Embracing the era of antimicrobial peptides with marine organisms

Quorum sensing inhibiting dihydropyrrol-2-ones embedded polymer/graphene oxide nanocomposite waterborne antimicrobial coatings

With increasing antibiotic resistance and hospital acquired microbial infections, there has been a growing interest to explore alternate antimicrobial approaches. This is particularly challenging when aiming to protect surfaces over a large area to avoid contact mediated infection transmission. Quorum sensing (QS) inhibition has emerged as an alternate antimicrobial approach overcoming evolutionary stress driven resistance observed in antibiotic treatment. However, specific surface orientation requirements and limited work on delivery of small molecule QS inhibiting compounds have limited their widespread applicability certainly when it comes to coating large surfaces. Here, we report antimicrobial nanocomposite coatings overcoming the dependence on molecular orientation of QS inhibiting dihydropyrrol-2-ones (DHP) analogues and release small molecule analogues. In a systematic study, we developed poly(styrene-stat-n-butyl acrylate)/graphene oxide (GO)/DHP analogue nanocomposite antimicrobial coatings that can be easily applied to surfaces of any length scale and studied their efficacy against Staphylococcus aureus. The polymer nanocomposite was designed to undergo coating formation at ambient temperature. The antimicrobial coatings exhibited DHP dose dependent antimicrobial response both in the supernatant growth media with a ∼7-log10 reduction in cell growth and virtually a complete inhibition in cell adhesion on the surface in the best coating compared to controls. When compared, DHP-Br coatings outperformed other DHP analogues (-F and -Ph) both in limiting the cell growth in the media and cellular adhesion on the coating surface. This is the first example of nanocomposite coatings comprising QS inhibiting compounds, and their exceptional performance is expected to pave the way for further research in the field.

A 14-amino acid cationic peptide Bolespleenin334-347 from the marine fish mudskipper Boleophthalmus pectinirostris exhibiting potent antimicrobial activity and therapeutic potential

Antimicrobial peptides (AMPs) are an important component of innate immunity in both vertebrates and invertebrates, and some of the unique characteristics of AMPs are usually associated with their living environment. The marine fish, mudskipper Boleophthalmus pectinirostris, usually live amphibiously in intertidal environments that are quite different from other fish species, which would be an exceptional source of new AMPs. In the study, an AMP named Bolespleenin334-347 was identified, which was a truncated peptide derived from a new functional gene found in B. pectinirostris, that was up-regulated in response to bacterial challenge. Bolespleenin334-347 had only 14 amino acid residues, including five consecutive arginine residues. It was found that the peptide had broad-spectrum antibacterial activity, good thermal stability and sodium ion tolerance. Bolespleenin334-347 killed Acinetobacter baumannii and Staphylococcus aureus by disrupting the structural integrity of the bacterial membrane, leading to leakage of the cellular contents, and inducing accumulation of bacterial endogenous reactive oxygen species (ROS). In addition, Bolespleenin334-347 effectively inhibited biofilm formation of A. baumannii and S. aureus and long-term treatment did not lead to the development of resistance. Importantly, Bolespleenin334-347 maintained stable activity against clinically multi-drug resistant bacterial strains. In addition, it was noteworthy that Bolespleenin334-347 showed superior efficacy to LL-37 and vancomycin in a constructed mouse model of MRSA-induced superficial skin infections, as evidenced by a significant reduction in bacterial load and more favorable wound healing. This study provides an effective antimicrobial agent for topical skin infections with potential therapeutic efficacy for infections with drug-resistant bacteria, including MRSA.

A review on the diversity of antimicrobial peptides and genome mining strategies for their prediction

Antibiotic resistance has become one of the most serious threats to human health in recent years. In response to the increasing microbial resistance to the antibiotics currently available, it is imperative to develop new antibiotics or explore new approaches to combat antibiotic resistance. Antimicrobial peptides (AMPs) have shown considerable promise in this regard, as the microbes develop low or no resistance against them. The discovery and development of AMPs still confront numerous obstacles such as finding a target, developing assays, and identifying hits and leads, which are time-consuming processes, making it difficult to reach the market. However, with the advent of genome mining, new antibiotics could be discovered efficiently using tools such as BAGEL, antiSMASH, RODEO, etc., providing hope for better treatment of diseases in the future. Computational methods used in genome mining automatically detect and annotate biosynthetic gene clusters in genomic data, making it a useful tool in natural product discovery. This review aims to shed light on the history, diversity, and mechanisms of action of AMPs and the data on new AMPs identified by traditional as well as genome mining strategies. It further substantiates the various phases of clinical trials for some AMPs, as well as an overview of genome mining databases and tools built expressly for AMP discovery. In light of the recent advancements, it is evident that targeted genome mining stands as a beacon of hope, offering immense potential to expedite the discovery of novel antimicrobials.

Waste to resource: Mining antimicrobial peptides in sludge from metagenomes using machine learning

The emergence of antibiotic-resistant bacteria poses a huge threat to the treatment of infections. Antimicrobial peptides are a class of short peptides that widely exist in organisms and are considered as potential substitutes for traditional antibiotics. Here, we use metagenomics combined with machine learning to find antimicrobial peptides from environmental metagenomes and successfully obtained 16,044,909 predicted AMPs. We compared the abundance of potential antimicrobial peptides in natural environments and engineered environments, and found that engineered environments also have great potential. Further, we chose sludge as a typical engineered environmental sample, and tried to mine antimicrobial peptides from it. Through metaproteome analysis and correlation analysis, we mined 27 candidate AMPs from sludge. We successfully synthesized 25 peptides by chemical synthesis, and experimentally verified that 21 peptides had antibacterial activity against the 4 strains tested. Our work highlights the potential for mining new antimicrobial peptides from engineered environments and demonstrates the effectiveness of mining antimicrobial peptides from sludge.

Heterologous Production of Antimicrobial Peptides: Notes to Consider

Heavy and irresponsible use of antibiotics in the last century has put selection pressure on the microbes to evolve even faster and develop more resilient strains. In the confrontation with such sometimes called "superbugs", the search for new sources of biochemical antibiotics seems to have reached the limit. In the last two decades, bioactive antimicrobial peptides (AMPs), which are polypeptide chains with less than 100 amino acids, have attracted the attention of many in the control of microbial pathogens, more than the other types of antibiotics. AMPs are groups of components involved in the immune response of many living organisms, and have come to light as new frontiers in fighting with microbes. AMPs are generally produced in minute amounts within organisms; therefore, to address the market, they have to be either produced on a large scale through recombinant DNA technology or to be synthesized via chemical methods. Here, heterologous expression of AMPs within bacterial, fungal, yeast, plants, and insect cells, and points that need to be considered towards their industrialization will be reviewed.

Characterization of a Novel Antimicrobial Peptide Bacipeptin against Foodborne Pathogens

The increasing emergence of multidrug-resistant pathogens and development of biopreservatives in food industries has increased the demand of novel and safe antimicrobial agents. In this study, a marine bacterial strain Bacillus licheniformis M1 was isolated and exhibited obvious antimicrobial activities against foodborne pathogens, especially against methicillin-resistant Staphylococcus aureus. The antimicrobial agent was purified and identified as a novel antimicrobial peptide, which was designated as bacipeptin, and the corresponding mechanism was further investigated by electron microscopy observation and transcriptomic analysis with biochemical validation. The results showed that bacipeptin could reduce the virulence of methicillin-resistant Staphylococcus aureus and exerted its antimicrobial activity by interfering with histidine metabolism, inducing the accumulation of reactive oxygen species and down-regulating genes related to Na+/H+ antiporter and the cell wall, thus causing damage to the cell wall and membrane. Overall, our study provides a novel natural product against foodborne pathogens and discloses the corresponding action mechanism.

In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes

Due to their potential application as an alternative to antibiotics, bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria, have received much attention in recent years. To identify bacteriocins within marine bacteria, most of the studies employed a culture-based method, which is more time-consuming than the in silico approach. For that, the aim of this study was to identify potential bacteriocin gene clusters and their potential producers in 51 marine Bacillota (formerly Firmicutes) genomes, using BAGEL4, a bacteriocin genome mining tool. As a result, we found out that a majority of selected Bacillota (60.78%) are potential bacteriocin producers, and we identified 77 bacteriocin gene clusters, most of which belong to class I bacteriocins known as RiPPs (ribosomally synthesized and post-translationally modified peptides). The identified putative bacteriocin gene clusters are an attractive target for further in vitro research, such as the production of bacteriocins using a heterologous expression system.

Aquiluscidin, a Cathelicidin from Crotalus aquilus, and the Vcn-23 Derivative Peptide, Have Anti-Microbial Activity against Gram-Negative and Gram-Positive Bacteria

Anti-microbial peptides play a vital role in the defense mechanisms of various organisms performing functions that range from the elimination of microorganisms, through diverse mechanisms, to the modulation of the immune response, providing protection to the host. Among these peptides, cathelicidins, a well-studied family of anti-microbial peptides, are found in various animal species, including reptiles. Due to the rise in anti-microbial resistance, these compounds have been suggested as potential candidates for developing new drugs. In this study, we identified and characterized a cathelicidin-like peptide called Aquiluscidin (Aq-CATH) from transcripts obtained from the skin and oral mucosa of the Querétaro's dark rattlesnake, Crotalus aquilus. The cDNA was cloned, sequenced, and yielded a 566-base-pair sequence. Using bioinformatics, we predicted that the peptide precursor contains a signal peptide, a 101-amino-acid conserved cathelin domain, an anionic region, and a 34-amino-acid mature peptide in the C-terminal region. Aq-CATH and a derived 23-amino-acid peptide (Vcn-23) were synthesized, and their anti-microbial activity was evaluated against various species of bacteria in in vitro assays. The minimal inhibitory concentrations against bacteria ranged from 2 to 8 μg/mL for both peptides. Furthermore, at concentrations of up to 50 μM, they exhibited no significant hemolytic activity (<2.3% and <1.2% for Aquiluscidin and Vcn-23, respectively) against rat erythrocytes and displayed no significant cytotoxic activity at low concentrations (>65% cell viability at 25 µM). Finally, this study represents the first identification of an antimicrobial peptide in Crotalus aquilus, which belongs to the cathelicidin family and exhibits the characteristic features of these peptides. Both Aq-CATH and its derived molecule, Vcn-23, displayed remarkable inhibitory activity against all tested bacteria, highlighting their potential as promising candidates for further antimicrobial research.

Novel Antimicrobial Peptide from the Hepatopancreas of the Red King Crab

Crustaceans have successfully adapted to survive in their natural habitat, rich in microorganisms, due to the presence of antimicrobial peptides (AMPs) in their organism. They achieve this adaptation despite lacking the highly specific adaptive immune system found in vertebrates. One valuable source of AMPs is the hepatopancreas, a waste product from crab fishery and its processing. Applying zymographic and spectrophotometric techniques, we discovered a small peptide (approximately 5 kDa) within a low molecular weight protein fraction extracted from the acetone powder of the red king crab hepatopancreas. This peptide hydrolyzes both M. lysodeikticus cell wall and M. lysodeikticus cell wall polysaccharide, while showing no activity against gelatin. The found peptide may be of interest for application in medicine, biotechnology, and the food industry, for example as a bio-preservative.