Ultrashort Antimicrobial Peptides with Antiendotoxin Properties

Antibacterial efficacy and mechanism of Cyprinus carpio chemokine-derived L-10 against multidrug-resistant Escherichia coli infections

OBJECTIVES

Antimicrobial resistance has raised concerns regarding untreatable infections and poses a growing threat to public health. Rational design of new AMPs is an ideal solution to this threat.

METHODS

In this study, we designed, modified, and synthesised an excellent AMP, L-10, based on the original sequence of the Cyprinus carpio chemokine. All experimental data were presented as the mean ± standard deviation (SD), and the two-tailed unpaired T-test method was used to analyze all data.

RESULTS

L-10 exhibited excellent antibacterial activity with negligible toxicity and improved the efficacy of a broad class of antibiotics against MDR Gram-negative pathogens, including tetracycline, meropenem, levofloxacin, and rifampin. Mechanistic studies have suggested that L-10 targets the bacterial membrane components, LPS and PG, to disrupt bacterial membrane integrity, thereby exerting antibacterial effects and enhancing the efficacy of antibiotics. Moreover, in animal infection models, L-10 significantly increased the survival rate of infected animals and effectively reduced the tissue bacterial load and inflammatory factor levels. In addition to its direct antibacterial activity, L-10 dramatically reduced pulmonary pathological alterations in a mouse model of endotoxemia and suppressed LPS-induced proinflammatory cytokines in vitro and in vivo. Lastly, L-10 was successfully expressed in Pichia pastoris and maintained antimicrobial activity against MDR Gram-negative pathogens in vivo and in vitro.

CONCLUSION

Collectively, these results reveal the potential of L-10 as an ideal candidate against MDR bacterial infections and provide new insights into the design, development, and clinical application of AMPs.

AMPFinder: A computational model to identify antimicrobial peptides and their functions based on sequence-derived information

Antimicrobial peptides (AMPs) called host defense peptides have existed among all classes of life with 5-100 amino acids generally and can kill mycobacteria, envelop viruses, bacteria, fungi, cancerous cells and so on. Owing to the non-drug resistance of AMP, it has been a wonderful agent to find novel therapies. Therefore, it is urgent to identify AMPs and predict their function in a high-throughput way. In this paper, we propose a cascaded computational model to identify AMPs and their functional type based on sequence-derived and life language embedding, called AMPFinder. Compared with other state-of-the-art methods, AMPFinder obtains higher performance both on AMP identification and AMP function prediction. AMPFinder shows better performance with improvement of F1-score (1.45%-6.13%), MCC (2.92%-12.86%) and AUC (5.13%-8.56%) and AP (9.20%-21.07%) on an independent test dataset. And AMPFinder achieve lower bias of R² on a public dataset by 10-fold cross-validation with an improvement of (18.82%-19.46%). The comparison with other state-of-the-art methods shows that AMP can accurately identify AMP and its function types. The datasets, source code and user-friendly application are available at https://github.com/abcair/AMPFinder.

Diversity-Oriented Synthesis (DOS) of On-DNA Peptidomimetics from Acid-Derived Phosphonium Ylides

The DNA-encoded library (DEL) technology represents a revolutionary drug-discovery tool with unprecedented screening power originating from the association of combinatorial chemistry and DNA barcoding. The chemical diversity of DELs and its chemical space will be further expanded as new DNA-compatible reactions are introduced. This work introduces the use of DOS in the context of on-DNA peptidomimetics. Wittig olefination of aspartic acid-derived on-DNA Wittig ylide, combined with a broad substrate scope of aldehydes, led to formation of on-DNA α ${\alpha }$ , β ${\beta }$ -unsaturated ketones. The synthesis of on-DNA multi-peptidyl-ylides was performed by incorporating sequential amino acids onto a monomeric ylide. Di-, tri- and tetrameric peptidyl-ylides were validated for Wittig olefination and led to on-DNA α ${\alpha }$ , β ${\beta }$ -unsaturated-based peptidomimetics, an important class of intermediates. One on-DNA aryl Wittig ylide was also developed and applied to Wittig olefination for synthesis of on-DNA chalcone-based molecules. Furthermore, DOS was used successfully with electron-deficient peptidomimetics and led to the development of different heterocyclic cores containing on-DNA peptidomimetics.

Synergy by Perturbing the Gram-Negative Outer Membrane: Opening the Door for Gram-Positive Specific Antibiotics

New approaches to target antibacterial agents toward Gram-negative bacteria are key, given the rise of antibiotic resistance. Since the discovery of polymyxin B nonapeptide as a potent Gram-negative outer membrane (OM)-permeabilizing synergist in the early 1980s, a vast amount of literature on such synergists has been published. This Review addresses a range of peptide-based and small organic compounds that disrupt the OM to elicit a synergistic effect with antibiotics that are otherwise inactive toward Gram-negative bacteria, with synergy defined as a fractional inhibitory concentration index (FICI) of <0.5. Another requirement for the inclusion of the synergists here covered is their potentiation of a specific set of clinically used antibiotics: erythromycin, rifampicin, novobiocin, or vancomycin. In addition, we have focused on those synergists with reported activity against Gram-negative members of the ESKAPE family of pathogens namely, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and/or Acinetobacter baumannii. In cases where the FICI values were not directly reported in the primary literature but could be calculated from the published data, we have done so, allowing for more direct comparison of potency with other synergists. We also address the hemolytic activity of the various OM-disrupting synergists reported in the literature, an effect that is often downplayed but is of key importance in assessing the selectivity of such compounds for Gram-negative bacteria.

High Level Expression and Purification of Cecropin-like Antimicrobial Peptides in Escherichia coli

Cecropins are a family of antimicrobial peptides (AMPs) that are widely found in the innate immune system of Cecropia moths. Cecropins exhibit a broad spectrum of antimicrobial and anticancer activities. The structures of Cecropins are composed of 34–39 amino acids with an N-terminal amphipathic α-helix, an AGP hinge and a hydrophobic C-terminal α-helix. KR12AGPWR6 was designed based on the Cecropin-like structural feature. In addition to its antimicrobial activities, KR12AGPWR6 also possesses enhanced salt resistance, antiendotoxin and anticancer properties. Herein, we have developed a strategy to produce recombinant KR12AGPWR6 through a salt-sensitive, pH and temperature dependent intein self-cleavage system. The His6-Intein-KR12AGPWR6 was expressed by E. coli and KR12AGPWR6 was released by the self-cleavage of intein under optimized ionic strength, pH and temperature conditions. The molecular weight and structural feature of the recombinant KR12AGPWR6 was determined by MALDI-TOF mass, CD, and NMR spectroscopy. The recombinant KR12AGPWR6 exhibited similar antimicrobial activities compared to the chemically synthesized KR12AGPWR6. Our results provide a potential strategy to obtain large quantities of AMPs and this method is feasible and easy to scale up for commercial production.

A Novel Antimicrobial Peptide Derived from Bony Fish IFN1 Exerts Potent Antimicrobial and Anti-Inflammatory Activity in Mammals

Type I interferons (IFN-Is) are critical antiviral cytokine in innate immunity but with limited direct defense ability against bacterial infections in mammals. In bony fish, despite all the IFN-Is (IFN1-4) act in antiviral immunity, studies demonstrate that IFN1 can remarkably contribute to host defense against bacterial infections. In this study, we found that IFN1 from grass carp (Ctenopharyngodon idella) contains an unusual cationic and amphipathic α-helical region (named as gcIFN-20, sequence: SYEKKINRHFKILKKNLKKK). The synthesized peptide gcIFN-20 could form α-helical structure in a membrane environment and exerts potent antimicrobial activity against multiple species of Gram-negative (G-) and Gram-positive (G+) bacteria with negligible toxicity. Mechanism studies showed gcIFN-20 kills G+ bacteria through membrane disruption and cytoplasm outflow while G- bacteria through membrane permeation and protein synthesis inhibition. In two mouse bacterial infection models, gcIFN-20 therapy could significantly reduce tissue bacterial loads and mortalities. In addition to the direct antibacterial activity, we also found that gcIFN-20 could significantly suppress the lipopolysaccharide (LPS)-induced pro-inflammatory cytokines in vitro and in vivo, obviously alleviated lung lesions in a mouse endotoxemia model. The mechanism is that gcIFN-20 interacts with LPS, causes LPS aggregation and neutralization. The antimicrobial and anti-inflammatory activities in vivo of gcIFN-20 in mammalian models suggested a promising agent for developing peptide-based antibacterial therapy. IMPORTANCE Type I interferons play crucial role in antiviral immunity in both vertebrates and invertebrates. The powerful antimicrobial activity is recently reported in nonmammalian vertebrates. The present study identified a novel antimicrobial peptide (gcIFN-20) derived from grass carp interferon 1, found gcIFN-20 exhibits forceful bactericidal and anti-inflammatory activity in mammals, and efficient therapeutic effect against two clinical severe extraintestinal pathogenic Escherichia coli and a mouse endotoxemia models. The antimicrobial mechanisms are membrane disruption and cytoplasm overflow for Gram-positive bacteria, while membrane permeation and protein synthesis inhibition for Gram-negative bacteria. The anti-inflammatory mechanisms can be aggregating and neutralizing lipopolysaccharide to attenuate the binding with receptors and facilitate phagocytosis. The results indicate that gcIFN-20 can be a promising novel therapeutic agent for bacterial diseases and inflammatory disorders, especially as a potential weapon for multidrug resistant strain infections.

Strategies employed in the design of antimicrobial peptides with enhanced proteolytic stability

Due to the alarming developing rate of multidrug-resistant bacterial pathogens, the development and modification of antimicrobial peptides (AMPs) are unprecedentedly active. Despite the fact that considerable efforts have been expended on the discovery and design strategies of AMPs, the clinical translation of peptide antibiotics remains inadequate. A large number of articles and reviews credited the limited success of AMPs to their poor stability in the biological environment, particularly their poor proteolytic stability. In the past forty years, various design strategies have been used to improve the proteolytic stability of AMPs, such as sequence modification, cyclization, peptidomimetics, and nanotechnology. Herein, we focus our discussion on the progress made in improving the proteolytic stability of AMPs and the principle, successes, and limitations of various anti-proteolytic design strategies. It is of prospective significance to extend current insights into the degradation-related inactivation of AMPs and also alleviate/overcome the problem.

Antimicrobial and anti-inflammatory activities of the neuropeptide antagonist SPA

Antimicrobial peptides have received increased attention due to the increasing prevalence of antibiotic-resistant bacteria. However, the development of antimicrobial peptides for clinical applications remains a huge challenge. SPA ([D-rg¹ , D-Trp^5,7,9 , Leu¹¹ ]SP), an analog of substance P, is a broad-spectrum neuropeptide antagonist. In this study, we found that SPA could efficiently kill Gram-positive and Gram-negative bacteria by membrane disruption, similar to antimicrobial peptides. In addition, SPA showed high killing activity toward bacteria rather than mammalian cells. Our results also demonstrated that SPA could significantly decrease the expression of proinflammatory cytokines and rescue mice from lethal septic shock induced by LPS. The impressive therapeutic potential of SPA, as indicated in this study, makes it a good template for developing effective antibiotics. Meanwhile, our study provides a new idea for developing multifunctional therapeutic agents to combat bacterial infections.

Boosting Synergistic Effects of Short Antimicrobial Peptides With Conventional Antibiotics Against Resistant Bacteria

The global spread of antibiotic-resistant infections has meant that there is an urgent need to develop new antimicrobial alternatives. In this study, we developed a strategy to boost and/or synergize the activity of conventional antibiotics by combination with antimicrobial peptides tagged with the bulky non-natural amino acid β-naphthylalanine (Nal) to their N- or C-terminus. A checkerboard method was used to evaluate synergistic effects of the parent peptide and the Nal-tagged peptides. Moreover, boron-dipyrro-methene labeled vancomycin was used to characterize the synergistic mechanism of action between the peptides and vancomycin on the bacterial strains. These Nal-tagged antimicrobial peptides also reduced the antibiotic-induced release of lipopolysaccharide from Gram-negative bacteria by more than 99.95%. Our results demonstrate that Nal-tagged peptides could help in developing antimicrobial peptides that not only have enhanced antibacterial activities but also increase the synergistic effects with conventional antibiotics against antibiotic-resistant bacteria.

Antimicrobial Peptides with Enhanced Salt Resistance and Antiendotoxin Properties

A strategy was described to design antimicrobial peptides (AMPs) with enhanced salt resistance and antiendotoxin activities by linking two helical AMPs with the Ala-Gly-Pro (AGP) hinge. Among the designed peptides, KR12AGPWR6 demonstrated the best antimicrobial activities even in high salt conditions (NaCl ~300 mM) and possessed the strongest antiendotoxin activities. These activities may be related to hydrophobicity, membrane-permeability, and α-helical content of the peptide. Amino acids of the C-terminal helices were found to affect the peptide-induced permeabilization of LUVs, the α-helicity of the designed peptides under various LUVs, and the LPS aggregation and size alternation. A possible model was proposed to explain the mechanism of LPS neutralization by the designed peptides. These findings could provide a new approach for designing AMPs with enhanced salt resistance and antiendotoxin activities for potential therapeutic applications.

Analysis of the anti-inflammatory effect of the aptamer LA27 and its binding mechanism

Lipopolysaccharide (LPS) is an important pathogenic factor and plays a key role in human diseases such as fever, shock, and sepsis. Blocking the toxicity of LPS through antagonism is considered the best choice for the treatment of LPS-induced diseases. In this research, nucleic acid aptamer LA27, which was previously selected and optimized by our group, was used as an LPS inhibitor to treat human HepG2 cells stimulated by LPS from four different sources (StLPS, EcoliLPS, PaLPS, and SeLPS): the levels of expression of three inflammatory cytokines factors (TNF-α, IL-1β, and IL-6) were evaluated by ELISA on LA27-treated and untreated cells incubated for 12 h with LPS. The results of the assays indicated that LA27 exhibited considerable anti-inflammatory activity. The binding site and interactions between aptamer LA27 and LPSs were also simulated using Molecular Operating Environment (MOE) 2018 software. MOE simulation results showed that, under a combination of the hydrophobic interaction, hydrogen bonding, and electrostatic interactions, the fatty acid chain of LPS could interact with the wide hydrophobic region of the aptamer, constituting its major groove, and formed stable complex of T-type. The present research indicated that LA27 might be a potential therapeutic agent for sepsis and other diseases, which provides a new path for the development of LPS antagonists.

Antimicrobial Peptides Display Strong Synergy with Vancomycin Against Vancomycin-Resistant E. faecium, S. aureus, and Wild-Type E. coli

There is an urgent and imminent need to develop new antimicrobials to fight against antibiotic-resistant bacterial and fungal strains. In this study, a checkerboard method was used to evaluate the synergistic effects of the antimicrobial peptide P-113 and its bulky non-nature amino acid substituted derivatives with vancomycin against vancomycin-resistant Enterococcus faecium, Staphylococcus aureus, and wild-type Escherichia coli. Boron-dipyrro-methene (BODIPY) labeled vancomycin was used to characterize the interactions between the peptides, vancomycin, and bacterial strains. Moreover, neutralization of antibiotic-induced releasing of lipopolysaccharide (LPS) from E. coli by the peptides was obtained. Among these peptides, Bip-P-113 demonstrated the best minimal inhibitory concentrations (MICs), antibiotics synergism, bacterial membrane permeabilization, and supernatant LPS neutralizing activities against the bacteria studied. These results could help in developing antimicrobial peptides that have synergistic activity with large size glycopeptides such as vancomycin in therapeutic applications.

Interactive association of lipopolysaccharide and free fatty acid with the prevalence of type 2 diabetes: A community-based cross-sectional study

AIMS/INTRODUCTION

Increased blood lipopolysaccharide (LPS) or free fatty acid (FFA) levels correlate with an increased risk of type 2 diabetes. The purpose of the present study was to evaluate the interactive effect of serum LPS and FFA levels on the prevalence of type 2 diabetes.

MATERIALS AND METHODS

This cross-sectional study included 2,553 community-dwelling Chinese adults. Fasting serum LPS levels were determined using the Limulus Amebocyte Lysate Chromogenic Endpoint assay, and FFA levels were determined using an enzymatic method. The participants were divided into three groups according to the tertiles of LPS or FFA levels or nine groups according to the tertiles of LPS and FFA levels. The odd ratios (ORs) for type 2 diabetes were estimated using logistic regression analysis.

RESULTS

We found that higher serum LPS or FFA levels were associated with higher high-sensitivity C-reactive protein levels (P < 0.001), homeostatic model assessment of insulin resistance levels (P < 0.001) and ORs for type 2 diabetes (P < 0.01). Meanwhile, there were significant interactions between LPS and FFA in terms of the high-sensitivity C-reactive protein level (P < 0.001), homeostatic model assessment of insulin resistance level (P < 0.001) and ORs for type 2 diabetes (P < 0.001). In the fully adjusted logistic regression model, the OR for participants with type 2 diabetes in the higher LPS and FFA level group were 6.58 (95% confidence interval 3.05-14.18, P < 0.001) compared with that in participants in the lower LPS and FFA level group.

CONCLUSIONS

The interaction between LPS and FFA was associated with an increased risk of type 2 diabetes in community-dwelling Chinese adults.

Blood Compatibility-An Important but Often Forgotten Aspect of the Characterization of Antimicrobial Peptides for Clinical Application

Acylation of antimicrobial peptides mimics the structure of the natural lipopeptide polymyxin B, and increases antimicrobial and endotoxin-neutralizing activities. In this study, the antimicrobial properties of lactoferrin-based LF11 peptides as well as blood compatibility as a function of acyl chain length were investigated. Beyond the classical hemolysis test, the biocompatibility was determined with human leukocytes and platelets, and the influence of antimicrobial peptides (AMPs) on the plasmatic coagulation and the complement system was investigated. The results of this study show that the acylation of cationic peptides significantly reduces blood tolerance. With increasing acyl chain length, the cytotoxicity of LF11 peptides to human blood cells also increased. This study also shows that acylated cationic antimicrobial peptides are inactivated by the presence of heparin. In addition, it could be shown that the immobilization of LF11 peptides leads to a loss of their antimicrobial properties.

Recent Advances in Anti-virulence Therapeutic Strategies With a Focus on Dismantling Bacterial Membrane Microdomains, Toxin Neutralization, Quorum-Sensing Interference and Biofilm Inhibition

Antimicrobial resistance constitutes one of the major challenges facing humanity in the Twenty-First century. The spread of resistant pathogens has been such that the possibility of returning to a pre-antibiotic era is real. In this scenario, innovative therapeutic strategies must be employed to restrict resistance. Among the innovative proposed strategies, anti-virulence therapy has been envisioned as a promising alternative for effective control of the emergence and spread of resistant pathogens. This review presents some of the anti-virulence strategies that are currently being developed, it will cover strategies focused on quench pathogen quorum sensing (QS) systems, disassemble of bacterial functional membrane microdomains (FMMs), disruption of biofilm formation and bacterial toxin neutralization.

Dependence on size and shape of non-nature amino acids in the enhancement of lipopolysaccharide (LPS) neutralizing activities of antimicrobial peptides

HYPOTHESIS

Release of lipopolysaccharides (LPS) from bacteria into bloodstream may cause serious unwanted stimulation of the host immune system. P-113 is a clinically active histidine-rich antimicrobial peptide. Nal-P-113, a β-naphthylalanine-substituted P-113, is salt-resistant but has limited LPS neutralizing activity. We suspected the size and shape of the non-natural bulky amino acid may affect its LPS neutralizing activity. Herein, antimicrobial, LPS neutralizing, and antiproteolytic effects of phenylalanine- (Phe-P-113), β-naphthylalanine- (Nal-P-113), β-diphenylalanine- (Dip-P-113), and β-(4,4'-biphenyl)alanine- (Bip-P-113) substituted P-113 were studied.

EXPERIMENTS

Structure-activity relationships of P-113, Phe-P-113, Nal-P-113, Dip-P-113, and Bip-P-113 were evaluated using antimicrobial activity assays, serum proteolytic assays, peptide-induced permeabilization of large unilamellar vesicles, zeta potential measurements, dynamic light scattering measurement of LPS aggregation, and Limulus amebocyte lysate assays for measuring LPS neutralization. In vitro and in vivo LPS neutralizing activities were further confirmed by LPS-induced inflammation inhibition in an endotoxemia mouse model.

FINDINGS

Bip-P-113 and Dip-P-113 had the longest and widest non-nature amino acids, respectively. Bip-P-113 enhanced salt resistance, serum proteolytic stability, peptide-induced permeabilization, zeta potential measurements, LPS aggregation, and in vitro and in vivo LPS neutralizing activities. These results could help design novel antimicrobial peptides that have enhanced stability in vivo and that can have potential therapeutic applications.

Role of β-naphthylalanine end-tags in the enhancement of antiendotoxin activities: Solution structure of the antimicrobial peptide S1-Nal-Nal in complex with lipopolysaccharide

Lipopolysaccharide (LPS, endotoxin) is the major component of Gram-negative bacterial outer surface membrane. LPS released from bacteria into bloodstream during infection may cause serious unwanted stimulation of host's immune system and lead to septic shock of the patient. Recently, we have developed a strategy to increase salt resistance and LPS neutralization of short antimicrobial peptides by adding β-naphthylalanine end-tags to their termini. Herein, correlations between membrane immersion depth, orientation, and antiendotoxin activities of the antimicrobial peptides S1 and S1-Nal-Nal have been investigated via solution structure, paramagnetic resonance enhancement, and saturation transfer difference NMR studies. Unlike the parent peptide S1, S1-Nal-Nal rotated its two terminal β-naphthylalanine residues into the hydrophobic lipid A motif of LPS micelles. The LPS-induced inflammation may then be prohibited by the blocked lipid A motif.

Antimicrobial activity and stability of the D-amino acid substituted derivatives of antimicrobial peptide polybia-MPI

Antimicrobial peptide has the potential to be developed as new kind of antimicrobial agents with novel action mechanism. However, the susceptibility to protease is a drawback for potential peptides to be clinical used. d-amino acid substitution can be one way to increase the proteolytic stability of peptides. In the present study, we synthesized the d-lysines substituted analog (d-lys-MPI) and the d-enantiomer of polybia-MPI (D-MPI) to improve the proteolytic resistance of polybia-MPI. Our results showed that, the stability of its d-amino acid partially substituted analog d-lys-MPI was increased. However, it lost antimicrobial activity at the tested concentration with the loss of α-helix content. As shown in the CD spectra, after substitution, the spectra of D-MPI is symmetrical to MPI, indicated it turned into left hand α-helical conformation. Excitingly, the stability of D-MPI toward the tested protease was improved greatly. Notably, the antimicrobial activity of D-MPI was comparable to its L-counterpart MPI, even improved. In addition, the hemolytic activity of D-MPI was lowered. This also indicated that the action target of antimicrobial peptide polybia-MPI was not chiral specific. So, D-MPI may offer a therapeutic strategy to defend the infection of microbes, considering its stability to protease and relatively lower cytotoxicity to human erythrocytes.

Structural basis for endotoxin neutralization by the eosinophil cationic protein

Acute infection by Gram-negative pathogens can induce an exacerbated immune response that leads to lethal septic shock syndrome. Bacterial lipopolysaccharide (LPS) is a major pathogen-associated molecular pattern molecule that can initiate massive and lethal immune system stimulation. Therefore, the development of new and effective LPS-neutralizing agents is a top priority. The eosinophil cationic protein (ECP) is an antimicrobial protein secreted in response to infection, with a remarkable affinity for LPS. In the present study, we demonstrate that ECP is able to neutralize bacterial LPS and inhibit tumor necrosis factor-α production in human macrophages. We also characterized ECP neutralizing activity using progressively truncated LPS mutants, and conclude that the polysaccharide moiety and lipid A portions are required for LPS-mediated neutralization. In addition, we mapped the structural determinants required for the ECP-LPS interaction by nuclear magnetic resonance. Our results show that ECP is able to neutralize LPS and therefore opens a new route for developing novel therapeutic agents based on the ECP structural scaffolding.