Karishma Patel; Louise J. Walport; James L. Walshe; Paul D. Solomon; Jason K. K. Low; Daniel H. Tran; Kevork S. Mouradian; Ana P. G. Silva; Lorna Wilkinson-White; Alexander Norman; Charlotte Franck; Jacqueline M. Matthews; J. Mitchell Guss; Richard J. Payne; Toby Passioura; Hiroaki Suga; Joel P. Mackay
Proc. Natl. Acad. Sci. USA, 2020, 117(43), 26728-26738
https://doi.org/10.1073/pnas.2003086117

Abstract

Large DNA-encoded libraries of cyclic peptides are emerging as powerful sources of molecules to tackle challenging drug targets. The structural and functional diversity contained within these libraries is, however, little explored. Here we demonstrate that one such library contains members that use unexpectedly diverse mechanisms to recognize the same surface on the same target proteins with high affinity and specificity. This range of binding modes is much larger than observed in natural ligands of the same proteins, demonstrating the power and versatility of the technology. Our data also reveal opportunities for the development of more sophisticated approaches to achieving specificity when trying to selectively target one member of a family of closely related proteins.
Cyclic peptide library screening technologies show immense promise for identifying drug leads and chemical probes for challenging targets. However, the structural and functional diversity encoded within such libraries is largely undefined. We have systematically profiled the affinity, selectivity, and structural features of library-derived cyclic peptides selected to recognize three closely related targets: the acetyllysine-binding bromodomain proteins BRD2, -3, and -4. We report affinities as low as 100 pM and specificities of up to 106-fold. Crystal structures of 13 peptide–bromodomain complexes reveal remarkable diversity in both structure and binding mode, including both α-helical and β-sheet structures as well as bivalent binding modes. The peptides can also exhibit a high degree of structural preorganization. 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.