Natural products dereplication by diffusion ordered NMR spectroscopy (DOSY)

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.

Functionalized magnetic particles coupled with LC-MS strategy facilitated discovery of trace thioalkaloids with potent immunosuppressive activity

Trace natural products (TNPs) are still the vital source of drug development. However, the mining of novel TNPs is becoming increasingly challenging due to their low abundance and complex interference. A comprehensive strategy was proposed in which the functionalized magnetic particles integrated with LC-MS for TNPs discovery. Under the guidance of the approach, fifteen trace Nuphar alkaloids including seven new ones, cyanopumiline A sulfoxide (1), cyanopumiline C sulfoxide (8) and cyanopumilines A-E (4-5, 10, 12-13) featuring an undescribed nitrile-containing 6/6/5/6/6 pentacyclic ring system were isolated from the rhizomes of Nuphar pumila. Their structures and absolute configurations were determined on the basis of detailed spectroscopic data analysis and single-crystal X-ray diffraction analysis. Notably, a concise method based on 13C NMR spectroscopy was established to determine the relative configurations of spiroatoms. Biologically, compounds 1-12 exhibited potent immunosuppressive activities with IC50 values ranging from 0.1-12.1 μM against anti-CD3/CD28 induced human peripheral T cell proliferation. Mechanistic studies revealed that 4 could dose-dependently decrease pro-inflammatory cytokines and the expression levels of CD25 and CD71.

Plant antibacterials: The challenges and opportunities

Nature possesses an inexhaustible reservoir of agents that could serve as alternatives to combat the growing threat of antimicrobial resistance (AMR). While some of the most effective drugs for treating bacterial infections originate from natural sources, they have predominantly been derived from fungal and bacterial species. However, a substantial body of literature is available on the promising antibacterial properties of plant-derived compounds. In this comprehensive review, we address the major challenges associated with the discovery and development of plant-derived antimicrobial compounds, which have acted as obstacles preventing their clinical use. These challenges encompass limited sourcing, the risk of agent rediscovery, suboptimal drug metabolism, and pharmacokinetics (DMPK) properties, as well as a lack of knowledge regarding molecular targets and mechanisms of action, among other pertinent issues. Our review underscores the significance of these challenges and their implications in the quest for the discovery and development of effective plant-derived antimicrobial agents. Through a critical examination of the current state of research, we give valuable insights that will advance our understanding of these classes of compounds, offering potential solutions to the global crisis of AMR. © 2017 Elsevier Inc. All rights reserved.

Structure Revision of Formyl Phloroglucinol Meroterpenoids: A Unified Approach Using NMR Fingerprinting and DFT NMR and ECD Analyses

NMR fingerprints are valuable tools for analyzing complex natural product mixtures and identifying incorrectly assigned structures in the literature. Our diagnostic NMR fingerprints for formyl phloroglucinol meroterpenoids revealed discrepancies in the structures reported for eucalyprobusal C (1a) and eucalypcamal K (2a). NMR fingerprinting PCA analyses identified 1a as an oxepine-diformyl phloroglucinol and 2a as an oxepine 3-acyl-1-formyl phloroglucinol, contrary to their initial assignments as pyrano-diformyl and pyrano 3-acyl-1-formyl phloroglucinols, respectively. Extensive reinterpretation of their reported one- and two-dimensional NMR data, coupled with GIAO DFT-calculated 1H and 13C NMR chemical shift and DP4+ analyses, supported the unequivocal reassignment of eucalyprobusal C to 1b and eucalypcamal K to 2b. The absolute configurations of the revised oxepine-containing phloroglucinol meroterpenoids were confirmed via the reinterpretation of their reported ROESY and NOESY NMR data, along with comparative TDDFT-calculated and experimental ECD spectra.

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.

Marine indole alkaloid diversity and bioactivity. What do we know and what are we missing?

Covering: marine indole alkaloids (n = 2048) and their reported bioactivities up to the end of 2021Despite increasing numbers of marine natural products (MNPs) reported each year, most have only been examined for cytotoxic, antibacterial, and/or antifungal biological activities with the majority found to be inactive in these assays. In this context, why are natural products continuing to be examined in assays they are unlikely to show significant activity in, and what targets might be more useful for expanding knowledge of their biologically relevant chemical space? We have undertaken a meta-analysis of the biological activities for 2048 marine indole alkaloids (MIAs), a diverse sub-class of MNPs reported up to the end of 2021, and this has highlighted that the bioactivity potentials for up to 86% of published MIAs remains underexplored and/or undefined. Although most published MIAs are not cytotoxic or antimicrobial, there is a continued focus on using these assays to evaluate new structurally related analogues. Using cheminformatics analyses, the chemical diversity of the 2048 MIAs were clustered using fragment based fingerprints and their reported bioactivity potency towards specific disease targets was assessed for structure activity trends. These analyses showed that there are groups of MIAs that possess potent and diverse activities and that many analogues, previously tested only in cellular toxicity assays, could be better exploited to generate structure activity relationships associated with leads to treat emerging diseases. A collection of indole drug and drug-lead structures from non-natural sources were also incorporated into the dataset providing complementary bioactivity profiles that were further used to predict underexplored areas of potential new activity and to better direct future testing of MIAs. Our findings clearly suggest the biological evaluation of MIAs continues to be conducted on a narrow range of bioassays and disease targets, and that shifting the focus to non-toxic disease targets should provide expanded knowledge of biologically relevant chemical space aimed at maximising the potential of MIAs for drug discovery.

Foaming with Starch: Exploring Faba Bean Aquafaba as a Green Alternative

The demand for sustainable and functional plant-based products is on the rise. Plant proteins and polysaccharides often provide emulsification and stabilization properties to food and food ingredients. Recently, chickpea cooking water, also known as aquafaba, has gained popularity as a substitute for egg whites in sauces, food foams, and baked goods due to its foaming and emulsifying capacities. This study presents a modified eco-friendly process to obtain process water from faba beans and isolate and characterize the foam-inducing components. The isolated material exhibits similar functional properties, such as foaming capacity, to aquafaba obtained by cooking pulses. To isolate the foam-inducing component, the faba bean process water was mixed with anhydrous ethanol, and a precipitated fraction was obtained. The precipitate was easily dissolved, and solutions prepared with the alcohol precipitate retained the foaming capacity of the original extract. Enzymatic treatment with α-amylase or protease resulted in reduced foaming capacity, indicating that both protein and carbohydrates contribute to the foaming capacity. The dried precipitate was found to be 23% protein (consisting of vicilin, α-legumin, and β-legumin) and 77% carbohydrate (amylose). Future investigations into the chemical structure of this foam-inducing agent can inform the development of foaming agents through synthetic or enzymatic routes. Overall, this study provides a potential alternative to aquafaba and highlights the importance of exploring plant-based sources for functional ingredients in the food industry.

Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation

Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.

NMR Fingerprints of Formyl Phloroglucinol Meroterpenoids and Their Application to the Investigation of Eucalyptus gittinsii subsp. gittinsii

NMR fingerprints provide powerful tools to identify natural products in complex mixtures. Principal component analysis and machine learning using ¹H and ¹³C NMR data, alongside structural information from 180 published formyl phloroglucinols, have generated diagnostic NMR fingerprints to categorize subclasses within this group. This resulted in the reassignment of 167 NMR chemical shifts ascribed to 44 compounds. Three pyrano-diformyl phloroglucinols, euglobal In-1 and psiguadiols E and G, contained ¹H and ¹³C NMR data inconsistent with their predicted phloroglucinol subclass. Subsequent reinterpretation of their 2D NMR data combined with DFT ¹³C NMR chemical shift and ECD calculations led to their structure revisions. Direct covariance processing of HMBC data permitted ¹H resonances for individual compounds in mixtures to be associated, and analysis of their ¹H/¹³C HMBC correlations using the fingerprint tool further classified components into phloroglucinol subclasses. NMR fingerprinting HMBC data obtained for six eucalypt flower extracts identified three subclasses of pyrano-acyl-formyl phloroglucinols from Eucalyptus gittinsii subsp. gittinsii. New, eucalteretial F and (+)-eucalteretial B, and known, (-)-euglobal VII and eucalrobusone C, compounds, each belonging to predicted subclasses, were isolated and characterized. Staphylococcus aureus and Plasmodium falciparum screening revealed eucalrobusone C as the most potent antiplasmodial formyl phloroglucinol to date.

Modern Trends in Natural Antibiotic Discovery

Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.

Marine natural products

Covering: January to December 2021This review covers the literature published in 2021 for marine natural products (MNPs), with 736 citations (724 for the period January to December 2021) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1425 in 416 papers for 2021), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of the number of authors, their affiliations, domestic and international collection locations, focus of MNP studies, citation metrics and journal choices is discussed.

A Sodium Sodate as Precursor for Lanthanide Bis(4-R-benzoxazol-2-yl)methanide Single-Molecule Magnets

From the sodium sodate precursor [(Na(thf)₆][Na{(4-Me-NCOC₆H₃)₂CH}₂] (1) three isostructural dinuclear lanthanide complexes [(μ-Cl)Ln^III{(4-MeNCOC₆H₃)₂CH}₂]₂ with Ln = Gd (2), Dy (3), and Er (4) based on the N,N'-chelating monoanionic bis(4-methylbenzoxazol-2-yl)methanide ligand (titled "Mebox") were synthesized and characterized by X-ray diffraction and magnetic measurements. The sodium precursor 1 was analyzed via X-ray diffraction and diffusion-ordered NMR spectroscopy experiments (DOSY-NMR) in order to investigate its aggregation in solution and the solid state. The sodium analog [(thf)₃Na(NCOC₆H₄)₂CH] (1') based on the bis(benzoxazol-2-yl)-methanide ligand (titled "box") was prepared and analyzed for comparison reasons. From the lanthanide derivatives 2-4, the Dy^III complex 3 displays slow relaxation of magnetization at zero field, with a relaxation barrier of U = 315.7 cm^-1. The coupling strength between the two lanthanide centers was estimated with the Gd^III equivalent 2, giving a weak antiferromagnetic coupling of J = -0.035 cm^-1.

How different are marine microbial natural products compared to their terrestrial counterparts?

Covering: 1877 to 2020A key challenge in natural products research is the selection of biodiversity to yield novel chemistry. Recently, marine microorganisms have become a preferred source. But how novel are marine microorganism natural products compared to those reported from terrestrial microbes? Cluster analysis of chemical fingerprints and molecular scaffold analysis of 55 817 compounds reported from marine and terrestrial microorganisms, and marine macro-organisms showed that 76.7% of the compounds isolated from marine microorganisms are closely related to compounds isolated from terrestrial microorganisms. Only 14.3% of marine microorganism natural products are unique when marine macro-organism natural products are also considered. Studies targeting marine specific and understudied microbial phyla result in a higher likelihood of finding marine specific compounds, whereas the depth and geographic location of microorganism collection have little influence. We recommend marine targeted strain isolation, incorporating early use of genomic sequencing to guide strain selection, innovation in culture media and cultivation techniques and the application of cheminformatics tools to focus on unique natural product diversity, rather than the dereplication of known compounds.