Probes
that covalently label protein targets facilitate the identification
of ligand-binding sites. Lysine residues are prevalent in the proteome,
making them attractive substrates for covalent probes. However, identifying
electrophiles that undergo amine-specific, regioselective reactions
with binding site lysine residues is challenging. Squarates can engage
in two sequential conjugate addition–elimination reactions
with amines. Nitrogen donation reduces the second reaction rate, making
the mono squaramide a mild electrophile. We postulated that this mild
electrophilicity would demand a longer residence time near the amine,
affording higher selectivity for binding site lysines. Therefore,
we compared the kinetics of squarate and monosquaramide amine substitution
to alternative amine bioconjugation handles. The data revealed that N-hydroxy succinimidyl esters react 4 orders of magnitude
faster, consistent with their labeling promiscuity. Squarate reactivity
can be tuned by a substitution pattern. Electron-withdrawing groups
on the vinylogous ester or amide increase reaction rates. Dithionosquarates
react more rapidly than squarates, while vinylogous thioester analogs,
dithiosquarates, react more slowly. We assessed squarate selectively
using the UDP-sugar processing enzyme GlfT2 from Mycobacterium
tuberculosis, which possesses 21 surface-exposed lysines.
The reaction predominately modified one lysine proximal to a binding
site to afford covalent inhibition. These findings demonstrate the
selectivity of squaric esters and squaramides, which is a critical
feature for affinity-based chemoproteomic probes.