Current and emerging tools and strategies for the identification of bioactive natural products in complex mixtures.

Covering: up to 2024The prompt identification of (bio)active natural products (NPs) from complex mixtures poses a significant challenge due to the presence of numerous compounds with diverse structures and (bio)activities. Thus, this review provides an overview of current and emerging tools and strategies for the identification of (bio)active NPs in complex mixtures. Traditional approaches of bioassay-guided fractionation (BGF), followed by nuclear magnetic resonance (NMR) and mass spectrometry (MS) analysis for compound structure elucidation, continue to play an important role in the identification of active NPs. However, recent advances (2018-2024) have led to the development of novel techniques such as (bio)chemometric analysis, dereplication and combined approaches, which allow efficient prioritization for the elucidation of (bio)active compounds. For researchers involved in the search for bioactive NPs and who want to speed up their discoveries while maintaining accurate identifications, this review highlights the strengths and limitations of each technique and provides up-to-date insights into their combined use to achieve the highest level of confidence in the identification of (bio)active natural products from complex matrices.

Looking for Actives in the Haystack: Merging HRMS2-Based Molecular Networking, Chemometrics, and 13C NMR-Based Dereplication Approaches.

The identification of bioactive natural products (NPs) in complex mixtures has become an important subject of contemporary NP research. In an attempt to address this challenge, the present work proposes an integrated strategy that combines tandem mass spectrometry (MS2)-based molecular networking (MN), a partial least-squares (PLS) chemometric model, as well as 13C NMR-based dereplication using MixONat software. In addition, an advanced glycation end product (AGEs) assay was used for activity evaluation. The approach was implemented on a Garcinia parvifolia bark extract that comprised a high content of prenylated xanthones and had previously shown a notable inhibitory effect on AGE formation. As a main result, the proposed strategy permitted the identification of potentially active metabolites within complex mixtures and their annotation with a higher level of confidence by NMR data. Overall, this comprehensive approach provides a powerful and efficient solution for the targeting and annotating of active compounds in complex NP mixtures.

Xanthone Inhibitors of Unfolded Protein Response Isolated from Calophyllum caledonicum.

The unfolded protein response (UPR) is a key component of fungal virulence. The prenylated xanthone γ-mangostin isolated from Garcinia mangostana (Clusiaceae) fruit pericarp, has recently been described to inhibit this fungal adaptative pathway. Considering that Calophyllum caledonicum (Calophyllaceae) is known for its high prenylated xanthone content, its stem bark extract was fractionated using a bioassay-guided procedure based on the cell-based anti-UPR assay. Four previously undescribed xanthone derivatives were isolated, caledonixanthones N-Q (3, 4, 8, and 12), among which compounds 3 and 8 showed promising anti-UPR activities with IC50 values of 11.7 ± 0.9 and 7.9 ± 0.3 µM, respectively.

A thorough evaluation of matrix-free laser desorption ionization on structurally diverse alkaloids and their direct detection in plant extracts.

Alkaloids represent a major group of natural products (NPs), derived from highly diverse organisms. These structurally varied specialized metabolites are widely used for medicinal purposes and also known as toxic contaminants in agriculture and dietary supplements. While the detection of alkaloids is generally facilitated by GC- or LC-MS, these techniques do require considerable efforts in sample preparation and method optimization. Bypassing these limitations and also reducing experimental time, matrix-free laser desorption ionization (LDI) and related methods may provide an interesting alternative. As many alkaloids show close structural similarities to matrices used in matrix-assisted laser desorption ionization (MALDI), they should ionize upon simple laser irradiation without matrix support. With this in mind, the current work presents a systematic evaluation of LDI properties of a wide range of structurally diverse alkaloids. Facilitating a direct comparison between LDI and ESI-MS fragmentation, all tested compounds were further studied by electrospray ionization (ESI). Moreover, crude plant extracts of Atropa belladonna, Cinchona succirubra, and Colchicum autumnale were analyzed by LDI in order to evaluate direct alkaloid detection and dereplication from complex mixtures. Finally, dose-dependent evaluation of MALDI and LDI detection using an extract of Rosmarinus officinalis spiked with atropine, colchicine, or quinine was conducted. Overall, present results suggest that LDI provides a versatile analytical tool for analyzing structurally diverse alkaloids as single compounds and from complex mixtures. It may further serve various potential applications ranging from quality control to the screening for toxic compounds as well as the build up of MS databases. Graphical abstract.

Absolute Configuration of Mycosporine-Like Amino Acids, Their Wound Healing Properties and In Vitro Anti-Aging Effects.

Mycosporine-like amino acids (MAAs) are water-soluble metabolites, reported to exhibit strong UV-absorbing properties. They have been found in a wide range of marine organisms, especially those that are exposed to extreme levels of sunlight, to protect them against solar radiation. In the present study, the absolute configuration of 14 mycosporine-like-amino acids was determined by combining the results of electronic circular dichroism (ECD) experiments and that of advanced Marfey's method using LC-MS. The crystal structure of a shinorine hydrate was determined from single crystal X-ray diffraction data and its absolute configuration was established from anomalous-dispersion effects. Furthermore, the anti-aging and wound-healing properties of these metabolites were evaluated in three different assays namely the inhibition of collagenase, inhibition of advanced glycation end products (AGEs) and wound healing assay (scratch assay).

Matrix-free laser desorption ionization mass spectrometry as a functional tool for the analysis and differentiation of complex phenolic mixtures in propolis: a new approach to quality control.

Matrix-free laser desorption ionization (LDI) is a rapid and versatile technique for the ionization of small, UV-light-absorbing molecules. Indeed, many natural products such as polyphenols exhibit inherent LDI properties, potentially facilitating their detection from highly complex samples such as crude extracts. With this in mind, the present work thoroughly evaluated the potential of LDI as an analytical tool for the chemical profiling and differentiation of propolis samples obtained from different global regions. Propolis is a complex bee product containing, among others, significant amounts of phenolic constituents that may show LDI effects. The present work will demonstrate that LDI not only provides reproducible and highly specific fingerprint spectra for each of the tested samples, it further allows their clear differentiation by principal compound analysis (PCA). Contrary to classical analytical approaches such as LC- or GC-MS, LDI does not require time-consuming sample preparation and method optimization procedures. Thus, the technique represents a most interesting analytical tool and potent supplement to classic LC-MS for quality control of herbal pharmaceuticals and dietary supplements. Present results clearly support this approach and further suggest the use of LDI as a versatile tool for the automated analysis of large sample batches on an industrial scale. Graphical abstract ᅟ.

The inherent matrix properties of lichen metabolites in matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

RATIONALE: Light-absorbing secondary metabolites from lichens were recently reported to exhibit promising Laser Desorption Ionization (LDI) properties, enabling their direct detection from crude lichen extracts. In addition, many of them display close structural homologies to commercial Matrix-Assisted Laser Desorption Ionization (MALDI) matrices, which is incentive for the evaluation of their matrical properties. The current study systematically evaluated the matrix effects of several structural classes of lichen metabolites: monoaromatic compounds, quinone derivatives, dibenzofuran-related molecules and the shikimate-derived vulpinic acid. Their matrical properties were tested against a wide range of structurally diverse analytes including alkaloids, coumarins, flavonoids and peptides. METHODS: Triplicate automatic positive-ion mode MALDI analyses were carried out and ionization efficiencies were compared with those of structurally related reference matrices (i.e. DHB, HCCA, dithranol and usnic acid) in terms of (i) analyte absolute intensities and (ii) Matrix Suppressing Effect (MSE) scores. RESULTS: Monoaromatic lichen metabolites revealed matrical properties similar to those of DHB when obtained under comparable experimental conditions. Likewise, anthraquinone metabolites triggered ionization of tested analytes in a similar way to the structurally related dithranol. Finally, dibenzofuran derivatives displayed a broad ionization profile, reminiscent of that of (+)-usnic acid. CONCLUSIONS: Lichen metabolites exhibit interesting MALDI matrix properties, especially for medium and low molecular weight analytes. For many of the tested molecules, matrix ion formation was very limited. This proof-of-concept study paves the way for follow-up investigations to assess the matrix properties of lichen metabolites against a wider array of analytes as well as adapting experimental settings to individually optimize the performance of successfully tested candidates.

Bithiophenic MALDI matrices as valuable leads for the selective detection of alkaloids.

Alkaloids represent a group of biologically most interesting compounds commonly used in modern medicines but also known for exhibiting severe toxic effects. Therefore, the detection of alkaloids is an important issue in quality control of plants, dietary supplements, and herbal pharmaceutical and mostly facilitated by methods such as GC or LC-MS. However, benefitting from the development of selective matrices as well as requiring very little sample preparation, MALDI-MS may also provide a valuable supplement to these standard analytical methods. With this in mind, the present study highlights recent advances in the development of bithiophenic matrix molecules designed for the selective detection of alkaloids. Overall four new bithiophenic matrix molecules (BMs) were tested on different analytes belonging to various chemical families such as alkaloids, curcuminoids, benzopyrones, flavonoids, steroids, and peptides (I). All BMs were further compared to the commercial matrices α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB) in terms of their signal response as well as their matrix noise formation (II). Based on these results the most promising candidate, 3-(5'-pentafluorophenylmethylsulfanyl-[2,2']bithiophenyl-5-ylsulfanyl)propionitrile (PFPT3P), was tested on highly complex samples such as the crude extracts of Colchicum autumnale, RYTMOPASC ® solution (a herbal pharmaceutical containing sparteine and rubijervine), as well as strychnine-spiked human plasma (III). For the latter, an evaluation of the limit of detection was performed. Eventually, a simplified protocol for the direct MALDI detection of major alkaloids from pulverized plant material of Atropa belladonna and Senecio vulgaris is presented (IV). Graphical abstract Selective MALDI MATRICES for Alkaloid Detection.

Bupleurum chinense Roots: a Bioactivity-Guided Approach toward Saponin-Type NF-κB Inhibitors.

The roots of Bupleurum chinense have a long history in traditional medicine to treat infectious diseases and inflammatory disorders. Two major compounds, saikosaponins A and D, were reported to exert potent anti-inflammatory activity by inhibiting NF-κB. In the present study, we isolated new saikosaponin analogues from the roots of B. chinese interfering with NF-κB activity in vitro. The methanol-soluble fraction of the dichloromethane extract of Radix Bupleuri was subjected to activity-guided isolation yielding 18 compounds, including triterpenoids and polyacetylenes. Their structures were determined by spectroscopic methods as saikogenin D (1), prosaikogenin D (2), saikosaponins B2 (3), W (4), B1 (5), Y (6), D (7), A (8), E (9), B4 (10), B3 (11), and T (12), saikodiyne A (13), D (14), E (15) and F (16), falcarindiol (17), and 1-linoleoyl-sn-glycero-3-phosphorylcholine (18). Among them, 4, 15, and 16 are new compounds, whereas 6, previously described as a semi-synthetic compound, is isolated from a natural source for the first time, and 13-17 are the first reports of polyacetylenes from this plant. Nine saponins/triterpenoids were tested for inhibition of NF-κB signaling in a cell-based NF-κB-dependent luciferase reporter gene model in vitro. Five of them (1, 2, 4, 6, and 8) showed strong (> 50%, at 30 µM) NF-κB inhibition, but also varying degrees of cytotoxicity, with compounds 1 and 4 (showing no significant cytotoxicity) presenting IC50 values of 14.0 µM and 14.1 µM in the cell-based assay, respectively.

Matrix-Free UV-Laser Desorption Ionization Mass Spectrometry as a Versatile Approach for Accelerating Dereplication Studies on Lichens.

The present study examined the suitability of laser desorption/ionization time-of-flight mass spectrometry (LDI-MS) for the rapid chemical fingerprinting of lichen extracts. Lichens are known to produce a wide array of secondary metabolites. Most of these compounds are unique to the symbiotic condition but some can be found in many species. Therefore, dereplication, that is, the rapid identification of known compounds within a complex mixture is crucial in the search for novel natural products. Over the past decade, significant advances were made in analytical techniques and profiling methods specifically adapted to crude lichen extracts, but LDI-MS has never been applied in this context. However, most classes of lichen metabolites have UV chromophores, which are quite similar to commercial matrix molecules used in matrix-assisted laser desorption ionization (MALDI). It is consequently postulated that these molecules could be directly detectable by matrix-free LDI-MS. The present study evaluated the versatility of this technique by investigating the LDI properties of a vast array of single lichen metabolites as well as lichen extracts of known chemical composition. Results from the LDI experiments were compared with those obtained by direct ESI-MS detection as well as LC-ESI-MS. It was shown that LDI ionization leads to strong molecular ion formation with little fragmentation, thus, facilitating straightforward spectra interpretation and representing a valuable alternative to time-consuming LC-MS analysis.

Cytotoxic constituents from Lobaria scrobiculata and a comparison of two bioassays for their evaluation.

Lichens are resilient organisms, known for their unique profiles of secondary metabolites and for exhibiting antioxidative, antibacterial, and cytotoxic effects. Analyzing the cytotoxic potential of Lobaria scrobiculata, a bioassay-guided fractionation strategy yielded seven known metabolites, with two of these compounds, 2 and 3, exhibiting cytotoxicity against HL-60 cells. In order to verify the potential impact of degradation on observed bioactivity, a purity and stability evaluation was conducted. The consistency of results obtained by the water-soluble tetrazolium salt-1 assay and trypan blue cytotoxicity assay was evaluated for selected compounds.

Polyyne hybrid compounds from Notopterygium incisum with peroxisome proliferator-activated receptor gamma agonistic effects.

In the search for peroxisome proliferator-activated receptor gamma (PPARγ) active constituents from the roots and rhizomes of Notopterygium incisum, 11 new polyacetylene derivatives (1-11) were isolated. Their structures were elucidated by NMR and HRESIMS as new polyyne hybrid molecules of falcarindiol with sesquiterpenoid or phenylpropanoid moieties, named notoethers A-H (1-8) and notoincisols A-C (9-11), respectively. Notoincisol B (10) and notoincisol C (11) represent two new carbon skeletons. When tested for PPARγ activation in a luciferase reporter assay with HEK-293 cells, notoethers A-C (1-3), notoincisol A (9), and notoincisol B (10) showed promising agonistic activity (EC50 values of 1.7 to 2.3 µM). In addition, notoincisol A (9) exhibited inhibitory activity on NO production of stimulated RAW 264.7 macrophages.

Polyacetylenes from Radix et Rhizoma Notopterygii incisi with an inhibitory effect on nitric oxide production in vitro.

Notopterygium roots (Qiang Huo) have been used in traditional Chinese medicine for treating colds, inflammatory diseases like rheumatoid arthritis, and as an analgesic. The anti-inflammatory activity of the roots of Notopterygium incisum has been evaluated by testing the inhibitory activity on nitric oxide production by inducible nitric oxide synthase. The apparent authenticity of the sample was checked by DNA sequence comparison. Using activity-guided isolation, different compounds were isolated and structurally characterized by means of NMR and mass spectroscopy. Eight polyacetylenes could be identified and were tested on their inhibitory activity on nitric oxide production in RAW 264.7 mouse macrophages using the Griess assay. Different 3-hydroxy allyl polyacetylenes exhibited significant activity (IC50: 8-acetoxyfalcarinol, 20.1 µM; falcarindiol, 9.2 µM; 9-epoxyfalcarindiol, 8.8 µM; and crithmumdiol, 23.6 µM).

Selective detection of alkaloids in MALDI-TOF: the introduction of a novel matrix molecule.

The current manuscript presents 3-[5'-(methylthio)-2,2'-bithiophen-5-ylthio]propanenitrile (MT3P), as a novel matrix molecule, which facilitates the selective ionization of alkaloids in matrix-assisted laser desorption/ionization mass spectrometry. Exhibiting strong ionizing properties at low levels of laser energy, MT3P was evaluated on 55 compounds belonging to various chemical families. The observed molecular ion yields induced by MT3P were compared with those obtained by commercially available matrices such as 1,8-dihydroxy-9,10-dihydroanthracen-9-one, α-cyano-4-hydroxycinnamic acid, 2,2':5',2"-terthiophene and 2,5-dihydroxybenzoic acid. In conclusion, MT3P displayed excellent ionization properties for 23 out of 25 investigated alkaloids, while showing little to no interaction with compounds from different chemical origin. Further, in comparison to other tested matrices, MT3P generally facilitated better ionization of alkaloids. Eventually, levels of laser energy were adjusted to obtain spectra with significantly reduced matrix noise.

Structure and anti-TB activity of trachylobanes from the liverwort Jungermannia exsertifolia ssp. cordifolia.

In the critical search for new antituberculosis lead compounds, bryophytes represent a largely untapped resource of chemically diverse structures. From the liverwort Jungermannia exsertifolia subsp. cordifolia, 11 new trachylobane diterpene derivatives, as well as three known compounds, were isolated. Their structures were elucidated by spectroscopic means, and full (1)H NMR spin analysis of one model compound confirmed the relative configurational assignments of the congeners. Four of the isolates exhibited noticeable activity against virulent Mycobacterium tuberculosis H(37)Rv with minimal inhibitory concentrations of 61-24 microg/mL. This finding suggests that bryophytes in general and trachylobanes in particular deserve further attention in the search for new antimycobacterial leads.

Matrix-Free Laser Desorption Ionization Mass Spectrometry as an Efficient Tool for the Rapid Detection of Opiates in Crude Extracts of Papaver somniferum.

Having a long history of traditional medicinal applications, Papaver somniferum is also known as a source of various pharmacologically highly active opiates. Consequently, their detection from plant extracts is an important analytical task and generally addressed by methods of GC-MS and LC-MS. However, opiates do also show structural similarities to matrix molecules used in matrix-assisted laser desorption ionization (LDI) and may therefore ionize upon simple laser irradiation. Following this analytical approach, the present work thoroughly evaluated the direct detection of opiates by matrix-free LDI in crude extracts of P. somniferum. The method facilitated the identification of 10 reported opiates by their molecular formulas without any chromatographic prepurification. Moreover, a principal component analysis based on LDI-MS data permitted the correct grouping of all extracts according to their inherent chemistry. Concluding experiments on serial dilutions of thebaine further evaluated potential quantitative applications of the method. Overall results highlight the promising potential of LDI-MS for the swift detection of opiates in complex mixtures.

E-notopterol.

THE TITLE COMPOUND (SYSTEMATIC NAME: 4-{[(2E)-5-hydr-oxy-3,7-dimethylocta-2,6-dien-1-yl]-oxy}-7H-furo[3,2-g][1]benzopyran-7-one), C(21)H(22)O(5), is a known furan-ocoumarin, which was isolated from the Chinese herbal product Radix seu Rhizoma Notopterygii. The crystal structure shows a weak O-H⋯O hydrogen bond.

Angelica sinensis and its alkylphthalides induce the detoxification enzyme NAD(P)H: quinone oxidoreductase 1 by alkylating Keap1.

The roots of Angelica sinensis (Oliv.) Diels (Dang Gui; Apiaceae) have a long history in traditional Chinese medicine as a remedy for women's disorders and are often called "lady's ginseng". Currently, extracts of A. sinensis are commonly included in numerous dietary supplements used for women's health and as antiaging products. In the present study, we examined the potential chemopreventive activity of A. sinensis extracts by measuring the relative ability to induce the detoxification enzyme, NAD(P)H:quinone oxidoreductase 1 (NQO1). The lipophilic partitions showed strong NQO1 induction with concentrations to double the enzyme activity (CD) of 5.5 +/- 0.7 (petroleum ether) and 3.9 +/- 0.5 microg/mL (chloroform). Fractionation led to the isolation of phenolic esters and alkylphthalides, especially Z-ligustilide, the main lipophilic compound, which showed strong NQO1 inducing properties (CD = 6.9 +/- 1.9 microM). Transcription of many detoxifying enzymes is regulated through the antioxidant response element (ARE) and its transcription factor Nrf2, which is repressed under basal conditions by Keap1. However, exposure to electrophilic inducers that alkylate Keap1 results in higher concentrations of free Nrf2 and ARE activation. The ARE reporter activity was therefore analyzed in HepG2-ARE-C8 cells after incubation with lipophilic extracts of A. sinensis or ligustilide for 24 h. Under these conditions, both the extract and the ligustilide increased ARE-luciferase reporter activity in a dose-dependent manner. Incubation of ligustilide with GSH and subsequent LC-MS-MS analysis revealed that ligustilide as well as oxidized ligustilide species covalently modified GSH. In addition, using MALDI-TOF mass spectrometry and LC-MS-MS, it was demonstrated that the lipophilic extracts, ligustilide, and monooxygenated ligustilide alkylated important cysteine residues in human Keap1 protein, thus activating Nrf2 and transcription of ARE regulated genes. These observations suggest that A. sinensis dietary supplements standardized to ligustilide have potential as chemopreventive agents through induction of detoxification enzymes.

High-content screening and mechanism-based evaluation of estrogenic botanical extracts.

Symptoms associated with menopause can greatly affect the quality of life for women. Botanical dietary supplements have been viewed by the public as safe and effective despite a lack of evidence indicating a urgent necessity to standardize these supplements chemically and biologically. Seventeen plants were evaluated for estrogenic biological activity using standard assays: competitive estrogen receptor (ER) binding assay for both alpha and beta subtypes, transient transfection of the estrogen response element luciferase plasmid into MCF-7 cells expressing either ER alpha or ER beta, and the Ishikawa alkaline phosphatase induction assay for both estrogenic and antiestrogenic activities. Based on the combination of data pooled from these assays, the following was determined: a) a high rate of false positive activity for the competitive binding assays, b) some extracts had estrogenic activity despite a lack of ability to bind the ER, c) one extract exhibited selective estrogen receptor modulator (SERM) activity, and d) several extracts show additive/synergistic activity. Taken together, these data indicate a need to reprioritize the order in which the bioassays are performed for maximal efficiency of programs involving bioassay-guided fractionation. In addition, possible explanations for the conflicts in the literature over the estrogenicity of Cimicifuga racemosa (black cohosh) are suggested.

Dynamic nature of the ligustilide complex.

Monomeric phthalides such as Z-ligustilide (1) and Z-butylidenephthalide (2) are major constituents of medicinal plants of the Apiaceae family. While 1 has been associated with a variety of observed biological effects, it is also known for its instability and rapid chemical degradation. For the purpose of isolating pure 1 and 2, a gentle and rapid two-step countercurrent isolation procedure was developed. From a supercritical CO2 fluid extract of Angelica sinensis roots, the phthalides were isolated with high GC-MS purities of 99.4% for 1 and 98.9% for 2 and consistently lower qHNMR purities of 98.1% and 96.4%, respectively. Taking advantage of molarity-based qHNMR methodology, a time-resolved study of the dynamic changes and residual complexity of pure 1 was conducted. GC-MS and (qH)NMR analysis of artificially degraded 1 provided evidence for the phthalide degradation pathways and optimized storing conditions. Parallel qHNMR analysis led to the recognition of variations in time- and process-dependent sample purity and has impact on the overall assessment of time-dependent changes in complex natural products systems. The study underscores the importance of independent quantitative monitoring as a prerequisite for the biological evaluation of labile natural products such as monomeric phthalides.