Cancer persists as a prominent global cause of mortality, highlighting an ongoing need for more effective therapies to enhance treatment efficacy and patient well-being. One hallmark of cancer is the rewiring of cellular metabolism, promoting proliferation and biosynthesis of cellular metabolites. Typically, this manifests as an increased reliance on glutamine and upregulation of malic enzyme 2 (ME2) expression, enhancing mitochondrial metabolism.
Human MEs exist in three isoforms: cytosolic ME1 and mitochondrial ME2/ME3. Elevated levels of ME1 and ME2 are implicated in various cancers and associated with the accumulation of ROS, decreased NADPH production, and induction of cellular senescence. ME2 emerges as a potential therapeutic target and is upregulated in pancreatic, melanoma, and lung cancers. ME2 currently presents an underexplored opportunity for therapeutic intervention. Small molecule inhibitors of ME2, including NPD-389 and embonic acid, may offer promise as potential drug leads for targeting cancer cell metabolism.
We expressed and characterised the kinetics of recombinant human ME1-3 isoforms. Kinetic analyses reveal novel data for the least well-studied ME3, characterising substrate (L-malate) and cofactor NAD(P)+ binding and inhibitory constants for NPD-389, an effective inhibitor across all isoforms. X-ray crystal structures of ME1-3 isoforms reveal the inhibitory binding mode for NPD-389, which selects a unique protein conformation. We have also tested NPD-389 on triple-negative breast cancer and generated novel inhibitory data. This unique protein conformation has been used for virtual screening, where we have since identified novel malic enzyme inhibitors and co-crystalised new enzyme-inhibitor complexes. We now aim to use these novel scaffolds to produce potent and soluble ME2-targeting molecules to advance towards clinical investigations targeting malic enzymes as adjunct cancer therapies alongside existing checkpoint or chemotherapy treatments.