Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data

Feature-based molecular networking (FBMN) is a popular analysis approach for liquid chromatography-tandem mass spectrometry-based non-targeted metabolomics data. While processing liquid chromatography-tandem mass spectrometry data through FBMN is fairly streamlined, downstream data handling and statistical interrogation are often a key bottleneck. Especially users new to statistical analysis struggle to effectively handle and analyze complex data matrices. Here we provide a comprehensive guide for the statistical analysis of FBMN results, focusing on the downstream analysis of the FBMN output table. We explain the data structure and principles of data cleanup and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. All code is shared in the form of Jupyter Notebooks ( https://github.com/Functional-Metabolomics-Lab/FBMN-STATS ). Additionally, the protocol is accompanied by a web application with a graphical user interface ( https://fbmn-statsguide.gnps2.org/ ) to lower the barrier of entry for new users and for educational purposes. Finally, we also show users how to integrate their statistical results into the molecular network using the Cytoscape visualization tool. Throughout the protocol, we use a previously published environmental metabolomics dataset for demonstration purposes. Together, the protocol, code and web application provide a complete guide and toolbox for FBMN data integration, cleanup and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking and can be easily adapted to other mass spectrometry feature detection, annotation and networking tools.

Unveiling biosynthetic potential of an Arctic marine-derived strain Aspergillus sydowii MNP-2

BACKGROUND

A growing number of studies have demonstrated that the polar regions have the potential to be a significant repository of microbial resources and a potential source of active ingredients. Genome mining strategy plays a key role in the discovery of bioactive secondary metabolites (SMs) from microorganisms. This work highlighted deciphering the biosynthetic potential of an Arctic marine-derived strain Aspergillus sydowii MNP-2 by a combination of whole genome analysis and antiSMASH as well as feature-based molecular networking (MN) in the Global Natural Products Social Molecular Networking (GNPS).

RESULTS

In this study, a high-quality whole genome sequence of an Arctic marine strain MNP-2, with a size of 34.9 Mb was successfully obtained. Its total number of genes predicted by BRAKER software was 13,218, and that of non-coding RNAs (rRNA, sRNA, snRNA, and tRNA) predicted by using INFERNAL software was 204. AntiSMASH results indicated that strain MNP-2 harbors 56 biosynthetic gene clusters (BGCs), including 18 NRPS/NRPS-like gene clusters, 10 PKS/PKS-like gene clusters, 8 terpene synthse gene clusters, 5 indole synthase gene clusters, 10 hybrid gene clusters, and 5 fungal-RiPP gene clusters. Metabolic analyses of strain MNP-2 grown on various media using GNPS networking revealed its great potential for the biosynthesis of bioactive SMs containing a variety of heterocyclic and bridge-ring structures. For example, compound G-8 exhibited a potent anti-HIV effect with an IC50 value of 7.2 nM and an EC50 value of 0.9 nM. Compound G-6 had excellent in vitro cytotoxicities against the K562, MCF-7, Hela, DU145, U1975, SGC-7901, A549, MOLT-4, and HL60 cell lines, with IC50 values ranging from 0.10 to 3.3 µM, and showed significant anti-viral (H1N1 and H3N2) activities with IC50 values of 15.9 and 30.0 µM, respectively.

CONCLUSIONS

These findings definitely improve our knowledge about the molecular biology of genus A. sydowii and would effectively unveil the biosynthetic potential of strain MNP-2 using genomics and metabolomics techniques.

New Dipyrroloquinones from a Plant-Derived Endophytic Fungus Talaromyces sp

Two new dipyrroloquinones, namely talaroterreusinones A (1) and B (2), together with four known secondary metabolites, terreusinone A (3), penicillixanthone A (4), isorhodoptilometrin (5), and chrysomutanin (6), were isolated from the solid culture of the endophytic fungus Talaromyces sp. by integrating mass spectrometry-based metabolic profiling and a bioassay-guided method. Their planar structures and stereochemistry were elucidated by comprehensive spectroscopic analysis including NMR and MS. The absolute configuration at C-1″ of terreusinone A (1) was established by applying the modified Mosher's method. Compounds 1-6 were evaluated for anti-inflammatory activity and cytotoxicity. As a result, 1-3 inhibited the LPS-stimulated NO production in macrophage RAW264.7 cells, with IC50 values of 20.3, 30.7, and 20.6 µM, respectively. Penicillixanthone A (4) exhibited potent cytotoxic activity against Hep G2 and A549 cell lines, with IC50 values of 117 nM and 212 nM, respectively, and displayed significant antitumour effects in A549 cells by inhibiting the PI3K-Akt-mTOR signalling pathway.

Cytotoxic pyridine alkaloids from a marine-derived fungus Arthrinium arundinis exhibiting apoptosis-inducing activities against small cell lung cancer

Small cell lung cancer (SCLC) is a kind of high-grade neuroendocrine carcinoma, which is characterized by a higher proliferative rate, earlier metastasis and more poor outcomes compared to non-small cell lung cancer (NSCLC). Under the guidance of MS/MS based molecular networking, three undescribed pyridone alkaloids, namely, arthpyrones M-O (1-3), together with two known pyridone derivatives, arthpyrones C (4) and G (5), were isolated from a sponge-derived Arthrinium arundinis. Their structures were determined through extensive spectroscopic analysis, ECD calculations, and X-ray single-crystal diffraction. Arthpyrone M (1) possessed a novel cage structure bearing an ether bridge functionality rarely reported in this class of metabolites. All isolated compounds were evaluated for their cytotoxicities against five cancer cell lines. As a result, compounds 1-5 showed cytotoxicity against some or all of the five cancer cell lines with IC₅₀ values ranging from 0.26 to 6.43 μM. Among them, arthpyrone O (3) not only exhibited potent efficacy against the proliferative activity of SCLC cells and induced apoptosis in vitro, but also significantly inhibited the growth of xenograft tumor based on SCLC cells in vivo, which indicated 4-hydroxy-2-pyridone alkaloids might been revised as privileged scaffolds in drug discovery.

Structural identification of pyridinopyrone compounds with anti-neuroinflammatory activity from streptomyces sulphureus DSM 40104

This study investigated the chemical composition and biosynthesis pathway of compounds produced by Streptomyces sulphureus DSM 40104. With the guild of molecular networking analysis, we isolated and identified six uncommon structural characteristics of compounds, including four newly discovered pyridinopyrones. Based on genomic analysis, we proposed a possible hybrid NRPS-PKS biosynthesis pathway for pyridinopyrones. Notably, this pathway starts with the use of nicotinic acid as the starting unit, which is a unique feature. Compounds 1-3 exhibited moderate anti-neuroinflammatory activity against LPS-induced BV-2 cell inflammation. Our study demonstrates the diversity of polyene pyrone compounds regarding their chemical structure and bioactivity while providing new insights into their biosynthesis pathway. These findings may lead to the development of new treatments for inflammation-related diseases.

Target isolation of cytotoxic diterpenoid esters and orthoesters from Daphne tangutica maxim based on molecular networking

Guiding by LC-MS/MS analysis and the GNPS Molecular Networking, five undescribed daphnane diterpenoids, tanguticanines A-E, and eleven known analogues were discovered from the whole plants of Daphne tangutica Maxim. Their structures and absolute configurations were determined via extensive NMR spectroscopic analysis, ECD calculations, and X-ray diffraction crystallography. Tanguticanine E (5) exhibited promising cytotoxicity against the HepG2 cell line with an IC₅₀ value of 9.93 ± 0.10 μM. Further flow cytometry experiment was performed to detect cell apoptosis, and the results indicated that cytotoxic diterpenoids (tanguticanines B, D and E, altadaphnan C, gniditrin, hirsein A and simplexin) exert their effects through induction of apoptosis.

Three unusual hybrid sorbicillinoids with anti-inflammatory activities from the deep-sea derived fungus Penicillium sp. SCSIO06868

Under the guidance of MS/MS based molecular networking, bisorbicillchaetones A-C, three undescribed hybrid sorbicillinoids, were isolated from cultures of the deep-sea derived fungus Penicillium sp. SCSIO06868. The planar structures and absolute configurations of these compounds were determined by extensive spectroscopic analyses. Bisorbicillchaetones are the first examples of hybrid sorbicillinoids containing a coniochaetone unit. Bisorbicillchaetones A and B exhibited moderate inhibitory effect on NO production in LPS activated RAW264.7 cells with the IC₅₀ values of 80.3 ± 3.6 μM and 38.4 ± 3.3 μM, respectively, without cytotoxicity observed.

Structural diversity and biological relevance of benzenoid and atypical ansamycins and their congeners

Covering: 2011 to 2021The structural division of ansamycins, including those of atypical cores and different lengths of the ansa chains, is presented. Recently discovered benzenoid and atypical ansamycin scaffolds are presented in relation to their natural source and biosynthetic routes realized in bacteria as well as their muta and semisynthetic modifications influencing biological properties. To better understand the structure-activity relationships among benzenoid ansamycins structural aspects together with mechanisms of action regarding different targets in cells, are discussed. The most promising directions for structural optimizations of benzenoid ansamycins, characterized by predominant anticancer properties, were discussed in view of their potential medical and pharmaceutical applications. The bibliography of the review covers mainly years from 2011 to 2021.

Ansafurantrienins, Unprecedented Ansatrienin Derivatives Formed via Photocatalytic Intramolecular [3 + 2] Oxidative Cycloaddition

Ansafurantrienins A-H, bearing a unique 5/6/8 dihydrofuran-fused benzo[b]azocine chromophore, were isolated from Streptomyces flaveolus. Their structures, especially in the dihydrofuran unit, were unambiguously established by spectroscopic analyses, molecular modeling, and TDDFT/ECD calculations. The ansafurantrienins were proposed to be generated via intramolecular [3 + 2] oxidative cycloaddition, which was achieved by photocatalytic reaction with UV light and oxygen and found to have solvent-dependent stereoselectivity. Ansafurantrienins showed significant antiproliferative effects against pancreatic cancer cells. The results led to a structural revision of strecacansamycins.

Vibsanoids A–D, four new subtypes of vibsane diterpenoids with a distinctive tricyclo[8.2.1.02,9]tridecane core from Viburnum odoratissimum

Four highly rearranged tetranorvibsane-type diterpenoids, vibsanoids A–D, with an unprecedented tricyclo[8.2.1.02,9]tridecane skeleton were isolated from Viburnum odoratissimum.

Applications and Restrictions of Integrated Genomic and Metabolomic Screening: An Accelerator for Drug Discovery from Actinomycetes?

Since the golden age of antibiotics in the 1950s and 1960s actinomycetes have been the most prolific source for bioactive natural products. However, the number of discoveries of new bioactive compounds decreases since decades. New procedures (e.g., activating strategies or innovative fermentation techniques) were developed to enhance the productivity of actinomycetes. Nevertheless, compound identification remains challenging among others due to high rediscovery rates. Rapid and cheap genome sequencing as well as the advent of bioinformatical analysis tools for biosynthetic gene cluster identification in combination with mass spectrometry-based molecular networking facilitated the tedious process of dereplication. In recent years several studies have been dedicated to accessing the biosynthetic potential of Actinomyces species, especially streptomycetes, by using integrated genomic and metabolomic screening in order to boost the discovery rate of new antibiotics. This review aims to present the various possible applications of this approach as well as the newly discovered molecules, covering studies between 2014 and 2021. Finally, the effectiveness of this approach with regard to find new bioactive agents from actinomycetes will be evaluated.

The natural product trienomycin A is a STAT3 pathway inhibitor that exhibits potent in vitro and in vivo efficacy against pancreatic cancer

BACKGROUND AND PURPOSE

Pancreatic cancer is an exceptionally fatal disease. However, therapeutic drugs for pancreatic cancer have presented a serious shortage over the past few decades. Signal transducer and activator of transcription-3 (STAT3) is persistently activated in many human cancers where it promotes tumour development and progression. Natural products serve as an inexhaustible source of anticancer drugs. Here, we identified the natural product trienomycin A (TA), an ansamycin antibiotic, as a potential inhibitor of the STAT3 pathway with potent activity against pancreatic cancer.

EXPERIMENTAL APPROACH

Effects of trienomycin A on transcriptional activity of STAT3 were assessed by the STAT3-luciferase (STAT3-luc) reporter system. In vitro and in vivo inhibitory activity of TA against pancreatic cancer made use of molecular docking, surface plasmon resonance (SPR) assay, MTS assay, colony formation assay, transwell migration/invasion assay, flow cytometric analysis, immunofluorescence staining, quantitative real-time polymerase chain reaction (PCR), western blotting, tumour xenograft model, haematoxylin and eosin (H&E) staining and immunohistochemistry.

KEY RESULTS

Trienomycin A directly bound to STAT3 and inhibited STAT3 (Tyr705) phosphorylation, thus inhibiting the STAT3 pathway. Trienomycin A also inhibited colony formation, proliferation, migration and invasion of pancreatic cancer cell lines. Trienomycin A also markedly blocked pancreatic tumour growth in vivo. More importantly, trienomycin A did not show obvious toxicity at the effective dose in mice.

CONCLUSIONS AND IMPLICATIONS

Trienomycin A exerted anti-neoplastic activity by suppressing STAT3 activation in pancreatic cancer. This natural product could be a novel therapeutic candidate for pancreatic cancer.