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Author: search.filters.author.Antunes, AgostinhoSubject: search.filters.subject.Complex networks

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    Item type:Publication,
    Unlocking Antimicrobial Peptides: In Silico Proteolysis and Artificial Intelligence-Driven Discovery from Cnidarian Omics
    (MDPI, 2025)
    Barroso, Ricardo Alexandre
    ;
    Agüero-Chapin, Guillermin
    ;
    Sousa, Rita
    ;
    Marrero Ponce, Yovani  
    ;
    Antunes, Agostinho
    Overcoming the growing challenge of antimicrobial resistance (AMR), which affects millions of people worldwide, has driven attention for the exploration of marine-derived antimicrobial peptides (AMPs) for innovative solutions. Cnidarians, such as corals, sea anemones, and jellyfish, are a promising valuable resource of these bioactive peptides due to their robust innate immune systems yet are still poorly explored. Hence, we employed an in silico proteolysis strategy to search for novel AMPs from omics data of 111 Cnidaria species. Millions of peptides were retrieved and screened using shallow- and deep-learning models, prioritizing AMPs with a reduced toxicity and with a structural distinctiveness from characterized AMPs. After complex network analysis, a final dataset of 3130 Cnidaria singular non-haemolytic and non-toxic AMPs were identified. Such unique AMPs were mined for their putative antibacterial activity, revealing 20 favourable candidates for in vitro testing against important ESKAPEE pathogens, offering potential new avenues for antibiotic development. ©The authors. ©MDPI.
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    Item type:Publication,
    Unveiling Encrypted Antimicrobial Peptides from Cephalopods' Salivary Glands: A Proteolysis-Driven Virtual Approach
    (American Chemical Society, 2024)
    Agüero-Chapin, Guillermin
    ;
    Domínguez-Pérez, Dany
    ;
    Marrero Ponce, Yovani  
    ;
    Castillo-Mendieta, Kevin
    ;
    Antunes, Agostinho
    Antimicrobial peptides (AMPs) have potential against antimicrobial resistance and serve as templates for novel therapeutic agents. While most AMP databases focus on terrestrial eukaryotes, marine cephalopods represent a promising yet underexplored source. This study reveals the putative reservoir of AMPs encrypted within the proteomes of cephalopod salivary glands via in silico proteolysis. A composite protein database comprising 5,412,039 canonical and noncanonical proteins from salivary apparatus of 14 cephalopod species was subjected to digestion by 5 proteases under three protocols, yielding over 9 million of nonredundant peptides. These peptides were effectively screened by a selection of 8 prediction and sequence comparative tools, including machine learning, deep learning, multiquery similarity-based models, and complex networks. The screening prioritized the antimicrobial activity while ensuring the absence of hemolytic and toxic properties, and structural uniqueness compared to known AMPs. Five relevant AMP datasets were released, ranging from a comprehensive collection of 542,485 AMPs to a refined dataset of 68,694 nonhemolytic and nontoxic AMPs. Further comparative analyses and application of network science principles helped identify 5466 unique and 808 representative nonhemolytic and nontoxic AMPs. These datasets, along with the selected mining tools, provide valuable resources for peptide drug developers. ©The authors ©ACS Omega.
    Scopus© Citations 1  13