Informatic search strategies to discover analogues and variants of natural product archetypes

Journal of Industrial Microbiology and Biotechnology

Volumn 43, Issue 2-3, 2016, Pages 293-298

  Johnston, Chad W ^a,b   Connaty, Alex D ^a,b   Skinnider, Michael A ^a,b   Li, Yong ^a,b   Grunwald, Alyssa ^c   Wyatt, Morgan A ^a,b   Kerr, Russell G ^c   Magarvey, Nathan A ^a,b  

^a MCMASTER UNIVERSITY   (Canada)

^b MCMASTER UNIVERSITY   (Canada)

^c UNIVERSITY OF PRINCE EDWARD ISLAND   (Canada)

Author keywords

Informatic platforms; LC MS MS; Natural products; Nonribosomal peptides; Peptaibols

Indexed keywords

PEPTAIBOL; ANTIFUNGAL AGENT; BIOLOGICAL PRODUCT; PEPTIDE; TRICHOPOLYN;

ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; FUNGUS ISOLATION; HYPOCREA; HYPOCREA MINUTISPORA; ION TRAP MASS SPECTROMETRY; NONHUMAN; SENSITIVITY ANALYSIS; CHEMISTRY; DRUG DEVELOPMENT; INFORMATION SCIENCE; MASS SPECTROMETRY; PROCEDURES;

ANTIFUNGAL AGENTS; BIOLOGICAL PRODUCTS; DRUG DISCOVERY; HYPOCREA; INFORMATICS; MASS SPECTROMETRY; PEPTAIBOLS; PEPTIDES;

EID: 84958120965     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-015-1675-9     Document Type: Article

References (19)

1. Bachmann BO, Van Lanen SG, Baltz RH (2014) Microbial genome mining for accelerated natural products discovery: is a renaissance in the making? J Ind Microbiol Biotechnol 41(2):175–184. doi:10.1007/s10295-013-1389-9
2. Backman TW, Cao Y, Girke T (2011) ChemMine tools: an online service for analyzing and clustering small molecules. Nucleic Acids Res 39(Web Server issue):W486W–491. doi:10.1093/nar/gkr320
3. Chugh JK, Wallace BA (2001) Peptaibols: models for ion channels. Biochem Soc Trans 29(Pt 4):565–570
4. Clardy J, Fischbach MA, Walsh CT (2006) New antibiotics from bacterial natural products. Nat Biotechnol 24(12):1541–1550. doi:10.1038/nbt1266
5. Degenkolb T, Kirschbaum J, Brückner H (2007) New sequences, constituents, and producers of peptaibiotics: an updated review. Chem Biodivers 4(6):1052–1067. doi:10.1002/cbdv.200790096
6. Fischbach MA, Clardy J (2007) One pathway, many products. Nat Chem Biol 3(7):353–355. doi:10.1038/nchembio0707-353
7. Ibrahim A, Yang L, Johnston C, Liu X, Ma B, Magarvey NA (2012) Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery. Proc Natl Acad Sci USA 109(47):19196–19201. doi:10.1073/pnas.1206376109
8. Iida A, Mihara T, Fujita T, Takaishi Y (1999) Peptidic immunosuppressants from the fungus Trichodermapolysporum. Bioorg Med Chem Lett 9(24):3393–3396. doi:10.1016/S0960-894X(99)00621-6
9. Koehn FE, Carter GT (2005) The evolving role of natural products in drug discovery. Nat Rev Drug Discov 4(3):206–220. doi:10.1038/nrd1657
10. Lam KS (2007) New aspects of natural products in drug discovery. Trends Microbiol 15(6):279–289. doi:10.1016/j.tim.2007.04.001
11. Li JW, Vederas JC (2009) Drug discovery and natural products: end of an era or an endless frontier? Science 325(5937):161–165. doi:10.1126/science.1168243
12. Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, Brewer HM, Pasa-Tolic L, Bandeira N, Moore BS, Pevzner PA, Dorrestein PC (2014) Automated genome mining of ribosomal peptide natural products. ACS Chem Biol 9(7):1545–1551. doi:10.1021/cb500199h
13. Mohimani H, Liu WT, Kersten RD, Moore BS, Dorrestein PC, Pevzner PA (2014) NRPquest: coupling mass spectrometry and genome mining for nonribosomal peptide discovery. J Nat Prod 77(8):1902–1909. doi:10.1021/np500370c
14. Mohimani H, Liu WT, Mylne JS, Poth AG, Colgrave ML, Tran D, Selsted ME, Dorrestein PC, Pevzner PA (2011) Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases. J Proteome Res 10(10):4505–4512. doi:10.1021/pr200323a
15. Ostrosky-Zeichner L, Casadevall A, Galgiani JN, Odds FC, Rex JH (2010) An insight into the antifungal pipeline: selected new molecules and beyond. Nat Rev Drug Discov 9(9):719–727. doi:10.1038/nrd3074
16. Schüller A, Hähnke V, Schneider G (2007) SmiLib v2.0: a Java-Based Tool for Rapid Combinatorial Library Enumeration. QSAR Comb Sci 26(3):407–410. doi:10.1002/qsar.200630101
17. Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC (2012) Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci USA 109(26):E1743–E1752. doi:10.1073/pnas.1203689109
18. Wright GD (2012) Antibiotics: a new hope. Chem Biol 19(1):3–10. doi:10.1016/j.chembiol.2011.10.019
19. Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, de Felicio R, Fenner A, Wong WR, Linington RG, Zhang L, Debonsi HM, Gerwick WH, Dorrestein PC (2013) Molecular networking as a dereplication strategy. J Nat Prod 76(9):1686–1699. doi:10.1021/np400413s