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.

Gaudêncio, Susana P.; Bayram, Engin; Bilela, Lada Lukic; Cueto, Mercedes; DIAZ MARRERO, ANA RAQUEL; Haznedaroglu, Berat Z.; Jimenez, Carlos; Mandalakis, Manolis; Pereira, Florbela; Reyes, Fernando; Tasdemir, Deniz.

Marine Drugs, 21(5), 308: 1-66 (2023)

Bifurcaria bifurcata extract exerts antioxidant effects on human Caco-2 cells

The present research study investigated the potential protective effect of Bifurcaria bifurcata extract on cell viability and antioxidant defences of cultured human Caco-2 cells submitted to oxidative stress induced by tert-butylhydroperoxide (tert-BOOH). Aqueous extracts were firstly characterized in terms of total phenolic contents. Concentrations of reduced glutathione (GSH) and malondialdehyde (MDA), generation of reactive oxygen species (ROS), nitric oxide (NO) production, antioxidant enzymes activities [NADPH quinone dehydrogenase 1 (NQO1) and glutathione S-transferase (GST)], caspase 3/7 activity and gene expression linked to apoptosis, proinflammation and oxidative stress signaling pathways were used as markers of cellular oxidative status. B. bifurcata extract prevented the cytotoxicity, the decrease of GSH, the increase of MDA levels and the ROS generation induced by tert-BOOH. B. bifurcata extract prevented the significant decrease of NQO1 and GST activities, and the significant increase of caspase 3/7 activity induced by tert-BOOH. B. bifurcata extract also caused an over-expression of GSTM2, Nrf2 and AKT1 transcriptors, as well as reduced ERK1, JNK1, Bax, BNIP3, NFκB1, IL-6 and HO-1 gene expressions induced by tert-BOOH suggesting an increase in cellular resistance against oxidative stress. The results of the biomarkers analyzed show that treatment of Caco-2 cells with B. bifurcata extract enhance antioxidant defences, which imply an improved cell response to an oxidative challenge. B. bifurcata extract possesses strong antioxidant properties and may be a potential effective alternative to oxidant agents in the functional food industry.

Martínez, María Aránzazu; Aedo, Hugo; López-Torres, Bernardo; Maximiliano, Jorge Enrique; Martínez-Larrañaga, María Rosa; Anadón, Arturo; Martínez, Marta; Peteiro, César; Cueto, Mercedes; Rubiño, Susana; Hortos, María; Ares, Irma

Environmental Research, 213, 116141: 1-15 (2023)

A Certification for Natural Wine? A Comparative Analysis of Consumer Drivers in Italy and Spain

The 2020 certification of natural wine (NW) in France has unleashed a heated debate in Europe. However, knowledge about NW consumer profiles and preferences in a comparative perspective remains scarce in the academic literature. This study aims to define the perceptions, preferences and profiles of wine consumers who support a NW label. For this purpose, we employed analysis of variance, aprioristic factor analysis and multiple regression analysis to examine data from a direct survey performed in Italy and Spain in 2020. Findings reveal that NW consumers in both countries deem it necessary to establish a certification for NW. However, we found significant differences regarding consumers’ profiles, as well as purchasing preferences. In Spain, demand for NW certification is linked to eco-healthy and proximity-craft attributes of wine, and is considered more important by non-professional consumers and those with lower educational level. In Italy, information on the label and the purchase experience are the most important factors to aid in recognizing NW, while women show a significant interest in the NW certification. These findings may help policy-makers to establish homogeneous parameters to differentiate and certify NW.

Parga-Dans, Eva; Vecchio, Riccardo; Annunziata, Azzurra; Alonso-González, Pablo; Otero Enríquez, Raimundo.

Wine economics and policy : 1-23 (2023)

Recirculating packed-bed biofilm photobioreactor combined with membrane ultrafiltration as advanced wastewater treatment

Packed-bed biofilm photobioreactor combined with ultrafiltration membrane was investigated for intensifying the process for secondary wastewater effluent treatment. Cylindrical glass carriers were used as supporting material for the microalgal-bacterial biofilm, which developed from indigenous microbial consortium. Glass carriers allowed adequate growth of the biofilm with limited suspended biomass. Stable operation was achieved after a start-up period of 1000 h, where supernatant biopolymer clusters were minimized and complete nitrification was observed. After that time, biomass productivity was 54 ± 18 mg·L−1·day−1. Green microalgae Tetradesmus obliquus and several strains of heterotrophic nitrification–aerobic denitrification bacteria and fungi were identified. Combined process exhibited COD, nitrogen and phosphorus removal rates of 56 ± 5%, 12 ± 2% and 20 ± 6%, respectively. Membrane fouling was mainly caused by biofilm formation, which was not effectively mitigated by air-scouring aided backwashing.

Díaz, Oliver; González, Enrique; Vera, Luisa; Fernández, Luis Javier; DIAZ MARRERO, ANA RAQUEL ; Fernández, José J.

Environmental Science and Pollution Research: 1-14 (2023)

Materia, vida y sociedad: Investigaciones del Instituto de Productos Naturales y Agrobiología

El artículo hace referencia a los objetivos y actividades, así como el papel científico que desempeña, el Instituto de Productos Naturales y Agrobiología (IPNA), institución que es una rareza entre los 121 centros que forman parte del Consejo Superior de Investigaciones Científicas (CSIC). Y lo es por varios motivos. El más evidente es su lejanía del continente y el hecho de que hasta 2022 fuera el único representante del CSIC en Canarias, algo que cambió con la incorporación del IEO y el IGME a la red. Esta circunstancia quizás sea la explicación de que en el IPNA se desarrollen estudios sobre las tres áreas claves del conocimiento: materia, vida y sociedad, las cuales se abordan y describen en el presente artículo, así como el impacto científico de este organismo, y los retos que afronta para el futuro.

Padrón, Juan I.; Pérez-Martín, Inés; Pérez Pérez, Beatriz.

Encuentros multidisciplinares, 73: 1-7 (2023)

Consumption of the lichen Roccella Gracilis by the large ground-finch Geospiza Magnirostris on the island of Daphne Major (Galápagos)

This note reports a trophic interaction of a passerine consuming lichens. On the islet of Daphne Major (Galápagos Archipelago), we made five observations of the Large Ground-Finch Geospiza magnirostris eating the fruticose lichen Roccella gracilis. This is an example of how island birds broaden their feeding niche in resource-poor environments.

Manuel Nogales, Sandra Hervías-Parejo.

Ornitología Neotropical, 34(1): 1-2 (2023)

Spatial ecology to strengthen invasive snake management on islands

Knowledge on the spatial ecology of invasive predators positively contributes to optimizing their management, especially when involving cryptic and secretive species, such as snakes. However, this information is lacking for most invasive snakes, particularly on islands, where they are known to cause severe ecological and socio-economic impacts. This research is focused on assessing the spatial ecology of the California kingsnake (Lampropeltis californiae) on Gran Canaria to strengthen management actions. We monitored 15 radio-tagged individuals once per day on 9–11 days per month from July 2020 to June 2021 to calculate the species' home range and describe annual activity patterns in the invaded range. To account for the species' diel activity during the emergence period, we additionally monitored snakes from January to May 2021 during three consecutive days per month in four different time intervals each day. We detected movement (consecutive detections at least 6 m apart) in 31.68% of the 1146 detections during the whole monitoring period. Movements most frequently detected were shorter than 100 m (82.24%), and among them the range 0–20 m was the most recurrent (27.03%). The mean distance of movement was 62.57 ± 62.62 m in 1–2 days. Average home range was 4.27 ± 5.35 ha—calculated with the Autocorrelated Kernel Density Estimator (AKDE) at 95%—and did not significantly vary with SVL nor sex. We detected an extremely low value of motion variance (0.76 ± 2.62 σ2m) compared to other studies, with a general inactivity period from November to February, January being the less active month of the year. Diel activity was higher during central and evening hours than during early morning and night. Our results should be useful to improve control programs for this invasive snake (e.g., trap placement and visual survey guidance) on Gran Canaria. Our research highlights the importance of gathering spatial information on invasive snakes to enhance control actions, which can contribute to the management of secretive invasive snakes worldwide.

Maestresalas, Borja; Piquet, Julien C.; López-Darias, Marta.

Scientific Reports, 13, 6731: 1-12 (2023)

Combined direct-sun ultraviolet and infrared spectroscopies at Popocatépetl volcano (Mexico)

Volcanic plume composition is strongly influenced by both changes in magmatic systems and plume-atmosphere interactions. Understanding the degassing mechanisms controlling the type of volcanic activity implies deciphering the contributions of magmatic gases reaching the surface and their posterior chemical transformations in contact with the atmosphere. Remote sensing techniques based on direct solar absorption spectroscopy provide valuable information about most of the emitted magmatic gases but also on gas species formed and converted within the plumes. In this study, we explore the procedures, performances and benefits of combining two direct solar absorption techniques, high resolution Fourier Transform Infrared Spectroscopy (FTIR) and Ultraviolet Differential Optical Absorption Spectroscopy (UV-DOAS), to observe the composition changes in the Popocatépetl’s plume with high temporal resolution. The SO2 vertical columns obtained from three instruments (DOAS, high resolution FTIR and Pandora) were found similar (median difference <12%) after their intercalibration. We combined them to determine with high temporal resolution the different hydrogen halide and halogen species to sulfur ratios (HF/SO2, BrO/SO2, HCl/SO2, SiF4/SO2, detection limit of HBr/SO2) and HCl/BrO in the Popocatépetl’s plume over a 2.5-years period (2017 to mid-2019). BrO/SO2, BrO/HCl, and HCl/SO2 ratios were found in the range of (0.63 ± 0.06 to 1.14 ± 0.20) × 10−4, (2.6 ± 0.5 to 6.9 ± 2.6) × 10−4, and 0.08 ± 0.01 to 0.21 ± 0.01 respectively, while the SiF4/SO2 and HF/SO2 ratios were found fairly constant at (1.56 ± 0.25) × 10−3 and 0.049 ± 0.001. We especially focused on the full growth/destruction cycle of the most voluminous lava dome of the period that took place between February and April 2019. A decrease of the HCl/SO2 ratio was observed with the decrease of the extrusive activity. Furthermore, the short-term variability of BrO/SO2 is measured for the first time at Popocatépetl volcano together with HCl/SO2, revealing different behaviors with respect to the volcanic activity. More generally, providing such temporally resolved and near-real-time time series of both primary and secondary volcanic gaseous species is critical for the management of volcanic emergencies, as well as for the understanding of the volcanic degassing processes and their impact on the atmospheric chemistry.

Taquet, N.; Rivera Cárdenas, C.; Stremme, W.; Boulesteix, Thomas; Bezanilla, A.; Grutter, M.; García, O.; Hase, F.; Blumenstock, T.

Frontiers in Earth Science, 11: 1-18 (2023)

Chamigrane-Type Sesquiterpenes from Laurencia dendroidea as Lead Compounds against Naegleria fowleri

Naegleria fowleri is an opportunistic protozoon that can be found in warm water bodies. It is the causative agent of the primary amoebic meningoencephalitis. Focused on our interest to develop promising lead structures for the development of antiparasitic agents, this study was aimed at identifying new anti-Naegleria marine natural products from a collection of chamigrane-type sesquiterpenes with structural variety in the levels of saturation, halogenation and oxygenation isolated from Laurencia dendroidea. (+)-Elatol (1) was the most active compound against Naegleria fowleri trophozoites with IC50 values of 1.08 μM against the ATCC 30808™ strain and 1.14 μM against the ATCC 30215™ strain. Furthermore, the activity of (+)-elatol (1) against the resistant stage of N. fowleri was also assessed, showing great cysticidal properties with a very similar IC50 value (1.14 µM) to the one obtained for the trophozoite stage. Moreover, at low concentrations (+)-elatol (1) showed no toxic effect towards murine macrophages and could induce the appearance of different cellular events related to the programmed cell death, such as an increase of the plasma membrane permeability, reactive oxygen species overproduction, mitochondrial malfunction or chromatin condensation. Its enantiomer (−)-elatol (2) was shown to be 34-fold less potent with an IC50 of 36.77 μM and 38.03 μM. An analysis of the structure–activity relationship suggests that dehalogenation leads to a significant decrease of activity. The lipophilic character of these compounds is an essential property to cross the blood-brain barrier, therefore they represent interesting chemical scaffolds to develop new drugs.

Arberas-Jiménez, Íñigo; Nocchi, Nathália; Chao-Pellicer, Javier; Sifaoui, Ines; Ribeiro Soares, Angélica; DIAZ MARRERO, ANA RAQUEL ; Fernández, José J.; Piñero, José E.; Lorenzo-Morales, Jacob.

Marine Drugs, 21(4), 224: 1-14 (2023)

Meroterpenoids from Gongolaria abies-marina against Kinetoplastids: In Vitro Activity and Programmed Cell Death Study

Leishmaniasis and Chagas disease affect millions of people worldwide. The available treatments against these parasitic diseases are limited and display multiple undesired effects. The brown alga belonging to the genus Gongolaria has been previously reported as a source of compounds with different biological activities. In a recent study from our group, Gongolaria abies-marine was proven to present antiamebic activity. Hence, this brown alga could be a promising source of interesting molecules for the development of new antiprotozoal drugs. In this study, four meroterpenoids were isolated and purified from a dichloromethane/ethyl acetate crude extract through a bioguided fractionation process targeting kinetoplastids. Moreover, the in vitro activity and toxicity were evaluated, and the induction of programmed cell death was checked in the most active and less toxic compounds, namely gongolarone B (2), 6Z-1′-methoxyamentadione (3) and 1′-methoxyamentadione (4). These meroterpenoids triggered mitochondrial malfunction, oxidative stress, chromatin condensation and alterations of the tubulin network. Furthermore, a transmission electron microscopy (TEM) image analysis showed that meroterpenoids (2–4) induced the formation of autophagy vacuoles and ER and Golgi complex disorganization. The obtained results demonstrated that the mechanisms of action at the cellular level of these compounds were able to induce autophagy as well as an apoptosis-like process in the treated parasites.

San Nicolás-Hernández, Desirée; Rodríguez-Expósito, Rubén L.; López-Arencibia, Atteneri; Bethencourt-Estrella, Carlos J.; Sifaoui, Ines; Salazar-Villatoro, Lizbeth; Omaña-Molina, Maritza; Fernández, José J.; DIAZ MARRERO, ANA RAQUEL ; Piñero, José E.; Lorenzo-Morales, Jacob.

Pharmaceuticals, 16(4), 476: 1-20 (2023)