Discovery of a covalent FGFR2-selective inhibitor overcoming clinically-acquired resistance mutations

Abnormal activation of fibroblast growth factor receptor 2 (FGFR2) drives tumorigenesis in various cancers. Clinical use of pan-FGFR inhibitors is limited due to emerging acquired resistance mutations within the FGFR2 kinase domain and adverse effects associated with FGFR1/4 off-target inhibition. Herein, we describe the structure-based discovery of LC-F2-1, an FGFR2-selective inhibitor that demonstrates irreversible covalent binding to the P-loop. Cellular assays confirm the high selectivity of LC-F2-1 for FGFR2 over FGFR1 and FGFR4, along with potent inhibition of FGFR2 signaling. LC-F2-1 maintains strong activity against clinically observed FGFR2 resistance variants, including gatekeeper, molecular brake, and activation loop variants. X-ray crystallography reveals conformational rearrangement of the kinase domain by LC-F2-1, which overcomes the recalcitrant V565F gatekeeper mutation. In vivo, LC-F2-1 induces tumor regression in xenograft models harboring FGFR2 resistance mutations without affecting serum phosphate levels. In this work, we identify LC-F2-1 as a therapeutic candidate for FGFR2-driven cancers. This study reports the structure-based discovery of LC-F2-1, a selective FGFR2 inhibitor that overcomes clinically observed resistance mutations in cancers. Its co-crystal structure with FGFR2V565F reveals how it may restore drug sensitivity.