Tag: Scientific Publications

Conformational, Aggregation, and Membrane Interaction Dynamics of Keratin-Derived Antimicrobial Peptides from Molecular Dynamics Simulations

Authors: Panagiotis Panagopoulos Papageorgiou, Katerina S. Karadima, Ioanna Papageorgiou, Georgios G. Vogiatzis and Vlasis G. Mavrantzas

Abstract

Keratin-derived antimicrobial peptides (KAMPs) from human corneal epithelial cells have received considerable attention due to their biocidal activity against both Gram-positive and Gram-negative bacteria without possessing the conventional characteristics of known antimicrobial peptides (AMPs), such as ordered secondary structure elements and a net positive charge. Here, we perform unbiased, all-atom molecular dynamics (MD) simulations for seven members of the glycine-rich KAMP family and for Pw-Antibac123, which is a distinct keratin-derived peptide obtained through chicken feather hydrolyzates. This study first aims to investigate the structural dynamics of these peptides in dilute and semidilute aqueous solutions. Our results verify the noncanonical structure of KAMPs and validate the molecular model of Pw-Antibac123 that has been proposed in the literature. Increasing the peptide concentration in the aqueous solution leads to self-assembly and peptide aggregation, due to the development of interpeptide hydrogen bonds and the strong effect of electrostatic interactions. The effect of intermolecular amino acid interactions on the secondary structure of KAMPs is also discussed, allowing us to identify strong synergies between specific amino acid pairs, such as serine and glycine, valine and leucine, and arginine and isoleucine. Subsequently, we focus on how KAMP-18C, an 18-residue-long KAMP, interacts with model Gram-positive lipid bilayers. Since spontaneous aggregation is not observed, we construct artificial pores and embed peptides within the membrane to assess the stability of these systems. We discuss how our findings correlate with proposed mechanisms of action for AMPs.

Follow the link to read the full paper: https://doi.org/10.1021/acs.jpcb.6c04420

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Copper-Modified Mesoporous Silica Nanoparticles for Antimicrobial Applications

Authors: Amaia M. Goitandia, Maialen Argaiz, Miren Blanco, Giorgia Grilli, Elisa Recchia, Alessandra Amoroso, Nathalie Totaro, Andrea Ciammarucon, Riccardo De Santis, Leire Ruiz Rubio, Fabiana Arduini and Florigio Lista

Abstract

The escalating global crisis of antimicrobial-resistant (AMR) bacterial infections, along with the continuous threat of viral outbreaks, poses a serious risk to public health worldwide and underscores the urgent need for innovative therapeutic strategies. In this study, mesoporous silica nanoparticles (MSNs) were successfully synthesized and subsequently functionalized with copper to impart broad-spectrum antimicrobial activity. The oxidation state of copper on the MSN surface was modulated through thermal treatments, allowing the evaluation of its influence on antimicrobial efficacy. The modified MSNs were tested against key bacterial pathogens, including Escherichia coli and Staphylococcus aureus, achieving complete bactericidal activity after 2 h of exposure to E. coli. Moreover, as well as influenza A (H1N1) pdm09, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and MS2 bacteriophage (MS2) were evaluated, reaching an efficiency higher than 80%, 90%, and 97%, respectively. The results indicated that copper-modified MSNs exhibit potent antibacterial and antiviral activity, highlighting their potential as an antibiotic-free alternative for preventing microbial infections while mitigating the development of AMR bacteria.

Follow the link to read the full paper: https://doi.org/10.3390/nano15241884

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Effect of pH, Temperature, Molecular Weight and Salt Concentration on the Structure and Hydration of Short Poly(N,N-dimethylaminoethyl methacrylate) Chains in Dilute Aqueous Solutions: A Combined Experimental and Molecular Dynamics Study

Authors: Dimitris G. Mintis, Marco Dompé, Panagiotis D. Kolokathis, Jasper van der Gucht, Antreas Afantitis and Vlasis G. Mavrantzas

Abstract

We study the microstructural properties and state of hydration of aqueous low-molecular-weight poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA) solutions and their dependence on polymer concentration and pH by means of detailed atomistic Molecular Dynamics (MD) simulations and experiments. For infinitely dilute solutions with a degree of polymerization of N = 30 at basic pH conditions, no temperature dependence is observed on the overall shape and state of hydration of the polyelectrolyte. This is supported by the experimental component of our work according to which the hydrodynamic radius, Rh, does not change dramatically with temperature. Small, but not drastic, changes are observed for solutions with longer PDMAEMA chains (N = 50, 70, and 110). Although the
MD simulations demonstrate that temperature and salt do affect the strength of hydrophobic interactions between PDMAEMA and water, apparently these effects are not strong enough to cause drastic changes to the overall shape of the polymer. MD simulations also reveal that Na+ salt ions strongly interact with the oxygen atoms located at the side chain of the polyelectrolyte. While no significant changes in the global shape or state of hydration of the PDMAEMA chain are found, a strong dependence is revealed for the aggregation behavior of the polymer on temperature and salt in slightly more concentrated solutions. A structural transition from a collapsed coil to a stretched conformation is also observed as we move from basic to acidic pH conditions, which is strongly correlated with the degree
of chain rigidity as a function of pH.

Follow the link to read the full article https://doi.org/10.3390/polym17162189

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An ecodesigned reagent-free paper-based electrochemical sensor modified with carbon black for the detection of essential oils

Authors: Luca Fiore, Arianna Antinucci, Giorgia Leotta, Laura Fabiani, Alessandro Iannini, Pierluca Galloni, Riccardo De Santis, Andrea Ciammaruconi, Giorgia Grilli, Elisa Recchia, Florigio Lista, Fabiana Arduini

A B S T R A C T
In the era of sustainability, the use of natural compounds as antimicrobial compounds is the rational selection to avoid the release of pollutants into the environment. Among natural compounds, essential oils are characterized by reliable antimicrobial activity and their use is estimated to grow in the future, thus their detection is an asked point. Herein, we report an electrochemical reagent-free paper-based device for the detection of essential oils, namely thymol, eugenol, and carvacrol by adding 5 µL of solution onto the electrode. We functionalized the working electrode with carbon black by drop casting, demonstrating for the first time the proved sensitivity in essential oil detection using this affordable nanomaterial. To deliver a reagent-free device, the paper-based electrode was loaded with the working buffer for asking the end-user only the addition of the sample. This sensor detected the selected essential oils in a dynamic linear range of up to 16 ppm, with a detection limit equal to 0.1, 0.1, and 0.2 ppm for thymol, eugenol, and carvacrol, respectively. Moreover, the sensor’s sustainability was evaluated using the RGBfast method, highlighting its whiteness compared to conventional chromatographic techniques. The reliable results obtained using the paper-based electrochemical sensor demonstrated the versatility, eco-friendliness, and practicality of this sensing tool, enlarging its use in essential oil detection.

Follow the link to read the full paper published in Green Analytical Chemistry https://doi.org/10.1016/j.greeac.2025.100217