Literature DB >> 23132949

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

Ashraf Ibrahim1, Lian Yang, Chad Johnston, Xiaowen Liu, Bin Ma, Nathan A Magarvey.   

Abstract

Nonribosomal peptides are highly sought after for their therapeutic applications. As with other natural products, dereplication of known compounds and focused discovery of new agents within this class are central concerns of modern natural product-based drug discovery. Development of a chemoinformatic library-based and informatic search strategy for natural products (iSNAP) has been constructed and applied to nonribosomal peptides and proved useful for true nontargeted dereplication across a spectrum of nonribosomal peptides and within natural product extracts.

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Year:  2012        PMID： 23132949      PMCID： PMC3511102          DOI： 10.1073/pnas.1206376109

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  21 in total

1.  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.

Authors:  Cindy Govaerts; Jef Rozenski; Jennifer Orwa; Eugène Roets; Ann Van Schepdael; Jos Hoogmartens
Journal:  Rapid Commun Mass Spectrom       Date:  2002       Impact factor: 2.419

Review 2.  Nonribosomal peptides: from genes to products.

Authors:  Dirk Schwarzer; Robert Finking; Mohamed A Marahiel
Journal:  Nat Prod Rep       Date:  2003-06       Impact factor: 13.423

Review 3.  Fragmentation pathways of protonated peptides.

Authors:  Béla Paizs; Sándor Suhai
Journal:  Mass Spectrom Rev       Date:  2005 Jul-Aug       Impact factor: 10.946

Review 4.  Biosynthesis of nonribosomal peptides1.

Authors:  Robert Finking; Mohamed A Marahiel
Journal:  Annu Rev Microbiol       Date:  2004       Impact factor: 15.500

Review 5.  Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms.

Authors:  Michael A Fischbach; Christopher T Walsh
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

6.  Sequence-scrambling fragmentation pathways of protonated peptides.

Authors:  Christian Bleiholder; Sandra Osburn; Todd D Williams; Sándor Suhai; Michael Van Stipdonk; Alex G Harrison; Béla Paizs
Journal:  J Am Chem Soc       Date:  2008-12-31       Impact factor: 15.419

7.  Dereplication and de novo sequencing of nonribosomal peptides.

Authors:  Julio Ng; Nuno Bandeira; Wei-Ting Liu; Majid Ghassemian; Thomas L Simmons; William H Gerwick; Roger Linington; Pieter C Dorrestein; Pavel A Pevzner
Journal:  Nat Methods       Date:  2009-07-13       Impact factor: 28.547

8.  A mass spectrometry-guided genome mining approach for natural product peptidogenomics.

Authors:  Roland D Kersten; Yu-Liang Yang; Yuquan Xu; Peter Cimermancic; Sang-Jip Nam; William Fenical; Michael A Fischbach; Bradley S Moore; Pieter C Dorrestein
Journal:  Nat Chem Biol       Date:  2011-10-09       Impact factor: 15.040

9.  PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification.

Authors:  Jing Zhang; Lei Xin; Baozhen Shan; Weiwu Chen; Mingjie Xie; Denis Yuen; Weiming Zhang; Zefeng Zhang; Gilles A Lajoie; Bin Ma
Journal:  Mol Cell Proteomics       Date:  2011-12-20       Impact factor: 5.911

10.  NORINE: a database of nonribosomal peptides.

Authors:  Ségolène Caboche; Maude Pupin; Valérie Leclère; Arnaud Fontaine; Philippe Jacques; Gregory Kucherov
Journal:  Nucleic Acids Res       Date:  2007-10-02       Impact factor: 16.971
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  25 in total

1.  Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries.

Authors:  Kenji L Kurita; Emerson Glassey; Roger G Linington
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-14       Impact factor: 11.205

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

Authors:  Chad W Johnston; Alex D Connaty; Michael A Skinnider; Yong Li; Alyssa Grunwald; Morgan A Wyatt; Russell G Kerr; Nathan A Magarvey
Journal:  J Ind Microbiol Biotechnol       Date:  2015-09-08       Impact factor: 3.346

3.  Non-direct sequence ions in the tandem mass spectrometry of protonated peptide amides--an energy-resolved study.

Authors:  Alex G Harrison; Cagdas Tasoglu; Talat Yalcin
Journal:  J Am Soc Mass Spectrom       Date:  2013-08-06       Impact factor: 3.109

Review 4.  The re-emergence of natural products for drug discovery in the genomics era.

Authors:  Alan L Harvey; RuAngelie Edrada-Ebel; Ronald J Quinn
Journal:  Nat Rev Drug Discov       Date:  2015-01-23       Impact factor: 84.694

5.  CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra.

Authors:  Jiří Novák; Karel Lemr; Kevin A Schug; Vladimír Havlíček
Journal:  J Am Soc Mass Spectrom       Date:  2015-07-21       Impact factor: 3.109

Review 6.  Mass spectrometry tools and workflows for revealing microbial chemistry.

Authors:  Tal Luzzatto-Knaan; Alexey V Melnik; Pieter C Dorrestein
Journal:  Analyst       Date:  2015-08-07       Impact factor: 4.616

7.  DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products.

Authors:  Nishanth J Merwin; Walaa K Mousa; Chris A Dejong; Michael A Skinnider; Michael J Cannon; Haoxin Li; Keshav Dial; Mathusan Gunabalasingam; Chad Johnston; Nathan A Magarvey
Journal:  Proc Natl Acad Sci U S A       Date:  2019-12-23       Impact factor: 11.205

8.  Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra.

Authors:  Alexey Gurevich; Alla Mikheenko; Alexander Shlemov; Anton Korobeynikov; Hosein Mohimani; Pavel A Pevzner
Journal:  Nat Microbiol       Date:  2018-01-22       Impact factor: 17.745

Review 9.  Mass spectrometry of natural products: current, emerging and future technologies.

Authors:  Amina Bouslimani; Laura M Sanchez; Neha Garg; Pieter C Dorrestein
Journal:  Nat Prod Rep       Date:  2014-05-07       Impact factor: 13.423

10.  MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis.

Authors:  Jan Přívratský; Jiří Novák
Journal:  J Cheminform       Date:  2021-07-07       Impact factor: 5.514
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