Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the
Satomi Kori1, Yuki Shibahashi2, Toru Ekimoto2
1Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Abstract:
The accumulation of epigenetic alterations is one of the major causes of tumorigenesis. Aberrant DNA methylation patterns cause genome instability and silencing of tumor suppressor genes in various types of tumors. Therefore, drugs that target DNA methylation-regulating factors have great potential for cancer therapy. Ubiquitin-like containing PHD and RING finger domain 1 (UHRF1) is an essential factor for DNA methylation maintenance. UHRF1 is overexpressed in various cancer cells and down-regulation of UHRF1 in these cells reactivates the expression of tumor suppressor genes, thus UHRF1 is a promising target for cancer therapy. We have previously shown that interaction between the tandem Tudor domain (TTD) of UHRF1 and DNA ligase 1 (LIG1) di/trimethylated on Lys126 plays a key role in the recruitment of UHRF1 to replication sites and replication-coupled DNA methylation maintenance. An arginine binding cavity (Arg-binding cavity) of the TTD is essential for LIG1 interaction, thus the development of inhibitors that target the Arg-binding cavity could potentially repress UHRF1 function in cancer cells. To develop such an inhibitor, we performed in silico screening using not only static but also dynamic metrics based on all-atom molecular dynamics simulations, resulting in efficient identification of 5-amino-2,4-dimethylpyridine (5A-DMP) as a novel TTD-binding compound. Crystal structure of the TTD in complex with 5A-DMP revealed that the compound stably bound to the Arg-binding cavity of the TTD. Furthermore, 5A-DMP inhibits the full-length UHRF1:LIG1 interaction in Xenopus egg extracts. Our study uncovers a UHRF1 inhibitor which can be the basis of future experiments for cancer therapy.
Insights
Researchers identified a novel compound, 5-amino-2,4-dimethylpyridine (5A-DMP), that inhibits UHRF1, a key factor in DNA methylation and cancer development. This discovery offers a new avenue for developing targeted cancer therapies.
Area of Science:
- Epigenetics
- Cancer Biology
- Drug Discovery
Background:
- Epigenetic alterations, particularly aberrant DNA methylation, are hallmarks of tumorigenesis, leading to genome instability and tumor suppressor gene silencing.
- Ubiquitin-like containing PHD and RING finger domain 1 (UHRF1) is crucial for DNA methylation maintenance and is overexpressed in many cancers, making it a promising therapeutic target.
Purpose of the Study:
- To identify novel inhibitors targeting the UHRF1 tandem Tudor domain (TTD) to disrupt its interaction with DNA ligase 1 (LIG1).
- To explore the potential of targeting the UHRF1-LIG1 interaction for cancer therapy.
Main Methods:
- In silico screening using molecular dynamics simulations to identify compounds binding to the UHRF1 TTD's arginine-binding cavity.
- X-ray crystallography to determine the binding mode of the identified compound.
- Biochemical assays using Xenopus egg extracts to assess the inhibition of UHRF1:LIG1 interaction.
Main Results:
- 5-amino-2,4-dimethylpyridine (5A-DMP) was identified as a novel compound that binds to the UHRF1 TTD's Arg-binding cavity.
- Crystal structure confirmed the stable binding of 5A-DMP within the target cavity.
- 5A-DMP effectively inhibited the interaction between full-length UHRF1 and LIG1 in vitro.
Conclusions:
- The study identified 5A-DMP as a potent inhibitor of the UHRF1-LIG1 interaction.
- This compound represents a promising starting point for developing new epigenetic drugs for cancer treatment targeting UHRF1.
