In silico identification of putative drug targets in Klebsiella pneumonia MGH78578

Indian Journal of Biotechnology

Volumn 10, Issue 4, 2011, Pages 432-439

  Georrge, John J ^a   Umrania, Valentina ^b  

^a Christ College   (India)

^b MVM Sc and HSc College   (India)

Author keywords

BLAST; DEG; Homologous proteins; KAAS server; Klebsiella pneumoniae; Potential drug targets; Reverse vaccinology

Indexed keywords

AZITHROMYCIN; ERYTHROMYCIN; MEMBRANE PROTEIN; PROTEOME; QUINUPRISTIN; RIFABUTIN; TIGECYCLINE;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL STRAIN; CELLULAR DISTRIBUTION; COMPUTER MODEL; DATA BASE; DRUG TARGETING; KLEBSIELLA PNEUMONIAE; NONHUMAN; PROTEIN ANALYSIS; PROTEIN FUNCTION;

EID: 83455221280     PISSN: 09725849     EISSN: 09750967     Source Type: Journal    
DOI: None     Document Type: Article

References (48)

1. De Groot A S, Sbai H, Aubin C S, McMurray J & Martin W, Immuno-informatics-mining the genomes for vaccine components, Immunol Cell Biol, 80 (2002) 255-269.
2. Galperin M Y & Koonin E V, Searching for drug targets in microbial genomes, Curr Opin Biotechnol, 10 (1999) 571-578.
3. Koonin E V, Tatusov R L & Galperin M Y, Beyond complete genomes: From sequence to structure and function, Curr Opin Struc Biol, 8 (1998) 355-363.
4. Barh D, Tiwari S, Jain N, Ali A, Santos A R et al, In silico subtractive genomics for target identification in human bacterial pathogens, Drug Develop Res, 72 (2011) 162-177. (DOI: 10.1002/ddr.20413)
5. Moriya Y, Itoh M, Okuda S, Yoshizawa A C & Kanehisa M, KAAS: An automatic genome annotation and pathway reconstruction server, Nucleic Acids Res, 35 (2007) W182-185
6. Zhang R & Lin Y, DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes, Nucleic Acids Res, 37 (2009), D455-D458.
7. Amineni U, Pradhan D &. Marisetty H, In silico identification of common putative drug targets in Leptospira interrogans, J Chem Biol, 3 (2010) 165-173.
8. Rathi B, Sarangi A N & Trivedi N, Genome subtraction for novel target definition in Salmonella typhi, Bioinformation, 4 (2009) 143-150.
9. Koteswara Reddy G, Nagamalleswara Rao K, Phani Rama Krishna B & Aravind S, In silico identification of potential therapeutic targets in Clostridium botulinum by the approach subtractive genomics, Int J Bioinform Res, 2 (2010) 12-16.
10. Dutta A, Singh S K, Ghosh P, Mukherjee R, Mitter S et al, In silico identification of potential therapeutic targets in the human pathogen Helicobacter pylori, In Silico Biol, 6 (2006) 43-47.
11. Sakharkar K R, Sakharkar M K & Chow V T, A novel genomics approach for the identification of drug targets in pathogens with special reference to Pseudomonas aeruginosa, In Silico Biol, 4 (2004) 355-360.
12. Gupta S K, Singh S, Gupta M K, Pant K K & Seth P K, Definition of potential targets in Mycoplasma pneumoniae through subtractive genome analysis, J Antivir Antiretrovir, 2 (2010) 38-42.
13. Allsop A E, Brooks G, Bruton G, Coulton S, Edwards P D et al, Penem inhibitors of bacterial signal peptidase, Bioorg Med Chem Lett, 5 (1995) 443-448.
14. Sharma V, Gupta P & Dixit A. In silico identification of putative drug targets from different metabolic pathways of Aeromonas hydrophila, In Silico Biol, 8 (2008) 331-338.
15. Barh D & Kumar A. In silico identification of candidate drug and vaccine targets from various pathways in Neisseria gonorrhoeae, In Silico Biol, 9 (2009) 225-231.
16. Singh S, Malik B K & Sharma D K. Metabolic pathway analysis of S. pneumoniae: An in silico approach towards drug-design, J Bioinform Comput Biol, 5 (2007) 135-53.
17. Anishetty S, Pulimi M & Pennathur G, Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis, Comput Biol Chem, 29 (2005) 368-378.
18. th edn (McGraw Hill Book Publishing Co, New York) 2004.
19. AHFS drug information (American Society of Health-System Pharmacists, Bethedsa, MD) 2006.
20. Rich M, Ritterhoff R & Hoffmann R, A fatal case of aplastic anemia following chloramphenicol (chloromycetin) therapy, Ann Intern Med, 33 (1950) 1459-1467.
21. Schaeffer A J, Co-trimoxazole use restricted, Drug Ther Bull, 33 (1995) 92-93.
22. De Champs C, Rich C, Chandezon P, Chanal C, Sirot D et al, Factors associated with antimicrobial resistance among clinical isolates of Klebsiella pneumoniae: 1-year survey in a French University hospital, Eur J Clin Microbiol Infect Dis, 23 (2004) 456-462.
23. Hasdemir U O, Chevalier J, Nordmann P & Pagès J M, Detection and prevalence of active drug efflux mechanism in various multidrug-resistant Klebsiella pneumoniae strains from Turkey, J Clin Microbiol, 42 (2004) 2701-2706.
24. Huang Y, Niu B, Gao Y, Fu L & Li W, CD-HIT Suite: A web server for clustering and comparing biological sequences, Bioinformatics, 26 (2010) 680-682.
25. Li W & Godzik A, Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, 22 (2006) 1658-1659.
26. Kerfeld C A & Scott K M, Using BLAST to Teach "E-valuetionary" concepts, PLoS Biol, 9 (2011) e1001014.
27. Waterman M S & Vingron M, Rapid and accurate estimates of statistical significance for sequence data base searches, Proc Natl Acad Sci USA, 91 (1994) 4625-4628.
28. Collins J F, Coulson A F & Lyall A, The significance of protein sequence similarities, Comput Appl Biosci, 4 (1988) 67-71.
29. Altschul S F, Gish W, Miller W, Myers E W & Lipman D J, Basic local alignment search tool, J Mol Biol, 215 (1990) 403-410.
30. Pearson W R, Effective protein sequence comparison. Methods Enzymol, 266 (1996) 227-258.
31. Pearson W R, Comparison of methods for searching protein sequence databases, Protein Sci, 4 (1995) 1145-1160.
32. Zhang R & Lin Y, DEG 5.0: A database of essential genes in both prokaryotes and eukaryotes, Nucleic Acids Res, 37 (2009), D455-D458.
33. Zhang C-T & Zhang R, Gene essentiality analysis based on DEG, a database of essential genes, Methods Mol Biol, 416 (2008) 391-400.
34. Moriya Y, Itoh M, Okuda S, Yoshizawa A C & Kanehisa M, KAAS: An automatic genome annotation and pathway reconstruction server, Nucleic Acids Res, 35 (2007) 182-185.
35. Knox C, Law V, Jewison T, Liu P, Ly S et al, DrugBank 3.0: A comprehensive resource for 'omics' research on drugs, Nucleic Acids Res, 39 (2011) D1035-D1041.
36. Chen X, Ji Z L & Chen Y Z, TTD: Therapeutic target database, Nucleic Acids Res, 30 (2002) 412-415.
37. Gao Z, Li H, Zhang H, Liu X, Kang L et al, PDTD: A webaccessible protein database for drug target identification, BMC Bioinformatics, 9 (2008) 104.
38. Ye H, Ye L, Kang H, Zhang D, Tao L et al, HIT: Linking herbal active ingredients to targets, Nucleic Acids Res, 39 (2011) D1055-D1059.
39. Yu N Y, Wagner J R, Laird M R, Melli G, Rey S et al, PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes, Bioinformatics, 26 (2010) 1608-1615.
40. Krogh A, Larsson B, von Heijne G & Sonnhammer E L, Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes, J Mol Biol, 305 (2001) 567-580.
41. Hu Y, Helm J S, Chen L, Ginsberg C, Gross B et al, Identification of selective inhibitors for the glycosyltransferase MurG via high-throughput screening, Chem Biol, 11 (2004) 703-711.
42. Matsushita M & Janda K D, Histidine kinases as targets for new antimicrobial agents, Bioorg Med Chem, 10 (2002) 855-867.
43. Selitrennikoff C P, Alex L, Miller T K, Clemons K V, Simon M I et al, COS-l, a putative two-component histidine kinase of Candida albicans, is an in vivo virulence factor, Med Mycol, 39 (2001) 69-74.
44. Labischinski H & Johannsen L, Cell wall targets in methicillin-resistant staphylococci, Drug Resist Updat, 2 (1999) 319-325.
45. Kulanthaivel P, Kreuzman A J, Strege M A, Belvo M D, Smitka T A et al, Novel lipoglycopeptides as inhibitors of bacterial signal peptidase I, J Biol Chem, 279 (2004) 36250-36258.
46. Gardy J L & Brinkman F S L, Methods for predicting bacterial protein subcellular localization, Nat Rev Microbiol, 4 (2006) 741-751.
47. Rappuoli R, Reverse vaccinology, Cur Opin Microbiol, 3 (2000) 445-450.
48. Pizza M, Scarlato V, Masignani V, Giuliani M M, Arico B et al, Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing, Science, 287 (2000) 1816-1820.