Anisaxins, helical antimicrobial peptides from marine parasites, kill resistant bacteria by lipid extraction and membrane disruption

Dual-Mechanism Peptide SR25 has Broad Antimicrobial Activity and Potential Application for Healing Bacteria-infected Diabetic Wounds

The rise of antibiotic resistance poses a significant public health crisis, particularly due to limited antimicrobial options for the treatment of infections with Gram-negative pathogens. Here, an antimicrobial peptide (AMP) SR25 is characterized, which effectively kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism without detectable resistance. Meanwhile, an SR25-functionalized hydrogel is developed for the efficient treatment of infected diabetic wounds. SR25 is obtained through genome mining from an uncultured bovine enteric actinomycete named Nonomuraea Jilinensis sp. nov. Investigations reveal that SR25 has two independent cellular targets, disrupting bacterial membrane integrity and restraining the activity of succinate:quinone oxidoreductase (SQR). In a diabetic mice wound infection model, the SR25-incorporated hydrogel exhibits high efficacy against mixed infections of Escherichia coli (E. coli) and methicillin-resistant Staphylococcus aureus (MRSA), accelerating wound healing. Overall, these findings demonstrate the therapeutic potential of SR25 and highlight the value of mining drugs with multiple mechanisms from uncultured animal commensals for combating challenging bacterial pathogens.

Embracing the era of antimicrobial peptides with marine organisms

Covering: 2018 to Jun of 2023The efficiency of traditional antibiotics has been undermined by the proliferation of antibiotic-resistant pathogenic microorganisms, necessitating the pursuit of innovative therapeutic agents. Antimicrobial peptides (AMPs), which are part of host defence peptides found ubiquitously in nature, exhibiting a wide range of activity towards bacteria, fungi, and viruses, offer a highly promising candidate solution. The efficacy of AMPs can frequently be augmented via alterations to their amino acid sequences or structural adjustments. Given the vast reservoir of marine life forms and their distinctive ecosystems, marine AMPs stand as a burgeoning focal point in the quest for alternative peptide templates extracted from natural sources. Advances in identification and characterization techniques have accelerated the discoveries of marine AMPs, thereby stimulating AMP customization, optimization, and synthesis research endeavours. This review presents an overview of recent discoveries related to the intriguing qualities of marine AMPs. Emphasis will be placed upon post-translational modifications (PTMs) of marine AMPs and how they may impact functionality and potency. Additionally, this review considers ways in which marine PTM might support larger-scale, heterologous AMP manufacturing initiatives, providing insights into translational applications of these important biomolecules.

Marine natural products

Covering: January to the end of December 2022This review covers the literature published in 2022 for marine natural products (MNPs), with 645 citations (633 for the period January to December 2022) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, the submerged parts of mangroves and other intertidal plants. The emphasis is on new compounds (1417 in 384 papers for 2022), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of NP structure class diversity in relation to biota source and biome is discussed.

From Simple Palladium(II) Monomers to 2D Heterometallic Sodium-Palladium(II) Coordination Networks with 2-Halonicotinates

The 2D heterometallic sodium-palladium(II) coordination polymers with 2-halonicotinates [2-chloropyridine-3-carboxylate (2-chloronicotinate), 2-Clnic- and 2-bromopyridine-3-carboxylate (2-bromonicotinate), 2-Brnic-], {[Na2(H2O)2(μ-H2O)4PdCl2(μ-2-Clnic-N:O')2]}n (1), and {[Na2(H2O)2(μ-H2O)4PdBr2(μ-2-Brnic-N:O')2]·2H2O}n (2) were prepared in aqueous solutions under the presence of NaHCO3, while palladium(II) monomers with the neutral 2-chloronicotinic and 2-bromonicotinic acid ligands, [PdCl2(2-ClnicH-N)2]·2DMF (3) and [PdCl2(2-BrnicH-N)2]·2DMF (4), were prepared in DMF/water mixtures (DMF = N,N'-dimethylformamide). The zigzag chains of water-bridged sodium ions are in turn bridged by [PdCl2(2-Clnic)2]2- moieties in 1 or by [PdBr2(2-Brnic)2]2- moieties in 2, leading to the formation of the infinite 2D coordination networks of 1 or 2. The DFT calculations showed the halosubstituents type (Cl vs Br) does not have an influence on the formation of either trans or cis isomers. The trans isomers were found in all reported compounds; being more stable for about 10 to 15 kJ mol-1. The 2D coordination networks 1 and 2 are more stabilized by the formation of Na-Ocarboxylate bonds, comparing to the stabilization of palladium(II) monomers 3 and 4 by hydrogen-bonding with DMF molecules. The difference in DFT calculated energy stabilization for 1 and 2 is ascribed to the type of halosubstituents and to the presence/absence of lattice water molecules in 1 and 2. The compounds show no antibacterial activity toward reference strains of Escherichia coli and Staphylococcus aureus bacteria and no antiproliferative activity toward bladder (T24) and lung (A549) cancer cell lines.

A review of current antibiotic resistance and promising antibiotics with novel modes of action to combat antibiotic resistance

The emergence and transmission of antibiotic resistance is a global public health crisis with significant burden on healthcare systems, resulting in high mortality and economic costs. In 2019, almost five million deaths were associated with drug-resistant infections, and if left unchecked, the global economy could lose $100 trillion by 2050. To effectively combat this crisis, it is essential for all countries to understand the current situation of antibiotic resistance. In this review, we examine the current driving factors leading to the crisis, impact of critical superbugs in three regions, and identify novel mechanisms of antibiotic resistance. It is crucial to monitor the phenotypic characteristics of drug-resistant pathogens and describe the mechanisms involved in preventing the emergence of cross-resistance to novel antimicrobials. Additionally, maintaining an active pipeline of new antibiotics is essential for fighting against diverse antibiotic-resistant pathogens. Developing antibacterial agents with novel mechanisms of action is a promising way to combat increasing antibiotic-resistant pathogens.

"AMP plus": Immunostimulant-Inspired Design Based on Chemotactic Motif-(PhHAhPH)n

Ability to stimulate antimicrobial immunity has proven to be a useful therapeutic strategy in treating infections, especially in the face of increasing antibiotic resistance. Natural antimicrobial peptides (AMPs) exhibiting immunomodulatory functions normally encompass complex activities, which make it difficult to optimize their therapeutic benefits. Here, a chemotactic motif was harnessed as a template to design a series of AMPs with immunostimulatory activities plus bacteria-killing activities ("AMP plus"). An amphipathic peptide ((PhHAhPH)n) was employed to improve the antimicrobial impact and expand the therapeutic potential of the chemotactic motif that lacked obvious bacteria-killing properties. A total of 18 peptides were designed and evaluated for their structure-activity relationships. Among the designed, KWH2 (1) potently killed bacteria and exhibited a narrow antimicrobial spectrum against Gram-negative bacteria and (2) activated macrophages (i.e., inducing Ca2+ influx, cell migration, and reactive oxygen species production) as a macrophage chemoattractant. Membrane permeabilization is the major antimicrobial mechanism of KWH2. Furthermore, the mouse subcutaneous abscess model supported the dual immunomodulatory and antimicrobial potential of KWH2 in vivo. The above results confirmed the efficiency of KWH2 in treating bacterial infection and provided a viable approach to develop immunomodulatory antimicrobial materials with desired properties.

Exploring the antimicrobial peptidome of nematodes through phylum-spanning in silico analyses highlights novel opportunities for pathogen control

Antimicrobial Peptides (AMPs) are key constituents of the invertebrate innate immune system and provide critical protection against microbial threat. Nematodes display diverse life strategies where they are exposed to heterogenous, microbe rich, environments highlighting their need for an innate immune system. Within the Ecdysozoa, arthropod AMPs have been well characterised, however nematode-derived AMP knowledge is limited. In this study the distribution and abundance of putative AMP-encoding genes was examined in 134 nematode genomes providing the most comprehensive profile of AMP candidates within phylum Nematoda. Through genome and transcriptome analyses we reveal that phylum Nematoda is a rich source of putative AMP diversity and demonstrate (i) putative AMP group profiles that are influenced by nematode lifestyle where free-living nematodes appear to display enriched putative AMP profiles relative to parasitic species; (ii) major differences in the putative AMP profiles between nematode clades where Clade 9/V and 10/IV species possess expanded putative AMP repertoires; (iii) AMP groups with highly restricted profiles (e.g. Cecropins and Diapausins) and others [e.g. Nemapores and Glycine Rich Secreted Peptides (GRSPs)] which are more widely distributed; (iv) complexity in the distribution and abundance of CSαβ subgroup members; and (v) that putative AMPs are expressed in host-facing life stages and biofluids of key nematode parasites. These data indicate that phylum Nematoda displays diversity in putative AMPs and underscores the need for functional characterisation to reveal their role and importance to nematode biology and host-nematode-microbiome interactions.

Novel antimicrobial peptide DvAMP serves as a promising antifungal agent against Cryptococcus neoformans

Cryptococcus neoformans is an important opportunistic human fungal pathogen that causes cryptococcosis in immunocompromised patients. However, the number of drugs for the treatment of cryptococcosis is restricted, and the development of novel antifungal drugs and innovative strategies for the treatment of cryptococcosis is urgently needed. In this study, we validated that DvAMP is a novel antimicrobial peptide with antimicrobial activity and that it was obtained by pre-screening from the UniProt database of more than three million unknown functional sequences based on the quantitative structure-activity relationships (QSARs) protocol (http://www.chemoinfolab.com/antifungal). The peptide exhibited satisfactory biosafety and physicochemical properties, and relatively rapid fungicidal activity against C. neoformans. Meanwhile, DvAMP was able to inhibit the static biofilm of C. neoformans and cause a reduction in the thickness of the capsule. In addition, DvAMP exerts antifungal effects through membrane-mediated mechanisms (membrane permeability and depolarization) and mitochondrial dysfunction, involving a hybrid multi-hit mechanism. Furthermore, by using the C. neoformans-Galleria mellonella infection model, we demonstrated that DvAMP has significant therapeutic effects in vivo and that it significantly reduces the mortality and fungal burden of infected larvae. These results suggest that DvAMP may be a potential antifungal drug candidate for the treatment of cryptococcosis.

How Alligator Immune Peptides Kill Gram-Negative Bacteria: A Lipid-Scrambling, Squeezing, and Extracting Mechanism Revealed by Theoretical Simulations

Alligator sinensis cathelicidins (As-CATHs) are antimicrobial peptides extracted from alligators that enable alligators to cope with diseases caused by bacterial infections. This study assessed the damaging effects of sequence-truncated and residue-substituted variants of As-CATH4, AS4-1, AS4-5, and AS4-9 (with decreasing charges but increasing hydrophobicity) on the membranes of Gram-negative bacteria at the molecular level by using coarse-grained molecular dynamics simulations. The simulations predicted that all the variants disrupt the structures of the inner membrane of Gram-negative bacteria, with AS4-9 having the highest antibacterial activity that is able to squeeze the membrane and extract lipids from the membrane. However, none of them can disrupt the structure of asymmetric outer membrane of Gram-negative bacteria, which is composed of lipopolysaccharides in the outer leaflet and phospholipids in the inner leaflet. Nonetheless, the adsorption of AS4-9 induces lipid scrambling in the membrane by lowering the free energy of a phospholipid flipping from the inner leaflet up to the outer leaflet. Upon binding onto the lipid-scrambled outer membrane, AS4-9s are predicted to squeeze and extract phospholipids from the membrane, AS4-5s have a weak pull-out effect, and AS4-1s mainly stay free in water without any lipid-extracting function. These findings provide inspiration for the development of potent therapeutic agents targeting bacteria.

Marine Resources Offer New Compounds and Strategies for the Treatment of Skin and Soft Tissue Infections

Bioprospecting of the marine environment for drug development has gained much attention in recent years owing to its massive chemical and biological diversity. Drugs for the treatment of skin and soft tissue infections have become part of the search, mainly with respect to enlarging the number of available antibiotics, with a special focus on multidrug-resistant Gram-positive bacteria, being the major causative agents in this field. Marine resources offer novel natural products with distinct biological activities of pharmaceutical importance, having the chance to provide new chemical scaffolds and new modes of action. New studies advance the field by proposing new strategies derived from an ecosystemic understanding for preventive activities against biofilms and new compounds suitable as disinfectants, which sustain the natural flora of the skin. Still, the development of new compounds is often stuck at the discovery level, as marine biotechnology also needs to overcome technological bottlenecks in drug development. This review summarizes its potential and shows these bottlenecks and new approaches.

Relating Molecular Dynamics Simulations to Functional Activity for Gly-Rich Membranolytic Helical Kiadin Peptides

Kiadins are in silico designed peptides with a strong similarity to diPGLa-H, a tandem sequence of PGLa-H (KIAKVALKAL) and with single, double or quadruple glycine substitutions. They were found to show high variability in their activity and selectivity against Gram-negative and Gram-positive bacteria, as well as cytotoxicity against host cells, which are influenced by the number and placing of glycine residues along the sequence. The conformational flexibility introduced by these substitutions contributes differently peptide structuring and to their interactions with the model membranes, as observed by molecular dynamics simulations. We relate these results to experimentally determined data on the structure of kiadins and their interactions with liposomes having a phospholipid membrane composition similar to simulation membrane models, as well as to their antibacterial and cytotoxic activities, and also discuss the challenges in interpreting these multiscale experiments and understanding why the presence of glycine residues in the sequence affected the antibacterial potency and toxicity towards host cells in a different manner.

Helminthic host defense peptides: using the parasite to defend the host

Parasitic helminths are destined to share niches with a variety of microbiota that inevitably influence their interaction with the host. To modulate the microbiome for their benefit and defend against pathogenic isolates, helminths have developed host defense peptides (HDPs) and proteins as integral elements of their immunity. These often exert a relatively nonspecific membranolytic activity toward bacteria, sometimes with limited or no toxicity toward host cells. With a few exceptions, such as nematode cecropin-like peptides and antibacterial factors (ABFs), helminthic HDPs are largely underexplored. This review scrutinizes current knowledge on the repertoire of such peptides in helminths and promotes their research as potential leads for an anti-infective solution to the burgeoning problem of antibiotic resistance.

Thinking on the Construction of Antimicrobial Peptide Databases: Powerful Tools for the Molecular Design and Screening

With the accelerating growth of antimicrobial resistance (AMR), there is an urgent need for new antimicrobial agents with low or no AMR. Antimicrobial peptides (AMPs) have been extensively studied as alternatives to antibiotics (ATAs). Coupled with the new generation of high-throughput technology for AMP mining, the number of derivatives has increased dramatically, but manual running is time-consuming and laborious. Therefore, it is necessary to establish databases that combine computer algorithms to summarize, analyze, and design new AMPs. A number of AMP databases have already been established, such as the Antimicrobial Peptides Database (APD), the Collection of Antimicrobial Peptides (CAMP), the Database of Antimicrobial Activity and Structure of Peptides (DBAASP), and the Database of Antimicrobial Peptides (dbAMPs). These four AMP databases are comprehensive and are widely used. This review aims to cover the construction, evolution, characteristic function, prediction, and design of these four AMP databases. It also offers ideas for the improvement and application of these databases based on merging the various advantages of these four peptide libraries. This review promotes research and development into new AMPs and lays their foundation in the fields of druggability and clinical precision treatment.

Glycerol and Antimicrobial Peptide-Modified Natural Latex for Bacteriostasis of Skin Wounds

This work aimed to develop a glycerol antimicrobial peptide natural latex film (NRL-GI-AMP film) for the treatment of skin wound infections. The contents of this work mainly include investigating the effect of adding glycerol (GI) and an antimicrobial peptide (AMP) on the physical and chemical properties of natural latex (NRL) and analyzing the cytocompatibility, bacteriostatic activity, and infected wound healing promotion of the NRL-GI-AMP film. The results showed that the addition of GI resulted in more pores in the internal structure of the NRL film, while the addition of G(LLKK)₃L AMP did not change the structure and properties of the NRL film. Compared with that of the NRL film, the infrared spectrum of the NRL-GI-AMP film did not produce new characteristic peaks, indicating that GI and AMP were non-covalently cross-linked with NRL. Addition of 10% GI reduces the toughness of the NRL-GI-AMP film by 62.0%, increases the water vapor transmission rate by 8.95 mg/(cm²·h), and reduces the water absorption and water retention distributions by 33.0 and 24.7%, respectively. AMP in the NRL-GI-AMP film could be released continuously for 40 h, and the release rate was about 45%. The NRL-GI-AMP film showed good biocompatibility and antibacterial activity and promoted the healing of infected wounds. Therefore, the NRL-GI-AP film has potential application in the development of dressings to inhibit skin wound infection and promote wound healing.

Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes

Antimicrobial peptides (AMPs) can be directed to specific membranes based on differences in lipid composition. In this study, we performed atomistic and coarse-grained simulations of different numbers of the designed AMP adepantin-1 with a eukaryotic membrane, cytoplasmic Gram-positive and Gram-negative membranes, and an outer Gram-negative membrane. At the core of adepantin-1's behavior is its amphipathic α-helical structure, which was implemented in its design. The amphipathic structure promotes rapid self-association of peptide in water or upon binding to bacterial membranes. Aggregates initially make contact with the membrane via positively charged residues, but with insertion, the hydrophobic residues are exposed to the membrane's hydrophobic core. This adaptation alters the aggregate's stability, causing the peptides to diffuse in the polar region of the membrane, mostly remaining as a single peptide or pairing up to form an antiparallel dimer. Thus, the aggregate's proposed role is to aid in positioning the peptide into a favorable conformation for insertion. Simulations revealed the molecular basics of adepantin-1 binding to various membranes, and highlighted peptide aggregation as an important factor. These findings contribute to the development of novel anti-infective agents to combat the rapidly growing problem of bacterial resistance to antibiotics.