Bulky substrates of isoleucine 2-epimerase: α-Neopentylglycine and NV-5138

Isoleucine 2-epimerase from Lactobacillus buchneri (LbIleE) catalyzes the pyridoxal 5′-phosphate-dependent, reversible, racemization or epimerization of nonpolar amino acids at the C-2 position. The integral role of the enzyme in the biosynthesis of branched-chain d-amino acids makes it a potential target for the development of antimicrobial agents. Probing the hydrophobic active-site pocket with a series of alkyl boronic acids, we show that the hydrophobic pocket accommodates the neopentyl group with enhanced binding affinity relative to the sec-butyl group. Subsequently, we show that LbIleE catalyzes the racemization of l- and d-α-neopentylglycine, exhibiting binding affinities for these substrates 6- and 24-fold greater than those for l-Ile and d-allo-Ile, but with catalytic efficiencies (k_cat/K_m) reduced 46- and 27-fold, respectively. NV-5138 is a ligand of the leucine-binding site of Sestrin2, which activates the mechanistic target of rapamycin complex1 (mTORC1) and is structurally similar to α-neopentylglycine. Our demonstration that LbIleE catalyzes the racemization of l-NV-5138 (k_cat/K_m = 2.2 ± 0.2 s⁻¹ mM⁻¹), along with the fact that L. buchneri can be present in the human gut microbiome, suggests that formation of d-NV-5138 could occur in humans when l-NV-5138 is used as a pharmacological intervention for depression.