Structure-based virtual screening and experimental validation of a MARK4 inhibitor for targeted cancer therapy

Microtubule affinity-regulating kinase 4 (MARK4) is a viable therapeutic target for neurodegenerative disorders and various solid cancers. To identify small molecule inhibitors targeting MARK4, a virtual high-throughput screening of a kinase-specific library and an in-house library was performed using Schrödinger Maestro suite. The study identified JMI-1094 (Docking score -8.486 kcal/mol) as a promising compound among top ten hits with high binding affinities for MARK4, exhibiting strong interactions with active site residues Lys85, Glu133, and Ala135. The binding potential is also supported by Prime/MM-GBSA binding free energy calculations. The stability of MARK4-JMI-1094 complex was also accessed through MD simulation studies of 100 ns. The analysis of MD trajectories in terms of root mean square deviation (RMSD) and root mean square fluctuation (RMSF) revealed that MARK4-JMI-1094 complex displayed lower RMSD values than the apoprotein, signifying a strong and stable binding of JMI-1094 with MARK4. Hydrogen bond interactions with Glu133 and Ala135 persisted for 99% of the simulation time. The cell-based tau-phosphorylation assay suggests that it substantially inhibits the activity of MARK4. Moreover, the efficacy of JMI-1094 was evaluated high MARK4 expressing cell lines from breast (MCF-7) and non-small cell lung cancer (A549) and it decreased the viability of these cell lines with an IC₅₀ value of 4.14 µM and 6.22 µM, respectively. The treatment with JMI-1094 significantly decreased the colonization and cell migration potential of MCF-7 and A549 cell lines, and induced apoptosis. These findings suggest JMI-1094 as a promising MARK4 inhibitor with potential future therapeutic implications in MARK4-mediated cancer(s).