2-Substituted indole-3-carbonitriles as new inhibitors of the protein kinase DYRK1A

Die Proteinkinase DYRK1A stellt eine interessante Zielstruktur zur Entwicklung neuer Inhibitoren dar, da ihre Überexpression vermutlich eine Ursache für die kognitiven Einschränkungen bei Menschen mit Down-Syndrom ist und ihre erhöhte Aktivität auch mit der Entwicklung der Alzheimer-Demenz in Verbindung gebracht wird. Von FALKE wurden 11H-Indolo[3,2-c]chinolin-6-carbonsäuren als potente Inhibitoren von DYRK1A identifiziert. Dabei stellte die 10-Iod-11H-indolo[3,2-c]chinolin-6-carbonsäure (KuFal194) das aktivste und gleichzeitig selektivste Derivat dar. Aufgrund des großen aromatischen Systems ist diese Verbindung allerdings sehr lipophil und nahezu unlöslich in Wasser, weshalb sie nicht als potentieller Arzneistoff geeignet ist. Daher wurde 7-Chlor-1H-indol-3-carbonitril als Analogon mit einem verkleinerten Grundkörper konstruiert, das verbesserte physikochemische Eigenschaften aufwies. Ausgehend von diesem Strukturfragment sollten in dieser Arbeit neue DYRK1A-Inhibitoren mit verbesserten Löslichkeitseigenschaften entwickelt werden. Durch docking-Studien wurde zunächst ein möglicher Bindemodus in der ATP-Bindetasche der Proteinkinase identifiziert, der als Grundlage für Modifikationen des Fragments diente. Dabei stellten sich der 7-Halogensubstituent und die Nitrilgruppe als essentiell für die Wechselwirkungen mit dem target heraus. Es wurde eine Serie an Indol-3-carbonitrilen mit verschiedenen Substituenten an Position 1, 2 und 7 des Indolgrundkörpers synthetisiert und ihre Hemmaktivität gegenüber den Kinasen der CMGC-Gruppe untersucht. 7-Iod-2-phenyl-1H-indol-3-carbonitril stellt den aktivsten DYRK1A-Inhibitor (IC50 = 10 nM) dieser Arbeit dar. Neben der kinaseinhibitorischen Aktivität wurden auch die physikochemischen Eigenschaften der Verbindungen evaluiert. Dazu wurden die thermodynamische und die kinetische Löslichkeit bestimmt und der logP-Wert berechnet. Im Vergleich zu KuFal194 zeigte die aktivste Verbindung dieser Arbeit weder eine geringere Lipophilie noch eine verbesserte Löslichkeit. Durch weitere Strukturmodifikationen konnte allerdings der logP-Wert gesenkt werden. Dadurch verbesserte sich die Löslichkeit, ohne dass sich die Hemmaktivität an DYRK1A deutlich verschlechterte.Because its overexpression is associated with mental retardation in people with Down syndrome and with the development of Alzheimer’s disease, the protein kinase DYRK1A represents an interesting target for the development of new inhibitors. FALKE identified 11H-indolo[3,2-c]quinoline-6-carboxylic acids as potent inhibitors of DYRK1A with 10-iodo-11H-indolo[3,2-c]quinoline-6-carboxylic acid (KuFal194) as the most potent and selective derivative. Due to the large aromatic system, this compound is very lipophilic, nearly insoluble in water and therefore not suitable for the potential use as a drug. The aim of this work was to develop new DYRK1A inhibitors with improved solubility related to KuFal194. By downsizing the ring system of KuFal194, the fragment 7-chloro-1H-indole-3-carbonitrile was created which showed improved physicochemical properties. Docking studies revealed a potential binding mode in the ATP binding pocket of DYRK1A that led to possible modifications of this fragment. The halogen substituent at position 7 and the nitrile group are essential for the interactions with the target and were not changed. A series of indole-3-carbonitriles with diverse substituents at positions 1, 2 and 7 of the indole core was synthesized and evaluated for their inhibitory activity against kinases of the CMGC group. Furthermore, the physicochemical properties of the compounds were evaluated by measuring the thermodynamic and the kinetic solubility and by calculating the logP value. 7-Iodo-2-phenyl-1H-indole-3-carbonitrile turned out to be the most potent DYRK1A inhibitor of this work (IC50 = 10 nM) but it displayed neither reduced lipophilicity nor improved solubility compared to KuFal194. Further modifications at position 2 of the indole led to decreased logP value and improved water solubility while the DYRK1A activity was only slightly diminished

7-Bromo-1-methyl-2-phenyl-1H-indole-3-carbonitrile

The title compound was prepared by electrophilic aromatic substitution of 7-bromo-1-methyl-2-phenyl-1H-indole with NCTS (N-cyano-N-phenyl-p-toluenesulfonamide). The structural identity of the title compound was proven by elemental analysis and spectroscopic methods (IR, NMR, APCI-MS). Purity was assessed by two independent HPLC methods

7-Iodo-1H-indole-3-carbonitrile

The title compound was prepared by a Friedel–Crafts acylation-oxime synthesis-decarboxylation/dehydration sequence starting from commercially available 7-iodoindole with 2-(7-iodo-1H-indol-3-yl)-2-oxoacetic acid as isolated intermediate. The structural identity of the title compound was proven by elemental analysis and spectroscopic methods (IR, NMR, EI-MS), and purity was assessed by two independent HPLC methods

7-Bromo-1-methyl-2-phenyl-1H-indole-3-carbonitrile

The title compound was prepared by electrophilic aromatic substitution of 7-bromo-1-methyl-2-phenyl-1H-indole with NCTS (N-cyano-N-phenyl-p-toluenesulfonamide). The structural identity of the title compound was proven by elemental analysis and spectroscopic methods (IR, NMR, APCI-MS). Purity was assessed by two independent HPLC methods

7-Bromo-1-methyl-2-phenyl-1H-indole-3-carbonitrile

The title compound was prepared by electrophilic aromatic substitution of 7-bromo-1-methyl-2-phenyl-1H-indole with NCTS (N-cyano-N-phenyl-p-toluenesulfonamide). The structural identity of the title compound was proven by elemental analysis and spectroscopic methods (IR, NMR, APCI-MS). Purity was assessed by two independent HPLC methods

7-Iodo-1H-indole-3-carbonitrile

The title compound was prepared by a Friedel–Crafts acylation-oxime synthesis-decarboxylation/dehydration sequence starting from commercially available 7-iodoindole with 2-(7-iodo-1H-indol-3-yl)-2-oxoacetic acid as isolated intermediate. The structural identity of the title compound was proven by elemental analysis and spectroscopic methods (IR, NMR, EI-MS), and purity was assessed by two independent HPLC methods

7-Iodo-1H-indole-3-carbonitrile

The title compound was prepared by a Friedel–Crafts acylation-oxime synthesis-decarboxylation/dehydration sequence starting from commercially available 7-iodoindole with 2-(7-iodo-1H-indol-3-yl)-2-oxoacetic acid as isolated intermediate. The structural identity of the title compound was proven by elemental analysis and spectroscopic methods (IR, NMR, EI-MS), and purity was assessed by two independent HPLC methods

Indole-3-Carbonitriles as DYRK1A Inhibitors by Fragment-Based Drug Design

Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a potential drug target because of its role in the development of Down syndrome and Alzheimer’s disease. The selective DYRK1A inhibitor 10-iodo-11H-indolo[3,2-c]quinoline-6-carboxylic acid (KuFal194), a large, flat and lipophilic molecule, suffers from poor water solubility, limiting its use as chemical probe in cellular assays and animal models. Based on the structure of KuFal194, 7-chloro-1H-indole-3-carbonitrile was selected as fragment template for the development of smaller and less lipophilic DYRK1A inhibitors. By modification of this fragment, a series of indole-3-carbonitriles was designed and evaluated as potential DYRK1A ligands by molecular docking studies. Synthesis and in vitro assays on DYRK1A and related protein kinases identified novel double-digit nanomolar inhibitors with submicromolar activity in cell culture assays