Genome-wide identification of antimicrobial peptides in the liver fluke, Clonorchis sinensis

Abstract

The increase in prevalence of antimicrobial resistance makes the search for new antibiotic agents imperative. Antimicrobial peptides (AMPs) from natural resources have been recognized as suitable tools to combat antibiotic-resistant bacteria. The liver fluke Clonorchis sinensis living in germ-filled environments could be a good source of antimicrobials. Here, we report the use of a rational protocol that combines AMP predictions based on their physicochemical properties and their in vivo stability to discover AMP candidates from the entire genome of C. sinensis. To screen AMP candidates, in silico analyses based on the physicochemical properties of known AMPs, such as length, charge, isoelectric point, and in vitro and in vivo aggregation values were performed. To enhance their in vivo stability, proteins having proteolytic cleavage sites were excluded. As a consequence, four high-activity, highstability peptides were identified. These peptides could be potential starting materials for the development of new AMPs via structural modification and optimization. Thus, this study proposes a refined computational method to develop new AMPs and identifies four AMP candidates, which could serve as templates for further development of peptide antibiotics.

Antimicrobial Protein Candidates from the Thermophilic Geobacillus sp. Strain ZGt-1: Production, Proteomics, and Bioinformatics Analysis

“…The Na 4 vSS values were 5.3, −6.6, and −2.4 for 6_35, 23_543, and 4_4, respectively ( Table 2 ). Previously reported AMPs have Na 4 vSS values within the range of −40 to 60 [ 36 , 42 ].…”

Analysis and Prediction of some Histone-derived Antimicrobial Peptides from Toads Duttaphrynus melanostictus and Phyrinoidis asper

“…In silico prediction of potent AMPs was conducted based on the methods used by Yoo et al [17] with a slight modification. Amino acid sequences of histone H2A were submitted to CAMP server [18] and each fragmented into 20 amino acid segments.…”

Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides

“…These methods are primarily homology-driven, using known sequences of large, well-characterised AMP families like cathelicidins and β-defensins to search for homologs (Dalla Valle et al 2012). A genomics-driven approach has been applied to discover novel AMPs from a range of non-model species (Peel et al 2016; Pérez de la Lastra et al 2021; Wang et al 2021; Yoo et al 2015). However, despite the evolutionary divergence of Australian frogs, none have yet been investigated for AMPs using a bioinformatic approach.…”