Issue 43, 2022

Pattern enrichment analysis for phage selection of stapled peptide ligands

Abstract

Phage display is the most widely used technique to discover de novo peptides that bind to target proteins. However, it is associated with some challenges such as compositional bias. In this study, to overcome these difficulties, we devised a ‘pattern enrichment analysis.’ In this method, two samples (one obtained by affinity selection, the other simply amplified without selection) are prepared, and the two sequence datasets read on next-generation sequencer are compared to find the three-residue pattern most enriched in the selected sample. This allows us to compare two sequence datasets with high coverage and facilitates the identification of peptide sequences and the key residues for binding. We also demonstrated that this approach in the combination with structured peptide libraries allowed spatial mapping of the enriched sequence patterns. Here, we prepared a phage library displaying chemically stapled helical peptides with the X1C2X3X4X5X6X7X8C9X10 sequence, where X is any amino acid. To validate our method, we performed screening against the HDM2 protein. The results showed that the hydrophobic residues (Phe, Tyr, Trp and Leu) that are key to interactions with HDM2 were clearly identified by the pattern enrichment analysis. We also performed selection targeting the SARS-CoV-2 spike RBD in the same manner. The results showed that similar patterns were enriched among the hit peptides that inhibited the protein–protein interaction.

Graphical abstract: Pattern enrichment analysis for phage selection of stapled peptide ligands

Supplementary files

Article information

Article type
Edge Article
Submitted
20 Jul 2022
Accepted
11 Oct 2022
First published
12 Oct 2022
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY license

Chem. Sci., 2022,13, 12634-12642

Pattern enrichment analysis for phage selection of stapled peptide ligands

T. Miki, K. Namii, K. Seko, S. Kakehi, G. Moro and H. Mihara, Chem. Sci., 2022, 13, 12634 DOI: 10.1039/D2SC04058A

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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