Nonribosomal peptides (NRPs) such as penicillin, vancomycin and related molecules isolated from microbial sources have been a staple for drug discovery for many decades. We propose to employ multi-stage mass-spectrometry (MSn) for de novo sequencing of NRPs, including cyclic NRPs. Analysis of MSn spectra of a cyclic peptide results in the difficult combinatorial problem of interpreting multiple linear peptides from the same spectrum. This proposal develops new combinatorial algorithms for solving this issue. Since the MSn based mass spectrometry analysis of NPRs is fast and inexpensive and requires minimal amounts of material (<1 5g), this approach opens a possibility of high-throughput sequencing of many unknown NRPs accumulated in large bioactivity marine cyanobacterial screening programs. In parallel to the automation of the NRPs sequencing efforts, we will harvest a set of orphan gene clusters from marine actinomycetes to generate a library of cyclic peptides. The algorithms developed in this proposal will be used to fully characterize this cyclic imine library. This work not only sets the stage for the automated characterization of NRPs but will also be applicable to the characterization of other peptidic natural products such as peptaibols, peptide derived toxins or lantibiotics.

Public Health Relevance

This project describes the development and application of a novel mass spectrometry based method and corresponding algorithms that allow the de novo sequencing of complex therapeutic agents that are non-ribosomally derived.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM086283-03
Application #
7924506
Study Section
Special Emphasis Panel (ZRG1-BCMB-H (50))
Program Officer
Hagan, Ann A
Project Start
2008-09-25
Project End
2012-08-31
Budget Start
2010-09-01
Budget End
2012-08-31
Support Year
3
Fiscal Year
2010
Total Cost
$331,419
Indirect Cost
Name
University of California San Diego
Department
Type
Schools of Pharmacy
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Mohimani, Hosein; Liu, Wei-Ting; Kersten, Roland D et al. (2014) NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery. J Nat Prod 77:1902-9
Gonzalez, David J; Vuong, Lisa; Gonzalez, Isaiah S et al. (2014) Phenol soluble modulin (PSM) variants of community-associated methicillin-resistant Staphylococcus aureus (MRSA) captured using mass spectrometry-based molecular networking. Mol Cell Proteomics 13:1262-72
Liu, Wei-Ting; Lamsa, Anne; Wong, Weng Ruh et al. (2014) MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus. J Antibiot (Tokyo) 67:99-104
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Boudreau, Paul D; Byrum, Tara; Liu, Wei-Ting et al. (2012) Viequeamide A, a cytotoxic member of the kulolide superfamily of cyclic depsipeptides from a marine button cyanobacterium. J Nat Prod 75:1560-70
Guthals, Adrian; Watrous, Jeramie D; Dorrestein, Pieter C et al. (2012) The spectral networks paradigm in high throughput mass spectrometry. Mol Biosyst 8:2535-44
Rath, Christopher M; Dorrestein, Pieter C (2012) The bacterial chemical repertoire mediates metabolic exchange within gut microbiomes. Curr Opin Microbiol 15:147-54
Gonzalez, David J; Xu, Yuquan; Yang, Yu-Liang et al. (2012) Observing the invisible through imaging mass spectrometry, a window into the metabolic exchange patterns of microbes. J Proteomics 75:5069-76
Gonzalez, David J; Okumura, Cheryl Y; Hollands, Andrew et al. (2012) Novel phenol-soluble modulin derivatives in community-associated methicillin-resistant Staphylococcus aureus identified through imaging mass spectrometry. J Biol Chem 287:13889-98
Xu, Ying; Kersten, Roland D; Nam, Sang-Jip et al. (2012) Bacterial biosynthesis and maturation of the didemnin anti-cancer agents. J Am Chem Soc 134:8625-32

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