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Structure-Based Virtual Ligand Screening on the XRCC4/DNA Ligase IV Interface
Grégory Menchon1,2, Oriane Bombarde1,2, Mansi Trivedi1
1Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France.
Abstract:
The association of DNA Ligase IV (Lig4) with XRCC4 is essential for repair of DNA double-strand breaks (DSBs) by Non-homologous end-joining (NHEJ) in humans. DSBs cytotoxicity is largely exploited in anticancer therapy. Thus, NHEJ is an attractive target for strategies aimed at increasing the sensitivity of tumors to clastogenic anticancer treatments. However the high affinity of the XRCC4/Lig4 interaction and the extended protein-protein interface make drug screening on this target particularly challenging. Here, we conducted a pioneering study aimed at interfering with XRCC4/Lig4 assembly. By Molecular Dynamics simulation using the crystal structure of the complex, we first delineated the Lig4 clamp domain as a limited suitable target. Then, we performed in silico screening of ~95,000 filtered molecules on this Lig4 subdomain. Hits were evaluated by Differential Scanning Fluorimetry, Saturation Transfer Difference-NMR spectroscopy and interaction assays with purified recombinant proteins. In this way we identified the first molecule able to prevent Lig4 binding to XRCC4 in vitro. This compound has a unique tripartite interaction with the Lig4 clamp domain that suggests a starting chemotype for rational design of analogous molecules with improved affinity.
Insights
Researchers identified the first molecule that disrupts the DNA repair protein complex XRCC4/DNA Ligase IV (Lig4). This finding offers a new strategy to enhance cancer therapy by targeting Non-homologous end-joining (NHEJ) DNA repair.
Area of Science:
- Biochemistry
- Molecular Biology
- Drug Discovery
Background:
- DNA Ligase IV (Lig4) and XRCC4 form a complex crucial for repairing DNA double-strand breaks (DSBs) via Non-homologous end-joining (NHEJ).
- Exploiting DSB cytotoxicity is a key strategy in anticancer therapy, making NHEJ a potential drug target.
- The strong interaction between XRCC4 and Lig4 presents a challenge for drug screening.
Purpose of the Study:
- To identify molecules that interfere with the XRCC4/Lig4 complex assembly.
- To develop novel therapeutic strategies for enhancing cancer treatment efficacy.
Main Methods:
- Molecular Dynamics simulations to identify suitable target regions on Lig4.
- In silico screening of approximately 95,000 molecules against the Lig4 clamp domain.
- In vitro validation using Differential Scanning Fluorimetry, Saturation Transfer Difference-NMR, and protein interaction assays.
Main Results:
- The Lig4 clamp domain was identified as a viable target for inhibiting XRCC4/Lig4 interaction.
- The first molecule capable of preventing Lig4 binding to XRCC4 in vitro was discovered.
- This molecule exhibits a unique tripartite interaction with the Lig4 clamp domain.
Conclusions:
- A novel chemotype was identified for the rational design of inhibitors targeting the XRCC4/Lig4 complex.
- This discovery opens new avenues for developing drugs to sensitize tumors to clastogenic anticancer treatments by inhibiting NHEJ.
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