Discovery of Selective Inhibitors of the Clostridium difficile Dehydroquinate Dehydratase

Abstract

A vibrant and healthy gut flora is essential for preventing the proliferation of Clostridium difficile, a pathogenic bacterium that causes severe gastrointestinal symptoms. In fact, most C. difficile infections (CDIs) occur after broad-spectrum antibiotic treatment, which, by eradicating the commensal gut bacteria, allows its spores to proliferate. Hence, a C. difficile specific antibiotic that spares the gut flora would be highly beneficial in treating CDI. Towards this goal, we set out to discover small molecule inhibitors of the C. difficile enzyme dehydroquinate dehydratase (DHQD). DHQD is the 3rd of seven enzymes that compose the shikimate pathway, a metabolic pathway absent in humans, and is present in bacteria as two phylogenetically and mechanistically distinct types. Using a high-throughput screen we identified three compounds that inhibited the type I C. difficile DHQD but not the type II DHQD from Bacteroides thetaiotaomicron, a highly represented commensal gut bacterial species. Kinetic analysis revealed that the compounds inhibit the C. difficile enzyme with Ki values ranging from 10 to 20 µM. Unexpectedly, kinetic and biophysical studies demonstrate that inhibitors also exhibit selectivity between type I DHQDs, inhibiting the C. difficile but not the highly homologous Salmonella enterica DHQD. Therefore, the three identified compounds seem to be promising lead compounds for the development of C. difficile specific antibiotics.

Transmissible microbial and metabolomic remodeling by soluble dietary fiber improves metabolic homeostasis

“…Alternatively, propionate may also promote phenylpropionate synthesis. Propionate can be converted to phosphoenolpyruvate, which in turn serves as substrate for the Shikimate pathway in commensal bacteria to produce phenylalanine and thus ultimately phenylpropionates 51 52 53 . The untargeted metabolomic platform used in this study was not able to identify SCFAs due to their polarity and volatility.…”

The rise of glyphosate and new opportunities for biosentinel early‐warning studies

“…The Shikimate pathway is not present in humans, but it is present in the bacteria living inside human intestines (Samsel & Seneff ; Ratia et al. ). It has been shown empirically that glyphosate‐induced imbalances in gut bacteria are linked to the development of many different chronic diseases including celiac disease, heart disease, cancer, and Alzheimer's disease (Samsel & Seneff , ; Seneff et al.…”

“…As a herbicide, glyphosate interrupts the Shikimate pathway responsible for the biosynthesis of essential aromatic amino acids and thus results in disruption of protein synthesis and eventually to plant death (Pérez et al 2011;Mesnage et al 2015). The Shikimate pathway is not present in humans, but it is present in the bacteria living inside human intestines (Samsel & Seneff 2013a;Ratia et al 2014). It has been shown empirically that glyphosate-induced imbalances in gut bacteria are linked to the development of many different chronic diseases including celiac disease, heart disease, cancer, and Alzheimer's disease (Samsel & Seneff 2013a, 2013bSeneff et al 2015).…”

Clostridium difficile Drug Pipeline: Challenges in Discovery and Development of New Agents

“…Ratia et al attempted to develop selective inhibitors of C. difficile by targeting the enzyme dehydroquinate dehydratase (DHQD), which is involved in the shikimate pathway for biosynthesis of chorismate, a precursor required for biosynthesis of three aromatic amino acids. 134 The shikimate pathway is not present in humans, but as DHQD is present in bacteria in two different subtypes, selective inhibitors could potentially be obtained by a target based drug discovery approach. The type I DHDQ is present in C. difficile , while the type II DHQD is present in commensal bacterial species such as Bacteroides thetaiotaomicron and Bifidobacterium longum .…”