Structure-Guided Development of Deoxycytidine Kinase Inhibitors with Nanomolar Affinity and Improved Metabolic Stability

Abstract

Recently, we have shown that small molecule dCK inhibitors in combination with pharmacological perturbations of de novo dNTP biosynthetic pathways could eliminate acute lymphoblastic leukemia cells in animal models. However, our previous lead compound had a short half-life in vivo. Therefore, we set out to develop dCK inhibitors with favorable pharmacokinetic properties. We delineated the sites of the inhibitor for modification, guided by crystal structures of dCK in complex with the lead compound and with derivatives. Crystal structure of the complex between dCK and the racemic mixture of our new lead compound indicated that the R-isomer is responsible for kinase inhibition. This was corroborated by kinetic analysis of the purified enantiomers, which showed that the R-isomer has >60-fold higher affinity than the S-isomer for dCK. This new lead compound has significantly improved metabolic stability, making it a prime candidate for dCK-inhibitor based therapies against hematological malignancies and, potentially, other cancers.

ATR inhibition facilitates targeting of leukemia dependence on convergent nucleotide biosynthetic pathways

“…1a ). To investigate whether ATR inhibition increases the dependence of T-ALL cells on dCK activity at the G1/S transition, CEM cells were synchronized in G1 using Palbociclib, a CDK4/6 inhibitor 36 , 37 , and then released into media containing VE-822 and/or DI-82, a high-affinity dCK inhibitor (dCKi) developed by our group 38 . At various time points following G1 release, cells were pulsed for 1 h with 5’-ethynyl-2’-deoxyuridine (EdU) to analyze cell cycle kinetics by flow cytometry.…”

SH479, a Betulinic Acid Derivative, Ameliorates Experimental Autoimmune Encephalomyelitis by Regulating the T Helper 17/Regulatory T Cell Balance

“…The human liver microsomal stability assay was performed by WuXi AppTec (Shanghai, People's Republic of China) according to the standard operating protocol. The plasma pharmacokinetics of SH479 in rats were determined by Shanghai Institute of Materia Medica (Shanghai, China) according to the standard protocol (Nomme et al, 2014). Briefly, Sprague Dawley rats (weighing 200-220 g) were intravenously injected with 10 mg/kg or fed 20 mg/kg SH479 by oral gavage.…”

[ 18 F]CFA as a clinically translatable probe for PET imaging of deoxycytidine kinase activity

“…In particular, [ 18 F]CFA may be useful as a pharmacokinetic PET stratification biomarker for its corresponding drug Clofarabine (Clolar; Genzyme) (39). Furthermore, as dCK inhibitors (5,6,25) (40), genetic defects in the purine nucleoside-catabolizing enzymes adenosine deaminase (ADA) and purine nucleoside phosphorylase (PNP) (41,42), and treatment of certain leukemias with ADA and PNP inhibitors (43,44). In addition to plasma dN levels, which should be determined in each patient scanned with [ (Fig.…”