Generation and Computational Characterization of a Complex Staphylococcus aureus Lipid Bilayer

Antibacterial activity of tamoxifen derivatives against methicillin-resistant Staphylococcus aureus

The development of new antimicrobial therapeutic strategies requires urgent attention to prevent the tens of millions of deaths predicted to occur by 2050 as a result of multidrug-resistant (MDR) bacterial infections. This study aimed to discover new tamoxifen derivatives with antimicrobial potential, particularly targeting methicillin-resistant Staphylococcus aureus (MRSA). The minimum inhibitory concentration (MIC) of 22 tamoxifen derivatives was determined against S. aureus reference and MRSA strains using microdilution assays. The antibacterial effects of selected tamoxifen derivatives against MRSA (USA7 strain) were assessed through bacterial growth assays. Additionally, bacterial membrane permeability and molecular dynamics (MD) simulation assays were performed. The MIC of the tamoxifen derivatives against reference S. aureus and MRSA strains ranged from to 16 to >64 μg/mL. Bacterial growth assays demonstrated that tamoxifen derivatives 2, 5, and 6, the only compounds bearing the electron-donating hydroxyl group in the para position on both phenyl rings of the tamoxifen skeleton, dose-dependently reduced the growth of the USA7 strain. Moreover, treatment of MRSA with derivatives 2 and 5 resulted in a slight increase of membrane permeabilization. Extensive MD simulations on the interaction between 5 and 6 and the S. aureus membrane model suggest that the compounds do not act by destabilizing the membrane integrity. These findings suggest that tamoxifen derivatives exhibit antibacterial activity against MRSA, potentially broadening the spectrum of available drug treatments for combating antimicrobial-resistant S. aureus.

Unraveling the molecular drivers of antibacterial prenylated (iso)flavonoids and chalcones against Streptococcus mutans

Given the negative side effects and increased resistance associated with conventional oral antimicrobials, prenylated phenolics are promising alternatives to combat the oral pathogen Streptococcus mutans. A total of 40 prenylated phenolics were evaluated for their antibacterial activity against S. mutans. Eleven prenylated phenolics were purified from licorice (Glycyrrhiza spp.) spent, including the newly discovered double prenylated 2-arylbenzofuran, isokanzonol V. Twenty-eight compounds showed similar potency as chlorhexidine. Activity was correlated with structural properties and novel structure-activity relationships were established: (i) Hydrophobic volume was the main driver associated to activity (double prenylated phenolics were consistently more active than single prenylated phenolics); (ii) the conversion of flavanones to chalcones by C-ring opening increases molecular length and planarity as well as antibacterial activity, and (iii) active single prenylated isoflavones have balanced molecular hydrophilicity. Hence, double or single prenylated phenolics featuring planarity, an extended configuration, and balanced hydrophilicity hold promise for S. mutans control.

Mycoidesin, a novel lantibiotic, exhibits potent bacteriostatic activity against Listeria monocytogenes and effectively controls its growth in beef

Listeria monocytogenes can cause severe listeriosis, with the consumption of contaminated food being an important route of its transmission. Biopreservatives can be used for the prevention and control of L. monocytogenes in food. In this study, we identified a novel lantibiotic, mycoidesin, with potent bacteriostatic activity against L. monocytogenes. It exhibited 4- to 16-fold higher bacteriostatic activity against the L. monocytogenes strains than nisin A. Analysis of the mode of action of mycoidesin revealed that it exerted bacteriostatic activity against L. monocytogenes ATCC 19111 at low and high concentrations (1×-32× MIC, 0.39-12.5 µM). It blocked cell wall synthesis by binding to Lipid II and inhibiting the growth of L. monocytogenes. For other sensitive strains, such as Bacillus cereus CMCC 63301, mycoidesin exerted a bacteriostatic effect at a low concentration (1× MIC, 1.56 µM) via the same mechanism, whereas it exerted a bactericidal effect at high concentrations (2×-8× MIC, 3.13-12.5 µM), which can damage the cell membrane and cause cell death. The stability test showed that mycoidesin had increased stability compared to nisin A. Additionally, mycoidesin showed low cytotoxic and hemolytic activity. Furthermore, mycoidesin effectively inhibited the growth of L. monocytogenes in beef and delayed the decline in beef quality. Our study demonstrates the potential of mycoidesin as a biopreservative to prevent L. monocytogenes contamination and improve the safety of meat and meat products in the food industry.

IMPORTANCE

This study aimed to identify highly effective, stable, and safe natural bacteriocin preservatives with anti-Listeria monocytogenes activity. We isolated a novel class II lantibiotic, mycoidesin, which exhibited more efficient bacteriostatic activity against L. monocytogenes and increased stability compared to the applied bacteriocin food preservative, nisin A. Mycoidesin also showed favorable biosafety. Moreover, mycoidesin could be effectively used for controlling L. monocytogenes in beef, demonstrating its potential as a biopreservative to prevent L. monocytogenes-related contamination and improve the safety of meat and meat products in the agricultural and food industries.

A dual antibacterial action of soft quaternary ammonium compounds: bacteriostatic effects, membrane integrity, and reduced in vitro and in vivo toxicity

Quaternary ammonium compounds (QACs) have served as essential antimicrobial agents for nearly a century due to their rapid membrane-disrupting action. However, the emergence of bacterial resistance and environmental concerns have driven interest in alternative designs, such as "soft QACs", which are designed for enhanced biodegradability and reduced resistance potential. In this study, we explored the antibacterial properties and mechanisms of action of our newly synthesized soft QACs containing a labile amide bond within a quinuclidine scaffold. Our findings revealed that these compounds primarily exhibit a bacteriostatic mode of action, effectively suppressing bacterial growth even at concentrations exceeding their minimum inhibitory concentrations (MICs). Unlike traditional QACs, fluorescence spectroscopy and microscopy demonstrated membrane preservation during treatment, with reduced membrane integration compared to cetylpyridinium chloride (CPC), as corroborated by parallel artificial membrane permeability assays. Additionally, molecular dynamics simulations revealed "hook-like" conformations that limit lipid bilayer penetration and promote the formation of larger aggregates, reducing their effective concentration and minimizing cytotoxic effects. Interestingly, secondary antibacterial mechanisms, including inhibition of protein synthesis, were observed, further enhancing their activity. Zebrafish embryotoxicity and in vitro cytotoxicity studies confirmed significantly lower toxicity compared to CPC. By addressing limitations associated with conventional QACs, including toxicity, resistance, and environmental persistence, these soft QACs provide a promising foundation for next-generation antimicrobials. This work advances the understanding of QAC mechanisms while paving the way for safer, eco-friendly applications in healthcare, agriculture, and industrial settings.

Imidazole-Rich, Four-Armed Host-Defense Peptidomimetics as Promising Narrow-Spectrum Antibacterial Agents and Adjuvants against Pseudomonas Aeruginosa Infections

The development of narrow-spectrum antimicrobial agents is paramount for swiftly eradicating pathogenic bacteria, mitigating the onset of drug resistance, and preserving the homeostasis of bacterial microbiota in tissues. Owing to the limited affinity between the hydrophobic lipid bilayer interior of bacterial cells and most hydrophilic, polar peptides, the construction of a distinctive class of four-armed host-defense peptides/peptidomimetics (HDPs) is proposed with enhanced specificity and membrane perturbation capability against Pseudomonas aeruginosa by incorporating imidazole groups. These groups demonstrate substantial affinity for unsaturated phospholipids, which are predominantly expressed in the cell membrane of P. aeruginosa, thereby enabling HDPs to exhibit narrow-spectrum activity against this bacterium. Computational simulations and experimental investigations have corroborated that the imidazole-rich, four-armed peptidomimetics exhibit notable selectivity toward bacteria over mammalian cells. Among them, 4H10, characterized by its abundant and densely distributed imidazole groups, exhibits impressive activity against various clinically isolated P. aeruginosa strains. Moreover, 4H10 has demonstrated potential as an antibiotic adjuvant, enhancing doxycycline accumulation and exerting effects on intracellular targets by efficiently disrupting bacterial cell membranes. Consequently, the hydrogel composed of 4H10 and doxycycline emerged as a promising topical agent, significantly diminishing the skin P. aeruginosa burden by 97.1% within 2 days while inducing minimal local and systemic toxicity.

Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations

Bacteria have evolved over 3 billion years, shaping our intrinsic and symbiotic coexistence with these single-celled organisms. With rising populations of drug-resistant strains, the search for novel antimicrobials is an ongoing area of research. Advances in high-performance computing platforms have led to a variety of molecular dynamics simulation strategies to study the interactions of antimicrobial molecules with different compartments of the bacterial cell envelope of both Gram-positive and Gram-negative species. In this review, we begin with a detailed description of the structural aspects of the bacterial cell envelope. Simulations concerned with the transport and associated free energy of small molecules and ions through the outer membrane, peptidoglycan, inner membrane and outer membrane porins are discussed. Since surfactants are widely used as antimicrobials, a section is devoted to the interactions of surfactants with the cell wall and inner membranes. The review ends with a discussion on antimicrobial peptides and the insights gained from the molecular simulations on the free energy of translocation. Challenges involved in developing accurate molecular models and coarse-grained strategies that provide a trade-off between atomic details with a gain in sampling time are highlighted. The need for efficient sampling strategies to obtain accurate free energies of translocation is also discussed. Molecular dynamics simulations have evolved as a powerful tool that can potentially be used to design and develop novel antimicrobials and strategies to effectively treat bacterial infections.

The antimicrobial potential of adarotene derivatives against Staphylococcus aureus strains

Multidrug-resistant (MDR) pathogens are severely impacting our ability to successfully treat common infections. Here we report the synthesis of a panel of adarotene-related retinoids showing potent antimicrobial activity on Staphylococcus aureus strains (including multidrug-resistant ones). Fluorescence and molecular dynamic studies confirmed that the adarotene analogues were able to induce conformational changes and disfunctions to the cell membrane, perturbing the permeability of the phospholipid bilayer. Since the major obstacle for developing retinoids is their potential cytotoxicity, a selected candidate was further investigated to evaluate its activity on a panel of human cell lines. The compound was found to be well tolerated, with IC50 5-15-fold higher than the MIC on S. aureus strains. Furthermore, the adarotene analogue had a good pharmacokinetic profile, reaching a plasma concentration of about 6 μM after 0.5 h after administration (150 mg/kg), at least twice the MIC observed against various bacterial strains. Moreover, it was demonstrated that the compound potentiated the growth-inhibitory effect of the poorly bioavailable rifaximin, when used in combination. Overall, the collected data pave the way for the development of synthetic retinoids as potential therapeutics for hard-to-treat infectious diseases caused by antibiotic-resistant Gram-positive pathogens.

Computational Design of Peptides for Biomaterials Applications

Computer-aided molecular design and protein engineering emerge as promising and active subjects in bioengineering and biotechnological applications. On one hand, due to the advancing computing power in the past decade, modeling toolkits and force fields have been put to use for accurate multiscale modeling of biomolecules including lipid, protein, carbohydrate, and nucleic acids. On the other hand, machine learning emerges as a revolutionary data analysis tool that promises to leverage physicochemical properties and structural information obtained from modeling in order to build quantitative protein structure-function relationships. We review recent computational works that utilize state-of-the-art computational methods to engineer peptides and proteins for various emerging biomedical, antimicrobial, and antifreeze applications. We also discuss challenges and possible future directions toward developing a roadmap for efficient biomolecular design and engineering.

Computing Individual Area per Head Group Reveals Lipid Bilayer Dynamics

Lipid bilayers express a range of phases from solid-like to gel-like to liquid-like as a function of temperature and lipid surface concentration. The area occupied per lipid head group serves as one useful indicator of the bilayer phase, in conjunction with the two-dimensional radial distribution function (i.e., structure factor) within the bilayer. Typically, the area per head group is determined by dividing the bilayer area equally among all head groups. Such an approach is less satisfactory for a multicomponent set of diverse lipids. In this work, area determination is performed on a lipid-by-lipid basis by attributing to a lipid the volume that surrounds each atom. Voronoi tessellation provides this division of the interfacial region on a per-atom basis. The method is applied to a multicomponent system of water, NaCl, and 19 phospholipid types that was devised recently [Langmuir2022, 38, 9481-9499] as a computational representation of the Gram-positive Staphylococcus aureus phospholipid bilayer. Results demonstrate that lipids and water molecules occupy similar extents of area within the interfacial region; ascribing area only to head groups implicitly incorporates assumptions about head group hydration. Results further show that lipid tails provide non-negligible contributions to area on the membrane side of the bilayer-water interface. Results for minimum and maximum area of individual lipids reveal that spontaneous fluctuations displace head groups more than 10 Å from the interfacial region during an NPT simulation at 310 K, leading to a zero contribution to total area at some times. Total area fluctuations and fluctuations per individual lipid relax with a correlation time of ∼10 ns. The method complements density profile as an approach to quantify the structure and dynamics of computational lipid bilayers.