mRNA display reveals a class of high-affinity bromodomain-binding motifs that are not found in the human proteome

Late-Stage Reshaping of Phage-Displayed Libraries to Macrocyclic and Bicyclic Landscapes using a Multipurpose Linchpin

Genetically encoded libraries (GEL) are increasingly being used for the discovery of ligands for "undruggable" targets that cannot be addressed with small molecules. Foundational GEL platforms like phage-, yeast-, ribosome-, and mRNA-display have enabled the display of libraries composed of 20 natural amino acids (20AA). Unnatural amino acids (UAA) and chemical post-translational modification (cPTM) expanded GEL beyond the 20AA space to yield unnatural linear, cyclic, and bicyclic peptides. The standard operating procedure incorporates UAA and cPTM into a "naive" library with 108-1012 compounds and uses a chemically upgraded library in multiple rounds of selection to discover target-binding hits. However, such an approach uses zero knowledge of natural peptide-receptor interactions that might have been discovered in selections performed with 20AA libraries. There is currently no consensus regarding whether "zero-knowledge" naive libraries or libraries with pre-existing knowledge can offer a more effective path to discovery of molecular interactions. In this manuscript, we evaluated the feasibility of discovery of macrocyclic and bicyclic peptides from "nonzero-knowledge" libraries. We approach this problem by late-stage chemical reshaping of a preselected phage-displayed landscape of 20AA binders to NS3aH1 protease. The reshaping is performed using a novel multifunctional C2-symmetric linchpin, 3,5-bis(bromomethyl)benzaldehyde (termed KYL), that combines two electrophiles that react with thiols and an aldehyde group that reacts with N-terminal amine. KYL diversified phage-displayed peptides into bicyclic architectures and delineated 2 distinct sequence populations: (i) peptides with the HXDMT motif that retained binding upon bicyclization and (ii) peptides without the HXDMT motif that lost binding once chemically modified. The same HXDMT family can be found in traditional selections starting from the naive KYL-modified library. Our report provides a case study for discovering advanced, chemically upgraded macrocycles and bicycles from libraries with pre-existing knowledge. The results imply that other selection campaigns completed in 20AA space, potentially, can serve for late-stage reshaping and as a starting point for the discovery of advanced peptide-derived ligands.

mRNA Display Identifies Potent, Paralog-Selective Peptidic Ligands for ARID1B

The ARID1A and ARID1B subunits are mutually exclusive components of the BAF variant of SWI/SNF chromatin remodeling complexes. Loss of function mutations in ARID1A are frequently observed in various cancers, resulting in a dependency on the paralog ARID1B for cancer cell proliferation. However, ARID1B has never been targeted directly, and the high degree of sequence similarity to ARID1A poses a challenge for the development of selective binders. In this study, we used mRNA display to identify peptidic ligands that bind with nanomolar affinities to ARID1B and showed high selectivity over ARID1A. Using orthogonal biochemical, biophysical, and chemical biology tools, we demonstrate that the peptides engage two different binding pockets, one of which directly involves an ARID1B-exclusive cysteine that could allow covalent targeting by small molecules. Our findings impart the first evidence of the ligandability of ARID1B, provide valuable tools for drug discovery, and suggest opportunities for the development of selective molecules to exploit the synthetic lethal relationship between ARID1A and ARID1B in cancer.