A high-throughput screen of pharmacologically active compounds for inhibitors of UHRF1 reveals epigenetic activity of anthracycline derivative chemotherapeutic drugs

// Hugh Giovinazzo 1 , 2 , 4 , * , David Walker 1 , 2 , 5 , * , Nicolas Wyhs 1 , 2 , Jianyong Liu 2 , David M. Esopi 2 , Ajay M. Vaghasia 2 , Yash Jain 2 , Akshay Bhamidipati 2 , Jianya Zhou 2 , 3 , William G. Nelson 1 , 2 and Srinivasan Yegnasubramanian 1 , 2 1 Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA 2 Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA 3 Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital College of Medicine, Zhejiang University, Hangzhou, China PR 4 Current Affiliation: Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA 5 Current Affiliation: Active Motif, Carlsbad, CA, USA * These authors contributed equally to this work Correspondence to: Srinivasan Yegnasubramanian, email: syegnasu@jhmi.edu William G. Nelson, email: bnelson@jhmi.edu Keywords: DNA methylation; UHRF1 inhibitors; SRA domain; TR-FRET; anthracyclines Received: March 20, 2019     Accepted: April 11, 2019     Published: April 30, 2019 ABSTRACT DNA methylation can mediate epigenetic silencing of tumor suppressor and cancer protective genes. The protein ubiquitin-like containing PHD and ring finger domains 1 (UHRF1) is an essential component in cells for DNA methylation maintenance. The SET- and RING-associated (SRA) domain of UHRF1 can bind hemimethylated DNA, and mediate recruitment of DNA methyltransferases to copy the methylation pattern to the newly synthesized daughter strand. Loss of UHRF1 function can lead to demethylation and re-expression of epigenetically silenced tumor suppressor genes and can reduce cancer cell growth and survival. We created a high-throughput time-resolved fluorescence resonance energy transfer (TR-FRET) assay to screen for inhibitors capable of disrupting the interaction between the UHRF1-SRA domain and hemimethylated DNA. Using this assay (Z’ factor of 0.74 in 384-well format) we screened the Library of Pharmacologically Active Compounds (LOPAC) for UHRF1-SRA inhibitors, and validated 7 hit compounds. These compounds included the anthracycline derivatives idarubicin and mitoxantrone, which are commonly used chemotherapeutic drugs known to mediate cytotoxicity by acting as class II topoisomerase (TOP2) poisons. In a panel of additional known topoisomerase poisons, only the anthracycline derivatives showed dose responsive inhibition of UHRF1-SRA. Additionally, mitoxantrone and doxorubicin showed dose-responsive global DNA demethylation and demonstrated a synergistic growth inhibition of multiple cancer cell lines when combined with the DNA methyltransferase (DNMT) inhibitor decitabine. These data validate a novel TR-FRET assay for identification of UHRF1 inhibitors, and revealed unexpected epigenetic properties of commonly used chemotherapeutic drugs that showed synergistic cytotoxicity of cancer cells when combined with a demethylating agent.