Insight into ponatinib resistance mechanisms in rhabdomyosarcoma caused by the mutations in FGFR4 tyrosine kinase using molecular modeling strategies.

Novel efficacious treatment of Rhabdomyosarcoma (RMS) with less toxicity has yet to emerge. Genomic analysis of RMS has reported that the receptor tyrosine kinase FGFR4 is highly expressed and frequently mutated in the tumor tissue. The V550E/L and N535D/K mutations of FGFR4 in RMS can lead to strong drug resistance to almost all of the type-I inhibitors. Previous report has demonstrated the type-II inhibitor ponatinib is the most potentially effective agent for RMS but still hard to starboard the V550E/L mutants. In this case, an ensemble of molecular modeling strategies was employed to theoretically uncover the resistance mechanisms. The binding free energy calculation results predicted by various strategies show that the V550E/L rather than N535D/K mutations indeed weaken the binding affinity of ponatinib, which are in good agreement with the experimental observations. Subsequently, the energy decomposition analysis mapped a knock-on effect on the diverse energy components of some key residues. Moreover, it is of great importance to report that there is an effective channel for type-II inhibitors sliding along the A-loop to prevent FGFR4 from phosphorylation and activation. Our results provide new insight into drug binding process and guide the development of effective inhibitors to surmount drug resistance in RMS.