Metabolic Profiling and Classification of Propolis Samples from Southern Brazil: An NMR-Based Platform Coupled with Machine Learning

Bee Species, Botanical Sources and the Chemical Composition of Propolis from Yucatan, Mexico

Propolis is used by corbiculated bees to protect the bee hive; it is mostly used to seal cracks, to reduce or prevent microbial growth and to embalm invaders. Different factors have been reported to influence the chemical composition of propolis, including bee species and the flora surrounding the hive. Nevertheless, the majority of the studies are focused on propolis produced by Apis mellifera, while studies on the chemical composition of propolis produced by stingless bees are still limited. In this investigation, the chemical composition of 27 propolis samples collected in the Yucatan Peninsula from A. mellifera beehives, together with 18 propolis samples from six different species of stingless bees, were analyzed by GC-MS. Results showed that lupeol acetate and β-amyrin were the characteristic triterpenes in propolis samples from A. mellifera, while grandiflorenic acid and its methyl ester were the main metabolites present in samples from stingless bees. Multivariate analyses were used to explore the relationship between bee species and botanical sources on the chemical composition of the propolis samples. Differences in body size and, therefore, foraging abilities, as well as preferences for specific botanical sources among bee species, could explain the observed variation in propolis chemical composition. This is the first report on the composition of propolis samples from the stingless bees Trigona nigra, Scaptotrigona pectoralis, Nannotrigona perilampoides, Plebeia frontalis and Partamona bilineata.

Computer Science Technology in Natural Products Research: A Review of Its Applications and Implications

Computational approaches to drug development are rapidly growing in popularity and have been used to produce significant results. Recent developments in information science have expanded databases and chemical informatics knowledge relating to natural products. Natural products have long been well-studied, and a large number of unique structures and remarkable active substances have been reported. Analyzing accumulated natural product knowledge using emerging computational science techniques is expected to yield more new discoveries. In this article, we discuss the current state of natural product research using machine learning. The basic concepts and frameworks of machine learning are summarized. Natural product research that utilizes machine learning is described in terms of the exploration of active compounds, automatic compound design, and application to spectral data. In addition, efforts to develop drugs for intractable diseases will be addressed. Lastly, we discuss key considerations for applying machine learning in this field. This paper aims to promote progress in natural product research by presenting the current state of computational science and chemoinformatics approaches in terms of its applications, strengths, limitations, and implications for the field.

NMR and HPLC profiling of bee pollen products from different countries

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Analysis using NMR and HPLC can be used to identify countries of origin but not producing years of bee pollens.

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Flavanoids in bee pollens from different countries were characterized using HPLC.

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Bee pollens from Spain and Australia were high in sucrose and adenosine.

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Bee pollens from China were high in trigonelline, uridine, and cytidine.

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Only the bee pollens from China contained acetic acid.

Bee pollen, a beehive product collected from flowers by honeybees, contains over 250 biological substances, and has attracted increasing attention as a functional food. However, commercial bee pollen products are often multifloral, and samples from different countries vary significantly. There is no universal standard for objective quality assessment of bee pollen based on its chemical composition. Here, we report metabolomic analysis of 11 bee pollen samples from Spain, China, and Australia for quality control. The characteristics of the samples depend on the sucrose, nucleoside, amino acid, and flavanol concentrations. Bee pollen samples from Spain and Australia had higher sucrose and adenosine concentrations, whereas those from China had higher trigonelline, uridine, and cytidine concentrations. Interestingly, acetic acid was only detected in samples from China. These components can be used to identify the country of origin. The obtained profiles of the samples will contribute to universal standard development for bee pollen products.

Quality assessment and chemical diversity of Australian propolis from Apis mellifera bees

The propolis industry is well established in European, South American and East Asian countries. Within Australia, this industry is beginning to emerge with a few small-scale producers. To contribute to the development of the Australian propolis industry, the present study aimed to examine the quality and chemical diversity of propolis collected from various regions across Australia. The results of testing 158 samples indicated that Australian propolis had pure resin yielding from 2 to 81% by weight, total phenolic content and total flavonoid content in one gram of dry extract ranging from a few up to 181 mg of gallic acid equivalent and 145 mg of quercetin equivalent, respectively. Some Australian propolis showed more potent antioxidant activity than the well-known Brazilian green, Brazilian red, and Uruguayan and New Zealand poplar-type propolis in an in vitro DPPH assay. In addition, an HPLC–UV analysis resulted in the identification of 16 Australian propolis types which can be considered as high-grade propolis owing to their high total phenolic content. Chemometric analysis of their ¹H NMR spectra revealed that propolis originating from the eastern and western coasts of Australia could be significantly discriminated based on their chemical composition.

Propolis: chemical diversity and challenges in quality control

Propolis is a resinous natural product produced by honeybees using beeswax and plant exudates. The chemical composition of propolis is highly complex, and varies with region and season. This inherent chemical variability presents several challenges to its standardisation and quality control. The present review was aimed at highlighting marker compounds for different types of propolis, produced by the species Apis mellifera, from different geographical origins and that display different biological activities, and to discuss strategies for quality control. Over 800 compounds have been reported in the different propolises such as temperate, tropical, birch, Mediterranean, and Pacific propolis; these mainly include alcohols, acids and their esters, benzofuranes, benzopyranes, chalcones, flavonoids and their esters, glycosides (flavonoid and diterpene), glycerol and its esters, lignans, phenylpropanoids, steroids, terpenes and terpenoids. Among these, flavonoids (> 140), terpenes and terpenoids (> 160) were major components. A broad range of biological activities, such as anti-oxidant, antimicrobial, anti-inflammatory, immunomodulatory, and anticancer activities, have been ascribed to propolis constituents, as well as the potential of these compounds to be biomarkers. Several analytical techniques, including non-separation and separation methods have been described in the literature for the quality control assessment of propolis. Mass spectrometry coupled with separation methods, followed by chemometric analysis of the data, was found to be a valuable tool for the profiling and classification of propolis samples, including (bio)marker identification. Due to the rampant chemotypic variability, a multiple-marker assessment strategy considering geographical and biological activity marker(s) with chemometric analysis may be a promising approach for propolis quality assessment.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11101-022-09816-1.

Metabolomic Analysis of Combretum lanceolatum Plants Interaction with Diaporthe phaseolorum and Trichoderma spirale Endophytic Fungi through 1 H-NMR

Endophytic fungi are an important class of microorganisms, able to interact with a host plant via a mutualistic mechanism without visible symptoms of the fungal colonization. The synergy between endophytic fungi and their host plant can promote morphological, physiological and biochemical changes through the expression of bioactive metabolites. This work aims to correlate metabolic changes in the Combretum lanceolatum plant metabolome with its endophytic fungi Diaporthe phaseolorum (Dp) and Trichoderma spirale (Ts), and to discover corresponding metabolite-biomarkers, with the principal focus being on its primary metabolism. The ¹ H-NMR metabolomic analysis of qualitative and quantitative changes was performed through multivariate statistical analysis and the identification of primary metabolites was achieved on the Madison Metabolomics Consortium Database. The presence of Dp significantly impacted the plant's metabolic pathways, improving the biosynthesis of primary metabolites such as threonine, malic acid and N-acetyl-mannosamine, which are precursors of special metabolites involved in plant self-defence. This work represents a valuable contribution to advanced studies on the metabolic profiles of the interaction of plants with endophytes.

Exploratory and discriminant analysis of plant phenolic profiles obtained by UV-vis scanning spectroscopy

Some species of cover crops produce phenolic compounds with allelopathic potential. The use of math, statistical and computational tools to analyze data obtained with spectrophotometry can assist in the chemical profile discrimination to choose which species and cultivation are the best for weed management purposes. The aim of this study was to perform exploratory and discriminant analysis using R package specmine on the phenolic profile of Secale cereale L., Avena strigosa L. and Raphanus sativus L. shoots obtained by UV-vis scanning spectrophotometry. Plants were collected at 60, 80 and 100 days after sowing and at 15 and 30 days after rolling in experiment in Brazil. Exploratory and discriminant analysis, namely principal component analysis, hierarchical clustering analysis, t-test, fold-change, analysis of variance and supervised machine learning analysis were performed. Results showed a stronger tendency to cluster phenolic profiles according to plant species rather than crop management system, period of sampling or plant phenologic stage. PCA analysis showed a strong distinction of S. cereale L. and A. strigosa L. 30 days after rolling. Due to the fast analysis and friendly use, the R package specmine can be recommended as a supporting tool to exploratory and discriminatory analysis of multivariate data.

Untargeted Ultrahigh-Performance Liquid Chromatography-Hybrid Quadrupole-Orbitrap Mass Spectrometry (UHPLC-HRMS) Metabolomics Reveals Propolis Markers of Greek and Chinese Origin

Chemical composition of propolis depends on the plant source and thus on the geographic and climatic characteristics of the site of collection. The aim of this study was to investigate the chemical profile of Greek and Chinese propolis extracts from different regions and suggest similarities and differences between them. Untargeted ultrahigh-performance liquid chromatography coupled to hybrid quadrupole-Orbitrap mass spectrometry (UHPLC-HRMS) method was developed and 22 and 23 propolis samples from Greece and China, respectively, were analyzed. The experimental data led to the observation that there is considerable variability in terms of quality of the distinctive propolis samples. Partial least squares - discriminant analysis (PLS-DA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) models were constructed and allowed the identification of significant features for sample discrimination, adding relevant information for the identification of class-determining metabolites. Chinese samples overexpressed compounds that are characteristic of the poplar type propolis, whereas Greek samples overexpress the latter and the diterpenes characteristic of the Mediterranean propolis type.

Metabolomics Reveals Discrimination of Chinese Propolis from Different Climatic Regions

The chemical profiles of propolis vary greatly due to the botanic sources and geographic origins, which limit its standardization for modern usages. Here, we proposed a reliable ¹H NMR-based metabolomic approach, to discriminate the function and quality of Chinese propolis. A total 63 Chinese propolis samples from different temperate regions were collected and extracted for NMR analysis. Twenty-one compositions in ethanol extracts were assigned based on characteristic chemical shifts and previous literature reports. Significant geographic indicators were identified after the PCA and orthogonal partial least squares discriminant analysis (OPLS-DA) analysis of the obtained ¹H NMR data. It was found that the composition discriminations arose from long-term acclimation of the different climates of botanic origin and caused the differences in the biological activities. This study provides us a reasonable instruction for the quality control of Chinese propolis.

NMR-based metabolomic study of asafoetida

Asafoetida, an oleo-gum-resin obtained from the exudates of Ferula assa-foetida L. roots, is traditionally used to treat various diseases including asthma, gastrointestinal disorders, and intestinal parasites. On the basis of Iranian traditional medicine, the main source of asafetida is F. assa-foetida roots. In folk medicine, however, different Ferula species have been used as sources of asafoetida. To identify the original asafoetida that possesses medicinal properties, we should compare metabolic profiles of different asafoetida sources which are commonly used for the oleo-gum-resin preparation.¹H-NMR based metabolomics was used to obtain metabolic profiles of eight asafoetida oleo-gum-resin samples and forty-six samples of Ferula species roots from two main regions of Iran. The acquired data were analyzed using multivariate principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and orthogonal projection to latent structures discriminant analysis (OPLS-DA) to identify the metabolic differences and similarities between the samples. Asafoetida is usually produced from Ferula species of southern and eastern regions of Iran. A clear metabolic differentiation was evident between asafoetida oleo-gum- resin samples from the southern and those of the eastern Iran. The distinguished metabolites, umbelliprenin, farnesiferol B, farnesiferol C, samarcandin and galbanic acid are significantly found in southern samples. Only southern asafoetida is obtained from F. assa-foetida. Asafoetida from eastern region of Iran is obtained from other species of Ferula such as F. alliacea and its metabolic profile is far different from that of southern asafoetida.

Natural deep eutectic solvents and aqueous solutions as an alternative extraction media for propolis

Ethanolic extracts of propolis are consumed for their health benefits even though direct consumption of alcoholic extracts is not always ideal. Natural Deep Eutectic Solvents (NADES) can potentially extract similar compounds as alcoholic extracts while being better for direct consumption. Therefore, in this work alternative solvents for the extraction of green propolis including its biomarker artepillin C were examined. Sixteen NADES made from low toxicity chemicals, including the essential amino acid l-lysine, were explored along with twelve individual NADES components and honey, which showed similar physical-chemical properties to NADES. At 50 °C NADES made from choline chloride-propylene glycol or lactic acid proved to be equal or better than the benchmark EtOH:Water 7:3 (v/v). Alternatively, aqueous l-lysine appeared as a potential solvent for the preparation of aqueous propolis extracts. From these findings NADES, honey and aqueous l-lysine solutions all demonstrated the potential to replace ethanol or water for extracting green propolis.

Comparative analysis of volatile compound profiles of propolis from different provenances

BACKGROUND

Propolis is a complex mixture that honey bees produce from the exudates of various plants and presents many medicinal properties. Its chemical composition varies according to the phytogeography characteristics of each region, among others. The aim of this study was to identify and characterize the volatile organic compounds (VOCs) present in Venezuelan propolis and compare with reference samples such as Brazilian and Argentinian propolis.

RESULTS

A total of 90 VOCs were identified in a series of propolis samples using both solid-phase microextraction and dynamic headspace (DHS), both coupled to a gas chromatograph-electron ionization mass spectrometer. In the case of Venezuelan propolis, sesquiterpenes, esters, aromatic compounds, and aliphatic hydrocarbons were identified. Limonene was found only in Venezuelan samples, this being the first time it has been identified in samples from this country. In the case of green propolis, β-caryophyllene and nerolidol were the major compounds. As for the Argentinian samples, prenyl acetate, benzyl acetate, and 2-phenylethyl acetate were detected only in these samples.

CONCLUSIONS

Possible chemical markers of natural sources such as limonene were detected using DHS extraction. Several compounds have also been identified for the first time in Venezuelan propolis. Cluster analysis allowed the relating of the propolis VOCs profile to their provenance. © 2017 Society of Chemical Industry.

A Chemometrics Approach for Nuclear Magnetic Resonance Data to Characterize the Partial Metabolome Banana Peels from Southern Brazil

Banana peels are well recognized as a source of important bioactive compounds, such as phenolics, carotenoids, biogenic amines, among others. As such, they have recently started to be used for industrial purposes. However, its composition seems to be strongly affected by biotic or abiotic ecological factors. Thus, this study aimed to investigate banana peels chemical composition, not only to get insights on eventual metabolic changes caused by the seasons, in southern Brazil, but also to identify the most relevant metabolites for these processes. To achieve this, a Nuclear magnetic resonance (NMR)-based metabolic profiling strategy was adopted, followed by chemometrics analysis, using the specmine package for the R environment, and metabolite identification. The results showed that the metabolomic approach adopted allowed identifying a series of primary and secondary metabolites in the aqueous extracts investigated. Besides, over the seasons the metabolic profiles of the banana peels showed to contain biologically active compounds relevant to the skin wound healing process, indicating the biotechnological potential of that raw material.

Synergistic Hepatoprotective and Antioxidant Effect of Artichoke, Fig, Blackberry Herbal Mixture on HepG2 Cells and Their Metabolic Profiling Using NMR Coupled with Chemometrics

The edible plants have long been reported to possess a lot of biological activities. Herein, the hepatoprotective and the antioxidant activities of the aqueous infusion of the edible parts of Cynara cardunculus, Ficus carica, and Morus nigra and their herbal mixture (CFM) was investigated in vitro using CCl₄ induced damage in HepG2 cells. The highest amelioration was observed via the consumption of CFM at 1 mg/ml showing 47.00% and 37.09% decline in aspartate transaminase and alanine transaminase and 77.32% and 101.02% increase in reduced glutathione and superoxide dismutase comparable to CCl₄ treated cells. Metabolic profiling of their aqueous infusions was done using nuclear magnetic resonance spectroscopic experiments coupled with chemometrics particularly hierarchical cluster analysis (HCA) and principal component analysis (PCA). The structural closeness of the various metabolites existing in black berry and the mixture as reflected in the PCA score plot and HCA processed from the ¹ H-NMR spectral data could eventually explained the close values in their biological behavior. For fig and artichoke, the existence of different phenolic metabolites that act synergistically could greatly interpret their potent biological behavior. Thus, it can be concluded that a herbal mixture composed of black berry, artichoke, and fig could afford an excellent natural candidate to combat oxidative stress and counteract hepatic toxins owing to its phenolic compounds.

Metabolomics study of Populus type propolis

Herein, we propose rapid and simple spectroscopic methods to determine the chemical composition of propolis derived from various Populus species using a metabolomics approach. In order to correlate variability in Populus type propolis composition with the altitude of its collection, NMR, IR, and UV spectroscopy followed by OPLS was conducted. The botanical origin of propolis was established by comparing propolis spectral data to those of buds of various Populus species. An O2PLS method was utilized to integrate two blocks of data. According to OPLS and O2PLS, the major compounds in propolis samples, collected from temperate continental climate above 500m, were phenolic glycerides originating from P. tremula buds. Flavonoids were predominant in propolis samples collected below 400m, originating from P. nigra and P. x euramericana buds. Samples collected at 400-500m were of mixed origin, with variable amounts of all detected metabolites.