scholarly journals NPBS database: a chemical data resource with relational data between natural products and biological sources

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Tingjun Xu ◽  
Weiming Chen ◽  
Junhong Zhou ◽  
Jingfang Dai ◽  
Yingyong Li ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Chemical Structure ◽  
Chemical Data ◽  
Relational Data ◽  
Data Link ◽  
Data Resource ◽  
Biological Sources ◽  
Specific Species

Abstract NPBS (Natural Products & Biological Sources) database is a chemical data resource with relational data between natural products and biological sources, manually curated from literatures of natural product researches. The relational data link a specific species and all the natural products derived from it and contrarily link a specific natural product and all the biological sources. The biological sources cover diverse species of plant, bacterial, fungal and marine organisms; the natural molecules have proper chemical structure data and computable molecular properties and all the relational data have corresponding references. NPBS database provides a wider choice of biological sources and can be used for dereplication to prevent re-isolation and re-characterization of already known natural products. Database URL: http://www.organchem.csdb.cn/scdb/NPBS

scholarly journals NPBS database: a chemical data resource with relational data between natural products and biological sources

2021 ◽  
Author(s):  
Tingjun Xu ◽  
Weiming Chen ◽  
Junhong Zhou ◽  
Jingfang Dai ◽  
Yingyong Li ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Marine Organism ◽  
Chemical Data ◽  
Relational Data ◽  
Data Resource ◽  
Data Links ◽  
Natural Product Research ◽  
Biological Sources ◽  
Specific Species

Abstract NPBS (Natural Products & Biological Sources) database is a chemical data resource with relational data between natural products and biological sources, manually curated from literatures of natural product research. The relational data links a specific species and all the natural products derived from it, contrarily, links a specific natural product and all the biological sources. The biological sources cover diverse species of plant, bacterial, fungal and marine organism, the natural molecules have proper chemical structure data and computable molecular properties, and all the relational data have corresponding references. NPBS database provides a wider choice of biological sources, and can be used for dereplication to prevent re-isolation and re-characterization of already known natural products.

scholarly journals NPDB: a natural product database with relational data between natural products and biological sources

2020 ◽  
Author(s):  
Tingjun Xu ◽  
Jingfang Dai ◽  
Weiming Chen ◽  
Yingyong Li ◽  
Yingli Zhao ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Product Information ◽  
Relational Data ◽  
Holistic View ◽  
Biological Sources

Abstract We designed a natural product database filled with hand-curated data of natural product information from journal literatures, to establish the relationships between natural products and biological sources. Therefore, we can figure out all the biological sources of a specific natural product reported in literatures, and also can inspect for the holistic view of a specific organism’s components, metabolites or extracts.

scholarly journals A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria

Marine Drugs ◽  
2021 ◽  
Vol 19 (1) ◽  
pp. 20
Author(s):  
Tiago Leão ◽  
Mingxun Wang ◽  
Nathan Moss ◽  
Ricardo da Silva ◽  
Jon Sanders ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Genome Mining ◽  
Gene Clusters ◽  
Microbial Interactions ◽  
Marine Cyanobacteria ◽  
Pharmaceutical Drugs ◽  
Genes Encoding ◽  
Microbial Natural Products

Microbial natural products are important for the understanding of microbial interactions, chemical defense and communication, and have also served as an inspirational source for numerous pharmaceutical drugs. Tropical marine cyanobacteria have been highlighted as a great source of new natural products, however, few reports have appeared wherein a multi-omics approach has been used to study their natural products potential (i.e., reports are often focused on an individual natural product and its biosynthesis). This study focuses on describing the natural product genetic potential as well as the expressed natural product molecules in benthic tropical cyanobacteria. We collected from several sites around the world and sequenced the genomes of 24 tropical filamentous marine cyanobacteria. The informatics program antiSMASH was used to annotate the major classes of gene clusters. BiG-SCAPE phylum-wide analysis revealed the most promising strains for natural product discovery among these cyanobacteria. LCMS/MS-based metabolomics highlighted the most abundant molecules and molecular classes among 10 of these marine cyanobacterial samples. We observed that despite many genes encoding for peptidic natural products, peptides were not as abundant as lipids and lipopeptides in the chemical extracts. Our results highlight a number of highly interesting biosynthetic gene clusters for genome mining among these cyanobacterial samples.

scholarly journals Asymmetric Alkene and Arene Halofunctionalization Reactions in Meroterpenoid Biosynthesis

Synlett ◽  
2017 ◽  
Vol 29 (04) ◽  
pp. 401-409 ◽  
Author(s):  
Bradley Moore
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Bioactive Molecules ◽  
Broad Distribution ◽  
Rearrangement Reactions

Meroterpenoid natural products are important bioactive molecules with broad distribution throughout nature. In Streptomyces bacteria, naphthoquinone-based meroterpenoids comprise a simple yet structurally fascinating group of natural product antibiotics that are enzymatically constructed through a series of asymmetric alkene and arene halofunctionalization reactions. This account article highlights our discovery and characterization of a group of vanadium-dependent chloroperoxidase enzymes that catalyze halogen-assisted cyclization and rearrangement reactions and have inspired biomimetic syntheses of numerous meroterpenoid natural products.1 Introduction2 Early Biosynthetic Insights and the Characterization of Alkene Halofunctionalization in Napyradiomycin Biosynthesis3 Discovery of the Merochlorin Natural Products and Enzymatic Aryl Halofunctionalization4 Discovery and Development of Unifying THN-Based Meroterpenoid Biosynthesis and Synthesis Approaches5 Insights into Naphterpin and Marinone Biosynthesis Involving Cryptic Aryl Halofunctionalization Reactions6 Closing Thoughts

scholarly journals Structure elucidation and biosynthesis of fuscachelins, peptide siderophores from the moderate thermophileThermobifida fusca

2008 ◽  
Vol 105 (40) ◽  
pp. 15311-15316 ◽  
Author(s):  
Eric J. Dimise ◽  
Paul F. Widboom ◽  
Steven D. Bruner
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Gene Cluster ◽  
Structure Elucidation ◽  
Biochemical Characterization ◽  
Gene Clusters ◽  
Biologically Active ◽  
Biosynthetic Gene ◽  
Nonribosomal Peptide

Bacteria belonging to the order Actinomycetales have proven to be an important source of biologically active and often therapeutically useful natural products. The characterization of orphan biosynthetic gene clusters is an emerging and valuable approach to the discovery of novel small molecules. Analysis of the recently sequenced genome of the thermophilic actinomyceteThermobifida fuscarevealed an orphan nonribosomal peptide biosynthetic gene cluster coding for an unknown siderophore natural product.T. fuscais a model organism for the study of thermostable cellulases and is a major degrader of plant cell walls. Here, we report the isolation and structure elucidation of the fuscachelins, siderophore natural products produced byT. fusca. In addition, we report the purification and biochemical characterization of the termination module of the nonribosomal peptide synthetase. Biochemical analysis of adenylation domain specificity supports the assignment of this gene cluster as the producer of the fuscachelin siderophores. The proposed nonribosomal peptide biosynthetic pathway exhibits several atypical features, including a macrocyclizing thioesterase that produces a 10-membered cyclic depsipeptide and a nonlinear assembly line, resulting in the unique heterodimeric architecture of the siderophore natural product.

scholarly journals Presence of Bromotyrosine Alkaloids in Marine Sponges Is Independent of Metabolomic and Microbiome Architectures

mSystems ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Ipsita Mohanty ◽  
Subhasish Tapadar ◽  
Samuel G. Moore ◽  
Jason S. Biggs ◽  
Christopher J. Freeman ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Marine Sponge ◽  
Solomon Islands ◽  
Florida Keys ◽  
Marine Sponges ◽  
Microbial Abundance ◽  
Chemical Structures ◽  
Geographical Dispersion

ABSTRACT Marine sponge holobionts are prolific sources of natural products. One of the most geographically widespread classes of sponge-derived natural products is the bromotyrosine alkaloids. A distinguishing feature of bromotyrosine alkaloids is that they are present in phylogenetically disparate sponges. In this study, using sponge specimens collected from Guam, the Solomon Islands, the Florida Keys, and Puerto Rico, we queried whether the presence of bromotyrosine alkaloids potentiates metabolomic and microbiome conservation among geographically distant and phylogenetically different marine sponges. A multi-omic characterization of sponge holobionts revealed vastly different metabolomic and microbiome architectures among different bromotyrosine alkaloid-harboring sponges. However, we find statistically significant correlations between the microbiomes and metabolomes, signifying that the microbiome plays an important role in shaping the overall metabolome, even in low-microbial-abundance sponges. Molecules mined from the polar metabolomes of these sponges revealed conservation of biosynthetic logic between bromotyrosine alkaloids and brominated pyrrole-imidazole alkaloids, another class of marine sponge-derived natural products. In light of prior findings postulating the sponge host itself to be the biosynthetic source of bromotyrosine alkaloids, our data now set the stage for investigating the causal relationships that dictate the microbiome-metabolome interconnectedness for marine sponges in which the microbiome may not contribute to natural product biogenesis. IMPORTANCE Our work demonstrates that phylogenetically and geographically distant sponges with very different microbiomes can harbor natural product chemical classes that are united in their core chemical structures and biosynthetic logic. Furthermore, we show that independent of geographical dispersion, natural product chemistry, and microbial abundance, overall sponge metabolomes tightly correlate with their microbiomes.

Recent advances in the use of vibrational chiroptical spectroscopic methods for stereochemical characterization of natural products

2015 ◽  
Vol 32 (9) ◽  
pp. 1280-1302 ◽  
Author(s):  
João M. Batista Jr. ◽  
Ewan W. Blanch ◽  
Vanderlan da Silva Bolzani
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Optical Activity ◽  
Spectroscopic Methods ◽  
Recent Advances

A comprehensive look into application of vibrational optical activity methods for conformational and configurational assignments in natural product molecules over the last 15 years is provided.

scholarly journals Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products

2020 ◽  
Author(s):  
Tessa B. Moyer ◽  
Nicole C. Parsley ◽  
Patric W. Sadecki ◽  
Wyatt J. Schug ◽  
Leslie M. Hicks
Keyword(s):  
Mass Spectrometry ◽  
Natural Products ◽  
Antimicrobial Peptide ◽  
Natural Product ◽  
Peptide Characterization

Strategies to accelerate natural product peptide characterization.

scholarly journals Thiocysteine lyases as polyketide synthase domains installing hydropersulfide into natural products and a hydropersulfide methyltransferase

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Song Meng ◽  
Andrew D. Steele ◽  
Wei Yan ◽  
Guohui Pan ◽  
Edward Kalkreuter ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Assembly Line ◽  
Polyketide Synthase ◽  
Genome Mining ◽  
Assembly Lines ◽  
Biologically Relevant ◽  
Peptide Synthetase ◽  
Adenosyl Methionine

AbstractNature forms S-S bonds by oxidizing two sulfhydryl groups, and no enzyme installing an intact hydropersulfide (-SSH) group into a natural product has been identified to date. The leinamycin (LNM) family of natural products features intact S-S bonds, and previously we reported an SH domain (LnmJ-SH) within the LNM hybrid nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) assembly line as a cysteine lyase that plays a role in sulfur incorporation. Here we report the characterization of an S-adenosyl methionine (SAM)-dependent hydropersulfide methyltransferase (GnmP) for guangnanmycin (GNM) biosynthesis, discovery of hydropersulfides as the nascent products of the GNM and LNM hybrid NRPS-PKS assembly lines, and revelation of three SH domains (GnmT-SH, LnmJ-SH, and WsmR-SH) within the GNM, LNM, and weishanmycin (WSM) hybrid NRPS-PKS assembly lines as thiocysteine lyases. Based on these findings, we propose a biosynthetic model for the LNM family of natural products, featuring thiocysteine lyases as PKS domains that directly install a -SSH group into the GNM, LNM, or WSM polyketide scaffold. Genome mining reveals that SH domains are widespread in Nature, extending beyond the LNM family of natural products. The SH domains could also be leveraged as biocatalysts to install an -SSH group into other biologically relevant scaffolds.

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