Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus

Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies

Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.

Injectable Liposome-Loaded Hydrogel Formulations with Controlled Release of Curcumin and α-Tocopherol for Dental Tissue Engineering

An injectable hydrogel formulation is developed utilizing low- and high-molecular-weight chitosan (LCH and HCH) incorporated with curcumin and α-tocopherol-loaded liposomes (Lip/Cur+Toc). Cur and Toc releases are delayed within the hydrogels. The injectability of hydrogels is proved via rheological analyses. In vitro studies are conducted using human dental pulp stem cells (hDPSCs) and human gingival fibroblasts (hGFs) to examine the biological performance of the hydrogels toward endodontics and periodontics, respectively. The viability of hDPSCs treated with the hydrogels with Lip/Cur+Toc is the highest till day 14, compared to the neat hydrogels. During odontogenic differentiation tests, alkaline phosphatase (ALP) enzyme activity of hDPSCs is induced in the Cur-containing groups. Biomineralization is enhanced mostly with Lip/Cur+Toc incorporation. The viability of hGFs is the highest in HCH combined with Lip/Cur+Toc while wound healing occurs almost 100% in both (Lip/Cur+Toc@LCH and Lip/Cur+Toc@HCH) after 2 days. Antioxidant activity of Lip/Cur+Toc@LCH on hGFs is significantly the highest among the groups. Antimicrobial tests demonstrate that Lip/Cur+Toc@LCH is more effective against Escherichia coli whereas so is Lip/Cur+Toc@HCH against Staphylococcus aureus. The antimicrobial mechanism of the hydrogels is investigated for the first time through various computational models. LCH and HCH loaded with Lip/Cur+Toc are promising candidates with multi-functional features for endodontics and periodontics.

Enhancing Mechanical and Antimicrobial Properties of Dialdehyde Cellulose-Silver Nanoparticle Composites through Ammoniated Nanocellulose Modification

Given the widespread prevalence of viruses, there is an escalating demand for antimicrobial composites. Although the composite of dialdehyde cellulose and silver nanoparticles (DAC@Ag1) exhibits excellent antibacterial properties, its weak mechanical characteristics hinder its practical applicability. To address this limitation, cellulose nanofibers (CNFs) were initially ammoniated to yield N-CNF, which was subsequently incorporated into DAC@Ag1 as an enhancer, forming DAC@Ag1/N-CNF. We systematically investigated the optimal amount of N-CNF and characterized the DAC@Ag1/N-CNF using FT-IR, XPS, and XRD analyses to evaluate its additional properties. Notably, the optimal mass ratio of N-CNF to DAC@Ag1 was found to be 5:5, resulting in a substantial enhancement in mechanical properties, with a 139.8% increase in tensile elongation and a 33.1% increase in strength, reaching 10% and 125.24 MPa, respectively, compared to DAC@Ag1 alone. Furthermore, the inhibition zones against Escherichia coli and Staphylococcus aureus were significantly expanded to 7.9 mm and 15.9 mm, respectively, surpassing those of DAC@Ag1 alone by 154.8% and 467.9%, indicating remarkable improvements in antimicrobial efficacy. Mechanism analysis highlighted synergistic effects from chemical covalent bonding and hydrogen bonding in the DAC@Ag1/N-CNF, enhancing the mechanical and antimicrobial properties significantly. The addition of N-CNF markedly augmented the properties of the composite film, thereby facilitating its broader application in the antimicrobial field.

Quaternary ammonium salts for water treatment with balanced rate of sterilization and degradation

The growing number of infections caused by drug-resistant bacteria which arise from the overuse of antibiotics has severely affected the normal operation of human society. The high antibacterial activity of QAS makes it promising as an alternative to antibiotics, but it suffers from secondary pollution due to its non-degradation. Here we have synthesized a class of gemini quaternary ammonium salts (GQAS) with different carbon chain lengths containing ester groups by using facile methylation reaction. Quaternary ammonium groups contribute to insert negatively charged bacterial membranes, resulting in membrane damage and bacteria death. Compared with conventional single-chain QAS, except for the more efficient antibacterial efficiency attribute to the presence of the second carbon chain, GQAS with alterable antibacterial properties can minimize the possibility of bacterial resistance and reduce the accumulation of GQAS in the environment through the introduction of degradable ester groups. GQAS is completely superior to the commercial bactericide benzalkonium chloride (BAC) in both antibacterial activity and degrade performance, which can be used as a more environmentally friendly bactericide.

A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria

The bacterial cell-wall peptidoglycan is made of glycan strands crosslinked by short peptide stems. Crosslinks are catalyzed by DD-transpeptidases (4,3-crosslinks) and LD-transpeptidases (3,3-crosslinks). However, recent research on non-model species has revealed novel crosslink types, suggesting the existence of uncharacterized enzymes. Here, we identify an LD-transpeptidase, LDTGo, that generates 1,3-crosslinks in the acetic-acid bacterium Gluconobacter oxydans. LDTGo-like proteins are found in Alpha- and Betaproteobacteria lacking LD3,3-transpeptidases. In contrast with the strict specificity of typical LD- and DD-transpeptidases, LDTGo can use non-terminal amino acid moieties for crosslinking. A high-resolution crystal structure of LDTGo reveals unique features when compared to LD3,3-transpeptidases, including a proline-rich region that appears to limit substrate access, and a cavity accommodating both glycan chain and peptide stem from donor muropeptides. Finally, we show that DD-crosslink turnover is involved in supplying the necessary substrate for LD1,3-transpeptidation. This phenomenon underscores the interplay between distinct crosslinking mechanisms in maintaining cell wall integrity in G. oxydans.

Chitosan/aloe vera gel coatings infused with orange peel essential oils for fruits preservation

Continuous fruit waste poses significant environmental and economic challenges, necessitating innovative fruit coating technologies. This research focuses on harnessing discarded orange peels to extract essential oil (OPEO), which is then integrated into a chitosan/aloe vera (CTS/AVG) matrix. The study comprehensively characterised the coating in terms of its physicochemical properties, antioxidant capacity, and antimicrobial efficacy. The investigation involved an analysis of particle size and distribution in the coating solutions, highlighting changes induced by the incorporation of orange peel essential oil (1 %, 2 % and 3 % v/w) into the chitosan/aloe vera (4:1 v/v) matrix, including particle size reduction and enhanced Brownian motion. The study quantifies a 33.21 % decrease in water vapour transmission rate and a reduction in diffusion coefficient from 9.26 × 10-11 m2/s to 6.20 × 10-11 m2/s following the addition of OPEO to CTS/AVG. Assessment of antioxidant potential employing DPPH radical scavenging assays, revealed that CTS/AVG/3 %OPEO exhibited notably superior radical scavenging activity compared to CTS/AVG, CTS/AVG/1 %OPEO, and CTS/AVG/2 %OPEO, demonstrated by its IC50 value of 17.01 ± 0.45 mg/mL. The study employs the well diffusion method, demonstrating a higher susceptibility of gram-negative bacteria to the coating solutions than gram-positive counterparts. Remarkably, CTS/AVG/3 %OPEO displayed the most pronounced inhibition against Escherichia coli, generating an inhibitory zone diameter of 14 ± 0.8 mm. The results collectively emphasised the potential of CTS/AVG/3 %OPEO as a viable natural alternative to synthetic preservatives within the fruit industry, attributed to its exceptional antioxidant and antimicrobial properties.

Molecular Modeling and Simulation of the Mycobacterial Cell Envelope: From Individual Components to Cell Envelope Assemblies

Unlike typical Gram-positive bacteria, the cell envelope of mycobacteria is unique and composed of a mycobacterial outer membrane, also known as the mycomembrane, a peptidoglycan layer, and a mycobacterial inner membrane, which is analogous to that of Gram-negative bacteria. Despite its importance, however, our understanding of this complex cell envelope is rudimentary at best. Thus, molecular modeling and simulation of such an envelope can benefit the scientific community by proposing new hypotheses about the biophysical properties of its different layers. In this Perspective, we present recent advances in molecular modeling and simulation of the mycobacterial cell envelope from individual components to cell envelope assemblies. We also show how modeling other types of cell envelopes, such as that of Escherichia coli, may help modeling part of the mycobacterial envelopes. We hope that the studies presented here are just the beginning of the road and more and more new modeling and simulation studies help us to understand crucial questions related to mycobacteria such as antibiotic resistance or bacterial survival in the host.

Mechanism of Synergistic Photoinactivation Utilizing Curcumin and Lauric Arginate Ethyl Ester against Escherichia coli and Listeria innocua

This study investigated the mechanism of how lauric arginate ethyl ester (LAE) improves the photoinactivation of bacteria by curcumin after diluting the 100 µmol/L stock curcumin-LAE micelle solution to the concentration used during the treatment based on the curcumin concentration. The photoinactivation of bacteria was conducted by irradiating the 1 µmol/L curcumin-LAE solution containing cocktails of Escherichia coli and Listeria innocua strains (7 log CFU/mL) for 5 min with UV-A light (λ = 365 nm). The changes in solution turbidity, curcumin stability, and bacterial morphology, viability, and recovery were observed using SEM, TEM, and live/dead cell assays. The study found that LAE enhances the photoinactivation of bacteria by increasing the permeability of cell membranes which could promote the interaction of reactive oxygen species produced by photosensitized curcumin with the cell components. The combination of curcumin and LAE was demonstrated to be more effective in inhibiting bacterial recovery at pH 3.5 for E. coli, while LAE alone was more effective at pH 7.0 for L. innocua.

Meta-Aerogel Electric Trap Enables Instant and Continuable Pathogen Killing in Face Masks

The tremendous menace of the COVID-19 pandemic has underscored the urgency for antipathogen masks to stop the transmission of airborne infectious diseases. Most prevailing antipathogen masks manifest a slower sterilization rate that lags behind the pathogen momentum traversing the masks, thereby engendering an elevated susceptibility to infection. Here we tailor nanofibrous meta-aerogel electric traps, 3D-assembled from self-knotted carbon nanotube networks in an all rigid nanofibrous skeleton. This superior configuration revolves around the creation of numerous "dielectrophoretic-aerodynamic grippers", which are capable of directional manipulation of microbes toward the region of the lethal intensive electric field. Based on this, we present a disinfection unit comprising a pair of aerogel electrodes that demonstrate a rapid killing rate (>99.99% biocidal efficacy within 0.016 s) and long-term durability (12 h of continuous operation). Additionally, a microbutton lithium cell is employed as a power supply to fabricate an antipathogen face mask with this disinfection unit, which exhibits superior pathogen inactivation efficacy compared to commercial masks. This scalable biocidal protective equipment holds great potential for use in emergency medical services.

Structure-Based Design of Dual Bactericidal and Bacteria-Releasing Nanosurfaces

Here, we report synergistic nanostructured surfaces combining bactericidal and bacteria-releasing properties. A polystyrene-block-poly(methyl methacrylate) (PS-block-PMMA) diblock copolymer is used to fabricate vertically oriented cylindrical PS structures ("PS nanopillars") on silicon substrates. The results demonstrate that the PS nanopillars (with a height of about 10 nm, size of about 50 nm, and spacing of about 70 nm) exhibit highly effective bactericidal and bacteria-releasing properties ("dual properties") against Escherichia coli for at least 36 h of immersion in an E. coli solution. Interestingly, the PS nanopillars coated with a thin layer (≈3 nm thick) of titanium oxide (TiO₂) ("TiO₂ nanopillars") show much improved dual properties against E. coli (a Gram-negative bacterium) compared to the PS nanopillars. Moreover, the dual properties emerge against Listeria monocytogenes (a Gram-positive bacterium). To understand the mechanisms underlying the multifaceted property of the nanopillars, coarse-grained molecular dynamics (MD) simulations of a lipid bilayer (as a simplified model for E. coli) in contact with a substrate containing hexagonally packed hydrophilic nanopillars were performed. The MD results demonstrate that when the bacterium-substrate interaction is strong, the lipid heads adsorb onto the nanopillar surfaces, conforming the shape of a lipid bilayer to the structure/curvature of nanopillars and generating high stress concentrations within the membrane (i.e., the driving force for rupture) at the edge of the nanopillars. Membrane rupture begins with the formation of pores between nanopillars (i.e., bactericidal activity) and ultimately leads to the membrane withdrawal from the nanopillar surface (i.e., bacteria-releasing activity). In the case of Gram-positive bacteria, the adhesion area to the pillar surface is limited due to the inherent stiffness of the bacteria, creating higher stress concentrations within a bacterial cell wall. The present study provides insight into the mechanism underlying the "adhesion-mediated" multifaceted property of nanosurfaces, which is crucial for the development of next-generation antibacterial surface coatings for relevant medical applications.