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Antimicrobial Agents: Synthesis and Design

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 20 September 2025 | Viewed by 687

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Special Issue Information

Dear Colleagues,

Multidrug-resistant (MDR) pathogens, often responsible for severe and incurable infections, are a worldwide concern urgently requiring efforts to find new treatment options. Both Gram-negative and Gram-positive MDR bacilli are emerging as clinically relevant superbugs, especially those included in the ESKAPE family, comprehending Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterococci. From years, several of such bacteria have demonstrated a promising sensitivity against natural cationic antimicrobial peptides (AMPs) acting by an extra-genomic mechanism with a low tendency to develop resistance, mainly based on cytoplasmic membrane disruption. On this evidence, more stable and low-cost cationic molecules and macromolecules, mimicking AMPs, are continuously synthesized and tested on various pathogenic bacterial species. Synthetic phosphonium bola-amphiphiles (BAs) molecules bearing two cationic triphenyl phosphonium groups, linked by a C12 hydrophobic chain, have recently revealed potent sterilizing effects against a series of environmental bacteria and very potent antibacterial effects against 50 clinical isolates of both Gram-positive and Gram-negative species with a difficult pattern of resistance, thus disabling the current viable to functioning. These recent achievements open a new area still largely unexplored, concerning the possible use of new antibacterial compounds, achievable by merging the properties of the known quaternary phosphonium and ammonium salts with the colloidal ones of BAs, which enable them to self-assemble nanomicelles in water. In a worrying scenario showing the incessant decline in the number of effective antibiotics and the rising healthcare costs due to increasingly frequent hospitalizations, this Special Issue aims to include articles and reviews on cationic natural and synthetic molecules and macromolecules, including BA and structural strategies to improve their antibacterial activity, selectivity, and carrying capacity, as well as studies investigating molecular mechanisms of action. Furthermore, studies of formulations of the developed agents, characterized by antibacterial activity and low cytotoxicity toward mammalian cells, will be welcome.

Prof. Dr. Silvana Alfei
Guest Editor

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Keywords

  • multi-drug resistant Gram-negative and Gram-positive pathogens
  • clinically relevant superbugs
  • severe and almost untreatable infections
  • immunocompromised individuals
  • synthetic antimicrobial cationic macromolecules
  • synthetic cationic dendrimers, polymers, and copolymers
  • polymerizing strategies
  • quaternary ammonium and phosphonium salts
  • amino-acid modified macromolecules
  • electrostatic interactions and membrane permeabilization
  • membrane disruptors
  • drug delivery systems
  • cationic bola-amphiphiles

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Published Papers (1 paper)

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Research

36 pages, 6758 KB  
Article
Integrative In Silico and Experimental Characterization of Endolysin LysPALS22: Structural Diversity, Ligand Binding Affinity, and Heterologous Expression
by Nida Nawaz, Shiza Nawaz, Athar Hussain, Maryam Anayat, Sai Wen and Fenghuan Wang
Int. J. Mol. Sci. 2025, 26(17), 8579; https://doi.org/10.3390/ijms26178579 - 3 Sep 2025
Viewed by 184
Abstract
Endolysins, phage-derived enzymes capable of lysing bacterial cell walls, hold significant promise as novel antimicrobials against resistant Gram-positive and Gram-negative pathogens. In this study, we undertook an integrative approach combining extensive in silico analyses and experimental validation to characterize the novel endolysin LysPALS22. [...] Read more.
Endolysins, phage-derived enzymes capable of lysing bacterial cell walls, hold significant promise as novel antimicrobials against resistant Gram-positive and Gram-negative pathogens. In this study, we undertook an integrative approach combining extensive in silico analyses and experimental validation to characterize the novel endolysin LysPALS22. Initially, sixteen endolysin sequences were selected based on documented lytic activity and enzymatic diversity, and subjected to multiple sequence alignment and phylogenetic analysis, which revealed highly conserved catalytic and binding domains, particularly localized to the N-terminal region, underscoring their functional importance. Building upon these sequence insights, we generated three-dimensional structural models using Swiss-Model, EBI-EMBL, and AlphaFold Colab, where comparative evaluation via Ramachandran plots and ERRAT scores identified the Swiss-Model prediction as the highest quality structure, featuring over 90% residues in favored conformations and superior atomic interaction profiles. Leveraging this validated model, molecular docking studies were conducted in PyRx with AutoDock Vina, performing blind docking of key peptidoglycan-derived ligands such as N-Acetylmuramic Acid-L-Alanine, which exhibited the strongest binding affinity (−7.3 kcal/mol), with stable hydrogen bonding to catalytic residues ASP46 and TYR61, indicating precise substrate recognition. Visualization of docking poses using Discovery Studio further confirmed critical hydrophobic and polar interactions stabilizing ligand binding. Subsequent molecular dynamics simulations validated the stability of the LysPALS22–NAM-LA complex, showing minimal structural fluctuations, persistent hydrogen bonding, and favorable interaction energies throughout the 100 ns trajectory. Parallel to computational analyses, LysPALS22 was heterologously expressed in Escherichia coli (E. coli) and Pichia pastoris (P. pastoris), where SDS-PAGE and bicinchoninic acid assays validated successful protein production; notably, the P. pastoris-expressed enzyme displayed an increased molecular weight (~45 kDa) consistent with glycosylation, and achieved higher volumetric yields (1.56 ± 0.31 mg/mL) compared to E. coli (1.31 ± 0.16 mg/mL), reflecting advantages of yeast expression for large-scale production. Collectively, these findings provide a robust structural and functional foundation for LysPALS22, highlighting its conserved enzymatic features, specific ligand interactions, and successful recombinant expression, thereby setting the stage for future in vivo antimicrobial efficacy studies and rational engineering efforts aimed at combating multidrug-resistant Gram-negative infections. Full article
(This article belongs to the Special Issue Antimicrobial Agents: Synthesis and Design)
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