Evaluation of the pharmacological descriptors related to the induction of antimicrobial activity by using QSAR and computational mutagenesis

Recent Trends on QSAR in the Pharmaeutical Perceptions

Volumn , Issue , 2012, Pages 63-98

  Avram, Speranta ^a   Buiu, Catalin ^a,b   Duda Seiman, Corina ^c   Borcan, Florin ^d   Duda Seiman, Daniel ^d   Mihailescu, Dan ^a  

^a UNIVERSITY OF BUCHAREST   (Romania)

^b UNIVERSITY POLITEHNICA OF BUCHAREST   (Romania)

^c WEST UNIVERSITY OF TIMISOARA   (Romania)

^d VICTOR BABES UNIVERSITY OF MEDICINE AND PHARMACY   (Romania)

Author keywords

Antimicrobial compounds; Computational mutagenesis; QSAR

Indexed keywords

EID: 84882857278     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.2174/978160805379711201010063     Document Type: Chapter

References (94)

1. Hilpert, K.; Elliott, M.R.; Volkmer-Engert, R. Sequence Requirements and an Optimization Strategy for Short Antimicrobial Peptides. Chem. Biol., 2006, 13(10), 1101-1107.
2. Rodriguez, C.H.; De Ambrosio, A.; Bajuk, M. In vitro antimicrobials activity against endemic Acinetobacter baumannii multiresistant clones. J. Infect. Dev. Ctries., 2010, 4(3), 164-167.
3. Brandenburg, K.; Schromm, A.B.; Gutsmann, T. Endotoxins: relationship between structure, function and activity. Subcell Biochem., 2010, 53, 53-67.
4. Bowdish, D.M.; Hancock, R.E. Anti-endotoxin properties of cationic host defence peptides and proteins. J. Endotoxin Res., 2005, 11(3), 230-236.
5. Periti, P.; Mazzei, T. New criteria for selecting the proper antimicrobial chemotherapy for severe sepsis and septic shock. Int. J. Antimicrob. Agents, 1999, 12, 97-105.
6. Zhu, W.L.; Song, Y.M.; Park, Y. Substitution of the leucine zipper sequence in melittin with peptoid residues affects self-association, cell selectivity and mode of action. Biochimica et Biophysica Acta, 2007, 1768, 1506-1517.
7. Zanetti, M.; Gennaro, R.; Skerlavaj, B.; Tomasinsig, L.; Circo, R. Cathelicidin peptides as candidates for a novel class of antimicrobials. Curr. Pharm. Des., 2002, 8, 779-793.
8. Zasloff, M. Antimicrobial peptides of multicellular organisms. N. Engl. J. Med., 2002, 347(15), 1199-2000.
9. Hancock, E.W.; Scott, MG. The role of antimicrobial peptides in animal defenses. Proc. Natl. Acad. Sci. U.S.A., 2000, 97, 8856-8861.
10. Maher, S.; McClean, S. Investigation of the cytotoxicity of eukaryotic and prokaryotic antimicrobial peptides in intestinal epithelial cells in vitro. Biochem Pharmacol., 2006, 71(9), 1289-1298.
11. Rosenfeld, Y.; Lev, N.; Shai, Y. Effect of the hydrophobicity to net positive charge ratio on antibacterial and anti-endotoxin activities of structurally similar antimicrobial peptides. Biochemistry, 2010, 49(5), 853-861.
12. Harris, F.; Dennison, S.R.; Phoenix, D.A. Anionic antimicrobial peptides from eukaryotic organisms. Curr. Protein Pept. Sci., 2009, 10(6), 585-606.
13. Hancock, R.E.; Rozek, A. Role of membranes in the activities of antimicrobial cationic peptides. FEMS Microbiol. Lett. 2002, 206, 143-149.
14. Jin, Y.; Hammer, J.; Pate, M. Antimicrobial activities and structures of two linear cationic peptide families with various amphipathic beta-sheet and alpha-helical potentials. Antimicrob. Agents Chemother., 2005, 49(12), 4957-4964.
15. Mahalka, A.K.; Kinnunen, P.K. Binding of amphipathic alpha-helical antimicrobial peptides to lipid membranes: lessons from temporins B and L. Biochim Biophys Acta, 2009, 1788(8), 1600-1609.
16. Subasinghage, A.P.; Conlon, J.M.; Hewage, C.M. Development of potent anti-infective agents from Silurana tropicalis: conformational analysis of the amphipathic, alpha-helical antimicrobial peptide XT-7 and its non-haemolytic analogue [G4K]XT-7. Biochim. Biophys. Acta, 2010, 1804(4), 1020-1028.
17. Chen, Y.; Mant, C.T.; Farmer, S.W.; Hancock, R.E.; Vasil, M.L.; Hodges, R.S. Rational design of a-helical antimicrobial peptides with enhanced activities and specificity/therapeutic index. J. Biol. Chem., 2005, 280, 12316-12329.
18. Auvynet, C.; Joanne, P.; Bourdais, J.; Nicolas, P.; Lacombe, C.; Rosenstein, Y. Dermaseptin DA4, although closely related to dermaseptin B2, presents chemotactic and Gram-negative selective bactericidal activities. FEBS J., 2009, 276(22), 6773-6786.
19. Davison, G.; Allgrove, J.; Gleeson, M. Salivary antimicrobial peptides (LL-37 and alphadefensins HNP1-3), antimicrobial and IgA responses to prolonged exercise. Eur. J. Appl. Physiol., 2009, 106(2), 277-284.
20. Hunter, H.N.; Fulton, D.B.; Ganz, T.; Vogel, H.J. The solution structure of human hepcidin, a peptide hormone with antimicrobial activity that is involved in iron uptake and hereditary hemochromatosis. J. Biol. Chem., 2002, 277, 37597.
21. Guenther, S.; Grobbel, M.; Heidemanns, K. First insights into antimicrobial resistance among faecal Escherichia coli isolates from small wild mammals in rural areas. Sci. Total Environ., 2010, 408 , 3519-3522.
22. Matsuzaki, K.; Murase, O.; Fujii, N.; Miyajima, K. Antimicrobial peptide, magainin 2, induced rapid flip-flop of phospholipids coupled with pore formation and peptide translocation. Biochemistry, 1996, 35, 11361-11368.
23. Powers, J.P.; Tan, A.; Ramamoorthy, A.; Hancock, R.E. Solution structure and interaction of the antimicrobial polyphemusins with lipid membranes. Biochemistry, 2005, 44(47), 15504-15513.
24. Epand, R.F.; Maloy, W.L.; Ramamoorthy, A.; Epand, R.M. Probing the "charge cluster mechanism" in amphipathic helical cationic antimicrobial peptides. Biochemistry, 2010, 49(19), 4076-4084.
25. Driessen, A.J.; van den Hooven, H.W.; Kuiper, W.; van de Kamp, M.; Sahl, H.G.; Konings, W.N. Mechanistic studies of lantibiotic-induced permeabilization of phospholipids vesicles. Biochemistry, 1995, 34, 1606-1614.
26. Chatterjee, C.; Paul, M.; Xie, L.; van der Donk, W.A. Biosynthesis and mode of action of lantibiotics. Chem. Rev., 2005, 105, 633-684.
27. Hwang, P.M.; Vogel, H.J. Structure-function relationships of antimicrobial peptides. Biochem. Cell Biol., 1998, 76, 235-246.
28. Yamamoto, N.; Tamura, A. Designed low amphipathic peptides with alpha-helical propensity exhibiting antimicrobial activity via a lipid domain formation mechanism. Peptides, 2010, 31(5), 794-805.
29. Park, C.; Lee, D.G. Melittin induces apoptotic features in Candida albicans. Biochem. Biophys. Res. Commun., 2010, 394(1), 170-172.
30. Vooturi, S.K.; Firestine, S.M. Synthetic membrane-targeted antibiotics. Curr. Med. Chem., 2010, 17(21), 2292-3000.
31. Pan, C.Y.; Rajanbabu, V.; Chen, J.Y.; Her, G.M.; Nan, F.H. Evaluation of the epinecidin-1 peptide as an active ingredient in cleaning solutions against pathogens. Peptides, 2010, 31(8), 1449-1458.
32. Bergsson, G.; Reeves, E.P.; McNally, P. LL-37 complexation with glycosaminoglycans in cystic fibrosis lungs inhibits antimicrobial activity, which can be restored by hypertonic saline. J. Immunol., 2009, 183(1), 543-551.
33. Leontiadou, H.; Mark, A.E.; Marrink, S.J. Antimicrobial peptides in action. J. Am. Chem. Soc., 2006, 128(37), 12156-12161.
34. Epand, R.F.; Maloy, L.; Ramamoorthy, A.; Epand, R.M. Amphipathic helical cationic antimicrobial peptides promote rapid formation of crystalline States in the presence of phosphatidylglycerol: lipid clustering in anionic membranes. Biophys. J., 2010, 98(11), 2564-2573.
35. Cruciani, R.A.; Barker, J.L.; Zasloff, M.; Chen, H.C.; Colamonici, O. Antibiotic magainins exert cytolytic activity against transformed cell lines through channel formation. Proc. Nat. Acad. Sci. U.S.A., 1991, 88(9), 3792-3796.
36. Matsuzaki, K.; Murase, O.; Miyajima, K. Kinetics of pore formation by an antimicrobial peptide, magainin 2, in phospholipid bilayers. Biochemistry, 1995, 34(39), 12553-12559.
37. Boggs, J.M.; Jo, E.; Polozov, I.V. Effect of magainin, class L, and class A amphipathic peptides on fatty acid spin labels in lipid bilayers. Biochim. Biophys. Acta., 2001, 1511(1), 28-41.
38. Matsuzaki, K.; Murase, O.; Fujii, N.; Miyajima, K. An antimicrobial peptide, magainin 2, induced rapid flip-flop of phospholipids coupled with pore formation and peptide translocation. Biochemistry, 1996, 35, 11361-11368.
39. Imura, Y.; Choda, N.; Matsuzaki, K. Magainin 2 in action: distinct modes of membrane permeabilization in living bacterial and mammalian cells. Biophys. J., 2008, 95(12), 5757- 5765.
40. Kulagina, N.V.; Shaffer, K.M.; Anderson, G.P.; Ligler, F.S.; Taitt, C.R. Antimicrobial peptide-based array for Escherichia coli and Salmonella screening. Anal. Chim. Acta, 2006, 575(1), 9-15.
41. Laughlin, T.F.; Ahmad, Z. Inhibition of Escherichia coli ATP synthase by amphibian antimicrobial peptides. Int. J. Biol. Macromol., 2010, 46(3), 367-374.
42. Baginski, M.; Resat, H.; Borowski, E. Comparative molecular dynamics simulations of amphotericin B-cholesterol/ergosterol membrane channels. Biochim. Biophys. Acta, 2002, 1567(1-2), 63-78.
43. Mally, M.; Majhenc, J.; Svetina, S.; Zeks, B. The response of giant phospholipid vesicles to pore-forming peptide melittin. Biochim. Biophys. Acta, 2007, 1768(5), 1179-1189.
44. Lam, Y.H.; Wassal, S.R.; Morton, C.J.; Smith, R.; Separovic, F. Solid-state NMR structure determination of melittin in a lipid environment. Biophys. J., 2001, 81, 2752-2761.
45. Hristova, K.; Dempsey, C.E.; White, S.H. Structure, location and lipid perturbations of melittin at the membrane interface. Biophys. J., 2001, 80, 801-811.
46. Olaru, A.; Gheorghiu, M.; David, S.; Wohland, T.; Gheorghiu E. Assessment of the multiphase interaction between a membrane disrupting peptide and a lipid membrane. J. Phys. Chem. B., 2009; 113(43); 14369-14380.
47. Mihajlovic, M.; Lazaridis, T. Antimicrobial peptides bind more strongly to membrane pores. Biochim. Biophys. Acta, 2010, 1798(8), 1494-1502.
48. Gevod, V.S.; Birdi, K.S. Melittin and the 8-26 fragment. Differences in ionophoric properties as measured by monolayer method. Biophys. J., 1984, 45, 1079-1083.
49. Werkmeister, J.A.; Kirkpatrick, A.; McKenzie, J.A.; Rivett, D.E. The effect of sequence variations and structure on the cytolytic activity of melittin peptides. Biochim. Biophys. Acta, 1993, 1157(1), 50-54.
50. Hongbiao, W.; Baolong, N.; Mengkui, X.; Lihua, H.; Weifeng, S.; Zhiqi, M. Biological activities of cecropin B-thanatin hybrid peptides. J. Pept. Res., 2005, 66(6), 382-386.
51. Yu, F.; Wang, J.; Zhang, P.; Hong, Y.; Liu, W. Fusion expression of cecropin B-like antibacterial peptide in Escherichia coli and preparation of its antiserum. Biotechnol. Lett., 2010, 32(5), 669-673.
52. Jan, P.S.; Huang, H.Y.; Chen, H.M. Expression of a synthesized gene encoding cationic peptide cecropin B in transgenic tomato plants protects against bacterial diseases. Appl. Environ. Microbiol., 2010, 76(3), 769-775.
53. Weinberg, E.D. Human lactoferrin: a novel therapeutic with broad spectrum potential. J. Pharm. Pharmacol., 2001, 53, 1303-1310.
54. Omata, Y.; Satake, M.; Maeda, R. Reduction of the infectivity of Toxoplasma gondii and Eimeria stiedai sporozoites by treatment with bovine lactoferricin. J. Vet. Med. Sci., 2001, 63, 187-190.
55. Jenssen, H.; Andersen, J.H.; Uhlin-Hansen, L.; Gutteberg, T.J.; Rekdal, Ø. Anti-HSV activity of lactoferricin analogues is only partly related to their affinity for heparan sulfate. Antiviral Res., 2004, 61(2), 101-109.
56. Cerovsky, V.; Slaninova, J.; Fucik, V. New potent antimicrobial peptides from the venom of Polistinae wasps and their analogs. Peptides, 2008, 29(6), 992-1003.
57. Mendes, M.A.; De Sousa, B.M.; Marques, M.R.; Palma, M.S. Structural and biological characterization of two novel peptides from the venom of the neotropical social wasp Agelaia pallipes palipes. Toxicon., 2004, 44, 67-74.
58. dos Santos Cabrera, M.P.; Costa, S.T.; de Souza, B.M.; Palma, M.S.; Ruggiero, J.R.; Ruggiero, N.J. Selectivity in the mechanism of action of antimicrobial mastoparan peptide Polybia-MP1. Eur. Biophys. J., 2008, 37(6), 879-891.
59. Akamatsu, M. Current state and perspectives of 3D-QSAR. Curr. Top. Med. Chem., 2002; 2; 1381-1394.
60. Frederic, C.; Cristine, A.C.; Erwan, A. JLK inhibitors: isocoumarin compounds as putative probes to selectively target the gamma-secretase pathway. Curr. Alzheimer Res., 2005, 2, 327-334.
61. Garg, A.; Tewari, R.; Raghava, G.P. KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials. BMC Bioinformatics., 2010, 11, 125.
62. Gundersen, E.; Fan, K.; Haas, K. Molecular-modeling based design, synthesis, and activity of substituted piperidines as gamma-secretase inhibitors. Bioorg. Med. Chem. Lett., 2005, 15, 1891-1894.
63. Prasad, C.V.; Vig, S.; Smith, D.W. 2,3-Benzodiazepin-1,4-diones as peptidomimetic inhibitors of gamma-secretase. Bioorg. Med. Chem. Lett., 2004, 14, 3535-3538.
64. Park, H.; Lee, S. Determination of the active site protonation state of beta-secretase from molecular dynamics simulation and docking experiment: implications for structure-based inhibitor design. J. Am. Chem. Soc., 2003, 125, 16416-16422.
65. Hu, J.; Cwi, C.L.; Smiley, D.L. Design and synthesis of statine-containing BACE inhibitors. Bioorg. Med. Chem. Lett., 2003, 13, 4335-4339.
66. Ghosh, A.K.; Devasamudram, T.; Hong, L. Structure-based design of cycloamide-urethanederived novel inhibitors of human brain memapsin 2 (beta-secretase). Bioorg. Med. Chem. Lett., 2005, 15, 15-20.
67. Snyder, R.D.; Hendry, L.B. Toward a greater appreciation of noncovalent chemical/DNA interactions: application of biological and computational approaches. Environ. Mol. Mutagen., 2005, 45, 100-105.
68. Zuo, Z.; Luo, X.; Zhu, W. Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with beta-secretase. Bioorg. Med. Chem., 2005, 13, 2121-2131.
69. Hayashi, Y.; Sakaguchi, K.; Kobayashi, M.; Kikuchi, Y.; Ichiishi, E. Molecular evaluation using in silico protein interaction profiles. Bioinformatics, 2003, 19, 1514-1523.
70. Oprea, T.I.; Waller, C.L.; Marshall, G.R. Three-dimensional quantitative structure-activity relationship of human immunodeficiency virus (I) protease inhibitors. 2. Predictive power using limited exploration of alternate binding modes. J. Med. Chem., 1994, 37, 2206-2215.
71. Cramer, R.D.3rd; Patterson, D.E.; Bunce, J.D. Recent advances in comparative molecular field analysis (CoMFA). Prog. Clin. Biol. Res., 1989, 291, 161-165.
72. Khedkar, S.A.; Malde, A.K.; Coutinho, E.C. CoMFA study of distamycin analogs binding to the minor-groove of DNA: a unified model for broad-spectrum activity. J. Mol. Model., 2007, 13(10), 1099-1108.
73. Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem., 1994, 37, 4130-4146.
74. Carosati, E.; Lemoine, H.; Spogli, R. Binding studies and GRIND/ALMOND-based 3D QSAR analysis of benzothiazine type K(ATP)-channel openers. Bioorg. Med. Chem., 2005, 13, 5581-5591.
75. Leontiadou, H.; Mark, A.E.; Marrink, S.J. Antimicrobial peptides in action. J. Am. Chem. Soc., 2006, 128(37), 12156-12161.
76. Manna, M.; Mukhopadhyay, C. Cause and effect of melittin-induced pore formation: a computational approach. Langmuir, 2009, 25(20), 12235-12242.
77. Neumann, A.; Czub, J.; Baginski, M. On the possibility of the amphotericin B-sterol complex formation in cholesterol- and ergosterol-containing lipid bilayers: a molecular dynamics study. J. Phys. Chem. B, 2009, 113(48), 15875-15885.
78. Mikut, R. Computer-based analysis, visualization, and interpretation of antimicrobial peptide activities. Methods Mol. Biol., 2010, 618, 287-299.
79. Montesinos, E.; Bardají, E. Synthetic antimicrobial peptides as agricultural pesticides for plant-diseasencontrol. Chem. Biodivers., 2008, 5(7), 1225-1237.
80. Barroso, J.M.; Besalú, E. Design of experiments applied to QSAR: ranking a set of compounds and establishing a statistical significance test. J. Mol. Struct., 2005, 727, 89-96.
81. Tong, J.; Liu, S.; Zhou, P.; Wu, B.; Li, Z. A novel descriptor of amino acids and its application in peptide QSAR. Theor. Biol., 2008, 253(1), 90-97.
82. Todeschini, R.; Gramatica, P.; Provenzani, R. Weighted holistic invariant molecular descriptor. Part 2. Theory development and applications on modeling physicochemical properties of polyaromatic hydrocarbons. Chemom. Intell. Lab. Syst., 1995, 27(2), 221-229.
83. Gramatica, P.; Corradi, M.; Consonni, V. Modeling and predication of soil sorption coefficients of nonionic organic pesticides by molecular descriptors. Chemosphere, 2000, 41(5), 763-777.
84. Di Marzio, W.; Galassi, S.; Todeschini, R.; Consolaro, F. Traditional versus WHIM molecular descriptors in QSAR approaches applied to fish toxicity studies. Chemosphere, 2001, 44(3), 401-406.
85. Tong, J.B.; Zhang, S.W. A new 3D descriptor of amino acids and its application in quantitative structure activity relationship of peptide drugs. Acta Phys. Chim. Sin., 2007, 23(1), 43-47.
86. Jenssen, H.; Fjell, C.D.; Cherkasov, A.; Hancock, R.E. QSAR modeling and computeraided design of antimicrobial peptides. J. Pept. Sci., 2008, 14(1), 110-114.
87. Hilpert, K.; Elliott, M.R.; Volkmer-Engert, R. Sequence requirements and an optimization strategy for short antimicrobial peptides. Chem. Biol., 2006, 13, 1101-1107.
88. Hilper, K.; Volkmer-Engert, R.; Walter, T.; Hancock, R.E.W. High throughput generation of small antibacterial peptides with improved activity. Nat. Biotechnol., 2005, 23, 1008-1012.
89. Collantes, E.R.; Dunn, W.J. Amino acid side chain descriptors for quantitative structure activity relationship studies of peptide analogues. J. Med. Chem., 1995, 38, 2705-2713.
90. Asthana, N.; Yadav, S.P.; Ghosh, J.K. Dissection of antibacterial and toxic activity of melittin: a leucine zipper motif plays a crucial role in determining its hemolytic activity but not antibacterial activity. J. Biol. Chem., 2004, 279(53), 55042-55050.
91. Boeckle, S.; Fahrmeir, J.; Roedl, W.; Ogris, M.; Wagner, E. Melittin analogs with high lytic activity at endosomal pH enhance transfection with purified targeted PEI polyplexes. Journal of Controlled Release, 2006, 112(2), 240-248.
92. Krajewski, K.; Marchand, C.; Long, Y.Q.; Pommier, Y.; Roller, P.P. Synthesis and HIV-1 integrase inhibitory activity of dimeric and tetrameric analogs of indolicidin. Bioorg. Med. Chem. Lett., 2004, 14, 5595-5598.
93. Sybyl by Tripos [Accessed on: 23rd May 2010].
94. Millions of documents and books. http://www.scribd.com. [Accessed May 2010].