Deciphering the Selectivity of CBL-B Inhibitors Using All-Atom Molecular Dynamics and Machine Learning

We employ a combination of accelerated molecular dynamics and machine learning to unravel how the dynamic characteristics of CBL-B and C–CBL confer their binding affinity and selectivity for ligands from subtle structural disparities within their binding pockets and dissociation pathways. Our predictive model of dissociation rate constants (koff) demonstrates a moderate correlation between predicted koff and experimental IC50 values, which is consistent with experimental koff and τ-random accelerated molecular dynamics (τRAMD) results. By employing a linear regression of dissociation trajectories, we identified key amino acids in binding pockets and along the dissociation paths responsible for activity and selectivity. These amino acids are statistically significant in achieving activity and selectivity and contribute to the primary structural discrepancies between CBL-B and C-CBL. Moreover, the binding free energies calculated from molecular mechanics with generalized Born and surface area solvation (MM/GBSA) highlight the ΔG difference between CBL-B and C-CBL. The koff prediction, together with the key amino acids, provides important guides for designing drugs with high selectivity.