Design, Synthesis and Biological Evaluation of 7-Chloro-9H-pyrimido[4,5-b]indole-based Glycogen Synthase Kinase-3β Inhibitors

Abstract

Glycogen synthase kinase-3β (GSK-3β) represents a relevant drug target for the treatment of neurodegenerative pathologies including Alzheimer’s disease. We herein report on the optimization of a novel class of GSK-3β inhibitors based on the tofacitinib-derived screen hit 3-((3R,4R)-3-((7-chloro-9H-pyrimido[4,5-b]indol-4-yl)(methyl)amino)-4-methylpiperidin-1-yl)-3-oxopropanenitrile (1). We synthesized a series of 19 novel 7-chloro-9H-pyrimido[4,5-b]indole-based derivatives and studied their structure–activity relationships with focus on the cyanoacetyl piperidine moiety. We unveiled the crucial role of the nitrile group and its importance for the activity of this compound series. A successful rigidization approach afforded 3-(3aRS,7aSR)-(1-(7-chloro-9H-pyrimido[4,5-b]indol-4-yl)octahydro-6H-pyrrolo[2,3-c]pyridin-6-yl)-propanenitrile (24), which displayed an IC50 value of 130 nM on GSK-3β and was further characterized by its metabolic stability. Finally, we disclosed the putative binding modes of the most potent inhibitors within the ATP binding site of GSK-3β by 1 µs molecular dynamics simulations.

Discovery and Evaluation of Enantiopure 9H-pyrimido[4,5-b]indoles as Nanomolar GSK-3β Inhibitors with Improved Metabolic Stability

“…We previously reported a synthetic route for the preparation of compound 2 [5]. This strategy demonstrated broad applicability within the herein presented study, as it provided access to the majority of final compounds with only minor alterations in the experimental protocols (Scheme 2).…”

“…Based on these results, we elected to maintain both moieties for further optimization and shifted our focus to other positions of the scaffold that are amenable to modification (Table 2). a IC 50 values were determined in an ADP Glo™ Kinase assay and are the means of at least two independent experiments; b data taken from [5].…”

“…The aliphatic side chain was then introduced by treatment of 4a-l with appropriate amines under basic conditions. In the case of 6a-l, we used racemic 1-Boc-3-(methylamino)piperidine, which was prepared as described previously [5]. For the synthesis of analogs (R)-5c,d and (S)-5c,d, enantiopure 1-Boc-3-aminopiperidine building blocks were utilized.…”

“…The water molecules were described with the TIP3P water model [30]. The production simulations of 1000 ns were run with NpT ensemble (T = 310 K, Nosé-Hoover method; p = 1.01325 bar, Martyna-Tobias-Klein method) with the default Desmond settings as described previously [5]. Before the actual production run, the default Desmond relaxation protocol was applied for both systems.…”

“…We hypothesized that the introduction of an acyl substituent on the piperidine nitrogen atom was a suitable approach to eliminate the potential metabolic hotspot. To this end, we refocused our attention on the reported amide derivative 2, which was 2.5-fold less active than 1 [5]. We used this compound as a template in order to design and optimize a series of novel amide-based GSK-3β inhibitors by applying a variety of structural modifications (Scheme 1).…”