Development of novel conformationally restricted selective Clk1/4 inhibitors through creating an intramolecular
Dalia S El-Gamil1, Ahmed K ElHady2, Po-Jen Chen3
1Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt; Department of Chemistry, Faculty of Pharmacy, Ahram Canadian University, Cairo, 12451, Egypt.
Abstract:
As prime regulators of pre-mRNA alternative splicing, different Clk isoforms were found to be overexpressed in various tumour types and have received much attention recently as potential targets for cancer therapy. Several studies have reported potent small-molecule Clk1/4 inhibitors with promising cellular anti-cancer activities; however, their clinical use was generally hampered by their compromised selectivity against off-targets, mainly Clk2 and Dyrk1A. In this study, we present a novel series of N-aroylated 5-methoxybenzothiophene-2-carboxamides (imides) as potent and selective Clk1/4 inhibitors. Potency of this series was found to be mainly dependent on the presence of an intramolecular H-bond between an ortho-methoxy group and the imide NH, that stabilizes a nearly coplanar conformation of high affinity to the ATP binding pocket(s) of Clk1/4. The two most potent hits in this series, compounds 20 (4-fluoro-2-methoxy) and 31 (5-chloro-2-methoxy) had cell free Clk1 IC50s of 4 and 9.7 nM, respectively, besides an unprecedented selectivity over Clk2 with 62- and 50-times higher affinities towards Clk1, respectively. 20 and 31 also exhibited remarkable selectivity over most common off-targets including Dyrk1A. Moreover, compounds 26 (2-ethoxy) and 31 showed growth inhibitory activities in T24 cancer cells with GI50s of <0.1 and 1.1 μM, respectively.
Insights
Researchers developed novel N-aroylated 5-methoxybenzothiophene-2-carboxamides as potent and selective inhibitors of Clk1/4 kinases. These compounds show promise for cancer therapy by targeting Clk1/4 while minimizing off-target effects on Clk2 and Dyrk1A.
Area of Science:
- Medicinal Chemistry
- Molecular Biology
- Cancer Therapeutics
Background:
- Cyclin-dependent kinase-like (Clk) kinases regulate alternative splicing and are overexpressed in various cancers.
- Existing Clk1/4 inhibitors often lack selectivity, primarily inhibiting Clk2 and Dyrk1A, limiting clinical applications.
- Targeting Clk isoforms presents a promising strategy for novel cancer therapies.
Purpose of the Study:
- To design and synthesize a novel series of N-aroylated 5-methoxybenzothiophene-2-carboxamides.
- To evaluate the inhibitory potency and selectivity of these compounds against Clk1/4 kinases.
- To assess the anti-cancer activity of lead compounds in relevant cancer cell lines.
Main Methods:
- Synthesis of N-aroylated 5-methoxybenzothiophene-2-carboxamides.
- In vitro kinase inhibition assays for Clk1, Clk2, and Dyrk1A.
- Cell-free assays to determine IC50 values.
- Cell growth inhibition assays (GI50) in T24 cancer cells.
Main Results:
- A novel series of potent and selective Clk1/4 inhibitors were identified.
- Compounds 20 and 31 demonstrated high affinity for Clk1 (IC50s of 4 nM and 9.7 nM) with significant selectivity over Clk2 (62- and 50-fold).
- Compounds 20 and 31 exhibited excellent selectivity against other off-targets, including Dyrk1A, and showed potent growth inhibition in T24 cancer cells.
Conclusions:
- N-aroylated 5-methoxybenzothiophene-2-carboxamides represent a promising class of potent and selective Clk1/4 inhibitors.
- The observed selectivity and potency suggest therapeutic potential for these compounds in cancer treatment.
- Further investigation into the mechanism of action and in vivo efficacy is warranted.
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