Synthetic fermentation of bioactive non-ribosomal peptides without organisms, enzymes or reagents

Nature Chemistry

Volumn 6, Issue 10, 2014, Pages 877-884

  Huang, Yi Lin ^a   Bode, Jeffrey W ^a,b  

^a ETH ZURICH   (Switzerland)

^b NAGOYA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIVIRUS AGENT; ISOXAZOLE DERIVATIVE; NS3 PROTEIN, HEPATITIS C VIRUS; PEPTIDE; PROTEINASE INHIBITOR; VIRUS PROTEIN;

ANTAGONISTS AND INHIBITORS; BACTERIA; BATCH CELL CULTURE; CHEMISTRY; METABOLISM;

ANTAGONISTS AND INHIBITORS; ANTIVIRAL AGENTS; BACTERIA; BATCH CELL CULTURE TECHNIQUES; CHEMISTRY; ISOXAZOLES; METABOLISM; PEPTIDES; PROTEASE INHIBITORS; VIRAL NONSTRUCTURAL PROTEINS;

EID: 84964282431     PISSN: 17554330     EISSN: 17554349     Source Type: Journal    
DOI: 10.1038/nchem.2048     Document Type: Article

References (50)

1. Fischbach, M. A. & Walsh, C. T. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem. Rev. 106, 3468-3496 (2006).
2. Marahiel, M. A., Stachelhaus, T. & Mootz, H. D. Modular peptide synthetases involved in nonribosomal peptide synthesis. Chem. Rev. 97, 2651-2674 (1997).
3. Roberts, A. A., Ryan, K. S., Moore, B. S. & Gulder, T. A. M. Total (bio)synthesis: strategies of nature and of chemists. Top. Curr. Chem. 297, 149-203 (2010).
4. vanWageningen, A. M. A. et al. Sequencing and analysis of genes involved in the biosynthesis of a vancomycin group antibiotic. Chem. Biol. 5, 155-162 (1998).
5. Weber, G., Schorgendorfer, K., Schneiderscherzer, E. & Leitner, E. The peptide synthetase catalyzing cyclosporine production in Tolypocladium niveum is encoded by a giant 45.8-kilobase open reading frame. Curr. Genet. 26, 120-125 (1994).
6. Duitman, E. H. et al. The mycosubtilin synthetase of Bacillus subtilis ATCC6633: a multifunctional hybrid between a peptide synthetase, an amino transferase, and a fatty acid synthase. Proc. Natl Acad. Sci. USA 96, 13294-13299 (1999).
7. Cane, D. E., Walsh, C. T. & Khosla, C. Biochemistry-harnessing the biosynthetic code: combinations, permutations, and mutations. Science 282, 63-68 (1998).
8. Wilkinson, B. & Micklefield, J. Mining and engineering natural-product biosynthetic pathways. Nature Chem. Biol. 3, 379-386 (2007).
9. Weist, S. & Sussmuth, R. D. Mutational biosynthesis-a tool for the generation of structural diversity in the biosynthesis of antibiotics. Appl. Microbiol. Biotechnol. 68, 141-150 (2005).
10. von Dohren, H., Keller, U., Vater, J. & Zocher, R. Multifunctional peptide synthetases. Chem. Rev. 97, 2675-2706 (1997).
11. Sattely, E. S., Fischbach, M. A. & Walsh, C. T. Total biosynthesis: in vitro reconstitution of polyketide and nonribosomal peptide pathways. Nat. Prod. Rep. 25, 757-793 (2008).
12. Aquino, C. et al. A biomimetic polyketide-inspired approach to small-molecule ligand discovery. Nature Chem. 4, 99-104 (2012).
13. Woerly, E. M., Roy, J. & Burke M. D. Synthesis of most polyene natural product motifs using just 12 building blocks and one coupling reaction. Nature Chem. 6, 484-491 (2014).
14. Carrillo, N., Davalos, E. A., Russak, J. A. & Bode, J. W. Iterative, aqueous synthesis of ?3-oligopeptides without coupling reagents. J. Am. Chem. Soc. 128, 1452-1453 (2006).
15. Yu, S. Y., Ishida, H., Juarez-Garcia, M. E. & Bode, J. W. Unified synthesis of enantiopure ?2h, ?3h and ?2, 3-amino acids. Chem. Sci. 1, 637-641 (2010).
16. Gerfaud, T., Chiang, Y. L., Kreituss, I., Russak, J. A. & Bode, J. W. Enantioselective, chromatography-free synthesis of ?3-amino acids with natural and unnatural side chains. Org. Process Res. Dev. 16, 687-696 (2012).
17. Njoroge, F. G., Chen, K. X., Shih, N. Y. & Piwinski, J. J. Challenges in modern drug discovery: a case study of boceprevir, an HCV protease inhibitor for the treatment of hepatitis C virus infection. Acc. Chem. Res. 41, 50-59 (2008).
18. Kwong, A. D., Kauffman, R. S., Hurter, P. & Mueller, P. Discovery and development of telaprevir: an NS3-4A protease inhibitor for treating genotype 1 chronic hepatitis C virus. Nature Biotechnol. 29, 993-1003 (2011).
19. Venkatraman, S. et al. Discovery of (1R, 5S)-N-[3-amino-1-(cyclobutylmethyl)-2, 3-dioxopropyl]-3-[2(S)-[[[(1, 1-dimethylethyl)amino]carbonyl]amino]-3, 3-dimethyl-1-oxobutyl]-6, 6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (SCH 503034), a selective, potent, orally bioavailable hepatitis C virus NS3 protease inhibitor: a potential therapeutic agent for the treatment of hepatitis C infection. J. Med. Chem. 49, 6074-6086 (2006).
20. Nett, M., Ikeda, H. & Moore, B. S. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat. Prod. Rep. 26, 1362-1384 (2009).
21. Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J. & Goodman, R. M. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5, R245-R249 (1998).
22. Wenzel, S. C. et al. Heterologous expression of a myxobacterial natural products assembly line in pseudomonads via red/ET recombineering. Chem. Biol. 12, 349-356 (2005).
23. Demain, A. L. & Adrio, J. L. Contributions of microorganisms to industrial biology. Mol. Biotechnol. 38, 41-55 (2008).
24. Schwarzer, D., Finking, R. & Marahiel, M. A. Nonribosomal peptides: from genes to products. Nat. Prod. Rep. 20, 275-287 (2003).
25. Keasling, J. D. Manufacturing molecules through metabolic engineering. Science 330, 1355-1358 (2010).
26. Walsh, C. T. Combinatorial biosynthesis of antibiotics: challenges and opportunities. ChemBioChem 3, 125-134 (2002).
27. Sieber, S. A. & Marahiel, M. A. Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics. Chem. Rev. 105, 715-738 (2005).
28. Linne, U. & Marahiel, M. A. Control of directionality in nonribosomal peptide synthesis: role of the condensation domain in preventing misinitiation and timing of epimerization. Biochemistry 39, 10439-10447 (2000).
29. Yeh, E., Kohli, R. M., Bruner, S. D. & Walsh, C. T. Type II thioesterase restores activity of a NRPS module stalled with an aminoacyl-S-enzyme that cannot be elongated. ChemBioChem 5, 1290-1293 (2004).
30. Uguru, G. C. et al. Active-site modifications of adenylation domains lead to hydrolysis of upstream nonribosomal peptidyl thioester intermediates. J. Am. Chem. Soc. 126, 5032-5033 (2004).
31. Smith, G. P. & Petrenko, V. A. Phage display. Chem. Rev. 97, 391-410 (1997).
32. Roberts, R.W. & Szostak, J.W. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc. Natl Acad. Sci. USA 94, 12297-12302 (1997).
33. Josephson, K., Hartman, M. C. T. & Szostak, J. W. Ribosomal synthesis of unnatural peptides. J. Am. Chem. Soc. 127, 11727-11735 (2005).
34. Terasaka, N. & Suga, H. Flexizymes-facilitated genetic code reprogramming leading to the discovery of drug-like peptides. Chem. Lett. 43, 11-19 (2014).
35. Mannocci, L., Leimbacher, M., Wichert, M., Scheuermann, J. & Neri, D. 20 years of DNA-encoded chemical libraries. Chem. Commun. 47, 12747-12753 (2011).
36. Lam, K. S., Lebl, M. & Krchnak, V. The 'one-bead-one-compound' combinatorial library method. Chem. Rev. 97, 411-448 (1997).
37. Ripka, W. C., Barker, G. & Krakover, J. High-throughput purification of compound libraries. Drug Discov. Today 6, 471-477 (2001).
38. Cooper, A. J., Ginos, J. Z. & Meister, A. Synthesis and properties of the ?-keto acids. Chem. Rev. 83, 321-358 (1983).
39. Dumas, A. M. & Bode, J. W. Synthesis of acyltrifluoroborates. Org. Lett. 14, 2138-2141 (2012).
40. Er?s, G., Kushida, Y. & Bode, J. W. A reagent for the one-step preparation of potassium acyltrifluoroborates (KATs) from aryl and heteroaryl halides. Angew. Chem. Int. Ed. 126, 7734-7737 (2014).
41. Ju, L., Bode, J. W., Toma, T. & Fukuyama, T. Amide formation by decarboxylative condensation of hydroxylamines and ?-ketoacids: N-[(1S)-1 phenylethyl]-benzeneacetamide. Org. Synth. 87, 218-225 (2010).
42. Narumi, T. & Bode, J. W. ?, ?-Dichloroisoxazolidinones for the synthesis and chemoselective peptide ligation of ?-peptide ?-ketoacids. Heterocycles 82, 1515-1525 (2011).
43. Juarez-Garcia, M. E., Yu, S. Y. & Bode, J. W. Asymmetric synthesis of enantiopure isoxazolidinone monomers for the synthesis of ?3-oligopeptides by chemoselective amide ligation. Tetrahedron 66, 4841-4853 (2010).
44. Frederickson, M., Grigg, R., Thornton-Pett, M. & Redpath, J. Palladium(II) catalysed oxime-metallo-nitrone-isoxazolidine cascade reactions of ?-imino aldoximes. Tetrahedron Lett. 38, 7777-7780 (1997).
45. Ogunkoya, A. O., Pattabiraman, V. R. & Bode, J. W. Sequential ?-ketoacidhydroxylamine (KAHA) ligations: synthesis of C-terminal variants of the modifier protein UFM1. Angew. Chem. Int. Ed. 51, 9693-9697 (2012).
46. Venanzi, M. & Kimura, S. Special issue: peptide materials. Polym. J. 45, 467 (2013).
47. Wennemers, H. Asymmetric catalysis with peptides. Chem. Commun. 47, 12036-12041 (2011).
48. Taliani M. et al. A continuous assay of hepatitis C virus protease based on resonance energy transfer depsipeptide substrates. Anal. Biochem. 240, 60-67 (1996).
49. Evans, B. S., Chen, Y. Q., Metcalf, W.W., Zhao, H. M. & Kelleher, N. L. Directed evolution of the nonribosomal peptide synthetase AdmK generates new andrimid derivatives in vivo. Chem. Biol. 18, 601-607 (2011).
50. Jin, M., Fischbach, M. A. & Clardy, J. A biosynthetic gene cluster for the acetyl-CoA carboxylase inhibitor andrimid. J. Am. Chem. Soc. 128, 10660-10661 (2006).