Antimicrobial peptides

Antimicrobial and Potent Anti-Biofilm Properties of Rationally Designed α-Helix Antimicrobial Peptides

The antimicrobial resistance (AMR) crisis represents a significant global threat. Unlike traditional antibiotics, antimicrobial peptides offer a promising pathway because of their primary mechanisms. This study aimed to evaluate and rationally design novel AMPs based on tobacco nectar's AMP (Pep 6) to combat antibiotic resistance issues. Substitution and truncation of some amino acids were applied. Four peptides, KF19, KF16, LK16, and LR16, were designed with enhanced net charge hydrophobicity. They were evaluated for their in vitro antibacterial activity. However, only promising AMPs were further evaluated for their hemolytic activity, time-killing kinetics, mode of action, and anti-biofilm properties. The results showed that only KF19 and LR16 have potent activity against Staphylococcus aureus ATCC25923 and resistant isolates with MIC values from 7.81 to 15.62 μg/mL. Hemolysis ratios were 2.38% and 2.24% at 125 μg/mL for KF19 and LR16, respectively. Both peptides were able to kill S. aureus ATCC25923 within 2 h. SEM results showed their ability to target the cell membrane. Both peptides destroyed the S. aureus biofilms significantly at 62.5 and 125 μg/mL (**p < 0.01, ***p < 0.001, ****p < 0.0001). This study supported rational design in developing new antibacterial agents and demonstrated the therapeutic potency of novel peptides that could solve the resistance issues.

Novel circular antimicrobial peptides to combat a critical listed bacterial pathogen multi drug resistant Acinetobacter baumannii

Acinetobacter baumannii, acritical nosocomial pathogen, is one of the leading causes of human mortality, globally. The extraordinary genetic plasticity of A. baumannii leads to a high propensity antimicrobial resistance trait that demands urgent attention for alternative therapeutics. The current study involves synthesis and purification of two synthetic antimicrobial peptides, i.e., Cyclized melittin (CMEL) and its analog CMEL-M1, to investigate their minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and mechanism of action on the ultrastructural alteration using scanning and transmission electron microscopy (SEM/TEM) against the clinical strains of multidrug-resistant A. baumannii. Mass spectrometry and Kaiser test was employed to assess the effect of cyclization and substitution of polar amino acids with basic amino acids, that created cyclic melittin and its analogue replacing threonine with arginine and lysine. By using broth dilution method, CMEL-M1 demonstrated 70 % strains had MIC value of 31.25 μg/mL, while in case of CMEL, only 20 % isolates exhibited MIC value of 31.25 μg/mL which suggested that CMEL-M1 is significantly effective against MDR- A. baumannii. Action mechanism of synthetic peptides using SEM/TEM depicted the altered cellular morphology leading to the disruption of membranes and the impairment of essential A. baumannii cellular functions. Hence, present findings clearly indicate the potential of CMEL and CMEL-M1 as therapeutic agents for the management of MDR- A. baumannii infections.

Insights into the antifungal properties and modes of action of a recombinant hepcidin, rAd-Hep from the shrimp scad, Alepes djedaba (Forsskål, 1775)

Antimicrobial peptides are short, mostly cationic and amphipathic molecules crucial for host defence. Among these, hepcidins are a family of cysteine rich peptides, with HAMP1 hepcidins playing a dual role in iron metabolism and antimicrobial defense. Recently, recombinantly produced Alepes djedaba hepcidin, rAd-Hep was characterized and its antibacterial potential against various pathogens have been discerned. Herein, we investigated the antifungal nature and modes of action of rAd-Hep against some fungal pathogens. The peptide was found to be active against both filamentous fungi and yeasts viz., Aspergillus flavus, Aspergillus sydowii, Fusarium solani, Penicillium citrinum, Candida albicans and Saccharomyces cerevisiae. The peptide acted via membrane permeabilization creating pores of ∼0.7-1.4 nm radii, ROS generation, chromatin condensation and DNA binding. The recombinant hepcidin, rAd-Hep can be considered as a promising candidate for future endeavors in antifungal therapies.

Data-Driven Visualization of the Dynamics of Antimicrobial Peptides in Cell Death

This study explores the current status, research hotspots, and emerging trends in AMP-induced cell death through bibliometric and data-driven visual analysis. The findings aim to provide researchers and clinical professionals with new insights and potential research directions. A total of 1,897 articles and reviews published between 2006 and 2024 were retrieved from the Web of Science Core Collection. Bibliometric and visual analyses were conducted using CiteSpace, VOSviewer, Scimago Graphica, Origin 2022, and WordClouds. The analysis focused on publication trends, contributing institutions, journals, authors, cited references, and keywords. China contributed the largest share of publications (28.15%). The Chinese Academy of Sciences emerged as the most collaborative institution, demonstrating the highest centrality. The author with the highest composite index was Chen, Jyh-Yih (2,985.27). Recent research hotspots have centered on elucidating the mechanisms of AMP-induced cell death and exploring the potential applications of AMPs in cancer therapy. Keywords such as anticancer peptides, mechanism, design, and antibiotic resistance currently dominate the field, reflecting its evolving focus. Research on the application of AMPs in cancer treatment is gaining momentum. The forefront of this field involves modifying and designing AMPs to address antibiotic-resistant bacterial infections and advance cancer therapeutics. However, further investigation is needed to uncover the specific molecular mechanisms underlying AMP-induced cell death, including necrosis, pyroptosis, and ferroptosis.

Prediction of Chemically Modified Antimicrobial Peptides and Their Sub-functional Activities Using Hybrid Features

Antimicrobial peptides (AMPs) demonstrate a broad spectrum of activities against various pathogens, thereby offering a promising strategy to mitigate the urgent challenge of antimicrobial resistance. Recent studies indicate that chemically modified AMPs (cmAMPs), which contain chemically modified amino acids, have the potential to alleviate the adverse effects commonly associated with conventional AMPs. Nevertheless, there remains a notable deficiency in computational methods specifically designed for the analysis and prediction of cmAMPs and their sub-function predictions. In this study, we proposed a two-layer model, termed as iCMAMP, aimed for the identification of cmAMPs and their sub-functional activities. The first layer, referred to as iCMAMP-1L, integrates three categories encompassing seven distinct groups of features, in conjunction with an ensemble method designed at enhancing predictive accuracy for cmAMPs. This ensemble approach effectively extracts relevant insights from a heterogeneous array of features sets while addressing potential dimensionality challenges. On the test dataset, iCMAMP-1L achieved an ACC of 0.934 and an MCC of 0.868, representing improvements of 3.4% and 6.8%, respectively, over AntiMPmod, which is the sole existing method for predicting cmAMPs. A comparative analysis between cmAMPs and their corresponding AMPs revealed that chemical modifications can significantly reduce hemolysis and toxicity associated with AMPs, while the functional characteristics of the peptides are primarily determined by their sequences. The second layer of our model, designated as iCMAMP-2L, employed a multi-label classification approach to predict the sub-functional activities of cmAMPs, with a specific focus on the dipeptide composition-based features. On the test dataset, iCMAMP-2L achieved an Accuracy of 0.390 and an Absolute true of 0.621. The data and Python code used in the iCMAMP model are available at https://github.com/swicher123/iCMAMP/tree/master .

Combatting Pseudomonas aeruginosa with β-Lactam Antibiotics: A Revived Weapon?

Pseudomonas aeruginosa is a significant threat to public health as an aggressive, opportunistic pathogen. The use of β-lactam antibiotics such as penicillins, cephalosporins, monobactams, and carbapenems remains a front-line treatment against P. aeruginosa. However, the widespread use of β-lactams has led to the emergence of β-lactam-resistant isolates that significantly increase the economic burden and risk of mortality in patients. With the declining productivity of the antibiotic discovery pipeline, research has investigated synergistic agents to revive the use of β-lactam antibiotics against β-lactam-resistant P. aeruginosa. In this review, we summarize the mechanism of β-lactam antibiotics and provide an overview of major mechanisms associated with β-lactam resistance in P. aeruginosa. We then describe the background and use of three promising classes of agents that have shown extensive beneficial effects with β-lactam antibiotics against P. aeruginosa, namely β-lactamase inhibitors, bacteriophages, and antimicrobial peptides. The current understanding of the mechanisms of these synergistic agents is discussed. Lastly, we provide an overview of the current barriers impeding antibiotic development, and offer a glimpse into recent advances of artificial intelligence-based discovery that may serve as a new foundation for antimicrobial discovery and treatment.

Serum-Stable, Cationic, α-Helical AMPs to Combat Infections of ESKAPE Pathogens and C. albicans

Expedition in the rate of development of antimicrobial resistance accompanied by the slowdown in the development of new antimicrobials has led to a dire necessity to develop an alternate class of antimicrobial agents. Antimicrobial peptides (AMPs), available in nature, are effective molecules that can combat microbial infections. However, due to several inherent shortcomings such as salt sensitivity of their potency, short systemic half-lives owing to protease and serum degradation, and cytotoxicity, their commercial success is limited. Inspired by α helical AMPs present in nature, here in this work, we have developed two short, cationic, helical AMPs RR-12 and FL-13. Both peptides exhibited high broad-spectrum antimicrobial activity, salt tolerance, prompt bactericidal activity, considerable serum stability, remaining non-cytotoxic and non-hemolytic at relevant microbicidal concentrations. The designed AMPs were membranolytic toward the microbial strains, though there were subtle differences in the mechanism owing to the variation in the composition of the cell membranes in different microbes. Rigorous experimental techniques and molecular dynamics (MD) simulations were performed to understand the structure, activity, and their mechanisms in detail. Positive charge, balanced hydrophobicity-hydrophilicity, and helical conformation were the different attributes that led to the development of the superior performance of the AMPs, making them valuable additions to the repertoire of therapeutically promising antimicrobials.

Novel hepcidin genes in gilthead seabream: Implications for immune response and iron metabolism

Antimicrobial peptides (AMPs) are highly conserved small molecules present in various organisms, including fish. In gilthead seabream (Sparus aurata), one hamp1 and 15 hamp2 genes have been identified. This study aimed to characterize two novel hamp2 genes, hamp2.0 and hamp2.15, located on chromosome 17 of the gilthead seabream genome. Evolutionary analysis revealed that orthologs of both genes first appeared in the Clupeocephala clade 229 million years ago. In silico analysis predicted that the mature peptides, Hamp2α and Hamp2Ω, possess antimicrobial properties. Both peptides exhibited bactericidal activity against Vibrio harveyi, with Hamp2α showing concentration-dependent inhibition and Hamp2Ω demonstrating time-dependent inhibition. Neither peptide displayed cytotoxicity against SAF-1 cells; instead, they promoted cell proliferation. Basal expression of both genes was observed in all tissues analyzed, with the highest levels in liver and gonad. In head kidney leucocytes (HKLs), expression of both genes increased upon stimulation with lypopolysaccharide, poly I:C, nodavirus, or V. anguillarum. In vivo, hamp2.0 expression significantly increased in various tissues of V. harveyi-infected fish, while hamp2.15 expression increased in liver, spleen, head kidney, skin, and brain. In nodavirus-infected fish, hamp2.15 expression decreased in head kidney and brain. Finally, both genes showed significantly increased expression in head kidney and liver 72 h post-iron dextran injection. These findings suggest that the two novel hamp2 genes in gilthead seabream play a role in the immune response to bacterial and viral infections and may be involved in iron metabolism regulation.

Design, Synthesis, and Biological Evaluation of New Analogs of Aurein 1.2 Containing Non-Proteinogenic Amino Acids

Extensive use of classical antibiotics has led to the growing emergence of many resistant strains of pathogenic bacteria. To combat this challenge, researchers have turned to the antimicrobial peptides (AMPs). Aurein 1.2 (GLFDIIKKIAESF-NH2) was demonstrated to have broad spectrum bi-functionality against bacterial and cancer cells. The Solid Phase Peptide Synthesis (Fmoc-strategy) was used for the synthesis of new analogs of aurein 1.2. The purity of all compounds was monitored by HPLC, and their structures were proven using mass spectrometry. Cytotoxicity and antiproliferative effects were studied using 3T3 NRU and MTT tests, respectively. The antibacterial activity was estimated against Gram-positive and Gram-negative bacteria using broth microdilution method in concentrations from 0 to 320 µg/mL to determine the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC). The antiproliferative activity test shows that the peptide analog EH [Orn]8 has the highest activity (IC50 = 44 ± 38 μM) for the three cell lines studied (MCF-12F, MCF-7, and MDA-MB-231). The same compound exhibited good antimicrobial activity. The obtained results reveal that replacement of Lys with non-proteinogenic amino acids can increase both the potency and activity spectra of natural template peptides, making them suitable candidates for new drug development.

Amphipathic Antimicrobial Peptides Illuminate a Reciprocal Relationship Between Self-assembly and Cytolytic Activity

Amphipathic character, encoded within the polar sequence patterns of antimicrobial peptides, is a critical structural feature that influences membrane disruptive behavior. Similarly, polar sequence patterns induce self-assembly of amphipathic peptides, which results in the formation of ordered supramolecular structures. The relationship between self-assembly and membrane activity remains an open question of relevance for the development of effective antimicrobial peptides. Here, we report the structural investigation of a class of lytic peptides that self-assemble into filamentous nanomaterials. CryoEM analysis was employed to determine the structure of one of the filaments, which revealed that the peptides are self-assembled into a bilayer nanotube, in which the interaction between layers of amphipathic α-helices was mediated through hydrophobic interactions. The relative stability of the filament peptide assemblies depended on the influence of sequence modifications on the helical conformation. Antimicrobial assays indicated that cytolytic activity was associated with dynamic disassociation of the filamentous assemblies under the assay conditions. Structural modifications of the peptides that stabilized the filaments abrogated lytic activity. These results illuminate a reciprocal relationship between self-assembly and antimicrobial activity in this class of amphipathic peptides and that reversible assembly was critical for the observation of biological activity.

Polymeric microneedle advancements in macromolecule drug delivery: current trends, challenges, and future perspectives

Microneedles (MNs) offer a transformative solution for delivering macromolecules, including proteins, RNA, and peptides. These are critical in treating complex diseases but face significant challenges such as immunogenicity, poor stability, high molecular weight, and delivery efficiency. Unlike conventional methods, MNs efficiently bypass biological barriers like the stratum corneum, enabling precise and minimally invasive transdermal drug delivery. This review explores various MN types such as solid, coated, hollow, hydrogel-forming, and dissolving and their therapeutic applications in cancer immunotherapy, diabetes management, and osteoporosis treatment. For instance, dissolving MNs have been employed for transdermal insulin delivery, enhancing patient compliance and therapeutic outcomes. Similarly, hydrogel MNs have shown promise in sustained drug release for immunotherapy applications. By addressing cost and scalability issues, polymeric MNs demonstrate significant potential for clinical translation, paving the way for innovations in macromolecule delivery, diagnostics, and personalised medicine. This review underscores the pivotal role of MNs in redefining drug delivery systems, offering improved efficacy, patient comfort, and accessibility.

Gene expression and characterization of an antimicrobial peptide from Medicago sativa "Sazova" cultivar

In recent years, the discovery of new antimicrobial agents has become necessary because of the increase in antibiotic resistance, the development of herbicides and fungicides resistance. Among the antimicrobial agents, antimicrobial peptides (AMPs) stand out due to their stable structure. In this study, the aim was to identify a thermostable AMP from the seeds of M. sativa "Sazova" cultivar and to analyze gene expression during germination. Antimicrobial tests were performed for the seed peptides after heat treatment (85 °C for 10 min), revealing antimicrobial effects against S. aureus, E. coli, and C. albicans. Subsequently, the peptide band corresponding to the inhibition zone was identified as M. sativa Defensin 2.1 (MsDef2.1, MW: 5.2048 kDa). The gene expression analysis of MsDef2.1 in Sazova cultivar showed that the gene was expressed different plant organs, and the expression was decreased over time. As a result of the gene analysis of two cultivars (Sazova and LegenDairy) it was found that there are 5 base differences in the coding sequence and 3 amino acid differences between the sequences of MsDef2.1 isoforms from the LegenDairy and Sazova cultivars. The physiochemical properties, secondary, and tertiary structure of the Sazova Defensin 2.1 were predicted by using bioinformatic tools. Due to the amino acid substitutions in γ-core structures, the antimicrobial activity of the isoforms is expected to differ from each other. These findings demonstrated that the defensin MsDef2.1 can differ in M. sativa cultivars in respect of the gene and amino acid sequences and has a potential for future applications.

Molecular interaction assays in silico of crotapotin from Crotalus durissus terrificus against the molecular target trypanothione reductase from Leishmania braziliensis

Background

Leishmaniasis is a neglected disease that mainly affects impoverished populations and receives limited attention from governments and research institutions. Current treatments are based on antimonial therapies, which present high toxicity and cause significant side effects, such as cardiotoxicity and hepatotoxicity. This study proposes using crotapotin, isolated from Crotalus durissus terrificus venom, as a potential inhibitor of the enzyme trypanothione reductase from Leishmania braziliensis (LbTR).

Methods

In silico assays were conducted to evaluate the interaction of crotapotin with LbTR using molecular docking and molecular dynamics techniques. Recombinant LbTR was expressed in E. coli, and its enzymatic activity was confirmed. The inhibitory action of crotapotin on LbTR was then tested in enzymatic assays.

Results

The stability of these interactions was confirmed over 200 ns molecular dynamics simulations, with a clustering analysis using the GROMACS method revealing a total of 12 distinct clusters. The five most representative clusters showed low RMSD values, indicating high structural stability of the LbTR-crotapotin complex. In particular, cluster 1, with 3,398 frames and an average RMSD of 0.189 nm from the centroid, suggests a dominant stable conformation of the complex. Additional clusters maintained average RMSD values between 0.173 nm and 0.193 nm, further reinforcing the robustness of the complex under physiological conditions. Recombinant LbTR expression was successful, yielding 4.8 mg/L with high purity, as verified by SDS-PAGE. In the enzymatic assays, crotapotin partially inhibited LbTR activity, with an IC50 of 223.4 μM.

Conclusion

The in silico findings suggest a stable and structured interaction between crotapotin and LbTR, with low structural fluctuation, although the inhibition observed in in vitro assays was moderate. These results indicate the potential of crotapotin as a promising basis for developing specific LbTR inhibitors, contributing to the bioprospecting of new antiparasitic agents.

Jelleine-I Membrane Interaction-related Biological Properties and Antimicrobial Activity against MDR, XDR, and PDR-Acinetobacter baumannii Clinical Isolates

Emerging bacterial infections pose a serious threat to human health. Acinetobacter baumannii is a particular concern due to its antimicrobial resistance phenotypes, especially to carbapenems. In this context, antimicrobial peptides appear as a promising class. Jelleine-I is a peptide identified from the royal jelly from Apis mellifera bee, which has demonstrated significant antibacterial effects against various microorganisms. This study aimed to characterize the activity of jelleine-I against clinical isolates of A. baumannii resistant to carbapenems (CRAB) and with different resistance phenotypes, in addition to investigating the peptide-membrane interaction in biomimetic media. Microbiological assays with jelleine-I performed against A. baumannii with MIC values of 8-16 μM were observed. Biophysical studies on the bacterial mimetic membrane show a possible disruption of the organization of the phospholipid bilayer. The significant affinity promoted by entropic and enthalpic contributions suggests that the main antimicrobial action occurs on the bacterial membrane. In addition, the negligible hemolytic activity and toxicity against VERO and HaCaT cells reveal jelleine-I as a potential novel antimicrobial agent, especially against microorganisms that exhibit high and diverse antimicrobial resistance, such as A. baumannii.

Antimicrobial peptide-fucoidan nanoplexes: A novel multifunctional biomimetic nanocarrier for enhanced vancomycin delivery against bacterial infections and sepsis

Sepsis, a critical medical emergency, continues to pose a substantial worldwide healthcare challenge that necessitates innovative approaches for enhanced treatment. Hence, this study aimed to develop multifunctional biomimetic vancomycin (VCM)-loaded nanoplexes (VCM-FU-PEP-NPs) utilizing a novel antimicrobial peptide (CC-19 peptide) and Fucoidan (FU) to target the Toll-like receptor (TLR) inflammatory pathway and augment the antibacterial efficacy against bacterial sepsis. The CC-19 peptide (CRPRKWIKIKFRCKSLKFC) was designed utilizing computer-aided drug design tools and subsequently synthesized. The biomimetic properties of FU were assessed through in silico and in vitro binding studies, demonstrating a strong affinity for TLR2. The formulated VCM-FU-PEP-NPs demonstrated appropriate physicochemical characteristics, physical stability, and biocompatibility. Moreover, VCM-FU-PEP-NPs exhibited a 2-fold increase in antibacterial efficacy against sensitive Staphylococcus aureus, superior and sustained antibacterial activity against MRSA over 72 h, 5-fold improvement in MRSA biofilm eradication, faster bacterial-killing kinetics, and significantly greater disruption of MRSA membranes, in comparison to bare VCM. Furthermore, VCM-FU-PEP-NPs exhibited excellent DPPH radical scavenging capacity and significant anti-inflammatory efficacy in cells exposed to bacterial toxins. Accordingly, VCM-FU-PEP-NPs demonstrate promise as a potential innovative, multifunctional antibiotic nanocarrier for advancing the treatment of sepsis.

Inhibitory Effect of Antimicrobial Peptides Bac7(17), PAsmr5-17 and PAβN on Bacterial Growth and Biofilm Formation of Multidrug-Resistant Acinetobacter baumannii

Acinetobacter (A.) baumannii is a major nosocomial pathogen in human and veterinary medicine. The emergence of certain international clones (ICs), often with multidrug-resistant (MDR) phenotypes and biofilm formation (BF), facilitates its spread in clinical environments. The global rise in antimicrobial resistance demands alternative treatment strategies, such as antimicrobial peptides (AMPs). In this study, 45 human and companion animal MDR-A. baumannii isolates, belonging to the globally spread IC1, IC2 and IC7, were tested for antimicrobial resistance and biofilm-associated genes (BAGs) and their capacity for BF. Of these, 13 were used to test the inhibitory effect of AMPs on bacterial growth (BG) and BF through the application of a crystal violet assay. The two novel AMP variants Bac7(17) (target cell inactivation) and Pasmr5-17 (efflux pump inhibition) and the well-known AMP phenylalanine-arginine-β-naphthylamide (PAβN) were tested at concentrations of 1.95 to 1000 µg/mL. Based on whole-genome sequence data, identical patterns of BAGs were detected within the same IC. AMPs inhibited BG and BF in a dose-dependent manner. Bac7(17) and PAsmr5-17 were highly effective against BG, with growth inhibition (GI) of >99% (62.5 and 125 µg/mL, respectively). PAβN achieved only 95.7% GI at 1000 µg/mL. Similar results were obtained for BF. Differences between the ICs were found for both GI and BF when influenced by AMPs. PAsmr5-17 had hardly any inhibitory effect on the BF of IC1 isolates, but for IC2 and IC7 isolates, 31.25 µg/mL was sufficient. Our data show that the susceptibility of animal MDR-A. baumannii to AMPs most likely resembles that of human isolates, depending on their assignment to a particular IC. Even low concentrations of AMPs had a significant effect on BG. Therefore, AMPs represent a promising alternative in the treatment of MDR-A. baumannii, either as the sole therapy or in combination with antibiotics.

Identification of antimicrobial peptides from the Ambystoma mexicanum displaying antibacterial and antitumor activity

Antibiotic resistance is a significant healthcare concern. Therefore, identifying target molecules that can serve as antibiotic substitutes is crucial. Among the promising candidates are antimicrobial peptides (AMPs). AMPs are defense mechanisms of the innate immune system which exist in almost all living organisms. Research on the AMPs of some amphibians has shown that, in addition to their antimicrobial effectiveness, AMPs also exhibit anti-inflammatory and anti-carcinogenic properties. In this study, we identify and characterize AMPs deriving from the skin mucus of the axolotl (Ambystoma mexicanum). Upon activity spectrum evaluation of the AMPs, we synthesized and ranked 22 AMPs according to antimicrobial efficacy by means of a prediction tool. To assess the AMPs' potential as antibacterial and anticarcinogenic compounds, we performed a minimum inhibitory concentration (MIC) assay for efficacy against methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA), and an apoptosis assay on T-47D mammary carcinoma cells. We identified four AMPs that showed significant inhibition of MRSA, of which three also demonstrated anticarcinogenic activity. Gene expression analysis was performed on AMP-stimulated carcinoma cells using a breast cancer-specific RT-PCR array. In cells stimulated with the AMPs, gene expression analysis showed upregulation of tumor suppressor genes and downregulation of oncogenes. Overall, our work demonstrates the antimicrobial and anticarcinogenic activity of axolotl-derived AMPs. The results of this work serve as a basis to further investigate the mode of action and potential use of axolotl AMPs as therapeutic anticancer or antibiotic agents.

Harnessing bacterial antimicrobial peptides: a comprehensive review on properties, mechanisms, applications, and challenges in combating antimicrobial resistance

Antimicrobial resistance (AMR) is a significant global health concern due to the persistence of pathogens and the emergence of resistance in bacterial infections. Bacterial-derived antimicrobial peptides (BAMPs) have emerged as a promising strategy to combat these challenges. Known for their diversity and multifaceted nature, BAMPs are notable bioactive agents that exhibit potent antimicrobial activities against various pathogens. This review explores the intricate properties and underlying mechanisms of BAMPs, emphasizing their diverse applications in addressing AMR. Additionally, the review investigates the mechanisms, analyses the challenges in utilizing BAMPs effectively, and examines their potential applications and associated deployment challenges providing comprehensive insights into how BAMPs can be harnessed to combat AMR across different domains. The significance of this review lies in highlighting the potential of BAMPs as transformative agents in combating AMR, offering sustainable and eco-friendly solutions to this pressing global health challenge.

Design of Natterins-based peptides improves antimicrobial and antiviral activities

The biochemical analysis of animal venoms has been intensifying over the years, enabling the prediction of new molecules derived from toxins, harnessing the therapeutic potential of these molecules. From the venom of the fish Thalassophryne nattereri, using in silico methods for predicting antimicrobial and cell-penetrating peptides, two peptides from Natterins with promising characteristics were synthesized and subjected to in vitro and in vivo analysis. The peptides were subjected to stability tests and antimicrobial assays, cytotoxicity in murine fibroblast cells, antiviral assays against the Chikungunya virus, and the toxicity on G. mellonella was also evaluated. The findings underscore the peptides' robust stability under varying temperatures and pH conditions and resistance to proteolytic degradation. The peptides demonstrated significant antimicrobial efficacy, minimal cytotoxicity, and low hemolytic activity. Although their antiviral efficacy was limited, they showed potential at specific stages of viral replication. The in vivo toxicity tests indicated a favorable safety profile. These findings suggest that this approach can aid in the development of antimicrobial agents, offering a faster and personalized method to combat microbial infections, and represent a promising discovery in venom biotechnology research.

Spatiotemporal Characteristics Determining the Multifaceted Nature of Reactive Oxygen, Nitrogen, and Sulfur Species in Relation to Proton Homeostasis

Significance: Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) act as signaling molecules, regulating gene expression, enzyme activity, and physiological responses. However, excessive amounts of these molecular species can lead to deleterious effects, causing cellular damage and death. This dual nature of ROS, RNS, and RSS presents an intriguing conundrum that calls for a new paradigm. Recent Advances: Recent advancements in the study of photosynthesis have offered significant insights at the molecular level and with high temporal resolution into how the photosystem II oxygen-evolving complex manages to prevent harmful ROS production during the water-splitting process. These findings suggest that a dynamic spatiotemporal arrangement of redox reactions, coupled with strict regulation of proton transfer, is crucial for minimizing unnecessary ROS formation. Critical Issues: To better understand the multifaceted nature of these reactive molecular species in biology, it is worth considering a more holistic view that combines ecological and evolutionary perspectives on ROS, RNS, and RSS. By integrating spatiotemporal perspectives into global, cellular, and biochemical events, we discuss local pH or proton availability as a critical determinant associated with the generation and action of ROS, RNS, and RSS in biological systems. Future Directions: The concept of localized proton availability will not only help explain the multifaceted nature of these ubiquitous simple molecules in diverse systems but also provide a basis for new therapeutic strategies to manage and manipulate these reactive species in neural disorders, pathogenic diseases, and antiaging efforts.

Antimicrobial Activity of the Peptide C14R Against Ab Initio Growing and Preformed Biofilms of Candida albicans, Candida parapsilosis and Candidozyma auris

Biofilms are the predominant lifeforms of microorganisms, contributing to over 80% of infections, including those caused by Candida species like C. albicans, C. parapsilosis and Candidozyma auris. These species form biofilms on medical devices, making infections challenging to treat, especially with the rise in drug-resistant strains. Candida infections, particularly hospital-acquired ones, are a significant health threat due to their resistance to antifungals and the risk of developing systemic infections (i.e., sepsis). We have previously shown that C14R reduces the viability of C. albicans and C. auris, but not of C. parapsilosis. Here, we show that C14R not only inhibits viability by pore formation, shown in a resazurin reduction assay, and in a C. parapsilosis and fluorescence-based permeabilization assay, but it also halts biofilm maturation and significantly reduces the biomass of preformed biofilms by over 70%. These findings suggest C14R could be an effective option for treating severe fungal infections, offering a potential new treatment approach for biofilm-related diseases. Further research is needed to fully understand its biofilm dispersal potential and to optimize its use for future applications as an antifungal in clinical settings.

Antimicrobial Polymer via ROMP of a Bioderived Tricyclic Oxanorbornene Lactam Derivative

The rapid emergence of multidrug-resistant (MDR) bacteria represents a critical global health threat, underscoring the urgent need for alternative antimicrobial strategies beyond conventional antibiotics. In this study, we report the synthesis of novel biobased antimicrobial polymers bearing quaternary ammonium salts, derived from sustainable feedstocks, maleic anhydride, dimethylaminobenzaldehyde, and furfurylamine. The functional tricyclic oxanorbornene lactam monomer is polymerized via ring opening metathesis polymerization, yielding well-defined polymers with controlled molar masses and low dispersity. Structural characterization is performed using 1D and 2D nuclear magnetic resonance (NMR) spectroscopy, and the polymerization kinetics is monitored by online 1H NMR spectroscopy. The quaternized biobased polymers demonstrate potent broad-spectrum antimicrobial activity against three clinically isolated MDR bacterial strains. They exhibit minimum inhibitory concentrations (MICs) that are significantly lower than those of several conventional antibiotics while also showing low hemolytic activity toward mammalian cells. This study highlights the potential of bioderived ROMP polymers as promising, sustainable antimicrobial polymers for combating the growing threat of antimicrobial resistance.

In vitro potentiation of tetracyclines in Pseudomonas aeruginosa by RW01, a new cyclic peptide

The pipeline for new drugs against multidrug-resistant Pseudomonas aeruginosa remains limited, highlighting the urgent need for innovative treatments. New strategies, such as membrane-targeting molecules acting as adjuvants, aim to enhance antibiotic effectiveness and combat resistance. RW01, a cyclic peptide with low antimicrobial activity, was selected as an adjuvant to enhance drug efficacy through membrane permeabilization. RW01's activity was evaluated via antimicrobial susceptibility testing in combination with existing antibiotics on 10 P. aeruginosa strains and analog synthesis. Synergy was assessed using checkerboard assays, and one-step mutants were generated to identify altered pathways through whole-genome sequencing and variant analysis. Permeabilizing activity was studied using flow cytometry and real-time fluorescence measurement. In vivo toxicity was assessed in female C57BL/6J mice, and possible interaction with mouse serum was also evaluated. Susceptibility testing revealed specific synergy with tetracyclines, with up to a 16-fold reduction in minimum inhibitory concentrations. Sequencing revealed that resistance to the RW01-minocycline combination involved mutations in the pmrB gene, affecting outer membrane lipopolysaccharide composition. This was further confirmed by the identification of cross-resistance to colistin in these mutants. RW01 reduced the mutant prevention concentration of minocycline from 64 to 8 mg/L. RW01 was demonstrated to enhance membrane permeabilization and therefore minocycline uptake with statistical significance. Synthetic derivatives of RW01 showed a complete loss of activity, highlighting the importance of RW01's D-proline(NH2) residue. No acute or cumulative in vivo toxicity was observed in mice. These findings suggest that RW01 could revitalize obsolete antimicrobials and potentially expand therapeutic options against multidrug-resistant P. aeruginosa.

Secretory Production of Heterologous Antimicrobial Peptides in Corynebacterium glutamicum

Antimicrobial peptides (AMPs) are host defense peptides that act against a broad spectrum of microorganisms. AMPs are of high interest as medicinal products, antimicrobial coatings, and for controlling biofilm formation. Applications and research of many AMPs are still hampered by insufficient titers and lack of production platforms that can tolerate high titers of AMPs. Corynebacterium glutamicum is an excellent microbial host for protein secretion and has been barely explored as a host for AMP production. Here, we report the successful production and secretion of two AMPs (amounts of up to 130 mg/L for liquid chromatography peak I [LCI] and 54 mg/L for Psoriasin) by C. glutamicum with low amounts of secreted byproducts.

Molecular Dynamics Simulations of Structurally Nanoengineered Antimicrobial Peptide Polymers Interacting with Bacterial Cell Membranes

Multidrug resistance (MDR) to conventional antibiotics is one of the most urgent global health threats, necessitating the development of effective and biocompatible antimicrobial agents that are less inclined to provoke resistance. Structurally nanoengineered antimicrobial peptide polymers (SNAPPs) are a novel and promising class of such alternatives. These star-shaped polymers are made of a dendritic core with multiple arms made of copeptides with varying amino acid sequences. Through a comprehensive set of in vivo experiments, we previously showed that SNAPPs with arms made of random blocks of lysine (K) and valine (V) residues exhibit sub-μM efficacy against Gram-negative and Gram-positive bacteria tested. Cryo-TEM images suggested pore formation by a SNAPP with random block copeptide arms as one of their modes of actions. However, the molecular mechanisms responsible for this mode of action of SNAPPs are not fully understood. To address this gap, we employed an atomistic molecular dynamics simulation technique to investigate the influence of three different sequences of amino acids, namely (1) alt-block KKV, (2) ran-block, and (3) diblock motifs on the secondary structure of their arms and SNAPP's overall configuration as well as their interactions with lipid bilayer. We, for the first time, identified a step-by-step mechanism through which alt-block and random SNAPPs interact with lipid bilayer and lead to "pore formation", hence, cell death. These insights provide a strong foundation for further optimization of the chemical structure of SNAPPs for maximum performance against MDR bacteria, therefore offering a promising avenue for addressing antibiotic resistance and the development of effective antibacterial agents.

Antimicrobial Peptides Against Arboviruses: Mechanisms, Challenges, and Future Directions

This review delves into the potential of antimicrobial peptides (AMPs) as promising candidates for combating arboviruses, focusing on their mechanisms of antiviral activity, challenges, and future directions. AMPs have shown promise in preventing arbovirus attachment to host cells, inducing interferon production, and targeting multiple viral stages, illustrating their multifaceted impact on arbovirus infections. Structural elucidation of AMP-viral complexes is explored to deepen the understanding of molecular determinants governing viral neutralization, paving the way for structure-guided design. Furthermore, this review highlights the potential of AMP-based combination therapies to create synergistic effects that enhance overall treatment outcomes while minimizing the likelihood of resistance development. Challenges such as susceptibility to proteases, toxicity, and scalable production are discussed alongside strategies to address these limitations. Additionally, the expanding applications of AMPs as vaccine adjuvants and antiviral delivery systems are emphasized, underscoring their versatility beyond direct antiviral functions.

Heterologous Production of Antimicrobial Peptides in Yeast Allows for Massive Assessment of the Activity of DNA-Encoded Antimicrobials In Situ

Antibiotic resistance threatens global healthcare. In clinical practice, conventional antibiotics are becoming gradually less effective. Moreover, the introduction of new antimicrobial agents into clinical practice leads to the emergence of resistant pathogenic strains within just a few years. Hence, the development of platforms for massive creation and screening of new antimicrobial agents is of particular importance. Massive parallel screening will greatly reduce the time required to identify the most promising drug candidates. Meanwhile, DNA-encoded antimicrobial agents offer unique opportunities for the high-throughput development of new antibiotics. Here, the yeast Pichia pastoris was engineered to produce a panel of antimicrobial peptides (AMPs), followed by high-throughput screening of AMP producers that inhibit bacterial growth in situ. Yeast clones producing thanatin and protegrin-1 exhibited the highest level of antimicrobial activity among the panel of AMPs under investigation. The production level of recombinant thanatin was significantly higher than that of protegrin-1, which correlates with its low toxicity. The designed technique of massive assessment of the activity of DNA-encoded antimicrobial agents enables the identification of drug candidates with an increased therapeutic index. Further development of methods for a rational design of artificial diversity in AMPs, followed by deep functional profiling of antimicrobial activity, will yield new AMPs with improved therapeutic characteristics.

sAMP-VGG16: Force-field assisted image-based deep neural network prediction model for short antimicrobial peptides

During the last three decades, antimicrobial peptides (AMPs) have emerged as a promising therapeutic alternative to antibiotics. The approaches for designing AMPs span from experimental trial-and-error methods to synthetic hybrid peptide libraries. To overcome the exceedingly expensive and time-consuming process of designing effective AMPs, many computational and machine-learning tools for AMP prediction have been recently developed. In general, to encode the peptide sequences, featurization relies on approaches based on (a) amino acid (AA) composition, (b) physicochemical properties, (c) sequence similarity, and (d) structural properties. In this work, we present an image-based deep neural network model to predict AMPs, where we are using feature encoding based on Drude polarizable force-field atom types, which can capture the peptide properties more efficiently compared to conventional feature vectors. The proposed prediction model identifies short AMPs (≤30 AA) with promising accuracy and efficiency and can be used as a next-generation screening method for predicting new AMPs. The source code is publicly available at the Figshare server sAMP-VGG16.

Cathelicidins in farm animals: Structural diversity, mechanisms of action, and therapeutic potential in the face of antimicrobial resistance

Cathelicidins are a diverse family of antimicrobial peptides found across many vertebrate species, playing a pivotal role in the innate immune system. These peptides exhibit a variety of structural motifs, including α-helices, β-hairpins, and random coils, contributing to their broad-spectrum antimicrobial activity. The structural diversity of cathelicidins allows them to interact with a wide range of microbial targets, thereby enhancing their antimicrobial efficacy. Distinct species produce specific cathelicidins, each adapted to meet their unique immune requirements. Cathelicidins primarily function by disrupting microbial membranes, leading to cell lysis. Beyond their direct antimicrobial action, they possess immunomodulatory properties that bolster host defense mechanisms. These properties include promoting chemotaxis, enhancing phagocytosis, and inducing cytokine production, thereby modulating the host immune response. The therapeutic potential of cathelicidins is significant, especially in light of the growing challenge of antimicrobial resistance (AMR). As conventional antibiotics lose efficacy, cathelicidins emerge as promising alternatives due to their unique mechanisms of action and reduced likelihood of inducing resistance. Recent research underscores their potential in treating infections, inflammatory diseases, and even cancer. Advances in synthetic biology offer promising prospects for effective cathelicidin-based therapies in the future. This review summarizes the diversity, modes of action, and clinical prospects of cathelicidins specific to farm animals.

AI Methods for Antimicrobial Peptides: Progress and Challenges

Antimicrobial peptides (AMPs) are promising candidates to combat multidrug-resistant pathogens. However, the high cost of extensive wet-lab screening has made AI methods for identifying and designing AMPs increasingly important, with machine learning (ML) techniques playing a crucial role. AI approaches have recently revolutionised this field by accelerating the discovery of new peptides with anti-infective activity, particularly in preclinical mouse models. Initially, classical ML approaches dominated the field, but recently there has been a shift towards deep learning (DL) models. Despite significant contributions, existing reviews have not thoroughly explored the potential of large language models (LLMs), graph neural networks (GNNs) and structure-guided AMP discovery and design. This review aims to fill that gap by providing a comprehensive overview of the latest advancements, challenges and opportunities in using AI methods, with a particular emphasis on LLMs, GNNs and structure-guided design. We discuss the limitations of current approaches and highlight the most relevant topics to address in the coming years for AMP discovery and design.

In vitro Antileishmanial Activity and In silico Molecular Modeling Studies of Novel Analogs of Dermaseptins S4 and B2

BACKGROUND

Leishmaniasis is responsible for approximately 65,000 annual deaths. Various Leishmania species are the predominant cause of visceral, cutaneous, or mucocutaneous leishmaniasis, affecting millions worldwide. The lack of a vaccine, emergence of resistance, and undesirable side effects caused by antileishmanial medications have prompted researchers to look for novel therapeutic approaches to treat this disease. Antimicrobial peptides (AMPs) offer an alternative for promoting the discovery of new drugs.

METHODS

In this study, we detail the synthesis process and investigate the antileishmanial activity against Leishmania (Viannia) braziliensis for peptides belonging to the dermaseptin (DS) family and their synthetic analogs. The MTT assay was performed to investigate the cytotoxicity of these peptides on the murine macrophage cell line RAW 264.7. Subsequently, we performed molecular modeling analysis to explore the structure-function correlation of the derivatives interacting with the parasitic membrane.

RESULTS

All examined derivatives displayed concentration-dependent antileishmanial effect at low concentrations. Their effectiveness varied according to the peptide's proprieties. Notably, peptides with higher levels of charge demonstrated the most pronounced activities. Cytotoxicity assays showed that all the tested peptides were not cytotoxic compared to the tested conventional drug. The structure-function relationships demonstrated that the charged N-terminus could be responsible for the antileishmanial effect observed on promastigotes.

CONCLUSION

Collectively, these results propose that dermaseptins (DS) might offer potential as promising candidates for the development of effective antileishmanial therapies.

In silico-driven identification and experimental confirmation of antifungal proteins (AFPs) against Candidaalbicans

Mycoses infect millions of people annually across the world. The most common mycosis agent, Candida albicans is responsible for a great deal of illness and death. C. albicans infection is becoming more widespread and the current antifungals polyenes, triazoles, and echinocandins are less efficient against it. Investigating antifungal peptides (AFPs) as therapeutic is gaining momentum. Therefore, we used MALDI-TOF/MS analysis to identify AFPs and protein-protein docking to analyze their interactions with the C. albicans target protein. Some microorganisms with strong antifungal action against C. albicans were selected for the isolation of AFPs. Using MALDI-TOF/MS, we identified 3 AFPs Chitin binding protein (ACW83017.1; Bacillus licheniformis), the bifunctional protein GlmU (BBQ13478.1; Stenotrophomonas maltophilia), and zinc metalloproteinase aureolysin (BBA25172.1; Staphylococcus aureus). These AFPs showed robust interactions with C. albicans target protein Sap5. We deciphered some important residues in identified APFs and highlighted interaction with Sap5 through hydrogen bonds, protein-protein interactions, and salt bridges using protein-protein docking and MD simulations. The three discovered AFPs-Sap5 complexes exhibit different levels of stability, as seen by the RMSD analysis and interaction patterns. Among protein-protein interactions, the remarkable stability of the BBQ25172.1-2QZX complex highlights the role of salt bridges and hydrogen bonds. Identified AFPs could be further studied for developing successful antifungal candidates and peptide-based new antifungal therapeutic strategies as fresh insights into addressing antifungal resistance also.

Roles of NET Peptides With Known Antimicrobial Activity and Toxicity in Immune Response

Antimicrobial peptides (AMPs) are crucial components of the innate immune system in all living organisms, playing a vital role in the body's defense against diseases and infections. The immune system's primary functions include preventing disease-causing agents from entering the body and eliminating them without causing harm. These peptides exhibit broad-spectrum activity against bacteria, viruses, fungi, parasites, and cancer cells. They are secreted by innate and epithelial cells and contribute to host defense by inducing cellular activities such as cell migration, proliferation, differentiation, cytokine production, angiogenesis, and wound healing. In response to the growing challenge of bacterial resistance to antimicrobial agents, alternative drugs and new antibacterial molecules are being explored. In a previous study, NET AMPs were synthesized and their antimicrobial effects were determined. The current study extends this work by assessing the effects of these peptides on the immune system through cell culture experiments and ELISA. Specifically, the study investigated how different concentrations of these peptides influence the secretion of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and interferon-γ (IFN-γ) in mouse macrophages. Among the synthesized peptides, NET1 and NET2 demonstrated low cytotoxicity in TIB-71 RAW 264.7 macrophages. These peptides induced an anti-inflammatory response and reduced IL-6 expression in the absence of LPS stimulation, while simultaneously increasing IFN-γ and TNF-α secretion. These findings suggest that NET1 and NET2 peptides possess both anti-inflammatory and pro-inflammatory properties, highlighting their potential role in modulating immune responses.

Accelerating antimicrobial peptide design: Leveraging deep learning for rapid discovery

Antimicrobial peptides (AMPs) are excellent at fighting many different infections. This demonstrates how important it is to make new AMPs that are even better at eliminating infections. The fundamental transformation in a variety of scientific disciplines, which led to the emergence of machine learning techniques, has presented significant opportunities for the development of antimicrobial peptides. Machine learning and deep learning are used to predict antimicrobial peptide efficacy in the study. The main purpose is to overcome traditional experimental method constraints. Gram-negative bacterium Escherichia coli is the model organism in this study. The investigation assesses 1,360 peptide sequences that exhibit anti- E. coli activity. These peptides' minimal inhibitory concentrations have been observed to be correlated with a set of 34 physicochemical characteristics. Two distinct methodologies are implemented. The initial method involves utilizing the pre-computed physicochemical attributes of peptides as the fundamental input data for a machine-learning classification approach. In the second method, these fundamental peptide features are converted into signal images, which are then transmitted to a deep learning neural network. The first and second methods have accuracy of 74% and 92.9%, respectively. The proposed methods were developed to target a single microorganism (gram negative E.coli), however, they offered a framework that could potentially be adapted for other types of antimicrobial, antiviral, and anticancer peptides with further validation. Furthermore, they have the potential to result in significant time and cost reductions, as well as the development of innovative AMP-based treatments. This research contributes to the advancement of deep learning-based AMP drug discovery methodologies by generating potent peptides for drug development and application. This discovery has significant implications for the processing of biological data and the computation of pharmacology.

Antimicrobial Activity of Copolymer Structures from Bio-Based Monomers

The urgent need for new antimicrobial compounds has led scientists to explore antimicrobial peptides (AMPs) and antimicrobial polymers as solutions for multidrug resistance. In this study, we synthesized copolymers with cationic and hydrophobic moieties by free-radical polymerization (FRP) using a chain transfer agent to control molecular weights. The potential of natural products as part of the hydrophobic moiety was evaluated, along with variations in their monomer content (13-25%) and the molecular weight (MW) of the copolymer (5000-20,000 g·mol-1). Hydrophobicity was evaluated using the theoretical Log Poct values and surface areas (SAs). Biological assays included antimicrobial activity against Escherichia coli and Staphylococcus aureus standard strains, hemolytic activity in red blood cells (RBC), and cytotoxicity tests against HEK293T cells. Keys findings indicate that copolymers with tropolone moieties, lower MWs, and an optimal balance between hydrophobic and cationic moieties show a promising basis for future generations of antimicrobials.

OmpH is Involved in the Decrease of Acinetobacter baumannii Biofilm by the Antimicrobial Peptide Cec4

Purpose

The emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) poses great difficulties in clinical treatment, and has been listed by the World Health Organization as a class of pathogens in urgent need of new antibiotic development. In our previous report, the novel antimicrobial peptide Cec4 showed great potential in decreasing the clinical CRAB biofilm, but its mechanism of action is still illusive. Therefore, in order to evaluate the clinical therapeutic potential of Cec4, it is necessary to explore the mechanism of how Cec4 decreases mature biofilms.

Methods

Key genes involved in the removal of CRAB biofilms by Cec4 were analyzed using transcriptomics. Based on the results of the bioinformatics analysis, the CRISPR-Cas9 method was used to construct the deletion strain of the key gene. The pYMAb2 plasmid was used for the complementation strain construction. Finally, the roles of key genes in biofilm removal by Cec4 were determined by crystal violet staining, podocyte staining, laser confocal imaging, and MBC and MBEC50.

Results

Combined with transcriptome analysis, we hypothesized that OmpH is a key gene involved in the removal of CRAB biofilms by Cec4. Deletion of the OmpH gene did not affect A. baumannii growth, but decreased A. baumannii capsule thickness, increasing biofilm production, and made biofilm-state A. baumannii more sensitive to Cec4.

Conclusion

Cec4 decreases biofilms formed by CRAB targeting OmpH. Deletion of the OmpH gene results in an increase in biofilms and greater sensitivity to Cec4, which enhances the removal of A. baumannii biofilms by Cec4.

Anti-Biofilm Performance of Resin Nanopillars Inspired from Cicada Wing Surface for Staphylococcus spp

The increase in infections derived from biofilms from Staphylococcal spp. prompted us to develop novel strategies to inhibit biofilm development. Nanoscale protrusion structures (nanopillars) observed on the wings of dragonflies and cicadas have recently gained notable attention owing to their physical, antimicrobial, and bactericidal properties. Thus, they are not only expected to reduce the damage caused by chemical antimicrobial agents to human health and the environment, but also to serve as a potential countermeasure against the emergence of antimicrobial-resistant bacteria (ARB). In this study, we evaluated the anti-biofilm effects of cyclo-olefin polymer (COP) nanopillars by changing the wettability of surfaces ranging in height from 100 to 500 nm against Staphylococcus spp., such as Staphylococcus aureus NBRC 100910 (MSSA), Staphylococcus aureus JCM 8702 methicillin-resistant S. aureus (MRSA), and Staphylococcus epidermidis ATCC 35984. The results clearly show that the fabricated nanopillar structures exhibited particularly strong biofilm inhibition against MRSA, with inhibition rates ranging from 51.2% to 62.5%. For MSSA, anti-biofilm effects were observed only at nanopillar heights of 100-300 nm, with relatively low hydrophobicity, with inhibition rates ranging from 23.9% to 40.8%. Conversely, no significant anti-biofilm effect was observed for S. epidermidis in any of the nanopillar structures. These findings suggest that the anti-biofilm properties of nanopillars vary among bacteria of the same species. In other words, by adjusting the height of the nanopillars, selective anti-biofilm effects against specific bacterial strains can be achieved.

Exploring the antimicrobial potential of crude peptide extracts from Allium sativum and Allium oschaninii against antibiotic-resistant bacterial strains

CONTEXT

Plant peptides garner attention for their potential antimicrobial properties amid the rising concern over antibiotic-resistant bacteria.

OBJECTIVE

This study investigates the antibacterial potential of crude peptide extracts from 27 Thai plants collected locally.

MATERIALS AND METHODS

Peptide extracts from 34 plant parts, derived from 27 Thai plants, were tested for their antimicrobial efficacy against four highly resistant bacterial strains: Streptococcus aureus MRSA, Pseudomonas aeruginosa, Acinetobacter baumannii, and Escherichia coli. The stability of these peptide extracts was examined at different temperatures, and the synergistic effects of two selected plant peptide extracts were investigated. Additionally, the time-kill kinetics of the individual extracts and their combination were determined against the tested pathogens.

RESULTS

Peptides from Allium sativum L. and Allium oschaninii O. Fedtsch (Amaryllidaceae) were particularly potent, inhibiting bacterial growth with MICs ranging from 1.43 to 86.50 µg/mL. The consistent MICs and MBCs of these extracts across various extraction time points highlight their reliability. Stability tests reveal that these peptides maintain their antimicrobial activity at -20 °C for over a month, emphasizing their durability for future exploration and potential applications in addressing antibiotic resistance. Time-kill assays elucidate the time and concentration-dependent nature of these antimicrobial effects, underscoring their potent initial activity and sustained efficacy over time.

DISCUSSION AND CONCLUSIONS

This study highlights the antimicrobial potential of Allium-derived peptides, endorsing them for combating antibiotic resistance and prompting further investigation into their mechanisms.

A review on the diversity of antimicrobial peptides and genome mining strategies for their prediction

Antibiotic resistance has become one of the most serious threats to human health in recent years. In response to the increasing microbial resistance to the antibiotics currently available, it is imperative to develop new antibiotics or explore new approaches to combat antibiotic resistance. Antimicrobial peptides (AMPs) have shown considerable promise in this regard, as the microbes develop low or no resistance against them. The discovery and development of AMPs still confront numerous obstacles such as finding a target, developing assays, and identifying hits and leads, which are time-consuming processes, making it difficult to reach the market. However, with the advent of genome mining, new antibiotics could be discovered efficiently using tools such as BAGEL, antiSMASH, RODEO, etc., providing hope for better treatment of diseases in the future. Computational methods used in genome mining automatically detect and annotate biosynthetic gene clusters in genomic data, making it a useful tool in natural product discovery. This review aims to shed light on the history, diversity, and mechanisms of action of AMPs and the data on new AMPs identified by traditional as well as genome mining strategies. It further substantiates the various phases of clinical trials for some AMPs, as well as an overview of genome mining databases and tools built expressly for AMP discovery. In light of the recent advancements, it is evident that targeted genome mining stands as a beacon of hope, offering immense potential to expedite the discovery of novel antimicrobials.

Antimicrobial hydrogel foam dressing with controlled release of gallium maltolate for infection control in chronic wounds

Effective treatment of infection in chronic wounds is critical to improve patient outcomes and prevent severe complications, including systemic infections, increased morbidity, and amputations. Current treatments, including antibiotic administration and antimicrobial dressings, are challenged by the increasing prevalence of antibiotic resistance and patients' sensitivity to the delivered agents. Previous studies have demonstrated the potential of a new antimicrobial agent, Gallium maltolate (GaM); however, the high burst release from the GaM-loaded hydrogel gauze required frequent dressing changes. To address this need, we developed a hydrogel foam-based wound dressing with GaM-loaded microspheres for sustained infection control. First, the minimal inhibitory and bactericidal concentrations (MIC and MBC) of GaM against two Staphylococcus aureus strains isolated from chronic wounds were identified. No significant adverse effects of GaM on dermal fibroblasts were shown at the MIC, indicating an acceptable selectivity index. For the sustained release of GaM, electrospraying was employed to fabricate microspheres with different release kinetics. Systematic investigation of loading and microsphere size on release kinetics indicated that the larger microsphere size and lower GaM loading resulted in a sustained GaM release profile over the target 5 days. Evaluation of the GaM-loaded hydrogel dressing demonstrated cytocompatibility and antibacterial activities with a zone of inhibition test. An equine distal limb wound model was developed and utilized to demonstrate the efficacy of GaM-loaded hydrogel foam in vivo. This antimicrobial hydrogel foam dressing displayed the potential to combat methicillin-resistant S. aureus (MRSA) infection with controlled GaM release to improve chronic wound healing.

Antimicrobial Peptides From Different Sources: Isolation, Purification, and Characterization to Potential Applications

Antimicrobial peptides (AMPs) are excellent promising candidates for biomedical applications owing to their structural properties, high biocompatibility, good biodegradability, and functional diversity. Unlike conventional antibiotics, AMPs have been shown to have broad-spectrum antimicrobial activity toward Gram-positive/negative bacteria, as well as antifungal and antiviral activity. These peptides have also been found to be cytotoxic to sperm and cancer cells. A range of AMPs has been isolated from various organisms, such as bacteria, fungi, plants, and animals. This review summarizes the latest studies on AMPs, covering their isolation, purification, and characterization as well as their potential biomedical applications and beyond.

Cycle-ESM: Generation-assisted classification of antifungal peptides using ESM protein language model

The rising prevalence of invasive fungal infections and the emergence of antifungal resistance highlight the urgent need for new antifungal medications. Antifungal peptides have emerged as promising alternatives to traditional antimicrobial agents. The identification of natural or synthetic antifungal peptides is crucial for advancing antifungal drug development. Typically, the availability of antifungal samples is limited, and significant sequence diversity exists among antifungal peptides, posing challenges for high-throughput screening. To address the identification challenge of antifungal peptides with limited sample availability, this study introduces the Cycle ESM method. Initially, the method utilises the ESM protein language model to generate additional data on antifungal peptides, serving as a data augmentation technique to enhance model training effectiveness. Subsequently, the ESM is employed in conjunction with a textCNN model to construct a classifier for peptide prediction, with a comprehensive exploration of peptide characteristics to improve prediction accuracy. Experimental results demonstrate that the performance of the Cycle ESM method surpasses that of existing methods across three distinct antifungal peptide datasets. This study presents a novel approach to antifungal peptide prediction and offers innovative insights for addressing classification problems with limited sample availability.

Ensemble Machine Learning and Predicted Properties Promote Antimicrobial Peptide Identification

The emergence of antibiotic-resistant microbes raises a pressing demand for novel alternative treatments. One promising alternative is the antimicrobial peptides (AMPs), a class of innate immunity mediators within the therapeutic peptide realm. AMPs offer salient advantages such as high specificity, cost-effective synthesis, and reduced toxicity. Although some computational methodologies have been proposed to identify potential AMPs with the rapid development of artificial intelligence techniques, there is still ample room to improve their performance. This study proposes a predictive framework which ensembles deep learning and statistical learning methods to screen peptides with antimicrobial activity. We integrate multiple LightGBM classifiers and convolution neural networks which leverages various predicted sequential, structural and physicochemical properties from their residue sequences extracted by diverse machine learning paradigms. Comparative experiments exhibit that our method outperforms other state-of-the-art approaches on an independent test dataset, in terms of representative capability measures. Besides, we analyse the discrimination quality under different varieties of attribute information and it reveals that combination of multiple features could improve prediction. In addition, a case study is carried out to illustrate the exemplary favorable identification effect. We establish a web application at http://amp.denglab.org to provide convenient usage of our proposal and make the predictive framework, source code, and datasets publicly accessible at https://github.com/researchprotein/amp .

Synergistic anticancer effects of interleukin-21 combined with therapeutic peptides in multiple cancer cells

BACKGROUND

Interleukin-21 (IL-21) is a cytokine produced by various cell types, including T cells, natural killer cells, myeloid cells, and B cells, and has a broad range of potential applications in cancer therapy. To improve the therapeutic index, we explored the use of fusion technologies that involved linking other anticancer peptides to the IL-21 gene using specific linkers.

OBJECTIVES

This study aimed to compare the anticancer potential of IL-21 and IL-21 fusion proteins.

METHODS

Antimicrobial peptides possessing anticancer properties were fused with IL-21 gene using a flexible linker (-GGGGS-), and the resulting construct was inserted into the pSecTag2a mammalian expression vector. The cassette was transfected into several cancer cell lines including H1 HeLa, HepG2, MCF-7, MDA-MB-231, HCT-116, HCC-1954, HEK-293, and SF-767. The cytotoxic effects of IL-21 and fusion proteins were evaluated using MTT, Caspase-3, LDH, and scratch assays.

RESULTS

The IL-21-Tachyplesin I fusion protein had the strongest antiproliferative activity against all tested cancer cells, followed by IL21-LPSBD2 and IL-21. In contrast, IL21-Cop A3, IL21-CSP I-Plus, and IL21-RGD Temporin-Las did not inhibit the viability of cancer cells.

CONCLUSION

Fusion technology is a promising therapeutic technique that can be used to enhance the cytotoxicity and antiproliferative activity of anticancer proteins such as IL-21.

Antimicrobial Peptides: The Game-Changer in the Epic Battle Against Multidrug-Resistant Bacteria

The rapid progress of antibiotic resistance among bacteria has prompted serious medical concerns regarding how to manage multidrug-resistant (MDR) bacterial infections. One emerging strategy to combat antibiotic resistance is the use of antimicrobial peptides (AMPs), which are amino acid chains that act as broad-spectrum antimicrobial molecules and are essential parts of the innate immune system in mammals, fungi, and plants. AMPs have unique antibacterial mechanisms that offer benefits over conventional antibiotics in combating drug-resistant bacterial infections. Currently, scientists have conducted multiple studies on AMPs for combating drug-resistant bacterial infections and found that AMPs are a promising alternative to conventional antibiotics. On the other hand, bacteria can develop several tactics to resist and bypass the effect of AMPs. Therefore, it is like a battle between the bacterial community and the AMPs, but who will win? This review provides thorough insights into the development of antibiotic resistance as well as detailed information about AMPs in terms of their history and classification. Furthermore, it addresses the unique antibacterial mechanisms of action of AMPs, how bacteria resist these mechanisms, and how to ensure AMPs win this battle. Finally, it provides updated information about FDA-approved AMPs and those that were still in clinical trials. This review provides vital information for researchers for the development and therapeutic application of novel AMPs for drug-resistant bacterial infections.

Phosphorylation as an Effective Tool to Improve Stability and Reduce Toxicity of Antimicrobial Peptides

Developing a straightforward and effective strategy to modify antimicrobial peptides (AMPs) is crucial in overcoming the challenges posed by their instability and toxicity. Phosphorylation can reduce toxicity and improve the stability of AMPs. Based on these, we designed a series of peptides and their corresponding phosphorylated forms. The results showed that all phosphorylated peptides displayed reduced toxicity and enhanced stability compared to their unphosphorylated counterparts. Among them, W3BipY8-P stood out as the most promising peptide, exhibiting similar antibacterial activity as its unphosphorylated analog W3BipY8 but with significantly reduced hemolytic activity (19-fold decrease), cytotoxicity (3.3-fold decrease), and an extended serum half-life 6.3 times longer than W3BipY8. W3BipY8-P exerted bactericidal effects by disrupting bacterial membranes. Notably, W3BipY8-P significantly prolonged the survival of bacteria-infected animals while its LD50 was 4.2 times higher than that of W3BipY8. These findings highlight phosphorylation as an effective strategy for improving the antimicrobial properties of AMPs.

Discovery of Highly Bioactive Peptides through Hierarchical Structural Information and Molecular Dynamics Simulations

Peptide drugs play an essential role in modern therapeutics, but the computational design of these molecules is hindered by several challenges. Traditional methods like molecular docking and molecular dynamics (MD) simulation, as well as recent deep learning approaches, often face limitations related to computational resource demands, complex binding affinity assessments, extensive data requirements, and poor model interpretability. Here, we introduce PepHiRe, an innovative methodology that utilizes the hierarchical structural information in peptide sequences and employs a novel strategy called Ladderpath, rooted in algorithmic information theory, to rapidly generate and enhance the efficiency and clarity of novel peptide design. We applied PepHiRe to develop BH3-like peptide inhibitors targeting myeloid cell leukemia-1, a protein associated with various cancers. By analyzing just eight known bioactive BH3 peptide sequences, PepHiRe effectively derived a hierarchy of subsequences used to create new BH3-like peptides. These peptides underwent screening through MD simulations, leading to the selection of five candidates for synthesis and subsequent in vitro testing. Experimental results demonstrated that these five peptides possess high inhibitory activity, with IC50 values ranging from 28.13 ± 7.93 to 167.42 ± 22.15 nM. Our study explores a white-box model driven technique and a structured screening pipeline for identifying and generating novel peptides with potential bioactivity.

Role of Peptide Associations in Enhancing the Antimicrobial Activity of Adepantins: Comparative Molecular Dynamics Simulations and Design Assessments

Adepantins are peptides designed to optimize antimicrobial biological activity through the choice of specific amino acid residues, resulting in helical and amphipathic structures. This paper focuses on revealing the atomistic details of the mechanism of action of Adepantins and aligning design concepts with peptide behavior through simulation results. Notably, Adepantin-1a exhibits a broad spectrum of activity against both Gram-positive and Gram-negative bacteria, while Adepantin-1 has a narrow spectrum of activity against Gram-negative bacteria. The simulation results showed that one of the main differences is the extent of aggregation. Both peptides exhibit a strong tendency to cluster due to the amphipathicity embedded during design process. However, the more potent Adepantin-1a forms smaller aggregates than Adepantin-1, confirming the idea that the optimal aggregations, not the strongest aggregations, favor activity. Additionally, we show that incorporation of the cell penetration region affects the mechanisms of action of Adepantin-1a and promotes stronger binding to anionic and neutral membranes.

Hybrid Planar Copolymer Membranes with Dual Functionality against Bacteria Growth

Antibacterial surfaces can be classified into two categories: passive surfaces, which repel bacteria by affecting surface wettability, and active surfaces, which have bactericidal properties that disrupt cell membranes upon contact. With the increasing demand for effective antibacterial solutions that combine these properties, advanced strategies are concentrating on developing surfaces with dual antimicrobial functionalities. Here, we present surfaces with nanotexture resulting from the phase separation of two different amphiphilic block copolymers displaying efficient dual functionality against bacteria growth. This approach combines the inherent antifouling properties of poly(ethylene oxide) as the hydrophilic domain of one copolymer with the antimicrobial effect of a peptide covalently attached to the hydrophilic domain of the second copolymer. The planar membranes are generated by self-assembly of the amphiphilic copolymer mixture deposited by Langmuir-Blodgett and Langmuir-Schaffer methods on a solid support, followed by covalent attachment of the antimicrobial peptides to one of the copolymers, specifically functionalized. Combining both copolymers, in terms of their properties and functionalities on the same surface, significantly limitsEscherichia colibiofilm formation and effectively eradicates bacteria during short-term incubation. While such multifunctional antimicrobial planar polymer membranes show promising potential in the design of fine coatings for small surgical or implantable devices, they are not limited to this application. Their use can be completely changed by attaching other active molecules or assemblies to induce specific multifunctionality for the targeted application.

The Human Mitochondrial Genome Encodes for an Interferon-Responsive Host Defense Peptide

The mitochondrial DNA (mtDNA) can trigger immune responses and directly entrap pathogens, but it is not known to encode for active immune factors. The immune system is traditionally thought to be exclusively nuclear-encoded. Here, we report the identification of a mitochondrial-encoded host defense peptide (HDP) that presumably derives from the primordial proto-mitochondrial bacteria. We demonstrate that MOTS-c (mitochondrial open reading frame from the twelve S rRNA type-c) is a mitochondrial-encoded amphipathic and cationic peptide with direct antibacterial and immunomodulatory functions, consistent with the peptide chemistry and functions of known HDPs. MOTS-c targeted E. coli and methicillin-resistant S. aureus (MRSA), in part, by targeting their membranes using its hydrophobic and cationic domains. In monocytes, IFNγ, LPS, and differentiation signals each induced the expression of endogenous MOTS-c. Notably, MOTS-c translocated to the nucleus to regulate gene expression during monocyte differentiation and programmed them into macrophages with unique transcriptomic signatures related to antigen presentation and IFN signaling. MOTS-c-programmed macrophages exhibited enhanced bacterial clearance and shifted metabolism. Our findings support MOTS-c as a first-in-class mitochondrial-encoded HDP and indicates that our immune system is not only encoded by the nuclear genome, but also by the co-evolved mitochondrial genome.