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Antibiotics
Special Issues
Structures and Functions of Antimicrobial Peptides
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Structures and Functions 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 (31 October 2021) | Viewed by 8073

Special Issue Editors

Dr. Didier Devaurs

E-Mail Website
Guest Editor
MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
Interests: structural bioinformatics; computational systems biology; quantitative biomedical research; protein mutation interpretation; molecular caging prediction; protein-ligand docking; integrative molecular modelling; molecular dynamics; protein-protein interactions
Dr. Dinler Amaral Antunes

E-Mail Website
Guest Editor
Department of Computer Science, Rice University, Houton, TX, USA
Interests: computational biology; structural bioinformatics;immunoinformatics; cancer immunotherapy; vaccine development; drug discovery

Special Issue Information

Dear Colleagues, 

Antimicrobial peptides (AMPs) are a diverse group of naturally-occurring molecules involved in the innate immune response of all multicellular organisms, but also produced by microbes to defend their environmental niche. They are potent antibiotics that can directly kill or inhibit the growth of foreign micro-organisms (such as bacteria, viruses, parasites, fungi, or yeasts), but also diseased cells, tumors, or biofilms. AMPs are often referred to as “host defense peptides” because of their various activities in modulating host cellular immunity in higher eukaryotic organisms. Recently, it has even been shown that AMPs can influence the composition of the microbiome in mammals. Interest in AMPs has been strongly renewed by the growing problem of bacterial resistance to conventional antibiotics. AMPs have the potential to become the next generation of prescribed anti-infection molecules, thanks to their more selective effects on pathogens. This Special Issue will focus on the analysis of the structure and function of AMPs and similar peptide-based drugs, as well as the various implications of such studies.

All submission types, including original research articles and comprehensive reviews, are welcome. Topics covered by this Special Issue include, but are not limited to the following: 

  • Structural diversity of AMPs
  • Structural classification of AMPS
  • Inter-species comparative studies
  • Evolutionary conservation of structural features
  • Impact of structure on the mechanisms of action
  • AMP binding/docking
  • AMP interactions with pathogens
  • Relationships between structure and expression/regulation
  • Antibiotic specificity/selectivity
  • Dynamic properties of AMPs
  • Role of flexibility in AMP activity
  • Cyclic/branched peptides
  • Post-translational modifications in AMPs
  • Peptide-based degradation
  • Anti-cancer peptides
  • Anti-biofilm peptides

Dr. Didier Devaurs
Dr. Dinler Amaral 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 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 peptide
  • host defense peptide
  • peptide-based drug
  • host immunity modulation
  • antibiotic resistance
  • antibiotic specificity
  • microbiome regulation
  • peptide immunotherapy
  • structural modeling
  • structure–function relationship

Published Papers (3 papers)

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Research

12 pages, 2116 KiB  
Article
Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors
by Jiří Czernek and Jiří Brus
Antibiotics 2021, 10(10), 1265; https://doi.org/10.3390/antibiotics10101265 - 18 Oct 2021
Viewed by 1935
Abstract
Alamethicin (ALM) is an antimicrobial peptide that is frequently employed in studies of the mechanism of action of pore-forming molecules. Advanced techniques of solid-state NMR spectroscopy (SSNMR) are important in these studies, as they are capable of describing the alignment of helical peptides, [...] Read more.
Alamethicin (ALM) is an antimicrobial peptide that is frequently employed in studies of the mechanism of action of pore-forming molecules. Advanced techniques of solid-state NMR spectroscopy (SSNMR) are important in these studies, as they are capable of describing the alignment of helical peptides, such as ALM, in lipid bilayers. Here, it is demonstrated how an analysis of the SSNMR measurements can benefit from fully periodic calculations, which employ the plane-wave density-functional theory (PW DFT) of the solid-phase geometry and related spectral parameters of ALM. The PW DFT calculations are used to obtain the structure of desolvated crystalline ALM and predict the NMR chemical shift tensors (CSTs) of its nuclei. A variation in the CSTs of the amidic nitrogens and carbonyl carbons along the ALM backbone is evaluated and included in simulations of the orientation-dependent anisotropic 15N and 13C chemical shift components. In this way, the influence of the site-specific structural effects on the experimentally determined orientation of ALM is shown in models of cell membranes. Full article
(This article belongs to the Special Issue Structures and Functions of Antimicrobial Peptides)
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12 pages, 1983 KiB  
Article
PhytoAFP: In Silico Approaches for Designing Plant-Derived Antifungal Peptides
by Atul Tyagi, Sudeep Roy, Sanjay Singh, Manoj Semwal, Ajit K. Shasany, Ashok Sharma and Ivo Provazník
Antibiotics 2021, 10(7), 815; https://doi.org/10.3390/antibiotics10070815 - 05 Jul 2021
Cited by 5 | Viewed by 2801
Abstract
Emerging infectious diseases (EID) are serious problems caused by fungi in humans and plant species. They are a severe threat to food security worldwide. In our current work, we have developed a support vector machine (SVM)-based model that attempts to design and predict [...] Read more.
Emerging infectious diseases (EID) are serious problems caused by fungi in humans and plant species. They are a severe threat to food security worldwide. In our current work, we have developed a support vector machine (SVM)-based model that attempts to design and predict therapeutic plant-derived antifungal peptides (PhytoAFP). The residue composition analysis shows the preference of C, G, K, R, and S amino acids. Position preference analysis shows that residues G, K, R, and A dominate the N-terminal. Similarly, residues N, S, C, and G prefer the C-terminal. Motif analysis reveals the presence of motifs like NYVF, NYVFP, YVFP, NYVFPA, and VFPA. We have developed two models using various input functions such as mono-, di-, and tripeptide composition, as well as binary, hybrid, and physiochemical properties, based on methods that are applied to the main data set. The TPC-based monopeptide composition model achieved more accuracy, 94.4%, with a Matthews correlation coefficient (MCC) of 0.89. Correspondingly, the second-best model based on dipeptides achieved an accuracy of 94.28% under the MCC 0.89 of the training dataset. Full article
(This article belongs to the Special Issue Structures and Functions of Antimicrobial Peptides)
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11 pages, 437 KiB  
Article
The Design of Alapropoginine, a Novel Conjugated Ultrashort Antimicrobial Peptide with Potent Synergistic Antimicrobial Activity in Combination with Conventional Antibiotics
by Ali Salama, Ammar Almaaytah and Rula M. Darwish
Antibiotics 2021, 10(6), 712; https://doi.org/10.3390/antibiotics10060712 - 13 Jun 2021
Cited by 11 | Viewed by 2218
Abstract
(1) Background: Antimicrobial resistance represents an urgent health dilemma facing the global human population. The development of novel antimicrobial agents is needed to face the rising number of resistant bacteria. Ultrashort antimicrobial peptides (USAMPs) are considered promising antimicrobial agents that meet the required [...] Read more.
(1) Background: Antimicrobial resistance represents an urgent health dilemma facing the global human population. The development of novel antimicrobial agents is needed to face the rising number of resistant bacteria. Ultrashort antimicrobial peptides (USAMPs) are considered promising antimicrobial agents that meet the required criteria of novel antimicrobial drug development. (2) Methods: Alapropoginine was rationally designed by incorporating arginine (R), biphenylalanine (B), and naproxen to create an ultrashort hexapeptide. The antimicrobial activity of alapropoginine was evaluated against different strains of bacteria. The hemolytic activity of alapropoginine was also investigated against human erythrocytes. Finally, synergistic studies with antibiotics were performed using the checkerboard technique and the determination of the fractional inhibitory index. (3) Results: Alapropoginine displayed potent antimicrobial activities against reference and multi-drug-resistant bacteria with MIC values of as low as 28.6 µg/mL against methicillin-resistant S. aureus. Alapropoginine caused negligible toxicity toward human red blood cells. Moreover, the synergistic studies showed improved activities for the combined conventional antibiotics with a huge reduction in their antimicrobial concentrations. (4) Conclusions: The present study indicates that alapropoginine exhibits promising antimicrobial activity against reference and resistant strains of bacteria with negligible hemolytic activity. Additionally, the peptide displays synergistic or additive effects when combined with several antibiotics. Full article
(This article belongs to the Special Issue Structures and Functions of Antimicrobial Peptides)
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