The isolation of water-soluble natural products - challenges, strategies and perspectives

Testacosides A-D, glycoglycerolipids produced by Microbacterium testaceum isolated from Tedania brasiliensis

Marine bacteria living in association with marine sponges have proven to be a reliable source of biologically active secondary metabolites. However, no studies have yet reported natural products from Microbacterium testaceum spp. We herein report the isolation of a M. testaceum strain from the sponge Tedania brasiliensis. Molecular networking analysis of bioactive pre-fractionated extracts from culture media of M. testaceum enabled the discovery of testacosides A-D. Analysis of spectroscopic data and chemical derivatizations allowed the identification of testacosides A-D as glycoglycerolipids bearing a 1-[α-glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol moiety connected to 12-methyltetradecanoic acid for testacoside A (1), 14-methylpentadecanoic acid for testacoside B (2), and 14-methylhexadecanoic acid for testacosides C (3) and D (4). The absolute configuration of the monosaccharide residues was determined by 1H-NMR analysis of the respective diastereomeric thiazolidine derivatives. This is the first report of natural products isolated from cultures of M. testaceum. KEY POINTS: • The first report of metabolites produced by Microbacterium testaceum. • 1-[α-Glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol lipids isolated and identified. • Microbacterium testaceum strain isolated from the sponge Tedania brasiliensis.

General Separation of Carbon Dots by Polyamide Chromatography

Carbon dot (C-dot) separation/purification is not only a fundamental chemical issue but also an essential precondition for revealing C-dots' true nature. To date, adequate separation of C-dots has remained an open question due to the lack of an appropriate fine separation system. Herein, we discover and reveal that polyamide chromatography can provide versatile and powerful performances for C-dot separation. By a joint study of experiments and all-atom molecular dynamics simulations, we demonstrate that multiple interaction forces, including electrostatic repulsion/attraction, hydrogen bond, and van der Waals effects, exist simultaneously among the stationary phase, mobile phase, and the separated C-dots. Furthermore, the magnitude of these forces is dependent on the surface chemistry of the separated C-dots and the nature of the used mobile phases, providing a theoretical basis and experimental operability for C-dot separation. So, the proposed system possesses the capacity for adequately separating hydrophilic, amphiphilic, and lipophilic C-dots. The polyamide chromatography, due to its versatile and powerful separation performances, not only provides more thorough separation effects but also helps to correct our false perceptions from inadequate purified C-dots.

Separation Methods of Phenolic Compounds from Plant Extract as Antioxidant Agents Candidate

In recent years, discovering new drug candidates has become a top priority in research. Natural products have proven to be a promising source for such discoveries as many researchers have successfully isolated bioactive compounds with various activities that show potential as drug candidates. Among these compounds, phenolic compounds have been frequently isolated due to their many biological activities, including their role as antioxidants, making them candidates for treating diseases related to oxidative stress. The isolation method is essential, and researchers have sought to find effective procedures that maximize the purity and yield of bioactive compounds. This review aims to provide information on the isolation or separation methods for phenolic compounds with antioxidant activities using column chromatography, medium-pressure liquid chromatography, high-performance liquid chromatography, counter-current chromatography, hydrophilic interaction chromatography, supercritical fluid chromatography, molecularly imprinted technologies, and high-performance thin layer chromatography. For isolation or purification, the molecularly imprinted technologies represent a more accessible and more efficient procedure because they can be applied directly to the extract to reduce the complicated isolation process. However, it still requires further development and refinement.

A guide to the use of bioassays in exploration of natural resources

Bioassays are the main tool to decipher bioactivities from natural resources thus their selection and quality are critical for optimal bioprospecting. They are used both in the early stages of compounds isolation/purification/identification, and in later stages to evaluate their safety and efficacy. In this review, we provide a comprehensive overview of the most common bioassays used in the discovery and development of new bioactive compounds with a focus on marine bioresources. We present a comprehensive list of practical considerations for selecting appropriate bioassays and discuss in detail the bioassays typically used to explore antimicrobial, antibiofilm, cytotoxic, antiviral, antioxidant, and anti-ageing potential. The concept of quality control and bioassay validation are introduced, followed by safety considerations, which are critical to advancing bioactive compounds to a higher stage of development. We conclude by providing an application-oriented view focused on the development of pharmaceuticals, food supplements, and cosmetics, the industrial pipelines where currently known marine natural products hold most potential. We highlight the importance of gaining reliable bioassay results, as these serve as a starting point for application-based development and further testing, as well as for consideration by regulatory authorities.

Fabrication of a biochar-doped monolithic adsorbent and its application for the extraction and determination of coumarins from Angelicae Pubescentis Radix

A monolithic adsorbent was designed aiming to the structure of osthole and columbianadin, and fabricated using diallyl phthalate as the monomer and ethylene dimethacrylate as the crosslinker with the addition of bamboo biochar, via polymerization reaction in a stainless-steel tube. The prepared composite adsorbent packed in the tube was used as a solid-phase extraction column for the extraction and determination of two coumarins (osthole and columbianadin) in Angelicae Pubescentis Radix, combing with a C18 analytical column through an HPLC instrument, which show excellent matrix-removal ability and good selectivity to osthole and columbianadin. Furthermore, the present adsorbent shows good applicability, which was used for the extraction of osthole from Duhuo Jisheng Pill. Compared to the commercial C18 and phenyl adsorbent, the present adsorbent own better selectivity and higher resolution. These results attributed to the enhanced specific surface area (141 m2/g) and enriched interaction sites of the resulting composite adsorbent, due to the doping of bamboo biochar, which can produce hydrogen bond, dipole-dipole, π-π and hydrophobic force interactions with the osthole and columbianadin. The methodology validation indicated that the present method showed good precision and good accuracy, and the composite adsorbent showed good preparative repeatability, which can be reused for no less than 100 times with the relative standard deviation ≤4.6 % (n = 100). The present work provided a simple and efficient method for the extraction and determination osthole and columbianadin from Angelicae Pubescentis Radix.

Novel Natural Carrier-Free Self-Assembled Nanoparticles for Treatment of Ulcerative Colitis by Balancing Immune Microenvironment and Intestinal Barrier

Ulcerative colitis (UC) is a chronic inflammatory illness affecting the colon and rectum, with current treatment methods being unable to meet the clinical needs of ulcerative colitis patients. Although nanomedicines are recognized as promising anti-inflammatory medicines, their clinical application is limited by their high cost and unpredictable safety risks. This study reveals that two natural phytochemicals, berberine (BBR) and hesperetin (HST), self-assemble directly to form binary carrier-free multi-functional spherical nanoparticles (BBR-HST NPs) through noncovalent bonds involving electrostatic interactions, π-π stacking, and hydrogen bonding. Because of their synergistic anti-inflammatory activity, berberine-hesperetin nanoparticles (BBR-HST NPs) exhibit significantly better therapeutic effects on UC and inhibitory effects on inflammation than BBR and HST at the same dose by regulating the immune microenvironment and repairing the damaged intestinal barrier. Furthermore, BBR-HST NPs exhibit good biocompatibility and biosafety. Thus, this study proves the potential of novel natural anti-inflammatory nanoparticles as therapeutic agents for UC, which could promote the progress of drug development for UC and eventually benefit patients who suffering from it.

In Situ Capture and Real-Time Enrichment of Marine Chemical Diversity

Analyzing the chemical composition of seawater to understand its influence on ecosystem functions is a long-lasting challenge due to the inherent complexity and dynamic nature of marine environments. Describing the intricate chemistry of seawater requires optimal in situ sampling. Here is presented a novel underwater hand-held solid-phase extraction device, I-SMEL (In Situ Marine moleculELogger), which aims to concentrate diluted molecules from large volumes of seawater in a delimited zone targeting keystone benthic species. Marine benthic holobionts, such as sponges, can impact the chemical composition of their surroundings possibly through the production and release of their specialized metabolites, hence termed exometabolites (EMs). I-SMEL was deployed in a sponge-dominated Mediterranean ecosystem at a 15 m depth. Untargeted MS-based metabolomics was performed on enriched EM extracts and showed (1) the chemical diversity of enriched seawater metabolites and (2) reproducible recovery and enrichment of specialized sponge EMs such as aerothionin, demethylfurospongin-4, and longamide B methyl ester. These EMs constitute the chemical identity of each targeted species: Aplysina cavernicola, Spongia officinalis, and Agelas oroides, respectively. I-SMEL concentrated sponge EMs from 10 L of water in a 10 min sampling time. The present proof of concept with I-SMEL opens new research perspectives in marine chemical ecology and sets the stage for further sustainable efforts in natural product chemistry.

Common fear molecules induce defensive responses in marine prey across trophic levels

Predator-prey interactions are a key feature of ecosystems and often chemically mediated, whereby individuals detect molecules in their environment that inform whether they should attack or defend. These molecules are largely unidentified, and their discovery is important for determining their ecological role in complex trophic systems. Homarine and trigonelline are two previously identified blue crab (Callinectes sapidus) urinary metabolites that cause mud crabs (Panopeus herbstii) to seek refuge, but it was unknown whether these molecules influence other species within this oyster reef system. In the current study, homarine, trigonelline, and blue crab urine were tested on juvenile oysters (Crassostrea virginica) to ascertain if the same molecules known to alter mud crab behavior also affect juvenile oyster morphology, thus mediating interactions between a generalist predator, a mesopredator, and a basal prey species. Oyster juveniles strengthened their shells in response to blue crab urine and when exposed to homarine and trigonelline in combination, especially at higher concentrations. This study builds upon previous work to pinpoint specific molecules from a generalist predator's urine that induce defensive responses in two marine prey from different taxa and trophic levels, supporting the hypothesis that common fear molecules exist in ecological systems.

Stress-driven metabolites of desert soil fungi

Microorganisms produce secondary metabolites to survive under stressful conditions. The effect of drought and heat stress on fungi isolated from Arabian desert soil during the hot (ca 40°C) and cool (ca 10°C) seasons was studied using the genome mining approach. The presence of three stress-related genes (calmodulin, polyketide synthase and beta tubulin) was analyzed molecularly using specific primers. The presence of the genes in desert fungi was compared to their antimicrobial (ten bacterial or fungal pathogens) and anticancer (liver, cervical and breast) properties and the production of thermostable enzymes (phytase and xylanase). The genes appeared to be present in the fungal sequence obtained during the summer, while none of the genes were present during winter. Appreciable differences were observed in enzyme activities, with summer activities high and winter low. The antagonistic activities of A. niger were relatively stable and varying, while those of P. chrysogenum were consistently higher in summer than in winter. The presence of the three genes seemed to correlate with the highly antagonistic activities of P. chrysogenum, while A. niger had relatively active winter isolates without any of the genes. The hot season in deserts yields fungal isolates with biological activities useful in biotechnological solutions.

Isolation and Purification of Natural Products from Microbial Cultures

Antibiotic natural products from microbes are characterized by diverse and mostly complex chemical structures, which challenge their total chemical synthesis and make biotechnological production to the predominant production route. In order to reach these valuable compounds in the fermentation broth, sophisticated recovery methods are required, and a high degree of purity is essential for a thorough exploration of their beneficial properties in subsequent assays. The isolation and purification of natural products from microbial cultures is mainly based on the repeated application of extraction and chromatographic separation methods.This chapter describes the general strategy of natural product recovery from microbial cultures, gives theoretical and practical insights to underlying methods-essentially compound extraction and preparative chromatography-and describes a specific methodical approach to isolate and purify the natural product fusarubin from the culture of the fungus Fusarium sp.

Diving into the Molecular Diversity of Aplysina cavernicola's Exometabolites: Contribution of Bromo-Spiroisoxazoline Alkaloids

Sponges are prolific producers of specialized metabolites with unique structural scaffolds. Their chemical diversity has always inspired natural product chemists working in drug discovery. As part of their metabolic filter-feeding activities, sponges are known to release molecules, possibly including their specialized metabolites. These released "Exo-Metabolites" (EMs) may be considered as new chemical reservoirs that could be collected from the water column while preserving marine biodiversity. The present work aims to determine the proportion and diversity of specialized EMs released by the sponge Aplysina cavernicola (Vacelet 1959). This Mediterranean sponge produces bromo-spiroisoxazoline alkaloids that are widely distributed in the Aplysinidae family. Aquarium experiments were designed to facilitate a continuous concentration of dissolved and diluted metabolites from the seawater around the sponges. Mass Spectrometry (MS)-based metabolomics combined with a dereplication pipeline were performed to investigate the proportion and identity of brominated alkaloids released as EMs. Chemometric analysis revealed that brominated features represented 12% of the total sponge's EM features. Consequently, a total of 13 bromotyrosine alkaloids were reproducibly detected as EMs. The most abundant ones were aerothionin, purealidin L, aerophobin 1, and a new structural congener, herein named aplysine 1. Their structural identity was confirmed by NMR analyses following their isolation. MS-based quantification indicated that these major brominated EMs represented up to 1.0 ± 0.3% w/w of the concentrated seawater extract. This analytical workflow and collected results will serve as a stepping stone to characterize the composition of A. cavernicola's EMs and those released by other sponges through in situ experiments, leading to further evaluate the biological properties of such EMs.

The antagonistic activity of Padina arborescens extracts on mPRα

The current study attempted to evaluate the antagonistic activity of compounds isolated and purified from the marine algae Padina arborescens during cultivation. The compounds were collected on a filter, concentrated on ODS columns and separated by HPLC. Two peaks that showed competitive progesterone binding activity with membrane progesterone receptor α (mPRα) were purified. Their physiological activity was further uncovered by in vitro and in vivo oocyte maturation and ovulation-inducing assays using zebrafish. The compounds inhibited the induction of oocyte maturation and ovulation. Moreover, the results showed that the compounds have antagonistic activity against mPRα. The purified compounds with antagonistic activity against mPRα would be considered as new pharmaceutical candidate.

Organobase-catalyzed 1,1-diborylation of terminal alkynes under metal-free conditions

An organobase-catalyzed 1,1-diborylation of terminal alkynes from propargylic derivatives with bis(2,4-dimethylpentane-2,4-glycolato)diboron (B₂oct₂) is first reported, regioselectively providing 1,1-diborylalkene products with high efficiency. The catalytic pathway is well postulated on the basis of DFT calculations.

An organobase-catalyzed 1,1-diborylation of terminal alkynes from propargylic derivatives with B₂oct₂ is first reported, providing 1,1-diborylalkene products with high efficiency. The catalytic pathway is well postulated on the basis of DFT calculations.

The phosphate ester group in secondary metabolites

Covering: 2000 to mid-2021The phosphate ester is a versatile, widespread functional group involved in a plethora of biological activities. Its presence in secondary metabolites, however, is relatively rare compared to other functionalities and thus is part of a rather unexplored chemical space. Herein, the chemistry of secondary metabolites containing the phosphate ester group is discussed. The text emphasizes their structural diversity, biological and pharmacological profiles, and synthetic approaches employed in the phosphorylation step during total synthesis campaigns, covering the literature from 2000 to mid-2021.

Palladium-catalyzed Lewis acid-regulated cascade annulation of alkynes with unactivated alkenes to access diverse α-methylene-γ-lactones

A palladium-catalyzed Lewis acid-regulated cascade annulation of alkynes with unactivated alkenes for the preparation of alkyl substituted α-methylene-γ-lactones with excellent Z/E selectivities was accomplished.