All Title Author
Keywords Abstract

PLOS ONE  2013 

LAMP: A Database Linking Antimicrobial Peptides

DOI: 10.1371/journal.pone.0066557

Full-Text   Cite this paper   Add to My Lib

Abstract:

The frequent emergence of drug-resistant bacteria has created an urgent demand for new antimicrobial agents. Traditional methods of novel antibiotic development are almost obsolete. Antimicrobial peptides (AMPs) are now regarded as a potential solution to revive the traditional methods of antibiotic development, although, until now, many AMPs have failed in clinical trials. A comprehensive database of AMPs with information about their antimicrobial activity and cytotoxicity will help promote the process of finding novel AMPs with improved antimicrobial activity and reduced cytotoxicity and eventually accelerate the speed of translating the discovery of new AMPs into clinical or preclinical trials. LAMP, a database linking AMPs, serves as a tool to aid the discovery and design of AMPs as new antimicrobial agents. The current version of LAMP has 5,547 entries, comprising 3,904 natural AMPs and 1,643 synthetic peptides. The database can be queried using either simply keywords or combinatorial conditions searches. Equipped with the detailed antimicrobial activity and cytotoxicity data, the cross-linking and top similar AMPs functions implemented in LAMP will help enhance our current understanding of AMPs and this may speed up the development of new AMPs for medical applications. LAMP is freely available at: http://biotechlab.fudan.edu.cn/database/?lamp.

References

[1]  IDSA (2010) The 10×'20 Initiative: pursuing a global commitment to develop 10 new antibacterial drugs by 2020. Clin Infect Dis 50: 1081–1083.
[2]  Hancock RE, Sahl HG (2006) Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat Biotechnol 24: 1551–1557.
[3]  Brogden KA (2005) Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Nat Rev Microbiol 3: 238–250.
[4]  Zasloff M (2002) Antimicrobial peptides of multicellular organisms. Nature 415: 389–395.
[5]  Gallo RL, Murakami M, Ohtake T, Zaiou M (2002) Biology and clinical relevance of naturally occurring antimicrobial peptides. J Allergy Clin Immunol 110: 823–831.
[6]  Eckert R (2011) Road to clinical efficacy: challenges and novel strategies for antimicrobial peptide development. Future Microbiol 6: 635–651.
[7]  Giuliani A, Rinaldi AC (2011) Beyond natural antimicrobial peptides: multimeric peptides and other peptidomimetic approaches. Cell Mol Life Sci 68: 2255–2266.
[8]  Brogden NK, Brogden KA (2011) Will new generations of modified antimicrobial peptides improve their potential as pharmaceuticals? Int J Antimicrob Agents 38: 217–225.
[9]  Jin-Jiang H, Jin-Chun L, Min L, Qing-Shan H, Guo-Dong L (2012) The Design and Construction of K11: A Novel α-Helical Antimicrobial Peptide. Internatinal Journal of Microbiology 2012.
[10]  Jiang Z, Vasil AI, Gera L, Vasil ML, Hodges RS (2011) Rational design of alpha-helical antimicrobial peptides to target Gram-negative pathogens, Acinetobacter baumannii and Pseudomonas aeruginosa: utilization of charge, 'specificity determinants,' total hydrophobicity, hydrophobe type and location as design parameters to improve the therapeutic ratio. Chem Biol Drug Des 77: 225–240.
[11]  Pag U, Oedenkoven M, Sass V, Shai Y, Shamova O, et al. (2008) Analysis of in vitro activities and modes of action of synthetic antimicrobial peptides derived from an alpha-helical 'sequence template'. J Antimicrob Chemother 61: 341–352.
[12]  Hammami R, Fliss I (2010) Current trends in antimicrobial agent research: chemo- and bioinformatics approaches. Drug Discov Today 15: 540–546.
[13]  Seshadri Sundararajan V, Gabere MN, Pretorius A, Adam S, Christoffels A, et al. (2012) DAMPD: a manually curated antimicrobial peptide database. Nucleic Acids Res 40: D1108–1112.
[14]  Tossi A, Sandri L (2002) Molecular diversity in gene-encoded, cationic antimicrobial polypeptides. Curr Pharm Des 8: 743–761.
[15]  Wang G, Li X, Wang Z (2009) APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res 37: D933–937.
[16]  Wang Z, Wang G (2004) APD: the Antimicrobial Peptide Database. Nucleic Acids Res 32: D590–592.
[17]  Thomas S, Karnik S, Barai RS, Jayaraman VK, Idicula-Thomas S (2010) CAMP: a useful resource for research on antimicrobial peptides. Nucleic Acids Res 38: D774–780.
[18]  Hammami R, Zouhir A, Le Lay C, Ben Hamida J, Fliss I (2010) BACTIBASE second release: a database and tool platform for bacteriocin characterization. BMC Microbiol 10: 22.
[19]  Hammami R, Ben Hamida J, Vergoten G, Fliss I (2009) PhytAMP: a database dedicated to antimicrobial plant peptides. Nucleic Acids Res 37: D963–968.
[20]  Gueguen Y, Garnier J, Robert L, Lefranc MP, Mougenot I, et al. (2006) PenBase, the shrimp antimicrobial peptide penaeidin database: sequence-based classification and recommended nomenclature. Dev Comp Immunol 30: 283–288.
[21]  Li Y, Chen Z (2008) RAPD: a database of recombinantly-produced antimicrobial peptides. FEMS Microbiol Lett 289: 126–129.
[22]  Wade D, Englund J (2002) Synthetic antibiotic peptides database. Protein Pept Lett 9: 53–57.
[23]  Seebah S, Suresh A, Zhuo S, Choong YH, Chua H, et al. (2007) Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. Nucleic Acids Res 35: D265–268.
[24]  Novkovic M, Simunic J, Bojovic V, Tossi A, Juretic D (2012) DADP: the database of anuran defense peptides. Bioinformatics 28: 1406–1407.
[25]  Wang CK, Kaas Q, Chiche L, Craik DJ (2008) CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering. Nucleic Acids Res 36: D206–210.
[26]  Wu H, Lu H, Huang J, Li G, Huang Q (2012) EnzyBase: a novel database for enzybiotic studies. BMC Microbiol 12: 54.
[27]  Whitmore L, Wallace BA (2004) The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols. Nucleic Acids Res 32: D593–594.
[28]  Fjell CD, Hancock RE, Cherkasov A (2007) AMPer: a database and an automated discovery tool for antimicrobial peptides. Bioinformatics 23: 1148–1155.
[29]  de Jong A, van Heel AJ, Kok J, Kuipers OP (2010) BAGEL2: mining for bacteriocins in genomic data. Nucleic Acids Res 38: W647–651.
[30]  Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37: D211–215.
[31]  Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235–242.

Full-Text

comments powered by Disqus

Contact Us

service@oalib.com

QQ:3279437679

微信:OALib Journal