Glutamate racemase as a target for drug discovery.
Bottom Line: Glutamate racemase, a member of the cofactor-independent, two-thiol-based family of amino acid racemases, has been implicated in the production and maintenance of sufficient d-glutamate pool levels required for growth.The subject of over four decades of research, it is now evident that the enzyme is conserved and essential for growth across the bacterial kingdom and has a conserved overall topology and active site architecture; however, several different mechanisms of regulation have been observed.These traits have recently been targeted in the discovery of both narrow and broad spectrum inhibitors.
Affiliation: Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. Stewart.Fisher@astrazeneca.comShow MeSH
Mentions: The recent report of selective, allosteric inhibitors of H. pylori glutamate racemase highlighted the structural and biochemical differences observed among bacterial species (Lundqvist et al., 2007). This series of inhibitors, which are based on derivatization of a pyrazolopyrimidinedione core scaffold as exemplified by analogues 8–12(see Fig. 5), were identified through a high‐throughput screening campaign of H. pylori enzyme activity. The series exhibits time‐independent, reversible, stoichiometric inhibition of the enzyme, but remarkably, substrate binding to the enzyme is required for inhibition. The requirement for substrate binding for inhibition (uncompetitive inhibition) is exceedingly rare for a single substrate enzyme and suggests that the inhibitor binds to a site that is distinct from the enzyme active site. Structural studies, using both NMR and X‐ray crystallography, on the enzyme with the inhibitor confirmed the inhibitor binds to a cryptic site on the enzyme ∼9 Å away from the catalytic centre that is primarily formed by a dislocation of the C‐terminal helix (see Fig. 6). Overlays with the native enzyme structure indicate that the inhibitor‐bound structure is highly similar and, importantly, no changes were observed in the active site. Upon dislocation of the C‐terminal helix, the inhibitor binding site is formed by a displacement and rotation of the W252 side‐chain; the pyrazolopyrimidinedione core forms a pi‐stacking interaction with the W252 indole ring and the biaryl ring system (naphthyl ring in analogue 8) fills the pocket vacated by the W252 ring movement (see fig. 3 in Lundqvist et al., 2007).
Affiliation: Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. Stewart.Fisher@astrazeneca.com