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

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.

Discovery of Anti-Hypertensive Oligopeptides from Adlay Based on In Silico Proteolysis and Virtual Screening

“…Then a 1000 ps NPT simulation was conducted, and pressure was coupled to 1.0 atm using the Parrinello−Rahman method. Upon completion of the two equilibration phases, the position restraints were released and the MD was performed for 15 ns with the v-rescale method and Parrinello–Rahman method [51,52]. The snapshot structures and energies were saved for every 10 ps.…”

The Role of the Core Non-Homologous End Joining Factors in Carcinogenesis and Cancer

“…However, it was recently published that SCR7 is neither a selective nor potent inhibitor of human LIG4, which brings this inhibitor into question [ 249 ]. Utilizing the crystal structure of the Lig4/XRCC4 complex, a recent study identified a compound that was able to prevent Lig4 binding to XRCC4 in vitro, suggesting that blocking the ability of Lig4 to interact with XRCC4 is a potential viable drug target [ 250 ]. Finally, the compound L189 was identified that competitively inhibits DNA Ligases I, III, and IV [ 251 ].…”

Druggable binding sites in the multicomponent assemblies that characterise DNA double-strand-break repair through non-homologous end joining

“…Disrupting the interaction between LigIV and XRCC4 through modulation of the PPI interface is therefore a challenging prospect, and design of a successful inhibitor might instead focus on stabilising the pre-rotational state of XRCC4 to prevent the conformational change associated with LigIV binding. Stabilising the unbound LigIV BRCT domains was an approach taken recently by Menchon and colleagues where they used virtual screening against the LigIV C-terminal clamp domain resulting in the discovery of molecule #3101, which they showed inhibited LigIV–XRCC4 interaction in vitro [ 110 ], thus presenting a promising future route for the development of an allosteric NHEJ inhibitor.…”