Application of unnatural amino acids to the de novo design of selective antibiotic peptides

Methods in Molecular Biology

Volumn 794, Issue , 2012, Pages 135-167

  Hicks, Rickey P ^a   Russell, Amanda L ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

Author keywords

Antimicrobial peptides; De novo; Organism selectivity; Unnatural amino acids

Indexed keywords

AMINO ACID; ANTIINFECTIVE AGENT; LIPOSOME; PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; DRUG DESIGN;

AMINO ACIDS; ANTI-BACTERIAL AGENTS; CIRCULAR DICHROISM; DRUG DESIGN; LIPOSOMES; MODELS, MOLECULAR; PEPTIDES;

BACTERIA (MICROORGANISMS);

EID: 80655144847     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-331-8_9     Document Type: Article

References (96)

1. Ma J S (2003) Unnatural amino acids in drug discovery. CHIMICA OGGI Chemistry Today, June, 65-68.
2. Hendrickson T L, de Crecy-Lagard V, Schimmel P (2004) Incorporation of nonnatural amino acids into proteins. Annu Rev Biochem 73, 147-176.
3. Padgett C L. et al. (2007) Unnatural amino acid mutagenesis of GABAa receptor binding site residues reveals a novel cation-pie interaction between GABA and b2 Tyr97. J Neurosci 27, 886-892. (Pubitemid 46174509)
4. Rodriquez E A, Lester H A, Dougherty D A (2006) In vivo incorporation of multiple unnatual amino acids through nonsense and frame shift suppression. PNAS 103, 8650-8655. (Pubitemid 43878075)
5. Yeaman M R, Yount N Y (2003) Mechanisms of antimicrobial peptide action and resistance. Pharmacol Rev 55, 27-55. (Pubitemid 36268398)
6. Dennison S R et al. (2005) Amphiphilic β-helical antimicrobial peptides and their structure/function relationships. Prot Pept Lett 12, 31-39. (Pubitemid 40068358)
7. Ganz T (2003) Defensins: antimicrobial peptides of innate immunity. Nature Reviews, Immun 3, 710-720. (Pubitemid 41070812)
8. Simmaco M, Mignogna G, Barra D (1999) Antimicrobial peptides from amphibian skin: what do they tell us? Biopolymers 47, 435-450.
9. Lee D G, et al. (2004) Structure-antiviral activity relationships of cecropin A-magainin 2 hybrid peptide and its analogues. J Pept Sci 10, 298-303. (Pubitemid 38594190)
10. Patch J A, Barron A E (2003) Helical peptoid mimics of magainin-2 amide. J Am Chem Soc 125, 12092-12093. (Pubitemid 37238834)
11. Jasir A et al. (2003) New antimicrobial cystatin C-based peptide active against gram-positive bacterial pathogens, including methicillin-resistant Staphylococcus aureus and multiresistant coagulase-negative staphylococci. APMIS 111, 1004-1010. (Pubitemid 37521893)
12. Deslouches B et al. (2005) Activity of the De Novo engineered antimicrobial peptide WLBU2 against pseudomonas aeruginosa in human serum and whole blood for systemic applications. Antimicro Agents Chemother 49, 3208-3216. (Pubitemid 41060563)
13. Conlon J M, Abraham B, Leprince J (2007) Strategies for transformation of naturallyoccurring amphibian antimicrobial peptides into therapeutically valuable anti-infective agents. Methods 42, 349-357. (Pubitemid 46856863)
14. Shlaes D M, Projan S J, Edwards J E (2004) Antibiotic discovery: state of the state. ASM News 70, 275-281. (Pubitemid 41246896)
15. Wang G, Li X, Wang Z (2009) APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res. 37, 933-937.
16. Khandelia H I, Mouritsen O G (2008) The impact of peptides on lipid membranes. Biochim Biophys Acta 1778, 1528-1536.
17. Hancock R E W, Lehrer R (1998) Cationic peptides: a new source of antibiotics. Trends Biotechnol 16, 82-88. (Pubitemid 28055477)
18. Toke O (2005) Antimicrobial peptides; new candidates in the fight against bacterial infections. Biopolymers 80, 717-735. (Pubitemid 43266580)
19. Zasloff M (2002) Antimicrobial peptides of multicellular organisms. Nature 415, 389-395. (Pubitemid 34100944)
20. Powers J-P S, Hancock R E W (2003) The relationship between peptide structure and antibacterial activity. Peptides 24, 1681-1691. (Pubitemid 38198075)
21. Brogden K A (2005) Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Nature Reviews Microbiol 3, 238-250. (Pubitemid 40298223)
22. Hicks R P et al. (2003) Comparison of the conformation and electrostatic surface properties of magainin peptides bound to SDS and DPC micelles: Insight into possible modes on antimicrobial activity. Biopolymers 68, 459-470. (Pubitemid 36427873)
23. Song Y M et al. (2005) Cell selectivity and mechanism of action of antimicrobial model peptides containing peptoid residues. Biochemistry 44, 12094-12106. (Pubitemid 41285707)
24. Papo N, Shai Y (2004) Effects of drastic sequence alteration and D-amino acid incorporation on the membrane binding behavior of lytic peptides. Biochemistry 43, 6393-6403. (Pubitemid 38697539)
25. Dathe M et al. (2002) General aspects of peptide selectivity towards lipid bilayers and cell membrane studied by variation of structural parameters of amphipathic β-helical model peptides. Biochim Biophys Acta 1558, 171-186. (Pubitemid 34075532)
26. Chen Y et al. (2005) Rational design of β-helical antimicrobial peptides with enhanced activities and specificity/therapeutic index. J Biol Chem 280, 12316-12329.
27. Oren Z, Hong J, Shai Y (1997) A repertoire of novel antibacterial diastereomeric peptides with selective cytolytic activity. J Biol Chem 272, 14643-14649. (Pubitemid 27251727)
28. Dathe M, Wiencek J M (1999) Structural features of helical antimicrobial peptides: their potential to modulate activity on model membranes and biological cells. Biochim Biophys Acta 1462, 71-87.
29. Papo N, Shai Y (2003) New lytic peptides based on the D,L amphipathic helix motif preferentially kill tumor cells compared to normal cells. Biochemistry 42, 9346-9354. (Pubitemid 36959242)
30. Giangaspero A, Sandri L, Tossi A (2001) Amphipathic β-helical antimicrobial peptides. Eur J Biochem 268, 5589-5600.
31. Azuma I et al. (1973) Cell wall of Mycobacterium lepraemurium strain Hawaii. J Bacteriology 113, 515-518.
32. Yeaman N R, Yount N Y (2003) Mechanisms of antimicrobial peptide action and resistance. Pharmacol Rev 55, 27-55. (Pubitemid 36268398)
33. Glukhov E et al. (2005) Basis for selectivity of cationic antimicrobial peptides for bacterial versus mammalian membranes. J Biol Chem 280, 33960-33967. (Pubitemid 41443116)
34. Zhang L, Harris S C, Falla T J (2005) Therapeutic application of innate immunity peptides. Horizon Bioscience, San Diego.
35. Bush K (2004) Why it is important to continue antibacterial drug discovery. ASM News 70, 282-287.
36. Klevens R M et al. (2007) Estimating health care-associated infections and deaths in U.S. hospitals.2002. Public Health Reports 122, 160-166.
37. Wang G L X, Wang Z ( 2009) APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res 37, D933-937.
38. Hancock R E, Patrzykat A (2002) Clinical development of cationic antimicrobial peptides: from natural to novel antibiotics. Curr Drug Targets Infect Disord 2, 79-83. (Pubitemid 34649857)
39. Kamysz W (2005) Are antimicrobial peptides an alternative for conventional antibiotics. Nuclear Med Reviews 8, 78-86. (Pubitemid 40916660)
40. Zhang L, Falla T J (2009) Host defense peptides for use as potential therapeutics. Curr Opin Investig Drugs 10, 164-171.
41. Nowick J S et al. (2000) An unnatural amino acid that mimics a tripeptide β-strand and forms β-sheet like hydrogen-bonded dimers. J Am Chem Soc 122, 7654-7661.
42. Nowick J S (2008) Exploring β-sheet structure and interactions with chemical model systems. Acc Chem Res 41, 1319-1330.
43. Grauer A A, Konig B (2009) Synthesis of new C tetrasubstituted β-amino acids. Beilstein J Org Chem 5, 5.
44. Kyle D J et al. (1993) NMR and computational evidence that high-affinity bradykinin receptor antagonists adopt C-terminal beta-turns. J Med Chem 36, 1450-1460. (Pubitemid 23164502)
45. Kyle D J et al. (1992) A novel beta-turn mimic useful for mapping the unknown topology of peptide receptors. Pept Res 5, 206-209.
46. Oh J E, Lee K H (1999) Synthesis of novel unnatural amino acid as a building block and its incorporation into an antimicrobial peptide. Bioorg & Med Chem 7, 2985-2990. (Pubitemid 30105873)
47. Bhonsle J B et al. (2007) Application of 3D-QSAR for identification of descriptors defining bioactivity of antimicrobial peptides. J Med Chem 50, 6545-6553. (Pubitemid 350309094)
48. Haug B E, Strom M B, Svendsen J S M (2007) The medicinal chemistry of short lactoferricin-based antibacterial peptides. Curr Med Chem 14, 1-18. (Pubitemid 46050301)
49. Venugopal D et al. (2010) Novel antimicrobial peptides that exhibit activity against select agents and other drug resistant bacteria. Bioorg & Med Chem 18, 5137-5147.
50. Hicks R P et al. (2007) De Novo design of selective antibiotic peptides by incorporation of unnatural amino acids. J Med Chem 50, 3026-3036. (Pubitemid 47001245)
51. Matsuzaki K. (1998) Magainins as paradigm for the mode of action of pore forming polypeptides. Biochim Biophys Acta 1376, 391-400. (Pubitemid 28517888)
52. Wenk M R, Seelig J (1998) Magainin 2 amide interaction with lipid membranes: calorimetric detection of peptide binding and pore formation. Biochemistry 37, 3909-3916. (Pubitemid 28162948)
53. Yang L et al. (2000) Crystallization of antimicrobial pores in membranes: magainin and protegrin. Biochemical J 79, 2002-2009.
54. Jing W et al. (2003) The structure of the antimicrobial peptide Ac-RRWWRF-NH2 bound to micelles and its interactions with phospholipid bilayers. J Pept Res 61, 219-229. (Pubitemid 36570796)
55. Watson R M et al. (2001) Conformational changes in pediocin AcH upon vesicle binding and approximation of the membrane-bound structure in detergent micelles. Biochemistry 40, 14037-14046. (Pubitemid 33078875)
56. Whitehead T L et al. (1998) Membraneinduced secondary structures of neuropeptides: a comparison of the solution conformations adopted by agonists and antagonists of the mammalian tachykinin NK1 receptor. J Med Chem 41, 1497-1506. (Pubitemid 28198978)
57. Whitehead T L, Hicks R P (2001) Rationale for using simple and complex micelles in polypeptide conformational analysis. Recent Res Devel Med Chem 1, 213-233.
58. Perrine S A et al. (2000) Solution structures in SDS micelles and functional activity at the bullfrog substance P receptor of ranatachykinin peptides. J Med Chem 43, 1741-1753. (Pubitemid 30305007)
59. Young J K, Hicks R P (1994) NMR and molecular modeling investigations of the neuropeptide bradykinin in three different solvent systems: DMSO, 9:1 dioxane/water, and in the presence of 7.4 mM lysophosphatidylcholine micelles. Biopolymers 34, 611-623.
60. Russell A L et al. (2010) Spectroscopic and thermodynamic evidence for antimicrobial peptide membrane selectivity. Chem Phys Lipids 163, 488-497.
61. Porter E A, Weisblum B, Gellman S H (2002) Mimicry of host defense peptides by unnatural oligomers: antimicrobial β-peptides. J Am Chem Soc 124, 7324-7330. (Pubitemid 34670441)
62. Tossi A, Sandri L, Glangaspero A. (2000) Amphipathic β-helical antimicrobial peptides. Biopolymers 55, 4-30.
63. Vasudev P G et al. (2010) Structural chemistry of peptides containing backbone expanded amino acid residues: Conformational features of and hybrid peptides. Chem Reviews 111, 657-687.
64. Turner J et al. (1998) Activites of LL-37, a cathelin-associated antimicrobial peptide of human neutrophilis. Antimicr Agents Chemother 42, 2206-2214. (Pubitemid 28420351)
65. Fuchs P F J et al. (2006) Kinetics and thermodynamics of type VIII β-turn formation: A CD, NMR and microsecond explicit molecular dynamics study of the GDNP tetrapeptide. Biophysical J 90, 2745-2759.
66. Perczel A, Fasman G D (1992) Quantitative analysis of cyclic β-turn models, Prot Sci 1, 378-395. (Pubitemid 23007305)
67. Crisma M et al. (2005) Turn stabilization in short peptides by C-methylated β-amino acids. Biopolymers 80, 279-293. (Pubitemid 40791058)
68. Toniolo C et al. (2002) Control of peptide conformation by the Thorpe-Ingold effect (C-tetrasubstitution). Pept Sci 60, 396-419. (Pubitemid 35000909)
69. Epand R F et al. (2004) Antimicrobial 14-helical β-peptides: Potent bilayer disrupting agents. Biochemistry 43, 9527-9535. (Pubitemid 38955486)
70. Seebach D, Matthews J L (1997) β-Peptides: a surprise at every turn. Chem Commun 2015-2022.
71. White S H, Wimley W C (1998) Hydrophobic interactions of peptides with membrane interfaces. Biochim Biophys Acta 1376, 339-352. (Pubitemid 28517884)
72. Wimley W C, White S H (1993) Membrane partitioning: distinguishing bilayer effects from hydrophobic effect. Biochemistry 32, 6307-6312. (Pubitemid 23208811)
73. Dathe M et al. (1997) Hydrophobicity, hydrophobic moment and angle subtended by charged residues modulate antibacterial and haemolytic activity of amphipathic helical peptides. FEBS Letter 403, 208-213.
74. Kiyota T, Lee S, Suqihara G (1996) Design and synthesis of amphiphilic alpha-helical model peptides with systematically varied hydrophobic-hydrophilic balance and their interaction with lipid-and bio-membranes. Biochemistry 35, 13196-13201.
75. Medina M L et al. (2002) Transient vesicle leakage initiated by synthetic apoptotic peptides derived from the death domain of neurotrophin receptor p75NTR. J Pept Sci 59, 149-158. (Pubitemid 34275835)
76. Wei S-T (2006) Solution structure of a novel tryptophan-rich peptide with bidirectional antimicrobial activity. J Bacteriology 188, 328-334.
77. Hunter H N et al. (2005) The interactions of antimicrobial peptides derived from lysozyme with model membrane systems. Biochim Biophys Acta, 1668, 175-189. (Pubitemid 40298921)
78. Wieprecht T et al. (2000) Membrane binding and pore formation of the antibacterial peptide PGLa: thermodynamic and mechanistic aspects. Biochemistry 39, 442-452. (Pubitemid 30056480)
79. Wieprecht T, Apostolov O, Seelig J (2000) Binding of the antibacterial peptide magainin 2 amide to small and large unilamellar vesicles. Biophys Chem 85, 187-198. (Pubitemid 30445262)
80. Wieprecht T, Beyermann M, Seelig J (2002) Thermodynamics of the coil β-helix transition of amphipathic peptides in a membrane environment: role of vesicle curvature. Biophys Chem 96, 191-201. (Pubitemid 34548232)
81. Wieprecht T, Seelig J (2002) Isothermal titration calorimetry for studying interactions between peptides and lipid membranes. In: Simon S A, McIntosh T J (eds), Peptide-Lipid Interactions, Academic Press, San Diego, pp 32-58.
82. Wen S (2007) Dicynthaurin (ala) monomer interaction with phospholipid bilayers studied by fluorescence leakages and isothermal titration calorimetry. J Phys Chem 111, 6280-6287. (Pubitemid 46966235)
83. Bringezu F et al. (2007) The insertion of the antimicrobial peptide dicynthaurin monomer in model membranes: thermodynamic and structural characterization. Biochemistry 46, 5678-5686. (Pubitemid 46764117)
84. Wieprecht T et al. (1996) Conformation and functional study of magainin 2 in model membrane environment using the new approach of systematic double D-amino acid replacement. Biochemistry 35, 10844-10853. (Pubitemid 26279666)
85. Dathe M (1996) Peptide helicity and membrane surface charge modulate the balance of electrostatic and hydrophobic interactions with lipid bilayers and biological membranes. Biochemistry 35, 12612-12622.
86. Tamba Y, Yamazaki M (2005) Single giant unilamellar vesicle method reveals effect of antimicrobial peptide Magainin 2 on membrane permeability. Biochemistry 44, 15823-15833. (Pubitemid 41746913)
87. Mahe E et al. (1998) Solid-phase synthesis, conformational analysis, and biological activity of AVR9 elicitor peptides of the fungal tomato pathogen Cladosporium fulvum. J Pept Res 52, 482-494. (Pubitemid 29029789)
88. Muri E M et al. (2004) N-t-Boc-amino acid esters of isomannide potential inhibitors of serine proteases. Amino Acids 27, 153-159. (Pubitemid 39506574)
89. Grant G A (2002) Synthetic Peptides, A user's guide, 2nd ed., Oxford University Press, New York, NY.
90. Birr C, Lochinger W, Wieland T (1969) Peptide synthesis. XLII. Comparison of several coupling methods. Justus Liebigs Annalen der Chemie 729, 213-216.
91. Bodanszky M (1985) In search of new methods in peptide synthesis. A review of the last three decades. Internat J Pep Prot Res 25, 449-474.
92. Benoiton N L (2006) Chemistry of Peptide Synthesis, Taylor and Francis (CRC Press), Boca-Raton, FL.
93. Gobbo M et al. (2002) Antimicrobial peptides: synthesis and antibacterial activity of linear and cyclic drosocin and apidaecin 1b analogues. J Med Chem 45, 4494-4505.
94. Whitehead T L, Jones L M, Hicks R P (2001) Effects of the incorporation of CHAPS into SDS micelles on neuropeptide-micelle binding: separation of the role of electrostatic interactions from hydrophobic interactions. Biopolymers 58, 593-605. (Pubitemid 32494238)
95. Whitehead T L, Jones L M, Hicks R P (2004) PFG-NMR investigations of the binding of cationic neuropeptides to anionic and zwitterionic micelles. J Biomol Struct Dyn 21, 567-576. (Pubitemid 38120957)
96. Vogel H J et al. (2002) Towards a structure-function analysis of bovine lactoferricin and related tryptophan-and arginine-containing peptides. Biochem Cell Bio 80, 49-63. (Pubitemid 34194228)