Antimicrobial Peptides: An Update on Classifications and Databases

Abstract

Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.

Antimicrobial peptides, conventional antibiotics, and their synergistic utility for the treatment of drug‐resistant infections

“…72 Databases covering various annotations of AMPs, including sequence, structure, activity, physical chemistry, patents, clinical, and references have been designed. For instance, the Antimicrobial Peptide Database (APD3, https://aps.unmc.edu/) is one of the largest databases (last accessed on October 18, 2021), 73 consisting of 3283 AMPs spanning six kingdoms of life (371 archaea bacteriocins/peptide antibiotics from bacteria, 5 from archaea, 8 from protists, 22 from fungi, 361 from plants, and 2431 from animals, including some synthetic peptides). The APD3 database also provides useful research tools to search, predict, and modify AMPs.…”

Strategies for Antimicrobial Peptides Immobilization on Surfaces to Prevent Biofilm Growth on Biomedical Devices

“…Based on these three-dimensional secondary and tertiary structures, which can be determined by NMR spectroscopy [ 49 ], AMPs are divided into four categories as depicted in Figure 4 : (i) α when the major secondary structure of the peptide is α-helical, (ii) β if the structure contains at least a pair of two-strands, (iii) αβ for peptides with both types of structure, (iv) non-αβ if none of the structures are present. The secondary and tertiary structures of AMPs are believed to play an important role in the mechanism of action against microbial cells, particularly in the process of integration in the cell membrane [ 47 ], albeit in 2021 only about 40% of AMPs have in fact a known 3D structure [ 50 ].…”

Application of Antimicrobial Peptides on Biomedical Implants: Three Ways to Pursue Peptide Coatings

“…Herein, the group of antimicrobial peptides (AMPs) has gained more and more attention as potent antibiotic surface coatings [13]. These peptides combine a broad spectrum of antimicrobial activity against a wide range of pathogens with a rather decent cytotoxicity against mammalian host cells [14]. Moreover, most AMPs facilitate a mechanism of action, which is usually not that easily adaptable by bacteria: they display high membrane-activity and lyse the bacterial outer membrane by membrane disruption [15].…”