Natural Products Dereplication: Databases and Analytical Methods

The development of efficient methods for dereplication has been critical in the re-emergence of the research in natural products as a source of drug leads. Current dereplication workflows rapidly identify already known bioactive secondary metabolites in the early stages of any drug discovery screening campaign based on natural extracts or enriched fractions. Two main factors have driven the evolution of natural products dereplication over the last decades. First, the availability of both commercial and public large databases of natural products containing the key annotations against which the biological and chemical data derived from the studied sample are searched for. Second, the considerable improvement achieved in analytical technologies (including instrumentation and software tools) employed to obtain robust and precise chemical information (particularly spectroscopic signatures) on the compounds present in the bioactive natural product samples. This chapter describes the main methods of dereplication, which rely on the combined use of large natural product databases and spectral libraries, alongside the information obtained from chromatographic, UV-Vis, MS, and NMR spectroscopic analyses of the samples of interest.

Rapid Chemical Profiling of Filipendula ulmaria Using CPC Fractionation, 2-D Mapping of 13C NMR Data, and High-Resolution LC-MS

Filipendula ulmaria, commonly known as meadowsweet, is a wild herbaceous flowering plant that is widely distributed in Europe. A range of salicylic acid derivatives and flavonol glycosides have been previously associated with the antirheumatic and diuretic properties of F. ulmaria. In the present work, a hydroalcoholic extract from F. ulmaria aerial parts was extensively profiled using an efficient NMR-based dereplication strategy. The approach involves the fractionation of the crude extract by centrifugal partition chromatography (CPC), 13C NMR analysis of the fractions, 2D-cluster mapping of the entire NMR dataset, and, finally, structure elucidation using a natural metabolite database, validated by 2D NMR data interpretation and liquid chromatography coupled with mass spectrometry. The chemodiversity of the aerial parts was extensive, with 28 compounds unambiguously identified, spanning various biosynthetic classes. The F. ulmaria extract and CPC fractions were screened for their potential to enhance skin epidermal barrier function and skin renewal properties using in vitro assays performed on Normal Human Epidermal Keratinocytes. Fractions containing quercetin, kaempferol glycosides, ursolic acid, pomolic acid, naringenin, β-sitosterol, and Tellimagrandins I and II were found to upregulate genes related to skin barrier function, epidermal renewal, and stress responses. This research is significant as it could provide a natural solution for improving hydration and skin renewal properties.

Lignans from the Roots and Rhizomes of Dysosma versipellis and Their Cytotoxic Activities

One new dibenzyltyrolactone lignan dysoslignan A (1), three new arylnaphthalide lignans dysoslignan B-C (2-4), along with fourteen known metabolites (5-18), were isolated from the roots and rhizomes of Dysosma versipellis. Their structures and stereochemistry were determined from analysis of NMR spectroscopic and circular dichroism (CD) data. Compound 2 represents the first report of naturally occurring arylnaphthalide lignan triglycoside. The cytotoxic activities of all isolated compounds were evaluated against A-549 and SMMC-7721 cell lines. Compounds 7-10 and 14-16 were more toxic than cisplatin in two tumor cell lines. This investigation clarifies the potential effective substance basis of D. versipellis in tumor treatment.

Dysosmaflavonoid A-F, new flavonols with potent DPPH radical scavenging activity from Dysosma versipellis

Six new flavonols, including four glucosylated flavonols (dysosmaflavonoid A-D), one phenylpropanoid-substituted flavonol (dysosmaflavonoid E), and one phenyl-substituted flavonol (dysosmaflavonoid F), together with five known analogues, were isolated from the roots and rhizomes of Dysosma versipellis. Their structures were elucidated by comprehensive analysis of their NMR, IR, UV, HRESIMS, and HPLC data. The antioxidant activities of all isolated compounds were examined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay. Compounds 2, 3, 5-8, and 12 exhibited significant DPPH scavenging capacity with IC₅₀ values of 33.95, 39.02, 31.17, 32.79, 31.85, 30.48, and 23.75 μM, respectively, in comparison with Trolox (IC₅₀, 15.80 μM). Compound 12 displayed more potent DPPH radical scavenging activity than prenylated and (or) glucosided derivatives (2-4, or 10). The preliminary structure-activity relationship showed that the catechol structure in flavonol is essential for DPPH radical scavenging effect.

Structurally diverse biflavonoids from Dysosma versipellis and their bioactivity

Five pairs of new biflavonoid enantiomers, (±)-dysosmabiflavonoids A–E (1–5), two new biflavonoids, dysosmabiflavonoids F–G (6–7), and four biosynthetically related precursors (8–11) were isolated from the roots and rhizomes of Dysosma versipellis.

Isolation of a new monoterpenoid glycoside from Anhua dark tea based on an NMR-guided method and its cytotoxic activity against MDA-MB-231 and SH-SY5Y cell lines

Based on an NMR-guided method, one new monoterpenoid glycoside (1) was isolated from Anhua dark tea, together with five known compounds (2-6). The structure of the new compound was determined as 3-(5,5-dimethyltetrahydrofuranyl)-1-buten-3-ol primeveroside, and trivially named anhuaterpenoside A (1), on the basis of detailed spectroscopic analyses, and acidic hydrolysis. Compound 1 exhibits cytotoxic activity against MDA-MB-231 and SH-SY5Y cell lines with IC₅₀ value of 23.26 μM and 18.57 μM, respectively.

Harnessing the Power of Optical Microscopic and Macroscopic Imaging for Natural Products as Cancer Therapeutics

Natural products (NPs) are an important source for new drug discovery over the past decades, which have been demonstrated to be effectively used in cancer prevention, treatment, and adjuvant therapy. Many methods, such as the genomic and metabolomic approaches, immunochemistry, mass spectrometry, and chromatography, have been used to study the effects of NPs on cancer as well as themselves. Because of the advantages in specificity, sensitivity, high throughput, and cost-effectiveness, optical imaging (OI) approaches, including optical microscopic imaging and macroscopic imaging techniques have also been applied in the studies of NPs. Optical microscopic imaging can observe NPs as cancer therapeutics at the cellular level and analyze its cytotoxicity and mechanism of action. Optical macroscopic imaging observes the distribution, metabolic pathway, and target lesions of NPs in vivo, and evaluates NPs as cancer therapeutics at the whole-body level in small living animals. This review focuses on the recent advances in NPs as cancer therapeutics, with particular emphasis on the powerful use of optical microscopic and macroscopic imaging techniques, including the studies of observation of ingestion by cells, anticancer mechanism, and in vivo delivery. Finally, we prospect the wider application and future potential of OI approaches in NPs as cancer therapeutics.

1H NMR-MS-based heterocovariance as a drug discovery tool for fishing bioactive compounds out of a complex mixture of structural analogues

Chemometric methods and correlation of spectroscopic or spectrometric data with bioactivity results are known to improve dereplication in classical bio-guided isolation approaches. However, in drug discovery from natural sources the isolation of bioactive constituents from a crude extract containing close structural analogues remains a significant challenge. This study is a ¹H NMR-MS workflow named ELINA (Eliciting Nature’s Activities) which is based on statistical heterocovariance analysis (HetCA) of ¹H NMR spectra detecting chemical features that are positively (“hot”) or negatively (“cold”) correlated with bioactivity prior to any isolation. ELINA is exemplified in the discovery of steroid sulfatase (STS) inhibiting lanostane triterpenes (LTTs) from a complex extract of the polypore fungus Fomitopsis pinicola.

Methanol linear gradient counter-current chromatography for the separation of natural products: Sinopodophyllum hexandrum as samples

Counter-current chromatography (CCC) is a unique, liquid-liquid partition chromatography process. Both the mobile and stationary phases are liquids, so no solid support matrix is used. CCC has gained wide acceptance as a preparative technique in a variety of fields. Because the mobile and stationary phases are both liquids, gradient elution is difficult to perform with CCC. Phase equilibrium must be maintained, so any change in the composition of one phase may induce a compositional change in the other. In this work, a new linear gradient elution method was developed for CCC. Biphasic solvent systems containing heptane, ethyl acetate, methanol, and water (HepEMWat) in various ratios were prepared and used to optimize both isocratic and linear gradient CCC separation with methanol. We first separated a test mixture of four standard compounds with partition coefficients ranging from 0.8 to 7.8. The separation resembled a reversed-phase process, and elution was performed while progressively decreasing the polarity of the mobile phase. Target molecules with small partition coefficients eluted first in the lower phase of the optimized HepEMWat solvent system. Elution of constituents with large partition coefficients was quite slow under isocratic conditions. Separation time was significantly reduced when elution was performed with a linear gradient using methanol and the optimal HepEMWat system. Elution with a 3:7:4:6 (v/v/v/v) HepEMWat system took approximately 200 min. This included an 80-min isocratic step, followed by gradient elution with methanol from 0% to 30%. The optimized methanol linear gradient CCC method was then used to separate a complex mixture of natural products isolated from Sinopodophyllum hexandrum (Royle) Ying roots. Twelve compounds with a wide range of polarities were well-resolved in a single separation. We have developed a convenient and cost-effective strategy for the separation of complex mixtures. No tedious mobile phase preparation step is required. The volume of unused mobile phase is minimal, so little solvent is wasted. The method is an important advance for the separation of mixtures that contain many compounds with a large range of polarities and partition coefficients, which are common features of natural products.

Preparative separation of flavone dimers from Dysosma versipellis by counter-current chromatography: Trifluoroacetic acid as a solvent system modifier

The separation of natural products is grueling and time-consuming work with repeated isolations needed to obtain purified compounds. However, using counter-current chromatography, a unique liquid-liquid partition chromatography, constituents can usually be purified efficiently. During the separation of flavone dimers from Dysosma versipellis (Hance) by counter-current chromatography, the separation resolution and sample loading was impeded by the emulsification of the sample. By screening, trifluoroacetic acid was selected as the solvent modifier to eliminate the emulsification. Then, a quaternary solvent system of hexane/ethyl acetate/methanol/water (4:6:5:5 v/v/v/v) with trifluoroacetic acid at a low concentration of 0.5% v/v was used to purify the components from D. versipellis. Compared to that without trifluoroacetic acid, the separation resolution as well as the sample loading both increased greatly. In addition, flavone dimers in low concentrations could be enriched and purified at high sample loading. As a result, five podophyllotoxins and 11 flavonoids were purified and characterized by interpretation of spectroscopic data, in which two of eight flavone dimers were new and a known flavone dimer was first separated from this species.

Sugaring-out strategy for counter-current chromatography isolation: podophyllotoxins and flavones from Dysosma versipellis as examples

In this work, we introduced a sugaring-out strategy for optimizing two-phase solvent systems for counter-current chromatography by adding some sugars into the selected two-phase solvent system.

A combination strategy for extraction and isolation of multi-component natural products by systematic two-phase solvent extraction-(13)C nuclear magnetic resonance pattern recognition and following conical counter-current chromatography separation: Podophyllotoxins and flavonoids from Dysosma versipellis (Hance) as examples

Despite of substantial developments of extraction and separation techniques, isolation of natural products from natural resources is still a challenging task. In this work, an efficient strategy for extraction and isolation of multi-component natural products has been successfully developed by combination of systematic two-phase liquid-liquid extraction-(13)C NMR pattern recognition and following conical counter-current chromatography separation. A small-scale crude sample was first distributed into 9 systematic hexane-ethyl acetate-methanol-water (HEMWat) two-phase solvent systems for determination of the optimum extraction solvents and partition coefficients of the prominent components. Then, the optimized solvent systems were used in succession to enrich the hydrophilic and lipophilic components from the large-scale crude sample. At last, the enriched components samples were further purified by a new conical counter-current chromatography (CCC). Due to the use of (13)C NMR pattern recognition, the kinds and structures of major components in the solvent extracts could be predicted. Therefore, the method could collect simultaneously the partition coefficients and the structural information of components in the selected two-phase solvents. As an example, a cytotoxic extract of podophyllotoxins and flavonoids from Dysosma versipellis (Hance) was selected. After the systematic HEMWat system solvent extraction and (13)C NMR pattern recognition analyses, the crude extract of D. versipellis was first degreased by the upper phase of HEMWat system (9:1:9:1, v/v), and then distributed in the two phases of the system of HEMWat (2:8:2:8, v/v) to obtain the hydrophilic lower phase extract and lipophilic upper phase extract, respectively. These extracts were further separated by conical CCC with the HEMWat systems (1:9:1:9 and 4:6:4:6, v/v). As results, total 17 cytotoxic compounds were isolated and identified. In general, whole results suggested that the strategy was very efficient for the systematic extraction and isolation of biological active components from the complex biomaterials.