Computational Approaches in Discovery and Design of Antimicrobial Peptides—3rd Edition

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antimicrobial Peptides".

Deadline for manuscript submissions: 30 November 2026 | Viewed by 262

Editors


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Facultad de Ingeniería, Universidad Panamericana, Augusto Rodin No. 498, Insurgentes Mixcoac, Benito Juárez, Ciudad de Mexico 03920, Mexico
Interests: drug discovery and molecular modeling; chemo-informatics; molecular descriptors definition for nucleic acids and proteins; molecular similarity and complex networks applied to analyze peptide databases; alignment-free models for protein classification problems
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Guest Editor
1. CIIMAR/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
2. Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
Interests: computational biology; biodiscovery; chemo- and bioinformatics; bioactive peptides; antimicrobial peptides (AMPs); biotechnology
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
1. CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal
2. Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
Interests: genomics (from animals to microorganisms); evolution, molecular ecology; conservation; biotechnology; bioinformatics; antimicrobial peptides
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The first two editions of the Special Issue “Computational Approaches in Discovery and Design of Antimicrobial Peptides” successfully brought together high-quality contributions from the scientific community, resulting in the publication of 10 and 8 articles receiving more than 72,200 and 30,500 views, respectively. The positive reception and growing interest in this topic have encouraged us to launch a third edition of this Special Issue.

Advances in modern artificial intelligence (AI) algorithms as well as computational biology, machine learning, and bioinformatics are rapidly transforming the discovery and design of antimicrobial peptides (AMPs), enabling more efficient identification, optimisation, and functional characterisation of novel peptide-based therapeutics.

This Special Issue welcomes original research articles that employ computational or in silico methodologies for the discovery, prediction, optimisation, or design of AMPs. Review articles addressing recent advances, methodological developments, and emerging computational strategies in AMP research are also encouraged.

We look forward to receiving your contributions and to further advancing the computational exploration of antimicrobial peptides.

Prof. Dr. Yovani Marrero-Ponce
Dr. Guillermin Agüero-Chapin
Prof. Dr. Agostinho Antunes
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • search/design of AMPs
  • bioinformatics
  • machine-learning
  • artificial intelligence
  • biodiscovery
  • computational analyses/tools
  • omics sciences
  • similarity networks
  • in vitro evaluations

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Published Papers (1 paper)

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Research

23 pages, 8444 KB  
Article
Diversity and Classification of the Actinopeptins: A New Family of Lanthipeptides Within the Genomes from the Phylum Actinomycetota
by Carlos García-Ausencio, Beatriz Ruiz-Villafán, Adelfo Escalante-Lozada, Martha Lydia Macías-Rubalcava, Romina Rodríguez-Sanoja and Sergio Sánchez
Antibiotics 2026, 15(8), 755; https://doi.org/10.3390/antibiotics15080755 - 5 Aug 2026
Abstract
Background/Objectives: Lanthipeptides are post-translationally modified compounds and have broad industrial potential. Six distinct classes of lanthipeptides are defined by the biosynthetic enzymes that install lanthionine and β-methyl-lanthionine. Notably, class II lanthipeptides are modified by the LanM enzyme and are encoded by specific biosynthetic [...] Read more.
Background/Objectives: Lanthipeptides are post-translationally modified compounds and have broad industrial potential. Six distinct classes of lanthipeptides are defined by the biosynthetic enzymes that install lanthionine and β-methyl-lanthionine. Notably, class II lanthipeptides are modified by the LanM enzyme and are encoded by specific biosynthetic clusters found in both Gram-positive and Gram-negative bacteria. Among bacterial phyla, the Actinomycetota is particularly notable for encoding a rich diversity of lanthipeptides. In this study, we investigated the diversity of a new class II lanthipeptide group, the actinopeptin family, within the phylum Actinomycetota. Methods: Using genome-mining tools, we analyzed 85 producer genomes encoding actinopeptins. Results: When comparing clusters, we found that high overall similarity is restricted to only a few sequences, whereas most clusters display marked differences, which highlights the broad diversity of this lanthipeptide family. Our comparative analysis revealed that while the leader peptide is conserved across this group, core peptides are highly diverse. Conclusions: This finding allowed us to categorize the entire family into distinct groups. We also identified clusters encoding multiple peptides modified by LanM, suggesting that it may exhibit substrate promiscuity. This study highlights the actinopeptin family as a promising source of new compounds. Full article
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