Development of Selective Covalent Janus Kinase 3 Inhibitors

Abstract

The Janus Kinases (JAKs) and their downstream effectors Signal Transducer and Activator of Transcription proteins (STATs) form a critical immune cell signaling circuit, which is of fundamental importance in innate immunity, inflammation and hematopoiesis and dysregulation is frequently observed in immune disease and cancer. The high degree of structural conservation of the JAK ATP binding pockets has posed a considerable challenge to medicinal chemists seeking to develop highly selective inhibitors as pharmacological probes and as clinical drugs. Here we report the discovery and optimization of 2,4-substituted pyrimidines as covalent JAK3 inhibitors that exploit a unique cysteine (Cys909) residue in JAK3. Investigation of structure-activity-relationship (SAR) utilizing biochemical and transformed Ba/F3 cellular assays resulted in identification of potent and selective inhibitors such as compounds 9 and 45. A 2.9 Å co-crystal structure of JAK3 in complex with 9 confirms the covalent interaction. Compound 9 exhibited decent pharmacokinetic properties and is suitable for use in vivo. These inhibitors provide a set of useful tools to pharmacologically interrogate JAK3-dependent biology.

Structure-guided development of covalent TAK1 inhibitors

“…Addition of a 6-amino group, which provides an additional hydrogen bond donor, did not help the hinge binding as in 1 but instead abrogated anti-TAK1 activity ( 16 ). Cyclization of the substitutions at 4- and 5-positions with a fused ring is a common strategy to optimize 2,4-disubstituted pyrimidine scaffolds [36]. However, the pyrrolopyrimidine core led to reduced activity in this case ( 17 ).…”

“…Switching the substitutions from 4- to 3-position slightly increased potency ( 20 , 21 ). Next we exploited 1-substituted-pyrazol-3-amine tails, which often maintain the potency for covalent inhibitors while reducing interaction with non-covalent off-targets compared to the aniline tails [36]. 1-methyl-1- H -pyrazol-3-amine ( 20 ) showed similar potency but decreased selectivity compared to 19 .…”

Selective JAK3 Inhibitors with a Covalent Reversible Binding Mode Targeting a New Induced Fit Binding Pocket

“…Very recently, Goedken et al. (2015) and Tan et al. (2015) reported irreversible JAK3 inhibitors showing good isoform selectivity but also potent off-target activity in the remaining kinome.…”

Discovery of host-targeted covalent inhibitors of dengue virus

“…Targeting functionally important cysteines has recently enabled the development of selective covalent inhibitors of a number of different human kinases (Backus et al, 2016; Cohen et al, 2007; Honigberg et al, 2010; Kwiatkowski et al, 2014; Lanning et al, 2014; Tan et al, 2015; Wu et al, 2014), as well as proteases (van der Linden et al, 2016), phosphatases, and E2 ubiquitin transferases (Singh et al, 2011). …”