Cyclic peptide library screening technologies show immense promise for identifying drug leads and chemical probes. They are especially powerful for challenging targets, such as protein-protein interactions, or to derive selective compounds for highly homologous targets. To date, however, the structural and functional diversity encoded within such libraries remains largely unexplored. We set out to explore this by systematically profiling the affinity, selectivity and structural features of de novo cyclic peptides selected against three closely related targets: individual bromodomains of the acetyllysine-binding bromodomain proteins BRD3 and BRD4. These targets were selected as despite their therapeutic promise in the treatment of a range of diseases, identification of highly selective small molecules inhibitors has proved elusive owing to the close structural conservation between bromodomain-containing proteins. Using a tailored library allowing incorporation of an acetyllysine warhead, we identified peptides with affinities as low as 100 pM and specificities of up to 106-fold between family members. All peptides were found to bind to the acetyllysine binding pocket, yet crystal structures of 13 peptide-bromodomain complexes revealed remarkable diversity in both structure and binding mode. These included both α-helical and β-sheet structures, as well as bivalent binding modes. NMR structures of the free peptides in solution demonstrated that some peptides also exhibit a high degree of structural pre-organization, likely contributing to the high binding affinities we observed. Overall, our data demonstrate the enormous potential within these libraries to provide diverse binding modes against a single target, which underpins their capacity to yield highly potent and selective ligands.

Diverse binding to a single interface: De novo cyclic peptides as inhibitors of the BET bromodomains

ACS Spring Meeting 2021

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.