Design, Synthesis, and Biological Evaluation of Indolin-2-one Derivatives as Novel Covalent Pan-FGFR Inhibitors for Overcoming Clinical Resistance

Abstract Oncogenic FGFR alterations drive the development of multiple cancers. However, acquired resistance to clinically approved inhibitors mediated by gatekeeper and molecular brake mutations poses a major therapeutic challenge. Herein, we describe the structure-based discovery of (Z)-3-(amino(phenyl)methylene)indolin-2-one derivatives as potent covalent pan-FGFR inhibitors. The representative compound, 9v, displayed high potency against FGFR1/2/3/4 (IC50 = 8.6, 5.4, 4.4, and 6.9 nM, respectively) and potent antiproliferative effects across a panel of FGFR-driven cancer cell lines (IC50 = 0.3−6.1 nM). Notably, 9v retained high efficacy against common resistance mutations, including the gatekeeper (FGFR1 V561M, FGFR2 V564F, and FGFR3 V555M) and “molecular brake” (FGFR2 N549K) variants, with IC50 values of <0.1 nM. Covalent modification of FGFR3 by 9v was confirmed through MALDI-TOF-MS and LC−MS/MS-based site mapping. Furthermore, 9v exhibited significant antitumor efficacy in an RT112/84 bladder cancer xenograft model, providing a promising strategy to overcome resistance in FGFR-targeted therapy.