Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 47, 2012, Pages 19196-19201

  Ibrahim, Ashraf ^a   Yang, Lian ^b   Johnston, Chad ^a   Liu, Xiaowen ^c   Ma, Bin ^b   Magarvey, Nathan A ^a  

^a MCMASTER UNIVERSITY   (Canada)

^b UNIVERSITY OF WATERLOO   (Canada)

^c INDIANA UNIVERSITY   (United States)

Author keywords

Antibiotic; Drug discovery; Genome mining; Secondary metabolite

Indexed keywords

BACITRACIN; BACITRACIN A; CYCLOSPORIN A; GRAMICIDIN A; KUTZNERIDE; NATURAL PRODUCT; NONRIBOSOMAL PEPTIDE; PEPTIDE; POLYMYXIN B; SEGLITIDE; SURFACTIN; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; BIOINFORMATICS; DRUG RESEARCH; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLITE; MOLECULE; NONRIBOSOMAL PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEOMICS; SCORING SYSTEM;

ALGORITHMS; BACILLUS; BACITRACIN; BIOLOGICAL PRODUCTS; COMPLEX MIXTURES; COMPUTATIONAL BIOLOGY; DATABASES, CHEMICAL; FERMENTATION; PEPTIDES; REPRODUCIBILITY OF RESULTS; RIBOSOMES; TANDEM MASS SPECTROMETRY;

EID: 84869792678     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1206376109     Document Type: Article

References (26)

1. Schwarzer D, Finking R, Marahiel MA (2003) Nonribosomal peptides: From genes to products. Nat Prod Rep 20(3):275-287.
2. Fischbach MA, Walsh CT (2006) Assembly-line enzymology for polyketide and non-ribosomal peptide antibiotics: Logic, machinery, and mechanisms. Chem Rev 106(8):3468-3496.
3. Caboche S, et al. (2008) NORINE: A database of nonribosomal peptides. Nucleic Acids Res 36(Database issue):D326-D331.
4. Li JW, Vederas JC (2009) Drug discovery and natural products: End of an era or an endless frontier? Science 325(5937):161-165.
5. McAlpine JB (2009) Advances in the understanding and use of the genomic base of microbial secondary metabolite biosynthesis for the discovery of new natural products. J Nat Prod 72(3):566-572.
6. Corre C, Challis GL (2009) New natural product biosynthetic chemistry discovered by genome mining. Nat Prod Rep 26(8):977-986.
7. Perkins DN, Pappin DJC, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18):3551-3567.
8. Finking R, Marahiel MA (2004) Biosynthesis of nonribosomal peptides. Annu Rev Microbiol 58:453-488.
9. Harrison AG, Young AB, Bleiholder C, Suhai S, Paizs B (2006) Scrambling of sequence information in collision-induced dissociation of peptides. J Am Chem Soc 128(32):10364-10365.
10. Eckart K (1994) Mass spectrometry of cyclic peptides. Mass Spectrom Rev 13(1):23-55.
11. Bleiholder C, et al. (2008) Sequence-scrambling fragmentation pathways of protonated peptides. J Am Chem Soc 130(52):17774-17789.
12. Liu WT, et al. (2009) Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Anal Chem 81(11):4200-4209.
13. Mohimani H, et al. (2011) Sequencing cyclic peptides by multistage mass spectrometry. Proteomics 11(18):3642-3650.
14. Ng J, et al. (2009) Dereplication and de novo sequencing of nonribosomal peptides. Nat Methods 6(8):596-599.
15. Kersten RD, et al. (2011) A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat Chem Biol 7(11):794-802.
16. Weininger D (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 28:31-36.
17. Paizs B, Suhai S (2004) Fragmentation pathways of protonated peptides. Mass Spectrom Rev 24(4):508-548.
18. Chamrad DC, et al. (2004) Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data. Proteomics 4(3):619-628.
19. Eng JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5(11):976-989.
20. Zhang J, et al. (2012) PEAKS DB: De novo sequencing assisted database search for sensitive and accurate peptide identification. Mol Cell Proteomics 11(4):M111.010587.
21. Razumovskaya J, et al. (2004) A computational method for assessing peptide-identification reliability in tandem mass spectrometry analysis with SEQUEST. Proteomics 4(4):961-969.
22. Govaerts C, et al. (2002) Mass spectrometric fragmentation of cyclic peptides belonging to the polymyxin and colistin antibiotics studied by ion trap and quadrupole/orthogonal-acceleration time-of-flight technology. Rapid Commun Mass Spectrom 16(9):823-833.
23. Vaisar T, Urban J (1998) Gas-phase fragmentation of protonated mono-N-methylated peptides. Analogy with solution-phase acid-catalyzed hydrolysis. J Mass Spectrom 33(6):505-524.
24. Broberg A, Menkis A, Vasiliauskas R (2006) Kutznerides 1-4, depsipeptides from the actinomycete Kutzneria sp. 744 inhabiting mycorrhizal roots of Picea abies seedlings. J Nat Prod 69(1):97-102.
25. Barber M, et al. (1992) An investigation of the tyrothricin complex by tandem mass spectrometry. Int J Mass Spectrom Ion Process 122:143-151.
26. Tang X, Thibault P, Boyd R (1992) Characterisation of the tyrocidine and gramicidin fraction of the tyrothricin complex from Bacillus brevis using liquid chromatography and mass spectrometry. Int J Mass Spectrom Ion Process 122:153-179.