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Target-driven design of a coumarinyl chalcone scaffold based novel EF2 Kinase inhibitor suppresses breast cancer growth in vivo

Eukaryotic elongation factor 2 kinase (eEF-2K), an unusual alpha kinase, is involved in protein synthesis through phosphorylation of elongation factor 2 (EF2). eEF-2K is indicated as one of the critical drivers of breast cancer and associated with poor clinical prognosis, representing a potential molecular target. The crystal structure of eEF-2K is unknown and there is no potent and effective eEF-2K inhibitor reported for clinical applications. To meet this challenge, we designed and synthesized several generations of potential inhibitor compounds and performed in silico studies. The effect of the inhibitors at the binding pocket of eEF-2K is analyzed after developing a 3D target model by homology modeling approaches using a domain of another α-kinase called myosin heavy-chain kinase A (MHCKA) that is closely resembling eEF-2K. Our results showed that compounds with coumarin-chalcone cores have a high predicted binding affinity for binding to eEF-2K. Following in vitro studies, we identified a compound that was highly effective in inhibiting eEF-2K activity at submicromolar concentrations and inhibited proliferation of various breast cancer cells with different features (BT20, MDA-MB-231, MDA-MB-436 and MCF-7) by induction of apoptosis while sparing normal cells. In vivo systemic administration of the the lead inhibitor encapsulated in single lipid-based nanoparticles twice a week significantly supressed growth of MDA-MB-231 tumors in orthotopic breast cancer models in nude mice. In conclusion, our study provides the first in vivo effective small molecule eEF-2K inhibitor that may be used for molecularly targeted precison medicine strategies in breast cancer or other eEF-2K-dependent tumors.