In silico Prediction of Malvaviscus arboreus Metabolites and Green Synthesis of Silver Nanoparticles - Opportunities for Safer Anti-Bacterial and Anti-Cancer Precision Medicine

The Substantial Role of Cell and Nanoparticle Surface Properties in the Antibacterial Potential of Spherical Silver Nanoparticles

Purpose

Although it is well known that the size, shape, and surface chemistry affect the biological potential of silver nanoparticles (AgNPs), the published studies that have considered the influence of AgNP surface on antibacterial activity have not provided conclusive results. This is the first study whose objective was to determine the significance of the surface net charge of AgNPs on their antibacterial potential, attraction to bacterial cells, and cell envelope disruption, considering differences in bacterial surface properties.

Methods

We evaluated five commercial AgNP colloids with identical size and shape but different surface ligands. We thoroughly characterized their physicochemical properties, including the zeta potential, hydrodynamic diameter, and polydispersity index, and determined the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC), along with silver absorption into bacterial cells. Moreover, we investigated structural changes in bacteria treated with AgNPs by using a crystal violet assay and electron microscopy.

Results

The zeta potential of AgNPs ranged from -47.6 to +68.5 mV, with a hydrodynamic diameter of 29-87 nm and a polydispersity index of 0.349-0.863. Bacterial susceptibility varied significantly (0.5 ≤ MIC ≤ 256 µg Ag/mL; 1 ≤ MBC ≤ 256 µg Ag/mL); we found the lowest susceptibility in bacteria with a cell wall or a polysaccharide capsule. The most active AgNPs (0.5 ≤ MIC ≤ 32 µg Ag/mL; 2 ≤ MBC ≤ 64 µg Ag/mL) had a moderate surface charge (-21.5 and +14.9 mV). The antibacterial potential was unrelated to ion dissolution or cell envelope disruption, and bacterial cells absorbed less of the most active AgNPs (1.75-7.65%).

Conclusion

Contrary to previous reports, we found that a moderate surface charge is crucial for the antibacterial activity of AgNPs, and that a significant attraction of the nanoparticle to the cell surface reduces the antibacterial potential of AgNPs. These findings challenge the existing views on AgNP antibacterial mechanisms and interactions with bacterial cells.

Composition and antimicrobial activity of hydroalcoholic extracts of Pleurotus eryngii var. ferulae and P. eryngii var. elaeoselini

Background

The basidiomycetes Pleurotus eryngii var. ferulae Lanzi and P. eryngii var. elaeoselini Venturella et al. belong to the P. eryngii species complex, acting as facultative biotrophs in association with members of Apiaceae family, i.e., Ferula communis L. and Elaeoselinum asclepium L., respectively. The consumption of these fungi has rapidly increased in recent decades, not only thanks to their nutritional properties and pleasant flavor, but also for their bioactive and medicinal properties.

Methods

A quantitative study of their hydroalcoholic extracts was carried out by liquid chromatography-mass spectrometry. The potential antimicrobial activity of the extracts was also tested against some phytopathogenic bacteria [Clavibacter michiganensis and Bacillus megaterium (Gram-positive), Pseudomonas viridiflava, Xanthomonas campestris, and Escherichia coli (Gram-negative)] and fungi (Aspergillus fumigatus, Penicillium italicum, Monilinia laxa, Botrytis cinerea, Cadophora sp., and Sclerotinia sclerotiorum).

Results

The chemical analysis allowed the identification of secondary metabolites belonging to different classes, as flavonoids, organic acids, amino acids, carbohydrates, vitamins, nucleic acids, fatty acids, and triterpenoids. Both extracts demonstrated antimicrobial activity against of the most tested microorganisms.

Conclusion

The results can broaden the knowledge on the possible use of these fungal species in the agricultural sector.

Impact of metallic nanoparticles on gut microbiota modulation in colorectal cancer: A review

Colorectal cancer (CRC) is the third most prevalent cancer. Ongoing research aims to uncover the causes of CRC, with a growing focus on the role of gut microbiota (GM) in carcinogenesis. The GM influences CRC development, progression, treatment efficacy, and therapeutic toxicities. For example, Fusobacterium nucleatum and Escherichia coli can regulate microbial gene expression through the incorporation of human small noncode RNA and potentially contribute to cancer progression. Metallic nanoparticles (MNPs) have both negative and positive impacts on GM, depending on their type. Several studies state that titanium dioxide may increase the diversity, richness, and abundance of probiotics bacteria, whereas other studies demonstrate dose-dependent GM dysbiosis. The MNPs offer cytotoxicity through the modulation of MAPK signaling pathways, NF-kB signaling pathways, PI3K/Akt signaling pathways, extrinsic signaling pathways, intrinsic apoptosis, and cell cycle arrest at G1, G2, or M phase. MNPs enhance drug delivery, enable targeted therapy, and may restore GM. However, there is a need to conduct well-designed clinical trials to assess the toxicity, safety, and effectiveness of MNPs-based CRC therapies.

Design rules applied to silver nanoparticles synthesis: A practical example of machine learning application

The synthesis of silver nanoparticles with controlled physicochemical properties is essential for governing their intended functionalities and safety profiles. However, synthesis process involves multiple parameters that could influence the resulting properties. This challenge could be addressed with the development of predictive models that forecast endpoints based on key synthesis parameters. In this study, we manually extracted synthesis-related data from the literature and leveraged various machine learning algorithms. Data extraction included parameters such as reactant concentrations, experimental conditions, as well as physicochemical properties. The antibacterial efficiencies and toxicological profiles of the synthesized nanoparticles were also extracted. In a second step, based on data completeness, we employed regression algorithms to establish relationships between synthesis parameters and desired endpoints and to build predictive models. The models for core size and antibacterial efficiency were trained and validated using a cross-validation approach. Finally, the features' impact was evaluated via Shapley values to provide insights into the contribution of features to the predictions. Factors such as synthesis duration, scale of synthesis and the choice of capping agents emerged as the most significant predictors. This study demonstrated the potential of machine learning to aid in the rational design of synthesis process and paves the way for the safe-by-design principles development by providing insights into the optimization of the synthesis process to achieve the desired properties. Finally, this study provides a valuable dataset compiled from literature sources with significant time and effort from multiple researchers. Access to such datasets notably aids computational advances in the field of nanotechnology.

Green synthesis of Brassica carinata microgreen silver nanoparticles, characterization, safety assessment, and antimicrobial activities

Nanotechnology has been a central focus of scientific investigation over the past decades owing to its versatile applications. The synthesis of silver nanoparticles (AgNPs) through plant secondary metabolites is a cost-effective and eco-friendly approach. The present study employed Brassica carinata microgreen extracts (BCME) to promote the reduction of silver nitrate (AgNO3) salt into Brassica carinata microgreen silver nanoparticles (BCM-AgNPs). The physicochemical properties of the biosynthesized AgNPs were characterized through both spectroscopy and microscopy techniques. Furthermore, the antimicrobial property of the biosynthesized AgNPs was assessed against six selected pathogenic microorganisms, and finally, their safety was evaluated on a normal Vero cell line through an MTT cytotoxicity assay. The UV-visible spectrum revealed that BCM-AgNPs exhibited an absorption peak at 420 nm. The potential functional groups involved in the biosynthesis of AgNPs were identified by Fourier transform infrared (FTIR) analysis. Scanning electron microscopy (SEM) revealed a spherical nature of the biosynthesized AgNPs. Transmission electron microscopy (TEM) analysis revealed the crystallinity of the AgNPs, averaging 34.68 nm in size. X-ray diffraction (XRD) investigation further confirmed the crystalline structure of the AgNPs. The zeta potential exhibited a significant value of - 22.5 ± 1.16 mV. Regarding the antimicrobial potential, BCM-AgNPs exhibited promising antimicrobial activity against the tested pathogens, with a minimum inhibitory concentration (MIC) of 62.5 µg/mL observed in Pseudomonas aeruginosa. Further cytotoxicity assessment of BCM-AgNPs conducted on Vero cells demonstrated their safety. This study presents a novel approach to synthesizing AgNPs using a nutraceutical microgreen, offering a biocompatible and promising alternative for combating multi-drug resistance.

Toden-E: Topology-Based and Density-Based Ensembled Clustering for the Development of Super-PAG in Functional Genomics using PAG Network and LLM

The integrative analysis of gene sets, networks, and pathways is pivotal for deciphering omics data in translational biomedical research. To significantly increase gene coverage and enhance the utility of pathways, annotated gene lists, and gene signatures from diverse sources, we introduced pathways, annotated gene lists, and gene signatures (PAGs) enriched with metadata to represent biological functions. Furthermore, we established PAG-PAG networks by leveraging gene member similarity and gene regulations. However, in practice, high similarity in functional descriptions or gene membership often leads to redundant PAGs, hindering the interpretation from a fuzzy enriched PAG list. In this study, we developed todenE (topology-based and density-based ensemble) clustering, pioneering in integrating topology-based and density-based clustering methods to detect PAG communities leveraging the PAG network and Large Language Models (LLM). In computational genomics annotation, the genes can be grouped/clustered through the gene relationships and gene functions via guilt by association. Similarly, PAGs can be grouped into higher-level clusters, forming concise functional representations called Super-PAGs. TodenE captures PAG-PAG similarity and encapsulates functional information through LLM, in characterizing network-based functional Super-PAGs. In synthetic data, we introduced a metric called the Disparity Index (DI), measuring the connectivity of gene neighbors to gauge clusterability. We compared multiple clustering algorithms to identify the best method for generating performance-driven clusters. In non-simulated data (Gene Ontology), by leveraging transfer learning and LLM, we formed a language-based similarity embedding. TodenE utilizes this embedding together with the topology-based embedding to generate putative Super-PAGs with superior performance in semantic and gene member inclusiveness.

Myco-fabricated silver nanoparticle by novel soil fungi from Saudi Arabian desert and antimicrobial mechanism

Biological agents are getting a noticeable concern as efficient eco-friendly method for nanoparticle fabrication, from which fungi considered promising agents in this field. In the current study, two fungal species (Embellisia spp. and Gymnoascus spp.) were isolated from the desert soil in Saudi Arabia and identified using 18S rRNA gene sequencing then used as bio-mediator for the fabrication of silver nanoparticles (AgNPs). Myco-synthesized AgNPs were characterized using UV-visible spectrometry, transmission electron microscopy, Fourier transform infrared spectroscopy and dynamic light scattering techniques. Their antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Klebsiella pneumoniae were investigated. In atrial to detect their possible antibacterial mechanism, Sodium dodecyl sulfate (SDS-PAGE) and TEM analysis were performed for Klebsiella pneumoniae treated by the myco-synthesized AgNPs. Detected properties of the fabricated materials indicated the ability of both tested fungal strains in successful fabrication of AgNPs having same range of mean size diameters and varied PDI. The efficiency of Embellisia spp. in providing AgNPs with higher antibacterial activity compared to Gymnoascus spp. was reported however, both indicated antibacterial efficacy. Variations in the protein profile of K. pneumoniae after treatments and ultrastructural changes were observed. Current outcomes suggested applying of fungi as direct, simple and sustainable approach in providing efficient AgNPs.

The antimicrobial activity of tea tree oil (Melaleuca alternifolia) and its metal nanoparticles in oral bacteria

Tea tree (Melaleuca alternifolia) oil (TTO) is an antimicrobial agent, and hence, its use in fabricating nanoparticles (NP) may be useful in providing more efficacious antimicrobial agents. The current research aimed to test the antimicrobial efficacy of TTO and its TTO-Metal-NPs against oral microbes: Porphyromonas gingivalis, Enterococcus faecalis, and Streptococcus mutans. The antimicrobial activity of TTO and zinc (Zn) and iron (Fe) nanoparticles (NPs) and the combined effects of antimicrobial agents were investigated using agar well diffusion assays. Fourier-transform infrared spectroscopy (FT-IR) was used to identify the phyto-constituents of TTO. Field emission scanning electron microscopy (FE-SEM), dynamic light scatter (DLS), and zeta potential were utilized to analyze the biogenic nanoparticles' morphology, size, and potential. The antimicrobial mode of action was determined by assessing the morphological changes under scanning electron microscopy (SEM). The TTO extracts converted Zn and Fe ions to NPs, having an average size of 97.50 (ZnNPs) and 102.4 nm (FeNPs). All tested agents had significant antibacterial efficacy against the tested oral microbes. However, the TTO extract was more efficacious than the NPs. Combination treatment of TTO with antibiotics resulted in partial additive effects against P. gingivalis and partial antagonistic effects against E. faecalis, S. mutans, and common mouthwashes (Oral B and chlorhexidine). TTO and NP-treated bacteria underwent morphological changes on treatment. M. alternifolia phytochemicals could be useful for further research and development of antimicrobial NPs. The current study highlights the variance in activity observed for different types of bacteria and antagonistic effects seen with common mouthwashes, which represent a threat to therapeutic efficacy and heighten the risk of clinical microbial resistance.