biostudies-literatureGhose DAHoward Hughes Medical InstituteNIGMS NIH HHS4496-4507https://www.ebi.ac.uk/biostudies/studies/S-EPMC12739935biostudies-literatureUnknown14(11)Toxin-antitoxin (TA) systems are widespread antiphage defense elements in bacteria that may impede successful phage therapy. Phage-encoded inhibitors of these systems have been discovered that enhance phage infection capacity. We used fragment-based design with deep-learning scoring functions to design peptide inhibitors of the toxin RelE. Our peptides extend a fragment of the native RelB antitoxin and are sufficient to inhibit RelE toxicity. Successful inhibitors share a highly conserved binding mode that mimics the native antitoxin but have diverse sequences, with alternative contacts used to form the peptide-protein interface. Designed peptides show different interaction specificities toward RelE family proteins, distinct from the wild-type RelB antitoxin, and inhibit the antiphage defeACS synthetic biologyDesign of Specific Peptide Inhibitors of Toxin-Antitoxin-Mediated Antiphage Defense.PMC12739935R35 GM149227Swanson SRGhose DALaub MTBirnbaum FKeating AEBritton DGan JLMahoney EMfalseDesign of Specific Peptide Inhibitors of Toxin-Antitoxin-Mediated Antiphage Defense.Toxin-antitoxin (TA) systems are widespread antiphage defense elements in bacteria that may impede successful phage therapy. Phage-encoded inhibitors of these systems have been discovered that enhance phage infection capacity. We used fragment-based design with deep-learning scoring functions to design peptide inhibitors of the toxin RelE. Our peptides extend a fragment of the native RelB antitoxin and are sufficient to inhibit RelE toxicity. Successful inhibitors share a highly conserved binding mode that mimics the native antitoxin but have diverse sequences, with alternative contacts used to form the peptide-protein interface. Designed peptides show different interaction specificities toward RelE family proteins, distinct from the wild-type RelB antitoxin, and inhibit the antiphage defe2025-01-01T00:00:00Z2025 Nov2026-06-06T05:56:05.226Z2026-05-27T03:11:53.059ZS-EPMC127399354113928510.1021/acssynbio.5c00498