Selection-based discovery of macrocyclic peptides for the next generation therapeutics

Current Opinion in Chemical Biology

Volumn 26, Issue , 2015, Pages 34-41

  Morioka, Tomomi ^a   Loik, Nikita D ^a   Hipolito, Christopher J ^a   Goto, Yuki ^a   Suga, Hiroaki ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; LIGAND; MACROCYCLIC COMPOUND; MACROCYCLIC PEPTIDE; UNCLASSIFIED DRUG; ALPHA,ALPHA'-DIBROMOXYLENE; BROMINATED HYDROCARBON; CYCLOPEPTIDE; DISUCCINIMIDYL GLUTARATE; PEPTIDE LIBRARY; SIRT2 PROTEIN, HUMAN; SIRTUIN 2; SUCCINIMIDE DERIVATIVE;

BIOTECHNOLOGY; CYCLIZATION; DRUG DESIGN; PEPTIDE LIBRARY; PROTEIN STRUCTURE; REVIEW; ANTAGONISTS AND INHIBITORS; BIOSYNTHESIS; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DEVELOPMENT; GENE EXPRESSION PROFILING; GENETICS; HUMAN; ISOLATION AND PURIFICATION; PROCEDURES; PROTEIN SYNTHESIS; RIBOSOME;

CYCLIZATION; DRUG DISCOVERY; GENE EXPRESSION PROFILING; HUMANS; HYDROCARBONS, BROMINATED; LIGANDS; MODELS, MOLECULAR; PEPTIDE LIBRARY; PEPTIDES, CYCLIC; PROTEIN BIOSYNTHESIS; RIBOSOMES; SIRTUIN 2; SUCCINIMIDES;

EID: 84923008655     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2015.01.023     Document Type: Review

References (62)

1. Houghten R.A., Pinilla C., Blondelle S.E., Appel J.R., Dooley C.T., Cuervo J.H. Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature 1991, 354:84-86.
2. Schreiber S.L. Target-oriented and diversity-oriented organic synthesis in drug discovery. Science 2000, 287:1964-1969.
3. Prien O. Target-family-oriented focused libraries for kinases-conceptual design aspects and commercial availability. ChemBioChem 2005, 6:500-505.
4. Boldi A.M. Libraries from natural product-like scaffolds. Curr Opin Chem Biol 2004, 8:281-286.
5. Thomas G.L., Wyatt E.E., Spring D.R. Enriching chemical space with diversity-oriented synthesis. Curr Opin Drug Discov Dev 2006, 9:700-712.
6. Vaino A.R., Janda K.D. Euclidean shape-encoded combinatorial chemical libraries. Proc Natl Acad Sci U S A 2000, 97:7692-7696.
7. Sidhu S.S. Phage display in pharmaceutical biotechnology. Curr Opin Biotechnol 2000, 11:610-616.
8. Gold L. mRNA display: diversity matters during in vitro selection. Proc Natl Acad Sci U S A 2001, 98:4825-4826.
9. Vale W., Brazeau P., Grant G., Nussey A., Burgus R., Rivier J., Ling N., Guillemi R. Observations on action mode of somatostatin, hypothalamic factor inhibiting growth-hormone secretion. Comptes Rendus Hebd Des Seances L Acad Des Sci Ser D 1972, 275:2913-2916.
10. Rowe L. Studies of oxytocin and vasopressin-the effect on frog melanophores. Endocrinology 1928, 12:663-670.
11. Su T. Micrococcin-an antibacterial substance formed by a strain of micrococcus. Br J Exp Pathol 1948, 29:473-481.
12. Ehlert F., Neu H.C. In vitro activity of LY146032 (Daptomycin), a new peptolide. Eur J Clin Microbiol 1987, 6:84-90.
13. Barber M., Waterworth P.M. Antibacterial activity of lincomycin and pristinamycin: a comparison with erythromycin. Br Med J 1964, 2:603-606.
14. Rüegger A., Kuhn M., Lichti H., Loosli H.R., Huguenin R., Quiquerez C., von Wartburg A. Cyclosporin A, ein immunsuppressiv wirksamer peptidmetabolit aus trichoderma polysporum (Link ex Pers.) Rifai. Helv Chim Acta 1976, 59:1075-1092.
15. Petcher T.J., Weber H.P., Rüegger A. Crystal and molecular structure of an iodo-derivative of the cyclic undecapeptide cyclosporin A. Helv Chim Acta 1976, 59:1480-1488.
16. Muttenthaler M., Andersson A., de Araujo A.D., Dekan Z., Lewis R.J., Alewood P.F. Modulating oxytocin activity and plasma stability by disulfide bond engineering. J Med Chem 2010, 53:8585-8596.
17. Lemmon M.A., Treutlein H.R., Adams P.D., Brünger A.T., Engelman D.M. A dimerization motif for transmembrane alpha-helices. Nat Struct Biol 1994, 1:157-163.
18. Russ W.P., Engelman D.M. The GxxxG motif: a framework for transmembrane helix-helix association. J Mol Biol 2000, 296:911-919.
19. Sparks A.B., Rider J.E., Hoffman N.G., Fowlkes D.M., Quillam L.A., Kay B.K. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCγ, Crk, and Grb2. Proc Natl Acad Sci U S A 1996, 93:1540-1544.
20. Kurakin A., Hoffman N.G., Kay B.K. Molecular recognition properties of the C-terminal Sh3 domain of the Cbl associated protein, Cap. J Pept Res 1998, 52:331-337.
21. Xu G., Wang W., Groves J.T., Hecht M.H. Self-assembled monolayers from a designed combinatorial library of de novo beta-sheet proteins. Proc Natl Acad Sci U S A 2001, 98:3652-3657.
22. Rickles R.J., Botfield M.C., Weng Z., Taylor J.A., Green O.M., Brugge J.S., Zoller M.J. Identification of Src, Fyn, Lyn, PI3K and Abl SH3 domain ligands using phage display libraries. EMBO J 1994, 13:5598-5604.
23. Haskell-Luevano C., Rosenquist Å., Souers A., Khong K.C., Ellman J.A., Cone R.D. Compounds that activate the mouse melanocortin-1 receptor identified by screening a small molecule library based upon the β-turn. J Med Chem 1999, 42:4380-4387.
24. Cochran A.G., Tong R.T., Starovasnik M.A., Park E.J., McDowell R.S., Theaker J.E., Skelton N.J. A minimal peptide scaffold for β-turn display: optimizing a strand position in disulfide-cyclized β-hairpins. J Am Chem Soc 2001, 123:625-632.
25. Whitby L.R., Ando Y., Setola V., Vogt P.K., Roth B.L., Boger D.L. Design, synthesis, and validation of a β-turn mimetic library targeting protein-protein and peptide-receptor interactions. J Am Chem Soc 2011, 133:10184-10194.
26. Souers A.J., Ellman J.A. β-Turn mimetic library synthesis: scaffolds and applications. Tetrahedron 2001, 57:7431-7448.
27. Nørholm M.H.H., Light S., Virkki M.T.I., Elofsson A., Von Heijne G., Daley D.O. Manipulating the genetic code for membrane protein production: what have we learnt so far?. Biochim Biophys Acta 2012, 1818:1091-1096.
28. Liu C.C., Mack A.V., Brustad E.M., Mills J.H., Groff D., Smider V.V., Schultz P.G. Evolution of proteins with genetically encoded "chemical warheads". J Am Chem Soc 2009, 131:9616-9617.
29. Heinis C., Rutherford T., Freund S., Winter G. Phage-encoded combinatorial chemical libraries based on bicyclic peptides. Nat Chem Biol 2009, 5:502-507.
30. Angelini A., Cendron L., Chen S., Touati J., Winter G., Zanotti G., Heinis C. Bicyclic peptide inhibitor reveals large contact interface with a protease target. ACS Chem Biol 2012, 7:817-821.
31. Chen S., Bertoldo D., Angelini A., Pojer F., Heinis C. Peptide ligands stabilized by small molecules. Angew Chem Int Ed 2014, 53:1602-1606.
32. Baeriswyl V., Calzavarini S., Gerschheimer C., Diderich P., Angelillo-Scherrer A., Heinis C. Development of a selective peptide macrocycle inhibitor of coagulation factor XII toward the generation of a safe antithrombotic therapy. J Med Chem 2013, 56:3742-3746.
33. Fukunaga K., Hatanaka T., Ito Y., Minami M., Taki M. Construction of a crown ether-like supramolecular library by conjugation of genetically-encoded peptide linkers displayed on bacteriophage T7. Chem Commun 2014, 50:3921-3923.
34. Jafari M.R., Deng L., Kitov P.I., Ng S., Matochko W.L., Tjhung K.F., Zeberoff A., Elias A., Klassen J.S., Derda R. Discovery of light-responsive ligands through screening of a light-responsive genetically encoded library. ACS Chem Biol 2014, 9:443-450.
35. Millward S.W., Takahashi T.T., Roberts R.W. A general route for post-translational cyclization of mRNA display libraries. J Am Chem Soc 2005, 127:14142-14143.
36. Guillen Schlippe Y.V., Hartman M.C.T., Josephson K., Szostak J.W. In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors. J Am Chem Soc 2012, 134:10469-10477.
37. Hipolito C.J., Suga H. Ribosomal production and in vitro selection of natural product-like peptidomimetics: the FIT and RaPID systems. Curr Opin Chem Biol 2012, 16:196-203.
38. Ito K., Passioura T., Suga H. Technologies for the synthesis of mRNA-encoding libraries and discovery of bioactive natural product-inspired non-traditional macrocyclic peptides. Molecules 2013, 18:3502-3528.
39. Shimizu Y., Inoue A., Tomari Y., Suzuki T., Yokogawa T., Nishikawa K., Ueda T. Cell-free translation reconstituted with purified components. Nat Biotechnol 2001, 19:751-755.
40. Ohuchi M., Murakami H., Suga H. The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. Curr Opin Chem Biol 2007, 11:537-542.
41. Morimoto J., Hayashi Y., Iwasaki K., Suga H. Flexizymes: their evolutionary history and the origin of catalytic function. Acc Chem Res 2011, 44:1359-1368.
42. Goto Y., Katoh T., Suga H. Flexizymes for genetic code reprogramming. Nat Protoc 2011, 6:779-790.
43. Passioura T., Suga H. Flexizyme-mediated genetic reprogramming as a tool for noncanonical peptide synthesis and drug discovery. Chemistry 2013, 19:6530-6536.
44. Ohta A., Murakami H., Higashimura E., Suga H. Synthesis of polyester by means of genetic code reprogramming. Chem Biol 2007, 14:1315-1322.
45. Kawakami T., Murakami H., Suga H. Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides. Chem Biol 2008, 15:32-42.
46. Goto Y., Suga H. Translation initiation with initiator tRNA charged with exotic peptides. J Am Chem Soc 2009, 131:5040-5041.
47. Yamagishi Y., Shoji I., Miyagawa S., Kawakami T., Katoh T., Goto Y., Suga H. Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library. Chem Biol 2011, 18:1562-1570.
48. Hayashi Y., Morimoto J., Suga H. In vitro selection of anti-Akt2 thioether-macrocyclic peptides leading to isoform-selective inhibitors. ACS Chem Biol 2012, 7:607-613.
49. Morimoto J., Hayashi Y., Suga H. Discovery of macrocyclic peptides armed with a mechanism-based warhead: isoform-selective inhibition of human deacetylase SIRT2. Angew Chem Int Ed 2012, 51:3423-3427.
50. Young T.S., Young D.D., Ahmad I., Louis J.M., Benkovic S.J., Schultz P.G. Evolution of cyclic peptide protease inhibitors. Proc Natl Acad Sci U S A 2011, 108:11052-11056.
51. Hipolito C.J., Tanaka Y., Katoh T., Nureki O., Suga H. A macrocyclic peptide that serves as a cocrystallization ligand and inhibits the function of a MATE family transporter. Molecules 2013, 18:10514-10530.
52. Tanaka Y., Hipolito C.J., Maturana A.D., Ito K., Kuroda T., Higuchi T., Katoh T., Kato H.E., Hattori M., Kumazaki K., et al. Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. Nature 2013, 496:247-251.
53. Kodan A., Yamaguchi T., Nakatsu T., Sakiyama K., Hipolito C.J., Fujioka A., Hirokane R., Ikeguchi K., Watanabe B., Hiratake J., et al. Structural basis for gating mechanisms of a eukaryotic P-glycoprotein homolog. Proc Natl Acad Sci U S A 2014, 111:4049-4054.
54. Yamagata K., Goto Y., Nishimasu H., Morimoto J., Ishitani R., Dohmae N., Takeda N., Nagai R., Komuro I., Suga H., et al. Structural basis for potent inhibition of SIRT2 deacetylase by a macrocyclic peptide inducing dynamic structural change. Structure 2014, 22:345-352.
55. Omote H., Hiasa M., Matsumoto T., Otsuka M., Moriyama Y. The MATE proteins as fundamental transporters of metabolic and xenobiotic organic cations. Trends Pharmacol Sci 2006, 27:587-593.
56. Hipolito C.J., Bashiruddin N.K., Suga H. Protein cocrystallization molecules originating from in vitro selected macrocyclic peptides. Curr Opin Struct Biol 2014, 26:24-31.
57. De Genst E., Silence K., Decanniere K., Conrath K., Loris R., Kinne J., Muyldermans S., Wyns L. Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies. Proc Natl Acad Sci U S A 2006, 103:4586-4591.
58. Rasmussen S.G.F., Choi H.J., Fung J.J., Pardon E., Casarosa P., Chae P.S., Devree B.T., Rosenbaum D.M., Thian F.S., Kobilka T.S., et al. Structure of a nanobody-stabilized active state of the β (2) adrenoceptor. Nature 2011, 469:175-180.
59. Ring A.M., Manglik A., Kruse A.C., Enos M.D., Weis W.I., Garcia K.C., Kobilka B.K. Adrenaline-activated structure of β2-adrenoceptor stabilized by an engineered nanobody. Nature 2013, 502:575-579.
60. Dryden S.C., Nahhas F.A., Nowak J.E., Goustin A.S., Tainsky M.A. Role for human SIRT2 NAD-dependent deacetylase activity in control of mitotic exit in the cell cycle. Mol Cell Biol 2003, 23:3173-3185.
61. +-dependent tubulin deacetylase. Mol Cell 2003, 11:437-444.
62. Vaquero A., Scher M.B., Dong H.L., Sutton A., Cheng H.L., Alt F.W., Serrano L., Sternglanz R., Reinberg D. SirT2 is a histone deacetylase with preference for histone H4 Lys 16 during mitosis. Genes Dev 2006, 20:1256-1261.