Literature DB >> 35296832

Strategies to access biosynthetic novelty in bacterial genomes for drug discovery.

Franziska Hemmerling1, Jörn Piel2.   

Abstract

Bacteria provide a rich source of natural products with potential therapeutic applications, such as novel antibiotic classes or anticancer drugs. Bioactivity-guided screening of bacterial extracts and characterization of biosynthetic pathways for drug discovery is now complemented by the availability of large (meta)genomic collections, placing researchers into the postgenomic, big-data era. The progress in next-generation sequencing and the rise of powerful computational tools provide unprecedented insights into unexplored taxa, ecological niches and 'biosynthetic dark matter', revealing diverse and chemically distinct natural products in previously unstudied bacteria. In this Review, we discuss such sources of new chemical entities and the implications for drug discovery with a particular focus on the strategies that have emerged in recent years to identify and access novelty.
© 2022. Springer Nature Limited.

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Year:  2022        PMID: 35296832     DOI: 10.1038/s41573-022-00414-6

Source DB:  PubMed          Journal:  Nat Rev Drug Discov        ISSN: 1474-1776            Impact factor:   84.694


  208 in total

Review 1.  Introducing the parvome: bioactive compounds in the microbial world.

Authors:  Julian Davies; Katherine S Ryan
Journal:  ACS Chem Biol       Date:  2011-11-17       Impact factor: 5.100

2.  Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics.

Authors:  Christopher J Schwalen; Graham A Hudson; Bryce Kille; Douglas A Mitchell
Journal:  J Am Chem Soc       Date:  2018-07-20       Impact factor: 15.419

3.  Computational approaches to natural product discovery.

Authors:  Marnix H Medema; Michael A Fischbach
Journal:  Nat Chem Biol       Date:  2015-09       Impact factor: 15.040

4.  RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links.

Authors:  Priyesh Agrawal; Shradha Khater; Money Gupta; Neetu Sain; Debasisa Mohanty
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

5.  PRISM 3: expanded prediction of natural product chemical structures from microbial genomes.

Authors:  Michael A Skinnider; Nishanth J Merwin; Chad W Johnston; Nathan A Magarvey
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

6.  A new genome-mining tool redefines the lasso peptide biosynthetic landscape.

Authors:  Jonathan I Tietz; Christopher J Schwalen; Parth S Patel; Tucker Maxson; Patricia M Blair; Hua-Chia Tai; Uzma I Zakai; Douglas A Mitchell
Journal:  Nat Chem Biol       Date:  2017-02-28       Impact factor: 15.040

7.  BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins.

Authors:  Auke J van Heel; Anne de Jong; Chunxu Song; Jakob H Viel; Jan Kok; Oscar P Kuipers
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

8.  antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.

Authors:  Kai Blin; Simon Shaw; Katharina Steinke; Rasmus Villebro; Nadine Ziemert; Sang Yup Lee; Marnix H Medema; Tilmann Weber
Journal:  Nucleic Acids Res       Date:  2019-07-02       Impact factor: 16.971

Review 9.  Genome mining strategies for ribosomally synthesised and post-translationally modified peptides.

Authors:  Alicia H Russell; Andrew W Truman
Journal:  Comput Struct Biotechnol J       Date:  2020-06-25       Impact factor: 6.155

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  2 in total

1.  Amino acid (acyl carrier protein) ligase-associated biosynthetic gene clusters reveal unexplored biosynthetic potential.

Authors:  Vesna Simunović; Ivan Grubišić
Journal:  Mol Genet Genomics       Date:  2022-10-22       Impact factor: 2.980

2.  Diaphorin, a Polyketide Produced by a Bacterial Symbiont of the Asian Citrus Psyllid, Inhibits the Growth and Cell Division of Bacillus subtilis but Promotes the Growth and Metabolic Activity of Escherichia coli.

Authors:  Nozomu Tanabe; Rena Takasu; Yuu Hirose; Yasuhiro Kamei; Maki Kondo; Atsushi Nakabachi
Journal:  Microbiol Spectr       Date:  2022-07-27
  2 in total

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