Exploration of Nonribosomal Peptide Families with an Automated Informatic Search Algorithm

Chemistry and Biology

Volumn 22, Issue 9, 2015, Pages 1259-1269

  Yang, Lian ^a   Ibrahim, Ashraf ^b   Johnston, Chad W ^c   Skinnider, Michael A ^c   Ma, Bin ^a   Magarvey, Nathan A ^b,c  

^a UNIVERSITY OF WATERLOO   (Canada)

^b MCMASTER UNIVERSITY   (Canada)

^c MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ANTIBIOTIC AGENT; GLYCINE; GUANIDINE; HISTIDINE; KETONE; LI FO; LOLOATIN; MONOMER; PEPTIDE; THREONINE; TRYPTOPHAN; TYROCIDINE; UNCLASSIFIED DRUG; BIOLOGICAL PRODUCT;

ALGORITHM; ARTICLE; BIOLOGICAL ACTIVITY; DRUG STRUCTURE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; PRIORITY JOURNAL; BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; LABORATORY AUTOMATION; METABOLOMICS; PRECLINICAL STUDY; PROCEDURES;

ALGORITHMS; AUTOMATION, LABORATORY; BIOLOGICAL PRODUCTS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DRUG EVALUATION, PRECLINICAL; METABOLOMICS; PEPTIDES;

EID: 84941944299     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2015.08.008     Document Type: Article

References (29)

1. J.M. Balkovec, D.L. Hughes, P.S. Masurekar, C.A. Sable, R.E. Schwartz, and S.B. Singh Discovery and development of first in class antifungal caspofungin (CANCIDAS®) - a case study Nat. Prod. Rep. 15 2014 15 34
2. T.C. Chou, X.G. Zhang, A. Balog, D.S. Su, D. Meng, K. Savin, J.R. Bertino, and S.J. Danishefsky Desoxyepothilone B: an efficacious microtubule-targeted antitumor agent with a promising in vivo profile relative to epothilone B Proc. Natl. Acad. Sci. USA 95 1998 9642 9647
3. B.I. Eisenstein, F.B. Oleson Jr., and R.H. Baltz Daptomycin: from the mountain to the clinic, with essential help from Francis Tally, MD Clin. Infect. Dis. 50 2010 S10 S15
4. A.M. Frank, N. Bandeira, Z. Shen, S. Tanner, S.P. Briggs, R.D. Smith, and P.A. Pevzner Clustering millions of tandem mass spectra J. Proteome. Res. 7 2008 113 122
5. J.M. Gerard, P. Haden, M.T. Kelly, and R.J. Andersen Loloatins A-D, cyclic decapeptide antibiotics produced in culture by a tropical marine bacterium J. Nat. Prod. 62 1999 80 85
6. J.W. Han, E.Y. Kim, J.M. Lee, Y.S. Kim, E. Bang, and B.S. Kim Site-directed modification of the adenylation domain of the fusaricidin nonribosomal peptide synthetase for enhanced production of fusaricidin analogs Biotechnol. Lett. 34 2012 1327 1334
7. H. He, R.T. Williamson, B. Shen, E.I. Graziani, H.Y. Yang, S.M. Sakya, P.J. Petersen, and G.T. Carter Mannopeptimycins, novel antibacterial glycopeptides from Streptomyces hygroscopicus, LL-AC98 J. Am. Chem. Soc. 124 2002 9729 9736
8. Y. Hou, D.R. Braun, C.R. Michel, J.L. Klassen, N. Adnani, T.P. Wyche, and T.S. Bugni Microbial strain prioritization using metabolomics tools for the discovery of natural products Anal. Chem. 84 2012 4277 4283
9. A. Ibrahim, L. Yang, C.W. Johnston, X. Liu, B. Ma, and N.A. Magarvey Dereplicating nonribosomal peptides using an informatic search algorithm for natural products Proc. Natl. Acad. Sci. USA 109 2012 19196 19201
10. R.D. Kersten, Y.L. Yang, Y. Xu, P. Cimermancic, S.J. Nam, W. Fenical, M.A. Fischbach, B.S. Moore, and P.C. Dorrestein A mass spectrometry-guided genome mining approach for natural product peptidogenomics Nat. Chem. Biol. 7 2011 794 802
11. P. Kulanthaivel, A.J. Kreuzman, M.A. Strege, M.D. Belvo, T.A. Smitka, M. Clemens, J.R. Swartling, K.L. Minton, F. Zheng, E.L. Angleton, and et al. Novel lipoglycopeptides as inhibitors of bacterial signal peptidase I J. Biol. Chem. 279 2004 36250 36258
12. J. Kuroda, T. Fukai, and T. Nomura Collision-induced dissociation of ring-opened cyclic depsipeptides with a guanidino group by electrospray ionization/ion trap mass spectrometry J. Mass. Spectrom. 36 2001 30 37
13. K. Kurusu, K. Ohba, T. Arai, and K. Fukushima New peptide antibiotics LI-F03, F04, F05, F07, and F08, produced by Bacillus polymyxa. I. Isolation and characterization J. Antibiot. 40 1987 1506 1514
14. Z. Lin, J.O. Falkinham, K.A. Tawfik, P. Jeffs, B. Bray, G. Dubay, J.E. Cox, and E.W. Schmidt Burkholdines from Burkholderia ambifaria: antifungal agents and possible virulence factors J. Nat. Prod. 75 2012 1518 1523
15. M.H. Medema, Y. Paalvast, D.D. Nguyen, A. Melnik, P.C. Dorrestein, E. Takano, and R. Breitling Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products PLoS Comput. Biol. 10 2014 e1003822
16. H. Mohimani, W.T. Liu, J.S. Mylne, A.G. Poth, M.L. Colgrave, D. Tran, M.E. Selsted, P.C. Dorrestein, and P.A. Pevzner Cycloquest: Identification of cyclopeptides via database search of their mass spectra against genome databases J. Proteome. Res. 10 2011 4505 4512
17. H. Mohimani, R.D. Kersten, W.T. Liu, M. Wang, S.O. Purvine, S. Wu, H.M. Brewer, L. Pasa-Tolic, N. Bandeira, B.S. Moore, and et al. Automated genome mining of ribosomal peptide natural products ACS Chem. Biol. 9 2014 1545 1551
18. H. Mohimani, W.T. Liu, R.D. Kersten, B.S. Moore, P.C. Dorrestein, and P.A. Pevzner NRPquest: Coupling mass spectrometry and genome mining for nonribosomal peptide discovery J. Nat. Prod. 77 2014 1902 1909
19. D.J. Newman, and G.M. Cragg Natural products as sources of drugs over the last 25 years J. Nat. Prod. 70 2007 461 477
20. J. Ng, N. Bandeira, W.T. Liu, M. Ghassemian, T.L. Simmons, W.H. Gerwick, R. Linington, P.C. Dorrestein, and P.A. Pevzner Dereplication and de novo sequencing of nonribosomal peptides Nat. Methods 6 2009 596 599
21. D.D. Nguyen, C.H. Wu, W.J. Moree, A. Lamsa, M.H. Medema, X. Zhao, R.G. Gavilan, M. Aparicio, L. Atencio, C. Jackson, and et al. MS/MS networking guided analysis of molecule and gene cluster families Proc. Natl. Acad. Sci. USA 110 2013 E2611 E2620
22. K. Scherlach, L.P. Partida-Martinez, H.M. Dahse, and C. Hertweck Antimitotic rhizoxin derivatives from a cultured bacterial endosymbiont of the rice pathogenic fungus Rhizopus microsporus J. Am. Chem. Soc. 128 2006 11529 11536
23. J. Schimana, K. Gebhardt, A. Höltzel, D.G. Schmid, R. Süssmuth, J. Müller, R. Pukall, and H.P. Fiedler Arylomycins A and B, new biaryl-bridged lipopeptide antibiotics produced by Streptomyces sp. Tü 6075. I. Taxonomy, fermentation, isolation and biological activities J. Antibiot. 55 2002 565 570
24. X.J. Tang, P. Thibault, and R.K. Boyd Characterisation of the tyrocidine and gramicidin fractions of the tyrothricin complex from Bacillus brevis using liquid chromatography and mass spectrometry Int. J. Mass. Spectrom. Ion. Process. 122 1992 153 179
25. C. Wang, L.M. Henkes, L.B. Doughty, M. He, D. Wang, F.J. Meyer-Almes, and Y.Q. Cheng Thailandepsins: bacterial products with potent histone deacetylase inhibitory activities and broad-spectrum antiproliferative activities J. Nat. Prod. 74 2011 2031 2038
26. J. Watrous, P. Roach, T. Alexandrov, B.S. Heath, J.Y. Yang, R.D. Kersten, M. van der Voort, K. Pogliano, H. Gross, J.M. Raaijmakers, and et al. Mass spectral molecular networking of living microbial colonies Proc. Natl. Acad. Sci. USA 109 2012 E1743 E1752
27. J.R. Winnikoff, E. Glukhov, J. Watrous, P.C. Dorrestein, and W.H. Gerwick Quantitative molecular networking to profile marine cyanobacterial metabolomes J. Antibiot. 67 2014 105 112
28. J.Y. Yang, L.M. Sanchez, C.M. Rath, X. Liu, P.D. Boudreau, N. Bruns, E. Glukhov, A. Wodtke, R. de Felicio, A. Fenner, and et al. Molecular networking as a dereplication strategy J. Nat. Prod. 76 2013 1686 1699
29. Z. Yu, S. Vodanovic-Jankovic, M. Kron, and B. Shen New WS9326A congeners from Streptomyces sp. 9078 inhibiting Brugia malayi asparaginyl-tRNA synthetase Org. Lett. 14 2012 4946 4949