Deciphering the resistance mechanism of RET kinase mutant against vandetanib and nintedanib using molecular dynamics simulations

Abstract

The RET protein is a transmembrane receptor tyrosine kinase (RTK) whose oncogenic mutations or fusions are closely related to human cancers such as thyroid and non-small cell lung cancer. Vandetanib as a clinical-approved protein-tyrosine kinase inhibitor (TKI) exhibits anti-cancer efficacy by blocking the RET ATP-binding site, but drug resistance was observed for the RETG810A mutant. Recent studies have identified another TKI nintedanib as an effective molecule to inhibit vandetanib-resistant RETG810A. However, there is no clear evidence of why nintedanib and vandetanib displayed different inhibitory activities towards RETG810A. Here, we exploited molecular dynamic (MD) simulations to compare the interactions of the RETG810A mutant with nintedanib and vandetanib. A higher structural flexibility of the activation loop was observed in the nintedanib-bound RETG810A, which may result in discrepant autophosphorylation activity in the nintedanib- and vandetanib-bound RET kinase, causing differentiated pharmacological effects of the two compounds. Molecular mechanics/Poisson-Bolzmann surface area method suggested that nintedanib had a higher affinity towards RETG810A over vandetanib, accounting for its better inhibitory effect as an ATP-competitive compound. These results depicted the underlying mechanism for the different inhibitory efficacy of nintedanib and vandetanib on RETG810A from both conformational and energetic aspects. Furthermore, we also found that both compounds maintained the ‘DFG-in, αC-helix-in, and activation loop-open’ conformation of RETG810A, which is the characteristic of the active state. Together, our results provide comprehensive mechanistic insights into nintedanib’s capability in inhibiting vandetanib-resistant RET mutant and enlighten future structural-based optimisation of RET TKIs to overcome drug resistance.