Constructing a Myxobacterial Natural Product Database to Facilitate NMR-Based Metabolomics Bioprospecting of Myxobacteria

Myxobacteria are fascinating prokaryotes featuring a potent capacity for producing a wealth of bioactive molecules with intricate chemical topology as well as intriguing enzymology, and thus it is critical to developing an efficient pipeline for bioprospecting. Herein, we construct the database MyxoDB, the first public compendium solely dedicated to myxobacteria, which enabled us to provide an overview of the structural diversity and taxonomic distribution of known myxobacterial natural products. Moreover, we demonstrated that the cutting-edge NMR-based metabolomics was effective to differentiate the biosynthetic priority of myxobacteria, whereby MyxoDB could greatly streamline the dereplication of multifarious known compounds and accordingly speed up the discovery of new compounds. This led to the rapid identification of a class of linear di-lipopeptides (archangimins) and a rare rearranged sterol (corasterol) that were endowed with unique chemical architectures and/or biosynthetic enzymology. We also showcased that NMR-based metabolomics, MyxoDB, and genomics can also work concertedly to accelerate the targeted discovery of a polyketidic compound pyxipyrrolone C. All in all, this study sets the stage for the discovery of many more novel natural products from underexplored myxobacterial resources.

Antiplasmodial and antimycobacterial activities of crude and lead-like enhanced extracts from Namibian medicinal plants

ETHNOPHARMACOLOGICAL RELEVANCE

Eight indigenous medicinal plants which are used traditionally for the treatment of tuberculosis (TB), malaria, and associated symptoms, were selected for this study.

AIM OF STUDY

The aim of this study was to evaluate the antiplasmodial and antimycobacterial activities of the organic and aqueous crude extracts of different plant parts, by comparing the activities of subfractions (lead-like enhanced [LLE] extracts and methanol fractions) prepared from the bioactive crude extracts.

MATERIALS & METHODS

Crude aqueous and organic extracts were prepared for 25 different plant parts obtained from eight plant species. In vitro antiplasmodial activity was evaluated using the parasite lactate dehydrogenase assay against chloroquine-sensitive Plasmodium falciparum NF54 and in vitro antimycobacterial activity determined against the Mycobacterium tuberculosis H37Rv-GFP strain in a standard broth microdilution assay. The bioactive crude extracts were subjected to solid phase extraction with Strata-X 33 μm reversed phase cartridges and eluted with 70:30 MeOH: H₂O:1% trifluoroacetic acid to yield the LLE extract, followed by a methanol rinse, herein referred to as the MeOH fraction. Both fractions were evaluated for antiplasmodial and antimycobacterial activity. Proton nuclear magnetic resonance spectroscopy (¹H-NMR) and ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) profiling of the crude and active fractions of the phytochemically unexplored Sarcocaulon marlothii Engl. were performed to aid the identification of a potential antiplasmodial lead compound.

RESULTS

Ten of the aqueous and organic crude extracts displayed antimycobacterial activity, with minimum inhibitory concentration (MIC₉₀) values ranging from 9.9 to 86.8 μg/mL, and four crude extracts showed antiplasmodial activity with inhibitory concentration (IC₅₀) values between 5.2 and 17.8 μg/mL. Although the stems of S. marlothii are traditionally used to treat TB and related symptoms, the two crude extracts displayed weak antimycobacterial activity (MIC₉₀ > 100 μg/mL) while the crude organic extract displayed moderate antiplasmodial activity with an IC₅₀ value of 8.8 μg/mL. None of the LLE extracts prepared from the ten antimycobacterial-active crudes displayed any significant activity (MIC₉₀ > 125 μg/mL). In contrast, fractionation of three antiplasmodial-active, crude organic extracts yielded MeOH fractions which displayed a 2-fold to 19-fold increase in activity. The ¹H-NMR profiles of the active MeOH fraction (IC₅₀ 4.3 μg/mL) of S. marlothii (organic, stem) revealed the likely presence of an unidentified trisubstituted cinnamic acid derivative as one of the major compounds and UPLC-MS/MS data provided additional evidence that the compound may be a hydroxycinnamic acid derivative. Unfortunately, owing to the paucity of the material obtained, we were unable to purify and unequivocally determine the structure of this active compound.

CONCLUSIONS

This is the first report on the phytochemical profiling of S. marlothii and, based on the antiplasmodial activity recorded, it merits an in-depth phytochemical analysis for the unequivocal characterization of a potential antiplasmodial lead compound. Results from this study lend support to the effectiveness of extract enrichment in combination with NMR fingerprinting for antiplasmodial lead identification.

Marine Actinomycetes-derived Natural Products

Actinomycetes is an abundant resource for discovering a large number of lead compounds, which play an important role in microbial drug discovery. Compared to terrestrial microorganisms, marine actinomycetes have unique metabolic pathways because of their special living environment, which has the potential to produce a variety of bioactive substances. In this paper, secondary metabolites isolated from marine actinomycetes are reviewed (2013-2018), most of which exhibited cytotoxic, antibacterial, and antiviral biological activities.

Efomycins K and L From a Termite-Associated Streptomyces sp. M56 and Their Putative Biosynthetic Origin

Two new elaiophylin derivatives, efomycins K (1) and L (2), and five known elaiophylin derivatives (3–7) were isolated from the termite-associated Streptomyces sp. M56. The structures were determined by 1D and 2D NMR and HR-ESIMS analyses and comparative CD spectroscopy. The putative gene cluster responsible for the production of the elaiophylin and efomycin derivatives was identified based on significant homology to related clusters. Phylogenetic analysis of gene cluster domains was used to provide a biosynthetic rational for these new derivatives and to demonstrate how a single biosynthetic pathway can produce diverse structures.

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

Screening and identification of novel biologically active natural compounds

With the advent of very rapid and cheap genome analyses and the linkage of these plus microbial metabolomics to potential compound structures came the realization that there was an immense sea of novel agents to be mined and tested. In addition, it is now recognized that there is significant microbial involvement in many natural products isolated from “nominally non-microbial sources”.

This short review covers the current screening methods that have evolved and one might even be tempted to say “devolved” in light of the realization that target-based screens had problems when the products entered clinical testing, with off-target effects being the major ones. Modern systems include, but are not limited to, screening in cell lines utilizing very modern techniques (a high content screen) that are designed to show interactions within cells when treated with an “agent”. The underlying principle(s) used in such systems dated back to unpublished attempts in the very early 1980s by the pharmaceutical industry to show toxic interactions within animal cells by using automated light microscopy. Though somewhat successful, the technology was not adequate for any significant commercialization. Somewhat later, mammalian cell lines that were “genetically modified” to alter signal transduction cascades, either up or down, and frequently linked to luciferase readouts, were then employed in a 96-well format. In the case of microbes, specific resistance parameters were induced in isogenic cell lines from approximately the mid-1970s. In the latter two cases, comparisons against parent and sibling cell lines were used in order that a rapid determination of potential natural product “hits” could be made. Obviously, all of these assay systems could also be, and were, used for synthetic molecules.

These methods and their results have led to a change in what the term “screening for bioactivity” means. In practice, versions of phenotypic screening are returning, but in a dramatically different scientific environment from the 1970s, as I hope to demonstrate in the short article that follows.

Revisiting biodiscovery from microbial sources in the light of molecular advances

Since the discovery of penicillin microorganisms have been an unexhausted source of novel bioactive compounds that served as scaffolds for potential drug candidates as well for the development of new antibiotics via fermentative processes. However, after 30 glorious years of biodiscovery begun in the 1940s, discovery of new antibiotic or therapeutic compounds with medicinal value entered a decline phase from the late 1970s onwards. At the same time, significant increases in the numbers of antibiotic or multi-drug resistant bacteria resulting in serious infections were reported. Although natural product discovery research was encouraged to continue due to the need to treat these infections only a few discoveries of potent antibiotics were made in the years of decline such as the discovery of Nikkomycin and Spinosyn. However, at the dawn of the 21st century advances in molecular biology such as genome mining and metabolic engineering changed the scene providing new avenues to the field of drug discovery. This article will highlight some of these advances.

Computational investigation of the interaction mechanism between the estrogen related receptor α and its agonists

The agonists may promote the binding of coactivator PGC-1α to ERRα by stabilizing the conformation and the site of H12.