Understanding the Kinetic Mechanism of Ligands Stabilizing the RAS–CYPA Interaction

Molecular
glues, including protein degraders and protein–protein
interaction (PPI) stabilizers, have emerged as a new paradigm of drug
design for regulating interactions between biomacromolecules; yet
it is still a challenge for rational design of molecular glues. KRAS,
as a prevalent oncogenic driver, is notoriously difficult to target
by traditional small molecular drugs due to its challenging binding
surface and frequent mutations. Although the small molecular drug
RMC7977 has been designed as a PPI stabilizer for stabilizing the
inherently weak RAS–CYPA interaction, the precise molecular
mechanism underlying its stabilization effect and selectivity difference
requires a deeper understanding. To this end, we leverage an integrated
computational strategy combining molecular dynamics (MD) simulation,
end-point binding free-energy calculation, and enhanced sampling technologies
to elucidate the dynamic characteristics of RAS–ligand–CYPA
interactions. Our result exhibits a high correlation between the predicted
binding affinities and the experimental observations, demonstrating
that RMC7977, acting as a strong PPI stabilizer, significantly enhances
the stability of the KRAS–CYPA interaction, where, by delicately
remodeling the protein–protein interface, the drug optimizes
various interactions. Moreover, the results also uncover the dynamic
process of stabilizer-mediated KRAS–CYPA stabilization and
the mechanistic origin of the binding selectivity. This study provides
essential molecular-level insights into RMC7977’s function
and offers a valuable computational framework for evaluating the stabilization
effect of ligands targeting the KRAS–CYPA and other challenging
PPI systems.