Deciphering the Atomic Mechanisms of Third-Generation Bisteric mTOR Inhibitors through Comparative Microsecond Molecular Dynamics Simulations

The mammalian target of rapamycin (mTOR) is a central regulator of cell growth and a key cancer therapeutic target. Although first-generation allosteric and second-generation ATP-competitive mTOR inhibitors have been developed, resistance due to mTOR mutations remains a challenge. Third-generation bisteric inhibitors, which bridge both allosteric and orthosteric sites via a flexible linker, offer a promising solution, yet their atomic mechanisms and optimal linker design are not fully understood. Here, we performed microsecond molecular dynamics simulations on six mTOR-bisteric inhibitor complexes. Our results reveal that (1) steric inhibitors stabilize the catalytic cleft of mTOR, (2) inhibitor potency correlates with cleft closure, and (3) optimal linker length promotes a more closed and stable conformation, enhancing binding affinity. These findings provide atomic-level insights to guide the rational design of next-generation mTOR inhibitors.