Design of Protegrin-1 Analogs with Improved Antibacterial Selectivity

Characterization of the first antimicrobial peptide from Sea Seal with potent therapeutic effect in septic mice

Marine organisms are a valuable source of natural bioactive substances, and an increasing number of marine antimicrobial peptides as the potential alternative to antibiotics are being developed. Nonetheless, antimicrobial peptides from Antarctic mammals have not been reported heretofore. In this context, we identified a Cathelicidin antimicrobial peptide, Cath-LW (RLRDLIRRGRQKIGRRINRLGRRIQDILKNLQPGKVS), from the whole-genome database of Leptonychotes weddellii, an Antarctic mammal. Cath-LW was characterized to exhibit a typical α-helix structure and broad-spectrum antimicrobial activity. Furthermore, Cath-LW was found to exert its antibacterial effect by destroying cytomembrane, binding to bacterial genome, and inhibiting DNA function. Additionally, Cath-LW could neutralize lipopolysaccharide (LPS) and inhibit LPS-induced inflammatory responses. Interestingly, Cath-LW also showed anticoagulant activity and suppressed FeCl3-induced carotid thrombosis in mice. Finally, in septic mice, Cath-LW was demonstrated to improve the survival rate by effectively alleviating organ inflammation and damage, as well as thrombus formation. These findings not only deepen our understanding of the survival strategies of L. weddellii against microbial infections but also provide a crucial template for developing a novel multifunctional anti-sepsis drug.

Antimicrobial peptides: from discovery to developmental applications

Antimicrobial resistance (AMR) has emerged as a significant crisis in global health. Due to their advantageous properties, antimicrobial peptides (AMPs) have garnered considerable attention as a potential alternative therapy to address the AMR crisis. These peptides might disrupt cell membranes or cell walls to exhibit antimicrobial activity, or modulate the immune response to promote recovery from diseases. In recent years, significant progress has been made in the research of AMPs, alongside the emergence of new challenges. This review first systematically summarizes and critically discusses recent advancements in understanding the characteristics and current landscapes of AMPs, as well as their regulatory mechanisms of action and practical applications, particularly those reported or approved within the last 5 years. Additionally, the principles, paths for their identification, and future research trends in AMPs are also analyzed following a discussion of the advantages and disadvantages of AMPs in comparison to conventional antibiotics. Unlike significant prior literature in this field, this report has summarized the latest major discovery methods for AMPs and, more importantly, emphasized their practical applications by supporting various viewpoints using selected examples of AMPs' applications in real-life scenarios. Besides, some emerging hot topics of AMPs, including those derived from gut microbiota and their potential synergistic effects in combating AMR, were profiled. All of these indicate the originality of the report and provide valuable references for future AMP discoveries and applications.

PMAP-37: A versatile cathelicidin for neutralizing bacteria and viruses

Antimicrobial peptides (AMPs), such as cathelicidins, show dual functionality by directly combating pathogens and indirectly eliminating them through stimulation of the immune system, generating interest in their therapeutic potential. Pigs have a large set of 11 cathelicidins, of which PMAP-37 is relatively understudied compared to some of the better-known cathelicidins. This study describes the effectiveness of PMAP-37 against both bacteria and viruses. PMAP-37 exhibited potent in vitro antimicrobial activity against both Gram-positive (Bacillus globigii) and Gram-negative bacteria (Escherichia coli) with minimum bactericidal concentrations (MBCs) of 2.5 and 5 μM, respectively. PMAP-37 caused a rapid permeabilization of E. coli's outer and inner membranes within 5 min, indicating its efficacy in disrupting bacterial cell membranes. Furthermore, PMAP-37 neutralized nitric oxide production in a macrophage cell line stimulated with various forms of LPS, Lipid A, or LTA in a dose-dependent manner. Flow cytometric analysis confirmed PMAP-37's capacity to inhibit LPS binding to macrophages, while zeta potential analysis showed the peptide's capacity to neutralize the negative charge of both the E. coli membrane and LPS micellular surfaces. Interestingly, PMAP-37 also exhibited antiviral activity against an important porcine pathogen, the porcine epidemic diarrhea virus (PEDV). These findings underscore the multifunctional properties of PMAP-37, and provide potential leads for future therapeutic use within the pig industry.

Protegrin-1 and Analogues Against Acinetobacter baumannii: A Narrative Review

A. baumannii is recognised as an important etiologic agent for hospital infections and increases the risk of postoperative complications, worsening mortality and prolonging hospitalisation. Protegrin-1 (PG-1) is one of the most promising antimicrobial peptides (AMPs) in the literature, since its antimicrobial action covers a wide range of Gram-positive and Gram-negative bacteria, including A. baumannii. PG-1 represents a valid new therapeutic option for the treatment of A. baumannii multi-drug resistant infections, showing synergic activity with traditional antibiotics, such as colistin. However, its clinical use in humans still requires studies, especially considering the haemolytic risk. For this reason, the use of PG-1 analogues, such as PLP-3, HV2, CDP-1, and IB367, seems to be the most promising way for the clinical use of this class of AMPs.

Novel antimicrobial peptides based on Protegrin-1: In silico and in vitro assessments

The development of antibiotic resistance has caused significant health problems. Antimicrobial peptides (AMPs) are considered next-generation antibiotics. Protegrin-1 (PG-1) is a β-hairpin AMP with a membrane-binding capacity. This study used twelve PG-1 analogs with different amino acid substitutions. Coarse-grained molecular dynamics (MD) simulations were used to assess these analogs, and their physicochemical properties were computed using the Antimicrobial Peptide Database. Three AMPs, PEP-D, PEP-C, and PEP-H, were chosen and synthesized for antibacterial testing. The microbroth dilution technique and hemolytic assays evaluated the antimicrobial efficacy and cellular toxicity. The checkerboard method was used to test the combined activity of AMP and standard antibiotics. Cell membrane permeability and electron microscopy were used to evaluate the mode of action. The chemical stability of the selective AMP, PEP-D, was assessed by a validated HPLC method. PEP-D consists of 16-18 amino acid residues and has a charge of +7 and a hydrophobicity of 44 %, similar to PG-1. It can efficiently inactivate bacteria by disrupting cell membranes and significantly reducing hemolytic activity. Chemical stability studies indicated that AMP was stable at 40 °C for six months under autoclave conditions. This study could introduce the potential therapeutic application of selective AMP as an anti-infective agent.

Cell Wall Binding Strategies Based on Cu3SbS3 Nanoparticles for Selective Bacterial Elimination and Promotion of Infected Wound Healing

Utilizing nanomaterials as an alternative to antibiotics, with a focus on maintaining high biosafety, has emerged as a promising strategy to combat antibiotic resistance. Nevertheless, the challenge lies in the indiscriminate attack of nanomaterials on both bacterial and mammalian cells, which limits their practicality. Herein, Cu3SbS3 nanoparticles (NPs) capable of generating reactive oxygen species (ROS) are discovered to selectively adsorb and eliminate bacteria without causing obvious harm to mammalian cells, thanks to the interaction between O of N-acetylmuramic acid in bacterial cell walls and Cu of the NPs. Coupled with the short diffusion distance of ROS in the surrounding medium, a selective antibacterial effect is achieved. Additionally, the antibacterial mechanism is then identified: Cu3SbS3 NPs catalyze the generation of O2•-, which has subsequently been conversed by superoxide dismutase to H2O2. The latter is secondary catalyzed by the NPs to form •OH and 1O2, initiating an in situ attack on bacteria. This process depletes bacterial glutathione in conjunction with the disruption of the antioxidant defense system of bacteria. Notably, Cu3SbS3 NPs are demonstrated to efficiently impede biofilm formation; thus, a healing of MRSA-infected wounds was promoted. The bacterial cell wall-binding nanoantibacterial agents can be widely expanded through diversified design.

Deep mutational scanning and machine learning for the analysis of antimicrobial-peptide features driving membrane selectivity

Many antimicrobial peptides directly disrupt bacterial membranes yet can also damage mammalian membranes. It is therefore central to their therapeutic use that rules governing the membrane selectivity of antimicrobial peptides be deciphered. However, this is difficult even for short peptides owing to the large combinatorial space of amino acid sequences. Here we describe a method for measuring the loss or maintenance of antimicrobial-peptide activity for thousands of peptide-sequence variants simultaneously, and its application to Protegrin-1, a potent yet toxic antimicrobial peptide, to determine the positional importance and flexibility of residues across its sequence while identifying variants with changes in membrane selectivity. More bacterially selective variants maintained a membrane-bound secondary structure while avoiding aromatic residues and cysteine pairs. A machine-learning model trained with our datasets accurately predicted membrane-specific activities for over 5.7 million Protegrin-1 variants, and identified one variant that showed substantially reduced toxicity and retention of activity in a mouse model of intraperitoneal infection. The high-throughput methodology may help elucidate sequence-structure-function relationships in antimicrobial peptides and inform the design of peptide-based synthetic drugs.

Waste to resource: Mining antimicrobial peptides in sludge from metagenomes using machine learning

The emergence of antibiotic-resistant bacteria poses a huge threat to the treatment of infections. Antimicrobial peptides are a class of short peptides that widely exist in organisms and are considered as potential substitutes for traditional antibiotics. Here, we use metagenomics combined with machine learning to find antimicrobial peptides from environmental metagenomes and successfully obtained 16,044,909 predicted AMPs. We compared the abundance of potential antimicrobial peptides in natural environments and engineered environments, and found that engineered environments also have great potential. Further, we chose sludge as a typical engineered environmental sample, and tried to mine antimicrobial peptides from it. Through metaproteome analysis and correlation analysis, we mined 27 candidate AMPs from sludge. We successfully synthesized 25 peptides by chemical synthesis, and experimentally verified that 21 peptides had antibacterial activity against the 4 strains tested. Our work highlights the potential for mining new antimicrobial peptides from engineered environments and demonstrates the effectiveness of mining antimicrobial peptides from sludge.

Novel BRICHOS-Related Antimicrobial Peptides from the Marine Worm Heteromastus filiformis: Transcriptome Mining, Synthesis, Biological Activities, and Therapeutic Potential

Marine polychaetes represent an extremely rich and underexplored source of novel families of antimicrobial peptides (AMPs). The rapid development of next generation sequencing technologies and modern bioinformatics approaches allows us to apply them for characterization of AMP-derived genes and the identification of encoded immune-related peptides with the aid of genome and transcriptome mining. Here, we describe a universal bioinformatic approach based on the conserved BRICHOS domain as a search query for the identification of novel structurally unique AMP families in annelids. In this paper, we report the discovery of 13 novel BRICHOS-related peptides, ranging from 18 to 91 amino acid residues in length, in the cosmopolitan marine worm Heteromastus filiformis with the assistance of transcriptome mining. Two characteristic peptides with a low homology in relation to known AMPs-the α-helical amphiphilic linear peptide, consisting of 28 amino acid residues and designated as HfBRI-28, and the 25-mer β-hairpin peptide, specified as HfBRI-25 and having a unique structure stabilized by two disulfide bonds-were obtained and analyzed as potential antimicrobials. Interestingly, both peptides showed the ability to kill bacteria via membrane damage, but mechanisms of their action and spectra of their activity differed significantly. Being non-cytotoxic towards mammalian cells and stable to proteolysis in the blood serum, HfBRI-25 was selected for further in vivo studies in a lethal murine model of the Escherichia coli infection, where the peptide contributed to the 100% survival rate in animals. A high activity against uropathogenic strains of E. coli (UPEC) as well as a strong ability to kill bacteria within biofilms allow us to consider the novel peptide HfBRI-25 as a promising candidate for the clinical therapy of urinary tract infections (UTI) associated with UPEC.