Evys Ancede-Gallardo

Correction for ‘Canonical Ru( ii ) tris-polypyridyl complexes as confocal-compatible stains for lignified secondary-wall domains in Arabidopsis thaliana stems’ by Ignacio Fuentes et al. , RSC Adv. , 2026, https://doi.org/10.1039/d6ra04630d.

The rhenium(I) tricarbonyl complex fac-[Re(CO)₃(5,6-epoxy-5,6-dihydro-1,10-phenanthroline)Br] (ReL) has previously demonstrated promising luminescent properties, enabling its direct application as a probe for walled cells such as Candida albicans and Salmonella enterica. In this new study, we present a significantly expanded and comprehensive characterization of ReL, incorporating a wide range of experimental and computational techniques not previously reported. These include variable-temperature ¹H and ¹³C NMR spectroscopy, CH-COSY, single-crystal X-ray diffraction, Hirshfeld surface analysis, DFT calculations, Fukui functions, non-covalent interaction (NCI) indices, and electrochemical profiling. Structural analysis confirmed a pseudo-octahedral geometry with the bromide ligand positioned cis to the epoxy group. NMR data revealed the coexistence of cis and trans isomers in solution, with the trans form being slightly more stable. DFT calculations and aromaticity descriptors indicated minimal electronic differences between isomers, supporting their unified treatment in subsequent analyses. Electrochemical studies revealed two oxidation and two reduction events, consistent with ECE and EEC mechanisms, including a Re(I) → Re(0) transition at −1.50 V vs. SCE. Theoretical redox potentials showed strong agreement with experimental data. Biological assays revealed a dose-dependent cytotoxic effect on HeLa cells, contrasting with previously reported low toxicity in microbial systems. These findings, combined with ReL’s luminescent and antimicrobial properties, underscore its multifunctional nature and highlight its potential as a bioactive and imaging agent for advanced therapeutic and microbiological applications.

Metal-free aminobenzoic acid-derived Schiff bases are attractive antimicrobial leads because their azomethine (–C=N–) functionality enables tunable electronic properties and target engagement. We investigated whether halogenation on the phenolic ring would modulate the redox behavior and enhance antibacterial potency, and hypothesized that heavier halogens would favorably tune physicochemical and electronic descriptors. We synthesized three derivatives (SB-3/Cl, SB-4/Br, and SB-5/I) and confirmed their structures using FTIR, ¹H- and ¹³C-NMR, UV-Vis, and HRMS. For SB-5, single-crystal X-ray diffraction and Hirshfeld analysis verified the intramolecular O–H⋯N hydrogen bond and key packing contacts. Cyclic voltammetry revealed an irreversible oxidation (aminobenzoic ring) and, for the halogenated series, a reversible reduction associated with the imine; peak positions and reversibility trends are consistent with halogen electronic effects and DFT-based MEP/LHS descriptors. Antimicrobial testing showed that SB-5 was selectively potent against Gram-positive aerobes, with low-to-mid micromolar MICs across the panel. Among anaerobes, activity was more substantial: Clostridioides difficile was inhibited at 0.1 µM, and SB-3/SB-5 reduced its sporulation at sub-MICs, while Blautia coccoides was highly susceptible (MIC 0.01 µM). No activity was detected against Gram-negative bacteria at the tested concentrations. In the fungal assay, Botrytis cinerea displayed only a transient fungistatic response without complete growth inhibition. In mammalian cells (HeLa), the compounds displayed clear concentration-dependent behavior. Overall, halogenation, particularly iodination, emerges as a powerful tool to couple redox tuning with selective Gram-positive activity and a favorable cellular tolerance window, nominating SB-5 as a promising scaffold for further antimicrobial optimization.

A new Schiff base, (E)-2-(((1,10-phenanthrolin-5-yl)imino)methyl)-4,6-di-tert-butylphenol (Fen-IHB), was designed to incorporate an intramolecular hydrogen bond (IHB) between the phenolic OH and the azomethine nitrogen with the goal of modulating its physicochemical and biological properties. Fen-IHB was synthesized by condensation of 5-amino-1,10-phenanthroline with 3,5-di-tert-butyl-2-hydroxybenzaldehyde and exhaustively characterized by HR-ESI-MS, FTIR, 1D/2D NMR (¹H, ¹³C, DEPT-45, HH-COSY, CH-COSY, D₂O exchange), and UV–Vis spectroscopy. Cyclic voltammetry in anhydrous CH₃CN revealed a single irreversible cathodic peak at −1.43 V (vs. Ag/Ag⁺), which is consistent with the intramolecular reductive coupling of the azomethine moiety. Density functional theory (DFT) calculations, including MEP mapping, Fukui functions, dual descriptor analysis, and Fukui potentials with dual descriptor potential, identified the exocyclic azomethine carbon as the principal nucleophilic site and the phenolic ring (hydroxyl oxygen and adjacent carbons) as the main electrophilic region. Noncovalent interaction (NCI) analysis further confirmed the strength and geometry of the intramolecular hydrogen bond (IHB). In vitro antimicrobial assays indicated that Fen-IHB was inactive against Gram-negative facultative anaerobes (Salmonella enterica serovar Typhimurium and Typhi, Escherichia coli) and strictly anaerobic Gram-positive species (Clostridioides difficile, Roseburia inulinivorans, Blautia coccoides), as any growth inhibition was indistinguishable from the DMSO control. Conversely, Fen-IHB displayed measurable activity against Gram-positive aerobes and aerotolerant anaerobes, including Bacillus subtilis, Streptococcus pyogenes, Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus haemolyticus. Overall, these comprehensive characterization results confirm the distinctive chemical and electronic properties of Fen-IHB, underlining the crucial role of the intramolecular hydrogen bond and electronic descriptors in defining its reactivity profile and selective biological activity.

Bacterial outer membrane vesicles (OMVs) are nanoscale extracellular structures produced by Gram-negative bacteria that are critical for microbial biology and host-pathogen interactions and have great potential in biotechnological applications. Despite the availability of fluorescent dyes for OMV studies, many are repurposed from eukaryotic extracellular vesicle research and are not explicitly optimized for OMVs, leading to challenges in achieving consistent labeling, minimizing background noise, and preserving vesicle integrity during analyses. This study evaluates B2, a benzimidazole-derived fluorophore, for OMV labeling in advanced techniques like flow cytometry and confocal microscopy. OMVs were isolated from Escherichia coli strains BL21 and O157, and their integrity was confirmed using transmission electron microscopy (TEM). B2 staining protocols were optimized for OMVs, and fluorescence analyses revealed specific interactions with the vesicle membranes, reducing aggregation and enhancing signal uniformity. Flow cytometry indicated near-complete labeling efficiency (98–100%) with minimal background interference. Confocal microscopy further validated B2’s effectiveness, showing evident OMV internalization into epithelial HT-29 cells and compatibility with other fluorophores. Density functional theory (DFT) calculations, including Fukui function analysis, identified key electrophilic and nucleophilic regions in B2 that facilitate specific hydrogen bonding and polar interactions with membrane components. Non-covalent interaction (NCI) analysis revealed pronounced intramolecular hydrogen bonding along with discrete regions of weak van der Waals interactions. Molecular dynamics simulations suggest that B2 exhibits an affinity for both the hydrophobic core of the lipid bilayer and the core oligosaccharide region of the LPS layer, which collectively ensures sustained retention of the dye. The findings presented in this study position B2 as a valuable fluorophore for OMV research.

This theoretical investigation aims to evaluate the influence of iodine substitutions on the phenolic moiety of the pyridine Schiff bases harboring an intramolecular hydrogen bond (PSB‐IHB) ancillary ligand within the monocationic. fac‐[Re(CO)₃(N,N)(PSB‐IHB)]⁺ architecture on photophysical properties, particularly emission range. Optimized structures of two Re(I) tricarbonyl complexes (C1 and C2) were analyzed, revealing a distorted octahedral coordination geometry. Geometric parameters were compared with experimental data from analogous complexes. NBO analysis confirmed the presence of intramolecular hydrogen bonds (IHBs) in both singlet and triplet states, providing significant stabilization. Theoretical calculations predicted three distinct absorption bands for all complexes in dichloromethane, indicating substantial electronic delocalization between the pyridinic and phenolic rings via the azomethine group. These findings underscore the crucial role of delocalization and donor–acceptor interactions in stabilizing Re(I) tricarbonyl complexes and their impact on photophysical properties. Emissions calculated for the C1 and C2 complexes were observed within the range of 632–643 nm. The presence of IHBs was found to be essential for modulating photophysical properties, with emissions attributed to ligand‐to‐ligand charge transfer transitions.

Alignment-free (AF) methodologies have increased in popularity in the last decades as alternative tools to alignment-based (AB) algorithms for performing comparative sequence analyses. They have been especially useful to detect remote homologs within the twilight zone of highly diverse gene/protein families and superfamilies. The most popular alignment-free methodologies, as well as their applications to classification problems, have been described in previous reviews. Despite a new set of graph theory-derived sequence/structural descriptors that have been gaining relevance in the detection of remote homology, they have been omitted as AF predictors when the topic is addressed. Here, we first go over the most popular AF approaches used for detecting homology signals within the twilight zone and then bring out the state-of-the-art tools encoding graph theory-derived sequence/structure descriptors and their success for identifying remote homologs. We also highlight the tendency of integrating AF features/measures with the AB ones, either into the same prediction model or by assembling the predictions from different algorithms using voting/weighting strategies, for improving the detection of remote signals. Lastly, we briefly discuss the efforts made to scale up AB and AF features/measures for the comparison of multiple genomes and proteomes. Alongside the achieved experiences in remote homology detection by both the most popular AF tools and other less known ones, we provide our own using the graphical–numerical methodologies, MARCH-INSIDE, TI2BioP, and ProtDCal. We also present a new Python-based tool (SeqDivA) with a friendly graphical user interface (GUI) for delimiting the twilight zone by using several similar criteria.

Background: The Ribonuclease III (RNase III) enzymatic class is involved in many important biological processes from bacteria to higher eukaryotes. Consequently, they have been useful as drug-target candidates for drug development. Despite their high molecular diversity, RNases III share common structural and catalytic features and some degree of enzymatic activity. However, the role of accessory domains as key determinants of substrate selectivity and over the biological function of each RNase III type is still under study. Results: The in vitro enzymatic activity of three RNase III members from class I (Escherichia coli RNase III, Schizosaccharomyces pombe Pac1 and Saccharomyces cerevisiae Rntp1) and the human Drosha placed in class II was revisited against four different substrates. These two RNase III classes comprise members showing different domain organization. Enzymatic activity differences were found among members of the class I, which were even higher when the human Drosha (class II) was tested. The substrate promiscuity of the E. coli RNase III was corroborated in vivo through its expression in S. cerevisiae, as reported previously, but was extended here to Pichia pastoris. The putative molecular mechanisms contributing for the lethal effect of the heterologous RNase III on the yeast lives were deeply discussed. Conclusion: The new generated biochemical data integrated with previous available information affirmed that RNases III substrate specificity as well as their cellular biological role is highly influenced by its protein structure architecture. This fact also allowed drawing evolutionary links between RNase III members from their structural and substrate specificity differences.

Background: Virtual Screening methodologies have emerged as efficient alternatives for the discovery of new drug candidates. At the same time, ensemble methods are nowadays frequently used to overcome the limitations of employing a single model in ligand-based drug design. However, many applications of ensemble methods to this area do not consider important aspects related to both virtual screening and the modeling process. During the application of ensemble methods to virtual screening the proper validation of the models in virtual screening conditions is often neglected. No analysis of the diversity of the ensemble members is performed frequently or no considerations regarding the applicability domain of the base models are being made. Methods: In this research, we review basic concepts and definitions related to virtual screening. We comment recent applications of ensemble methods to ligand-based virtual screening and highlight their advantages and limitations. Results: Next, we propose a method based on genetic algorithms optimization for the generation of virtual screening tailored ensembles which address the previously identified problems in the current applications of ensemble methods to virtual screening. Conclusion: Finally, the proposed methodology is successfully applied to the generation of ensemble models for the ligand-based virtual screening of dual target A2A adenosine receptor antagonists and MAO-B inhibitors as potential Parkinson’s disease therapeutics.