Large-scale culture as a complementary and practical method for discovering natural products with novel skeletons

2021 ◽  
Author(s):  
Zhengxi Hu ◽  
Ying Ye ◽  
Yonghui Zhang
Keyword(s):  
Natural Products ◽  
Large Scale ◽  
Genome Mining ◽  
Practical Method ◽  
Large Scale Culture

Large-scale culture is a complementary and practical method for genome mining and OSMAC approaches to discover natural products of unprecedented skeletal classes from fungi.

Antiviral activity of arylnaphthalene and aryldihydronaphthalene lignans

2000 ◽  
Vol 78 (5) ◽  
pp. 553-561 ◽  
Author(s):  
Christopher Cow ◽  
Carmen Leung ◽  
James L Charlton
Keyword(s):  
Natural Products ◽  
Antiviral Activity ◽  
Human Cytomegalovirus ◽  
Large Scale ◽  
Practical Method ◽  
The Common ◽  
Large Scale Synthesis ◽  
Regioselective Reactions

A practical method for large scale synthesis of 1-arylnaphthalene and 1-aryl-1,2-dihydronaphthalene lignans is described. The method makes use of the classic Stobbe condensation followed by regioselective reactions that provide access to both the common and retrolactone lignans, e.g., 2 and 3. A total of 25 compounds, many of which are known natural products, were prepared and their antiviral activity against human cytomegalovirus measured.Key words: lignan, Stobbe, arylnaphthalene, antiviral.

scholarly journals Coupling Mass Spectral and Genomic Information to Improve Bacterial Natural Product Discovery Workflows

Marine Drugs ◽  
2021 ◽  
Vol 19 (3) ◽  
pp. 142 ◽  
Author(s):  
Max Crüsemann
Keyword(s):  
Mass Spectrometry ◽  
Natural Products ◽  
Natural Product ◽  
Large Scale ◽  
Genome Mining ◽  
Structural Diversity ◽  
Gene Clusters ◽  
Genomic Information ◽  
Mass Spectral ◽  
Natural Product Discovery

Bacterial natural products possess potent bioactivities and high structural diversity and are typically encoded in biosynthetic gene clusters. Traditional natural product discovery approaches rely on UV- and bioassay-guided fractionation and are limited in terms of dereplication. Recent advances in mass spectrometry, sequencing and bioinformatics have led to large-scale accumulation of genomic and mass spectral data that is increasingly used for signature-based or correlation-based mass spectrometry genome mining approaches that enable rapid linking of metabolomic and genomic information to accelerate and rationalize natural product discovery. In this mini-review, these approaches are presented, and discovery examples provided. Finally, future opportunities and challenges for paired omics-based natural products discovery workflows are discussed.

scholarly journals An Interpreted Atlas of Biosynthetic Gene Clusters from 1000 Fungal Genomes

2020 ◽  
Author(s):  
Matthew T. Robey ◽  
Lindsay K. Caesar ◽  
Milton T. Drott ◽  
Nancy P. Keller ◽  
Neil L. Kelleher
Keyword(s):  
Natural Products ◽  
Large Scale ◽  
Ad Hoc ◽  
Chemical Space ◽  
Genome Mining ◽  
Fold Increase ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Fungal Genomes

AbstractFungi are prolific producers of natural products, compounds which have had a large societal impact as pharmaceuticals, mycotoxins, and agrochemicals. Despite the availability of over 1000 fungal genomes and several decades of compound discovery efforts from fungi, the biosynthetic gene clusters (BGCs) encoded by these genomes and the associated chemical space have yet to be analyzed systematically. Here we provide detailed annotation and analyses of fungal biosynthetic and chemical space to enable genome mining and discovery of fungal natural products. Using 1037 genomes from species across the fungal kingdom (e.g., Ascomycota, Basidiomycota, and non-Dikarya taxa), 36,399 predicted BGCs were organized into a network of 12,067 gene cluster families (GCFs). Anchoring these GCFs with reference BGCs enabled automated annotation of 2,026 BGCs with predicted metabolite scaffolds. We performed parallel analyses of the chemical repertoire of Fungi, organizing 15,213 fungal compounds into 2,945 molecular families (MFs). The taxonomic landscape of fungal GCFs is largely species-specific, though select families such as the equisetin GCF are present across vast phylogenetic distances with parallel diversifications in the GCF and MF. We compare these fungal datasets with a set of 5,453 bacterial genomes and their BGCs and 9,382 bacterial compounds, revealing dramatic differences between bacterial and fungal biosynthetic logic and chemical space. These genomics and cheminformatics analyses reveal the large extent to which fungal and bacterial sources represent distinct compound reservoirs. With a >10-fold increase in the number of interpreted strains and annotated BGCs, this work better regularizes the biosynthetic potential of fungi for rational compound discovery.Significance StatementFungi represent an underexploited resource for new compounds with applications in the pharmaceutical and agriscience industries. Despite the availability of >1000 fungal genomes, our knowledge of the biosynthetic space encoded by these genomes is limited and ad hoc. We present results from systematically organizing the biosynthetic content of 1037 fungal genomes, providing a resource for data-driven genome mining and large-scale comparison of the genetic and molecular repertoires produced in fungi and compare to those present in bacteria.

scholarly journals Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes

2015 ◽  
Vol 112 (39) ◽  
pp. 12175-12180 ◽  
Author(s):  
Kou-San Ju ◽  
Jiangtao Gao ◽  
James R. Doroghazi ◽  
Kwo-Kwang A. Wang ◽  
Christopher J. Thibodeaux ◽  
...  
Keyword(s):  
Natural Products ◽  
Phosphonic Acid ◽  
Large Scale ◽  
Genome Mining ◽  
Gene Clusters ◽  
High Rate ◽  
Phosphonic Acids ◽  
Strain Collection ◽  
Gene Level ◽  
Products Analysis

Although natural products have been a particularly rich source of human medicines, activity-based screening results in a very high rate of rediscovery of known molecules. Based on the large number of natural product biosynthetic genes in microbial genomes, many have proposed “genome mining” as an alternative approach for discovery efforts; however, this idea has yet to be performed experimentally on a large scale. Here, we demonstrate the feasibility of large-scale, high-throughput genome mining by screening a collection of over 10,000 actinomycetes for the genetic potential to make phosphonic acids, a class of natural products with diverse and useful bioactivities. Genome sequencing identified a diverse collection of phosphonate biosynthetic gene clusters within 278 strains. These clusters were classified into 64 distinct groups, of which 55 are likely to direct the synthesis of unknown compounds. Characterization of strains within five of these groups resulted in the discovery of a new archetypical pathway for phosphonate biosynthesis, the first (to our knowledge) dedicated pathway for H-phosphinates, and 11 previously undescribed phosphonic acid natural products. Among these compounds are argolaphos, a broad-spectrum antibacterial phosphonopeptide composed of aminomethylphosphonate in peptide linkage to a rare amino acid N5-hydroxyarginine; valinophos, an N-acetyl l-Val ester of 2,3-dihydroxypropylphosphonate; and phosphonocystoximate, an unusual thiohydroximate-containing molecule representing a new chemotype of sulfur-containing phosphonate natural products. Analysis of the genome sequences from the remaining strains suggests that the majority of the phosphonate biosynthetic repertoire of Actinobacteria has been captured at the gene level. This dereplicated strain collection now provides a reservoir of numerous, as yet undiscovered, phosphonate natural products.

Expanding the Natural Products Heterologous Expression Repertoire in the Model Cyanobacterium Anabaena sp. Strain PCC 7120: Production of Pendolmycin and Teleocidin B-4

2019 ◽  
Author(s):  
Patrick Videau ◽  
Kaitlyn Wells ◽  
Arun Singh ◽  
Jessie Eiting ◽  
Philip Proteau ◽  
...  
Keyword(s):  
Natural Products ◽  
Genome Mining ◽  
Gene Clusters ◽  
Combinatorial Biosynthesis ◽  
Test Case ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Cyanobacterium Anabaena ◽  
Anabaena Sp ◽  
Pcc 7120

Cyanobacteria are prolific producers of natural products and genome mining has shown that many orphan biosynthetic gene clusters can be found in sequenced cyanobacterial genomes. New tools and methodologies are required to investigate these biosynthetic gene clusters and here we present the use of <i>Anabaena </i>sp. strain PCC 7120 as a host for combinatorial biosynthesis of natural products using the indolactam natural products (lyngbyatoxin A, pendolmycin, and teleocidin B-4) as a test case. We were able to successfully produce all three compounds using codon optimized genes from Actinobacteria. We also introduce a new plasmid backbone based on the native <i>Anabaena</i>7120 plasmid pCC7120ζ and show that production of teleocidin B-4 can be accomplished using a two-plasmid system, which can be introduced by co-conjugation.

A Simple Synthesis of the Anticancer Drug Altretamine

2020 ◽  
Vol 17 (8) ◽  
pp. 628-630
Author(s):  
Vu Binh Duong ◽  
Pham Van Hien ◽  
Tran Thai Ngoc ◽  
Phan Dinh Chau ◽  
Tran Khac Vu
Keyword(s):  
Aqueous Solution ◽  
Anticancer Drug ◽  
Potassium Hydroxide ◽  
Large Scale ◽  
Synthesis Method ◽  
Practical Method ◽  
Cyanuric Chloride ◽  
Simple Synthesis ◽  
High Yield ◽  
One Step

A simple and practical method for the synthesis on a large scale of altretamine (1), a wellknown antitumor drug, has been successfully developed. The synthesis method involves the conversion of cyanuric chloride (2) into altretamine (1) by dimethylamination of 2 with an aqueous solution of 40% dimethylamine and potassium hydroxide in 1, -dioxan 4in one step to give altretamine (1) in high yield.

scholarly journals Biosynthetic pathways and enzymes involved in the production of phosphonic acid natural products

2021 ◽  
Vol 85 (1) ◽  
pp. 42-52
Author(s):  
Taro Shiraishi ◽  
Tomohisa Kuzuyama
Keyword(s):  
Natural Products ◽  
Biosynthetic Pathway ◽  
Organophosphorus Compounds ◽  
Genome Mining ◽  
Biological Molecules ◽  
Antibacterial Drug ◽  
Gene Encoding ◽  
Quarter Century ◽  
Lead Compounds ◽  
Biosynthetic Machinery

Abstract Phosphonates are organophosphorus compounds possessing a characteristic C−P bond in which phosphorus is directly bonded to carbon. As phosphonates mimic the phosphates and carboxylates of biological molecules to potentially inhibit metabolic enzymes, they could be lead compounds for the development of a variety of drugs. Fosfomycin (FM) is a representative phosphonate natural product that is widely used as an antibacterial drug. Here, we review the biosynthesis of FM, which includes a recent breakthrough to find a missing link in the biosynthetic pathway that had been a mystery for a quarter-century. In addition, we describe the genome mining of phosphonate natural products using the biosynthetic gene encoding an enzyme that catalyzes C–P bond formation. We also introduce the chemoenzymatic synthesis of phosphonate derivatives. These studies expand the repertoires of phosphonates and the related biosynthetic machinery. This review mainly covers the years 2012-2020.

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