Structural and positional studies of the antimicrobial peptide brevinin‐1BYa in membrane‐mimetic environments

Mechanistic Insight into the Early Stages of Toroidal Pore Formation by the Antimicrobial Peptide Smp24

The antimicrobial peptide Smp24, originally derived from the venom of Scorpio maurus palmatus, is a promising candidate for further drug development. However, before doing so, greater insight into the mechanism of action is needed to construct a reliable structure-activity relationship. The aim of this study was to specifically investigate the critical early stages of peptide-induced membrane disruption. Single-channel current traces were obtained via planar patch-clamp electrophysiology, with multiple types of pore-forming events observed, unlike those expected from the traditional, more rigid mechanistic models. To better understand the molecular-level structures of the peptide-pore assemblies underlying these observed conductance events, molecular dynamics simulations were used to investigate the peptide structure and orientation both before and during pore formation. The transition of the peptides to transmembrane-like states within disordered toroidal pores occurred due to a peptide-induced bilayer-leaflet asymmetry, explaining why pore stabilization does not always follow pore nucleation in the experimental observations. To fully grasp the structure-activity relationship of antimicrobial peptides, a more nuanced view of the complex and dynamic mechanistic behaviour must be adopted.

Going Beyond Host Defence Peptides: Horizons of Chemically Engineered Peptides for Multidrug-Resistant Bacteria

Multidrug-resistant (MDR) bacteria are considered a health threat worldwide, and this problem is set to increase over the decades. The ESKAPE, a group of six pathogens including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. is the major source of concern due to their high death incidence and nosocomial acquired infection. Host defence peptides (HDPs) are a class of ribosomally synthesised peptides that have shown promising results in combating MDR, including the ESKAPE group, in- and outside bacterial biofilms. However, their poor pharmacokinetics in physiological mediums may impede HDPs from becoming viable clinical candidates. To circumvent this problem, chemical engineering of HDPs has been seen as an emergent approach to not only improve their pharmacokinetics but also their efficacy against pathogens. In this review, we explore several chemical modifications of HDPs that have shown promising results, especially against ESKAPE pathogens, and provide an overview of the current findings with respect to each modification.

Peptidomic analysis of the host-defense peptides in skin secretions of the Amazon River frog Lithobates palmipes (Ranidae)

Skin secretions of certain frog species represent a source of host-defense peptides (HDPs) with therapeutic potential and their primary structures provide insight into taxonomic and phylogenetic relationships. Peptidomic analysis was used to characterize the HDPs in norepinephrine-stimulated skin secretions from the Amazon River frog Lithobates palmipes (Ranidae) collected in Trinidad. A total of ten peptides were purified and identified on the basis of amino acid similarity as belonging to the ranatuerin-2 family (ranatuerin-2PMa, -2PMb, -2PMc, and-2PMd), the brevinin-1 family (brevinin-1PMa, -1PMb, -1PMc and des(8-14)brevinin-1PMa) and the temporin family (temporin-PMa in C-terminally amidated and non-amidated forms). Deletion of the sequence VAAKVLP from brevinin-1PMa (FLPLIAGVAAKVLPKIFCAISKKC) in des[(8-14)brevinin-1PMa resulted in a 10-fold decrease in potency against Staphylococcus aureus (MIC = 31 μM compared with 3 μM) and a > 50-fold decrease in hemolytic activity but potency against Echerichia coli was maintained (MIC = 62.5 μM compared with 50 μM). Temporin-PMa (FLPFLGKLLSGIF.NH₂) inhibited growth of S. aureus (MIC = 16 μM) but the non-amidated form of the peptide lacked antimicrobial activity. Cladistic analysis based upon the primary structures of ranaturerin-2 peptides supports the division of New World frogs of the family Ranidae into the genera Lithobates and Rana. A sister-group relationship between L. palmipes and Warszewitsch's frog Lithobates warszewitschii is indicated within a clade that includes the Tarahumara frog Lithobates tarahumarae. The study has provided further evidence that peptidomic analysis of HDPs in frog skin secretions is a valuable approach to elucidation of the evolutionary history of species within a particular genus.

Design, characterization and structure-function analysis of novel antimicrobial peptides based on the N-terminal CATH-2 fragment

The emergence of multidrug resistance coupled with shrinking antibiotic pipelines has increased the demand of antimicrobials with novel mechanisms of action. Therefore, researchers across the globe are striving to develop new antimicrobial substances to alleviate the pressure on conventional antibiotic therapies. Host-Defence Peptides (HDPs) and their derivatives are emerging as effective therapeutic agents against microbial resistance. In this study, five analogs (DP1-5) of the N-terminal (N-15) fragment of CATH-2 were designed based on the delicate balance between various physicochemical properties such as charge, aliphatic character, amphipathicity and hydrophobicity. By means of in-silico and in-vitro studies a novel peptide (DP1) with the sequence “RFGRFLRKILRFLKK” was found to be more effective and less toxic than the N-terminal CATH-2 peptide. Circular dichroism spectroscopy and differential scanning calorimetry were applied for structural insights. Antimicrobial, haemolytic, and cytotoxic activities were also assessed. The resulting peptide was characterized by low cytotoxicity, low haemolytic activity, and efficient anti-microbial activity. Structurally, it displayed strong helical properties irrespective of the solvent environment and was stable in membrane-mimicking environments. Taken together, the data suggests that DP1 can be explored as a promising therapeutic agent with possible clinical applications.

Membrane mechanism of temporin-1CEc, an antimicrobial peptide isolated from the skin secretions of Rana chensinensis, and its systemic analogs

Antimicrobial peptides (AMPs) are new and powerful target molecules in the development of new antibacterial agents. Temporin-1CEc, a natural peptide isolated and purified from the skin secretions of the Chinese brown frog Rana chensinensis, exhibits low or no antibacterial activity against gram-negative and gram-positive bacteria, which limits its potential therapeutic use; however, it displays low hemolysis to human erythrocytes. Here, a series of temporin-1CEc analogs was designed and synthesized by amino acid residue substitutions based on cationicity, hydrophobicity, amphipathicity and secondary structure to understand the structure-activity relationships of this peptide in depth. The results showed that all of the analogs, except for 2K and 4K, had significantly improved antibacterial activity against the tested standard bacterial strains and multidrug-resistant bacterial strains compared to temporin-1CEc. 2K2L and 2K4L, but not 4K2L and 4K4L, showed the strongest antibacterial activity compared with their parent peptides 2K and 4K, suggesting that peptide hydrophobicity plays a more important role in antibacterial activity than cationicity for this series of AMPs. However, the antibacterial activity of the 6 Trp-containing analogs of 2K4L decreased with a further increase in hydrophobicity based on the results of 2K4L, indicating that it is more important to balance cationicity and hydrophobicity. Moreover, an increase in AMP hydrophobicity led to hemolysis. Notably, all of the peptides adopted α-helical structures in 50% trifluoroethanol/water and 30 mM SDS solutions. 2K2L and 2K4L displayed broad-spectrum antibacterial activity against sensitive and multidrug-resistant bacteria, effectively killing the tested multidrug resistant strain Staphylococcus epidermidis (MRSE1208). 2K2L and 2K4L were able to increase the permeability of the outer and inner membranes by depolarization and disturb the integration of the cytoplasmic membrane of MRSE1208 cells, leading to leakage of its cellular contents. In addition, 2K2L and 2K4L at low concentrations inhibited biofilm formation and degraded mature 1-day-old MRSE1208 biofilms. Notably, 2K2L and 2K4L inhibited the formation of MRSE1208 biofilms at concentrations below its MIC value, suggesting that the peptide may exert an inhibitory effect through not only direct antimicrobial activity but also a biofilm-specific mechanism. Collectively, these results suggest that 2K2L and 2K4L could be effective antibiotics against multidrug-resistant bacterial strains.

Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca

Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defence peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dimensional structure in a 50/50% water/2,2,2-trifluoroethanol-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$d_{3}$$\end{document}d3 mixture. The structure is defined by an \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\alpha$$\end{document}α-helix that spans between Ile\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{6}$$\end{document}6-Ala\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{26}$$\end{document}26, and a cyclic disulfide-bridged domain at the C-terminal end of the peptide sequence, between residues 23 and 29. A molecular dynamics simulation was employed to model the peptide’s interactions with sodium dodecyl sulfate micelles, a widely used bacterial membrane-mimicking environment. Throughout the simulation, the peptide was found to maintain its \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\alpha$$\end{document}α-helical conformation between residues Ile\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{6}$$\end{document}6-Ala\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{26}$$\end{document}26, while adopting a position parallel to the surface to micelle, which is energetically-favourable due to many hydrophobic and electrostatic contacts with the micelle.

APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures

Good knowledge of a peptide's tertiary structure is important for understanding its function and its interactions with its biological targets. APPTEST is a novel computational protocol that employs a neural network architecture and simulated annealing methods for the prediction of peptide tertiary structure from the primary sequence. APPTEST works for both linear and cyclic peptides of 5-40 natural amino acids. APPTEST is computationally efficient, returning predicted structures within a number of minutes. APPTEST performance was evaluated on a set of 356 test peptides; the best structure predicted for each peptide deviated by an average of 1.9Å from its experimentally determined backbone conformation, and a native or near-native structure was predicted for 97% of the target sequences. A comparison of APPTEST performance with PEP-FOLD, PEPstrMOD and PepLook across benchmark datasets of short, long and cyclic peptides shows that on average APPTEST produces structures more native than the existing methods in all three categories. This innovative, cutting-edge peptide structure prediction method is available as an online web server at https://research.timmons.eu/apptest, facilitating in silico study and design of peptides by the wider research community.

ENNAVIA is a novel method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides

Viruses represent one of the greatest threats to human health, necessitating the development of new antiviral drug candidates. Antiviral peptides often possess excellent biological activity and a favourable toxicity profile, and therefore represent a promising field of novel antiviral drugs. As the quantity of sequencing data grows annually, the development of an accurate in silico method for the prediction of peptide antiviral activities is important. This study leverages advances in deep learning and cheminformatics to produce a novel sequence-based deep neural network classifier for the prediction of antiviral peptide activity. The method outperforms the existent best-in-class, with an external test accuracy of 93.9%, Matthews correlation coefficient of 0.87 and an Area Under the Curve of 0.93 on the dataset of experimentally validated peptide activities. This cutting-edge classifier is available as an online web server at https://research.timmons.eu/ennavia, facilitating in silico screening and design of peptide antiviral drugs by the wider research community.

Biophysical study of the structure and dynamics of the antimicrobial peptide maximin 1

Maximin 1 is a cationic, amphipathic antimicrobial peptide found in the skin secretions and brains of the Chinese red belly toad Bombina maxima. The 27 amino acid residue-long peptide is biologically interesting as it possesses a variety of biological activities, including antibacterial, antifungal, antiviral, antitumour and spermicidal activities. Its three-dimensional structural model was obtained in a 50/50% water/2,2,2-trifluoroethanol-d₃ mixture using two-dimensional NMR spectroscopy. Maximin 1 was found to adopt an α-helical structure from residue Ile² to Ala²⁶ . The peptide is amphipathic, showing a clear separation between polar and non-polar residues. The interactions with sodium dodecyl sulfate micelles, a widely-used bacterial membrane-mimicking environment, were modelled using molecular dynamics simulations. The peptide maintains an α-helical conformation, occasionally displaying a flexibility around the Gly⁹ and Gly¹⁶ residues, which is likely responsible for the peptide's low haemolytic activity. It is found to preferentially adopt a position parallel to the micellar surface, establishing a number of hydrophobic and electrostatic interactions with the micelle.

Brevinin-1GHd: a novel Hylarana guentheri skin secretion-derived Brevinin-1 type peptide with antimicrobial and anticancer therapeutic potential

Host-defense antimicrobial peptides (AMPs) from amphibians are usually considered as one of the most promising next-generation antibiotics because of their excellent antimicrobial properties and low cytotoxicity. In the present study, one novel Brevinin-1 type peptide, Brevinin-1GHd, was isolated and characterized from the skin secretion of the frog, Hylarana guentheri. Brevinin-1GHd was found to possess a wide range of antimicrobial activity through penetrating the bacterial membrane within a short time while showing low hemolysis at bactericidal concentrations, even against the resistant strains. It also inhibited and eradicated biofilms that are thought to be closely related to the rise in resistance. Meanwhile, Brevinin-1GHd exhibited wide-spectrum anti-proliferation activity toward human cancer lines. Taken together, these results indicate that Brevinin-1GHd with its excellent antimicrobial and anticancer activities is a promising candidate for a novel antibiotic agent, and study of its structure–activity relationships also provided a rational template for further research and peptide analog design.

ENNAACT is a novel tool which employs neural networks for anticancer activity classification for therapeutic peptides

The prevalence of cancer as a threat to human life, responsible for 9.6 million deaths worldwide in 2018, motivates the search for new anticancer agents. While many options are currently available for treatment, these are often expensive and impact the human body unfavourably. Anticancer peptides represent a promising emerging field of anticancer therapeutics, which are characterized by favourable toxicity profile. The development of accurate in silico methods for anticancer peptide prediction is of paramount importance, as the amount of available sequence data is growing each year. This study leverages advances in machine learning research to produce a novel sequence-based deep neural network classifier for anticancer peptide activity. The classifier achieves performance comparable to the best-in-class, with a cross-validated accuracy of 98.3%, Matthews correlation coefficient of 0.91 and an Area Under the Curve of 0.95. This innovative classifier is available as a web server at https://research.timmons.eu/ennaact, facilitating in silico screening and design of new anticancer peptide chemotherapeutics by the research community.

A Novel Amphibian Antimicrobial Peptide, Phylloseptin-PV1, Exhibits Effective Anti-staphylococcal Activity Without Inducing Either Hepatic or Renal Toxicity in Mice

In order to part address the problem of drug-resistant pathogens, antimicrobial peptides (AMPs) have been proposed as alternatives to traditional antibiotics. Herein, a novel phylloseptin peptide, named phylloseptin-PV1 (PPV1), is described from the defensive skin secretion of the Neotropical white-lined leaf frog, Phyllomedusa vaillantii. The peptide was synthesized by solid phase peptide synthesis (SPPS) and purified by RP-HPLC, prior to assessment of its biological activities. PPV1 not only demonstrated potent antimicrobial activity against planktonic ESKAPE microorganisms and the yeast, Candida albicans, but also inhibited and eradicated Staphylococcus aureus and MRSA biofilms. The antimicrobial mechanism was shown to include permeabilization of target cell membranes. The in vivo antimicrobial activity of the peptide was then evaluated using mice. PPV1 also exhibited antiproliferative activity against the cancer cell lines, H157, MCF-7, and U251MG, but had a lower potency against the normal cell line, HMEC-1. Although, the peptide possessed a moderate hemolytic action on mammalian red blood cells in vitro, it did not induce significant hepatic or renal toxicity in injected infected mice. These studies have thus found PPV1 to be a potent phylloseptin group AMP, which can effectively inhibit staphylococci, both in vitro and in vivo, without eliciting toxicity. These data thus provide support for further evaluation of PPV1 as a novel antimicrobial agent with therapeutic potential.

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.

HAPPENN is a novel tool for hemolytic activity prediction for therapeutic peptides which employs neural networks

The growing prevalence of resistance to antibiotics motivates the search for new antibacterial agents. Antimicrobial peptides are a diverse class of well-studied membrane-active peptides which function as part of the innate host defence system, and form a promising avenue in antibiotic drug research. Some antimicrobial peptides exhibit toxicity against eukaryotic membranes, typically characterised by hemolytic activity assays, but currently, the understanding of what differentiates hemolytic and non-hemolytic peptides is limited. This study leverages advances in machine learning research to produce a novel artificial neural network classifier for the prediction of hemolytic activity from a peptide's primary sequence. The classifier achieves best-in-class performance, with cross-validated accuracy of [Formula: see text] and Matthews correlation coefficient of 0.71. This innovative classifier is available as a web server at https://research.timmons.eu/happenn , allowing the research community to utilise it for in silico screening of peptide drug candidates for high therapeutic efficacies.

Brevinin-2GHk from Sylvirana guentheri and the Design of Truncated Analogs Exhibiting the Enhancement of Antimicrobial Activity

Brevinins are an important antimicrobial peptide (AMP) family discovered in the skin secretions of Ranidae frogs. The members demonstrate a typical C-terminal ranabox, as well as a diverse range of other structural characteristics. In this study, we identified a novel brevinin-2 peptide from the skin secretion of Sylvirana guentheri, via cloning transcripts, and identifying the expressed mature peptide, in the skin secretion. The confirmed amino acid sequence of the mature peptide was designated brevinin-2GHk (BR2GK). Moreover, as a previous study had demonstrated that the N-terminus of brevinin-2 is responsible for exerting antimicrobial activity, we also designed a series of truncated derivatives of BR2GK. The results show that the truncated derivatives exhibit significantly improved antimicrobial activity and cytotoxicity compared to the parent peptide, except a Pro¹⁴ substituted analog. The circular dichroism (CD) analysis of this analog revealed that it did not fold into a helical conformation in the presence of either lipopolysaccharides (LPS) or TFE, indicating that position 14 is involved in the formation of the α-helix. Furthermore, three more analogs with the substitutions of Ala, Lys and Arg at the position 14, respectively, revealed the influence on the membrane disruption potency on bacteria and mammalian cells by the structural changes at this position. Overall, the N-terminal 25-mer truncates demonstrated the potent antimicrobial activity with low cytotoxicity.