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Antibiotics
Special Issues
Accelerating the Discovery and Characterization of Antimicrobial Peptides
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Accelerating the Discovery and Characterization of Antimicrobial Peptides

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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 7808

Special Issue Editors

Dr. Carlos A. Brizuela

E-Mail Website
Guest Editor
Computer Science Department, CICESE Research Center, Ensenada, Baja California 22860, Mexico
Interests: design of AI algorithms for the identification of antimicrobial peptides; computational biology and drug discovery
Dr. Gabriel Del Río Guerra

E-Mail Website
Guest Editor
Department of Biochemistry and Structural Biology, Instituto de Fisiologia Celular, UNAM, Mexico City 04510, Mexico
Interests: computer aided design of multifunctional peptides; protein structure–function relationship by network analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The last decade has witnessed a remarkable increase in the number of alignment-free, machine learning-based approaches for the prediction of antimicrobial peptides. The accuracy of shallow and deep learning methods to discriminate AMPs from non-AMPs has reached 95% or more. Once a sequence is identified as antimicrobial, its specific activity, target pathogen and MIC must be determined. Furthermore, antimicrobial peptides are also able to penetrate cells and activate autophagy in mammalian cells, as well as to modulate the immune system. In summary, the activities embedded within these peptides include anti-viral, anti-fungal, anti-parasite, anti-bacterial, pro-autophagy and immunomodulator. Such multi-functionality imposes the need to further characterize these peptides to evaluate which activities are present, not only out of curiosity, but also as a requirement if these peptides are aimed to be used as pharmaceuticals. Thus, further developments of these predictors and experimental systems are required to match the current development of the field.

Methodological challenges to match this increasing need to further characterize antimicrobial peptides include the lack of a profound analysis of the available data, representation aspects of both shallow and deep models and high-throughput assays. A well-known drawback of machine-learning methods is the lack of negative experimentally validated sets. The development of high-throughput experiments assessing the different activities of antimicrobial peptides will be of extreme value.

This Special Issue of Antibiotics invites authors to publish original research including peptide data analysis, methodological aspects of machine learning-based approaches and high-throughput assays intended to achieve the abovementioned goal.

Dr. Carlos A. Brizuela
Dr. Gabriel Del Río Guerra
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 100 words) can be sent to the Editorial Office for announcement on this website.

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-blind 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

  • antimicrobial peptides
  • high-throughput assays
  • peptides database analysis
  • target and MIC prediction
  • negative sets generation
  • assay standardization

Published Papers (4 papers)

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Research

15 pages, 2123 KiB  
Article
Embedded-AMP: A Multi-Thread Computational Method for the Systematic Identification of Antimicrobial Peptides Embedded in Proteome Sequences
by Germán Meléndrez Carballo, Karen Guerrero Vázquez, Luis A. García-González, Gabriel Del Rio and Carlos A. Brizuela
Antibiotics 2023, 12(1), 139; https://doi.org/10.3390/antibiotics12010139 - 10 Jan 2023
Viewed by 1924
Abstract
Antimicrobial peptides (AMPs) have gained the attention of the research community for being an alternative to conventional antimicrobials to fight antibiotic resistance and for displaying other pharmacologically relevant activities, such as cell penetration, autophagy induction, immunomodulation, among others. The identification of AMPs had [...] Read more.
Antimicrobial peptides (AMPs) have gained the attention of the research community for being an alternative to conventional antimicrobials to fight antibiotic resistance and for displaying other pharmacologically relevant activities, such as cell penetration, autophagy induction, immunomodulation, among others. The identification of AMPs had been accomplished by combining computational and experimental approaches and have been mostly restricted to self-contained peptides despite accumulated evidence indicating AMPs may be found embedded within proteins, the functions of which are not necessarily associated with antimicrobials. To address this limitation, we propose a machine-learning (ML)-based pipeline to identify AMPs that are embedded in proteomes. Our method performs an in-silico digestion of every protein in the proteome to generate unique k-mers of different lengths, computes a set of molecular descriptors for each k-mer, and performs an antimicrobial activity prediction. To show the efficiency of the method we used the shrimp proteome, and the pipeline analyzed all k-mers between 10 and 60 amino acids in length to predict all AMPs in less than 20 min. As an application example we predicted AMPs in different rodents (common cuy, common rat, and naked mole rat) with different reported longevities and found a relation between species longevity and the number of predicted AMPs. The analysis shows as the longevity of the species is higher, the number of predicted AMPs is also higher. The pipeline is available as a web service. Full article
(This article belongs to the Special Issue Accelerating the Discovery and Characterization of Antimicrobial Peptides)
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22 pages, 4583 KiB  
Article
In Vitro, In Vivo and In Silico Assessment of the Antimicrobial and Immunomodulatory Effects of a Water Buffalo Cathelicidin (WBCATH) in Experimental Pulmonary Tuberculosis
by Jacqueline Barrios Palacios, Jorge Barrios-Payán, Dulce Mata-Espinosa, Jacqueline V. Lara-Espinosa, Juan Carlos León-Contreras, Gerald H. Lushington, Tonatiuh Melgarejo and Rogelio Hernández-Pando
Antibiotics 2023, 12(1), 75; https://doi.org/10.3390/antibiotics12010075 - 31 Dec 2022
Cited by 1 | Viewed by 1569
Abstract
Tuberculosis (TB) is considered the oldest pandemic in human history. The emergence of multidrug-resistant (MDR) strains is currently considered a serious global health problem. As components of the innate immune response, antimicrobial peptides (AMPs) such as cathelicidins have been proposed to have efficacious [...] Read more.
Tuberculosis (TB) is considered the oldest pandemic in human history. The emergence of multidrug-resistant (MDR) strains is currently considered a serious global health problem. As components of the innate immune response, antimicrobial peptides (AMPs) such as cathelicidins have been proposed to have efficacious antimicrobial activity against Mycobacterium tuberculosis (Mtb). In this work, we assessed a cathelicidin from water buffalo, Bubalus bubalis, (WBCATH), determining in vitro its antitubercular activity (MIC), cytotoxicity and the peptide effect on bacillary loads and cytokines production in infected alveolar macrophages. Our results showed that WBCATH has microbicidal activity against drug-sensitive and MDR Mtb, induces structural mycobacterial damage demonstrated by electron microscopy, improves Mtb killing and induces the production of protective cytokines by murine macrophages. Furthermore, in vivo WBCATH showed decreased bacterial loads in a model of progressive pulmonary TB in BALB/c mice infected with drug-sensitive or MDR mycobacteria. In addition, a synergistic therapeutic effect was observed when first-line antibiotics were administered with WBCATH. These results were supported by computational modeling of the potential effects of WBCATH on the cellular membrane of Mtb. Thus, this water buffalo-derived cathelicidin could be a promising adjuvant therapy for current anti-TB drugs by enhancing a protective immune response and potentially reducing antibiotic treatment duration. Full article
(This article belongs to the Special Issue Accelerating the Discovery and Characterization of Antimicrobial Peptides)
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22 pages, 4116 KiB  
Article
Targeted Modification and Structure-Activity Study of GL-29, an Analogue of the Antimicrobial Peptide Palustrin-2ISb
by Siyan Liu, Yaxian Lin, Jiachen Liu, Xiaoling Chen, Chengbang Ma, Xinping Xi, Mei Zhou, Tianbao Chen, James F. Burrows and Lei Wang
Antibiotics 2022, 11(8), 1048; https://doi.org/10.3390/antibiotics11081048 - 03 Aug 2022
Cited by 4 | Viewed by 1575
Abstract
Antimicrobial peptides (AMPs) are considered as promising antimicrobial agents due to their potent bioactivity. Palustrin-2 peptides were previously found to exhibit broad-spectrum antimicrobial activity with low haemolytic activity. Therefore, GL-29 was used as a template for further modification and study. Firstly, the truncated [...] Read more.
Antimicrobial peptides (AMPs) are considered as promising antimicrobial agents due to their potent bioactivity. Palustrin-2 peptides were previously found to exhibit broad-spectrum antimicrobial activity with low haemolytic activity. Therefore, GL-29 was used as a template for further modification and study. Firstly, the truncated analogue, GL-22, was designed to examine the function of the ‘Rana box’, which was confirmed to have no impact on antimicrobial activity. The results of antimicrobial activity assessment against seven microorganisms demonstrated GL-22 to have a broad-spectrum antimicrobial activity, but weak potency against Candida albicans (C. albicans). These data were similar to those of GL-29, but GL-22 showed much lower haemolysis and lower cytotoxicity against HaCaT cells. Moreover, GL-22 exhibited potent in vivo activity at 4 × MIC against Staphylococcus aureus (S. aureus)-infected larvae. Several short analogues, from the C-terminus and N-terminus of GL-22, were modified to identify the shortest functional motif. However, the results demonstrated that the shorter peptides did not exhibit potent antimicrobial activity, and the factors that affect the bioactive potency of these short analogues need to be further studied. Full article
(This article belongs to the Special Issue Accelerating the Discovery and Characterization of Antimicrobial Peptides)
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16 pages, 3479 KiB  
Article
Antimicrobial and Immunomodulatory Effects of Selected Chemokine and Antimicrobial Peptide on Cytokine Profile during Salmonella Typhimurium Infection in Mouse
by Astrid Tuxpan-Pérez, Marco Antonio Ibarra-Valencia, Blanca Elisa Estrada, Herlinda Clement, Ligia Luz Corrales-García, Gerardo Pavel Espino-Solis and Gerardo Corzo
Antibiotics 2022, 11(5), 607; https://doi.org/10.3390/antibiotics11050607 - 30 Apr 2022
Cited by 5 | Viewed by 2207
Abstract
The antimicrobial and immunomodulatory capacities of the peptide Css54 and the chemokine MCP-1 were tested. The first, a peptide isolated from the venom of the scorpion Centruroides suffusus suffusus was synthesized chemically. In contrast, the second is a monocyte chemoattractant expressed as a [...] Read more.
The antimicrobial and immunomodulatory capacities of the peptide Css54 and the chemokine MCP-1 were tested. The first, a peptide isolated from the venom of the scorpion Centruroides suffusus suffusus was synthesized chemically. In contrast, the second is a monocyte chemoattractant expressed as a recombinant protein in our lab. It was observed in vitro that Css54 inhibited the growth of Salmonella enterica serovar Typhimurium (6.2 µg/mL). At high concentrations, it was toxic to macrophages (25 µg/mL), activated macrophage phagocytosis (1.5 µg/mL), and bound Salmonella LPS (3 µg/mL). On the other hand, the recombinant MCP-1 neither inhibited the growth of Salmonella Typhimurium nor was it toxic to macrophages (up to 25 µg/mL), nor activated macrophage phagocytosis or bound Salmonella LPS (up to 3 µg/mL). Although it was observed in vivo in mice Balb/C that both Css54 and MCP-1 did not resolve the intraperitoneal infection by S. Typhimurium, Css54 decreased the expression of IL-6 and increased IL-10, IL-12p70, and TNF-α levels; meanwhile, MCP-1 decreased the expression of IFN-γ and increased IL-12p70 and TNF-α. It was also observed that the combination of both molecules Css54 and MCP-1 increased the expression of IL-10 and TNF-α. Full article
(This article belongs to the Special Issue Accelerating the Discovery and Characterization of Antimicrobial Peptides)
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