De novo generation of cationic antimicrobial peptides: influence of length and tryptophan substitution on antimicrobial activity

Lipidated SNAPP-Stars Target and Kill Multidrug-Resistant Bacteria within Minutes

The fast emergence of bacteria resistance has already threatened global health, and immediate action is required before the emergence of another global pandemic. Despite substantial progress in the chemical synthesis of novel antimicrobial compounds and advancements in understanding antimicrobial resistance, there has been only a handful of new antibiotics coming to the market. Structurally Nanoengineered Antimicrobial Peptide Polymers (SNAPP-stars) are a new class of antimicrobials. Here, we show that lipidation of lysine-valine 16-armed SNAPP-star, S16 (lipo-SNAPP-star) where the N-terminal arms are conjugated with different fatty acids (caproic, C6, lauric, C12, and stearic acid, C18) enhanced the antimicrobial activity toward S. aureus and MRSA. Lipidation enhanced activity by targeting the SNAPP-stars to the bacterial surface by binding to peptidoglycan, leading to greater inner membrane disruption and depolarization. Lipo-SNAPP-stars killed bacteria in under a minute, whereas vancomycin took >16 h. Lipo-SNAPP-stars were found to preferentially target and kill MRSA rather than S. aureus in a mixed bacteria model. Lipid chain length affected activity, with C6-S16 having greater activity compared to C12-S16 > C18-S16. Lauric and stearic acid enhanced SNAPP-star binding to the bacterial surface and membrane depolarization but impeded SNAPP-stars' ability to transit through the peptidoglycan layer to disrupt the inner membrane. Microbial flow cytometry showed that lipidation aided binding to bacteria via lipoteichoic acid and specifically to peptidoglycan. Further, lipid length enhanced bacterial binding with C18-S16 > C12-S16 > C6-S16 = S16, which contrasts the activity order of C6-S16 > S16 ≫ C12-S16 ≫ C18-S16. Our data demonstrate that lipidation enhances antimicrobial activity by targeting and binding an antimicrobial to peptidoglycan, but increasing lipid length reduces activity by retaining the antimicrobial in the outer layer. Lipidation of SNAPP-stars did not increase cytotoxicity, with C6-S16 having an improved therapeutic index compared to S16. Our data show how lipidation of SNAPP-stars enhances its antimicrobial activity, resulting in a highly biocompatible antimicrobial that targets and kills the "superbug" MRSA within minutes.

Machine learning-driven discovery of highly selective antifungal peptides containing non-canonical β-amino acids

Antimicrobial peptides (AMPs) are promising compounds for the treatment and prevention of multidrug-resistant infections because of their ability to directly disrupt microbial membranes, a mechanism that is less likely to lead to resistance compared to antibiotics. Unfortunately, natural AMPs are prone to proteolytic cleavage in vivo and have relatively low selectivity for microbial versus human cells, motivating the development of synthetic peptidomimetics of AMPs with improved peptide stability, activity, and selectivity. However, a lack of understanding of structure-activity relationships for peptidomimetics constrains development to rational design or experimental predictors, both of which are cost and time prohibitive, especially when the design space of possible sequences scales exponentially with the number of amino acids. To address these challenges, we developed an iterative Gaussian process regression (GPR) approach to explore a large design space of 336 000 synthetic α/β-peptide analogues of a natural AMP, aurein 1.2, based on an initial training set of 147 sequences and their biological activities against microbial pathogens and selectivity for microbes vs. mammalian cells. We show that the quantification of prediction uncertainty provided by GPR can guide the exploration of this design space via iterative experimental measurements to efficiently discover novel sequences with up to a 52-fold increase in antifungal selectivity compared to aurein 1.2. The highest selectivity peptide discovered using this approach features an unconventional substitution of cationic amino acids in the hydrophobic face and would be unlikely to be explored by conventional rational design. Overall, this work demonstrates a generalizable approach that integrates computation and experiment to accurately predict the selectivity of AMPs containing synthetic amino acids, which we employed to discover new α/β-peptides that hold promise as selective antifungal agents to combat the antimicrobial resistance crisis.

Cyclization of Two Antimicrobial Peptides Improves Their Activity

One promising strategy to combat worldwide antimicrobial resistance involves using cyclic peptides as antibacterial agents. Cyclization of peptides can confer several advantages, including enhanced stability to proteolysis, decreased toxicity and increased bactericidal efficacy. This paper examines two cyclic peptides CE-03 (12 AAs) and CE-05 (16 AAs) and evaluates their effectiveness in combating bacterial infections, their stability and toxicity. We compare them to their linear versions. Circular dichroism (CD) reveals that CE-03 and CE-05 both adopt random coil and β-sheet structures in lipid model membranes (LMMs) mimicking G(-) and G(+) bacteria, where they are both bactericidal. Using X-ray diffuse scattering (XDS), their effects on lipid model membranes show a deep penetration of both peptides into eukaryotic LMMs where they are nontoxic, while a headgroup location in bacterial LMMs correlates with bacterial killing. Neutron reflectometry (NR) confirms the AMP locations determined using XDS. Further, solution small-angle X-ray scattering demonstrates that both peptides induce vesicle fusion in bacterial LMMs without affecting eukaryotic LMMs. Proteolytic degradation studies show that both CE-05 and CE-03 do not lose activity when incubated with the elastase enzyme, while the helical E2-35 AMP becomes inactive upon proteolysis.

Antibacterials with Novel Chemical Scaffolds in Clinical Development

The rise of antimicrobial resistance represents a significant global health threat, driven by the diminishing efficacy of existing antibiotics, a lack of novel antibacterials entering the market, and an over- or misuse of existing antibiotics, which accelerates the evolution of resistant bacterial strains. This review focuses on innovative therapies by highlighting 19 novel antibacterials in clinical development as of June 2024. These selected compounds are characterized by new chemical scaffolds, novel molecular targets, and/or unique mechanisms of action, which render their potential to break antimicrobial resistance particularly high. A detailed analysis of the scientific foundations behind each of these compounds is provided, including their pharmacodynamic profiles, current development state, and potential for overcoming existing limitations in antibiotic therapy. By presenting this subset of chemically novel antibacterials, the review highlights the ability to innovate in antibiotic drug development to counteract bacterial resistance and improve treatment outcomes.

Machine learning and genetic algorithm-guided directed evolution for the development of antimicrobial peptides

INTRODUCTION

Antimicrobial peptides (AMPs) are valuable alternatives to traditional antibiotics, possess a variety of potent biological activities and exhibit immunomodulatory effects that alleviate difficult-to-treat infections. Clarifying the structure-activity relationships of AMPs can direct the synthesis of desirable peptide therapeutics.

OBJECTIVES

In this study, the lipopolysaccharide-binding domain (LBD) was identified through machine learning-guided directed evolution, which acts as a functional domain of the anti-lipopolysaccharide factor family of AMPs identified from Marsupenaeus japonicus.

METHODS

LBDA-D was identified as an output of this algorithm, in which the original LBDMj sequence was the input, and the three-dimensional solution structure of LBDB was determined using nuclear magnetic resonance. Furthermore, our study involved a comprehensive series of experiments, including morphological studies and in vitro and in vivo antibacterial tests.

RESULTS

The NMR solution structure showed that LBDB possesses a circular extended structure with a disulfide crosslink at the terminus and two 310-helices and exhibits a broad antimicrobial spectrum. In addition, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) showed that LBDB induced the formation of a cluster of bacteria wrapped in a flexible coating that ruptured and consequently killed the bacteria. Finally, coinjection of LBDB, Vibrio alginolyticus and Staphylococcus aureus in vivo improved the survival of M. japonicus, demonstrating the promising therapeutic role of LBDB for treating infectious disease.

CONCLUSIONS

The findings of this study pave the way for the rational drug design of activity-enhanced peptide antibiotics.

Dhvar5- and MSI78-coated titanium are bactericidal against methicillin-resistant Staphylococcus aureus, immunomodulatory and osteogenic

Infection is one of the major issues associated with the failure of orthopedic devices, mainly due to implant bacterial colonization, biofilm formation, and associated antibiotic resistance. Antimicrobial peptides (AMP) are a promising alternative to conventional antibiotics given their broad-spectrum of activity, low propensity to induce bacterial resistance, and ability to modulate host immune responses. Dhvar5 (LLLFLLKKRKKRKY) and MSI78 (GIGKFLKKAKKFGKAFVKILKK) are two AMP with broad-spectrum activity against bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), one of the most problematic etiologic agents in Orthopedic Devices-Related Infections (ODRI). This work aims to evaluate the bactericidal, immunomodulatory and osteogenic potential of Dhvar5- and MSI78-coated titanium surfaces (AMP-Ti). Two AMP-Ti surfaces were successfully obtained by grafting Dhvar5 (0.8 ± 0.1 µM/mm2) or MSI78 (0.5 ± 0.3 µM/mm2) onto titanium substrates through a polydopamine layer. Both AMP-Ti were bactericidal against MRSA, eradicating bacteria upon contact for 6 h in a culture medium supplemented with human plasma proteins. The AMP-Ti immunomodulatory potential was evaluated using human primary macrophages, by assessing surfaces capacity to induce pro-/anti-inflammatory (M1/M2) markers and cytokines. While in naïve conditions both AMP-Ti surfaces slightly promoted the M2 marker CD163, in response to LPS and IFN-γ (simulating a bacterial infection), both AMP increased the M1 marker CCR7 and enhanced macrophage secretion of pro-inflammatory IL-6 and TNF-α cytokines, particularly for Ti-MSI78 surfaces. Additionally, both AMP-Ti surfaces were cytocompatible and promoted osteoblastic cell differentiation. This proof-of-concept study demonstrated the high potential of Dhvar5- and MSI78-Ti as antimicrobial coatings for ODRI prevention. STATEMENT OF SIGNIFICANCE: This study investigates the bactericidal effects of the antimicrobial peptides Dhvar5 and MSI78, immobilized on titanium (Ti) surfaces through a polydopamine coating, aiming at the prevention of Orthopedic-Device Related Infections (ODRIs). The developed coatings displayed MRSA-sterilizing activity, while revealing an immunomodulatory potential towards macrophages and promoting osteoblastic cell differentiation. This strategy allows a quick and easy immobilization of high quantities of AMP, unlike most other approaches, thus favoring its clinical translation.

Comparative Properties of Helical and Linear Amphipathicity of Peptides Composed of Arginine, Tryptophan, and Valine

BACKGROUND

The persistence of antibiotic resistance has incited a strong interest in the discovery of agents with novel antimicrobial mechanisms. The direct killing of multidrug-resistant bacteria by cationic antimicrobial peptides (AMPs) underscores their importance in the fight against infections associated with antibiotic resistance. Despite a vast body of AMP literature demonstrating a plurality in structural classes, AMP engineering has been largely skewed toward peptides with idealized amphipathic helices (H-amphipathic). In contrast to helical amphipathicity, we designed a series of peptides that display the amphipathic motifs in the primary structure. We previously developed a rational framework for designing AMP libraries of H-amphipathic peptides consisting of Arg, Trp, and Val (H-RWV, with a confirmed helicity up to 88% in the presence of membrane lipids) tested against the most common MDR organisms.

METHODS

In this study, we re-engineered one of the series of the H-RWV peptides (8, 10, 12, 14, and 16 residues in length) to display the amphipathicity in the primary structure by side-by-side (linear) alignment of the cationic and hydrophobic residues into the 2 separate linear amphipathic (L-amphipathic) motifs. We compared the 2 series of peptides for antibacterial activity, red blood cell (RBC) lysis, killing and membrane-perturbation properties.

RESULTS

The L-RWV peptides achieved the highest antibacterial activity at a minimum length of 12 residues (L-RWV12, minimum optimal length or MOL) with the lowest mean MIC of 3-4 µM, whereas the MOL for the H-RWV series was reached at 16 residues (H-RWV16). Overall, H-RWV16 displayed the lowest mean MIC at 2 µM but higher levels of RBC lysis (25-30%), while the L-RWV series displayed minor RBC lytic effects at the test concentrations. Interestingly, when the S. aureus strain SA719 was chosen because of its susceptibility to most of the peptides, none of the L-RWV peptides demonstrated a high level of membrane perturbation determined by propidium iodide incorporation measured by flow cytometry, with <50% PI incorporation for the L-RWV peptides. By contrast, most H-RWV peptides displayed almost up to 100% PI incorporation. The results suggest that membrane perturbation is not the primary killing mechanism of the L-amphipathic RWV peptides, in contrast to the H-RWV peptides.

CONCLUSIONS

Taken together, the data indicate that both types of amphipathicity may provide different ideal pharmacological properties that deserve further investigation.

How Unnatural Amino Acids in Antimicrobial Peptides Change Interactions with Lipid Model Membranes

This study investigates the potential of antimicrobial peptides (AMPs) as alternatives to combat antibiotic resistance, with a focus on two AMPs containing unnatural amino acids (UAAs), E2-53R (16 AAs) and LE-54R (14 AAs). In both peptides, valine is replaced by norvaline (Nva), and tryptophan is replaced by 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic). Microbiological studies reveal their potent activity against both Gram-negative (G(-)) and Gram-positive (G(+)) bacteria without any toxicity to eukaryotic cells at test concentrations up to 32 μM. Circular dichroism (CD) spectroscopy indicates that these peptides maintain α-helical structures when interacting with G(-) and G(+) lipid model membranes (LMMs), a feature linked to their efficacy. X-ray diffuse scattering (XDS) demonstrates a softening of G(-), G(+) and eukaryotic (Euk33) LMMs and a nonmonotonic decrease in chain order as a potential determinant for bacterial membrane destabilization. Additionally, XDS finds a significant link between both peptides' interfacial location in G(-) and G(+) LMMs and their efficacy. Neutron reflectometry (NR) confirms the AMP locations determined using XDS. Lack of toxicity in eukaryotic cells may be related to their loss of α-helicity and their hydrocarbon location in Euk33 LMMs. Both AMPs with UAAs offer a novel strategy to wipe out antibiotic-resistant strains while maintaining human cells. These findings are compared with previously published data on E2-35, which consists of the natural amino acids arginine, tryptophan, and valine.

Discovery and engineering of a novel peptide, Temporin-WY2, with enhanced in vitro and in vivo efficacy against multi-drug resistant bacteria

Infections by drug-resistant microorganisms are a threat to global health and antimicrobial peptides are considered to be a new hope for their treatment. Temporin-WY2 was identified from the cutaneous secretion of the Ranidae frog, Amolops wuyiensis. It presented with a potent anti-Gram-positive bacterial efficacy, but its activity against Gram-negative bacteria and cancer cell lines was unremarkable. Also, it produced a relatively high lytic effect on horse erythrocytes. For further improvement of its functions, a perfect amphipathic analogue, QUB-1426, and two lysine-clustered analogues, 6K-WY2 and 6K-1426, were synthesised and investigated. The modified peptides were found to be between 8- and 64-fold more potent against Gram-negative bacteria than the original peptide. Additionally, the 6K analogues showed a rapid killing rate. Also, their antiproliferation activities were more than 100-fold more potent than the parent peptide. All of the peptides that were examined demonstrated considerable biofilm inhibition activity. Moreover, QUB-1426, 6K-WY2 and 6K-1426, demonstrated in vivo antimicrobial activity against MRSA and E. coli in an insect larvae model. Despite observing a slight increase in the hemolytic activity and cytotoxicity of the modified peptides, they still demonstrated a improved therapeutic index. Overall, QUB-1426, 6K-WY2 and 6K-1426, with dual antimicrobial and anticancer functions, are proposed as putative drug candidates for the future.

Antimicrobial peptide A20L: in vitro and in vivo antibacterial and antibiofilm activity against carbapenem-resistant Klebsiella pneumoniae

Antimicrobial resistance has become a growing public health threat in recent years. Klebsiella pneumoniae is one of the priority pathogens listed by the World Health Organization. Antimicrobial peptides are considered promising alternatives to antibiotics due to their broad-spectrum antibacterial activity and low resistance. In this study, we investigated the antibacterial activity of antimicrobial peptide A20L against K. pneumoniae. In vitro antibacterial activity of A20L against K. pneumoniae was demonstrated by broth microdilution method. We confirmed the in vivo efficacy of A20L by Galleria mellonella infection model. In addition, we found that A20L also had certain antibiofilm activity by crystal violet staining. We also evaluated the safety and stability of A20L, and the results revealed that at a concentration of ≤128 µg/mL, A20L exhibited negligible toxicity to RAW264.7 cells and no substantial toxicity to G. mellonella. A20L was stable at different temperatures and with low concentration of serum [5% fetal bovine serum (FBS)]; however, Ca2+, Mg2+, and high serum concentrations reduced the antibacterial activity of A20L. Scanning electron microscope (SEM) and membrane permeability tests revealed that A20L may exhibit antibacterial action by damaging bacterial cell membranes and increasing the permeability of outer membrane. Taken together, our results suggest that A20L has significant development potential as a therapeutic antibiotic alternative, which provides ideas for the treatment of K. pneumoniae infection.

IMPORTANCE

A20L showed antibacterial and anti-infective efficacy in vitro and in vivo against Klebsiella pneumoniae. It can have an antibacterial effect by disrupting the integrity of cell membranes. A20L displayed anti-biofilm and anti-inflammatory activity against carbapenem-resistant K. pneumoniae and certain application potential in vivo, which provides a new idea for the clinical treatment of biofilm-associated infections.

Novel design of simplified β-hairpin antimicrobial peptide as a potential food preservative based on Trp-pocket backbone

Food contamination from microbial deterioration requires the development of potent antimicrobial peptides (AMPs). The deployment of approved AMPs as dietary preservatives is limited due to barriers such as instability, toxicity, and high synthetic costs. This exploration utilizes the primary structural elements of the Trp-pocket backbone to engineer a series of β-hairpin AMPs (XWRWRPGXKXXR-NH2, X representing I, V, F, and/or L). Peptides WpLF, with Phe as X and Leu arranged at the 11th position, demonstrated exceptional selectivity index (SI = 123.08) and sterilization effects both in vitro and in vivo. WpLF consistently exhibited stable bacteriostasis, regardless of physiological salts, serum, and extreme pH. Mechanistic analysis indicated that the peptide penetrates microbial cell membranes, inducing membrane disruption, thereby impeding drug resistance evolution. Conclusively, AMPs engineered by the Trp-pocket skeleton hold substantial potential as innovative biological preservatives in food preservation, providing valuable insights for sustainable and safe peptide-based food preservatives.

Novel non-helical antimicrobial peptides insert into and fuse lipid model membranes

This research addresses the growing menace of antibiotic resistance by exploring antimicrobial peptides (AMPs) as alternatives to conventional antibiotics. Specifically, we investigate two linear amphipathic AMPs, LE-53 (12-mer) and LE-55 (16-mer), finding that the shorter LE-53 exhibits greater bactericidal activity against both Gram-negative (G(-)) and Gram-positive (G(+)) bacteria. Remarkably, both AMPs are non-toxic to eukaryotic cells. The heightened effectiveness of LE-53 is attributed to its increased hydrophobicity (H) compared to LE-55. Circular dichroism (CD) reveals that LE-53 and LE-55 both adopt β-sheet and random coil structures in lipid model membranes (LMMs) mimicking G(-) and G(+) bacteria, so secondary structure is not the cause of the potency difference. X-ray diffuse scattering (XDS) reveals increased lipid chain order in LE-53, a potential key distinction. Additionally, XDS study uncovers a significant link between LE-53's upper hydrocarbon location in G(-) and G(+) LMMs and its efficacy. Neutron reflectometry (NR) confirms the AMP locations determined using XDS. Solution small angle X-ray scattering (SAXS) demonstrates LE-53's ability to induce vesicle fusion in bacterial LMMs without affecting eukaryotic LMMs, offering a promising strategy to combat antibiotic-resistant strains while preserving human cell integrity, whereas LE-55 has a smaller ability to induce fusion.

Cathelicidin AS-12W Derived from the Alligator sinensis and Its Antimicrobial Activity Against Drug-Resistant Gram-Negative Bacteria In Vitro and In Vivo

Antimicrobial peptides (AMPs) have the potential to treat multidrug-resistant bacterial infections. Cathelicidins are a class of cationic antimicrobial peptides that are found in nearly all vertebrates. Herein, we determined the mature peptide region of Alligator sinensis cathelicidin by comparing its cathelicidin peptide sequence with those of other reptiles and designed nine peptide mutants based on the Alligator sinensis cathelicidin mature peptide. According to the antibacterial activity and cytotoxicity screening, the peptide AS-12W demonstrated broad-spectrum antibacterial activity and exhibited low erythrocyte hemolytic activity. In particular, AS-12W exhibited strong antibacterial activity and rapid bactericidal activity against carbapenem-resistant Pseudomonas aeruginosa in vitro. Additionally, AS-12W effectively removed carbapenem-resistant P. aeruginosa from blood and organs in vivo, leading to improved survival rates in septic mice. Furthermore, AS-12W exhibited good stability and tolerance to harsh conditions such as high heat, high salt, strong acid, and strong alkali, and it also displayed high stability toward trypsin and simulated gastric fluid (SGF). Moreover, AS-12W showed significant anti-inflammatory effects in vitro by inhibiting the production of proinflammatory factors induced by lipopolysaccharide (LPS). Due to its antibacterial mechanism against Escherichia coli, we found that this peptide could neutralize the negative charge on the surface of the bacteria and disrupt the integrity of the bacterial cell membrane. In addition, AS-12W has the ability to bind to the genomic DNA of bacteria and stimulate the production of reactive oxygen species (ROS) within bacteria, which is believed to be the reason for the good antibacterial activity of AS-12W. These results demonstrated that AS-12W exhibits remarkable antibacterial activity, particularly against carbapenem-resistant P. aeruginosa. Therefore, it is a potential candidate for antibacterial drug development.

Antibacterial agents active against Gram Negative Bacilli in phase I, II, or III clinical trials

INTRODUCTION

Antimicrobial resistance is a major threat to modern healthcare, and it is often regarded that the antibiotic pipeline is 'dry.'

AREAS COVERED

Antimicrobial agents active against Gram negative bacilli in Phase I, II, or III clinical trials were reviewed.

EXPERT OPINION

Nearly 50 antimicrobial agents (28 small molecules and 21 non-traditional antimicrobial agents) active against Gram-negative bacilli are currently in clinical trials. These have the potential to provide substantial improvements to the antimicrobial armamentarium, although it is known that 'leakage' from the pipeline occurs due to findings of toxicity during clinical trials. Significantly, a lack of funding for large phase III clinical trials is likely to prevent trials occurring for the indications most relevant to loss of life attributed to antimicrobial resistance such as ventilator-associated pneumonia. Non-traditional antimicrobial agents face issues in clinical development such as a lack of readily available and reliable susceptibility tests, and the potential need for superiority trials rather than non-inferiority trials. Most importantly, concrete plans must be made during clinical development for access of new antimicrobial agents to areas of the world where resistance to Gram negative bacilli is most frequent.

Accelerating Antimicrobial Peptide Discovery for WHO Priority Pathogens through Predictive and Interpretable Machine Learning Models

The escalating menace of multidrug-resistant (MDR) pathogens necessitates a paradigm shift from conventional antibiotics to innovative alternatives. Antimicrobial peptides (AMPs) emerge as a compelling contender in this arena. Employing in silico methodologies, we can usher in a new era of AMP discovery, streamlining the identification process from vast candidate sequences, thereby optimizing laboratory screening expenditures. Here, we unveil cutting-edge machine learning (ML) models that are both predictive and interpretable, tailored for the identification of potent AMPs targeting World Health Organization's (WHO) high-priority pathogens. Furthermore, we have developed ML models that consider the hemolysis of human erythrocytes, emphasizing their therapeutic potential. Anchored in the nuanced physical-chemical attributes gleaned from the three-dimensional (3D) helical conformations of AMPs, our optimized models have demonstrated commendable performance-boasting an accuracy exceeding 75% when evaluated against both low-sequence-identified peptides and recently unveiled AMPs. As a testament to their efficacy, we deployed these models to prioritize peptide sequences stemming from PEM-2 and subsequently probed the bioactivity of our algorithm-predicted peptides vis-à-vis WHO's priority pathogens. Intriguingly, several of these new AMPs outperformed the native PEM-2 in their antimicrobial prowess, thereby underscoring the robustness of our modeling approach. To elucidate ML model outcomes, we probe via Shapley Additive exPlanations (SHAP) values, uncovering intricate mechanisms guiding diverse actions against bacteria. Our state-of-the-art predictive models expedite the design of new AMPs, offering a robust countermeasure to antibiotic resistance. Our prediction tool is available to the public at https://ai-meta.chem.ncu.edu.tw/amp-meta.

BsR1, a broad-spectrum antibacterial peptide with potential for plant protection

IMPORTANCE

This study addresses the critical need for new antibacterial drugs in the face of bacterial multidrug resistance resulting from antibiotic overuse. It highlights the significance of antimicrobial peptides as essential components of innate immunity in animals and plants, which have been proven effective against multidrug-resistant bacteria and are difficult to develop resistance against. This study successfully synthesizes a broad-spectrum antibacterial peptide, BsR1, with strong inhibitory activities against various Gram-positive and Gram-negative bacteria. BsR1 demonstrates favorable stability and a mode of action that damages bacterial cell membranes, leading to cell death. It also exhibits biological safety and shows potential in enhancing disease resistance in rice. This research offers a novel approach and potential medication for antibacterial drug development, presenting a valuable tool in combating pathogenic microorganisms, particularly in plants.

The antimicrobial peptide database is 20 years old: Recent developments and future directions

In 2023, the Antimicrobial Peptide Database (currently available at https://aps.unmc.edu) is 20-years-old. The timeline for the APD expansion in peptide entries, classification methods, search functions, post-translational modifications, binding targets, and mechanisms of action of antimicrobial peptides (AMPs) has been summarized in our previous Protein Science paper. This article highlights new database additions and findings. To facilitate antimicrobial development to combat drug-resistant pathogens, the APD has been re-annotating the data for antibacterial activity (active, inactive, and uncertain), toxicity (hemolytic and nonhemolytic AMPs), and salt tolerance (salt sensitive and insensitive). Comparison of the respective desired and undesired AMP groups produces new knowledge for peptide design. Our unification of AMPs from the six life kingdoms into "natural AMPs" enabled the first comparison with globular or transmembrane proteins. Due to the dominance of amphipathic helical and disulfide-linked peptides, cysteine, glycine, and lysine in natural AMPs are much more abundant than those in globular proteins. To include peptides predicted by machine learning, a new "predicted" group has been created. Remarkably, the averaged amino acid composition of predicted peptides is located between the lower bound of natural AMPs and the upper bound of synthetic peptides. Synthetic peptides in the current APD, with the highest cationic and hydrophobic amino acid percentages, are mostly designed with varying degrees of optimization. Hence, natural AMPs accumulated in the APD over 20 years have laid the foundation for machine learning prediction. We discuss future directions for peptide discovery. It is anticipated that the APD will continue to play a role in research and education.

Self-assembled and Zn(II)-coordinated dipeptide nanoparticles with membrane-rupturing action on bacteria

Metal ion-coordinated self-assembled short-chain amino acid peptide molecules with multi-photon excitation wavelengths and their photoluminescence properties are advantageous for fluorescence-based diagnostics and treatments of biological diseases based on their extra features of antibacterial agents. We have designed a novel strategy based on tryptophan molecule coordinated with Zn(II) ions in the form of biocompatible spherical nanoparticles of diameter 30-80 nm which have been used for antibacterial treatments against different kinds of pathogenic bacteria (Escherichia coli, Salmonella typhimurium, and Pseudomonas). Preferably, we have used tryptophan-phenylalanine (Trp-Phe), a dipeptide molecule having tryptophan as principal material against E. coli strains as antimicrobial agents for surface rupturing and killing purposes. Furthermore, based on single amino acid, tryptophan, self-assembled and Zn(II)-coordinated dipeptide nanoparticles (Zn-DPNPs) were studied against three types of multi-drug-resistant bacteria as an active antimicrobial agent. These antibacterial efficient nanoparticles may have best alternative of antibiotic drugs for clinical applications. The capability of self-assembled fluorescence behavior of Zn-coordinated dipeptide molecules and higher hydrophobicity against bacterial cell wall will perform as antimicrobial fluorescent agents. KEY POINTS: • Zn(II) and Cu(II) better coordinated into self-assembled NPs. • Fluorescence signals showed interaction of NPs with gram -ve cell wall. • Significant surface-damaging effects were observed in the case of Cu-DPNPs and Zn-DPNPs.

Plant defensin MtDef4-derived antifungal peptide with multiple modes of action and potential as a bio-inspired fungicide

Chemical fungicides have been instrumental in protecting crops from fungal diseases. However, increasing fungal resistance to many of the single-site chemical fungicides calls for the development of new antifungal agents with novel modes of action (MoA). The sequence-divergent cysteine-rich antifungal defensins with multisite MoA are promising starting templates for design of novel peptide-based fungicides. Here, we experimentally tested such a set of 17-amino-acid peptides containing the γ-core motif of the antifungal plant defensin MtDef4. These designed peptides exhibited antifungal properties different from those of MtDef4. Focused analysis of a lead peptide, GMA4CG_V6, showed that it was a random coil in solution with little or no secondary structure elements. Additionally, it exhibited potent cation-tolerant antifungal activity against the plant fungal pathogen Botrytis cinerea, the causal agent of grey mould disease in fruits and vegetables. Its multisite MoA involved localization predominantly to the plasma membrane, permeabilization of the plasma membrane, rapid internalization into the vacuole and cytoplasm, and affinity for the bioactive phosphoinositides phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. The sequence motif RRRW was identified as a major determinant of the antifungal activity of this peptide. While topical spray application of GMA4CG_V6 on Nicotiana benthamiana and tomato plants provided preventive and curative suppression of grey mould disease symptoms, the peptide was not internalized into plant cells. Our findings open the possibility that truncated and modified defensin-derived peptides containing the γ-core sequence could serve as promising candidates for further development of bio-inspired fungicides.

Novel Helical Trp- and Arg-Rich Antimicrobial Peptides Locate Near Membrane Surfaces and Rigidify Lipid Model Membranes

Antibiotics are losing effectiveness as bacteria become resistant to conventional drugs. To find new alternatives, antimicrobial peptides (AMPs) are rationally designed with different lengths, charges, hydrophobicities (H ), and hydrophobic moments (μH ), containing only three types of amino acids: arginine, tryptophan, and valine. Six AMPs with low minimum inhibitory concentrations (MICs) and <25% toxicity to mammalian cells are selected for biophysical studies. Their secondary structures are determined using circular dichroism (CD), which finds that the % α -helicity of AMPs depends on composition of the lipid model membranes (LMMs): gram-negative (G ( - ) ) inner membrane (IM) >gram-positive (G ( + ) ) > Euk33 (eukaryotic with 33 mol% cholesterol). The two most effective peptides, E2-35 (16 amino acid [AA] residues) and E2-05 (22 AAs), are predominantly helical in G ( - ) IM and G ( + ) LMMs. AMP/membrane interactions such as membrane elasticity, chain order parameter, and location of the peptides in the membrane are investigated by low-angle and wide-angle X-ray diffuse scattering (XDS). It is found that headgroup location correlates with efficacy and toxicity. The membrane bending modulus K C displays nonmonotonic changes due to increasing concentrations of E2-35 and E2-05 in G ( - ) and G ( + ) LMMs, suggesting a bacterial killing mechanism where domain formation causes ion and water leakage.

Boosting stability and therapeutic potential of proteolysis-resistant antimicrobial peptides by end-tagging β-naphthylalanine

Recently, much emphasis has been placed on solving the intrinsic defects of antimicrobial peptides (AMPs), especially their susceptibility to protease digestion for the systemic application of antibacterial biomaterials. Although many strategies have increased the protease stability of AMPs, antimicrobial activity was severely compromised, thereby substantially weakening their therapeutic effect. To address this issue, we introduced hydrophobic group modifications at the N-terminus of proteolysis-resistant AMPs D1 (AArIIlrWrFR) through end-tagging with stretches of natural amino acids (W and I), unnatural amino acid (Nal) and fatty acids. Of these peptides, N1 tagged with a Nal at N-terminus showed the highest selectivity index (GM_SI = 19.59), with a 6.73-fold improvement over D1. In addition to potent broad-spectrum antimicrobial activity, N1 also exhibited high antimicrobial stability toward salts, serum and proteases in vitro and ideal biocompatibility and therapeutic efficacy in vivo. Furthermore, N1 killed bacteria through multiple mechanisms, involving disruption of bacterial membranes and inhibition of bacterial energy metabolism. Indeed, appropriate terminal hydrophobicity modification opens up new avenues for developing and applying high-stability peptide-based antibacterial biomaterials. STATEMENT OF SIGNIFICANCE: To improve the potency and stability of proteolysis-resistant antimicrobial peptides (AMPs) without increasing toxicity, we constructed a convenient and tunable platform based on different compositions and lengths of hydrophobic end modifications. By tagging an Nal at the N-terminal, the obtained target compound N1 exhibited strong antimicrobial activity and desirable stability under multifarious environments in vitro (protease, salts and serum), and also showed favorable biocompatibility and therapeutic efficacy in vivo. Notably, N1exerted its bactericidal effect by damaging bacterial cell membranes and inhibiting bacterial energy metabolism in a dual mode. The findings provide a potential method for designing or optimizing proteolysis-resistant AMPs thus promoting the development and application of peptide-based antibacterial biomaterial.

Development of Neuropeptide Hemokinin-1 Analogues with Antimicrobial and Wound-Healing Activity

Wound healing is a complex process that can be delayed in some pathological conditions, such as infection and diabetes. Following skin injury, the neuropeptide substance P (SP) is released from peripheral neurons to promote wound healing by multiple mechanisms. Human hemokinin-1 (hHK-1) has been identified as an SP-like tachykinin peptide. Surprisingly, hHK-1 shares similar structural features with antimicrobial peptides (AMPs), but it does not display efficient antimicrobial activity. Therefore, a series of hHK-1 analogues were designed and synthesized. Among these analogues, AH-4 was found to display the greatest antimicrobial activity against a broad spectrum of bacteria. Furthermore, AH-4 rapidly killed bacteria by membrane disruption, similar to most AMPs. More importantly, AH-4 showed favorable healing activity in all tested mouse full-thickness excisional wound models. Overall, this study suggests that the neuropeptide hHK-1 can be used as a desirable template for developing promising therapeutics with multiple functions for wound healing.

The Unusual Aggregation and Fusion Activity of the Antimicrobial Peptide W-BP100 in Anionic Vesicles

Cationic antimicrobial peptides (CAMPs) offer a promising strategy to counteract bacterial resistance, mostly due to their membrane-targeting activity. W-BP100 is a potent broad-spectrum cecropin-melittin CAMP bearing a single N-terminal Trp, which was previously found to improve its antibacterial activity. W-BP100 has high affinity toward anionic membranes, inducing membrane saturation at low peptide-to-lipid (P/L) ratios and membrane permeabilization, with the unique property of promoting the aggregation of anionic vesicles only at specific P/L ratios. Herein, we aimed to investigate this unusual behavior of W-BP100 by studying its aggregation and fusion properties with negatively-charged large (LUVs) or giant (GUVs) unilamellar vesicles using biophysical tools. Circular dichroism (CD) showed that W-BP100 adopted an α-helical conformation in anionic LUVs, neutralizing its surface charge at the aggregation P/L ratio. Its fusion activity, assessed by Förster resonance energy transfer (FRET) using steady-state fluorescence spectroscopy, occurred mainly at the membrane saturation/aggregation P/L ratio. Confocal microscopy studies confirmed that W-BP100 displays aggregation and detergent-like effects at a critical P/L ratio, above which it induces the formation of new lipid aggregates. Our data suggest that W-BP100 promotes the aggregation and fusion of anionic vesicles at specific P/L ratios, being able to reshape the morphology of GUVs into new lipid structures.

Pharmaceutical nanotechnology: Antimicrobial peptides as potential new drugs against WHO list of critical, high, and medium priority bacteria

Nanobiotechnology is a relatively unexplored area that has, nevertheless, shown relevant results in the fight against some diseases. Antimicrobial peptides (AMPs) are biomacromolecules with potential activity against multi/extensively drug-resistant bacteria, with a lower risk of generating bacterial resistance. They can be considered an excellent biotechnological alternative to conventional drugs. However, the application of several AMPs to biological systems is hampered by their poor stability and lifetime, inactivating them completely. Therefore, nanotechnology plays an important role in the development of new AMP-based drugs, protecting and carrying the bioactive to the target. This is the first review article on the different reported nanosystems using AMPs against bacteria listed on the WHO priority list. The current shortage of information implies a nanobiotechnological potential to obtain new drugs or repurpose drugs based on the AMP-drug synergistic effect.

Expanding the Landscape of Amino Acid-Rich Antimicrobial Peptides: Definition, Deployment in Nature, Implications for Peptide Design and Therapeutic Potential

Unlike the α-helical and β-sheet antimicrobial peptides (AMPs), our knowledge on amino acid-rich AMPs is limited. This article conducts a systematic study of rich AMPs (>25%) from different life kingdoms based on the Antimicrobial Peptide Database (APD) using the program R. Of 3425 peptides, 724 rich AMPs were identified. Rich AMPs are more common in animals and bacteria than in plants. In different animal classes, a unique set of rich AMPs is deployed. While histidine, proline, and arginine-rich AMPs are abundant in mammals, alanine, glycine, and leucine-rich AMPs are common in amphibians. Ten amino acids (Ala, Cys, Gly, His, Ile, Lys, Leu, Pro, Arg, and Val) are frequently observed in rich AMPs, seven (Asp, Glu, Phe, Ser, Thr, Trp, and Tyr) are occasionally observed, and three (Met, Asn, and Gln) were not yet found. Leucine is much more frequent in forming rich AMPs than either valine or isoleucine. To date, no natural AMPs are simultaneously rich in leucine and lysine, while proline, tryptophan, and cysteine-rich peptides can simultaneously be rich in arginine. These findings can be utilized to guide peptide design. Since multiple candidates are potent against antibiotic-resistant bacteria, rich AMPs stand out as promising future antibiotics.

Antimicrobial peptides for bone tissue engineering: Diversity, effects and applications

Bone tissue engineering has been becoming a promising strategy for surgical bone repair, but the risk of infection during trauma repair remains a problematic health concern worldwide, especially for fracture and infection-caused bone defects. Conventional antibiotics fail to effectively prevent or treat bone infections during bone defect repair because of drug-resistance and recurrence, so novel antibacterial agents with limited resistance are highly needed for bone tissue engineering. Antimicrobial peptides (AMPs) characterized by cationic, hydrophobic and amphipathic properties show great promise to be used as next-generation antibiotics which rarely induce resistance and show potent antibacterial efficacy. In this review, four common structures of AMPs (helix-based, sheet-based, coil-based and composite) and related modifications are presented to identify AMPs and design novel analogs. Then, potential effects of AMPs for bone infection during bone repair are explored, including bactericidal activity, anti-biofilm, immunomodulation and regenerative properties. Moreover, we present distinctive applications of AMPs for topical bone repair, which can be either used by delivery system (surface immobilization, nanoparticles and hydrogels) or used in gene therapy. Finally, future prospects and ongoing challenges are discussed.

Important Roles and Potential Uses of Natural and Synthetic Antimicrobial Peptides (AMPs) in Oral Diseases: Cavity, Periodontal Disease, and Thrush

Numerous epithelial cells and sometimes leukocytes release AMPs as their first line of defense. AMPs encompass cationic histatins, defensins, and cathelicidin to encounter oral pathogens with minimal resistance. However, their concentrations are significantly below the effective levels and AMPs are unstable under physiological conditions due to proteolysis, acid hydrolysis, and salt effects. In parallel to a search for more effective AMPs from natural sources, considerable efforts have focused on synthetic stable and low-cytotoxicy AMPs with significant activities against microorganisms. Using natural AMP templates, various attempts have been used to synthesize sAMPs with different charges, hydrophobicity, chain length, amino acid sequence, and amphipathicity. Thus far, sAMPs have been designed to target Streptococcus mutans and other common oral pathogens. Apart from sAMPs with antifungal activities against Candida albicans, future endeavors should focus on sAMPs with capabilities to promote remineralization and antibacterial adhesion. Delivery systems using nanomaterials and biomolecules are promising to stabilize, reduce cytotoxicity, and improve the antimicrobial activities of AMPs against oral pathogens. Nanostructured AMPs will soon become a viable alternative to antibiotics due to their antimicrobial mechanisms, broad-spectrum antimicrobial activity, low drug residue, and ease of synthesis and modification.

Engineered peptide PLG0206 overcomes limitations of a challenging antimicrobial drug class

The absence of novel antibiotics for drug-resistant and biofilm-associated infections is a global public health crisis. Antimicrobial peptides explored to address this need have encountered significant development challenges associated with size, toxicity, safety profile, and pharmacokinetics. We designed PLG0206, an engineered antimicrobial peptide, to address these limitations. PLG0206 has broad-spectrum activity against >1,200 multidrug-resistant (MDR) ESKAPEE clinical isolates, is rapidly bactericidal, and displays potent anti-biofilm activity against diverse MDR pathogens. PLG0206 displays activity in diverse animal infection models following both systemic (urinary tract infection) and local (prosthetic joint infection) administration. These findings support continuing clinical development of PLG0206 and validate use of rational design for peptide therapeutics to overcome limitations associated with difficult-to-drug pharmaceutical targets.

Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation

In an effort to combat rising antimicrobial resistance, our labs have rationally designed cationic, helical, amphipathic antimicrobial peptides (AMPs) as alternatives to traditional antibiotics since AMPs incur bacterial resistance in weeks, rather than days. One highly positively charged AMP, WLBU2 (+13e), (RRWV RRVR RWVR RVVR VVRR WVRR), has been shown to be effective in killing both Gram-negative (G(-)) and Gram-positive (G(+)) bacteria by directly perturbing the bacterial membrane nonspecifically. Previously, we used two equilibrium experimental methods: synchrotron X-ray diffuse scattering (XDS) providing lipid membrane thickness and neutron reflectometry (NR) providing WLBU2 depth of penetration into three lipid model membranes (LMMs). The purpose of the present study is to use the results from the scattering experiments to guide molecular dynamics (MD) simulations to investigate the detailed biophysics of the interactions of WLBU2 with LMMs of Gram-negative outer and inner membranes, and Gram-positive cell membranes, to elucidate the mechanisms of bacterial killing. Instead of coarse-graining, backmapping, or simulating without bias for several microseconds, all-atom (AA) simulations were guided by the experimental results and then equilibrated for ∼0.5 μs. Multiple replicas of the inserted peptide were run to probe stability and reach a combined time of at least 1.2 μs for G(-) and also 2.0 μs for G(+). The simulations with experimental comparisons help rule out certain structures and orientations and propose the most likely set of structures, orientations, and effects on the membrane. The simulations revealed that water, phosphates, and ions enter the hydrocarbon core when WLBU2 is positioned there. For an inserted peptide, the three types of amino acids, arginine, tryptophan, and valine (R, W, V), are arranged with the 13 Rs extending from the hydrocarbon core to the phosphate group, Ws are located at the interface, and Vs are more centrally located. For a surface state, R, W, and V are positioned relative to the bilayer interface as expected from their hydrophobicities, with Rs closest to the phosphate group, Ws close to the interface, and Vs in between. G(-) and G(+) LMMs are thinned ∼1 Å by the addition of WLBU2. Our results suggest a dual anchoring mechanism for WLBU2 both in the headgroup and in the hydrocarbon region that promotes a defect region where water and ions can flow across the slightly thinned bacterial cell membrane.

Tryptophan, more than just an interfacial amino acid in the membrane activity of cationic cell-penetrating and antimicrobial peptides

Trp is unique among the amino acids since it is involved in many different types of noncovalent interactions such as electrostatic and hydrophobic ones, but also in π-π, π-cation, π-anion and π-ion pair interactions. In membranotropic peptides and proteins, Trp locates preferentially at the water-membrane interface. In antimicrobial or cell-penetrating peptides (AMPs and CPPs respectively), Trp is well-known for its strong role in the capacity of these peptides to interact and affect the membrane organisation of both bacteria and animal cells at the level of the lipid bilayer. This essential amino acid can however be involved in other types of interactions, not only with lipids, but also with other membrane partners, that are crucial to understand the functional roles of membranotropic peptides. This review is focused on this latter less known role of Trp and describes in details, both in qualitative and quantitative ways: (i) the physico-chemical properties of Trp; (ii) its effect in CPP internalisation; (iii) its importance in AMP activity; (iv) its role in the interaction of AMPs with glycoconjugates or lipids in bacteria membranes and the consequences on the activity of the peptides; (v) its role in the interaction of CPPs with negatively charged polysaccharides or lipids of animal membranes and the consequences on the activity of the peptides. We intend to bring highlights of the physico-chemical properties of Trp and describe its extensive possibilities of interactions, not only at the well-known level of the lipid bilayer, but with other less considered cell membrane components, such as carbohydrates and the extracellular matrix. The focus on these interactions will allow the reader to reevaluate reported studies. Altogether, our review gathers dedicated studies to show how unique are Trp properties, which should be taken into account to design future membranotropic peptides with expected antimicrobial or cell-penetrating activity.

Tools and techniques for rational designing of antimicrobial peptides for aquaculture

Fisheries and aquaculture industries remain essential sources of food and nutrition for millions of people worldwide. Indiscriminate use of antibiotics has led to the emergence of antimicrobial-resistant bacteria and posed a severe threat to public health. Researchers have opined that antimicrobial peptides (AMPs) can be the best possible alternative to curb the rising tide of antimicrobial resistance in aquaculture. AMPs may also help to achieve the objectives of one health approach. The natural AMPs are associated with several shortcomings, like less in vivo stability, toxicity to host cell, high cost of production and low potency in a biological system. In this review, we have provided a comprehensive outline about the strategies for designing synthetic mimics of natural AMPs with high potency. Moreover, the freely available AMP databases and the information about the molecular docking tools are enlisted. We also provided in silico template for rationally designing the AMPs from fish piscidins or other peptides. The rationally designed piscidin (rP1 and rp2) may be used to tackle microbial infections in aquaculture. Further, the protocol can be used to develop the truncated mimics of natural AMPs having more potency and protease stability.

Effect of Leu/Val Mutation on the Energetics of Antimicrobial Peptide:Micelle Binding

Recently, we had reported a synthetic positively charged leucine-rich 14-residue-long antimicrobial peptide (AMP, LL-14: NH₃⁺-LKWLKKLLKWLKKL-CONH₂), which was highly active and cytotoxic relative to its valine analogue (VV-14). However, the thermodynamics underlying this differential toxicity and antimicrobial activity was unclear. Understanding the energetics of peptide binding to micelles (simplest membrane mimic, viz., SDS as a bacterial membrane and DPC as a eukaryotic membrane) and the effect of Leu → Val peptide mutations on the stability of the peptide:micelle complexes are of great academic interest and relevant for the rational design of potent and selective AMPs for therapeutic use. Here, we have reported the molecular dynamics free energy simulations that allowed us to quantitatively estimate the strength of peptide discrimination (based on single- or multiple-site Leu/Val mutations in LL-14) by membrane mimetic micelles (SDS and DPC) and decipher the energetics underlying peptide selectivity by micelles. The Leu-containing peptide (LL-14) was found to be preferred for micelle (SDS and DPC) binding relative to its Val analogues (single or multiple Val mutants). The strength of the preference depended on the position of the Leu/Val mutation in the peptide. Surprisingly, the N-terminal LL-14 single mutation (Leu → Val: L1V) was found to fine-tune the electrostatic interactions, resulting in the highest peptide selectivity (ΔΔG ∼ 8 kcal/mol for both SDS and DPC). However, the mechanism of L1V peptide selectivity was distinctly different for SDS and DPC micelles. SDS ensured high selectivity by disrupting the peptide:micelle salt bridge, whereas DPC desolvated the broken-peptide-backbone hydrogen bond in the V1 peptide:micelle complex. Mutations (Leu → Val) in the middle positions of the LL-14 (4th, 7th, 8th, and 11th) were disfavored by the micelles primarily due to the loss of peptide:micelle hydrophobic interactions. Peptides differing at the C-terminal (i.e., L14V) were recognized by SDS micelles (ΔΔG ∼ 4 kcal/mol) by altering peptide:micelle interactions. L14V mutation, on the other hand, did not play any role in the peptide:DPC binding, as no direct interactions between the C-terminal and DPC micelle were observed due to obvious electrostatic reasons. The strength of selectivity favoring LL-14 binding against VV-14 was found to be much higher for DPC micelles (ΔΔG ∼ 25 kcal/mol) relative to SDS micelles (ΔΔG ∼ 19 kcal/mol). The loss of the peptide:micelle hydrophobic contact in response to LL-14 → VV-14 mutation was found to be significantly larger for DPC relative to SDS micelles, resulting in higher discriminatory power for the former. Peptide:SDS salt bridges seemed to prevent the loss of peptide:micelle hydrophobic contact to some extent, leading to weaker selectivity for SDS micelles. High selectivity of DPC micelles provided an efficient mechanism for VV-14 dissociation from DPC micelles, whereas low-selectivity of SDS micelles ensured binding of both LL-14 and VV-14. To the best of our knowledge, this is the first study in which the experimental observations (antimicrobial activity and toxicity) between leucine-rich and valine-rich peptides have been explained by establishing a direct link between the energetics and structures.

Rational Framework for the Design of Trp- and Arg-Rich Peptide Antibiotics Against Multidrug-Resistant Bacteria

The threat of antibiotic resistance warrants the discovery of agents with novel antimicrobial mechanisms. Antimicrobial peptides (AMPs) directly disrupting bacterial membranes may overcome resistance to traditional antibiotics. AMP development for clinical use has been mostly limited to topical application to date. We developed a rational framework for systematically addressing this challenge using libraries composed of 86 novel Trp- and Arg-rich engineered peptides tested against clinical strains of the most common multidrug-resistant bacteria known as ESKAPE pathogens. Structure-function correlations revealed minimum lengths (as low as 16 residues) and Trp positioning for maximum antibacterial potency with mean minimum inhibitory concentration (MIC) of 2–4 μM and corresponding negligible toxicity to mammalian cells. Twelve peptides were selected based on broad-spectrum activity against both gram-negative and -positive bacteria and <25% toxicity to mammalian cells at maximum test concentrations. Most of the selected PAX remained active against the colistin-resistant clinical strains. Of the selected peptides, the shortest (the 16-residue E35) was further investigated for antibacterial mechanism and proof-of-concept in vivo efficacy. E35 killed an extensively-resistant isolate of Pseudomonas aeruginosa (PA239 from the CDC, also resistant to colistin) by irreversibly disrupting the cell membranes as shown by propidium iodide incorporation, using flow cytometry and live cell imaging. As proof of concept, in vivo toxicity studies showed that mice tolerated a systemic dose of up to 30 mg/kg peptide and were protected with a single 5 mg/kg intravenous (IV) dose against an otherwise lethal intraperitoneal injection of PA239. Efficacy was also demonstrated in an immune-compromised Klebsiella pneumoniae infection model using a daily dose of 4mg/kg E35 systemically for 2 days. This framework defines the determinants of efficacy of helical AMPs composed of only cationic and hydrophobic amino acids and provides a path for a potential departure from the restriction to topical use of AMPs toward systemic application.

An Overview of Antiviral Peptides and Rational Biodesign Considerations

Viral diseases have contributed significantly to worldwide morbidity and mortality throughout history. Despite the existence of therapeutic treatments for many viral infections, antiviral resistance and the threat posed by novel viruses highlight the need for an increased number of effective therapeutics. In addition to small molecule drugs and biologics, antimicrobial peptides (AMPs) represent an emerging class of potential antiviral therapeutics. While AMPs have traditionally been regarded in the context of their antibacterial activities, many AMPs are now known to be antiviral. These antiviral peptides (AVPs) have been shown to target and perturb viral membrane envelopes and inhibit various stages of the viral life cycle, from preattachment inhibition through viral release from infected host cells. Rational design of AMPs has also proven effective in identifying highly active and specific peptides and can aid in the discovery of lead peptides with high therapeutic selectivity. In this review, we highlight AVPs with strong antiviral activity largely curated from a publicly available AMP database. We then compile the sequences present in our AVP database to generate structural predictions of generic AVP motifs. Finally, we cover the rational design approaches available for AVPs taking into account approaches currently used for the rational design of AMPs.

Designing Anti-Microbial Peptides Against Major β-Lactamase Enzymes in Clinically Important Gram-Negative Bacterial Pathogens: An In-Silico Study

Anti-microbial resistance (AMR) creating healthcare concerns worldwide requires ardent exploration of therapeutic alternatives. Although anti-microbial peptides (AMP) are popular for broad-spectrum activity, recent evidence of increasing resistance to membrane-acting AMPs by ESKAPE pathogens has compelled us to design novel AMPs as therapeutic candidates. A library of 60 AMPs comprising natural AMPs and their mutants was constructed through in-silico methods. After physico-chemical property evaluations, each peptide in the library was subjected to flexible molecular docking against four major β-lactamases in Gram-negative ESKAPE pathogens. Among the potent AMP mutants, a Lactoferricin B-Mutant (M4) possessed uniformly high affinity with SHV1, OXA48, NDM1, and AmpC having energies -842.0Kcal/mol, -774.8Kcal/mol, -1103.3Kcal/mol, and -858.8Kcal/mol respectively. Coarse-grained clustering and flexibility analysis further accounted for the residue-level stable configurations of the protein-peptide complexes with high affinity. Highest affinity of Lactoferricin B_M4 was found with NDM1 due to H-bonds, salt-bridges, and hydrophobic interactions with the metallo-β-lactamase domain including crucial active-site residue Asp124. Molecular dynamics simulation further confirmed the stability of Lactoferricin B_M4-NDM1 complex having low residue-level root-mean square deviations (RMSD), atomic-level fluctuations, and radius of gyration (Rg). The study encourages experimental validations and similar methods to identify potential AMPs against drug-resistant pathogens.

The Potential of Modified and Multimeric Antimicrobial Peptide Materials as Superbug Killers

Antimicrobial peptides (AMPs) are found in nearly all living organisms, show broad spectrum antibacterial activity, and can modulate the immune system. Furthermore, they have a very low level of resistance induction in bacteria, which makes them an ideal target for drug development and for targeting multi-drug resistant bacteria 'Superbugs'. Despite this promise, AMP therapeutic use is hampered as typically they are toxic to mammalian cells, less active under physiological conditions and are susceptible to proteolytic degradation. Research has focused on addressing these limitations by modifying natural AMP sequences by including e.g., d-amino acids and N-terminal and amino acid side chain modifications to alter structure, hydrophobicity, amphipathicity, and charge of the AMP to improve antimicrobial activity and specificity and at the same time reduce mammalian cell toxicity. Recently, multimerisation (dimers, oligomer conjugates, dendrimers, polymers and self-assembly) of natural and modified AMPs has further been used to address these limitations and has created compounds that have improved activity and biocompatibility compared to their linear counterparts. This review investigates how modifying and multimerising AMPs impacts their activity against bacteria in planktonic and biofilm states of growth.

Antimicrobial peptides, conventional antibiotics, and their synergistic utility for the treatment of drug-resistant infections

Antimicrobial peptides (AMPs), also known as host defense peptides (HDPs), are important effector immune defense molecules in multicellular organisms. AMPs exert their antimicrobial activities through several mechanisms; thus far, induction of drug resistance through AMPs has been regarded as unlikely. Therefore, they have great potential as new generation antimicrobial agents. To date, more than 30 AMP-related drugs are in the clinical trial phase. In recent years, studies show that some AMPs and conventional antibiotics have synergistic effects. The combined use of AMPs and antibiotics can kill drug-resistant pathogens, prevent drug resistance, and significantly improve the therapeutic effects of antibiotics. In this review, we discuss the progress in synergistic studies on AMPs and conventional antibiotics. An overview of the current understanding of the functional scope of AMPs, ongoing clinical trials, and challenges in the development processes are also presented.

Advances in the development of antimicrobial peptides and proteins for inhaled therapy

Antimicrobial peptides and proteins (APPs) are becoming increasingly important in targeting multidrug-resistant (MDR) bacteria. APPs is a rapidly emerging area with novel molecules being produced and further optimised to enhance antimicrobial efficacy, while overcoming issues associated with biologics such as potential toxicity and low bioavailability resulting from short half-life. Inhalation delivery of these agents can be an effective treatment of respiratory infections owing to the high local drug concentration in the lungs with lower exposure to systemic circulation hence reducing systemic toxicity. This review describes the recent studies on inhaled APPs, including in vitro and in vivo antimicrobial activities, toxicity assessments, and formulation strategies whenever available. The review also includes studies on combination of APPs with other antimicrobial agents to achieve enhanced synergistic antimicrobial effect. Since different APPs have different biological and chemical stabilities, a targeted formulation strategy should be considered for developing stable and inhalable antimicrobial peptides and proteins. These strategies include the use of sodium chloride to reduce electrostatic interaction between APP and extracellular DNA in sputum, the use of D-enantiomers or dendrimers to minimise protease-mediated degradation and or the use of prodrugs to reduce toxicity. Although great effort has been put towards optimising the biological functions of APPs, studies assessing biological stability in inhalable aerosols are scarce, particularly for novel molecules. As such, formulation and manufacture of inhalable liquid and powder formulations of APPs are underexplored, yet they are crucial areas of research for clinical translation.

The Engineered Antibiotic Peptide PLG0206 Eliminates Biofilms and Is a Potential Treatment for Periprosthetic Joint Infections

Antimicrobial peptides (AMPs) have recently gained attention for their potential to treat diseases related to bacterial and viral infections, as many traditional antimicrobial drugs have reduced efficacy in treating these infections due to the increased prevalence of drug-resistant pathogens. PLG0206, an engineered cationic antibiotic peptide that is 24 residues long, has been designed to address some limitations of other natural AMPs, such as toxicity and limited activity due to pH and ion concentrations. Nonclinical studies have shown that PLG0206 is highly selective for targeting bacterial cells and is not toxic to human blood cells. Antibiofilm experiments demonstrated that PLG0206 is effective at reducing both biotic and abiotic biofilm burdens following direct biofilm contact. PLG0206 has rapid and broad-spectrum activity against both Gram-positive and Gram-negative bacteria that are implicated as etiologic agents in periprosthetic joint infections, including multidrug-resistant ESKAPE pathogens and colistin-resistant isolates. A recent first-in-human study demonstrated that PLG0206 is well tolerated and safe as an intravenous infusion in healthy volunteers. Studies are planned to determine the efficacy of PLG0206 in patients for the treatment of periprosthetic joint infections. This review summarizes the chemistry, pharmacology, and microbiology of PLG0206 and explores its current preclinical, clinical, and regulatory status.

Structure-activity trend analysis between amino-acids and minimal inhibitory concentration of antimicrobial peptides

Antimicrobial peptides (AMPs) provide large structural libraries of molecules with high variability of constitutional amino-acids (AAs). Highlighting structural organization and structure-activity trends in such molecular systems provide key information on structural associations and functional conditions that could usefully help for drug design. This work presents link analyses between minimal inhibitory concentration (MIC) and different types of constitutional AAs of anti-Pseudomonas aeruginosa AMPs. This scope was based on a dataset of 328 published molecules. Regulation levels of AAs in AMPs were statistically ordinated by correspondence analysis helping for classification of the 328 AMPs into nine structurally homogeneous peptide clusters (PCs 1-9) characterized by high/low relative occurrences of different AAs. Within each PC, negative trends between MIC and AAs were highlighted by iterated multiple linear regression models built by bootstrap processes (bagging). MIC-decrease was linked to different AAs that varied with PCs: alcohol type AAs (Thr, Ser) in Cys-rich and low Arg PCs (PCs 1-3); basic AAs (Lys, Arg) in Pro-rich and low Val PCs (PCs 4-8); Trp (heterocyclic AA) in Arg-rich PCs (PCs 6, 7, 9). Aliphatic AAs (more particularly Gly) showed MIC-reduction effects in different PCs essentially under interactive forms.

Synergism between WLBU2 peptide and antibiotics against methicillin-resistant Staphylococcus aureus and extended-spectrum beta-lactamase-producing Enterobacter cloacae

Infections caused by Methicillin-Resistant Staphylococcus aureus (MRSA) and Extended-Spectrum Beta-Lactamase (ESBL) producing Enterobacter cloacae are considered as major therapeutic challenge due to their multidrug-resistant (MDR) phenotype against conventional antibiotics. WLBU2 is an engineered cationic peptide with potent antimicrobial activity. This in-vitro study aimed to evaluate the effects of WLBU2 against clinical isolates of the aforementioned bacteria and assess whether synergistic effects can be achieved upon combination with conventional antibiotics. The minimum inhibitory concentrations (MICs) of antimicrobial agents against bacterial clinical isolates (n = 30/strain) were determined using the microbroth dilution assay. The minimum bactericidal concentrations (MBCs) of WLBU2 were determined from microbroth dilution (MICs) tests by subculturing to agar plates. MICs of WLBU2 were evaluated in the presence of physiological concentrations of salts including NaCl, CaCl2 and MgCl2. To identify bacterial resistance profile, MRSA were treated with Oxacillin, Erythromycin and Vancomycin, while Ceftazidime, Ceftriaxone, Ciprofloxacin and Imipenem were used against Enterobacter cloacae. Combination treatments of antibiotics and sub-inhibitory concentrations of WLBU2 were conducted when MICs indicated intermediate/resistant susceptibility. The MICs/MBCs of WLBU2 were identical for each respective bacteria with values of 0.78-6.25 μM and 1.5-12.5 μM against MRSA and Enterobacter cloacae, respectively. WLBU2 was found as salt resistant. Combination treatment showed that synergistic and additive effects were achieved in many isolates of MRSA and Enterobacter cloacae. Our data revealed that WLBU2 is a potent peptide with bactericidal activity. In addition, it demonstrated the selective advantage of WLBU2 as a potential therapeutic agent under physiological solutions. Our findings also support the combination of WLBU2 and conventional antibiotics with potential application for treatment of resistant bacteria.

Biomaterial-Interrelated Bacterial Sweeper: Simplified Self-Assembled Octapeptides with Double-Layered Trp Zipper Induces Membrane Destabilization and Bacterial Apoptosis-Like Death

Treatment of microbial-associated infections continues to be hampered by impaired antibacterial efficiency and the variability in nanomedicines. Herein, an octapeptide library with a double-layered zipper, constructed via a systematic arrangement, simplifying the sequence and optimizing the structure (diverse motifs including surfactant-like, central-bola, and end-bola), is assessed in terms of biological efficiency and self-assembly properties. The results indicate that peptides with double-layered Trp zipper exhibit significant antimicrobial activity. Extracellularly, affinity interactions between micelles and bacteria induce the lateral flow of the membrane and electric potential perturbation. Intracellularly, lead molecules cause apoptosis-like death, as indicated by excessive accumulation of reactive oxygen species, generation of a DNA ladder, and upregulation of mazEF expression. Among them, RW-1 performs the best in vivo and in vitro. The intersecting combination of Trp zipper and surfactants possesses overwhelming superiority with respect to bacterial sweepers (therapeutic index [TI] = 52.89), nanostructures (micelles), and bacterial damage compared to RW-2 (central-bola) and RW-3 (end-bola). These findings confirm that the combination of double-layered Trp zipper and surfactants has potential for application as a combined motif for combating microbial infection and connects the vast gap between antimicrobial peptides and self-assembly, such as Jacob's ladder.

Chemical modifications to increase the therapeutic potential of antimicrobial peptides

The continued use of antibiotics has been accompanied by the rapid emergence and spread of antibiotic-resistant strains of bacteria. Antimicrobial peptides (AMPs), also known as host defense peptides, show multiple features as an ideal antimicrobial agent, including potent, rapid, and broad-spectrum antimicrobial activity, low promotion of antimicrobial resistance, potent anti-biofilm activity, and lethality against metabolically inactive microorganisms. However, several crucial drawbacks constrain the use of AMPs as clinical drugs, e.g., liability in vivo, toxicity when used systemically, and high production costs. Based on recent findings and our own experiences, here we summarize some chemical modifications and key design strategies to increase the therapeutic potential of AMPs, including 1) enhancing antimicrobial activities, 2) improving in vivo effectiveness, and 3) reduction in toxicity, which may facilitate the design and optimization of AMPs for the development of drug candidates. We also discuss the present challenges in the optimization of AMPs and future concerns about the resistance and cross-resistance to AMPs in the development of AMPs as therapeutic drugs.

A Phase 1 Study of Safety, Tolerability and Pharmacokinetics of Single Ascending Doses of a First in Human Engineered Cationic Peptide, PLG0206, Intravenously Administered in Healthy Subjects

Background: In this first in human study, PLG0206, a novel engineered cationic antimicrobial peptide was evaluated for safety, tolerability and pharmacokinetics when intravenously administered as a single dose to healthy subjects. Methods: Six cohorts of 8 subjects received escalating single IV infusions of PLG0206 at 0.05, 0.125, 0.25, 0.5, or 1 mg/kg dose or placebo over 1-to-4-hours. Subjects were randomized to receive either PLG0206 (6 per cohort) or placebo (2 per cohort). Serial pharmacokinetic samples were taken prior to infusion and up to 48 hours post infusion. Safety and tolerability were assessed throughout the study. Results: The demographic characteristics of subjects were comparable between those treated with PLG0206 and placebo and between dose groups. The incidence of treatment emergent adverse events (TEAE) related to PLG0206 was low and most events were mild in severity and were similar between the PLG0206 treatment and placebo groups. The most common adverse events reported for PLG0206 were infusion related reactions, which were mitigated with increasing infusion time and volume. There were no serious adverse events (SAE), life-threatening events, or deaths throughout the study. IV PLG0206 exhibited linear pharmacokinetics over the dose range of 0.05 to 1.0 mg/kg. The median terminal half-life (t_½) ranged from 7.37 to 19.97 hours. Conclusion: Following a single IV infusion to healthy subjects, PLG0206 was safe and well tolerated and exhibited linear PK at doses ranging from 0.05 to 1 mg/kg. These findings support the ongoing development of IV PLG0206 as an antimicrobial agent.

Conjugation of Silver Nanoparticles with De Novo Engineered Cationic Antimicrobial Peptides: An Exploratory Proposal

Background

Cationic antimicrobial peptides have broad antimicrobial activity and provide a novel way of targeting multidrug-resistant bacteria in the era of increasing antimicrobial resistance. Current developments show positive prospects for antimicrobial peptides and silver nanoparticles (AgNPs) individually.

Objective

The primary objective is to propose another method for enhancing antimicrobial activity by conjugating AgNPs with cationic antimicrobial peptides, with a subsequent preliminary assessment of the minimum inhibitory concentration of multidrug-resistant bacteria. The secondary objective is to evaluate the safety of the conjugated compound and assess its viability for in vivo use.

Methods

The proposal involves 3 stages. First, WLBU2C, a modified version of the antimicrobial peptide WLBU2 with an added cysteine group, needs to be synthesized using a standard Fmoc procedure. It can then be stably conjugated with AgNPs ideally through photochemical means. Second, the WLBU2C-AgNP conjugate should be tested for antimicrobial activity according to the Clinical & Laboratory Standards Institute manual on standard minimum inhibitory concentration testing. Third, the cytotoxicity of the conjugate should be tested using cell lysis assays if the above stages are completed.

Results

I-TASSER (iterative threading assembly refinement) simulation revealed that the modified peptide WLBU2C has a secondary structure similar to that of the original WLBU2 peptide. No other results have been obtained at this time.

Conclusions

The addition of AgNPs to already developed de novo–engineered antimicrobial peptides provides an opportunity for the development of potent antimicrobials. Future prospects include emergency last-line therapy and treatment for current difficult-to-eradicate bacterial colonization, such as in cystic fibrosis, implantable medical devices, cancer, and immunotherapy. As I do not anticipate funding at this time, I hope this proposal provides inspiration to other researchers.

International Registered Report Identifier (IRRID)

PRR1-10.2196/28307

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.

Tandem Repeat of a Short Human Chemerin-Derived Peptide and Its Nontoxic d-Lysine-Containing Enantiomer Display Broad-Spectrum Antimicrobial and Antitubercular Activities

To design novel antimicrobial peptides by utilizing the sequence of the human host defense protein, chemerin, a seven-residue amphipathic stretch located in the amino acid region, 109-115, was identified, which possesses the highest density of hydrophobic and positively charged residues. Although this 7-mer peptide was inactive toward microorganisms, its 14-mer tandem repeat (Chem-KVL) was highly active against different bacteria including methicillin-resistant Staphylococcus aureus, a multidrug-resistant Staphylococcus aureus strain, and slow- and fast-growing mycobacterial species. The selective enantiomeric substitutions of its two l-lysine residues were attempted to confer cell selectivity and proteolytic stability to Chem-KVL. Chem-8dK with a d-lysine replacement in its middle (eighth position) showed the lowest hemolytic activity against human red blood cells among Chem-KVL analogues and maintained high antimicrobial properties. Chem-8dK showed in vivo efficacy against Pseudomonas aeruginosa infection in BALB/c mice and inhibited the development of resistance in this microorganism up to 30 serial passages and growth of intracellular mycobacteria in THP-1 cells.

Discovery, Optimization, and Clinical Application of Natural Antimicrobial Peptides

Antimicrobial peptides (AMPs) are widespread in multicellular organisms. These structurally diverse molecules are produced as the first line of defense against pathogens such as bacteria, viruses, fungi, and parasites. Also known as host defense peptides in higher eukaryotic organisms, AMPs display immunomodulatory and anticancer activities. During the last 30 years, technological advances have boosted the research on antimicrobial peptides, which have also attracted great interest as an alternative to tackling the antimicrobial resistance scenario mainly provoked by some bacterial and fungal pathogens. However, the introduction of natural AMPs in clinical trials faces challenges such as proteolytic digestion, short half-lives, and cytotoxicity upon systemic and oral application. Therefore, some strategies have been implemented to improve the properties of AMPs aiming to be used as effective therapeutic agents. In the present review, we summarize the discovery path of AMPs, focusing on preclinical development, recent advances in chemical optimization and peptide delivery systems, and their introduction into the market.