Design, synthesis and biological evaluation of novel cyclic malonamide derivatives as selective RIPK1 inhibitors.

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) plays a key role in cell death and inflammation. RIPK1 is a well-established therapeutic target, due to the presence of a unique kinase-regulating allosteric pocket, which enables selective inhibition. Herein we used GSK2982772 as our starting point in our discovery campaign. Applying isosteric replacement, we successfully identified the malonamide scaffold, instead of the well-established serine template. Further structural optimization led to the design and synthesis of a series of analog inhibitors. The enantiomers of the most promising compound were tested on 97 different kinases. The active enantiomer proved to be kinase selective.

Controlling receptor function from the extracellular vestibule of G-protein coupled receptors.

Receptor function is traditionally controlled from the orthosteric binding site of G-protein coupled receptors. Here, we show that the functional activity and signalling of human dopamine D2 and D3 receptor ligands can be fine-tuned from the extracellular secondary binding pocket (SBP) located far from the signalling interface suggesting optimization of the SBP binding part of bitopic ligands might be a useful strategy to develop GPCR ligands with designed functional and signalling profile.

Multiple fragment docking and linking in primary and secondary pockets of dopamine receptors.

A sequential docking methodology was applied to computationally predict starting points for fragment linking using the human dopamine D3 receptor crystal structure and a human dopamine D2 receptor homology model. Two focused fragment libraries were docked in the primary and secondary binding sites, and best fragment combinations were enumerated. Similar top scoring fragments were found for the primary site, while secondary site fragments were predicted to convey selectivity. Three linked compounds were synthesized that had 9-, 39-, and 55-fold selectivity in favor of D3 and the subtype selectivity of the compounds was assessed on a structural basis.

Virtual fragment screening on GPCRs: a case study on dopamine D3 and histamine H4 receptors.

Prospective structure based virtual fragment screening methodologies on two GPCR targets namely the dopamine D3 and the histamine H4 receptors with a library of 12,905 fragments were evaluated. Fragments were docked to the X-ray structure and the homology model of the D3 and H4 receptors, respectively. Representative receptor conformations for ensemble docking were obtained from molecular dynamics trajectories. In vitro confirmed hit rates ranged from 16% to 32%. Hits had high ligand efficiency (LE) values in the range of 0.31-0.74 and also acceptable lipophilic efficiency. The X-ray structure, the homology model and structural ensembles were all found suitable for docking based virtual screening of fragments against these GPCRs. However, there was little overlap among different hit sets and methodologies were thus complementary to each other.

In vitro and in vivo comparison of [³H](+)-PHNO and [³H]raclopride binding to rat striatum and lobes 9 and 10 of the cerebellum: a method to distinguish dopamine D3 from D2 receptor sites.

In vitro binding characteristics of the dopamine D3/D2 antagonist [³H]raclopride were compared to the D3/D2 agonist [³H](+)-PHNO in membrane preparations from rat striatum, cerebellum Lobules 9 and 10 (CB L9,10), and other cerebellar regions. In striatum, both radioligands labeled a single binding site. [³H](+)-PHNO showed higher affinity, though lower B(max) , compared with [³H]raclopride and was sensitive to inhibition by Gpp(NH)p. [³H](+)-PHNO showed significant specific binding to CB L9,10 membranes with higher affinity compared to striatal membranes. [³H](+)-PHNO binds to a high- and a low-affinity binding site in CB L9,10 membranes; the high-affinity site was not Gpp(NH)p-sensitive. [³H](+)-PHNO did not significantly bind cerebellum left hemisphere membranes. Very low specific binding of [³H]raclopride was found in CB L9,10. The selective dopamine D3 antagonist SB-277011 did not displace the binding of either ligand to striatal membranes but potently inhibited the binding of [³H](+)-PHNO in CB L9,10 membranes. The highly selective D2 antagonist SV-156 showed the opposite profile. In vivo experiments were consistent with and supported by in vitro results. In summary, [³H](+)-PHNO and [³H]raclopride mainly label dopamine D2 receptors in rat striatum, with [³H](+)-PHNO labeling a D2(High) population. In vitro and in vivo, [³H](+)-PHNO labels CB L9,10 dopamine D3 receptors that are apparently in a high affinity state whereas [³H]raclopride gave only very low signal in this region. The present approaches appear useful for selectively labeling dopamine D3 and D2 receptors in different rat brain regions and offer the possibility to demonstrate D3 versus D2 receptor selectivity of compounds using native rat brain tissue.