Thinking on the Construction of Antimicrobial Peptide Databases: Powerful Tools for the Molecular Design and Screening

Abstract

With the accelerating growth of antimicrobial resistance (AMR), there is an urgent need for new antimicrobial agents with low or no AMR. Antimicrobial peptides (AMPs) have been extensively studied as alternatives to antibiotics (ATAs). Coupled with the new generation of high-throughput technology for AMP mining, the number of derivatives has increased dramatically, but manual running is time-consuming and laborious. Therefore, it is necessary to establish databases that combine computer algorithms to summarize, analyze, and design new AMPs. A number of AMP databases have already been established, such as the Antimicrobial Peptides Database (APD), the Collection of Antimicrobial Peptides (CAMP), the Database of Antimicrobial Activity and Structure of Peptides (DBAASP), and the Database of Antimicrobial Peptides (dbAMPs). These four AMP databases are comprehensive and are widely used. This review aims to cover the construction, evolution, characteristic function, prediction, and design of these four AMP databases. It also offers ideas for the improvement and application of these databases based on merging the various advantages of these four peptide libraries. This review promotes research and development into new AMPs and lays their foundation in the fields of druggability and clinical precision treatment.

Impact of bacteriocins on multidrug‐resistant bacteria and their application in aquaculture disease prevention and control

“…Identification and annotation of bacteriocins or bacteriocin‐like proteins can be facilitated with the help of several bioinformatics tools. There are several antibacterial compound databases available for reference, such as the antimicrobial peptides database (APD), the collection of antimicrobial peptides (CAMP), the BACTIBASE, the database of antimicrobial activity and structure of peptides (DBAASP) and the database of antimicrobial peptides 90 . The APD contains information on 2619 antibacterial compounds and 261 bacteriocins, including producer organism, peptide sequence, chemical modifications, structure and additional functions of the peptide, target organism, mode of action, discovery year and author.…”

Molecular Modification of Kex2 P1’ Site Enhances Expression and Druggability of Fungal Defensin

“…There is a good preliminary foundation in our team regarding the modification, expression, and efficacy studies of this class of antimicrobial peptides, which are expected to have good development prospects for antibiotic substitution and combination administration to hinder drug resistance [ 18 , 19 , 20 , 21 , 22 , 23 ]. We know that defensins take over half of AMPs in quantity from the AMP databases [ 24 , 25 ]. Looking back and thinking about the historic experience during the discovery of new antibiotics, we are impressed by the fact that, on one hand, the most defensin produced by fungi or other microorganisms has the better druggability and is more suitable being as new sources of candidate antimicrobials to dig and follow, which is superior to that of plants and animals with more difficulties to validate their druggability.…”

Site Mutation Improves the Expression and Antimicrobial Properties of Fungal Defense

“…In view of these actual situations, development expectations, and our previous experience in similar directions over the years, the structure of Plectasin will be modified and optimized in this study to obtain candidates with high expression and antibacterial activity, no/low toxicity, and better druggability. A challenge has been how to use AMP databases in the actual field to design and construct new AMPs [ 3 , 38 , 39 ]; thus, our aim would try to follow and solidate a clue from the AMP databases for new candidate derivatives by enhancing the combination of theory and application.…”