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

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

doi:10.1038/s41598-020-80588-4

Cited by 25 publications

(28 citation statements)

References 71 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Since UHRF1 is overexpressed in a wide variety of solid tumours and it is not required in non-replicating cells, its downregulation could be used to overcome the resistance to DNA damaging agents by impairing DNA repair mechanisms. While several approaches have been tested to inhibit the different domains of UHRF1 ( 149 , 150 ), a recent work focused specifically on targeting UHRF1 functions in DNA damage repair ( 151 ). Here it is shown that in prostate cancer cells, the combined treatment with HDAC and PARP inhibitors (SAHA and veliparib) disrupts the interaction between UHRF1 and BRCA1 and decreases UHRF1 and BRCA1 levels, resulting in inhibition of the HR pathway and cell death ( 151 ).…”

Section: Uhrf1 In Dna Damage Response As a Potential Therapeutic Targetmentioning

confidence: 99%

The multi-functionality of UHRF1: epigenome maintenance and preservation of genome integrity

Mancini

Magnani

Macchi

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

During S phase, the cooperation between the macromolecular complexes regulating DNA synthesis, epigenetic information maintenance and DNA repair is advantageous for cells, as they can rapidly detect DNA damage and initiate the DNA damage response (DDR). UHRF1 is a fundamental epigenetic regulator; its ability to coordinate DNA methylation and histone code is unique across proteomes of different species. Recently, UHRF1’s role in DNA damage repair has been explored and recognized to be as important as its role in maintaining the epigenome. UHRF1 is a sensor for interstrand crosslinks and a determinant for the switch towards homologous recombination in the repair of double-strand breaks; its loss results in enhanced sensitivity to DNA damage. These functions are finely regulated by specific post-translational modifications and are mediated by the SRA domain, which binds to damaged DNA, and the RING domain. Here, we review recent studies on the role of UHRF1 in DDR focusing on how it recognizes DNA damage and cooperates with other proteins in its repair. We then discuss how UHRF1’s epigenetic abilities in reading and writing histone modifications, or its interactions with ncRNAs, could interlace with its role in DDR.

show abstract

Section: Uhrf1 In Dna Damage Response As a Potential Therapeutic Targetmentioning

confidence: 99%

The multi-functionality of UHRF1: epigenome maintenance and preservation of genome integrity

Mancini

Magnani

Macchi

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Considering the number of structurally unique protein domains required to coordinate DNA repair on chromatin, it is not surprising that many small molecule inhibitors are available that are potentially capable of disrupting the functions of these domains ( Arrowsmith and Schapira, 2019 ; Mio et al, 2019 ). Chemical or peptide based inhibitors have recently been developed to target several domains that are found within DDR proteins including tandem tudor domains ( Chang L. et al, 2021 ), PRC1 chromodomains ( Stuckey et al, 2016 ), PHD zinc fingers ( Wagner et al, 2012 ), bromodomains ( Filippakopoulos et al, 2010 ) and ubiquitin interacting motifs (UIM) ( Manczyk et al, 2019 ). In addition to their potential clinical applications, the development and availability to researchers of specific inhibitors of these repair-chromatin interactions will be advantageous for untangling and defining the specific contribution of individual contacts within these proteins and their ability to mediate DNA repair.…”

Section: Discussionmentioning

confidence: 99%

Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin

et al. 2021

View full text Add to dashboard Cite

DNA double-strand breaks (DSBs) are hazardous to genome integrity and can promote mutations and disease if not handled correctly. Cells respond to these dangers by engaging DNA damage response (DDR) pathways that are able to identify DNA breaks within chromatin leading ultimately to their repair. The recognition and repair of DSBs by the DDR is largely dependent on the ability of DNA damage sensing factors to bind to and interact with nucleic acids, nucleosomes and their modified forms to target these activities to the break site. These contacts orientate and localize factors to lesions within chromatin, allowing signaling and faithful repair of the break to occur. Coordinating these events requires the integration of several signaling and binding events. Studies are revealing an enormously complex array of interactions that contribute to DNA lesion recognition and repair including binding events on DNA, as well as RNA, RNA:DNA hybrids, nucleosomes, histone and non-histone protein post-translational modifications and protein-protein interactions. Here we examine several DDR pathways that highlight and provide prime examples of these emerging concepts. A combination of approaches including genetic, cellular, and structural biology have begun to reveal new insights into the molecular interactions that govern the DDR within chromatin. While many questions remain, a clearer picture has started to emerge for how DNA-templated processes including transcription, replication and DSB repair are coordinated. Multivalent interactions with several biomolecules serve as key signals to recruit and orientate proteins at DNA lesions, which is essential to integrate signaling events and coordinate the DDR within the milieu of the nucleus where competing genome functions take place. Genome architecture, chromatin structure and phase separation have emerged as additional vital regulatory mechanisms that also influence genome integrity pathways including DSB repair. Collectively, recent advancements in the field have not only provided a deeper understanding of these fundamental processes that maintain genome integrity and cellular homeostasis but have also started to identify new strategies to target deficiencies in these pathways that are prevalent in human diseases including cancer.

show abstract

“…Recently, there has been great interest in identifying compounds that target UHRF1 as potential anticancer agents 42–46 . The mechanism of action of several of these compounds involves disrupting the histone binding activities of the TTD or TTD‐PHD domains 44–46 .…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Recently, there has been considerable interest in UHRF1 as a therapeutic target via inhibiting its DNA and histone reader function through small molecule inhibition 8,42–46 . In particular, several compounds have been identified using high throughput screening strategies that disrupt the histone binding activities of the TTD and TTD‐PHD 44–46 . However, given the distinct cellular functions of UHRF1 and UHRF2 and their frequently dissimilar roles in cancer, each protein must be targeted without affecting the epigenetic reader function of the other.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Molecular investigation of the tandem Tudor domain and plant homeodomain histone binding domains of the epigenetic regulator UHRF2

et al. 2021

View full text Add to dashboard Cite

Ubiquitin‐like containing PHD and ring finger (UHRF)1 and UHRF2 are multidomain epigenetic proteins that play a critical role in bridging crosstalk between histone modifications and DNA methylation. Both proteins contain two histone reader domains, called tandem Tudor domain (TTD) and plant homeodomain (PHD), which read the modification status on histone H3 to regulate DNA methylation and gene expression. To shed light on the mechanism of histone binding by UHRF2, we have undergone a detailed molecular investigation with the TTD, PHD and TTD‐PHD domains and compared the binding activity to its UHRF1 counterpart. We found that unlike UHRF1 where the PHD is the primary binding contributor, the TTD of UHRF2 has modestly higher affinity toward the H3 tail, while the PHD has a weaker binding interaction. We also demonstrated that like UHRF1, the aromatic amino acids within the TTD are important for binding to H3K9me3 and a conserved aspartic acid within the PHD forms an ionic interaction with R2 of H3. However, while the aromatic amino acids in the TTD of UHRF1 contribute to selectivity, the analogous residues in UHRF2 contribute to both selectivity and affinity. We also discovered that the PHD of UHRF2 contains a distinct asparagine in the H3R2 binding pocket that lowers the binding affinity of the PHD by reducing a potential electrostatic interaction with the H3 tail. Furthermore, we demonstrate the PHD and TTD of UHRF2 cooperate to interact with the H3 tail and that dual domain engagement with the H3 tail relies on specific amino acids. Lastly, our data indicate that the unique stretch region in the TTD of UHRF2 can decrease the melting temperature of the TTD‐PHD and represents a disordered region. Thus, these subtle but important mechanistic differences are potential avenues for selectively targeting the histone binding interactions of UHRF1 and UHRF2 with small molecules.

show abstract

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

Cited by 25 publications

References 71 publications

The multi-functionality of UHRF1: epigenome maintenance and preservation of genome integrity

The multi-functionality of UHRF1: epigenome maintenance and preservation of genome integrity

Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin

Molecular investigation of the tandem Tudor domain and plant homeodomain histone binding domains of the epigenetic regulator UHRF2

Contact Info

Product

Resources

About