Disulfide-rich peptides (DRPs) are an interesting and promising molecular format for drug discovery and development. However, the engineering and application of DRPs rely on the foldability of the peptides into specific structures with correct disulfide pairing, which strongly hinders the development of designed DRPs with randomly encoded sequences. Design or discovery of new DRPs with robust foldability would provide valuable scaffolds for developing peptide-based probes or therapeutics. Herein we report a cell-based selection system leveraging cellular protein quality control (termed PQC-select) to select DRPs with robust foldability from random sequences. By correlating the foldability of DRPs with their expression levels on the cell surface, thousands of sequences that can fold properly have been successfully identified. We anticipated that PQC-select will be applicable to many other designed DRP scaffolds in which the disulfide frameworks and/or the disulfide-directing motifs can be varied, enabling the generation of a variety of foldable DRPs with new structures and superior potential for further developments.
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