Rational Design and Synthesis of D-galactosyl Lysophospholipids as Selective Substrates and non-ATP-competitive Inhibitors of Phosphatidylinositol Phosphate Kinases

Phosphatidylinositol phosphate kinases (PIPKs) produce lipid signaling molecules and have been attracting increasing attention as drug targets for cancer, neurodegenerative diseases, and viral infection. Given the potential cross-inhibition of kinases and other ATP-utilizing enzymes by ATP-competitive inhibitors, targeting the unique lipid substrate binding site represents a superior strategy for PIPK inhibition. Here, by taking advantage of the nearly identical stereochemistry between myo-inositol and D-galactose, we designed and synthesized a panel of D-galactosyl lysophospholipids, one of which was found to be a selective substrate of phosphatidylinositol 4-phosphate 5-kinase. Derivatization of this compound led to the discovery of a human PIKfyve inhibitor with an apparent IC50 of 6.2 mu M, which significantly potentiated the inhibitory effect of Apilimod, an ATP-competitive PIKfyve inhibitor under clinical trials against SARS-CoV-2 infection and amyotrophic lateral sclerosis. Our results provide the proof of concept that D-galactose-based phosphoinositide mimetics can be developed into artificial substrates and new inhibitors of PIPKs.

Automated summary

Phosphatidylinositol phosphate kinases (PIPKs) are enzymes that produce lipid signaling molecules and have become attractive drug targets for various diseases. Researchers have designed and synthesized D-galactosyl lysophospholipids, which can selectively target phosphatidylinositol 4-phosphate 5-kinase. This study also discovered a human PIKfyve inhibitor that enhances the inhibition of Apilimod, an ATP-competitive PIKfyve inhibitor, in clinical trials for SARS-CoV-2 infection and amyotrophic lateral sclerosis. These findings demonstrate the potential of D-galactose-based phosphoinositide mimetics as artificial substrates and inhibitors of PIPKs.