MRNA display: From basic principles to macrocycle drug discovery

Drug Discovery Today

Volumn 19, Issue 4, 2014, Pages 388-399

  Josephson, Kristopher ^a   Ricardo, Alonso ^a   Szostak, Jack W ^b  

^a Ra Pharmaceuticals   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AURILIDE; COTRANSIN; CYCLOSPORIN; ENZYME INHIBITOR; LARGAZOLE; MACROCYCLIC COMPOUND; MONOCLONAL ANTIBODY; NATURAL PRODUCT; PROTEIN INHIBITOR; PUROMYCIN; TACROLIMUS; TRANSFER RNA; UNCLASSIFIED DRUG; BIOLOGICAL PRODUCT; MESSENGER RNA; PEPTIDE; PEPTIDE LIBRARY;

CHEMICAL MODIFICATION; CHEMICAL REACTION; COMPLEX FORMATION; CYCLIZATION; DRUG BINDING; DRUG BIOAVAILABILITY; DRUG DESIGN; DRUG PENETRATION; DRUG SCREENING; DRUG SELECTIVITY; DRUG STRUCTURE; DRUG SYNTHESIS; GENE TECHNOLOGY; IN VITRO STUDY; MRNA DISPLAY; PEPTIDE LIBRARY; REVIEW; CHEMISTRY; DRUG DEVELOPMENT;

BIOLOGICAL PRODUCTS; DRUG DISCOVERY; PEPTIDE LIBRARY; PEPTIDES; RNA, MESSENGER;

EID: 84899578138     PISSN: 13596446     EISSN: 18785832     Source Type: Journal    
DOI: 10.1016/j.drudis.2013.10.011     Document Type: Review

References (55)

1. J. Grünewald, and M.A. Mahariel Chemoenzymatic and template-directed synthesis of bioactive macrocyclic peptides Microbiol. Mol. Biol. Rev. 70 2006 121 146
2. C. Hertweck The biosynthetic logic of polyketide diversity Angew. Chem. Int. Ed. 48 2009 4688 4716
3. S. Fahnestock, and A. Rich Ribosome-catalyzed polyester formation Science 23 1971 340 343
4. L. Du et al. Hybrid peptide-polyketide natural products: biosynthesis and prospects toward engineering novel molecules Metab. Eng. 3 2001 78 95
5. A.A. Bowers Biochemical and biosynthetic preparation of natural product-like cyclic peptide libraries Med. Chem. Commun. 3 2012 905 915
6. T. Kawakami Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids J. Am. Chem. Soc. 130 2008 16861 16863
7. J.A. McIntosh et al. Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds Nat. Prod. Rep. 26 2009 537 559
8. S. Caboche et al. Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity J. Bacteriol. 192 2010 5143 5150
9. J. Chatterjee et al. N-methylation of peptides and proteins: an important element for modulating biological functions Angew. Chem. Int. Ed. 52 2013 254 269
10. R. Mahalakshmi, and P. Balaram The use of d-amino acids in peptide design R. Konno, In d-Amino Acids: A New Frontier in Amino Acid and Protein Research 1st edn 2007 Nova Science Publishers 415 430
11. N. Bionda et al. Effects of cyclic lipodepsipeptide structural modulation on stability, antibacterial activity and human cell toxicity ChemMedChem 7 2012 871 882
12. L. Zhang, and G. Bulaj Converting peptides into drug leads by lipidation Curr. Med. Chem. 19 2012 1602 1618
13. J.E. Bock et al. Getting in shape: controlling peptide bioactivity and bioavailability using conformational constrains ACS Chem. Biol. 8 2013 488 499
14. J. Chatterjee et al. N-Methylated cyclic pentaalanine peptides as template structures J. Am. Chem. Soc. 128 2006 15164 15172
15. T.R. White et al. On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds Nat. Chem. Biol. 7 2011 810 817
16. J. Chatterjee et al. N-methylation of peptides: a new perspective in medicinal chemistry Acc. Chem. Res. 41 2008 1331 1342
17. A.C. Rand Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance Med. Chem. Commun. 3 2012 1282 1289
18. J.G. Beck Intestinal permeability of cyclic peptides: common key backbone motifs identified J. Am. Chem. Soc. 134 2012 12125 12133
19. S.S.F. Leung Testing physical models of passive membrane permeability J. Chem. Inf. Model. 52 2012 1621 1636
20. T. Rezai et al. Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers J. Am. Chem. Soc. 128 2006 2510 2511
21. H. Loosli et al. Peptide conformations. Part 31. The conformation of cyclosporine A in the crystal and in solution Helv. Chim. Acta 68 1985 682 704
22. R.W. Roberts, and J.W. Szostak RNA-peptide fusions for the in vitro selection of peptides and proteins Proc. Natl. Acad. Sci. U. S. A. 94 1997 12297 12302
23. S.S. Sidhu et al. Phage display for selection of novel binding peptides Methods Enzymol. 328 2000 333 363
24. Y. Shimizu et al. Cell-free translation reconstituted with purified components Nat. Biotechnol. 19 2001 751 755
25. A.C. Forster et al. A simplified reconstitution of mRNA-directed peptide synthesis: activity of the epsilon enhancer and an unnatural amino acid Anal. Biochem. 297 2001 60 70
26. K. Josephson et al. Ribosomal synthesis of unnatural peptides J. Am. Chem. Soc. 127 2005 11727 11735
27. M.C.T. Hartman et al. An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides PLoS ONE 10 2007 e972
28. A. Ohta et al. Polymerization of α-hydroxy acids by ribosomes ChemBioChem 9 2008 2773 2778
29. J. Ellman et al. Biosynthetic method for introducing unnatural amino acids site specifically into proteins Methods Enzymol. 202 1991 301 336
30. C. Merryman, and R. Green Transformation of aminoacyl tRNAs for the in vitro selection of "drug like" molecules Chem. Biol. 11 2004 575 582
31. Y. Goto et al. Flexizymes for genetic code reprogramming Nat. Protoc. 6 2011 779 790
32. T. Fujino et al. Reevaluation of the d-amino acid compatibility with the elongation event in translation J. Am. Chem. Soc. 135 2013 1830 1837
33. T. Kawakami et al. Messenger RNA-programmed incorporation of multiple N-methyl-amino-acids into linear and cyclic peptides Chem. Biol. 15 2008 32 42
34. K. Muller et al. Fluorine in pharmaceuticals looking beyond intuition Science 317 2007 1881 1886
35. F.P. Seebeck, and J.W. Szostak Ribosomal synthesis of dehydroalanine-containing peptides J. Am. Chem. Soc. 128 2006 7150 7151
36. Y. Goto et al. Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides ACS Chem. Biol. 3 2008 120 129
37. Y.V. Guillen-Schlippe et al. In vitro selection of highly modified cyclic peptides that act as tight inhibitors J. Am. Chem. Soc. 134 2012 10469 10477
38. S.W. Millward et al. A general route for post-translational cyclization of mRNA display libraries J. Am. Chem. Soc. 127 2005 14142 14143
39. Q. Wang et al. Bioconjugation by copper(I)-catalyzed azide-alkyne [3+2] cycloaddition J. Am. Chem. Soc. 125 2003 3192 3193
40. S. Li, and R.W. Roberts A novel strategy for in vitro selection of peptide-drug conjugates Chem. Biol. 10 2003 233 239
41. D.E. Scott et al. Fragment-based approaches in drug discovery and chemical biology Biochemistry 51 2012 4990 5003
42. Y. Hayashi et al. In vitro selection of anti-Akt2 thioether-macrocyclic peptides leading to isoform-selective inhibitors ACS Chem. Biol. 7 2012 607 613
43. Y. Yamagishi et al. Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library Chem. Biol. 18 2011 1562 1570
44. J. Morimoto et al. Discovery of macrocyclic peptides armed with a mechanism-based war head: isoform-selective inhibition of human deacetylase SIRT2 Angew. Chem. 51 2012 3423 3427
45. T. Kawakami et al. In vitro selection of multiple libraries created by genetic code reprogramming to discover macrocyclic peptides that antagonize VEGFR2 activity in living cells ACS Chem. Biol. 2013 [Epub ahead of print]
46. F.J. LaRiviere et al. Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation Science 294 2001 165 168
47. K. Ieong et al. Inefficient delivery but fast peptide bond formation of unnatural l-aminoacyl-tRNAs in translation J. Am. Chem. Soc. 134 2012 17955 17962
48. S.J. Chapman et al. Histidine 66 in Escherichia coli elongation factor Tu selectively stabilizes aminoacyl-tRNAs J. Biol. Chem. 287 2012 1229 1234
49. S. Lee et al. A facile strategy for selective incorporation of phosphoserine into histones Angew. Chem. 52 2013 5771 5775
50. J.M. Schrader et al. Understanding the sequence specificity of tRNA binding to elongation factor Tu using tRNA mutagenesis J. Mol. Biol. 386 2009 1255 1264
51. H. Neumann et al. Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome Nature 464 2010 441 444
52. S. Sato et al. Marine natural product aurilide activates the OPA1-mediated apoptosis by binding to prohibitin Chem. Biol. 18 2011 131 139
53. Y. Liu et al. A histone deacetylase inhibitor, largazole, decreases liver fibrosis and angiogenesis by inhibiting transforming growth factor-β and vascular endothelial growth factor signaling Liver Int. 33 2013 504 515
54. J.L. Garrison et al. A substrate-specific inhibitor of protein translocation into the endoplasmatic reticulum Nature 436 2005 285 289
55. R. Venkataramanan et al. Pharmacokinetics of FK506 following oral administration: a comparison of FK506 and cyclosporine Transplant. Proc. 23 1991 931 933