Design, Synthesis and Biological Evaluation of 7‑(1-Methyl‑1H‑indole-3-yl)‑5H‑pyrrolo[2,3‑b]pyrazine Derivatives as Novel Covalent pan-FGFR Inhibitors to Overcome Clinical Resistance

Aberrant activation of fibroblast growth factor receptors (FGFRs) plays a critical role in tumorigenesis across multiple cancer types, driving the development of various FGFR inhibitors. Despite clinical advances, therapeutic efficacy remains limited by the emergence of drug resistance, primarily mediated by gatekeeper mutations in FGFRs. To overcome this challenge, we designed and synthesized a novel series of 7-(1-methyl-1H-indole-3-yl)-5H-pyrrolo[2,3-b]pyrazine derivatives as covalent pan-FGFR inhibitors targeting both wild-type and gatekeeper mutants. Compound 9p demonstrated potent nanomolar inhibitory activity against FGFR1–3 and gatekeeper mutants in biochemical and cellular assays. Structural characterization using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) and X-ray crystallography confirmed covalent binding of 9p to FGFR1. Additionally, 9p showed significant in vivo antitumor efficacy in nude mice bearing the RT112 bladder cancer xenograft model. These findings establish 9p as a promising lead for further development of FGFR-targeted anticancer therapies.