Unveiling Encrypted Antimicrobial Peptides from Cephalopods' Salivary Glands: A Proteolysis-Driven Virtual Approach

Abstract

Antimicrobial peptides (AMPs), with their versatile actions, offer promise against antimicrobial resistance and as templates for novel therapeutic agents. While existing AMP databases primarily feature AMPs from terrestrial eukaryotes, marine sources are gaining attention, with cephalopods emerging as a promising but still underexplored source. This study unveils the potential reservoir of AMPs encrypted within the proteome of cephalopods’ salivary glands using in silico proteolysis. A composite protein database comprising canonical and non-canonical proteins from cephalopods' salivary apparatus was used as the substrate for five proteases involved in three digestion protocols. The resulting millions of peptides were screened using machine learning, deep learning, multi-query similarity-based models, and complex networks. The screening prioritizes antimicrobial activity, the absence of haemolytic and toxic attributes, and structural distinctiveness compared to characterized AMPs. Diverse publicly accessible AMP datasets are produced, catering to various research needs, ranging from those focused solely on antimicrobial activity to refined datasets of non-haemolytic and non-toxic AMPs. Comparative analyses and network science principles were applied to identify singular and representative subsets from non-haemolytic and non-toxic AMPs. All these sets of AMPs and the proposed mining tools serve as valuable assets for peptide drug developers.