Process Development and Scale-Up of RLY-2139: A Selective CDK2 Inhibitor Targeting ER+/HER2– Breast Cancer

RLY-2139 is a potent and selective orthosteric CDK2/Cyclin E inhibitor in development for the treatment of ER+/HER2– breast cancer. It showed an on target IC 50 of 4 nM for CDK2/CycE and good biochemical selectivity, e.g., 100× for CDK1/CycB, 320× for CDK6/CycD3, and 2400× for CDK9/CycT1. We report the route optimization and scale-up of a robust, cGMP-compliant synthesis for RLY-2139 to support preclinical and early clinical supply. The convergent route couples two advanced intermediates 1 and 2 followed by deprotections and functional group transformations to deliver the drug substance. Key optimizations included replacing T3P with CMPI to address operational constraints, substituting HF·TEA with aqueous TBAF to improve safety, and employing N, N′ -disuccinimidyl carbonate (DSC) in place of phenyl chloroformate to eliminate phenolic byproducts and enable telescoping. Rearranging late-stage steps improved impurity control and process robustness, while scalable recrystallization replaced column chromatography. The optimized sequence was successfully demonstrated on multi-kilogram scale, delivering 14.7 kg of crystalline RLY-2139 (67% overall yield from 1 ) with >99.9% chemical purity (LCAP) and 100% chiral purity.