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Peptide Antimicrobial Agents 3.0
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Peptide Antimicrobial Agents 3.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 12497

Special Issue Editors

Prof. Dr. Gábor Tóth

E-Mail Website
Guest Editor
Department of Medical Chemistry, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary
Interests: protein and peptide synthesis; protein bioconjugation; bioactive peptides; bioorganic chemistry; synthesis of multiple disulfide containing polypeptides; posttranslationally modified peptides; ion channel blockers
Special Issues, Collections and Topics in MDPI journals
Dr. Györgyi Váradi

E-Mail Website
Guest Editor
Department of Medical Chemistry, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary
Interests: antimicrobial peptides; antifungal proteins; structure-activity relationships of antifungal proteins; peptide and protein synthesis; native chemical ligation; selective formation of disulfide bridges
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antibiotic resistance—when germs (bacteria and fungi) develop the ability to defeat the antibiotics designed to kill them—is one of the greatest global health challenges of modern time. Currently, at least 700,000 people die each year due to drug-resistant diseases, including 230,000 people who die from multidrug-resistant tuberculosis. More and more common diseases, including respiratory tract infections, sexually transmitted infections and urinary tract infections, are untreatable. The ever-increasing episodes of antibiotic resistance in bacteria and other microorganisms pose a serious threat to human health. Antimicrobial peptides (AMPs) are ribosomally synthesized natural antibiotics produced by nearly all organisms, from bacteria to plants and animals. AMPs are the first line of innate defense present in most living organisms, from bacteria to humans, against invading pathogens. Certain AMPs show an exceptionally broad spectrum of activity against Gram-negative and Gram-positive bacteria and fungi as well as viruses and parasites. Therefore, AMPs or their derivatives may represent potentially new classes of antimicrobial drugs. In this context, antimicrobial peptides (AMPs) have emerged as promising alternatives owing to their unique structural and functional characteristics. They have various modes of action; this diversity in the activity of the AMPs lead to the very-slow or negligible development of resistance against them in contrast to conventional antibiotics, which generally have a fixed intracellular target. This has led to significant advances in the area of AMP research in the last few decades for potential drugs of the future.

Prof. Dr. Gábor Tóth
Dr. Györgyi Váradi
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Published Papers (6 papers)

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Research

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13 pages, 1614 KiB  
Article
Prediction of Antifungal Activity of Antimicrobial Peptides by Transfer Learning from Protein Pretrained Models
by Fernando Lobo, Maily Selena González, Alicia Boto and José Manuel Pérez de la Lastra
Int. J. Mol. Sci. 2023, 24(12), 10270; https://doi.org/10.3390/ijms241210270 - 17 Jun 2023
Cited by 4 | Viewed by 1442
Abstract
Peptides with antifungal activity have gained significant attention due to their potential therapeutic applications. In this study, we explore the use of pretrained protein models as feature extractors to develop predictive models for antifungal peptide activity. Various machine learning classifiers were trained and [...] Read more.
Peptides with antifungal activity have gained significant attention due to their potential therapeutic applications. In this study, we explore the use of pretrained protein models as feature extractors to develop predictive models for antifungal peptide activity. Various machine learning classifiers were trained and evaluated. Our AFP predictor achieved comparable performance to current state-of-the-art methods. Overall, our study demonstrates the effectiveness of pretrained models for peptide analysis and provides a valuable tool for predicting antifungal peptide activity and potentially other peptide properties. Full article
(This article belongs to the Special Issue Peptide Antimicrobial Agents 3.0)
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15 pages, 4539 KiB  
Article
Unleashing the Influence of cAMP Receptor Protein: The Master Switch of Bacteriocin Export in Pectobacterium carotovorum subsp. carotovorum
by Chung-Pei Chang, Ruchi Briam James Sersenia Lagitnay, Tzu-Rong Li, Wei-Ting Lai, Reymund Calanga Derilo and Duen-Yau Chuang
Int. J. Mol. Sci. 2023, 24(11), 9752; https://doi.org/10.3390/ijms24119752 - 05 Jun 2023
Cited by 1 | Viewed by 1400
Abstract
Pectobacterium carotovorum subsp. carotovorum (Pcc) is a Gram-negative phytopathogenic bacterium that produces carocin, a low-molecular-weight bacteriocin that can kill related strains in response to factors in the environment such as UV exposure or nutritional deficiency. The function of the catabolite activator [...] Read more.
Pectobacterium carotovorum subsp. carotovorum (Pcc) is a Gram-negative phytopathogenic bacterium that produces carocin, a low-molecular-weight bacteriocin that can kill related strains in response to factors in the environment such as UV exposure or nutritional deficiency. The function of the catabolite activator protein (CAP), also known as the cyclic AMP receptor protein (CRP), as a regulator of carocin synthesis was examined. The crp gene was knocked out as part of the investigation, and the outcomes were assessed both in vivo and in vitro. Analysis of the DNA sequence upstream of the translation initiation site of carocin S3 revealed two putative binding sites for CRP that were confirmed using a biotinylated probe pull-down experiment. This study revealed that the deletion of crp inhibited genes involved in extracellular bacteriocin export via the flagellar type III secretion system and impacted the production of many low-molecular-weight bacteriocins. The biotinylated probe pull-down test demonstrated that when UV induction was missing, CRP preferentially attached to one of the two CAP sites while binding to both when UV induction was present. In conclusion, our research aimed to simulate the signal transduction system that controls the expression of the carocin gene in response to UV induction. Full article
(This article belongs to the Special Issue Peptide Antimicrobial Agents 3.0)
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13 pages, 562 KiB  
Article
Enhanced Antibacterial Activity of Substituted Derivatives of NCR169C Peptide
by Dian H. O. Howan, Sándor Jenei, János Szolomajer, Gabriella Endre, Éva Kondorosi and Gábor K. Tóth
Int. J. Mol. Sci. 2023, 24(3), 2694; https://doi.org/10.3390/ijms24032694 - 31 Jan 2023
Cited by 2 | Viewed by 1419
Abstract
Medicago truncatula in symbiosis with its rhizobial bacterium partner produces more than 700 nodule-specific cysteine-rich (NCR) peptides with diverse physicochemical properties. Most of the cationic NCR peptides have antimicrobial activity and the potential to tackle antimicrobial resistance with their novel modes of action. [...] Read more.
Medicago truncatula in symbiosis with its rhizobial bacterium partner produces more than 700 nodule-specific cysteine-rich (NCR) peptides with diverse physicochemical properties. Most of the cationic NCR peptides have antimicrobial activity and the potential to tackle antimicrobial resistance with their novel modes of action. This work focuses on the antibacterial activity of the NCR169 peptide derivatives as we previously demonstrated that the C-terminal sequence of NCR169 (NCR169C17–38) has antifungal activity, affecting the viability, morphology, and biofilm formation of various Candida species. Here, we show that NCR169C17–38 and its various substituted derivatives are also able to kill ESKAPE pathogens such as Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. The replacement of the two cysteines with serines enhanced the antimicrobial activity against most of the tested bacteria, indicating that the formation of a disulfide bridge is not required. As tryptophan can play role in the interaction with bacterial membranes and thus in antibacterial activity, we replaced the tryptophans in the NCR169C17–38C12,17/S sequence with various modified tryptophans, namely 5-methyl tryptophan, 5-fluoro tryptophan, 6-fluoro tryptophan, 7-aza tryptophan, and 5-methoxy tryptophan, in the synthesis of NCR169C17–38C12,17/S analogs. The results demonstrate that the presence of modified fluorotryptophans can significantly enhance the antimicrobial activity without notable hemolytic effect, and this finding could be beneficial for the further development of new AMPs from the members of the NCR peptide family. Full article
(This article belongs to the Special Issue Peptide Antimicrobial Agents 3.0)
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21 pages, 4768 KiB  
Article
A Novel Antimicrobial Peptide Spampcin56–86 from Scylla paramamosain Exerting Rapid Bactericidal and Anti-Biofilm Activity In Vitro and Anti-Infection In Vivo
by Manyu Jiang, Roushi Chen, Jingrong Zhang, Fangyi Chen and Ke-Jian Wang
Int. J. Mol. Sci. 2022, 23(21), 13316; https://doi.org/10.3390/ijms232113316 - 01 Nov 2022
Cited by 8 | Viewed by 1926
Abstract
The abuse of antibiotics leads to the increase of bacterial resistance, which seriously threatens human health. Therefore, there is an urgent need to find effective alternatives to antibiotics, and antimicrobial peptides (AMPs) are the most promising antibacterial agents and have received extensive attention. [...] Read more.
The abuse of antibiotics leads to the increase of bacterial resistance, which seriously threatens human health. Therefore, there is an urgent need to find effective alternatives to antibiotics, and antimicrobial peptides (AMPs) are the most promising antibacterial agents and have received extensive attention. In this study, a novel potential AMP was identified from the marine invertebrate Scylla paramamosain and named Spampcin. After bioinformatics analysis and AMP database prediction, four truncated peptides (Spa31, Spa22, Spa20 and Spa14) derived from Spampcin were screened, all of which showed potent antimicrobial activity with different antibacterial spectrum. Among them, Spampcin56–86 (Spa31 for short) exhibited strong bactericidal activity against a variety of clinical pathogens and could rapidly kill the tested bacteria within minutes. Further analysis of the antibacterial mechanism revealed that Spa31 disrupted the integrity of the bacterial membrane (as confirmed by scanning electron microscopy observation, NPN, and PI staining assays), leading to bacterial rupture, leakage of cellular contents (such as elevated extracellular ATP), increased ROS production, and ultimately cell death. Furthermore, Spa31 was found to interact with LPS and effectively inhibit bacterial biofilms. The antibacterial activity of Spa31 had good thermal stability, certain ion tolerance, and no obvious cytotoxicity. It is worth noting that Spa31 could significantly improve the survival rate of zebrafish Danio rerio infected with Pseudomonas aeruginosa, indicating that Spa31 played an important role in anti-infection in vivo. This study will enrich the database of marine animal AMPs and provide theoretical reference and scientific basis for the application of marine AMPs in medical fields. Full article
(This article belongs to the Special Issue Peptide Antimicrobial Agents 3.0)
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14 pages, 1742 KiB  
Article
Improving Fmoc Solid Phase Synthesis of Human Beta Defensin 3
by Aleksandra Walewska, Paulina Kosikowska-Adamus, Marta Tomczykowska, Bartosz Jaroszewski, Adam Prahl and Grzegorz Bulaj
Int. J. Mol. Sci. 2022, 23(20), 12562; https://doi.org/10.3390/ijms232012562 - 19 Oct 2022
Viewed by 1590
Abstract
Human β-defensin 3, HBD-3, is a 45-residue antimicrobial and immunomodulatory peptide that plays multiple roles in the host defense system. In addition to interacting with cell membranes, HBD-3 is also a ligand for melanocortin receptors, cytokine receptors and voltage-gated potassium channels. Structural and [...] Read more.
Human β-defensin 3, HBD-3, is a 45-residue antimicrobial and immunomodulatory peptide that plays multiple roles in the host defense system. In addition to interacting with cell membranes, HBD-3 is also a ligand for melanocortin receptors, cytokine receptors and voltage-gated potassium channels. Structural and functional studies of HBD-3 have been hampered by inefficient synthetic and recombinant expression methods. Herein, we report an optimized Fmoc solid-phase synthesis of this peptide using an orthogonal disulfide bonds formation strategy. Our results suggest that utilization of an optimized resin, coupling reagents and pseudoproline dipeptide building blocks decrease chain aggregation and largely improve the amount of the target peptide in the final crude material, making the synthesis more efficient. We also present an alternative synthesis of HBD-3 in which a replacement of a native disulfide bridge with a diselenide bond improved the oxidative folding. Our work enables further biological and pharmacological characterization of HBD-3, hence advancing our understanding of its therapeutic potential. Full article
(This article belongs to the Special Issue Peptide Antimicrobial Agents 3.0)
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Review

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32 pages, 2197 KiB  
Review
Antimicrobial Peptides: Challenging Journey to the Pharmaceutical, Biomedical, and Cosmeceutical Use
by Anna Mazurkiewicz-Pisarek, Joanna Baran and Tomasz Ciach
Int. J. Mol. Sci. 2023, 24(10), 9031; https://doi.org/10.3390/ijms24109031 - 20 May 2023
Cited by 11 | Viewed by 4121
Abstract
Antimicrobial peptides (AMPs), or host defence peptides, are short proteins in various life forms. Here we discuss AMPs, which may become a promising substitute or adjuvant in pharmaceutical, biomedical, and cosmeceutical uses. Their pharmacological potential has been investigated intensively, especially as antibacterial and [...] Read more.
Antimicrobial peptides (AMPs), or host defence peptides, are short proteins in various life forms. Here we discuss AMPs, which may become a promising substitute or adjuvant in pharmaceutical, biomedical, and cosmeceutical uses. Their pharmacological potential has been investigated intensively, especially as antibacterial and antifungal drugs and as promising antiviral and anticancer agents. AMPs exhibit many properties, and some of these have attracted the attention of the cosmetic industry. AMPs are being developed as novel antibiotics to combat multidrug-resistant pathogens and as potential treatments for various diseases, including cancer, inflammatory disorders, and viral infections. In biomedicine, AMPs are being developed as wound-healing agents because they promote cell growth and tissue repair. The immunomodulatory effects of AMPs could be helpful in the treatment of autoimmune diseases. In the cosmeceutical industry, AMPs are being investigated as potential ingredients in skincare products due to their antioxidant properties (anti-ageing effects) and antibacterial activity, which allows the killing of bacteria that contribute to acne and other skin conditions. The promising benefits of AMPs make them a thrilling area of research, and studies are underway to overcome obstacles and fully harness their therapeutic potential. This review presents the structure, mechanisms of action, possible applications, production methods, and market for AMPs. Full article
(This article belongs to the Special Issue Peptide Antimicrobial Agents 3.0)
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