In silico characterization of Cnidarian’s antimicrobial peptides

Abstract

The characterization of active compounds in Cnidaria sheds light on a large bank of substances against multiresistant bacteria related to diseases in humans, which makes it a cutting edge with a repertoire of antimicrobial molecules worthy of bioprospecting analysis. Thus, the main nabof this research was to characterize antimicrobial peptides (AMP) belonging to the defensin family in different species of Cnidarians through bioinformatic approaches. To this, an exhaustive search was carried out for sequences homologous to antimicrobial peptides belonging to the defensin family in genomes availables for Cnidarians. Also, 3D models of AMP were obtained by modeling based on homology, functional characterization of peptides found was performed with machine learning approaches. Characterization of twelve peptides derived from 11 Cnidarian species was possible due to 3D modeling, which showed structural similarity with defensins reported in several species such as Nasonia vitripennis, Pisum sativum, Solanum lycopersicum, and Aurelia aurita. Also, different physicochemical properties such as hydrophobic moment, hydrophobicity, net charge, amphiphilic index, and isoelectric point were evaluated. These peptides showed values ​​that are ideal for AMP. Further, functional characterization showed a bactericidal potential of 20 peptides against multiresistant bacteria Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. These peptides with action potential were found in 17 species from Cnidarians and obtained by homology through the defensin Aurelin, described in the Cnidarian Aurelia aurita, and Mus musculus’ Beta-defensin 7. Finally, a phylogenetic tree was performed, it showed that defensins are distributed in all Cnidarians regardless of the taxonomic group. Thus, the origin of defensins in the Phylum Cnidaria is not monophyletic. Our results show that Cnidaria has AMP with structural and physicochemical characteristics similar to those described in defensins of insects, mammals, and plants. The structural characteristics of these peptides, their physicochemical properties, and their functional potential outline them as promising templates for the discovery of new antibiotics.

Novel technologies uncover novel ‘anti’-microbial peptides in Hydra shaping the species-specific microbiome

“…However, one AMP family, the defensins [35], appears to be omnipresent in the animal kingdom, in plants and fungi. Numerous defensin genes were in silico predicted from the genomes of Cnidaria as well [36][37][38] and few of them were empirically validated [39]. However, no members of the defensin family have been described in Hydra so far.…”

“…H. viridissima and Cassiopea xamachana are, in fact, rather exceptions among the hydrozoans [ 68 ]. Although some recent studies attempt to create a comprehensive survey of AMPs in Cnidaria [ 36 ], their focus remains bound to exclusively conserved gene families. Implementation of novel highly automatized algorithms for AMP detection and annotation, such as the MLAs, promises a major progress in understanding the link between AMP repertoire and holobiont architecture in Cnidaria.…”

Bioprospecting and marine ‘omics’: surfing the deep blue sea for novel bioactive proteins and peptides

“…Apart from employing in silico tools for discovering physicochemical proprieties and predicting 3D structures for putative proteins, they also synthesised a few peptides and performed successful antimicrobial assays, thus highlighting the already acknowledged interest of cone snails for biotechnologists. In turn, Leal et al (2022) performed a high-throughput search for antimicrobial peptides, but this time instead the analysis was purely in silico. This study on Gastropoda characterised several putative peptides and bioactivity was determined using PASS (Pirtskhalava et al, 2021).…”