Abstract
Plant homeodomain (PHD) zinc fingers are histone reader domains that are often associated with human diseases. Despite this, they constitute a poorly targeted class of readers, suggesting low ligandability. Here, we describe a successful fragment-based campaign targeting PHD fingers from the proteins BAZ2A and BAZ2B as model systems. We validated a pool of in silico fragments both biophysically and structurally and solved the first crystal structures of PHD zinc fingers in complex with fragments bound to an anchoring pocket at the histone binding site. The best-validated hits were found to displace a histone H3 tail peptide in competition assays. This work identifies new chemical scaffolds that provide suitable starting points for future ligand optimization using structure-guided approaches. The demonstrated ligandability of the PHD reader domains could pave the way for the development of chemical probes to drug this family of epigenetic readers.
Highlights
Plant homeodomain (PHD) zinc fingers are histone reader domains that are often associated with human diseases
Unlike other reader domains,[6] PHD fingers have been proven difficult to target with small molecules, and no chemical probe has been reported to date against them
Further motivation came from an ultimate goal to develop chemical probes that could inform on the biological function of these proteins
Summary
Previous research has shown that BAZ2 PHDs recognize preferentially unmodified H3 histone tail promoting helicity in the H3 peptide upon binding.[10,11] It was shown that the mutation to alanine of the second and third residues of the H3 histone tail abolishes binding.[11,20] we hypothesized that the H3 N-terminal 3-mer motif “ART” might be essential to anchor the histone tail to the surface of BAZ2 PHDs. In silico ligandability analysis highlighted two potential druggable pockets and targeted virtual screening identified a set of fragments that were validated experimentally for protein binding From this set, we were able to solve the co-crystal structure of one compound (Fr19) bound to the histone pocket, which guided further in silico optimization of the binding mode, resulting in two more fragments successfully soaked in BAZ2 PHDs. To the best of our knowledge, these are the first fragment-bound crystal structures revealing protein− ligand interactions at the histone pocket of a PHD zinc finger domain. Improved ligands could be conjugated to E3 ubiquitin ligase ligands, yielding bifunctional chemical degraders to induce proteasomal degradation of the BAZ2 proteins.[30,31]
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