Protein aggregation as an antibiotic design strategy

Abstract

Taking advantage of the xenobiotic nature of bacterial infections, we tested whether the cytotoxicity of protein aggregation can be targeted to bacterial pathogens without affecting their mammalian hosts. In particular, we examined if peptides encoding aggregation-prone sequence segments of bacterial proteins can display antimicrobial activity by initiating toxic protein aggregation in bacteria, but not in mammalian cells. Unbiased in vitro screening of aggregating peptide sequences from bacterial genomes lead to the identification of several peptides that are strongly bactericidal against methicillin-resistant Staphylococcus aureus. Upon parenteral administration in vivo, the peptides cured mice from bacterial sepsis without apparent toxic side effects as judged from histological and hematological evaluation. We found that the peptides enter and accumulate in the bacterial cytosol where they cause aggregation of bacterial polypeptides. Although the precise chain of events that leads to cell death remains to be elucidated, the ability to tap into aggregation-prone sequences of bacterial proteomes to elicit antimicrobial activity represents a rich and unexplored chemical space to be mined in search of novel therapeutic strategies to fight infectious diseases.

Amyloid Structures as Biofilm Matrix Scaffolds

“…Bednarska and collaborators developed an ingenious strategy in this regard: they designed peptides carrying aggregationprone sequence stretches of bacterial proteins, some of them with an amyloid-like nature, that specifically penetrate bacteria, causing aggregation of polypeptides in the cytosol and ultimately leading to bacterial death. The interesting point is that these peptides had no detectable effects on host cells (94).…”

De novo design of a biologically active amyloid

“…Moreover, the two homologs share 84% sequence identity overall and 90% in the TANGO-regions. To derive peptide sequences that are likely to form amyloid structure in isolation, but also have a high potential for forming soluble oligomers (29), we devised a strategy (30,31) that makes use of a sequence feature of functional amyloids and yeast prions, which often contain several Aggregation Prone Regions (APR) (32) closely connected by disordered regions (33). Hence we placed two APRs in a peptide, separated by a rigid proline-proline linker, mimicking these repeat patterns.…”

Sequence-specific protein aggregation generates defined protein knockdowns in plants

“…As charged residues are enriched at the flanks of APRs to decrease aggregation and function as natural "aggregation gatekeepers" (De Baets et al, 2014), five to six naturally flanking (NF) amino acids were added to the BIN2 249-257 APR and expressed, including the first six amino acids of the BIN2 protein (MADDKE) in a single copy (BIN2 [249][250][251][252][253][254][255][256][257] NF) or in tandem (T) (BIN2 [249][250][251][252][253][254][255][256][257] NFT) (Supplemental Table S3). The aim of the tandem constructs was to amplify the aggregation potential by mimicking the repeating patterns of APRs that are observed in naturally occurring functional amyloids, such as the yeast prions (Bednarska et al, 2016).…”