Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery

Lyra Chang,Banumathi Sankaran,Kevin Tran,Shiva K R Guduru,Kevin R Mackenzie,Prashi Jain,Conrad Santini,Idris O Raji,Damian W Young,Michelle Nguyen,James Campbell,Bethany C Taylor,Prasanna Kandel,Matthew V Holt,Navneet K Venugopal,Errol L G Samuel,Nicolas L Young,Steven Liu

doi:10.1038/s41598-020-80588-4

Abstract

Despite the established roles of the epigenetic factor UHRF1 in oncogenesis, no UHRF1-targeting therapeutics have been reported to date. In this study, we use fragment-based ligand discovery to identify novel scaffolds for targeting the isolated UHRF1 tandem Tudor domain (TTD), which recognizes the heterochromatin-associated histone mark H3K9me3 and supports intramolecular contacts with other regions of UHRF1. Using both binding-based and function-based screens of a ~ 2300-fragment library in parallel, we identified 2,4-lutidine as a hit for follow-up NMR and X-ray crystallography studies. Unlike previous reported ligands, 2,4-lutidine binds to two binding pockets that are in close proximity on TTD and so has the potential to be evolved into more potent inhibitors using a fragment-linking strategy. Our study provides a useful starting point for developing potent chemical probes against UHRF1.

Highlights

DNA methylation at gene promoters is associated with transcriptional r epression[1] and erroneous DNA methylation marks are linked to cancer development[2]
To identify compounds that block this internal tandem Tudor domain (TTD):polybasic region (PBR) interaction, we developed an assay using AlphaScreen (Amplified Luminescent Proximity Homogeneous Assay, Perkin Elmer) technology that detects the interaction between biotinylated-AviTag-N-UHRF1 and FLAG-C-UHRF1 (Fig. 1A,C)
Despite being an attractive drug target, no highly potent UHRF1-targeting cancer therapeutics or chemical probes have been developed to date

Summary

Introduction

DNA methylation at gene promoters is associated with transcriptional r epression[1] and erroneous DNA methylation marks are linked to cancer development[2]. The TTD makes functional intramolecular interactions with the polybasic region (PBR; aa 647–678) and the linker (L2) between TTD and PHD domains (Fig. 1A) that control UHRF1 conformational s tates[9,10,27,32,33,34,38], and it can drive high affinity interaction with DNA ligase 1 (LIG1)[39], which joins the lagging strand Okazaki fragments that are generated during DNA replication and prevents the formation of “nicked” DNA and genetic m utations[40] Given these important roles, compounds that target UHRF1-TTD activities could be useful chemical probes for studying UHRF1 functions and determining which domain contributes to cancer.

Methods

Results

Conclusion