Structure-Guided Evolution of Potent and Selective CHK1 Inhibitors through Scaffold Morphing

Abstract

Pyrazolopyridine inhibitors with low micromolar potency for CHK1 and good selectivity against CHK2 were previously identified by fragment-based screening. The optimization of the pyrazolopyridines to a series of potent and CHK1-selective isoquinolines demonstrates how fragment-growing and scaffold morphing strategies arising from a structure-based understanding of CHK1 inhibitor binding can be combined to successfully progress fragment-derived hit matter to compounds with activity in vivo. The challenges of improving CHK1 potency and selectivity, addressing synthetic tractability, and achieving novelty in the crowded kinase inhibitor chemical space were tackled by multiple scaffold morphing steps, which progressed through tricyclic pyrimido[2,3-b]azaindoles to N-(pyrazin-2-yl)pyrimidin-4-amines and ultimately to imidazo[4,5-c]pyridines and isoquinolines. A potent and highly selective isoquinoline CHK1 inhibitor (SAR-020106) was identified, which potentiated the efficacies of irinotecan and gemcitabine in SW620 human colon carcinoma xenografts in nude mice.

Discovery of 3-Alkoxyamino-5-(pyridin-2-ylamino)pyrazine-2-carbonitriles as Selective, Orally Bioavailable CHK1 Inhibitors

“…During the evolution of the lead compound 6 by scaffold morphing from a purine fragment hit, 20 pyridines represented by compound 7 had been prepared and evaluated. 19 Compound 7 lacked the potent cellular activity or cellular selectivity of 6 but showed good microsomal stability and equivalent permeability (Figure 2, Table 1). We therefore investigated hybridization of the two scaffolds represented by 6 and 7 to give novel 3-alkoxyamino-5-(pyridin-2-ylamino)pyrazine-2-carbonitriles that could allow the maintenance of the cellular potency and selectivity of 6 while conferring the improved in vitro ADME properties observed for 7 .…”

“…The importance of the cyanopyrazine and aminoalkoxy groups in binding to selectivity determinants in the CHK1 ATP site had previously been shown by the X-ray structure of 6 complexed with CHK1. 19 The 4-aminomethyl substituent retained in the hybrid molecule was anticipated to generate a pseudobicycle to replace the isoquinoline of 6 through forming an intramolecular hydrogen bond to the adjacent ester. Compound 8 showed equivalent potency and cellular activities to 6 .…”

“…For CHK1, specificity of binding in the ATP site is aided by the presence of structural features, such as protein-bound water molecules and polar residues deep in the ATP pocket, that are unique to CHK1 and are effectively targeted by the 5-amino-3-(alkoxyamino)pyrazine-2-carbonitrile group. 19,20,31,33,42 …”

“…The enantiomerically pure 1-(dimethylamino)propan-2-ols were prepared from the appropriate enantiomer of glycidol as previously described. 19 …”

“…N 2 was passed through a mixture of 49 (0.532 g, 2.38 mmol), 30 (19) (0.526 g, 2.38 mmol), xantphos (0.275 g, 0.476 mmol), Pd 2 dba 3 (0.218 g, 0.238 mmol), and Cs 2 CO 3 (1.55 g, 0.593 mmol) in dioxane (24 mL) for 10 min. The mixture was heated at 100 °C for 17 h. The cooled mixture was absorbed onto SCX-II acidic ion-exchange resin (20 g) and eluted with MeOH/CH 2 Cl 2 and then with 2 M NH 3 in MeOH and finally with 7 M NH 3 in MeOH.…”