The first dual-function assay for human serine racemase
(hSR),
the only bona fide racemase in human biology, is reported. The hSR
racemization function is essential for neuronal signaling, as the
product, d-serine (d-Ser), is a potent N-methyl d-aspartate (NMDA) coagonist, important for learning
and memory, with dysfunctional d-Ser-signaling being observed
in some neuronal disorders. The second hSR function is β-elimination
and gives pyruvate; this activity is elevated in colorectal cancer.
This new NMR-based assay allows one to monitor both α-proton-exchange
chemistry and β-elimination using only the native l-Ser substrate and hSR and is the most sensitive such assay. The
assay judiciously employs segregated dual 13C-labeling
and 13C/2H crosstalk, exploiting both the splitting
and shielding effects of deuterium. The assay is deployed to screen
a 1020-compound library and identifies an indolo-chroman-2,4-dione
inhibitor family that displays allosteric site binding behavior (noncompetitive
inhibition vs l-Ser substrate; competitive inhibition vs
adenosine 5′-triphosphate (ATP)). This assay also reveals important
mechanistic information for hSR; namely, that H/D exchange is ∼13-fold
faster than racemization, implying that K56 protonates the carbanionic
intermediate on the si-face much faster than does
S84 on the re-face. Moreover, the 13C
NMR peak pattern seen is suggestive of internal return, pointing to
K56 as the likely enamine-protonating residue for β-elimination.
The 13C/2H-isotopic crosstalk assay has also
been applied to the enzyme tryptophan synthase and reveals a dramatically
different partition ratio in this active site (β-replacement: si-face protonation ∼6:1 vs β-elimination: si-face protonation ∼1:3.6 for hSR), highlighting
the value of this approach for fingerprinting the pyridoxal phosphate
(PLP) enzyme mechanism.