Data Base similarity (DBsimilarity) of natural products to aid compound identification on MS and NMR pipelines, similarity networking, and more

INTRODUCTION

We developed Data Base similarity (DBsimilarity), a user-friendly tool designed to organize structure databases into similarity networks, with the goal of facilitating the visualization of information primarily for natural product chemists who may not have coding experience.

METHOD

DBsimilarity, written in Jupyter Notebooks, converts Structure Data File (SDF) files into Comma-Separated Values (CSV) files, adds chemoinformatics data, constructs an MZMine custom database file and an NMRfilter candidate list of compounds for rapid dereplication of MS and 2D NMR data, calculates similarities between compounds, and constructs CSV files formatted into similarity networks for Cytoscape.

RESULTS

The Lotus database was used as a source for Ginkgo biloba compounds, and DBsimilarity was used to create similarity networks including NPClassifier classification to indicate biosynthesis pathways. Subsequently, a database of validated antibiotics from natural products was combined with the G. biloba compounds to identify promising compounds. The presence of 11 compounds in both datasets points to possible antibiotic properties of G. biloba, and 122 compounds similar to these known antibiotics were highlighted. Next, DBsimilarity was used to filter the NPAtlas database (selecting only those with MIBiG reference) to identify potential antibacterial compounds using the ChEMBL database as a reference. It was possible to promptly identify five compounds found in both databases and 167 others worthy of further investigation.

CONCLUSION

Chemical and biological properties are determined by molecular structures. DBsimilarity enables the creation of interactive similarity networks using Cytoscape. It is also in line with a recent review that highlights poor biological plausibility and unrealistic chromatographic behaviors as significant sources of errors in compound identification.

High-speed countercurrent chromatography with offline detection by electrospray mass spectrometry and nuclear magnetic resonance detection as a tool to resolve complex mixtures: A practical approach using Coffea arabica leaf extract

INTRODUCTION

Many secondary metabolites isolated from plants have been described in the literature owing to their important biological properties and possible pharmacological applications. However, the identification of compounds present in complex plant extracts has remained a great scientific challenge, is often laborious, and requires a long research time with high financial cost.

OBJECTIVES

The aim of this study was to develop a method that allows the identification of secondary metabolites in plant extracts with a high degree of confidence in a short period of time.

MATERIAL AND METHODS

In this study, an ethanolic extract of Coffea arabica leaves was used to validate the proposed method. Countercurrent chromatography was chosen as the initial step for extraction fractionation using gradient elution. Resulting fractions presented a variation of compounds concentrations, allowing for statistical total correlation spectroscopy (STOCSY) calculations between liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-HRMS/MS) and NMR across fractions.

RESULTS

The proposed method allowed the identification of 57 compounds. Of the annotated compounds, 20 were previously described in the literature for the species and 37 were reported for the first time. Among the inedited compounds, we identified flavonoids, alkaloids, phenolic acids, coumarins, and terpenes.

CONCLUSION

The proposed method presents itself as a valid alternative for the study of complex extracts in an effective, fast, and reliable way that can be reproduced in the study of other extracts.

NMR as a tool for compound identification in mixtures

INTRODUCTION

Natural products and metabolomics are intrinsically linked through efforts to analyze complex mixtures for compound annotation. Although most studies that aim for compound identification in mixtures use MS as the main analysis technique, NMR has complementary advances that are worth exploring for enhanced structural confidence.

OBJECTIVE

This review aimed to showcase a portfolio of the main tools available for compound identification using NMR.

MATERIALS AND METHODS

COLMAR, SMART-NMR, MADByTE, and NMRfilter are presented using examples collected from real samples from the perspective of a natural product chemist. Data are also made available through Zenodo so that readers can test each case presented here.

CONCLUSION

The acquisition of ¹ H NMR, HSQC, TOCSY, HSQC-TOCSY, and HMBC data for all samples and fractions from a natural products study is strongly suggested. The same is valid for MS analysis to create a bridged analysis between both techniques in a complementary manner. The use of NOAH supersequences has also been suggested and demonstrated to save NMR time.

Data Fusion-based Discovery (DAFdiscovery) pipeline to aid compound annotation and bioactive compound discovery across diverse spectral data

INTRODUCTION

Data Fusion-based Discovery (DAFdiscovery) is a pipeline designed to help users combine mass spectrometry (MS), nuclear magnetic resonance (NMR), and bioactivity data in a notebook-based application to accelerate annotation and discovery of bioactive compounds. It applies Statistical Total Correlation Spectroscopy (STOCSY) and Statistical HeteroSpectroscopy (SHY) calculation in their data using an easy-to-follow Jupyter Notebook.

METHOD

Different case studies are presented for benchmarking, and the resultant outputs are shown to aid natural products identification and discovery. The goal is to encourage users to acquire MS and NMR data from their samples (in replicated samples and fractions when available) and to explore their variance to highlight MS features, NMR peaks, and bioactivity that might be correlated to accelerated bioactive compound discovery or for annotation-identification studies.

RESULTS

Different applications were demonstrated using data from different research groups, and it was shown that DAFdiscovery reproduced their findings using a more straightforward method.

CONCLUSION

DAFdiscovery has proven to be a simple-to-use method for different situations where data from different sources are required to be analyzed together.

Larvicidal Activity of Secondary Plant Metabolites inAedes aegyptiControl: An Overview of the Previous 6 Years

Aedes aegypti is the main transmitter of several arboviruses, mainly dengue. It occurs, recently, in more than 100 countries and majority of the world population lives in areas of mosquito incidence, marking its control relevant and necessary. Presently, the main form of vector control is the use of synthetic insecticides; however, its continuous application has led to inefficiency due to resistance development. Based on this fact, the insecticides from natural sources appear as a friendly alternative for man and the environment. This study provides an overview of the larvicidal compounds isolated from plant extracts while controlling A. aegypti, in the previous 6 years (2013-2018), and aims to impart more knowledge regarding the described metabolites and to encourage the search for new bioactive compounds. In addition, the proposals for mechanisms of action and structure-activity relationships that may justify the larvicidal potential are also discussed.

Preparative mass-spectrometry profiling of minor concentrated metabolites in Salicornia gaudichaudiana Moq by high-speed countercurrent chromatography and off-line electrospray mass-spectrometry injection

Salicornia species have just been introduced to the European market as a vegetable named 'samphire', 'green asparagus', or 'sea asparagus'. Due to its increasing attention, and associated value, minor compounds of Salicornia gaudichaudiana Moq were investigated. The use of countercurrent chromatography and mass spectrometry enabled the search for known, as well as potentially novel natural products. Their identification was achieved based on molecular weights and mass-spectrometric fragmentation data. Low detection limits enabled the visualization of all compounds with their identification in almost real time close to the preparative countercurrent chromatography experiment. A list of known natural products from Salicornia genus guided the identification process of compounds occurring in Salicornia gaudichaudiana Moq by tandem mass spectrometry fragment comparison. The natural product classes were divided into four groups: chlorogenic acid derivatives; flavonoid derivatives; pentacyclic triterpenoid saponins; and other compounds.

Countercurrent chromatography separation of saponins by skeleton type from Ampelozizyphus amazonicus for off-line ultra-high-performance liquid chromatography/high resolution accurate mass spectrometry analysis and characterisation

Ampelozizyphus amazonicus Ducke (Rhamnaceae), a medicinal plant used to prevent malaria, is a climbing shrub, native to the Amazonian region, with jujubogenin glycoside saponins as main compounds. The crude extract of this plant is too complex for any kind of structural identification, and HPLC separation was not sufficient to resolve this issue. Therefore, the aim of this work was to obtain saponin enriched fractions from the bark ethanol extract by countercurrent chromatography (CCC) for further isolation and identification/characterisation of the major saponins by HPLC and MS. The butanol extract was fractionated by CCC with hexane - ethyl acetate - butanol - ethanol - water (1:6:1:1:6; v/v) solvent system yielding 4 group fractions. The collected fractions were analysed by UHPLC-HRMS (ultra-high-performance liquid chromatography/high resolution accurate mass spectrometry) and MSn. Group 1 presented mainly oleane type saponins, and group 3 showed mainly jujubogenin glycosides, keto-dammarane type triterpene saponins and saponins with C31 skeleton. Thus, CCC separated saponins from the butanol-rich extract by skeleton type. A further purification of group 3 by CCC (ethyl acetate - ethanol - water (1:0.2:1; v/v)) and HPLC-RI was performed in order to obtain these unusual aglycones in pure form.

Gradient Elution in Countercurrent Chromatography

Countercurrent chromatography is a form of liquid-liquid partition chromatography in which the stationary liquid phase is retained in the apparatus without the use of a solid support. Gradient elution in countercurrent chromatography can be used in many different ways, such as linear gradients, stepwise elution gradients, pH gradients, etc. The main goal of using the gradient approach is to shorten the duration of the separation and improve resolution, especially when the retention range of the sample to be purified is broadening and, thus, the compounds cannot be purified by only one solvent system. The principle is based on modifying the mobile phase to increase the elution strength with no or minimum changes in the stationary phase, which can be a difficult task since both phases are in intimate contact all the time. The most common ways to perform gradients in countercurrent chromatography are changing the mobile's phase polarity, flow rate, and pH, what is called linear or step gradient, flow rate gradient, pH gradient, respectively.

Solvent system selectivities in countercurrent chromatography using Salicornia gaudichaudiana metabolites as practical example with off-line electrospray mass-spectrometry injection profiling

For the development of an efficient two-stage isolation process for high-speed countercurrent chromatography (HSCCC) with focus on principal metabolites from the ethyl acetate extract of the halophyte plant Salicornia gaudichaudiana, separation selectivities of two different biphasic solvent systems with similar polarities were evaluated using the elution and extrusion approach. Efficiency in isolation of target compounds is determined by the solvent system selectivity and their chronological use in multiple separation steps. The system n-hexane-ethyl acetate-methanol-water (0.5:6:0.5:6, v/v/v/v) resulted in a comprehensive separation of polyphenolic glycosides. The system n-hexane-n-butanol-water (1:1:2, v/v/v) was less universal but was highly efficient in the fractionation of positional isomers such as di-substituted cinnamic acid quinic acid derivatives. Multiple metabolite detection performed on recovered HSCCC tube fractions was done with rapid mass-spectrometry profiling by sequential off-line injections to electrospray mass-spectrometry (ESI-MS/MS). Selective ion traces of metabolites delivered reconstituted preparative HSCCC runs. Molecular weight distribution of target compounds in single HSCCC tube fractions and MS/MS fragment data were available. Chromatographic areas with strong co-elution effects and fractions of pure recoverable compounds were visualized. In total 11 metabolites have been identified and monitored. Result of this approach was a fast isolation protocol for S. gaudichaudiana metabolites using two solvent systems in a strategic sequence. The process could easily be scaled-up to larger lab-scale or industrial recovery.

Isolation of phenolics from Rhizophora mangle by combined counter-current chromatography and gel-filtration

Nine phenolic compounds, quercetin, epi-catechin, catechin, 4-hydroxybenzoic acid, kaempferol 3-O-β-glucopyranoside, quercetin 3-O-β-glucopyranoside, quercetin 3-O-6"-trans-coumaroyl-β-glucoside, kaempferol 3-O-β-rutinoside and quercetin 3-O-β-rutinoside, were isolated from the EtOAc leaf extract of Rhizophora mangle (Rhizophoraceae) combining counter-current chromatography (CCC) and gel-filtration. A solvent system of n-hexane-ethyl acetate-methanol-water (1.5:6:1.5:6) was employed at the preliminary stage of EtOAc extract fractionation as it was shown to contain compounds that differed highly in their hydrophobicity. The obtained fractions were further purified by either CCC or gel-filtration depending on their complexity. The isolated compounds were analyzed by NMR spectroscopy and the proposed structures were confirmed by HRES/ESI/TOF MS. Some of these compounds were isolated and/or identified for the first time in R. mangle.

Isolation of Phenolics from Rhizophora mangle by Combined Counter-current Chromatography and Gel-Filtration

Nine phenolic compounds, quercetin, epi-catechin, catechin, 4-hydroxybenzoic acid, kaempferol 3- O-β-glucopyranoside, quercetin 3- O-β-glucopyranoside, quercetin 3- O-6″- trans-coumaroyl-β-glucoside, kaempferol 3- O-β-rutinoside and quercetin 3- O-β-rutinoside, were isolated from the EtOAc leaf extract of Rhizophora mangle (Rhizophoraceae) combining counter-current chromatography (CCC) and gel-filtration. A solvent system of n-hexane-ethyl acetate-methanol-water (1.5:6:1.5:6) was employed at the preliminary stage of EtOAc extract fractionation as it was shown to contain compounds that differed highly in their hydrophobicity. The obtained fractions were further purified by either CCC or gel-filtration depending on their complexity. The isolated compounds were analyzed by NMR spectroscopy and the proposed structures were confirmed by HRES/ESI/TOF MS. Some of these compounds were isolated and/or identified for the first time in R. mangle.

Changes in the mobile phase composition on a stepwise counter-current chromatography elution for the isolation of flavonoids from Siparuna glycycarpa

This paper describes the isolation of flavonoids and other aromatic compounds from an ethyl acetate extract of leaves of Siparuna glycycarpa using stepwise elution counter-current chromatography (CCC). The elution profile yielded the following compounds: diglycosylated flavonoids, quercetin 3-O-rutinoside and quercetin 7-O-rutinoside, followed by monoglycosylated flavonoids, kaempferol-3-O-β-glucopyranoside, kaempferol-3-O-β-rhamnopiranoside, kaempferol-3-O-β-6''(p-coumaroyl) glucopyranoside, and quercetin-3-O-β-glucopyranoside, and then free phenolics, protocatechuic acid, and 2',6'-dihydroxy-4, 4'-dimethoxydihydrochalcone, which shows that this type of elution covers a broader range of polarity than the traditional isocratic mode. This makes it more suitable to perform separations of mixtures containing large differences in hydrophobicity. A GC analysis of a blank CCC run was performed to determine if changes in the mobile phase composition affect the chromatographic process. Results showed a gradual variation of the composition of the mobile phase emerging after the step gradient, favoring the selectivity of the solvent system.

Strategies of solvent system selection for the isolation of flavonoids by countercurrent chromatography

Flavonoids form a large class of important naturally occurring bioactive compounds. Their isolation and purification from natural sources can sometimes be very difficult and time-consuming when traditional phytochemical techniques are used. Countercurrent chromatography (CCC), a support-free liquid-liquid partition chromatography technique, is very useful for the isolation of polar compounds and its use is increasing in the natural products field. In this paper, we propose strategies of solvent system selection for the isolation of flavonoids by CCC, based on data from the literature, plus incorporation of own practical experiences. The selected references report the isolation of over 300 different flavonoid compounds from more than 100 plant species, using 40 different solvent systems, showing the versatility of this technique. The solvent system hexane-ethylacetate-methanol-water is proposed as a starting point for the separation of samples containing free flavonoids, as it was cited in more than 60% of the papers. A "fine tuning" step is proposed at each level of this solvent family. Other modifications include exchanging the alcohol in the system as well as introducing a fifth solvent. The solvent system ethyl-acetate-butanol-water is proposed as the starting point for glycosylated flavonoids. Other solvent systems are also discussed. The use of gradients is proposed for samples containing both free and glycosylated flavonoids, as the polarity window is larger in these cases. High-speed countercurrent chromatography was used in 89% of the reviewed data.