Decrypting a cryptic allosteric pocket in H. pylori glutamate racemase

One of our greatest challenges in drug design is targeting cryptic allosteric pockets in enzyme targets. Drug leads that do bind to these cryptic pockets are often discovered during HTS campaigns, and the mechanisms of action are rarely understood. Nevertheless, it is often the case that the allosteric pocket provides the best option for drug development against a given target. In the current studies we present a successful way forward in rationally exploiting the cryptic allosteric pocket of H. pylori glutamate racemase, an essential enzyme in this pathogen's life cycle. A wide range of computational and experimental methods are employed in a workflow leading to the discovery of a series of natural product allosteric inhibitors which occupy the allosteric pocket of this essential racemase. The confluence of these studies reveals a fascinating source of the allosteric inhibition, which centers on the abolition of essential monomer-monomer coupled motion networks. Protein-ligand binding can induce the formation of cryptic allosteric pockets not found in the unbound protein, but predicting this computationally can be challenging. Here a combined computational and experimental workflow identifies ligands for H. pyloriglutamate racemase, finding that coupled dynamics of the enzyme dimer are dampened by ligand binding.

Automated summary

One of the challenges in drug design is targeting cryptic allosteric pockets in enzyme targets, which can provide the best option for drug development. Using computational and experimental methods, a successful approach has been presented in rationally exploiting the cryptic allosteric pocket of H. pylori glutamate racemase, leading to the discovery of a series of natural product allosteric inhibitors. These studies reveal the source of allosteric inhibition and how protein-ligand binding affects enzyme dynamics.