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An Atomistic Understanding of Allosteric Inhibition of Glutamate Racemase: a Dampening of Native Activation Dynamics
Journal article

An Atomistic Understanding of Allosteric Inhibition of Glutamate Racemase: a Dampening of Native Activation Dynamics

Katie R Witkin, Nicholas R Vance, Colleen Caldwell, Quinn Li, Liping Yu and M Ashley Spies
ChemMedChem, Vol.15(4), pp.376-384
02/17/2020
DOI: 10.1002/cmdc.201900642
PMCID: PMC7337235
PMID: 31876113

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Abstract

Glutamate racemases (GR) are members of the family of bacterial enzymes known as cofactor-independent racemases and epimerases and catalyze the stereoinversion of glutamate. D-amino acids are universally important for the proper construction of viable bacterial cell walls, and thus have been repeatedly validated as attractive targets for novel antimicrobial drug design. Significant aspects of the mechanism of this challenging stereoinversion remain unknown. The current study employs a combination of MD and QM/MM computational approaches to show that the GR from H. pylori must proceed via a pre-activation step, which is dependent on the enzyme's flexibility. This mechanism is starkly different from previously proposed mechanisms. These findings have immediate pharmaceutical relevance, as the H. pylori GR enzyme is a very attractive allosteric drug target. The results presented in this study offer a distinctly novel understanding of how AstraZeneca's lead series of inhibitors cripple the H. pylori GR's native motions, via prevention of this critical chemical pre-activation step. Our experimental studies, using SPR, fluorescence and NMR WaterLOGSY, show that H. pylori GR is not inhibited by the uncompetitive mechanism originally put forward by Lundqvist et al.. The current study supports a deep connection between native enzyme motions and chemical reactivity, which has strong relevance to the field of allosteric drug discovery.
 Allosteric Regulation - drug effects Amino Acid Isomerases - antagonists & inhibitors Amino Acid Isomerases - metabolism Anti-Bacterial Agents - chemistry Anti-Bacterial Agents - pharmacology Dose-Response Relationship, Drug Enzyme Inhibitors - chemistry Enzyme Inhibitors - pharmacology Helicobacter pylori - drug effects Helicobacter pylori - enzymology Microbial Sensitivity Tests Molecular Dynamics Simulation Molecular Structure Structure-Activity Relationship

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