Spectroscopic, zeta potential and molecular dynamics studies of the interaction of antimicrobial peptides with model bacterial membrane

Recent Advances on Antimicrobial Peptides from Milk: Molecular Properties, Mechanisms, and Applications

Traditional antibiotics are facing a tremendous challenge due to increased antimicrobial resistance; hence, there is an urgent need to find novel antibiotic alternatives. Milk protein-derived antimicrobial peptides (AMPs) are currently attracting substantial attention considering that they showcase an extensive spectrum of antimicrobial activities, with slower development of antimicrobial resistance and safety of raw materials. This review summarizes the molecular properties, and activity mechanisms and highlights the applications and limitations of AMPs derived from milk proteins comprehensively. Also the analytical technologies, especially bioinformatics methodologies, applied in the process of screening, identification, and mechanism illustration of AMPs were underlined. This review will give some ideas for further research and broadening of the applications of milk protein-derived AMPs in the food field.

Development and challenges of antimicrobial peptide delivery strategies in bacterial therapy: A review

The escalating global prevalence of antimicrobial resistance poses a critical threat, prompting concerns about its impact on public health. This predicament is exacerbated by the acute shortage of novel antimicrobial agents, a scarcity attributed to the rapid surge in bacterial resistance. This review delves into the realm of antimicrobial peptides, a diverse class of compounds ubiquitously present in plants and animals across various natural organisms. Renowned for their intrinsic antibacterial activity, these peptides provide a promising avenue to tackle the intricate challenge of bacterial resistance. However, the clinical utility of peptide-based drugs is hindered by limited bioavailability and susceptibility to rapid degradation, constraining efforts to enhance the efficacy of bacterial infection treatments. The emergence of nanocarriers marks a transformative approach poised to revolutionize peptide delivery strategies. This review elucidates a promising framework involving nanocarriers within the realm of antimicrobial peptides. This paradigm enables meticulous and controlled peptide release at infection sites by detecting dynamic shifts in microenvironmental factors, including pH, ROS, GSH, and reactive enzymes. Furthermore, a glimpse into the future reveals the potential of targeted delivery mechanisms, harnessing inflammatory responses and intricate signaling pathways, including adenosine triphosphate, macrophage receptors, and pathogenic nucleic acid entities. This approach holds promise in fortifying immunity, thereby amplifying the potency of peptide-based treatments. In summary, this review spotlights peptide nanosystems as prospective solutions for combating bacterial infections. By bridging antimicrobial peptides with advanced nanomedicine, a new therapeutic era emerges, poised to confront the formidable challenge of antimicrobial resistance head-on.

Detecting the Mechanism of Action of Antimicrobial Peptides by Using Microscopic Detection Techniques

Increasing antibiotic resistance has shifted researchers’ focus to antimicrobial peptides (AMPs) as alternatives to antibiotics. AMPs are small, positively charged, amphipathic peptides with secondary helical structures. They have the ability to disrupt the bacterial membrane and create wedges due to electrostatic differences. Water molecules enter the pathogens through those wedges and disrupt their normal cellular functioning, eventually causing the death of the pathogens. Keeping in mind the importance of AMPs, this review compiles recent data and is divided into three parts. The first part explains the AMP structure and properties, the second part comprises the spectroscopy techniques currently used for evaluating the AMP-bacterial targeting mechanism as well as its structure and safety; and the third part describes the production of AMPs from an animal source (whey protein). Most of the peptides that were used in recent studies have been either the precursors of a natural peptide or synthetic peptides with some modifications, but data on the exploitation of dairy protein are scarce. Among the little-studied milk proteins and peptides, in the last three years, whey protein has been studied the least based on the reported data. Because whey protein is a leftover part of cheese making that often drains out as cheese waste, causing soil and environmental pollution, today, the need of the hour is to produce safe AMPs from whey protein. The use of whey protein that is based on hydrolyzing lactic acid bacteria with some structural modifications can increase AMPs’ potency, stability, and safety, and it can also help to avoid soil and environmental pollution as a result of whey drainage.

Usnic acid induced changes in biomolecules and their association with apoptosis in squamous carcinoma (A-431) cells: A flow cytometry, FTIR and DLS spectroscopic study

Many natural products induce apoptotic cell death in cancer cells, though studies on their interactions with macromolecules are limited. For the first time, this study demonstrated the cytotoxic potential of usnic acid (UA) against squamous carcinoma (A-431) cells and the associated changes in cell surface proteins, lipids and DNA by attenuated total reflection- fourier transform infrared spectroscopy (ATR-FTIR) and dynamic light scattering (DLS) spectroscopic studies. The IC₅₀ for UA was 98.9 µM after treatment of A-431 cells for 48 h, while the IC₅₀ reduced to 39.2 µM after 72 h of incubation time. UA induced oxidative stress in treated cells as confirmed by DCFHDA flow cytometry assay, depletion in reduced glutathione and increase in lipid peroxidation. The oxidative stress resulted in conformation change in amide I, amide II protein bands and DNA as observed by ATR-FTIR in UA treated A-431 cells. Shift in secondary structures of proteins from α helix to β sheets and structural changes in DNA was observed in UA treated A-431 cells. An increase in the band intensity of phospholipids, increased distribution of lipid and change in membrane potential was noted in UA treated cells, which was confirmed by externalization of phosphatidylserine to the outer membrane by annexin V-FITC/PI assay. Increase in mitochondrial membrane potential, cell cycle arrest at G0/G1 phase by flow cytometry and activation of caspase-3/7 dependent proteins confirmed the UA induced apoptosis in treated A-431 cells. FTIR and DLS spectroscopy confirmed the changes in biomolecules after UA treatment, which were associated with apoptosis, as observed by flow cytometry.

Is It Possible to Find an Antimicrobial Peptide That Passes the Membrane Bilayer with Minimal Force Resistance? An Attempt at a Predictive Approach by Molecular Dynamics Simulation

There is still no answer to the mechanism of penetration of AMP peptides through the membrane bilayer. Several mechanisms for such a process have been proposed. It is necessary to understand whether it is possible, using the molecular dynamics method, to determine the ability of peptides of different compositions and lengths to pass through a membrane bilayer. To explain the passage of a peptide through a membrane bilayer, a method for preparing a membrane phospholipid bilayer was proposed, and 656 steered molecular dynamics calculations were carried out for pulling 7 amyloidogenic peptides with antimicrobial potential, and monopeptides (homo-repeats consisting of 10 residues of the same amino acid: Poly (Ala), Poly (Leu), Poly (Met), Poly (Arg), and Poly (Glu)) with various sequences through the membrane. Among the 15 studied peptides, the peptides exhibiting the least force resistance when passing through the bilayer were found, and the maximum reaction occurred at the boundary of the membrane bilayer entry. We found that the best correlation between the maximum membrane reaction force and the calculated parameters corresponds to the instability index (the correlation coefficient is above 0.9). One of the interesting results of this study is that the 10 residue amyloidogenic peptides and their extended peptides, with nine added residue cell-penetrating peptides and four residue linkers, both with established antimicrobial activity, have the same bilayer resistance force. All calculated data are summarized and posted on the server.

An evidence of pores in phospholipid membrane induced by an antimicrobial peptide NK-2

NK-2, a peptide derived from a cationic core region of NK-lysin, has emerged as a promising candidate for new antibiotics. In contrast to classical antibiotics, antimicrobial peptides target bacterial membranes and disintegrate the membrane by forming the transmembrane pores. However, complete understanding of the precise mechanisms of cellular apoptosis and molecular basis of membrane selectivity is still in dispute. In the present study, we have shown that NK-2 forms trans-membrane pores on negatively charged phospholipid membranes using phase contrast microscopy. As bacteria mimicking membranes, we have chosen large unilamellar vesicles (LUV) and giant unilamellar vesicles (GUV) composed of negatively charged phospholipid, dioleoyl phosphatidyl glycerol (DOPG) and neutral phospholipid, dioleoyl phophatidylcholine (DOPC). Leakage of internal fluid of giant unilamellar vesicles (GUV), leading to decrease in intensity in the halo region of phase contrast micrographs, suggests the formation of transmembrane pores. No such reduction of intensity in the halo region of DOPC was observed, indicating, neutral vesicles does not exhibit pores. Rate constant reckoned from the decaying intensity in the halo region was found to be 0.007 s^-1. Further, significant interaction of NK-2 with anionic membranes has been envisaged from zeta potential and dynamic light scattering. Binding free energy and other interaction parameters have been delineated using theoretical ansatz. A proliferation of average Size of anionic LUV on increasing NK-2 concentration indicates membrane-membrane interaction leading to peptide induced large aggregates of vesicles.

Spectroscopic study of antimicrobial peptides: Structure and functional activity

Amphibians are a natural source of a large number of peptides with a wide range of functional activities. Here, a complex of spectroscopic methods including NMR-, FTIR-, CD-, and UV-spectroscopy was applied to characterize the structure and functional activity of megin-1, a peptide isolated from amphibian skin. The three-dimensional structure of two forms of the peptide was determined using solution NMR spectroscopy. Thermodynamic characteristics of the process of peptide transformation from linear to cyclic form were obtained. Antibacterial and antimycotic properties of the peptide, as well as its protease inhibitory activities, were analyzed.

Antimicrobial Peptides: An Update on Classifications and Databases

Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.

The effect of acidic pH on the adsorption and lytic activity of the peptides Polybia-MP1 and its histidine-containing analog in anionic lipid membrane: a biophysical study by molecular dynamics and spectroscopy

Antimicrobial peptides (AMPs) are part of the innate immune system of many species. AMPs are short sequences rich in charged and non-polar residues. They act on the lipid phase of the plasma membrane without requiring membrane receptors. Polybia-MP1 (MP1), extracted from a native wasp, is a broad-spectrum bactericide, an inhibitor of cancer cell proliferation being non-hemolytic and non-cytotoxic. MP1 mechanism of action and its adsorption mode is not yet completely known. Its adsorption to lipid bilayer and lytic activity is most likely dependent on the ionization state of its two acidic and three basic residues and consequently on the bulk pH. Here we investigated the effect of bulk acidic (pH 5.5) and neutral pH (7.4) solution on the adsorption, insertion, and lytic activity of MP1 and its analog H-MP1 to anionic (7POPC:3POPG) model membrane. H-MP1 is a synthetic analog of MP1 with lysines replaced by histidines. Bulk pH changes could modulate this peptide efficiency. The combination of different experimental techniques and molecular dynamics (MD) simulations showed that the adsorption, insertion, and lytic activity of H-MP1 are highly sensitive to bulk pH in opposition to MP1. The atomistic details, provided by MD simulations, showed peptides contact their N-termini to the bilayer before the insertion and then lay parallel to the bilayer. Their hydrophobic faces inserted into the acyl chain phase disturb the lipid-packing.

Modulatory Effects of Acidic pH and Membrane Potential on the Adsorption of pH-Sensitive Peptides to Anionic Lipid Membrane

Anionic lipid membrane electrostatic potential and solution pH can influence cationic peptide adsorption to these bilayers, especially those containing simultaneously acid and basic residues. Here, we investigate the effects of the pH solution on MP1 (IDWKKLLDAAKQIL-NH2) adsorption to anionic (7POPC:3POPG) lipid vesicles in comparison to its analog H-MP1, with histidines substituting lysines. We used the association of adsorption isotherms and constant pH molecular dynamic simulations (CpHMD) to explore the effects of membrane potential and pH on peptides' adsorption on this lipid membrane. We analyzed the fluorescence and zeta potential adsorption isotherms using the Gouy-Chapman theory. In CpHMD simulations for the peptides in solution and adsorbed on the lipid bilayer, we used the conformations obtained by conventional MD simulations at a μs timescale. Non-equilibrium Monte Carlo simulations provided the protonation states of acidic and basic residues. CpHMD showed average pKa shifts of two to three units, resulting in a higher net charge for the analog than for MP1, strongly modulating the peptide adsorption. The fractions of the protonation of acidic and basic residues and the peptides' net charges obtained from the analysis of the adsorption isotherms were in reasonable agreement with those from CpHMD. MP1 adsorption was almost insensitive to solution pH. H-MP1 was much more sensitive to partitioning, at acidic pH, with an affinity ten times higher than in neutral ones.

Palladium-catalyzed selective defluorinative arylation for the efficient stereospecific synthesis of (E)-β-fluoroacrylamides

A practical and efficient method for the synthesis of (E)-β-fluoroacrylamides was developed by the selective defluorinative arylation of trifluoropropanamides with arylboronic acids.

Copper-Catalyzed Selective Defluorinative Sulfuration of Trifluoropropanamides Leading to α-Fluorothioacrylamides

A practical and efficient method for the synthesis of α-fluorothioacrylamide was developed from selective defluorinative sulfuration of trifluoropropanamides with disulfides. The N-chelation-assisted copper-catalyzed defluorination and sulfurization reactions feature excellent functional group tolerance and incorporation of both sulfur atoms of disulfides into acrylamides.

Preparation and Characterization of a Composite Dust Suppressant for Coal Mines

In an effort to effectively control coal dust pollution and thereby reduce the harm of coal dust to human health, we prepared a highly efficient composite dust suppressant. First, dynamic contact angle and zeta potential measurements were used to select sodium dodecyl sulfonate (SDS) over sodium carboxymethyl cellulose and trisodium methyl silicon as the complementary additive to soy protein isolate for the dust suppressant. We employed viscosity and wind erosion resistance tests to compare the performance of the composite dust suppressant with three common, commercially available suppressants. As the concentration of the composite dust suppressant was increased, the viscosity increased, reaching a maximum value of 22.7 mPa·s at a concentration of 5 wt%. The 5 wt% concentration of the composite dust suppressant provided the lowest wind erosion rate (20.62%) at a wind speed of 12 m/s. The composite dust suppressant also had good bonding performance and wind erosion resistance. Scanning electron microscopy, X-ray diffraction, and thermogravimetric analysis were used to characterize the properties of the dust suppressants. The dust suppressant, which had a crystal-like structure, could easily capture coal dust and form an effective package. In addition, the density of the dust suppressant film increased as its crystallinity increased. The increased density was beneficial in that it enabled the dust suppressant to form a hard, solidified shell on the surface of coal dust, which improved dust suppression. The composite dust suppressant also had good thermal stability.

The Best Peptidomimetic Strategies to Undercover Antibacterial Peptides

Health-care systems that develop rapidly and efficiently may increase the lifespan of humans. Nevertheless, the older population is more fragile, and is at an increased risk of disease development. A concurrently growing number of surgeries and transplantations have caused antibiotics to be used much more frequently, and for much longer periods of time, which in turn increases microbial resistance. In 1945, Fleming warned against the abuse of antibiotics in his Nobel lecture: "The time may come when penicillin can be bought by anyone in the shops. Then there is the danger that the ignorant man may easily underdose himself and by exposing his microbes to non-lethal quantities of the drug make them resistant". After 70 years, we are witnessing the fulfilment of Fleming's prophecy, as more than 700,000 people die each year due to drug-resistant diseases. Naturally occurring antimicrobial peptides protect all living matter against bacteria, and now different peptidomimetic strategies to engineer innovative antibiotics are being developed to defend humans against bacterial infections.