Identification Of Natural Products Research Articles

Time-Dependent Comparison of the Structural Variations of Natural Products and Synthetic Compounds.

The identification of natural products (NPs) has played a pivotal role in drug discovery and shaped the evolution of synthetic compounds (SCs). However, the extent to which NPs have historically influenced the structural characteristics of SCs remains unclear. In this study, we conducted a comprehensive, time-dependent chemoinformatic analysis to investigate the impact of NPs on the structural evolution of SCs. The physicochemical properties, molecular fragments, biological relevance, and chemical space of the molecules from the Dictionary of Natural Products were compared in a time series fashion with a synthetic compound collection sourced from 12 databases. Our findings reveal that NPs have become larger, more complex, and more hydrophobic over time, exhibiting increased structural diversity and uniqueness. Conversely, SCs exhibit a continuous shift in physicochemical properties, yet these changes are constrained within a defined range governed by drug-like constraints. SCs possess a broader range of synthetic pathways and structural diversity, albeit with a decline in biological relevance. The chemical space of NPs has become less concentrated compared to that of SCs. In conclusion, our study suggests that the structural evolution of SCs is influenced by NPs to some extent; however, SCs have not fully evolved in the direction of NPs.

Recent strategies in target identification of natural products: Exploring applications in chronic inflammation and beyond.

Natural products are a treasure trove for drug discovery, especially in the areas of infection, inflammation and cancer, due to their diverse bioactivities and complex, and varied structures. Chronic inflammation is closely related to many diseases, including complex diseases such as cancer and neurodegeneration. Improving target identification for natural products contributes to elucidating their mechanism of action and clinical progress. It also facilitates the discovery of novel druggable targets and the elimination of undesirable ones, thereby significantly enhancing the productivity of drug discovery and development. Moreover, the rise of polypharmacological strategies, considered promising for the treatment of complex diseases, will further increase the demand for target deconvolution. This review underscores strategies for identifying natural product targets (NPs) in the context of chronic inflammation over the past 5 years. These strategies encompass computational methodologies for early target discovery and the anticipation of compound binding sites, proteomics-driven approaches for target delineation and experimental biology techniques for target validation and comprehensive mechanistic exploration.

Sanyensin with an Unprecedented Architecture: An Effective Strategy from Discovery to Stereochemical Identification of Flexible Natural Products.

Under the guidance of genome mining combined with bioassay-coupled metabolomic analyses, an unprecedented macrodiolide sanyensin (1), with two flexible macrolides fused by the rigid oxabicyclo[3.3.1]nonane core, was isolated from the deep-sea-derived Streptomyces sp. OUCT16-30. The stereochemistry of 1 was established by NOEs (nuclear Overhauser effects), J-based configuration analysis, Marfey's analysis, and together with a newly introduced stereochemical study workflow, which greatly shortens the time to obtain correct conformations of flexible structures based on the NMR constraints, thus leading to reliable quantum chemical calculations to establish the absolute configurations. This workflow is expected to have broad applicability for elucidating the stereochemistry of flexible natural products. The macrodiolide framework of 1 is proposed to be formed through a biocatalytic cyclodimerization, followed by a series of nonenzymatic reactions. This work leads to new insights into the unexplored biosynthetic potential of deep-sea microbes and also provides a practical streamline for efficient mining of novel natural products, from discovery to stereochemical finalization.

LC–MS coupled with diagnostic ion strategy facilitated the discovery of 5-methylcoumarin meroterpenoids from Gerbera piloselloides

Plant-derived natural products remain crucial in drug development. However, the identification of undescribed natural products is becoming increasingly challenging. A comprehensive strategy combining LC–MS with diagnostic ions was proposed for the discovery of undescribed 5-methylcoumarin meroterpenoids. Thirteen undescribed 5-methylcoumarin meroterpenoids, including five pairs of enantiomers (1a/1b and 5a/5b–8a/8b), were isolated from the whole plant of Gerbera piloselloides. Their structures and absolute configurations were unambiguously determined based on their spectroscopic data, calculated and experimental ECD data and X-ray diffraction analysis. Bioassays conducted on scopolamine-induced injury PC12 cells revealed that compounds 5a/5b, 7a/7b and 8a/8b possessed mild protective effects. Additionally, compounds 2 and 8 showed notable IL-6 inhibition in lipopolysaccharide-induced BEAS-2B cells.

Secondary metabolites with antimicrobial activity produced by thermophilic bacteria from a high-altitude hydrothermal system.

Thermophilic microorganisms possess several adaptations to thrive in high temperature, which is reflected as biosynthesis of proteins and thermostable molecules, isolation and culture represent a great methodological challenge, therefore High throughput sequencing enables screening of the whole bacterial genome for functional potential, providing rapid and cost-effective information to guide targeted cultures for the identification and characterization of novel natural products. In this study, we isolated two thermophilic bacterial strains corresponding to Bacillus LB7 and Streptomyces LB8, from the microbial mats in the Atacama Desert. By combining genome mining, targeted cultures and biochemical characterization, we aimed to identify their capacity to synthesize bioactive compounds with antimicrobial properties. Additionally, we determined the capability to produce bioactive compounds under controlled in vitro assays and detected by determining their masses by Thin-Layer Chromatography/Mass Spectrometry (TLC/MS). Overall, both isolates can produce antimicrobial (e.g., Myxalamide C by-product) and antioxidants (e.g. Dihydroxymandelic Acid, Amide biotine and Flavone by-products) compounds. Bacillus LB7 strain possesses a more diverse repertoire with 51.95% of total metabolites unmatched, while Streptomyces LB8 favors mainly antioxidants, but has over 70% of unclassified compounds, highlighting the necessity to study and elucidate the structure of novel compounds. Based on these results, we postulate that the uncultured or rare cultured thermophiles inhabiting high-altitude hydrothermal ecosystems in the Atacama Desert offer a promising opportunity to the study of novel microbial bioactive compounds.

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.

Natural Photosensitizers in Clinical Trials

Photodynamic therapy (PDT) is a minimally invasive therapeutic method with high selectivity of action. It has gained great popularity in recent years as a new therapy for the treatment of cancer, but is also used in dermatology, ophthalmology, and antimicrobial treatment, among others. The therapeutic regimen involves the administration of a photosensitizer (PS) that selectively accumulates in tumor cells or is present in the blood vessels of the tumor prior to irradiation with light at a wavelength corresponding to the absorbance of the photosensitizer, leading to the generation of reactive oxygen species (ROS). Choosing the right PS is one of the most important steps in PDT and is crucial to the effectiveness of the therapy. Despite the many compounds discovered, the search for new molecules that could fulfill the functions of an optimal photosensitizer and improve the efficiency of PDT is still ongoing. Compounds of natural origin could contribute to achieving this goal. A number of photoactive substances as effective as synthetic photosensitizers have been described in various plant and fungal species. With the increasing identification of photoactive natural products, many new photosensitizers are expected to emerge. Some have already been clinically tested with promising results. In our work, we provide insights into this research and molecules, analyze their advantages and disadvantages, and point out gaps in current knowledge and future directions for their development. We also present natural photosensitizers not yet tested in clinical trials and point out future potential directions for their development.

Computer-Aided Drug Discovery Approaches in the Identification of Natural Products against SARS-CoV-2: A Review.

The COVID-19 pandemic is raising a worldwide search for compounds that could act against the disease, mainly due to its mortality. With this objective, many researchers invested in the discovery and development of drugs of natural origin. To assist in this search, the potential of computational tools to reduce the time and cost of the entire process is known. Thus, this review aimed to identify how these tools have helped in the identification of natural products against SARS-CoV-2. For this purpose, a literature review was carried out with scientific articles with this proposal where it was possible to observe that different classes of primary and, mainly, secondary metabolites were evaluated against different molecular targets, mostly being enzymes and spike, using computational techniques, with emphasis on the use of molecular docking. However, it is noted that in silico evaluations still have much to contribute to the identification of an anti-SARS-CoV-2 substance, due to the vast chemical diversity of natural products, identification and use of different molecular targets and computational advancement.

Bioassay-Guided Identification of Natural Products for Biocontrol by Thin Layer Chromatography-Direct Bioautography.

Thin layer chromatography-direct bioautography (TLC-DB) is a well-established bioassay used to separate and identify natural products (NPs) that are antagonistic against a target pathogen. It is a rapid, inexpensive, and simple option for the bioassay-guided isolation and identification of NPs that hinges on separation by TLC coupled with the direct application of a target pathogen to examine bioactivity. It is typically used for the analysis of bioactive plant extracts, detecting inhibitory activity against bacteria, fungi, and enzymes. That being said, it has great potential in bacterial NP discovery, particularly for evaluating bacterial NPs against pertinent agricultural pathogens, which is valuable for discovering and developing novel biopesticides for the agriculture industry. Furthermore, it is a tunable protocol that could be applied to other target pathogens or sources of NPs in research programs concerning the discovery and identification of bioactive compounds. Herein, we describe a model system for discovering and identifying biopesticide NPs using TLC-DB with Bacillus spp. and the agricultural pathogen Sclerotinia sclerotiorum.

Amazon Rainforest Hidden Volatiles-Part I: Unveiling New Compounds from Acmella oleracea (L.) R.K. Jansen Essential Oil.

Motivated by the culinary and ethnopharmacological use of Acmella oleracea (L.) R.K. Jansen, this study aimed to unveil new chemical compounds from its essential oil (EO). Acmella oleracea, known for its anesthetic and spicy properties, has been used in traditional medicine and cuisine, particularly in Northern Brazil. Through a detailed GC-MS analysis, 180 constituents were identified, including 12 tentatively identified long-chain α-keto esters of various acids. Additionally, 18 new esters were synthesized for structural verification. This research expands the known chemical diversity of A. oleracea EO, providing a basis for potential pharmacological applications. The identification of new natural products, including homologs and analogs of acmellonate, underscores the EO's rich chemical profile and its potential for novel bioproduct development.

Eco-Friendly Preservation of Pharaonic Wooden Artifacts using Natural Green Products

The biodeterioration of wooden cultural heritage is a severe problem worldwide and fungi are the main deteriorating agents. The identification of effective natural products, safer for humans and the environment, is a current challenge. Ten deteriorated archaeological objects (a wooden statue of a seated man, an anthropoid wooden coffin with a cartonnage mummy of Nespathettawi, and a wooden box of Padimen’s son), stored at the Egyptian museum in Cairo, were considered here. The wood species of the three most deteriorated objects were previously identified as Acacia nilotica, Ficus sycomorus, and Tamarix gennessarensis. Twenty-six fungal species were isolated and identified from the wooden objects and the four most frequent species belonged to the genus Aspergillus. Fourteen fungal species among those isolated showed the greatest biodeterioration activity on the experimental wood blocks of the archaeological objects. The antifungal activities of several eco-friendly plant essential oils (from cinnamon, eucalyptus, frankincense, geranium, lavender, lemongrass, menthe, rosemary, tea tree, and thyme) and plant extracts (from basil, eucalyptus, henna, melia, and teak) were tested against the fungal species with the greatest biodeterioration activity. The essential oils (Eos) were more effective than the plant extracts. Thyme EO, followed by geranium and cinnamon ones, was the most active (minimum inhibitory concentrations: 0.25–1 µL/mL). These EO; also showed inhibitory effects on the enzymatic activities (cellulase, amylase, and protease) of the four most dominant fungal species. Thymol and p-cymene were the two main components of thyme oil, while geraniol and beta-citronellol were those of geranium oil; eugenol and caryophyllene were those of the cinnamon EO. Thyme oil applied to the most deteriorated experimental aged A. nilotica wooden cubes inoculated with the four highly frequent fungal species was effective in wood preservation. Moreover, no significant interference was observed in the wood before and after thyme treatment. Thyme oil seems to be a promising eco-friendly antifungal agent for the preservation of archaeological wooden artefacts.

Application of 3Rs in Caenorhabditis elegans Research for the Identification of Health-Promoting Natural Products.

The average age of the population is increasing worldwide, which has a profound impact on our society. This leads to an increasing demand for medicines and requires the development of new strategies to promote health during the additional years. In the search for resources and therapeutics for improved health during an extended life span, attention has to be paid to environmental exposure and ecosystem burdens that inevitably emerge with the extended consumption of medicines and drug development, even in the preclinical stage. The hereby introduced sustainable strategy for drug discovery is built on 3Rs, "R: obustness, R: eliability, and saving R: esources", inspired by both the 3Rs used in animal experiments and environmental protection, and centers on the usefulness and the variety of the small model organism Caenorhabditis elegans for detecting health-promoting natural products. A workflow encompassing a multilevel screening approach is presented to maximize the amount of information on health-promoting samples, while considering the 3Rs. A detailed, methodology- and praxis-oriented compilation and discussion of proposed C. elegans health span assays and more disease-specific assays are presented to offer guidance for scientists intending to work with C. elegans, thus facilitating the initial steps towards the integration of C. elegans assays in their laboratories.

Virtual screening, MMGBSA, and molecular dynamics approaches for identification of natural products from South African biodiversity as potential Onchocerca volvulus pi-class glutathione S-transferase inhibitors

We investigated 1012 molecules from natural products previously isolated from the South African biodiversity (SANCDB, https://sancdb.rubi.ru.ac.za/), for putative inhibition of Onchocerca volvulus pi-class glutathione S-transferase (Ov-GST2) by virtual screening, MMGBSA, and molecular dynamics approaches. ADMET, docking, and MMGBSA shortlisted 12 selected homoisoflavanones-type hit molecules, among which two namely SANC00569, and SANC00689 displayed high binding affinities of −46.09 and −46.26 kcal mol−1, respectively towards π-class Ov-GST2, respectively. The molecular dynamics results of SANC00569 showed the presence of intermolecular H-bonding, hydrophobic interactions between the ligand and key amino acids of Ov-GST2, throughout the simulation period. This hit molecule had a stable binding pose and occupied the binding pockets throughout the 200 ns simulation. To the best of our knowledge, there is no report of any alleged anti–onchocerciasis activity referring to homoisoflavanones or flavonoids. Nevertheless, homoisoflavanones, which are a subclass of flavonoids, exhibit a plethora of biological activities. All these results led to the conclusion that SANC00569 is the most hypothetical Ov-GST2, which could lead the development of new drugs against Onchocerca volvulus pi-class glutathione S-transferase. Further validation of these findings through in vitro and in vivo studies is required.

Inhibition of Clinical MRSA Isolates by Coagulase Negative Staphylococci of Human Origin.

Staphylococcus aureus is frequently highlighted as a priority for novel drug research due to its pathogenicity and ability to develop antibiotic resistance. Coagulase-negative staphylococci (CoNS) are resident flora of the skin and nares. Previous studies have confirmed their ability to kill and prevent colonization by S. aureus through the production of bioactive substances. This study screened a bank of 37 CoNS for their ability to inhibit the growth of methicillin-resistant S. aureus (MRSA). Deferred antagonism assays, growth curves, and antibiofilm testing performed with the cell-free supernatant derived from overnight CoNS cultures indicated antimicrobial and antibiofilm effects against MRSA indicators. Whole genome sequencing and BAGEL4 analysis of 11 CoNS isolates shortlisted for the inhibitory effects they displayed against MRSA led to the identification of two strains possessing complete putative bacteriocin operons. The operons were predicted to encode a nukacin variant and a novel epilancin variant. From this point, strains Staphylococcus hominis C14 and Staphylococcus epidermidis C33 became the focus of the investigation. Through HPLC, a peptide identical to previously characterized nukacin KQU-131 and a novel epilancin variant were isolated from cultures of C14 and C33, respectively. Mass spectrometry confirmed the presence of each peptide in the active fractions. Spot-on-lawn assays demonstrated both bacteriocins could inhibit the growth of an MRSA indicator. The identification of natural products with clinically relevant activity is important in today's climate of escalating antimicrobial resistance and a depleting antibiotic pipeline. These findings also highlight the prospective role CoNS may play as a source of bioactive substances with activity against critical pathogens.

Chemical characterization, multivariate analysis and comparison of biological activities of different parts of Fraxinus mandshurica.

Fraxinus mandshurica (Oleaceae) is used as a traditional medicinal plant for the treatment of red eyes, menstrual disorders, excessive leucorrhea, chronic bronchitis and psoriasis. To perform chemical characterization of the secondary metabolites of F. mandshurica roots, bark, stems and leaves, 32 samples were collected from eight provinces in this study. A total of 64 chemical components were detected from four different parts of F. mandshurica by ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Meanwhile, a total of nine secoiridoids were obtained by natural product chemical extraction, isolation and identification methods. Quantitative analysis by high-performance liquid chromatography-diode array detection-mass spectrometry showed the highest total content of secoiridoids in the bark, which is also consistent with the traditional medicinal parts. The results of methodological validation showed that the correlation coefficient (R2) values were all >0.9993, indicating a good linear range of the standard curve, while the relative standard deviations of precision, reproducibility and stability were <3%, and the spiked recoveries ranged from 98.22 to 102.27%, indicating that the experimental method was reliable and stable. In addition, fingerprinting and a heatmap were established to demonstrate the content trends of F. mandshurica more visually from different origins. Multivariate analysis, including principal component analysis and partial least squares discriminant analysis, was performed to determine the chemical characteristics of different parts of F. mandshurica, and six characteristic secoiridoids that could be used to distinguish different origins were screened. Finally, the inhibition of tyrosinase, α-glucosidase, acetylcholinesterase and pancreatic lipase activities by the nine characteristic compounds and extracts from different parts were investigated, and the results showed that they all exhibited different degrees of enzyme activity inhibition and thus have potential applications in whitening and blemish removal, hypoglycemia, anti-Alzheimer's disease and anti-obesity as a new source of natural enzyme activity inhibitors. This study establishes an identification and evaluation method applicable to phytochemistry of different origins, which is a guideline for quality control, origin evaluation and clinical application of traditional medicinal plants. This is also an unprecedented study on the identification of the chemical composition of different parts of F. mandshurica, characteristic compounds and the inhibition of enzyme activity of extracts from different parts.

Identification of fungal natural products with potent inhibition in Toxoplasma gondii.

Current therapeutics for treating toxoplasmosis remain insufficient, demonstrating high cytotoxicity, poor bioavailability, limited efficacy, and drug resistance. Additional research is needed to develop novel compounds with high efficacy and low cytotoxicity. The success of artemisinin and other natural products in treating malaria highlights the potential of natural products as anti-protozoan therapeutics. However, the exploration of natural products in T. gondii drug discovery has been less comprehensive, leaving untapped potential. By leveraging the resources available for the malaria drug discovery campaign, we conducted a phenotypic screen utilizing a set of natural products previously screened against Plasmodium falciparum. Our study revealed 18 compounds with high potency and low cytotoxicity in T. gondii, including four novel scaffolds with no previously reported activity in T. gondii. These new scaffolds may serve as starting points for the development of toxoplasmosis therapeutics but could also serve as tool compounds for target identification studies using chemogenomic approach.

Genome-guided purification of high amounts of the siderophore ornibactin and detection of potentially novel burkholdine derivatives produced by Burkholderia catarinensis 89T.

The increased availability of genome sequences has enabled the development of valuable tools for the prediction and identification of bacterial natural products. Burkholderia catarinensis 89T produces siderophores and an unknown potent antifungal metabolite. The aim of this work was to identify and purify natural products of B. catarinensis 89T through a genome-guided approach. The analysis of B. catarinensis 89T genome revealed 16 clusters putatively related to secondary metabolism and antibiotics production. Of particular note was the identification of a nonribosomal peptide synthetase (NRPS) cluster related to the production of the siderophore ornibactin, a hybrid NRPS-polyketide synthase Type 1 cluster for the production of the antifungal glycolipopeptide burkholdine, and a gene cluster encoding homoserine lactones (HSL), probably involved in the regulation of both metabolites. We were able to purify high amounts of the ornibactin derivatives D/C6 and F/C8, while also detecting the derivative B/C4 in mass spectrometry investigations. A group of metabolites with molecular masses ranging from 1188 to 1272Da could be detected in MS experiments, which we postulate to be new burkholdine analogs produced by B. catarinensis. The comparison of B. catarinensis BGCs with other Bcc members corroborates the hypothesis that this bacterium could produce new derivatives of these metabolites. Moreover, the quorum sensing metabolites C6-HSL, C8-HSL, and 3OH-C8-HSL were observed in LC-MS/MS analysis. The new species B. catarinensis is a potential source of new bioactive secondary metabolites. Our results highlight the importance of genome-guided purification and identification of metabolites of biotechnological importance.

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.

Characterization and identification of bioactive natural products in the ethanol extracts of Acacia nilotica, Melia azedarach, and Euphorbia hirta from Cholistan desert, Pakistan

Characterization and identification of bioactive natural products in the ethanol extracts of Acacia nilotica, Melia azedarach, and Euphorbia hirta from Cholistan desert, Pakistan

Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products.

Covering: 1995 to 2023Advances in bioanalytical methods, particularly mass spectrometry, have provided valuable molecular insights into the mechanisms of life. Non-targeted metabolomics aims to detect and (relatively) quantify all observable small molecules present in a biological system. By comparing small molecule abundances between different conditions or timepoints in a biological system, researchers can generate new hypotheses and begin to understand causes of observed phenotypes. Functional metabolomics aims to investigate the functional roles of metabolites at the scale of the metabolome. However, most functional metabolomics studies rely on indirect measurements and correlation analyses, which leads to ambiguity in the precise definition of functional metabolomics. In contrast, the field of natural products has a history of identifying the structures and bioactivities of primary and specialized metabolites. Here, we propose to expand and reframe functional metabolomics by integrating concepts from the fields of natural products and chemical biology. We highlight emerging functional metabolomics approaches that shift the focus from correlation to physical interactions, and we discuss how this allows researchers to uncover causal relationships between molecules and phenotypes.