Background: Given the diverse roles of cyclin A2 both in cell cycle regulation and in
DNA damage response, identifying small molecule regulators of cyclin A2 activity carries significant
potential to regulate diverse cellular processes in both ageing/neurodegeneration and in cancer.
Objective: Based on cyclin A2’s recently discovered role in DNA repair, we hypothesized that
small molecule inhibitors that were predicted to bind to both cyclin A2 and CDK2 will be useful
as a radiosensitizer of cancer cells. In this study, we used structure-based drug discovery to find
inhibitors that target both cyclin A2 and CDK2.
Methods: 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 dual cyclin A2 and CDK2 inhibitors. Based on a consensus score of
docked poses from Glide and AutoDock Vina, we identified about 40 promising hit compounds,
where all PAINS scaffolds were removed from consideration. A biochemical luminescence assay
of cyclin A2-CDK2 function was used for experimental verification.
Results: Four lead inhibitors of cyclin A2-CDK2 complex have been identified using a relaxed complex
scheme virtual screen have been verified in a biochemical luminescence assay of cyclin A2-
CDK2 function. Two of the four lead inhibitors had inhibitory concentrations in the nanomolar range.
Conclusion: The four cyclin A2-CDK2 complex inhibitors are the first reported inhibitors that
were specifically designed not to target the cyclin A2-CDK2 protein-protein interface. Overall, our
results highlight the potential of combined advanced computational tools and biochemical verification
to discover novel binding scaffolds.