Mechanisms of action and inhibition of [4Fe-4S] proteins IspG and IspH in isoprenoid biosynthesis

The methylerythritol phosphate pathway (also known as the non-mevalonate pathway) of isoprenoid biosynthesis is potentially an important anti-bacterial and anti-malarial drug target. However, the catalytic mechanisms of the last two enzymes in this pathway, IspG (also known as GcpE) and IspH (also known as LytB) were largely unknown, and there were no inhibitors targeting these two enzymes. These two enzymes both are [4Fe-4S] proteins with one unique iron not bonded to any cysteine residue, and catalyze 2e-/2H+ reductions. In this study, bioorganometallic mechanisms are proposed for IspG and IspH catalyses, where direct iron-carbon interactions play important roles. This is a new type of catalytic mechanism of iron-sulfur enzymes, and is supported by extensive characterizations of trapped reaction intermediates: in IspG catalysis, a reaction intermediate with Fe-C and Fe-O bonding has been identified; whereas in IspH catalysis, an alkoxide complex, a weak π-complex, and an η3-allyl complex has been discovered along the reaction pathway. No free radical intermediates were observed. In addition, the first potent inhibitors against IspG and IspH have been discovered. Based on the catalytic mechanism of IspH enzyme, alkyne diphosphate inhibitors against both enzymes were rationally designed; pyridine diphosphate inhibitors against Aquifex aeolicus IspH were discovered by compound library screening. The binding modes of both types of inhibitors have also been determined. The work reported here is of broad general interest, since it clarifies the nature of the reaction mechanisms of IspG and IspH catalyses, and opens up new routes to inhibitor design, of interest in the context of both anti-bacterial as well as anti-malarial drugs