Computational resources and tools for antimicrobial peptides

Abstract

Antimicrobial peptides (AMPs), as evolutionarily conserved components of innate immune system, protect against pathogens including bacteria, fungi, viruses, and parasites. In general, AMPs are relatively small peptides (<10 kDa) with cationic nature and amphipathic structure and have modes of action different from traditional antibiotics. Up to now, there are more than 19 000 AMPs that have been reported, including those isolated from nature sources or by synthesis. They have been considered to be promising substitutes of conventional antibiotics in the quest to address the increasing occurrence of antibiotic resistance. However, most AMPs have modest direct antimicrobial activity, and their mechanisms of action, as well as their structure-activity relationships, are still poorly understood. Computational strategies are invaluable assets to provide insight into the activity of AMPs and thus exploit their potential as a new generation of antimicrobials. This article reviews the advances of AMP databases and computational tools for the prediction and design of new active AMPs. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Prediction and Characterization of Cationic Arginine-Rich Plant Antimicrobial Peptide SM-985 From Teosinte (Zea mays ssp. mexicana)

“…In our lab, we screened cDNA libraries for AMPs via expression systems (Kong et al, 2018;Wu et al, 2020), but this is also a time-and cost-consuming approach. In silico prediction is a time-and cost-effective approach for large-scale screening and detection of AMPs (Liu et al, 2017). The detection of AMPs from databases has drawn interest as a field of structural genomics and bioinformatics.…”

Molecular Design of Peptide-Fc Fusion Drugs

“…In this situation, structure-free peptide design is a good alternative solution. With the rapid increasing of available bioactive peptide database and the advance of artificial intelligence, predicting peptide leads based on sequence information has become popular [61][62][63][64][65][66][67][68][69][70][71][72][73][74]. However, there is a big problem for the current structure-free peptide design methods.…”

Promising Approaches to Optimize the Biological Properties of the Antimicrobial Peptide Esculentin-1a(1–21)NH2: Amino Acids Substitution and Conjugation to Nanoparticles

“…Remarkably, unlike conventional antibiotics, this non-specific mechanism of action of AMPs very rarely induces resistance (Bechinger and Gorr, 2017) and makes them an interesting class of molecules for the development of new antimicrobial compounds (Mazer-Amirshahi et al, 2016). To date, thousands of AMPs have been characterized from a variety of natural sources as well as their synthetic derivatives (Liu et al, 2016). Noteworthy, an increasing number of AMPs has already entered into advanced stages of clinical trials for topical treatment of different types of infections.…”