahk YY, Kim SA, Kim JS et al (2004) Antigens secreted from Mycobacterium tuberculosis : identi fication by proteomics approach and test for diagnostic marker. Proteomics 4: 3299-3307
13. Mawuenyega KG, Forst CV, Dobos KM et al (2005) Mycobacterium tuberculosis functional network analysis by global subcellular protein pro filing. Mol Biol Cell 16:396-404
14. Mattow J, Siejak F, Hagens K et al (2007) An improved strategy for selective and ef ficient enrichment of integral plasma membrane proteins of mycobacteria. Proteomics 7:1687-1701
15. Malen H, Berven FS, Fladmark KE et al (2007) Comprehensive analysis of exported proteins from Mycobacterium tuberculosis H37Rv. Proteomics 7:1702-1718
16. Gonzalez-Zamorano M, Mendoza-Hernandez G, Xolalpa W et al (2009) Mycobacterium tuberculosis glycoproteomics based on ConAlectin af finity capture of mannosylated proteins. J Proteome Res 8:721-733
17. Sarker M, Chopra S, Mortelmans K et al (2011) In silico pathway analysis predicts metabolites that are potential antimicrobial targets. J Comput Sci Syst Biol 4:021-026
18. Munger J, Bennett BD, Parikh A et al (2008) Systems-level metabolic flux pro filing identi fies fatty acid synthesis as a target for antiviral therapy. Nat Biotechnol 26:1179-1186
19. Kim HU, Kim TY, Lee SY (2010) Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE. Mol Biosyst 6:339-348
20. Kim TY, Kim HU, Lee SY (2010) Metabolitecentric approaches for the discovery of antibacterials using genome-scale metabolic networks. Metab Eng 12:105-111
21. Kim HU, Kim SY, Jeong H et al (2011) Integrative genome-scale metabolic analysis of Vibrio vulni ficus for drug targeting and discovery. Mol Syst Biol 7:460
22. Schilling CH, Palsson BO (2000) Assessment of the metabolic capabilities of Haemophilus in fluenzae Rd through a genome-scale pathway analysis. J Theor Biol 203:249-283
23. Yeh I, Hanekamp T, Tsoka S et al (2004) Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res 14:917-924
24. Rahman SA, Schomburg D (2006) Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks. Bioinformatics 22:1767-1774
25. Jamshidi N, Palsson BO (2007) Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst Biol 1:26
26. Chavali AK, Whittemore JD, Eddy JA et al (2008) Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol Syst Biol 4:177
27. Mazumdar V, Snitkin ES, Amar S et al (2009) Metabolic network model of a human oral pathogen. J Bacteriol 191:74-90
28. Oberhardt MA, Goldberg JB, Hogardt M et al (2010) Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection. J Bacteriol 192:5534-5548
29. Raghunathan A, Shin S, Dae fler S (2010) Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis . BMC Syst Biol 4:118
30. Crowther GJ, Shanmugam D, Carmona SJ et al (2010) Identi fication of attractive drug targets in neglected-disease pathogens using an in silico approach. PLoS Negl Trop Dis 4:e804
31. Plata G, Hsiao TL, Olszewski KL et al (2010) Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Mol Syst Biol 6:408
32. Navratil V, De Chassey B, Combe CR et al (2011) When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases. BMC Syst Biol 5:13
33. Fatumo S, Plaimas K, Adebiyi E et al (2011) Comparing metabolic network models based on genomic and automatically inferred enzyme information from Plasmodium and its human host to de fine drug targets in silico. Infect Genet Evol 11:708-715
34. Fang K, Zhao H, Sun C et al (2011) Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. BMC Syst Biol 5:83
35. Ng A, Bursteinas B, Gao Q et al (2006) Resources for integrative systems biology: from data through databases to networks and dynamic system models. Brief Bioinform 7:318-330
36. Jagarlapudi SA, Kishan KV (2009) Database systems for knowledge-based discovery. Methods Mol Biol 575:159-172
37. Ghosh S, Matsuoka Y, Asai Y et al (2011) Software for systems biology: from tools to integrated platforms. Nat Rev Genet 12:821-832