Connecting peptide physicochemical and antimicrobial properties by a rational prediction model

PLoS ONE

Volumn 6, Issue 2, 2011, Pages

  Torrent, Marc ^a,b   Andreu, David ^b   Nogués, Victòria M ^a   Boix, Ester ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE ANTIBIOTIC AGENT; ANTIMICROBIAL CATIONIC PEPTIDE;

ALPHA HELIX; AMINO ACID SEQUENCE; ANTIBIOTIC RESISTANCE; ANTIMICROBIAL ACTIVITY; ARTICLE; ARTIFICIAL NEURAL NETWORK; BACTERIAL INFECTION; BACTERIAL STRAIN; BETA SHEET; BIOINFORMATICS; CONTROLLED STUDY; DRUG DESIGN; DRUG INDUSTRY; DRUG MECHANISM; DRUG POTENCY; HYDROPHOBICITY; ISOELECTRIC POINT; PREDICTION; PROTEIN AGGREGATION; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; METHODOLOGY; PHYSICAL CHEMISTRY; PROTEIN CONFORMATION; REGRESSION ANALYSIS;

BACTERIA (MICROORGANISMS);

AMINO ACID SEQUENCE; ANTIMICROBIAL CATIONIC PEPTIDES; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); PHYSICOCHEMICAL PROCESSES; PROTEIN CONFORMATION; REGRESSION ANALYSIS;

EID: 79951801514     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016968     Document Type: Article

References (38)

1. Jenssen H, Hamill P, Hancock RE, (2006) Peptide antimicrobial agents. Clin Microbiol Rev 19: 491-511.
2. Beisswenger C, Bals R, (2005) Functions of antimicrobial peptides in host defense and immunity. Curr Protein Pept Sci 6: 255-264.
3. Hancock RE, Sahl HG, (2006) Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat Biotechnol 24: 1551-1557.
4. Andres E, Dimarcq JL, (2004) Cationic antimicrobial peptides: update of clinical development. J Intern Med 255: 519-520.
5. Oyston PC, Fox MA, Richards SJ, Clark GC, (2009) Novel peptide therapeutics for treatment of infections. J Med Microbiol 58: 977-987.
6. Poole K, (2003) Overcoming multidrug resistance in gram-negative bacteria. Curr Opin Investig Drugs 4: 128-139.
7. Guani-Guerra E, Santos-Mendoza T, Lugo-Reyes SO, Teran LM, (2010) Antimicrobial peptides: general overview and clinical implications in human health and disease. Clin Immunol 135: 1-11.
8. Nguyen LT, Chau JK, Perry NA, de Boer L, Zaat SA, et al. (2010) Serum stabilities of short tryptophan- and arginine-rich antimicrobial peptide analogs. PLoS One 5.
9. Sieprawska-Lupa M, Mydel P, Krawczyk K, Wojcik K, Puklo M, et al. (2004) Degradation of human antimicrobial peptide LL-37 by Staphylococcus aureus-derived proteinases. Antimicrob Agents Chemother 48: 4673-4679.
10. Lata S, Mishra NK, Raghava GP, (2010) AntiBP2: improved version of antibacterial peptide prediction. BMC Bioinformatics 11 (Suppl 1): S19.
11. Torrent M, Nogues VM, Boix E, (2009) A theoretical approach to spot active regions in antimicrobial proteins. BMC Bioinformatics 10: 373.
12. Frecer V, Ho B, Ding JL, (2004) De novo design of potent antimicrobial peptides. Antimicrob Agents Chemother 48: 3349-3357.
13. Jenssen H, Lejon T, Hilpert K, Fjell CD, Cherkasov A, et al. (2007) Evaluating different descriptors for model design of antimicrobial peptides with enhanced activity toward P. aeruginosa. Chem Biol Drug Des 70: 134-142.
14. Jenssen H, Fjell CD, Cherkasov A, Hancock RE, (2008) QSAR modeling and computer-aided design of antimicrobial peptides. J Pept Sci 14: 110-114.
15. Frecer V, (2006) QSAR analysis of antimicrobial and haemolytic effects of cyclic cationic antimicrobial peptides derived from protegrin-1. Bioorg Med Chem 14: 6065-6074.
16. Cherkasov A, Jankovic B, (2004) Application of 'inductive' QSAR descriptors for quantification of antibacterial activity of cationic polypeptides. Molecules 9: 1034-1052.
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. Taboureau O, Olsen OH, Nielsen JD, Raventos D, Mygind PH, et al. (2006) Design of novispirin antimicrobial peptides by quantitative structure-activity relationship. Chem Biol Drug Des 68: 48-57.
19. Fjell CD, Jenssen H, Hilpert K, Cheung WA, Pante N, et al. (2009) Identification of novel antibacterial peptides by chemoinformatics and machine learning. J Med Chem 52: 2006-2015.
20. Bulet P, Stocklin R, Menin L, (2004) Anti-microbial peptides: from invertebrates to vertebrates. Immunol Rev 198: 169-184.
21. Taboureau O, (2010) Methods for building quantitative structure-activity relationship (QSAR) descriptors and predictive models for computer-aided design of antimicrobial peptides. Methods Mol Biol 618: 77-86.
22. Shai Y, (2002) Mode of action of membrane active antimicrobial peptides. Biopolymers 66: 236-248.
23. Deslouches B, Phadke SM, Lazarevic V, Cascio M, Islam K, et al. (2005) De novo generation of cationic antimicrobial peptides: influence of length and tryptophan substitution on antimicrobial activity. Antimicrob Agents Chemother 49: 316-322.
24. Gorr SU, Sotsky JB, Shelar AP, Demuth DR, (2008) Design of bacteria-agglutinating peptides derived from parotid secretory protein, a member of the bactericidal/permeability increasing-like protein family. Peptides 29: 2118-2127.
25. Torrent M, Badia M, Moussaoui M, Sanchez D, Nogues MV, et al. (2010) Comparison of human RNase 3 and RNase 7 bactericidal action at the Gram-negative and Gram-positive bacterial cell wall. FEBS J 277: 1713-1725.
26. Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L, (2004) Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22: 1302-1306.
27. Conchillo-Sole O, de Groot NS, Aviles FX, Vendrell J, Daura X, et al. (2007) AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. BMC Bioinformatics 8: 65.
28. de Groot NS, Ventura S, (2010) Protein aggregation profile of the bacterial cytosol. PLoS One 5: e9383.
29. Giuliani A, Pirri G, Bozzi A, Di Giulio A, Aschi M, et al. (2008) Antimicrobial peptides: natural templates for synthetic membrane-active compounds. Cell Mol Life Sci 65: 2450-2460.
30. Brown LR, Lauterwein J, Wuthrich K, (1980) High-resolution 1H-NMR studies of self-aggregation of melittin in aqueous solution. Biochim Biophys Acta 622: 231-244.
31. Oren Z, Lerman JC, Gudmundsson GH, Agerberth B, Shai Y, (1999) Structure and organization of the human antimicrobial peptide LL-37 in phospholipid membranes: relevance to the molecular basis for its non-cell-selective activity. Biochem J 341 (Pt 3): 501-513.
32. Kustanovich I, Shalev DE, Mikhlin M, Gaidukov L, Mor A, (2002) Structural requirements for potent versus selective cytotoxicity for antimicrobial dermaseptin S4 derivatives. J Biol Chem 277: 16941-16951.
33. Feder R, Dagan A, Mor A, (2000) Structure-activity relationship study of antimicrobial dermaseptin S4 showing the consequences of peptide oligomerization on selective cytotoxicity. J Biol Chem 275: 4230-4238.
34. Rosenfeld Y, Barra D, Simmaco M, Shai Y, Mangoni ML, (2006) A synergism between temporins toward Gram-negative bacteria overcomes resistance imposed by the lipopolysaccharide protective layer. J Biol Chem 281: 28565-28574.
35. Mangoni ML, Marcellini HG, Simmaco M, (2007) Biological characterization and modes of action of temporins and bombinins H, multiple forms of short and mildly cationic anti-microbial peptides from amphibian skin. J Pept Sci 13: 603-613.
36. Shai Y, (1999) Mechanism of the binding, insertion and destabilization of phospholipid bilayer membranes by alpha-helical antimicrobial and cell non-selective membrane-lytic peptides. Biochim Biophys Acta 1462: 55-70.
37. Allende D, Simon SA, McIntosh TJ, (2005) Melittin-induced bilayer leakage depends on lipid material properties: evidence for toroidal pores. Biophys J 88: 1828-1837.
38. He K, Ludtke SJ, Worcester DL, Huang HW, (1996) Neutron scattering in the plane of membranes: structure of alamethicin pores. Biophys J 70: 2659-2666.