Discovery of Potent and Selective Inhibitors of Cdc2-Like Kinase 1 (CLK1) as a New Class of Autophagy Inducers

Abstract

Autophagy inducers represent new promising agents for the treatment of a wide range of medical illnesses. However, safe autophagy inducers for clinical applications are lacking. Inhibition of cdc2-like kinase 1 (CLK1) was recently found to efficiently induce autophagy. Unfortunately, most of the known CLK1 inhibitors have unsatisfactory selectivity. Herein, we report the discovery of a series of new CLK1 inhibitors containing the 1H-[1,2,3]triazolo[4,5-c]quinoline scaffold. Among them, compound 25 was the most potent and selective, with an IC value of 2 nM against CLK1. The crystal structure of CLK1 complexed with compound 25 was solved, and the potency and kinase selectivity of compound 25 were interpreted. Compound 25 was able to induce autophagy in in vitro assays and displayed significant hepatoprotective effects in the acetaminophen (APAP)-induced liver injury mouse model. Collectively, due to its potency and selectivity, compound 25 could be used as a chemical probe or agent in future mechanism-of-action or autophagy-related disease therapy studies.

Cdc-Like Kinases (CLKs): Biology, Chemical Probes, and Therapeutic Potential

“…In addition, CLK1 can regulate autophagy—CLK1 inhibition or knockout induces autophagy via activation of the mTOR/PI3K pathway [ 90 , 91 ].…”

“…In 2017, Compound 25 ( Figure 19 ) was published as a CLK1 inhibitor [ 90 ]. While the compound exhibits the highest potency towards CLK1 (IC 50 = 2 nM), it is also highly active towards CLK2 and CLK4 (IC 50 = 31 nM and 8 nM, respectively), but practically inactive against CLK3.…”

“…In addition, Compound 25 induced autophagy in BNL CL.2 and SKOV-3 (human ovarian cancer cell line) cell lines. The pharmacokinetic profile (in mice) is also available in the original publication [ 90 ]. Unfortunately, an inactive control compound as well as the determination of cellular target engagement are missing.…”

Autoregulation of the human splice factor kinase CLK1 through exon skipping and intron retention

“…CLK activity is increasingly associated with the development and progression of cancer (Naro and Sette, 2013;Corkery et al, 2015;Czubaty and Piekielko-Witknowska, 2017). As a result there is considerable interest in developing selective CLK inhibitors that block tumour growth (Schmitt et al, 2014;ElHady et al, 2017;Murar et al, 2017;Sun et al, 2017;Riggs et al, 2017;Walter et al, 2017). CLK1 is also a potential target in the treatment of Alzheimer's (Jain et al, 2014) and has been earmarked for the treatment of Duchenne's muscular dystrophy as its inhibition causes the skipping of a mutated exon (Ogawa and Hagiwara, 2012;Sako et al, 2017).…”

Molecular structures of cdc2-like kinases in complex with a new inhibitor chemotype

“…1 μM TG693 inhibited the activities of DYRK1A by 84% and of CLK1 by 93%, exhibiting some selectivity for the latter enzyme [ 30 ]. Recently, the [ 1 , 2 , 3 ]triazolo[4,5- c ]quinoline 7 was reported as potent and selective CLK1 inhibitor, inducing autophagy in vitro and showing hepatoprotective effects in vivo in an acetaminophen-induced liver injury mouse model [ 31 ]. We here report 6,7-dihydropyrrolo[3,4- g ]indol-8(1 H )-ones as another class of CLK inhibitors.…”