Structure-Based Virtual Ligand Screening on the XRCC4/DNA Ligase IV Interface

• Published in: Scientific reports 2016-03, Vol.6 (1), p.22878-22878, Article 22878
• Main Authors: Menchon, Grégory, Bombarde, Oriane, Trivedi, Mansi, Négrel, Aurélie, Inard, Cyril, Giudetti, Brigitte, Baltas, Michel, Milon, Alain, Modesti, Mauro, Czaplicki, Georges, Calsou, Patrick
• Format: Article
• Language: English
• Subjects: 101/6; 631/154; 631/154/1435; 631/154/1435/2418; Affinity; Binding Sites; Biochemistry, Molecular Biology; Cancer; Crystal structure; Cytotoxicity; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - metabolism; DNA Breaks, Double-Stranded; DNA damage; DNA ligase (ATP); DNA Ligase ATP - chemistry; DNA Ligase ATP - metabolism; DNA Repair; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - metabolism; Drug screening; Humanities and Social Sciences; Humans; Life Sciences; LIG4 protein; Ligands; Magnetic resonance spectroscopy; Models, Molecular; Molecular Conformation; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; multidisciplinary; NMR; Non-homologous end joining; Nuclear magnetic resonance; Protein Binding; Protein Interaction Domains and Motifs; Reproducibility of Results; Scanning; Science; Structural Biology; Structure-Activity Relationship; Tumors
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep22878

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.