Abstract B089: Targeting metabolic vulnerabilities in cancer through structure-guided discovery of novel malic enzyme inhibitors

Abstract

Cancer remains a major global health challenge and urgently requires therapies that improve clinical outcomes and patient quality of life. Tumor cells frequently reprogram metabolism to sustain proliferation and survival, notably by increasing glutamine dependence and upregulating mitochondrial malic enzyme 2 (ME2), which generates pyruvate and NAD(P)H. ME2 is overexpressed in pancreatic, melanoma, and lung cancers, making it a compelling yet underexplored therapeutic target. Recombinant human ME1, ME2, and ME3 were expressed and kinetically characterized in the presence and absence of inhibitors. We solved a complete set of X-ray crystal structures for all three isoforms bound to a potent malic enzyme inhibitor, defining ligand and metal coordination and capturing an unexpected enzyme conformation. These structures guided virtual screening of a curated library of ∼14 million drug-like and fragment molecules to identify novel malic enzyme inhibitors. Biochemical hits were advanced to cellular assays; lead compounds NPD-389 and FLA were evaluated for antiproliferative activity in melanoma and triple-negative breast cancer cell lines. Kinetic analyses revealed distinct activity and inhibition profiles across ME isoforms. X-ray crystallography visualized the isoform-nonselective inhibitor NPD-389 bound in a metal-coordinating mode and stabilizing an unanticipated malic enzyme conformation. Structure-based virtual screening against this conformation yielded multiple novel scaffolds with biochemical inhibitory activity. One scaffold, FLA, displayed a unique selectivity profile and was found bound to ME2 in a previously cryptic pocket that rearranges upon ligand engagement and lies adjacent to the NAD+ cofactor and malate-binding site. In melanoma and triple-negative breast cancer models, both NPD-389 and FLA reduced proliferation, supporting their potential as chemical leads. These findings establish mitochondrial malic enzymes, particularly ME2/ME3, as tractable metabolic targets for cancer therapy. Structural elucidation of NPD-389’s metal-binding mode and FLA’s cryptic/allosteric pocket provides a strong foundation for rational optimization of potency and isoform selectivity. Selective ME inhibitors, either isoform-specific or mitochondrially targeted, represent promising candidates for combination strategies with checkpoint inhibitors or chemotherapy to more effectively disrupt metabolic dependencies in cancer. Ben Krinkel, Yuliana Yosaatmadja, Mark Slayton, Jin Heon Jeon, Jack Flanagan, Sofia Merajver, Christopher Squire, Kerry Loomes. Targeting metabolic vulnerabilities in cancer through structure-guided discovery of novel malic enzyme inhibitors [abstract]. In: Proceedings of AACR Drug Discovery and Development (AACR D3) Conference; 2026 Jul 21-24; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(14_Suppl):Abstract nr B089.