Fulcrum Occupancy–Leverage Perturbation Strategy Enables Rapid Discovery of Potent CDK2–Cyclin A2 Interaction Inhibitors

Abstract

AbstractTraditional strategies for developing small‐molecule inhibitors of protein–protein interactions (PPIs) are time‐consuming and often yield low success rates due to the flat and dynamic interfaces of PPIs. To enable the rapid design of highly potent PPI inhibitors, we proposed a novel strategy named “Fulcrum Occupancy–Leverage Perturbation (FOLP)”. In this strategy, high‐affinity fragments serve as the “Fulcrum” by binding to the orthosteric pocket, while suitable moieties extend into allosteric sites near the PPI interface as “Leverage” to modulate the protein–protein interaction. As a proof of concept, the potent CDK2–Cyclin A2 PPI inhibitor LC‐K2CAin‐3, which fits the “FOLP” paradigm, was discovered with an IC50 of 32.1 nM for inhibiting the interaction. Molecular dynamics simulations and cryptic pocket identification were employed, revealing the activation loop (A‐loop) of CDK2 was flexible and targetable. X‐ray crystallography and hydrogen deuterium exchange mass spectrometry (HDX‐MS) analysis showed that LC‐K2CAin‐3 indeed bound to and stabilized the A‐loop. LC‐K2CAin‐3 effectively inhibited the CDK2–Cyclin A2 interaction in CDK2 highly expressed melanoma cells, leading to cell cycle arrest and apoptosis and inhibition of CDK2 mediated signaling. In conclusion, the “FOLP” strategy offers a novel approach for PPI inhibitor discovery and could accelerate the development of PPI inhibitors.