Characterizing the structure-function relationship reveals the mode of action of a novel antimicrobial peptide, P1, from jumper ant Myrmecia pilosula

The biological role of charge distribution in linear antimicrobial peptides

INTRODUCTION

Antimicrobial peptides (AMP) have received particular attention due to their capacity to kill bacteria. Although much is known about them, peptides are currently being further researched. A large number of AMPs have been discovered, but only a few have been approved for topical use, due to their promiscuity and other challenges, which need to be overcome.

AREAS COVERED

AMPs are diverse in structure. Consequently, they have varied action mechanisms when targeting microorganisms or eukaryotic cells. Herein, the authors focus on linear peptides, particularly those that are alpha-helical structured, and examine how their charge distribution and hydrophobic amino acids could modulate their biological activity.

EXPERT OPINION

The world currently needs urgent solutions to the infective problems caused by resistant pathogens. In order to start the race for antimicrobial development from the charge distribution viewpoint, bioinformatic tools will be necessary. Currently, there is no software available that allows to discriminate charge distribution in AMPs and predicts the biological effects of this event. Furthermore, there is no software available that predicts the side-chain length of residues and its role in biological functions. More specialized software is necessary.

[Design, screening and antibacterial activity evaluation of the novel antibacterial peptide KR-1]

OBJECTIVE

To design novel antimicrobial peptides with high activity and low toxicity and evaluate their effect against Streptococcus mutans and other oral bacteria for prevention and treatment of dental caries.

OBJECTIVE

We synthesized two antimicrobial peptides (KR-1 and KR-2) using Dhvar4 (a histatins5 mimic) as the template. The antimicrobial peptides with high activity and low toxicity were screened using minimal inhibitory concentration (MIC) test, hemolysis test, and CCK-8 assay. Streptococcus mutans biofilms cultured in 96-well plates were divided into experimental group (KR-1) and positive control group (CHX) and treated with concentration gradients (0.6×, 0.8×, 1× and 2× MICs) of KR-1 and CHX, respectively. Crystal violet staining was used for quantitative analysis of the changes of the biofilms after the treatments. The structural changes of the biofilms were observed with laser confocal microscopy after KR-1 treatment at 10 × MIC. The antimicrobial activity of KR-1 against oral Streptococcus was analyzed based on the time required for sterilization after KR-1 treatment.

OBJECTIVE

The MIC of KR-1 and KR-2 for S. mutans was 3.2 μmol/L and 12.8 μmol/L, respectively. Under the effective concentration, KR-1 and KR-2 resulted in hemolysis rates of 0.35% and 48.8% in rabbit red blood cells and lowered the survival rates of gingival fibroblasts to 88.7% and 21.94%, respectively. KR-1 treatment significantly reduced biofilm formation with a minimum biofilm inhibition concentration (MBIC₅₀) lower than 1.92 μmol/L, and showed an even stronger antimicrobial than CHX at the concentration of 2.56 μmol/L (P=0.001). Confocal laser scanning microscopy revealed that the biofilm structure became loosened after KR-1 treatment, which was capable of killing about 90% of the bacteria within 5 min.

OBJECTIVE

The antimicrobial peptide KR-1 has a stronger antibacterial activity and a low toxicity with a good inhibitory effect against S. mutans biofilm.

Heterodimeric Insecticidal Peptide Provides New Insights into the Molecular and Functional Diversity of Ant Venoms

Ants use venom for predation, defense, and communication; however, the molecular diversity, function, and potential applications of ant venom remains understudied compared to other venomous lineages such as arachnids, snakes and cone snails. In this work, we used a multidisciplinary approach that encompassed field work, proteomics, sequencing, chemical synthesis, structural analysis, molecular modeling, stability studies, and in vitro and in vivo bioassays to investigate the molecular diversity of the venom of the Amazonian Pseudomyrmex penetrator ants. We isolated a potent insecticidal heterodimeric peptide Δ-pseudomyrmecitoxin-Pp1a (Δ-PSDTX-Pp1a) composed of a 27-residue long A-chain and a 33-residue long B-chain cross-linked by two disulfide bonds in an antiparallel orientation. We chemically synthesized Δ-PSDTX-Pp1a, its corresponding parallel AA and BB homodimers, and its monomeric chains and demonstrated that Δ-PSDTX-Pp1a had the most potent insecticidal effects in blowfly assays (LD₅₀ = 3 nmol/g). Molecular modeling and circular dichroism studies revealed strong α-helical features, indicating its cytotoxic effects could derive from cell membrane pore formation or disruption. The native heterodimer was substantially more stable against proteolytic degradation (t _1/2 = 13 h) than its homodimers or monomers (t _1/2 < 20 min), indicating an evolutionary advantage of the more complex structure. The proteomic analysis of Pseudomyrmex penetrator venom and in-depth characterization of Δ-PSDTX-Pp1a provide novel insights in the structural complexity of ant venom and further exemplifies how nature exploits disulfide-bond formation and dimerization to gain an evolutionary advantage via improved stability, a concept that is highly relevant for the design and development of peptide therapeutics, molecular probes, and bioinsecticides.

In Silico Structural Evaluation of Short Cationic Antimicrobial Peptides

Cationic peptides with antimicrobial properties are ubiquitous in nature and have been studied for many years in an attempt to design novel antibiotics. However, very few molecules are used in the clinic so far, sometimes due to their complexity but, mostly, as a consequence of the unfavorable pharmacokinetic profile associated with peptides. The aim of this work is to investigate cationic peptides in order to identify common structural features which could be useful for the design of small peptides or peptido-mimetics with improved drug-like properties and activity against Gram negative bacteria. Two sets of cationic peptides (AMPs) with known antimicrobial activity have been investigated. The first reference set comprised molecules with experimentally-known conformations available in the protein databank (PDB), and the second one was composed of short peptides active against Gram negative bacteria but with no significant structural information available. The predicted structures of the peptides from the first set were in excellent agreement with those experimentally-observed, which allowed analysis of the structural features of the second group using computationally-derived conformations. The peptide conformations, either experimentally available or predicted, were clustered in an “all vs. all” fashion and the most populated clusters were then analyzed. It was confirmed that these peptides tend to assume an amphipathic conformation regardless of the environment. It was also observed that positively-charged amino acid residues can often be found next to aromatic residues. Finally, a protocol was evaluated for the investigation of the behavior of short cationic peptides in the presence of a membrane-like environment such as dodecylphosphocholine (DPC) micelles. The results presented herein introduce a promising approach to inform the design of novel short peptides with a potential antimicrobial activity.