Consensus Virtual Screening Identified [1,2,4]Triazolo[1,5-b]isoquinolines As MELK Inhibitor Chemotypes

Abstract

Maternal Embryonic Leucine-zipper Kinase (MELK) is a current oncotarget involved in a diverse range of human cancers, with the usage of MELK inhibitors being explored clinically. Here, we aimed to discover new MELK inhibitor chemotypes from our in-house compound library with a consensus-based virtual screening workflow, employing three screening concepts. After careful retrospective validation, prospective screening and in vitro enzyme inhibition testing revealed a series of [1,2,4]triazolo[1,5-b]isoquinolines as a new structural class of MELK inhibitors, with the lead compound of the series exhibiting a sub-micromolar inhibitory activity. The structure-activity relationship of the series was explored by testing further analogs based on a structure-guided selection process. Importantly, the present work marks the first disclosure of the synthesis and bioactivity of this class of compounds.

Keywords: MELK inhibitor; docking; isoquinoline; kinase; virtual screening.

Figure 1

Workflow of the computational screening and experimental testing steps, with the respective compound counts. Three virtual screening concepts (docking, pharmacophore and shape screening) were used in parallel. These were validated retrospectively and applied prospectively to our in‐house compound database. Compounds that are predicted as actives by at least two out of three screening concepts were considered as virtual hits and selected for primary in vitro testing, followed by an SAR analysis of the [1,2,4]triazolo[1,5‐b]isoquinoline scaffold.

Figure 2

Structure‐guided selection of further analogues for testing. A) Predicted binding mode of compound 18 (green sticks) overlaid on the binding mode of dorsomorphin (white sticks, PDB: 6GVX ^[31] ). In addition to the good overlay of the respective cores, the 4‐OMe group of 18 mimics the larger, solvent‐exposed substituent of dorsomorphin, while the 10‐ethyl group extends inside the binding pocket. B) Predicted binding mode of compound 11 (green sticks) overlaid on the binding mode of the MELK inhibitor NVS‐MELK8F (white sticks, PDB: 5IHA ^[32] ). Here, the heterocyclic nitrogen of the pyridyl unit can act as the anchoring group against the backbone NH group of the hinge residue C89, while the advantageous position of the 10‐methyl group is supported by the hydrophobic group of NVS‐MELK8F in the same position.

Figure 3

ROC curves with AUC values (and 95 % confidence intervals ^[47] ) of the retrospective docking. Ensemble docking based on the minimum, maximum and geometric mean of the seven docking scores is better than using any single structure. Based on our earlier results, we have selected the geometric mean from the available data fusion rules.