Design, synthesis, biological and computational evaluation of Thieno[3,2-d]pyrimidine-based inhibitors of JAK3 kinase

JAK3 is a non-receptor tyrosine kinase that plays an important role in immune signaling pathways. It has long been indicated as a potential target for autoimmune diseases. In this work, a set of 28 novel JAK3 inhibitors were designed around a thieno[3,2-d]pyrimidine core, with aromatic moieties at the 2-position, and a range of alkyl linkers connected to electrophillic groups at the 4-position. Structure-based design has been employed in an attempt to maximize activity through direct reaction of the inhibitor electrophile and Cys909 residue located within the JAK3 active site. We identified the acrylamide containing compound 42 as a potent inhibitor of JAK3, with an IC₅₀ of 6.2 nM and selectivity of 23.4-fold over the related JAK2 enzyme. This compares to 1.4 nM and 53.1-fold, respectively, for the 1st generation JAK3 inhibitor Tofacitinib. 42 also demonstrated good selectivity against 10 diverse kinases at a screening concentration of 1 μM, a low logD_7.4 of 1.51 and good phosphate buffer solubility (1030.8 μg/ml). Computational analysis was undertaken to help rationalize the SAR in the form of molecular dynamics simulations and quantum chemical cluster calculations of electrophile-nucleophile reactivity.