Combining structure-based pharmacophore modeling, virtual screening, and in silico ADMET analysis to discover novel tetrahydro-quinoline based pyruvate kinase isozyme M2 activators with antitumor activity

Abstract

Compared with normal differentiated cells, cancer cells upregulate the expression of pyruvate kinase isozyme M2 (PKM2) to support glycolytic intermediates for anabolic processes, including the synthesis of nucleic acids, amino acids, and lipids. In this study, a combination of the structure-based pharmacophore modeling and a hybrid protocol of virtual screening methods comprised of pharmacophore model-based virtual screening, docking-based virtual screening, and in silico ADMET (absorption, distribution, metabolism, excretion and toxicity) analysis were used to retrieve novel PKM2 activators from commercially available chemical databases. Tetrahydroquinoline derivatives were identified as potential scaffolds of PKM2 activators. Thus, the hybrid virtual screening approach was applied to screen the focused tetrahydroquinoline derivatives embedded in the ZINC database. Six hit compounds were selected from the final hits and experimental studies were then performed. Compound 8 displayed a potent inhibitory effect on human lung cancer cells. Following treatment with Compound 8, cell viability, apoptosis, and reactive oxygen species (ROS) production were examined in A549 cells. Finally, we evaluated the effects of Compound 8 on mice xenograft tumor models in vivo. These results may provide important information for further research on novel PKM2 activators as antitumor agents.

Keywords:

• pharmacophore
• molecular docking
• pyruvate kinase
• virtual screening

Supplementary materials

Figure S1 Superimposition of seven PKM2-activator complexes.

Abbreviation: PKM, pyruvate kinase isozyme.

Figure S2 Binding modes and important binding site residues of Compound 8 located in the binding site of PKM2 (ligands in magenta, PKM2 domain in green and cyan, respectively).

Note: The A and B represent two different directional views of Compound 8 located in the binding site of PKM2.

Abbreviation: PKM, pyruvate kinase isozyme.

Acknowledgments

We gratefully acknowledge the support from the National Natural Science Foundation of China (No. 30901837, 81001357 and 81273471), the Fund of the Health Department of Sichuan Province (No.120487), and the Open Research Fund of State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine.

Disclosure

The authors report no conflicts of interest in this work.