University of Bath develops bacterial platform for stapled peptide drug discovery

Researchers at the University of Bath have developed a new system that uses bacteria to produce, chemically stabilize, and test millions of peptide molecules inside living cells in a single, streamlined process. Published in Cell Chemical Biology, the approach is designed to provide a faster, cleaner, and more scalable way to identify potential therapies for proteins that have long resisted conventional drug development.

Peptide therapeutics are experiencing a surge of interest, with more than 80 peptide drugs already on the market and hundreds more in clinical and preclinical development. The global market for peptide-based therapeutics is expected to grow to $68.83 billion by 2028. Despite their promise, peptides are often structurally flexible, easily degraded by enzymes in the body, and can struggle to enter cells, limiting their stability and effectiveness as drugs.

One strategy to overcome these challenges is peptide stapling, a technique that chemically locks peptides into a stable shape. In the Bath system, stapled peptides are produced directly inside living bacterial cells rather than synthesized and then chemically stapled afterwards. The system uses genetically encoded libraries, with each cell producing a unique sequence, and small bis-alkylating molecules that cross the bacterial membrane and react with pairs of cysteine residues engineered into the peptides, forming the staple and cyclizing the molecule inside the living cell.

This approach allows millions of candidate molecules to be generated simultaneously inside bacteria, reducing the need for complex, multi-step synthesis and purification that traditionally slows peptide drug development. The researchers said the biology effectively selects both the peptide sequence and the optimal constraint geometry at the same time.

The screening step uses the Transcription Block Survival (TBS) assay, which links peptide activity directly to bacterial survival. In this setup, bacteria are engineered so that a transcription factor blocks the expression of an essential gene. If the transcription factor is active, the cell cannot grow, but if a peptide successfully blocks the transcription factor, the block is lifted and the cell survives.

According to the researchers, the TBS assay automatically filters out sequences that are unstable, non-specific, toxic, or poorly expressed. Only peptides that are stable, functional, and able to selectively engage the target inside the cell are enriched by survival in the screen.