Chem-Bio Hybrid Synthesis Enables Reengineering of Natural Product-Based Methionine Aminopeptidase 2 Inhibitors for Treating Amebiasis.

Natural products remain a vital source of therapeutic innovation, but their structural complexity often limits the systematic optimization and clinical translation. This challenge is exemplified by the fungal metabolite fumagillin, a covalent inhibitor of methionine aminopeptidase 2 (MetAP2), which advanced toward clinical development but whose semisynthetic derivatives were discontinued in trials for cancer and obesity because of adverse effects. To overcome these barriers, we reengineered the fumagillin biosynthetic pathway in Aspergillus nidulans to expand chemical diversity, uncovering its natural analog ovalicin as a more potent agent active against Entamoeba histolytica. Although ovalicin had never been developed clinically, our analyses revealed that its rapid degradation by hepatic cytochrome P450 enzymes underlies its therapeutic ineffectiveness in preclinical studies. We then established a chem-bio hybrid platform that integrates pathway-engineered biosynthesis with site-selective chemical derivatization to address this metabolic fragility. Introduction of a C6-hydroxyl group as a built-in functional handle enabled preparative-scale diversification and the synthesis of about 30 analogs. Several C6-modified derivatives maintained subnanomolar MetAP2 inhibition, resisted P450-mediated metabolism, and exhibited negligible cytotoxicity. Two optimized compounds, YOK24 and NS-181, achieved complete resolution of amebic liver abscess in hamsters after both subcutaneous and oral administration. Together, these findings establish a general and broadly applicable strategy for the biosynthetic reprogramming of natural products, providing a blueprint for expanding the chemical and therapeutic space of complex metabolites beyond conventional synthetic and biosynthetic limits.