Hydroxybenzothiophene Ketones Are Efficient Pre-mRNA Splicing Modulators Due to Dual Inhibition of Dyrk1A and Clk1/4

Abstract

Dysregulated usage of pre-mRNA splicing sites contributes to the progression of cancer, neurodegenerative diseases, and viral infections. Serine/arginine-rich (SR) proteins play major roles in the splice site recognition and are largely regulated by phosphorylation. This provides an option for the pharmacological correction of aberrant splicing by inhibiting the relevant kinases. Cdc2-like kinases (Clks) and dual specificity tyrosine phosphorylation-regulated kinases (Dyrks) were both reported to phosphorylate numerous SR proteins in vitro and in vivo. In this study, we describe the discovery of new selective dual Clk/Dyrk1A/1B inhibitors, which are able to modulate alternative pre-mRNA splicing of model gene transcripts in cells with submicromolar potencies. The optimization process yielded a dual Clk and Dyrk inhibitor with exceptionally high ligand efficiency. Our results suggested that dual inhibition of both Clk1 and Dyrk1A increased the efficacy of pre-mRNA splicing modulation.

Structure‐Based Design and Synthesis of Harmine Derivatives with Different Selectivity Profiles in Kinase versus Monoamine Oxidase Inhibition

“…Modification of the ring NH group was achieved by introducing differently functionalized alkyl chains. N-Methyl derivative 7 bearing the smallest substituent in this position retained harmine'sa ctivity against both targets.B yi ncreasing the size of the substituent (see compounds [8][9][10][11][12][13][14][15], we observed as ignificant drop in MAO-A inhibition, whereas the affinity toward DYRK1A remained similar.P ropyl (see compound 8)a nd isopropyl (see compound 9)s ubstitu- tion was equallyt olerated, ase xpected on the basis of the structureo fD YRK1A, as theses ubstituents are projected toward the solvent-exposed area.V ariation in the polarity of the Ns ubstituent in the analogues of 8,a se xpected, did not restoreM AO-A binding buti nsteadl ed to some variations in DYRK1Aa ffinity.E ster-bearingc ompound 10 remained equipotent, whereas benzyl derivative 11 and amide analogue 14 were 6-to 8-fold less potent.T he least potent compound in this series wasa cid derivative 13.T he loss of potency for 13 and 14 might be attributed to desolvation (see compound 4), whereas the benzyl group of 11 might clash with the glycine loop of DYRK1A (omitted from Figure 1f or clarity). These results demonstrate that by proper functionalization of the ring NH group of harmine, one might obtain potent DYRK1Ainhibitors that are devoid of MAO-A inhibition.…”

“…Owing to the pharmacological interest in selective DYRK1A and MAO‐A inhibitors, harmine is positioned ideally as a starting point for the structure‐based design of such harmine derivatives that maintain the parent structure's DYRK1A or MAO‐A inhibition potency while being devoid of inhibiting the other target. Some recent papers described benzothiazole derivatives that showed inhibitory potency and kinase selectivity similar to those of harmine without inhibiting MAO‐A . The decrease in MAO‐A inhibition through N‐substitution of β‐carbolines while maintaining DYRK1A inhibition was also elegantly demonstrated by Becker …”

“…Some recent papers described benzothiazole derivatives that showed inhibitory potency and kinase selectivity similar to those of harmine without inhibiting MAO-A. [13,14] The decrease in MAO-A inhibition through N-substitutiono fb-carbolines whilem aintaining DYRK1Ai nhibition was also elegantly demonstratedb y Becker. [15]…”

Mutations in spliceosome genes and therapeutic opportunities in myeloid malignancies

“…First, alterations of splicing regulatory proteins have been observed in diverse cancer subtypes and have become apparent antineoplastic targets. Inhibiting the SRSF2 kinases SPRK and CLK, as well as the SF3B1 kinase DYRK have been linked to effects on splicing factor phosphorylation, localization, and alternative splicing . A large‐scale screen for more selective splicing factor kinase inhibitors discovered three related compounds, Cpd‐1, Cpd‐2, and Cpd‐3 that seem to specifically inhibit SPRK1, SRPK2, and/or CLK1,2 and modulated pre‐mRNA splicing resulting in cell growth suppression and apoptosis .…”

Modulation of alternative splicing by anticancer drugs

“…Other kinases such as Cdc2‐like kinases (Clks) and dual specificity tyrosine phosphorylation‐regulated kinases (Dyrks) phosphorylate numerous SR proteins in vitro and in vivo . Inhibitors of Clk and Dyrk1A resulted in the modulation of alternative splicing . Phosphorylation‐mediated regulation of alternative splicing has been extensively reviewed …”