Potent macrocycle inhibitors of the human SAGA deubiquitinating module

The SAGA complex is a transcriptional coactivator that plays multiple roles in activating transcription and is conserved from yeast to humans. One of SAGAs activities is the removal of ubiquitin from histone H2B-K120 by the deubiquitinating module (DUBm), a four-protein subcomplex containing the catalytic subunit, USP22, bound to three proteins that are required for catalytic activity and targeting to nucleosomes. Overexpression of USP22 is correlated with cancers with a poor prognosis that are resistant to available therapies. We used the RaPID (Random non-standard Peptides Integrated Discovery) system to identify cyclic peptides that are potent and highly specific inhibitors of USP22. Peptide binding did not impact the overall integrity of the DUBm complex as judged by small-angle x-ray scattering, indicating that the inhibitors do not disrupt subunit interactions required for USP22 activity. Cells treated with peptide had increased levels of H2B monoubiquitination, demonstrating the ability of the cyclic peptides to enter human cells and inhibit H2B deubiquitination. The macrocycle inhibitors we have identified in this work thus exhibit favorable drug-like properties and constitute, to our knowledge, the first reported inhibitors of USP22/SAGA DUB module.