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Jaione Saez Cabodevilla

New inhibitors of quinolinate synthase as potential antibacterial drugs

Published on 6 December 2018

Thesis presented December 06, 2018

Resistance to antibiotics is becoming a world-wide threat. Microorganisms are able to withstand drugs leading to persistence of diseases. This is why the research of new drugs is of great importance nowadays.
Nicotinamide adenine dinucleotide (NAD) is an essential cofactor and substrate in numerous biological reactions. For this reason, both the enzymes that use it as a substrate and those participating on its biosynthetic pathway are largely studied as potential antibacterial targets. In this context, we are interested in the development of new antibacterial drugs against quinolinate synthase enzyme (NadA). This enzyme participates in the prokaryotic NAD de novo biosynthetic pathway and is essential in two pathogens: Helicobacter pylori, cause of gastric ulcers and cancers, and Mycobacterium leprae, responsible of leprosy. The fact that NadA only exists in prokaryotes and the fact that it is essential for these two pathogens make it an interesting target for the design of new antibacterial drugs. Quinolinate synthase is a [4Fe-4S] cluster enzyme, where one of the Fe sites is coordinated by a water molecule in the resting state, and plays a Lewis acid role during catalysis. The reaction catalyzed by NadA consists in the formation of quinolinic acid (QA), precursor of NAD, from iminoaspartate and dihydroxyacetone phosphate. Based on the discovery in our laboratory of the first inhibitor of NadA (DTHPA) that coordinates irreversibly the catalytic iron site of the cluster, we designed and synthesized a family of molecules as potential more specific NadA inhibitors. These molecules contain a benzene/pyridine or pyrazine ring, two vicinal carboxylates and a thiol as an iron coordinating group: 4-mercaptophthalic acid (4MP), 6-mercaptopyridine-2, 3-dicarboxylic acid (6MPDC), 5-mercaptopyrazine-2, 3-dicarboxylic acid (5MPzDC) and 5-mercaptopyridine-2, 3-dicarboxylic acid (5MPDC). We demonstrated that these molecules inhibit NadA enzyme in vitro in the same range as DTHPA. Using different spectroscopies and crystallography, we demonstrated that inhibition occurs by coordination of the molecules to the catalytic iron site through their thiol group. We investigated also in vitro the specificity of these molecules. We demonstrated that 4MP and 5MPDC molecules are specific NadA inhibitors when assayed on bacterial aconitase B, a [4Fe-4S] enzyme, whose cluster displays functional and structural properties similar to those of NadA.
Finally, we investigated the QA pathway inhibition activity of the four molecules in cellulo, in an Escherichia coli strain. Whereas, 6MPDC and 5MPzDC molecules inhibit E. coli growth in a QA biosynthetic pathway independent manner, 4MP and 5MPDC (the two in vitro specific inhibitors) did not show any in cellulo inhibition activity. Since this lack of activity might be due to a lack of penetration of the molecules inside bacteria, we thought about assisting the penetration of the molecules using a transmembrane carrier, a simplified analogue of the tetra-cyclopeptide FR235222 natural product. We synthetized and coupled the cyclopeptide to the 4MP inhibitor. Unfortunately, no E. coli growth inhibition was observed. The Ph.D ended by investigating the penetration of the tetra-cyclopeptide inside bacteria, using some fluorophore agents.

Antibacterial, Quinolinate synthase, Inhibition, Prodrug, Penetration

On-line thesis.