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.

scholarly journals Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors

Marine Drugs ◽  
2020 ◽  
Vol 18 (2) ◽  
pp. 124 ◽  
Author(s):  
Ipsita Mohanty ◽  
Sheila Podell ◽  
Jason S. Biggs ◽  
Neha Garg ◽  
Eric E. Allen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Natural Products ◽  
Candidate Gene ◽  
Marine Sponge ◽  
Gene Clusters ◽  
Marine Sponges ◽  
Quantitative Comparison ◽  
Filter Feeding ◽  
Chemical Structures ◽  
Ecological Relevance

Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor a far greater diversity of low-abundance natural products that have evaded discovery. While these low-abundance natural products may not be feasible to isolate, insights into their chemical structures can be gleaned by careful curation of mass fragmentation spectra. Sponges are also some of the most complex, multi-organismal holobiont communities in the oceans. We overlay sponge metabolomes with their microbiome structures and detailed metagenomic characterization to discover candidate gene clusters that encode production of sponge-derived natural products. The multi-omic profiling strategy for sponges that we describe here enables quantitative comparison of sponge metabolomes and microbiomes to address, among other questions, the ecological relevance of sponge natural products and for the phylochemical assignment of previously undescribed sponge identities.

scholarly journals Biological and Chemical Diversity of Marine Sponge-Derived Microorganisms over the Last Two Decades from 1998 to 2017

Molecules ◽  
2020 ◽  
Vol 25 (4) ◽  
pp. 853 ◽  
Author(s):  
Mei-Mei Cheng ◽  
Xu-Li Tang ◽  
Yan-Ting Sun ◽  
Dong-Yang Song ◽  
Yu-Jing Cheng ◽  
...  
Keyword(s):  
Natural Products ◽  
Secondary Metabolites ◽  
Natural Product ◽  
Marine Sponge ◽  
Marine Sponges ◽  
Chemical Diversity ◽  
Comprehensive Overview ◽  
Bioactive Secondary Metabolites ◽  
The Relationship ◽  
Product Chemistry

Marine sponges are well known as rich sources of biologically natural products. Growing evidence indicates that sponges harbor a wealth of microorganisms in their bodies, which are likely to be the true producers of bioactive secondary metabolites. In order to promote the study of natural product chemistry and explore the relationship between microorganisms and their sponge hosts, in this review, we give a comprehensive overview of the structures, sources, and activities of the 774 new marine natural products from sponge-derived microorganisms described over the last two decades from 1998 to 2017.

Unzipping Natural Products: Improved Natural Product Structure Predictions by Ensemble Modeling and Fingerprint Matching

2018 ◽  
Author(s):  
William A. Shirley ◽  
Brian P. Kelley ◽  
Yohann Potier ◽  
John H. Koschwanez ◽  
Robert Bruccoleri ◽  
...  
Keyword(s):  
Natural Products ◽  
Open Source ◽  
Natural Product ◽  
Gene Cluster ◽  
Public Domain ◽  
Product Structure ◽  
Fingerprint Matching ◽  
Ensemble Modeling ◽  
Chemical Structures ◽  
Source Gene

This pre-print explores ensemble modeling of natural product targets to match chemical structures to precursors found in large open-source gene cluster repository antiSMASH. Commentary on method, effectiveness, and limitations are enclosed. All structures are public domain molecules and have been reviewed for release.

scholarly journals Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB

Metabolites ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 48
Author(s):  
Marc Feuermann ◽  
Emmanuel Boutet ◽  
Anne Morgat ◽  
Kristian Axelsen ◽  
Parit Bansal ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Semantic Web Technologies ◽  
Knowledge Resources ◽  
Web Technologies ◽  
Chemical Structures ◽  
Biological Interest ◽  
Catalyzed Reactions ◽  
Enzyme Catalyzed Reactions ◽  
Practical Demonstration

The UniProt Knowledgebase UniProtKB is a comprehensive, high-quality, and freely accessible resource of protein sequences and functional annotation that covers genomes and proteomes from tens of thousands of taxa, including a broad range of plants and microorganisms producing natural products of medical, nutritional, and agronomical interest. Here we describe work that enhances the utility of UniProtKB as a support for both the study of natural products and for their discovery. The foundation of this work is an improved representation of natural product metabolism in UniProtKB using Rhea, an expert-curated knowledgebase of biochemical reactions, that is built on the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Knowledge of natural products and precursors is captured in ChEBI, enzyme-catalyzed reactions in Rhea, and enzymes in UniProtKB/Swiss-Prot, thereby linking chemical structure data directly to protein knowledge. We provide a practical demonstration of how users can search UniProtKB for protein knowledge relevant to natural products through interactive or programmatic queries using metabolite names and synonyms, chemical identifiers, chemical classes, and chemical structures and show how to federate UniProtKB with other data and knowledge resources and tools using semantic web technologies such as RDF and SPARQL. All UniProtKB data are freely available for download in a broad range of formats for users to further mine or exploit as an annotation source, to enrich other natural product datasets and databases.

scholarly journals Estudo do tautomerismo ceto-enólico da 7-epi-clusianona através de cálculos teóricos de deslocamentos químicos de RMN

2020 ◽  
Author(s):  
Ana Carolina Ferreira de Albuquerque ◽  
José Walkimar de Mesquita Carneiro ◽  
Fernando Martins dos Santos Junior
Keyword(s):  
Natural Products ◽  
Structural Characterization ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Spectroscopic Techniques ◽  
Chemical Structures ◽  
Nmr Parameters

The properties of natural products, including their biological and pharmacological activities, are directly correlated with their chemical structures. Thus, a correct structural characterization of these compounds is a crucial step to the understanding of their biological activities. However, despite the recent advances in spectroscopic techniques, structural studies of natural products can be challenging. This way, theoretical calculations of Nuclear Magnetic Resonance (NMR) parameters (such as chemical shifts and coupling constants) have proven to be a powerful and low-cost tool for the aid to experimental techniques traditionally used for the structural characterization of natural products. One of the several applications of quantum-mechanical calculations of NMR parameters is the study of tautomerism. Since chemical shifts are sensitive to the tautomeric equilibrium, this technique can provide crucial informations. In this work, it was applied a protocol for theoretical calculations of ¹³C chemical shifts in order to study the tautomerism of the natural product 7-epi-clusianone, isolated from Rheedia gardneriana. This protocol consists in a Monte Carlo conformational search, followed by geometry optimization and shielding tensors calculations, both using a density functional level of theory. After comparison of theoretical and experimental data, it was possible to confirm the two tautomers present in equilibrium in the experimental solution. Furthermore, this study highlights how this theoretical protocol can be an effective method in identifying the preferred tautomeric form in solution.

scholarly journals All-carbon [3 + 2] cycloaddition in natural product synthesis

2020 ◽  
Vol 16 ◽  
pp. 3015-3031
Author(s):  
Zhuo Wang ◽  
Junyang Liu
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Structural Features ◽  
Single Step ◽  
Natural Product Synthesis ◽  
Synthetic Chemistry ◽  
Quaternary Centers ◽  
Chemical Structures ◽  
Quaternary Center ◽  
Medicinal Properties

Many natural products possess interesting medicinal properties that arise from their intriguing chemical structures. The highly-substituted carbocycle is one of the most common structural features in many structurally complicated natural products. However, the construction of highly-substituted, stereo-congested, five-membered carbocycles containing all-carbon quaternary center(s) is, at present, a distinct challenge in modern synthetic chemistry, which can be accessed through the all-carbon [3 + 2] cycloaddition. More importantly, the all-carbon [3 + 2] cycloaddition can forge vicinal all-carbon quaternary centers in a single step and has been demonstrated in the synthesis of complex natural products. In this review, we present the development of all-carbon [3 + 2] cycloadditions and illustrate their application in natural product synthesis reported in the last decade covering 2011–2020 (inclusive).

A Recent Look into Natural Products that have Potential to Inhibit Cholinesterases and Monoamine Oxidase B: Update for 2010-2019

2020 ◽  
Vol 23 (9) ◽  
pp. 862-876
Author(s):  
Hayrettin O. Gulcan ◽  
Ilkay E. Orhan
Keyword(s):  
Natural Products ◽  
Monoamine Oxidase ◽  
Natural Product ◽  
Biological Activities ◽  
Treatment Options ◽  
Monoamine Oxidase B ◽  
Chemical Structures ◽  
Natural Agents ◽  
Natural Product Research ◽  
Multiple Receptors

With respect to the unknowns of pathophysiology of Alzheimer’s Disease (AD)-, and Parkinson’s Disease (PD)-like neurodegenerative disorders, natural product research is still one of the valid tools in order to provide alternative and/or better treatment options. At one hand, various extracts of herbals provide a combination of actions targeting multiple receptors, on the other hand, the discovery of active natural products (i.e., secondary metabolites) generally offers alternative chemical structures either ready to be employed in clinical studies or available to be utilized as important scaffolds for the design of novel agents. Regarding the importance of certain enzymes (e.g. cholinesterase and monoamine oxidase B), for the treatment of AD and PD, we have surveyed the natural product research within this area in the last decade. Particularly novel natural agents discovered within this period, concomitant to novel biological activities displayed for known natural products, are harmonized within the present study.

scholarly journals A Review of the Secondary Metabolites From the Marine Sponges of the Genus Aaptos

2020 ◽  
Vol 15 (9) ◽  
pp. 1934578X2095143
Author(s):  
Qianqian He ◽  
Shuang Miao ◽  
Na Ni ◽  
Yuqing Man ◽  
Kaikai Gong
Keyword(s):  
Natural Products ◽  
Secondary Metabolites ◽  
Natural Product ◽  
Chemical Ecology ◽  
Marine Natural Products ◽  
Organic Molecules ◽  
Biological Activities ◽  
Marine Sponges ◽  
Marine Natural Product ◽  
Natural Product Research

Marine sponges, which belong to the phylum Porifera (Metazoa), are considered the single best source of marine natural products. Among them, members of the genus Aaptos are attractive targets for marine natural product research owing to their abundant biogenetic ability to produce aaptamine derivatives. Apart from aaptamine alkaloids, there are also reports of other compounds from Aaptos sponges. This work reviews the secondary metabolites isolated from Aaptos species from 1982 to 2020, with 46 citations referring to 62 compounds (47 for aaptamines and 15 for others). The emphasis is placed on the structure of the organic molecules, relevant biological activities, chemical ecology aspects, and biosynthesis studies, which are described in the classifications of aaptamines and other compounds in the order of the published year.

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 Targeting Multiple Myeloma Cancer Stem Cells with Natural Products – Lessons from Other Hematological Malignancies

Planta Medica ◽  
2017 ◽  
Vol 83 (09) ◽  
pp. 752-760 ◽  
Author(s):  
Mark Issa ◽  
Sylvian Cretton ◽  
Muriel Cuendet
Keyword(s):  
Stem Cells ◽  
Multiple Myeloma ◽  
Natural Products ◽  
Cancer Stem Cells ◽  
Hematological Malignancies ◽  
Plasma Cells ◽  
Chemical Structures ◽  
Recent Advances ◽  
Promising Therapeutic Approach

AbstractMultiple myeloma is characterized by the accumulation of malignant plasma cells in the bone marrow. Multiple myeloma is the second most frequently diagnosed hematological malignancy, predominantly affecting the elderly. Despite recent advances in the development of novel therapies, multiple myeloma remains an incurable malignancy where the majority of patients relapse, develop resistance, and eventually die from the disease. This has been attributed to the fact that conventional therapy currently in use targets mainly the bulk of tumor cells, but not the tumor-initiating cancer stem cells. Cancer stem cells are a highly resistant subpopulation of cells believed to be responsible for the initiation, progression, metastasis, and relapse of cancer. Enormous efforts have been invested in the characterization of cancer stem cells. These efforts led to the characterization of key cellular signaling pathways responsible for conferring stem cell characteristics including self-renewal, differentiation, migratory, survival, and intracellular detoxification capabilities. Targeting these protective mechanisms offers a valuable strategy that may help combat a major driving force behind cancers. The use of natural products offers a promising therapeutic approach for targeting cancer stem cells. In this review, recent advances achieved in the characterization of cancer stem cells derived from hematological malignancies, with a particular focus on multiple myeloma, are discussed and major natural products that target cancer stem cells are presented. As natural products remain an essential source of novel chemical structures and medicinal leads, the exploitation of this immense reservoir is used to draw lessons in targeting multiple myeloma-cancer stem cells.

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