Discovery of Small-Molecule Antagonists of the H3K9me3 Binding to UHRF1 Tandem Tudor Domain

Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is a multidomain protein that plays a critical role in maintaining DNA methylation patterns through concurrent recognition of hemimethylated DNA and histone marks by various domains, and recruitment of DNA methyltransferase 1 (DNMT1). UHRF1 is overexpressed in various cancers, including breast cancer. The tandem tudor domain (TTD) of UHRF1 specifically and tightly binds to histone H3 di- or trimethylated at lysine 9 (H3K9me2 or H3K9me3, respectively), and this binding is essential for UHRF1 function. We developed an H3K9me3 peptide displacement assay, which was used to screen a library of 44,000 compounds for small molecules that disrupt the UHRF1-H3K9me3 interaction. This screen resulted in the identification of NV01, which bound to UHRF1-TTD with a K_d value of 5 μM. The structure of UHRF1-TTD in complex with NV01 confirmed binding to the H3K9me3-binding pocket. Limited structure-based optimization of NV01 led to the discovery of NV03 (K_d of 2.4 μM). These well-characterized small-molecule antagonists of the UHRF1-H3K9me2/3 interaction could be valuable starting chemical matter for developing more potent and cell-active probes toward further characterizing UHRF1 function, with possible applications as anticancer therapeutics.

Increasing role of UHRF1 in the reading and inheritance of the epigenetic code as well as in tumorogenesis

Epigenetic mechanisms such as DNA methylation and histone posttranslational modifications, allow cells to maintain the phenotype throughout successive mitosis. UHRF1 plays a major role in the inheritance of some epigenetic marks from mother cells to daughter cells due to its particular structural domains. The originality of UHRF1 lies in the fact that it can read epigenetic marks and recruit the enzymes that catalyze the same epigenetic mark. The SRA domain senses the presence of a methylated cytosine on one DNA strand allowing the recruitment of DNMT1, which methylates the cytosine on the newly synthesized DNA. The recently identified tudor domain of UHRF1 senses the presence of methylated histone H3 conducting UHRF1 to recruit histone methyltransferases. Recent studies deciphering the relationships between some of the structural domains of UHRF1 provides new insights on the reading of the epigenetic code over a larger portion of histone tail than usually expected. Furthermore, latest developments highlights that UHRF1 is one of the proteins which is able to directly connect DNA methylation to histone epigenetic marks. This paper reviews the principles how UHRF1 acts as an epigenetic reader and discusses the properties of UHRF1 to be a biomarker as well as a therapeutic target.