A Molecular Tool Targeting the Base‐Flipping Activity of Human UHRF1

Abstract

During DNA replication, ubiquitin‐like, containing PHD and RING fingers domains 1 (UHRF1) plays key roles in the inheritance of methylation patterns to daughter strands by recognizing through its SET and RING‐associated domain (SRA) the methylated CpGs and recruiting DNA methyltransferase 1 (DNMT1). Herein, our goal is to identify UHRF1 inhibitors targeting the 5′‐methylcytosine (5mC) binding pocket of the SRA domain to prevent the recognition and flipping of 5mC and determine the molecular and cellular consequences of this inhibition. For this, we used a multidisciplinary strategy combining virtual screening and molecular modeling with biophysical assays in solution and cells. We identified an anthraquinone compound able to bind to the 5mC binding pocket and inhibit the base‐flipping process in the low micromolar range. We also showed in cells that this hit impaired the UHRF1/DNMT1 interaction and decreased the overall methylation of DNA, highlighting the critical role of base flipping for DNMT1 recruitment and providing the first proof of concept of the druggability of the 5mC binding pocket. The selected anthraquinone appears thus as a key tool to investigate the role of UHRF1 in the inheritance of methylation patterns, as well as a starting point for hit‐to‐lead optimizations.

Insights into the computer-aided drug design and discovery based on anthraquinone scaffold for cancer treatment: A systematic review

“…None of the studies used ligand-based method alone since the crystal structure of all identified targets in the studies were either available in the protein databases [ 55 , 56 , 58 – 60 , 62 – 67 , 69 – 75 , 77 – 86 ] or successfully created by homology modelling [ 57 , 61 , 68 , 76 ].…”

“…The use of both structure-based and ligand-based methods were combined in either a parallel manner [ 58 , 78 , 80 ] or performed one after another in sequence, termed as sequential screening [ 59 , 71 , 76 , 77 , 83 , 85 , 86 ]. The sequential approach was more popular as it enabled efficient computation in which the more straightforward and quicker ligand-based virtual screening served as the pre-docking filter to reduce the size of the screening library before the more computational-demanding docking job took place.…”

Exploring the Potential of Anthraquinone‐Based Hybrids for Identifying a Novel Generation of Antagonists for the Smoothened Receptor in HH‐Dependent Tumour

“…The prominent anthraquinone‐based drugs doxorubicin, mitoxantrone, as well as more recent epirubicin, idarubicin, and valrubicin, are successfully used in chemotherapy of haematological malignancies and solid tumours [32] . The anthraquinone core remains a promising scaffold for discovering novel drug candidates [30,31,33,34] …”

“…[32] The anthraquinone core remains a promising scaffold for discovering novel drug candidates. [30,31,33,34] Based on these findings, this work provides an innovative exploitation of the chemical versatility as well as the affinity for the HH pathway of the anthraquinone scaffold by combining it with the active portion of well-known SMO antagonists (Taladegib and Anta XV) to design, synthesize and test specific antagonists. Our strategy implied the design, supported by computer-aided methods, and synthesis of a library of anthraquinone derivatives featuring variously substituted piperazine linkers, able to interact in silico with the SMO receptor, and the investigation of the HH inhibitory properties of the synthesized compounds, to validate the computational modelling predictions.…”

A Fast Ubiquitination of UHRF1 Oncogene Is a Unique Feature and a Common Mechanism of Thymoquinone in Cancer Cells

“…The ubiquitin-like containing PHD and ring finger 1 (UHRF1) oncogene is overexpressed in many human cancers and serves as a master regulator of the epigenome (DNA methylation and histone modifications) through its five functional domains [1][2][3][4][5][6][7], including the RING domain, which is the only domain of UHRF1 that exhibits enzymatic activity [2,8]. Indeed, UHRF1 belongs to the ring finger-type E3-ubiquitin ligases, which have in vitro autoubiquitination activity [8][9][10] and are currently viewed as promising anticancer drug targets due to their roles in the regulation of many tumor suppressor proteins [8,11].…”