Elucidating the catalytic power of glutamate racemase by investigating a series of covalent inhibitors

Nicholas Robert Vance  Katie R. Witkin  Patrick W. Rooney  Yalan Li  Marshall Pope Michael Ashley Spies

ChemMedChem 2018, doi: 10.1002/cmdc.201800592

The application of covalent inhibitors has experienced a renaissance within drug discovery programs in the last decade. To leverage the superior potency and drug target residence time of covalent inhibitors, there have been extensive efforts to develop highly specific covalent modifications to reduce off‐target liabilities. Herein, we present a series of covalent inhibitors of an antimicrobial drug target, glutamate racemase, discovered though structure‐based virtual screening. A combination of enzyme kinetics, mass spectrometry, and surface‐plasmon resonance experiments details a highly specific 1,4‐conjugate addition of a small molecule inhibitor with a catalytic cysteine of glutamate racemase. Molecular dynamics simulations and quantum mechanics‐molecular mechanics geometry optimizations reveal the chemistry of the conjugate addition. Two compounds from this series of inhibitors display antimicrobial potency comparable to β‐lactam antibiotics, with significant activity against methicillin‐resistant S. aureus strains. This study elucidates a detailed chemical rationale for covalent inhibition and provides a platform for the development of antimicrobials with a novel mechanism of action against a target in the cell wall biosynthesis pathway.