Membrane-active antimicrobial peptide identified in Rana arvalis by targeted DNA sequencing

Hybrid 2D/3D-quantitative structure-activity relationship studies on the bioactivities and molecular mechanism of antibacterial peptides

Antimicrobial peptide (AMP) is the polypeptide, which protects the organism avoiding attack from pathogenic bacteria. Studies have shown that there were some antimicrobial peptides with molecular action mechanism involved in crossing the cell membrane without inducing severe membrane collapse, then interacting with cytoplasmic target-nucleic acid, and exerting antibacterial activity by interfacing the transmission of genetic information of pathogenic microorganisms. However, the relationship between the antibacterial activities and peptide structures was still unclear. Therefore, in the present work, a series of AMPs with a sequence of 20 amino acids was extracted from DBAASP database, then, quantitative structure-activity relationship (QSAR) methods were conducted on these peptides. In addition, novel antimicrobial peptides with  stronger antimicrobial activities were designed according to the information originated from the constructed models. Hence, the outcome of this study would lay a solid foundation for the in-silico design and exploration of novel antibacterial peptides with improved activity activities.

Tandem Mass Spectrometry de novo Sequencing of the Skin Defense Peptides of the Central Slovenian Agile Frog Rana dalmatina

Peptides released on frogs' skin in a stress situation represent their only weapon against micro-organisms and predators. Every species and even population of frog possesses its own peptidome being appropriate for their habitat. Skin peptides are considered potential pharmaceuticals, while the whole peptidome may be treated as a taxonomic characteristic of each particular population. Continuing the studies on frog peptides, here we report the peptidome composition of the Central Slovenian agile frog Rana dalmatina population. The detection and top-down de novo sequencing of the corresponding peptides was conducted exclusively by tandem mass spectrometry without using any chemical derivatization procedures. Collision-induced dissociation (CID), higher energy collision-induced dissociation (HCD), electron transfer dissociation (ETD) and combined MS3 method EThcD with stepwise increase of HCD energy were used for that purpose. MS/MS revealed the whole sequence of the detected peptides including differentiation between isomeric Leu/Ile, and the sequence portion hidden in the disulfide cycle. The array of the discovered peptide families (brevinins 1 and 2, melittin-related peptides (MRPs), temporins and bradykinin-related peptides (BRPs)) is quite similar to that of R. temporaria. Since the genome of this frog remains unknown, the obtained results were compared with the recently published transcriptome of R. dalmatina.

Mass Spectrometry Differentiation between Rana arvalis Populations Based on Their Skin Peptidome Composition

Skin secretion of amphibians often represents the only weapon of these species against pathogens and predators. Peptides constitute the major portion of active molecules of that weapon and may be treated as potential pharmaceuticals for future generations. The first step of their efficient use involves establishing of their primary structure, i.e., sequencing. De novo sequencing by means of mass spectrometry was applied to Rana arvalis species, collected in the spring 2021 in Central Slovenia (vicinity of Ljubljana). HPLC-ESI-HRMS/MS with Orbitrap instruments was used to establish the skin peptidome of these species and compare it with the earlier identified skin peptidome of the Moscow population of Rana arvalis. Application of CID, HCD, ETD, and EThcD enabled detecting and sequencing 18 peptides; five of them were novel and may be treated as possible biomarkers of the Ljubljana population of Rana arvalis. Interestingly, representatives of two peptide families (temporins and brevinins 2) were not found in the Moscow population. MS³ modes, first of all EThcD, demonstrated their great potential in the de novo sequencing, including extraction of the sequence information from the intact peptides with disulfide cycle (rana box) in their structure and differentiation of isomeric Leu/Ile residues. Thus, all six isomeric residues were reliably distinguished in the novel melittin-related peptide AK-23-1. In addition, another post-translational modification dealing with carbonylation of the N-terminal Gly of novel temporin AVa was established using the MS³ mode. The obtained results demonstrate the efficiency of the use of MS³ tools in proteomics/peptidomics.

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

An infecting and propagating parasite relies on its innate defense system to evade the host's immune response and to survive challenges from commensal bacteria. More so for the nematode Anisakis, a marine parasite that during its life cycle encounters both vertebrate and invertebrate hosts and their highly diverse microbiotas. Although much is still unknown about how the nematode mitigates the effects of these microbiota, its antimicrobial peptides likely play an important role in its survival. We identified anisaxins, the first cecropin-like helical antimicrobial peptides originating from a marine parasite, by mining available genomic and transcriptomic data for Anisakis spp. These peptides are potent bactericidal agents in vitro, selectively active against Gram-negative bacteria, including multi-drug resistant strains, at sub-micromolar concentrations. Their interaction with bacterial membranes was confirmed by solid state NMR (ssNMR) and is highly dependent on the peptide concentration as well as peptide to lipid ratio, as evidenced by molecular dynamics (MD) simulations. MD results indicated that an initial step in the membranolytic mode of action involves membrane bulging and lipid extraction; a novel mechanism which may underline the peptides' potency. Subsequent steps include membrane permeabilization leading to leakage of molecules and eventually cell death, but without visible macroscopic damage, as shown by atomic force microscopy and flow cytometry. This membranolytic antibacterial activity does not translate to cytotoxicity towards human peripheral blood mononuclear cells (HPBMCs), which was minimal at well above bactericidal concentrations, making anisaxins promising candidates for further drug development. STATEMENT OF SIGNIFICANCE: Witnessing the rapid spread of antibiotic resistance resulting in millions of infected and dozens of thousands dying worldwide every year, we identified anisaxins, antimicrobial peptides (AMPs) from marine parasites, Anisakis spp., with potent bactericidal activity and selectivity towards multi-drug resistant Gram-negative bacteria. Anisaxins are membrane-active peptides, whose activity, very sensitive to local peptide concentrations, involves membrane bulging and lipid extraction, leading to membrane permeabilization and bacterial cell death. At the same time, their toxicity towards host cells is negligible, which is often not the case for membrane-active AMPs, therefore making them suitable drug candidates. Membrane bulging and lipid extraction are novel concepts that broaden our understanding of peptide interactions with bacterial functional structures, essential for future design of such biomaterials.

Rationally design of electrospun polysaccharides polymeric nanofiber webs by various tools for biomedical applications: A review

Nanofibers have a particular benefit when delivering a spectrum of therapeutic drugs for diverse biomedical applications. Nanofibers are easily fabricated from cellulose acetate, chitosan, polycaprolactone, and other polymers with regulated morphology and release profiles due to nanotechnology's recent advancement. This review will provide the latest approaches to the fabrication of electrospun nanofibers containing herbal extracts, antimicrobial peptides, and antibiotics for wound-healing potential. Besides, synthesis and evaluation of nanofibrous mats, including conducting polymer and evaluate their possibility for wound healing. In addition, nanofibers are loaded with some drugs for skin cancer treatment and contain growth factors for tissue regeneration. Also, the current two-dimensional nanofibers limitations and the various techniques for convert two-dimensional to three-dimension nanofibers to avoid these drawbacks. Moreover, the future direction in improving the three-dimensional structure and functionality has been including.

Probing the Mode of Antibacterial Action of Silver Nanoparticles Synthesized by Laser Ablation in Water: What Fluorescence and AFM Data Tell Us

We aim to elucidate the mode of antibacterial action of the laser-synthesized silver colloid against Escherichia coli. Membrane integrity was studied by flow cytometry, while the strain viability of the treated culture was determined by plating. The spectrofluorometry was used to obtain the time development of the reactive oxygen species (ROS) inside the nanoparticle-treated bacterial cells. An integrated atomic force and bright-field/fluorescence microscopy system enabled the study of the cell morphology, Young modulus, viability, and integrity before and during the treatment. Upon lethal treatment, not all bacterial cells were shown to be permeabilized and have mostly kept their morphology with an indication of cell lysis. Young modulus of untreated cells was shown to be distinctly bimodal, with randomly distributed softer parts, while treated cells exhibited exponential softening of the stiffer parts in time. Silver nanoparticles and bacteria have shown a masking effect on the raw fluorescence signal through absorbance and scattering. The contribution of cellular ROS in the total fluorescence signal was resolved and it was proven that the ROS level inside the lethally treated cells is not significant. It was found that the laser-synthesized silver nanoparticles mode of antibacterial action includes reduction of the cell's Young modulus in time and subsequently the cell leakage.

A Rapid Fluorescence-Based Microplate Assay to Investigate the Interaction of Membrane Active Antimicrobial Peptides with Whole Gram-Positive Bacteria

Background: Membrane-active antimicrobial peptides (AMPs) are interesting candidates for the development of novel antimicrobials. Although their effects were extensively investigated in model membrane systems, interactions of AMPs with living microbial membranes are less known due to their complexity. The aim of the present study was to develop a rapid fluorescence-based microplate assay to analyze the membrane effects of AMPs in whole Staphylococcus aureus and Staphylococcus epidermidis. Methods: Bacteria were exposed to bactericidal and sub-inhibitory concentrations of two membrane-active AMPs in the presence of the potential-sensitive dye 3,3′-dipropylthiadicarbocyanine iodide (diSC₃(5)) and the DNA staining dye propidium iodide (PI), to simultaneously monitor and possibly distinguish membrane depolarization and membrane permeabilization. Results: The ion channel-forming gramicidin D induced a rapid increase of diSC₃(5), but not PI fluorescence, with slower kinetics at descending peptide concentrations, confirming killing due to membrane depolarization. The pore-forming melittin, at sub-MIC and bactericidal concentrations, caused, respectively, an increase of PI fluorescence in one or both dyes simultaneously, suggesting membrane permeabilization as a key event. Conclusions: This assay allowed the distinction between specific membrane effects, and it could be applied in the mode of action studies as well as in the screening of novel membrane-active AMPs.

Halogenated boroxine dipotassium trioxohydroxytetrafluorotriborate K2[B3O3F4OH] inhibits emerging multidrug-resistant and β-lactamase-producing opportunistic pathogens

Halogenated boroxine dipotassium trioxohydroxytetrafluorotriborate, K₂[B₃O₃F₄OH] (boroxine) was previously shown to be very effective in inhibition of several carcinoma cell lines, including the skin cancer. Here, we investigated its antimicrobial potential by targeting the multidrug-resistant opportunistic pathogens associated with skin and wound infections. The antimicrobial testing against eleven bacterial and four fungal species revealed good activity of boroxine against pathogenic filamentous fungi Penicillium funiculosum and Aspergillus niger (MIC₅₀ 64 and 128 µg/ml), and a moderate bioactivity against the yeast Candida albicans (MIC₅₀ 512 µg/ml). Among the tested multidrug-resistant bacteria, the best antibacterial effect, stable over a 24-h period, was observed against the methicillin-resistant Staphylococcus aureus strain (MRSA) at MIC of 1024 µg/ml. The atomic force microscopy (AFM) used to investigate the morphology of S. aureus cells revealed indentations on its cell envelope after the boroxine exposure. These results show that in addition to the antitumor effect, boroxine exerts wide spectrum antimicrobial activity, thus may help preventing the development of skin and wound-related opportunistic infections.