Natural Cyclic Peptides from DBAASP Database

Antimicrobial peptides (AMPs) have emerged as a novel class of anti-infectives to combat microbial resistance. However, their intrinsic characteristics, including low target affinity and limited in vivo stability, present obstacles to their therapeutic development. Macrocyclic peptides, a diverse peptide family, offer improved metabolic and proteolytic stability along with high target affinity. In this work, we performed an analysis of the DBAASP database to enhance our understanding of small cyclic peptides, nature’s defense mechanisms for living organisms. To our knowledge, this is the first effort to characterize cyclic peptides originated from either non-ribosomal or post-ribosomal peptide synthesis and reveal shared and distinctive cyclization patterns. The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) provides invaluable data on structural characteristics and experimental testing of AMPs, encompassing over 4,400 cyclic AMPs. Natural peptides within DBAASP are categorized based on their synthesis type: ribosomal and non-ribosomal. Currently, DBAASP contains 1346 ribosomal and 475 non-ribosomal cyclic AMPs. We conducted an analysis of this dataset, considering peptide length, amino acid composition, intrachain bonding for cyclization, and mechanisms of action. The methods of cyclization, types of cycles, and their peculiarities in the composition of small cyclic peptides have also been explored. Analysing this wealth of information not only deepens our understanding of cyclic AMPs but also inspires strategies for designing novel AMPs with enhanced therapeutic potential.