Structure-Based Design of Potent Selective Nanomolar Type-II Inhibitors of Glycogen Synthase Kinase-3β

For the first time, the in
silico design, screening,
and in vitro validation of potent GSK-3β type-II
inhibitors are presented. In the absence of crystallographic evidence
for a DFG-out GSK-3β activation loop conformation, computational
models were designed using an adapted DOLPHIN approach and a method
consisting of Prime loop refinement, induced-fit docking, and molecular
dynamics. Virtual screening of the Biogenics subset from the ZINC
database led to an initial selection of 20 Phase I compounds revealing
two low micromolar inhibitors in an isolated enzyme assay. Twenty
more analogues (Phase II compounds) related to the hit [pyrimidin-2-yl]­amino–furo­[3,2-b]­furyl–urea scaffold were selected for structure–activity
relationship analysis. The Phase II studies led to five highly potent
nanomolar inhibitors, with compound 23 (IC50 =0.087 μM) > 100 times more potent than the best Phase
I inhibitor,
and selectivity for GSK-3β inhibition compared to homologous
kinases was observed. Ex vivo experiments (SH-SY5Y
cell lines) for tau hyperphosphorylation revealed promising neuroprotective
effects at low micromolar concentrations. The type-II inhibitor design
has been unraveled as a potential route toward more clinically effective
GSK-3β inhibitors.