Probing the Substrate Specificity of 3-Deoxy-D-arabino-Heptulosonate 7-Phosphate Synthase and 3-Deoxy-D-manno-Octulosonate 8-Phosphate Synthase using Analogues of Phosphoenolpyruvate

Abstract

3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) synthase and 3-deoxy-D-mannooctulosonate 8-phosphate (KD08P) synthase are two bacterial enzymes that are vital for host virulence. DAH7P synthase catalyses the first commited step of the shikimate pathway that results in the biosynthesis of aromatic metabolites. KD08P synthase catalyses the formation of the sugar KDO, which is an essential component of the cell wall of Gram-negative bacteria. The enzymes that catalyse these reactions are not present in animals, and therefore they are attractive targets for anti-bacterial agents. Interestingly, these two enzymes catalyse very similar aldol-like reactions and share a common substrate, phosphoenolpyruvate (PEP). In this thesis, the synthesis of various analogues to the shared substrate, PEP, has been described. Alterations to PEP include; substitution of a vinylic proton for either a fluorine, a bromine, a chlorine, a methyl group or deuterium; substitution of the carboxylic acid group for a methylchloride or a phosphonate; reduction of the double bond, and substituting the phosphate bridging oxygen for a methylene group. These analogues were tested as competitive inhibitors, and some as substrates and irreversible inhibitors against DAH7P synthase (from E. coli) and KD08P synthase (from N. meningitidis). 3-FluoroPEP was observed to act as a substrate for both DAH7P synthase and KD08P synthase. However, following the reaction progress via ¹⁹F NMR spectroscopy showed that in the KD08P synthase reaction the (Z)-isomer was processed much slower than the (E)isomer, whereas in the DAH7P synthase reaction both isomers were processed at a similar rate. Chloro, bromo and methyl 3-substituted PEP analogues were found to be reasonable competitive inhibitors of DAH7P synthase and KD08P synthase . DAH7P synthase was shown to have better inhibition with the (E)-isomers of these 3-substituted PEP analogues, whereas in KD08P synthase this varied. l-(Chloromethyl)vinyl phosphate was shown to be a poor competitive inhibitor of both DAH7P synthase and KD08P synthase. However, this compound showed time-dependent covalent inactivation of both DAH7P synthase and KD08P synthase. DiphosphoPEP was shown to be a reasonable competitive inhibitor towards DAH7P synthase, and was a poor competitive inhibitor of KD08P synthase (at pH 6.5). Lowering the pH to 5.3 resulted in significantly greater inhibition of KD08P synthase. DiphosphoPEP was shown not to act as a substrate to both enzymes. The (R)-isomer of 2-phospholactic acid was found to be the best competitive inhibitor of DAH7P synthase, from the PEP analogues tested, and the (S)-isomer had approximately 6-fold weaker inhibition. Inhibition of KD08P synthase with 2-phospholactic acid was poor, with slightly better inhibition with the (R)-isomer. The phosphonate of PEP was shown to be a reasonable competitive inhibitor towards DAH7P synthase and close to no inhibition was observed ofKD08P synthase (at pH 6.5). Lowering the pH to 5.3 resulted in some inhibition of KD08P synthase.