Revealing Acquired Resistance Mechanisms of Kinase-Targeted Drugs Using an on-the-Fly, Function-Site Interaction Fingerprint Approach

Although kinase-targeted drugs have
achieved significant clinical
success, they are frequently subject to the limitations of drug resistance,
which has become a primary vulnerability to targeted drug therapy.
Therefore, deciphering resistance mechanisms is an important step
in designing more efficacious, antiresistant drugs. Here we studied
two FDA-approved kinase drugs: Crizotinib and Ceritinib, which are
first- and second-generation anaplastic lymphoma kinase (ALK) targeted
inhibitors, to unravel drug-resistance mechanisms. We used an on-the-fly,
function-site interaction fingerprint (on-the-fly Fs-IFP) approach,
combining binding free-energy surface calculations with the Fs-IFPs.
Establishing the potentials of mean force and monitoring the atomic-scale
protein–ligand interactions, before and after L1196M-induced
drug resistance, revealed insights into drug-resistance/antiresistant
mechanisms. Crizotinib prefers to bind the wild-type ALK kinase domain,
whereas Ceritinib binds more favorably to the mutated ALK kinase domain,
in agreement with experimental results. We determined that ALK kinase–drug
interactions in the region of the front pocket are associated with
drug resistance. Additionally, we find that the L1196M mutation does
not simply alter the binding modes of inhibitors but also affects
the flexibility of the entire ALK kinase domain. Our work provides
an understanding of the mechanisms of ALK drug resistance, confirms
the usefulness of the on-the-fly Fs-IFP approach, and provides a practical
paradigm to study drug-resistance mechanisms in prospective drug discovery.