Development of a backbone cyclic peptide library as potential antiparasitic therapeutics using microwave irradiation

Journal of Visualized Experiments

Volumn 2016, Issue 107, 2016, Pages

  Qvit, Nir ^a   Kornfeld, Opher S ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Backbone cyclization; Chemistry; Cyclic peptide; Issue 107; Microwave irradiation; Microwave assisted synthesis; Peptides; Peptidomimetics; Protein protein interactions; Solid phase peptide synthesis

Indexed keywords

ANTIPARASITIC AGENT; CYCLOPEPTIDE; PEPTIDE; PEPTIDE LIBRARY;

ANIMAL; CHEMISTRY; CYCLIZATION; DRUG EFFECTS; HUMAN; LEISHMANIA DONOVANI; MICROWAVE RADIATION; PEPTIDE LIBRARY; PROTEIN CONFORMATION; SYNTHESIS;

ANIMALS; ANTIPARASITIC AGENTS; CYCLIZATION; HUMANS; LEISHMANIA DONOVANI; MICROWAVES; PEPTIDE LIBRARY; PEPTIDES; PEPTIDES, CYCLIC; PROTEIN CONFORMATION;

EID: 85000716806     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/53589     Document Type: Article

References (93)

1. Wells, J. A., & McClendon, C. L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature. 450 (7172), 1001-1009 (2007).
2. Arkin, M. R., & Wells, J. A. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov.(4), 301-317 (2004).
3. Mandell, D. J., & Kortemme, T. Computer-aided design of functional protein interactions. Nat. Chem. Biol. 5 (11), 797-807 (2009).
4. Friedler, A. et al. Backbone cyclic peptide, which mimics the nuclear localization signal of human immunodeficiency virus type 1 matrix protein, inhibits nuclear import and virus production in nondividing cells. Biochemistry. 37 (16), 5616-5622 (1998).
5. Brandman, R., Disatnik, M. H., Churchill, E., & Mochly-Rosen, D. Peptides derived from the C2 domain of protein kinase C epsilon (epsilon PKC) modulate epsilon PKC activity and identify potential protein-protein interaction surfaces. J. Biol. Chem. 282 (6), 4113-4123 (2007).
6. Vlieghe, P., Lisowski, V., Martinez, J., & Khrestchatisky, M. Synthetic therapeutic peptides: science and market. Drug discov today. 15 (1-2), 40-56 (2010).
7. Marx, V. Watching Peptide Drugs Grow Up. Chemical & Engineering News. 83, 17-24 American Chemical Society, (2005).
8. Denicourt, C., & Dowdy, S. F. Medicine. Targeting apoptotic pathways in cancer cells. Science. 305 (5689), 1411-1413 (2004).
9. Qvit, N. et al. Synthesis of a novel macrocyclic library: discovery of an IGF-1R inhibitor. J Comb Chem. 10 (2), 256-266 (2008).
10. Patch, J. A., & Barron, A. E. Mimicry of bioactive peptides via non-natural, sequence-specific peptidomimetic oligomers. Curr. Opin. Chem. Biol. 6 (6), 872-877 (2002).
11. Kessler, H. Peptide Conformations.19. Conformation and Biological-Activity of Cyclic-Peptides. Angew. Chem. Int. Ed. Engl. 21 (7), 512-523 (1982).
12. Gazal, S., Gelerman, G., & Gilon, C. Novel Gly building units for backbone cyclization: synthesis and incorporation into model peptides. Peptides. 24 (12), 1847-1852 (2003).
13. Fesik, S. W. et al. NMR studies of [U-13C]cyclosporin A bound to cyclophilin: bound conformation and portions of cyclosporin involved in binding. Biochemistry. 30 (26), 6574-6583 (1991).
14. Kornfeld, O. S. et al. Mitochondrial Reactive Oxygen Species at the Heart of the Matter: New Therapeutic Approaches for Cardiovascular Diseases. Circ. Res. 116 (11), 1783-1799 (2015).
15. Boguslavsky, V., Hruby, V. J., O’Brien, D. F., Misicka, A., & Lipkowski, A. W. Effect of peptide conformation on membrane permeability. J. Pept. Res. 61 (6), 287-297 (2003).
16. Eguchi, M. et al. Solid-phase synthesis and structural analysis of bicyclic beta-turn mimetics incorporating functionality at the i to i+3 positions. J. Am. Chem. Soc. 121 (51), 12204-12205 (1999).
17. Altstein, M. et al. Backbone cyclic peptide antagonists, derived from the insect pheromone biosynthesis activating neuropeptide, inhibit sex pheromone biosynthesis in moths. J. Biol. Chem. 274 (25), 17573-17579 (1999).
18. Cheng, M. F., & Fang, J. M. Liquid-phase combinatorial synthesis of 1,4-benzodiazepine-2,5-diones as the candidates of endothelin receptor antagonism. J. Comb. Chem. 6 (1), 99-104 (2004).
19. Merrifield, R. B. Solid Phase Peptide Synthesis I. the Synthesis of a Tetrapeptide. J. Am. Chem. Soc. 85 (2149-2154) (1963).
20. Pfeiffer, C. T., & Schafmeister, C. E. Solid phase synthesis of a functionalized bis-peptide using ‘safety catch’ methodology. J Vis Exp.63, e4112 (2012).
21. Coin, I., Beyermann, M., & Bienert, M. Solid-phase peptide synthesis: from standard procedures to the synthesis of difficult sequences. Nat. Protoc. 2 (12), 3247-3256 (2007).
22. Qvit, N. et al. Design and synthesis of backbone cyclic phosphorylated peptides: the IkB model. Biopolymers. 91 (2), 157-168 (2009).
23. Sainlos, M., & Imperiali, B. Tools for investigating peptide-protein interactions: peptide incorporation of environment-sensitive fluorophores through SPPS-based ‘building block’ approach. Nat. Protoc. 2 (12), 3210-3218 (2007).
24. Hilpert, K., Winkler, D. F., & Hancock, R. E. Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat. Protoc. 2 (6), 1333-1349 (2007).
25. Qi, X., Qvit, N., Su, Y. C., & Mochly-Rosen, D. A novel Drp1 inhibitor diminishes aberrant mitochondrial fission and neurotoxicity. J. Cell Sci. 126 (Pt 3), 789-802 (2013).
26. Beaucage, S. L. Solid-phase synthesis of siRNA oligonucleotides. Curr. Opin. Drug Discovery Dev. 11 (2), 203-216 (2008).
27. Dhanawat, M., & Shrivastava, S. K. Solid-Phase Synthesis of Oligosaccharide Drugs: A Review. Mini Rev Med Chem. 9 (2), 169-185 (2009).
28. Seeberger, P. H., & Werz, D. B. Synthesis and medical applications of oligosaccharides. Nature. 446 (7139), 1046-1051 (2007).
29. Plante, O. J., Palmacci, E. R., & Seeberger, P. H. Automated solid-phase synthesis of oligosaccharides. Science. 291 (5508), 1523-1527 (2001).
30. Komiyama, M., Aiba, Y., Ishizuka, T., & Sumaoka, J. Solid-phase synthesis of pseudo-complementary peptide nucleic acids. Nat. Protoc. 3, 646-654 (2008).
31. Christensen, L. et al. Solid-Phase synthesis of peptide nucleic acids. J. Pept. Sci. 1 (3), 175-183 (1995).
32. Qvit, N. et al. Development of bifunctional photoactivatable benzophenone probes and their application to glycoside substrates. Biopolymers. 90 (4), 526-536 (2008).
33. O’Neill, J. C., & Blackwell, H. E. Solid-phase and microwave-assisted syntheses of 2,5-diketopiperazines: small molecules with great potential. Comb Chem High Throughput Screen. 10 (10), 857-876 (2007).
34. Qvit, N., Barda, Y., Shalev, D., & Gilon, C. A Laboratory Preparation of Aspartame Analogs Using Simultaneous Multiple Parallel Synthesis Methodology. J. Chem. Educ. 84 (12), 1988-1991 (2007).
35. Truran, G. A., Aiken, K. S., Fleming, T. R., Webb, P. J., & Markgraf, J. H. Solid phase organic synthesis and combinatorial chemistry: A laboratory preparation of oligopeptides. J. Chem. Educ. 79 (1), 85-86 (2002).
36. Verlander, M. Industrial applications of solid-phase peptide synthesis - A status report. Int. J. Pept. Res. Ther. 13 (1-2), 75-82 (2007).
37. Bray, B. L. Large-scale manufacture of peptide therapeutics by chemical synthesis. Nature reviews. Drug discovery. 2 (7), 587-593 (2003).
38. Qvit, N. Development and therapeutic applications of oligonucleotides and peptides. chimica Oggi/CHEMISTRY today. 29 (2), 4-7 (2011).
39. Carpino, L. A., & Han, G. Y. 9-Fluorenylmethoxycarbonyl Amino-Protecting Group. J. Org. Chem. 37 (22), 3404-3409 (1972).
40. Gedye, R. et al. The use of microwave ovens for rapid organic synthesis. Tetrahedron Lett. 27 (3), 279-282 (1986).
41. Giguere, R. J., Bray, T. L., Duncan, S. M., & Majetich, G. Application of commercial microwave ovens to organic synthesis. Tetrahedron Lett. 27 (41), 4945-4948 (1986).
42. Kappe, C. O., & Dallinger, D. The impact of microwave synthesis on drug discovery. Nature reviews. Drug discovery. 5 (1), 51-63 (2006).
43. Kappe, C. O. Controlled microwave heating in modern organic synthesis. Angew. Chem. Int. Ed. Engl. 43 (46), 6250-6284 (2004).
44. de la Hoz, A., Diaz-Ortiz, A., & Moreno, A. Microwaves in organic synthesis. Thermal and non-thermal microwave effects. Chem. Soc. Rev. 34 (2), 164-178 (2005).
45. Yu, H. M., Chen, S. T., & Wang, K. T. Enhanced coupling efficiency in solid-phase peptide synthesis by microwave irradiation. J. Org. Chem. 57 (18), 4781-4784 (1992).
46. Mingos, D. M. P., & Baghurst, D. R. Tilden Lecture. Applications of microwave dielectric heating effects to synthetic problems in chemistry. Chem. Soc. Rev. 20 (1), 1-47 (1991).
47. Gabriel, C., Gabriel, S., Grant, E.H., Halstead, B.S. J., & Mingos, D. M. P. Dielectric parameters relevant to microwave dielectric heating. Chem. Soc. Rev. 27 (3), 213-224 (1998).
48. Sabatino, G., & Papini, A. M. Advances in automatic, manual and microwave-assisted solid-phase peptide synthesis. Curr. Opin. Drug Discovery Dev. 11 (6), 762-770 (2008).
49. Banerjee, J., Hanson, A. J., Muhonen, W. W., Shabb, J. B., & Mallik, S. Microwave-assisted synthesis of triple-helical, collagen-mimetic lipopeptides. Nat. Protoc. 5 (1), 39-50 (2010).
50. Bacsa, B., & Kappe, C. O. Rapid solid-phase synthesis of a calmodulin-binding peptide using controlled microwave irradiation. Nat. Protoc. 2 (9), 2222-2227 (2007).
51. Murray, J. K., & Gellman, S. H. Parallel synthesis of peptide libraries using microwave irradiation. Nat. Protoc. 2 (3), 624-631 (2007).
52. Palasek, S. A., Cox, Z. J., & Collins, J. M. Limiting racemization and aspartimide formation in microwave-enhanced Fmoc solid phase peptide synthesis. J Pept Sci. 13 (3), 143-148 (2007).
53. Murray, J. K., Aral, J., & Miranda, L. P. Solid-Phase Peptide Synthesis Using Microwave Irradiation. Methods Mol. Biol. Vol. 716 73-88 (2011).
54. Galanis, A. S., Albericio, F., & Grotli, M. Solid-Phase Peptide Synthesis in Water Using Microwave-Assisted Heating. Organic Letters. 11 (20), 4488-4491 (2009).
55. Rizzolo, F., Sabatino, G., Chelli, M., Rovero, P., & Papini, A. M. A convenient microwave-enhanced solid-phase synthesis of difficult peptide sequences: Case study of Gramicidin A and CSF114(Glc). Int. J. Pept. Res. Ther. 13 (1-2), 203-208 (2007).
56. Matsushita, T., Hinou, H., Kurogochi, M., Shimizu, H., & Nishimura, S. Rapid microwave-assisted solid-phase glycopeptide synthesis. Org Lett. 7 (5), 877-880 (2005).
57. Nagaike, F. et al. Efficient microwave-assisted tandem N- to S-acyl transfer and thioester exchange for the preparation of a glycosylated peptide thioester. Org Lett. 8 (20), 4465-4468 (2006).
58. Naruchi, K. et al. Construction and structural characterization of versatile lactosaminoglycan-related compound library for the synthesis of complex glycopeptides and glycosphingolipids. J. Org. Chem. 71 (26), 9609-9621 (2006).
59. Brandt, M., Gammeltoft, S., & Jensen, K. J. Microwave heating for solid-phase peptide synthesis: General evaluation and application to 15- mer phosphopeptides. Int. J. Pept. Res. Ther. 12 (4), 349-357 (2006).
60. Harris, P. W. R., Williams, G. M., Shepherd, P., & Brimble, M. A. The Synthesis of Phosphopeptides Using Microwave-assisted Solid Phase Peptide Synthesis. Int. J. Pept. Res. Ther. 14 (4), 387-392 (2008).
61. Qvit, N. Microwave-assisted Synthesis of Cyclic Phosphopeptide on Solid Support. Chem. Biol. Drug Des. 85 (3), 300-305 (2014).
62. Kato, D., Verhelst, S. H., Sexton, K. B., & Bogyo, M. A general solid phase method for the preparation of diverse azapeptide probes directed against cysteine proteases. Org Lett. 7 (25), 5649-5652 (2005).
63. Olivos, H. J., Alluri, P. G., Reddy, M. M., Salony, D., & Kodadek, T. Microwave-assisted solid-phase synthesis of peptoids. Org Lett. 4 (23), 4057-4059 (2002).
64. Gorske, B. C., Jewell, S. A., Guerard, E. J., & Blackwell, H. E. Expedient synthesis and design strategies for new peptoid construction. Org Lett. 7 (8), 1521-1524 (2005).
65. Grieco, P. et al. Design and microwave-assisted synthesis of novel macrocyclic peptides active at melanocortin receptors: discovery of potent and selective hMC5R receptor antagonists. J. Med. Chem. 51 (9), 2701-2707 (2008).
66. Boutard, N., Jamieson, A. G., Ong, H., & Lubell, W. D. Structure-Activity Analysis of the Growth Hormone Secretagogue GHRP-6 by alpha- and beta-Amino gamma-Lactam Positional Scanning. Chem. Biol. Drug Des. 75 (1), 40-50 (2010).
67. Jamieson, A. G. et al. Positional scanning for peptide secondary structure by systematic solid-phase synthesis of amino lactam peptides. J. Am. Chem. Soc. 131 (22), 7917-7927 (2009).
68. Hossain, M. A., Bathgate, R. A. D., Tregear, G., & Wade, J. D. in Relaxin and Related Peptides: Fifth International Conference. Vol. 1160 Annals of the New York Academy of Sciences. (eds G. D. BryantGreenwood, C. A. Bagnell, & R. A. D. Bathgate) 16-19 (2009).
69. Fowler, S. A., Stacy, D. M., & Blackwell, H. E. Design and synthesis of macrocyclic peptomers as mimics of a quorum sensing signal from Staphylococcus aureus. Org Lett. 10 (12), 2329-2332 (2008).
70. Cemazar, M., & Craik, D. J. Microwave-assisted Boc-solid phase peptide synthesis of cyclic cysteine-rich peptides. J Pept Sci. 14 (6), 683-689 (2008).
71. Miles, S. M., Leatherbarrow, R. J., Marsden, S. P., & Coates, W. J. Synthesis and bio-assay of RCM-derived Bowman-Birk inhibitor analogues. Org Biomol Chem. 2 (3), 281-283 (2004).
72. Murray, J. K. et al. Efficient synthesis of a beta-peptide combinatorial library with microwave irradiation. J. Am. Chem. Soc. 127 (38), 13271-13280 (2005).
73. Churchill, E. N., Qvit, N., & Mochly-Rosen, D. Rationally designed peptide regulators of protein kinase C. Trends Endocrinol. Metab. 20 (1), 25-33 (2009).
74. Mochly-Rosen, D., & Qvit, N. Peptide inhibitors of protein-protein interactions. chimica Oggi/CHEMISTRY today. 28 (1), 14-16 (2010).
75. Qvit, N., & Mochly-Rosen, D. Highly specific modulators of protein kinase C localization: applications to heart failure. Drug Discov. Today Dis. Mech. 7 (2), e87-e93 (2010).
76. Mougneau, E. et al. Expression cloning of a protective Leishmania antigen. Science. 268 (5210), 563-566 (1995).
77. Kelly, B. L., Stetson, D. B., & Locksley, R. M. Leishmania major LACK antigen is required for efficient vertebrate parasitization. J. Exp. Med. 198 (11), 1689-1698 (2003).
78. Choudhury, K. et al. Trypanosomatid RACK1 orthologs show functional differences associated with translation despite similar roles in Leishmania pathogenesis. PLoS One. 6 (6), e20710 (2011).
79. Gonzalez-Aseguinolaza, G., Taladriz, S., Marquet, A., & Larraga, V. Molecular cloning, cell localization and binding affinity to DNA replication proteins of the p36/LACK protective antigen from Leishmania infantum. Eur. J. Biochem. 259 (3), 909-916 (1999).
80. Gump, J. M., & Dowdy, S. F. TAT transduction: the molecular mechanism and therapeutic prospects. Trends Mol. Med. 13 (10), 443-448 (2007).
81. Aletras, A., Barlos, K., Gatos, D., Koutsogianni, S., & Mamos, P. Preparation of the very acid-sensitive Fmoc-Lys(Mtt)-OH. Application in the synthesis of side-chain to side-chain cyclic peptides and oligolysine cores suitable for the solid-phase assembly of MAPs and TASPs. Int. J. Pept. Protein Res. 45 (5), 488-496 (1995).
82. Li, D., & Elbert, D. L. The kinetics of the removal of the N-methyltrityl (Mtt) group during the synthesis of branched peptides. J. Pept. Res. 60 (5), 300-303 (2002).
83. Bourel, L., Carion, O., Gras-Masse, H., & Melnyk, O. The deprotection of Lys(Mtt) revisited. J Pept Sci. 6 (6), 264-270 (2000).
84. Tran, H., Gael, S. L., Connolly, M. D., & Zuckermann, R. N. Solid-phase submonomer synthesis of peptoid polymers and their self-assembly into highly-ordered nanosheets. J Vis Exp. 57, e3373 (2011).
85. Kaiser, E., Colescot, R. L., Bossinge, C. D., & Cook, P. I. Color Test for Detection of Free Terminal Amino Groups in Solid-Phase Synthesis of Peptides. Anal. Biochem. 34 (2), 595-598 (1970).
86. Christensen, T. Qualitative Test for Monitoring Coupling Completeness in Solid-Phase Peptide-Synthesis Using Chloranil. Acta Chem. Scand. Ser.B-Org. Chem. Biochem. 33 (10), 763-766 (1979).
87. Qvit, N., & Crapster, J. A. Peptides that Target Protein-Protein Interactions as an Anti-Parasite Strategy. chimica Oggi/ CHEMISTRY today. 32 (6), 62-66 (2014).
88. Byk, G. et al. Synthesis and biological activity of NK-1 selective, N-backbone cyclic analogs of the C-terminal hexapeptide of substance P. J. Med. Chem. 39 (16), 3174-3178 (1996).
89. King, D. S., Fields, C. G., & Fields, G. B. A cleavage method which minimizes side reactions following Fmoc solid phase peptide synthesis. Int. J. Pept. Protein Res. 36 (3), 255-266 (1990).
90. Pedersen, S. L., Tofteng, A. P., Malik, L., & Jensen, K. J. Microwave heating in solid-phase peptide synthesis. Chemical Society Reviews. 41, 1826-1844 (2012).
91. Colangelo, A. M. et al. A new nerve growth factor-mimetic peptide active on neuropathic pain in rats. J. Neurosci. 28 (11), 2698-2709 (2008).
92. Mesfin, F. B., Andersen, T. T., Jacobson, H. I., Zhu, S., & Bennett, J. A. Development of a synthetic cyclized peptide derived from alpha- fetoprotein that prevents the growth of human breast cancer. J. Pept. Res. 58 (3), 246-256 (2001).
93. Mizejewski, G. J., Muehlemann, M., & Dauphinee, M. Update of alpha fetoprotein growth-inhibitory peptides as biotherapeutic agents for tumor growth and metastasis. Chemotherapy. 52 (2), 83-90 (2006).