Design and optimization of potent, selective, and peripherally acting JNK3 inhibitors for chronic kidney disease

Chronic kidney disease (CKD) is characterized by progressive fibrosis and podocyte injury driven in part by TGF-β-dependent MAPK signaling. Although pan-JNK inhibition has shown antifibrotic efficacy, isoform selectivity and safety remain major challenges. Herein, we report the design, synthesis, and biological evaluation of a new class of 2-aryl-3-pyrimidin-4-yl-1H-indole derivatives as potent and peripherally acting JNK3 inhibitors for CKD. A modular synthetic strategy enabled systematic diversification of the indole core and pyrimidine substituents, allowing detailed structure-activity relationship studies. Selective optimization of hydroxy substitution and aryl groups yielded multiple low-nanomolar JNK3 inhibitors. Among them, 50b (IC₅₀ = 2.08 nM) and 50d (IC₅₀ = 1.44 nM) emerged as the most potent compounds. Induced-fit docking supported conserved hinge binding to Met149 and highlighted enhanced hydrophobic engagement and sulfur-π interactions for both compounds. Kinome-wide profiling against a 50-kinase panel demonstrated a largely restricted activity spectrum with meaningful selectivity over JNK1, JNK2, and p38α. In human podocytes stimulated with TGF-β1, selected compounds effectively suppressed c-Jun phosphorylation without cytotoxicity. Notably, 50b showed the most pronounced reduction of profibrotic markers (COL1A1 and PAI-1) and robust restoration of E-cadherin expression, indicating functional protection against podocyte injury. Both 50b and 50d exhibited favorable plasma stability, moderate microsomal stability, and low BBB permeability in BBB-PAMPA, consistent with SwissADME predictions. Collectively, this study identifies 50b and 50d as promising lead candidates and establishes the 2-aryl-3-pyrimidin-4-yl-1H-indole scaffold as a viable chemotype for developing selective, non-CNS-penetrant JNK3 inhibitors for CKD.