Structure-Based Design of 4‑(1-Methyl‑1H‑indol-3-yl)pyrimidin-2-amine Derivatives as the First Covalent FGFR3 Selective Inhibitors

Aberrant fibroblast growth factor receptor 3 (FGFR3)
activation
drives bladder carcinogenesis in humans, but currently approved pan-FGFR
inhibitors lack FGFR3 isoform selectivity and fail to counter clinically
acquired resistance mutations (e.g., FGFR3 V555M/L). Herein, we report
the structure-based drug design of 4-(1-methyl-1H-indol-3-yl)pyrimidin-2-amine derivatives as the first covalent FGFR3
selective inhibitors. The representative compound 10s displayed high potency against FGFR3 (IC50 = 6.8 nM)
and 5–60-fold selectivity over FGFR1/2/4. It was also effective
against the common clinically acquired FGFR3V555M resistance
mutation with an IC50 value of 19.2 nM. Furthermore, 10s exhibited strong antiproliferative effects in FGFR3-driven
RT112/84 cells (IC50 = 9.2 nM). Structural characterization
using MALDI-TOF-MS and X-ray crystallography confirmed covalent binding
of 10s to FGFR3. Compound 10s also showed
significant antitumor efficacy in the RT112/84 bladder cancer xenograft
model, offering a promising compound to address both selectivity and
resistance in FGFR3-targeted therapy.