Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors

Abstract

It has been shown that dysfunction in tight regulation of DNA repair pathways can induce various syndromes, increase the risk of cancer, and trigger neurological defect. However, there are cases where inhibition of DNA repair process is necessary. For example, after treating cancer cells with radiotherapy, it is essential to inhibit DNA repair function of the radiation-induced cancer cells for successful apoptosis. Therefore, the key is to target a protein that is responsible for controlling the rapid and proper resolution of DNA strand breaks. The recent discovery of CCNA2 (cyclin A2), the main mammalian S-phase cyclin, as a regulator of neuronal genomic stability and DNA repair positioned cyclin A2 as a potential therapeutic target for DNA repair dysfunction and as a radiation sensitizer. Thus, identifying small molecule regulators of cyclin A2 activity carries significant potential to regulate diverse cellular processes in both ageing/neurodegeneration and in cancer. No functional modulators of cyclin A2 are known to date. Here, we identified a potential allosteric cyclin A2 ligand binding pocket based on high-resolution structural data. Molecular dynamics simulations were used to generate diverse binding pocket conformations for application of the relaxed complex scheme. We then used structure-based virtual screening to find potential cyclin A2 inhibitors. Based on a consensus score of docked poses from Glide and AutoDock Vina, we identified about 60 promising hit compounds, where all PAINS scaffolds were removed from consideration. A biochemical luminescence assay of cyclin A2 function was used for experimental verification and identified three nanomolar inhibitors of cyclin A2. These novel cyclin A2 inhibitors are the first reported cyclin A2 inhibitors that do not target the cyclin A2 - CDK 2 protein-protein interface.