In silico identification of dual ability of n. gonorrhoeae ddl for developing drug and vaccine against pathogenic neisseria and other human pathogens

Journal of Proteomics and Bioinformatics

Volumn 3, Issue 3, 2010, Pages 082-090

  Barh, Debmalya ^a   Misra, Amarendra Narayan ^b   Kumar, Anil ^c  

^a Institute of Integrative Omics and Applied Biotechnology IIOAB   (India)

^b FAKIR MOHAN UNIVERSITY   (India)

^c DEVI AHILYA UNIVERSITY   (India)

Author keywords

Broad spectrum target; Computational prediction; Epitope design; Immunoinformatics; Sexually transmitted disease

Indexed keywords

BACTERIA (MICROORGANISMS); NEISSERIA; NEISSERIA GONORRHOEAE;

EID: 77950121219     PISSN: None     EISSN: 0974276X     Source Type: Journal    
DOI: 10.4172/jpb.1000125     Document Type: Article

References (46)

1. Arockiasamy A, Krishnaswamy S (1995) Prediction of B-cell epitopes for Salmonella typhi OmpC. J Biosci 20: 235-243.
2. Arévalo-Herrera M, Valencia AZ, Vergara J, Bonelo A, Fleischhauer K, et al. (2002) Identification of HLA-A2 restricted CD8(+) T-lymphocyte responses to Plasmodium vivax circumsporozoite protein in individuals naturally exposed to malaria. Parasite Immunol 24: 161-169.
3. Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics 22: 195-201.
4. Barbosa-Cesnik CT, Gerbase A, Heymann D (1997) STD vaccines an overview. Genitourin Med 73: 336-342.
5. Barh D, Kumar A (2009) In silico identification of candidate drug and vaccine targets from various pathways in Neisseria gonorrhoeae. In Silico Biol 9: 0019.
6. Barh D, Misra AN (2009) In silico Identification of membrane associated candidate drug targets in Neisseria gonorrhoeae. International Journal of Integrative Biology 6: 65-67.
7. Baú D, Martin AJ, Mooney C, Vullo A, Walsh I, et al. (2006) Distill: A suite of web servers for the prediction of one-, twoand three-dimensional structural features of proteins. BMC Bioinformatics 7: 402.
8. Bos MP, Tefsen B, Voet P, Weynants V, van Putten JP, et al. (2005) Function of neisserial outer membrane phospholipase a in autolysis and assessment of its vaccine potential. Infect Immun 73: 2222-2231.
9. Centers for Disease Control and Prevention (CDC): Sexually transmitted disease surveillance 2006. Atlanta: U.S. Department of Health and Human Services, 2007.
10. Cornelissen CN (2008) Identification and characterization of gonococcal iron transport systems as potential vaccine antigens. Future Microbiol 3: 287-298.
11. Doytchinova IA, Flower DR (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 8: 4.
12. El-Manzalawy Y, Dobbs D, Honavar V (2008) Predicting linear B-cell epitopes using string kernels. J Mol Recognit 21: 243-255.
13. Fan C, Park IS, Walsh CT, Knox JR (1997) D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. Biochemistry 36: 2531-2538.
14. Furuya R, Tanaka M (2009) Neisseria gonorrhoeae infections. Nippon Rinsho 67: 129-135.
15. Gholizadeh Y, Prevost M, Van Bambeke F, Casadewall B, Tulkens PM, Courvalin P (2001) Sequencing of the ddl gene and modeling of the mutated D-alanine:Dalanine ligase in glycopeptide-dependent strains of Enterococcus faecium. Protein Sci 10: 836-844.
16. Guan P, Doytchinova IA, Zygouri C, Flower DR (2003) MHCPred: A server for quantitative prediction of peptide-MHC binding. Nucleic Acids Res 31: 3621-3624.
17. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18: 2714-2723.
18. Gulati S, Ngampasutadol J, Yamasaki R, McQuillen DP, Rice PA (2001) Strategies for mimicking Neisserial saccharide epitopes as vaccines. Int Rev Immunol 20: 229-250.
19. Hansen JK, Demick KP, Mansfield JM, Forest KT (2007) Conserved regions from Neisseria gonorrhoeae pilin are immunosilent and not immunosuppressive. Infect Immun 75: 4138-4147.
20. Kovac A, Majce V, Lenarsic R, Bombek S, Bostock JM, et al. (2007) Diazenedicarboxamides as inhibitors of D-alanine-D-alanine ligase (Ddl). Bioorg Med Chem Lett 17: 2047-2054.
21. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-80.
22. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26: 283-291.
23. Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33: W89-W93.
24. Liu S, Chang JS, Herberg JT, Horng MM, Tomich PK, et al. (2006) Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies. Proc Natl Acad Sci 103: 15178-15183.
25. McCoy AJ, Maurelli AT (2005) Characterization of Chlamydia MurC-Ddl, a fusion protein exhibiting D-alanyl-D-alanine ligase activity involved in peptidoglycan synthesis and D-cycloserine sensitivity. Mol Microbiol 57: 41-52.
26. Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217.
27. Pancré V, Gras-Masse H, Delanoye A, Herno J, Capron A, et al. (1996) Induction of cytotoxic T-cell activity by the protective antigen of Schistosoma mansoni Sm28GST or its derived C-terminal lipopeptide. Scand J Immunol 44: 485-492.
28. Prévost M, Van Belle D, Tulkens PM, Courvalin P,Van Bambeke F (2000) Modeling of Enterococcus faecalis D-alanine:D-alanine ligase: structure-based study of the active site in the wild-type enzyme and in glycopeptide-dependent mutants. J Mol Microbiol Biotechnol 2: 321-330.
29. Price GA, Masri HP, Hollander AM, Russell MW, Cornelissen CN (2007) Gonococcal transferrin binding protein chimeras induce bactericidal and growth inhibitory antibodies in mice. Vaccine 25: 7247-7260.
30. Price GA, Russell MW, Cornelissen CN (2005) Intranasal administration of recombinant Neisseria gonorrhoeae transferrin binding proteins A and B conjugated to the cholera toxin B subunit induces systemic and vaginal antibodies in mice. Infect Immun 73: 3945-3953.
31. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, et al. (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33: W116-120.
32. Rothbard JB, Fernandez R, Wang L, Teng NN, Schoolnik GK (1985) Antibodies to peptides corresponding to a conserved sequence of gonococcal pilins block bacterial adhesion. Proc Natl Acad Sci 82: 915-919.
33. Sharma V, Gupta P, Dixit A (2008) In silico identification of putative drug targets from different metabolic pathways of Aeromonas hydrophila. In Silico Biol 8: 0026.
34. Singh H, Raghava GP (2001) ProPred: prediction of HLA-DR binding sites. Bioinformatics 17: 1236-1237.
35. Singh H, Raghava GP (2003) ProPred1: prediction of promiscuous MHC ClassI binding sites. Bioinformatics 19: 1009-1014.
36. Sollner J, Grohmann R, Rapberger R, Perco P, Lukas A, et al. (2008) Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins. Immunome Res 4: 1.
37. Tapsall J (2006) Antibiotic resistance in Neisseria gonorrhoeae is diminishing available treatment options for gonorrhea: some possible remedies. Expert Rev Anti Infect Ther 4: 619-628.
38. Thomas CE, Zhu W, Van Dam CN, Davis NL, Johnston RE, et al. (2006) Vaccination of mice with gonococcal TbpB expressed in vivo from Venezuelan equine encephalitis viral replicon particles. Infect Immun 74: 1612-1620.
39. Toes RE, Nussbaum AK, Degermann S, Schirle M, Emmerich NP, et al. (2001) Discrete cleavage motifs of constitutive and immunoproteasomes revealed by quantitative analysis of cleavage products. J Exp Med 194: 1-12.
40. Triola G, Wetzel S, Ellinger B, Koch MA, Hübel K, et al. (2009) ATP competitive inhibitors of D-alanine-D-alanine ligase based on protein kinase inhibitor scaffolds. Bioorg Med Chem 17: 1079-1087.
41. Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35: W407-410.
42. Workowski KA, Berman SM, Douglas JM Jr (2008) Emerging antimicrobial resistance in Neisseria gonorrhoeae: urgent need to strengthen prevention strategies. Ann Intern Med 148: 606-613.
43. Wu D, Kong Y, Han C, Chen J, Hu L, et al. (2008) D-Alanine:D-alanine ligase as a new target for the flavonoids quercetin and apigenin. Int J Antimicrob Agents 32: 421-426.
44. Zawadzke LE, Bugg TD, Walsh CT (1991) Existence of two D-alanine:D-alanine ligases in Escherichia coli: cloning and sequencing of the ddlA gene and purification and characterization of the DdlA and DdlB enzymes. Biochemistry 30: 1673-1682.
45. Zhang R, Ou HY, Zhang CT (2004) DEG: A database of essential genes. Nucleic Acids Res 32: D271-D272.
46. Zhu W, Thomas CE, Sparling PF (2004) DNA immunization of mice with a plasmid encoding Neisseria gonorrhea PorB protein by intramuscular injection and epidermal particle bombardment. Vaccine 22: 660-669.