Using natural products for drug discovery: the impact of the genomics era

DNA sequencing technologies: 2006–2016

(2017) Elaine R Mardis   Nature Protocols

Computational strategies for genome-based natural product discovery and engineering in fungi

(2016) Theo A.J. van der Lee et al.   FUNGAL GENETICS AND BIOLOGY

Natural product discovery: past, present, and future

(2016) Leonard Katz et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Natural Products as Sources of New Drugs from 1981 to 2014

(2016) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

Natural Product Discovery through Improved Functional Metagenomics in Streptomyces

(2016) Hala A. Iqbal et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The evolution of genome mining in microbes – a review

(2016) Nadine Ziemert et al.   NATURAL PRODUCT REPORTS

Engineering microbial hosts for production of bacterial natural products

(2016) Mingzi M. Zhang et al.   NATURAL PRODUCT REPORTS

Recent advances in engineering nonribosomal peptide assembly lines

(2016) M. Winn et al.   NATURAL PRODUCT REPORTS

New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters

(2016) Yunzi Luo et al.   NATURAL PRODUCT REPORTS

Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology

(2016) Kira J. Weissman   NATURAL PRODUCT REPORTS

Human commensals producing a novel antibiotic impair pathogen colonization

(2016) Alexander Zipperer et al.   NATURE

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching

(2016) Chris A Dejong et al.   Nature Chemical Biology

Discovery of MRSA active antibiotics using primary sequence from the human microbiome

(2016) John Chu et al.   Nature Chemical Biology

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Synthetic biology to access and expand nature's chemical diversity

(2016) Michael J. Smanski et al.   NATURE REVIEWS MICROBIOLOGY

Plant metabolic clusters - from genetics to genomics

(2016) Hans-Wilhelm Nützmann et al.   NEW PHYTOLOGIST

Multiplexed CRISPR/Cas9- and TAR-Mediated Promoter Engineering of Natural Product Biosynthetic Gene Clusters in Yeast

(2016) Hahk-Soo Kang et al.   ACS Synthetic Biology

One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces

(2015) He Huang et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

Engineering of Secondary Metabolism

(2015) Sarah E. O'Connor   Annual Review of Genetics

Highly efficient editing of the actinorhodin polyketide chain length factor gene in Streptomyces coelicolor M145 using CRISPR/Cas9-CodA(sm) combined system

(2015) Hu Zeng et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

Identification and analysis of the bacterial endosymbiont specialized for production of the chemotherapeutic natural product ET-743

(2015) Michael M. Schofield et al.   ENVIRONMENTAL MICROBIOLOGY

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Culture-independent discovery of natural products from soil metagenomes

(2015) Micah Katz et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Connecting Phenotype and Chemotype: High-Content Discovery Strategies for Natural Products Research

(2015) Kenji L. Kurita et al.   JOURNAL OF NATURAL PRODUCTS

Targeted Metagenomics: Finding Rare Tryptophan Dimer Natural Products in the Environment

(2015) Fang-Yuan Chang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Investigation of Interspecies Interactions within Marine Micromonosporaceae Using an Improved Co-Culture Approach

(2015) Navid Adnani et al.   Marine Drugs

Targeted activation of silent natural product biosynthesis pathways by reporter-guided mutant selection

(2015) Fang Guo et al.   METABOLIC ENGINEERING

A new antibiotic kills pathogens without detectable resistance

(2015) Losee L. Ling et al.   NATURE

Minimum Information about a Biosynthetic Gene cluster

(2015) Marnix H Medema et al.   Nature Chemical Biology

Computational approaches to natural product discovery

(2015) Marnix H Medema et al.   Nature Chemical Biology

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

(2015) Alan L. Harvey et al.   NATURE REVIEWS DRUG DISCOVERY

Discovery of microbial natural products by activation of silent biosynthetic gene clusters

(2015) Peter J. Rutledge et al.   NATURE REVIEWS MICROBIOLOGY

Highly efficient CRISPR/Cas9-mediated TAR cloning of genes and chromosomal loci from complex genomes in yeast

(2015) Nicholas C.O. Lee et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Genome-guided investigation of plant natural product biosynthesis

(2015) Franziska Kellner et al.   PLANT JOURNAL

Evolution of chemical diversity by coordinated gene swaps in type II polyketide gene clusters

(2015) Maureen E. Hillenmeyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors

(2015) Jeremy G. Owen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants

(2015) Clarissa S. Sit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant diterpene synthases: exploring modularity and metabolic diversity for bioengineering

(2015) Philipp Zerbe et al.   TRENDS IN BIOTECHNOLOGY

Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics

(2015) Pierre-Yves Colin et al.   Nature Communications

CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

(2015) Yaojun Tong et al.   ACS Synthetic Biology

Motif-independent de novo detection of secondary metabolite gene clusters—toward identification from filamentous fungi

(2015) Myco Umemura et al.   Frontiers in Microbiology

Reprogramming Nonribosomal Peptide Synthetases for “Clickable” Amino Acids

(2014) Hajo Kries et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Rational Design of Modular Polyketide Synthases: Morphing the Aureothin Pathway into a Luteoreticulin Assembly Line

(2014) Yuki Sugimoto et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

Lassomycin, a Ribosomally Synthesized Cyclic Peptide, Kills Mycobacterium tuberculosis by Targeting the ATP-Dependent Protease ClpC1P1P2

(2014) Ekaterina Gavrish et al.   CHEMISTRY & BIOLOGY

In silico tools for the analysis of antibiotic biosynthetic pathways

(2014) Tilmann Weber   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

NP/MS since 1970: from the basement to the bench top

(2014) Guy T. Carter   NATURAL PRODUCT REPORTS

Emerging capabilities of mass spectrometry for natural products

(2014) Alan K. Jarmusch et al.   NATURAL PRODUCT REPORTS

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

Functional optimization of gene clusters by combinatorial design and assembly

(2014) Michael J Smanski et al.   NATURE BIOTECHNOLOGY

A microbial biomanufacturing platform for natural and semisynthetic opioids

(2014) Kate Thodey et al.   Nature Chemical Biology

De novo biosynthesis of terminal alkyne-labeled natural products

(2014) Xuejun Zhu et al.   Nature Chemical Biology

Escherichia coli as a cell factory for heterologous production of nonribosomal peptides and polyketides

(2014) Jian Li et al.   New Biotechnology

Improved Lanthipeptide Detection and Prediction for antiSMASH

(2014) Kai Blin et al.   PLoS One

High-throughput platform for the discovery of elicitors of silent bacterial gene clusters

(2014) M. R. Seyedsayamdost   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A

(2014) Kazuya Yamanaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Efficiency Multiplex Genome Editing of Streptomyces Species Using an Engineered CRISPR/Cas System

(2014) Ryan E. Cobb et al.   ACS Synthetic Biology

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis

(2014) Marnix H. Medema et al.   PLoS Computational Biology

Activation and identification of five clusters for secondary metabolites inStreptomyces albus J1074

(2014) Carlos Olano et al.   Microbial Biotechnology

Arimetamycin A: Improving Clinically Relevant Families of Natural Products through Sequence-Guided Screening of Soil Metagenomes

(2013) Hahk-Soo Kang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Multiplexing of Combinatorial Chemistry in Antimycin Biosynthesis: Expansion of Molecular Diversity and Utility

(2013) Yan Yan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Bacterium Induces Cryptic Meroterpenoid Pathway in the Pathogenic FungusAspergillus fumigatus

(2013) Claudia C. König et al.   CHEMBIOCHEM

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

High-level semi-synthetic production of the potent antimalarial artemisinin

(2013) C. J. Paddon et al.   NATURE

BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides

(2013) Auke J. van Heel et al.   NUCLEIC ACIDS RESEARCH

MS/MS networking guided analysis of molecule and gene cluster families

(2013) D. D. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules

(2013) R. D. Kersten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products

(2013) J. G. Owen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expanding the Fluorine Chemistry of Living Systems Using Engineered Polyketide Synthase Pathways

(2013) M. C. Walker et al.   SCIENCE

Discovery of a family of γ-aminobutyrate ureas via rational derepression of a silent bacterial gene cluster

(2013) John D. Sidda et al.   Chemical Science

Interspecies Interactions Stimulate Diversification of the Streptomyces coelicolor Secreted Metabolome

(2013) M. F. Traxler et al.   mBio

Activation and characterization of a cryptic polycyclic tetramate macrolactam biosynthetic gene cluster

(2013) Yunzi Luo et al.   Nature Communications

Selective Enrichment of Environmental DNA Libraries for Genes Encoding Nonribosomal Peptides and Polyketides by Phosphopantetheine Transferase-Dependent Complementation of Siderophore Biosynthesis

(2012) Zachary Charlop-Powers et al.   ACS Chemical Biology

Neutral Loss Fragmentation Pattern Based Screening for Arginine-Rich Natural Products in Xenorhabdus and Photorhabdus

(2012) Sebastian W. Fuchs et al.   ANALYTICAL CHEMISTRY

Learning from nature: new approaches to the metabolic engineering of plant defense pathways

(2012) Jan Jirschitzka et al.   CURRENT OPINION IN BIOTECHNOLOGY

A functional screen for recovery of 4′-phosphopantetheinyl transferase and associated natural product biosynthesis genes from metagenome libraries

(2012) J. G. Owen et al.   ENVIRONMENTAL MICROBIOLOGY

Two Separate Gene Clusters Encode the Biosynthetic Pathway for the Meroterpenoids Austinol and Dehydroaustinol in Aspergillus nidulans

(2012) Hsien-Chun Lo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A genomic approach to the cryptic secondary metabolome of the anaerobic world

(2012) Anne-Catrin Letzel et al.   NATURAL PRODUCT REPORTS

Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting

(2012) Jun Fu et al.   NATURE BIOTECHNOLOGY

The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity

(2012) Nadine Ziemert et al.   PLoS One

Genome streamlining and chemical defense in a coral reef symbiosis

(2012) J. C. Kwan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Myxoprincomide: A Natural Product from Myxococcus xanthus Discovered by Comprehensive Analysis of the Secondary Metabolome

(2011) Niña Socorro Cortina et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Directed Evolution of the Nonribosomal Peptide Synthetase AdmK Generates New Andrimid Derivatives In Vivo

(2011) Bradley S. Evans et al.   CHEMISTRY & BIOLOGY

Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler

(2011) Zengyi Shao et al.   Molecular BioSystems

A close relationship between primary nucleotides sequence structure and the composition of functional genes in the genome of prokaryotes

(2011) Juan A.L. Garcia et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A mass spectrometry–guided genome mining approach for natural product peptidogenomics

(2011) Roland D Kersten et al.   Nature Chemical Biology

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in Streptomyces ambofaciens

(2011) L. Laureti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria

(2010) J. W. Craig et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mycolic Acid-Containing Bacteria Induce Natural-Product Biosynthesis inStreptomycesSpecies

(2010) Hiroyasu Onaka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species

(2010) D. Nichols et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Aspernidine A and B, prenylated isoindolinone alkaloids from the model fungus Aspergillus nidulans

(2010) Kirstin Scherlach et al.   JOURNAL OF ANTIBIOTICS

Rare earth elements activate the secondary metabolite–biosynthetic gene clusters in Streptomyces coelicolor A3(2)

(2010) Yukinori Tanaka et al.   JOURNAL OF ANTIBIOTICS

Tailoring Enzyme-Rich Environmental DNA Clones: A Source of Enzymes for Generating Libraries of Unnatural Natural Products

(2010) Jacob J. Banik et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Post-PKS tailoring steps in natural product-producing actinomycetes from the perspective of combinatorial biosynthesis

(2010) Carlos Olano et al.   NATURAL PRODUCT REPORTS

NMR of natural products at the ‘nanomole-scale’

(2010) Tadeusz F. Molinski   NATURAL PRODUCT REPORTS

Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

(2010) P. K. Ajikumar et al.   SCIENCE

Natural Products from Environmental DNA Hosted inRalstonia metallidurans

(2009) Jeffrey W. Craig et al.   ACS Chemical Biology

Automated genome mining for natural products

(2009) Michael HT Li et al.   BMC BIOINFORMATICS

Identifying Natural Product Biosynthetic Genes from a Soil Metagenome by Using T7 Phage Selection

(2009) Keya Zhang et al.   CHEMBIOCHEM

Functional metagenomics for enzyme discovery: challenges to efficient screening

(2009) Taku Uchiyama et al.   CURRENT OPINION IN BIOTECHNOLOGY

Development of an Analysis Program of Type I Polyketide Synthase Gene Clusters Using Homology Search and Profile Hidden Markov Model

(2009) Kiejung Park   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Myxobacteria—‘microbial factories’ for the production of bioactive secondary metabolites

(2009) Silke C. Wenzel et al.   Molecular BioSystems

Genomic basis for natural product biosynthetic diversity in the actinomycetes

(2009) Markus Nett et al.   NATURAL PRODUCT REPORTS

Epigenome manipulation as a pathway to new natural product scaffolds and their congeners

(2009) Robert H. Cichewicz   NATURAL PRODUCT REPORTS

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Antibacterial discovery in actinomycetes strains with mutations in RNA polymerase or ribosomal protein S12

(2009) Takeshi Hosaka et al.   NATURE BIOTECHNOLOGY

Chromatin-level regulation of biosynthetic gene clusters

(2009) Jin Woo Bok et al.   Nature Chemical Biology

NtcA—A negative regulator of secondary metabolite biosynthesis in Sorangium cellulosum

(2008) S. Rachid et al.   JOURNAL OF BIOTECHNOLOGY

Extracellular signalling, translational control, two repressors and an activator all contribute to the regulation of methylenomycin production inStreptomyces coelicolor

(2008) Sean O'Rourke et al.   MOLECULAR MICROBIOLOGY

Epigenetic remodeling of the fungal secondary metabolome

(2008) Russell B. Williams et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

A chemical epigenetics approach for engineering the in situbiosynthesis of a cryptic natural product from Aspergillus niger

(2008) Jon C. Henrikson et al.   ORGANIC & BIOMOLECULAR CHEMISTRY